2010-07-09  jbednar

	* [r11154] topo/command/analysis.py:
	  Minor cleanup of organization

	* [r11153] examples/lissom_whisker_barrels.ty:
	  Minor cleanup

2010-07-09  ceball

	* [r11152] Makefile,
	  topo/tests/__init__.py,
	  topo/tests/test_script.py:
	  Semi-permanent test data is stored in 'default output path'/tests
	  (created if necessary). Locations of test data being read and
	  saved are now printed. Updated test paths.

	* [r11151] topo/misc/genexamples.py:
	  Made find_examples() and print_examples() functions.

2010-07-09  jbednar

	* [r11150] examples/lissom_whisker_barrels.ty:
	  Further cleanup

2010-07-09  ceball

	* [r11149] topo/tests/gca_lissom.ty_SPEEDDATA,
	  topo/tests/lissom_fsa.ty_SPEEDDATA:
	  Removed 'speed data', which should not be checked in (it is
	  machine-specific).

2010-07-09  jbednar

	* [r11148] examples/lissom_whisker_barrels.ty:
	  Partly cleaned up to match conventions

	* [r11147] examples/lissom_whisker_barrels.ty:
	  Partly cleaned up to match conventions

	* [r11146] examples/lissom_whisker_barrels.ty:
	  Slightly corrected version from Stuart

2010-07-09  ceball

	* [r11145] param/parameterized.py:
	  Added repr() for Parameter, so they are represented reasonably.
	  When displayed as part of help(parameterized), parameters'
	  default values, bounds, etc, will be shown.

	* [r11144]
	  doc/Developer_Manual/imports_text.php,
	  param/parameterized.py,
	  topo/analysis/vision.py,
	  topo/command/basic.py,
	  topo/command/pylabplot.py,
	  topo/misc/commandline.py,
	  topo/tests/__init__.py,
	  topo/tkgui/topoconsole.py:
	  Added Command(ParameterizedFunction) class. Commands should
	  inherit from this class, so that exceptions when calling them can
	  be handled gracefully. Added mechanism to allow code that depends
	  on an optional module to create classes etc to be run, deferring
	  the ImportException to the point of use (allows user to learn
	  about possibilties even if he/she is missing an optional module).
	  Made Matplotlib be optional.

	* [r11143] topo/misc/genexamples.py:
	  Print where the examples were found. Also some cleaning and
	  corrections.

2010-07-08  ceball

	* [r11142]
	  doc/Developer_Manual/installation_text.php:
	  Minor tidying.

2010-07-07  antolikjan

	* [r11141] contrib/JanA/LSCSM.py:
	  new version

	* [r11140] contrib/JanA/LSCSM.py:
	  new version

2010-07-07  ceball

	* [r11139] topo/misc/genexamples.py:
	  Added missing path.

	* [r11138] examples/run.py,
	  topo/misc/genexamples.py:
	  Moved examples/run.py to topo/misc/genexamples.py, and made it
	  work however Topographica was installed.

	* [r11137] Makefile,
	  contrib/jaanalysis.py,
	  contrib/jacommands.py,
	  contrib/jsldefs.py,
	  contrib/modelfit.py,
	  contrib/surround_analysis.py,
	  doc/Developer_Manual/coding_text.php,
	  examples/lissom_or_movie.ty,
	  param/__init__.py,
	  param/tk.py,
	  topo/__init__.py,
	  topo/analysis/vision.py,
	  topo/command/analysis.py,
	  topo/command/basic.py,
	  topo/command/pylabplot.py,
	  topo/misc/__init__.py,
	  topo/misc/commandline.py,
	  topo/misc/filepath.py,
	  topo/misc/trace.py,
	  topo/pattern/audio.py,
	  topo/pattern/image.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testCompositeSheetMasks.txt,
	  topo/tests/test_map_measurement.py,
	  topo/tests/test_script.py,
	  topo/tests/testbitmap.py,
	  topo/tests/testimage.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testsnapshots.py,
	  topo/tkgui/editor.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Moved resolve_path, normalize_path, and Filename out of
	  topo.misc.filepath and into topo.param. Cleaned up 'special
	  paths' (application_path, output_path, package_path).

	* [r11136] doc/Developer_Manual,
	  doc/Downloads,
	  doc/Downloads/git_text.php:
	  Updated ignore lists and added comment.

	* [r11135] doc/Developer_Manual/index_text.php,
	  doc/Developer_Manual/installation_text.php,
	  doc/Developer_Manual/revisioncontrol_text.php,
	  doc/Downloads/bzr_text.php,
	  doc/Downloads/cvs_text.php,
	  doc/Downloads/existingpython_text.php,
	  doc/Downloads/git_text.php,
	  doc/Downloads/index_text.php,
	  doc/FAQ/index_text.php:
	  Reorganized download documentation. 'Basic' installation page is
	  supposed to be simpler, but with the chance for developers or
	  experienced python users to jump to more complex options.

2010-07-07  jbednar

	* [r11134] topo/pattern/audio.py:
	  Tweaked error message

	* [r11133] topo/pattern/audio.py:
	  Restored old error handling for when pyaudiolab is not present

	* [r11132] doc/News/index_text.php:
	  Removed note

	* [r11131] topo/command/analysis.py:
	  Cleaned up formatting

	* [r11130] topo/pattern/basic.py:
	  Changed default min_frequency to a nonzero value to make it work
	  with log10, so that AudioFile can be instantiated with default
	  parameters

	* [r11129] topo/base/projection.py:
	  Removed unused parameters

	* [r11128] topo/tests/testaudio.py:
	  Brought Audio test up to date

	* [r11127] topo/tkgui/editor.py,
	  topo/tkgui/topoconsole.py,
	  topo/transferfn/optimized.py:
	  Removed unused import

2010-07-06  ceball

	* [r11126] setup.py:
	  setup.py now installs examples to
	  prefix/share/topographica/examples.

2010-07-05  ceball

	* [r11125] examples/lissom.ty:
	  Corrected out-of-date name for individual normalization.

	* [r11124] param/__init__.py:
	  Fixed bug where default value was a list.

2010-07-05  jbednar

	* [r11123] topo/pattern/basic.py:
	  Cleaned up docs and comments. Marked PowerSpectrum and
	  Spectrogram abstract for now, as they are not useful in the GUI.
	  Provided a more useful default for PowerSpectrum.window_length.
	  Removed default value for the signal argument, as it is not
	  currently usable with default values anyway. Added sanity check
	  on window size.

	* [r11122] topo/pattern/audio.py:
	  Made AudioFile and AudioFolder disappear entirely if pyaudiolab
	  is not available.

2010-07-05  ceball

	* [r11121] contrib/basic.py,
	  contrib/lissom_rgb.ty,
	  examples/gca_lissom.ty,
	  examples/lissom.ty,
	  param/__init__.py,
	  topo/coordmapper/basic.py,
	  topo/pattern/image.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testEnumerationParameter.txt,
	  topo/tkgui/editor.py:
	  Simplified param.ObjectSelector by removing 'allow_None'.
	  param.ObjectSelector now restricts values to be among specified
	  objects by default (whereas if no objects are supplied, values
	  are not restricted).

2010-07-05  jbednar

	* [r11120] doc/Makefile:
	  Enabled classtrees in reference manual

	* [r11119] topo/command/basic.py:
	  Force non-XML pickles to be opened in binary mode on all
	  platforms

2010-07-05  ceball

	* [r11118]
	  topo/tests/testEnumerationParameter.txt:
	  Updated test after removing param.Enumeration.

	* [r11117] param/__init__.py:
	  Temporary fix to ObjectSelector: when check_value() is called as
	  the parameter is being created, and the default value fails the
	  check, attrib_name has not yet been set.

	* [r11116] param/tk.py:
	  Added missing return statement, which had been preventing
	  topoconsole's 'refresh_plots_menu() from working under some
	  circumstances.

	* [r11115] contrib/basic.py,
	  contrib/lissom_rgb.ty,
	  examples/gca_lissom.ty,
	  examples/lissom.ty,
	  param/__init__.py,
	  topo/coordmapper/basic.py,
	  topo/misc/legacy.py,
	  topo/pattern/basic.py,
	  topo/pattern/image.py,
	  topo/tkgui/editor.py:
	  Removed redundant param.Enumeration (replaced with
	  param.ObjectSelector); SF #2630230.

	* [r11114] topo/command/pylabplot.py:
	  File missed from previous commit (svn does some strange
	  things...).

	* [r11113] external/Makefile:
	  Made python depend on zlib, since we are now including zlib (and
	  Python skips building some modules if zlib is not available).

	* [r11112] doc/FAQ/index_text.php,
	  doc/User_Manual/commandline_text.php,
	  doc/User_Manual/noise_text.php,
	  doc/User_Manual/overview_text.php,
	  doc/User_Manual/patterns_text.php,
	  doc/User_Manual/plotting_text.php,
	  doc/buildbot/bbanalysis.py,
	  topo/tests/reference/lissom_fsa_reference.ty:
	  Updated documentation after recent reorganizations.

	* [r11111] examples/lissom.ty,
	  examples/run.py,
	  topo/analysis/vision.py,
	  topo/command/pylabplots.py,
	  topo/misc/legacy.py,
	  topo/sheet/slissom.py,
	  topo/tests/gui_tests.py,
	  topo/tests/test_map_measurement.py,
	  topo/tests/testimage.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Renamed topo.command.pylabplots to topo.command.pylabplot (SF
	  #2631254).

	* [r11110] topo/misc/generatorsheet.py,
	  topo/sheet/basic.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py:
	  Moved definition of GeneratorSheet from topo.sheet to
	  topo.misc.generatorsheet so that it can be used independently of
	  importing topo.sheet library (partially addresses SF #2657028).

	* [r11109] Makefile:
	  Fixed missing argument from recent change.

	* [r11108] contrib/cc_lesi_final.ty,
	  contrib/cc_lesi_final_new.ty,
	  contrib/cc_lesi_oo_or.ty,
	  contrib/cc_lesi_oo_or_new.ty,
	  contrib/cc_lissom_oo_or_simple_rv.ty,
	  contrib/gc_alissom.ty,
	  contrib/gc_lissom_oo_or_homeostatic_new.ty,
	  contrib/jacommands.py,
	  contrib/jm_cc_lissom.ty,
	  contrib/lesi_whisker_barrels.ty,
	  contrib/lissom_oo_or_homeostatic.ty,
	  contrib/lissom_oo_or_homeostatic_tracked.ty,
	  contrib/lissom_oo_or_homeostatic_tracked_new.ty,
	  contrib/lissom_oo_or_noshrinking.ty,
	  contrib/modelfit.py,
	  contrib/sparse_connectivity_LESI.ty,
	  contrib/sparse_connectivity_model.ty,
	  contrib/species_cf_jitter.ty,
	  contrib/species_lat_jitter.ty,
	  contrib/species_pf_jitter.ty,
	  examples/gca_lissom.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  topo/misc/legacy.py,
	  topo/pattern/basic.py,
	  topo/transferfn/basic.py,
	  topo/transferfn/misc.py:
	  Moved TransferFns with complex dependencies out of
	  transferfn.basic into transferfn.misc. Fixes SF #2945499.

2010-07-04  ceball

	* [r11107] examples/leaky_lissom_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/saccade_demo.ty:
	  Examples missed from previous commit.

	* [r11106] contrib/basic.py,
	  contrib/cc_lesi_final.ty,
	  contrib/cc_lesi_final_new.ty,
	  contrib/cc_lesi_oo_or.ty,
	  contrib/cc_lesi_oo_or_new.ty,
	  contrib/cc_lissom_oo_or_simple_rv.ty,
	  contrib/gc_alissom.ty,
	  contrib/gc_lissom_oo_or_homeostatic_new.ty,
	  contrib/helper.py,
	  contrib/jacommands.py,
	  contrib/jm_cc_lissom.ty,
	  contrib/jm_plotting.py,
	  contrib/lesi.ty,
	  contrib/lesi_judethesisversion.ty,
	  contrib/lesi_whisker_barrels.ty,
	  contrib/lgn_lateral.ty,
	  contrib/lissom_oo_or_homeostatic.ty,
	  contrib/lissom_oo_or_homeostatic_tracked.ty,
	  contrib/lissom_oo_or_homeostatic_tracked_new.ty,
	  contrib/lissom_oo_or_noshrinking.ty,
	  contrib/lissom_oo_or_noshrinking_latswitch.ty,
	  contrib/lissom_or_noshrinking.ty,
	  contrib/lissom_or_noshrinking_latswitch.ty,
	  contrib/modelfit.py,
	  contrib/sparse_connectivity_LESI.ty,
	  contrib/sparse_connectivity_model.ty,
	  contrib/species_cf_jitter.ty,
	  contrib/species_lat_jitter.ty,
	  contrib/species_pf_jitter.ty,
	  contrib/surround_analysis.py,
	  topo/analysis/vision.py,
	  topo/command/analysis.py,
	  topo/coordmapper/basic.py,
	  topo/misc/__init__.py,
	  topo/misc/legacy.py,
	  topo/misc/numbergenerator.py,
	  topo/pattern/basic.py,
	  topo/tests/gui_tests.py,
	  topo/tests/testCompositePatternGenerators.txt,
	  topo/tests/testDynamicParameter.txt,
	  topo/tests/testNumberParameter.txt,
	  topo/tests/test_pattern_present.txt,
	  topo/tests/testcfsom.py,
	  topo/tests/testgmpynumber.txt,
	  topo/tests/testparameterizedobject.py,
	  topo/tests/testpatterngenerator.py,
	  topo/transferfn/basic.py:
	  Removed topo.misc.numbergenerator (SF #2631258).

	* [r11105] Makefile,
	  create_topographica_script.py:
	  When Topographica and its dependencies are built from source,
	  Python's site.USER_SITE is ignored by passing '-s' to Python.
	  Fixes sf.net bug 2965099.

	* [r11104]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Fixed typo.

	* [r11103] param/tk.py:
	  Added GUI support for Filename parameter. Fixes sf.net bugs
	  2970815 and 2725796.

2010-07-04  jbednar

	* [r11102] doc/Home/news_text.php,
	  doc/News/index_text.php:
	  Brought news up to date

	* [r11101] topo/pattern/basic.py:
	  Cleaned up whitespace

	* [r11100] ChangeLog.txt:
	  Updated to r11099

2010-07-02  ceball

	* [r11099] Makefile:
	  Fixed typo.

	* [r11098] Makefile:
	  Should have been included in the previous commit.

	* [r11097] Makefile:
	  Fixed quotation marks error.

	* [r11096] Makefile:
	  Cleaned up deb generation, adding support for 'release' debs.

2010-07-01  ceball

	* [r11095] debian/control:
	  Added python-dev dependency to Ubuntu package.

2010-06-30  ceball

	* [r11094] doc/Forums/index_text.php,
	  doc/Forums/problems_text.php:
	  Removed out-of-date link to Windows Forum, and improved links to
	  bug reports and feature requests.

2010-06-29  ceball

	* [r11093] /branches/kkudryavtsev_branch:
	  Removed Konstantin's aborted MPI branch (latest version is
	  http://gitorious.org/topographica, mpi2 branch).

	* [r11092] doc/buildbot/master.cfg:
	  Doozy was upgraded to Ubuntu 10.04.

2010-06-23  ceball

	* [r11091] doc/buildbot/master.cfg:
	  Added Lucid to list of debs to be uploaded.

2010-06-22  ceball

	* [r11090] topo/base/simulation.py,
	  topo/command/basic.py,
	  topo/misc/picklemain.py:
	  Added ALERTs.

2010-06-20  ceball

	* [r11089] doc/buildbot/master.cfg:
	  Added generation of Reference Manual to one builder (also
	  uploaded to buildbot.topographica.org/doc/).

2010-06-17  ceball

	* [r11088] topo/base/functionfamily.py,
	  topo/responsefn/optimized.py:
	  Added comments.

	* [r11087] external/zlib-1.2.5.tar.gz:
	  Identical version of zlib, but extracted and recompressed on a
	  linux machine (apparently there is some problem with gzip on
	  recent linux;
	  https://bugs.launchpad.net/ubuntu/+source/gzip/+bug/524366).
	  Fixes bug #3015804.

	* [r11086] Makefile:
	  Fixed Ubuntu version name errors.

	* [r11085] Makefile:
	  Fixed quoting mistake.

	* [r11084] Makefile:
	  Ubuntu package moved to 'Lucid' (10.04 LTS). Not yet tested.

	* [r11083]
	  doc/Developer_Manual/optimization_text.php:
	  Added comment.

	* [r11082]
	  doc/Developer_Manual/optimization_text.php:
	  Updated optimization page and tried to make the example coherent.

	* [r11081]
	  doc/Developer_Manual/optimization_text.php:
	  Fixed various typos and updated a link.

2010-06-13  ceball

	* [r11080] external:
	  More to ignore.

2010-06-04  antolikjan

	* [r11079] contrib/cc_lesi_final.ty:
	  small optimization

	* [r11078] contrib/cc_lesi_final.ty:
	  add init ring size parameter

	* [r11077] contrib/surround_analysis.py:
	  multiple plotting changes

	* [r11076] contrib/pybrainstuff.py:
	  changes

	* [r11075] contrib/jacommands.py:
	  small changes

	* [r11074] topo/analysis/vision.py:
	  small changes to complexity analysis

2010-06-03  jbednar

	* [r11073] topo/transferfn/basic.py:
	  Made HomeostaticResponse picklable even before first use, so that
	  run_batch (which presents an initial test pattern) would work for
	  gca_lissom.ty

2010-05-28  jbednar

	* [r11072] examples/gca_lissom.ty:
	  Added ALERT

	* [r11071] topo/transferfn/basic.py:
	  Minor doc and formatting cleanup. Removed unused sheet_name
	  parameter

2010-05-27  ceball

	* [r11070] topo/pattern/random.py:
	  Added ALERT.

	* [r11069] examples/gca_lissom.ty,
	  topo/base/arrayutil.py,
	  topo/tests/gca_lissom.ty_DATA,
	  topo/transferfn/basic.py:
	  New version to match GCA paper. Intermediate checkin - some
	  documentation and minor changes to come.

	* [r11068] external/Makefile,
	  external/zlib-1.2.5.tar.gz:
	  Added zlib (a not-always-available dependency of libpng).

	* [r11067] external/Makefile,
	  external/m4-1.4.9.tar.gz:
	  Added M4 (a not-always-available dependency of GMP).

2010-05-24  antolikjan

	* [r11066] contrib/JanA/glm.py:
	  update

	* [r11065] contrib/JanA/glm.py:
	  update

2010-05-20  antolikjan

	* [r11064] contrib/JanA/glm.py:
	  update

	* [r11063] contrib/JanA/glm.py:
	  update

	* [r11062] contrib/JanA/noiseEstimation.py:
	  update

	* [r11061] contrib/modelfit.py:
	  update

2010-05-18  antolikjan

	* [r11060] contrib/JanA/glm.py:
	  update

2010-05-18  ceball

	* [r11059] topo/tests/utils.py:
	  Added note.

2010-05-17  antolikjan

	* [r11058] contrib/JanA/glm.py:
	  update

	* [r11057] contrib/JanA/glm.py:
	  update

	* [r11056] contrib/JanA/glm.py:
	  update

	* [r11055] contrib/JanA/dataimport.py:
	  update

	* [r11054] contrib/JanA/glm.py:
	  update

2010-05-14  antolikjan

	* [r11053] contrib/JanA/glm.py:
	  update

	* [r11052] contrib/JanA/glm.py:
	  update

	* [r11051] contrib/JanA/glm.py:
	  update

2010-05-13  antolikjan

	* [r11050] contrib/JanA/dataimport.py:
	  corrected cutoff

	* [r11049] contrib/JanA/dataimport.py:
	  corrected cutoff

	* [r11048] contrib/JanA/glm.py:
	  corrected bug with number of subplots

2010-05-12  antolikjan

	* [r11047] contrib/JanA/glm.py:
	  update

	* [r11046] contrib/modelfit.py:
	  update

	* [r11045] contrib/dd.py:
	  update

	* [r11044] contrib/JanA/LSCSM.py,
	  contrib/JanA/dataimport.py,
	  contrib/JanA/glm.py,
	  contrib/JanA/noiseEstimation.py,
	  contrib/JanA/sparsness_analysis.py,
	  contrib/JanA/stim_comparison.py:
	  reorganization of the fitting code

2010-05-10  antolikjan

	* [r11043] contrib/JanA/noiseEstimation.py:
	  got rid of dependency

2010-05-09  ceball

	* [r11042] doc/buildbot/master.cfg:
	  Added Ubuntu server buildslave (no X server installed).

2010-05-07  antolikjan

	* [r11041] contrib/JanA/glm.py:
	  improvements

2010-05-07  ceball

	* [r11040]
	  topo/tests/testparametersframe_tk.py:
	  Change missed from r11038.

2010-05-06  ceball

	* [r11039] Makefile,
	  external/Makefile:
	  Added variable 'GUI' to control whether or not to build tk and
	  related packages.

	* [r11038] topo/tests/__init__.py,
	  topo/tests/testmatplotlib_tk.py,
	  topo/tests/testmatplotlibtk.py,
	  topo/tests/testparameterizedobject_tk.py,
	  topo/tests/testparametersframe.py,
	  topo/tests/testparametersframe_tk.py,
	  topo/tests/testtkparameterizedobject.py:
	  Test files that import Tkinter now have a name that ends in '_tk'
	  so that importing them can be avoided if tk is not available.

	* [r11037] param/external.py:
	  Removed dependency of param.external on Tkinter.

2010-05-06  antolikjan

	* [r11036] contrib/modelfit.py:
	  changes

	* [r11035] contrib/helper.py:
	  image preprocessing

	* [r11034] contrib/dd.py:
	  module for organazing my analysis results

2010-05-05  antolikjan

	* [r11033] contrib/JanA/glm.py:
	  correction

	* [r11032] contrib/JanA/glm.py:
	  small changes

	* [r11031] contrib/JanA,
	  contrib/JanA/__init__.py,
	  contrib/JanA/__init__.pyc,
	  contrib/JanA/glm.py,
	  contrib/JanA/glm.pyc,
	  contrib/JanA/noiseEstimation.py,
	  contrib/JanA/noiseEstimation.pyc,
	  contrib/JanA/stim_comparison.py,
	  contrib/JanA/stim_comparison.pyc:
	  with the increasing number of analysis files I added I decided to
	  make a subdirectory for them

	* [r11030] contrib/modelfit.py:
	  lot of changes

2010-04-14  antolikjan

	* [r11029] contrib/modelfit.py:
	  lot of changes

2010-04-10  ceball

	* [r11028] topo/command/basic.py:
	  When snapshot fails to load, show original error as well the one
	  raised after legacy support has been loaded.

2010-04-10  bilalkhancnsg

	* [r11027] contrib/lissom_audio.ty,
	  topo/command/analysis.py:
	  Removed svn tagging accidentally left in command.analysis

	* [r11026] contrib/lissom_audio.ty:
	  Updated connections to to calibrated values, put a HalfRectify on
	  MGB.

	* [r11025] contrib/lissom_audio.ty:
	  Added calibration sheet to test out STRFs, resized all other
	  sheets to calibrated dimensions, cochlea now 100 msecs by 10
	  octaves.

	* [r11024] contrib/lissom_audio.ty:
	  Changed command line params (densities) to more appropraite
	  values.

	* [r11023] contrib/lissom_audio.ty:
	  Updated audio input pattern to millsecond increments per
	  timestep, cleaned up to use latest version of audio pattern
	  generator.

	* [r11022] contrib/lissom_audio.ty:
	  Moved log gaussian and sigmoided difference of log gaussian to
	  lissom_audio till the quirks can be worked out of them.

	* [r11021] sounds/sine_waves/00020hz.wav,
	  sounds/sine_waves/*.wav,
	  sounds/square_waves/*.wav,
	  Old sound files deleted.

	* [r11020] sounds/complex/ReadMe.txt,
	  sounds/complex/daisy.wav,
	  sounds/sine_waves/ReadMe.txt,
	  sounds/sine_waves/normalized,
	  sounds/sine_waves/normalized/*_sine.wav,
	  sounds/sine_waves/raw,
	  sounds/sine_waves/raw/*_sine.wav,
	  sounds/square_waves/ReadMe.txt,
	  sounds/square_waves/normalized,
	  sounds/square_waves/normalized/*_square.wav,
	  sounds/square_waves/raw,
	  sounds/square_waves/raw/*_square.wav,
	  Added normalised versions of sine and square waves, updated
	  ReadMe files accordingly.

	* [r11019] topo/analysis/featureresponses.py,
	  topo/pattern/audio.py,
	  topo/pattern/basic.py:
	  Minor spacing corrections.

	* [r11018] topo/command/analysis.py:
	  Modified frequency map measurement to use Line instead of
	  RawRectangle, added a selectivity as well as preference output

	* [r11017] topo/pattern/audio.py:
	  Added ability to multiplicatively amplify a frequency range.
	  Changed AudioFolder to employ AudioFile, previous concat of audio
	  signal behavior does not scale.

	* [r11016] topo/pattern/audio.py:
	  Updated AudioFile to use new Spectrogram/PowerSpectrum structure.
	  AudioFile now outputs in dB.

	* [r11015] topo/pattern/basic.py:
	  Segmented PowerSpectrum for cleaner inheritance, fixed window
	  overlap bug where sample window shrunk instead of overlapping.
	  Updated Spectrogram to use new PowerSpectrum

	* [r11014] topo/pattern/basic.py:
	  Added precendence values for sigmoidedDoG pattern params, removed
	  eroneous sigmoid x offset from sigmoidedDog.

2010-04-09  bilalkhancnsg

	* [r11013] topo/pattern/basic.py:
	  Added dedicted difference of gaussians pattern

	* [r11012] topo/pattern/basic.py:
	  Replaced rectangular smoothing window with a simpler
	  implementation.

	* [r11011] topo/pattern/basic.py:
	  Removed log gaussian and difference of log gaussians, they don't
	  work predictably

	* [r11010] topo/misc/patternfn.py:
	  Removed log gaussian function, it doesnt work predictably

2010-04-05  ceball

	* [r11009] topo/transferfn/basic.py:
	  Added comment about ActivityAveragingTF.

2010-03-31  ceball

	* [r11008] topo/base/simulation.py:
	  Added enhancement note.

2010-03-26  ceball

	* [r11007] topo/base/arrayutil.py:
	  No visible change (renamed internal variable).

	* [r11006] topo/base/arrayutil.py:
	  Simplified array_argmax(). Should be no change to results.

	* [r11005] topo/base/arrayutil.py:
	  Simplified clip_lower() and clip_upper(). New implementation is
	  presumably faster, but I have not verified that. Should be no
	  change to any results.

	* [r11004] topo/pattern/image.py:
	  Simpified PatternSampler.__call__() (no longer any need to create
	  'empty' pattern sample in advance). Should be no change to
	  results.

	* [r11003] topo/pattern/image.py:
	  Simplified image sampling (also gives vast speedup for presenting
	  images). Should cause no change to results.

2010-03-19  aplebe

	* [r11002] topo/command/key_angles.png:
	  initial static image for angle prefernce map

	* [r11001] topo/command/analysis.py:
	  Added preference map for angle between two segments,
	  independently from the
	  segment orientations, and related image with hue coding of the
	  angles

2010-03-18  ceball

	* [r11000] COPYING.txt,
	  LICENSE.txt, README.txt,
	  debian/copyright,
	  doc/Team_Members/index_text.php,
	  setup.py,
	  topo/__init__.py:
	  Changed from GPL to BSD license. Changed copyright statement to
	  refer to 'Topographica Developers' (individuals are listed on the
	  Team Members page).

2010-03-15  jbednar

	* [r10999] sounds/sine_waves/ReadMe.txt,
	  sounds/square_waves/ReadMe.txt:
	  Fixed missing newlines

2010-03-14  ceball

	* [r10998] topo/misc/legacy.py:
	  Leagacy support for OneDPowerSpectrum->Spectrogram.

	* [r10997] topo/misc/commandline.py:
	  Fixed typo (resulting in IPython being unavailable; sf.net bug
	  #2969832).

2010-03-14  bilalkhancnsg

	* [r10996] topo/pattern/audio.py:
	  Corrected typo.

	* [r10995] contrib/lissom_audio.ty,
	  topo/pattern/audio.py:
	  Added ability for pattern.audio to load a folder of sound files
	  back to back, sample rates must be consistent between files. Can
	  also specify a length of gap to insert between each consecutive
	  sound file. Updated lissom_audio to use new audio load methods.

	* [r10994] topo/pattern/basic.py:
	  Changed the 'fft results to sheet mapping' so it takes into
	  account ALL amplitudes when drawing on the sheet, this fixes the
	  previous erroneous behaviour where only a tiny subset of
	  amplitudes were employed which caused the bulk of information to
	  be lost, hence distinct bands were seen even on pure tone ffts.
	  It also fixes the problem where the sheet needed normalisation
	  before anything was visible. Lastly it fixes corollary discrete
	  frequency problems since the frequency is now continuous along
	  the sheet (the resolution is directly proportional to the density
	  of the sheet). As a consequence changed lin and logspace mapping
	  such that it now returns all possible frequency indices between
	  user specified min and max (unconstrained by sheet divisions). It
	  also now rounds properly (used to use floor to get int index
	  values). Made some commenting clearer.

	* [r10993] topo/command/analysis.py:
	  Added class to measure frequency preference maps in mgb and a1.

	* [r10992] contrib/lissom_audio.ty:
	  Added imports and code for swapping window functions in
	  lissom_audio

2010-03-13  ceball

	* [r10991] Makefile:
	  Fixed bug where system python was being used to create
	  topographica script, rather than Topographica's python. Changed
	  'other python' target to use the 'other python' to create the
	  topographica script.

2010-03-13  bilalkhancnsg

	* [r10990] topo/pattern/basic.py:
	  Removed the overridden size parameter from LogGaussian.

	* [r10989] topo/misc/patternfn.py:
	  Added a line to sigmoid to explain what is meant by axis.

	* [r10988] contrib/lissom_audio.ty:
	  updated lissom_audio to use new square wave files.

	* [r10987] sounds/sine_waves/ReadMe.txt,
	  sounds/square_waves/*.wav,
	  sounds/square_waves/ReadMe.txt:
	  Added ReadMe files to the sine and square wave sound file folders
	  explaining the format and how they were generated. Added square
	  waves for each frequency currently in sine waves.

	* [r10986] contrib/lissom_audio.ty:
	  Corrected sheet dimensions such that mgb and a1 aren't so small
	  they only cover half the sheet below them. Each sheet is now
	  smaller than the one below it by a perimeter of half a connection
	  field. Updated so the new Audio function from topo.pattern.audio
	  is employed. Removed cochlea aspect ratio code as its not useful.

	* [r10985] topo/pattern/basic.py:
	  Defined a new kind of smoothing window, rectangular, which
	  actually means no smoothing is applied. Set this to be the
	  default.

	* [r10984] topo/pattern/audio.py:
	  Changed class name from Spectrogram back to Audio (Audio now
	  inherits from Spectrogram). Removed all spectrogram specific
	  code, retaining only that relevant to the importing of audio
	  files.

	* [r10983] topo/pattern/basic.py:
	  Moved Spectrogram from topo.pattern.audio to topo.pattern.basic.
	  Spectrogram inherits from new PowerSpectrum, so code content
	  remains largely unchanged, merely restructured to fit the new
	  PowerSpectrum. The changes that have occurred: Spectrogram now
	  pushes new data onto the left side, with older information on the
	  right, and frequencies go from lowest at the bottom to highest at
	  the top - this is how it should have been all along.

	* [r10982] topo/pattern/basic.py:
	  Renamed class OneDPowerSpectrum to PowerSpectrum. Combined its
	  methods _generate_frequency_indices and _create_indices. Shifted
	  fft calculation into its own function for cleaner inheritance.
	  Commented everything, as a result found and corrected bug where
	  default window parameters were not being overridden in
	  PowerSpectrum.

	* [r10981] topo/plotting/plotgroup.py:
	  Minor typo correction

2010-03-12  ceball

	* [r10980] external/Makefile:
	  Removed unused variable (was for building via msys on Windows,
	  which does not work).

	* [r10979] MANIFEST.in,
	  Makefile,
	  create_topographica_script.py,
	  setup.py:
	  Fixed some recently introduced bugs in setup.py-related commands.

2010-03-11  jbednar

	* [r10978] topo/misc/patternfn.py:
	  Minor updates and fixes to messages and documentation

	* [r10977] topo/misc/commandline.py,
	  topo/misc/patternfn.py:
	  Minor updates and fixes to messages and documentation

	* [r10976] Makefile,
	  topo/__init__.py:
	  Minor updates and fixes to messages and documentation

2010-03-11  bilalkhancnsg

	* [r10975] contrib/lissom_audio.ty,
	  topo/pattern/audio.py:
	  Modified paths in lissom audio to reflect new sounds folder
	  structure, modified pattern.audio to use a log space for
	  spctrogram.

	* [r10974] topo/pattern/basic.py:
	  Added class for Sigmoided Difference of Log Gaussians.

	* [r10973] sounds/multipletones,
	  sounds/puretones,
	  sounds/sine_waves,
	  sounds/sine_waves/*.wav,
	  sounds/square_waves,
	  sounds/square_waves/sqr-100Hz.wav,
	  sounds/square_waves/sqr-1kHz.wav:
	  Could not locate the original source to credit for the pure tone
	  sound files so i generated a new one of each. The waveforms of
	  mine appear to be a little cleaner also. Renamed pure tone to
	  sine wave and multiple tone to square wave as this is far
	  clearer.

	* [r10972] topo/misc/patternfn.py,
	  topo/pattern/basic.py:
	  Added class for logarithmic gaussian pattern in
	  topo.pattern.basic. Added log_gaussian function to
	  topo.misc.patternfn

	* [r10971] topo/misc/patternfn.py,
	  topo/pattern/audio.py,
	  topo/pattern/basic.py:
	  Removed spectrogram code from OneDPowerSpectrum, as the name
	  implies it should only return a one dimensional structure.
	  Spectrogram code is now in pattern/audio. Fft no longer employs a
	  smoothing function (i.e. it operates on a rectangualr window)
	  which produces slightly better results. Moved fft calculation to
	  its own method to make inheritence cleaner. In pattern/audio
	  renamed class Audio to class Spectrogram as this is really what
	  it should have been doing all along (and is now doing). Moved the
	  function aspect of the sigmoid pattern to topo/patternfn as this
	  is conforms to how every other class is doing it.

2010-03-10  jbednar

	* [r10970]
	  doc/Developer_Manual/optimization_text.php:
	  Minor fixes

2010-03-10  ceball

	* [r10969] setup.py:
	  Minor alterations to setup.py

	* [r10968] setup.py:
	  Fixed typo.

	* [r10967] setup.py:
	  Minor updates to docs.

	* [r10966] setup.py:
	  Remove capitalization of 'topographica' package name.

	* [r10965] setup.py:
	  Uncommented code that was disabled for testing (should have been
	  part of previous commit).

	* [r10964] setup.py:
	  Support easy_install without depending on setuptools.

	* [r10963] Makefile,
	  create_topographica_script.py:
	  Fixed bugs with svnversion variables.

2010-03-10  bilalkhancnsg

	* [r10962] sounds/complex,
	  sounds/complex/daisy.wav,
	  sounds/daisy.wav,
	  sounds/multipletones,
	  sounds/multipletones/sqr-100Hz.wav,
	  sounds/multipletones/sqr-1kHz.wav,
	  sounds/puretones,
	  sounds/puretones/*.wav,
	  sounds/sqr-1kHz.wav,
	  sounds/test.wav:
	  Added 20 sound files of pure tones of ascending frequency ranging
	  from 20Hz to 20000Hz to a folder named 'puretones', added 2 sound
	  files of square waves (test of multiple frequencies) to the
	  'multipletones' folder, and finally, created a folder named
	  'complex' to house the spectral and termporally variant rich test
	  sound (daisy).

2010-03-07  ceball

	* [r10961] setup.py:
	  Added description for pypi page.

	* [r10960] MANIFEST.in,
	  Makefile, setup.py:
	  More minor packaging cleanup.

	* [r10959] Makefile,
	  setup.py:
	  Packaging cleanup.

	* [r10958] topo/__init__.py,
	  topo/misc/commandline.py,
	  topo/tests/__init__.py:
	  Allow Topographica to run without gmpy or fixedpoint.

	* [r10957] external/Makefile:
	  fixedpoint-uninstall was leaving files behind.

	* [r10956] MANIFEST.in,
	  Makefile,
	  create_topographica_script.py,
	  setup.py:
	  Simplified distutils pypi commands.

2010-03-06  ceball

	* [r10955] topo/misc/commandline.py:
	  Made IPython be optional.

	* [r10954] MANIFEST.in:
	  Added missing file.

	* [r10953] MANIFEST.in,
	  Makefile, _setup.py,
	  external/Makefile,
	  setup.py, setup_app.py,
	  setup_exe.py,
	  setup_ez.py:
	  Focus on Python's distutils only: drop setuptools, easy_install,
	  py2exe, and py2app (all of which are incompatible with code in
	  Topographica or at least one of its dependencies in various
	  ways). Also, removed incomplete support for building via MSYS on
	  Windows.

2010-03-03  bilalkhancnsg

	* [r10952] contrib/lissom_audio.ty:
	  Modified the mgb afferent strength so a1 isn't flooded with
	  input. Changed the mgb's weights on the cochlea so it better
	  resembles known strf data.

	* [r10951] sounds/daisy.wav:
	  Added a new test sound: the song Daisy Bell, this allows us to
	  see how the audio pattern generator holds up to a more complex
	  spectrogram. (Daisy Bell in tribute to the IBM 704 which in 1962
	  became the first ever computer to 'sing')

	* [r10950] topo/command/analysis.py:
	  Modified the _feature_list method of class measure_rfs such that
	  it no longer assumes a square sheet

2010-03-02  bilalkhancnsg

	* [r10949] topo/pattern/basic.py:
	  Commented out Gamma for now, it't not presently needed and
	  requires more time to fix than i can currently give it.

2010-03-02  jbednar

	* [r10948] topo/pattern/basic.py:
	  Cleaned up docstrings

2010-03-02  bilalkhancnsg

	* [r10947] topo/command/basic.py:
	  Added an extra section to the documentation of method
	  pattern_present explaining the back arrow history mechanism
	  availible in the gui to view just presented patterns. Removed the
	  time.sleep command added to pattern_present which attempted to
	  achieve similar functionality.

	* [r10946] topo/analysis/featureresponses.py:
	  Reverted class Feature to its previous state, the modification of
	  parameter 'range' was duplication of the functionality provided
	  by the parameter 'value'.

	* [r10945] contrib/lissom_audio.ty:
	  Changed the density parameter to density_multiplier so as to
	  better convey its purpose. Changed the value of
	  density_multiplier to 1.0 and the densities of the cochlea, mgbv
	  and a1 sheets to reasonable values

	* [r10944] topo/pattern/basic.py:
	  Changed the name of GammaDistribution to Gamma. Gamma now
	  utilises the SciPy implementation for the generalised gamma
	  distribution. Accordingly much improved the documentation for
	  Gamma.

	* [r10943] topo/misc/patternfn.py:
	  Removed my implementations of gamma and factorial in favour of
	  those from scipy, the scipy versions are one liners so they're
	  now placed directly in topo.pattern.basic where they're utilised.

2010-03-01  jbednar

	* [r10942] topo/misc/patternfn.py,
	  topo/pattern/basic.py:
	  Cleaned up docstrings and comments

2010-03-01  bilalkhancnsg

	* [r10941] topo/command/analysis.py,
	  topo/command/basic.py,
	  topo/misc/patternfn.py:
	  CORRECTION TO REVISION 10936: misunderstood the CEBENHANCEMENT
	  about visualising motion, changed the code to reflect this

	* [r10940] contrib/lissom_audio.ty:
	  Added a density parameter such that cochlea, mgbv and a1
	  densities can all be multiplicatively modified through a single
	  parameter on the command line. Changed cochlea, mgbv and a1
	  densities to unit densities relative to each other. Changed
	  dimensions of mgbv and a1 sheets to be rectangular and congruent
	  to the cochlea. Added a SigmoidedDoG weights generator to the
	  cochlea afferent connection and oriented and scaled it correctly

	* [r10939] topo/pattern/basic.py:
	  Added a Gamma Distribution class to utilise the gamma function
	  from topo.misc.patternfn. Changed the default x position of
	  SigmoidedDoG from -1.5 to 0. Changed the gaussians such that
	  modifying the global size parameter multiplies the individual
	  size of both.

	* [r10938] topo/misc/patternfn.py:
	  Added new definitions for gamma and recursive factorial (which is
	  employed by gamma). Note that gamma is one dimensional.

	* [r10937] topo/misc/patternfn.py:
	  Added new definitions for gamma and recursive factorial (which is
	  employed by gamma). Note that gamma is one dimensional.

	* [r10936] topo/command/basic.py:
	  Added ability to slow down presentation of patterns in
	  pattern_present so as to be able to visualise them

	* [r10935] topo/analysis/featureresponses.py:
	  Added ability for the class FeatureMaps to accept single values
	  for its range

2010-02-25  jbednar

	* [r10934] topo/coordmapper/basic.py:
	  Fixed ConstantMapper parameter bounds and documentation

2010-02-23  jbednar

	* [r10933] examples/obermayer_pnas90.ty:
	  Removed outdated reference to topo.param that prevented it from
	  being run

2010-02-23  ceball

	* [r10932] external/Cython-0.12.1.tar.gz,
	  external/Cython-0.9.8.1.1.tar.gz,
	  external/Makefile:
	  Upgraded Cython to 0.12.1.

2010-02-22  antolikjan

	* [r10931] contrib/jacommands.py:
	  further changes to measre_histogram

2010-02-21  antolikjan

	* [r10930] contrib/jacommands.py:
	  various changes to measure activity histogram

2010-02-21  ceball

	* [r10929] debian/install.ex,
	  debian/menu.ex,
	  debian/topographica.desktop:
	  (Ubuntu package) Added files for creating menu entry in the
	  future - currently unused.

	* [r10928] Makefile:
	  (Ubuntu package) Add tk-tile as dependency for Ubuntu 8.04.

2010-02-18  ceball

	* [r10927] contrib/lissom_audio.ty:
	  Added normal svn properties.

	* [r10926] doc/buildbot/master.cfg:
	  (Buildbot) Fixed another typo.

	* [r10925] doc/buildbot/master.cfg:
	  (buildbot) Fixed typos.

2010-02-17  ceball

	* [r10924] doc/buildbot/master.cfg:
	  (Buildbot) Fixed package uploading.

2010-02-16  ceball

	* [r10923] Makefile:
	  (Ubuntu package) Fixed path error for rpm creation.

	* [r10922] doc/buildbot/master.cfg:
	  Added deb and rpm generation.

2010-02-16  antolikjan

	* [r10921] topo/command/pylabplots.py:
	  improved plotting of modulation ratios

	* [r10920] topo/analysis/vision.py:
	  improved plotting of modulation ratio histograms

2010-02-16  ceball

	* [r10919] Makefile:
	  (Ubuntu package) Renamed a target.

	* [r10918] Makefile:
	  (Ubuntu package) Removed 'PRERELEASE' variable.

2010-02-15  ceball

	* [r10917] Makefile:
	  (Ubuntu package) debuild source after binaries, so checksums
	  match for subsequent dput.

	* [r10916] Makefile:
	  (Ubuntu package) Restored hardy deb.

	* [r10915] debian/pyversions:
	  (Ubuntu package) File removed from previous commit.

	* [r10914] debian/control:
	  (Ubuntu package) Fix python dependency confusion.

	* [r10913] Makefile:
	  Added some notes.

	* [r10912] Makefile:
	  Fixed typo.

	* [r10911] Makefile:
	  (Ubuntu package) Commented out Hardy package building.

	* [r10910] Makefile,
	  doc/buildbot/dot-dput.cf:
	  (Ubuntu package) Cleanup plus generation of rpm files.

2010-02-13  ceball

	* [r10909] debian/control:
	  (Ubuntu package) Attempt to allow building on Hardy (LTS).

	* [r10908] Makefile:
	  (Ubuntu package) Continued attempt to upload debs for multiple
	  versions of Ubuntu.

	* [r10907] Makefile:
	  (Ubuntu package) Attempt to upload debs for multiple versions of
	  Ubuntu.

	* [r10906] Makefile:
	  (Ubuntu package) Automated process now working for Ubuntu Jaunty
	  target.

	* [r10905] Makefile:
	  (Ubuntu package) Attempt to create Ubuntu Jaunty deb.

	* [r10904] Makefile:
	  (Ubuntu package) Continued attempting to get automatic PPA upload
	  to work.

	* [r10903] Makefile:
	  (Ubuntu package) Testing PPA.

	* [r10902] Makefile:
	  (Ubuntu package) Simplified the commands.

	* [r10901] Makefile:
	  (Ubuntu package) Create valid changelog.

	* [r10900] Makefile:
	  (Ubuntu package) Fixed mistake in previous commit.

	* [r10899] Makefile,
	  debian/changelog:
	  (Ubuntu package) Continued attempting to automate deb creation.

	* [r10898] debian/control,
	  debian/rules:
	  Reverted earlier confused change of pycentral to pysupport.

2010-02-12  ceball

	* [r10897] debian/pyversions:
	  (Ubuntu packaging) Fixed syntax error.

	* [r10896] Makefile,
	  debian/pyversions:
	  More deb packaging updates.

	* [r10895] Makefile,
	  debian/control:
	  More updates for Karmic Koala build machine.

	* [r10894] create_topographica_script.py:
	  Fixed typo in previous commit.

	* [r10893] Makefile,
	  create_topographica_script.py:
	  Began implementing deb creation via Makefile.

	* [r10892] debian/compat,
	  debian/rules:
	  Updates for Ubuntu Karmic Koala (as the packaging machine).

2010-02-10  jbednar

	* [r10891] contrib/lissom_audio.ty,
	  topo/pattern/audio.py,
	  topo/pattern/basic.py:
	  Cleaned up formatting and docstrings to match Topographica
	  conventions. Should be no change in behavior apart from the
	  arrangement in the Model Editor

2010-02-10  bilalkhancnsg

	* [r10890] contrib/lissom_audio.ty,
	  topo/pattern/basic.py:
	  SigmoidedDoG now with doc info, which lissom audio now employs as
	  its weights generator

	* [r10889] contrib/lissom_audio.ty,
	  topo/pattern/basic.py:
	  lissom audio sans happyface, and SigmoidedDoG pattern working

	* [r10888] topo/pattern/basic.py:
	  SigmoidedDoGs changed to SigmoidedDoG since it now only employs
	  one diff of gaussians

2010-02-09  ceball

	* [r10887]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Change missed from previous commit.

	* [r10886]
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/reference/topo_or_defs.py:
	  Changes missed when converting CFProjection's n_units() method to
	  an attribute.

2010-02-05  ceball

	* [r10885] doc/Downloads/git_text.php:
	  Some updates about sharing work.

2010-02-04  ceball

	* [r10884] external:
	  Updated ignore list.

2010-02-04  jbednar

	* [r10883]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Fixed apparent typo

2010-02-04  ceball

	* [r10882] external/Makefile:
	  Added Python 2.5 directories to clean and uninstall.

	* [r10881] doc/buildbot/index.html,
	  doc/buildbot/master.cfg:
	  Made current svn documentation available from buildbot.

2010-02-03  bilalkhancnsg

	* [r10880] topo/pattern/basic.py:
	  Updated doc info for Sigmoid and SigmoidedDoGs, changed param
	  names in SigmoidedDoGs to be generic and also changed soft and
	  hard bounds to reasonable values

	* [r10879] contrib/lissom_audio.ty,
	  topo/misc/patternfn.py,
	  topo/pattern/basic.py:
	  Added new pattern (Sigmoid) for generating sigmoids along the
	  horizontal, and added a new pattern (SigmoidedDoGs) consisting of
	  two differences of gaussians summed and subsequently multiplied
	  by a sigmoid

2010-02-02  ceball

	* [r10878] doc/buildbot/master.cfg:
	  New Mac buildslave does not yet have necessary tools installed to
	  build docs, so stop warning (it's not a failure of docs to build
	  on Mac). No slow-tests on Windows, because msys shell interacts
	  badly with buildbot, giving false failures.

	* [r10877] doc/buildbot/index.html:
	  Updated links.

2010-02-01  ceball

	* [r10876] param/tk.py:
	  Restored compatibility setting for Tk versions less than 8.5 (for
	  Windows).

	* [r10875] external/Makefile:
	  Try to address mysterious, intermittent buildbot error by
	  avoiding pipe in matplotlib unpacking.

	* [r10874] topo/misc/legacy.py:
	  Added legacy support for CFProjection's n_units() method being
	  removed (r10871).

2010-01-31  ceball

	* [r10873] topo/projection/basic.py:
	  Fixed bug in n_bytes() (hadn't been updated after flattening cfs
	  list.

	* [r10872] topo/base/cf.py,
	  topo/base/projection.py:
	  Minor changes to comments.

	* [r10871] topo/base/cf.py,
	  topo/sheet/lissom.py:
	  Made CFProjection's n_units() method into an attribute, since the
	  number of units is fixed (should make distribution easier).
	  ResizableCFProjection's n_units is updated when the bounds are
	  changed.

	* [r10870] topo/base/cf.py:
	  CFProjection.n_units() uses the mask template to count the number
	  of units, rather than the mask of the central CF. Should be no
	  change to existing simulations.

	* [r10869] topo/projection/basic.py:
	  Fixed bug where incorrect mask was being stored on shared cf;
	  this resulted in n_units() returning the wrong value (but this
	  had no effect on existing simulations because learning is not
	  implemented for shared weight CFPs).

	* [r10868] topo/base/cf.py:
	  Removed proj from CFIter.

	* [r10867] topo/base/cf.py,
	  topo/learningfn/optimized.py,
	  topo/learningfn/projfn.py,
	  topo/responsefn/optimized.py,
	  topo/responsefn/projfn.py,
	  topo/transferfn/optimized.py:
	  Use flatcfs and flattened activity array (see svn r10838). Use
	  cf_type stored in CFIter rather than from projection.

	* [r10866] topo/base/cf.py,
	  topo/learningfn/optimized.py,
	  topo/learningfn/projfn.py:
	  CFPLearningFn.constant_sum_connection_rate() takes n_units
	  directly, rather than proj then accessing proj.n_units(), so that
	  CFIter only needs to store n_units.

	* [r10865] topo/base/cf.py:
	  Made CFIter store activity, flatcfs, and mask (in preparation for
	  it no longer storing the projection).

	* [r10864] topo/base/cf.py:
	  Fixed CFPLearningFn call signature.

2010-01-29  antolikjan

	* [r10863] contrib/modelfit.py:
	  changes

2010-01-28  ceball

	* [r10862] Makefile:
	  Pylint warnings should not appear as errors until we have
	  eliminated all of the invalid warnings.

2010-01-27  ceball

	* [r10861] _setup.py,
	  external/Makefile,
	  external/Python-2.5.1.tgz,
	  external/Python-2.6.4.tgz,
	  external/Python_64bit_pickle.diff,
	  external/Tkinter_bool_none.diff,
	  external/freetype-2.3.9.tar.gz,
	  external/idle_tk8.5.patch,
	  external/libpng-1.2.40.tar.gz,
	  external/numpy-1.2.1.tar.gz,
	  external/numpy-1.3.0.tar.gz,
	  setup_app.py,
	  setup_exe.py,
	  setup_ez.py:
	  Upgraded to Python 2.6. Includes: upgrade to numpy 1.3 (necessary
	  for Windows and Mac); freetype and libpng so they are no longer
	  dependencies that must be installed from elsewhere.
	  
	  (I.e. merge branch 'python26' from ceball_fiver.)

2010-01-24  antolikjan

	* [r10860]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  correction of standard retinal waves

2010-01-16  bilalkhancnsg

	* [r10859] contrib/lissom_audio.ty,
	  topo/pattern/audio.py,
	  topo/pattern/basic.py:
	  the audio pattern generator now populates a sheet with a
	  spectrogram, new signal transforms are pushed to the right,
	  oldest fall off the left, size of history is dictated by sheet
	  size

2010-01-15  aplebe

	* [r10858] topo/transferfn/optimized.py:
	  Added a check on the cumulative weight value in
	  CFPOF_DivisiveNormalizeL1_opt
	  and CFPOF_DivisiveNormalizeL1, to avoid dividing by 0 - it is
	  especially
	  deceitful for the optimized version, because no error is issued
	  and "NaN"
	  non-value are stored in the weights

2010-01-14  jbednar

	* [r10857]
	  topo/tests/lissom_oo_or_t000100.00_Size_Tuning.data:
	  Checked in new data for buildbot to pass; must be verified by J.
	  Antolik

	* [r10856] doc/Home/index_text.php:
	  Removed outdated qualifier

	* [r10855] doc/Home/news_text.php,
	  doc/News/index_text.php:
	  Cleaned up news for publishing

	* [r10854] topo/base/simulation.py:
	  Added alert

	* [r10853] topo/pattern/audio.py:
	  Clarified how Audio differs from OneDPowerSpectrum

2010-01-13  jbednar

	* [r10852] doc/News/index_text.php:
	  First pass at list of recent post-0.9.6 features

	* [r10851] ChangeLog.txt:
	  Brought up to date as of 9 Jan 2010

2010-01-11  bilalkhancnsg

	* [r10850] examples/run.py:
	  Commented a path check in examples/run.py when debugging on my
	  system, accidently uploaded it in that state. Now back to as it
	  should be

2010-01-10  bilalkhancnsg

	* [r10849] contrib/lissom_audio.ty,
	  examples/run.py,
	  sounds/sqr-1kHz.wav:
	  1. Connected Cochlea to MGBv with correct edge adjustments,
	  connected MGBv to A1 with correct edge adjustments, put in
	  lateral excitory and inhibitory connections in A1 as in V1, not
	  sure about these entirely at this stage. 2. Sounds can now be
	  placed in the sounds folder and loaded into the file, currently
	  there is a 1kHz square wave and a small drumbeat in there. 3.
	  Cochlea sheet gets populated with the frequency bands (fourier
	  analysis), these are passed up to the MGBv and from there to A1 -
	  i see the patterns of activity pass up but am not sure its 100%
	  correct at this stage (not quite sure how it should look)

2010-01-09  bilalkhancnsg

	* [r10848] contrib/lissom_audio.ty:
	  Added connections (afferent from mgb) and AI sheet based on
	  lissom, not accurate to AI yet, currently commented out till
	  discussion as to most appropriate parameters

	* [r10847] contrib/lissom_audio.ty:
	  Dimensions of cochlea are now accurate, errors in cochlea
	  orientation and connection corrected.

2010-01-09  jbednar

	* [r10846] ChangeLog.txt:
	  Brought up to date as of 11 Dec 2009

	* [r10845] topo/base/cf.py:
	  Upgraded alert

2010-01-05  antolikjan

	* [r10844] contrib/surround_analysis.py:
	  bug

	* [r10843] contrib/surround_analysis.py:
	  bug

	* [r10842] contrib/surround_analysis.py:
	  added FREQ parameter

	* [r10841] topo/base/cf.py:
	  bug correction

2010-01-05  aplebe

	* [r10840] topo/pattern/basic.py:
	  Minor modification of GaussiansCorner: two additional parameters,
	  the internal
	  angle and the control on the intersection points of the two
	  Gaussians. Now it is
	  possible to combina e cross shape, as before, and also a corner
	  shape, with
	  arbitrary angle. The dafault values of the new parameters
	  preserve
	  the behaviour of the previous version of the pattern.

2010-01-04  antolikjan

	* [r10839] contrib/surround_analysis.py:
	  small changes

2009-12-29  ceball

	* [r10838] topo/base/cf.py,
	  topo/base/projection.py,
	  topo/learningfn/optimized.py,
	  topo/learningfn/projfn.py,
	  topo/learningfn/som.py,
	  topo/misc/legacy.py,
	  topo/responsefn/optimized.py,
	  topo/sheet/basic.py,
	  topo/sheet/optimized.py,
	  topo/tests/testcf.py,
	  topo/transferfn/optimized.py:
	  Added flatcfs and made CFIter use it. Adjusted
	  CFPOF_DivisiveNormalizeL1_opt, CFPLF_Hebbian_opt,
	  CFPRF_DotProduct_opt, and optimized joint normalization to use
	  flatcfs. Removed CFProjection's _cfs attribute.

	* [r10837] topo/base/cf.py,
	  topo/base/projection.py:
	  Removed MaskedCFIter. CFIter is now MaskedCFIter, unless
	  ignore_sheet_mask is True. Simplified CFIter.

	* [r10836] topo/base/cf.py,
	  topo/base/projection.py,
	  topo/learningfn/optimized.py,
	  topo/sheet/optimized.py,
	  topo/transferfn/optimized.py:
	  CFPOF_DivisiveNormalizeL1_opt, CFPLF_Hebbian_opt, and optimized
	  joint normalization now respect the sheet mask.

	* [r10835] topo/base/cf.py,
	  topo/base/projection.py,
	  topo/projection/basic.py,
	  topo/sheet/basic.py,
	  topo/sheet/lissom.py,
	  topo/sheet/optimized.py,
	  topo/transferfn/optimized.py:
	  Moved 'activity masking' into CFIter and made active_units_mask
	  be a switch for apply_learn_output_fns and weight normalization.

	* [r10834] topo/base/cf.py,
	  topo/learningfn/optimized.py,
	  topo/projection/basic.py,
	  topo/sheet/basic.py,
	  topo/sheet/optimized.py,
	  topo/transferfn/optimized.py:
	  Tried to document the 'activity mask' used to decide whether or
	  not to apply weights_output_fns. Added ALERTs about sheet mask
	  being ignored by several functions.

2009-12-11  antolikjan

	* [r10833] contrib/modelfit.py:
	  many many changes

	* [r10832] contrib/surround_analysis.py:
	  numerouse modifications

	* [r10831] topo/command/pylabplots.py:
	  added frequency to features of orientation contrast measurement

2009-12-04  ceball

	* [r10830] topo/misc/util.py:
	  Added to comment.

	* [r10829] contrib/parameter_analysis,
	  contrib/parameter_analysis.cfg:
	  Bug fixes, cleaning, and simplification.

	* [r10828] contrib/lissom_oo_dr.ty:
	  Updated to use global_params, and for changes to Topographica's
	  code (e.g. output_fn -> output_fns).

2009-12-03  ceball

	* [r10827] contrib/parameter_analysis,
	  contrib/parameter_analysis.cfg,
	  doc/User_Manual/batch_text.php:
	  Added 'parameter_analysis' script for generating simple reports
	  from collections of batch runs.

2009-12-02  ceball

	* [r10826] contrib/parameter_search:
	  parameter_search prints where output will go.

	* [r10825] contrib/parameter_search,
	  contrib/parameter_search.cfg:
	  Updated parameter_search to allow it to be used simultaneously
	  from the same directory by different machines (by distinguishing
	  the names of generated scripts; this makes it clearer anyway).

2009-12-01  bilalkhancnsg

	* [r10824] contrib/lissom_audio.ty:
	  Added audio pattern generator.

2009-12-01  antolikjan

	* [r10823] contrib/modelfit.py:
	  load of changes

2009-11-30  ceball

	* [r10822] topo/command/basic.py:
	  Silently ignore parameter names in param_formatter.map that are
	  not present among the actual params.

	* [r10821] topo/command/basic.py:
	  Added ALERT.

	* [r10820] topo/misc/picklemain.py:
	  When pickling main, skip items beginning with an underscore.
	  Unlikely to have any effect on existing code.

	* [r10819] topo/misc/legacy.py:
	  Added missing import.

2009-11-30  jbednar

	* [r10818] doc/Downloads/index_text.php:
	  Added m4 to ubuntu prerequisites

	* [r10817] topo/pattern/basic.py:
	  Minor fixes to comments

2009-11-30  ceball

	* [r10816] topo/pattern/basic.py:
	  Added comment.

	* [r10815] topo/pattern/audio.py,
	  topo/pattern/basic.py:
	  Removed warnings.

	* [r10814] topo/pattern/audio.py,
	  topo/pattern/basic.py:
	  Moved OneDPowerSpectrum into topo/pattern/basic.py.

	* [r10813] topo/pattern/audio.py:
	  Finished implementing Audio and OneDPowerSpectrum pattern
	  generators.

2009-11-29  ceball

	* [r10812] topo/command/basic.py:
	  Allow specification of order for params in run_batch's directory
	  name.

2009-11-29  antolikjan

	* [r10811] contrib/surround_analysis.py:
	  updatez

2009-11-28  antolikjan

	* [r10810] topo/command/pylabplots.py:
	  bug correction in orientation contrast

	* [r10809] topo/command/pylabplots.py:
	  bug correction in orientation contrast

	* [r10808] contrib/surround_analysis.py:
	  bug correction

	* [r10807] topo/command/pylabplots.py:
	  minor changes to orientation contrast analysis

	* [r10806] topo/command/pylabplots.py:
	  made orientation center an explicit parameter in orientation
	  contrast analysis

2009-11-27  ceball

	* [r10805] doc/Downloads/git_text.php:
	  Added git admin info for sf.net.

2009-11-26  ceball

	* [r10804] topo/base/cf.py:
	  Fixed bug in change_bounds() introduced in r10792.

	* [r10803] topo/command/basic.py:
	  Fixed saving of script parameters that were specified to
	  run_batch().

	* [r10802] topo/command/basic.py:
	  Allow run_batch's directory name to use abbreviated parameter
	  names.

	* [r10801] topo/command/basic.py:
	  Made order_params_by_name() actually sort the names.

	* [r10800] topo/command/basic.py:
	  Added dirname_params_filter to run_batch(), allowing control over
	  how parameters will appear in the output directory name.

	* [r10799] topo/command/basic.py:
	  Added notes.

	* [r10798] param/parameterized.py,
	  topo/tests/testparameterizedobject.py:
	  Allow ParameterizedFunction.instance()s to pickle.

	* [r10797]
	  topo/tests/testparameterizedobject.py:
	  Repeat ParameterizedFunction tests on an instance (previously,
	  only the class was tested).

	* [r10796]
	  topo/tests/testparameterizedobject.py:
	  Minor alteration to test to make it easier to subclass.

2009-11-24  bilalkhancnsg

	* [r10795] contrib/lissom_audio.ty:
	  Initial version.

2009-11-24  ceball

	* [r10794] topo/pattern/audio.py:
	  Cleaned up formatting (no other change).

2009-11-24  antolikjan

	* [r10793] contrib/gc_alissom.ty:
	  made t_init external parameter in Relative HF

2009-11-24  ceball

	* [r10792] topo/base/cf.py,
	  topo/projection/basic.py:
	  Allow ConnectionFields to be instantiated easily by fixing
	  default arguments to __init__.

2009-11-22  antolikjan

	* [r10791] contrib/jacommands.py:
	  added lgn gain param

2009-11-21  antolikjan

	* [r10790] topo/transferfn/basic.py:
	  corrected bug in HalfRectify

	* [r10789] topo/transferfn/basic.py:
	  added gain to HalfRectify

	* [r10788] contrib/cc_lesi_final.ty:
	  added V1 Inh gain

2009-11-21  ceball

	* [r10787] doc/Downloads/git_text.php:
	  Added missing 'fetch' command and some formatting to git
	  documentation.

2009-11-20  ceball

	* [r10786] Makefile,
	  _setup.py,
	  create_topographica_script.py,
	  setup.py, setup_exe.py,
	  setup_ez.py:
	  Made a python script to create the topographica script. Now there
	  is only one routine to create the topographica script (except
	  that topographica-win also needs to be adjusted to use the new
	  script). Added 'topographica-other-python' target to Makefile,
	  for creating the topographica script when using some external
	  python interpreter.

	* [r10785] doc/Downloads/git_text.php:
	  Added more git documentation.

2009-11-20  antolikjan

	* [r10784] contrib/cc_lesi_final.ty:
	  lateral learning rate modification

2009-11-18  antolikjan

	* [r10783] contrib/cc_lesi_final.ty:
	  lateral learning rate modification

2009-11-18  ceball

	* [r10782] external/Makefile,
	  external/weave_keyerror.patch:
	  Fix KeyError problem with weave and Python 2.6
	  (http://projects.scipy.org/scipy/ticket/855).

	* [r10781] param/tk.py:
	  Fixed multiple 'ignored' Exception RuntimeErrors when starting
	  the gui with Python 2.6.

2009-11-18  KKudryavtsev

	* [r10780] /branches/kkudryavtsev_branch/topographica/mpidemo*:
	  Created branch for MPI work

2009-11-17  KKudryavtsev

	* [r10779] /branches/kkudryavtsev_branch:
	  

	* [r10778]
	  contrib/cc_lissom_oo_or_simple_rv.ty,
	  contrib/gc_lissom_oo_or_homeostatic_new.ty,
	  contrib/lgn_lateral.ty,
	  contrib/sparse_connectivity_model.ty,
	  examples/lissom_oo_or.ty,
	  examples/tiny.ty,
	  external/Makefile,
	  mpidemo, setup_ez.py:
	  

	* [r10777] examples/lissom_oo_or.ty,
	  examples/tiny.ty,
	  external/Makefile,
	  mpidemo*:
	  Mistakenly added files to trunk instead of branch

2009-11-17  antolikjan

	* [r10776] contrib/surround_analysis.py:
	  bug correction

2009-11-17  ceball

	* [r10775] topo/command/basic.py:
	  Added option to run_batch() for saving global_params to a pickle
	  for future inspection.

	* [r10774] topo/command/basic.py:
	  Added more info for git vc info in run_batch().

	* [r10773] topo/command/basic.py:
	  Added more information about the version of Topographica used for
	  batch runs.

	* [r10772] topo/command/basic.py:
	  Added information about host to batch output.

2009-11-16  ceball

	* [r10771] Makefile:
	  Restored xvfb-run's -a option, accidentally removed in a previous
	  commit.

	* [r10770] Makefile:
	  Restored warning if xvfb-run not found.

	* [r10769] Makefile:
	  Tried to simplify detection of xvfb-run.

	* [r10768] external:
	  Updated ignore list.

	* [r10767] external/libsndfile-1.0.20.tar.gz,
	  external/scikits.audiolab-0.10.2.tar.gz,
	  external/setuptools-0.6c11.tar.gz,
	  sounds/test.wav:
	  Fixed svn:mime-type on recently added files.

	* [r10766] Makefile:
	  Try to use xvfb-run for tests.

	* [r10765] external/Makefile,
	  sounds, sounds/test.wav,
	  topo/pattern/audio.py,
	  topo/tests/__init__.py,
	  topo/tests/testaudio.py:
	  Added sounds/ directory, and test sound from scikits.audiolab.
	  Added test file for audio.py.

	* [r10764] external/Makefile,
	  topo/pattern/audio.py:
	  Updated to new API for scikits.audiolab.

	* [r10763] external/Makefile,
	  external/libsndfile-1.0.17.tar.gz,
	  external/libsndfile-1.0.20.tar.gz,
	  external/pyaudiolab-0.6.6.tar.gz,
	  external/scikits.audiolab-0.10.2.tar.gz,
	  external/setuptools-0.6c11.tar.gz,
	  topo/pattern/audio.py:
	  Updated topo.pattern.audio and its dependencies to the stage that
	  at least the Audio PatternGenerator can be called without error.

2009-11-15  antolikjan

	* [r10762] contrib/gc_alissom.ty:
	  changes

2009-11-14  antolikjan

	* [r10761] contrib/modelfit.py:
	  parameter changes

2009-11-13  judelaw

	* [r10760] contrib/jacommands.py:
	  added surround size parameter to AddGC

2009-11-12  antolikjan

	* [r10759] contrib/surround_analysis.py:
	  bug correction

	* [r10758] contrib/surround_analysis.py:
	  bug correction

	* [r10757] contrib/modelfit.py:
	  parameter changes

2009-11-12  jbednar

	* [r10756] topo/base/cf.py,
	  topo/command/analysis.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotgroup.py:
	  Fix Projection Activity plots to show the correct label for the
	  source of the projection

2009-11-12  antolikjan

	* [r10755] contrib/modelfit.py:
	  parameter changes

	* [r10754] contrib/modelfit.py:
	  parameter changes

	* [r10753] contrib/surround_analysis.py:
	  bug correction

2009-11-12  ceball

	* [r10752] topo/tests/testplotfilesaver.py:
	  Minor change to error message.

	* [r10751] topo/tests/testplotfilesaver.py:
	  Improved error message.

2009-11-12  antolikjan

	* [r10750] contrib/surround_analysis.py:
	  bug correction

2009-11-11  antolikjan

	* [r10749] contrib/surround_analysis.py:
	  changed the orientation contrast preffered orientation
	  computation

2009-11-10  antolikjan

	* [r10748] contrib/modelfit.py:
	  parameter changes

2009-11-10  ceball

	* [r10747] topo/command/basic.py:
	  Extended VC info to include 'svn info' and 'svn status' (or
	  equivalents).

	* [r10746] topo/command/basic.py:
	  Fixed longstanding bug where 'Differences from' prefix could be
	  printed at the end of the diff file.

	* [r10745] topo/command/basic.py:
	  Added support for git and bzr version control systems when
	  recording diffs.

2009-11-10  antolikjan

	* [r10744] contrib/jacommands.py:
	  parameter changes

	* [r10743] contrib/modelfit.py:
	  parameter changes

2009-11-07  antolikjan

	* [r10742] contrib/modelfit.py:
	  added complex cell analysis stuff

2009-11-07  ceball

	* [r10741] param/tk.py:
	  GUI does not suspend when there is an error.

	* [r10740] topo/command/analysis.py:
	  Fix for SF.net #2872925: no more 'Projection Activity errors for
	  mousing'.

2009-11-06  antolikjan

	* [r10739] contrib/modelfit.py:
	  added complex cell analysis stuff

2009-11-04  kkudryavtsev

	* [r10738]
	  doc/Developer_Manual/optimization_text.php:
	  New version of optimisation page from Developers Manual

2009-11-04  ceball

	* [r10737] examples/lissom.ty:
	  Added notes about some known problems with the CR model in this
	  file (fixed in other versions).

2009-11-04  antolikjan

	* [r10736] contrib/modelfit.py:
	  changes

	* [r10735] contrib/modelfit.py:
	  changes

2009-11-04  ceball

	* [r10734] external/Makefile:
	  Updated note about MPI on DICE, and updated OpenMPI uninstall.

	* [r10733] param:
	  Added files to ignore.

	* [r10732] external:
	  More to ignore.

	* [r10731]
	  external/PyFlakes-divmod_r17780.tar.gz:
	  Fixed error in directory name.

	* [r10730] external/Makefile,
	  external/PyFlakes-divmod_r17780.tar.gz,
	  external/pyflakes-0.3.0.tar.gz:
	  Updated PyFlakes to a recent SVN version.

2009-11-04  antolikjan

	* [r10729] contrib/modelfit.py:
	  changes

	* [r10728] contrib/modelfit.py:
	  changes

	* [r10727] contrib/modelfit.py:
	  bug correction

	* [r10726] contrib/modelfit.py:
	  change of dataset#

2009-11-03  ceball

	* [r10725] external/Makefile,
	  external/pyflakes-0.3.0.tar.gz:
	  Added pyflakes (another tool like Lint).

	* [r10724] external/Makefile:
	  Added to comment about MPI on Eddie.

	* [r10723] external/Makefile,
	  external/Twisted-8.2.0.tar.gz,
	  external/foolscap-0.4.2.tar.gz,
	  external/ipython-0.10.tar.gz,
	  external/ipython-0.8.4.tar.gz,
	  external/pyOpenSSL-0.9.tar.gz,
	  external/zope.interface-3.3.0.tar.gz:
	  Upgraded to IPython 0.10. Added optional dependencies for
	  parallel IPython. Reverted r10721 (environment variables removed
	  in that commit are required under Ubuntu, at least). Added
	  various missing items from the 'clean' and 'uninstall' lists.

	* [r10722] external/Makefile:
	  Minor alterations to comments.

	* [r10721] external/Makefile:
	  Minor simplification.

	* [r10720] external/Makefile:
	  Fixed typo.

2009-11-03  antolikjan

	* [r10719] contrib/surround_analysis.py:
	  changed default contrasts

	* [r10718] contrib/modelfit.py:
	  change of dataset#

2009-11-03  ceball

	* [r10717] external/Makefile:
	  Fixed system MPI build of mpi4py, and added notes.

2009-11-03  antolikjan

	* [r10716] contrib/modelfit.py:
	  change of dataset#

2009-11-03  ceball

	* [r10715] external/Makefile,
	  external/mpi4py-1.1.0.tar.gz,
	  external/openmpi-1.3.3.tar.gz:
	  'make -C external mpi4py' seems to work on DICE and Ubuntu. Also
	  added a second mpi4py section, for using the system MPI (which I
	  couldn't get to work on DICE).

2009-11-03  antolikjan

	* [r10714] contrib/modelfit.py:
	  change of dataset#

	* [r10713] contrib/modelfit.py:
	  change of dataset#

	* [r10712] contrib/modelfit.py:
	  changes

	* [r10711] contrib/modelfit.py:
	  changes

2009-11-02  ceball

	* [r10710] external/Makefile:
	  Added sections for OpenMPI and mpi4py (but haven't uploaded
	  binaries).

2009-11-02  antolikjan

	* [r10709] contrib/modelfit.py:
	  change of datasets

	* [r10708] contrib/modelfit.py:
	  change of datasets

	* [r10707] contrib/modelfit.py:
	  change of datasets

	* [r10706] contrib/modelfit.py:
	  change of datasets

	* [r10705] contrib/modelfit.py:
	  change of datasets

	* [r10704] contrib/modelfit.py:
	  change of datasets

	* [r10703] contrib/modelfit.py:
	  change of datasets

2009-11-01  jbednar

	* [r10702] topo/sheet/basic.py:
	  Fixed typo in debug message

2009-11-01  ceball

	* [r10701] doc/buildbot/master.cfg:
	  Buildslave 'sunny' upgraded to latest Ubuntu (9.10).

	* [r10700] topo/tkgui/topoconsole.py:
	  Allow printing of full traceback from errors that occur during
	  gui callbacks.

2009-11-01  antolikjan

	* [r10699] contrib/cc_lesi_final_new.ty:
	  cclesi with inhibitory neurons in L4C

2009-11-01  ceball

	* [r10698] param/tk.py,
	  topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/__init__.py:
	  Allow param.tk to work with an external Tkinter.Tk instance.

2009-11-01  antolikjan

	* [r10697] contrib/cc_lesi_final.ty:
	  added treshold to V1Complex

	* [r10696] contrib/cc_lesi_final.ty:
	  bug correction

	* [r10695] contrib/cc_lesi_final.ty:
	  switched off noise in V1Complex

2009-10-31  ceball

	* [r10694] external/Makefile,
	  external/ipythonTk.diff,
	  external/ipythonTk.tar.gz,
	  external/ipython_view.diff,
	  topo/misc/commandline.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/topoconsole.py:
	  Removed IPythonTk-related code (which was all experimental: there
	  is too much to do to make it complete).

	* [r10693] contrib/complex_shapes_analysis.py,
	  contrib/expressionparam.py,
	  contrib/jm_plotting.py,
	  contrib/jsldefs.py,
	  contrib/rgbimages.py:
	  Changes in contrib/ missed when moving topo.param to param.

2009-10-31  antolikjan

	* [r10692] contrib/surround_analysis.py:
	  change title in neural dynamics figure

2009-10-30  antolikjan

	* [r10691] contrib/surround_analysis.py:
	  change title in neural dynamics figure

	* [r10690] contrib/surround_analysis.py:
	  change of parameters

2009-10-29  antolikjan

	* [r10689] contrib/jacommands.py:
	  bug correction

	* [r10688] contrib/jacommands.py:
	  change of parameters

2009-10-29  ceball

	* [r10687] doc/Future_Work/current_text.php:
	  Cleaned up by moving some tasks to trackers and reorganizing some
	  of the comments. Added my non-phd-related Topographica tasks
	  (commented out, until they find a better home).

	* [r10686] doc/Downloads/git_text.php,
	  doc/Future_Work/current_text.php:
	  Moved some git notes to the git document; deleted obsolete notes.

	* [r10685] doc/Forums/index_text.php:
	  Replaced tracker links with ones that show only open items, and
	  have the items ordered by priority.

2009-10-29  antolikjan

	* [r10684] contrib/surround_analysis.py:
	  change of parameters

	* [r10683] contrib/surround_analysis.py:
	  change of parameters

	* [r10682] contrib/surround_analysis.py:
	  change of parameters

	* [r10681] contrib/surround_analysis.py:
	  change of parameters

	* [r10680] contrib/surround_analysis.py:
	  change of parameters

	* [r10679] contrib/cc_lesi_final.ty:
	  made feedback delay external parameter

	* [r10678] contrib/cc_lesi_final.ty:
	  made smoothening external parameter

2009-10-28  antolikjan

	* [r10677] contrib/surround_analysis.py:
	  added saving of settling figure

	* [r10676] contrib/cc_lesi_final.ty:
	  made time constant external parameter

2009-10-28  ceball

	* [r10675] doc/Downloads/git_text.php:
	  Documented how to handle rebasing when the remote repository is
	  shared.

	* [r10674] doc/FAQ/index_text.php:
	  Removed platform-specific FAQ. Only contained one entry (for
	  Mac), and that was out of date.

	* [r10673] Makefile:
	  Added to notes.

	* [r10672] topo/__init__.py,
	  topo/analysis/featureresponses.py,
	  topo/analysis/vision.py,
	  topo/base/__init__.py,
	  topo/base/arrayutil.py,
	  topo/base/boundingregion.py,
	  topo/base/cf.py,
	  topo/base/functionfamily.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/base/sheetview.py,
	  topo/base/simulation.py,
	  topo/command/analysis.py,
	  topo/command/basic.py,
	  topo/command/pylabplots.py,
	  topo/coordmapper/basic.py,
	  topo/ep/basic.py,
	  topo/learningfn/basic.py,
	  topo/learningfn/optimized.py,
	  topo/learningfn/projfn.py,
	  topo/learningfn/som.py,
	  topo/misc/commandline.py,
	  topo/misc/filepath.py,
	  topo/misc/legacy.py,
	  topo/misc/picklemain.py,
	  topo/misc/robotics.py,
	  topo/misc/trace.py,
	  topo/misc/util.py,
	  topo/numbergen/basic.py,
	  topo/pattern/audio.py,
	  topo/pattern/basic.py,
	  topo/pattern/image.py,
	  topo/pattern/random.py,
	  topo/pattern/rds.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/projection/basic.py,
	  topo/responsefn/optimized.py,
	  topo/responsefn/projfn.py,
	  topo/sheet/basic.py,
	  topo/sheet/lissom.py,
	  topo/sheet/optimized.py,
	  topo/sheet/saccade.py,
	  topo/sheet/slissom.py,
	  topo/tests/__init__.py,
	  topo/tests/testCompositeParameter.txt,
	  topo/tests/testDynamicParameter.txt,
	  topo/tests/testEnumerationParameter.txt,
	  topo/tests/testNumberParameter.txt,
	  topo/tests/testParamOverrides.txt,
	  topo/tests/test_map_measurement.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testgmpynumber.txt,
	  topo/tests/testparameterizedobject.py,
	  topo/tests/testparametersframe.py,
	  topo/tests/testplot.py,
	  topo/tests/testsheetview.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/editor.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py,
	  topo/transferfn/basic.py,
	  topo/transferfn/optimized.py:
	  Whole directory missed from r10668. Subversion appears to have
	  trouble tracking directory moves!

2009-10-27  ceball

	* [r10671] Makefile:
	  make clean-pyc now removes pyc files from main directory.

	* [r10670] _setup.py:
	  Updated setup.py code for separate param package.

	* [r10669] param/parameterized.py:
	  Revert an unrelated change accidentally included in the previous
	  checkin.

	* [r10668] contrib/cbmisc.py,
	  contrib/cc_lesi_final.ty,
	  contrib/cc_lesi_oo_or.ty,
	  contrib/cc_lesi_oo_or_new.ty,
	  contrib/cc_lissom_oo_or_simple_rv.ty,
	  contrib/expressionparam.py,
	  contrib/hegdeessen.py,
	  contrib/jacommands.py,
	  contrib/jj_tiny.ty,
	  contrib/jm_cc_lissom.ty,
	  contrib/jm_cf_matrix.py,
	  contrib/jsldefs.py,
	  contrib/lesi_whisker_barrels.ty,
	  contrib/lissom_happyface.ty,
	  contrib/lissom_or_noshrinking_latswitch.ty,
	  contrib/lissom_rgb.ty,
	  contrib/rgbimages.py,
	  contrib/sparse_connectivity_LESI.ty,
	  contrib/sparse_connectivity_model.ty,
	  contrib/surround_analysis.py,
	  contrib/tracker.py,
	  doc/Developer_Manual/gui_text.php,
	  doc/FAQ/index_text.php,
	  doc/News/index_text.php,
	  doc/Reference_Manual/index_text.php,
	  doc/User_Manual/commandline_text.php,
	  doc/User_Manual/interfacing_text.php,
	  doc/User_Manual/overview_text.php,
	  doc/User_Manual/parameters_text.php,
	  doc/User_Manual/scripts_text.php,
	  examples/gca_lissom.ty,
	  examples/goodhill_network90.ty,
	  examples/hierarchical.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/perrinet_retina.ty,
	  examples/saccade_demo.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/tiny.ty, param,
	  param/__init__.py,
	  param/external.py,
	  param/externaltk,
	  param/externaltk/README,
	  param/externaltk/scrodget-2.1,
	  param/externaltk/scrodget-2.1/pkgIndex.tcl,
	  param/externaltk/scrodget-2.1/scrodget.tcl,
	  param/externaltk/snit-2.2.1,
	  param/externaltk/snit-2.2.1/main1.tcl,
	  param/externaltk/snit-2.2.1/main1_83.tcl,
	  param/externaltk/snit-2.2.1/main2.tcl,
	  param/externaltk/snit-2.2.1/pkgIndex.tcl,
	  param/externaltk/snit-2.2.1/snit.tcl,
	  param/externaltk/snit-2.2.1/snit2.tcl,
	  param/externaltk/snit-2.2.1/snit_tcl83_utils.tcl,
	  param/externaltk/snit-2.2.1/validate.tcl,
	  param/externaltk/tooltip-1.4,
	  param/externaltk/tooltip-1.4/pkgIndex.tcl,
	  param/externaltk/tooltip-1.4/tipstack.tcl,
	  param/externaltk/tooltip-1.4/tooltip.tcl,
	  param/parameterized.py,
	  param/tk.py, topo/param:
	  Moved topo.param to param.

2009-10-27  jbednar

	* [r10667] contrib/surround_analysis.py:
	  Fixed missing newline at end of file

	* [r10666] topo/pattern/basic.py:
	  Fixed TwoRectangles to allow non-square patterns

2009-10-27  antolikjan

	* [r10665] topo/sheet/basic.py:
	  made continuos to activate during learning step

	* [r10664] contrib/surround_analysis.py:
	  parameter changes

	* [r10663] contrib/surround_analysis.py:
	  parameter changes

	* [r10662] contrib/surround_analysis.py:
	  moved legend

	* [r10661] contrib/surround_analysis.py:
	  moved legend

2009-10-26  antolikjan

	* [r10660] contrib/surround_analysis.py:
	  bug correction

	* [r10659] contrib/surround_analysis.py:
	  parameter changes

	* [r10658] contrib/surround_analysis.py:
	  bug correction

	* [r10657] contrib/surround_analysis.py:
	  bug correction

	* [r10656] contrib/surround_analysis.py:
	  bug correction

	* [r10655] contrib/surround_analysis.py:
	  bug correction

	* [r10654] contrib/surround_analysis.py:
	  adadded run_dynamics_analysis

	* [r10653] contrib/surround_analysis.py:
	  added neuron analysis function

	* [r10652] contrib/surround_analysis.py:
	  added neuron analysis function

2009-10-18  antolikjan

	* [r10651] contrib/surround_analysis.py:
	  change of parameters

2009-10-17  antolikjan

	* [r10650] contrib/cc_lesi_final.ty:
	  more parameter changes

	* [r10649] contrib/cc_lesi_final.ty:
	  delay paremeter change

2009-10-16  antolikjan

	* [r10648] contrib/cc_lesi_final.ty:
	  Adding newest version of CCLESI

	* [r10647] contrib/surround_analysis.py:
	  bugg correction

	* [r10646] contrib/surround_analysis.py:
	  changes

	* [r10645] contrib/surround_analysis.py:
	  changes

	* [r10644] contrib/surround_analysis.py:
	  changes

	* [r10643] contrib/surround_analysis.py:
	  changes

2009-10-14  antolikjan

	* [r10642] contrib/modelfit.py:
	  moved Image to FileImage

	* [r10641] contrib/modelfit.py:
	  changes

	* [r10640] contrib/surround_analysis.py:
	  bug correction

2009-10-13  antolikjan

	* [r10639] contrib/surround_analysis.py:
	  bug correction

	* [r10638] contrib/surround_analysis.py:
	  changes

	* [r10637] contrib/surround_analysis.py:
	  change of parameters

2009-10-12  ceball

	* [r10636] doc/buildbot/master.cfg:
	  cider.csres was updated to OS X 10.6 (Snow Leopard).

2009-10-11  antolikjan

	* [r10635]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  corrected V1Simple lateral connections

2009-10-09  ceball

	* [r10634] setup.py:
	  Added note about creating pypi entry.

	* [r10633] _setup.py,
	  debian/control,
	  external/Makefile,
	  setup_app.py,
	  setup_ez.py,
	  topo/param/externaltk/README:
	  Updated information about external packages.

	* [r10632] doc/Downloads/index_text.php:
	  Added missing dependency from Ubuntu example.

	* [r10631] external/Makefile,
	  topo/param/externaltk,
	  topo/param/externaltk/scrodget-2.1,
	  topo/param/externaltk/scrodget-2.1/pkgIndex.tcl,
	  topo/param/externaltk/scrodget-2.1/scrodget.tcl,
	  topo/param/externaltk/snit-2.2.1,
	  topo/param/externaltk/snit-2.2.1/main1.tcl,
	  topo/param/externaltk/snit-2.2.1/main1_83.tcl,
	  topo/param/externaltk/snit-2.2.1/main2.tcl,
	  topo/param/externaltk/snit-2.2.1/pkgIndex.tcl,
	  topo/param/externaltk/snit-2.2.1/snit.tcl,
	  topo/param/externaltk/snit-2.2.1/snit2.tcl,
	  topo/param/externaltk/snit-2.2.1/snit_tcl83_utils.tcl,
	  topo/param/externaltk/snit-2.2.1/validate.tcl,
	  topo/param/externaltk/tooltip-1.4,
	  topo/param/externaltk/tooltip-1.4/pkgIndex.tcl,
	  topo/param/externaltk/tooltip-1.4/tipstack.tcl,
	  topo/param/externaltk/tooltip-1.4/tooltip.tcl,
	  topo/param/tk.py,
	  topo/tkgui/__init__.py:
	  Moved snit, scrodget, and tooltip into topo.param so that they do
	  not appear as external dependencies.

	* [r10630] doc/Downloads/git_text.php:
	  Fixed a few formatting errors.

2009-10-05  antolikjan

	* [r10629]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  Image -> FileImage

2009-10-04  ceball

	* [r10628] Makefile:
	  Added info about rpm generation.

	* [r10627] Makefile,
	  debian/python-scrodget.debhelper.log,
	  debian/python-scrodget.postinst.debhelper,
	  debian/python-scrodget.preinst.debhelper,
	  debian/python-scrodget.prerm.debhelper,
	  debian/python-scrodget.substvars:
	  Cleaned up debian/ directory.

	* [r10626] external:
	  Updated ignore list.

	* [r10625] debian/control:
	  Updated package dependencies (scrodget, not pyscrodget).

	* [r10624] _setup.py,
	  setup_ez.py:
	  Updated info about scrodget.

	* [r10623] external/Makefile,
	  external/pyscrodget-0.0.2_2.1.tar.gz,
	  external/scrodget-2.1.tar.gz,
	  topo/param/tk.py:
	  Moved pyscrodget wrapper to topo.param.tk.

	* [r10622] Makefile:
	  Added transcript of uploading .deb based on svn version of
	  Topographica.

	* [r10621] Makefile:
	  More to clean.

	* [r10620] external:
	  More to ignore.

2009-10-03  ceball

	* [r10619] Makefile:
	  Added info about signing deb.

	* [r10618] Makefile:
	  Corrected ppa upload command.

	* [r10617] Makefile:
	  Minor addition.

	* [r10616] Makefile,
	  debian/changelog,
	  debian/docs:
	  Added doc/ and examples/ to deb package.

	* [r10615] Makefile,
	  debian, debian/changelog,
	  debian/compat,
	  debian/control,
	  debian/copyright,
	  debian/docs,
	  debian/pycompat,
	  debian/python-scrodget.debhelper.log,
	  debian/python-scrodget.postinst.debhelper,
	  debian/python-scrodget.preinst.debhelper,
	  debian/python-scrodget.prerm.debhelper,
	  debian/python-scrodget.substvars,
	  debian/rules:
	  Sketch of creating an Ubuntu deb file.

	* [r10614] _setup.py,
	  setup.py, setup_app.py:
	  Topographica's 'python setup.py install' can work on Ubuntu 9.04
	  and Mac OS X 10.6 (with MacPorts).

	* [r10613] external/Makefile,
	  topo/__init__.py,
	  topo/base/sheetcoords.py,
	  topo/param/__init__.py,
	  topo/param/parameterized.py:
	  Added some notes relating to Python 2.6.

2009-10-01  ceball

	* [r10612] setup_ez.py:
	  First version that appears to work, depending only on Python,
	  Tcl/Tk, and GMP.

	* [r10611] topo/__init__.py:
	  Support setuptools-based installations of PIL.

	* [r10610] topo/misc/legacy.py,
	  topo/pattern/image.py:
	  Removed old 'Image=FileImage' hack.

2009-10-01  antolikjan

	* [r10609]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  Removed ExpLinear

2009-09-30  ceball

	* [r10608] doc/Downloads/git_text.php:
	  Added more info to git docs about sharing.

	* [r10607] doc/Downloads/git_text.php:
	  Added more to git docs.

	* [r10606] doc/Downloads/git_text.php:
	  Added more to git docs.

	* [r10605] doc/Downloads/git_text.php:
	  Added clarification.

	* [r10604] doc/Downloads/git_text.php:
	  Updated sharing command.

	* [r10603] doc/Downloads/git_text.php:
	  Added warning.

	* [r10602] doc/Downloads/git_text.php:
	  Added more info about sharing git repository.

	* [r10601] doc/Downloads/git_text.php:
	  Began extending git documentation to cover more advanced usage.

	* [r10600] external/Makefile:
	  Added link to relevant mailing list item.

	* [r10599] external/Makefile,
	  external/matplotlib-0.91.4.tar.gz,
	  external/matplotlib-0.99.1.1.tar.gz,
	  topo/command/pylabplots.py:
	  Upgraded to matplotlib 0.99.1.1.

	* [r10598] doc/buildbot/index.html,
	  doc/buildbot/master.cfg:
	  Added jupiter3 buildslave.

2009-09-26  ceball

	* [r10597] external/Makefile,
	  external/weave.diff:
	  Changes missed from r10596 (patch to make weave not depend on
	  scipy).

	* [r10596] external/Makefile:
	  Fixed installation of weave. SF #2791212 is now fixed.

2009-09-24  antolikjan

	* [r10595] external/Makefile:
	  corrected dependency of weave on old scipy

2009-09-23  antolikjan

	* [r10594] external/Makefile,
	  external/numpy-1.1.1.tar.gz,
	  external/numpy-1.2.1.tar.gz,
	  external/numpy.diff,
	  external/scipy-0.5.2.tar.gz,
	  external/scipy-0.7.1.tar.gz,
	  external/scipy-site.cfg:
	  Upgraded numpy and scipy, and edited the example scipy-site.cfg
	  to be suitable for DICE.

2009-09-22  antolikjan

	* [r10593] contrib/surround_analysis.py:
	  further modifications

2009-09-22  jbednar

	* [r10592] topo/plotting/plotgroup.py:
	  Trivial fixes to comments and docstrings

2009-09-21  antolikjan

	* [r10591]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  changes to lateral connectivity in layer 4C

2009-09-19  antolikjan

	* [r10590] contrib/cc_lesi_oo_or_new.ty:
	  added treshold to V1 complex

2009-09-18  ceball

	* [r10589] topo/base/boundingregion.py,
	  topo/pattern/image.py:
	  Small changes reducing attribute lookups inside two particular
	  loops, improving the performance of the Image pattern generators.

	* [r10588] topo/transferfn/basic.py:
	  Clean up DivisiveNormalizeLinf (to use numpy max and abs; vastly
	  improves performance).

2009-09-17  ceball

	* [r10587] doc/buildbot/master.cfg:
	  buildbot: examples/ and doc/ no longer split from 'python
	  setup.py install' archive.

	* [r10586] Makefile:
	  Archive produced for 'python setup.py install' now contains
	  examples/ and doc/.

	* [r10585] topo/param/tk.py:
	  If Topographica doesn't have 'grab', don't try to get grab for
	  window causing the error.

2009-09-16  antolikjan

	* [r10584] contrib/surround_analysis.py:
	  few more changes

2009-09-16  ceball

	* [r10583] doc/buildbot/master.cfg:
	  Added archive-making slave.

2009-09-15  antolikjan

	* [r10582] contrib/surround_analysis.py:
	  few more changes

2009-09-14  antolikjan

	* [r10581] contrib/surround_analysis.py:
	  few more changes

2009-09-13  ceball

	* [r10580] setup_ez.py:
	  Various updates. Getting closer to working...

	* [r10579] doc/Developer_Manual:
	  More to ignore.

	* [r10578] external:
	  Updated files to ignore.

	* [r10577] Makefile:
	  First go at making archives suitable for packaging.

	* [r10576] _setup.py,
	  setup.py:
	  setup.py fixes.

	* [r10575] topo/command/analysis.py:
	  Renamed variable (to avoid potential clash). Should be no visible
	  change.

2009-09-10  antolikjan

	* [r10574] contrib/surround_analysis.py:
	  few parameter changes

2009-09-08  antolikjan

	* [r10573] contrib/modelfit.py:
	  further improvements

	* [r10572]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  further improvements

2009-09-07  antolikjan

	* [r10571] contrib/modelfit.py:
	  further improvements

	* [r10570] contrib/surround_analysis.py:
	  moved surround analysis from jaccomands into sepparate file

2009-09-06  antolikjan

	* [r10569] contrib/modelfit.py:
	  few more changes

	* [r10568] contrib/modelfit.py:
	  few more changes

	* [r10567]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  few more changes

2009-09-02  ceball

	* [r10566] topo/tkgui/topoconsole.py:
	  Added ALERT.

	* [r10565] topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/sheet/basic.py:
	  Moved definition of output_fns to Sheet. (Fixes problem where
	  state_push()/pop() assume output_fns are present in Sheet.)

2009-08-30  ceball

	* [r10564] topo/command/pylabplots.py,
	  topo/plotting/plotgroup.py:
	  Minor clarifcation of docs.

	* [r10563] topo/plotting/plotgroup.py:
	  Renamed normalize='Joint' to normalize='JointProjections'.

	* [r10562] topo/plotting/plotgroup.py:
	  Renamed normalize='All' to normalize='AllTogether'.

	* [r10561] topo/command/analysis.py,
	  topo/command/pylabplots.py,
	  topo/plotting/plotgroup.py,
	  topo/sheet/basic.py:
	  Renamed normalize='Independent' to normalize='Individually'.

	* [r10560] topo/tkgui/topoconsole.py:
	  Hide any error generated while trying to find an appropriate
	  status bar for displaying messages.

	* [r10559] topo/param/tk.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Progress bars, messages, warnings, and errors should now display
	  on the appropriate status bar. This is quite a significant
	  change, and is likely to need tuning based on feedback from
	  users.

	* [r10558] topo/param/__init__.py,
	  topo/tkgui/projectionpanel.py:
	  Hacked support for exclusive right and top bounds when editing
	  parameters in the GUI.

2009-08-26  antolikjan

	* [r10557]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  new external parameter lgn_tresh

2009-08-22  antolikjan

	* [r10556]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  new external parameter lgn_density

2009-08-21  antolikjan

	* [r10555]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  new external parameter RingScale

	* [r10554]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  further changes

	* [r10553]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  further changes

2009-08-20  antolikjan

	* [r10552]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  further changes

2009-08-18  antolikjan

	* [r10551] contrib/jacommands.py:
	  surround modulation analysis, change of contrast parameters

2009-08-14  antolikjan

	* [r10550]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  added external parameterers and made latencies shorter

	* [r10549] contrib/jacommands.py:
	  surround modulation analysis minor changes

2009-08-13  antolikjan

	* [r10548] contrib/jaanalysis.py:
	  lot of changes imported from Eddie version

2009-08-07  antolikjan

	* [r10547] contrib/jacommands.py:
	  Further improvements to the surround modulation analysis

2009-08-06  antolikjan

	* [r10546] contrib/jacommands.py:
	  Improvements to the surround modulation analysis

2009-08-04  antolikjan

	* [r10545]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  Parameter changes

	* [r10544]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  Parameter changes

	* [r10543]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  Parameter changes

2009-08-03  jbednar

	* [r10542] examples/lissom.ty:
	  Fixed outdated dims='All' to work as dims=[] instead. Fixed SF
	  map measurement to set frequencies parameter before instantiation
	  of measure_sine_pref, so that the value will be respected.

	* [r10541] topo/command/analysis.py:
	  Added PhaseDisparity Preference&Selectivity plot

2009-08-03  antolikjan

	* [r10540] contrib/jacommands.py:
	  Corrected some bugs in surround modulation measurements

	* [r10539] contrib/cc_lesi_oo_or_new.ty:
	  Addapted to new GC parameters

	* [r10538]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  Made to use expander

2009-08-03  jbednar

	* [r10537] doc/Downloads/index_text.php,
	  topo/transferfn/basic.py:
	  Minor fix to doc

2009-08-02  antolikjan

	* [r10536] contrib/jacommands.py:
	  Added new pattern generator - Expander - increases size of
	  patterns

2009-07-30  ceball

	* [r10535] topo/base/simulation.py:
	  Added note.

	* [r10534] doc/Downloads/index_text.php:
	  Mentioned about using a 64-bit platform for large simulations.

2009-07-29  jbednar

	* [r10533] contrib/basic.py,
	  contrib/cc_lesi_oo_or.ty,
	  contrib/cc_lissom_oo_or_simple_rv.ty,
	  contrib/jsldefs.py,
	  contrib/lesi_judethesisversion.ty,
	  contrib/lesi_whisker_barrels.ty,
	  contrib/lissom.ty,
	  contrib/lissom_oo_or_homeostatic.ty,
	  contrib/lissom_oo_or_homeostatic_tracked.ty,
	  contrib/lissom_rgb.ty,
	  contrib/modelfit.py,
	  contrib/rgbhsv.py,
	  contrib/sparse_connectivity_LESI.ty,
	  contrib/sparse_connectivity_model.ty,
	  contrib/species_cf_jitter.ty,
	  contrib/species_lat_jitter.ty,
	  contrib/species_pf_jitter.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lissom.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/perrinet_retina_pynest.py,
	  examples/sullivan_neurocomputing04.ty,
	  examples/tiny.ty,
	  topo/analysis/featureresponses.py,
	  topo/analysis/vision.py,
	  topo/base/cf.py,
	  topo/base/sheetcoords.py,
	  topo/base/sheetview.py,
	  topo/command/analysis.py,
	  topo/command/basic.py,
	  topo/command/pylabplots.py,
	  topo/coordmapper/basic.py,
	  topo/learningfn/basic.py,
	  topo/learningfn/optimized.py,
	  topo/learningfn/projfn.py,
	  topo/learningfn/som.py,
	  topo/pattern/basic.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/projection/basic.py,
	  topo/responsefn/optimized.py,
	  topo/responsefn/projfn.py,
	  topo/sheet/lissom.py,
	  topo/sheet/slissom.py,
	  topo/tests/testoutputfnsbasic.py,
	  topo/tests/testplot.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testsheet.py,
	  topo/tests/testsheetview.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/editor.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py,
	  topo/transferfn/basic.py:
	  Expanded tabs to spaces to avoid problems with some editors

	* [r10532] contrib/hegdeessen.py:
	  Fixed typos

2009-07-28  ceball

	* [r10531] topo/analysis/featureresponses.py:
	  Fixed variable name. (Hue map measurement for separate R, G, and
	  B retinas has presumably been broken since I added support for
	  hue map measurement using a single RGB retina.)

2009-07-27  ceball

	* [r10530] topo/plotting/bitmap.py:
	  When enlarging an image by an integer factor, avoid PIL by using
	  numpy (PIL has a bug). Mitigates SF #2820821.

2009-07-26  ceball

	* [r10529] topo/misc/commandline.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/topoconsole.py:
	  Simplified dock-by-default for -G option.

	* [r10528] topo/plotting/plot.py:
	  Fix for #1962478 ('Status bar information bug on the map
	  window'). Actually caused by TemplatePlot instances sharing the
	  same view_dict (the Sheet's sheet_views dictionary).

2009-07-25  ceball

	* [r10527] topo/plotting/plotgroup.py:
	  Fixed mistake in r10524 (mistakenly introduced a space into plot
	  labels).

	* [r10526] topo/analysis/featureresponses.py:
	  Set MeasureResponseCommand's pattern_presenter parameter to
	  instantiate its value, since the value will be mutable.

	* [r10525] contrib/cbmisc.py:
	  Updated my analysis function.

2009-07-24  ceball

	* [r10524] examples/lissom.ty,
	  topo/command/analysis.py,
	  topo/command/pylabplots.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/testpattern.py:
	  Implemented joint normalization for plotting (SF #1829844).
	  Includes some clean-up of the PlotGroup classes. Various parts of
	  plotgroup.py and plot.py still require cleaning, and the GUI's
	  normalization widget placement also needs to be sorted out.

	* [r10523] topo/param/__init__.py:
	  Fix for SF #2661510. (Intermediate checkin: will be cleaned up.

2009-07-23  ceball

	* [r10522] doc/Downloads/git_text.php:
	  Added link and hint.

	* [r10521] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Fixed GUI's dynamic coordinates: now there is no systematic
	  offset (SF #2127012), and coordinates work on projection and CF
	  panels (ALERT). Also: changed plot borders to be drawn by tk
	  rather than by us.

	* [r10520] _setup.py:
	  Removed package that no longer exists.

	* [r10519] topo/command/basic.py:
	  Added comment about pickling.

	* [r10518] Makefile:
	  File missed from previous commit.

	* [r10517] external/Makefile,
	  external/idle_tk8.5.patch:
	  Experimental: 'make topographicagui; ./topographicagui' to try
	  using Topographica with IDLE.

	* [r10516] external/Makefile,
	  external/ipythonTk.diff,
	  external/ipythonTk.tar.gz,
	  external/ipython_view.diff,
	  topo/ipythonTk,
	  topo/tkgui/topoconsole.py:
	  Moved topo.ipythonTk to an external package (plus patches to fix
	  some problems). The package contains unmodified copies of
	  ipython_view.py from Accerciser and ipythonTk.py from CCP1GUI.
	  ipython_view.py is now part of new IPython releases, so we should
	  just use IPython's version eventaully. (IPython focuses on wx,
	  though, so there is no equivalent of ipythonTk.py in IPython.)

2009-07-22  ceball

	* [r10515] topo/tkgui/__init__.py:
	  File missed from previous commit.

	* [r10514] topo/misc/commandline.py:
	  Hack to allow -G to have windows docked by default.

	* [r10513] topo/ipythonTk/ipython_view.py:
	  ipythonTk: Apparently fixed tab completion.

2009-07-17  jmoudrik

	* [r10512] contrib/jm_plotting.py:
	  Added title for the Phase preference scatter plot

2009-07-15  antolikjan

	* [r10511] contrib/modelfit.py:
	  added backpropagation

2009-07-14  antolikjan

	* [r10510]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  switching back to uncorrelated

2009-07-13  antolikjan

	* [r10509] contrib/modelfit.py:
	  changed default density

	* [r10508] contrib/modelfit.py:
	  added learning rate parameter'

	* [r10507] contrib/modelfit.py:
	  made the file 'executable'

	* [r10506] contrib/modelfit.py:
	  added external parameters

2009-07-13  ceball

	* [r10505] topo/param/parameterized.py:
	  Updated comment.

2009-07-13  machalekj

	* [r10504] contrib/complex_shapes_analysis.py:
	  Added python header info to analysis plots.

2009-07-12  machalekj

	* [r10503] contrib/complex_shapes_analysis.py,
	  contrib/hegdeessen.py:
	  Modification of Hegde and Van Essen stimuli as were used in
	  complex shapes analysis in bachalor thesis of Machalek. Added
	  script with analysis plots.

2009-07-12  jmoudrik

	* [r10502] contrib/jm_analysis.py,
	  contrib/jm_cc_lissom.ty,
	  contrib/jm_cf_matrix.py,
	  contrib/jm_plotting.py,
	  contrib/jm_smooth.py:
	  Merged jm_smooth into jm_analysis; jm_analysis splitted to
	  analysis and plotting (jm_plotting).
	  Added an extension of complex cell model.

2009-07-12  antolikjan

	* [r10501] contrib/gc_alissom.ty:
	  increased the retinal density in order to improve RV LGN response

2009-07-11  antolikjan

	* [r10500]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  switching of correlated RV

2009-07-09  ceball

	* [r10499] contrib/cbmisc.py:
	  Updated my analysis functions.

2009-07-09  antolikjan

	* [r10498] contrib/modelfit.py:
	  new models

2009-07-08  ceball

	* [r10497] contrib/cbmisc.py:
	  Added function to create single-eye plotgroups. Added function I
	  use for OR/OD/CR simulations.

	* [r10496] topo/analysis/featureresponses.py:
	  Added generator_sheets parameter to MeasureResponseCommand, to
	  simplify setting this parameter on the PatternPresenter.

	* [r10495] topo/analysis/featureresponses.py:
	  Added sheet_views_prefix to allow distinction between e.g.
	  OrientationPreference and LeftRetina OrientationPreference.

	* [r10494] topo/analysis/featureresponses.py:
	  Put blank patterns in GeneratorSheets that are not being used.

	* [r10493] topo/analysis/featureresponses.py:
	  Added generator_sheets parameter to PatternPresenter (allowing
	  restriction of set of GeneratorSheets).

	* [r10492] topo/analysis/featureresponses.py:
	  Set instantiate=True for pattern_presenter pararameter of
	  SinusoidalMeasureResponseCommand (since it defaults to a mutable
	  object).

2009-07-07  jbednar

	* [r10491] examples/lissom.ty:
	  Added speed parameter, and allowed linear interpolation between
	  integer values

	* [r10490] topo/misc/util.py:
	  Added linearly_interpolate

2009-07-03  ceball

	* [r10489] contrib/parameter_search,
	  contrib/parameter_search.cfg:
	  Tidying. Should be no visible change.

	* [r10488] contrib/parameter_search,
	  contrib/parameter_search.cfg:
	  Saves combinations file. Saves command used to launch
	  parameter_search. Saves everything (all run_batch() directories,
	  combinations file, etc) into one directory.

	* [r10487] contrib/parameter_search,
	  contrib/parameter_search.cfg:
	  Added ability to pass dirname_prefix to run_batch().

	* [r10486] topo/command/basic.py:
	  Added name_time_format parameter to run_batch().

	* [r10485] topo/command/basic.py:
	  Added optional dirname_prefix to run_batch().

2009-07-01  ceball

	* [r10484] topo/base/cf.py:
	  Removed unused import.

	* [r10483] topo/base/sheetview.py:
	  Replaced tabs with spaces.

	* [r10482] topo/base/sheetcoords.py:
	  Removed unused import.

2009-07-01  antolikjan

	* [r10481]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  Minnor changes

2009-06-30  ceball

	* [r10480] doc/Downloads/git_text.php,
	  doc/Downloads/index_text.php:
	  Updated some documentation relating to git.

2009-06-26  ceball

	* [r10479] topo/base/cf.py,
	  topo/misc/legacy.py,
	  topo/projection/basic.py,
	  topo/tests/testcf.py:
	  ConnectionField no longer stores x and y.

	* [r10478] topo/base/sheet.py:
	  Removed never-been-used sheet_offset() method.

	* [r10477] examples/hierarchical.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  topo/base/cf.py,
	  topo/projection/basic.py,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty:
	  Added ResizableCFProjection and removed bounds-changing-related
	  code from CFProjection and ConnectionField.

	* [r10476] topo/base/cf.py:
	  Added _generate_coords() method to CFProjection, with the
	  intention of allowing subclasses to e.g. store the generated
	  coords. Improved simple_vectorize() to handle functions with any
	  number of outputs.

	* [r10475] topo/base/sheet.py:
	  Added method to get arrays of X and Y sheet coordinates.

	* [r10474] topo/base/cf.py,
	  topo/projection/basic.py:
	  Tried to simplify CFProjection by adding a _create_cf() method
	  and avoiding a visible loop through the dest sheet units.

	* [r10473] topo/base/sheet.py:
	  Added ALERT.

2009-06-26  antolikjan

	* [r10472]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  Minor changes

2009-06-25  ceball

	* [r10471] topo/param/__init__.py:
	  Added ALERT.

2009-06-25  antolikjan

	* [r10470] contrib/jacommands.py:
	  variouse changes to surround analysis

	* [r10469] topo/command/pylabplots.py:
	  corrected the units in measure_orientation_contrast

	* [r10468] contrib/gc_alissom.ty:
	  Minor changes

2009-06-23  ceball

	* [r10467] topo/base/cf.py,
	  topo/base/sheetcoords.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/projection/basic.py,
	  topo/tests/testsheet.py:
	  Slice no longer stores bounds. Reduces memory usage (as recorded
	  in 'memuse_rSlice_no_bounds.out'). Could increase plotting times
	  - not sure.

	* [r10466] topo/base/cf.py:
	  Corrected an error in CFProjection.change_bounds(): the
	  bounds_template that is stored after changing bounds is now that
	  which corresponds exactly to the slice. Should make no change to
	  any of our simulations, because the correct slice was being
	  passed to the ConnectionField; CFProjection's bounds_template is
	  not currently used by anything after the point it is stored.

2009-06-23  antolikjan

	* [r10465] contrib/modelfit.py:
	  Added motion to the model

	* [r10464] contrib/gc_alissom.ty:
	  Overhaul of gain control and consequently parameters

	* [r10463]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  Overhaul of gain control and consequently parameters

	* [r10462] contrib/jacommands.py:
	  GC update and LGN channel randomization updates

	* [r10461] topo/command/basic.py:
	  Adding the wipe_out_activity and clear_even_queue into the
	  analysis pre-presentation hooks

	* [r10460] topo/sheet/basic.py:
	  Addjusted the JointNormalizingCFSheet_Continuous such that it
	  works more in line with LISSOM

	* [r10459] topo/analysis/featureresponses.py:
	  pre presentation hooks are now set in different place

	* [r10458] topo/tkgui/testpattern.py:
	  Adjusted test pattern so it clears the activity and state of the
	  network properly before presenting stimulus

2009-06-19  ceball

	* [r10457] doc/buildbot/master.cfg:
	  Fixed 'warn on errors' in various cases (e.g. for make lint-base,
	  which niow only causes warnings even if pylint reports errors
	  with the code).

2009-06-18  jbednar

	* [r10456] topo/responsefn/optimized.py:
	  Replaced C code with macros; verified that the .cpp code did not
	  change

	* [r10455] topo/misc/inlinec.py:
	  Added macro for looking up contiguous array from slot

	* [r10454] topo/responsefn/optimized.py:
	  Further reorganized C code to match macros

	* [r10453] topo/responsefn/optimized.py:
	  Reorganized C code to match macros

2009-06-18  ceball

	* [r10452] topo/tests/test_script.py:
	  Run current density combinations to 20000 rather than 1000.

2009-06-17  ceball

	* [r10451] external:
	  Ignore guppy.

	* [r10450] external/Makefile,
	  external/logilab-astng-0.17.2.tar.gz,
	  external/logilab-astng-0.19.0.tar.gz,
	  external/logilab-common-0.25.0.tar.gz,
	  external/logilab-common-0.41.0.tar.gz,
	  external/pylint-0.14.0.tar.gz,
	  external/pylint-0.18.0.tar.gz:
	  Upgraded pylint.

2009-06-17  antolikjan

	* [r10449] contrib/gc_alissom.ty:
	  added two new natural image datasets

2009-06-16  antolikjan

	* [r10448] contrib/cc_lesi_oo_or_new.ty:
	  made V1 complex inh neurons have external parameter defining
	  their threshold

2009-06-16  machalekj

	* [r10447] contrib/hegdeessen.py:
	  48 Grating and 80 contour stimuli used in Hegde and Van Essen
	  works. 5 new patterns classes added.

2009-06-15  antolikjan

	* [r10446] contrib/cc_lesi_oo_or_new.ty:
	  made V1 complex inh neurons have external parameter defining
	  their threshold

	* [r10445] topo/command/pylabplots.py:
	  Modified the Orientation Contrast analysis so it better reflects
	  the published figures

	* [r10444] contrib/jacommands.py:
	  Added surround modulation analysis batch test

	* [r10443] contrib/cc_lesi_oo_or.ty:
	  minor parameter changes

	* [r10442] topo/pattern/basic.py:
	  Removed some spurious parameters in the OrientationContrast
	  pattern

2009-06-15  ceball

	* [r10441] topo/base/cf.py,
	  topo/misc/legacy.py,
	  topo/projection/basic.py:
	  ConnectionField no longer stores input_sheet.

	* [r10440] topo/projection/basic.py:
	  Fixed SharedWeightCFProjection.n_bytes(): count
	  input_sheet_slice, not weights_slice.

2009-06-14  ceball

	* [r10439] topo/misc/legacy.py:
	  File missed from the previous checkin.

	* [r10438] topo/base/cf.py,
	  topo/projection/basic.py:
	  ConnectionField no longer stores weights_slice.

	* [r10437] topo/projection/basic.py:
	  Fixed error in recent commit.

	* [r10436] topo/base/cf.py,
	  topo/misc/legacy.py,
	  topo/projection/basic.py:
	  Made ConnectionField no longer have a __dict__ (to save memory).

	* [r10435] examples/saccade_demo.ty,
	  topo/base/cf.py,
	  topo/projection/basic.py:
	  Moved min_matrix_radius from cf to projection.

	* [r10434] topo/base/cf.py,
	  topo/param/parameterized.py,
	  topo/projection/basic.py:
	  Made ConnectionField inherit from object rather than
	  Parameterized (to reduce memory usage). Intermediate checkin:
	  added slots for all attributes except _has_norm_total; still have
	  to remove __dict__.

	* [r10433] topo/misc/legacy.py:
	  Added support for __setstate__ for classes that used to - but no
	  longer - have __setstate__.

	* [r10432] topo/misc/legacy.py:
	  Removed stray import.

2009-06-14  antolikjan

	* [r10431]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  made LGN center size external parameter

2009-06-14  jbednar

	* [r10430] topo/learningfn/optimized.py,
	  topo/responsefn/optimized.py,
	  topo/sheet/optimized.py,
	  topo/transferfn/optimized.py:
	  Changed double * to npfloat * to allow changing float type ;
	  should be no change in function or performance

	* [r10429] topo/sheet/basic.py:
	  Removed unused import

2009-06-13  jbednar

	* [r10428] topo/learningfn/optimized.py:
	  Simplified C code based on new macros in c_header

	* [r10427] topo/misc/inlinec.py:
	  Added c_header with declarations and macros

	* [r10426] topo/learningfn/optimized.py:
	  Reordered statements and renamed temporaries to match macro
	  version to be checked in next, to allow direct comparison of .cpp
	  code

	* [r10425] topo/base/sheet.py:
	  Made numpy float type explicit

2009-06-13  ceball

	* [r10424] doc/Downloads/index_text.php,
	  external/Makefile:
	  Added documentation about package required for antialiased fonts
	  (fixes SF #2791479).

	* [r10423] _setup.py:
	  Added list of dependencies in the form of what I had to install
	  on Ubuntu 9.04.

2009-06-12  jbednar

	* [r10422]
	  doc/Developer_Manual/memuse_text.php:
	  Fixed typo

	* [r10421] topo/analysis/featureresponses.py:
	  Removed changes from r10404, making a correct fix for RF plots
	  instead

	* [r10420] doc/shared/util.php:
	  Added fns for building the Developer Manual

	* [r10419] topo/command/basic.py:
	  Added docstring

	* [r10418] doc/Developer_Manual/index_text.php,
	  doc/Developer_Manual/memuse_text.php,
	  doc/Developer_Manual/optimization_text.php,
	  topo/misc/memuse.py:
	  Added documentation about optimizing memory usage

2009-06-12  judelaw

	* [r10417] contrib/laminar_oo_or.ty,
	  contrib/laminar_or.ty,
	  contrib/lissom_oo_or_species.ty,
	  contrib/lissom_oo_or_species_tracked.ty,
	  contrib/species_lateral_sparsity.ty:
	  removed old versions replaced by newer files

	* [r10416] contrib/lesi_judethesisversion.ty:
	  Version which matches simulations presented in thesis

	* [r10415] contrib/species_lat_jitter.ty:
	  Updated to match simulations presented in thesis

	* [r10414] contrib/species_pf_jitter.ty:
	  Updated to match simulations presented in thesis

	* [r10413] contrib/jsldefs.py,
	  contrib/lesi.ty,
	  contrib/species_cf_jitter.ty,
	  topo/command/pylabplots.py,
	  topo/coordmapper/basic.py:
	  added NormalJitter for jitter chosen from a Normal distribution

	* [r10412] topo/base/arrayutil.py:
	  added clip_upper function

	* [r10411] topo/transferfn/basic.py:
	  added Threshold function that sets values below a particular
	  value to zero but leaves others unchanged

	* [r10410] topo/analysis/featureresponses.py:
	  added multiplier and offset parameters to Feature class so that
	  individual SheetViews can be maipulated separately for each
	  feature

2009-06-12  ceball

	* [r10409] topo/param/tk.py:
	  Fixed typo.

	* [r10408] topo/param/tk.py:
	  Fixed part of SF bug #2805379 (only Parameterized classes can be
	  represented by ClassSelector, but GUI was attempting to use
	  ClassSelector for e.g. floats when editing a list).

2009-06-11  jbednar

	* [r10407] topo/misc/memuse.py:
	  Made topsize work for small-size process ids

2009-06-11  ceball

	* [r10406] Makefile,
	  topo/tkgui/topoconsole.py:
	  Allow exit status to be passed to quit_topographica(), and use it
	  for gui-tests.

	* [r10405] topo/tkgui/topoconsole.py:
	  Attempt to fix strange Windows 'unusual termination' error: one
	  cause of the error is quitting with matplotlib windows open.

2009-06-11  jbednar

	* [r10404] topo/analysis/featureresponses.py:
	  Updated ReverseCorrelation to match recent changes to
	  FeatureResponses; may help fix RF plots

	* [r10403] topo/analysis/featureresponses.py:
	  Suppressed message about number of test patterns being printed

	* [r10402] topo/misc/memuse.py:
	  Shortened default message length

	* [r10401] topo/projection/basic.py:
	  Removed Python variables from n_bytes so that it more accurately
	  reflects weight and activity array sizes

	* [r10400] topo/misc/memuse.py:
	  Initial version; code for measuring memry usage

	* [r10399] topo/misc/asizeof.py:
	  Copied recipe
	  http://aspn.activestate.com/ASPN/Cookbook/Python/Recipe/546530
	  verbatim

2009-06-11  ceball

	* [r10398] external/Makefile,
	  external/guppy-r70.tar.gz:
	  Added guppy (which provides heapy, for memory profiling), from
	  https://guppy-pe.svn.sourceforge.net/svnroot/guppy-pe/trunk/guppy
	  r70.

	* [r10397] topo/tests/test_map_measurement.py:
	  Added support for Parameterized BoundingRegions in pickled map
	  test data.

2009-06-10  ceball

	* [r10396] topo/base/boundingregion.py:
	  Removed redundant __init__ methods.

	* [r10395] topo/base/boundingregion.py,
	  topo/misc/legacy.py,
	  topo/param/parameterized.py:
	  BoundingRegion is now just an object (no longer inherits from
	  Parameterized). Reduces memory consumption of "./topographica -i
	  -p 'cortex_density=retina_density=1' -p lgn_density=20 -p
	  'dims=[or,od,dr,cr,sf]' examples/lissom.ty" from 435 to 334 MB
	  (as reported by top). Also added legacy support.

	* [r10394] topo/tests/testsnapshots.py:
	  Added preferred search_path. (Avoids conflict with any unrelated
	  testsnapshot.typ that happens to be in a default search path.)

	* [r10393] topo/base/sheetcoords.py:
	  Added __slots__ to Slice. Reduces memory consumption of
	  "./topographica -i -p 'cortex_density=retina_density=1' -p
	  lgn_density=20 -p 'dims=[or,od,dr,cr,sf]' examples/lissom.ty"
	  from 525 to 435 MB (as reported by top).

2009-06-10  jbednar

	* [r10392] topo/base/cf.py,
	  topo/base/projection.py,
	  topo/projection/basic.py:
	  Made n_bytes be implemented at the Projection level

	* [r10391] topo/projection/basic.py:
	  Added missing n_conns method

2009-06-10  antolikjan

	* [r10390]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  made sure all random generators are seeded

2009-06-10  ceball

	* [r10389] topo/base/sheetcoords.py:
	  Added ALERT.

2009-06-09  jbednar

	* [r10388] topo/command/basic.py:
	  Added print_sizes command, which is now called in run_batch (but
	  can also be called explicitly)

	* [r10387] topo/projection/basic.py:
	  Added more SharedCF overhead

	* [r10386] topo/base/cf.py:
	  Minor cleanup

	* [r10385] topo/base/cf.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/command/basic.py,
	  topo/projection/basic.py:
	  Added n_bytes() and n_conns() methods and global commands to
	  calculate memory size and number of connections in the current
	  simulation

2009-06-09  ceball

	* [r10384] contrib/parameter_search,
	  contrib/parameter_search.cfg:
	  Moved some options into a config file.

2009-06-08  ceball

	* [r10383] contrib/parameter_search:
	  Minor simplification.

	* [r10382] contrib/parameter_search:
	  Use simpler string formatting.

	* [r10381] setup_app.py:
	  Added notes.

	* [r10380]
	  external/pyscrodget-0.0.2_2.1.tar.gz:
	  Accidentally left in the build/ directory in previous version.

	* [r10379] _setup.py,
	  setup.py, setup_app.py,
	  setup_exe.py,
	  setup_ez.py:
	  Added create_topographica_script() to _setup.py. Previously, the
	  topographica script had to be created by make before running
	  setup.

2009-06-06  ceball

	* [r10378] doc/Future_Work/current_text.php,
	  setup_app.py:
	  Added info about icons from future work doc.

	* [r10377] setup_app.py:
	  Began attempting to include external packages.

	* [r10376] setup_ez.py:
	  Added docstring.

	* [r10375] Makefile,
	  easysetup.py,
	  setup_app.py,
	  setup_exe.py,
	  setup_ez.py,
	  win_build_exe.py:
	  Made setup script naming more consistent. Added beginnings of
	  py2app script.

	* [r10374] Makefile:
	  More files to delete from distribution.

	* [r10373] doc/Downloads/index_text.php:
	  Added comment.

2009-06-05  ceball

	* [r10372] topo/plotting/plotgroup.py:
	  Fixed bogus 'self'.

	* [r10371] easysetup.py,
	  setup.py:
	  Added some documentation.

	* [r10370] easysetup.py:
	  Fixed typos.

	* [r10369] _setup.py,
	  easysetup.py, setup.py:
	  Moved code common to distutils and setuptools into _setup.py.

	* [r10368] easysetup.py:
	  Beginnings of 'easy_install topographica'

	* [r10367] topo/misc/filepath.py:
	  Removed erroneous use of set() (search paths were not being
	  searched in order). It doesn't matter if a path appears more than
	  once.

	* [r10366] topo/misc/filepath.py:
	  Fixed (presumably accidental) mutable default argument.

	* [r10365] topo/tests/testsnapshots.py:
	  Simplified paths.

	* [r10364] topo/misc/filepath.py:
	  Added output_path to resolve_path()'s list of search_paths.

	* [r10363]
	  topo/tests/testCompositeSheetMasks.txt:
	  Fixed path.

	* [r10362] topo/tests/__init__.py:
	  Skip gmpy/Number tests if gmpy not available.

	* [r10361] topo/tests/testNumberParameter.txt,
	  topo/tests/testgmpynumber.txt:
	  Split gmpy/Number tests from other Number tests.

	* [r10360] setup.py:
	  Added more missing files.

	* [r10359] topo/analysis/vision.py,
	  topo/command/analysis.py,
	  topo/tests/testbitmap.py,
	  topo/tests/testimage.py,
	  topo/tkgui/plotgrouppanel.py:
	  Cleaned up file paths.

2009-06-05  antolikjan

	* [r10358]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  added missing import

2009-06-05  ceball

	* [r10357]
	  external/pyscrodget-0.0.2_2.1.tar.gz:
	  Forgot to gzip previous version.

	* [r10356]
	  external/pyscrodget-0.0.2_2.1.tar.gz:
	  Minor update to path finding.

	* [r10355] topo/plotting/bitmap.py:
	  Added level to vera.ttf detection hack, so that vera.ttf can be
	  found when topo is installed as a package.

	* [r10354] setup.py:
	  Added missing files.

	* [r10353]
	  external/pyscrodget-0.0.2_2.1.tar.gz:
	  Corrected typo in package info.

	* [r10352] external/Makefile,
	  external/pyscrodget-0.0.1_2.1.tar.gz,
	  external/pyscrodget-0.0.2_2.1.tar.gz:
	  Minor alterations to pyscrodget package.

	* [r10351] topo/misc/filepath.py:
	  Expanded comment.

	* [r10350] external/Makefile,
	  external/Tile.py,
	  external/odict.py,
	  topo/param/external.py,
	  topo/param/tk.py,
	  topo/tkgui/editor.py,
	  topo/tkgui/topoconsole.py:
	  Moved odict and tilewrapper to topo.param.external module.

	* [r10349] setup.py:
	  Added a comment.

	* [r10348] setup.py,
	  topo/misc/filepath.py,
	  topo/tests/testsnapshots.py:
	  Fixed error introduced into testsnapshots (I mistakenly thought
	  testsnapshot.typ was checked in).

2009-06-04  ceball

	* [r10347] topo/tests/testplotfilesaver.py:
	  Simplified temporary file handling.

	* [r10346] topo/tests/testsnapshots.py:
	  Use resolve_path() to locate the snapshot file.

	* [r10345] setup.py:
	  Added some notes.

	* [r10344] topo/tests/testsnapshots.py:
	  Removed out-of-date ALERT.

	* [r10343] topo/command/basic.py:
	  Tried to simplify handling snapshots that might or might not be
	  xml, when gnosis (for xml pickles) might or might not be
	  available. Will probably have to revisit this if we also add
	  hdf5.

	* [r10342] topo/param/tk.py:
	  Adjustment to paths now that package_path is available.

	* [r10341] topo/misc/commandline.py,
	  topo/tests/test_map_measurement.py,
	  topo/tkgui/topoconsole.py:
	  Adjustment to paths now that topo.misc.filepath.package_path is
	  available. Not yet complete: other uses of
	  application_path/normalize_path/resolve_path might need to be
	  updated.

	* [r10340] topo/plotting/bitmap.py:
	  Added comment.

	* [r10339] topo/misc/filepath.py:
	  Added 'package_path' (the location of the topo module), which is
	  often what is needed when 'application_path' is currently used.
	  (Some uses of 'application_path' should be 'output_path'.)

	* [r10338] topo/tests/testplotfilesaver.py:
	  Cleaned up temporary file creation.

	* [r10337] topo/param/tk.py:
	  Removed unused output_path variable.

	* [r10336] topo/misc/trace.py:
	  Removed unused import.

	* [r10335] setup.py,
	  topo/__init__.py:
	  Added missing numbergen package.

	* [r10334] topo/misc/util.py:
	  Made pstats & cProfile dependencies optional.

	* [r10333] topo/misc/filepath.py:
	  topo.misc.filepath.output_path is set to ~/topographica if the
	  application_path is not writable.

2009-06-04  antolikjan

	* [r10332]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  change of default parameters

	* [r10331]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  Added intrinsic noise and parametrization of V1 afferent extents

2009-06-04  ceball

	* [r10330] setup.py:
	  Added installation of topographica script.

	* [r10329] topo/misc/inlinec.py:
	  Check for scipy.weave if weave module is not found (for e.g.
	  Ubuntu package).

	* [r10328] topo/command/basic.py:
	  Removed topo.command.basic's dependency on gnosis module (making
	  it optional).

	* [r10327] setup.py:
	  Initial version.

2009-06-04  jbednar

	* [r10326] doc/User_Manual/overview_text.php:
	  Added note about one-to-one and all-to-all connections

2009-06-03  jbednar

	* [r10325] contrib/jj_tiny.ty:
	  Added missing imports

	* [r10324] contrib/jj_tiny.ty:
	  Simple starting point for John to optimize

2009-05-31  ceball

	* [r10323] doc/buildbot/master.cfg:
	  svn backup and build scheduled at different times. Skip docs on
	  mac build.

	* [r10322] topo/__init__.py,
	  topo/misc/legacy.py:
	  Replace gmpy.mpq with fixedpoint.FixedPoint if gmpy is
	  unavailable.

	* [r10321] topo/misc/util.py:
	  Added warning.

	* [r10320] topo/misc/legacy.py,
	  topo/misc/util.py:
	  More advanced module faking: the fake module is not created until
	  an attempt is made to import the module. So far, only gmpy faking
	  uses this. Should make no visible change to legacy support for
	  gmpy.

	* [r10319] topo/misc/legacy.py:
	  Removed testing code (accidentally left in).

2009-05-29  jbednar

	* [r10318] topo/analysis/featureresponses.py:
	  Cleaned up docstring

2009-05-28  ceball

	* [r10317] doc/buildbot/master.cfg:
	  Set up windows build. Added svn checkout retries (to avoid
	  clobbering the checkout quite so readily). Reduced frequency of
	  performance tests. The windows build's VM is on doozy, so added
	  doozy_lock to windows build.

	* [r10316] doc/Downloads/index_text.php:
	  Updated info about using fink to build docs.

2009-05-28  antolikjan

	* [r10315] contrib/gc_alissom.ty:
	  change the default parameters of retinal waves

2009-05-28  ceball

	* [r10314] topo/misc/legacy.py:
	  Fixed support for no gmpy.mpq: numbers like '5/7' couldn't be
	  parsed by FixedPoint, so the number is first eval'd (using float
	  division).

	* [r10313] external/gmpy-1.04.tar.gz:
	  Latest release of gmpy.

	* [r10312]
	  topo/tests/reference/topo_or_defs.py:
	  Corrected typo.

	* [r10311]
	  topo/tests/reference/topo_or_defs.py:
	  Updated output_fn -> output_fns.

	* [r10310]
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty:
	  Updated output_fn to output_fns.

	* [r10309] doc/buildbot/index.html:
	  Various simplifications.

	* [r10308] doc/buildbot/master.cfg:
	  Cleaned up. Added Ubuntu 9.04 builder.

2009-05-28  jbednar

	* [r10307] doc/buildbot/master.cfg:
	  Fixed typo

2009-05-27  ceball

	* [r10306] doc/buildbot/master.cfg:
	  Simplification of builders.

2009-05-27  jmoudrik

	* [r10305] contrib/jm_analysis.py,
	  contrib/jm_cf_matrix.py,
	  contrib/jm_smooth.py:
	  files for complex analysis and an improved CFProjection

2009-05-27  ceball

	* [r10304] topo/misc/legacy.py:
	  Added missing import statement.

	* [r10303] doc/buildbot/doozy-buildbot.tac:
	  Removed out-of-date file.

	* [r10302] doc/buildbot/index.html:
	  Updated links.

	* [r10301] doc/buildbot/master.cfg:
	  Beginnings of reorganization. Added new machines cider (OS X) and
	  light (Windows XP).

	* [r10300] doc/buildbot/master.cfg:
	  Unoptimized train-tests TESTDP reverted to 5. Changes have been
	  running on buildbot for a while.

2009-05-26  antolikjan

	* [r10299] topo/command/pylabplots.py:
	  added parameter to size tuning curve measurment function which
	  defines the size of the maximum disk grating

	* [r10298] contrib/jacommands.py:
	  added surround modulation analysis function

	* [r10297] contrib/cc_lesi_oo_or_new.ty:
	  removed double retina

	* [r10296] contrib/gc_alissom.ty:
	  made Hysteresis optional

	* [r10295] topo/analysis/featureresponses.py:
	  deleted the debugging info and renamed num_repetitions to
	  repetitions

2009-05-26  ceball

	* [r10294]
	  doc/Developer_Manual/testing_text.php:
	  Added note.

	* [r10293] doc/Downloads/index_text.php:
	  Minor reorganization.

2009-05-24  jbednar

	* [r10292] external/Makefile,
	  external/gmp-4.2.2.tar.gz,
	  external/gmp-4.3.1.tar.gz:
	  Upgraded gmp to 4.3.1 to fix CPU detection problem on some Macs

2009-05-22  antolikjan

	* [r10291] topo/command/analysis.py:
	  Set correct default duration for corner orientation map
	  measurement

2009-05-21  antolikjan

	* [r10290] topo/analysis/featureresponses.py:
	  Implemented the repetitions paradigm

2009-05-20  antolikjan

	* [r10289]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  Made only single fake retina

	* [r10288] contrib/cc_lesi_oo_or_new.ty:
	  changed default contrasts where tuning curves are measured

	* [r10287] contrib/jacommands.py:
	  made hysteresis in V2 reset

2009-05-18  jbednar

	* [r10286] topo/projection/basic.py:
	  Clarified docstring

2009-05-17  jbednar

	* [r10285]
	  /releases/0.9.6/topographica/doc/User_Manual/overview_text.php:
	  Added note about one-to-one and all-to-all connections

2009-05-15  antolikjan

	* [r10284] contrib/jacommands.py:
	  switched off V1 plasticity in outputfn after adding V2

	* [r10283] contrib/jacommands.py:
	  changes to AddV2 function

	* [r10282] contrib/jacommands.py:
	  changes to AddV2 function

	* [r10281] contrib/v2_cc_lesi_oo_or.ty:
	  loads a simulation, adds V2

2009-05-11  antolikjan

	* [r10280] contrib/cc_lesi_oo_or_new.ty:
	  Added SimpleHomeoLinear

2009-05-09  jbednar

	* [r10279] ChangeLog.txt:
	  Added recent changes

2009-05-06  ceball

	* [r10278] contrib/parameter_search:
	  Minor fix to work with Python 2.3.

	* [r10277] contrib/parameter_search:
	  Minor correction in docstring.

	* [r10276] doc/Downloads/git_text.php:
	  Removed draft notes that were turning into a git tutorial.

2009-05-04  jbednar

	* [r10275]
	  contrib/gc_lissom_oo_or_homeostatic_new.ty,
	  contrib/laminar_oo_or.ty,
	  contrib/laminar_or.ty,
	  contrib/lesi.ty,
	  contrib/lesi_whisker_barrels.ty,
	  contrib/lgn_lateral.ty,
	  contrib/lissom_oo_or_homeostatic.ty,
	  contrib/lissom_oo_or_homeostatic_tracked.ty,
	  contrib/lissom_oo_or_homeostatic_tracked_new.ty,
	  contrib/lissom_oo_or_noshrinking.ty,
	  contrib/lissom_oo_or_noshrinking_latswitch.ty,
	  contrib/lissom_oo_or_species.ty,
	  contrib/lissom_oo_or_species_tracked.ty,
	  contrib/lissom_or_noshrinking.ty,
	  contrib/lissom_or_noshrinking_latswitch.ty,
	  contrib/sparse_connectivity_LESI.ty,
	  contrib/sparse_connectivity_model.ty,
	  contrib/species_cf_jitter.ty,
	  contrib/species_lateral_sparsity.ty:
	  Fixed outdated ref to topo.sheet.generator

	* [r10274] contrib/gc_alissom.ty:
	  Fixed typo

	* [r10273] contrib/cc_lesi_oo_or_new.ty:
	  Added newlines

	* [r10272] topo/command/basic.py:
	  Formatted docstring

2009-05-04  ceball

	* [r10271] doc/buildbot/master.cfg:
	  Reduced accuracy of unoptimized tests and altered an email
	  address. Changes have been live on buildbot for at least a month.

2009-05-03  antolikjan

	* [r10270] contrib/gc_alissom.ty:
	  switched of attribute tracking when fixed treshold output
	  function is active

	* [r10269] contrib/cc_lesi_oo_or_new.ty:
	  reduced number of contrasts at which tuning curves are computed

2009-05-02  antolikjan

	* [r10268] contrib/cc_lesi_oo_or_new.ty:
	  complex cell model with exactly the same connectivity (except
	  strength) as in the lesi model in layer 2/3

2009-05-01  antolikjan

	* [r10267] topo/analysis/vision.py:
	  Corrected potential division by zero bug

2009-04-30  antolikjan

	* [r10266] contrib/gc_alissom.ty:
	  Added fixed treshold output function

	* [r10265] topo/transferfn/basic.py:
	  Extended HalfRectify with random treshold

2009-04-30  ceball

	* [r10264] contrib/parameter_search:
	  Added note.

2009-04-30  antolikjan

	* [r10263] contrib/gc_alissom.ty:
	  Removed JointScaling_opt

	* [r10262] contrib/jacommands.py:
	  Corrected SimpleHomeoLinear to set the initial y_avg to MU

2009-04-30  jbednar

	* [r10261] doc/Tutorials/lissom_oo_or_text.php:
	  Minor clarification

	* [r10260] Makefile:
	  Delete generated info directory from distribution

	* [r10259] topo/sheet/optimized.py:
	  Removed unnecessary JointScaling_Opt class, and clarified
	  docstring for LISSOM_Opt

2009-04-29  antolikjan

	* [r10258] contrib/cc_lesi_oo_or.ty:
	  allowd for homeostasis also in layer 4C

2009-04-29  ceball

	* [r10257] contrib/parameter_search:
	  Corrected path to python.

2009-04-29  antolikjan

	* [r10256] contrib/gc_alissom.ty:
	  changed the t_init parameter

	* [r10255] contrib/jacommands.py:
	  corrected bug with state_push/pop stack

2009-04-29  ceball

	* [r10254] contrib/parameter_search:
	  Tidied up script and documentation; should be no visible change.

2009-04-29  antolikjan

	* [r10253] topo/analysis/vision.py:
	  made the modulation ratio to scale to 0-1.0 scale in order to
	  achieve correct plotting

	* [r10252]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  corrected bug with external parametriazation

2009-04-29  ceball

	* [r10251] contrib/parameter_search:
	  Removed out-of-date note.

2009-04-28  ceball

	* [r10250] contrib/parameter_search:
	  Initial version of script to help start multiple batch
	  simulations.

2009-04-27  ceball

	* [r10249] topo/param/tk.py,
	  topo/tkgui/plotgrouppanel.py:
	  Addition to SF #2122761: pre_plot_hooks etc now also do not
	  scroll.

2009-04-26  ceball

	* [r10248] topo/command/basic.py:
	  Added max_name_length parameter to run_batch() to avoid
	  generating experiment directory names that are too long for the
	  filesystem.

2009-04-25  jbednar

	* [r10247] topo/transferfn/basic.py:
	  Clarified docs

2009-04-25  ceball

	* [r10246] topo/param/tk.py,
	  topo/tkgui/plotgrouppanel.py:
	  Fix SF #2122761: PlotGroup control buttons now do not scroll.

	* [r10245] topo/param/tk.py:
	  Simplification - no visible change.

2009-04-23  ceball

	* [r10244] topo/param/parameterized.py:
	  Minor clarification.

2009-04-20  antolikjan

	* [r10243] contrib/jacommands.py:
	  Corrected a bug

	* [r10242] topo/transferfn/basic.py:
	  Corrected docstring of state_push/pop in TranfserFnWithState

	* [r10241] topo/base/sheet.py:
	  state_push/pop in Sheet now checks for existing state_push/pop
	  function in output functions

2009-04-17  ceball

	* [r10240] examples/gca_lissom.ty:
	  Added missing import.

2009-04-16  antolikjan

	* [r10239] topo/sheet/optimized.py:
	  corrected bug with importing of JointScaling

	* [r10238] contrib/gc_alissom.ty:
	  Chaneged JointScaling to JointScaling_Opt

	* [r10237] topo/sheet/optimized.py:
	  Added optimized version of JointScaling

	* [r10236] topo/base/sheet.py:
	  state_push/pop in Sheet now check whether a given output function
	  is of class TransferFnWithState begfore it calls its
	  state_push/pop

	* [r10235] topo/base/functionfamily.py:
	  Removed the stat_push/pop from TransferFn (they were moved to
	  TransferFnWithState)

	* [r10234] topo/transferfn/basic.py:
	  Removed IntrinsicNoise function, moved the definition of
	  state_push/pop into TranfserFnWithState, and made Hysteresis have
	  sheet_name parameter

	* [r10233] contrib/gc_alissom.ty:
	  Replaced the IntrinsicNoise transfer function with existing
	  composite equivalent

2009-04-12  jbednar

	* [r10232] topo/transferfn/basic.py:
	  Cleaned up docs and fixed spelling error on parameter

2009-04-10  antolikjan

	* [r10231] topo/transferfn/basic.py:
	  corrected the IntrinsicNoise OF

	* [r10230] contrib/gc_alissom.ty:
	  changed the default analysis input scale

2009-04-09  antolikjan

	* [r10229] topo/transferfn/basic.py:
	  Added Intrinsic Noise output function and corrected some issues
	  with state_push/pop

	* [r10228] topo/analysis/vision.py:
	  corrected the measure_and_analyze_complexity to be derived from
	  the right class

	* [r10227] contrib/jacommands.py:
	  various minor changes

	* [r10226] contrib/gc_alissom.ty:
	  added intrinsic noise and made relative adaptation and gain
	  control optional

	* [r10225]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  added external parameter

	* [r10224] topo/base/sheet.py:
	  Made sheet to call state_push/pop on all output functions when
	  its state_push/pop is called

2009-04-06  antolikjan

	* [r10223] contrib/gc_alissom.ty:
	  made the size of V1 to be external parameter

2009-04-04  ceball

	* [r10222]
	  /releases/0.9.6/topographica-win/common/python_topo.tar.gz:
	  Added missing python25.dll

	* [r10221] /trunk/topographica-win/create_installer/README.txt:
	  Added 10217 from 0.9.6 (note in release instructions).

	* [r10220]
	  /trunk/topographica-win/create_installer/topographica.iss:
	  Added a step to instructions for Windows release.

2009-04-04  antolikjan

	* [r10219]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  added external parameters

	* [r10218] contrib/cc_lesi_oo_or.ty:
	  added external parameters

2009-04-04  ceball

	* [r10217]
	  /releases/0.9.6/topographica-win/create_installer/README.txt:
	  Added note.

2009-04-03  ceball

	* [r10216] topo/learningfn/optimized.py:
	  Added ALERT.

	* [r10215] /releases/0.9.6/topographica/examples/gca_lissom.ty:
	  Applied r10212 from trunk: in gca_lissom, "replaced
	  CFPLF_Scaled_opt with CFPLF_Hebbian_opt - we do not use different
	  learning rates for individual neurons anymore".

2009-04-03  antolikjan

	* [r10214] contrib/cc_lesi_oo_or.ty:
	  change of default parameters

	* [r10213] contrib/cc_lesi_oo_or.ty:
	  allowed for changing the lateral connections learning rate

	* [r10212] examples/gca_lissom.ty:
	  replaced CFPLF_Scaled_opt with CFPLF_Hebbian_opt - we do not use
	  different learning rates for individual neurons anymore

2009-04-02  ceball

	* [r10211]
	  /releases/0.9.6/topographica/doc/User_Manual/noise_text.php:
	  Applied change that was missed from r10209 (r10203 - class name
	  qualification in the noise documentation).

	* [r10210]
	  /releases/0.9.6/topographica/topo/tkgui/templateplotgrouppanel.py:
	  Applied r10202 from trunk ('Applied strength-only hack to
	  refresh_plots() (previously, it was only applied to
	  redraw_plots()). Fixes SF #2724032.')

	* [r10209]
	  /releases/0.9.6/topographica/doc/User_Manual/noise_text.php:
	  Applied r10183, r10204, and r10205 from trunk (fixes to noise
	  documentation).

	* [r10208] /releases/0.9.6/topographica/Makefile:
	  Applied r10167 and r10168 from trunk ("Added separate
	  win-distclean target so that python_topo/ can be preserved during
	  distclean on Windows. (Want to keep the binaries for Windows
	  distribution, but usually during clean we do want to remove
	  python_topo/)").

	* [r10207] /releases/0.9.6/topographica/examples/Makefile:
	  Applied r10164 from trunk ("Removed references to cfsom_or").

	* [r10206]
	  /releases/0.9.6/topographica/topo/tests/test_map_measurement.py:
	  Applied r10161 from trunk ("Removed 'Retinotopy' from the list of
	  map measurements to test").

	* [r10205] doc/User_Manual/noise_text.php:
	  Commented out 'weight adjustment noise' example, since this
	  specific code cannot currently be used.

	* [r10204] doc/User_Manual/noise_text.php:
	  Described how to get dynamic numbers for weight generation.

	* [r10203] doc/User_Manual/noise_text.php:
	  Qualified some names with the module (e.g. PatternCombine ->
	  transferfn.PatternCombine.

2009-04-01  ceball

	* [r10202]
	  topo/tkgui/templateplotgrouppanel.py:
	  Applied strength-only hack to refresh_plots() (previously, it was
	  only applied to redraw_plots()). Fixes SF #2724032.

	* [r10201] /trunk/topographica-win/README.txt,
	  /trunk/topographica-win/common/python_topo.tar.gz,
	  /trunk/topographica-win/common/setup.py,
	  /trunk/topographica-win/create_installer/README.txt,
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat,
	  /trunk/topographica-win/create_installer/topographica.iss,
	  /trunk/topographica-win/create_python_topo/PIL-1.1.5.win32-py2.5.exe,
	  /trunk/topographica-win/create_python_topo/PIL-1.1.6.win32-py2.5.exe,
	  /trunk/topographica-win/create_python_topo/README.txt,
	  /trunk/topographica-win/create_python_topo/distutils_compiler_quoting.diff,
	  /trunk/topographica-win/create_python_topo/pyreadline-1.5-win32-setup.exe,
	  /trunk/topographica-win/create_python_topo/setup.bat,
	  /trunk/topographica-win/setup_cvs_copy/README.txt,
	  /trunk/topographica-win/setup_cvs_copy/setup.bat,
	  /trunk/topographica-win/util/gzip.exe:
	  Merged changes r10135:10191 from releases/0.9.6/topographica-win
	  into the trunk version of topographica-win.

	* [r10200] /releases/0.9.6/topographica/Makefile:
	  Applied 10199 from trunk: fixes missing images/ellen_arthur.pgm.

	* [r10199] Makefile:
	  Preserve images/ellen_arthur.pgm in release distribtions. Fixes
	  SF #2724036.

2009-03-31  jbednar

	* [r10198] /releases/0.9.6/topographica/examples/som_retinotopy.ty:
	  Fixed density to match tutorial

	* [r10197] examples/som_retinotopy.ty:
	  Fixed cortex_density; in r9809 it was mistakenly set to 48
	  instead of 10.

2009-03-30  antolikjan

	* [r10196] topo/transferfn/basic.py:
	  made Hysteresis to push/pop state

	* [r10195] topo/base/functionfamily.py:
	  Introduced push pop function for all output fns

	* [r10194] topo/analysis/vision.py:
	  Made the measure_and_analyse_complexity be a measure_or_pref
	  class

	* [r10193] contrib/jacommands.py:
	  Big revamp after the move from Eclipse to command line svn

	* [r10192]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  Changed to use shouval dataset

2009-03-28  ceball

	* [r10191] /releases/0.9.6/topographica-win/common/setup.py:
	  Fixed a typo.

	* [r10190]
	  /releases/0.9.6/topographica-win/common/python_topo.tar.gz:
	  Updated with recent changes.

	* [r10189]
	  /releases/0.9.6/topographica-win/create_python_topo/setup.bat:
	  Fixed a typo resulting in odict being missed (odict isn't missing
	  from existing binaries because it was copied in manually).

	* [r10188]
	  /releases/0.9.6/topographica-win/create_python_topo/README.txt:
	  Fixed a typo.

	* [r10187]
	  /releases/0.9.6/topographica-win/create_python_topo/setup.bat:
	  Correction to location of weave's compiled code cache.

	* [r10186]
	  /releases/0.9.6/topographica-win/create_python_topo/distutils_compiler_quoting.patch:
	  Deletion missed from an earlier commit.

	* [r10185] /releases/0.9.6/topographica-win/common/setup.py:
	  Added extra directory to PATH (required for non-admin Vista
	  users?).

2009-03-28  machalekj

	* [r10184] contrib/basic.py,
	  contrib/hegdeessen.py,
	  contrib/patternfn.py:
	  Implementation of Hegde and Van Essen grating and contour
	  stimuli. Four new basic patterns added to allow this.

2009-03-26  jbednar

	* [r10183] doc/User_Manual/noise_text.php:
	  Clarified how scale and offset work

	* [r10182] topo/base/projection.py:
	  Fixed whitespace

2009-03-24  antolikjan

	* [r10181] contrib/cc_lesi_oo_or.ty:
	  the lesie version of the complex cell model

2009-03-23  ceball

	* [r10180] contrib/cbmisc.py,
	  contrib/rgbhsv.py,
	  contrib/rgbimages.py:
	  Reorganization of some of my code.

	* [r10179] examples/gca_lissom.ty:
	  Fixed another typo in code ('Nature' dataset can now be used).

	* [r10178] examples/gca_lissom.ty:
	  Fixed typo in code (p.lgn_density was being ignored).

2009-03-18  ceball

	* [r10177]
	  /releases/0.9.6/topographica-win/create_python_topo/pyreadline-1.5-win32-setup.exe,
	  /releases/0.9.6/topographica-win/create_python_topo/setup.bat:
	  Added pyreadline.

2009-03-18  antolikjan

	* [r10176] contrib/jacommands.py:
	  made the lgn channel afferent strength normalization uniform
	  random

2009-03-18  ceball

	* [r10175]
	  /releases/0.9.6/topographica-win/create_python_topo/distutils_compiler_quoting.diff,
	  /releases/0.9.6/topographica-win/create_python_topo/setup.bat:
	  Changed distutils_compiler_quoting patch into a format that works
	  with the Windows version of patch.

	* [r10174]
	  /releases/0.9.6/topographica-win/create_python_topo/distutils_compiler_quoting.patch,
	  /releases/0.9.6/topographica-win/create_python_topo/setup.bat:
	  http://bugs.python.org/issue4508

	* [r10173]
	  /releases/0.9.6/topographica-win/create_installer/topographica.iss:
	  Removed debugging test.

	* [r10172]
	  /releases/0.9.6/topographica-win/create_installer/topographica.iss:
	  Added check for required Windows system dlls; if they are
	  missing, and the user is not running the installation program as
	  a Power User or Administrator, the installation is aborted (with
	  a message to that effect, and the instruction to re-run with
	  appropriate privileges). Also updated paths to match my current
	  setup.

2009-03-16  ceball

	* [r10171]
	  /releases/0.9.6/topographica-win/setup_cvs_copy/README.txt:
	  Added more info.

	* [r10170]
	  /releases/0.9.6/topographica-win/create_installer/topographica.iss:
	  Added conditional installation of some required .dll files.

	* [r10169]
	  /releases/0.9.6/topographica-win/create_installer/README.txt:
	  Updated to use win-distclean.

	* [r10168] Makefile:
	  Fixed command for renaming.

	* [r10167] Makefile:
	  Added separate win-distclean target so that python_topo/ can be
	  preserved during distclean on Windows. (Want to keep the binaries
	  for Windows distribution, but usually during clean we do want to
	  remove python_topo/.)

	* [r10166]
	  /releases/0.9.6/topographica-win/create_installer/prepare_for_installer.bat:
	  Minor clarification.

	* [r10165]
	  doc/Developer_Manual/releases_text.php:
	  Minor updates.

	* [r10164] examples/Makefile:
	  Removed references to cfsom_or.

	* [r10163]
	  /releases/0.9.6/topographica-win/create_installer/README.txt,
	  /releases/0.9.6/topographica-win/create_installer/topographica.iss:
	  Clarified instructions.

	* [r10162]
	  /releases/0.9.6/topographica-win/create_installer/README.txt:
	  Clarified documentation.

	* [r10161] topo/tests/test_map_measurement.py:
	  Removed 'Retinotopy' from the list of map measurements to test.

2009-03-15  ceball

	* [r10160]
	  /releases/0.9.6/topographica-win/setup_cvs_copy/README.txt:
	  Fixed typo.

	* [r10159]
	  /releases/0.9.6/topographica-win/create_installer/README.txt:
	  Cut down on duplicated instructions.

	* [r10158] topo/numbergen/basic.py:
	  Fixed syntax and import error.

	* [r10157]
	  /releases/0.9.6/topographica-win/setup_cvs_copy/setup.bat:
	  Correction to printed instruction.

2009-03-14  ceball

	* [r10156] /releases/0.9.6/topographica-win/common/setup.py:
	  Added missing newline character.

2009-03-14  jbednar

	* [r10155] /releases/0.9.6/topographica/examples/gca_lissom.ty,
	  /releases/0.9.6/topographica/examples/lissom_oo_or.ty,
	  /releases/0.9.6/topographica/examples/tiny.ty,
	  /releases/0.9.6/topographica/topo/base/patterngenerator.py,
	  /releases/0.9.6/topographica/topo/tkgui/plotgrouppanel.py:
	  Ported bugfixes from the main branch

	* [r10154] topo/numbergen/basic.py:
	  Minor clarifications to docstrings; added softbounds

2009-03-13  ceball

	* [r10153] topo/analysis/featureresponses.py:
	  For 'hue', PatternPresenter detects whether there are three
	  separate retinas for the color dimension, allowing e.g.
	  measure_hue_pref() to work with a single, color retina, or with
	  three separate retinas. (Should be no change to the measurement
	  for each case.)

	* [r10152] topo/analysis/featureresponses.py:
	  Simplifications - should be no visible change.

2009-03-12  ceball

	* [r10151] examples/lissom.ty:
	  Added ALERT.

	* [r10150] contrib/rgbimages.py:
	  Added handling of cache parameter to ColorImage.

	* [r10149] doc/Future_Work/current_text.php:
	  Test commit.

2009-03-11  antolikjan

	* [r10148] contrib/gc_alissom.ty:
	  parameter changes

2009-03-10  jbednar

	* [r10147] /releases/0.9.6/topographica/doc/shared/trailer.php:
	  Updated sf.net logo as they requested

2009-03-09  ceball

	* [r10146] contrib/rgbimages.py:
	  Now uses weave versions of rgb/hsv conversion functions.

	* [r10145] /releases/0.9.6/topographica-win/README.txt,
	  /releases/0.9.6/topographica-win/create_python_topo/README.txt:
	  Clarified and moved note about running setup.bat files.

	* [r10144]
	  /releases/0.9.6/topographica-win/common/python_topo.tar.gz:
	  Updated external packages.

	* [r10143]
	  /releases/0.9.6/topographica-win/create_python_topo/setup.bat:
	  Added odict

	* [r10142]
	  /releases/0.9.6/topographica-win/setup_cvs_copy/README.txt:
	  Added a note about MSVCP71.DLL

	* [r10141]
	  /releases/0.9.6/topographica-win/create_python_topo/README.txt,
	  /releases/0.9.6/topographica-win/create_python_topo/setup.bat:
	  Simplified instructions.

	* [r10140] /releases/0.9.6/topographica-win/util/gzip.exe:
	  Added gzip.

	* [r10139]
	  /releases/0.9.6/topographica-win/create_python_topo/setup.bat:
	  Minor alteration to text.

	* [r10138]
	  /releases/0.9.6/topographica-win/create_python_topo/README.txt:
	  Minor addition to text.

	* [r10137]
	  /releases/0.9.6/topographica-win/create_python_topo/setup.bat:
	  Missed from previous commit.

	* [r10136]
	  /releases/0.9.6/topographica-win/create_python_topo/PIL-1.1.5.win32-py2.5.exe,
	  /releases/0.9.6/topographica-win/create_python_topo/PIL-1.1.6.win32-py2.5.exe:
	  Updated to PIL 1.16

	* [r10135] doc/Downloads/cvs_text.php:
	  Fixed links.

2009-03-09  jbednar

	* [r10134] doc/User_Manual/noise_text.php:
	  Fixed typo

2009-03-08  jbednar

	* [r10133] topo/base/patterngenerator.py:
	  Made __setup_xy and __create_and_rotate_coordinate_arrays not be
	  private, because it prevented __call__ from being reimplemented
	  with minor changes in a subclass

2009-03-06  jbednar

	* [r10132] topo/base/patterngenerator.py,
	  topo/tests/lissom_oo_or_t000100.00_Retinotopy.data:
	  Changed mask_shape to calculate its x, y, and orientation
	  relative to those of the owning pattern, to allow the mask to be
	  offset or a different size from the main pattern. These
	  parameters were previously ignored, and they must now be set to
	  1.0, 1.0, and 0.0 to get the same results as before. Thus it is
	  possible for this change to change results for a pattern using
	  mask_shape, but the old behavior should be easily obtainable by
	  adding parameter settings.

	* [r10131] topo/analysis/featureresponses.py,
	  topo/command/pylabplots.py,
	  topo/misc/legacy.py,
	  topo/pattern/basic.py:
	  Added explicit size specification for pattern masks, so that they
	  can later respect their given size

	* [r10130] topo/command/pylabplots.py:
	  Reverted Rectangle to RawRectangle to make tests pass

	* [r10129] doc/News/index_text.php:
	  Added list of new pattern generators, as a comment

	* [r10128] doc/News/index_text.php:
	  Added list of new pattern generators, as a comment

	* [r10127] contrib/lissom_happyface.ty,
	  examples/leaky_lissom_or.ty,
	  topo/analysis/featureresponses.py,
	  topo/command/pylabplots.py,
	  topo/misc/legacy.py,
	  topo/misc/patternfn.py,
	  topo/pattern/basic.py,
	  topo/tests/testpatterngenerator.py:
	  Moved Arc, Curve, and SmoothedRectangle classes into topo/,
	  renaming the old Rectangle class to RawRectangle (possibly to be
	  removed?), and changing SmoothedRectangle to Rectangle. Old code
	  that uses Rectangle will now have a small amount of smoothing by
	  default; to avoid this change Rectangle to RawRectangle in the
	  old code, or set smoothing to zero.

	* [r10126] contrib/lissom_happyface.ty:
	  Major cleanup of documentation, spacing, floating-point errors
	  for parameter values of 0.0, and parameter names. Changed default
	  smoothing values, arc_end to arc_length

	* [r10125] topo/base/patterngenerator.py,
	  topo/misc/patternfn.py,
	  topo/pattern/basic.py:
	  Increased soft bounds on size and aspect_ratio to make working
	  with them in the GUI easier. Added guards for case of zero
	  smoothing, to avoid floating-point errors in extreme cases. Fixes
	  HACKALERT.

2009-03-05  jbednar

	* [r10124] topo/pattern/basic.py:
	  Added ExponentialDecay pattern.

	* [r10123] examples/gca_lissom.ty,
	  topo/tests/gca_lissom.ty_DATA:
	  Changed y position seed to match lissom_oo_or.ty; will change
	  results

	* [r10122] topo/misc/patternfn.py:
	  Fixed errors in Gabor when aspect_ratio or size was zero

	* [r10121] topo/misc/patternfn.py:
	  Added ExponentialDecay pattern. Fixed errors in Gaussian when
	  aspect_ratio or size was zero

2009-03-04  rczhao

	* [r10120] contrib/lissom_happyface.ty:
	  Replaced Boolean parameter in class Curve with Enumeration.

2009-03-03  ceball

	* [r10119] contrib/rgbhsv.py:
	  File missed from previous checkin (r10118).

	* [r10118] contrib/rgbimages.py:
	  Undid changes to ColorImage from 10111. Corrected how mask,
	  scale, offset, output_fns are applied. (Also changed from RGB
	  values on [0,255] to [0,1]; I'd misread the colorsys module
	  documentation.)

2009-03-03  rczhao

	* [r10117] contrib/lissom_happyface.ty:
	  Revised class Curve and function arc_by_center so that Curve can
	  draw both constant-length and constant-width curves.

2009-03-03  jbednar

	* [r10116] topo/tkgui/editor.py:
	  Added import removed in previous revision; was breaking gui-tests

2009-03-03  ceball

	* [r10115] examples/tiny.ty:
	  Fixed list of imports.

2009-03-03  jbednar

	* [r10114]
	  doc/Developer_Manual/optimization_text.php:
	  Fixed attribution

	* [r10113] topo/tkgui/editor.py:
	  Removed duplicate importing of sheets and projections

	* [r10112] examples/gca_lissom.ty,
	  examples/lissom_oo_or.ty:
	  Fixed area scaling; had not been using the right area or number
	  of inputs for large areas

2009-03-02  ceball

	* [r10111] contrib/rgbimages.py:
	  Simplified code for ColorImage by overriding __call__ instead of
	  function().

	* [r10110] contrib/rgbimages.py:
	  Fixed ColorImage: scale, offset, mask, and output_fns were not
	  being applied to the color channels.

2009-02-27  ceball

	* [r10109] topo/command/analysis.py:
	  save_plotgroup() now uses Parameterized's set_param() method to
	  set parameters on the plotgroup, thereby giving an error if the
	  wrong name is given for a plotgroup parameter (e.g.
	  save_plotgroup('Activity',normalized=True).

	* [r10108] topo/param/parameterized.py:
	  Added set_param() method to Parameterized, for use when setting
	  parameters (instead of setattr(), which does not check for that
	  the named attribute is actually a Parameter).

2009-02-27  jbednar

	* [r10107] examples/gca_lissom.ty:
	  Added support for area parameter

	* [r10106] topo/tkgui/plotgrouppanel.py:
	  Made it possible to open Test Pattern window for a simulation
	  created in the Model Editor

2009-02-25  jbednar

	* [r10105] topo/pattern/basic.py:
	  Added HalfPlane pattern from Stuart

2009-02-24  jbednar

	* [r10104] contrib/lissom_happyface.ty:
	  Fixed RectangleWithSmoothing to be smoothed in both directions.
	  Changed Arc.arc_end to increase from zero as angles do. Fixed
	  hiding of Curve.arc_end.

2009-02-24  rczhao

	* [r10103] contrib/lissom_happyface.ty:
	  Revised Arc class and rectangle()

2009-02-23  ceball

	* [r10102] contrib/lissom_rgb.ty:
	  Updated dataset=Gaussian to work with color retina.

	* [r10101] contrib/rgbimages.py,
	  topo/analysis/featureresponses.py:
	  Added ListGenerator, to create lists dynamically. Changed
	  ExtendToRGB's channel_strengths to relative_channel_strengths.

	* [r10100] images/mcgill/foliage_b/01.png,
	  images/mcgill/foliage_b/02.png,
	  images/mcgill/foliage_b/03.png,
	  images/mcgill/foliage_b/04.png,
	  images/mcgill/foliage_b/05.png,
	  images/mcgill/foliage_b/06.png,
	  images/mcgill/foliage_b/07.png,
	  images/mcgill/foliage_b/08.png,
	  images/mcgill/foliage_b/09.png,
	  images/mcgill/foliage_b/10.png,
	  images/mcgill/foliage_b/11.png,
	  images/mcgill/foliage_b/12.png,
	  images/mcgill/foliage_b/13.png,
	  images/mcgill/foliage_b/14.png,
	  images/mcgill/foliage_b/15.png,
	  images/mcgill/foliage_b/16.png,
	  images/mcgill/foliage_b/17.png,
	  images/mcgill/foliage_b/18.png,
	  images/mcgill/foliage_b/19.png,
	  images/mcgill/foliage_b/20.png,
	  images/mcgill/foliage_b/21.png,
	  images/mcgill/foliage_b/22.png,
	  images/mcgill/foliage_b/23.png,
	  images/mcgill/foliage_b/24.png,
	  images/mcgill/foliage_b/25.png:
	  Added single-file (i.e. color) versions of existing images (the
	  existing images will be deleted in the future).

	* [r10099] examples/lissom.ty:
	  Simplified parentheses.

	* [r10098] topo/base/projection.py:
	  Simplified SheetMask's sheet and data properties by making them
	  both overridable properties. Should be no visible change.

	* [r10097] topo/param/parameterized.py,
	  topo/pattern/image.py:
	  Renamed Oproperty to overridable_property, and cleaned up docs
	  and spacing.

2009-02-23  jbednar

	* [r10096] contrib/rgbimages.py:
	  Fixed typo

2009-02-23  ceball

	* [r10095] topo/pattern/image.py:
	  Added comment.

	* [r10094] topo/pattern/image.py:
	  Fixed error deleting PatternSampler's cache of the image.

	* [r10093] contrib/rgbimages.py,
	  topo/pattern/image.py:
	  Simplified PatternSampler by removing the caching of image array.
	  (The cache no longer appeared to be having much of an impact on
	  performance, since PIL.Image can now be efficiently converted to
	  an array.) Created base class ImageSampler, from which
	  PatternSampler and FastImageSampler (formerly FastPatternSampler)
	  now inherit. Simplified GenericImage's _get_image().

	* [r10092] topo/base/projection.py,
	  topo/param/parameterized.py:
	  Added Oproperty, an implementation of 'property' that allows
	  subclasses to override the get/set/del methods.

	* [r10091] contrib/rgbimages.py:
	  Updated docs.

	* [r10090] contrib/lissom_rgb.ty:
	  Initial version.

	* [r10089] contrib/rgbimages.py:
	  Added ALERT, plus minor cleanup (should be no visible change).

	* [r10088] topo/param/tk.py:
	  Fixed bug with ListWidget where e.g. right clicking on output_fns
	  list in the Test Pattern window caused an error. (The 'disabled'
	  attribute was not being created during __init__.)

2009-02-21  rczhao

	* [r10087] contrib/lissom_happyface.ty:
	  Many improvements.

2009-02-20  ceball

	* [r10086] contrib/rgbimages.py:
	  Simplified application of channel_strengths (now applies in both
	  color and monochrome cases.

	* [r10085] contrib/rgbimages.py:
	  If ColorImage gets a grayscale image, sets R, G, and B channels
	  to the same (each to 1/3 of grayscale) rather than giving an
	  error.

	* [r10084] examples/lissom.ty:
	  Removed accidentally duplicated line (which I think was having no
	  effect).

	* [r10083] topo/command/analysis.py,
	  topo/command/basic.py,
	  topo/command/pylabplots.py,
	  topo/param/parameterized.py:
	  Fixed problem that became apparent in r10076: e.g. p.x=y (where p
	  is a ParamOverrides instance) would be lost when passing on p via
	  **p, because p.x did not result in x being put into the
	  ParamOverrides dictionary (it was only set as an attribute, and
	  hence was lost on converting ParamOverrides to a dictionary via
	  **). ParamOverrides now inserts into its dictionary any attribute
	  that does not start with an underscore. Genuine attributes of
	  ParamOverrides (e.g. extra_keywords) have now been renamed to
	  begin with an underscore (this is better anyway because it
	  reduces the chance for a parameter to have the same name as an
	  attribute of ParamOverrides).

2009-02-19  ceball

	* [r10082] topo/pattern/image.py:
	  Added ALERT.

	* [r10081] contrib/rgbimages.py:
	  Simplified RotatedHuesImage's random number generation.

	* [r10080] contrib/rgbimages.py:
	  ParamOverrides-related renaming for consistency. Should be no
	  visible change.

	* [r10079] topo/pattern/image.py:
	  Removed ability to override PatternSampler's parameter when
	  calling it (was unused).

	* [r10078] contrib/rgbimages.py,
	  topo/pattern/image.py:
	  Removed PatternSampler's _initialize_image() method, and made its
	  whole_pattern_output_fns and background_value_fn be constant
	  parameters.

	* [r10077] topo/param/tk.py:
	  Added support to ListWidget for constant List parameters (i.e.
	  don't show a popup menu for a right click if the parameter is
	  constant).

2009-02-19  jbednar

	* [r10076] topo/pattern/basic.py,
	  topo/pattern/random.py,
	  topo/pattern/rds.py:
	  Updated to use cleaner parameter accessing style and to fix cases
	  where parameters supplied in the call to a PatternGenerator
	  instance would be ignored. Should be no change in results except
	  for cases where instances were called with explicit parameters

2009-02-19  ceball

	* [r10075] contrib/rgbimages.py:
	  Restored line that went missing sometime recently.

	* [r10074] topo/pattern/basic.py:
	  Removed unused parameter.

	* [r10073] topo/pattern/image.py:
	  Made ParamOverrides-related naming more consistent. Should be no
	  visible change.

	* [r10072] topo/pattern/basic.py:
	  Some patterns' __call__ methods were ignoring some parameters if
	  they were passed in.

	* [r10071] topo/pattern/basic.py:
	  Made ParamOverrides-related naming more consistent. Should be no
	  visible change.

	* [r10070] topo/base/patterngenerator.py:
	  Minor code simplification.

	* [r10069] topo/base/patterngenerator.py:
	  Fixed bug in Constant pattern generator; since output_fn was
	  changed to output_fns, Constant has not been working whenever it
	  has had any output_fns.

	* [r10068] topo/base/patterngenerator.py:
	  Made ParamOverrides-related naming more consistent. Should be no
	  visible change.

	* [r10067] topo/pattern/image.py:
	  Ensure FileImage's _get_image() uses a filename that's passed
	  into __call__().

2009-02-18  jbednar

	* [r10066] contrib/rgbimages.py:
	  Cleaned up docs, some code

2009-02-18  ceball

	* [r10065] contrib/rgbimages.py:
	  Made ExtendToRGB have red, green, blue attributes on creation.

	* [r10064] topo/sheet/basic.py:
	  Added ALERT.

	* [r10063] topo/analysis/featureresponses.py:
	  Added commented-out code for measuring hue maps with a single
	  color retina.

	* [r10062] contrib/rgbimages.py:
	  More simplification. Should be no visible change.

	* [r10061] contrib/rgbimages.py:
	  Simplified ColorImageSheet: automatically wraps input_generator
	  in ExtendToRGB.

	* [r10060] contrib/rgbimages.py:
	  More renaming of variables.

	* [r10059] contrib/rgbimages.py,
	  topo/command/analysis.py:
	  Various RGB-related renaming and documentation.

	* [r10058] contrib/rgbimages.py:
	  Simplified ColorImage after recent changes to GenericImage.

	* [r10057] topo/pattern/image.py:
	  Made PatternSampler's __call__ not change the supplied x and y
	  matrices. (Changing the supplied x any matrices prevents their
	  reuse e.g. in a subclass of GenericImage that makes more than one
	  sample.)

	* [r10056] topo/pattern/image.py:
	  Reverted change accidentally introduced during recent
	  reorganization.

	* [r10055] topo/pattern/image.py:
	  Added to comment.

2009-02-18  jbednar

	* [r10054] contrib/lissom_happyface.ty:
	  Reorganized Arc; added Curve class; still needs more work

2009-02-18  antolikjan

	* [r10053]
	  contrib/cc_lissom_oo_or_simple_rv.ty:
	  decreased the density of retina to increase speed

2009-02-18  rczhao

	* [r10052] contrib/lissom_happyface.ty:
	  Arc class now can draw an arc by either specifying start and end
	  radian, or by specifying the arc width and height.

2009-02-18  antolikjan

	* [r10051] topo/command/pylabplots.py:
	  made the tuning curves plotting use larger fonts and thicker
	  plots lines

2009-02-18  ceball

	* [r10050] topo/pattern/image.py,
	  topo/tests/testimage.py:
	  Simplified GenericImage and PatternSampler by removing duplicate
	  parameters size_normalization and whole_image_output_fns from
	  GenericImage.

	* [r10049] topo/pattern/image.py:
	  Intermediate checkin: changing GenericImage to have a
	  PatternSampler instance, rather than creating one from a type
	  each time. Should simplify code and cut down on parameter
	  duplication.

	* [r10048] examples/lissom.ty:
	  Removed redundant check.

2009-02-18  jbednar

	* [r10047] topo/pattern/image.py:
	  Fixed formatting of docstrings; minor clarifications

	* [r10046] topo/plotting/bitmap.py:
	  Removed unused import

2009-02-18  ceball

	* [r10045] topo/pattern/image.py:
	  Changed some of PatternSampler's various method arguments to be
	  parameters. Should be no visible change.

2009-02-17  ceball

	* [r10044] topo/pattern/image.py:
	  Restored Float argument accidentally deleted in previous commit.

	* [r10043] topo/pattern/image.py:
	  Simplified converting PIL Image into array (became possible after
	  upgrading to PIL 1.1.6). Should be no visible change.

	* [r10042] examples/lissom.ty:
	  Fixed typo.

	* [r10041] contrib/rgbimages.py:
	  Code simplification: no visible change.

2009-02-17  antolikjan

	* [r10040] contrib/gc_alissom.ty:
	  selectivity multiplier change

2009-02-17  ceball

	* [r10039] examples/lissom.ty:
	  Updated doc (for script-level parameters).

2009-02-16  ceball

	* [r10038] contrib/rgbimages.py:
	  Corrected import.

2009-02-13  rczhao

	* [r10037] contrib/lissom_happyface.ty:
	  A LISSOM-based happy face (cartoon face with a curved mouth)
	  simulation.

2009-02-12  jbednar

	* [r10036] /releases/0.9.6:
	  Create release 0.9.6

	* [r10035] /tags/LATEST_STABLE/trunk:
	  Update LATEST_STABLE.

	* [r10034] doc/Team_Members/index_text.php:
	  Updated team

	* [r10033] doc/Tutorials/gca_lissom_text.php,
	  doc/Tutorials/images/gca_natural_image_oo_or.png:
	  Fixed refs to LISSOM. Updated image of face

	* [r10032] Makefile,
	  examples/README.txt:
	  Fixed syntax for distclean. Added gca_lissom.ty to list to keep

	* [r10031] ChangeLog.txt:
	  Updated with current changes

2009-02-12  ceball

	* [r10030] etc/update_095_to_096:
	  Added 'output_fn=X'->'output_fns=[X'.

	* [r10029] doc/Reference_Manual/index_text.php:
	  Added info about Cython.

2009-02-12  antolikjan

	* [r10028] contrib/gc_alissom.ty:
	  made default map measurment with higher number of orientations

2009-02-12  ceball

	* [r10027] topo/param/tk.py:
	  Fixed SF #2572627 (assumed all widgets were managed by grid, but
	  some are managed by pack).

	* [r10026] topo/param/tk.py:
	  Fixed bug in GUI where a new list item could not be added
	  sometimes (caused by a parameter's representation was not being
	  removed).

	* [r10025] doc/Tutorials:
	  More to ignore.

2009-02-12  jbednar

	* [r10024] README.txt,
	  doc/Downloads/index_text.php,
	  doc/Future_Work/current_text.php,
	  doc/Future_Work/index_text.php,
	  doc/Reference_Manual/index_text.php,
	  topo/__init__.py:
	  Updated for new release

	* [r10023]
	  doc/Developer_Manual/releases_text.php:
	  Minor clarification

2009-02-12  ceball

	* [r10022] topo/param/tk.py:
	  Removed debugging aid left in by mistake.

2009-02-12  jbednar

	* [r10021] /trunk/topographica-win/common/setup.py,
	  /trunk/topographica-win/create_installer/topographica.iss:
	  Updated to declare version 0.9.6

	* [r10020] examples/gca_lissom.ty:
	  Added item_scale to make Model Editor look better

2009-02-12  ceball

	* [r10019] topo/param/tk.py:
	  Fixed bug where TaggedSliders' sliders were not being refreshed
	  when the Defaults button was pressed.

	* [r10018]
	  doc/Tutorials/som_retinotopy_text.php:
	  Updated locals() -> global_params.

	* [r10017] doc/Tutorials/gca_lissom_text.php:
	  More changes to convert from lissom_oo_or to gca_lissom.

	* [r10016] topo/command/basic.py:
	  Changed snapshot info print statement to debug statement.

	* [r10015] doc/Tutorials/gca_lissom_text.php,
	  doc/Tutorials/lissom_oo_or_text.php,
	  doc/User_Manual/plotting_text.php:
	  Reduced section about display=True during map measurement.

2009-02-12  jbednar

	* [r10014] Makefile:
	  Updated stated release; still needs 'make new-version'

2009-02-11  jbednar

	* [r10013] topo/command/pylabplots.py:
	  Fixed pylabplots titles; missing since r9557

2009-02-11  ceball

	* [r10012] doc/Tutorials/gca_lissom_text.php,
	  doc/Tutorials/images/lissom_network_diagram_oo.png,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Minor updates (including lissom_oo_or network diagram.

	* [r10011] doc/Tutorials/gca_lissom_text.php,
	  doc/Tutorials/images/gca_lissom_network_diagram.png:
	  More updates: network size, network diagram.

	* [r10010] doc/Tutorials/gca_lissom_text.php,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Minor updates.

	* [r10009] doc/Tutorials/gca_lissom_text.php,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Updated command.

	* [r10008] doc/Tutorials/gca_lissom_text.php,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Fixed minor typo.

	* [r10007] topo/param/tk.py:
	  Fixed typo.

	* [r10006] topo/param/tk.py:
	  Remove newline characters from script_reprs in the GUI. Partially
	  addresses SF bug #2590268.

2009-02-11  antolikjan

	* [r10005] contrib/jacommands.py:
	  repaired some more problems with imports

2009-02-11  ceball

	* [r10004] topo/param/tk.py:
	  Fixed SF #2585687 by restoring code to wipe all displayed widgets
	  (should not have been removed).

	* [r10003]
	  doc/Downloads/update_script_text.php:
	  Fixed minor typo.

2009-02-11  antolikjan

	* [r10002] contrib/jacommands.py:
	  added some missing imports

	* [r10001] contrib/gc_alissom.ty:
	  change to some parameters

2009-02-11  ceball

	* [r10000]
	  topo/tkgui/templateplotgrouppanel.py:
	  Made strength-only hack safe between instances of
	  TemplatePlotGroupPanels. Fixes SF #2585560.

	* [r9999] doc/Downloads/update_script_text.php:
	  Minor typo.

	* [r9998] topo/param/tk.py:
	  Implemented ClassSelector support for List parameters that have a
	  valid class_. SF feature #2581878.

2009-02-11  jbednar

	* [r9997] doc/News/index_text.php:
	  Reorganized order; no new items

	* [r9996] doc/Home/news_text.php,
	  doc/News/index_text.php:
	  Updated with recent news and to announce version 0.9.6

	* [r9995] doc/Downloads/update_script_text.php:
	  Updated for 0.9.6

	* [r9994]
	  doc/Developer_Manual/optimization_text.php:
	  Added line-by-line target. Reduced line length to work in
	  browser.

2009-02-11  ceball

	* [r9993] topo/sheet/lissom.py:
	  Increased JointScaling's precedence above that of LISSOM's.

	* [r9992] topo/plotting/plotgroup.py:
	  Fixed bug in PlotGroup's _create_images() where plots were being
	  constructed twice for TemplatePlotGroups.

2009-02-11  jbednar

	* [r9991] examples/tiny.ty:
	  Made import style match other examples

	* [r9990] doc/Tutorials/gca_lissom_text.php,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Made spelling consistent

	* [r9989] Makefile:
	  Sped up ChangeLog generation

	* [r9988] ChangeLog.txt:
	  Fixed some bogus checkin messages

	* [r9987] ChangeLog.txt,
	  doc/News/index_text.php:
	  Updated with recent changes

2009-02-11  ceball

	* [r9986] doc/Tutorials/gca_lissom_text.php:
	  Updated introduction to GCA-LISSOM tutorial.

2009-02-11  jbednar

	* [r9985] doc/News/index_text.php:
	  Updated with recent changes

	* [r9984] topo/base/cf.py:
	  Added mask_threshold value (fixes ALERT)

2009-02-11  ceball

	* [r9983] doc/Tutorials/gca_lissom_text.php,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Added section about visualizing map measurement.

	* [r9982] doc/Tutorials/lissom_oo_or_text.php:
	  Fixed link to GeneratorSheet reference.

2009-02-11  jbednar

	* [r9981] topo/plotting/plot.py:
	  Suppressed extra staleness_warnings

	* [r9980] examples/gca_lissom.ty:
	  Changed defaults for map measurement to match lissom_oo_or.ty

	* [r9979]
	  topo/command/disp_key_white_vert_small.png:
	  Cleaned up number spacing

2009-02-11  ceball

	* [r9978] doc/Tutorials/gca_lissom_text.php,
	  doc/Tutorials/images/gca_lissom_activity_010000.png,
	  doc/Tutorials/images/gca_lissom_activity_010000_or.png,
	  doc/Tutorials/images/gca_lissom_cf_center_010000.png,
	  doc/Tutorials/images/gca_lissom_cf_center_010000_or.png,
	  doc/Tutorials/images/gca_lissom_cf_vertical_010000_or.png,
	  doc/Tutorials/images/gca_lissom_network_diagram.png,
	  doc/Tutorials/images/gca_lissom_or_pref_010000.png,
	  doc/Tutorials/images/gca_lissom_ormap_ft.png,
	  doc/Tutorials/images/gca_lissom_projection_010000.png,
	  doc/Tutorials/images/gca_lissom_test_pattern.png,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Initial version of GCA-LISSOM tutorial.

	* [r9977] examples/run.py:
	  Added 'gca_lissom_10000.typ' target.

2009-02-10  jbednar

	* [r9976] doc/Tutorials/lissom_oo_or_text.php,
	  doc/Tutorials/lissom_or_text.php:
	  Fixed broken URL

	* [r9975] topo/tkgui/editor.py:
	  Fixed activity and density display options

	* [r9974] contrib/jacommands.py,
	  topo/sheet/lissom.py:
	  Moved add_gc back to jacommands now that gca_lissom.ty does not
	  need it

2009-02-10  antolikjan

	* [r9973] contrib/gc_alissom.ty:
	  bug repair

	* [r9972] contrib/gc_alissom.ty:
	  some more minor simplifications and parameter changes

	* [r9971] contrib/cc_lissom_oo_or_simple_rv.ty:
	  change of default parameter value

2009-02-10  jbednar

	* [r9970] examples/gca_lissom.ty:
	  Removed dependence on add_gc, and fixed selectivity_multiplier

	* [r9969] topo/base/arrayutil.py:
	  Made divide_with_constant available globally

2009-02-10  ceball

	* [r9968]
	  doc/Tutorials/images/activity_line_oo.png,
	  doc/Tutorials/images/activity_line_oo_or.png,
	  doc/Tutorials/images/lissom_oo_or_activity_rightclick.png,
	  doc/Tutorials/images/lissom_oo_or_orpref_ft.png,
	  doc/Tutorials/images/natural_image_oo_or.png,
	  doc/Tutorials/images/oo_or_map.png,
	  doc/Tutorials/images/projection_oo.png,
	  doc/Tutorials/images/test_pattern_oo.png,
	  doc/Tutorials/images/unit_weights_0_0_oo.png,
	  doc/Tutorials/images/unit_weights_0_0_oo_or.png,
	  doc/Tutorials/images/unit_weights_41_24_oo_or.png,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Updated lissom_oo_or tutorial images.

2009-02-10  antolikjan

	* [r9967] contrib/cc_lissom_oo_or_simple_rv.ty:
	  change of default parameter value

2009-02-10  ceball

	* [r9966]
	  doc/Tutorials/images/topographica_console.png,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Files missed from r9965.

	* [r9965]
	  doc/Tutorials/images/som_topographica_console.png,
	  doc/Tutorials/images/topographica_console.png,
	  doc/Tutorials/som_retinotopy_text.php:
	  Renamed som_retinotopy's topographica_console.png to
	  som_topographica_console.png (tutorials can't share a console
	  image now the simulation name is displayed).

	* [r9964]
	  doc/Tutorials/images/som_activity_000000.png,
	  doc/Tutorials/images/som_activity_000001.png,
	  doc/Tutorials/images/som_cog_000000.png,
	  doc/Tutorials/images/som_cog_005000.png,
	  doc/Tutorials/images/som_projection_000000.png,
	  doc/Tutorials/images/som_projection_000001.png,
	  doc/Tutorials/images/som_projection_000005.png,
	  doc/Tutorials/images/som_projection_010000.png,
	  doc/Tutorials/images/som_projection_040000.png,
	  doc/Tutorials/images/som_projection_activity_000001.png,
	  doc/Tutorials/images/topographica_console.png,
	  doc/Tutorials/som_retinotopy_text.php:
	  Updated SOM retinotopy tutorial with new screenshots.

2009-02-10  antolikjan

	* [r9963] contrib/gc_alissom.ty:
	  parameter value change

2009-02-10  ceball

	* [r9962] doc/User_Manual/commandline_text.php,
	  doc/User_Manual/plotting_text.php,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py:
	  More renaming related to update_command -> pre_plot_hooks.

2009-02-09  jbednar

	* [r9961] topo/transferfn/basic.py:
	  Fixed typo

	* [r9960] topo/sheet/lissom.py:
	  Expanded comment

	* [r9959] topo/analysis/featureresponses.py:
	  Removed unused imports

	* [r9958] topo/plotting/plotgroup.py:
	  Fixed to provide a default sheet in more cases

	* [r9957] topo/transferfn/basic.py:
	  Minor cleanup

	* [r9956] topo/base/simulation.py:
	  Changed EventProcessor.input_event to deepcopy the data only
	  once, regardles of the number of destinations for the message

2009-02-09  ceball

	* [r9955] contrib/jacommands.py:
	  Added links to classes recently removed.

	* [r9954] examples/gca_lissom.ty,
	  topo/transferfn/basic.py:
	  Renamed ActivityHysteresis to Hysteresis, and updated docs.

	* [r9953] contrib/jacommands.py,
	  examples/gca_lissom.ty,
	  topo/sheet/lissom.py:
	  Moved contrib.jacommands.AddGC() to topo.sheet.lissom.add_gc().

	* [r9952] contrib/jacommands.py,
	  examples/gca_lissom.ty:
	  AddGC() now takes arguments rather than looking in __main__, and
	  works on one sheet at a time.

	* [r9951] contrib/jacommands.py,
	  examples/gca_lissom.ty,
	  topo/transferfn/basic.py:
	  Moved ActivityHysteresis from contrib.jacommands to
	  topo.transferfn.basic.

	* [r9950] contrib/jacommands.py:
	  Minor changes (should be no visible change).

	* [r9949] contrib/jacommands.py,
	  examples/gca_lissom.ty,
	  topo/transferfn/basic.py:
	  Moved HomeostaticResponse from contrib.jacommands to
	  topo.transferfn.basic.

	* [r9948] contrib/jacommands.py,
	  examples/gca_lissom.ty:
	  Renamed SimpleHomeoLinearRelative to HomeostaticResponse (and
	  made minor formatting changes).

	* [r9947] examples/gca_lissom.ty:
	  Added missing svn properties to gca_lissom.ty.

2009-02-09  jbednar

	* [r9946] examples/gca_lissom.ty:
	  Fixed comment

	* [r9945] Makefile,
	  examples/Makefile,
	  examples/gc_alissom.ty,
	  examples/gca_lissom.ty,
	  topo/tests/gc_alissom.ty_DATA,
	  topo/tests/gc_alissom.ty_SPEEDDATA,
	  topo/tests/gca_lissom.ty_DATA,
	  topo/tests/gca_lissom.ty_SPEEDDATA:
	  Renamed gc_alissom to gca_lissom to make it pronounceable

	* [r9944] examples/gc_alissom.ty:
	  Added defaults to match lissom_oo_or.ty. Changed feature curves
	  as Jan did in contrib

2009-02-06  antolikjan

	* [r9943] contrib/cc_lissom_oo_or_simple_rv.ty:
	  added half rectified TF option for V1Simple

	* [r9942] topo/transferfn/basic.py:
	  modified half rectified TFs to use threshold

	* [r9941] contrib/gc_alissom.ty:
	  changed the selectivity multiplier

2009-02-06  ceball

	* [r9940] doc/User_Manual/plotting_text.php,
	  topo/command/analysis.py:
	  Added note about alternative implementation of measure_or_pref().

	* [r9939] doc/User_Manual/images/edit_list.png,
	  doc/User_Manual/images/list_item_properties.png,
	  doc/User_Manual/plotting_text.php:
	  Updated to show list editing via the GUI.

2009-02-06  jbednar

	* [r9938] doc/User_Manual/scripts_text.php:
	  Fixed typo

2009-02-06  ceball

	* [r9937] topo/misc/commandline.py:
	  Fixed quotation error.

	* [r9936] doc/Tutorials/lissom_oo_or_text.php,
	  doc/Tutorials/som_retinotopy_text.php,
	  doc/User_Manual/batch_text.php,
	  doc/User_Manual/scripts_text.php,
	  topo/misc/commandline.py:
	  Updated documentation relating to -p and global_params.

2009-02-06  antolikjan

	* [r9935] contrib/cc_lissom_oo_or_simple_rv.ty:
	  allowed for parametrization for the strength of the LGN channels
	  strength randomization

	* [r9934] topo/analysis/vision.py:
	  reduced the number of samples for phase scatter plot to match
	  DeAngelis 1999

2009-02-06  ceball

	* [r9933] examples/run.py:
	  Updated location of some commands (now in pylabplots).

2009-02-05  ceball

	* [r9932] topo/misc/legacy.py:
	  Added comment.

	* [r9931] topo/param/parameterized.py:
	  Minor modification to snapshot warning messages.

	* [r9930] topo/param/parameterized.py:
	  Snapshot loading: made Parameter restoration warning message more
	  useful (can now see more work needs to be done on legacy support
	  even for the lissom_oo_or.ty snapshot).

	* [r9929] topo/command/basic.py:
	  Removed unused import.

	* [r9928] topo/param/parameterized.py:
	  Fixed command for importing module while restoring class
	  attributes (previous command committed by mistake during other
	  work).

	* [r9927] contrib/rgbimages.py:
	  Updated to match recent changes to output_fns.

	* [r9926] doc/Downloads/git_text.php:
	  Minor additions to git documentation.

	* [r9925] contrib/rgbhsv.py:
	  Inital version (from CSNG repository).

	* [r9924] contrib/rgbimages.py:
	  Various changes to rgb-related classes. Added various online
	  analysis classes.

2009-02-04  jbednar

	* [r9923] topo/command/analysis.py:
	  Suppressed rarely-useful message

	* [r9922] doc/Future_Work/current_text.php:
	  Removed some completed tasks

	* [r9921] doc/Future_Work/index_text.php:
	  Added link to pytables, and new spiking model

	* [r9920] doc/User_Manual/commandline_text.php:
	  Added example of looking up a SheetView

2009-02-04  antolikjan

	* [r9919] contrib/gc_alissom.ty:
	  made changes regarding the new output function mechanism

	* [r9918] contrib/cc_lissom_oo_or_simple_rv.ty:
	  made changes regarding output function updates

	* [r9917] contrib/cc_lissom_oo_or_simple_rv.ty:
	  bug repair

2009-02-04  jbednar

	* [r9916] topo/tests/lissom_fsa.ty_DATA,
	  topo/tests/lissom_fsa.ty_SPEEDDATA:
	  Committed 2008-10-02 results of running the lissom_fsa.ty tests

2009-02-04  ceball

	* [r9915] external:
	  More to ignore.

2009-02-04  antolikjan

	* [r9914] contrib/cc_lissom_oo_or_simple_rv.ty:
	  got rid of PipelineTF

	* [r9913] contrib/gc_alissom.ty:
	  got rid of PipelineTF

2009-02-04  jbednar

	* [r9912] topo/analysis/featureresponses.py:
	  Changed _fullmatrix handling to work the same for subclasses as
	  for FeatureResponses

2009-02-03  ceball

	* [r9911] etc/update_095_to_096:
	  Attempt to make update script. Still unusable.

	* [r9910] etc/update_095_to_096:
	  More things to update. Still a sketch.

	* [r9909] topo/misc/legacy.py,
	  topo/param/parameterized.py:
	  Support change of output_fn=x to output_fns=[x]. Plus some
	  additional cleanup.

2009-02-03  antolikjan

	* [r9908] topo/analysis/featureresponses.py:
	  made _fullmatrix in FeatureResponses static

	* [r9907] contrib/gc_alissom.ty:
	  decreased the default selectivity multiplier

2009-02-03  ceball

	* [r9906] topo/param/tk.py:
	  Uncommented code to get buttons on list widget.

2009-02-03  jbednar

	* [r9905] topo/tkgui/icons/arrow-down-2.0.png,
	  topo/tkgui/icons/arrow-up.png,
	  topo/tkgui/icons/edit_add.png,
	  topo/tkgui/icons/edit_remove.png,
	  topo/tkgui/icons/star-button.png,
	  topo/tkgui/icons/stop-2.1.png,
	  topo/tkgui/icons/trashcan_empty-2.1.png:
	  Committed results of 'make -C external bluesphere to get icons
	  for list widget

2009-02-03  ceball

	* [r9904] topo/param/tk.py:
	  Upgraded list editing in the GUI. Can now add, remove, and
	  reorder items. Need to add icons for buttons. But: what started
	  out as simple code to implement this feature has become a mess,
	  for various irrelevant reasons; some specific problems are noted
	  in the commit.

	* [r9903] topo/misc/legacy.py:
	  Added comment.

	* [r9902] topo/misc/legacy.py:
	  Cleaned up teststimuli support.

2009-02-02  ceball

	* [r9901] doc/Future_Work/current_text.php,
	  doc/User_Manual/commandline_text.php,
	  doc/User_Manual/noise_text.php,
	  doc/User_Manual/overview_text.php,
	  doc/User_Manual/parameters_text.php:
	  Updated documentation about output functions/transfer functions.

	* [r9900] topo/base/cf.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/pattern/image.py,
	  topo/projection/basic.py,
	  topo/sheet/basic.py:
	  Restored type specification to some output_fns HookLists (didn't
	  restore in cases where type specification should be inherited
	  from a parent class). Removed output_fns parameter in some cases
	  (where I believe the parameter is already suitably specified in a
	  parent class.

2009-02-02  jbednar

	* [r9899]
	  external/BlueSphere-SVG-snapshot-Nov-29-2002_Makefile:
	  Added more icons to topo/tkgui for Chris's list widget

2009-02-02  ceball

	* [r9898] topo/misc/legacy.py:
	  Added legacy support for PipelineOF. Presumably not yet complete,
	  but current snapshot-compatibility-tests now pass without errors
	  or warnings.

	* [r9897] contrib/jacommands.py,
	  doc/User_Manual/commandline_text.php,
	  doc/User_Manual/plotting_text.php,
	  examples/gc_alissom.ty,
	  examples/hierarchical.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/tiny.ty,
	  topo/analysis/featureresponses.py,
	  topo/base/cf.py,
	  topo/base/functionfamily.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/command/analysis.py,
	  topo/command/basic.py,
	  topo/misc/legacy.py,
	  topo/pattern/image.py,
	  topo/pattern/random.py,
	  topo/pattern/rds.py,
	  topo/projection/basic.py,
	  topo/sheet/basic.py,
	  topo/sheet/lissom.py,
	  topo/sheet/slissom.py,
	  topo/tests/gui_tests.py,
	  topo/tests/testimage.py,
	  topo/transferfn/basic.py:
	  Changed output_fn parameters to be HookLists, and renamed
	  output_fn (and related) variable names to output_fns. No legacy
	  support yet.

2009-02-01  ceball

	* [r9896] topo/param/tk.py:
	  Fixed bug introduced in an earlier checkin.

	* [r9895] topo/param/tk.py:
	  Fixed bug introduced in previous checkin.

	* [r9894] topo/param/tk.py:
	  More cleanup. Should be no visible change.

	* [r9893] topo/param/tk.py:
	  More cleanup. Should be no visible change.

	* [r9892] topo/param/tk.py:
	  More cleanup. Should be no visible change.

	* [r9891] topo/param/tk.py:
	  More cleanup. Should be no visible change.

	* [r9890] topo/param/tk.py:
	  Cleanup - should be no visible change.

	* [r9889] topo/param/tk.py:
	  Simplified on_set() and on_modify().

	* [r9888] topo/param/tk.py:
	  Minor simplification: don't need to store row information (grid()
	  stores it already).

	* [r9887] topo/param/tk.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Renamed on_change() to on_set() (to distinguish from on_modify().

	* [r9886] etc/update_095_to_096,
	  topo/command/basic.py:
	  Cleaned up some notices about filing bug reports.

	* [r9885] topo/misc/legacy.py:
	  More simplification of legacy support.

	* [r9884] topo/param/parameterized.py:
	  When unpickling class attributes, no longer uses
	  __main__.__dict__ as a space in which to work. Added note about
	  intention to remove try/catches around class attribute
	  unpickling.

	* [r9883] topo/misc/legacy.py:
	  Fixed bug in legacy's module_redirect() (for cases where a
	  module's parent is already a redirected module). Added support
	  for OneDPowerSpectrum's moves between topo.pattern.audio and
	  .basic.

2009-01-30  antolikjan

	* [r9882] topo/analysis/featureresponses.py:
	  corrected the problem with ACDC tuning curve and added hook to
	  FeatureCurves

2009-01-30  jbednar

	* [r9881] examples/gc_alissom.ty:
	  Cleaned up and reorganized to match lissom_oo_or.ty

	* [r9880] examples/gc_alissom.ty:
	  Removed unused bounding box

	* [r9879] examples/gc_alissom.ty:
	  Converted locals to parameters

	* [r9878] topo/analysis/featureresponses.py:
	  Temporarily commented out broken code

	* [r9877] examples/hierarchical.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/perrinet_retina.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/tiny.ty:
	  Added note explaining parameters

2009-01-30  antolikjan

	* [r9876] topo/analysis/vision.py:
	  corrected and import problem

	* [r9875] contrib/gc_alissom.ty:
	  added NoisyDisks and the change from NoisyDisks to Natural into
	  the simulation

2009-01-30  ceball

	* [r9874] topo/param/tk.py:
	  Disabled ListEntry text box, but made foreground color same as
	  normal text box (otherwise nobody will try clicking on it...).

	* [r9873] topo/param/tk.py:
	  Changed list widget to have right-click menu with 'properties' on
	  it for editing a list (rather than it being a left click).

2009-01-29  jbednar

	* [r9872] examples/gc_alissom.ty:
	  Converted imports to new simpler style

2009-01-29  antolikjan

	* [r9871] topo/analysis/vision.py:
	  repaired circular imports

	* [r9870] topo/command/pylabplots.py:
	  corrected circular import bug

	* [r9869] contrib/cc_lissom_oo_or_simple_rv.ty:
	  one parameter change and one import renaming

	* [r9868] contrib/jacommands.py:
	  tiny cosmetic changes

	* [r9867] topo/analysis/featureresponses.py:
	  plugged in the new ACDC way of computing tuning curves

	* [r9866] topo/analysis/vision.py:
	  added new way of computing tuning curves - the AC DC max

	* [r9865] contrib/gc_alissom.ty:
	  a working version of the same file in examples

2009-01-29  jbednar

	* [r9864] Makefile,
	  topo/tests/gc_alissom.ty_DATA,
	  topo/tests/gc_alissom.ty_SPEEDDATA:
	  Added gc_alissom.ty tests

	* [r9863] examples/gc_alissom.ty:
	  Changed name of density parameters to match other examples

2009-01-29  ceball

	* [r9862] topo/tests/test_script.py:
	  Reduced combinations of densities for c++ comparisons. See SF.net
	  #2545559.

	* [r9861] doc/buildbot/master.cfg:
	  Removed fixed-parameters c++ lissom comparisons.

	* [r9860] Makefile,
	  topo/tests/reference/Makefile,
	  topo/tests/reference/fixed_params:
	  Removed fixed-parameters C++ lissom comparisons.

2009-01-28  ceball

	* [r9859] Makefile:
	  Rearranged comment; no visible change.

	* [r9858] doc/buildbot/master.cfg:
	  Set cloud to use 'clobber'. Reduced unoptimized matching
	  requirement from 7 dp to 6 dp.

	* [r9857] topo/tests/test_script.py:
	  Added print out of no. of decimal places on failure.

	* [r9856] topo/misc/legacy.py:
	  Legacy support: simplified; should be no visible change.

	* [r9855] topo/misc/legacy.py:
	  Further simplifications.

	* [r9854] topo/misc/legacy.py:
	  Simplified support for package name changes.

	* [r9853] topo/misc/legacy.py:
	  Simplified support for module name changes. Still more to go...

2009-01-28  jbednar

	* [r9852] doc/News/index_text.php:
	  Fixed typo that was breaking doc build

	* [r9851] external/Makefile:
	  Fixed broken odict clean and uninstall targets

2009-01-27  antolikjan

	* [r9850]
	  contrib/lissom_oo_or_homeostatic_tracked_new.ty:
	  some more parameter changes

	* [r9849] examples/gc_alissom.ty:
	  made default lateral exc. learning rate 0

	* [r9848]
	  contrib/lissom_oo_or_homeostatic_tracked_new.ty:
	  changed some parameters

	* [r9847] examples/gc_alissom.ty:
	  allowed for lat exc connections to learn

2009-01-27  ceball

	* [r9846] topo/misc/legacy.py:
	  Fixed problem with fake_package() where wrong module was being
	  returned by __import__.

	* [r9845] external/Imaging.diff,
	  external/Imaging_OSX.diff:
	  Restored Imaging.diff and removed Imaging_OSX.diff (wrong one
	  mistakenly removed in r9728).

2009-01-27  jbednar

	* [r9844] topo/command/pylabplots.py:
	  Fixed tuning curve plots to show full coordinates, instead of
	  cropped to integers

	* [r9843] doc/News/index_text.php,
	  topo/tkgui/plotgrouppanel.py:
	  Added right-click option for plotting orientation tuning curves

	* [r9842] topo/param/parameterized.py:
	  Fixed typo in doc

2009-01-27  ceball

	* [r9841] topo/outputfn:
	  Removed topo.outputfn; apparently removal didn't carry over from
	  git.

2009-01-26  ceball

	* [r9840] topo/param/tk.py:
	  Can now edit lists in the GUI. Clicking on a list parameter
	  brings up a new window with the list entries. Initial version:
	  cannot add or remove items from the list (plus see other bugs on
	  sf.net). Works by representing the list with a Parameterized
	  object.

	* [r9839] external/Makefile:
	  Added odict to default target (provides OrderedDictionary).

	* [r9838] topo/param/parameterized.py:
	  Fixed ParameterizedFunction's script_repr() method (so that it
	  includes '.instance()').

	* [r9837] topo/param/parameterized.py:
	  Fixed typo in code.

	* [r9836] topo/param/parameterized.py:
	  Delete params() cache when adding a new parameter to a class.

2009-01-25  ceball

	* [r9835] doc/User_Manual:
	  More to ignore.

	* [r9834] topo/transferfn:
	  Set svn:ignore on topo/transferfn/

	* [r9833] external:
	  More to ignore.

	* [r9832] etc/update_095_to_096:
	  Initial version.

	* [r9831] contrib/cc_lissom_oo_or_simple_rv.ty,
	  contrib/gc_lissom_oo_or_homeostatic_new.ty,
	  contrib/jacommands.py,
	  contrib/jsldefs.py,
	  contrib/laminar_oo_or.ty,
	  contrib/laminar_or.ty,
	  contrib/lesi.ty,
	  contrib/lesi_whisker_barrels.ty,
	  contrib/lgn_lateral.ty,
	  contrib/lissom.ty,
	  contrib/lissom_oo_dr.ty,
	  contrib/lissom_oo_or_homeostatic.ty,
	  contrib/lissom_oo_or_homeostatic_tracked.ty,
	  contrib/lissom_oo_or_homeostatic_tracked_new.ty,
	  contrib/lissom_oo_or_noshrinking.ty,
	  contrib/lissom_oo_or_noshrinking_latswitch.ty,
	  contrib/lissom_oo_or_species.ty,
	  contrib/lissom_oo_or_species_tracked.ty,
	  contrib/lissom_or_noshrinking.ty,
	  contrib/lissom_or_noshrinking_latswitch.ty,
	  contrib/modelfit.py,
	  contrib/sparse_connectivity_LESI.ty,
	  contrib/sparse_connectivity_model.ty,
	  contrib/species_cf_jitter.ty,
	  contrib/species_lateral_sparsity.ty,
	  contrib/wordcolor.ty,
	  doc/Developer_Manual/imports_text.php,
	  doc/Developer_Manual/optimization_text.php,
	  doc/FAQ/index_text.php,
	  doc/Future_Work/current_text.php,
	  doc/Future_Work/index_text.php,
	  doc/Reference_Manual/index_text.php,
	  doc/User_Manual/commandline_text.php,
	  doc/User_Manual/noise_text.php,
	  doc/User_Manual/overview_text.php,
	  doc/User_Manual/scripts_text.php,
	  examples/gc_alissom.ty,
	  examples/hierarchical.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/tiny.ty,
	  topo/__init__.py,
	  topo/base/cf.py,
	  topo/base/functionfamily.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/command/basic.py,
	  topo/command/pylabplots.py,
	  topo/learningfn/som.py,
	  topo/misc/legacy.py,
	  topo/outputfn/__init__.py,
	  topo/outputfn/basic.py,
	  topo/outputfn/optimized.py,
	  topo/outputfn/projfn.py,
	  topo/pattern/image.py,
	  topo/pattern/random.py,
	  topo/pattern/rds.py,
	  topo/projection/basic.py,
	  topo/sheet/basic.py,
	  topo/sheet/lissom.py,
	  topo/sheet/optimized.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/testimage.py,
	  topo/tests/testoutputfnsbasic.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/__init__.py,
	  topo/transferfn,
	  topo/transferfn/__init__.py,
	  topo/transferfn/basic.py,
	  topo/transferfn/optimized.py,
	  topo/transferfn/projfn.py:
	  Renamed topo.outputfn to topo.transferfn. Renamed OutputFn to
	  TransferFn. Renamed OFs to TFs. Added legacy support.

	* [r9830] topo/command/basic.py:
	  Added snapshot version printing to load_snapshot().

2009-01-24  ceball

	* [r9829] topo/analysis/featureresponses.py,
	  topo/base/functionfamily.py:
	  Renamed after_analysis_session to post_analysis_session_hooks. No
	  legacy support added.

	* [r9828] topo/analysis/featureresponses.py,
	  topo/base/functionfamily.py:
	  Renamed before_analysis_session to pre_analysis_session_hooks. No
	  legacy support added.

	* [r9827] topo/analysis/featureresponses.py,
	  topo/base/functionfamily.py:
	  Renamed after_pattern_presentation to post_presentation_hooks. No
	  legacy support added.

	* [r9826] contrib/jacommands.py,
	  topo/analysis/featureresponses.py,
	  topo/base/functionfamily.py:
	  Renamed before_pattern_presentation to pre_presentation_hooks. No
	  legacy support added.

	* [r9825] topo/__init__.py,
	  topo/param/parameterized.py:
	  Updated comments.

	* [r9824] topo/__init__.py,
	  topo/base/simulation.py,
	  topo/misc/legacy.py,
	  topo/param/__init__.py:
	  Added general support for pickling/copying instance methods.
	  Removed InstanceMethodWrapper and wrap_callable.

	* [r9823] doc/buildbot/master.cfg:
	  Added cloud as a buildslave.

	* [r9822] doc/buildbot/master.cfg:
	  Reorganization of buildmaster configuration: should be no visible
	  change.

	* [r9821] Makefile:
	  Renamed default_density etc.

	* [r9820] examples/som_retinotopy.ty:
	  Undid accidental change to default retina_density (changed from
	  from 24.0 to 10.0 in r9809).

	* [r9819] topo/tests/test_script.py:
	  Added support for old test data files containing
	  'default_density' etc.

	* [r9818] topo/tests/lissom.ty_DATA:
	  Data from r9776 (after random seed change).

	* [r9817] topo/tests/test_script.py:
	  Added support for test data that contains old 'default_'
	  arguments.

	* [r9816] topo/tests/test_script.py:
	  TestScript now prints arguments that were specifed for a script
	  (so that we can see what arguments were used).

2009-01-23  jbednar

	* [r9815] examples/Makefile:
	  Removed long-gone or_dr simulation. Added gc_alissom simulation.

	* [r9814] examples/perrinet_retina.ty:
	  Added URL and minor notes, plus made sim time controllable and
	  forced density to be an integer (as NEST requires)

	* [r9813] topo/learningfn/optimized.py:
	  Removed redundant option

2009-01-22  ceball

	* [r9812] contrib/expressionparam.py:
	  Initial version.

	* [r9811] external/Makefile,
	  external/termcap-1.3.1.tar.gz:
	  Added termcap, and made readline depend on it. Made Python depend
	  on readline, and passed EXTRA_CFLAGS to Python's make so that
	  Topographica's include directory is used. Added readline and
	  termcap to uninstall and clean targets.

2009-01-22  antolikjan

	* [r9810] examples/gc_alissom.ty:
	  added external parameters and made activity to reset between
	  input presentations

2009-01-21  jbednar

	* [r9809] examples/som_retinotopy.ty:
	  Converted locals() calls to explicit global parameters

	* [r9808] doc/News/index_text.php:
	  Updated with a recent change

	* [r9807] Makefile:
	  Removed cfsom_or references

	* [r9806] topo/tests/test_script.py:
	  Changed default_density to cortex_density to match changes in
	  examples/; still needs work

	* [r9805] examples/leaky_lissom_or.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/perrinet_retina.ty,
	  examples/sullivan_neurocomputing04.ty:
	  Converted locals() calls to explicit global parameters

	* [r9804] examples/hierarchical.ty:
	  Updated to match lissom.ty style parameters

	* [r9803] examples/tiny.ty:
	  Updated to match lissom.ty style parameters

	* [r9802] doc/Future_Work/current_text.php,
	  doc/User_Manual/commandline_text.php,
	  doc/User_Manual/scripts_text.php,
	  examples/cfsom_or.ty,
	  examples/run.py:
	  Removed unused cfsom_or.ty example file

	* [r9801] examples/tiny.ty:
	  Updated to match lissom.ty style parameters

	* [r9800] examples/lissom_oo_or.ty:
	  Fixed previous checkin

	* [r9799] examples/lissom.ty,
	  examples/lissom_oo_or.ty:
	  Cleaned up and expanded docs and params

	* [r9798] examples/lissom.ty:
	  Cleaned up and expanded docs and params

	* [r9797] examples/lissom.ty:
	  Renamed density parameters to avoid confusing 'default'

2009-01-20  antolikjan

	* [r9796]
	  contrib/lissom_oo_or_homeostatic_tracked_new.ty:
	  loads of small changes

2009-01-20  ceball

	* [r9795] contrib/lissom.ty,
	  examples/lissom.ty,
	  topo/command/pylabplots.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Renamed Plotgroup's plot_command to plot_hooks.

	* [r9794] contrib/jsldefs.py,
	  contrib/lesi.ty,
	  contrib/lesi_whisker_barrels.ty,
	  contrib/lissom.ty,
	  contrib/lissom_oo_or_species_tracked.ty,
	  contrib/species_cf_jitter.ty,
	  contrib/species_lateral_sparsity.ty,
	  doc/User_Manual/commandline_text.php,
	  examples/lissom.ty,
	  examples/lissom_whisker_barrels.ty,
	  topo/analysis/featureresponses.py,
	  topo/analysis/vision.py,
	  topo/command/analysis.py,
	  topo/command/pylabplots.py,
	  topo/param/parameterized.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/gui_tests.py,
	  topo/tests/test_map_measurement.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Renamed Plotgroup's update_command to pre_plot_hooks.

2009-01-20  jbednar

	* [r9793] topo/misc/legacy.py:
	  Minor fix to comment

2009-01-20  ceball

	* [r9792] topo/param/__init__.py:
	  Added some comments.

	* [r9791] topo/tkgui/projectionpanel.py:
	  UnitsPanel now knows which sheet bounds are exclusive, and passes
	  that information to its sliders.

	* [r9790] topo/param/tk.py:
	  TaggedSlider now supports exclusive bounds.

	* [r9789] topo/misc/legacy.py,
	  topo/param/__init__.py:
	  Allow Number to work with exclusive bounds.

2009-01-18  jbednar

	* [r9788] examples/lissom.ty:
	  Cleaned up parameter formatting

2009-01-18  ceball

	* [r9787] topo/command/pylabplots.py:
	  Removed stray print statement.

	* [r9786] topo/base/parameterclasses.py,
	  topo/tests/testsheetview.py:
	  Removed topo/base/parameterclasses.py.

	* [r9785] doc/User_Manual/commandline_text.php,
	  examples/gc_alissom.ty,
	  examples/goodhill_network90.ty,
	  examples/leaky_lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/saccade_demo.ty,
	  examples/tiny.ty,
	  topo/command/analysis.py,
	  topo/command/basic.py,
	  topo/misc/legacy.py,
	  topo/sheet/generator.py,
	  topo/sheet/saccade.py,
	  topo/tests/gui_tests.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/testCompositePatternGenerators.txt,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testsnapshots.py,
	  topo/tests/utils.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py:
	  Removed topo/sheet/generator.py.

	* [r9784] examples/lissom.ty:
	  Fixed typo (introduced during a git merge).

	* [r9783] examples/lissom.ty:
	  Simplified setting of default value of default_retina_density.

	* [r9782] topo/param/parameterized.py:
	  Added set_default() to Parameterized. x.set_default(name,val) is
	  a simple way of doing x.params(name).default=val, or,
	  equivalently, setattr(type(x),name,val).

	* [r9781] topo/misc/commandline.py:
	  Renamed -s to -p (for parameter setting, to match 'p' used
	  elsewhere.

	* [r9780] examples/lissom.ty:
	  Import global_params as p to match existing convention.

	* [r9779] examples/lissom.ty:
	  Simplified setting of default_retina_density.

	* [r9778] examples/lissom.ty:
	  Begin to use global_params in lissom.ty.

	* [r9777] examples/lissom.ty:
	  Fixed typo.

	* [r9776] examples/lissom.ty:
	  Random input pattern parameters now use a seed generated from a
	  single base seed, allowing all random input parameters to be
	  changed at once. Simulations using Gaussian input patterns will
	  now have different results (differences should be insignificant)
	  because the input seeds have changed in that case.

2009-01-15  antolikjan

	* [r9775] topo/command/pylabplots.py:
	  Made orientation tuning curve plots have limited number of xticks
	  (they will allways now have 7)

2009-01-15  ceball

	* [r9774] topo/misc/commandline.py:
	  GlobalParams: set name to 'global_params' to match other uses.

	* [r9773] topo/misc/commandline.py:
	  GlobalParams: added warning for duplicate parameter specification
	  after any scripts have been executed (already detects duplicate
	  specifications before scripts are executed.

2009-01-15  antolikjan

	* [r9772] topo/analysis/vision.py:
	  improved the phase scatter plot

	* [r9771] topo/command/pylabplots.py:
	  more update to plot_modulation_ratio

2009-01-15  ceball

	* [r9770] examples/lissom.ty:
	  Image inputs: all random streams (i.e. all random parameters for
	  all images) now have a distinct seed. Shouldn't change results
	  significantly.

2009-01-15  antolikjan

	* [r9769] topo/command/pylabplots.py:
	  repaired plot_modultion_ratio

2009-01-15  ceball

	* [r9768] examples/lissom.ty:
	  Image inputs: made selection of input patch (x and y), plus
	  orientation of the patch, have dfferent random number streams for
	  each image (rather than every different image having the same
	  stream of x, y, and orientation). Although simulation results
	  will change, they should not be different in any significant way.

2009-01-15  jbednar

	* [r9767] topo/pattern/image.py:
	  Fixed confusing attribute name

	* [r9766] topo/base/sheetview.py,
	  topo/plotting/plot.py:
	  Made row_precedence always be 0.5 by default, to fix sf bug
	  #2456002

2009-01-15  antolikjan

	* [r9765] examples/gc_alissom.ty:
	  changes to external parametrization

2009-01-13  ceball

	* [r9764] doc/Downloads/git_text.php,
	  doc/Future_Work/current_text.php:
	  More cleaning of git documentation.

	* [r9763] topo/base/simulation.py:
	  Fixed typo.

	* [r9762] doc/Downloads/git_text.php:
	  Minor cleanup.

2009-01-12  antolikjan

	* [r9761] contrib/cc_lissom_oo_or_simple_rv.ty:
	  chaneged some external parametrization

2009-01-12  ceball

	* [r9760] topo/command/basic.py:
	  Use global_params.set_in_context(), rather than
	  .exec_in_context(), for setting parameter values.

	* [r9759] topo/misc/commandline.py:
	  Added set_in_context() method to GlobalParams.

2009-01-12  antolikjan

	* [r9758]
	  contrib/gc_lissom_oo_or_homeostatic_new.ty:
	  changed SimpleHomeoLinear to SimpleHomeoLinearRelative

2009-01-12  ceball

	* [r9757] topo/command/basic.py:
	  Made snaphots include the GlobalParams instance.

	* [r9756] topo/misc/commandline.py:
	  Made GlobalParams not save its context attribute when it is
	  pickled.

	* [r9755] topo/param/parameterized.py:
	  Clarified a comment.

2009-01-12  antolikjan

	* [r9754] topo/analysis/vision.py:
	  small change to scatter plot : change of diameter and small bug
	  correction

2009-01-11  ceball

	* [r9753] doc/Future_Work/current_text.php:
	  Added some links for my future reference.

	* [r9752] examples/tiny.ty:
	  Changed to use global_params instead of locals().

	* [r9751] topo/command/basic.py:
	  Converted run_batch() to use global_params. Should be no change
	  for current users of run_batch(), except that warnings will be
	  printed about values being unused.

	* [r9750] topo/misc/commandline.py,
	  topo/param/__init__.py:
	  Moved MainParams class and mainparams variable from topo.param to
	  topo.misc. Renamed MainParams to GlobalParams, and mainparams to
	  global_params.

2009-01-09  jbednar

	* [r9749]
	  doc/Developer_Manual/optimization_text.php:
	  Fixed bogus title, and other minor cleanup for line-by-line
	  profiling

	* [r9748] topo/learningfn/optimized.py:
	  Added missing import

2009-01-09  antolikjan

	* [r9747] examples/gc_alissom.ty:
	  adding gc_allissom

2009-01-07  ceball

	* [r9746] topo/misc/legacy.py:
	  Added support for SineGratingDisk, SineGratingRectangle, and
	  SineGratingRing. Removed broken support for
	  topo.pattern.teststimuli (fixes failing snapshot test); support
	  could be restored if required.

2009-01-06  ceball

	* [r9745] topo/tests/utils.py:
	  Added docstring.

	* [r9744]
	  doc/Developer_Manual/optimization_text.php:
	  Added information about line-by-line profiling. SF.net feature
	  request #2478100.

	* [r9743] topo/misc/commandline.py:
	  Added -s (--set-parameters) option.

	* [r9742] topo/param/__init__.py:
	  MainParams: for specifically defined parameters (script-level
	  parameters specified on the commandline via -s), warn if
	  duplicate values are specified, and keep track of parameter names
	  so that unused parameters can be detected.

2009-01-04  ceball

	* [r9741] topo/param/__init__.py:
	  Added MainParams: support for script-level parameters.

	* [r9740] topo/base/simulation.py,
	  topo/param/parameterized.py:
	  Moved OptionalSingleton from topo.base.simulation to
	  topo.base.parameterized.

	* [r9739] topo/param/parameterized.py:
	  Made Parameterized._add_parameter() be callable by a class or
	  instance.

	* [r9738] topo/param/parameterized.py:
	  Added method to Parameterized allowing new Parameter objects to
	  be installed into a Parameterized class.

	* [r9737] topo/param/parameterized.py:
	  ParameterizedMetaclass: moved parameter initialization
	  (inheritance, attribute name setting) into a separate method.
	  Should be no visible change.

2009-01-03  ceball

	* [r9736] topo/param/parameterized.py:
	  When instantiating Parameters, avoid redundantly instantiating
	  objects from superclasses.

	* [r9735] topo/param/parameterized.py,
	  topo/tests/testparameterizedobject.py:
	  Fixed inheritance for Parameter's instantiate slot (SF #2483932).

	* [r9734] topo/misc/trace.py:
	  Fixed variable name in InMemoryRecorder's get_data().

	* [r9733] topo/sheet/basic.py:
	  Clarified ALERT.

2009-01-02  ceball

	* [r9732] topo/tests/utils.py:
	  Added wrapper that gives simple access to a generator (for test
	  files).

	* [r9731] contrib/tracker.py:
	  Classes for tracking attribute access.

2008-12-31  ceball

	* [r9730] external/Makefile,
	  external/line_profiler-582df342463a.tar.gz:
	  Added line_profiler, for line-by-line profiling. From
	  http://www.enthought.com/~rkern/cgi-bin/hgwebdir.cgi/line_profiler/
	  (last change: Sat, 29 Nov 2008 21:32:35 -0600).

	* [r9729] external/Cython-0.9.8.1.1.tar.gz,
	  external/Makefile:
	  Added Cython 0.9.8.1.1 from cython.org.

2008-12-27  ceball

	* [r9728] external/Imaging.diff,
	  external/Makefile:
	  Removed PIL patch that is no longer required (at least, it isn't
	  required on Sake).

2008-12-21  ceball

	* [r9727] contrib/rgbimages.py:
	  Use multiple input images in example.

	* [r9726] topo/command/analysis.py:
	  Added combined RedActivity, GreenActivity, BlueActivity plot.

	* [r9725] topo/analysis/featureresponses.py:
	  Removed unnecessary line; should have no effect.

	* [r9724] examples/lissom.ty:
	  Added row_precedence specifications.

	* [r9723] topo/tkgui/plotgrouppanel.py:
	  Added row_precedence handling to PlotGroupPanel.

	* [r9722] topo/analysis/featureresponses.py,
	  topo/analysis/vision.py,
	  topo/base/sheet.py,
	  topo/base/sheetview.py,
	  topo/command/analysis.py,
	  topo/command/pylabplots.py,
	  topo/plotting/plot.py:
	  Added row_precedence to Sheet, to allow grouping before
	  precedence is applied. (Handling of parameters by SheetView etc
	  needs to be cleaned up; this change just copies previous code in
	  that respect.)

2008-12-20  ceball

	* [r9721] external/Makefile,
	  external/Tkinter_bool_none.diff,
	  topo/param/tk.py:
	  GUI: Added support for None in boolean variables.

	* [r9720] topo/param/parameterized.py,
	  topo/param/tk.py:
	  Made GUI use script_repr() rather than repr() for displaying
	  ordinary Parameters. Currently has the side effect that full
	  paths are displayed (e.g.
	  'topo.command.analysis.update_command()' rather than just
	  'update_command()').

	* [r9719] topo/param/tk.py:
	  Added parameter to control whether or not labels are displayed on
	  ParametersFrames.

2008-12-19  jbednar

	* [r9718] topo/pattern/basic.py:
	  Fixed typo

	* [r9717] topo/pattern/teststimuli.py:
	  Removed now-unused file

	* [r9716] topo/pattern/random.py:
	  Removed outdated note

	* [r9715] topo/misc/legacy.py:
	  Added note about faking SineGratingDisk

	* [r9714] topo/analysis/featureresponses.py,
	  topo/command/pylabplots.py,
	  topo/pattern/basic.py:
	  Added new, simpler OrientationContrast pattern, and changed
	  clients of OrientationContrastPattern to use it instead.

	* [r9713] topo/command/pylabplots.py,
	  topo/tests/lissom_oo_or_t000100.00_Retinotopy.data:
	  Changed SineGratingRectangle to
	  SineGrating(mask_shape=Rectangle()). Updated saved Retinotopy
	  data array; plot hasn't visibly changed, but apparently the
	  underlying matrix values differ.

	* [r9712] topo/analysis/featureresponses.py:
	  Replaced SineGratingDisk with SineGrating(mask_shape=Disk())

	* [r9711] topo/base/patterngenerator.py:
	  Changed pattern mask to be applied before scaling and offset, to
	  allow mask to be used to set the shape but otherwise leave the
	  pattern acting like other patterns.

	* [r9710]
	  contrib/lissom_oo_or_species_tracked.ty,
	  contrib/species_cf_jitter.ty,
	  contrib/species_lateral_sparsity.ty,
	  topo/analysis/featureresponses.py,
	  topo/command/pylabplots.py,
	  topo/pattern/teststimuli.py,
	  topo/tkgui/editor.py:
	  Fixed 'centre' to be 'center' to make spelling consistent

	* [r9709]
	  contrib/lissom_oo_or_homeostatic_tracked_new.ty:
	  Fixed typo

2008-12-19  ceball

	* [r9708] external/Makefile:
	  Enabled patch to address SF #2119256 (32-bit/64-bit machines &
	  snapshots).

	* [r9707] external/Makefile,
	  external/Python_64bit_pickle.diff:
	  Added commented-out patch to Python to address problem loading
	  32-bit pickles on 64-bit machines (and vice versa).

2008-12-18  antolikjan

	* [r9706]
	  contrib/lissom_oo_or_homeostatic_tracked_new.ty:
	  minor changes

2008-12-18  jbednar

	* [r9705] topo/command/pylabplots.py:
	  Removed outdated processing of sheet and coords params

2008-12-18  antolikjan

	* [r9704] contrib/cc_lissom_oo_or_simple_rv.ty:
	  minor changes

2008-12-18  jbednar

	* [r9703] topo/command/pylabplots.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Moved implementation of FFT plots out of the GUI and into
	  pytlabplots, to make it possible to call in batch mode. Fixed
	  parameter passing for gradientplots, for the same reason.

2008-12-17  antolikjan

	* [r9702] topo/analysis/vision.py:
	  removed default parameters from measure_and_analyze_complexity
	  measure_or_pref call

2008-12-17  ceball

	* [r9701] external:
	  Updated svn:ignore.

	* [r9700] external/Makefile,
	  external/tcl8.5.1-src.tar.gz,
	  external/tcl8.5.5-src.tar.gz,
	  external/tk8.5.1-src.tar.gz,
	  external/tk8.5.5-src.tar.gz:
	  Upgraded to Tcl/Tk 8.5.5.

	* [r9699] external/Imaging-1.1.5.tgz,
	  external/Imaging-1.1.6.tgz,
	  external/Makefile:
	  Upgraded to PIL 1.1.6.

	* [r9698] topo/plotting/plotfilesaver.py:
	  Explicitly specified array dtype in preparation for upgrade to
	  PIL 1.1.6.

2008-12-16  ceball

	* [r9697] examples/lissom.ty:
	  Fixed bug introduced in r9682 (when I fixed the bug where scale
	  was varying when there was no OD, I inadvertently removed the
	  'scalingfactors' for natural images).

	* [r9696] topo/pattern/basic.py:
	  Altered Selector's get_current_generator() so that it does not
	  cause the index to advance.

2008-12-16  antolikjan

	* [r9695]
	  contrib/lissom_oo_or_homeostatic_tracked_new.ty:
	  minor changes

	* [r9694] contrib/jacommands.py:
	  Changed to use x_avg instead of lr_x_avg in
	  SimpleHomeoLinearRelative

	* [r9693] contrib/jsldefs.py:
	  Commented out some things and also change lr_x_avg to x_avg

	* [r9692] topo/sheet/lissom.py:
	  Made it possible to switch off scaling with parameter

2008-12-15  ceball

	* [r9691] contrib/rgbimages.py:
	  Initial sketch of RGB image support; work in progress.

	* [r9690] topo/pattern/basic.py:
	  Added method to Selector allowing external access to the current
	  generator.

	* [r9689] topo/pattern/image.py:
	  Removed _create_pattern_sampler() (should be no visible change).

	* [r9688] topo/pattern/image.py:
	  Removed apparently unused method.

	* [r9687] topo/pattern/image.py:
	  Renamed __setup_pattern_sampler() to _create_pattern_sampler()
	  (so it can be used by subclasses).

2008-12-15  antolikjan

	* [r9686] contrib/cc_lissom_oo_or_simple_rv.ty:
	  minor parameter changes

	* [r9685]
	  contrib/lissom_oo_or_homeostatic_tracked_new.ty:
	  made LGN and Retina bigger to get rid of edge effects

	* [r9684] contrib/cc_lissom_oo_or_simple_rv.ty:
	  made new default scale for map measurment

2008-12-12  antolikjan

	* [r9683] contrib/jacommands.py:
	  changed the activity histogram measurement

2008-12-12  ceball

	* [r9682] examples/lissom.ty:
	  Fixed input pattern scale where 'od' not in dims (SF #2413540).

2008-12-11  chrisjeffery

	* [r9681] contrib/lissom.ty:
	  added new direction map measurement, which is not working. Also
	  added changes from examples/lissom.ty for preference maps.

2008-12-10  antolikjan

	* [r9680]
	  contrib/gc_lissom_oo_or_homeostatic_new.ty:
	  enlarged LGN and Retina to get rid of edge effects

2008-12-10  ceball

	* [r9679] contrib/lissom_oo_dr.ty:
	  Adjusted parameters to match lissom.ty dims=or,dr.

2008-12-09  antolikjan

	* [r9678] contrib/cc_lissom_oo_or_simple_rv.ty:
	  added simple linear homeostatic control

2008-12-09  chrisjeffery

	* [r9677] contrib/lissom.ty:
	  Forked lissom.ty for separate development of new dr model.
	  Currently broken, just checking in to keep track of changes.
	  Removed multiple sheets for direction, and changed connections to
	  use staggered delays. Inputs are not set up correctly yet.

2008-12-08  jbednar

	* [r9676] examples/lissom.ty:
	  Updated combined plots definitions to match recent changes in
	  topo.command.

	* [r9675] topo/command/pylabplots.py:
	  Made overlaid_plots arguments into documented Parameters.

2008-12-08  ceball

	* [r9674] topo/param/tk.py:
	  More simplification of param.tk.Menu. Should be no visible
	  change.

	* [r9673] topo/param/tk.py:
	  Should be no visible change: updated documentation of
	  param.tk.Menu

	* [r9672] topo/param/tk.py:
	  Fixed SF #2406957 (right-click menus broken).

2008-12-08  antolikjan

	* [r9671] contrib/cc_lissom_oo_or_simple_rv.ty:
	  Made some consolidation/simplification of the code

2008-12-08  jbednar

	* [r9670] doc/News/index_text.php:
	  Added recent news (up to r9630)

	* [r9669] topo/command/pylabplots.py:
	  Fixed circular import and made topo.analysis.vision be loaded
	  only when required

2008-12-06  jbednar

	* [r9668] topo/tkgui/topoconsole.py:
	  Removed unused plot

2008-12-05  jbednar

	* [r9667] topo/analysis/featureresponses.py,
	  topo/command/pylabplots.py,
	  topo/plotting/plotgroup.py:
	  Changed update_command and plot_command into HookLists, now
	  requiring lists rather than commands or strings. Changed passing
	  of sheet, input_sheet, projection, and coords arguments to be
	  done by calling the instance with those values, rather than the
	  previous indirect, complicated, and error-prone method of setting
	  various class attributes. Changed default_measureable_sheet and
	  default_input_sheet to be calculated in the plotgroup rather than
	  separately in the update_command and plot_command (with the
	  accompanying difficulty making the values match).

2008-12-05  antolikjan

	* [r9666] contrib/jacommands.py:
	  SimpleHomeoLinearRelative

2008-12-05  jbednar

	* [r9665] contrib/jacommands.py:
	  Typo fixes

2008-12-05  antolikjan

	* [r9664]
	  contrib/lissom_oo_or_homeostatic_tracked_new.ty:
	  Modified version of judes homeostatic model with GC

	* [r9663] contrib/jacommands.py:
	  Added SimpleHomeoLinear and SimpleHomeoLinearRelative

2008-12-05  jbednar

	* [r9662] ChangeLog.txt:
	  Added recent changes

	* [r9661] doc/Home/news_text.php:
	  Updated release date estimate

	* [r9660] topo/command/basic.py:
	  Added ALERT

2008-12-04  jbednar

	* [r9659] topo/command/analysis.py:
	  Removed unused imports

	* [r9658] topo/command/pylabplots.py,
	  topo/plotting/plotgroup.py:
	  Converted plot_commands from strings to lists of callables. Added
	  parameters to measure_cog.

2008-12-04  ceball

	* [r9657] contrib/lissom_oo_dr.ty,
	  topo/analysis/featureresponses.py,
	  topo/command/basic.py:
	  Added direction map measurement for new motion model.

2008-12-04  jbednar

	* [r9656] topo/plotting/plotgroup.py:
	  Added support for plot_command lists

	* [r9655] topo/command/analysis.py,
	  topo/command/pylabplots.py,
	  topo/tests/gui_tests.py,
	  topo/tests/test_map_measurement.py:
	  Moved all plots requiring MatPlotLib to pylabplots.py, so that
	  they can switch plot_command from strings to actual commands
	  (which much thus have all imports be available). Should not
	  change behavior at all.

	* [r9654] doc/User_Manual/commandline_text.php:
	  Minor update to example

	* [r9653] contrib/lesi_whisker_barrels.ty,
	  examples/lissom.ty,
	  examples/lissom_whisker_barrels.ty,
	  topo/analysis/featureresponses.py,
	  topo/analysis/vision.py,
	  topo/command/analysis.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/gui_tests.py:
	  Changed ParameterizedFunction update_commands to use .instance()
	  to allow flexible handling of their parameters. Changed plot
	  update_commands into lists, to allow them to be declared as type
	  HookList and to provide a simple [] empty default. Cleaned up
	  PatternPresenter warnings to avoid overwhelming output.

	* [r9652] doc/Tutorials/lissom_oo_or_text.php:
	  Minor clarification

2008-12-04  ceball

	* [r9651] contrib/lissom_oo_dr.ty,
	  topo/pattern/basic.py:
	  Moved Translator(PatternGenerator) to topo.pattern.basic.

2008-12-03  ceball

	* [r9650] examples/lissom.ty:
	  Initial version of ocular preference overlaid with hue preference
	  boundaries.

	* [r9649] examples/lissom.ty,
	  topo/command/analysis.py:
	  Moved combined plots to lissom.ty; script selects appropriate
	  combinations (depending on dims).

2008-12-02  ceball

	* [r9648] topo/tkgui/topoconsole.py:
	  Added method to allow Plots menu to be refreshed.

	* [r9647] topo/param/tk.py:
	  param.tk.Menu: fixed deletion of a range.

	* [r9646] topo/param/tk.py:
	  Cleaned up tk.param.Menu (simplified code and fixed deletion of
	  items).

	* [r9645] topo/tkgui/topoconsole.py:
	  Change missed from r9644.

	* [r9644] topo/param/tk.py:
	  tk.param.Menu: Renamed 'entries' to 'named_commands'; Menu now
	  only stores commands in named_commands if they are actually
	  named.

	* [r9643] topo/param/tk.py:
	  Change missed from r9641 (insert() now adds the index as a
	  string).

	* [r9642] topo/param/tk.py:
	  param.tk.Menu: fixed delete() method, which removed the internal
	  index before actually deleting the associated menu item.

	* [r9641] topo/param/tk.py:
	  Made param.tk.Menu's internal indexing more consistent (if an
	  index has no name associated with it, its string representation
	  is used as a key in the internal name-index dictionary, to match
	  how named items are stored). Should have no visible impact.

	* [r9640] topo/tkgui/topoconsole.py:
	  Topoconsole now alphabetically sorts Plot submenu items.

2008-12-01  ceball

	* [r9639] topo/param/parameterized.py:
	  Fixed ParameterizedFunction's __reduce__ (was resulting in
	  reconstructed instances reverting to ParameterizedFunctions,
	  instead of whatever subclass they were).

2008-12-01  antolikjan

	* [r9638] contrib/sparse_connectivity_model.ty:
	  Made few parameters external

	* [r9637]
	  contrib/gc_lissom_oo_or_homeostatic_new.ty:
	  Made few parameters external

2008-11-29  ceball

	* [r9636] topo/plotting/bitmap.py:
	  Minor simplification: should be no visible change.

	* [r9635] topo/misc/filepath.py:
	  Made resolve_path() raise an error if a file is not found when an
	  absolute path is supplied (it already raises an error when an
	  unfound relative path is supplied, so now it is more consistent).

	* [r9634] doc/User_Manual/batch_text.php:
	  Fixed reference.

2008-11-27  rczhao

	* [r9633] /trunk/facespace/fs1mf.ty:
	  Added measure_or_in_face function

2008-11-25  ceball

	* [r9632] topo/plotting/plot.py:
	  Removed unused import.

2008-11-25  jbednar

	* [r9631] topo/command/analysis.py:
	  Removed unused measure_rfs_noise class

2008-11-24  ceball

	* [r9630] examples/lissom.ty:
	  Fixed typo.

2008-11-23  jbednar

	* [r9629] examples/lissom_oo_or_cr.ty:
	  Updated path to images that have been moved.

2008-11-23  ceball

	* [r9628] examples/lissom.ty:
	  Corrected position of ValueError for unknown dataset.

	* [r9627] images/mcgill/foliage_a,
	  images/mcgill/foliage_a/00_0.png,
	  images/mcgill/foliage_a/00_1.png,
	  images/mcgill/foliage_a/00_2.png,
	  images/mcgill/foliage_a/01_0.png,
	  images/mcgill/foliage_a/01_1.png,
	  images/mcgill/foliage_a/01_2.png,
	  images/mcgill/foliage_a/02_0.png,
	  images/mcgill/foliage_a/02_1.png,
	  images/mcgill/foliage_a/02_2.png,
	  images/mcgill/foliage_a/03_0.png,
	  images/mcgill/foliage_a/03_1.png,
	  images/mcgill/foliage_a/03_2.png,
	  images/mcgill/foliage_a/04_0.png,
	  images/mcgill/foliage_a/04_1.png,
	  images/mcgill/foliage_a/04_2.png,
	  images/mcgill/foliage_a/05_0.png,
	  images/mcgill/foliage_a/05_1.png,
	  images/mcgill/foliage_a/05_2.png:
	  Images missed (by Subversion, in my opinion) from the previous
	  commit.

	* [r9626] examples/lissom.ty,
	  images/colormap,
	  images/mcgill,
	  images/mcgill/foliage_b,
	  images/mcgill/foliage_b/01_0.png,
	  images/mcgill/foliage_b/01_1.png,
	  images/mcgill/foliage_b/01_2.png,
	  images/mcgill/foliage_b/02_0.png,
	  images/mcgill/foliage_b/02_1.png,
	  images/mcgill/foliage_b/02_2.png,
	  images/mcgill/foliage_b/03_0.png,
	  images/mcgill/foliage_b/03_1.png,
	  images/mcgill/foliage_b/03_2.png,
	  images/mcgill/foliage_b/04_0.png,
	  images/mcgill/foliage_b/04_1.png,
	  images/mcgill/foliage_b/04_2.png,
	  images/mcgill/foliage_b/05_0.png,
	  images/mcgill/foliage_b/05_1.png,
	  images/mcgill/foliage_b/05_2.png,
	  images/mcgill/foliage_b/06_0.png,
	  images/mcgill/foliage_b/06_1.png,
	  images/mcgill/foliage_b/06_2.png,
	  images/mcgill/foliage_b/07_0.png,
	  images/mcgill/foliage_b/07_1.png,
	  images/mcgill/foliage_b/07_2.png,
	  images/mcgill/foliage_b/08_0.png,
	  images/mcgill/foliage_b/08_1.png,
	  images/mcgill/foliage_b/08_2.png,
	  images/mcgill/foliage_b/09_0.png,
	  images/mcgill/foliage_b/09_1.png,
	  images/mcgill/foliage_b/09_2.png,
	  images/mcgill/foliage_b/10_0.png,
	  images/mcgill/foliage_b/10_1.png,
	  images/mcgill/foliage_b/10_2.png,
	  images/mcgill/foliage_b/11_0.png,
	  images/mcgill/foliage_b/11_1.png,
	  images/mcgill/foliage_b/11_2.png,
	  images/mcgill/foliage_b/12_0.png,
	  images/mcgill/foliage_b/12_1.png,
	  images/mcgill/foliage_b/12_2.png,
	  images/mcgill/foliage_b/13_0.png,
	  images/mcgill/foliage_b/13_1.png,
	  images/mcgill/foliage_b/13_2.png,
	  images/mcgill/foliage_b/14_0.png,
	  images/mcgill/foliage_b/14_1.png,
	  images/mcgill/foliage_b/14_2.png,
	  images/mcgill/foliage_b/15_0.png,
	  images/mcgill/foliage_b/15_1.png,
	  images/mcgill/foliage_b/15_2.png,
	  images/mcgill/foliage_b/16_0.png,
	  images/mcgill/foliage_b/16_1.png,
	  images/mcgill/foliage_b/16_2.png,
	  images/mcgill/foliage_b/17_0.png,
	  images/mcgill/foliage_b/17_1.png,
	  images/mcgill/foliage_b/17_2.png,
	  images/mcgill/foliage_b/18_0.png,
	  images/mcgill/foliage_b/18_1.png,
	  images/mcgill/foliage_b/18_2.png,
	  images/mcgill/foliage_b/19_0.png,
	  images/mcgill/foliage_b/19_1.png,
	  images/mcgill/foliage_b/19_2.png,
	  images/mcgill/foliage_b/20_0.png,
	  images/mcgill/foliage_b/20_1.png,
	  images/mcgill/foliage_b/20_2.png,
	  images/mcgill/foliage_b/21_0.png,
	  images/mcgill/foliage_b/21_1.png,
	  images/mcgill/foliage_b/21_2.png,
	  images/mcgill/foliage_b/22_0.png,
	  images/mcgill/foliage_b/22_1.png,
	  images/mcgill/foliage_b/22_2.png,
	  images/mcgill/foliage_b/23_0.png,
	  images/mcgill/foliage_b/23_1.png,
	  images/mcgill/foliage_b/23_2.png,
	  images/mcgill/foliage_b/24_0.png,
	  images/mcgill/foliage_b/24_1.png,
	  images/mcgill/foliage_b/24_2.png,
	  images/mcgill/foliage_b/25_0.png,
	  images/mcgill/foliage_b/25_1.png,
	  images/mcgill/foliage_b/25_2.png:
	  Moved images/colormap/*.png to images/mcgill/foliage_a, and moved
	  images/colormap/rgb/*.png to images/mcgill/foliage_b.

	* [r9625] examples/lissom.ty:
	  Corrected mistake in docstring, introduced when I added the
	  'colormap' label.

	* [r9624] topo/param/parameterized.py:
	  Added commented-out __deepcopy__ method for Parameterized.

	* [r9623] topo/base/boundingregion.py:
	  Removed redundant method.

	* [r9622] topo/param/parameterized.py:
	  Clarified comment.

	* [r9621] topo/command/basic.py,
	  topo/misc/util.py:
	  Files accidentally missed from previous commit.

	* [r9620] topo/misc/legacy.py:
	  Removed ExtraPickler. Includes no longer restoring things that
	  had been held in ExtraPickler (I assume that was only
	  topo.plotting.plotgroups).

	* [r9619] topo/param/parameterized.py:
	  Should be no visible change: changed ParameterizedFunction's
	  _true_new() to use Parameterized.__new__ rather than
	  object.__new__, and allowed args to be passed to _true_new when
	  creating an instance.

	* [r9618] topo/param/parameterized.py:
	  Fix bug with ParameterizedFunction: control copy/pickle's use of
	  __new__ (avoids calling instance when trying to recreate it).

	* [r9617] topo/misc/filepath.py:
	  Fixed warning message that hadn't been updated (Parameter's
	  attrib_name() method was removed some time ago).

2008-11-21  jbednar

	* [r9616] topo/analysis/featureresponses.py,
	  topo/command/basic.py,
	  topo/plotting/plotgroup.py:
	  Changed Subplotting to keep track of last arguments and restore
	  them on load_snapshot. Removed pickling of plotgroups, which
	  should no longer be necessary (and was causing many problems).

	* [r9615] examples/lissom.ty:
	  Added commented-out examples of generating complete list of
	  combinations in measure_sine_pref

	* [r9614] topo/command/analysis.py:
	  Added direction and speed to the list of features supported by
	  measure_sine_pref

	* [r9613] topo/analysis/featureresponses.py:
	  Changed PatternGenerator to use given ocular and phasedisparity
	  rather than relying on them being set on the input generators

	* [r9612] topo/pattern/basic.py:
	  Added phase property to Sweeper for use in measure_sine_pref.

2008-11-20  jbednar

	* [r9611] topo/command/analysis.py:
	  Fixed bug in orientation maps measured using measure_dr_pref by
	  adding round(x,13) to compute_orientation_from_direction so that
	  wrapped orientations have exactly the same value. Previously the
	  OR map was heavily biased towards 0.5/pi, because one wrapped
	  value was nearly but not identical to the unwrapped one. Usually
	  that would have no effect on a vector sum, but with
	  keep_peak=True, the result is to weight the duplicated value
	  twice as strongly, pulling all values towards it. Made
	  num_speeds=0 legal to allow strict comparison between
	  measure_sine_pref and measure_dr_pref.

	* [r9610] topo/analysis/featureresponses.py:
	  Cleaned up present_permutation; no change in behavior. Added
	  optional offset for a Feature. Relaxed direction handling in
	  PatternPresenter so that it will work on any network, at speed 0.

	* [r9609] topo/misc/distribution.py:
	  Added bins() method

	* [r9608] images/colormap/rgb/11_0.pgm:
	  Fixed stray uncommitted change

2008-11-19  ceball

	* [r9607] examples/lissom.ty:
	  Added dataset label 'colormap' to distinguish from Nature
	  (Shouval) images. (Need a better label than 'colormap'.)

2008-11-19  jbednar

	* [r9606] examples/lissom.ty,
	  examples/lissom_oo_or_cr.ty,
	  images/colormap/rgb/01_0.pgm,
	  images/colormap/rgb/01_0.png,
	  images/colormap/rgb/01_1.pgm,
	  images/colormap/rgb/01_1.png,
	  images/colormap/rgb/01_2.pgm,
	  images/colormap/rgb/01_2.png,
	  images/colormap/rgb/02_0.pgm,
	  images/colormap/rgb/02_0.png,
	  images/colormap/rgb/02_1.pgm,
	  images/colormap/rgb/02_1.png,
	  images/colormap/rgb/02_2.pgm,
	  images/colormap/rgb/02_2.png,
	  images/colormap/rgb/03_0.pgm,
	  images/colormap/rgb/03_0.png,
	  images/colormap/rgb/03_1.pgm,
	  images/colormap/rgb/03_1.png,
	  images/colormap/rgb/03_2.pgm,
	  images/colormap/rgb/03_2.png,
	  images/colormap/rgb/04_0.pgm,
	  images/colormap/rgb/04_0.png,
	  images/colormap/rgb/04_1.pgm,
	  images/colormap/rgb/04_1.png,
	  images/colormap/rgb/04_2.pgm,
	  images/colormap/rgb/04_2.png,
	  images/colormap/rgb/05_0.pgm,
	  images/colormap/rgb/05_0.png,
	  images/colormap/rgb/05_1.pgm,
	  images/colormap/rgb/05_1.png,
	  images/colormap/rgb/05_2.pgm,
	  images/colormap/rgb/05_2.png,
	  images/colormap/rgb/06_0.pgm,
	  images/colormap/rgb/06_0.png,
	  images/colormap/rgb/06_1.pgm,
	  images/colormap/rgb/06_1.png,
	  images/colormap/rgb/06_2.pgm,
	  images/colormap/rgb/06_2.png,
	  images/colormap/rgb/07_0.pgm,
	  images/colormap/rgb/07_0.png,
	  images/colormap/rgb/07_1.pgm,
	  images/colormap/rgb/07_1.png,
	  images/colormap/rgb/07_2.pgm,
	  images/colormap/rgb/07_2.png,
	  images/colormap/rgb/08_0.pgm,
	  images/colormap/rgb/08_0.png,
	  images/colormap/rgb/08_1.pgm,
	  images/colormap/rgb/08_1.png,
	  images/colormap/rgb/08_2.pgm,
	  images/colormap/rgb/08_2.png,
	  images/colormap/rgb/09_0.pgm,
	  images/colormap/rgb/09_0.png,
	  images/colormap/rgb/09_1.pgm,
	  images/colormap/rgb/09_1.png,
	  images/colormap/rgb/09_2.pgm,
	  images/colormap/rgb/09_2.png,
	  images/colormap/rgb/10_0.pgm,
	  images/colormap/rgb/10_0.png,
	  images/colormap/rgb/10_1.pgm,
	  images/colormap/rgb/10_1.png,
	  images/colormap/rgb/10_2.pgm,
	  images/colormap/rgb/10_2.png,
	  images/colormap/rgb/11_0.png,
	  images/colormap/rgb/11_1.pgm,
	  images/colormap/rgb/11_1.png,
	  images/colormap/rgb/11_2.pgm,
	  images/colormap/rgb/11_2.png,
	  images/colormap/rgb/12_0.pgm,
	  images/colormap/rgb/12_0.png,
	  images/colormap/rgb/12_1.pgm,
	  images/colormap/rgb/12_1.png,
	  images/colormap/rgb/12_2.pgm,
	  images/colormap/rgb/12_2.png,
	  images/colormap/rgb/13_0.pgm,
	  images/colormap/rgb/13_0.png,
	  images/colormap/rgb/13_1.pgm,
	  images/colormap/rgb/13_1.png,
	  images/colormap/rgb/13_2.pgm,
	  images/colormap/rgb/13_2.png,
	  images/colormap/rgb/14_0.pgm,
	  images/colormap/rgb/14_0.png,
	  images/colormap/rgb/14_1.pgm,
	  images/colormap/rgb/14_1.png,
	  images/colormap/rgb/14_2.pgm,
	  images/colormap/rgb/14_2.png,
	  images/colormap/rgb/15_0.pgm,
	  images/colormap/rgb/15_0.png,
	  images/colormap/rgb/15_1.pgm,
	  images/colormap/rgb/15_1.png,
	  images/colormap/rgb/15_2.pgm,
	  images/colormap/rgb/15_2.png,
	  images/colormap/rgb/16_0.pgm,
	  images/colormap/rgb/16_0.png,
	  images/colormap/rgb/16_1.pgm,
	  images/colormap/rgb/16_1.png,
	  images/colormap/rgb/16_2.pgm,
	  images/colormap/rgb/16_2.png,
	  images/colormap/rgb/17_0.pgm,
	  images/colormap/rgb/17_0.png,
	  images/colormap/rgb/17_1.pgm,
	  images/colormap/rgb/17_1.png,
	  images/colormap/rgb/17_2.pgm,
	  images/colormap/rgb/17_2.png,
	  images/colormap/rgb/18_0.pgm,
	  images/colormap/rgb/18_0.png,
	  images/colormap/rgb/18_1.pgm,
	  images/colormap/rgb/18_1.png,
	  images/colormap/rgb/18_2.pgm,
	  images/colormap/rgb/18_2.png,
	  images/colormap/rgb/19_0.pgm,
	  images/colormap/rgb/19_0.png,
	  images/colormap/rgb/19_1.pgm,
	  images/colormap/rgb/19_1.png,
	  images/colormap/rgb/19_2.pgm,
	  images/colormap/rgb/19_2.png,
	  images/colormap/rgb/20_0.pgm,
	  images/colormap/rgb/20_0.png,
	  images/colormap/rgb/20_1.pgm,
	  images/colormap/rgb/20_1.png,
	  images/colormap/rgb/20_2.pgm,
	  images/colormap/rgb/20_2.png,
	  images/colormap/rgb/21_0.pgm,
	  images/colormap/rgb/21_0.png,
	  images/colormap/rgb/21_1.pgm,
	  images/colormap/rgb/21_1.png,
	  images/colormap/rgb/21_2.pgm,
	  images/colormap/rgb/21_2.png,
	  images/colormap/rgb/22_0.pgm,
	  images/colormap/rgb/22_0.png,
	  images/colormap/rgb/22_1.pgm,
	  images/colormap/rgb/22_1.png,
	  images/colormap/rgb/22_2.pgm,
	  images/colormap/rgb/22_2.png,
	  images/colormap/rgb/23_0.pgm,
	  images/colormap/rgb/23_0.png,
	  images/colormap/rgb/23_1.pgm,
	  images/colormap/rgb/23_1.png,
	  images/colormap/rgb/23_2.pgm,
	  images/colormap/rgb/23_2.png,
	  images/colormap/rgb/24_0.pgm,
	  images/colormap/rgb/24_0.png,
	  images/colormap/rgb/24_1.pgm,
	  images/colormap/rgb/24_1.png,
	  images/colormap/rgb/24_2.pgm,
	  images/colormap/rgb/24_2.png,
	  images/colormap/rgb/25_0.pgm,
	  images/colormap/rgb/25_0.png,
	  images/colormap/rgb/25_1.pgm,
	  images/colormap/rgb/25_1.png,
	  images/colormap/rgb/25_2.pgm,
	  images/colormap/rgb/25_2.png:
	  Changed pgm to png files to save space

	* [r9605] topo/analysis/featureresponses.py,
	  topo/command/analysis.py:
	  Added mechanism for computing feature values from other permuted
	  ones, and added computed orientation map for measure_dr_pref

2008-11-18  jbednar

	* [r9604] examples/lissom.ty:
	  Changed order of map measurement to make subplotting work and to
	  ensure that the best versions of each map are used. Made
	  expand_sf_test_range optional and off by default, for speed.
	  Removed disparity and hue testing from measure_sine_pref command,
	  to avoid combinatorial explosion.

	* [r9603] topo/command/analysis.py:
	  Added more informative messages for save_plotgroup in batch mode.
	  Changed measure_disparity to use a vertical test pattern, for
	  speed, rather than being part of measure_sine_pref.

	* [r9602] topo/analysis/featureresponses.py:
	  Added more informative messages in batch mode. Fixed passing of
	  parameters by keyword for FeatureMaps (name, in this case)

2008-11-18  ceball

	* [r9601] topo/param/parameterized.py:
	  Simplified ParameterizedFunction.instance(), and corrected naming
	  of class object.

	* [r9600] topo/param/parameterized.py:
	  Added instance() to ParameterizedFunction.

2008-11-17  jbednar

	* [r9599] topo/command/pylabplots.py:
	  Removed unused plotrctg command. Removed unused extra_keyword
	  support from plot_modulation_ratio

	* [r9598] topo/command/basic.py:
	  Enabled result caching for plots; should give significant speedup
	  for lissom.ty

	* [r9597] topo/command/analysis.py:
	  Finished save_plotgroup update_command caching support; should be
	  safe to use now (though it is not turned on by default).

	* [r9596] topo/command/analysis.py:
	  Changed most update_commands to callable objects rather than
	  strings, to allow parameters to be edited in the GUI.

2008-11-17  ceball

	* [r9595] topo/misc/picklemain.py:
	  Removed stray line from previous checkin.

	* [r9594] topo/command/basic.py,
	  topo/misc/picklemain.py,
	  topo/misc/util.py:
	  Moved MainPickler and associated code into a new module,
	  topo.misc.picklemain.

2008-11-17  jbednar

	* [r9593] topo/command/analysis.py,
	  topo/plotting/plotgroup.py:
	  Removed proj_name<->projection conversion from
	  UnitMeasurementCommands, to simplify it and ensure that
	  everything is done via Parameters rather than ad-hoc attributes

2008-11-17  ceball

	* [r9592] topo/command/basic.py,
	  topo/misc/util.py,
	  topo/param/parameterized.py:
	  Added support for pickling functions and classes defined in
	  __main__.

2008-11-16  ceball

	* [r9591] examples/cfsom_or.ty:
	  Restored cfsom_or's results to previous values (they had changed
	  in r9582) by explicitly setting parameters of the connection's
	  weights_generator, rather than relying on defaults (which had
	  changed).

	* [r9590] topo/pattern/image.py:
	  Fix for SF #2276819: loading snapshots of simulations using
	  FileImage now works.

2008-11-16  jbednar

	* [r9589] topo/plotting/plotgroup.py,
	  topo/tests/test_map_measurement.py:
	  Added support for update_command and plot_command that are
	  callable objects rather than strings for exec. For now, this
	  changes the representation in the GUI to include quotation marks,
	  but these should go away as we change the various commands to
	  objects rather than strings

2008-11-15  jbednar

	* [r9588] topo/command/analysis.py,
	  topo/tests/lissom_oo_or_t000100.00_Spatial_Frequency_Preference.data:
	  Changed default spatial frequency preference plot to test only
	  one frequency, primarily for speed but also to avoid enforcing
	  special defaults that are more difficult for .ty scripts to
	  override

	* [r9587] examples/lissom.ty:
	  Added support for measure_sine_pref

	* [r9586] topo/command/analysis.py:
	  Converted save_plotgroup to a ParameterizedFunction, adding
	  experimental use_cached_results option (disabled by default).
	  Added comprehensive measure_sine_pref command, which should
	  eventually replace measure_or_pref, measure_od_pref,
	  measure_phasedisparity, measure_hue_pref, etc.

2008-11-14  jbednar

	* [r9585] topo/analysis/featureresponses.py:
	  Minor tweaks; should be no change in normal behavior

2008-11-14  ceball

	* [r9584] contrib/lissom_oo_dr.ty:
	  Translator: Implemented episode intervals.

	* [r9583] contrib/lissom_oo_dr.ty:
	  Translator: simplified 'last_time' and calls to float().

2008-11-14  jbednar

	* [r9582] topo/pattern/basic.py:
	  Changed default size and aspect_ratio of Gaussian to avoid
	  confusion -- pattern looked vertical but had an actual
	  orientation of 0.

	* [r9581] contrib/lissom_oo_dr.ty:
	  Cleaned up docs, parameter names, defaults, etc. for Translator.
	  Fixed self references that should have been p.

2008-11-14  ceball

	* [r9580] contrib/lissom_oo_dr.ty:
	  Translator: when drawing underlying pattern, uses that pattern's
	  parameters to offset the pattern's position or rotate the
	  pattern's orientation.

	* [r9579] contrib/lissom_oo_dr.ty:
	  x, y, and direction are now set on the Translator itself.

	* [r9578] contrib/lissom_oo_dr.ty:
	  Translator: moved orientation parameter back to generator, to be
	  consistent with x and y (which are also on the generator).

	* [r9577] contrib/lissom_oo_dr.ty:
	  Minor changes to Translator (no visible change).

	* [r9576] contrib/lissom_oo_dr.ty:
	  Changed Translator.__call__ to use ParamOverrides.

	* [r9575] contrib/lissom_oo_dr.ty,
	  topo/pattern/basic.py:
	  Continued cleaning up Translator. Should be no change to
	  behavior, although the random stream might be being used
	  differently.

	* [r9574] contrib/lissom_oo_dr.ty:
	  Added missing svn properties.

	* [r9573] contrib/lissom_oo_dr.ty:
	  Translator: commented out more unused code, altered some
	  documentation, and added some commented-out parameters. No change
	  to the behavior.

	* [r9572] topo/projection/basic.py:
	  Changed SharedWeightCFProjection to handle creation of CF slices
	  in the same way as CFProjection. (Intermediate checkin: I'm
	  planning to reorganize the CF hierarchy; meanwhile, this should
	  improve start times dominated by creation of
	  SharedWeightCFProjections.)

2008-11-13  jbednar

	* [r9571] topo/command/basic.py:
	  Added plot measurement at time zero

	* [r9570] contrib/lissom_oo_or_homeostatic.ty:
	  Made frequency scaling and target_lr be automatic for each
	  dataset. Changed Natural dataset to Nature, to match the CMVC
	  book. Added error in case of no dataset specified

2008-11-13  ceball

	* [r9569] topo/misc/legacy.py,
	  topo/param/parameterized.py:
	  No visible change: removed stray print statement and added an
	  ALERT.

	* [r9568] topo/misc/legacy.py:
	  Support missing allow_None in old snapshots: addresses SF
	  #2270680. Snapshots saved before allow_None was added to
	  Parameters will be loaded with allow_None set to False in all
	  cases.

	* [r9567] topo/misc/legacy.py:
	  Upgraded preprocess_state() to allow more operations (by having
	  functions also accept the instance they are working on).

	* [r9566] topo/param/parameterized.py:
	  Tried to clarify warning message about restoring class
	  attributes.

	* [r9565] topo/misc/legacy.py:
	  Snapshot compatibility: Made replacement of gmpy.mpq by
	  fixedpoint.FixedPoint only happen if gmpy.mpq is not available.

2008-11-12  ceball

	* [r9564] topo/misc/legacy.py:
	  Added support for loading snapshots when gmpy.mpq is not present
	  (SF #2221332).

	* [r9563] topo/misc/legacy.py:
	  Changed fake_a_module() so that parent can be None.

2008-11-12  judelaw

	* [r9562] topo/command/pylabplots.py:
	  corrected error in plot_tracked_attributes - changed filename to
	  p.filename

	* [r9561] contrib/jsldefs.py:
	  corrected error and brought up to date with current version

2008-11-10  jbednar

	* [r9560] contrib/jaanalysis.py,
	  contrib/jacommands.py,
	  contrib/jsldefs.py,
	  contrib/modelfit.py:
	  Updated contrib files to match changes in pylabplots

	* [r9559] topo/command/pylabplots.py:
	  Added typical defaults for attribute tracking times

	* [r9558] topo/command/analysis.py,
	  topo/command/pylabplots.py:
	  Removed now-unneeded matrixplot_hsv

	* [r9557] topo/command/pylabplots.py:
	  Converted remaining pylab commands to ParameterizedFunctions
	  using PylabPlotCommand. The order of arguments accepted will have
	  changed, but it should be rare that a positional argument is used
	  beyond the first two, and those have been preserved. All but
	  plot_tracked_attributes have been tested for basic function, but
	  there are few automatic tests for these commands, and thus there
	  may be some new bugs.

	* [r9556] topo/command/analysis.py:
	  Updated to use new tuning curve commands; should not change any
	  results relative to previous version

	* [r9555] topo/command/pylabplots.py:
	  Added tuning curve implementation using ParameterizedFunction;
	  will allow significant simplification and generalization, but the
	  old version is still in the file (as tuning_curve_old and
	  or_tuning_curve, replaced by tuning_curve and
	  cyclic_tuning_curve) for comparison. The old tuning_curve and
	  or_tuning_curve commands have been generalized as well, as an
	  intermediate step, to eliminate the need for tuning_curve_batch
	  and or_tuning_curve_batch. The only change to results should be
	  that the x axis will no longer have a gap on the last item for
	  tuning_curve plots, which changes the tick marks (but not the
	  quantities plotted).

2008-11-08  ceball

	* [r9554] contrib/lesi_whisker_barrels.ty:
	  Attempt to correct svn:keywords on
	  contrib/lesi_whisker_barrels.ty.

2008-11-07  jbednar

	* [r9553] contrib/lissom_oo_dr.ty:
	  Added input_period variable, and scaled time by it

2008-11-07  ceball

	* [r9552] contrib/lissom_oo_dr.ty:
	  Inserted a modified version of contrib.jacommands.Translator
	  (fixed faulty initial reset period; removed Null() every
	  reset_period; removed index parameter and associated code). Work
	  in progress.

2008-11-07  jbednar

	* [r9551] topo/command/pylabplots.py:
	  Merged functionality of or_tuning_curve_batch into
	  or_tuning_curve

2008-11-05  jbednar

	* [r9550] contrib/lesi_whisker_barrels.ty:
	  Trivial fix to revision number string

	* [r9549] contrib/lesi_whisker_barrels.ty:
	  Initial version from Stuart with fixes for the latest version of
	  Topographica

	* [r9548] contrib/lissom_oo_dr.ty:
	  Partial update to use a single retina and LGN ON/OFF pair instead
	  of four of each of those; seems to work but the pattern generator
	  will need to be updated to present inputs moving over time

	* [r9547] contrib/lissom_oo_dr.ty:
	  Added missing import

2008-11-04  rczhao

	* [r9546] /trunk/facespace/fs1mf.ty:
	  Merged with ~/.topographicarc so that simulation of face space
	  doesn't need specific startup files.

	* [r9545] /trunk/facespace/pattern_fs.py:
	  minor update

2008-11-02  ceball

	* [r9544] topo/param/parameterized.py:
	  Parameterized classes now have a name attribute (set to the class
	  __name__).

2008-10-31  jbednar

	* [r9543] topo/command/pylabplots.py:
	  Made Orientation Preference and Complexity possible to use with
	  networks other than contrib/cc_*, but it still needs significant
	  generalization. Removed duplication of suffix in saved pylab
	  filenames.

	* [r9542] topo/analysis/vision.py:
	  Made Orientation Preference and Complexity possible to use with
	  networks other than contrib/cc_*, but it still needs significant
	  generalization. Removed duplication of suffix in saved pylab
	  filenames.

	* [r9541]
	  contrib/sparese_connectivity_model.ty:
	  Fixed filename

	* [r9540]
	  contrib/sparese_connectivity_LESIE.ty,
	  contrib/sparse_connectivity_LESI.ty:
	  Fixed filename

2008-10-31  ceball

	* [r9539] doc/Future_Work/current_text.php:
	  Removed tasks that have been added on sf.net.

2008-10-30  jbednar

	* [r9538] topo/base/arrayutil.py:
	  Added note about wrap usually being unnecessary.

2008-10-30  ceball

	* [r9537] doc/buildbot/bbanalysis.py:
	  Added annotation (for r9395) to buildbot graph.

	* [r9536] doc/buildbot/bbanalysis.py:
	  Updated buildbot analysis script (had previously been running on
	  an old copy of Topographica).

	* [r9535] doc/buildbot/bbanalysis.py:
	  Fixed typo in buildbot analysis script.

	* [r9534] topo/tests/gui_tests.py:
	  Fixed failing Test Pattern window test. (Correct fix would be to
	  stop None appearing from sheet lists in GUI; we hope to do this
	  soon.)

	* [r9533] topo/plotting/plotgroup.py:
	  Fixed copy/paste error from r9521.

2008-10-28  antolikjan

	* [r9532]
	  contrib/sparese_connectivity_LESIE.ty:
	  changed the afferent projection initial connection fields

	* [r9531] contrib/cc_lissom_oo_or_simple_rv.ty:
	  changed parameters and renamed some projections

2008-10-28  rczhao

	* [r9530] /trunk/facespace/face_space_patterns.py:
	  

	* [r9529] /trunk/facespace/face_space.ty:
	  

	* [r9528] /trunk/facespace/evofacemodel/fs1mf.m:
	  Generate a face on a male/female trajectory given a strength
	  (morphing) value.

	* [r9527] /trunk/facespace/evofacemodel/fs1mf_init.m:
	  Initialization of the face database

	* [r9526] /trunk/facespace/evofacemodel:
	  MATLAB codes that generates faces from Evo-Face model database.
	  Note that the database and some original codes are not included
	  in this public repository.

2008-10-24  jbednar

	* [r9525] topo/command/analysis.py:
	  Minor expansion of doc

	* [r9524] topo/command/analysis.py:
	  Rearranged all of the plot definitions for readability and in
	  preparation for making update_command into a callable rather than
	  a string, hopefully without changing anything at all

	* [r9523] contrib/lissom_oo_dr.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  topo/analysis/featureresponses.py,
	  topo/command/analysis.py,
	  topo/command/pylabplots.py,
	  topo/plotting/plotgroup.py:
	  Renamed ParameterizdFunction abstract base classes for commands
	  to end in Command rather than Function, for clarity

	* [r9522] contrib/jaanalysis.py,
	  contrib/jacommands.py,
	  contrib/jsldefs.py,
	  contrib/lesi.ty,
	  contrib/lissom_oo_or_homeostatic_tracked.ty:
	  Updated contrib directory to match changes in commands/analysis

	* [r9521] contrib/lissom_oo_dr.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  topo/analysis/featureresponses.py,
	  topo/command/analysis.py,
	  topo/command/pylabplots.py,
	  topo/plotting/plotgroup.py:
	  Moved abstract ParameterizedFunction definitions to
	  topo.analysis.featureresponses and topo.plotting.plotgroup

	* [r9520] topo/analysis/__init__.py:
	  Fixed bogus list of files for __all__

	* [r9519] topo/command/analysis.py,
	  topo/plotting/plotgroup.py:
	  Added common base class for connectionfield and projection plots.
	  Made all analysis parameter setting use abstract classes for
	  generality

	* [r9518] topo/command/analysis.py,
	  topo/plotting/plotgroup.py:
	  Removed now-unused module-level interface to command parameter
	  defaults

2008-10-24  antolikjan

	* [r9517]
	  contrib/sparese_connectivity_LESIE.ty:
	  Made more parameters to be modifiable from command line

2008-10-24  jbednar

	* [r9516] topo/command/analysis.py,
	  topo/command/pylabplots.py,
	  topo/plotting/plotgroup.py:
	  Changed sheet_name and input_sheet name parameters to sheet and
	  input_sheet, so that they could have defaults computed and then
	  shared appropriately.

	* [r9515] topo/command/analysis.py:
	  Added UnitCurveFunction to group FeatureCurveFunctions that work
	  on a set of units

2008-10-24  rczhao

	* [r9514] /trunk/facespace/pattern_fs.py:
	  A simpler face generator to replace face-space.ty; currently only
	  implemented a class dealing with one-dimensional face space with
	  data from external MATLAB database

2008-10-24  ceball

	* [r9513] topo/param/__init__.py:
	  Corrected error introduced into get_range() in previous checkin.

2008-10-24  rczhao

	* [r9512] /trunk/facespace/fs1mf.ty:
	  A simpler face space script to replace face-space.ty; deals with
	  one-dimensional face space only and get data from external MATLAB
	  database

2008-10-24  ceball

	* [r9511] topo/param/__init__.py:
	  Added compute_default() method to ObjectSelector.

	* [r9510] topo/param/__init__.py:
	  ObjectSelector now ensures that the default value is in its list
	  of objects.

	* [r9509] topo/param/parameterized.py:
	  Added optional name argument to params(), so that one parameter
	  object can be requested.

	* [r9508] topo/param/__init__.py:
	  ObjectSelector now defaults to having instantiate=False, which
	  makes more sense because we usually use it to select from a list
	  of existing objects.

2008-10-24  jbednar

	* [r9507] topo/command/analysis.py,
	  topo/command/basic.py,
	  topo/tests/test_map_measurement.py:
	  Provide global default value for sheet_name parameter

	* [r9506] topo/command/analysis.py:
	  Made helper functions private

	* [r9505] topo/command/analysis.py:
	  Consolidated handling of input_sheet_name. Broke up RF Projection
	  to match other functions. Commented-out RF Projection (noise)
	  until further investigation.

	* [r9504] topo/command/analysis.py:
	  Removed unused RF CoG plot. Made measure_retinotopy into a
	  ParameterizedFunction.

2008-10-23  jbednar

	* [r9503] topo/command/analysis.py,
	  topo/tests/lissom_oo_or_t000100.00_Retinotopy.data:
	  Changed measure_retinotopy to use duration=0.175 and
	  apply_output_fn=False by default, to make map data match once
	  it's converted to a ParameterizedFunction

	* [r9502]
	  topo/tests/lissom_oo_or_t000100.00_Retinotopy.data,
	  topo/tests/test_map_measurement.py:
	  Added test for Retinotopy

2008-10-23  ceball

	* [r9501] topo/param/tk.py:
	  Moved (hacked) right-click editing up to TkParameterizedObject so
	  that it works for any parameter. (Many changes come from changing
	  various methods to 'protected' rather than 'private'.)

2008-10-23  jbednar

	* [r9500] topo/command/analysis.py:
	  Made measure_orientation_contrast into a ParameterizedFunction.

	* [r9499] topo/param/parameterized.py:
	  Changed ParameterizedFunction names to avoid unique number

	* [r9498] doc/Developer_Manual/coding_text.php:
	  Added note about spelling.

2008-10-23  ceball

	* [r9497] topo/param/tk.py:
	  ParametersFrame: now you can right click on any Parameterized
	  instance in a text box to access its properties.

2008-10-23  antolikjan

	* [r9496]
	  contrib/sparese_connectivity_LESIE.ty:
	  parameter changes

2008-10-23  ceball

	* [r9495] topo/param/parameterized.py:
	  When a ParameterizedFunction is called, the temporary instance is
	  now also initialized. Fixes problem with missing name.

2008-10-23  jbednar

	* [r9494] topo/command/analysis.py:
	  Added control over curve value printing format. Converted
	  measure_contrast_response to a ParameterizedFunction.

	* [r9493] topo/command/analysis.py:
	  Simplified and generalized curve implementation. Updated
	  docstrings. Converted measure_size_response to a
	  ParameterizedFunction.

2008-10-23  antolikjan

	* [r9492] topo/analysis/vision.py:
	  change in parameters

2008-10-23  jbednar

	* [r9491] topo/command/analysis.py:
	  Minor simplification

	* [r9490] topo/misc/commandline.py:
	  Fixed intermittent problem with Emacs temporary files interfering
	  with startup

2008-10-22  jbednar

	* [r9489] topo/command/analysis.py,
	  topo/plotting/plotgroup.py:
	  Generalized FeatureCurveFunction to handle or_tuning as well, and
	  made measure_or_tuning into a ParameterizedFunction based on it.
	  Made measure_or_tuning support a list of units to measure, though
	  only in batch mode at present.

2008-10-22  ceball

	* [r9488] contrib/lissom_oo_dr.ty:
	  Uncommented scheduled events.

2008-10-22  jbednar

	* [r9487] contrib/lissom_oo_dr.ty:
	  Added hints for the analysis routines

	* [r9486] topo/command/analysis.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/test_map_measurement.py:
	  Made measure_or_tuning_fullfield into a ParameterizedFunction

2008-10-22  antolikjan

	* [r9485] contrib/jacommands.py:
	  minor changes

2008-10-22  ceball

	* [r9484] contrib/lissom_oo_dr.ty:
	  File for working on implementation of models of motion. Based on
	  a cleaned up version of examples/lissom_oo_dr.ty (from r9313).

2008-10-22  antolikjan

	* [r9483]
	  contrib/sparese_connectivity_LESIE.ty:
	  parameter changes

	* [r9482]
	  contrib/sparese_connectivity_LESIE.ty:
	  The big complex cell model

2008-10-22  jbednar

	* [r9481] examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  topo/command/analysis.py:
	  Cleaned up handling of duration and apply_output_fn, making the
	  defaults always be 1.0 and True, but overridable at the
	  PatternPresenter or MeasureResponseFunction levels (to allow easy
	  control in the GUI or from scripts). Made scripts that should
	  typically use 0.175 and False to set that up explicitly. Cleaned
	  up PatternPresenter's arguments, making them Parameters, except
	  pattern_generator, which is typically used as a positional
	  parameter.

	* [r9480] topo/command/analysis.py,
	  topo/tests/lissom_oo_or_t000100.00_Corner_OR_Preference.data:
	  Changed default duration and apply_output_fn for Corner
	  Orientation Preference, in preparation for next revision

	* [r9479] topo/command/analysis.py,
	  topo/tests/lissom_oo_or_t000100.00_Corner_OR_Preference.data:
	  Changed default duration and apply_output_fn for Corner
	  Orientation Preference, in preparation for next revision

2008-10-21  jbednar

	* [r9478] topo/command/analysis.py:
	  Converted measure_cog to a ParameterizedFunction, and extended it
	  to have a reasonable default in nearly every feedforward network
	  (instead of only having a useful default for things with a
	  projection named Afferent)

	* [r9477] topo/command/basic.py:
	  Replaced run_batch with ParameterizedFunction version; should be
	  no change in behavior

2008-10-18  ceball

	* [r9476] topo/command/basic.py:
	  Replaced 'args' parameter of run_batch2() with access to extra
	  keywords via ParamOverrides.

	* [r9475] topo/base/patterngenerator.py,
	  topo/param/parameterized.py,
	  topo/pattern/random.py,
	  topo/pattern/rds.py:
	  Moved _check_params from Parameterized to ParamOverrides. Added
	  an option to ParamOverrides to allow extra (non-Parameter)
	  keywords to be handled without printing a warning.

2008-10-18  jbednar

	* [r9474] topo/command/analysis.py,
	  topo/plotting/plotgroup.py:
	  Converted unit, projection, and RF plotting to use
	  ParameterizedFunctions.

	* [r9473] topo/tkgui/projectionpanel.py:
	  Fixed RF measurement plot broken since r9414

	* [r9472] topo/command/analysis.py:
	  Reimplemented most map measurement commands as
	  ParameterizedFunctions so that their default values can be
	  controlled by users

2008-10-17  jbednar

	* [r9471] topo/base/patterngenerator.py:
	  Removed support for position parameter, probably temporarily.
	  Brought closer to using param override decorator syntax, but
	  still calling ParamOverrides explicitly

2008-10-17  antolikjan

	* [r9470] contrib/sparse_connectivity_model.ty:
	  further external parametrization added

2008-10-17  ceball

	* [r9469] topo/command/basic.py:
	  Made run_batch2's script_file be an argument rather than a
	  parameter.

	* [r9468] topo/param/parameterized.py:
	  Added support for positional arguments to ParameterizedFunction.

2008-10-17  chrisjeffery

	* [r9467] examples/lissom.ty:
	  Dummy checkin for testing

2008-10-17  jbednar

	* [r9466] topo/param/__init__.py:
	  Minor clarification to docstring

	* [r9465] topo/tkgui/editor.py:
	  Added canvas_width attribute so that it can be overridden

	* [r9464] topo/tests/test_map_measurement.py:
	  Added missing import

2008-10-17  ceball

	* [r9463] topo/param/parameterized.py:
	  Added getattr to ParamOverrides (allows dot-style access to the
	  parameterized object being overridden).

2008-10-16  jbednar

	* [r9462] topo/command/basic.py:
	  Enabled arg processing for run_batch2

	* [r9461] topo/command/basic.py:
	  Added test run_batch2 ParameterizedFunction

	* [r9460] topo/param/parameterized.py:
	  Clarified docstring, and declared ParameterizedFunction to be
	  __abstract

	* [r9459] topo/tkgui/testpattern.py:
	  Minor cleanup; shouldn't be any significant change to behavior

	* [r9458] doc/Tutorials/lissom_oo_or_text.php:
	  Updated runtimes to match performance boost

	* [r9457] doc/News/index_text.php:
	  More news

2008-10-15  jbednar

	* [r9456] topo/numbergen/basic.py,
	  topo/param/__init__.py:
	  Trivial fix to docs and comments

	* [r9455] topo/command/basic.py:
	  Added version control revision and diff printing and .ty file
	  copying to run_batch. Reorganized error and message printing.

2008-10-15  judelaw

	* [r9454] contrib/lissom_oo_or_homeostatic.ty:
	  fixed typing error in last commit

	* [r9453] contrib/lissom_oo_or_homeostatic.ty,
	  contrib/lissom_oo_or_homeostatic_tracked.ty:
	  replaced CFPLF_PluginScaled with optimized version

	* [r9452] contrib/lesi.ty:
	  replaced CFPLF_PluginScaled with optimized version

	* [r9451] contrib/species_cf_jitter.ty:
	  version of mouse/cat models with connection field jitter

	* [r9450] contrib/species_lateral_sparsity.ty:
	  version of mouse/cat models with sparse lateral connections
	  rather than feed-forward jitter

	* [r9449] contrib/jsldefs.py:
	  latest version of analysis code

2008-10-15  ceball

	* [r9448] topo/param/parameterized.py:
	  Added handling of types (not just instances of specific types) to
	  script_repr().

2008-10-14  ceball

	* [r9447] topo/command/basic.py,
	  topo/param/parameterized.py:
	  Added warning count.

	* [r9446] topo/param/parameterized.py:
	  Added ALERT.

	* [r9445] topo/param/__init__.py,
	  topo/param/parameterized.py,
	  topo/tests/testparameterizedobject.py:
	  Added ParameterizedFunction.

	* [r9444] topo/command/basic.py:
	  Added number of errors to the end of run_batch's output (stdout
	  and log file).

	* [r9443] topo/command/basic.py,
	  topo/misc/util.py:
	  Renamed MultiOut to MultiFile, since it's actually written
	  generally (in theory...).

	* [r9442] topo/command/basic.py:
	  Changed run_batch() to shadow - rather than divert - stdout to a
	  file. run_batch() also now updates the output file as often as it
	  prints messages to the screen (rather than writing the whole file
	  at the end of the run.

	* [r9441] topo/misc/util.py:
	  Added class MultiOut, allowing e.g. output to be sent to multiple
	  file-like objects.

	* [r9440] topo/numbergen/basic.py:
	  Added calls to super's __init__ missing from Unary and
	  BinaryOperator. Fixes problem with instances having name=None.

2008-10-14  jbednar

	* [r9439] topo/command/analysis.py:
	  Removed duplicate function measure_sf_pref; now just calls
	  measure_or_pref with more frequencies.

2008-10-13  jbednar

	* [r9438] examples/lissom.ty:
	  Fixed typo in previous checkin

	* [r9437] topo/param/parameterized.py:
	  Generalized to handle name=None, now that it is allowed to be

	* [r9436] examples/lissom.ty:
	  Added shortcut for modelling all dimensions

	* [r9435] topo/param/__init__.py,
	  topo/param/parameterized.py:
	  Moved String from param to param.parameterized, in order to make
	  Parameterized.name be a String

	* [r9434] topo/param/__init__.py:
	  Generalized String to allow_None

2008-10-13  antolikjan

	* [r9433] examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/lgn_lateral.ty:
	  Deleting files that were moved to contrib

2008-10-12  jbednar

	* [r9432] topo/learningfn/optimized.py:
	  Added unoptimized equivalents. Cleaned up definition of
	  CFPLF_Hebbian.

	* [r9431] Makefile:
	  Updated sf-web-site command to match changes at sf.net

	* [r9430] doc/Home/news_text.php,
	  doc/News/index_text.php:
	  Announced upcoming 0.9.6 release

2008-10-11  jbednar

	* [r9429]
	  contrib/gc_lissom_oo_or_homeostatic_new.ty,
	  contrib/lesi.ty,
	  contrib/lissom_oo_or_homeostatic.ty,
	  contrib/lissom_oo_or_homeostatic_tracked.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  topo/base/cf.py:
	  Removed duplicate CFPLF_PluginScaled class; the correct version
	  is in topo.learningfn.projfn

	* [r9428] ChangeLog.txt:
	  Added recent updates

	* [r9427] examples/lissom.ty:
	  Added separate control over LGN density. Set up appropriate
	  default preference maps for run_batch to measure

	* [r9426] topo/command/analysis.py:
	  Added speed preference plots to Direction Preference plotgroup

	* [r9425] topo/command/basic.py:
	  Added option to run_batch for saving a snapshot

2008-10-10  ceball

	* [r9424]
	  topo/tests/testtkparameterizedobject.py:
	  Updated test now None is a possible value for Selector
	  Parameters.

2008-10-10  antolikjan

	* [r9423] contrib/cc_lissom_oo_or_simple_rv.ty:
	  Minor parameter changes

	* [r9422] contrib/sparse_connectivity_model.ty:
	  

2008-10-09  jbednar

	* [r9421] topo/command/analysis.py:
	  Removed accidental import of pylabplots; fixes bug #2155124

2008-10-09  antolikjan

	* [r9420]
	  contrib/sparese_connectivity_model.ty:
	  Added simple V1Complex layer

	* [r9419]
	  contrib/sparese_connectivity_model.ty:
	  A LISSOM analogue model utilising sparse lateral connectivity and
	  BCM learning rule

2008-10-09  jbednar

	* [r9418] topo/tkgui/templateplotgrouppanel.py:
	  Added missing right-click menu option for printing a plot matrix

2008-10-08  ceball

	* [r9417] topo/param/parameterized.py:
	  script_repr() now handles function pointers. (Partially addresses
	  SF #2072507.)

	* [r9416] topo/param/tk.py:
	  Changes on a right-click properties window now cause the same
	  changes as changes on the parent window.

	* [r9415] topo/tkgui/testpattern.py:
	  Temporary changes to handle None in the 'edit sheet' list.

	* [r9414] topo/param/__init__.py:
	  Enabled 'allow_None' for ObjectSelectors.

	* [r9413] topo/param/tk.py:
	  None is now handled properly for all selector parameter
	  translators.

2008-10-07  jbednar

	* [r9412] topo/command/basic.py:
	  Fixed typo in run_batch in previous checkin.

	* [r9411] topo/command/basic.py:
	  Made pattern_present handle typical case of one input either to
	  one sheet or to all sheets more easily. Generalized
	  default_analysis_function to work with any set of input sheet
	  names. Added time scaling to run_batch.

	* [r9410] doc/Downloads/cvs_text.php,
	  doc/Downloads/index_text.php:
	  Cleaned up SVN docs

2008-10-07  ceball

	* [r9409] topo/tkgui/topoconsole.py:
	  SF.net #2125087 (a window no longer has the simulation title
	  repeatedly prefixed to its title when docked repeatedly).

	* [r9408] external/Makefile:
	  Fixed SF.net #2127024 (make always rebuilt on OS X and Win).

2008-10-06  jbednar

	* [r9407] contrib/wordcolor.ty:
	  Made initial changes to match Alessio's sim

	* [r9406] contrib/wordcolor.ty:
	  Copied from lissom_oo_or.ty r9405

	* [r9405] examples/lissom_oo_or.ty:
	  Made default_area be controllable separately from the bounding
	  boxes

	* [r9404] topo/command/analysis.py:
	  Reverted to revision 9401; need to figure out how to handle the
	  background offset level for the masked patterns

	* [r9403] external/Makefile,
	  external/readline-5.2.tar.gz:
	  Added readline to try to get it to be used on all platforms; on
	  some platforms it was not being found for some reason

2008-10-06  judelaw

	* [r9402] topo/command/analysis.py:
	  changed teststimuli patterns to be SineGratings with masks
	  instead of SineGratingDisk and SineGratingRectangle

2008-10-04  jbednar

	* [r9401] doc/Tutorials/lissom_oo_or_text.php:
	  Added notes about using mask_shape

	* [r9400] doc/News/index_text.php,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Added notes about using mask_shape

	* [r9399] topo/base/patterngenerator.py:
	  Changed mask_shape to be a ClassSelector to allow it to be
	  selected in the GUI

	* [r9398] topo/param/__init__.py:
	  Added None to the list of possible objects for ClassSelector;
	  still should be added to ObjectSelector

2008-10-04  ceball

	* [r9397] topo/param/tk.py:
	  Added hack to compensate for missing variable traces.

2008-10-04  jbednar

	* [r9396] topo/pattern/basic.py:
	  Trivial formatting fix

2008-10-03  ceball

	* [r9395] topo/param/tk.py:
	  Fixed faulty handling of None by CSPTranslator.

	* [r9394] doc/buildbot/bbanalysis.py:
	  Fixed minor syntax error.

	* [r9393] doc/buildbot/bbanalysis.py:
	  Cleaned up and added some real information for the legend.

	* [r9392] doc/buildbot/bbanalysis.py:
	  Cleaned up labeling.

	* [r9391] doc/buildbot/bbanalysis.py:
	  Times are looked up automatically if left as None.

	* [r9390] doc/buildbot/bbanalysis.py:
	  More simplification of performance graph plotting.

2008-10-03  jbednar

	* [r9389] doc/User_Manual/noise_text.php:
	  Trivial typo fix

	* [r9388] topo/base/patterngenerator.py,
	  topo/pattern/random.py:
	  Moved mask application to a method to allow it to be called from
	  Constant and Random

	* [r9387] topo/base/cf.py:
	  Added note

2008-10-03  judelaw

	* [r9386] contrib/lesi.ty:
	  current version - has full homeostatic (scaling+ triesch) in
	  excitatory sheet and option to have triesch rule in inhibitory
	  sheet, works ok with gaussians and natural images but still work
	  in progress

2008-10-03  ceball

	* [r9385] doc/buildbot/bbanalysis.py:
	  Added version to legend.

2008-10-03  jbednar

	* [r9384] topo/pattern/basic.py:
	  Fixed scale and offset for Composite patterns -- had been
	  applying once per subpattern, instead of simply applying to the
	  complete Composite pattern array. Also fixed missing import; was
	  preventing GaussiansCorner from working.

2008-10-03  ceball

	* [r9383] doc/buildbot/bbanalysis.py:
	  Corrected mistake in previous checkin.

2008-10-03  jbednar

	* [r9382] topo/pattern/teststimuli.py:
	  Cleaned up docstrings and comments. Added commented-out example
	  of using mask_shape to construct these patterns

	* [r9381] topo/base/patterngenerator.py:
	  Added mask_shape parameter, to make it simple to use a
	  PatternGenerator for the mask. The mask parameter is now hidden,
	  and perhaps should change to an attribute rather than a parameter

	* [r9380] topo/param/__init__.py:
	  Added support for Parameters that can allow None to be a valid
	  value

	* [r9379] topo/pattern/random.py:
	  Added aspect_ratio parameter to GaussianCloud. Changed to
	  evaluate parameters when called, rather than when constructed,
	  for use in the Test Pattern window

	* [r9378] topo/param/tk.py:
	  Removed redundant method

2008-10-03  ceball

	* [r9377] doc/buildbot/bbanalysis.py:
	  Changed key to be a KeyedList rather than dict so order is
	  maintained.

	* [r9376] doc/buildbot/bbanalysis.py:
	  Fixed error in path to image.

	* [r9375] doc/buildbot/bbanalysis.py:
	  Added function to write out results to a web page.

2008-10-03  antolikjan

	* [r9374]
	  topo/tests/lissom_oo_or_t000100.00_Contrast_Response.data,
	  topo/tests/lissom_oo_or_t000100.00_Corner_OR_Preference.data,
	  topo/tests/lissom_oo_or_t000100.00_Orientation_Preference.data,
	  topo/tests/lissom_oo_or_t000100.00_Orientation_Tuning.data,
	  topo/tests/lissom_oo_or_t000100.00_Orientation_Tuning_Fullfield.data,
	  topo/tests/lissom_oo_or_t000100.00_Position_Preference.data,
	  topo/tests/lissom_oo_or_t000100.00_Size_Tuning.data,
	  topo/tests/lissom_oo_or_t000100.00_Spatial_Frequency_Preference.data:
	  measure maps tests have been changed because of the difference to
	  apply_output_fn parameter handling

	* [r9373] topo/command/basic.py:
	  changed pattern_present such that only sheets with measure_maps
	  True have their apply_output_fn parameter changed

	* [r9372] topo/command/analysis.py:
	  removed wipe_out_activity and event_clear from PatternPresenter -
	  not needed anymore

	* [r9371] contrib/cc_lissom_oo_or_simple_rv.ty:
	  removed Habituation

2008-10-03  judelaw

	* [r9370] topo/projection/basic.py:
	  added ability to use a coordmapperfunction on a Shared
	  WeightCFProjection

	* [r9369] topo/outputfn/basic.py:
	  added saving of first_call state to HomeostaticMaxEnt to avoid
	  errors when pushing/popping state and measuring maps before any
	  patterns have been presented

2008-10-02  ceball

	* [r9368] doc/buildbot/bbanalysis.py:
	  Gave up hope of having reasonable key on the plot itself.

2008-10-02  jbednar

	* [r9367] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Cleaned up plot titles

2008-10-02  ceball

	* [r9366] doc/buildbot/bbanalysis.py:
	  Added missing import.

	* [r9365] doc/buildbot/bbanalysis.py:
	  Attempt at adding a key to bb graph.

	* [r9364] doc/buildbot/bbanalysis.py:
	  Now doesn't print any information after first exclusion.

	* [r9363] doc/buildbot/bbanalysis.py:
	  Invalid results permanently excluded (rather than being
	  re-checked every time).

2008-10-02  jbednar

	* [r9362] doc/News/index_text.php,
	  doc/User_Manual/noise_text.php,
	  topo/base/cf.py:
	  Changed share_mask_for_connection_fields to
	  same_cf_shape_for_all_cfs, to make the connection to cf_shape
	  clear

2008-10-02  ceball

	* [r9361] doc/buildbot/bbanalysis.py:
	  Fixed 'exclusions' and cleaned up a little.

2008-10-02  jbednar

	* [r9360] images/ellen_arthur.pgm:
	  Committed change missed from last week

	* [r9359] topo/base/functionfamily.py,
	  topo/misc/robotics.py,
	  topo/sheet/lissom.py:
	  Cleaned up docstrings and line formatting. Changed Parameter to
	  HookList where appropriate

	* [r9358] topo/analysis/featureresponses.py,
	  topo/command/basic.py:
	  Fixed broken snapshot tests by adding clear_event_queue instead
	  of storing topo.sim.event_clear in a Parameter as-is

	* [r9357] topo/plotting/plotgroup.py:
	  Cleaned up docstring formatting

	* [r9356] topo/misc/robotics.py,
	  topo/param/__init__.py:
	  Added HookList parameter type since they are becoming ubiquitous

2008-10-02  antolikjan

	* [r9355] contrib/jacommands.py:
	  Minor parameter adjustment

	* [r9354] contrib/jacommands.py:
	  moved CascadeHomeostatic here

	* [r9353] topo/outputfn/basic.py:
	  Removed CascadeHomeostatic and moving into jacommands

	* [r9352] contrib/cc_lissom_oo_or_simple_rv.ty,
	  contrib/gc_lissom_oo_or_homeostatic_new.ty,
	  contrib/lgn_lateral.ty:
	  Moved the still active example files from examples to contrib

	* [r9351] topo/tkgui/testpattern.py:
	  event_clear has now default parameter EPConnection so I removed
	  it from the code

	* [r9350] topo/sheet/lissom.py:
	  Made LISSOM to have also hook lists - one is activated at the
	  beginning of new iteration and one at the end

	* [r9349] topo/learningfn/optimized.py:
	  added CFPLF_Scaled_opt and BCMFixed_opt

	* [r9348] topo/command/pylabplots.py:
	  tiny bug correction in plot_modulation_ratio

	* [r9347] topo/analysis/featureresponses.py:
	  made FeatureResponses to inherit from PatternDrivenAnalysis and
	  the related modifications

	* [r9346] topo/analysis/vision.py:
	  minor changes to update commands of measure complexity

	* [r9345] topo/base/simulation.py:
	  made the function event_clear parameter event_type a default
	  EPConnectionEvent

	* [r9344] topo/base/cf.py:
	  Made it possible for each CF have different mask

	* [r9343] topo/base/functionfamily.py:
	  Added the class PatternDrivenAnalysis

	* [r9342]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  Added possibility to have Homeostatic plasticity, moved from
	  Translator to Jiterrer

	* [r9341] contrib/jacommands.py:
	  Added new Class Jiterrer and Habituation and few other minor
	  modifications

2008-10-02  jbednar

	* [r9340] doc/News/index_text.php:
	  Added more news

2008-10-02  ceball

	* [r9339] doc/buildbot/bbanalysis.py:
	  Exclude an invalid result from the buildbot speed graph.

	* [r9338] topo/tests/test_script.py:
	  Fixed bug in reading old speed-test data files: first digit from
	  number of iterations was being missed.

2008-10-02  judelaw

	* [r9337] topo/base/cf.py:
	  re-added CFPLF_PluginScaled, somehow got l;ost in last update

2008-10-02  jbednar

	* [r9336] ChangeLog.txt:
	  Updated

	* [r9335] Makefile:
	  Removed unnecessary targets

2008-10-01  ceball

	* [r9334] Makefile:
	  Re-enabled lissom.ty and lissom_fsa.ty for slow-tests.

	* [r9333] Makefile:
	  Removed specification of sheet to inspect from special speed
	  tests (data not inspected during speed tests).

2008-10-01  jbednar

	* [r9332] Makefile:
	  Added SPEEDDATA targets for special .ty files; not yet enabled by
	  default

2008-10-01  ceball

	* [r9331] topo/tests/test_script.py:
	  Fixed bug in new-style speed tests (wasn't pickling/unpickling
	  the data).

2008-10-01  jbednar

	* [r9330] Makefile:
	  Removed lissom.ty from SCRIPTS for the moment, as it causes
	  problems for the speed tests

	* [r9329] examples/lissom_whisker_barrels.ty:
	  Minor cleanup. Fixed default_density processing.

	* [r9328] examples/lissom.ty:
	  Minor cleanup to docstring. Added missing import

	* [r9327] Makefile,
	  topo/tests/lissom.ty_DATA:
	  Added special _DATA targets for unusual .ty files

2008-10-01  judelaw

	* [r9326] contrib/lesi.ty:
	  Current version with homeostatic plasticity in Exc sheet but no
	  afferent scaling, works well with gaussians

2008-09-30  ceball

	* [r9325] topo/tests/test_script.py:
	  Cleaned up train-tests section (no change to results). Made
	  speed-tests more flexible (can specify densities etc; should be
	  no change but not yet tested). Removed out-of-date ALERTs
	  (Windows ALERT was invalid because we use an MSYS terminal to run
	  these tests on Windows).

	* [r9324] topo/tests/test_script.py:
	  Added flexibility to data generation command, allowing any
	  'startup parameters' for a script to be set (e.g.
	  default_density, default_retina_density, etc).

	* [r9323] Makefile:
	  Updated data generation command for train-tests, showing how to
	  set command-line arguments for a script, and how to specify the
	  name of the sheet to inspect.

	* [r9322] doc/Future_Work/current_text.php:
	  Added tasks so that I don't forget about them.

2008-09-28  jbednar

	* [r9321] examples/lissom.ty:
	  Added more progress reports in hopes of making unoptimized tests
	  to pass on buildbot

	* [r9320] examples/whiskers:
	  Removed no-longer-used Matlab whisker support files

	* [r9319] topo/command/analysis.py:
	  Removed outdated whisker support

	* [r9318] topo/tests/lissom_oo_or_dy.ty_DATA:
	  Removed test file for obsolete script

	* [r9317] topo/tests/lissom_oo_od.ty_DATA,
	  topo/tests/sullivan_nn06.ty_DATA:
	  Removed test data for outdated scripts

2008-09-27  jbednar

	* [r9316] examples/lissom_whisker_barrels.ty,
	  examples/whiskers/dfl_key_white_vert.png,
	  topo/command/dfl_key_white_vert.png:
	  Moved deflection key from examples/whiskers to topo/command with
	  the other color keys

2008-09-26  ceball

	* [r9315] topo/misc/legacy.py:
	  Removed legacy redirection of topo.sheets.cfsom to
	  topo.sheet.cfsom now that CFSOM has been deleted. We could add
	  legacy support for the CFSOM class if necessary.

	* [r9314] examples/lissom_oo_dr.ty:
	  Removed unused example (duplicates lissom.ty).

2008-09-26  jbednar

	* [r9313] examples/lissom_whisker_barrels.ty:
	  Fixed problems that made previous release unrunnable

	* [r9312] topo/numbergen/basic.py:
	  Expanded docstrings and added missing VonMisesRandom class

	* [r9311] examples/lissom_whisker_barrels.ty:
	  Updated to Stuart's current version; results slightly different
	  from the J. Neuroscience paper submission due to change in random
	  number code

	* [r9310] examples/lissom_whisker_barrels.ty:
	  Updated to version used for J. Neuroscience paper submission; not
	  runnable in the current Topographica

2008-09-26  judelaw

	* [r9309] contrib/laminar_oo_or.ty:
	  re added correct copy of laminar_oo_or.ty

	* [r9308] contrib/laminar_oo_or.ty,
	  contrib/laminar_oo_or.ty*:
	  removing file commited in error

	* [r9307] contrib/jsldefs.py,
	  contrib/laminar_oo_or.ty,
	  contrib/laminar_oo_or.ty*,
	  contrib/laminar_or.ty,
	  contrib/lesi.ty,
	  contrib/lissom_oo_or_homeostatic.ty,
	  contrib/lissom_oo_or_homeostatic_tracked.ty,
	  contrib/lissom_oo_or_noshrinking.ty,
	  contrib/lissom_oo_or_noshrinking_latswitch.ty,
	  contrib/lissom_oo_or_species.ty,
	  contrib/lissom_oo_or_species_tracked.ty,
	  contrib/lissom_or_noshrinking.ty,
	  contrib/lissom_or_noshrinking_latswitch.ty:
	  added inprogress example files

	* [r9306] examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/lesi.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_homeostatic_tracked.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_oo_or_species.ty,
	  examples/lissom_oo_or_species_tracked.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty:
	  moved inprogress example files to contrib/

2008-09-26  jbednar

	* [r9305] examples/lissom.ty:
	  Minor cleanup; should be no change to results

	* [r9304] examples/lissom_or.ty:
	  Changed to use schedule_event; should be no change in results

	* [r9303] topo/sheet/lissom.py:
	  Fixed longstanding tiny bug in parameter values -- the upper
	  threshold change at 500 iterations was being skipped for the
	  lissom_oo_or*.ty simulations, compared to the parameters in the
	  CMVC book. Changed it to match the book value, which does not
	  affect slow-tests (which only test to 250), but does affect the
	  final organized map slightly.

	* [r9302] examples/lissom_fsa.ty:
	  Simplified by using standard set of scheduled events, and
	  improved convergence, though it is still not as good as the
	  published version. The afferent learning rates and most of the
	  scheduled events are now different from the previous version, and
	  thus the results have changed significantly.

	* [r9301] topo/sheet/lissom.py:
	  Added control over afferent learning rate scaling

2008-09-25  jbednar

	* [r9300] examples/lissom_fsa.ty:
	  Cleaned up formatting; should be no change in results

	* [r9299] Makefile:
	  Removed tests for obsolete scripts

	* [r9298] examples/ellen_arthur.pgm,
	  topo/pattern/image.py,
	  topo/tests/testcfsom.py:
	  Moved sample image out of examples/ and into images/

	* [r9297] topo/sheet/cfsom.py:
	  Removed obsolete code; see examples/cfsom_or.ty for current
	  approach

	* [r9296]
	  examples/sullivan_neurocomputing04.ty:
	  Changed to use current SOM implementation, to allow cfsom.py to
	  be deleted

	* [r9295]
	  examples/sullivan_neurocomputing04.ty:
	  Cleaned up formatting; should be no change in results

	* [r9294] Makefile,
	  examples/README.txt,
	  examples/sullivan_nn06.ty:
	  Removed sullivan_nn06.ty; never completed.

	* [r9293] examples/leaky_lissom_or.ty:
	  Clarified docstring

	* [r9292] examples/ohzawa_science90.ty:
	  Removed; not very useful

	* [r9291] examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty:
	  Obsolete; DY simulation now in lissom.ty, though these files
	  produce somewhat different results and may still have some
	  information relevant to reproducing the Ramtohul (2006) thesis.
	  In particular, lissom_oo_or_dy_photo.ty shows how to use stereo
	  pair image inputs.

	* [r9290] examples/lissom_oo_od.ty:
	  Obsolete; OD simulation now in lissom.ty

	* [r9289] examples/lissom_or_sf.ty:
	  Obsolete; basic SF simulation now in lissom.ty, and Chris Palmer
	  has newer more complex SF sims

	* [r9288] examples/lissom_photo_or.ty:
	  Obsolete; photo simulation now in lissom.ty

	* [r9287] examples/lissom_oo_or_cr.ty:
	  Changed to use schedule_events; should be no change in results
	  (though not verified)

	* [r9286] examples/lissom_oo_or_cr.ty:
	  Cleaned up to match lissom.ty. May be deleted, as it can be
	  reproduced by lissom.ty, but kept as an example for now.

	* [r9285] examples/lissom.ty:
	  Minor simplification

	* [r9284] examples/lissom_oo_or_rg.ty:
	  Results can be reproduced using lissom.ty

	* [r9283] examples/lissom.ty,
	  topo/sheet/lissom.py:
	  Generalized schedule_events for use in lissom.ty; should have no
	  change in results for any simulation

	* [r9282] topo/sheet/lissom.py:
	  Fixed apparent bug in previous checkin

	* [r9281] examples/lissom.ty:
	  Cleaned up, shortened lines, simplified, and changed to style of
	  lissom_oo_or.ty; should have no change in results

2008-09-24  jbednar

	* [r9280] examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_species.ty,
	  examples/lissom_whisker_barrels.ty,
	  topo/sheet/lissom.py:
	  Moved scheduled events into a shared sheet.lissom.schedule_events
	  command

	* [r9279] Makefile:
	  Added test for lissom.ty

	* [r9278] topo/tests/lissom.ty_DATA:
	  Current version, for reference

	* [r9277] examples/laminar_or.ty,
	  examples/lissom_or_noshrinking_latswitch.ty:
	  Minor cleanup, removing unused code. Should have no change in
	  results

	* [r9276] examples/lissom_or.ty:
	  Cleaned up formatting to match lissom_oo_or.ty; no change in
	  results

	* [r9275] examples/lissom_oo_or.ty:
	  Trivial cleanup of formatting; no change in results

	* [r9274] examples/lissom_or.ty:
	  Partial update to match style of lissom_oo_or.ty; should be no
	  change in results.

	* [r9273]
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/lesi.ty:
	  Fixed references to old topo directory names

2008-09-23  gerasymo

	* [r9272] examples/lissom_oo_or_od_dr_dy.ty:
	  Results of this file can be obtained from lissom.ty with
	  dims=['or','od','dr','dy']

	* [r9271]
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty:
	  Results of this file can be obtained from lissom.ty with
	  dims=['or','od','dr','dy','sf','rg','cr']

2008-09-22  ceball

	* [r9270] topo/tkgui/plotgrouppanel.py:
	  Changed missed from r9269.

	* [r9269] topo/tkgui/plotgrouppanel.py:
	  Simplified getting sheet coordinates from mouse events during
	  subsequent processing: store (x,y) of cell center in the event
	  (addresses ALERT: simplifies r9219 and r9265; should be no
	  visible change).

2008-09-22  jbednar

	* [r9268] doc/Downloads/index_text.php,
	  doc/FAQ/index_text.php:
	  Moved outdated warning into a FAQ

	* [r9267] topo/outputfn/basic.py:
	  Fixed formatting and docstring for recent changes. Simplified
	  first_call changes for HomeostaticMaxEnt

	* [r9266] topo/base/cf.py,
	  topo/learningfn/optimized.py,
	  topo/learningfn/projfn.py:
	  Moved CFPLF_PluginScaled out of base and into learningfn
	  directory with the other learningfns. Fixed formatting on recent
	  changes.

2008-09-22  chrispalmer

	* [r9265] topo/tkgui/plotgrouppanel.py:
	  corrects reporting of pixel coord values in status bar and pop up
	  window to centre of pixel

	* [r9264] topo/tkgui/plotgrouppanel.py:
	  adds current file name to window titles

2008-09-22  jbednar

	* [r9263] examples/perrinet_retina_pynest.py:
	  Reformatted and cleaned up for release

2008-09-21  ceball

	* [r9262] /trunk/topographica-win/create_python_topo/setup.bat:
	  Fixed tile installation.

	* [r9261] topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py:
	  Files missed from previous check-in.

	* [r9260] topo/tests/__init__.py:
	  Removed unused function and added comment.

	* [r9259] /trunk/topographica-win/create_python_topo/setup.bat:
	  Now prints fewer messages (in the hope of making error messages
	  visible).

2008-09-20  ceball

	* [r9258] doc/Downloads/index_text.php:
	  Updated win/msys instructions.

	* [r9257] topo/tkgui/__init__.py:
	  Allow win/msys's tcl to find extra packages.

	* [r9256] topo/plotting/bitmap.py:
	  Fixed TITLE_FONT for MSYS/Windows (as opposed to binary Windows).

	* [r9255] external/matplotlib-0.91.4.tar.gz:
	  Re-archived and re-compressed version to try to get MSYS to work
	  with it (should be no other changes).

	* [r9254] doc/Downloads/cvs_text.php,
	  doc/Downloads/index_text.php:
	  Further attempts to unify the installation instructions.

	* [r9253] topo/param/parameterized.py:
	  Added note to myself that has been lying around for ages.

	* [r9252] external/Makefile_win_msys.diff:
	  Updated win-msys-patch.

	* [r9251] external/Makefile_OSX_tk.diff:
	  Removed unused patch.

	* [r9250] Makefile:
	  Removed unnecessary 'else'.

	* [r9249] external/Makefile:
	  Added in windows/msys packages to skip (rather than applying via
	  patch).

	* [r9248] Makefile:
	  win-msys-patch is applied by default when the Makefile is run on
	  Windows/MSYS.

	* [r9247] topo/tkgui/__init__.py:
	  Fixed test for wm forget (docking); was broken on linux.

2008-09-19  ceball

	* [r9246] /trunk/topographica-win/README.txt:
	  Updated to reflect current status.

	* [r9245] /trunk/topographica-win/create_python_topo/README.txt:
	  Updated to reflect current status.

	* [r9244]
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat:
	  Minor corrections.

	* [r9243] Makefile:
	  Don't delete topographica-win on Windows (it's done later).

	* [r9242] /trunk/topographica-win/create_installer/README.txt,
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat:
	  Untested simplifications to Windows's .exe creation routine.

	* [r9241] /trunk/topographica-win/common/setup.py:
	  Allow Windows's topographica script to work from msys (works
	  without the gui, but hangs with the gui - still useful for
	  developers to run all but make gui-tests).

	* [r9240] /trunk/topographica-win/create_python_topo/setup.bat:
	  Added patching of gnosis utils.

	* [r9239] topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/__init__.py:
	  Made sure param.tk tests start tkgui so that tests can run
	  successfully on platforms without tk 8.5 (hack).

	* [r9238] /trunk/topographica-win/create_python_topo/setup.bat,
	  /trunk/topographica-win/create_python_topo/tile0.8.2.tar.gz:
	  Added tile 0.8.2 binary.

	* [r9237] topo/tkgui/__init__.py,
	  topo/tkgui/plotgrouppanel.py:
	  Hide docking if Tk version doesn't support it.

	* [r9236] external/Makefile:
	  Added pyttk build steps, for future use.

	* [r9235] topo/tkgui/__init__.py:
	  Added support for versions of Tk below 8.5. If Tk 8.5 is not
	  installed, then tile 0.8.2 or greater must be available.

	* [r9234] topo/plotting/bitmap.py:
	  TITLE_FONT: Restored option accidentally removed in previous
	  commit, and simplified default call.

	* [r9233] topo/plotting/bitmap.py:
	  Fixed TITLE_FONT for Windows.

	* [r9232] Makefile:
	  Added command for generating map tests data.

	* [r9231]
	  topo/tests/lissom_oo_or_t000100.00_Contrast_Response.data,
	  topo/tests/lissom_oo_or_t000100.00_Corner_OR_Preference.data,
	  topo/tests/lissom_oo_or_t000100.00_Orientation_Preference.data,
	  topo/tests/lissom_oo_or_t000100.00_Orientation_Tuning.data,
	  topo/tests/lissom_oo_or_t000100.00_Orientation_Tuning_Fullfield.data,
	  topo/tests/lissom_oo_or_t000100.00_Position_Preference.data,
	  topo/tests/lissom_oo_or_t000100.00_Size_Tuning.data,
	  topo/tests/lissom_oo_or_t000100.00_Spatial_Frequency_Preference.data:
	  Data generated with current version of lissom_oo_or.ty. (Results
	  match previous ones to 4 d.p.)

	* [r9230] topo/misc/legacy.py:
	  Added support for old snapshots (ConnectionField's bounds
	  property). Addresses SF.net #2118376.

	* [r9229] topo/param/parameterized.py,
	  topo/projection/basic.py:
	  Extracted get_all_slots() from Parameter so that it can also be
	  used in Parameterized objects that have slots. Added slot
	  handling to Parameterized instance pickling. Addresses part of
	  SF.net #2118376 (still need to add legacy support).

2008-09-19  chrispalmer

	* [r9228] topo/command/analysis.py:
	  correction to fix spacing presentation of pixel by pixel stimulus
	  to correction receptive field measurement by reverse correlation

2008-09-19  jbednar

	* [r9227] doc/User_Manual/interfacing_text.php:
	  Fixed spacing

2008-09-19  ceball

	* [r9226] doc/User_Manual/interfacing_text.php:
	  Fixed an indentation problem, and made minor changes to text.

2008-09-19  jbednar

	* [r9225] doc/News/index_text.php:
	  Added pointer to interfacing page

2008-09-18  jbednar

	* [r9224]
	  doc/User_Manual/images/perrinet_retina_modeleditor2.png,
	  doc/User_Manual/interfacing_text.php:
	  Minor fixes to interfacing page

	* [r9223]
	  doc/User_Manual/images/perrinet_retina_modeleditor2.png:
	  Added for interfacing page

	* [r9222] doc/User_Manual/index_text.php,
	  doc/User_Manual/interfacing_text.php:
	  Added page about interfacing; adapted from my fin08 submission

2008-09-17  ceball

	* [r9221] topo/tkgui/plotgrouppanel.py:
	  Added ALERT.

2008-09-17  chrispalmer

	* [r9220] topo/tkgui/plotgrouppanel.py:
	  changed title of individual receptive field display to give more
	  info

	* [r9219] topo/tkgui/plotgrouppanel.py:
	  fixed right click request to display indiviual unit connection
	  fields and receptive fields

2008-09-17  antolikjan

	* [r9218]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  Repaired bug in image presentation

	* [r9217]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  Repaired bug in image presentation

2008-09-17  ceball

	* [r9216] topo/base/cf.py:
	  File missed from r9215.

	* [r9215] topo/learningfn/optimized.py:
	  Converted CFPLF_Hebbian_opt to access weights, input_sheet_slice,
	  and mask as slots.

	* [r9214] topo/outputfn/optimized.py:
	  Converted CFPOF_DivisiveNormalizeL1_opt to access weights and
	  input_sheet_slice as slots.

	* [r9213] topo/responsefn/optimized.py:
	  Simplified handling of weights_obj.

	* [r9212] topo/responsefn/optimized.py:
	  Simplified handling of slice_obj.

	* [r9211] topo/base/cf.py,
	  topo/responsefn/optimized.py:
	  Made ConnectionField's weights and input_sheet_slice be slots,
	  allowing fast access from optimized C functions. No longer need a
	  shadow list of weights and slices.

2008-09-17  antolikjan

	* [r9210]
	  examples/gc_lissom_oo_or_homeostatic_new.ty:
	  Moved to the new images set

	* [r9209]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  Changed to new image set

2008-09-15  ceball

	* [r9208] /trunk/topographica-win/create_python_topo/setup.bat:
	  Added tooltip and snit to Windows binary installation.

	* [r9207] /trunk/topographica-win/setup_cvs_copy/setup.bat:
	  Minor update.

	* [r9206] /trunk/topographica-win/create_python_topo/setup.bat:
	  Minor updates to Windows' binary setup.

	* [r9205] /trunk/topographica-win/create_python_topo/setup.bat:
	  Corrections to create_python_topo's setup.bat

	* [r9204]
	  /trunk/topographica-win/create_python_topo/psyco-1.5.2.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/setup.bat:
	  Updating Topographica's Windows binary installation...

	* [r9203]
	  /trunk/topographica-win/create_python_topo/PIL-1.1.5.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/PIL-1.1.5.win32-py2.5.exe,
	  /trunk/topographica-win/create_python_topo/gmpy-1.03-gmp-4.2.1.win32-py2.5.exe,
	  /trunk/topographica-win/create_python_topo/ipython-0.8.4.win32-setup.exe,
	  /trunk/topographica-win/create_python_topo/libsndfile-1_0_17.zip,
	  /trunk/topographica-win/create_python_topo/setup.bat:
	  Updating Topographica's Windows binary installation...

2008-09-15  antolikjan

	* [r9202] contrib/jacommands.py:
	  Renamed import pathes related to the new renaming scheme

2008-09-15  ceball

	* [r9201] /trunk/topographica-win/create_python_topo/README.txt,
	  /trunk/topographica-win/create_python_topo/matplotlib-0.90.1.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/matplotlib-0.91.4.win32-py2.5.exe,
	  /trunk/topographica-win/create_python_topo/setup.bat:
	  

	* [r9200]
	  /trunk/topographica-win/create_python_topo/matplotlib-0.90.0.win32-py2.4.exe:
	  Updating Topographica's Windows binary installation...

	* [r9199]
	  /trunk/topographica-win/create_python_topo/numpy-1.0.2.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/numpy-1.1.1-win32-superpack-python2.5.exe,
	  /trunk/topographica-win/create_python_topo/scipy-0.5.2.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/scipy-0.6.0.win32-py2.5.exe:
	  Updating Windows binary packages...

2008-09-15  jbednar

	* [r9198] doc/Downloads/index_text.php:
	  Added notes about installing documentation on Mac

2008-09-15  ceball

	* [r9197] doc/buildbot/master.cfg:
	  Updated mac build procedure. Changes have been running on the
	  actual buildbot for a while already.

2008-09-14  jbednar

	* [r9196] examples/perrinet_retina.ty:
	  Made Topographica be in charge of the network size. Added Model
	  Editor layout.

2008-09-13  jbednar

	* [r9195] examples/perrinet_retina.ty:
	  Minor reformatting and simplification. Changed processing to
	  occur in input_event rather than process_current_time for
	  simplicity. Made input vary as a demo

2008-09-13  judelaw

	* [r9194] topo/outputfn/basic.py:
	  changed HomeostaticMaxEnt state_push and state_pop to allow them
	  to be called before the parameters have been initialized

2008-09-12  jbednar

	* [r9193] doc/News/index_text.php:
	  Added notes about updates since 0.9.5

2008-09-12  judelaw

	* [r9192]
	  examples/lissom_oo_or_species_tracked.ty:
	  brought up to date with release 0.95 using conversion script

	* [r9191]
	  examples/lissom_oo_or_species_tracked.ty:
	  added missing import

2008-09-11  ceball

	* [r9190] Makefile,
	  examples/lissom_oo_or.ty,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty:
	  Switched lissom_oo_or example and reference test to use optimized
	  joint normalization function. Reduced slow-tests matching
	  requirement to 7 dp.

	* [r9189] topo/sheet/optimized.py:
	  Uncommented 'provide unoptimized equivalent' of
	  compute_joint_norm_totals_opt.

	* [r9188] examples/perrinet_retina.ty:
	  Fixed typo.

2008-09-10  jbednar

	* [r9187] examples/perrinet_retina.ty,
	  examples/perrinet_retina_pynest.py:
	  Greatly cleaned-up version of code originally developed at
	  CodeJam07

	* [r9186] topo/sheet/basic.py:
	  Added ActivityCopy sheet

	* [r9185] topo/base/projection.py,
	  topo/base/simulation.py:
	  Trivial clarification -- swapped declaration order of src and
	  dest ports to match chronological order of processing

	* [r9184] topo/tkgui/editor.py:
	  Generalized Model Editor to have a representation for
	  EventProcessor distinct from Sheet, and for EPConnection distinct
	  from CFProjection.

	* [r9183] topo/tkgui/editor.py:
	  Fixed broken warning message. Simplified handling of Simulation
	  objects.

2008-09-10  ceball

	* [r9182] topo/pattern/image.py:
	  Fixed bug pickling GenericImage when image_cache==False.

	* [r9181] topo/sheet/basic.py,
	  topo/sheet/optimized.py:
	  Extracted JointNormalizingCFSheet's compute_joint_norm_totals()
	  method into a function. JointNormalizingCFSheets now have a
	  joint_norm_fn parameter, allowing compute_joint_norm_totals_opt()
	  to be used independently of LISSOM_Opt (although the results
	  using compute_joint_norm_totals_opt() have not been verified
	  yet).

	* [r9180] etc/update_094_to_095:
	  Fixed bug in update script.

2008-09-10  jbednar

	* [r9179] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_oo_or.ty,
	  examples/som_retinotopy.ty:
	  Shortened import lists

	* [r9178] topo/param/parameterized.py:
	  Fixed typo in docs

	* [r9177] topo/misc/commandline.py:
	  Added verbose and debugging commandline options

2008-09-10  judelaw

	* [r9176]
	  examples/lissom_oo_or_species_tracked.ty:
	  took out references to exponential jitter, changed module
	  importing plotgroups from

	* [r9175] examples/lesi.ty,
	  examples/lissom_oo_or_species_tracked.ty:
	  work in progress

	* [r9174] contrib/jsldefs.py:
	  added function for plotting out connections of units in a
	  projection (plot_out_connections())

2008-09-10  ceball

	* [r9173] etc/update_094_to_095:
	  Set svn:executable ON

	* [r9172] topo/param/parameterized.py:
	  Avoid state_push() and state_pop() being called on classes.
	  Addresses SF.net #2103756.

2008-09-10  jbednar

	* [r9171] examples/Makefile:
	  Fixed broken paths to commands

	* [r9170] doc/Downloads/index_text.php:
	  Minor clarification

2008-09-09  ceball

	* [r9169]
	  topo/tests/reference/common_control.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/support_clissom/lissom5.gz:
	  Version of C++ lissom that outputs angle in radians rather than
	  degrees (removes added complexity of angle conversions). Also
	  added check of weights+activities just before first bounds
	  change, to aid detection of incorrect bounds changes. OO DR
	  simulation reverted to LISSOM (had been switched to LISSOM_Opt by
	  mistake).

	* [r9168]
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/oo_dir_map.param:
	  Simplification of parameters; Topographcia and c++ reference oo
	  dr simulations now match until the first bounds change.

	* [r9167]
	  topo/tests/reference/lissom_oo_dr_reference.ty:
	  Removed fixedpoint.

	* [r9166]
	  topo/tests/reference/oo_dir_map.param:
	  Set Precision on generators.

	* [r9165]
	  topo/tests/reference/support_clissom/lissom5.gz:
	  Compiled from CVS after fixing handling of Precision.

	* [r9164]
	  topo/tests/reference/lissom_oo_dr_reference.ty:
	  Fixed import error.

2008-09-08  ceball

	* [r9163] topo/base/cf.py,
	  topo/projection/basic.py:
	  Made ConnectionField's x and y be constant parameters. Removed
	  superfluous code in ConnectionField's __init__ relating to x and
	  y.

2008-09-06  ceball

	* [r9162] doc/Team_Members/index_text.php:
	  Added OS X credit.

	* [r9161]
	  topo/tests/reference/lissom_oo_dr_reference.ty:
	  Removed comment that does not apply to this file (copied from
	  oo_or version).

	* [r9160]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Added minor note to mac users about .DS_* files.

	* [r9159] topo/base/cf.py:
	  Added handling of del to weight_arrays and slice_arrays (missed
	  from previous commit).

	* [r9158] topo/base/cf.py,
	  topo/projection/basic.py:
	  Made _weight_arrays and _slice_arrays optimization more robust
	  (by making them properties, the lists of arrays can be created
	  when they are requested - which allows e.g. old snapshots to work
	  and means e.g. subclasses of CFProjection don't have to call code
	  to create the arrays). Haven't evaluated performance, but this
	  change should have little impact.

2008-09-05  ceball

	* [r9157] topo/base/cf.py,
	  topo/projection/basic.py,
	  topo/responsefn/optimized.py:
	  Added demo of providing c with faster access to CF weights and
	  slices. Reduces run time over first 300 iterations of
	  lissom_oo_or density=48 to about 65% of original.

	* [r9156]
	  doc/Developer_Manual/releases_text.php:
	  Added ALERT.

	* [r9155] Makefile:
	  Simplified list of scripts to keep for distribution.

2008-09-05  jbednar

	* [r9154] topo/sheet/lissom.py:
	  Removed extra copy of class

2008-09-05  ceball

	* [r9153] Makefile:
	  Removed unnecessary step during make LATEST_STABLE.

	* [r9152] /tags/LATEST_STABLE:
	  Update LATEST_STABLE.

	* [r9151] /tags/LATEST_STABLE:
	  Update LATEST_STABLE.

	* [r9150] /releases/0.9.5/trunk:
	  Create release 0.9.5

	* [r9149] doc/News/index_text.php:
	  Update to news list.

	* [r9148] doc/Downloads/index_text.php:
	  Added note that binaries are coming soon for Windows.

	* [r9147]
	  topo/tests/lissom_oo_or_t000100.00_Corner_OR_Preference.data,
	  topo/tests/test_map_measurement.py:
	  New data for Corner OR Preference after defaults were altered.

	* [r9146] ChangeLog.txt:
	  Updated ChangeLog.

	* [r9145] /releases/0.9.5:
	  Create release 0.9.5

	* [r9144] /tags/LATEST_STABLE:
	  Update LATEST_STABLE.

	* [r9143] /tags/LATEST_STABLE:
	  Update LATEST_STABLE.

2008-09-04  ceball

	* [r9142] doc/FAQ/index_text.php:
	  Made OS X's readline instructions more explicit.

	* [r9141] doc/User_Manual:
	  More to ignore.

	* [r9140] doc/Downloads/index_text.php,
	  doc/FAQ/index_text.php:
	  Added section to FAQ for platform-specific questions.

	* [r9139] external/Makefile:
	  Added target to avoid building tcl, tk, and blt on OS X.

2008-09-04  jbednar

	* [r9138] doc/Home/news_text.php,
	  doc/News/index_text.php:
	  Updated release date

	* [r9137] doc/Home/news_text.php,
	  doc/News/index_text.php:
	  Declared ready for release

	* [r9136] doc/News/index_text.php,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/noise_text.php:
	  Added page about noise

	* [r9135] doc/Developer_Manual/coding_text.php,
	  doc/Developer_Manual/imports_text.php,
	  doc/Developer_Manual/optimization_text.php,
	  doc/Developer_Manual/refactoring_text.php,
	  doc/Developer_Manual/releases_text.php:
	  Minor edits

	* [r9134] topo/tkgui/projectionpanel.py:
	  Fixed coordinate display so that it doesn't make the window size
	  change when dragging sliders

2008-09-04  ceball

	* [r9133] doc/Future_Work/current_text.php:
	  Updated and cleaned up tasks.

2008-09-04  antolikjan

	* [r9132]
	  examples/gc_lissom_oo_or_homeostatic_new.ty:
	  Minor parameter changes

	* [r9131]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  parameter changes

	* [r9130] contrib/modelfit.py:
	  Minor input changes

	* [r9129] contrib/jacommands.py:
	  Few minor changes

	* [r9128] topo/tkgui/testpattern.py:
	  corrected some indentition problems

	* [r9127] topo/sheet/lissom.py:
	  Added the JointNormalizingCFSheet_Continuous class

	* [r9126] topo/outputfn/basic.py:
	  Added the HalfRectifyAndPower output function

	* [r9125] topo/learningfn/optimized.py:
	  

	* [r9124] topo/command/analysis.py:
	  

2008-09-04  ceball

	* [r9123]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Added more info about using svn.

	* [r9122] doc/Downloads/index_text.php,
	  doc/Reference_Manual/index_text.php:
	  Updated some information.

	* [r9121] doc/Downloads,
	  doc/User_Manual:
	  More to ignore.

	* [r9120] doc/Downloads/index_text.php,
	  doc/User_Manual/commandline_text.php,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/scripts_text.php:
	  Added missing scripts page to User Manual, and updated links to
	  it.

	* [r9119] doc/images/080903_plotting2_mac.png:
	  Cropped image.

	* [r9118]
	  doc/Developer_Manual/releases_text.php:
	  Updated release procedure.

	* [r9117] Makefile:
	  Added target to create svn copy of release.

	* [r9116] Makefile:
	  Restored mistakenly removed log message in make LATEST_STABLE.

	* [r9115] /tags/LATEST_STABLE:
	  Updating LATEST_STABLE.

	* [r9114] /tags/LATEST_STABLE:
	  Updating LATEST_STABLE

	* [r9113] Makefile:
	  Fixed LATEST_STABLE target.

2008-09-04  jbednar

	* [r9112] doc/shared/util.php:
	  Reorganized menu

	* [r9111] doc/Downloads/cvs_text.php,
	  doc/FAQ/index_text.php,
	  doc/Forums/index_text.php,
	  doc/Links/index_text.php,
	  doc/News/index_text.php,
	  doc/Team_Members/index_text.php,
	  doc/Tutorials/lissom_oo_or_text.php,
	  doc/Tutorials/som_retinotopy_text.php,
	  doc/User_Manual/batch_text.php,
	  doc/User_Manual/introduction_text.php.m4,
	  doc/User_Manual/modeleditor_text.php,
	  doc/User_Manual/overview_text.php,
	  doc/User_Manual/parameters_text.php,
	  doc/User_Manual/plotting_text.php:
	  Misc fixes and cleanup

2008-09-03  ceball

	* [r9110] topo/tests/reference/Makefile:
	  Fixed deletion of directories from reference runs.

	* [r9109] topo/pattern/audio.py,
	  topo/pattern/basic.py:
	  Temporarily moved OneDPowerSpectrum(PatternGenerator) from
	  topo.pattern.basic to topo.pattern.audio because
	  OneDPowerSpectrum should not yet appear in lists such as those
	  presented in the GUI.

	* [r9108] doc/Home/news_text.php:
	  Added Mac screenshot.

	* [r9107] doc/images/080903_plotting2_mac.png:
	  Added screenshot showing plotting on Mac.

	* [r9106] doc/Home/news_text.php:
	  Updated screenshot links for 0.9.5.

	* [r9105]
	  doc/images/080903_modeleditor_fedora.png:
	  Added screenshot showing model editor.

	* [r9104] doc/images/080903_docking_fedora.png:
	  Added screenshot showing docking.

	* [r9103]
	  doc/images/080903_plotting1_fedora.png:
	  Added new screenshot.

	* [r9102] doc/News/index_text.php,
	  doc/shared/topo.css:
	  Added div tags around individual items, and set up the divs to
	  indent lines after the first one.

	* [r9101] doc/Downloads/update_script_text.php,
	  doc/News/index_text.php:
	  Added info about updating old scripts.

	* [r9100] topo/misc/legacy.py:
	  Added snapshot support for topo.outputfns.homeostatic. Added
	  demonstration code for supporting old scripts as well as old
	  snapshots (i.e. for scripts that haven't been/can't be updated).

	* [r9099] etc/update_094_to_095:
	  Minor changes.

	* [r9098] etc/update_094_to_095:
	  Added Id string to update script, since Revision didn't seem to
	  work.

	* [r9097] etc/update_094_to_095:
	  Moved notes to the end and added Revision string.

	* [r9096] etc/update_094_to_095,
	  etc/update_094_to_095.py:
	  Removed .py suffix from update_094_to_095.py

	* [r9095] etc/update_094_to_095.py:
	  Made renaming script a little friendlier.

	* [r9094] topo/misc/commandline.py:
	  Added '-l' install legacy support option.

	* [r9093] etc/update_094_to_095.py:
	  Initial version.

	* [r9092] topo/misc/legacy.py:
	  Restored full support for non-existent DynamicNumber class. Added
	  an 'install_legacy_support()' function - currently just a
	  convenience function for installing snapshot support.

	* [r9091] doc/User_Manual/overview_text.php:
	  Replaced CFSOM example with SaccadeController.

	* [r9090] Makefile:
	  Remove contrib/ from release.

	* [r9089] Makefile:
	  Keep ChangeLog in release.

	* [r9088] doc/User_Manual/overview_text.php:
	  Replaced example of sensor that isn't currently supported.

	* [r9087] examples/README.txt:
	  Updated list of examples.

	* [r9086] Makefile:
	  'make dist' now deletes all examples except those on the list to
	  include (syntax of command could be improved).

2008-09-03  jbednar

	* [r9085] doc/Team_Members/index_text.php:
	  Fixed ending date

2008-09-03  ceball

	* [r9084] doc/Team_Members/index_text.php:
	  Minor alteration to formatting.

	* [r9083] doc/Downloads/index_text.php:
	  Minor alteration to description around Mac instructions.

2008-09-03  jbednar

	* [r9082] doc/News/index_text.php:
	  Minor reformatting

	* [r9081] /trunk/topographica-win/common/setup.py,
	  /trunk/topographica-win/create_installer/topographica.iss:
	  Updated release number

	* [r9080] Makefile:
	  Updated release number

	* [r9079] doc/Downloads/index_text.php,
	  doc/Home/news_text.php,
	  doc/News/index_text.php:
	  Minor fixes

	* [r9078] README.txt,
	  doc/Home/index_text.php,
	  doc/Team_Members/index_text.php,
	  doc/User_Manual/about_text.php,
	  topo/__init__.py:
	  Updated develop list and copyright dates

2008-09-03  ceball

	* [r9077] doc/User_Manual/overview_text.php:
	  Minor change.

	* [r9076] Makefile:
	  More examples to remove (list is probably slightly brutal and
	  probably omits some that should be removed); we need to change to
	  a list of examples to keep.

	* [r9075] Makefile:
	  More to clean when making distribution.

	* [r9074]
	  doc/Developer_Manual/releases_text.php:
	  Minor addition.

	* [r9073] topo/tests/reference/Makefile:
	  Added Makefile to clean out reference test dirs.

2008-09-02  ceball

	* [r9072] topo/numbergen:
	  Added svn:ignore.

	* [r9071]
	  doc/Developer_Manual/releases_text.php:
	  Minor additions to release procedure.

	* [r9070]
	  doc/Developer_Manual/releases_text.php:
	  Replaced CVS with SVN.

	* [r9069] doc/Tutorials/lissom_oo_or_text.php:
	  Cleanup of text recently added to lissom tutorial.

	* [r9068] Makefile,
	  doc/Downloads/index_text.php,
	  external/Makefile:
	  Made important action of osx-tk-patch be applied automatically on
	  mac (now tcl, tk, and blt are unnecessarily built on mac - but
	  the manual patch step is now not required).

	* [r9067] Makefile:
	  Temporarily removed lissom_oo_or_homeostatic simulations from the
	  list of those to test.

	* [r9066] examples/cfsom_or.ty:
	  Updated to make better use of namespaces.

	* [r9065] examples/hierarchical.ty:
	  Removed unused import (numpy).

	* [r9064] examples/som_retinotopy.ty:
	  Removed unused import (numpy).

	* [r9063] examples/hierarchical.ty:
	  Updated to make better use of namespaces.

2008-09-02  jbednar

	* [r9062] README.txt:
	  Minor fixes

2008-09-02  ceball

	* [r9061]
	  doc/Tutorials/som_retinotopy_text.php:
	  Commented out reference to obermayer_pnas90 example.

	* [r9060] doc/News/index_text.php:
	  Commented out link to git instructions because they are not yet
	  finished, and we can't definitely support git usage yet.

	* [r9059] doc/User_Manual/commandline_text.php:
	  Updated section about customizing command prompt.

	* [r9058]
	  doc/Tutorials/som_retinotopy_text.php:
	  Dealt with ALERT.

	* [r9057] topo/misc/commandline.py:
	  Fixed erroneous reference to 'self' variable. Removed duplicate
	  and out-of-date class CommandPrompt. Updated link to IPython
	  documentation.

	* [r9056] doc/News/index_text.php:
	  Added model editor's dynamic parameter support + note that it's
	  described in the tutorial.

	* [r9055] topo/tkgui/testpattern.py:
	  Added note.

	* [r9054] doc/Tutorials/lissom_oo_or_text.php:
	  Added section about using the Model Editor to install a pattern
	  for learning. (Reinstated from c++ lissom.)

	* [r9053] topo/param/tk.py:
	  Added workaround to GUI to allow it to set a GeneratorSheet's
	  input_generator.

	* [r9052] topo/param/tk.py:
	  Fixed bug in GUI: right clicking on a parameter wasn't working
	  because of a missing 'self' argument (not sure how this error was
	  introduced...).

	* [r9051] doc/Tutorials/lissom_oo_or_text.php:
	  Clarified description of 'refresh' button.

	* [r9050]
	  doc/Developer_Manual/imports_text.php:
	  Removed ALERT.

	* [r9049] topo/base/simulation.py:
	  Switched info about mxNumber to gmpy.

	* [r9048] doc/Downloads/index_text.php:
	  Added info about unsuccessful attempts to get tools required to
	  build docs on mac.

	* [r9047] doc/Downloads/cvs_text.php:
	  Changed ALERT to ENHANCEMENT.

	* [r9046] doc/Reference_Manual/index_text.php:
	  Addressed ALERT: added description of gmpy.

	* [r9045]
	  doc/Tutorials/som_retinotopy_text.php:
	  Minor alteration to text.

	* [r9044]
	  doc/Tutorials/som_retinotopy_text.php:
	  Minor alterations to text.

2008-09-01  ceball

	* [r9043] doc/Downloads/index_text.php:
	  Updated comment about mac.

	* [r9042] topo/param/tk.py:
	  Made AppWindow's status bar have a width equal to the window's
	  (i.e. stopped it altering the master window's width);
	  unfortunately, this seems to mean I have to fix its height as
	  well. Should address SF.net #2087402. Needs testing on non-linux
	  platforms.

	* [r9041] doc/News/index_text.php:
	  Altered some commented-out items (including removing some).

2008-09-01  jbednar

	* [r9040] doc/Future_Work/index_text.php:
	  Reordered and updated big to-do items

	* [r9039] doc/Home/news_text.php,
	  doc/News/index_text.php:
	  Updated with recent changes in preparation for 0.9.5 release

2008-09-01  ceball

	* [r9038] doc/Tutorials/lissom_oo_or_text.php:
	  Minor updates to lissom_oo_or tutorial.

	* [r9037] doc/Downloads/cvs_text.php:
	  Clarification for Windows/MSYS users.

	* [r9036] doc/Downloads/index_text.php,
	  doc/User_Manual/commandline_text.php,
	  doc/User_Manual/index_text.php:
	  Created a 'running scripts interactively' section in the user
	  manual (by moving and editing text from the downloads and
	  commandline pages).

2008-09-01  jbednar

	* [r9035] doc/News/index_text.php:
	  Minor updates to new features, plus more complete list as a
	  comment for now

2008-08-28  ceball

	* [r9034] doc/User_Manual/commandline_text.php:
	  First pass at an 'imports' section.

	* [r9033] topo/command/basic.py:
	  Corrected reference in a docstring.

	* [r9032] doc/User_Manual/modeleditor_text.php:
	  Removed out-of-date statement that model editor doesn't support
	  dynamic numbers.

	* [r9031] doc/User_Manual/commandline_text.php:
	  Fixed typo.

	* [r9030] topo/base/cf.py:
	  Corrected CFProjection's 'cleanup' code (CFs could be None).

	* [r9029] doc/FAQ/index_text.php,
	  doc/User_Manual/commandline_text.php,
	  examples/hierarchical.ty,
	  topo/command/basic.py,
	  topo/tests/testplot.py:
	  Renamed some missed instances of 'parameterizedobject' to
	  'parameterized'.

	* [r9028] topo/misc/legacy.py,
	  topo/pattern/basic.py:
	  Removed duplicate SineGratingDisk class.

	* [r9027] doc/Future_Work/current_text.php,
	  topo/base/cf.py,
	  topo/base/simulation.py:
	  Fixed memory leak with load_snapshot() (SF.net #2065608).

	* [r9026] doc/Downloads/index_text.php:
	  Made an explicit 'all platforms' section. Entire text now needs
	  reviewing for coherence.

2008-08-27  gerasymo

	* [r9025] examples/lissom.ty:
	  New doc string about further publications that can be replicated
	  with this file.

2008-08-27  jbednar

	* [r9024] examples/lissom_oo_or.ty:
	  Allowed command-line overriding of LGN density

	* [r9023] examples/lissom_oo_or.ty,
	  examples/som_retinotopy.ty:
	  Updated to reflect new recommended conventions on imports and
	  file organization

	* [r9022] topo/outputfn/basic.py:
	  Updated alert.

	* [r9021] topo/sheet/__init__.py,
	  topo/sheet/basic.py,
	  topo/sheet/generator.py,
	  topo/sheet/lissom.py:
	  Added basic.py and moved the basic Sheet classes into it, for
	  consistency with other library directories. Also made BoundingBox
	  available from topo.sheet, because it's required for using
	  Sheets.

	* [r9020] topo/tests/testcfsom.py:
	  Added missing import

	* [r9019] topo/misc/numbergenerator.py,
	  topo/numbergen,
	  topo/numbergen/__init__.py,
	  topo/numbergen/basic.py:
	  Moved NumberGenerator classes into their own directory for
	  consistency with other library directories

	* [r9018] topo/pattern/random.py:
	  Added GaussianCloud pattern to simplify initial weights

2008-08-27  gerasymo

	* [r9017]
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty:
	  Results of this file can be obtained from lissom.ty with
	  dims=['or','od','dr','dy','rg','cr']

	* [r9016]
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty:
	  Right BoundingBox size: 0.27083 instead of 0.25; other trivial
	  changes.

2008-08-27  jbednar

	* [r9015] examples/som_retinotopy.ty:
	  Sorted imports

	* [r9014] ChangeLog.txt:
	  Fixed confusing date

2008-08-27  ceball

	* [r9013] examples/som_retinotopy.ty:
	  Updated to use namespaces better.

2008-08-26  ceball

	* [r9012] doc/Downloads/cvs_text.php,
	  doc/Downloads/index_text.php:
	  First pass at updating and reorganizing Topographica's download
	  instructions.

2008-08-26  jbednar

	* [r9011] ChangeLog.txt,
	  Makefile:
	  Changed svn2cl to work on repository instead of just the trunk,
	  in order to catch the tags marking releases

2008-08-26  ceball

	* [r9010] topo/command/basic.py:
	  Added missing close() for file (although I think it makes no
	  difference in this case because the file should have been closed
	  anyway when the function ended).

2008-08-26  antolikjan

	* [r9009] contrib/jacommands.py:
	  

	* [r9008]
	  examples/gc_lissom_oo_or_homeostatic_new.ty:
	  

	* [r9007]
	  examples/gc_lissom_oo_or_homeostatic_new.ty:
	  

	* [r9006] contrib/jacommands.py:
	  
2008-08-25  ceball

	* [r9005] topo/tkgui/editor.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Moved model editor code into one files (i.e. moved
	  editortools.py, editorwindow.py, and editorobjects.py into
	  editor.py).

2008-08-25  jbednar

	* [r9004] ChangeLog.txt:
	  Generated new ChangeLog based on svn (not CVS) sources, for the
	  complete history

	* [r9003] Makefile,
	  external/Makefile,
	  external/svn2cl-0.10.tar.gz:
	  Added svn2cl and changed ChangeLog.txt target to use it

	* [r9002] examples/lissom.ty:
	  Fixed string join. Added control over LGN density using
	  default_retina_density

2008-08-25  ceball

	* [r9001] /releases/0.9.4, /tags/release_0_9_4:
	  Moved tags/release_0_9_4 to releases/0.9.4

	* [r9000] /releases/0.9.3, /tags/release_0_9_3:
	  Moved tags/release_0_9_3 to releases/0.9.3

	* [r8999] /releases/0.9.2, /tags/release_0_9_2:
	  Moved tags/release_0_9_2 to releases/0.9.2

	* [r8998] /releases/0.9.1, /tags/release_0_9_1:
	  Moved tags/release_0_9_1 to releases/0.9.1

	* [r8997] /releases/0.9.0, /tags/release_0_9_0:
	  Moved tags/release_0_9_0 to releases/0.9.0

	* [r8996] /releases/0.8.2, /tags/release_0_8_2:
	  Moved tags/release_0_8_2 to releases/0.8.2

	* [r8995] /releases/0.8.1, /tags/release_0_8_1:
	  Moved tags/release_0_8_1 to releases/0.8.1

	* [r8994] /releases/0.8.0, /tags/release_0_8_0:
	  Moved tags/release_0_8_0 to releases/0.8.0

2008-08-25  jbednar

	* [r8993] doc/User_Manual/publishing_text.php:
	  Updated ref to cite

2008-08-25  ceball

	* [r8992] doc/User_Manual/overview_text.php,
	  doc/User_Manual/parameters_text.php,
	  topo/param/tk.py:
	  Some renaming that was missed earlier.

	* [r8991] contrib/jacommands.py,
	  examples/lissom_or_movie.ty,
	  topo/misc/__init__.py,
	  topo/misc/legacy.py,
	  topo/misc/trace.py,
	  topo/misc/traces.py:
	  Renamed topo.misc.traces to topo.misc.trace. Also updated
	  parameter names in trace.py.

	* [r8990] topo/plotting/bitmap.py:
	  Restored TITLE_FONT, which had been temporarily disabled.

	* [r8989] topo/tests/testparametersframe.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/testpattern.py:
	  Removed placeholder topo/tkgui/parametersframe.py.

	* [r8988] contrib/ae.py,
	  doc/Developer_Manual/optimization_text.php,
	  examples/ohzawa_science90.ty,
	  topo/analysis/featureresponses.py,
	  topo/command/analysis.py,
	  topo/command/basic.py,
	  topo/coordmapper/basic.py,
	  topo/misc/__init__.py,
	  topo/misc/legacy.py,
	  topo/misc/traces.py,
	  topo/misc/util.py,
	  topo/misc/utils.py,
	  topo/plotting/plotgroup.py,
	  topo/projection/basic.py,
	  topo/sheet/composer.py,
	  topo/sheet/generator.py,
	  topo/sheet/saccade.py,
	  topo/tests/test_script.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testsheetview.py,
	  topo/tkgui/editorobjects.py:
	  Renamed topo.misc.utils to topo.misc.util

	* [r8987]
	  doc/Developer_Manual/imports_text.php:
	  Updated import list.

	* [r8986]
	  examples/sullivan_neurocomputing04.ty,
	  topo/__init__.py,
	  topo/misc/__init__.py,
	  topo/misc/legacy.py,
	  topo/misc/patternfn.py,
	  topo/misc/patternfns.py,
	  topo/pattern/basic.py,
	  topo/pattern/teststimuli.py:
	  Renamed topo.misc.patternfns to topo.misc.patternfn

	* [r8985] contrib/jacommands.py,
	  contrib/modelfit.py,
	  doc/User_Manual/patterns_text.php,
	  examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/cfsom_or.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/hierarchical.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lesi.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_homeostatic_tracked.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_oo_or_od_dr_dy.ty,
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty,
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty,
	  examples/lissom_oo_or_rg.ty,
	  examples/lissom_oo_or_species.ty,
	  examples/lissom_oo_or_species_tracked.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/saccade_demo.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  topo/analysis/vision.py,
	  topo/command/analysis.py,
	  topo/coordmapper/basic.py,
	  topo/misc/__init__.py,
	  topo/misc/legacy.py,
	  topo/misc/numbergenerator.py,
	  topo/misc/numbergenerators.py,
	  topo/pattern/basic.py,
	  topo/pattern/teststimuli.py,
	  topo/tests/gui_tests.py,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/testCompositePatternGenerators.txt,
	  topo/tests/testDynamicParameter.txt,
	  topo/tests/testNumberParameter.txt,
	  topo/tests/test_pattern_present.txt,
	  topo/tests/testcfsom.py,
	  topo/tests/testparameterizedobject.py,
	  topo/tests/testpatterngenerator.py:
	  Renamed topo.misc.numbergenerators to topo.misc.numbergenerator.

	* [r8984] topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/widgets.py:
	  Removed the placeholder file topo/tkgui/widgets.py.

2008-08-24  ceball

	* [r8983] contrib/jaanalysis.py,
	  contrib/jacommands.py,
	  contrib/jsldefs.py,
	  doc/Developer_Manual/coding_text.php,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_or_movie.ty,
	  topo/analysis/vision.py,
	  topo/command/basic.py,
	  topo/command/pylabplots.py,
	  topo/misc/__init__.py,
	  topo/misc/commandline.py,
	  topo/misc/filepath.py,
	  topo/misc/filepaths.py,
	  topo/misc/traces.py,
	  topo/param/tk.py,
	  topo/pattern/audio.py,
	  topo/pattern/image.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/testCompositeSheetMasks.txt,
	  topo/tests/test_map_measurement.py,
	  topo/tests/test_script.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Renamed topo.misc.filepaths to topo.misc.filepath

	* [r8982]
	  doc/Developer_Manual/optimization_text.php,
	  doc/User_Manual/overview_text.php,
	  examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/cfsom_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  topo/learningfn/optimized.py,
	  topo/learningfn/projfn.py,
	  topo/learningfn/projfns.py,
	  topo/misc/legacy.py,
	  topo/outputfn/optimized.py,
	  topo/outputfn/projfn.py,
	  topo/outputfn/projfns.py,
	  topo/responsefn/optimized.py,
	  topo/responsefn/projfn.py,
	  topo/responsefn/projfns.py:
	  Renamed topo.X.projfns to topo.X.projfn for X in
	  [outputfn,learningfn,responsefn].

	* [r8981] contrib/jacommands.py,
	  contrib/jsldefs.py,
	  contrib/modelfit.py,
	  doc/Developer_Manual/optimization_text.php,
	  doc/Future_Work/current_text.php,
	  doc/User_Manual/overview_text.php,
	  examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/ohzawa_science90.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  topo/base/__init__.py,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/functionfamily.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/command/basic.py,
	  topo/coordmapper/basic.py,
	  topo/learningfn/basic.py,
	  topo/learningfn/optimized.py,
	  topo/learningfn/projfns.py,
	  topo/misc/legacy.py,
	  topo/outputfn/basic.py,
	  topo/outputfn/optimized.py,
	  topo/pattern/rds.py,
	  topo/projection/basic.py,
	  topo/responsefn/basic.py,
	  topo/responsefn/optimized.py,
	  topo/responsefn/projfns.py,
	  topo/sheet/generator.py,
	  topo/sheet/lissom.py,
	  topo/sheet/optimized.py:
	  Renamed topo.base.functionfamilies to topo.base.functionfamily

	* [r8980] contrib/ae.py,
	  doc/Developer_Manual/coding_text.php,
	  doc/Developer_Manual/optimization_text.php,
	  examples/ohzawa_science90.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  topo/base/__init__.py,
	  topo/base/arrayutil.py,
	  topo/base/arrayutils.py,
	  topo/command/analysis.py,
	  topo/command/pylabplots.py,
	  topo/learningfn/som.py,
	  topo/misc/distribution.py,
	  topo/outputfn/basic.py,
	  topo/pattern/basic.py,
	  topo/responsefn/projfns.py,
	  topo/sheet/cfsom.py,
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/testdistribution.py,
	  topo/tests/testfeaturemap.py:
	  Renamed topo.base.arrayutils to topo.base.arrayutil.

	* [r8979] doc/Team_Members/index_text.php:
	  Updated my information.

	* [r8978] doc/FAQ/index_text.php:
	  Minor alteration to snapshot question.

	* [r8977] doc/Developer_Manual/coding_text.php,
	  doc/Developer_Manual/gui_text.php,
	  doc/Developer_Manual/imports_text.php,
	  doc/Developer_Manual/index_text.php,
	  doc/Developer_Manual/optimization_text.php,
	  doc/Developer_Manual/releases_text.php,
	  doc/Developer_Manual/testing_text.php,
	  topo/param/tk.py:
	  Updated Developer Manual.

	* [r8976] doc/Reference_Manual/index_text.php:
	  Updated Reference Manual's index page.

	* [r8975] topo/__init__.py,
	  topo/commands,
	  topo/coordmapperfns,
	  topo/eps,
	  topo/learningfns,
	  topo/outputfns,
	  topo/patterns,
	  topo/projections,
	  topo/responsefns,
	  topo/sheets:
	  Removed old directories from topo/ and updated topo.__init__.

	* [r8974] doc/User_Manual/about_text.php:
	  Added minor ALERT.

	* [r8973] doc/User_Manual/publishing_text.php:
	  Added minor ALERT.

	* [r8972] doc/User_Manual/modeleditor_text.php:
	  Minor updates to model editor section of User Manual.

	* [r8971] doc/User_Manual/plotting_text.php:
	  Updated plotting section of User Manual.

	* [r8970] doc/User_Manual/patterns_text.php:
	  Updated patterns section of user manual.

2008-08-23  ceball

	* [r8969] doc/User_Manual/parameters_text.php:
	  Updated text and simplified examples.

	* [r8968] doc/User_Manual/commandline_text.php:
	  Minor changes.

2008-08-22  ceball

	* [r8967] doc/User_Manual/space_text.php:
	  Fixed minor typo.

	* [r8966] doc/User_Manual/commandline_text.php:
	  Quick update of most of the commandline documentation.

	* [r8965] topo/base/sheet.py:
	  Added read-only density property to sheet, so that users can
	  request to see the true density of a sheet (without having to
	  find out about xdensity or ydensity). True bounds are already
	  available as .bounds

	* [r8964] doc/User_Manual/time_text.php:
	  Fixed minor typo.

	* [r8963] doc/User_Manual/batch_text.php,
	  doc/User_Manual/commandline_text.php,
	  doc/User_Manual/overview_text.php,
	  doc/User_Manual/parameters_text.php,
	  doc/User_Manual/patterns_text.php,
	  doc/User_Manual/plotting_text.php,
	  doc/User_Manual/publishing_text.php:
	  Updated User Manual after renaming directories.

	* [r8962] doc/User_Manual/overview_text.php:
	  Updated module names. Also made some corrections to text and
	  added ALERTs.

2008-08-21  ceball

	* [r8961] topo/command/basic.py:
	  No visible change (removed code accidentally added in previous
	  checkin.

	* [r8960] topo/command/basic.py:
	  Tidied load_snapshot() error messages a little.

	* [r8959] Makefile,
	  topo/param/parameterized.py:
	  Fixed SF #1856728: script_repr() & namespace. Still room for
	  improvement, but we get runnable representations now (added
	  simple test).

	* [r8958] topo/command,
	  topo/coordmapper,
	  topo/ep, topo/learningfn,
	  topo/outputfn,
	  topo/pattern,
	  topo/projection,
	  topo/responsefn,
	  topo/sheet:
	  Added svn:ignore.

	* [r8957] doc/Future_Work/current_text.php:
	  Updated tasks.

	* [r8956] topo/command/__init__.py,
	  topo/command/basic.py:
	  Promoted functions from command.basic.

	* [r8955] topo/command/analysis.py,
	  topo/plotting/plotgroup.py:
	  Made save_plotgroup() work with a copy of the plotgroup.

	* [r8954] topo/tests/testsimulation.py:
	  Added commented-out test for garbage collection of Simulation
	  objects.

	* [r8953] topo/misc/commandline.py:
	  Change missed when renaming topo.commands to topo.command.

2008-08-21  jbednar

	* [r8952] examples/joublin_bc96.ty:
	  Removed outdated example; would need rewriting to work in current
	  version, probably by throwing away all of the custom CF-related
	  files and implementing using the standard classes now (which
	  should work or nearly work for this purpose nowadays).

	* [r8951] topo/base/simulation.py:
	  Removed alert; checked all cases that we know about

2008-08-21  ceball

	* [r8950] Makefile,
	  contrib/ae.py,
	  contrib/jaanalysis.py,
	  contrib/jacommands.py,
	  contrib/jsldefs.py,
	  contrib/modelfit.py,
	  examples/goodhill_network90.ty,
	  examples/lesi.ty,
	  examples/lissom_oo_or_homeostatic_tracked.ty,
	  examples/lissom_oo_or_species_tracked.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/ohzawa_science90.ty,
	  examples/run.py,
	  examples/sullivan_nn06.ty,
	  topo/analysis/featureresponses.py,
	  topo/analysis/vision.py,
	  topo/command,
	  topo/command/__init__.py,
	  topo/command/analysis.py,
	  topo/command/basic.py,
	  topo/command/disp_key_white_vert_small.png,
	  topo/command/dr_key_white_vert_small.png,
	  topo/command/or_key_white_horiz.pdf,
	  topo/command/or_key_white_vert.pdf,
	  topo/command/or_key_white_vert.png,
	  topo/command/or_key_white_vert_small.png,
	  topo/command/pylabplots.py,
	  topo/commands/__init__.py,
	  topo/commands/analysis.py,
	  topo/commands/basic.py,
	  topo/commands/disp_key_white_vert_small.png,
	  topo/commands/dr_key_white_vert_small.png,
	  topo/commands/or_key_white_horiz.pdf,
	  topo/commands/or_key_white_vert.pdf,
	  topo/commands/or_key_white_vert.png,
	  topo/commands/or_key_white_vert_small.png,
	  topo/commands/pylabplots.py,
	  topo/misc/commandline.py,
	  topo/misc/legacy.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/sheet/slissom.py,
	  topo/tests/test_map_measurement.py,
	  topo/tests/test_pattern_present.txt,
	  topo/tests/test_script.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testimage.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testsnapshots.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py:
	  Moved topo.commands to topo.command.

	* [r8949] topo/misc/legacy.py:
	  Minor cleanup - should be no visible change.

	* [r8948] topo/commands/basic.py:
	  Only install legacy support if snapshot loading fails initially.

	* [r8947] topo/misc/legacy.py:
	  Hacked til make snapshot-tests worked.

	* [r8946] topo/misc/legacy.py:
	  Reverted line that was changed by mistake.

	* [r8945] topo/misc/legacy.py:
	  Partial snapshot support for recent renaming.

	* [r8944] contrib/jaanalysis.py,
	  contrib/jsldefs.py,
	  examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/cfsom_or.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/goodhill_network90.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lesi.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_homeostatic_tracked.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_oo_or_od_dr_dy.ty,
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty,
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty,
	  examples/lissom_oo_or_rg.ty,
	  examples/lissom_oo_or_species.ty,
	  examples/lissom_oo_or_species_tracked.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/saccade_demo.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  topo/commands/analysis.py,
	  topo/commands/basic.py,
	  topo/sheet/generator.py,
	  topo/sheet/generatorsheet.py,
	  topo/sheet/saccade.py,
	  topo/tests/gui_tests.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/testCompositePatternGenerators.txt,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testsheetview.py,
	  topo/tests/testsnapshots.py,
	  topo/tests/utils.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py:
	  Renamed topo.sheet.generatorsheet to topo.sheet.generator

	* [r8943] contrib/ae.py,
	  contrib/jacommands.py,
	  contrib/jsldefs.py,
	  contrib/modelfit.py,
	  examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/cfsom_or.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/goodhill_network90.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lesi.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_homeostatic_tracked.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_oo_or_od_dr_dy.ty,
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty,
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty,
	  examples/lissom_oo_or_rg.ty,
	  examples/lissom_oo_or_species.ty,
	  examples/lissom_oo_or_species_tracked.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/saccade_demo.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  topo/__init__.py,
	  topo/commands/analysis.py,
	  topo/commands/basic.py,
	  topo/learningfn/som.py,
	  topo/misc/robotics.py,
	  topo/outputfn/basic.py,
	  topo/param/parameterized.py,
	  topo/param/tk.py,
	  topo/pattern,
	  topo/pattern/__init__.py,
	  topo/pattern/audio.py,
	  topo/pattern/basic.py,
	  topo/pattern/image.py,
	  topo/pattern/random.py,
	  topo/pattern/rds.py,
	  topo/pattern/teststimuli.py,
	  topo/patterns/__init__.py,
	  topo/patterns/audio.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/patterns/rds.py,
	  topo/patterns/teststimuli.py,
	  topo/tests/gui_tests.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/testCompositePatternGenerators.txt,
	  topo/tests/test_pattern_present.txt,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testimage.py,
	  topo/tests/testpatterngenerator.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testsnapshots.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/__init__.py:
	  Renamed topo.patterns to topo.pattern

	* [r8942] contrib/jaanalysis.py,
	  contrib/jacommands.py,
	  contrib/jsldefs.py:
	  Missed from previous renaming of component libraries.

	* [r8941] examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/hierarchical.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lesi.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_homeostatic_tracked.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_oo_or_od_dr_dy.ty,
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty,
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty,
	  examples/lissom_oo_or_rg.ty,
	  examples/lissom_oo_or_species.ty,
	  examples/lissom_oo_or_species_tracked.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/ohzawa_science90.ty,
	  examples/saccade_demo.ty,
	  examples/sullivan_nn06.ty,
	  topo/projection,
	  topo/projection/__init__.py,
	  topo/projection/basic.py,
	  topo/projection/optimized.py,
	  topo/projections/__init__.py,
	  topo/projections/basic.py,
	  topo/projections/optimized.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tkgui/__init__.py,
	  topo/tkgui/editortools.py:
	  Renamed topo.projections to topo.projection

	* [r8940] examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/cfsom_or.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/goodhill_network90.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lesi.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_homeostatic_tracked.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_oo_or_od_dr_dy.ty,
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty,
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty,
	  examples/lissom_oo_or_rg.ty,
	  examples/lissom_oo_or_species.ty,
	  examples/lissom_oo_or_species_tracked.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/saccade_demo.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  topo/commands/analysis.py,
	  topo/commands/basic.py,
	  topo/ep/__init__.py,
	  topo/misc/robotics.py,
	  topo/sheet,
	  topo/sheet/__init__.py,
	  topo/sheet/cfsom.py,
	  topo/sheet/composer.py,
	  topo/sheet/generatorsheet.py,
	  topo/sheet/lissom.py,
	  topo/sheet/optimized.py,
	  topo/sheet/saccade.py,
	  topo/sheet/slissom.py,
	  topo/sheets/__init__.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/composer.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py,
	  topo/sheets/optimized.py,
	  topo/sheets/saccade.py,
	  topo/sheets/slissom.py,
	  topo/tests/gui_tests.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/testCompositePatternGenerators.txt,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testsnapshots.py,
	  topo/tests/utils.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py:
	  Renamed topo.sheets to topo.sheet

	* [r8939] topo/ep,
	  topo/ep/__init__.py,
	  topo/ep/basic.py,
	  topo/eps/__init__.py,
	  topo/eps/basic.py,
	  topo/tests/testsimulation.py,
	  topo/tkgui/__init__.py:
	  Renamed topo.eps to topo.ep.

	* [r8938] examples/lissom_oo_or_species.ty,
	  examples/lissom_oo_or_species_tracked.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/saccade_demo.ty,
	  topo/__init__.py,
	  topo/coordmapper,
	  topo/coordmapper/__init__.py,
	  topo/coordmapper/basic.py,
	  topo/coordmapperfns/__init__.py,
	  topo/coordmapperfns/basic.py,
	  topo/sheets/saccade.py,
	  topo/tkgui/__init__.py:
	  Renamed topo.coordmapperfns to topo.coordmapperfn.

	* [r8937] examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/cfsom_or.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lesi.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_homeostatic_tracked.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_oo_or_od_dr_dy.ty,
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty,
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty,
	  examples/lissom_oo_or_rg.ty,
	  examples/lissom_oo_or_species.ty,
	  examples/lissom_oo_or_species_tracked.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/saccade_demo.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  topo/__init__.py,
	  topo/responsefn,
	  topo/responsefn/__init__.py,
	  topo/responsefn/basic.py,
	  topo/responsefn/optimized.py,
	  topo/responsefn/projfns.py,
	  topo/responsefns/__init__.py,
	  topo/responsefns/basic.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/testplotgroup.py,
	  topo/tkgui/__init__.py:
	  Renamed topo.responsefns to topo.responsefn.

	* [r8936] examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/cfsom_or.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lesi.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_homeostatic_tracked.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_oo_or_od_dr_dy.ty,
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty,
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty,
	  examples/lissom_oo_or_rg.ty,
	  examples/lissom_oo_or_species.ty,
	  examples/lissom_oo_or_species_tracked.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  topo/__init__.py,
	  topo/base/cf.py,
	  topo/learningfn,
	  topo/learningfn/__init__.py,
	  topo/learningfn/basic.py,
	  topo/learningfn/optimized.py,
	  topo/learningfn/projfns.py,
	  topo/learningfn/som.py,
	  topo/learningfns/__init__.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py,
	  topo/learningfns/projfns.py,
	  topo/learningfns/som.py,
	  topo/projections/basic.py,
	  topo/sheets/cfsom.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testplotgroup.py,
	  topo/tkgui/__init__.py:
	  Renamed topo.learningfns to topo.learningfn.

	* [r8935] examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/cfsom_or.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lesi.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_homeostatic_tracked.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_oo_or_od_dr_dy.ty,
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty,
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty,
	  examples/lissom_oo_or_rg.ty,
	  examples/lissom_oo_or_species.ty,
	  examples/lissom_oo_or_species_tracked.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  topo/__init__.py,
	  topo/base/functionfamilies.py,
	  topo/learningfns/som.py,
	  topo/outputfn,
	  topo/outputfn/__init__.py,
	  topo/outputfn/basic.py,
	  topo/outputfn/optimized.py,
	  topo/outputfn/projfns.py,
	  topo/outputfns/__init__.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/optimized.py,
	  topo/outputfns/projfns.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/projections/basic.py,
	  topo/sheets/lissom.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/testimage.py,
	  topo/tests/testoutputfnsbasic.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/__init__.py:
	  Renamed topo.outputfns to topo.outputfn

2008-08-20  ceball

	* [r8934] topo/base/cf.py:
	  Reverted CFSheet's precedence to its previous value.

	* [r8933] topo/tkgui/editortools.py:
	  Added default_sheet parameter to model editor.

	* [r8932] contrib:
	  Added svn:ignore to contrib/.

2008-08-19  gerasymo

	* [r8931] examples/lissom_oo_or_od_dr_dy_rg.ty:
	  Results of this file can be obtained from lissom.ty with
	  dims=['or','od','dr','dy','rg']

	* [r8930] examples/lissom_oo_or_od_dr_dy_rg.ty:
	  Right BoundingBox size: 0.27083 instead of 0.25.

2008-08-19  ceball

	* [r8929] topo/base/arrayutils.py,
	  topo/base/simulation.py,
	  topo/param/parameterized.py:
	  Simplified script_repr() function. Should be no visible change to
	  output.

	* [r8928] topo/base/arrayutils.py:
	  Added support for script_repr() of ufuncs. SF #2051244.

	* [r8927] topo/base/simulation.py,
	  topo/param/parameterized.py:
	  Extracted basic functionality of Parameterized's script_repr()
	  method into a function that can be called on any object. Added
	  support to script_repr() for recursing into tuples as well as
	  lists. Added script_repr_dict, allowing custom functions to be
	  installed to handle specific types. script_repr() appears to work
	  as before in other cases, but not extensively tested.

2008-08-19  gerasymo

	* [r8926] examples/lissom_oo_or_od_dr_dy.ty:
	  BoundingBox size set correctly. Default max_disparity increased
	  from 2 to 4.

	* [r8925] examples/lissom.ty:
	  No need for initial uniform weights, it was just for testing
	  reasons.

	* [r8924] examples/lissom.ty:
	  New comment line.

2008-08-19  ceball

	* [r8923] doc/Future_Work/current_text.php:
	  Downgraded priority of a task because it will probably have
	  little externally visible impact, and because I want to do it at
	  the same time as the other cf.py tasks.

	* [r8922] external,
	  external/numpy-1.0.2.tar.gz:
	  Removed numpy 1.0.2 and cleaned up svn:ignore list for external/.

2008-08-19  gerasymo

	* [r8921] examples/lissom_oo_or_od_dr.ty:
	  Results of this file can be obtained from
	  lissom_oo_or_od_dr_dy_sf_rg_cr.ty by setting
	  dims=['or','od','dr'].

	* [r8920] examples/lissom_oo_or_od_dr.ty:
	  BoundingBox size set correctly. Missing condition for natural
	  images added.

2008-08-19  ceball

	* [r8919] external/Makefile,
	  external/matplotlib-0.91.2.tar.gz,
	  external/matplotlib-0.91.4.tar.gz:
	  Upgraded to matplotlib 0.91.4.

2008-08-19  gerasymo

	* [r8918] examples/lissom_oo_or_rg.ty:
	  Right BoundingBox size: 0.27083 instead of 0.25.

	* [r8917] examples/lissom_oo_or_cr.ty:
	  Right BoundingBox size: 0.27083 instead of 0.25.

	* [r8916]
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty:
	  Retinotopy added: larger circles instead of gaussians. For image
	  simulations cache_image set to false to avoid memory error.

	* [r8915]
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty:
	  Different size of gaissians for SF added. Default disparity
	  increased from 2 to 4.

2008-08-18  ceball

	* [r8914] doc/buildbot/bbanalysis.py:
	  buildbot analysis: added handling of case where build exited
	  prematurely.

	* [r8913] doc/buildbot/bbanalysis.py:
	  Updated buildbot analysis after step was added to make
	  slow-tests.

	* [r8912] doc/Future_Work/current_text.php:
	  Removed a task: couldn't reproduce reported memory problem (as
	  documented in 'memory leak?' emails between CB and JAB).

	* [r8911] external/numpy.diff:
	  Updated patch for numpy 1.1.1.

	* [r8910] external/Makefile,
	  external/numpy-1.1.1.tar.gz:
	  Upgraded numpy to 1.1.1.

	* [r8909] Makefile:
	  Lowered precision required for matching slow-tests from 14 dp to
	  12 dp so that the results of lissom_oo_or_homoestatic*.ty on
	  Windows match those from linux. SF #2053544.

2008-08-18  gerasymo

	* [r8908]
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty:
	  Sizes of retina and LGNs parametrized according to SF: parameters
	  v1aff_radius, lgnaff_radius, sf_spacing added.

2008-08-18  ceball

	* [r8907] Makefile:
	  Updates to comments - no visible change.

2008-08-15  ceball

	* [r8906] doc/Future_Work/current_text.php:
	  Moved idle branch decision to 1.0.

	* [r8905] doc/Future_Work/current_text.php,
	  topo/base/simulation.py,
	  topo/param/__init__.py,
	  topo/param/parameterized.py:
	  InstanceMethodWrapper still required to pickle instance methods,
	  so deleted notes about removing it.

	* [r8904] doc/Future_Work/current_text.php:
	  Cleaned up task list. Moved some tasks to sf.net trackers.

2008-08-15  gerasymo

	* [r8903]
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty:
	  SF for the RG and CR cases incorporated.

	* [r8902]
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty:
	  Too deep indention corrected.

2008-08-15  jbednar

	* [r8901] doc/Future_Work/current_text.php:
	  Added rf_radius buffer cleanup task

2008-08-15  ceball

	* [r8900] doc/Downloads/cvs_text.php,
	  doc/Downloads/index_text.php:
	  Updated OS X instructions.

2008-08-15  gerasymo

	* [r8899]
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty:
	  Bounding boxes' size corrected and parametrized. SF for cases of
	  natural images without color added.

2008-08-14  ceball

	* [r8898] topo/base/simulation.py:
	  Altered quotation marks in CommandEvent's script_repr() as
	  suggested by JAB. Fixes SF #2051251.

	* [r8897] topo/base/simulation.py:
	  Minor correction to documentation.

2008-08-14  jbednar

	* [r8896] topo/base/projection.py:
	  Fixed outdated docs

2008-08-14  ceball

	* [r8895]
	  topo/tests/lissom_oo_or_homeostatic.ty_DATA,
	  topo/tests/lissom_oo_or_homeostatic_tracked.ty_DATA:
	  Corrected svn:mime-type properties.

	* [r8894] examples/lissom_oo_or_dy_photo.ty:
	  Removed mistaken note.

	* [r8893] examples/lissom_oo_or_dy_photo.ty,
	  topo/patterns/image.py:
	  Made lissom_oo_or_dy_photo run without crashing.

	* [r8892]
	  topo/tests/lissom_oo_or_homeostatic.ty_DATA,
	  topo/tests/lissom_oo_or_homeostatic_tracked.ty_DATA:
	  Checked in data from r8891.

2008-08-13  ceball

	* [r8891] topo/misc/commandline.py:
	  Removed psyco option (users can still enable psyco in their
	  .topographicarc files).

	* [r8890] topo/outputfns/basic.py:
	  Removed hacks from OutputFnWithRandomState classes; results of
	  simulations using these functions will now change because of
	  having different streams of random numbers.

	* [r8889] topo/outputfns/basic.py,
	  topo/tests/testoutputfnsbasic.py:
	  Created OutputFnWithRandomState, which allows output functions to
	  have a random number generator, and to save and restore its
	  state. Made PoissonSample and HomeostaticMaxEnt inherit from
	  OutputFnWithRandomState. For now, results of simulations using
	  these two output functions will not have changed (because of a
	  temporary hack; lissom_oo_or_homeostatic.ty checked).

2008-08-13  judelaw

	* [r8888]
	  topo/tests/testtkparameterizedobject.py:
	  Added call to update() (required for tkinter on os x when there's
	  no mainloop(); SF.net #2027001).

2008-08-13  ceball

	* [r8887] examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_homeostatic_tracked.ty,
	  topo/outputfns/basic.py:
	  Homeostatic output function no longer uses global numpy.random
	  RandomState - instead, it temporarily uses topo.patterns.random's
	  (so results of simulations depending on it have not changed).

	* [r8886] examples/lissom_oo_or_dy_photo.ty:
	  Added note that this example will be using different random
	  numbers.

	* [r8885] examples/lissom_or_sf.ty:
	  Made lissom_or_sf have same results after no longer using
	  numpy.random's global RandomState.

	* [r8884] examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/cfsom_or.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lesi.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_cr.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_oo_or_od_dr.ty,
	  examples/lissom_oo_or_od_dr_dy.ty,
	  examples/lissom_oo_or_od_dr_dy_rg.ty,
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty,
	  examples/lissom_oo_or_rg.ty,
	  examples/lissom_oo_or_species.ty,
	  examples/lissom_oo_or_species_tracked.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  topo/patterns/random.py:
	  patterns.random.RandomGenerator now has a
	  numpy.random.RandomState instance, rather than relying on
	  numpy.random's global RandomState instance. Examples where the
	  results change - or might have changed - have not yet been
	  altered (i.e. currently they have or are likely to have different
	  results because of different streams of random numbers).

2008-08-13  gerasymo

	* [r8883]
	  examples/lissom_oo_or_od_dr_dy_sf_rg_cr.ty:
	  File for merging SF with existing dimensions created, just copied
	  from lissom_oo_or_od_dr_dy_rg_cr.ty with new doc comment.

	* [r8882]
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty:
	  CR merged with OR/OD/DR/DY/RG.

2008-08-12  gerasymo

	* [r8881] images/colormap/rgb,
	  images/colormap/rgb/01_0.pgm,
	  images/colormap/rgb/01_1.pgm,
	  images/colormap/rgb/01_2.pgm,
	  images/colormap/rgb/02_0.pgm,
	  images/colormap/rgb/02_1.pgm,
	  images/colormap/rgb/02_2.pgm,
	  images/colormap/rgb/03_0.pgm,
	  images/colormap/rgb/03_1.pgm,
	  images/colormap/rgb/03_2.pgm,
	  images/colormap/rgb/04_0.pgm,
	  images/colormap/rgb/04_1.pgm,
	  images/colormap/rgb/04_2.pgm,
	  images/colormap/rgb/05_0.pgm,
	  images/colormap/rgb/05_1.pgm,
	  images/colormap/rgb/05_2.pgm,
	  images/colormap/rgb/06_0.pgm,
	  images/colormap/rgb/06_1.pgm,
	  images/colormap/rgb/06_2.pgm,
	  images/colormap/rgb/07_0.pgm,
	  images/colormap/rgb/07_1.pgm,
	  images/colormap/rgb/07_2.pgm,
	  images/colormap/rgb/08_0.pgm,
	  images/colormap/rgb/08_1.pgm,
	  images/colormap/rgb/08_2.pgm,
	  images/colormap/rgb/09_0.pgm,
	  images/colormap/rgb/09_1.pgm,
	  images/colormap/rgb/09_2.pgm,
	  images/colormap/rgb/10_0.pgm,
	  images/colormap/rgb/10_1.pgm,
	  images/colormap/rgb/10_2.pgm,
	  images/colormap/rgb/11_0.pgm,
	  images/colormap/rgb/11_1.pgm,
	  images/colormap/rgb/11_2.pgm,
	  images/colormap/rgb/12_0.pgm,
	  images/colormap/rgb/12_1.pgm,
	  images/colormap/rgb/12_2.pgm,
	  images/colormap/rgb/13_0.pgm,
	  images/colormap/rgb/13_1.pgm,
	  images/colormap/rgb/13_2.pgm,
	  images/colormap/rgb/14_0.pgm,
	  images/colormap/rgb/14_1.pgm,
	  images/colormap/rgb/14_2.pgm,
	  images/colormap/rgb/15_0.pgm,
	  images/colormap/rgb/15_1.pgm,
	  images/colormap/rgb/15_2.pgm,
	  images/colormap/rgb/16_0.pgm,
	  images/colormap/rgb/16_1.pgm,
	  images/colormap/rgb/16_2.pgm,
	  images/colormap/rgb/17_0.pgm,
	  images/colormap/rgb/17_1.pgm,
	  images/colormap/rgb/17_2.pgm,
	  images/colormap/rgb/18_0.pgm,
	  images/colormap/rgb/18_1.pgm,
	  images/colormap/rgb/18_2.pgm,
	  images/colormap/rgb/19_0.pgm,
	  images/colormap/rgb/19_1.pgm,
	  images/colormap/rgb/19_2.pgm,
	  images/colormap/rgb/20_0.pgm,
	  images/colormap/rgb/20_1.pgm,
	  images/colormap/rgb/20_2.pgm,
	  images/colormap/rgb/21_0.pgm,
	  images/colormap/rgb/21_1.pgm,
	  images/colormap/rgb/21_2.pgm,
	  images/colormap/rgb/22_0.pgm,
	  images/colormap/rgb/22_1.pgm,
	  images/colormap/rgb/22_2.pgm,
	  images/colormap/rgb/23_0.pgm,
	  images/colormap/rgb/23_1.pgm,
	  images/colormap/rgb/23_2.pgm,
	  images/colormap/rgb/24_0.pgm,
	  images/colormap/rgb/24_1.pgm,
	  images/colormap/rgb/24_2.pgm,
	  images/colormap/rgb/25_0.pgm,
	  images/colormap/rgb/25_1.pgm,
	  images/colormap/rgb/25_2.pgm:
	  Images for CR model.

	* [r8880] examples/lissom_oo_or_cr.ty:
	  Another image set is used.

2008-08-12  ceball

	* [r8879] topo/plotting/plotgroup.py:
	  Renamed TwoDThingPlotGroup to GridPlotGroup.

2008-08-12  jbednar

	* [r8878] doc/Future_Work/current_text.php:
	  Formatted alert list for HTML. Updated priorities for the coming
	  release, and removed some completed tasks

2008-08-12  gerasymo

	* [r8877]
	  examples/lissom_oo_or_od_dr_dy_rg_cr.ty:
	  File for merging CR with existing maps created, just copied from
	  lissom_oo_or_od_dr_dy_rg.ty.

	* [r8876] topo/misc/numbergenerators.py:
	  For BinaryOperator global name error corrected.

	* [r8875] examples/lissom_oo_or_od_dr_dy_rg.ty:
	  Code for creating color map with gaussians added.

2008-08-11  jbednar

	* [r8874] topo/misc/numbergenerators.py:
	  Added optional argument processing to BinaryOperator for symmetry

	* [r8873] topo/misc/numbergenerators.py:
	  Added docstring

	* [r8872] topo/base/cf.py:
	  Boosted precedence of CFSheet to make it the default in the model
	  editor

2008-08-11  gerasymo

	* [r8871] topo/misc/numbergenerators.py:
	  class UnaryOperator extended to be able to handle functions with
	  several parameters.

	* [r8870] topo/commands/analysis.py:
	  Different settings for overlaid plot of OR and Hue.

	* [r8869] topo/commands/pylabplots.py:
	  Parameter normalize added to overlaid_plots() to control
	  normalization.

2008-08-07  ceball

	* [r8868] external/Makefile,
	  external/odict.py:
	  odict: an ordered dictionary, from
	  http://pypi.python.org/pypi/Ordered Dictionary/ (note that it
	  seems like an ordered dictionary will be in Python 2.6).

	* [r8867] doc/Future_Work/current_text.php:
	  Added note to myself.

	* [r8866] topo/tkgui/editortools.py:
	  Model editor: sort sheets and projections by preference (sf.net
	  #1951493).

	* [r8865] topo/base/cf.py,
	  topo/base/projection.py,
	  topo/projections/basic.py:
	  Added precedence to Projections.

2008-08-07  gerasymo

	* [r8864] examples/lissom_oo_or_od_dr_dy_rg.ty:
	  Lateral excitatory learning rate changed according to ids
	  parameter.

	* [r8863] examples/lissom_oo_or_rg.ty:
	  Lateral excitatory learning rates changed also according to ids
	  parameter (average number of activation blobs in V1).

2008-08-06  ceball

	* [r8862] topo/base/parameterclasses.py:
	  Added warning to parameterclasses.

	* [r8861] topo/base/simulation.py:
	  Added some documentation.

	* [r8860] topo/base/simulation.py:
	  Updated documentation of OptionalSingleton (no visible change).

	* [r8859]
	  topo/tests/reference/common_control.py:
	  Added comment.

	* [r8858] topo/tests/test_script.py:
	  Changed combinations of densities for reference testing.

	* [r8857] doc/Future_Work/current_text.php:
	  Minor changes.

2008-08-04  ceball

	* [r8856] /trunk/topographica-win/msys,
	  /trunk/topographica-win/msys/MinGW.7z,
	  /trunk/topographica-win/msys/README.txt,
	  /trunk/topographica-win/msys/msys.7z:
	  Added MSYS 1.0.11 and MingGW 5.1.4, which should give an
	  environment suitable for building topographica on Windows.

2008-08-04  gerasymo

	* [r8855]
	  topo/commands/dr_key_white_vert_small.png:
	  Image of direction arrows flipped around according to the
	  previous change.

	* [r8854] topo/commands/pylabplots.py:
	  Signs of arrow's coordinates in the overlaid OR/DR changed,
	  because image is with lower origin (flipped around), so arrows
	  must also be flipped around.

	* [r8853] examples/lissom_oo_or_od_dr_dy_rg.ty:
	  Display the simulation name according to dims added.

	* [r8852] topo/commands/analysis.py:
	  For phase disparity, measurement made possible with other
	  dimensions (case when number of input sheets > 2). For ocularity
	  measurement, just trivial changes.

	* [r8851] examples/lissom_oo_or_od_dr_dy_rg.ty:
	  Default dimensions changed, RG excluded because computationally
	  intensive.

2008-08-02  ceball

	* [r8850] external/Makefile,
	  external/psyco-dist-svn42201.tar.gz,
	  external/psyco-dist-svn52800.tar.gz,
	  external/psyco-dist-svn56930.tar.gz:
	  Updated to psyco svn 56930.

2008-08-01  ceball

	* [r8849] doc/buildbot/master.cfg:
	  buildbot: added buildslave Heavy (msys on Windows); added OS X
	  aqua Tkinter patch. Changes have been live on buildbot for some
	  time.

	* [r8848] Makefile,
	  win_build_exe.py:
	  Added beginnings of automatic exe creation.

2008-08-01  gerasymo

	* [r8847] topo/commands/analysis.py:
	  For the case that input sheets don't start with defining strings
	  (e.g. Left-, Right-, Red- or Green-), search for a substring will
	  be done in the name.

2008-08-01  antolikjan

	* [r8846] contrib/jacommands.py:
	  minor parameter changes in AddV2 and AddGC

	* [r8845]
	  examples/gc_lissom_oo_or_homeostatic_new.ty:
	  minor parameter changes

2008-08-01  gerasymo

	* [r8844] examples/lissom_oo_or_od_dr_dy_rg.ty:
	  File tested. With dataset Gaussians results are identical to
	  previous lissom_oo_or_od_dr_dy.ty in all dims combinations
	  (provided initial uniform distribution od weights), because input
	  for both (red and green) retinas are identical gaussians. With
	  dataset Nature in OR/RG mode results are identical to basic color
	  model of lissom_oo_or_rg.ty (again if initial weights set to
	  uniform).

2008-07-31  gerasymo

	* [r8843] examples/lissom_oo_or_od_dr_dy_rg.ty:
	  Red and green retinas added with necessary LGNs. Both retinas
	  receive identical input, so results of the file working with
	  gaussians and dims=['or'] and dims=['or', 'rg'] are both
	  identical to simple OR model (if initial weights are uniformly
	  distributed). Work in progress.

	* [r8842] examples/lissom_oo_or_od_dr_dy_rg.ty:
	  Loops for potential different cone types and different LGN
	  opponent types added. But their lists are still empty, that's why
	  results still identical to lisssom_oo_or_od_dr_dy.ty. Work in
	  progress.

	* [r8841] examples/lissom_oo_or_od_dr_dy_rg.ty:
	  Merging OR/OD/DR/DY with RG basic color model. Initially, file
	  copied from lissom_oo_or_od_dr_dy.ty and only LGN DoG were
	  separated. So, results still identical to the source file.

	* [r8840] examples/lissom_oo_or_od_dr_dy.ty:
	  Missing condition for learning rate definition added.

2008-07-30  antolikjan

	* [r8839]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  minor parameter changes

2008-07-30  gerasymo

	* [r8838] examples/lissom_oo_or_cr.ty:
	  Blue retina connected to LGNs, LGNs to V1, so all necessary
	  connections for a complete color model are there. Work in
	  progress.

	* [r8837] examples/lissom_oo_or_cr.ty:
	  Blue retina created, but not yet connected to any LGN, so resuts
	  still identical to lissom_oo_or_rg model.

	* [r8836] examples/lissom_oo_or_rg.ty:
	  This file contains a basic red-green model. The
	  lissom_oo_or_cr.ty will be extended beyond that to include also
	  bue color.

2008-07-29  antolikjan

	* [r8835] contrib/jacommands.py:
	  Modified the homeostatic_analysis_function() to count in the new
	  ActivityHysteresis function

	* [r8834]
	  examples/gc_lissom_oo_or_homeostatic_new.ty:
	  Added ActivityHomeostasis

	* [r8833]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  minor parameter changes

2008-07-28  antolikjan

	* [r8832] topo/patterns/basic.py:
	  Removed Translator class

	* [r8831]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  Made the simulation to use ActivityHysteresis output function and
	  some minor parameter changes

	* [r8830] topo/tkgui/testpattern.py:
	  Deleted code related to now removed support for continuous
	  activity in ProjectionSheet

	* [r8829] topo/commands/analysis.py:
	  Deleted the code related to now removed support for continuos
	  activity in ProjectionSheet

	* [r8828] topo/base/projection.py:
	  Removed the part of code from ProjectionSheet that was allowing
	  to have continuouse activity in sheets - it has been now replaced
	  with a new output function ActivityHysteresis which is for now
	  only in contrib.jacommands

	* [r8827] contrib/jacommands.py:
	  Added ActivityHysteresis as a new output_fn and moved Translator
	  pattern generator to this file from topo

2008-07-23  ceball

	* [r8826] external/Makefile_win_msys.diff:
	  Windows/MSys build: more path fixes.

	* [r8825] external/Makefile_win_msys.diff:
	  Corrected typo.

	* [r8824] external/Makefile_win_msys.diff:
	  Another attempt to fix the paths for msys build.

	* [r8823] external/Makefile_win_msys.diff:
	  Corrected whitespace error.

	* [r8822] external/Makefile_win_msys.diff:
	  Fixed paths that were mistakenly swapped around.

	* [r8821] Makefile,
	  external/msys_path.py:
	  Updated win-msys-patch to allow topographica directory to be
	  anywhere.

	* [r8820] external/Makefile_win_msys.diff:
	  Updated windows msys patch to allow the Topographica directory to
	  be anywhere.

	* [r8819] external/Makefile:
	  Reverted Makefile to previous version (changes committed by
	  mistake).

	* [r8818] topo/plotting/bitmap.py:
	  Temporarily commented out title font code in bitmap (while
	  testing buildbot on Windows).

2008-07-22  ceball

	* [r8817] doc/buildbot/master.cfg:
	  Added pyc-clean to slow-tests. Reduced frequency of lodestar
	  tests (although going to move to another machine eventually).
	  These changes have been in effect on buildbot for a while
	  already.

	* [r8816] Makefile:
	  Don't use 'time' on msys, but restore for other platforms.

	* [r8815] Makefile:
	  Msys: updated patch (work in progress).

	* [r8814] external/win32_static.tar.gz:
	  From matplotlib's sf.net site.

	* [r8813] Makefile,
	  external/Makefile,
	  external/Makefile_win_msys.diff:
	  Building Topographica on Windows using msys; work in progress.

	* [r8812] topo/plotting/bitmap.py:
	  Added ERRORALERT.

2008-07-20  ceball

	* [r8811] topo/tkgui/templateplotgrouppanel.py:
	  Added missing import.

2008-07-18  ceball

	* [r8810] contrib/ae.py:
	  Moved TAE measurement into a function. Added DAE measurement
	  (total hack, unlikely to be correct).

	* [r8809] contrib/ae.py:
	  Initial version. Original script by rczhao, cleanup by JAB
	  (emailed 2007-11-15), minor updates by CB. (Intention is to
	  generalize this code and put it in topo.)

	* [r8808] topo/base/parameterclasses.py:
	  Minor simplification.

	* [r8807] topo/misc/legacy.py:
	  Restored handling of DynamicNumber in old snapshots (had been
	  temporarily commented out while parameterclasses was removed).

	* [r8806] topo/base/parameterclasses.py:
	  Restored topo.base.parameterclasses while contrib/ and possibly
	  other user code depends on it. (The legacy support installed to
	  replace it is only applied for snapshots by default.)

	* [r8805] examples/saccade_demo.ty:
	  Updated import statement.

	* [r8804] examples/lesi.ty:
	  Removed unused import.

	* [r8803] topo/base/__init__.py,
	  topo/tkgui/editortools.py:
	  Fixed import errors.

	* [r8802] topo/commands/analysis.py:
	  Changed Parameter to param.Parameter (Parameter is no longer
	  imported in this file).

	* [r8801] topo/patterns/teststimuli.py:
	  Changed Number to param.Number (Number is no longer imported in
	  this file).

	* [r8800] topo/base/parameterclasses.py,
	  topo/misc/legacy.py:
	  Added legacy support for topo.base.parameterized,
	  topo.base.parameterizedobject, and topo.base.parameterclasses.
	  Removed topo.base.parameterclasses.

2008-07-18  judelaw

	* [r8799]
	  examples/lissom_oo_or_species_tracked.ty:
	  lissom_oo_or_homeostatic.ty which can be tuned to various species
	  and tracked during development

	* [r8798] examples/lesi.ty:
	  added work in progress, laminar_oo_or.ty combined with
	  lissom_oo_or_homeostatic.ty

	* [r8797] topo/commands/analysis.py:
	  added retinotopy measurement and orientation contrast measurement

	* [r8796] topo/commands/pylabplots.py:
	  added matrixplot_hsv which plots values in range 0-1 in colour
	  rather than greyscale

	* [r8795] topo/patterns/teststimuli.py:
	  added SineGratingRectangle for retinotopy measurement and added
	  control over contrast in OrientationContrastPattern (i.e. scale
	  and contrast)

	* [r8794] topo/analysis/featureresponses.py:
	  added norm factor in FeatureMaps for special case of measuring
	  retinotopy which is the number of squares the retina is divided
	  into

	* [r8793] contrib/jsldefs.py:
	  added analysis functions for lesi.ty and
	  lissom_oo_or_specise_tracked.ty, added function for plotting
	  out-connections from lgn to v1

2008-07-17  ceball

	* [r8792] topo/base/parameterclasses.py:
	  Restored mistakenly removed, transitional imports in
	  topo.base.parameterclasses. (Users will likely have code that
	  depends on these imports. The file will eventually be deleted.)

	* [r8791] topo/params:
	  Removed topo/params (git-svn dcommit appears not to have
	  succeeded in removing it).

	* [r8790] topo/param:
	  Files to ignore.

	* [r8789] contrib/jacommands.py,
	  contrib/jsldefs.py,
	  examples/sullivan_neurocomputing04.ty,
	  topo/tests/testcfsom.py,
	  topo/tests/testparameterizedobject.py,
	  topo/tests/testtkparameterizedobject.py:
	  Continued moving to topo.params. 'make tests' and 'make
	  slow-tests' now pass. Still more tidying up to go (docs, removing
	  leftover files).

	* [r8788]
	  topo/tests/testCompositeParameter.txt,
	  topo/tests/testDynamicParameter.txt,
	  topo/tests/testEnumerationParameter.txt,
	  topo/tests/testNumberParameter.txt:
	  Fixed params imports in doctests (move to topo.param; tests still
	  fail).

	* [r8787] topo/sheets/saccade.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py:
	  Fixed params.tk imports (move to topo.param; tests still fail).

	* [r8786] examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/cfsom_or.ty,
	  examples/goodhill_network90.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/tiny.ty,
	  topo/commands/analysis.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testparameterizedobject.py:
	  Continued cleaning up imports (move to topo.param); tests still
	  fail. (Imports in examples/ really need sorting out...)

	* [r8785] topo/analysis/featureresponses.py,
	  topo/misc/legacy.py,
	  topo/patterns/basic.py,
	  topo/patterns/teststimuli.py,
	  topo/plotting/plotfilesaver.py,
	  topo/sheets/optimized.py,
	  topo/sheets/saccade.py,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/testCompositeParameter.txt,
	  topo/tests/testCompositePatternGenerators.txt,
	  topo/tests/testDynamicParameter.txt,
	  topo/tests/testEnumerationParameter.txt,
	  topo/tests/testNumberParameter.txt,
	  topo/tkgui/editorobjects.py:
	  Continued cleaning up imports (move to topo.param); tests still
	  fail.

	* [r8784] examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  topo/analysis/featureresponses.py,
	  topo/commands/analysis.py,
	  topo/coordmapperfns/basic.py,
	  topo/misc/filepaths.py,
	  topo/misc/traces.py,
	  topo/outputfns/basic.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/sheets/lissom.py,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/testDynamicParameter.txt,
	  topo/tests/testcfsom.py,
	  topo/tests/testparameterizedobject.py,
	  topo/tests/testparametersframe.py,
	  topo/tests/testsheetview.py,
	  topo/tests/testtkparameterizedobject.py:
	  Replaced Parameter with param.Parameter (continuing partial
	  checkin; tests still fail).

	* [r8783] topo/__init__.py,
	  topo/analysis/featureresponses.py,
	  topo/analysis/vision.py,
	  topo/base/cf.py,
	  topo/base/parameterclasses.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheetcoords.py,
	  topo/commands/analysis.py,
	  topo/commands/basic.py,
	  topo/commands/pylabplots.py,
	  topo/coordmapperfns/basic.py,
	  topo/eps/basic.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py,
	  topo/learningfns/projfns.py,
	  topo/learningfns/som.py,
	  topo/misc/distribution.py,
	  topo/misc/filepaths.py,
	  topo/misc/robotics.py,
	  topo/misc/traces.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/optimized.py,
	  topo/patterns/audio.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/patterns/rds.py,
	  topo/patterns/teststimuli.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/projections/basic.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/composer.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py,
	  topo/sheets/optimized.py,
	  topo/sheets/saccade.py,
	  topo/sheets/slissom.py,
	  topo/tests/gui_tests.py,
	  topo/tests/sheetmask_setup.py,
	  topo/tests/test_map_measurement.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testparameterizedobject.py,
	  topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py:
	  Continuing move to topo.param: cleaned up import statements
	  (many, but not all).

	* [r8782] topo/base/parameterclasses.py,
	  topo/plotting/bitmap.py:
	  Replaced NumericTuple with param.NumericTuple (continuing partial
	  checkin; tests still fail).

	* [r8781] examples/goodhill_network90.ty,
	  examples/lissom_whisker_barrels.ty,
	  topo/misc/traces.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/patterns/rds.py,
	  topo/plotting/bitmap.py,
	  topo/sheets/lissom.py,
	  topo/tkgui/projectionpanel.py:
	  Replaced Integer and Magnitude with param.Integer and
	  param.Magnitude, respectively (continuing partial checkin; tests
	  still fail).

	* [r8780] doc/Future_Work/current_text.php,
	  examples/lissom_oo_or_dy_photo.ty,
	  topo/base/parameterclasses.py,
	  topo/coordmapperfns/basic.py,
	  topo/patterns/image.py,
	  topo/plotting/palette.py,
	  topo/tests/testDynamicParameter.txt,
	  topo/tests/testEnumerationParameter.txt,
	  topo/tests/testparameterizedobject.py,
	  topo/tkgui/editorobjects.py:
	  Replaced Enumeration and Dynamic with param.Enumeration and
	  param.Dynamic, respectively (continuing partial checkin; tests
	  still fail).

	* [r8779] topo/commands/analysis.py,
	  topo/coordmapperfns/basic.py,
	  topo/misc/robotics.py,
	  topo/misc/traces.py,
	  topo/outputfns/basic.py,
	  topo/patterns/basic.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/plotgroup.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/slissom.py:
	  Replaced List/DictParameter with param.List/Dict (continuing
	  partial checkin; tests still fail).

	* [r8778] examples/joublin_bc96.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  topo/learningfns/optimized.py,
	  topo/learningfns/projfns.py,
	  topo/learningfns/som.py,
	  topo/misc/robotics.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/optimized.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/plotting/plotgroup.py,
	  topo/projections/basic.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py,
	  topo/sheets/saccade.py,
	  topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/testpattern.py:
	  Replaced Class/ObjectSelectorParameter with
	  param.Class/ObjectSelector (continuing partial checkin; tests
	  still fail).

	* [r8777] topo/misc/traces.py,
	  topo/plotting/bitmap.py,
	  topo/tests/testCompositeParameter.txt:
	  Replaced CompositeParameter with param.Composite (continuing
	  partial checkin; tests still fail).

	* [r8776] topo/sheets/saccade.py:
	  Replaced CallableParameter with param.Callable (continuing
	  partial checkin; tests still fail).

	* [r8775] examples/lissom_whisker_barrels.ty,
	  topo/commands/analysis.py,
	  topo/coordmapperfns/basic.py,
	  topo/learningfns/projfns.py,
	  topo/misc/robotics.py,
	  topo/misc/traces.py,
	  topo/outputfns/basic.py,
	  topo/patterns/image.py,
	  topo/plotting/plotgroup.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py,
	  topo/sheets/saccade.py,
	  topo/sheets/slissom.py,
	  topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Replaced BooleanParameter with param.Boolean (continuing partial
	  checkin; tests still fail).

	* [r8774] topo/misc/traces.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py:
	  Replaced StringParameter with param.String (continuing partial
	  checkin; tests still fail).

	* [r8773] doc/Future_Work/current_text.php,
	  examples/goodhill_network90.ty,
	  examples/joublin_bc96.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/tiny.ty,
	  topo/analysis/featureresponses.py,
	  topo/coordmapperfns/basic.py,
	  topo/eps/basic.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py,
	  topo/learningfns/projfns.py,
	  topo/learningfns/som.py,
	  topo/misc/robotics.py,
	  topo/misc/traces.py,
	  topo/outputfns/basic.py,
	  topo/param/tk.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/patterns/rds.py,
	  topo/patterns/teststimuli.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/projections/basic.py,
	  topo/responsefns/projfns.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py,
	  topo/sheets/saccade.py,
	  topo/sheets/slissom.py,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/testCompositeParameter.txt,
	  topo/tests/testNumberParameter.txt,
	  topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/testpattern.py:
	  Replaced Number with param.Number (incomplete checkin; make tests
	  fails).

	* [r8772] examples/joublin_bc96.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  topo/analysis/featureresponses.py,
	  topo/base/__init__.py,
	  topo/base/boundingregion.py,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/parameterclasses.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/base/sheetview.py,
	  topo/base/simulation.py,
	  topo/commands/analysis.py,
	  topo/commands/basic.py,
	  topo/coordmapperfns/basic.py,
	  topo/misc/filepaths.py,
	  topo/misc/legacy.py,
	  topo/misc/numbergenerators.py,
	  topo/misc/traces.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/optimized.py,
	  topo/param,
	  topo/param/__init__.py,
	  topo/param/parameterized.py,
	  topo/param/tk.py,
	  topo/params/__init__.py,
	  topo/params/parameterized.py,
	  topo/params/tk.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/patterns/rds.py,
	  topo/patterns/teststimuli.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/sheets/lissom.py,
	  topo/sheets/optimized.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/testCompositeParameter.txt,
	  topo/tests/testDynamicParameter.txt,
	  topo/tests/testEnumerationParameter.txt,
	  topo/tests/testNumberParameter.txt,
	  topo/tests/testParamOverrides.txt,
	  topo/tests/testcfsom.py,
	  topo/tests/testparameterizedobject.py,
	  topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/widgets.py:
	  Moved topo.params to topo.param.

	* [r8771] topo/base/boundingregion.py,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/base/sheetview.py,
	  topo/base/simulation.py:
	  Continued moving to topo.params (in topo.base); going to rename
	  'topo.params' to 'topo.param'.

	* [r8770] external/Makefile:
	  Added --prefix option to all 'setup.py install' commands,
	  allowing us to control installation location even when not using
	  our own Python (e.g. on Windows).

2008-07-15  ceball

	* [r8769] topo/base/functionfamilies.py,
	  topo/base/sheet.py,
	  topo/base/simulation.py,
	  topo/outputfns/basic.py,
	  topo/params/__init__.py,
	  topo/params/parameterized.py,
	  topo/tests/testparameterizedobject.py:
	  Moved state_push() and _pop() up from EventProcessor to
	  Parameterized; Parameterized instances now save the state of
	  dynamic values. Addresses SF #2014250.

	* [r8768] doc/Future_Work/current_text.php:
	  Added task.

2008-07-14  ceball

	* [r8767] topo/base/cf.py:
	  Removed duplicate import.

	* [r8766] topo/base/parameterizedobject.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Continued move to topo.params.

	* [r8765] topo/base/boundingregion.py,
	  topo/base/cf.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheetview.py,
	  topo/base/simulation.py,
	  topo/commands/basic.py,
	  topo/coordmapperfns/basic.py,
	  topo/misc/filepaths.py,
	  topo/misc/legacy.py,
	  topo/params/__init__.py,
	  topo/patterns/random.py,
	  topo/patterns/rds.py,
	  topo/patterns/teststimuli.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/testCompositeParameter.txt,
	  topo/tests/testDynamicParameter.txt,
	  topo/tests/testEnumerationParameter.txt,
	  topo/tests/testNumberParameter.txt,
	  topo/tests/testParamOverrides.txt,
	  topo/tests/testcfsom.py,
	  topo/tests/testparameterizedobject.py,
	  topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py:
	  Continued move to topo.params.

	* [r8764] doc/Developer_Manual/gui_text.php,
	  doc/FAQ/index_text.php,
	  doc/Future_Work/current_text.php,
	  doc/Team_Members/index_text.php,
	  doc/User_Manual/commandline_text.php,
	  doc/User_Manual/overview_text.php,
	  doc/User_Manual/parameters_text.php,
	  examples/joublin_bc96.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  topo/analysis/featureresponses.py,
	  topo/base/boundingregion.py,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/parameterclasses.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheetview.py,
	  topo/base/simulation.py,
	  topo/commands/analysis.py,
	  topo/commands/basic.py,
	  topo/misc/filepaths.py,
	  topo/misc/traces.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/optimized.py,
	  topo/params/__init__.py,
	  topo/params/tk.py,
	  topo/patterns/image.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/sheets/lissom.py,
	  topo/sheets/optimized.py,
	  topo/tests/reference/fixed_params/lissom_oo_or_reference_fixed.ty,
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/testparameterizedobject.py,
	  topo/tests/testparametersframe.py,
	  topo/tests/testplot.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py:
	  Began replacing calls to contents of
	  topo.base.parameterizedobject with ones to topo.params.

	* [r8763] doc/News:
	  Added ignore list.

	* [r8762] doc/Downloads:
	  Updated ignore list.

	* [r8761] external:
	  Updated svn:ignore.

	* [r8760] external:
	  Removed misnamed property.

2008-07-14  jbednar

	* [r8759] topo/misc/commandline.py,
	  topo/tkgui/topoconsole.py:
	  Moved stty workarounds to the same place and simplified them;
	  still not very clean

2008-07-14  ceball

	* [r8758] topo/tkgui/__init__.py:
	  Added apparently required import statement.

	* [r8757] external/Makefile_OSX_tk.diff:
	  Simplified after changes to Makefile.

	* [r8756] external/Makefile:
	  Removed unnecessary dependencies.

	* [r8755] external/Makefile:
	  Updated targets (missed from previous checkin).

	* [r8754] external/Makefile,
	  external/tklib-CVS20080114.tar.gz,
	  external/tooltip-1.4.tar.gz:
	  Made snit and tooltip installation procedures more compatible
	  with OS X. Removed tklib, just keeping tooltip module (this
	  tooltip is from tklib CVS, 2008/01/14).

	* [r8753] external/Makefile:
	  Removed superfluous target from default.

	* [r8752] external/Makefile,
	  external/snit-2.2.1.tar.gz,
	  external/snit1.0.tar.gz:
	  Upgraded snit to new version designed for Tk 8.5; should be no
	  visible change except performance. This version of snit comes
	  from tcllib-1.10.

2008-07-13  ceball

	* [r8751] external/Python_OSX_tk.diff:
	  Patch was missing file's location.

	* [r8750] Makefile:
	  Fixed typo from previous checkin.

	* [r8749] Makefile,
	  external/Makefile_OSX_tk.diff,
	  external/Python_OSX_tk.diff,
	  topo/tkgui/__init__.py:
	  Added (untested) patch to allow OS X to work with tcl/tk from
	  /Library/Frameworks.

	* [r8748] doc/Downloads/cygwin_text.php:
	  Added up-to-date story about building on Cygwin (and moved
	  previous one down the page; diffs don't really make sense now).

2008-07-10  ceball

	* [r8747] topo/projections/__init__.py,
	  topo/projections/basic.py:
	  Made basic Projection classes available from topo.projections.

	* [r8746] topo/learningfns/__init__.py,
	  topo/learningfns/basic.py:
	  Made basic LearningFn classes available from topo.learningfns.

	* [r8745] topo/responsefns/__init__.py,
	  topo/responsefns/basic.py:
	  Made basic ResponseFn classes available from topo.responsefns.

	* [r8744] topo/coordmapperfns/__init__.py,
	  topo/coordmapperfns/basic.py:
	  Made basic CoordinateMapperFn classes available from
	  topo.coordmapperfns.

2008-07-09  ceball

	* [r8743] topo/analysis/vision.py,
	  topo/commands/pylabplots.py,
	  topo/misc/commandline.py:
	  Made exception explicit so that other problems are not hidden
	  (e.g. I got this 'could not import matplotlib' warning, but I
	  found I could import matplotlib normally - topographica was
	  actually giving a hidden IOError).

	* [r8742] topo/misc/commandline.py:
	  Made hack prompt-printing hack for emacs only run when emacs is
	  detected.

2008-07-09  gerasymo

	* [r8741] examples/lissom_oo_or_od_dr_dy.ty:
	  Extended to be able to build DY maps for natural images.

2008-07-08  gerasymo

	* [r8740] topo/commands/analysis.py:
	  Command for creation of combined OR map with DY contours added.

	* [r8739] examples/lissom_oo_or_od_dr_dy.ty:
	  Unnecessary condition deleted. Some trivial changes made.

2008-07-07  gerasymo

	* [r8738] topo/commands/analysis.py:
	  Normalization set to true for measure_phasedisparity().

	* [r8737] examples/lissom_oo_or_od_dr_dy.ty:
	  OR/OD/DR extended to include disparity (DY). DY map possible
	  first only with gaussians. Work in process.

2008-07-03  antolikjan

	* [r8736] contrib/jacommands.py:
	  improved axis scaling for activity histograms

	* [r8735] contrib/jacommands.py:
	  

	* [r8734] contrib/jacommands.py:
	  A corrected minor bug

2008-07-02  antolikjan

	* [r8733] contrib/jacommands.py:
	  Rewritten the part of code for measuring histogram of activity

2008-07-01  antolikjan

	* [r8732] contrib/jacommands.py:
	  updated the histogram measuring tool

2008-07-01  ceball

	* [r8731] doc/Future_Work/current_text.php:
	  Added some tasks.

2008-06-30  antolikjan

	* [r8730]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  

	* [r8729]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  added external parametrization

	* [r8728] topo/analysis/vision.py:
	  In MR (modulation ratio) computing code I have added a line that
	  subtracts 'spontaneous' activity from the measured activity -
	  because that one is normally not taken into account

2008-06-27  jbednar

	* [r8727] topo/plotting/plot.py:
	  Fixed up docstring and added alert

2008-06-27  gerasymo

	* [r8726] topo/commands/analysis.py:
	  Subplotting of OR map activated.

	* [r8725] topo/commands/analysis.py:
	  Normalization set to true for hue map.

	* [r8724] topo/commands/analysis.py:
	  num_phase set to 12 and num_hue to 8.

	* [r8723] topo/commands/analysis.py:
	  Implementation of measure_hue_pref() without HSVBitmap class but
	  with the same results; no need for parameters scale and offset in
	  measure_hue_pref().

	* [r8722] topo/plotting/bitmap.py:
	  No need for rgb matrices to be class attributes, reverted back to
	  be just local variables.

	* [r8721] topo/commands/analysis.py:
	  Confidence:OrientationSelectivity added for overlaid plots.

2008-06-27  jbednar

	* [r8720] examples/obermayer_pnas90.ty:
	  Added alert

	* [r8719] examples/lissom_oo_or_species.ty:
	  Added command-line control over jitter_scale

	* [r8718] topo/patterns/teststimuli.py:
	  Removed unused import

2008-06-26  gerasymo

	* [r8717] topo/commands/pylabplots.py:
	  Edge color of arrows changed to white.

	* [r8716] topo/commands/analysis.py:
	  Update in measure_hue_pref(); now using scale of SineGrating
	  pattern.

	* [r8715] examples/lissom_oo_or_cr.ty:
	  No need to change the selectivity multiplier, since selectivity
	  map can also be normalized now.

	* [r8714] topo/plotting/plot.py:
	  Preference&Selectivity plot made affected by normalization (by
	  checking the normalization box on the Preference window).

	* [r8713] topo/commands/analysis.py:
	  New implementation of measure_hue_pref(); now it handles every
	  hue value from range (0.0,1.0).

	* [r8712] topo/plotting/bitmap.py:
	  In the class HSVBitmap three local variables converted to class
	  attributes, to be able to manipulate rgb channels.

2008-06-26  antolikjan

	* [r8711]
	  examples/gc_lissom_oo_or_homeostatic.ty:
	  

	* [r8710]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  minor changes to some parameters

2008-06-26  gerasymo

	* [r8709] examples/lissom_oo_or_cr.ty:
	  Selectivity multiplier set to lower value (4 instead of 17) to
	  better identify the unselective areas.

2008-06-25  antolikjan

	* [r8708]
	  examples/gc_lissom_oo_or_homeostatic_new.ty:
	  minnor upgrades

	* [r8707] contrib/jacommands.py:
	  added CascadeHomeostatic function

2008-06-25  gerasymo

	* [r8706] examples/lissom_oo_or_od_dr.ty:
	  Size of the presented photos changed.

	* [r8705] topo/commands/pylabplots.py:
	  Edgecolor of arrows set to black in overlaid OR/DR plots.

2008-06-24  jbednar

	* [r8704] topo/commands/analysis.py:
	  Removed bogus else clauses after exception raising

2008-06-24  gerasymo

	* [r8703] topo/commands/analysis.py:
	  Green contour to overlaid OR/CR plot added.

	* [r8702] topo/commands/analysis.py:
	  Right color coding for hue map. Command for creating OR map
	  overlaid with hue preference created.

	* [r8701] examples/lissom_oo_or_cr.ty:
	  Different size of presented photos (size=10).

2008-06-23  jbednar

	* [r8700] topo/commands/analysis.py:
	  Minor doc and formatting fixes

	* [r8699]
	  examples/lissom_oo_or_homeostatic_tracked.ty:
	  Minor typo fixes

2008-06-23  antolikjan

	* [r8698]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  repaired bug with __main__

2008-06-23  gerasymo

	* [r8697] examples/lissom_oo_or_cr.ty:
	  Wrong condition deleted.

2008-06-23  antolikjan

	* [r8696] topo/sheets/lissom.py:
	  removed the apply_output_fn_init parameter

	* [r8695] topo/base/simulation.py:
	  removed the apply_output_fn_init handling

2008-06-23  gerasymo

	* [r8694] examples/lissom_oo_or_cr.ty:
	  Parameters specific for natural images added.

2008-06-22  gerasymo

	* [r8693] topo/commands/analysis.py:
	  Command for creating Hue Preference maps added. Work in progress.

2008-06-22  ceball

	* [r8692]
	  examples/lissom_oo_or_homeostatic_tracked.ty:
	  Added missing imports (that were causing slow-tests to fail).

	* [r8691]
	  topo/tests/lissom_oo_or_t000100.00_Contrast_Response.data,
	  topo/tests/lissom_oo_or_t000100.00_Corner_OR_Preference.data,
	  topo/tests/lissom_oo_or_t000100.00_Orientation_Preference.data,
	  topo/tests/lissom_oo_or_t000100.00_Orientation_Tuning.data,
	  topo/tests/lissom_oo_or_t000100.00_Orientation_Tuning_Fullfield.data,
	  topo/tests/lissom_oo_or_t000100.00_Position_Preference.data,
	  topo/tests/lissom_oo_or_t000100.00_Size_Tuning.data,
	  topo/tests/lissom_oo_or_t000100.00_Spatial_Frequency_Preference.data,
	  topo/tests/test_map_measurement.py:
	  Updated 'map testing' to include curves (still need to rename
	  test).

2008-06-21  gerasymo

	* [r8690] examples/lissom_oo_or_cr.ty:
	  Different input for Red and Green retinas.

	* [r8689] examples/lissom_oo_or_od_dr.ty:
	  Array of afferent strength from retina to LGN adjusted according
	  to speed.

2008-06-21  jbednar

	* [r8688] topo/outputfns/basic.py:
	  Made a_init and b_init into Parameters, not Numbers, to fix
	  errors.

2008-06-21  ceball

	* [r8687] topo/tests/__init__.py:
	  Removed test_map_measurement from list of unit tests.

2008-06-20  jbednar

	* [r8686] examples/lissom_oo_or_od_dr.ty:
	  Minor reformatting of docstrings

2008-06-20  gerasymo

	* [r8685] examples/lissom_oo_or_od_dr_photo.ty:
	  File was integrated to lissom_oo_or_od_dr.ty; results can be
	  obtained by running the latter with variable dataset='Nature'.

	* [r8684] examples/lissom_oo_or_od_dr.ty:
	  Former file merged with lissom_oo_or_od_dr_photo.ty. So variable
	  dataset added with default value Gaussian, which then produces
	  the same map as former lissom_oo_or_od_dr.ty; when
	  dataset=Nature, maps identical to lissom_oo_or_od_dr_photo.ty are
	  build (with natural photos as input). Parameters for photos are
	  set according to CMVC A.5.2 Natural images.

2008-06-20  judelaw

	* [r8683] Makefile:
	  added lissom_oo_or_homeostatic.ty and
	  lissom_oo_or_homeostatic_tracked.ty to SCRIPTS list for testing

	* [r8682] contrib/jsldefs.py:
	  added missing import and removed alert

	* [r8681] topo/outputfns/basic.py:
	  added a_init and b_init parameters to HomeostaticMaxEnt to kmake
	  sure that documentation is kept even if the default=None

	* [r8680]
	  examples/lissom_oo_or_homeostatic_tracked.ty:
	  added code to make sure selecitivity_multipler=1.0 for
	  reproducing results

2008-06-20  antolikjan

	* [r8679]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  changed locals() to __main__.__dict__ in order to make external
	  parameter setting work also in the secondStage() function

2008-06-20  jbednar

	* [r8678] topo/commands/analysis.py:
	  Moved corner's topographic_grid() from update_command to
	  plot_command to fix ALERT.

2008-06-20  ceball

	* [r8677] topo/tests/test_map_measurement.py:
	  Made test work across platforms (map measurement results don't
	  match exactly).

	* [r8676] Makefile,
	  topo/tests/lissom_oo_or_t000100.00_Orientation_Preference.data,
	  topo/tests/lissom_oo_or_t000100.00_Position_Preference.data,
	  topo/tests/lissom_oo_or_t000100.00_Spatial_Frequency_Preference.data,
	  topo/tests/test_map_measurement.py:
	  Added beginnings of test of map measurement.

	* [r8675] doc/Future_Work/current_text.php:
	  Added a note for myself.

	* [r8674] topo/commands/analysis.py:
	  Added ALERT.

	* [r8673] Makefile,
	  topo/tests/test_script.py:
	  Undid changes from r8672 (i.e. reverted to r8671). I didn't check
	  in the required data file previously, and anyway I've decided to
	  do something different.

	* [r8672] Makefile,
	  topo/tests/test_script.py:
	  Added basic test of orientation map measurement.

2008-06-19  gerasymo

	* [r8671] examples/lissom_oo_or_od_dr_photo.ty:
	  Input scaled differently for right and left retinas, so OD map
	  can be built.

2008-06-19  jbednar

	* [r8670] topo/patterns/image.py:
	  Added cache_image parameter

2008-06-19  gerasymo

	* [r8669] examples/lissom_oo_or_od_dr_photo.ty:
	  Image specific parameters added.

2008-06-18  gerasymo

	* [r8668] examples/lissom_oo_or_od_dr_photo.ty:
	  Copied from lissom_oo_or_od_dr.ty -r 8656 and adjusted to receive
	  images as input. Doesn't have image specific parameters yet.
	  Produces OR and DR maps, but no OD, since scale for both eyes is
	  identical.

2008-06-18  antolikjan

	* [r8667]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  further parameter changes: slope of the transfer function

2008-06-18  ceball

	* [r8666] topo/commands/analysis.py:
	  Added ALERT.

2008-06-17  gerasymo

	* [r8665] topo/commands/analysis.py:
	  One unnecessary statement deleted.

	* [r8664] topo/commands/analysis.py:
	  Warning added to prevent the case that directions map is measured
	  when there is no lagged input.

2008-06-17  judelaw

	* [r8663] contrib/jsldefs.py:
	  added state_push and state_pop to JointScaling_lronly and
	  JointScaling_affonly. Added temporary changing of homeostatic
	  parameters during orientation preference map measurement in
	  homeostatic_analysis_function. This is to allow comparison of map
	  selectivity for different simulations and at different timepoints
	  during development

	* [r8662] topo/sheets/lissom.py:
	  added state_push and state_pop in JointScaling so that state can
	  be saved to the __curent_state_stack and restored at a later time
	  (for example when measuring orientation selectivity maps)

	* [r8661] topo/outputfns/basic.py:
	  added state_push and state_pop in HomeostaticMaxEnt so that state
	  can be saved to the __curent_state_stack and restored at a later
	  time (for example when measuring orientation selectivity maps)

	* [r8660] topo/base/functionfamilies.py:
	  added state_push and state_pop to PipelineOF so that Output
	  functions in a pipeline can save and restore their state if they
	  have a state_push and state_pop function

2008-06-17  antolikjan

	* [r8659]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  naming bug corrected

2008-06-17  gerasymo

	* [r8658] examples/lissom_oo_or_dr.ty:
	  This model is integrated in the lissom_oo_or_od_dr.ty and the
	  same results (map) can be obtained by running the latter file
	  with dims=['or','dr'].

	* [r8657] examples/lissom_oo_or_od.ty:
	  This model is integrated in the lissom_oo_or_od_dr.ty and the
	  same results (map) can be obtained by running the latter file
	  with dims=['or','od'].

	* [r8656] examples/lissom_oo_or_od_dr.ty:
	  Comment added how to turn on and off OD and DR dimensions. It is
	  also specified to which figures from CMVC the resulting maps
	  correspond.

2008-06-17  judelaw

	* [r8655] contrib/jsldefs.py:
	  added file containing code specific to
	  lissom_oo_or_homeostatic_tracked.ty

	* [r8654]
	  examples/lissom_oo_or_homeostatic_tracked.ty:
	  removed code used only in this example and put it in
	  contrib/jsldefs.py

2008-06-17  antolikjan

	* [r8653]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  and more parameters changes

	* [r8652]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  parameter changes

2008-06-17  jbednar

	* [r8651] topo/base/cf.py:
	  Minor docstring cleanup

	* [r8650] examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/cc_lissom_oo_or_pokus.ty,
	  examples/cc_lissom_oo_or_simple_rv.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/lissom_oo_or_homeostatic.ty:
	  Removed obsolete FixedPoint uses

2008-06-16  judelaw

	* [r8649] examples/lissom_oo_or_homeostatic.ty:
	  corrected syntax error

	* [r8648]
	  examples/lissom_oo_or_homeostatic_tracked.ty:
	  Version of lissom_oo_or_homeostatic.ty with all necessary
	  functionality for reproducing published figures, including
	  counter examples where simulation doesn't work. Also includes all
	  tracking and analysis functions. Not yet fully tested.

	* [r8647] examples/lissom_oo_or_homeostatic.ty:
	  Brought up to date with version to be published. Removed all
	  debugging and tracking code and replaced with separate file
	  (lissom_oo_or_homeostatic_tracked.ty). Renamed sparsity as
	  frequency and type_input as dataset

	* [r8646] topo/outputfns/basic.py:
	  Changed HomeostaticMaxEnt so that if initial a and b parameters
	  are not specified they are randomly generated (within realistic
	  bounds)

2008-06-16  ceball

	* [r8645] doc/buildbot/bbanalysis.py:
	  Began to add annotations to buildbot graph.

	* [r8644] doc/buildbot/index.html:
	  Added minor changes to buildbot's index page (these changes have
	  been live on buildbot for some time).

	* [r8643] topo/base/arrayutils.py:
	  Added commented-out alternative to array_argmax().

2008-06-15  gerasymo

	* [r8642] examples/lissom_oo_or_od_dr.ty:
	  Array dims added, with the help of which it is possible to create
	  different combinations of maps running one file
	  (lissom_oo_or_od_dr.ty)with appropriate dims values. E.g.
	  dims=['or'] will give OR map identical to that created with
	  lissom_oo_or.ty(if in the latter scale is chosen from [0,2]);
	  dims=['or','od'] gives OR and OD maps identical to those from
	  lissom_oo_or_od.ty(if in the latter only one gaussian is
	  inputed); etc.

2008-06-13  antolikjan

	* [r8641]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  corrected some indentition problems

	* [r8640]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  one more external parameter addition

	* [r8639]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  some further parameter changes and additional sheaduled commands

	* [r8638] contrib/jacommands.py:
	  added hacked randomized LGN projection strength

2008-06-12  antolikjan

	* [r8637]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  Some parameter changes

2008-06-11  jbednar

	* [r8636] topo/tkgui/projectionpanel.py:
	  Fixed bug in RF Projection plot -- fairly recent generalization
	  of Projection/ProjectionSheet handling broke it

	* [r8635] topo/commands/analysis.py:
	  Fixed to work with old snapshots

2008-06-11  ceball

	* [r8634] topo/tkgui/topoconsole.py:
	  Minor simplification - no visible change.

	* [r8633]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Added svn ignore commands (still commented out).

	* [r8632] topo/ipythonTk:
	  Files to ignore.

	* [r8631] topo/misc/commandline.py,
	  topo/tkgui/topoconsole.py:
	  Files missed from r8630.

	* [r8630] topo/ipythonTk,
	  topo/ipythonTk/__init__.py,
	  topo/ipythonTk/ipythonTk.py,
	  topo/ipythonTk/ipython_view.py,
	  topo/tkgui/ipythonTk:
	  Moved topo.tkgui.ipythonTk to topo.ipythonTk.

	* [r8629] topo/misc/commandline.py,
	  topo/tkgui/__init__.py:
	  Added experimental -G option to have an IPython console in the
	  GUI. (Notes: do not rely on this for your work; mock-up
	  implementation is simply to help us evaluate where to take the
	  GUI.)

	* [r8628] topo/tkgui/topoconsole.py:
	  Added experimental support for an IPython console.

	* [r8627] topo/tkgui/ipythonTk/ipythonTk.py:
	  Allowed specification of the user dictionary for IterableIPShell.

2008-06-11  jbednar

	* [r8626]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Minor clarifications

2008-06-10  gerasymo

	* [r8625] examples/lissom_oo_or_od_dr.ty:
	  Names of variables (for model configuration) changed for
	  consistency reason; same performance.

	* [r8624] examples/lissom_oo_or_cr.ty:
	  Names of variables (for model configuration) changed for
	  consistency reason; same performance.

2008-06-10  ceball

	* [r8623] external:
	  Updated ignore list.

	* [r8622] external/Makefile,
	  external/ipython-0.8.2.tar.gz:
	  Changes missed from r8621.

	* [r8621] external/ipython-0.8.4.tar.gz:
	  Upgraded to IPython 0.8.4.

	* [r8620] topo/misc/commandline.py,
	  topo/tkgui/ipythonTk/ipythonTk.py:
	  Added (experimental) methods to try out different ways of running
	  tkgui.

	* [r8619] topo/tkgui/__init__.py:
	  Allowed start() to make use of an existing Tk instance (if one is
	  optionally supplied).

	* [r8618] topo/misc/commandline.py:
	  Removed unused import.

	* [r8617] topo/tkgui/ipythonTk/ipythonTk.py:
	  Removed dependence on Pmw.

	* [r8616] topo/tkgui/ipythonTk,
	  topo/tkgui/ipythonTk/__init__.py,
	  topo/tkgui/ipythonTk/ipythonTk.py,
	  topo/tkgui/ipythonTk/ipython_view.py:
	  Added code to allow IPython to be embedded in Tkinter. (Code
	  copied from ccp1gui.sf.net.)

2008-06-09  antolikjan

	* [r8615]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  few parameter changes

2008-06-08  ceball

	* [r8614] topo/tkgui/topoconsole.py:
	  Minor bug fix: previously, if no simulation was loaded or a
	  simulation had None for a name, the GUI crashed when a progress
	  meter opened.

2008-06-06  jbednar

	* [r8613] examples/lissom_oo_or_od_dr.ty:
	  Minor reformatting

2008-06-06  ceball

	* [r8612] doc/buildbot/master.cfg:
	  Updated creation of shell commands to work with new buildbot
	  version 0.7.7 (fixes SF #1981218).

	* [r8611] doc/buildbot/master.cfg:
	  Added cleaning of pyc files and renamed c++ reference builder.
	  (These changes have been in effect on the buildbot itself for at
	  least a month.)

2008-06-05  gerasymo

	* [r8610] examples/lissom_oo_or_cr.ty:
	  No changes in respect of content, just how it looks like.

	* [r8609] examples/lissom_oo_or_cr.ty:
	  Third LGN layer added, so now there are all needed layers for
	  basic color model (Red/Green, Green/Red, Luminosity).Because of
	  the identical input pattern for both red and green retinas,
	  resulted activities and OR preference map is identical to
	  lissom_oo_or.ty.

2008-06-04  gerasymo

	* [r8608] examples/lissom_oo_or_cr.ty:
	  Two layers of LGN (Red/Green and Green/Red) added. For Red/Green,
	  the center input comes from red retina, the surrounding from the
	  green retina, respectively for Green/Red. Learning rates
	  adjusted, so maps identical to lissom_oo_or.ty are built, because
	  of the identical input patterns on both red and green retinas.

	* [r8607] examples/lissom_oo_or_cr.ty:
	  Mistake in the connections corrected.

	* [r8606] examples/lissom_oo_or_cr.ty:
	  Instead of one, there are now two identical retinas, so one LGN
	  receives input from two retinas: central part from one and
	  surrounding part from the second retina. Because of the identical
	  input patterns on both retinas, no effect on the map - the same
	  map as lissom_oo_or.ty

	* [r8605] examples/lissom_oo_or_cr.ty:
	  Inputs for central and surround gaussians of LGN separated, but
	  because of only one retina it still doesnt't have any effect. So
	  maps identical to lissom_oo_or.ty can be built. Model editor
	  temporarily commented.

2008-06-04  antolikjan

	* [r8604] examples/cc_lissom_oo_or_pokus.ty:
	  Changed some parameters to be configurable through -c option

2008-06-03  gerasymo

	* [r8603] topo/commands/analysis.py:
	  New plotgroup created for building OR map overlaid with both OD
	  contours and DR arrows. It can be temporarily accessed in the
	  Combined Preference Maps category.

	* [r8602] examples/lissom_oo_or_od_dr.ty:
	  Two eyes added with inputs scaled differently as required for OD.
	  Also model editor extended to suit the model. OR/OD/DR maps can
	  be build.

	* [r8601] topo/commands/analysis.py:
	  Changes in patterns presented for ocular preference map
	  measurement. Difference in scale for inputs to the left and right
	  retinas made independent of the number of input sheets; scale
	  depends only on whether the input goes to the left or right.

	* [r8600] topo/commands/analysis.py:
	  Changes in presented input for direction map measurement. Lag
	  numbers are made to correspond to the Sweeper step, so e.g. by
	  two eyes, inputs to different eyes with the same lag number get
	  the same translation.

2008-06-03  antolikjan

	* [r8599]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  

	* [r8598]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  

	* [r8597] examples/cc_lissom_oo_or_pokus.ty:
	  

	* [r8596]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  

	* [r8595] topo/tkgui/testpattern.py:
	  

	* [r8594] topo/sheets/lissom.py:
	  

	* [r8593] topo/patterns/basic.py:
	  

	* [r8592] topo/commands/analysis.py:
	  

	* [r8591] topo/base/projection.py:
	  

	* [r8590] topo/base/simulation.py:
	  

	* [r8589] topo/base/cf.py:
	  

	* [r8588] examples/cc_lissom_oo_or_pokus.ty:
	  

	* [r8587]
	  examples/cc_lissom_oo_or_simple_rv.ty:
	  

2008-06-02  gerasymo

	* [r8586] topo/commands/analysis.py:
	  Command for creation of overlaid plots adjusted to the change in
	  the function overlaid_plots.

	* [r8585] topo/commands/pylabplots.py:
	  Function overlaid_plots and overlaid_plots_arrows combined into
	  one function overlaid_plots, which can produce plots with both
	  types of overlay, contours and/or arrows.

	* [r8584] topo/commands/pylabplots.py:
	  In the overlaid_plot_arrow function scaling of arrows according
	  to direction selectivity added.

2008-06-02  antolikjan

	* [r8583] topo/analysis/featureresponses.py:
	  

	* [r8582] topo/analysis/vision.py:
	  

	* [r8581] contrib/jaanalysis.py:
	  

	* [r8580] contrib/jaanalysis.py:
	  

	* [r8579] contrib/jansanalyzisfunctions.py,
	  contrib/modelfit.py:
	  

2008-05-30  jbednar

	* [r8578] topo/commands/analysis.py:
	  Fixed minor typos

	* [r8577] topo/commands/pylabplots.py:
	  Fixed minor typo

2008-05-30  gerasymo

	* [r8576] topo/commands/analysis.py:
	  Command for building plots of OR maps overlaid with DR arrows
	  created (temporarily). Measure direction preferences command
	  corrected.

	* [r8575] topo/commands/pylabplots.py:
	  Plot function for overlaid plots with arrows created (for OR maps
	  overlaid with DR arrows). Work in progress.

	* [r8574]
	  topo/commands/dr_key_white_vert_small.png:
	  Added arrows key image for measuring direction.

2008-05-29  jbednar

	* [r8573] topo/commands/pylabplots.py:
	  Minor fix to docstring

	* [r8572] topo/analysis/vision.py,
	  topo/commands/pylabplots.py,
	  topo/misc/commandline.py:
	  Allowed GUI to run even when pylab is unavailable, to make
	  porting to problematic platforms easier (e.g. Mac)

	* [r8571] images/colormap/00_0.pgm,
	  images/colormap/00_0.png,
	  images/colormap/00_1.pgm,
	  images/colormap/00_1.png,
	  images/colormap/00_2.pgm,
	  images/colormap/00_2.png,
	  images/colormap/01_0.pgm,
	  images/colormap/01_0.png,
	  images/colormap/01_1.pgm,
	  images/colormap/01_1.png,
	  images/colormap/01_2.pgm,
	  images/colormap/01_2.png,
	  images/colormap/02_0.pgm,
	  images/colormap/02_0.png,
	  images/colormap/02_1.pgm,
	  images/colormap/02_1.png,
	  images/colormap/02_2.pgm,
	  images/colormap/02_2.png,
	  images/colormap/03_0.pgm,
	  images/colormap/03_0.png,
	  images/colormap/03_1.pgm,
	  images/colormap/03_1.png,
	  images/colormap/03_2.pgm,
	  images/colormap/03_2.png,
	  images/colormap/04_0.pgm,
	  images/colormap/04_0.png,
	  images/colormap/04_1.pgm,
	  images/colormap/04_1.png,
	  images/colormap/04_2.pgm,
	  images/colormap/04_2.png,
	  images/colormap/05_0.pgm,
	  images/colormap/05_0.png,
	  images/colormap/05_1.pgm,
	  images/colormap/05_1.png,
	  images/colormap/05_2.pgm,
	  images/colormap/05_2.png:
	  Converted to PNG format to save space and loading time

	* [r8570] images/colormap/06_0.pgm,
	  images/colormap/06_1.pgm,
	  images/colormap/06_2.pgm,
	  images/colormap/07_0.pgm,
	  images/colormap/07_1.pgm,
	  images/colormap/07_2.pgm,
	  images/colormap/08_0.pgm,
	  images/colormap/08_1.pgm,
	  images/colormap/08_2.pgm,
	  images/colormap/09_0.pgm,
	  images/colormap/09_1.pgm,
	  images/colormap/09_2.pgm,
	  images/colormap/10_0.pgm,
	  images/colormap/10_1.pgm,
	  images/colormap/10_2.pgm,
	  images/colormap/11_0.pgm,
	  images/colormap/11_1.pgm,
	  images/colormap/11_2.pgm,
	  images/colormap/12_0.pgm,
	  images/colormap/12_1.pgm,
	  images/colormap/12_2.pgm,
	  images/colormap/13_0.pgm,
	  images/colormap/13_1.pgm,
	  images/colormap/13_2.pgm,
	  images/colormap/14_0.pgm,
	  images/colormap/14_1.pgm,
	  images/colormap/14_2.pgm,
	  images/colormap/15_0.pgm,
	  images/colormap/15_1.pgm,
	  images/colormap/15_2.pgm,
	  images/colormap/16_0.pgm,
	  images/colormap/16_1.pgm,
	  images/colormap/16_2.pgm,
	  images/colormap/17_0.pgm,
	  images/colormap/17_1.pgm,
	  images/colormap/17_2.pgm,
	  images/colormap/18_0.pgm,
	  images/colormap/18_1.pgm,
	  images/colormap/18_2.pgm,
	  images/colormap/19_0.pgm,
	  images/colormap/19_1.pgm,
	  images/colormap/19_2.pgm,
	  images/colormap/20_0.pgm,
	  images/colormap/20_1.pgm,
	  images/colormap/20_2.pgm,
	  images/colormap/21_0.pgm,
	  images/colormap/21_1.pgm,
	  images/colormap/21_2.pgm,
	  images/colormap/22_0.pgm,
	  images/colormap/22_1.pgm,
	  images/colormap/22_2.pgm,
	  images/colormap/23_0.pgm,
	  images/colormap/23_1.pgm,
	  images/colormap/23_2.pgm,
	  images/colormap/24_0.pgm,
	  images/colormap/24_1.pgm,
	  images/colormap/24_2.pgm,
	  images/colormap/25_0.pgm,
	  images/colormap/25_1.pgm,
	  images/colormap/25_2.pgm,
	  images/colormap/26_0.pgm,
	  images/colormap/26_1.pgm,
	  images/colormap/26_2.pgm,
	  images/colormap/27_0.pgm,
	  images/colormap/27_1.pgm,
	  images/colormap/27_2.pgm,
	  images/colormap/28_0.pgm,
	  images/colormap/28_1.pgm,
	  images/colormap/28_2.pgm,
	  images/colormap/29_0.pgm,
	  images/colormap/29_1.pgm,
	  images/colormap/29_2.pgm,
	  images/colormap/30_0.pgm,
	  images/colormap/30_1.pgm,
	  images/colormap/30_2.pgm,
	  images/colormap/31_0.pgm,
	  images/colormap/31_1.pgm,
	  images/colormap/31_2.pgm,
	  images/colormap/32_0.pgm,
	  images/colormap/32_1.pgm,
	  images/colormap/32_2.pgm,
	  images/colormap/33_0.pgm,
	  images/colormap/33_1.pgm,
	  images/colormap/33_2.pgm,
	  images/colormap/34_0.pgm,
	  images/colormap/34_1.pgm,
	  images/colormap/34_2.pgm,
	  images/colormap/35_0.pgm,
	  images/colormap/35_1.pgm,
	  images/colormap/35_2.pgm,
	  images/colormap/36_0.pgm,
	  images/colormap/36_1.pgm,
	  images/colormap/36_2.pgm,
	  images/colormap/37_0.pgm,
	  images/colormap/37_1.pgm,
	  images/colormap/37_2.pgm,
	  images/colormap/38_0.pgm,
	  images/colormap/38_1.pgm,
	  images/colormap/38_2.pgm,
	  images/colormap/39_0.pgm,
	  images/colormap/39_1.pgm,
	  images/colormap/39_2.pgm,
	  images/colormap/40_0.pgm,
	  images/colormap/40_1.pgm,
	  images/colormap/40_2.pgm,
	  images/colormap/41_0.pgm,
	  images/colormap/41_1.pgm,
	  images/colormap/41_2.pgm,
	  images/colormap/42_0.pgm,
	  images/colormap/42_1.pgm,
	  images/colormap/42_2.pgm,
	  images/colormap/43_0.pgm,
	  images/colormap/43_1.pgm,
	  images/colormap/43_2.pgm,
	  images/colormap/44_0.pgm,
	  images/colormap/44_1.pgm,
	  images/colormap/44_2.pgm,
	  images/colormap/45_0.pgm,
	  images/colormap/45_1.pgm,
	  images/colormap/45_2.pgm,
	  images/colormap/46_0.pgm,
	  images/colormap/46_1.pgm,
	  images/colormap/46_2.pgm,
	  images/colormap/47_0.pgm,
	  images/colormap/47_1.pgm,
	  images/colormap/47_2.pgm,
	  images/colormap/48_0.pgm,
	  images/colormap/48_1.pgm,
	  images/colormap/48_2.pgm,
	  images/colormap/49_0.pgm,
	  images/colormap/49_1.pgm,
	  images/colormap/49_2.pgm,
	  images/colormap/50_0.pgm,
	  images/colormap/50_1.pgm,
	  images/colormap/50_2.pgm,
	  images/colormap/51_0.pgm,
	  images/colormap/51_1.pgm,
	  images/colormap/51_2.pgm,
	  images/colormap/52_0.pgm,
	  images/colormap/52_1.pgm,
	  images/colormap/52_2.pgm,
	  images/colormap/53_0.pgm,
	  images/colormap/53_1.pgm,
	  images/colormap/53_2.pgm,
	  images/colormap/54_0.pgm,
	  images/colormap/54_1.pgm,
	  images/colormap/54_2.pgm,
	  images/colormap/55_0.pgm,
	  images/colormap/55_1.pgm,
	  images/colormap/55_2.pgm,
	  images/colormap/56_0.pgm,
	  images/colormap/56_1.pgm,
	  images/colormap/56_2.pgm,
	  images/colormap/57_0.pgm,
	  images/colormap/57_1.pgm,
	  images/colormap/57_2.pgm,
	  images/colormap/58_0.pgm,
	  images/colormap/58_1.pgm,
	  images/colormap/58_2.pgm,
	  images/colormap/59_0.pgm,
	  images/colormap/59_1.pgm,
	  images/colormap/59_2.pgm,
	  images/colormap/60_0.pgm,
	  images/colormap/60_1.pgm,
	  images/colormap/60_2.pgm,
	  images/colormap/61_0.pgm,
	  images/colormap/61_1.pgm,
	  images/colormap/61_2.pgm,
	  images/colormap/62_0.pgm,
	  images/colormap/62_1.pgm,
	  images/colormap/62_2.pgm,
	  images/colormap/63_0.pgm,
	  images/colormap/63_1.pgm,
	  images/colormap/63_2.pgm,
	  images/colormap/64_0.pgm,
	  images/colormap/64_1.pgm,
	  images/colormap/64_2.pgm,
	  images/colormap/65_0.pgm,
	  images/colormap/65_1.pgm,
	  images/colormap/65_2.pgm,
	  images/colormap/66_0.pgm,
	  images/colormap/66_1.pgm,
	  images/colormap/66_2.pgm,
	  images/colormap/67_0.pgm,
	  images/colormap/67_1.pgm,
	  images/colormap/67_2.pgm,
	  images/colormap/68_0.pgm,
	  images/colormap/68_1.pgm,
	  images/colormap/68_2.pgm,
	  images/colormap/69_0.pgm,
	  images/colormap/69_1.pgm,
	  images/colormap/69_2.pgm,
	  images/colormap/70_0.pgm,
	  images/colormap/70_1.pgm,
	  images/colormap/70_2.pgm,
	  images/colormap/71_0.pgm,
	  images/colormap/71_1.pgm,
	  images/colormap/71_2.pgm,
	  images/colormap/72_0.pgm,
	  images/colormap/72_1.pgm,
	  images/colormap/72_2.pgm,
	  images/colormap/73_0.pgm,
	  images/colormap/73_1.pgm,
	  images/colormap/73_2.pgm:
	  Removed large images not needed for basic RG color map

2008-05-29  gerasymo

	* [r8569] images/colormap,
	  images/colormap/00_0.pgm,
	  images/colormap/00_1.pgm,
	  images/colormap/00_2.pgm,
	  images/colormap/01_0.pgm,
	  images/colormap/01_1.pgm,
	  images/colormap/01_2.pgm,
	  images/colormap/02_0.pgm,
	  images/colormap/02_1.pgm,
	  images/colormap/02_2.pgm,
	  images/colormap/03_0.pgm,
	  images/colormap/03_1.pgm,
	  images/colormap/03_2.pgm,
	  images/colormap/04_0.pgm,
	  images/colormap/04_1.pgm,
	  images/colormap/04_2.pgm,
	  images/colormap/05_0.pgm,
	  images/colormap/05_1.pgm,
	  images/colormap/05_2.pgm,
	  images/colormap/06_0.pgm,
	  images/colormap/06_1.pgm,
	  images/colormap/06_2.pgm,
	  images/colormap/07_0.pgm,
	  images/colormap/07_1.pgm,
	  images/colormap/07_2.pgm,
	  images/colormap/08_0.pgm,
	  images/colormap/08_1.pgm,
	  images/colormap/08_2.pgm,
	  images/colormap/09_0.pgm,
	  images/colormap/09_1.pgm,
	  images/colormap/09_2.pgm,
	  images/colormap/10_0.pgm,
	  images/colormap/10_1.pgm,
	  images/colormap/10_2.pgm,
	  images/colormap/11_0.pgm,
	  images/colormap/11_1.pgm,
	  images/colormap/11_2.pgm,
	  images/colormap/12_0.pgm,
	  images/colormap/12_1.pgm,
	  images/colormap/12_2.pgm,
	  images/colormap/13_0.pgm,
	  images/colormap/13_1.pgm,
	  images/colormap/13_2.pgm,
	  images/colormap/14_0.pgm,
	  images/colormap/14_1.pgm,
	  images/colormap/14_2.pgm,
	  images/colormap/15_0.pgm,
	  images/colormap/15_1.pgm,
	  images/colormap/15_2.pgm,
	  images/colormap/16_0.pgm,
	  images/colormap/16_1.pgm,
	  images/colormap/16_2.pgm,
	  images/colormap/17_0.pgm,
	  images/colormap/17_1.pgm,
	  images/colormap/17_2.pgm,
	  images/colormap/18_0.pgm,
	  images/colormap/18_1.pgm,
	  images/colormap/18_2.pgm,
	  images/colormap/19_0.pgm,
	  images/colormap/19_1.pgm,
	  images/colormap/19_2.pgm,
	  images/colormap/20_0.pgm,
	  images/colormap/20_1.pgm,
	  images/colormap/20_2.pgm,
	  images/colormap/21_0.pgm,
	  images/colormap/21_1.pgm,
	  images/colormap/21_2.pgm,
	  images/colormap/22_0.pgm,
	  images/colormap/22_1.pgm,
	  images/colormap/22_2.pgm,
	  images/colormap/23_0.pgm,
	  images/colormap/23_1.pgm,
	  images/colormap/23_2.pgm,
	  images/colormap/24_0.pgm,
	  images/colormap/24_1.pgm,
	  images/colormap/24_2.pgm,
	  images/colormap/25_0.pgm,
	  images/colormap/25_1.pgm,
	  images/colormap/25_2.pgm,
	  images/colormap/26_0.pgm,
	  images/colormap/26_1.pgm,
	  images/colormap/26_2.pgm,
	  images/colormap/27_0.pgm,
	  images/colormap/27_1.pgm,
	  images/colormap/27_2.pgm,
	  images/colormap/28_0.pgm,
	  images/colormap/28_1.pgm,
	  images/colormap/28_2.pgm,
	  images/colormap/29_0.pgm,
	  images/colormap/29_1.pgm,
	  images/colormap/29_2.pgm,
	  images/colormap/30_0.pgm,
	  images/colormap/30_1.pgm,
	  images/colormap/30_2.pgm,
	  images/colormap/31_0.pgm,
	  images/colormap/31_1.pgm,
	  images/colormap/31_2.pgm,
	  images/colormap/32_0.pgm,
	  images/colormap/32_1.pgm,
	  images/colormap/32_2.pgm,
	  images/colormap/33_0.pgm,
	  images/colormap/33_1.pgm,
	  images/colormap/33_2.pgm,
	  images/colormap/34_0.pgm,
	  images/colormap/34_1.pgm,
	  images/colormap/34_2.pgm,
	  images/colormap/35_0.pgm,
	  images/colormap/35_1.pgm,
	  images/colormap/35_2.pgm,
	  images/colormap/36_0.pgm,
	  images/colormap/36_1.pgm,
	  images/colormap/36_2.pgm,
	  images/colormap/37_0.pgm,
	  images/colormap/37_1.pgm,
	  images/colormap/37_2.pgm,
	  images/colormap/38_0.pgm,
	  images/colormap/38_1.pgm,
	  images/colormap/38_2.pgm,
	  images/colormap/39_0.pgm,
	  images/colormap/39_1.pgm,
	  images/colormap/39_2.pgm,
	  images/colormap/40_0.pgm,
	  images/colormap/40_1.pgm,
	  images/colormap/40_2.pgm,
	  images/colormap/41_0.pgm,
	  images/colormap/41_1.pgm,
	  images/colormap/41_2.pgm,
	  images/colormap/42_0.pgm,
	  images/colormap/42_1.pgm,
	  images/colormap/42_2.pgm,
	  images/colormap/43_0.pgm,
	  images/colormap/43_1.pgm,
	  images/colormap/43_2.pgm,
	  images/colormap/44_0.pgm,
	  images/colormap/44_1.pgm,
	  images/colormap/44_2.pgm,
	  images/colormap/45_0.pgm,
	  images/colormap/45_1.pgm,
	  images/colormap/45_2.pgm,
	  images/colormap/46_0.pgm,
	  images/colormap/46_1.pgm,
	  images/colormap/46_2.pgm,
	  images/colormap/47_0.pgm,
	  images/colormap/47_1.pgm,
	  images/colormap/47_2.pgm,
	  images/colormap/48_0.pgm,
	  images/colormap/48_1.pgm,
	  images/colormap/48_2.pgm,
	  images/colormap/49_0.pgm,
	  images/colormap/49_1.pgm,
	  images/colormap/49_2.pgm,
	  images/colormap/50_0.pgm,
	  images/colormap/50_1.pgm,
	  images/colormap/50_2.pgm,
	  images/colormap/51_0.pgm,
	  images/colormap/51_1.pgm,
	  images/colormap/51_2.pgm,
	  images/colormap/52_0.pgm,
	  images/colormap/52_1.pgm,
	  images/colormap/52_2.pgm,
	  images/colormap/53_0.pgm,
	  images/colormap/53_1.pgm,
	  images/colormap/53_2.pgm,
	  images/colormap/54_0.pgm,
	  images/colormap/54_1.pgm,
	  images/colormap/54_2.pgm,
	  images/colormap/55_0.pgm,
	  images/colormap/55_1.pgm,
	  images/colormap/55_2.pgm,
	  images/colormap/56_0.pgm,
	  images/colormap/56_1.pgm,
	  images/colormap/56_2.pgm,
	  images/colormap/57_0.pgm,
	  images/colormap/57_1.pgm,
	  images/colormap/57_2.pgm,
	  images/colormap/58_0.pgm,
	  images/colormap/58_1.pgm,
	  images/colormap/58_2.pgm,
	  images/colormap/59_0.pgm,
	  images/colormap/59_1.pgm,
	  images/colormap/59_2.pgm,
	  images/colormap/60_0.pgm,
	  images/colormap/60_1.pgm,
	  images/colormap/60_2.pgm,
	  images/colormap/61_0.pgm,
	  images/colormap/61_1.pgm,
	  images/colormap/61_2.pgm,
	  images/colormap/62_0.pgm,
	  images/colormap/62_1.pgm,
	  images/colormap/62_2.pgm,
	  images/colormap/63_0.pgm,
	  images/colormap/63_1.pgm,
	  images/colormap/63_2.pgm,
	  images/colormap/64_0.pgm,
	  images/colormap/64_1.pgm,
	  images/colormap/64_2.pgm,
	  images/colormap/65_0.pgm,
	  images/colormap/65_1.pgm,
	  images/colormap/65_2.pgm,
	  images/colormap/66_0.pgm,
	  images/colormap/66_1.pgm,
	  images/colormap/66_2.pgm,
	  images/colormap/67_0.pgm,
	  images/colormap/67_1.pgm,
	  images/colormap/67_2.pgm,
	  images/colormap/68_0.pgm,
	  images/colormap/68_1.pgm,
	  images/colormap/68_2.pgm,
	  images/colormap/69_0.pgm,
	  images/colormap/69_1.pgm,
	  images/colormap/69_2.pgm,
	  images/colormap/70_0.pgm,
	  images/colormap/70_1.pgm,
	  images/colormap/70_2.pgm,
	  images/colormap/71_0.pgm,
	  images/colormap/71_1.pgm,
	  images/colormap/71_2.pgm,
	  images/colormap/72_0.pgm,
	  images/colormap/72_1.pgm,
	  images/colormap/72_2.pgm,
	  images/colormap/73_0.pgm,
	  images/colormap/73_1.pgm,
	  images/colormap/73_2.pgm:
	  Added images for color model.

2008-05-28  gerasymo

	* [r8568] examples/lissom_oo_or_cr.ty:
	  Created file for basic color model. Copied from
	  lissom_oo_or_dr.ty -r 8562, but without translation and with one
	  LGN layer. So at this stage maps identical to lissom_oo_or.ty can
	  be buit.

	* [r8567] topo/commands/pylabplots.py:
	  Small cosmetic changes made to overlaid_plots.

2008-05-27  gerasymo

	* [r8566] topo/commands/analysis.py:
	  Combined Preference Maps category in the Plots menu is added. It
	  has an option of plotting the Orientation and Ocular Preference
	  map, that is OR map overlaid with OD boundaries with the help of
	  overlaid_plots function.

	* [r8565] topo/commands/pylabplots.py:
	  Function overlaid_plots added for creating combined plots.
	  Combined plot is build from a template plot overlaid with
	  contours of another map, both specified in parameters.

2008-05-26  gerasymo

	* [r8564] topo/commands/analysis.py:
	  Scale of the presented input patterns for direction map
	  measurement increased to 0.6.

2008-05-23  jbednar

	* [r8563] examples/lissom_oo_or_od_dr.ty:
	  Added warnings

2008-05-23  gerasymo

	* [r8562] examples/lissom_oo_or_dr.ty,
	  topo/base/simulation.py,
	  topo/tkgui/editorwindow.py:
	  Added a variable item_scale, which determines the size of items
	  in diagram, to the Simulation class. It is used in editorwindow
	  for scaling determination. In lissom_oo_or_dr.ty, it can be
	  overwritten by the grid_layout as its parameter.

	* [r8561] examples/lissom_oo_or_dr.ty:
	  Set speed to be independent of retinal units.

	* [r8560]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Added note about enabling auto-props

	* [r8559] topo/commands/analysis.py:
	  Scale of presented input patterns for direction preference map
	  increased to 0.5; number of tested direction set to 6; max_speed
	  set to ensure equal distance moved with respect to sheet
	  coordinates.

2008-05-22  jbednar

	* [r8558] examples/lissom_oo_or_dr.ty,
	  examples/lissom_oo_or_od_dr.ty:
	  Fixed keywords

	* [r8557] topo/params/__init__.py:
	  Minor clarification

2008-05-22  gerasymo

	* [r8556] examples/lissom_oo_or_dr.ty:
	  Build default locations for Model editor.

	* [r8555] examples/lissom_oo_or_od_dr.ty:
	  Copied from lissom_oo_or_dr.ty -r 8527

	* [r8554] topo/commands/analysis.py:
	  Change for the direction map measurement: scale increased to 0.4,
	  because the previous of 0.2 was to low to be detected; max_speed
	  set according to the density of retina.

2008-05-21  gerasymo

	* [r8553] examples/lissom_oo_or_dr.ty:
	  Variable speed added for variation of translation speed of an
	  input pattern on the different retinas. Array strength added,
	  which is indexed by the variable speed and stores the LGN
	  afferent scale for different speeds to make the response stronger
	  (as in CMVC).

2008-05-20  jbednar

	* [r8552] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Temporarily (?) enabled docking to allow people to check it out

2008-05-20  gerasymo

	* [r8551] examples/lissom_oo_or_dr.ty:
	  Speed increased.

2008-05-19  jbednar

	* [r8550] examples/lissom_oo_or_dr.ty:
	  Minor fix to doc

2008-05-19  gerasymo

	* [r8549] examples/lissom_oo_or_dr.ty:
	  Simulation number corrected.

2008-05-19  jbednar

	* [r8548] topo/commands/basic.py:
	  Improved run_batch handling of filenames for command-line
	  parameters that are lists, so that dimensions=['OR','OD','DR']
	  gives dimensions=OR_OD_DR instead of something with brackets and
	  quotations

2008-05-19  gerasymo

	* [r8547] examples/lissom_oo_or_dr.ty:
	  Orientation of an input pattern set to zero at first; it is
	  defined later in Sweeper.

2008-05-19  jbednar

	* [r8546] doc/Future_Work/current_text.php:
	  Minor fix

	* [r8545] topo/plotting/plotgroup.py:
	  Added note

	* [r8544] topo/misc/numbergenerators.py:
	  Changed to use new organization of params/ as an example

	* [r8543] topo/params/__init__.py:
	  Temporarily (?) added Parameterized to simplify imports

2008-05-18  gerasymo

	* [r8542] examples/lissom_oo_or_dr.ty:
	  Added Sweeper for translation of input on retinas.

2008-05-18  ceball

	* [r8541] topo/base/cf.py,
	  topo/base/projection.py:
	  Moved get_projection_view() up to Projection, since it appears to
	  be valid for all Projections.

	* [r8540] topo/tkgui/topoconsole.py:
	  Improvement to docking (when windows start undocked, the dock
	  manager no longer appears then disappears).

	* [r8539] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Minor fixes for docking.

	* [r8538] topo/params/tk.py,
	  topo/tests/testplotgrouppanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py:
	  Renamed FrameManager to DockManager and made it work with
	  Toplevels that are turned into Frames (rather than Frames that
	  are turned into Toplevels). Made various related changes,
	  including fixes for SF #1963861 ('Problem opening and closing
	  Activity windows') and #1951348 ('Windows resize when Go is
	  clicked'). Code still requires cleanup in several places.

2008-05-17  gerasymo

	* [r8537] examples/lissom_oo_or_dr.ty:
	  Added Sweeper for translation of input patterns for different
	  retinas, but still with speed=0; so builds the same map as
	  lissom_oo_or.ty

	* [r8536] examples/lissom_oo_or_dr.ty:
	  Substituted class Opposite through arithmetic expression doing
	  the same.

	* [r8535] examples/lissom_oo_or_od.ty:
	  Deleted import copy; no need for this now since class Opposite,
	  which was using it, is no longer there.

2008-05-16  jbednar

	* [r8534] topo/base/sheet.py:
	  Cleaned up docstrings

	* [r8533] doc/News/index_text.php:
	  Added recent news

	* [r8532] examples/lissom_oo_or_od.ty:
	  Removed Opposite class now that NumberGenerators support
	  arithmetic.

	* [r8531] topo/misc/numbergenerators.py:
	  Added explicit NumberGenerator base class to provide support for
	  using NumberGenerators in arithmetic expressions (yielding other
	  NumberGenerators)

	* [r8530] examples/lissom_oo_or_od.ty:
	  Restored brightness differences between the two eyes, probably
	  omitted by mistake in previous checkin.

	* [r8529] topo/misc/commandline.py:
	  Added hack to make behavior in Emacs shell mode less confusing

	* [r8528] topo/base/arrayutils.py,
	  topo/base/cf.py,
	  topo/base/sheetcoords.py,
	  topo/misc/distribution.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py:
	  Removed obsolete references to Numeric in docstrings and comments

2008-05-15  gerasymo

	* [r8527] examples/lissom_oo_or_dr.ty:
	  Added 4 retinas and LGN lags; still identical input patterns for
	  all retinas (without translation), so produces the same map as
	  lissom_oo_or.ty

	* [r8526] examples/lissom_oo_or_dr.ty:
	  Copied from lissom_oo_or.ty -r 8223; then identical code for
	  different eyes and response types substituted with loops;
	  produces the same map as lissom_oo_or.ty

2008-05-14  jbednar

	* [r8525] doc/Reference_Manual/index_text.php:
	  Minor update

2008-05-14  ceball

	* [r8524] topo/__init__.py,
	  topo/base/__init__.py:
	  Corrected error in previous commit (moved numpy ufunc pickle
	  support to topo.__init__).

	* [r8523] topo/base/__init__.py,
	  topo/base/arrayutils.py:
	  Moved numpy ufunc pickle support from topo.base.arrayutils to
	  topo.__init__ so that it is always executed by Topographica.
	  Fixes unreported bug where a snapshot could not be saved if an
	  instance used a ufunc somewhere, but no function from
	  topo.base.arrayutils was imported.

	* [r8522] topo/misc/legacy.py:
	  Updated Simulation time_type legacy code. Fixes SF #1962509.

2008-05-13  gerasymo

	* [r8521] examples/lissom_oo_or_od.ty:
	  Added Opposite class and other infrastructure for running OD
	  sims, but still with identical patterns in the two eyes, and thus
	  still should match lissom_oo_or.ty. Also fixed to allow a single
	  eye again, with eyes=[''].

2008-05-13  jbednar

	* [r8520] topo/tkgui/projectionpanel.py:
	  Made Connection Field window title more useful

	* [r8519] doc/Reference_Manual/index_text.php:
	  Minor clarifications

	* [r8518] doc/News/index_text.php:
	  Added notes about -p and movies

	* [r8517] doc/Future_Work/current_text.php:
	  Removed unnecessary or completed tasks; added note to try Sphinx
	  instead of epydoc

	* [r8516] doc/Developer_Manual/ood_text.php,
	  doc/Developer_Manual/optimization_text.php:
	  Added useful links

	* [r8515] topo/patterns/random.py:
	  Added BinaryUniformRandom

	* [r8514] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Added simulation name to window titles

2008-05-12  jbednar

	* [r8513] examples/lissom_oo_or_od.ty:
	  Set keywords properly

2008-05-12  gerasymo

	* [r8512] examples/lissom_oo_or_od.ty:
	  Added two eyes; otherwise identical to lissom_oo_or.ty

	* [r8511] examples/lissom_oo_or_od.ty:
	  Rewritten with loops; only one eye; identical with
	  lissom_oo_or.ty

	* [r8510] examples/lissom_oo_or_od.ty:
	  Copied from lissom_oo_or.ty -r 8223; not yet any change to add OD

2008-05-10  ceball

	* [r8509] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py:
	  Cleanup of valid_context() and populate_*_param().

	* [r8508] topo/params/tk.py:
	  Made widgets in parameters frame expand horizontally to fill
	  space.

	* [r8507] doc/User_Manual/parameters_text.php,
	  doc/User_Manual/patterns_text.php,
	  topo/base/cf.py:
	  Made CFProjection set dynamic time fn to None for
	  weights_generator.

	* [r8506] topo/params/parameterized.py,
	  topo/patterns/basic.py,
	  topo/tests/testpatterngenerator.py:
	  Allowed Parameterized.set_dynamic_time_fn() to accept an
	  attribute name containing a list of subobjects (e.g.
	  'generators'). Avoids the need for subclasses to override
	  set_dynamic_time_fn().

2008-05-09  ceball

	* [r8505] doc/Future_Work/current_text.php:
	  Added some notes I've begun writing about parameters and dynamic
	  parameters (unfinished).

	* [r8504] topo/tests/testpatterngenerator.py:
	  Added beginning of test for Selector.

	* [r8503] topo/tests/testDynamicParameter.txt:
	  Added tests for set_dynamic_time_fn().

	* [r8502] topo/patterns/basic.py:
	  Made selector.set_dynamic_time_fn() apply also to generators.

	* [r8501] topo/params/__init__.py,
	  topo/params/parameterized.py:
	  Allowed set_dynamic_time_fn() to work for classes and instances.

	* [r8500] topo/tkgui/projectionpanel.py:
	  No visible change: removed parentheses I left behind by mistake.

2008-05-07  ceball

	* [r8499] topo/params/__init__.py,
	  topo/params/parameterized.py:
	  Allowed Parameterized instances to override dynamic parameters'
	  time_fns (trial).

2008-05-06  ceball

	* [r8498] topo/tkgui/projectionpanel.py:
	  Fixed GUI projection panel's laying out of CFs for non-square
	  projection bounds. (Fixes sf.net #1862101.)

	* [r8497] topo/plotting/plotgroup.py:
	  Fixed swapped axes. Saved projection plotgroups are now correct
	  for non-square CF bounds. Addresses part of sf.net #1862101.

	* [r8496] topo/tkgui/plotgrouppanel.py:
	  Ensure busy cursor is always replaced after a function has
	  finished executing.

	* [r8495] topo/params/tk.py:
	  Made TkParameterized 'change checking' code include a test for
	  identity if the test for equality fails.

	* [r8494] topo/params/__init__.py,
	  topo/params/parameterized.py,
	  topo/tests/testNumberParameter.txt:
	  Fixed comparison with None during parameter slot inheritance.
	  Fixes sf.net #1958401 (Can't use an mpq of FixedPoint instance as
	  a default value).

	* [r8493] topo/tests/testNumberParameter.txt:
	  Added comments.

	* [r8492] topo/tests/testplotgrouppanel.py:
	  Fixed failing test.

2008-05-05  ceball

	* [r8491] topo/params/tk.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py:
	  Moved status bars outside of scrollable region (info on status
	  bars should now always be visible - sf.net #1884341). Model
	  editor's parametersframe is now a themed window (i.e. has icon,
	  etc). These changes are mixed in with several other experimental
	  alterations to docking (should have no visible effect right now).

2008-05-04  ceball

	* [r8490] topo/params/tk.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Removed (trial) status bar from ParametersFrame. Improved status
	  bar handling for TkParameterizedObjects (there are still hacks in
	  a few places, but most windows now display reasonable information
	  in their own status bar while parameters are being edited).

2008-05-04  jbednar

	* [r8489] doc/Reference_Manual/index_text.php,
	  topo/base/__init__.py:
	  Updated to match recent changes in directory structure

	* [r8488] external/Makefile,
	  external/epydoc-3.0.1.tar.gz,
	  external/epydoc-3.0beta1.tar.gz:
	  Updated epydoc to handle . and .. imports

2008-05-04  ceball

	* [r8487] topo/params/tk.py:
	  Corrected copy method for CSPTranslator.

	* [r8486] topo/params/tk.py,
	  topo/tkgui/plotgrouppanel.py:
	  Added statusbar to ParametersFrame (trial). Minor cleanup.

	* [r8485] topo/params/__init__.py,
	  topo/params/parameterized.py,
	  topo/params/tk.py:
	  Updated svn:keywords.

	* [r8484] topo/params/tk.py:
	  No visible change - removed comment-out code.

	* [r8483] topo/params/tk.py:
	  Cleaned up type check. Removed another redundant one.

	* [r8482] topo/params/tk.py:
	  Fixed mistake in previous checkin.

	* [r8481] topo/params/tk.py:
	  Clarified an import.

	* [r8480] Makefile:
	  Fixed comparisons.

	* [r8479] Makefile:
	  Split cleaning pyc files from cleaning compiled c code.

2008-05-03  ceball

	* [r8478] topo/params/tk,
	  topo/params/tk.py:
	  Moved tk parameter support from package to module (i.e.
	  topo.params.tk is now a module).

	* [r8477] topo/tests/testplotgrouppanel.py:
	  Fixed import.

	* [r8476] topo/params/tk/__init__.py,
	  topo/params/tk/widgets.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/widgets.py:
	  Moved contents of topo.params.tk.widgets into
	  topo.params.tk.__init__

	* [r8475] topo/params/tk/widgets.py:
	  Clarified ALERT and cleaned up some formatting - no visible
	  change.

	* [r8474] topo/tests/testplotgrouppanel.py:
	  Fixed failing test.

	* [r8473] topo/params/tk/widgets.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/topowidgets.py:
	  Began incorporating status bar into default window. Moved
	  topoconsole-related widgets out of topowidgets and into
	  topoconsole.

	* [r8472] topo/params/tk/widgets.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/topoconsole.py:
	  Moved ControllableMenu from topo.params.tk to
	  topo.tkgui.topoconsolve.

	* [r8471] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  No visible change - silenced pylint warnings.

	* [r8470] topo/params/tk/__init__.py,
	  topo/params/tk/widgets.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/widgets.py:
	  Renamed TkguiWindow to AppWindow.

	* [r8469] topo/params/tk/__init__.py:
	  Minor cleanup - no visible changes.

	* [r8468] topo/tkgui/__init__.py:
	  Cleaned imports (no visible change).

	* [r8467] topo/params/tk/__init__.py:
	  Cleaned up initial docstring, and removed ERRORALERT about number
	  comparisons not matching (was fixed in an earlier revision).

	* [r8466] topo/params/parameterized.py:
	  No visible change - renamed a variable and converted a comment to
	  an ALERT.

	* [r8465] topo/patterns/__init__.py:
	  Restored 'del f' to patterns.__init__.

2008-05-02  jbednar

	* [r8464] examples/hierarchical.ty:
	  Cleaned up importing of outputfns and patterns

2008-05-02  ceball

	* [r8463] examples/hierarchical.ty,
	  topo/patterns/__init__.py,
	  topo/patterns/basic.py:
	  Imported classes from topo.patterns.basic into topo.patterns.

	* [r8462] topo/params/tk/__init__.py:
	  Removed topo.params.tk's depency on topo.

	* [r8461] topo/params/tk/__init__.py,
	  topo/tkgui/plotgrouppanel.py:
	  Removed params.tk's dependence on topo.guimain.

	* [r8460] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py,
	  topo/params/__init__.py,
	  topo/params/parameterized.py,
	  topo/params/tk/__init__.py,
	  topo/params/tk/widgets.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Renamed ParameterizedObject to Parameterized. (Updates to
	  topo/params/tk/ are only by search-and-replace - documentation
	  still needs editing.)

2008-04-29  jbednar

	* [r8459] Makefile:
	  Added uninstall target to main Makefile

2008-04-28  ceball

	* [r8458]
	  topo/tests/reference/lissom_oo_dr_reference.ty:
	  Fixed import.

	* [r8457] topo/tests/reference/common.param,
	  topo/tests/reference/lissom5.gz,
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/measure_dir_pref,
	  topo/tests/reference/measure_or_pref,
	  topo/tests/reference/or_defs,
	  topo/tests/reference/save_all_units.command,
	  topo/tests/reference/set_thresholds.command,
	  topo/tests/reference/support_clissom,
	  topo/tests/reference/support_clissom/common.param,
	  topo/tests/reference/support_clissom/lissom5.gz,
	  topo/tests/reference/support_clissom/measure_dir_pref,
	  topo/tests/reference/support_clissom/measure_or_pref,
	  topo/tests/reference/support_clissom/or_defs,
	  topo/tests/reference/support_clissom/save_all_units.command,
	  topo/tests/reference/support_clissom/set_thresholds.command:
	  Moved c++ lissom support files into a subdirectory (makes it
	  clear that these template files are not used by c++ lissom - only
	  copies in the binary directory are used).

	* [r8456]
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/oo_or_map_topo.param:
	  More cleanup after moving out old reference simulation.

	* [r8455] topo/tests/reference,
	  topo/tests/reference/010910_or_map_512MB.log.gz,
	  topo/tests/reference/Makefile,
	  topo/tests/reference/oo_dir_map.log.gz:
	  More tidy-up after moving out old reference simulation.

	* [r8454] topo/tests/reference/fixed_params:
	  Updated svn:ignore.

	* [r8453] Makefile, topo/tests/reference/:
	  Moved old, fixed-data reference simulation to new directory to
	  save clutter.

	* [r8452]
	  topo/tests/reference/lissom_log_parser.py:
	  Was missing a file to copy into the new simulation directory (had
	  no effect since c++ lissom was finding the file in the parent
	  directory - can that be prevented from happening?).

2008-04-27  ceball

	* [r8451] topo/params/tk/__init__.py:
	  Minor change to docstring.

	* [r8450] topo/tkgui/plotgrouppanel.py:
	  Changed to use new topo.params namespace.

	* [r8449] topo/params/tk/__init__.py,
	  topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Continued moving tk-parameter interface out of tkgui.

	* [r8448] topo/params/tk/widgets.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/topowidgets.py:
	  Moved StatusBar to tkgui.

	* [r8447] topo/params/tk/widgets.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/topowidgets.py:
	  Continued cleaning up locations of tkgui classes.

	* [r8446] topo/tkgui/widgets.py:
	  File missed from r8445.

	* [r8445] topo/params/tk,
	  topo/params/tk/__init__.py,
	  topo/params/tk/widgets.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Created topo.params.tk and began to move code from topo.tkgui.

	* [r8444] topo/tkgui/parametersframe.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Moved contents of parametersframe.py into tkparameterized.py (in
	  anticipation of tkparameterized.py's removal to
	  topo/params/tk/__init__.py).

	* [r8443] topo/tkgui/parametersframe.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/widgets.py:
	  Made TkguiWindow more general (apart from the name).

	* [r8442] topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/topowidgets.py,
	  topo/tkgui/widgets.py:
	  Moved TkguiWindow into widgets (TkguiWindow will be generalized
	  in the future.

	* [r8441] topo/tkgui/topowidgets.py:
	  Removed unused code.

	* [r8440] topo/misc/utils.py:
	  File missed from r8439.

	* [r8439] topo/tkgui/parametersframe.py:
	  Moved keys_sorted_by_value() to tkgui/parametersframe (the only
	  place it's used), and removed values_sorted_by_key() (which has
	  remained unused for almost 2 years).

	* [r8438] topo/misc/utils.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/tkparameterizedobject.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/widgets.py:
	  Began cleanup of imports for moving out parameter interface
	  (intermediate checkin).

2008-04-26  ceball

	* [r8437] topo/params:
	  Updated svn:ignore

	* [r8436] /trunk/topographica:
	  Updated svn:ignore

	* [r8435] external:
	  Updated svn:ignore

	* [r8434] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py,
	  topo/params,
	  topo/params/__init__.py,
	  topo/params/parameterized.py:
	  Began moving Parameters to topo/params.

	* [r8433]
	  topo/tests/testtkparameterizedobject.py:
	  Updates to match new handling of numbers in GUI.

	* [r8432] topo/misc/utils.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Removed eval_atof().

	* [r8431] topo/tkgui/tkparameterizedobject.py:
	  Removed special handling of numbers from the GUI (now they are
	  handled just as Parameters are - the same as if they were typed
	  at the commandline).

	* [r8430] doc/Downloads/cvs_text.php:
	  Updated links to buildbot builds (not sure if linking to 'Fedora,
	  OS X 10.5, Ubuntu 7' is the most helpful way for users).

	* [r8429] doc/buildbot/index.html,
	  doc/buildbot/master.cfg:
	  Added lodestar buildslave, tried to simplify names so we know
	  which build is which.

2008-04-25  ceball

	* [r8428] topo/tkgui/topoconsole.py:
	  Fixed Help menu items (fixed creation of 1-tuples).

	* [r8427] topo/tkgui/plotgrouppanel.py:
	  Fixed removal of panel from topoconsole's auto_refresh_panels.

	* [r8426] external/pyscrodget-0.0.1_2.1.tar.gz:
	  Marked gz gile as binary.

	* [r8425] topo/tkgui/topoconsole.py:
	  Added workaround for problem with 'Quit' dialog box.

	* [r8424] Makefile:
	  Stop make clean from halting if it can't remove
	  ~/.python2*_compiled.

	* [r8423] external/Makefile:
	  Added back blt to python target. Fixed 'clean' and 'uninstall'
	  targets by removing things that had crept back in during various
	  merges.

	* [r8422] topo/tkgui/topoconsole.py:
	  Commented out topoconsole's frame manager (since there is
	  currently no docking).

	* [r8421] topo/tkgui/editorobjects.py,
	  topo/tkgui/widgets.py:
	  Commented out balloon tagbind() calls (I think they were not
	  working anyway).

	* [r8420] topo/tkgui/plotgrouppanel.py:
	  Commented out dock option. Clarified an ALERT.

	* [r8419] topo/tkgui/plotgrouppanel.py:
	  Added ALERT.

	* [r8418] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Uncommented frame manager, and fixed some problems. (I think some
	  changes I made disappeared a while ago in one of the trips this
	  branch has taken between svn, bazaar, and git.)

	* [r8417] topo/tkgui/parametersframe.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Added right-click menu for parameters, allowing switching between
	  dynamic and non-dynamic represenations for Dynamic parameters.

	* [r8416] topo/tkgui/parametersframe.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Began to update code to allow switching of dynamic numbers in
	  GUI. (This change is untested.)

	* [r8415] topo/tkgui/widgets.py:
	  TaggedSlider: mouse <Leave>s tag is now the same as tag losing
	  focus.

	* [r8414] topo/tkgui/__init__.py:
	  Removed ALERT.

	* [r8413] topo/tkgui/widgets.py:
	  Removed stray variable.

	* [r8412] topo/tkgui/widgets.py:
	  Generalized cursor handling (old cursor put back, not all widgets
	  have cursor(?).

	* [r8411] topo/tkgui/topoconsole.py:
	  FrameManager currently not being used, so stopped it from being
	  displayed.

	* [r8410] topo/tkgui/__init__.py,
	  topo/tkgui/topoconsole.py:
	  Menubar on every OS X window (this version not actually tested on
	  OS X).

	* [r8409] topo/tests/gui_tests.py:
	  Removed outdated test.

	* [r8408] topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py:
	  Restored model editor display customizations (so it's suitable
	  for use now; hoses tile compatibility).

	* [r8407] topo/tkgui/tkparameterizedobject.py:
	  Added BoolTranslator. Fixes test errors, but is it really
	  necessary? What changed about BooleanVar between 8.4 and 8.5?

	* [r8406] topo/tests/testplotgrouppanel.py:
	  Updated PlotGroupPanel opening (console no longer passed around).

	* [r8405] topo/tkgui/featurecurvepanel.py:
	  Updated FeatureCurvePanel (was missed in a previous commit -
	  console no longer passed around).

	* [r8404] topo/tkgui/plotgrouppanel.py:
	  Hide dock option (for now).

	* [r8403] topo/tkgui/topoconsole.py:
	  Fixed error creating ProgressController.

	* [r8402] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Fixed plot centering.

	* [r8401] topo/tkgui/editortools.py:
	  Added ALERT.

	* [r8400] topo/tkgui/topoconsole.py,
	  topo/tkgui/widgets.py:
	  Made windows automatically resize again even after manual
	  adjustment.

	* [r8399] topo/tkgui/tkparameterizedobject.py:
	  Removed unused import statement.

	* [r8398] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Added hack to keep Combobo readonly.

	* [r8397] external/Makefile:
	  Removed blt requirement (didn't test blt, it might work fine with
	  tcl/tk 8.5)

	* [r8396] topo/tkgui/tkparameterizedobject.py,
	  topo/tkgui/widgets.py:
	  Replaced obsolete OptionMenu (and EditableOptionMenu) with
	  Combobox.

	* [r8395] topo/tkgui/parametersframe.py:
	  Removed unused method.

	* [r8394] topo/tkgui/editortools.py:
	  Removed unused import.

	* [r8393] external/Makefile,
	  external/Pmw.diff,
	  external/Pmw.tgz,
	  external/Tile.py,
	  external/Tile.py.gz,
	  external/pybwidget-0.1.2_1.7.0.tar.gz,
	  external/pybwidget-0.1.2_1.8.0.tar.gz,
	  external/pyscrodget-0.0.1_2.1.tar.gz,
	  external/snit1.0.tar.gz,
	  external/tcl8.4.13-src.tar.gz,
	  external/tcl8.5.1-src.tar.gz,
	  external/tile-0.7.8.tar.gz,
	  external/tk8.4.13-src.tar.gz,
	  external/tk8.5.1-src.tar.gz,
	  external/tklib-CVS20080114.tar.gz,
	  topo/tests/testtemplateplotgrouppanel.py,
	  topo/tests/testtopoconsole.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/tkparameterizedobject.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/topowidgets.py,
	  topo/tkgui/widgets.py:
	  Multiple changes from broken Git repository:
	  
	  Author: C. E. Ball <ceball@users.sf.net>
	  Date: Thu Feb 21 01:08:12 2008 +0000
	  
	  Switched from OptionMenu to read-only Combobox.
	  
	  Author: C. E. Ball <ceball@users.sf.net>
	  Date: Thu Feb 21 01:07:38 2008 +0000
	  
	  Switch to use 'classic' theme so that any themed widgets do not
	  stand out too much for the moment.
	  
	  Author: C. E. Ball <ceball@users.sf.net>
	  Date: Thu Feb 21 01:06:33 2008 +0000
	  
	  Added hack to work round strange parsing of list for Combobox's
	  values.
	  
	  Author: C. E. Ball <ceball@users.sf.net>
	  Date: Wed Feb 20 23:09:32 2008 +0000
	  
	  Updated ProgressWindow with changes to TkguiWindow.
	  
	  Author: C. E. Ball <ceball@users.sf.net>
	  Date: Wed Feb 20 19:05:39 2008 +0000
	  
	  Hacks to deal with the fact that users of ScrolledFrame must use
	  its content attribute as their master.
	  
	  Author: C. E. Ball <ceball@users.sf.net>
	  Date: Wed Feb 20 18:11:35 2008 +0000
	  
	  FrameManager deals with ScrolledFrames instead of Frames.
	  
	  Author: C. E. Ball <ceball@users.sf.net>
	  Date: Wed Feb 20 18:00:59 2008 +0000
	  
	  Made ScrolledWindow use ScrolledFrame.
	  
	  Author: C. E. Ball <ceball@users.sf.net>
	  Date: Wed Feb 20 17:48:37 2008 +0000
	  
	  Added ScrolledFrame.
	  
	  Author: C. E. Ball <ceball@users.sf.net>
	  Date: Wed Feb 20 17:36:27 2008 +0000
	  
	  Upgraded tcl/tk to 8.5.1.
	  
	  Author: C. E. Ball <ceball@users.sf.net>
	  Date: Mon Feb 18 07:06:45 2008 +0800
	  
	  Imported launchpad.net bzr r7822, plus minor alterations to some
	  docstrings.

2008-04-24  jbednar

	* [r8392] contrib/jacommands.py:
	  Removed obsolete FixedPoint

2008-04-24  antolikjan

	* [r8391]
	  examples/gc_lissom_oo_or_homeostatic.ty:
	  updated to use the new projection activity integration mechanism

	* [r8390] contrib/jacommands.py:
	  updated to use the new projection activity integration mechanism

	* [r8389]
	  examples/gc_lissom_oo_or_homeostatic_new.ty:
	  updated to use the new projection activity integration mechanism

2008-04-24  jbednar

	* [r8388] examples/goodhill_network90.ty:
	  Removed stray import

2008-04-24  ceball

	* [r8387] examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/ohzawa_science90.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty:
	  Removed explicit specification of mpq for connection delay
	  (because the delay is coerced into an mpq anyway when added to
	  the simulation time).

2008-04-23  jbednar

	* [r8386] examples/cc_lissom_oo_or.ty,
	  examples/cc_lissom_oo_or_new.ty,
	  examples/gc_lissom_oo_or_homeostatic.ty,
	  examples/gc_lissom_oo_or_homeostatic_new.ty,
	  examples/goodhill_network90.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/saccade_demo.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty:
	  Removed references to FixedPoint

2008-04-23  ceball

	* [r8385] doc/Future_Work/current_text.php:
	  Added task.

	* [r8384] doc/Future_Work/current_text.php,
	  doc/News/index_text.php:
	  Updates to reflect recent changes.

	* [r8383] external/Makefile:
	  Added gmpy to the list of default targets.

2008-04-22  ceball

	* [r8382] external/Makefile:
	  Made gmpy installation able to find our copy of gmp.

	* [r8381] topo/base/parameterclasses.py,
	  topo/tests/testEnumerationParameter.txt:
	  Cleaned up Enumeration.

	* [r8380] topo/patterns/basic.py,
	  topo/patterns/teststimuli.py:
	  Removed unused import.

	* [r8379] topo/__init__.py:
	  Added pickle support for gmpy.mpq (I have no idea how to patch
	  gmpy itself).

	* [r8378] topo/__init__.py:
	  Switched from mxnumber to gmpy.

	* [r8377] external/Makefile:
	  Added gmpy to 'clean' and 'uninstall' targets.

	* [r8376] topo/misc/commandline.py:
	  Use topo.sim.timestr() to format the command prompt time.

2008-04-21  ceball

	* [r8375] external/gmpy-sources-101.tar.gz:
	  Fixed direcdtory name error.

	* [r8374] external/Makefile,
	  external/gmpy-sources-101.tar.gz:
	  Added gmpy (wraps GMP; repackaged from .zip file at gmpy.sf.net)

2008-04-20  ceball

	* [r8373] topo/patterns/basic.py:
	  No visible change - removed unnecessary variable.

	* [r8372] topo/patterns/basic.py:
	  Simplified and corrected Translator (or, misunderstood its
	  purpose and removed required code).

	* [r8371] topo/patterns/basic.py:
	  Added ALERT.

	* [r8370] examples/lissom_oo_dr.ty:
	  No visible changes: cleanup of formatting (to fit my screen
	  width...).

	* [r8369]
	  topo/tests/reference/common_control.py,
	  topo/tests/reference/lissom_log_parser.py:
	  Simplifications to checking: always checks both weights and
	  activities (at the expense of using more disk space and taking
	  slightly longer to run).

2008-04-19  jbednar

	* [r8368] doc/Future_Work/current_text.php:
	  Added notes about coverage testing

	* [r8367] topo/base/functionfamilies.py:
	  Removed outdated docstring

	* [r8366] topo/commands/basic.py:
	  Moved activity plot after OR map for run_batch, to get correct
	  colorizations. Added LGN OFF (and all other afferents) plot

	* [r8365] contrib/__init__.py:
	  Removed bogus items inherited when copied from
	  topo/commands/__init__.py

2008-04-16  antolikjan

	* [r8364] topo/base/projection.py:
	  updated the mechanism of activity integration over projections in
	  the ProjectionSheet.activate method. The ports are not used any
	  more to identify projection groups

2008-04-12  ceball

	* [r8363]
	  topo/tests/reference/common_control.py:
	  Fixed minor mistake where activities were checked before weights.

	* [r8362]
	  topo/tests/reference/lissom_oo_dr_reference.ty:
	  Continued setting up to try to match c++ simulation (now the
	  topographica and c++ lissom simulations look similar, but the
	  initial pattern on the retina is very slightly different).

	* [r8361]
	  topo/tests/reference/lissom_log_parser.py:
	  Fixed problem where minus signs were not detected in lissom's log
	  file (and also changed method for retrieving sign from lissom's
	  log file - which I did because I thought the original method was
	  broken, until I found the minus sign problem; the newer method is
	  clearer anyway).

2008-04-12  jbednar

	* [r8360] topo/base/projection.py:
	  Undid previous change to ProjectionSheet.activate() until it can
	  be done consistently

2008-04-12  ceball

	* [r8359]
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/measure_dir_pref:
	  Added measure_dir_pref from c++ lissom.

	* [r8358]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Include exc_rad in parameters passed to c++ lissom.

2008-04-11  jprovost

	* [r8357] topo/base/projection.py:
	  Moved .send_output() call from ProjectionSheet.activate() into
	  ProjectionSheet.process_current_time() to improve modularity.

	* [r8356] topo/misc/playerrobot.py,
	  topo/misc/robotics.py:
	  Changes toward eventual support of true multiprocessing for the
	  player polling loop.

2008-04-11  antolikjan

	* [r8355] topo/base/projection.py:
	  first step in updating projection.activate()

2008-04-11  ceball

	* [r8354]
	  topo/tests/reference/lissom_log_parser.py:
	  Added in extra weights saving to c lissom command.

	* [r8353] topo/tests/reference/topo_or_defs.py:
	  All initial radii for weights now end in .5 (for odd weights
	  matrices, and so that the radii are exactly half the matrix
	  width).

	* [r8352]
	  topo/tests/reference/lissom_or_reference.ty:
	  Include exc_rad in params passed to lissom.

	* [r8351]
	  topo/tests/reference/common_control.py,
	  topo/tests/reference/lissom_log_parser.py:
	  Set exc_rad in param file. Added function to check only array
	  sizes (the comparisons functions already check sizes, but this
	  function is to check only the sizes).

2008-04-10  antolikjan

	* [r8350] contrib/mycommands.py:
	  

2008-04-09  jprovost

	* [r8349] doc/Reference_Manual/index_text.php:
	  Added blurb about the processing external package.

2008-04-09  ceball

	* [r8348]
	  topo/tests/reference/lissom_oo_dr_reference.ty:
	  Copied Sweeper class into oo_dr reference file so I can modify it
	  while testing.

	* [r8347]
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/oo_dir_map.param:
	  Updated oo_dr reference simulations.

	* [r8346]
	  topo/tests/reference/010910_oo_or_map_512MB.param,
	  topo/tests/reference/010910_or_map_512MB.param,
	  topo/tests/reference/common.param:
	  Simplified param files for c++ lissom; should be no visible
	  change.

	* [r8345] topo/tests/reference/topo_or_defs.py:
	  Added min_exc_rad for change_bounds.

	* [r8344]
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty:
	  Corrected mistake in previous checkin.

	* [r8343]
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty:
	  Use min_exc_rad when creating lateral excitatory connections.

	* [r8342]
	  topo/tests/reference/common_control.py,
	  topo/tests/reference/lissom_log_parser.py:
	  Made weights tests match times when bounds change.

	* [r8341]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Minor simplification - no visible change.

	* [r8340]
	  topo/tests/reference/common_control.py,
	  topo/tests/reference/lissom_log_parser.py:
	  Made tests check weights before activities; added extra weights
	  test.

	* [r8339] topo/tests/reference/topo_or_defs.py:
	  Simplified typing for changing excitatory bounds (should be no
	  visible change). Added min_exc_rad.

2008-04-08  jprovost

	* [r8338] topo/sheets/generatorsheet.py:
	  Stored periodic event in SequenceGenerator sheet, for future
	  reference.

2008-04-08  ceball

	* [r8337]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Removed duplicate scheduled action.

	* [r8336]
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/topo_or_defs.py:
	  Continued generalizing oo_or reference simulation.

	* [r8335]
	  topo/tests/reference/010910_oo_or_map_512MB.param,
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Continued simplifying oo_or reference simulation.

2008-04-07  jprovost

	* [r8334] external/Makefile,
	  external/processing-0.51.tar.gz:
	  - Added processing library.
	  - Added support for using config flags with player.

2008-04-06  ceball

	* [r8333]
	  topo/tests/reference/010910_oo_or_map_512MB.param,
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Continued simplifying oo_or reference simulation.

	* [r8332] Makefile:
	  Made compare_oo_or continue to use checked-in data (for now).

	* [r8331] topo/tests/reference/topo_or_defs.py:
	  Added rf_radius_scale to topo_or_defs.

	* [r8330]
	  topo/tests/reference/lissom_oo_dr_reference.ty:
	  oo_dr reference simulation: Correction to input parameters.

	* [r8329]
	  topo/tests/reference/common_control.py,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty:
	  Use sheets' precedence values to determine order of checking.

	* [r8328]
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/oo_dir_map.param:
	  Began simplifying oo_dr reference simulation.

	* [r8327]
	  topo/tests/reference/010910_oo_or_map_512MB.param,
	  topo/tests/reference/common_control.py,
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Copied oo_or_map_topo.param to 010910_oo_or_map_512MB.param.

2008-04-05  ceball

	* [r8326] Makefile,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference_old.ty,
	  topo/tests/reference/oo_or_map_topo.param,
	  topo/tests/reference/oo_or_map_topo_old.param:
	  Simplified oo_or reference simulation.

	* [r8325]
	  topo/tests/reference/oo_or_map_topo_old.param:
	  Copied oo_or_map_topo.param, so that we still have a version for
	  use with the checked-in data.

	* [r8324] topo/tests/test_script.py:
	  Allowed specification of script for 'multiple densities' test
	  function.

	* [r8323]
	  topo/tests/reference/lissom_oo_or_reference_old.ty:
	  Copied lissom_oo_or_reference.ty to
	  lissom_oo_or_reference_old.ty, so we still have a version that
	  uses checked-in data.

	* [r8322]
	  topo/tests/reference/lissom_or_reference.ty:
	  Minor changes - should be no visible change.

	* [r8321]
	  topo/tests/reference/lissom_log_parser.py:
	  Fixed error when writing rf_radius into params file.

	* [r8320]
	  topo/tests/reference/common_control.py,
	  topo/tests/reference/save_all_units.command:
	  Made save_all_units.command (and equivalent topo testing fn) skip
	  some units.

	* [r8319]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Minor cleanup - no visible change.

	* [r8318]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Began simplifying oo_or reference (should be no visible change).

	* [r8317]
	  topo/tests/reference/lissom_or_reference.ty:
	  Made minor formatting changes.

2008-04-04  jbednar

	* [r8316] topo/commands/pylabplots.py:
	  Updated usage tip

2008-04-04  judelaw

	* [r8315] topo/commands/pylabplots.py:
	  removed references to matplotlib.use for specifying a backend,
	  now done in commandline.py

	* [r8314] topo/commands/basic.py:
	  removed references to matplotlib.use for specifying a backend,
	  now done in commandline.py

2008-04-03  jprovost

	* [r8313] topo/sheets/saccade.py:
	  Added SaccadeController.command_mapper parameter, that can take a
	  CoordMapperFn to remap the saccade command after it is computed
	  from the sheet activity.

	* [r8312] topo/base/cf.py:
	  Clarified docstring.

2008-04-02  jbednar

	* [r8311] examples/lissom_oo_or_species.ty:
	  Fixed too-high density

	* [r8310] examples/lissom_oo_or_species.ty:
	  Initial version using rough parameters worked out with Tom

2008-04-02  judelaw

	* [r8309] topo/misc/commandline.py:
	  Removed print statement from debugging matplotlib backend

	* [r8308] topo/misc/commandline.py:
	  Made sure that matplotlib uses Agg as default backend unless gui
	  is used, in which case it defaults to TkAgg

2008-04-02  ceball

	* [r8307]
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/reference/topo_or_defs.py:
	  Moved scheduled actions into topo_or_defs.py.

	* [r8306]
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/reference/topo_or_defs.py,
	  topo/tests/test_script.py:
	  Restricted matching tests to densities high enough to get weights
	  of at least 3x3.

2008-04-01  ceball

	* [r8305]
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/reference/topo_or_defs.py:
	  Moved definitions of variables into new file.

	* [r8304]
	  topo/tests/reference/lissom_or_reference.ty:
	  Update to docstring.

	* [r8303]
	  topo/tests/reference/common_control.py,
	  topo/tests/reference/lissom_or_reference.ty:
	  Minor simplification.

	* [r8302]
	  topo/tests/reference/common_control.py,
	  topo/tests/reference/lissom_or_reference.ty:
	  Moved out common comparison code from lissom_or_reference.py into
	  common_control.py

	* [r8301]
	  topo/tests/reference/lissom_or_reference.ty:
	  No visible change - renamed a function.

	* [r8300]
	  topo/tests/reference/lissom_or_reference.ty:
	  Removed unnecessary n_units() function.

	* [r8299]
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/lissom_or_reference.ty:
	  No visible change: moved general functions out of
	  lissom_or_reference.ty, into lissom_log_parser.py.

	* [r8298]
	  topo/tests/reference/lissom_or_reference.ty:
	  No visible change: fixes to formatting.

	* [r8297] doc/Future_Work/current_text.php:
	  Added task.

	* [r8296]
	  topo/tests/reference/lissom_oo_dr_reference.ty:
	  Set learning rate on all afferents.

	* [r8295]
	  topo/tests/reference/lissom_log_parser.py:
	  Fixed recovery of sign in input params.

2008-03-31  antolikjan

	* [r8294] contrib/jaanalysis.py:
	  applying the renaming

	* [r8293] contrib/jaanalysis.py:
	  renaming

	* [r8292] contrib/jacommands.py:
	  renaming

	* [r8291] contrib/mycommands.py:
	  added movie saving

2008-03-30  ceball

	* [r8290]
	  topo/tests/reference/lissom_or_reference.ty:
	  Made inh and aff weight matrices be odd (whatever densities are
	  specified), to match what Topographica already enforces.

2008-03-29  ceball

	* [r8289]
	  topo/tests/reference/lissom_or_reference.ty:
	  Turned off autosize_mask.

	* [r8288]
	  topo/tests/reference/lissom_or_reference.ty:
	  Allowed 1x1 CFs.

	* [r8287]
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/test_script.py:
	  Various improvements to output of multiple density comparisons,
	  plus fixed return code error.

	* [r8286] topo/tests/test_script.py:
	  Removed mistake in previous commit.

	* [r8285] Makefile,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/test_script.py:
	  Made the output of multiple density comparisons easier to
	  understand.

	* [r8284]
	  topo/tests/reference/lissom_log_parser.py:
	  Missed from previous checkin.

	* [r8283]
	  topo/tests/reference/lissom_log_parser.py:
	  Added more info to exceptions.

2008-03-28  ceball

	* [r8282] doc/buildbot/master.cfg:
	  Added or_comparisons to c++ tests.

	* [r8281]
	  topo/tests/reference/lissom_or_reference.ty:
	  Made lissom5 binary executable for or_comparisons.

	* [r8280] Makefile:
	  Added or_comparisons target.

	* [r8279]
	  topo/tests/reference/lissom_or_reference.ty:
	  Added temporary option to or_reference to allow shorter
	  comparison.

	* [r8278] topo/tests/test_script.py:
	  Added function to run combinations of densities for or_reference.

	* [r8277]
	  topo/tests/reference/lissom_log_parser.py:
	  Made C++ comparison functions print out a little more info.

	* [r8276]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Specified FixedPoint explicitly.

	* [r8275] Makefile,
	  topo/tests/reference/lissom_or_reference.ty:
	  Clunky modifications to allow specification of BaseRN and BaseN
	  from commandline, along with auto-generation of appropriate C++
	  lissom data.

	* [r8274]
	  topo/tests/reference/010910_or_map_512MB.param:
	  Minor alteration to formatting - no visible change.

	* [r8273]
	  topo/tests/reference/lissom_or_reference.ty:
	  Added weights tests at first few iterations.

	* [r8272] Makefile:
	  Removed lissom_or_noshrinking from list of scripts for
	  slow-tests.

	* [r8271] doc/buildbot/master.cfg:
	  Various simplifications.

2008-03-27  antolikjan

	* [r8270] topo/outputfns/basic.py:
	  removed debugging printouts

2008-03-27  ceball

	* [r8269] topo/outputfns/basic.py:
	  Commented out lines with faulty indentation.

	* [r8268] topo/patterns/basic.py:
	  Added question.

2008-03-26  antolikjan

	* [r8267]
	  examples/gc_lissom_oo_or_homeostatic_new.ty:
	  

	* [r8266] examples/cc_lissom_oo_or_new.ty:
	  made core_size work properly

	* [r8265] examples/cc_lissom_oo_or.ty:
	  made core_size work properly

	* [r8264] contrib/mycommands.py:
	  

	* [r8263] contrib/jansanalyzisfunctions.py:
	  

	* [r8262] topo/outputfns/basic.py:
	  Added new output function CascadeHomeostatic

	* [r8261] examples/v2_cc_lissom_oo_or.ty:
	  Deleting

	* [r8260] examples/cc_lissom_oo_or.ty:
	  

	* [r8259]
	  examples/gc_lissom_oo_or_homeostatic_new.ty:
	  

	* [r8258] topo/patterns/basic.py:
	  Modified Translator to allow zero stimuly between sweeps

	* [r8257] contrib/mycommands.py:
	  

	* [r8256] examples/cc_lissom_oo_or_new.ty:
	  changed loads of things

2008-03-26  ceball

	* [r8255]
	  topo/tests/reference/lissom_or_reference.ty:
	  Altered c++ lissom command to avoid production of ppm plots.

	* [r8254]
	  topo/tests/reference/lissom_or_reference.ty:
	  Specify FixedPoint explicitly.

	* [r8253]
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/reference/save_all_units.command:
	  Added c++ lissom command to save .matrix files for all units.
	  Made lissom_or_reference compare all units' weights (and reduced
	  number of times the weights comparisons happen). (This commit is
	  from multiple git commits; I get a segmentation fault whenever
	  trying to 'git-svn dcommit').

	* [r8252]
	  topo/tests/reference/lissom_or_reference.ty:
	  Corrected setting of exc_rad (has no effect at density 24).

	* [r8251] doc/Downloads/cvs_text.php:
	  Added comment.

	* [r8250] doc/Downloads/cvs_text.php:
	  Added some comments.

	* [r8249] external/Makefile:
	  Removed mxnumber from the default target because it causes a
	  problem with snapshots (needs to be resolved). Added mxnumber and
	  gmp to clean and uninstall targets.

	* [r8248] Makefile,
	  topo/misc/inlinec.py:
	  Cleaned up 'import_weave'.

	* [r8247] external/psyco-dist-svn52800.tar.gz:
	  Initial version.

	* [r8246] topo/misc/commandline.py:
	  Removed a change accidentally committed in previous version.

	* [r8245] topo/misc/commandline.py:
	  Added a trial 'psyco' startup option.

	* [r8244] external/Makefile:
	  Added mxnumber to default target (so lissom_oo_or will use
	  mx.Number.Float; the other examples are still setup to use
	  FixedPoint).

2008-03-25  ceball

	* [r8243] doc/buildbot/master.cfg:
	  Simplified creation of builders (should be no visible change).

2008-03-24  ceball

	* [r8242] doc/Future_Work/current_text.php:
	  Added note to myself.

2008-03-23  jbednar

	* [r8241] topo/base/simulation.py:
	  Cleaned up docs

2008-03-22  ceball

	* [r8240] doc/Future_Work/current_text.php,
	  topo/tests/test_script.py:
	  Added task. Minor change to comment.

2008-03-21  antolikjan

	* [r8239] examples/cc_lissom_oo_or_new.ty:
	  few parameter modifications

2008-03-21  ceball

	* [r8238] doc/Future_Work/current_text.php:
	  Moved task to tracker.

	* [r8237] doc/Future_Work/current_text.php:
	  Updated task assignments.

	* [r8236]
	  topo/tests/reference/lissom_or_reference.ty:
	  Simplified weights checks. Test should be unchanged.

	* [r8235]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Changed to use unsituate() function rather than specifying slice
	  for each weights comparison: test should be unchanged.

	* [r8234]
	  topo/tests/reference/lissom_log_parser.py:
	  Added function to guess at unsituated weights from c++ lissom.
	  Also made various minor changes to other functions.

2008-03-20  antolikjan

	* [r8233]
	  examples/gc_lissom_oo_or_homeostatic_new.ty:
	  updated version of gc_lissom_oo_or_homeostatic

	* [r8232]
	  examples/gc_lissom_oo_or_homeostatic.ty:
	  adapted to new AttributeTrackingOF

	* [r8231] topo/analysis/vision.py:
	  changed default analysis parameters

	* [r8230] contrib/mycommands.py:
	  

	* [r8229] contrib/jansanalyzisfunctions.py:
	  corrected few import bugs

2008-03-19  ceball

	* [r8228] topo/misc/legacy.py:
	  Added support for old snapshots: create cfs array if it doesn't
	  already exist.

	* [r8227] topo/base/cf.py,
	  topo/commands/analysis.py,
	  topo/learningfns/projfns.py,
	  topo/plotting/plotgroup.py,
	  topo/projections/basic.py,
	  topo/responsefns/projfns.py,
	  topo/sheets/lissom.py,
	  topo/sheets/optimized.py,
	  topo/tests/testcf.py:
	  Made CFProjection hold the CFs in an array (the list of lists of
	  cfs remains as _cfs for access by optimized weave functions).

	* [r8226] doc/buildbot/master.cfg:
	  Added unoptimized train-tests to buildbot's linux slow-tests.

	* [r8225] Makefile,
	  topo/misc/inlinec.py:
	  Hacks to allow buildbot to run slow-tests with unoptimized
	  components.

	* [r8224] topo/base/simulation.py:
	  Fixed Simulation's handling of register, so that a Simulation is
	  correctly a singleton or not. Moved most of the
	  singleton-specific code into a separate class. Although the
	  'register' behavior is now correct and passes the unit tests, the
	  implementation might change.

	* [r8223] examples/cfsom_or.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/som_retinotopy.ty:
	  Removed explicit request for FixedPoint from some examples.
	  (These examples will continue to use FixedPoint by default, since
	  mxNumber is not yet built by default.)

2008-03-18  jprovost

	* [r8222] examples/lissom_or_movie.ty,
	  topo/misc/traces.py,
	  topo/plotting/bitmap.py:
	  Some improvements to font and title handling for MontageBitmaps
	  and ActivityMovies.

2008-03-18  jbednar

	* [r8221] examples/lissom_or_movie.ty:
	  Set up with an always-available TTF font, made work regardless of
	  where it was run in the filesystem, added missing import, and
	  cleaned up docs slightly

2008-03-18  jprovost

	* [r8220] examples/lissom_or_movie.ty,
	  topo/plotting/bitmap.py:
	  Added an example of how to generate activity movies.

2008-03-18  ceball

	* [r8219]
	  examples/gc_lissom_oo_or_homeostatic.ty:
	  Missed from a previous commit: weights_shape was renamed to
	  cf_shape.

	* [r8218] doc/Future_Work/current_text.php:
	  Added note.

	* [r8217] examples/cfsom_or.ty,
	  examples/goodhill_network90.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/saccade_demo.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  topo/base/simulation.py:
	  Added set_time_type to Simulation to allow scripts to choose a
	  new type of time easily. Examples should be unchanged, since they
	  remain using FixedPoint.

	* [r8216] topo/__init__.py:
	  Set Simulation's default time_type to mx.Number.Float (if
	  available - otherwise, uses fixedpoint.FixedPoint).

	* [r8215] topo/base/simulation.py:
	  Added time_type and time_type_args parameters to Simulation.

	* [r8214] topo/base/parameterizedobject.py:
	  Made as_uninitialized be a function. Should be no visible change.

	* [r8213] topo/tests/testsimulation.py:
	  Added test to show that when unpickling a Simulation, the class's
	  register value is used (rather than that from the instance being
	  unpickled).

	* [r8212] topo/base/simulation.py:
	  Fixed copying of register=False simulations.

	* [r8211] topo/tests/testsimulation.py:
	  More corrections to register=False test (still fails, which is
	  correct).

	* [r8210] topo/tests/testsimulation.py:
	  Testing Simulation's register parameter: Made pickle use protocol
	  2 (the same as we use in save_snapshot), and corrected
	  register_is_false test to show that copy & deepcopy of a
	  Simulation(register=False) instance are currently broken.

	* [r8209] topo/base/simulation.py:
	  Clarified comments about Simulation.

2008-03-17  jbednar

	* [r8208] topo/commands/pylabplots.py:
	  Trivial simplification

2008-03-17  ceball

	* [r8207] topo/base/cf.py:
	  Fixed typo in change_bounds, which was causing the old bounds
	  template to be used, rather than the new one.

	* [r8206] topo/base/cf.py:
	  Same fix as in r8204, but for change_bounds().

2008-03-17  judelaw

	* [r8205] topo/commands/pylabplots.py:
	  updated plot_tracked_attributes() to only show unit coordinates
	  on graph key to 2 decimal places

2008-03-16  ceball

	* [r8204] topo/base/cf.py:
	  Copy mask into each CF: fixes strange problem with artefacts
	  being introduced into weights by optimized learning function
	  (this problem began in r8079).

	* [r8203] topo/base/simulation.py:
	  Updates to comments about copying Simulation.

	* [r8202] topo/base/simulation.py,
	  topo/tests/testsimulation.py:
	  Made simulation(register=False) not be a singleton (i.e. only one
	  instance of Simulation(register=True) can exist, but
	  Simulation(register=False) instances exist as normal objects).

2008-03-15  ceball

	* [r8201] topo/__init__.py:
	  Added svn version to 'about' text.

	* [r8200] topo/base/simulation.py,
	  topo/tests/testsimulation.py:
	  Made Simulation be a singleton (unimportant change from it being
	  a 'monostate' class). Added methods to control copying and
	  pickling. Simulation's 'register' parameter no longer affects the
	  Simulation's status as a singleton.

	* [r8199] topo/tests/test_pattern_present.txt,
	  topo/tests/utils.py:
	  Made topo.tests.utils.new_simulation() return the created
	  simulation.

2008-03-14  antolikjan

	* [r8198] examples/cc_lissom_oo_or_new.ty:
	  

2008-03-14  judelaw

	* [r8197] examples/lissom_oo_or_homeostatic.ty:
	  Removed comment about saving snapshot error

2008-03-14  ceball

	* [r8196] doc/Future_Work/current_text.php:
	  Added tasks about missing tests.

	* [r8195]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Made lissom_oo_or_reference include weights comparisons at 500
	  and 20000.

	* [r8194]
	  topo/tests/reference/oo_or_map_topo.020000.wts.Ganglia00.Afferent0.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.020000.wts.Ganglia00.Afferent0.012_012.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.020000.wts.Ganglia01.Afferent0.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.020000.wts.Ganglia01.Afferent0.012_012.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.020000.wts.Primary.Afferent00.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.020000.wts.Primary.Afferent00.023_023.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.020000.wts.Primary.Afferent01.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.020000.wts.Primary.Afferent01.023_023.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.020000.wts.Primary.LateralExcitatory.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.020000.wts.Primary.LateralExcitatory.023_023.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.020000.wts.Primary.LateralInhibitory.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.020000.wts.Primary.LateralInhibitory.023_023.matrix.gz:
	  Added c++ lissom oo_or weights at iteration 20000.

	* [r8193]
	  topo/tests/reference/oo_or_map_topo.000500.wts.Ganglia00.Afferent0.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000500.wts.Ganglia00.Afferent0.012_012.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000500.wts.Ganglia01.Afferent0.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000500.wts.Ganglia01.Afferent0.012_012.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000500.wts.Primary.Afferent00.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000500.wts.Primary.Afferent00.023_023.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000500.wts.Primary.Afferent01.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000500.wts.Primary.Afferent01.023_023.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000500.wts.Primary.LateralExcitatory.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000500.wts.Primary.LateralExcitatory.023_023.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000500.wts.Primary.LateralInhibitory.000_000.matrix.gz:
	  Added c++ lissom oo_or weights at iteration 500.

2008-03-13  jbednar

	* [r8192] topo/commands/analysis.py:
	  Cleaned up docstrings

	* [r8191] topo/commands/pylabplots.py:
	  Removed outdated alert

	* [r8190]
	  /branches/cnv_course_2008/topographica/topo/base/functionfamilies.py:
	  Updated with changes from trunk

	* [r8189]
	  /branches/cnv_course_2008/topographica/topo/outputfns/basic.py,
	  /branches/cnv_course_2008/topographica/topo/projections/basic.py:
	  Updated with changes from trunk

	* [r8188] topo/base/functionfamilies.py:
	  Fixed PipelineOF to work with ParametersFrame

2008-03-13  antolikjan

	* [r8187] examples/cc_lissom_oo_or_new.ty:
	  

	* [r8186] examples/cc_lissom_oo_or_new.ty:
	  

2008-03-13  jbednar

	* [r8185]
	  /branches/cnv_course_2008/topographica/topo/base/functionfamilies.py,
	  /branches/cnv_course_2008/topographica/topo/commands/basic.py,
	  /branches/cnv_course_2008/topographica/topo/coordmapperfns/basic.py,
	  /branches/cnv_course_2008/topographica/topo/outputfns/optimized.py,
	  /branches/cnv_course_2008/topographica/topo/plotting/plotfilesaver.py:
	  Brought up to date with changes on the trunk that were made
	  specifically for the CNV course

	* [r8184] topo/patterns/random.py:
	  Again removed PoissonRandom class; not sure why it reappeared

	* [r8183] topo/coordmapperfns/basic.py:
	  Added missing import

	* [r8182] examples/lissom_oo_or.ty:
	  Reverted to 8137 to erase bogus checkin

	* [r8181] topo/coordmapperfns/basic.py,
	  topo/patterns/random.py:
	  Added Jitter class

2008-03-12  jbednar

	* [r8180] topo/patterns/random.py:
	  Removed temporary checkin of PoissonRandom class

	* [r8179] doc/News,
	  doc/News/index_text.php,
	  examples/lissom_oo_or.ty,
	  topo/base/functionfamilies.py,
	  topo/patterns/random.py:
	  Made PipelineOF work for norm_total

	* [r8178] topo/outputfns/optimized.py:
	  Fixed comments

	* [r8177] topo/outputfns/basic.py:
	  Fixed to work with non-square arrays

2008-03-12  judelaw

	* [r8176] examples/lissom_oo_or_homeostatic.ty:
	  separated out tracking and non tracking components for debugging

	* [r8175] topo/outputfns/basic.py:
	  added error to AttributeTrackingOF to avoid coordframe being
	  overwritten if tracked object is already a SheetCoordinateSystem

	* [r8174] topo/base/functionfamilies.py:
	  removed _get_attribute__ fn from PipelineOF which was causing
	  problems for saving snapshots

	* [r8173] examples/lissom_oo_or_homeostatic.ty:
	  Added an option to turn off tracking so that snapshots can be
	  saved

	* [r8172] examples/lissom_oo_or_homeostatic.ty:
	  Updated with latest changes

	* [r8171] topo/commands/pylabplots.py:
	  added option to save raw data from plot_tracked_attributes

	* [r8170] topo/base/cf.py:
	  Corrected error in CFPLF_PluginScaled,
	  learning_rate_scaling_factor should be same shape as
	  output_activity not input_activity

	* [r8169] examples/lissom_oo_or_noshrinking.ty:
	  Corrected smoothing parameter to account for change in definition
	  to 1-smoothing in HomeostaticMaxEnt and changes to
	  AttributeTrackingOF

	* [r8168] topo/outputfns/basic.py:
	  Corrected defaults for HomeostaticMaxEnt to make sure example
	  file outputs aren't affected, changed AttributeTrackingOF so that
	  it uses sheet coordinates instead of matrix coordinates

2008-03-12  ceball

	* [r8167]
	  topo/tests/reference/lissom_fsa_reference.ty,
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty:
	  Renamed weights_shape to cf_shape (missed from a previous
	  commit).

	* [r8166] doc/Downloads/git_text.php:
	  Added note.

2008-03-11  jbednar

	* [r8165] topo/projections/basic.py:
	  Minor fix to docs

	* [r8164] topo/commands/basic.py:
	  Added saving of projection and test pattern plots to
	  default_analysis function

	* [r8163] topo/plotting/plotfilesaver.py:
	  Added filename_suffix option

2008-03-11  judelaw

	* [r8162] topo/outputfns/basic.py:
	  Added step parameter to HomeostaticMaxEnt to allow parameters to
	  be updated at different durations

2008-03-11  antolikjan

	* [r8161] examples/cc_lissom_oo_or_new.ty:
	  New attempt on complex cells

2008-03-11  jbednar

	* [r8160] external/Makefile:
	  Trivial spacing fix

	* [r8159] Makefile:
	  Fixed previous checkin

	* [r8158] Makefile:
	  Added cleanup of compiled weave files, for safety

	* [r8157] doc/Future_Work/current_text.php:
	  Minor cleanup

	* [r8156] external/Makefile:
	  Added more to clean up

2008-03-10  antolikjan

	* [r8155]
	  examples/gc_lissom_oo_or_homeostatic.ty:
	  Enlarged LGN to get rid of border effects

	* [r8154] contrib/mycommands.py:
	  

	* [r8153] contrib/jansanalyzisfunctions.py:
	  

2008-03-08  ceball

	* [r8152] topo/tests/testparametersframe.py:
	  Added test demonstrating problem with parameter setting in GUI.

2008-03-07  antolikjan

	* [r8151] contrib/jansanalyzisfunctions.py,
	  contrib/mycommands.py:
	  repaired some import bugs

	* [r8150] contrib/mycommands.py:
	  added import copy

	* [r8149]
	  examples/gc_lissom_oo_or_homeostatic.ty:
	  changed the import of SimpleHomeo

	* [r8148] contrib/mycommands.py:
	  moved here the SimpleHomeo function

	* [r8147] examples/cc_lissom_oo_or.ty:
	  some updates

2008-03-07  ceball

	* [r8146] topo/analysis/vision.py:
	  Fixed import error.

2008-03-07  antolikjan

	* [r8145]
	  examples/gc_lissom_oo_or_homeostatic.ty:
	  lissom_oo_or_homeostatic witg Gain Control

	* [r8144] topo/commands/analysis.py:
	  corrected bug in measure_corner_or_pref

	* [r8143] topo/commands/basic.py:
	  made it work in batch mode with Agg instead of TkAgg

	* [r8142] topo/analysis/vision.py:
	  made the plotting of phase scatter plot use normalized_path

	* [r8141] contrib/jansanalyzisfunctions.py:
	  my analyzis functions

	* [r8140] topo/commands/pylabplots.py:
	  Did some minor improvements to plot_modulation_ratio

2008-03-07  ceball

	* [r8139] doc/Future_Work/current_text.php,
	  topo/base/cf.py,
	  topo/learningfns/optimized.py,
	  topo/sheets/optimized.py:
	  Stopped optimized functions from causing redundant calls when
	  setting norm_total (I assume this was the original intention).

	* [r8138] doc/Reference_Manual/index_text.php:
	  Fixed a typo.

	* [r8137] doc/Future_Work/current_text.php,
	  examples/cc_lissom_oo_or.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/v2_cc_lissom_oo_or.ty,
	  topo/base/cf.py:
	  Renamed CFProjection.weights_shape to CFProjection.cf_shape.

	* [r8136] doc/Future_Work/current_text.php,
	  topo/base/cf.py:
	  Removed an ALERT and a couple of completed tasks.

	* [r8135] doc/Reference_Manual/index_text.php:
	  Added some useful links for external packages. Added IPython
	  section.

2008-03-06  jbednar

	* [r8134] doc/Future_Work/current_text.php:
	  Prioritized current tasks

	* [r8133] doc/Future_Work/index_text.php:
	  Removed completed task

	* [r8132] topo/base/cf.py,
	  topo/base/projection.py,
	  topo/base/sheet.py:
	  Cleaned up outdated and unnecessary alerts

2008-03-06  ceball

	* [r8131] doc/Future_Work/current_text.php:
	  Removed irrelevant task.

	* [r8130] doc/Future_Work/current_text.php:
	  Rearranged tasks. Moved right-click-menu task to tracker. Added
	  some notes.

	* [r8129] doc/Future_Work/current_text.php:
	  Added link to useful article.

	* [r8128] external/Makefile,
	  external/egenix-mx-experimental-3.0.0.tar.gz,
	  external/gmp-4.2.2.tar.gz:
	  Added GNU MP and mxNumber.

2008-03-05  ceball

	* [r8127] doc/buildbot/index.html:
	  Added link to performance tests. Also added 'useful links' and
	  updated some other links (changes that have existed on the live
	  buildbot page for some time).

2008-03-05  antolikjan

	* [r8126] topo/misc/commandline.py:
	  Undid the use('Agg') bug

	* [r8125] contrib/__init__.py:
	  Just to make contrib directory work

2008-03-05  ceball

	* [r8124] topo/tests/gui_tests.py:
	  Added test of orientation tuning window.

2008-03-05  antolikjan

	* [r8123] topo/analysis/vision.py:
	  Decreased the area in which the scatter plot takes data from

	* [r8122] topo/misc/commandline.py:
	  Added call to matplotlib and use('Agg') to enable plotting in non
	  XWindows envinronemnts

2008-03-05  ceball

	* [r8121] doc/buildbot/master.cfg:
	  Made buildbot plot performance results to
	  buildbot.topographica.org/p/

	* [r8120] doc/buildbot/bbanalysis.py:
	  Fixed import error.

	* [r8119] doc/buildbot/bbanalysis.py:
	  Allow exclusion of specific builds. Fixed some figure() errors.

	* [r8118] doc/buildbot/bbanalysis.py:
	  Use Agg backend for matplotlib.

	* [r8117] doc/buildbot/bbanalysis.py:
	  Fixed typos.

	* [r8116] doc/Future_Work/current_text.php:
	  Added note.

	* [r8115] doc/buildbot/bbanalysis.py:
	  Added basic plotting of perfomance tests.

2008-03-04  antolikjan

	* [r8114] contrib,
	  contrib/mycommands.py:
	  A directory where people can add thier custom code

2008-03-04  ceball

	* [r8113] topo/misc/filepaths.py:
	  Added __getstate__ for Filename (to avoid search_paths from being
	  pickled). Not yet finished (need to solve a strange test
	  problem).

	* [r8112] topo/patterns/image.py:
	  Added ALERT.

	* [r8111] doc/Future_Work/current_text.php:
	  Moved tasks to sf.net tracker. Removed tile task.

2008-03-04  jbednar

	* [r8110] topo/base/patterngenerator.py,
	  topo/patterns/basic.py:
	  Trivial whitespace and line formatting cleanup

2008-03-04  ceball

	* [r8109] doc/Future_Work/current_text.php:
	  Updates to tasks. Added in beginnings of overview of ALERTs in
	  base.

2008-03-03  antolikjan

	* [r8108] topo/sheets/lissom.py:
	  Added strict_tsettle parameter that if defined tells the LISSOM
	  not to send the afferent output to next layer until
	  strict_tsettle steps

2008-03-03  jbednar

	* [r8107] topo/learningfns/optimized.py:
	  Added missing import

	* [r8106] external/Makefile_OSX_X11.diff:
	  Updated to match changes in Makefile

2008-03-02  antolikjan

	* [r8105] topo/base/projection.py:
	  Added code that allows to specify constant in the divisive and
	  multiplicative projection types

2008-03-01  ceball

	* [r8104] topo/plotting/bitmap.py:
	  Cleaned up copying of Bitmap. Minor plotting speed improvement.

2008-02-29  ceball

	* [r8103] topo/base/cf.py:
	  Clarified a comment.

2008-02-28  ceball

	* [r8102] topo/base/sheetcoords.py:
	  Disabled erroneous pylint error (attribute that does exist
	  claimed to be non-existent).

	* [r8101] topo/base/cf.py:
	  Updated some numpy imports.

	* [r8100] topo/base/patterngenerator.py:
	  Updated numpy imports.

	* [r8099] external/Makefile,
	  external/logilab-astng-0.17.1.tar.gz,
	  external/logilab-astng-0.17.2.tar.gz:
	  Updated pylint support (logilab-astng).

	* [r8098] external/Makefile,
	  external/pylint-0.13.2.tar.gz,
	  external/pylint-0.14.0.tar.gz:
	  Upgraded pylint to 0.14.0

	* [r8097] topo/base/simulation.py:
	  Added a note.

	* [r8096] topo/base/parameterizedobject.py:
	  Demonstrated replacement of lambda by itemgetter and attrgetter
	  (as per PEP 0290, which indicates these new methods are faster
	  than lambda).

2008-02-26  jbednar

	* [r8095] topo/commands/or_key_white_horiz.pdf,
	  topo/commands/or_key_white_vert.pdf:
	  Fixed color keys to match order in Topographica

	* [r8094] doc/User_Manual/publishing_text.php,
	  topo/commands/or_key_white_horiz.pdf,
	  topo/commands/or_key_white_vert.pdf:
	  Added PDF versions of color keys for use in publications

	* [r8093] examples/cc_lissom_oo_or.ty,
	  examples/v2_cc_lissom_oo_or.ty,
	  topo/analysis/vision.py:
	  Fixed keywords and eol type properties for svn

2008-02-26  ceball

	* [r8092] topo/base/cf.py:
	  Added comment.

	* [r8091] topo/base/cf.py:
	  Restored an array copy during CF's change_bounds(), because
	  substantially it's faster.

	* [r8090] doc/Future_Work/current_text.php:
	  Added note.

	* [r8089] topo/base/cf.py:
	  Moved mask-generating code back into CFProjection (at least for
	  the moment; because of the class hierarchy, it is otherwise
	  tricky to deal with autosize_mask for SharedWeightCF
	  (autosize_mask is required for c++ lissom matching)).

	* [r8088] topo/tests/utils.py:
	  Replaced function that had been mistakenly removed.

2008-02-25  ceball

	* [r8087] topo/base/cf.py:
	  Fixed typo in code.

	* [r8086] topo/base/cf.py,
	  topo/projections/basic.py:
	  Cleanup - should be no visible change.

	* [r8085] topo/base/cf.py:
	  Minor cleanup; should be no visible change.

	* [r8084] topo/base/cf.py:
	  ConnectionField: Removed unnecessary array copy during
	  change_bounds().

	* [r8083] topo/base/cf.py:
	  Moved min_matrix_radius and autosize_mask to ConnectionField.
	  Cleanup of some documentation and ALERTs.

	* [r8082] topo/tests/test_script.py:
	  File missed from r8081.

	* [r8081] topo/tests/gui_tests.py,
	  topo/tests/setup_simulation.py,
	  topo/tests/test_pattern_present.txt,
	  topo/tests/testimage.py,
	  topo/tests/testpatterngenerator.py,
	  topo/tests/testsnapshots.py,
	  topo/tests/utils.py:
	  Use numpy.testing functions for array equality (rather than our
	  own in utils). Moved new_simulation() to utils.

	* [r8080] topo/base/cf.py:
	  Change missed from r8079.

	* [r8079] topo/base/cf.py:
	  Made mask array be shared between CFs (rather than copying mask
	  for each CF).

2008-02-24  jbednar

	* [r8078] external/Makefile,
	  external/blt2.4z.tar.gz:
	  Added blt package, used by tkinter but not always installed with
	  a compatible version (e.g. on utcs)

2008-02-24  ceball

	* [r8077]
	  topo/tests/reference/lissom_log_parser.py:
	  Fixed mistake getting input parameters when only one eye.

	* [r8076] topo/base/cf.py:
	  Corrected another error from previous checkin (r8073).

	* [r8075] topo/base/cf.py:
	  Corrected naming error from previous checkin (r8073).

	* [r8074] topo/plotting/plot.py,
	  topo/projections/basic.py:
	  Files missed from previous commit (r8073).

	* [r8073] examples/joublin_bc96.ty,
	  topo/base/boundingregion.py,
	  topo/base/cf.py,
	  topo/base/patterngenerator.py,
	  topo/base/sheet.py,
	  topo/base/sheetcoords.py,
	  topo/misc/legacy.py,
	  topo/tests/testsheet.py:
	  Intermediate checkin - cleaning up Slice and ConnectionField.
	  Moved Slice from topo.base.sheet to topo.base.sheetcoords.
	  Implemented __copy__ for Slice and altered code in
	  ConnectionField to copy() slices rather than deepcopy() them.
	  (Startup time improvement.) Avoid unnecessary creation of
	  BoundingBox objects (alter exising ones): BoundingRegion has
	  set() method. (Startup time improvement). Moved bounds2slice()
	  and slice2bounds from SheetCoordinateSystem to Slice and avoided
	  unnecessary creation of BoundingBox objects; still needs work.
	  (Startup time improvement.) Moved ConnectionField's
	  slice-construction methods into Slice (needs cleanup).
	  ConnectionField takes one 'template' argument rather than a
	  required BoundingRegion and an optional Slice; the template could
	  be a BoundingRegion or a Slice. (Passing a Slice instead of a
	  BoundingRegion is more complex, but avoids duplication of
	  calculations for every CF.) Moved mask-creation code from
	  CFProjection to ConnectionField (not yet sure this change will
	  stay). Updated topo.misc.legacy.

2008-02-23  ceball

	* [r8072] topo/base/sheet.py:
	  Added support for deepcopying Slice. Should have no effect on
	  existing examples. Intermediate checkin - part of larger
	  reorganization.

2008-02-22  ceball

	* [r8071] doc/buildbot/bbanalysis.py:
	  buildbot analysis script: various fixes.

	* [r8070] doc/buildbot/bbanalysis.py:
	  Assume recent startup timings tests happened at 99% cpu.

	* [r8069] Makefile:
	  Added unix 'time' command to more tests (should we just add it to
	  all tests?).

	* [r8068] doc/buildbot/bbanalysis.py:
	  Added collection of startup timings (script needs to be cleaned
	  up).

	* [r8067] doc/Downloads/git_text.php:
	  Git: described how to revert last commit.

	* [r8066] doc/Downloads/git_text.php:
	  Basic conflict resolution.

	* [r8065] doc/Downloads/git_text.php:
	  Added note to myself.

2008-02-21  jbednar

	* [r8064] topo/commands/pylabplots.py:
	  Added note that SVG is supported

	* [r8063] doc/Downloads/index_text.php:
	  Updated instructions for OS X

	* [r8062] topo/commands/pylabplots.py:
	  Added batch support to most commands

	* [r8061] topo/tests/testmatplotlib.py,
	  topo/tests/testmatplotlibtk.py:
	  Cleaned up matplotlib backend selection

	* [r8060] topo/commands/basic.py,
	  topo/commands/pylabplots.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Cleaned up matplotlib backend selection

	* [r8059] external/Makefile,
	  external/matplotlib-0.90.1.tar.gz,
	  external/matplotlib-0.91.2.tar.gz:
	  Upgraded matplotlib to latest version

	* [r8058] examples/lissom_photo_or.ty:
	  Fixed typo in previous checkin

	* [r8057] topo/misc/inlinec.py:
	  Turned off warnings from weave about code that doesn't use all
	  the generated variables

	* [r8056] doc/Downloads/git_text.php:
	  Tried getting the entire repository; documented the results

	* [r8055] Makefile,
	  external/Makefile,
	  external/Makefile_OSX.diff:
	  Added automatic detection of platform, instead of manual patch
	  application; not tested yet.

	* [r8054] doc/Home/news_text.php,
	  doc/Home/oldnews_text.php,
	  doc/shared/util.php:
	  Moved old_news to new News directory, and made it a proper item
	  on the menu, leaving only a stub on the front page

	* [r8053] doc/Home/oldnews_text.php:
	  Updated to contain complete list of news, not just older items

	* [r8052] examples/lissom_photo_or.ty:
	  Trivial cleanup

2008-02-21  ceball

	* [r8051] topo/base/cf.py:
	  Various changes to comments and ALERTs; should be no visible
	  change.

2008-02-21  jbednar

	* [r8050] doc/Downloads/git_text.php:
	  

2008-02-21  ceball

	* [r8049] topo/base/parameterclasses.py:
	  Made Class and ObjectSelectorParameter use super(). Removed
	  unused import.

	* [r8048] topo/base/cf.py,
	  topo/base/sheet.py,
	  topo/base/sheetcoords.py:
	  Temporary change to assess performance impact of unnecessary
	  creation of BoundingBoxes (rather than replacement of their
	  AARectangles). Should be no visible change except for a
	  significant startup time reduction.

	* [r8047] doc/Downloads/bzr_text.php:
	  Minor additions to bzr text (including recommendation to use Git
	  instead).

	* [r8046] topo/misc/legacy.py:
	  Added placeholder for legacy DynamicNumber support.

	* [r8045] doc/Downloads/git_text.php:
	  Git: info about dcommitting.

	* [r8044] topo/base/cf.py:
	  Fixed some whitespace.

	* [r8043] doc/Downloads/git_text.php:
	  Some cleanup and simplification of git instructions.

	* [r8042]
	  topo/tests/testparameterizedobject.py:
	  Minor additions to docstrings.

	* [r8041]
	  topo/tests/testparameterizedobject.py:
	  Added tests for read-only parameters: make sure they are also
	  constant, and that they are not instantiated.

2008-02-20  jbednar

	* [r8040] external/Makefile:
	  Removed -o option to tar; not supported on OS X

2008-02-20  ceball

	* [r8039] doc/Downloads/git_text.php:
	  More updates to Git documentation.

	* [r8038] /branches/tkgui-tk85:
	  Migrated tkgui-tk85 to a git repository that tracks trunk/.

2008-02-20  jbednar

	* [r8037] doc/Downloads/git_text.php:
	  Minor cleanup

2008-02-20  ceball

	* [r8036] topo/misc/legacy.py:
	  Allow old snapshots to work after removing 'suffix_to_lose' from
	  ClassSelectorParameter.

	* [r8035] examples/joublin_bc96.ty,
	  examples/sullivan_nn06.ty:
	  Removed PatternGeneratorParameter (missed from a previous
	  checkin).

2008-02-19  jbednar

	* [r8034]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Minor addition

2008-02-19  ceball

	* [r8033] topo/base/parameterizedobject.py:
	  Parameter: Made readonly imply constant (but still do not
	  instantiate read-only parameters). Minor alterations to
	  documentation.

	* [r8032] topo/base/functionfamilies.py:
	  Removed unused imports.

	* [r8031] topo/base/parameterclasses.py:
	  Removed unused 'suffix_to_lose' from ClassSelectorParameter.

	* [r8030] topo/learningfns/optimized.py,
	  topo/outputfns/optimized.py,
	  topo/responsefns/optimized.py:
	  Made optimized functions have read-only single_cf_fns. (Also,
	  added explicit declaration of single_cf_fn from some places
	  missing such a declaration.)

	* [r8029] topo/base/cf.py,
	  topo/base/patterngenerator.py,
	  topo/learningfns/som.py,
	  topo/misc/legacy.py,
	  topo/outputfns/basic.py,
	  topo/patterns/basic.py,
	  topo/projections/basic.py,
	  topo/sheets/generatorsheet.py:
	  Removed PatternGeneratorParameter

	* [r8028]
	  doc/Developer_Manual/revisioncontrol_text.php,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/misc/legacy.py,
	  topo/projections/basic.py:
	  Removed CoordinateMapperFnParameter.

	* [r8027]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Added ~/.subversion/config info.

	* [r8026] topo/commands/basic.py,
	  topo/misc/legacy.py,
	  topo/misc/utils.py:
	  Moved snapsot support to topo.misc.legacy.

2008-02-19  jbednar

	* [r8025] doc/Downloads/git_text.php:
	  Added some motivation

	* [r8024] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  Removed unneccessary references to topo in comments

2008-02-19  judelaw

	* [r8023] topo/base/functionfamilies.py:
	  Added __add__ function to PipelineOF that returns a single new
	  pipeline rather than a nested pipeline

	* [r8022] topo/base/cf.py:
	  Removed debug_output_function from CFProjection which was only
	  for debugging and checked in by mistake

2008-02-19  ceball

	* [r8021] topo/commands/basic.py,
	  topo/misc/utils.py:
	  No visible change (automated the class faking).

	* [r8020] topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/simulation.py,
	  topo/misc/utils.py:
	  Collected together hacks to support snapshots that use legacy
	  classes (there are probably others I don't know about or have
	  forgotten).

	* [r8019] topo/base/cf.py,
	  topo/base/parameterizedobject.py,
	  topo/base/sheet.py,
	  topo/base/simulation.py,
	  topo/commands/basic.py,
	  topo/misc/utils.py:
	  Moved pickle hacks (largely regarding instance attributes) into
	  one place.

2008-02-19  jbednar

	* [r8018] topo/outputfns/basic.py:
	  Declared OutputFnWithState to be abstract

2008-02-19  ceball

	* [r8017] topo/base/cf.py,
	  topo/base/functionfamilies.py:
	  Temporary fix to allow old snapshots to load: fake old
	  xFnParameters.

	* [r8016] topo/base/parameterizedobject.py:
	  Fixed error converting Parameter's old 'hidden' attribute.

	* [r8015] examples/joublin_bc96.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/sullivan_neurocomputing04.ty:
	  Removed OutputFnParameter, ResponseFnParameter, and
	  LearningFnParameter (missed from previous checkins).

	* [r8014] topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py,
	  topo/learningfns/projfns.py,
	  topo/projections/basic.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py,
	  topo/tkgui/__init__.py:
	  Removed LearningFnParameter and ResponseFnParameter. Also cleaned
	  up some import statements.

	* [r8013] topo/base/functionfamilies.py:
	  PipelineOF raises an error if a nested output_fn has a
	  non-callable attribute by the name requested.

2008-02-19  jbednar

	* [r8012] topo/commands/analysis.py:
	  Removed unused import

	* [r8011] topo/commands/pylabplots.py:
	  Minor fix to docstring

2008-02-18  jbednar

	* [r8010] topo/base/projection.py,
	  topo/base/simulation.py:
	  Simplified self.verbose() messages to allow easy replacement

	* [r8009] topo/base/functionfamilies.py,
	  topo/outputfns/basic.py:
	  Moved OutputFnWithState from functionfamilies.py to
	  outputfns/basic.py

	* [r8008] topo/plotting/plot.py:
	  Added alert

2008-02-18  antolikjan

	* [r8007] topo/commands/pylabplots.py:
	  defined new batch versions of tuning curves plotting

	* [r8006] topo/analysis/vision.py:
	  corrected small bug with import

2008-02-18  ceball

	* [r8005] topo/base/simulation.py:
	  Removed out-of-date alert.

	* [r8004] topo/base/sheet.py:
	  Disabled pylint warning about Sheet.input_event().

	* [r8003] topo/misc/numbergenerators.py:
	  Updated comments.

	* [r8002] topo/base/arrayutils.py:
	  Altered imports: should be no visible change.

	* [r8001] topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/optimized.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/patterns/teststimuli.py,
	  topo/projections/basic.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py,
	  topo/sheets/optimized.py,
	  topo/tkgui/__init__.py:
	  Removed OutputFnParameter and CFPOutputFnParameter.

	* [r8000] topo/base/functionfamilies.py,
	  topo/base/projection.py:
	  Removed override_plasticity_state() and
	  restore_plasticity_state() from OutputFn, reverting OutputFn to a
	  more general class; users of OutputFns must test for presence of
	  the methods (rather than assuming they exist). Added mechanism to
	  allow a method called on PipelineOF to be called on all of its
	  output_fns (testing); removed restore_plasticity_state() and
	  override_plasticity_state() from PipelineOF.

	* [r7999] doc/Downloads/git_text.php:
	  More git notes.

2008-02-18  jbednar

	* [r7998] examples/v2_cc_lissom_oo_or.ty:
	  Removed unused import

	* [r7997] examples/v2_cc_lissom_oo_or.ty:
	  Minor alert and whitespace changes

2008-02-18  ceball

	* [r7996] doc/Downloads/git_text.php:
	  More Git notes.

	* [r7995] doc/Downloads/bzr_text.php:
	  bzr doc: minor revisions.

	* [r7994] doc/Downloads/git_text.php:
	  Git: added some notes and references.

	* [r7993] doc/Downloads/git_text.php:
	  First semi-coherent description of working with Git.

	* [r7992] doc/Downloads/git_text.php:
	  Topographica with Git: added more info (still incoherent).

2008-02-17  ceball

	* [r7991]
	  /branches/tkgui-tk85/topographica/doc/Downloads/bzr_text.php,
	  /branches/tkgui-tk85/topographica/topo/base/functionfamilies.py,
	  /branches/tkgui-tk85/topographica/topo/base/patterngenerator.py,
	  /branches/tkgui-tk85/topographica/topo/base/projection.py,
	  /branches/tkgui-tk85/topographica/topo/base/sheet.py,
	  /branches/tkgui-tk85/topographica/topo/commands/basic.py,
	  /branches/tkgui-tk85/topographica/topo/sheets/generatorsheet.py,
	  /branches/tkgui-tk85/topographica/topo/tkgui/__init__.py,
	  /branches/tkgui-tk85/topographica/topo/tkgui/plotgrouppanel.py,
	  /branches/tkgui-tk85/topographica/topo/tkgui/topoconsole.py:
	  Merged in bzr changes up to bzr rev 7821 (various svn merges and
	  now FrameManager's ejected windows have a title and icon, and
	  panels default to undocked).

	* [r7990] /branches/tkgui-tk85/topographica:
	  Restore topographica-tkgui_with_tile from r7944
	  
	  --This line, and those below, will be
	  ignored--
	  
	  A
	  https://topographica.svn.sourceforge.net/svnroot/topographica/branches/tkgui-tk85/topographica

	* [r7989] /branches/tkgui-tk85:
	  New home for using Tk8.5 with tkgui.

	* [r7988] doc/Downloads/git_text.php:
	  Continued writing.

	* [r7987] doc/Downloads/git_text.php:
	  Initial version.

	* [r7986]
	  topo/tests/reference/lissom_oo_dr_reference.ty:
	  Added sign to match C++ lissom (still got speed - and probably
	  more - to match). (Also, removed some code that was copy-pasted
	  from lissom_oo_or_reference.)

	* [r7985]
	  topo/tests/reference/lissom_log_parser.py:
	  Made get_input_params() also recover 'sign'.

2008-02-16  ceball

	* [r7984]
	  topo/tests/reference/lissom_oo_dr_reference.ty:
	  Removed unused import.

	* [r7983] topo/base/patterngenerator.py:
	  Fixed HACKALERT: corrected test for IdentityOF instance.

	* [r7982] topo/base/patterngenerator.py:
	  Delayed production of two verbose statements. (Makes lissom_oo_or
	  startup time 4-5% faster.)

	* [r7981] topo/base/simulation.py,
	  topo/sheets/generatorsheet.py:
	  Reverted Event to object (rather than ParameterizedObject -
	  because of small performance hit).

	* [r7980] topo/base/parameterizedobject.py,
	  topo/tkgui/parametersframe.py:
	  Reduced number of ALERTS related to 'defaults()' method.

	* [r7979] topo/base/parameterizedobject.py:
	  Updates to comments.

	* [r7978] topo/learningfns/basic.py:
	  Import IdentityLF into learningfns.basic

	* [r7977] topo/misc/utils.py:
	  Minor changes to profile()'s output.

	* [r7976] topo/base/parameterizedobject.py:
	  Fixed mistake in comment.

	* [r7975] topo/base/parameterizedobject.py,
	  topo/tests/testparameterizedobject.py:
	  Addressed SF.net request #1829846: added 'readonly' to Parameter,
	  allowing Parameters that can only be set when they are declared.
	  (Also added unit test, and unit test for constant Parameters.)

	* [r7974] topo/tkgui/testpattern.py:
	  File missed from commit 7973 (name Parameter is constant).

	* [r7973] topo/base/parameterizedobject.py,
	  topo/commands/analysis.py:
	  ParameterizedObject: made name a constant Parameter; provided
	  _set_name() for when the name really does need to change; tried
	  to simplify controlling the 'initialized' flag by providing a
	  decorator function to manage it.

	* [r7972] topo/base/simulation.py:
	  Made Simulation's name not be constant.

	* [r7971] topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py:
	  Made EditorObject and ModelEditor inherit from object rather than
	  ParameterizedObject (they should both have ParameterizedObject as
	  a parent, but that requires more than just changing the parent
	  class to ParameterizedObject - e.g. initializing the parent
	  class).

2008-02-15  antolikjan

	* [r7970] topo/analysis/vision.py:
	  Corrected import bug

	* [r7969] topo/commands/analysis.py:
	  Moved complex analysis to topo.commands.analysis and added corner
	  orientation preffernce analysis

	* [r7968] topo/analysis/vision.py:
	  Added phase prefference plot and moved complex analysis from
	  topo.commands.analysis

2008-02-15  jbednar

	* [r7967] topo/misc/traces.py,
	  topo/plotting/bitmap.py:
	  Cleaned up comments, whitespace, and docstrings. Added some
	  alerts.

2008-02-15  ceball

	* [r7966] topo/base/simulation.py:
	  Removed out-of-date ERRORALERT.

	* [r7965] topo/base/boundingregion.py:
	  Added comment.

	* [r7964] topo/base/parameterizedobject.py,
	  topo/base/sheet.py:
	  SnapshotCompatibility: added option to call superclass's setstate
	  when overriding a class's setstate.

	* [r7963] topo/base/simulation.py:
	  Moved Simulation's pickle hack into a separate function.

	* [r7962] topo/base/cf.py:
	  Moved CF's pickle hack into a separate function.

	* [r7961] topo/base/sheet.py:
	  Moved Slice's pickle hack into a separate function call. Added
	  new pickle hack to allow loading of snapshots that were created
	  before SheetCoordinateSystem was made to store its shape.

	* [r7960] topo/base/parameterizedobject.py:
	  Created SnapshotCompatibility class, offering functions to
	  control aspects of unpickling. Parameter's __setstate__
	  picklehack moved to separate function call.

2008-02-15  jbednar

	* [r7959] doc/User_Manual/publishing_text.php:
	  Fixed broken link

2008-02-15  ceball

	* [r7958] topo/base/sheetcoords.py:
	  Made SheetCoordinateSystem's xdensity and ydensity read-only
	  properties, and made shape property return a stored shape rather
	  than calculating each time (fixes ALERT).

2008-02-15  jbednar

	* [r7957] examples/cc_lissom_oo_or.ty,
	  examples/v2_cc_lissom_oo_or.ty,
	  topo/analysis/featureresponses.py,
	  topo/analysis/vision.py,
	  topo/base/cf.py,
	  topo/base/projection.py,
	  topo/base/simulation.py,
	  topo/commands/analysis.py,
	  topo/commands/pylabplots.py,
	  topo/patterns/basic.py,
	  topo/sheets/lissom.py:
	  Cleaned up docstrings, comments, and whitespace

	* [r7956] topo/learningfns/optimized.py:
	  Added unoptimized equivalent for CFPLF_Trace_opt

	* [r7955] topo/commands/basic.py:
	  Simplified wipe_out_activity()

	* [r7954] topo/sheets/lissom.py:
	  Cleaned up docstrings and comments

2008-02-14  jbednar

	* [r7953] topo/sheets/optimized.py:
	  Fixed compilation problem in C code by forcing matradius to be an
	  integer

	* [r7952] doc/Future_Work/current_text.php:
	  Added note for future work

2008-02-14  ceball

	* [r7951] doc/Downloads/bzr_text.php:
	  More updates to bzr instructions.

	* [r7950] doc/Downloads/bzr_text.php:
	  Added some more notes to bzr instructions.

	* [r7949] doc/Downloads/bzr_text.php:
	  First coherent Bazaar instructions (will remain a work in
	  progress for a while now).

2008-02-13  jbednar

	* [r7948] topo/base/functionfamilies.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/sheets/generatorsheet.py:
	  Cleaned up docs and comments about plasticity_state

2008-02-13  judelaw

	* [r7947] topo/base/functionfamilies.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/commands/basic.py,
	  topo/sheets/generatorsheet.py:
	  Changed disable_plasticity and restore_plasticity functions to
	  override_plasticity_state/disable_plasticity_state to allow
	  plastic to also be set temporarily to True

2008-02-13  ceball

	* [r7946] /branches/topographica-tkgui_with_tile:
	  Moved til branch to
	  https://code.launchpad.net/~topographica-developers/topographica/tk85
	  (bzr 7818 corresponds to svn 7944, apart from some deliberately
	  dropped external packages).

	* [r7945] doc/Downloads/bzr_text.php:
	  More bzr instructions.

	* [r7944]
	  /branches/topographica-tkgui_with_tile/doc/Downloads/bzr_text.php:
	  Merged r7939:7943 from trunk.

2008-02-12  ceball

	* [r7943] /branches/topographica-tkgui_with_tile/:
	  Merged in changes r7794:7939 from trunk.

	* [r7942] doc/Downloads/bzr_text.php:
	  Corrected 'pull' instructions.

	* [r7941] doc/Downloads/bzr_text.php:
	  Minor updates to text.

	* [r7940] doc/Downloads/bzr_text.php:
	  Continued writing instructions.

	* [r7939] examples/lissom_or_noshrinking.ty:
	  Updated import statement.

	* [r7938] doc/Downloads/bzr_text.php:
	  Added notes.

	* [r7937] doc/Downloads/bzr_text.php:
	  Initial version.

	* [r7936] external/Makefile:
	  Restored python configure options that were removed (presumably
	  by mistake) in r7849.

	* [r7935] external/ipython-0.7.3.tar.gz:
	  Removed old ipython version.

	* [r7934] topo/tests/testDynamicParameter.txt:
	  Fixed failing unit tests (caused by failure to remove
	  DynamicNumber from tests.

2008-02-11  ceball

	* [r7933] topo/base/parameterclasses.py:
	  Removed class supporting old DynamicNumbers.

	* [r7932] examples/joublin_bc96.ty,
	  examples/lissom_or_noshrinking_latswitch.ty:
	  Renamed variables that should have been updated in the past.

	* [r7931] topo/commands/basic.py:
	  If gzip cannot be imported, try to load the snapshot as a normal
	  file.

2008-02-11  jbednar

	* [r7930] topo/outputfns/basic.py:
	  Added ALERT

	* [r7929] examples/cc_lissom_oo_or.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/v2_cc_lissom_oo_or.ty:
	  Removed DynamicNumber and did basic testing, fixing some other
	  longstanding unrelated problems in some files. Not all scripts
	  modified have been tested thoroughly.

2008-02-11  ceball

	* [r7928] topo/base/parameterizedobject.py:
	  Simplified Parameter's _set_names().

	* [r7927] topo/base/parameterizedobject.py:
	  Removed tests for __slots__ on Parameter classes (and renamed
	  some variables).

	* [r7926] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  Decided to restrict storage of objtype to Parameters that
	  explicitly declare an objtype slot.

2008-02-11  judelaw

	* [r7925] examples/cc_lissom_oo_or.ty,
	  examples/laminar_oo_or.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/ohzawa_science90.ty,
	  examples/v2_cc_lissom_oo_or.ty:
	  updated examples with new plastic parameter replacing learning
	  parameter

	* [r7924] topo/base/functionfamilies.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/commands/analysis.py,
	  topo/commands/basic.py,
	  topo/outputfns/basic.py,
	  topo/projections/basic.py,
	  topo/sheets/lissom.py,
	  topo/tkgui/testpattern.py:
	  renamed stop and restore updating, updating and learning
	  parameter to plastic renamed _updating_state to
	  _plasticity_setting_stack

2008-02-11  ceball

	* [r7923] topo/base/parameterclasses.py:
	  Cleaned up some error messages.

	* [r7922] topo/base/boundingregion.py:
	  Simplified AARectangle's pickling; should be no visible change.

	* [r7921] topo/base/parameterizedobject.py:
	  No visible change: renamed a variable for consistency.

	* [r7920] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  Generalized Jeff's objtype slot to all Parameters (i.e. all
	  Parameters owned by ParameterizedObject classes (which should be
	  all Parameters) are told their owning class when the owning class
	  is created). This saves Parameters from having to lookup their
	  owning class later on, during use.

	* [r7919] topo/base/parameterclasses.py:
	  Moved some documentation.

2008-02-10  ceball

	* [r7918] topo/base/boundingregion.py,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py,
	  topo/base/patterngenerator.py,
	  topo/base/simulation.py:
	  Made ParameterMetaclass add __slots__=[] to any class that does
	  not already define __slots__.

2008-02-10  judelaw

	* [r7917] topo/commands/analysis.py:
	  Removed changes commited in error

	* [r7916] examples/cc_lissom_oo_or.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/lissom_oo_or_homeostatic.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/v2_cc_lissom_oo_or.ty,
	  topo/commands/analysis.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/homeostatic.py:
	  Merged homeostatic.py into basic.py

2008-02-10  ceball

	* [r7915] topo/base/boundingregion.py,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py,
	  topo/base/patterngenerator.py,
	  topo/base/simulation.py,
	  topo/misc/filepaths.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Added metaclass for Parameter, allowing the class docstring to be
	  displayed for help(parameter class), and the object doc slot to
	  be displayed for help(parameter object). Removes need for all
	  parameter subclasses to declare __doc__.

	* [r7914] topo/base/sheet.py,
	  topo/base/sheetcoords.py,
	  topo/patterns/image.py:
	  Removed matrixidx2sheet_array and sheetidx2matrix_array, and made
	  the previously scalar-only equivalents handle arrays.
	  sheet2matrixidx() involves a 'hasattr' test, though, so it's not
	  clearly an improvement.

	* [r7913] topo/base/sheetcoords.py:
	  Updated numpy imports, and use arange() instead of array() and
	  range().

	* [r7912] topo/base/sheet.py:
	  Simplified sheet_rows and sheet_cols().

	* [r7911] topo/analysis/featureresponses.py:
	  Attempted to simplify another for loop (again, I'm not sure it's
	  any simpler now).

	* [r7910] topo/analysis/featureresponses.py:
	  Attempted to simplify creation of distribution_matrix using
	  vectorize(), but I'm not sure it's any simpler now.

	* [r7909] topo/sheets/generatorsheet.py:
	  Made GeneratorSheet draw its pattern into its existing activity
	  array.

	* [r7908] topo/sheets/generatorsheet.py:
	  Added to comment.

	* [r7907] topo/base/sheet.py:
	  Fixed whitespace and some imports.

	* [r7906] doc/buildbot/pylintrc:
	  Made pylint flag 'oldnumeric'.

	* [r7905] doc/buildbot/pylintrc:
	  Made pylint ignore 'more than one statement on a line'.

2008-02-09  ceball

	* [r7904] topo/base/simulation.py:
	  Updated documentation.

	* [r7903] topo/base/parameterizedobject.py:
	  Fixed typos in error messages.

	* [r7902] topo/__init__.py,
	  topo/base/simulation.py,
	  topo/misc/utils.py:
	  Removed SimSingleton and made Simulation a monostate class. (A
	  simplification, because now topo.sim is the Simulation rather
	  than just a proxy.)

	* [r7901]
	  /branches/topographica-cfs_list_to_array/topographica/responsefnsoptimized.py:
	  Fixed mistake - now matches previous C version.

	* [r7900]
	  /branches/topographica-cfs_list_to_array/topographica/learningfnsoptimized.py:
	  Fixed another mistake; function now matches previous c version.

2008-02-08  ceball

	* [r7899]
	  /branches/topographica-cfs_list_to_array/topographica/learningfnsoptimized.py,
	  /branches/topographica-cfs_list_to_array/topographica/responsefnsoptimized.py:
	  Fixed mistake (still more mistakes to find in these two...).

	* [r7898]
	  /branches/topographica-cfs_list_to_array/topographica/outputfnsoptimized.py:
	  Fixed error in cfpofdivnorml1opt; now matches previous c code.

	* [r7897]
	  /branches/topographica-cfs_list_to_array/topographica/learningfnsoptimized.py,
	  /branches/topographica-cfs_list_to_array/topographica/responsefnsoptimized.py:
	  Fixed TypeErrors.

	* [r7896]
	  /branches/topographica-cfs_list_to_array/topographica/learningfnsoptimized.py:
	  No visible change.

	* [r7895]
	  /branches/topographica-cfs_list_to_array/topographica/outputfnsoptimized.py:
	  No visible change.

	* [r7894]
	  /branches/topographica-cfs_list_to_array/topographica/responsefnsoptimized.py,
	  /branches/topographica-cfs_list_to_array/topographica/topo/responsefns/optimized.py:
	  Untested replacement of CFPRF_DotProduct_opt by C code for
	  Instant.

	* [r7893]
	  /branches/topographica-cfs_list_to_array/topographica/learningfnsoptimized.py,
	  /branches/topographica-cfs_list_to_array/topographica/topo/learningfns/optimized.py:
	  Untested replacement of CFPLF_Hebbian_opt by C code for Instant.

2008-02-08  jbednar

	* [r7892] images/shouval/README:
	  Fixed whitespace

2008-02-08  ceball

	* [r7891]
	  /branches/topographica-cfs_list_to_array/topographica/outputfnsoptimized.py,
	  /branches/topographica-cfs_list_to_array/topographica/topo/outputfns/optimized.py:
	  Initial version of replacement for CFPOF_DivisiveNormalizeL1_opt.

	* [r7890]
	  /branches/topographica-cfs_list_to_array/topographica/anotherfile.py:
	  Renamed 'a' to 'cfs'.

	* [r7889]
	  /branches/topographica-cfs_list_to_array/topographica/anotherfile.py:
	  Added 'mask'.

	* [r7888]
	  /branches/topographica-cfs_list_to_array/topographica/anotherfile.py:
	  C code for Instant that I'm starting to make look like
	  outputfns/optimized.py's code.

2008-02-08  jbednar

	* [r7887] examples/lissom_oo_or_homeostatic.ty:
	  Changed to use shouval images distributed with Topographica

	* [r7886] Makefile,
	  examples/lissom_photo_or.ty,
	  images, images/shouval,
	  images/shouval/README,
	  images/shouval/combined01.png,
	  images/shouval/combined02.png,
	  images/shouval/combined03.png,
	  images/shouval/combined04.png,
	  images/shouval/combined05.png,
	  images/shouval/combined06.png,
	  images/shouval/combined07.png,
	  images/shouval/combined08.png,
	  images/shouval/combined09.png,
	  images/shouval/combined10.png,
	  images/shouval/combined11.png,
	  images/shouval/combined12.png,
	  images/shouval/combined13.png,
	  images/shouval/combined14.png,
	  images/shouval/combined15.png,
	  images/shouval/combined16.png,
	  images/shouval/combined17.png,
	  images/shouval/combined18.png,
	  images/shouval/combined19.png,
	  images/shouval/combined20.png,
	  images/shouval/combined21.png,
	  images/shouval/combined22.png,
	  images/shouval/combined23.png,
	  images/shouval/combined24.png,
	  images/shouval/combined25.png:
	  Added standard set of photos, and enabled testing of
	  lissom_photo.ty

	* [r7885] topo/commands/basic.py:
	  Removed obsolete alerts

2008-02-08  ceball

	* [r7884] doc/buildbot/bbanalysis.py:
	  Only log performance if results didn't change.

	* [r7883]
	  /branches/topographica-cfs_list_to_array/,
	  Merged in changes r7658:7882 from trunk.

	* [r7882] doc/buildbot/master.cfg:
	  Updated timeouts, corrected call to analysis script, c++ lissom
	  comparison runs once per week.

	* [r7881] doc/buildbot/bbanalysis.py:
	  Multiple corrections.

2008-02-07  jbednar

	* [r7880] Makefile:
	  Removed just-added lissom_oo_or_homeostatic.ty from list of
	  scripts to check; defaults are not coded in a density-independent
	  way

	* [r7879] Makefile:
	  Added lissom_oo_or_homeostatic.ty to list of scripts to check

	* [r7878] topo/base/projection.py:
	  Added updating parameter to Projection for ScaledCFProjection to
	  use.

	* [r7877] topo/base/functionfamilies.py,
	  topo/base/projection.py,
	  topo/projections/basic.py,
	  topo/sheets/lissom.py:
	  Cleaned up docstrings, comments, and whitespace. Removed
	  duplicate implementations of updating, stop_updating, and
	  restore_updating

2008-02-07  ceball

	* [r7876] doc/buildbot/master.cfg:
	  Added start of c++ results and speed comparisons.

	* [r7875] doc/buildbot/bbanalysis.py:
	  Initial version.

	* [r7874] Makefile:
	  Added target for buildbot running c++ lissom comparison.

	* [r7873]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Added option for profiling.

	* [r7872]
	  topo/tests/reference/lissom_log_parser.py:
	  Comparisons optionally raise assertion error on failure.

2008-02-07  jbednar

	* [r7871] topo/tkgui/plotgrouppanel.py:
	  Added alert

	* [r7870] topo/base/functionfamilies.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/homeostatic.py:
	  Moved implementation of stop_updating and restore_updating to a
	  new base class OutputFnWithState, to remove rampant code
	  duplication. Cleaned up comments, docstrings, and spacing.

	* [r7869] topo/base/sheet.py,
	  topo/sheets/lissom.py:
	  Cleaned up comments, docstrings, and spacing.

	* [r7868] topo/base/parameterizedobject.py,
	  topo/base/projection.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/homeostatic.py,
	  topo/projections/basic.py:
	  Cleaned up docstrings, comments, and whitespace

	* [r7867] topo/patterns/teststimuli.py:
	  Removed unused parameter

2008-02-07  ceball

	* [r7866] topo/base/parameterizedobject.py:
	  Allow old snapshots to load after removing Parameter's 'hidden'
	  slot.

	* [r7865] Makefile:
	  Added 'time' command to speed tests.

	* [r7864] Makefile:
	  Added 'time' command to slow-tests.

	* [r7863] topo/base/simulation.py:
	  Fixed some whitespace and disabled a pylint message.

	* [r7862] topo/base/parameterizedobject.py:
	  Fixed or disabled numerous pylint complaints.

	* [r7861] topo/base/cf.py,
	  topo/base/parameterizedobject.py,
	  topo/base/patterngenerator.py,
	  topo/base/sheet.py,
	  topo/patterns/basic.py,
	  topo/patterns/random.py,
	  topo/patterns/rds.py,
	  topo/patterns/teststimuli.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Addressed SF.net feature 1869380: Replaced hidden with negative
	  precedence. GUI has settable display_threshold.

	* [r7860] external/Makefile:
	  Removed stray 'ctypes'.

	* [r7859] examples/goodhill_network90.ty:
	  Removed unused import and fixed SyntaxError (from __future__ ...
	  must appear at the top of a file).

2008-02-06  jprovost

	* [r7858] topo/misc/traces.py:
	  Added ActivityMovie class.

	* [r7857] topo/sheets/generatorsheet.py:
	  Fix to accomodate changed Event API.

	* [r7856] topo/base/simulation.py:
	  Added ALERT.

	* [r7855] topo/misc/traces.py:
	  Bug fixes and upgrades to getting ranges and individual
	  timepoints from a DataRecorder object.

	* [r7854] topo/plotting/bitmap.py:
	  Added MontageBitmap class for compositing bitmaps together into a
	  larger bitmap.

2008-02-06  judelaw

	* [r7853] topo/projections/basic.py:
	  updated documentation for ScaledCFProjection

	* [r7852] examples/lissom_oo_or_homeostatic.ty:
	  updated to account for changes in AttributeTrackingOF

2008-02-06  jprovost

	* [r7851] topo/sheets/generatorsheet.py:
	  Changed SequenceGeneratorSheet to default to behave like a plain
	  GeneratorSheet if no sequence is provided.

	* [r7850] topo/tkgui/projectionpanel.py:
	  Fix Projection GUI to omit sheets with no CFProjections.

	* [r7849] external/Imaging_OSX.diff,
	  external/Makefile,
	  external/Makefile_OSX.diff,
	  external/Makefile_OSX_X11.diff:
	  Build in PIL font support on Mac OS.

2008-02-06  ceball

	* [r7848] topo/base/parameterizedobject.py:
	  Made pylint ignore 'bothmethods' not using self.

	* [r7847] topo/base/arrayutils.py:
	  Removed old references to Numeric.

	* [r7846] topo/base/simulation.py:
	  Converted Event into a ParameterizedObject.

	* [r7845] topo/base/arrayutils.py:
	  Aimed pylint message more specifically.

	* [r7844] topo/base/arrayutils.py:
	  Corrected pylint message id.

	* [r7843] topo/base/cf.py,
	  topo/base/projection.py:
	  Moved declaration of output_fn from CFProjection up to
	  Projection. Fixed whitespace in projection.py.

	* [r7842] doc/buildbot/pylintrc:
	  More for pylint to ignore.

	* [r7841] doc/buildbot/pylintrc:
	  Made Pylint ignore warnings about relative imports. (We tell
	  people to do it in our manual.)

	* [r7840] topo/base/arrayutils.py:
	  Tried to deal with pylint complaints in arrayutils.

	* [r7839] doc/buildbot/pylintrc:
	  Minor adjustment to pylint's options.

2008-02-06  judelaw

	* [r7838] topo/outputfns/basic.py:
	  made changes to AttributeTrackingOF to fix bug when using
	  script_repr()

2008-02-06  ceball

	* [r7837] topo/base/arrayutils.py,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/parameterizedobject.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/base/sheetcoords.py,
	  topo/base/sheetview.py:
	  Removed unused imports, as detected by make lint-base.

	* [r7836] topo/base/parameterizedobject.py:
	  Removed duplicate import.

	* [r7835] topo/base/arrayutils.py,
	  topo/base/parameterclasses.py:
	  Removed unused imports.

	* [r7834] topo/base/simulation.py:
	  Removed unused import.

	* [r7833] topo/base/simulation.py:
	  Re-enabled a debug statement that had previously been slowing
	  down simulations whatever the print_level; appears to make no
	  impact now (when print level is below debug).

	* [r7832] Makefile:
	  Removed scripts that have been deleted from slow-tests.

	* [r7831] doc/buildbot/master.cfg:
	  Added -k to make slow-tests.

	* [r7830] topo/base/parameterizedobject.py:
	  Functions can be passed to debug(), message(), etc, allowing us
	  to avoid building complex strings unless the print_level requires
	  it.

2008-02-06  judelaw

	* [r7829] topo/commands/analysis.py:
	  Changed default duration in measure_or_pref back to 0.175

2008-02-06  ceball

	* [r7828] topo/base/simulation.py:
	  Added ALERT about parent class of Event.

	* [r7827] topo/base/simulation.py:
	  Made run() docstring clearer (to me).

	* [r7826]
	  /branches/topographica-cfs_list_to_array/topographica/objectsiter.py:
	  Minor edit (no change to C code).

	* [r7825]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py,
	  /branches/topographica-cfs_list_to_array/topographica/objectsiter.py:
	  Made Instant and Weave code examples match.

	* [r7824]
	  /branches/topographica-cfs_list_to_array/topographica/instant_inline_demo.py:
	  Demonstrate looping through and modifying weights of (fake) CFs
	  from C++ using instant.

	* [r7823]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py:
	  Avoid conversion error by casting a py::object to PyObject; now
	  get a segmentation fault.

	* [r7822]
	  /branches/topographica-cfs_list_to_array/topographica/doublesiter.py,
	  /branches/topographica-cfs_list_to_array/topographica/doublesloop.py,
	  /branches/topographica-cfs_list_to_array/topographica/objectsiter.py,
	  /branches/topographica-cfs_list_to_array/topographica/objectsloop.py:
	  Added Instant demonstrations (object versions have pointer errors
	  corrected from e-mail versions.

	* [r7821]
	  /branches/topographica-cfs_list_to_array/topographica/external/Makefile,
	  /branches/topographica-cfs_list_to_array/topographica/external/instant-0.9.2.tar.gz:
	  Added Instant from fenics.org.

	* [r7820]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py:
	  Added test loop using a numpy iterator (fails to compile).

2008-02-05  judelaw

	* [r7819] topo/sheets/lissom.py:
	  added 'JointNormalize' to _grouped_in_projections in JointScaling

	* [r7818] examples/lissom_oo_or_homeostatic.ty:
	  removed imports of missing functions

	* [r7817] examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_or_homeoscale.ty,
	  topo/base/cf.py,
	  topo/outputfns/homeostatic.py,
	  topo/projections/basic.py,
	  topo/responsefns/optimized.py:
	  Removed old examples now replaced by lissom_oo_or_homeostatic.ty

	* [r7816] topo/sheets/lissom.py:
	  Added learning rate scaling to JointScaling sheet

	* [r7815] topo/outputfns/basic.py:
	  Merged SheetAttributeTrackingOF with AttributeTrackingOF

	* [r7814] examples/lissom_oo_or_homeostatic.ty:
	  Removed afferent learning rate decay, added new input types

2008-02-04  jbednar

	* [r7813] external/Makefile,
	  external/stage-2.1.0rc1.tar.bz2:
	  Added stage; made player install the playerc module

	* [r7812] external/Makefile,
	  external/player-2.1.0rc1.tar.bz2:
	  Updated to player 2.10rc1

	* [r7811] doc/Team_Members/index_text.php:
	  Fixed Jeff's info to match his web pages

	* [r7810] external/Makefile:
	  Minor update

	* [r7809] doc/shared/trailer.php:
	  Removed dependence on cs.utexas

2008-02-01  jbednar

	* [r7808] examples/lgn_lateral.ty:
	  Resolved more conflicts

	* [r7807] examples/lissom_oo_or_homeostatic.ty:
	  Cleaned up docstring

	* [r7806] examples/lissom_oo_or_homeostatic.ty:
	  Fixed docstring keywords

	* [r7805] examples/lgn_lateral.ty:
	  Fixed docstring keywords, added alert, and removed bogus conflict
	  characters

2008-02-01  antolikjan

	* [r7804] examples/v2_cc_lissom_oo_or.ty:
	  renamed JointNormalizingCFSheet_Continouse

	* [r7803] examples/cc_lissom_oo_or.ty:
	  renamed JointNormalizingCFSheet_Continouse

	* [r7802] examples/lgn_lateral.ty:
	  Reflected the changes

	* [r7801] topo/base/simulation.py:
	  made event_clear such that you specify which type of events to
	  clear

	* [r7800] topo/commands/analysis.py:
	  corrected to use new event_clear(),correcting orientation tuning
	  curve,

	* [r7799] topo/sheets/lissom.py:
	  removed _port_match(self,key,portlist) and renamed
	  JointNormalizingCFSheet_Continouse

	* [r7798] topo/tkgui/testpattern.py:
	  corrected to work with nw event_clear()

	* [r7797] topo/analysis/vision.py:
	  corrected some bugs in complexity function

	* [r7796] topo/analysis/featureresponses.py:
	  removed _complexity_rec

2008-02-01  ceball

	* [r7795] /branches/topographica-tkgui_with_tile/:
	  Merged in trunk changes r7685:7794

	* [r7794] /branches/topographica-tkgui_with_tile/external/Makefile,
	  /branches/topographica-tkgui_with_tile/external/Pmw.diff,
	  /branches/topographica-tkgui_with_tile/external/Pmw.tgz,
	  /branches/topographica-tkgui_with_tile/external/pybwidget-0.1.2_1.7.0.tar.gz,
	  /branches/topographica-tkgui_with_tile/external/pybwidget-0.1.2_1.8.0.tar.gz:
	  Removed unused external packages.

	* [r7793] /branches/topographica-tkgui_with_tile/external/Makefile,
	  /branches/topographica-tkgui_with_tile/external/tile-0.8.2.tar.gz:
	  Removed tile (it's part of Tk 8.5).

2008-01-31  ceball

	* [r7792] topo/sheets/lissom.py:
	  Fixed minor typo.

	* [r7791] topo/misc/utils.py:
	  Removed old profile() function.

2008-01-31  jbednar

	* [r7790] Makefile:
	  Removed references to CVS. Updated LATEST_STABLE target to work
	  with SVN.

2008-01-31  ceball

	* [r7789] /tags/LATEST_STABLE:
	  Update LATEST_STABLE.

	* [r7788] /tags/LATEST_STABLE:
	  Updating LATEST_STABLE.

	* [r7787] examples/lissom_or_homeoscale.ty:
	  Use numpy's own array clip() method. Fixes buildbot slow-tests
	  failure on build 141.

	* [r7786] examples/ohzawa_science90.ty:
	  Removed unused import.

	* [r7785] examples/sullivan_nn06.ty:
	  Removed unused import.

2008-01-31  rczhao

	* [r7784] /trunk/facespace/perception_3d.ty:
	  Measure perception based on the new face space

2008-01-30  rczhao

	* [r7783] /trunk/facespace/face_space_patterns.py:
	  Added a new FaceSpace5D_mlab class to work with external MATLAB
	  data.

	* [r7782] /trunk/facespace/face_space.ty:
	  Simulation changes to new FaceSpace class.

2008-01-30  ceball

	* [r7781] Makefile:
	  Added date and svnversion printing to slow-tests (for benefit of
	  buildbot log analysis.

	* [r7780] topo/base/simulation.py:
	  CommandEvent raises an error (rather than warning) if a syntax
	  error is detected when the event is created. CommandEvent now
	  also raises an error if there is an error while executing the
	  command (rather than warning). Additionally, CommandEvent now
	  tests the syntax on creation by using the compile() function,
	  rather than by exec()ing the string in another namespace.

	* [r7779] topo/base/arrayutils.py:
	  Added comment about clip_lower().

	* [r7778] topo/base/arrayutils.py,
	  topo/outputfns/basic.py:
	  Removed our clip_in_place(); numpy's array now has a clip method
	  that can operate in place.

	* [r7777] topo/base/parameterizedobject.py:
	  Updated ParamOverrides to use Python 2.5-only method. Minor
	  changes to other comments.

	* [r7776] topo/base/parameterizedobject.py,
	  topo/tests/testCompositeParameter.txt,
	  topo/tests/testDynamicParameter.txt,
	  topo/tkgui/tkparameterizedobject.py:
	  Renamed repr_value() to get_value_generator().

	* [r7775] topo/base/parameterizedobject.py:
	  Removed out-of-date ALERT.

	* [r7774] topo/base/parameterizedobject.py:
	  script_repr_suppress_defaults and dbprint_prefix are no longer
	  Parameters (previously they were Parameters of no
	  ParameterizedObject). Also, minor alterations to other comments.

	* [r7773] topo/base/sheet.py:
	  Allow snapshots created between 7547 and 7763 to load without
	  error.

2008-01-30  jbednar

	* [r7772] doc/Tutorials/lissom_oo_or_text.php,
	  doc/Tutorials/som_retinotopy_text.php:
	  Merged changes from 7643:7758 on cnv_course_2008 branch to fix
	  various issues with the tutorials

	* [r7771]
	  /branches/cnv_course_2008/topographica/doc/Tutorials/lissom_oo_or_text.php:
	  Enabled command-line param setting now that it works properly

	* [r7770]
	  /branches/cnv_course_2008/topographica/examples/lissom_oo_or.ty,
	  /branches/cnv_course_2008/topographica/topo/base/cf.py,
	  /branches/cnv_course_2008/topographica/topo/base/sheet.py:
	  Merged Chris's changes from trunk to fix bugs

2008-01-30  ceball

	* [r7769] topo/base/parameterizedobject.py:
	  Replaced 'curry' with python's own partial() function. Should be
	  no visible change.

	* [r7768] doc/Future_Work/current_text.php:
	  Added some tasks.

2008-01-29  ceball

	* [r7767] topo/plotting/plotgroup.py:
	  Fixed bug in UnitPlotGroup: was failing to set unit coordinate in
	  topo.commands.analysis.

	* [r7766] topo/commands/basic.py:
	  Removed print statement.

	* [r7765] topo/commands/analysis.py:
	  Removed comment.

	* [r7764] topo/base/sheet.py:
	  No visible change: removed stray comment.

	* [r7763] topo/base/sheet.py:
	  Fix SF.net bug 1881582 (Plotgroup's situate doesn't work after
	  loading snapshot). Slice(ndarray) did not have its non-ndarray
	  attributes pickled, so ConnectionFields' bounds were None;
	  plotting uses those bounds for unsituated plots.

	* [r7762] doc/Forums/problems_text.php:
	  Updated link for reporting a bug.

	* [r7761] doc/Forums/problems_text.php:
	  Cleaned up bug report procedure.

	* [r7760] examples/lissom_oo_or.ty:
	  Reverted lissom_oo_or to fixed-point time; run() does not work
	  with floating-point time.

	* [r7759] topo/base/cf.py:
	  Fixed bug where using an integer learning rate led to an inter
	  division happening in constant_sum_connection_rate().

2008-01-28  jbednar

	* [r7758]
	  /branches/cnv_course_2008/topographica/doc/Tutorials/lissom_oo_or_text.php:
	  Updated to match the actual output shown in the figures

	* [r7757]
	  /branches/cnv_course_2008/topographica/doc/Tutorials/som_retinotopy_text.php:
	  Minor update

	* [r7756]
	  /branches/cnv_course_2008/topographica/doc/Tutorials/som_retinotopy_text.php:
	  Fixed outdated bits from the tutorial

2008-01-28  antolikjan

	* [r7755] topo/base/simulation.py:
	  Removed some print statements that I forgot in the code of
	  event_clear()

	* [r7754] topo/sheets/lissom.py:
	  Resolved the conflict and submitting the changes to LISSOM -
	  appropriate handling of the case when tsettle == 0, moving port
	  matching code to Projection and adding a new class
	  JointNormalizingCFSheet_Continouse

	* [r7753] topo/analysis/vision.py:
	  corrected bug with fft

2008-01-28  jbednar

	* [r7752] doc/Links/index_text.php:
	  Removed new qualifier from CMVC book

2008-01-28  ceball

	* [r7751] topo/misc/patternfns.py:
	  Made patternfns more readable: no visible change, except that the
	  change is incompatible with Python 2.4.

	* [r7750] doc/Home/index_text.php:
	  Updated expected release date.

2008-01-28  jbednar

	* [r7749] doc/Future_Work/index_text.php:
	  Updated to-do dates

	* [r7748] doc/Home/news_text.php:
	  Simplified news and made lines shorter to fit on smaller windows

	* [r7747]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Clarified that the : is required for CVS/SVN keywords

	* [r7746] examples/lissom_oo_or_dy.ty:
	  Added note about status

	* [r7745] doc/Future_Work/current_text.php:
	  Added to-do item

	* [r7744] doc/Downloads/cvs_text.php:
	  Minor clarifications

	* [r7743] doc/Home/news_text.php:
	  Updated with recent news

	* [r7742] topo/commands/basic.py:
	  Clarified docstring

2008-01-27  jbednar

	* [r7741] /branches/topographica-tkgui_with_tile/external/Makefile:
	  Added required step

2008-01-27  ceball

	* [r7740]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/testpattern.py:
	  More updates for panels opening on console.

	* [r7739]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/editorobjects.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/editorwindow.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/parametersframe.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/plotgrouppanel.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topoconsole.py:
	  More updates for panels opening on console.

	* [r7738]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/__init__.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/plotgrouppanel.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/projectionpanel.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/templateplotgrouppanel.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/testpattern.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topoconsole.py:
	  Try allowing plotgrouppanels to be free or on console.

2008-01-27  antolikjan

	* [r7737] examples/cc_lissom_oo_or.ty:
	  The complex cells model

2008-01-27  ceball

	* [r7736] /branches/topographica-tkgui_with_tile/external/Tile.py:
	  Initial version, from
	  http://tkinter.unpythonic.net/wiki/TileWrapper.

	* [r7735]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/__init__.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topoconsole.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topowidgets.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/widgets.py:
	  Began to clean up window parentage. Made topoconsole be a
	  TkParameterizedObject.

2008-01-26  ceball

	* [r7734] doc/Downloads/cvs_text.php:
	  Updated buildbot links.

	* [r7733] topo/misc/commandline.py:
	  Stop IPython performing its 'namespace hack' (see link included
	  in comments).

	* [r7732] external/Makefile,
	  external/scipy-site.cfg:
	  Added a site.cfg for scipy, so that scipy should at least build
	  on DICE.

	* [r7731]
	  topo/tests/reference/lissom_oo_dr_reference.ty,
	  topo/tests/reference/oo_dir_map.log.gz,
	  topo/tests/reference/oo_dir_map.param:
	  Initial version of oo_dir c++ lissom comparison - untested.

	* [r7730]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Added note to write up later.

	* [r7729]
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty:
	  Updated lissom_log_parser to handle data from more than one eye.

	* [r7728] topo/commands/analysis.py:
	  Uncommented direction map code (with minor changes to
	  formatting).

	* [r7727] doc/buildbot/master.cfg:
	  Added svn rsync backup. Renamed builders so display is clearer.

2008-01-25  antolikjan

	* [r7726] topo/analysis/vision.py:
	  changed to not use scipy anymore

2008-01-24  rczhao

	* [r7725] /trunk/facespace/face_space_patterns.py:
	  The latest working version for 2-D face space on Topographica as
	  of SVN 2007-12-07.

	* [r7724] /trunk/facespace/face_space.ty:
	  The latest working version for 2-D face space on Topographica as
	  of SVN 2007-12-07.

	* [r7723] /trunk/facespace/perception.ty:
	  The latest working version for 2-D face space on Topographica as
	  of SVN 2007-12-07.

2008-01-24  antolikjan

	* [r7722] examples/v2_cc_lissom_oo_or.ty:
	  New file that contains complex cell LISSOM model with added V2

	* [r7721] examples/cc_lissom_oo_or.ty:
	  New file that contains complex cell LISSOM model

	* [r7720] topo/base/projection.py:
	  New code allowing for divisive and multiplicative connections

	* [r7719] topo/outputfns/basic.py:
	  New Naka-Rushton output function (used for gain control)

	* [r7718] topo/learningfns/optimized.py:
	  new optimized Trace learning rule

	* [r7717] topo/patterns/basic.py:
	  New Translator pattern that allows movement of stimuly

	* [r7716] topo/commands/analysis.py:
	  new function that displays also modulation ratio of cells

	* [r7715] topo/commands/pylabplots.py:
	  New function that can compute modulation ratio - a indicator of
	  how phase invariant a cell is

	* [r7714] topo/analysis/featureresponses.py:
	  The new FullMatrix class added that stores all the info collected
	  during analysis for further processing

	* [r7713] topo/tkgui/testpattern.py:
	  Added wiping out activity and events before pattern presentation
	  for simulations that ignore tsettle

	* [r7712] topo/commands/basic.py:
	  added wipe_out_activity function that resets the activity in all
	  sheets and projections to zero

	* [r7711] topo/base/simulation.py:
	  New function event_clear that cleans up event que from leftover
	  events before analysis - it is a HACK for now!

	* [r7710] topo/analysis/vision.py:
	  The new file containing analysis code for vision specific models

2008-01-24  ceball

	* [r7709]
	  /branches/topographica-tkgui_with_tile/external/tklib-CVS20080114.tar.gz:
	  Previous version had directory missing; this version is straight
	  from cvs.

2008-01-23  ceball

	* [r7708] topo/analysis/featureresponses.py:
	  Removed unused import.

	* [r7707] topo/commands/analysis.py:
	  Added commented-out code for measuring a direction map.

	* [r7706] topo/base/parameterizedobject.py:
	  Allow snapshots to load if a class for which parameters were
	  saved can no longer be found.

	* [r7705] examples/lissom_oo_dr.ty:
	  Updated to new dynamic number syntax.

2008-01-23  jbednar

	* [r7704] Makefile:
	  Added dependencies to force topographica script to rebuild

	* [r7703] Makefile:
	  Made SVN version info be collected when make is run, rather than
	  on every startup

	* [r7702] doc/User_Manual/publishing_text.php:
	  Removed outdated instruction

2008-01-23  ceball

	* [r7701]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/__init__.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/widgets.py:
	  Require tooltip package inside the Balloon widget. Cleanup
	  tkgui/__init__.

	* [r7700]
	  /branches/topographica-tkgui_with_tile/topo/tests/testtopoconsole.py:
	  Removed useless test file.

	* [r7699]
	  /branches/topographica-tkgui_with_tile/topo/tests/testtemplateplotgrouppanel.py:
	  Removed apparently useless test.

	* [r7698]
	  /branches/topographica-tkgui_with_tile/topo/tests/gui_tests.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topoconsole.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/widgets.py:
	  Removed Command Prompt, removed Combobox wrapper.

	* [r7697]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/editorobjects.py:
	  Converted connections list to OptionMenu.

	* [r7696]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/editortools.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/editorwindow.py:
	  Converted model editor's comboboxes to optionmenus. (I think
	  there is something wrong with the parentage of frames in the
	  model editor hierarchy; pack takes quite a long time to solve the
	  layout.)

2008-01-22  ceball

	* [r7695]
	  /branches/topographica_tkgui-with-idle/topo/tkgui/tk_thread.py:
	  Initial version.

	* [r7694] /branches/topographica_tkgui-with-idle:
	  Created branch to hold IDLE-with-tkgui experiment.

2008-01-22  judelaw

	* [r7693] topo/outputfns/basic.py:
	  removed an alert

	* [r7692] topo/sheets/lissom.py:
	  combined do_joint_scaling and get_sf functions in JointScaling,
	  added alerts

	* [r7691] examples/lissom_oo_or_homeostatic.ty:
	  Changed name of CFPLF_Plugin_scaled to CFPLF_PluginScaled

	* [r7690] topo/base/cf.py:
	  Changed name of CFPLF_Plugin_scaled to CFPLF_PluginScaled

2008-01-22  ceball

	* [r7689]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/widgets.py:
	  TaggedSlider no longer shows value above slider (as in trunk).

	* [r7688] /branches/topographica-tkgui_with_tile/Makefile,
	  /branches/topographica-tkgui_with_tile/doc/Downloads/cvs_text.php,
	  /branches/topographica-tkgui_with_tile/doc/Forums/problems_text.php,
	  /branches/topographica-tkgui_with_tile/doc/buildbot/master.cfg,
	  /branches/topographica-tkgui_with_tile/doc/buildbot/pylintrc,
	  /branches/topographica-tkgui_with_tile/examples/lissom_oo_or_homeostatic.ty,
	  /branches/topographica-tkgui_with_tile/topo/base/cf.py,
	  /branches/topographica-tkgui_with_tile/topo/outputfns/basic.py,
	  /branches/topographica-tkgui_with_tile/topo/outputfns/homeostatic.py,
	  /branches/topographica-tkgui_with_tile/topo/patterns/rds.py,
	  /branches/topographica-tkgui_with_tile/topo/sheets/lissom.py:
	  Merged in trunk changes 7647:7685.

2008-01-22  jbednar

	* [r7687] doc/Downloads/cvs_text.php:
	  Added a note about branching

	* [r7686] doc/Downloads/cvs_text.php:
	  Minor clarification

2008-01-22  ceball

	* [r7685] /branches/topographica-tkgui_with_tile/external/Makefile,
	  /branches/topographica-tkgui_with_tile/external/tklib-CVS20080114.tar.gz:
	  Added tklib.

	* [r7684] doc/Forums/problems_text.php:
	  Don't need svn status in bug reports.

	* [r7683]
	  /branches/topographica-cfs_list_to_array/topographica/doc/Downloads/cvs_text.php:
	  Undid change to doc that has now been made on trunk/.

	* [r7682] doc/Downloads/cvs_text.php:
	  Jim's change to SVN documentation (accidentally committed to a
	  branch before).

	* [r7681] doc/Forums/problems_text.php:
	  Updated problem-reporting guidelines (for SVN).

2008-01-21  ceball

	* [r7680] /branches/topographica-tkgui_with_tile/external/Makefile,
	  /branches/topographica-tkgui_with_tile/external/tcl8.5.0-src.tar.gz,
	  /branches/topographica-tkgui_with_tile/external/tk8.5.0-src.tar.gz,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/__init__.py:
	  Upgrade to tcl/tk 8.5 (experiment). (Note that to use this branch
	  right now you must install tklib and patch tooltip.tcl for Tile.
	  This will be added to the repository some time soon.).

2008-01-21  jbednar

	* [r7679]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py:
	  Works, but not in any reasonable way

	* [r7678]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py:
	  Added row, column info; made some of the obj array work

	* [r7677]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py:
	  Updated to Chris's new my_test.py

	* [r7676]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py:
	  Hacked to allow it to compile

	* [r7675]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py:
	  Updated to match my_test.py from Chris

2008-01-21  judelaw

	* [r7674] examples/lissom_oo_or_homeostatic.ty:
	  Added new example file for stable development of orientation maps
	  with LISSOM using homeostatic mechanisms

	* [r7673] topo/outputfns/basic.py:
	  changed definition of smoothing parameter for exponential
	  averaging, added SheetAttributeTrackingOF for debugging

	* [r7672] topo/outputfns/homeostatic.py:
	  changed definition of smoothing parameter for exponential
	  averaging, removed JointScalingOF and AdaptingHomeostaticMaxEnt

	* [r7671] topo/sheets/lissom.py:
	  added JointScaling sheet which scales afferent projection
	  activity, for use in lissom_oo_or_homeostatic.ty

	* [r7670] topo/base/cf.py:
	  added a new learning function CFPLF_Plugin_scaled for use in
	  lissom_oo_or_homeostatic.ty

2008-01-21  jbednar

	* [r7669]
	  /branches/topographica-cfs_list_to_array/topographica/doc/Downloads/cvs_text.php:
	  Added note about SVN 1.3

	* [r7668]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py:
	  Added double version for testing

	* [r7667]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py:
	  Reverted to previous, plus some additions from Jim

2008-01-21  ceball

	* [r7666]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py:
	  Tried to turn example C function into something more useful.

	* [r7665]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py:
	  Cleanup to example (used to be for lists).

	* [r7664]
	  /branches/topographica-cfs_list_to_array/topographica/array_obj_test.py:
	  Added small test example to work C access to arrays of objects.

2008-01-21  jbednar

	* [r7663] topo/patterns/rds.py:
	  Removed unused import

2008-01-21  ceball

	* [r7662]
	  /branches/topographica-cfs_list_to_array/topographica/topo/base/cf.py,
	  /branches/topographica-cfs_list_to_array/topographica/topo/projections/basic.py:
	  First pass at changing CFProjection's list of CFs into an array
	  (no change to optimized functions yet).

	* [r7661]
	  /branches/topographica-cfs_list_to_array/topographica/external/Makefile:
	  Corrected another mistake in earlier checkin.

	* [r7660]
	  /branches/topographica-cfs_list_to_array/topographica/external/Makefile:
	  Corrected typo in previous checkin.

	* [r7659]
	  /branches/topographica-cfs_list_to_array/topographica/external/Makefile,
	  /branches/topographica-cfs_list_to_array/topographica/external/weave-3852.tar.gz,
	  /branches/topographica-cfs_list_to_array/topographica/weave.diff:
	  Added current SVN weave and a patch to support arrays of objects
	  (maybe).

	* [r7658] /branches/topographica-cfs_list_to_array/topographica:
	  Created branch for transforming CFProjection's list of CFs to be
	  an array of CFs.

	* [r7657] /branches/topographica-cfs_list_to_array:
	  Created branch for transforming CFProjection's list of CFs to be
	  an array of CFs.

2008-01-20  jbednar

	* [r7656] doc/Downloads/cvs_text.php:
	  Updated Windows SVN instructions

2008-01-19  ceball

	* [r7655] doc/buildbot/pylintrc:
	  Made pylint output 'parseable' as it was before using the rc
	  file.

	* [r7654] doc/buildbot/master.cfg:
	  buildbot now runs make lint-base.

	* [r7653] Makefile:
	  Pylint manual recommends using module names rather than passing
	  in separate files. Seems to produce the same output, anyway.

	* [r7652] Makefile,
	  doc/buildbot/pylintrc:
	  Updated pylint command to work with current version of pylint.
	  Added pylintrc file generated from previous pylint command (minus
	  incompatible options).

2008-01-17  ceball

	* [r7651] /branches/topographica-tkgui_with_tile/external/Makefile:
	  Added missing target.

	* [r7650]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topowidgets.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/widgets.py:
	  Replaced bwidget's progressbar with tile's.

	* [r7649] /branches/topographica-tkgui_with_tile/external/Makefile:
	  Fixed minor mistake from merge.

	* [r7648] /branches/topographica-tkgui_with_tile/:
	  Merged in changes 7597:7647 from trunk.

	* [r7647] /branches/topographica-tkgui_with_tile/external/Makefile,
	  /branches/topographica-tkgui_with_tile/external/tcl8.4.13-src.tar.gz,
	  /branches/topographica-tkgui_with_tile/external/tcl8.4.17-src.tar.gz,
	  /branches/topographica-tkgui_with_tile/external/tk8.4.13-src.tar.gz,
	  /branches/topographica-tkgui_with_tile/external/tk8.4.17-src.tar.gz,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/__init__.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/editorobjects.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/editortools.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/templateplotgrouppanel.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/tkparameterizedobject.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topoconsole.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topowidgets.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/widgets.py:
	  Multiple changes: removed Pmw, upgraded to tcl/tk 8.4.17.

	* [r7646] /trunk/facespace/.DS_Store:
	  Deleted file presumably committed by accident (I thought I had
	  already deleted this once?).

	* [r7645] doc/Downloads/index_text.php:
	  Minor modification for Python 2.5.

	* [r7644] /branches/cnv_course_2008/topographica:
	  Created cnv_course_2008 branch from 7643.

	* [r7643] /branches/cnv_course_2008:
	  Make directory to hold cnv_course_2008 topographica.

	* [r7642] /branches/cnv_course_2008:
	  Deleted cnv_2008_course branch: the directory structure is wrong
	  (missing topographica/ level).

	* [r7641] topo/tests/test_pattern_present.txt:
	  Commented out faulty test.

	* [r7640] topo/plotting/bitmap.py,
	  topo/plotting/plot.py:
	  Switch to use numpy.array's own methods in some parts of plotting
	  (e.g. numpy's sum() for python's); should be no visible change
	  except a speedup to plotting. Presumably, more of these simple
	  replacements are possible (and would be indicated by profiling
	  the plotting).

	* [r7639] /tags/CNV_COURSE, /tags/cnv_course_2006:
	  Renamed CNV_COURSE to cnv_course_2006.

	* [r7638] /branches/cnv_course_2008:
	  Created cnv_course_2008 branch.

	* [r7637] doc/Tutorials/lissom_oo_or_text.php,
	  doc/Tutorials/som_retinotopy_text.php,
	  topo/tkgui/plotgrouppanel.py:
	  Minor changes to documentation.

	* [r7636] topo/base/simulation.py:
	  Added some comments.

	* [r7635] topo/commands/basic.py:
	  Fix failing test: save_input_generators() does topo.sim.run(0) to
	  start generator sheets.

	* [r7634] topo/tests/test_pattern_present.txt:
	  Added test to show that save_input_generators() causes a problem
	  with the event queue.

	* [r7633] topo/tests/testpatternpresent.py:
	  Removed redundant test.

	* [r7632] topo/plotting/plot.py:
	  Fixed oversight in previous checkin.

	* [r7631] topo/plotting/plot.py,
	  topo/tkgui/plotgrouppanel.py:
	  Improvement on r7630: better workaround for SF.net bug 1860837
	  (plot creation no longer happens, rather than happening but not
	  being displayed).

2008-01-16  ceball

	* [r7630] topo/tkgui/plotgrouppanel.py:
	  Added temporary workaround for SF.net bug 1860837 (i.e. avoid
	  plotting weights when only the hue+confidence are present).

2008-01-16  jbednar

	* [r7629] topo/misc/keyedlist.py:
	  Removed warning

2008-01-16  ceball

	* [r7628] topo/misc/utils.py:
	  Fixed bug where ExtraPickler was not being used (forgot to change
	  pickling method when I altered Singleton).

	* [r7627] doc/Tutorials/lissom_oo_or_text.php:
	  Minor updates to lissom_oo_or tutorial.

	* [r7626] topo/tkgui/tkparameterizedobject.py:
	  Fixed bug where Default was not properly being restored
	  (Eval_ReprTranslator now caches last object and its string
	  representation when object2string is called).

	* [r7625] topo/tkgui/parametersframe.py:
	  On opening a ParametersFrame, set the initial state of the Apply
	  button.

	* [r7624] topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Apply button is disabled if there are no changes. Fixed bug where
	  looking up default value for a ClassSelectorParameter overwrote
	  the current value.

	* [r7623]
	  /trunk/topographica-win/create_python_topo/ctypes-1.0.1.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/python-2.4.4.msi,
	  /trunk/topographica-win/create_python_topo/python-2.5.1.msi:
	  Update to Python 2.5.1

	* [r7622] external/Makefile:
	  Corrected error in a previous checkin (ctypes had not been fully
	  removed.)

	* [r7621] external,
	  external/Python-2.4.4.tgz,
	  external/pylint-0.7.0.tar.gz:
	  Cleaned up external/ directory.

	* [r7620] external/Makefile,
	  external/ctypes-1.0.1.tar.gz:
	  Switch to Python 2.5.

	* [r7619] doc/Downloads/cvs_text.php,
	  doc/Downloads/index_text.php:
	  First pass at updating SVN procedure for Windows.

2008-01-15  ceball

	* [r7618] topo/tkgui/parametersframe.py,
	  topo/tkgui/tkparameterizedobject.py:
	  'Value changed' (blue) status only happens when there is an
	  'Apply' button.

	* [r7617] topo/misc/commandline.py:
	  Minor simplifications to startup process.

	* [r7616] external/Makefile,
	  topo/misc/commandline.py:
	  Changed to use IPython by default. (Make Ipython by default;
	  CommandPrompt classes now relate to IPython.)

	* [r7615] topo/misc/commandline.py:
	  Changed default prompt to 'topo_tn>>>' where n is
	  topo.sim.time().

2008-01-15  jbednar

	* [r7614] Makefile:
	  Removed outdated alert

2008-01-15  ceball

	* [r7613] topo/tkgui/parametersframe.py:
	  Fixed bug where a sub-ParametersFrame could not be displayed for
	  a Parameter of a class (class objects have name=None).

	* [r7612] topo/tkgui/tkparameterizedobject.py:
	  When representing a ClassSelectorParameter, the choices (classes)
	  are not instantiated until an object is actually required.

	* [r7611] topo/misc/commandline.py:
	  Added mechanism to allow prompt control for IPython.

	* [r7610] external/Makefile,
	  external/ipython-0.8.2.tar.gz:
	  Upgraded IPython to 0.8.2.

	* [r7609] Makefile,
	  topo/misc/commandline.py:
	  Experiment: made IPython only start if -i (or -g) is given.
	  (Change only affects those who have IPython built.)

	* [r7608] external/Makefile,
	  external/progressbar-2.2.tar.gz:
	  Added progressbar from http://pypi.python.org/pypi/progressbar/.

2008-01-14  jprovost

	* [r7607] Makefile:
	  Fixed version check so it works from outside TOPOROOT. Also added
	  pissy comment about same.

2008-01-14  ceball

	* [r7606] topo/tkgui/parametersframe.py:
	  Undid part of previous commit: accidentally committed code to
	  change the apply button color.

	* [r7605] topo/tkgui/parametersframe.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Default value for a parameter is shown in pop-up help. Changed
	  status indications: red widget text for an error, and blue widget
	  text for an unapplied change.

2008-01-14  jbednar

	* [r7604] examples/tiny.ty,
	  topo/base/cf.py,
	  topo/base/parameterclasses.py,
	  topo/commands/analysis.py,
	  topo/plotting/plotgroup.py:
	  Minor alert

2008-01-14  ceball

	* [r7603] topo/tkgui/projectionpanel.py:
	  PlotGroupPanel's auto_refresh was moved to plotgroup so there
	  should no longer be a Parameter declaration in any subclasses.

2008-01-13  ceball

	* [r7602]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/plotgrouppanel.py:
	  Removed dependence on Pmw and bwidget. Fixed busy cursor (at
	  least on ubuntu linux).

	* [r7601]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topoconsole.py:
	  Replace Pmw messagebar.

	* [r7600]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/__init__.py:
	  More widgets to use Tile.

	* [r7599]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/widgets.py:
	  Added Statusbar class and with_busy_cursor decorator. Fixed a
	  Tile incompatibility.

	* [r7598] /branches/topographica-tkgui_with_tile/external/Makefile,
	  /branches/topographica-tkgui_with_tile/external/Tile.py.gz:
	  Removed Tilewrapper.

	* [r7597] /branches/topographica-tkgui_with_tile/:
	  Merged in changes 7567:7596 from trunk/topographica/.

	* [r7596]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/__init__.py:
	  More changes for Tile.

	* [r7595]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/widgets.py:
	  Added an ALERT.

	* [r7594]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/testpattern.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topoconsole.py:
	  Commented out tile-incompatible code.

	* [r7593]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/__init__.py:
	  Make more widgets use tile.

	* [r7592]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/widgets.py:
	  scrodget was renamed to Scrodget.

	* [r7591]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/plotgrouppanel.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/tkparameterizedobject.py:
	  Commented out lines incompatible with Tile.

	* [r7590] /branches/topographica-tkgui_with_tile/external/Makefile,
	  /branches/topographica-tkgui_with_tile/external/snit1.0.tar.gz:
	  Added snit (snit is from http://www.wjduquette.com/snit). Build
	  tile by default.

	* [r7589] /branches/topographica-tkgui_with_tile/external/Makefile:
	  Added scrodget. Commented out Tilewrapper (which we don't use).

	* [r7588]
	  /branches/topographica-tkgui_with_tile/external/pyscrodget-0.0.1_2.1.tar.gz:
	  Scrodget wrapped for Tkinter. (Package does not exist elsewhere.)

	* [r7587]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topoconsole.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topowidgets.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/widgets.py:
	  Added new scrolled window that uses scrodget. No longer have to
	  work around bwidget's ScrollableWindow bugs.

2008-01-12  ceball

	* [r7586] /branches/topographica-tkgui_with_tile/external/Makefile:
	  Upgrade to Tile 0.8.2 (missed from previous checkin).

	* [r7585]
	  /branches/topographica-tkgui_with_tile/external/tile-0.7.8.tar.gz,
	  /branches/topographica-tkgui_with_tile/external/tile-0.8.2.tar.gz,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/__init__.py:
	  Upgraded to Tile 0.8.2.

	* [r7584] examples/lissom_oo_or.ty:
	  Made lissom_oo_or.ty use floating-point time.

	* [r7583] /branches/topographica-float-sim-time:
	  Delete topographica-float-sim-time branch: finished making
	  changes to Simulation time.

	* [r7582] topo/base/simulation.py:
	  Fix to previous commit: support previously saved snapshots.

	* [r7581] examples/*.ty,
	  topo/base/simulation.py,
	  topo/tests/test_pattern_present.txt:
	  Merged branches/topographica-float-sim-time changes r7566:7580
	  into the trunk (i.e. make Simulation time be float rather than
	  FixedPoint by default, but keep all existing example scripts
	  using FixedPoint). Should be no visible change to existing
	  example scripts.

	* [r7580]
	  /branches/topographica-float-sim-time/:
	  Made use of FixedPoint simulation time explicit (simulations
	  should all be identical to when Simualtion's time was FixedPoint
	  by default.

	* [r7579] doc/Downloads/index_text.php:
	  Added direct link to SF.net Windows download page.

	* [r7578] doc/Future_Work/current_text.php:
	  Moved tasks to SF.net trackers.

	* [r7577] doc/Future_Work/current_text.php:
	  Moved tasks to SF.net tracker.

2008-01-11  ceball

	* [r7576]
	  /branches/topographica-tkgui_with_tile/topo/tkgui/__init__.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/editortools.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/editorwindow.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/topoconsole.py,
	  /branches/topographica-tkgui_with_tile/topo/tkgui/widgets.py:
	  Removed some Tile-incompatible code.

2008-01-11  jbednar

	* [r7575]
	  doc/Tutorials/som_retinotopy_text.php:
	  Clarified how to get a CoG plot

	* [r7574]
	  doc/Tutorials/som_retinotopy_text.php:
	  Clarified how to get a CoG plot

	* [r7573] examples/tiny.ty:
	  Added control over retina density

	* [r7572]
	  doc/Tutorials/som_retinotopy_text.php:
	  Clarified how to get a Projection plot

	* [r7571] topo/tkgui/templateplotgrouppanel.py:
	  Fixed bug in saving PNG plots from right-click menu

2008-01-11  ceball

	* [r7570]
	  /branches/topographica-float-sim-time/examples/lissom_oo_or.ty:
	  After switching Simulation's default time type to be float,
	  revert lissom_oo_or's time type to be FixedPoint.

	* [r7569]
	  /branches/topographica-float-sim-time/topo/tests/test_pattern_present.txt:
	  Changed test to work whatever the time type.

	* [r7568]
	  /branches/topographica-float-sim-time/topo/base/simulation.py:
	  Added set_time() method to allow Simulation time's type to be
	  changed. Changed default time_type to be float.

	* [r7567] /branches/topographica-tkgui_with_tile:
	  Creating branch for modifying tkgui to work with Tile.

	* [r7566] /branches/topographica-float-sim-time:
	  Creating branch for conversion of Simulation time.

2008-01-10  ceball

	* [r7565] topo/base/parameterclasses.py,
	  topo/tests/testNumberParameter.txt:
	  Clarified current limitation of Number/FixedPoint combination.

	* [r7564] topo/base/cf.py:
	  Provide backwards compatibility for snapshots created before
	  ConnectionField's slice_array was renamed to input_sheet_slice.
	  (Fixes failing snapshot-compatibility-tests.)

	* [r7563] topo/base/simulation.py:
	  Fixed bug in Singleton: previously, there could be more than one
	  instance of Singleton after copying or pickling - now there can
	  only ever be one. This fixes a bug in snapshot loading: after
	  more than one save-load sequence, topo.sim was no longer being
	  set to the Simulation being unpickled.

	* [r7562] doc/Downloads/win32notes_text.php:
	  Clarifications to Windows-specific notes.

	* [r7561]
	  /trunk/topographica-win/create_installer/topographica.iss:
	  Added missing 'WorkingDir' specification to desktop icon.

2008-01-09  ceball

	* [r7560] doc/buildbot/master.cfg:
	  buildbot's slow-tests separates performance tests from
	  snapshot-tests.

	* [r7559] Makefile:
	  Removed snapshot-tests from slow-tests in Makefile (temporary -
	  for buildbot).

	* [r7558] topo/base/patterngenerator.py:
	  Removed experimental optimization of PatternGenerator (i.e. undo
	  changes 7524 and 7525). (The change made very little performance
	  improvement, and appears to cause a problem with Image.)

2008-01-09  rczhao

	* [r7557] topo/patterns/basic.py:
	  Bugs fixed - changed all orientation=['orientation'] to
	  orientation=params['orientation']

2008-01-09  ceball

	* [r7556] topo/base/cf.py,
	  topo/projections/basic.py:
	  More cleanup of ConnectionField; should be no visible change.

	* [r7555] topo/base/sheet.py:
	  Added some comments about Slice.

	* [r7554] topo/responsefns/projfns.py:
	  Removed unused import.

2008-01-09  jbednar

	* [r7553] doc/Tutorials/lissom_oo_or_text.php:
	  Minor clarification

2008-01-08  jbednar

	* [r7552] doc/Downloads/index_text.php:
	  Added note about not running as root. Added explicit apt-get
	  command for Ubuntu

	* [r7551] external/Makefile:
	  Added o option to tar so that it is safe to run as root

2008-01-08  ceball

	* [r7550] Makefile:
	  Switch order of slow-tests so that pickle failures don't stop
	  performance data from being collected.

	* [r7549] topo/base/cf.py:
	  Added comments and questions related to ConnectionFields.

	* [r7548] topo/base/cf.py,
	  topo/commands/analysis.py,
	  topo/learningfns/optimized.py,
	  topo/outputfns/optimized.py,
	  topo/projections/basic.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py:
	  Renamed ConnectionField's 'slice_array' to 'input_sheet_slice'.

	* [r7547] topo/base/cf.py,
	  topo/base/sheet.py,
	  topo/tests/testsheet.py:
	  Converted our Slice object into a subclass of numpy.ndarray.

2008-01-07  jbednar

	* [r7546] topo/base/parameterizedobject.py:
	  Clarified error and debug messages

	* [r7545] topo/outputfns/optimized.py,
	  topo/outputfns/projfns.py:
	  Fixed recent changes to importing __all__

	* [r7544] external/Makefile:
	  Fixed pmw not to rebuild every time make is called

	* [r7543] doc/Downloads/win32notes_text.php:
	  Fixed backslash

2008-01-07  ceball

	* [r7542] topo/tests/test_script.py:
	  Minor adjustment to startup-speed-tests so output can be
	  distinguished from speed-tests output.

	* [r7541] topo/base/sheet.py:
	  Made Slice be consistent about representing __slice (was
	  sometimes an array, sometimes a tuple; now it's always a tuple,
	  but it should be changed to be an array). Should be no visible
	  change.

	* [r7540] topo/base/parameterizedobject.py:
	  Minor optimization (should be no visible change): _check_params()
	  is called many times, so it is worthwhile to reduce the number of
	  attribute lookups it performs. (Also corrected warning message.)

	* [r7539] topo/base/parameterizedobject.py:
	  Replaced our classlist function with one from the standard
	  library. (Should improve startup speed slightly.)

	* [r7538] topo/base/cf.py,
	  topo/misc/utils.py:
	  Removed apparently unnecessary copying of bounds_template and
	  slice_template.

	* [r7537] topo/base/cf.py:
	  Moved copying of mask_template inside ConnectionField. Should be
	  no visible change.

	* [r7536] topo/base/cf.py:
	  Moved copying of bounds_template inside ConnectionField. Should
	  be no visible change.

	* [r7535] topo/base/cf.py,
	  topo/projections/basic.py:
	  Added some default values to ConnectionField. (No visible change,
	  but arguments have been swapped around; not yet finished.)

	* [r7534] topo/misc/commandline.py:
	  Fixed mistakes in previous checkin: restored an accidentally
	  removed call to gui(); if -g is passed, don't need to call
	  interactive() again.

	* [r7533] topo/misc/commandline.py:
	  Restored printing of BANNER if topographica is invoked with no
	  options or the -g option. Tried to simplify handling of
	  'interactive' use.

	* [r7532] Makefile,
	  topo/tests/test_script.py:
	  Added startup-speed-tests.

2008-01-06  ceball

	* [r7531] /releases:
	  Created releases directory.

	* [r7530] doc/Downloads/cvs_text.php:
	  Simplfications and corrections to SVN instructions.

	* [r7529] /tags/LATEST_STABLE:
	  Update LATEST_STABLE from 7484 to 7514 (correction to path).

	* [r7528] /tags/LATEST_STABLE:
	  Correct LATEST_STABLE path error in previous commit.

	* [r7527] /tags/LATEST_STABLE:
	  Update LATEST_STABLE from 7484 to 7514.

	* [r7526] /tags/LATEST_STABLE:
	  Update LATEST_STABLE from 7484 to 7514.

2008-01-05  ceball

	* [r7525] topo/base/patterngenerator.py:
	  PatternGenerator: (add hack to) allow earlier snapshot to load.

	* [r7524] topo/base/patterngenerator.py:
	  PatternGenerator: try caching some stages of generating patterns
	  (experiment to try on buildbot; might revert).

	* [r7523] topo/base/parameterizedobject.py:
	  Minor optimization of Parameter.__get__: avoid a method call if
	  possible.

	* [r7522] topo/outputfns/homeostatic.py:
	  Removed unused import.

	* [r7521] topo/base/parameterclasses.py:
	  ListParameter: removed check for being set to Dynamic value
	  generator before calling check_value(). Presumably the test was
	  always useless?

	* [r7520] topo/base/parameterclasses.py,
	  topo/tests/testNumberParameter.txt:
	  Added commented-out test to show that Number does not work with
	  FixedPoint.

	* [r7519] topo/responsefns/projfns.py:
	  Removed unused import.

	* [r7518] topo/base/parameterclasses.py:
	  Cleaned up Number parameter: no visible change.

	* [r7517] topo/base/parameterclasses.py:
	  Minor internal cleanup of Dynamic: no visible change.

	* [r7516] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  Cleaned up which Dynamic method to check for when performing
	  different operations.

	* [r7515] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py,
	  topo/tests/testCompositeParameter.txt,
	  topo/tests/testDynamicParameter.txt,
	  topo/tkgui/tkparameterizedobject.py:
	  Clean up of Dynamic parameter (documentation, method names).
	  Visible change: only callables are suitable for producing dynamic
	  values. (Previously, anything with a next() method could also be
	  used, but since we can't use iterators anyway, that was
	  misleading [SF.net 1864370].)

	* [r7514] Makefile:
	  Reorganized snapshot-tests (to consist of
	  snapshot-compatibility-tests and simulation-snapshot-tests).
	  Fixed simulation-snapshot-tests's rm command (removed erroneous
	  quotation marks).

	* [r7513] Makefile,
	  topo/tests/test_script.py:
	  Altered slow snapshot tests so that they check real simulations
	  run the same after loading as they would have done if no snapshot
	  had been involved (rather than simply that snapshots save and
	  load; would have caught recent snapshot-with-Dynamic parameters
	  bug that our unit test of snapshots could not catch).

	* [r7512] Makefile:
	  Modified topographica's version-setting command so that we get
	  something closer to the code's actual version number.

	* [r7511] topo/base/simulation.py:
	  Added ALERT.

	* [r7510] topo/misc/commandline.py:
	  Fixed mistake in earlier checkin: './topographica' is the same as
	  './topographica -i'.

	* [r7509] topo/base/simulation.py:
	  Fixed bug where Dynamic parameters did not work after loading a
	  snapshot (Dynamic.time_fn did not point to the unpickled
	  simulation).

	* [r7508] topo/base/parameterizedobject.py:
	  Added support for loading snapshots when parameter names have
	  been changed. Added unrelated ALERT about repr of
	  ParameterizedObjects with Dynamic parameters.

	* [r7507] Makefile:
	  Added comment to topographica script.

	* [r7506] topo/base/parameterizedobject.py:
	  Corrected error message: when loading a snapshot, if a parameter
	  from the snapshot cannot be set on the current class, it is not
	  because the parameter's name has changed (most likely it is
	  because the Parameter object has changed).

	* [r7505] topo/base/parameterizedobject.py:
	  When restoring a snapshot, set parameter values directly on the
	  class rather than first temporarily storing the values in
	  __main__.__dict__.

	* [r7504] topo/misc/commandline.py:
	  Fixed bug where 'topographica -i' and 'topographica -g' did not
	  stay open if there was an error in a '-c' command.

	* [r7503] topo/tkgui/tkparameterizedobject.py:
	  Added commented-out logging code for tkgui.

2008-01-04  ceball

	* [r7502] topo/base/parameterizedobject.py:
	  Simplified some code that sets a class attribute (now we can set
	  underscore attributes on ParameterizedObjectMetaclasses without
	  getting a warning).

	* [r7501] topo/base/parameterizedobject.py:
	  Corrected warning message.

	* [r7500] topo/base/parameterizedobject.py:
	  Cleaned up mess surrounding ParameterizedObject's __getstate__
	  method (i.e. now it can be removed without getting myseterious
	  warnings; the myseterious warnings are from
	  ParameterizedObjectMetaclass complaining about __slotnames__
	  being cached on the class by python itself).
	  ParameterizedObjectMetaclass now does not warn about a
	  non-Parameter class attribute being set if the attribute name
	  starts with an underscore (_).

	* [r7499] topo/base/arrayutils.py:
	  Replaced an ALERT with a note.

	* [r7498] topo/outputfns/homeostatic.py,
	  topo/outputfns/optimized.py,
	  topo/outputfns/projfns.py:
	  Finished implementing the 'promoting basic.py' plan for outputfns
	  (i.e. added __all__ to the outputfns modules that were missing
	  it).

	* [r7497] topo/tkgui/editortools.py:
	  Model Editor no longer displays a popup to ask for a new Sheet's
	  name (i.e. revert to code from r7481; the EP-name bug has been
	  fixed elsewhere, so you can now add sheets before setting 'name'
	  without an error).

	* [r7496] Makefile:
	  Fixed quotation mark error in previous checkin.

	* [r7495] topo/__init__.py:
	  The topographica script tries to store the Subversion version
	  number in topo.version. (File missed from previous checkin.)

	* [r7494] Makefile,
	  topo/commands/basic.py:
	  The topographica script tries to store the Subversion version
	  number in topo.version.

	* [r7493] topo/base/parameterizedobject.py:
	  Fixed bug where EPs could be created with name=None.

	* [r7492] doc/Future_Work/current_text.php:
	  Removed cvs2svn task from future work.

2008-01-03  ceball

	* [r7491] doc/Downloads/cvs_text.php:
	  Changed references to 'topographica.svn.sf.net' to
	  'topographica.svn.sourceforge.net' because SF's https certificate
	  is only valid for sourceforge.net (i.e. avoid people seeing
	  'certificate validation' warnings).

	* [r7490] doc/buildbot/master.cfg:
	  Switched buildbot to use SVNPoller instead of email changesource.

	* [r7489] doc/buildbot/master.cfg:
	  Updated buildbot configuration to work with SVN rather than CVS.

	* [r7488]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  First pass at updating developmer manual revision control from
	  CVS to SVN.

	* [r7487] doc/Developer_Manual/index_text.php,
	  doc/Downloads/cvs_text.php:
	  Moved 'joining as a developer' from downloads page to developer
	  manual front page.

	* [r7486] doc/Downloads/cvs_text.php,
	  doc/Downloads/index_text.php:
	  First pass at converting download instructions from CVS to SVN.
	  Windows instructions not yet changed at all.

	* [r7485] /trunk/facespace/aam_fit_data.h5:
	  Changed properties: the file is binary.

	* [r7484] /tags/*/*/*/.cvsignore:
	  Information in .cvsignore already exists (in svn:ignore).

	* [r7483] topo/base/parameterclasses.py:
	  Added some notes.

	* [r7482] topo/base/simulation.py:
	  Added some ALERTs.

	* [r7481] topo/tkgui/editortools.py:
	  Ask for sheet name when creating a sheet.

2008-01-02  ceball

	* [r7480] doc/Future_Work/current_text.php:
	  Adjustment to cvs2svn procedure: taking LATEST_STABLE with us.
	  (Also, added some code that has no home in a note at the end of
	  the file.)

	* [r7479] external/Makefile:
	  Previous checkin was an accident - revert to version 1.98

	* [r7478] doc/Future_Work/current_text.php,
	  external/Makefile:
	  Added extra notes for cvs2svn conversion.

2008-01-01  rczhao

	* [r7477] /trunk/facespace/perception.ty:
	  Totally new version; now able to demonstrate face adaptation
	  aftereffects in one-dimensional face space

	* [r7476] /trunk/facespace/face_space.ty:
	  Set presented face interval 0.01.

2007-12-30  ceball

	* [r7475] examples/run.py:
	  Fixed 'default_density' position bug. Fortunately it wasn't
	  affecting the tutorial (only use of this script so far).

	* [r7474] topo/sheets/generatorsheet.py:
	  Temporarily use Constant() as input generator when
	  push_generator() is called.

	* [r7473] topo/base/parameterizedobject.py:
	  Added comment.

2007-12-30  ceball_cvs2svn

	* [r7472] /tags/release_0_9_4, /tags/release_0_9_4/facespace:
	  This commit was manufactured by cvs2svn to create tag
	  'release_0_9_4'.

	* [r7471] /tags/LATEST_STABLE, /tags/LATEST_STABLE/facespace:
	  This commit was manufactured by cvs2svn to create tag
	  'LATEST_STABLE'.

2007-12-30  ceball

	* [r7470] doc/Future_Work/current_text.php:
	  Note to myself.

	* [r7469] topo/base/parameterizedobject.py:
	  Added 'bothmethod' decorator (c.f. 'classmethod'). Use bothmethod
	  to decorate force_new_dynamic_value(), inspect_value(), and
	  repr_value() so that all three can be called on both instances
	  and classes. (Fixes missing functionality that was most obvious
	  in the model editor: couldn't add new sheets.)

	* [r7468] topo/base/parameterclasses.py:
	  Made some of Dynamic's __get__-related method signatures match
	  Parameter's __get__ better. Not really an important change. The
	  place to read about the confusion is Parameter.__get__ itself.

	* [r7467] topo/base/simulation.py:
	  Added ALERT (might not actually be ALERT, but at least needs some
	  documentation).

	* [r7466] topo/tkgui/testpattern.py:
	  Added topo.sim.run(0) call to Present() (because it push()es the
	  simulation state). Fixes failing TestPattern test.

	* [r7465] topo/tests/gui_tests.py:
	  Added TestPattern Present-before-simulation-run test (currently
	  fails).

	* [r7464] topo/base/simulation.py,
	  topo/commands/basic.py:
	  Removed 'fake' hack; pattern_present calls run(0.0) before doing
	  anything else, instead.

	* [r7463] topo/sheets/generatorsheet.py:
	  pusgh_input_generator now puts the current input_generator on the
	  stack and leaves a *copy* in place.

	* [r7462] topo/tests/test_pattern_present.txt:
	  Added test to show bug in save_input_generators()
	  (GeneratorSheet's push_input_generator).

	* [r7461] topo/sheets/generatorsheet.py:
	  Fixed bug in error message.

2007-12-29  ceball

	* [r7460] topo/tests/setup_simulation.py:
	  Specify sheet bounds because the defaults are overridden in other
	  tests.

	* [r7459] topo/tests/testboundingregion.py:
	  Removed stray blank line.

	* [r7458] topo/tests/testoutputfnsoptimized.py:
	  Added HACKALERT.

	* [r7457] topo/tests/testplotfilesaver.py:
	  Stopped tests running twice by correcting class hierarchy.

	* [r7456] topo/tests/testbitmap.jpg:
	  Reduced size to 100x55 to speed up unit tests.

	* [r7455] topo/tests/testplotfilesaver.py:
	  No change - marginal speedup by reducing density.

	* [r7454] Makefile,
	  topo/tests/lissom_oo_or.ty_pickle_test.typ:
	  Added snapshot-compatibility-test (and added it to slow-tests).
	  Not yet going to guarantee snapshots will keep working, but at
	  least we'll know when we break them. The snapshot comes from
	  current CVS. (Might want to add more snapshots from other
	  examples in the future.)

	* [r7453] topo/base/simulation.py,
	  topo/commands/basic.py:
	  Added flag to run() so that pattern_present can avoid clearing
	  out the list of eps to start (with ALERT). Fixes failing test
	  test_pattern_present (or it would, but the test itself has a bug
	  that causes it to fail when run with make tests - on its own it
	  now passes fine.

	* [r7452] doc/Future_Work/current_text.php:
	  Updated cvs2svn procedure (diff command for checking).

	* [r7451] /trunk/facespace/__init__.py:
	  Fixed up some strange line endings (most were fine - seems odd).

	* [r7450] topo/tests/test_pattern_present.txt:
	  Removed mistaken line (that's not testing anything).

	* [r7449] doc/Downloads/cygwin_packages:
	  Converted to unix format using dos2unix. Unix format is fine if
	  we handle this file in Cygwin on Windows.

	* [r7448] doc/Future_Work/current_text.php:
	  Updates to cvs2svn procedure (checking svn matches cvs).

	* [r7447] doc/Future_Work/current_text.php:
	  Fixed typos: options were in wrong place.

	* [r7446] doc/Future_Work/current_text.php:
	  Update to cvs2svn procedure (svn:eol=native).

	* [r7445] topo/tests/test_pattern_present.txt:
	  Inserted pattern_present() before any topo.sim.run(); test now
	  fails.

	* [r7444] topo/tests/test_pattern_present.txt:
	  Clarified test. Currently passes. pattern_present() bug is when
	  it's called before time is advanced at all.

	* [r7443] topo/tests/test_pattern_present.txt:
	  Initial version. Shows problem with pattern_present().

	* [r7442] topo/tests/setup_simulation.py:
	  Initial version.

2007-12-28  ceball

	* [r7441] external,
	  external/.cvsignore,
	  external/Makefile:
	  Roll back to Python 2.4.

	* [r7440] topo/base/parameterizedobject.py:
	  Make ParamOverrides compatible with python 2.4.

	* [r7439] topo/tkgui/topowidgets.py,
	  topo/tkgui/widgets.py:
	  Moved ResizableScrollableFrame into the same place as the windows
	  themselves (so all the code that could be replaced is together).

	* [r7438] doc/Future_Work/current_text.php:
	  Updates to cvs2svn procedure.

	* [r7437] topo/tkgui/projectionpanel.py:
	  When changing sheet, update the widget's list now that the option
	  menu is editable (rather than replacing the whole widget). Fixes
	  failing test test_projection in gui_tests.

	* [r7436] topo/tkgui/tkparameterizedobject.py:
	  Added update_selector(). String_ObjectTranslators replace their
	  caches on update().

	* [r7435] topo/tkgui/widgets.py:
	  Addded replace_list() to EditableOptionMenu.

	* [r7434] topo/tests/gui_tests.py:
	  Update test_projection to swtich sheets and projections.

	* [r7433] topo/tkgui/tkparameterizedobject.py:
	  set_parameter_value() updates the corresponding tkvar, and
	  __setattr__ uses set_parameter_value() to set parameter values.
	  Grouped related methods together.

	* [r7432] topo/tkgui/tkparameterizedobject.py:
	  Removed 'param_has_modifyable_choices'.

	* [r7431] topo/tkgui/projectionpanel.py:
	  Reverted to version 1.160 - the previous checkin was accidental.

2007-12-27  ceball

	* [r7430] topo/tests/gui_tests.py:
	  Added test that shows changing sheet on projection window is not
	  working.

	* [r7429] topo/tests/functionaltest.py:
	  Added further check to catch errors.

	* [r7428] topo/tests/gui_tests.py:
	  Create a more complex simulation.

	* [r7427] doc/Future_Work/current_text.php:
	  Update to cvs2svn procedure.

	* [r7426] doc/Future_Work/current_text.php:
	  Update to cvs2svn procedure.

	* [r7425] doc/Future_Work/current_text.php:
	  Update to cvs2svn procedure.

	* [r7424] doc/Future_Work/current_text.php:
	  Updated cvs2svn procedure.

2007-12-24  jbednar

	* [r7423] topo/base/parameterclasses.py:
	  Fixed typo

2007-12-23  ceball

	* [r7422] topo/base/parameterclasses.py:
	  Enable warnings for code using old DynamicNumber-in-a-Number
	  syntax.

	* [r7421] examples/cfsom_or.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_or_homeoscale.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_sf.ty,
	  examples/saccade_demo.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  topo/tests/testCompositePatternGenerators.txt,
	  topo/tests/testDynamicParameter.txt:
	  Removed old DynamicNumber-in-a-Number syntax.

	* [r7420] topo/patterns/basic.py:
	  Renamed 'pos' to 'params' (ParamOverrides) and fixed some missing
	  calls to ParamOverrides (some PatternGenerators have no test
	  coverage).

	* [r7419] topo/base/parameterizedobject.py:
	  Added ALERT.

	* [r7418]
	  examples/sullivan_neurocomputing04.ty,
	  topo/base/patterngenerator.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/patterns/rds.py,
	  topo/patterns/teststimuli.py,
	  topo/tkgui/projectionpanel.py:
	  Renamed 'pos' to 'params' (ParamOverrides).

	* [r7417] examples/joublin_bc96.ty:
	  Use ParamOverrides in the PatternGenerator.

	* [r7416] doc/Future_Work/current_text.php:
	  Added task.

	* [r7415] doc/Future_Work/current_text.php:
	  Added step to cvs2svn procedure.

	* [r7414] topo/tkgui/plotgrouppanel.py:
	  Fix a bug in panels when __update_widgets_for_history() is
	  called: sometimes setting a widget's state fails (not sure why).

2007-12-22  ceball

	* [r7413]
	  examples/sullivan_neurocomputing04.ty:
	  Revert to dynamic parameters not controlled by simulation time
	  (need to investigate this script).

	* [r7412] topo/misc/commandline.py:
	  Removed unused import and ALERT that was fixed.

	* [r7411] topo/tests/testpatterngenerator.py:
	  Updated test for time-controlled dynamic parameters.

	* [r7410]
	  topo/tests/testCompositeParameter.txt:
	  Removed test that is no longer meaningful (with time-controlled
	  dynamic parameters).

	* [r7409] topo/base/simulation.py,
	  topo/patterns/basic.py:
	  Switched to time-controlled Dynamic Parameters.

	* [r7408]
	  topo/tests/testCompositePatternGenerators.txt:
	  Removed outdated comments.

	* [r7407] topo/base/parameterizedobject.py:
	  Cleanup of Dynamic-related methods; should be no visible change.

	* [r7406] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  Removed '_dynamically_generated' slot from Dynamic.

	* [r7405] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  Dynamic's last time and last value are stored on the generator
	  rather than the Parameter/ParameterizedObject. (Working, but
	  needs to be cleaned up.)

	* [r7404] topo/tests/testDynamicParameter.txt:
	  Commented out test for generators and iterators; we don't (yet)
	  support those.

	* [r7403]
	  topo/tests/testCompositeParameter.txt:
	  Replaced iter as a Dynamic value with a class (no change to
	  test). Note that although the previous version worked before,
	  using iter does not work in general (e.g. for the default value,
	  or when pickling).

2007-12-21  ceball

	* [r7402] topo/tests/testDynamicParameter.txt:
	  Corrections to previous commit (don't change failure outcome).

2007-12-20  ceball

	* [r7401] topo/tests/testDynamicParameter.txt:
	  Test shared generator and some common generator types. (Test now
	  fails.)

2007-12-19  jbednar

	* [r7400] doc/Future_Work/current_text.php:
	  Added info about PsychoPy and VisionEgg

2007-12-18  jbednar

	* [r7399] topo/base/projection.py:
	  Minor fix to docstrings

2007-12-18  ceball

	* [r7398] examples/cfsom_or.ty:
	  Stop Composite and subclasses causing unused dynamic parameter
	  value accesses.

	* [r7397] topo/base/parameterizedobject.py,
	  topo/patterns/basic.py,
	  topo/tests/cfsom_or.ty_DATA,
	  topo/tests/lissom_oo_or.ty_DATA,
	  topo/tests/lissom_oo_or_homeomaxent.ty_DATA,
	  topo/tests/lissom_or.ty_DATA,
	  topo/tests/lissom_or_homeomaxent.ty_DATA,
	  topo/tests/lissom_or_noshrinking.ty_DATA:
	  Stop Composite and subclasses causing unused dynamic parameter
	  value accesses.

	* [r7396] external,
	  external/.cvsignore:
	  Changed to Python-2.5.1

	* [r7395]
	  examples/sullivan_neurocomputing04.ty,
	  topo/base/patterngenerator.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/patterns/rds.py,
	  topo/patterns/teststimuli.py:
	  Replaced params.get('x',self.x) with ParamOverrides. Some
	  variables will need to be renamed to improve clarity, and the
	  code should be tidied in several places. Should be no visible
	  change (unless maybe someone whose code is not checked in was
	  using a (Separated)Composite with a subpattern that had
	  previously undetected duplicate 'params.get()' lines causing two
	  unused advances of dynamic numbers - which is unlikely).

	* [r7394] topo/base/parameterizedobject.py:
	  Make ParamOverrides simulate old params.get('x',self.x) behavior
	  by accessing an attribute (which causes random numbers to be
	  skipped) if the overridden object is a PatternGenerator belonging
	  to Composite.

	* [r7393] topo/base/parameterizedobject.py,
	  topo/tests/testParamOverrides.txt:
	  Changed to pass a dict to ParamOverrides.

	* [r7392] topo/base/parameterizedobject.py,
	  topo/tests/testParamOverrides.txt:
	  Initial version of ParamOverrides.

2007-12-17  jprovost

	* [r7391] topo/misc/robotics.py:
	  Support for swapping sense positive/negative left/right sense for
	  saccade amplitude in PTZ object.

	* [r7390] topo/sheets/generatorsheet.py:
	  Added outputfn support ot GeneratorSheets.

	* [r7389] topo/misc/commandline.py:
	  Made 'topographica -i <file>' stay open at a command prompt when
	  there's an error in <file>.

	* [r7388] topo/patterns/basic.py:
	  Added PatternGeneratorParameter

	* [r7387] topo/tests/sheetmask_setup.py,
	  topo/tests/testCompositeSheetMasks.txt:
	  Tests for CompositeSheetMasks.

	* [r7386] topo/base/projection.py:
	  Added CompositeSheetMask, AndMask, and OrMask.

2007-12-16  ceball

	* [r7385]
	  topo/tests/testCompositePatternGenerators.txt:
	  Initial version; shows bug in Composite PatternGenerators used
	  with dynamic numbers.

	* [r7384] doc/buildbot/master.cfg:
	  Build test now runs unit tests too.

	* [r7383] doc/Future_Work/current_text.php:
	  Updated cvs2svn conversion procedure.

	* [r7382] doc/buildbot/index.html:
	  Initial version of buildbot's public_html/index page.

	* [r7381] doc/Downloads/cvs_text.php:
	  Minor simplification.

	* [r7380] doc/buildbot/master.cfg:
	  Removed prefix. Directories in changes should show up ok because
	  I patched
	  /usr/lib/python2.5/site-packages/buildbot/changes/mail.py.

2007-12-15  jbednar

	* [r7379] topo/outputfns/__init__.py:
	  Added auto-import from basic.py, to simplify access for common
	  items

	* [r7378] topo/outputfns/basic.py:
	  Added declaration of __all__ to provide a clean 'from x import *'

2007-12-15  ceball

	* [r7377] doc/buildbot/master.cfg:
	  Tried a new prefix for mail source.

	* [r7376] doc/buildbot/master.cfg:
	  Added cvs mail change source; not sure about prefix.

	* [r7375] doc/Downloads/cvs_text.php:
	  Added links to build status.

	* [r7374] doc/Downloads/cvs_text.php:
	  Added links to specific builders (to see status of latest cvs
	  version.

	* [r7373] topo/tkgui/topoconsole.py:
	  Removed commented-out 'plot gallery' code.

2007-12-14  ceball

	* [r7372] doc/buildbot/master.cfg:
	  Updated to buildbot-0.7.6 format. Added beginnings of Windows
	  tester. Changed to better html status. Max of 1 buildbot action
	  at any one time on sake and doozy. Separated gui-tests. Only
	  emails when the status changes from pass to fail. If make fails,
	  the subsequent tests are skipped. OS X built for Aqua.

	* [r7371] topo/tkgui/parametersframe.py:
	  Quick fix to Defaults button (fixes failing gui test).

	* [r7370] topo/tests/gui_tests.py:
	  Fixed error in test_test_pattern() (no visible change - test was
	  correctly failing).

	* [r7369] topo/base/parameterizedobject.py:
	  No visible change: method changed from __ to _.

	* [r7368] topo/tests/testDynamicParameter.txt:
	  Removed ParameterizedObject.is_dynamically_generated.

	* [r7367] topo/base/parameterizedobject.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Removed ParameterizedObject.is_dynamically_generated.

	* [r7366] topo/base/parameterizedobject.py:
	  Clarified a comment.

	* [r7365] topo/tests/functionaltest.py,
	  topo/tests/gui_tests.py:
	  Moved the test 'framework' into a separate file. (Not sure if it
	  will ever be helpful other than for gui_tests...)

	* [r7364] topo/tests/gui_tests.py:
	  No visible change: moved titling into _run().

	* [r7363] topo/tests/gui_tests.py:
	  Moved comments into assertion statements to improve output.

	* [r7362] Makefile:
	  For GUI tests, return the number of errors.

	* [r7361] topo/tests/gui_tests.py:
	  Added a simple framework to make running gui tests simpler, and
	  the output more useful.

2007-12-13  ceball

	* [r7360] external/Makefile_OSX.diff:
	  Updated patch: no need to build tk on OS X when using Aqua.

	* [r7359] external/Makefile:
	  Removed unnecessary dependence of bwidget on tk.

2007-12-13  jbednar

	* [r7358] ChangeLog.txt:
	  Updated with recent changes

2007-12-13  ceball

	* [r7357] topo/base/parameterizedobject.py,
	  topo/tests/testparameterizedobject.py:
	  Fixed bug in ParameterizedObject.params(), where the params cache
	  for a class could hide the parameters of its superclasses (i.e.
	  the bug preventing Connection Fields windows from opening through
	  a right click.) Added test of params().

2007-12-12  jbednar

	* [r7356] doc/Home/news_text.php:
	  Updated with recent changes

	* [r7355] external/Pmw.diff:
	  Fixed Pmw patch per Jeff's suggestion

	* [r7354] external/Makefile,
	  external/Pmw.diff:
	  Added Pmw patch to fix bug in error reporting

2007-12-12  ceball

	* [r7353] topo/base/parameterizedobject.py:
	  Minor addition to comment.

	* [r7352] topo/tkgui/topoconsole.py:
	  Added ERRORALERT (about Step button).

	* [r7351] topo/patterns/basic.py:
	  Corrected a mistake in the previous checkin.

	* [r7350] topo/patterns/basic.py:
	  Fixed mistake in previous checkin.

	* [r7349] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py,
	  topo/patterns/basic.py:
	  Intermediate checkin (anticipates some changes for when Dynamic
	  uses topo.sim.time() but doesn't change any current results).
	  Dynamic caches whether or not its value is being dynamically
	  generated; Parameter caches internal_name; added
	  force_new_dynamic_value() to ParameterizedObject;
	  SeparatedComposite uses force_new_dynamic_value().

	* [r7348] topo/base/parameterizedobject.py:
	  Added comment.

	* [r7347] topo/base/simulation.py:
	  Commented out expensive debug() statement; improves performance
	  of half-density lissom_oo_or by about 4%.

2007-12-11  judelaw

	* [r7346] topo/commands/pylabplots.py:
	  added an option to plot_tracked_attributes for putting a label on
	  the y axis

	* [r7345] topo/sheets/lissom.py:
	  Removed OPTNORM and added post_initialization_weights_output_fn
	  to LISSOM to allow the weights outputfn to be changed after an
	  initial normalization step

	* [r7344] topo/outputfns/homeostatic.py:
	  Changed ScalingOF and JointScalingOF to calculate scaling factor
	  with old average. Corrected JointScalingOF to scale individual
	  projection activities rather than totals

2007-12-11  ceball

	* [r7343] external/Makefile_OSX_X11.diff:
	  Fixed path error in original checkin.

	* [r7342] Makefile:
	  Added osx-x11-patch.

	* [r7341] external/Makefile_OSX_X11.diff,
	  external/Python_OSX_X11.diff:
	  For building Python with X11 Tkinter on OS X.

2007-12-10  jbednar

	* [r7340] topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/homeostatic.py:
	  Cleaned up docs and spacing

	* [r7339] topo/commands/basic.py:
	  Removed duplicate processing of ProjectionSheets

2007-12-10  judelaw

	* [r7338] topo/commands/pylabplots.py:
	  Fixed bug in plot_tracked_attributes to plot the correct time
	  values

	* [r7337] topo/sheets/lissom.py:
	  added new OPTNORM lissom sheet which can optionally turn off
	  normalization after an initial normalization step

	* [r7336] topo/outputfns/homeostatic.py:
	  added new ScalingOF and JointScalingOF, added stop_updating and
	  restore_updating functions to allow freezing of state during e.g.
	  pattern_present

	* [r7335] topo/outputfns/basic.py:
	  added stop_updating and restore_updating functions to
	  AttributeTrackingOF and ActivityAveragingOF to allow freezing if
	  their state during e.g. pattern_present

	* [r7334] topo/commands/basic.py:
	  replaced turning learning flag off in pattern_present with
	  calling stop_updating() and restore_updating()

	* [r7333] topo/base/sheet.py:
	  added stop_updating and restore_updating functions to Sheet to
	  allow learning to be turned off during e.g. pattern_present

	* [r7332] topo/base/projection.py:
	  added stop_updating and restore_updating functions to Projection
	  and ProjectionSheet to allow freezing of their state during e.g.
	  pattern_present

	* [r7331] topo/base/functionfamilies.py:
	  added stop_updating and restore_updating functions to OutputFn
	  and PipelineOF to allow functions with state to freeze their
	  state during e.g. pattern_present

2007-12-09  ceball

	* [r7330] topo/base/parameterizedobject.py:
	  Cache the result of params() because we call it often (via
	  __repr__).

	* [r7329] topo/base/parameterclasses.py:
	  Added some comments.

	* [r7328] topo/base/parameterclasses.py:
	  Removed is_iterator() - we only care if the object has a next()
	  method.

	* [r7327] topo/base/parameterclasses.py:
	  Improve speed of is_iterator() by replacing 'x in dir(obj)' with
	  hasattr(obj,x) (no visible change).

	* [r7326] topo/misc/utils.py:
	  Added comment.

2007-12-08  ceball

	* [r7325] topo/misc/utils.py:
	  Fixed typo in code from last commit.

	* [r7324] topo/misc/utils.py:
	  profile() uses cProfile (python 2.5). (If cProfile can't be
	  imported, the previous profile function - now old_profile() - is
	  used.)

	* [r7323] external,
	  external/.cvsignore:
	  Upgraded several packages.

	* [r7322] external/Makefile:
	  Upgraded to Python 2.5.1

	* [r7321] external/Makefile:
	  Upgraded pylint.

	* [r7320] external/Makefile:
	  Uncommented and finished logilab-astng target.

	* [r7319] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  Set instantiate through a method because its value can also
	  depend on constant.

	* [r7318] topo/tests/__init__.py:
	  Minor cleanup - should be no changes to behavior.

2007-12-07  ceball

	* [r7317] Makefile:
	  Renamed osx-patch-clean to osx-patch-uninstall.

2007-12-07  rczhao

	* [r7316] external/Makefile:
	  Rolled back to older version of pytables as the latest version
	  2.0.2 doesn't work for numpy 1.0.2 currently installed on
	  Topographica

	* [r7315] external/pytables-20070518.tar.gz:
	  Rolled back to this old version as the latest 2.0.2 version has
	  to be run with numpy 1.0.3 but current numpy in Topographica is
	  1.0.2.

2007-12-07  ceball

	* [r7314] topo/base/parameterclasses.py:
	  Undid keep-instantiate-updated change (causes surprising
	  behavior); intermediate checkin.

	* [r7313] topo/tkgui/parametersframe.py:
	  Minor simplification - no visible change.

2007-12-07  rczhao

	* [r7312] external/Makefile:
	  Updated pytables and hdf5 building commands so that they can be
	  built properly now.

	* [r7311] external/hdf5-1.6.6.tar.gz:
	  Utility for managing extremely large and complex data
	  collections. Required for pytables

	* [r7310] external/pytables-2.0.2.tar.gz:
	  A Python-HDF5 interface, enabling hierarchical dataset for
	  handling large amounts of datasets

	* [r7309] external/pytables-20070518.tar.gz:
	  To be replaced by latest version 2.0.2

2007-12-07  ceball

	* [r7308] topo/tkgui/tkparameterizedobject.py:
	  Minor cleanup - no visible change.

2007-12-07  rczhao

	* [r7307] /trunk/facespace/aam_fit.pyx,
	  /trunk/facespace/face_space_patterns.py:
	  Fixed a bug in generating faces.

	* [r7306] /trunk/facespace/face_space.ty:
	  Removed OutputFnDebugger

2007-12-07  ceball

	* [r7305] topo/tkgui/parametersframe.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Removed unnecessary parameters() function.

	* [r7304] topo/tkgui/tkparameterizedobject.py:
	  Use ParameterizedObject's is_dynamically_generated() method.

	* [r7303] topo/base/parameterizedobject.py:
	  Fixed error in is_dynamically_generated().

	* [r7302] topo/tests/testDynamicParameter.txt:
	  Test 'is_dynamically_generated'.

	* [r7301] topo/base/parameterizedobject.py:
	  Added convenience method 'is_dynamically_generated()' to
	  ParameterizedObject.

	* [r7300] topo/base/parameterclasses.py:
	  Renamed a method.

	* [r7299] topo/base/parameterclasses.py:
	  Fixed ERRORALERT in Number.

	* [r7298] topo/tests/testNumberParameter.txt:
	  Initial version.

	* [r7297] topo/base/parameterclasses.py:
	  Added ERRORALERT for Number.

	* [r7296] topo/base/parameterizedobject.py:
	  Removed unused Parameter.count.

	* [r7295] topo/base/parameterclasses.py:
	  Added some documentation to Dynamic's methods and made a minor
	  simplification (should be no change to behavior).

2007-12-06  ceball

	* [r7294] topo/base/parameterclasses.py:
	  Added comment and made minor simplification.

	* [r7293] topo/tests/testDynamicParameter.txt:
	  Added tests of time_fn.

	* [r7292] topo/tests/testDynamicParameter.txt:
	  Added more tests to show Dynamic's behavior.

	* [r7291] topo/base/parameterclasses.py:
	  Dynamic: now keeps instantiate up to date for the default value.

2007-12-06  jbednar

	* [r7290] external,
	  external/.cvsignore:
	  Updated Gnosis version

	* [r7289] external/Gnosis_Utils.diff,
	  external/Makefile:
	  Added patch for gnosis xml to avoid spurious 'FATAL ERROR
	  <unknown>:1:0: not well-formed (invalid token)' message when
	  testing whether a snapshot is xml or not

2007-12-06  ceball

	* [r7288] external/Makefile:
	  Added commented-out (and unfinished) section for logilab-astng,
	  required for new version of pylint.

	* [r7287] external/logilab-astng-0.17.1.tar.gz:
	  From www.logilab.org.

	* [r7286] doc/buildbot/pycheckrc:
	  Special methods have been added to pychecker now. limit now
	  defaults to a low number - we need it to be higher.

	* [r7285] external/Makefile:
	  Upgrade to CVS version of pychecker.

	* [r7284]
	  external/pychecker-0.8.18-CVS-200712061936.tar.gz:
	  From pychecker.cvs.sf.net (time is CST by mistake).

	* [r7283]
	  external/logilab-common-0.25.0.tar.gz,
	  external/pylint-0.13.2.tar.gz:
	  From logilab.org.

	* [r7282] external/Makefile:
	  Removed copy-and-paste errors (epydoc and docutils don't depend
	  on common).

	* [r7281] topo/base/parameterizedobject.py:
	  Minor simplification - no visible change.

	* [r7280] topo/base/parameterizedobject.py:
	  Clarified 'gensym'.

2007-12-05  jbednar

	* [r7279] topo/misc/utils.py:
	  Moved misplaced alert

2007-12-05  judelaw

	* [r7278] topo/commands/pylabplots.py:
	  renamed param_names as attrib_names

	* [r7277] examples/lissom_oo_or_noshrinking.ty:
	  changed param_names to attrib_names in AttributeTrackingOF

	* [r7276] topo/outputfns/basic.py:
	  added learning parameter to AttributeTrackingOF and
	  ActivityAveragingOF so that tracking and averaging can be turned
	  off during map measurement, renamed param_names to attrib_names
	  in AttributeTrackingOF

	* [r7275] topo/commands/basic.py:
	  Fixed pattern_present so that sheet and projection output_fns
	  learning parameter can be set to false even when embedded in a
	  PipelineOF

2007-12-04  ceball

	* [r7274] topo/base/parameterizedobject.py:
	  Added ERRORALERT.

	* [r7273] topo/base/parameterizedobject.py:
	  Removed caching of Parameter's _internal_name (makes code a
	  little simpler).

	* [r7272] topo/base/parameterizedobject.py:
	  Removed a comment, modified another.

	* [r7271] topo/base/parameterclasses.py:
	  Renamed get_name() to internal_name().

	* [r7270] topo/base/parameterizedobject.py:
	  Updated documentation for Parameter. Simplified Parameter 'name'
	  in the code and documentation. (Removed ALERT about instantiating
	  constant parameters.)

2007-12-03  judelaw

	* [r7269] examples/lissom_oo_or_noshrinking.ty:
	  made compatible with new AttributeTrackingOF which replaces
	  OutputFnDebugger

	* [r7268] topo/commands/pylabplots.py:
	  made compatible with changes to AttributeTrackingOF

	* [r7267] topo/outputfns/homeostatic.py:
	  moved AttributeTrackingOF and ActivityAveragingOF to
	  outputfns/basic

	* [r7266] topo/outputfns/basic.py:
	  added AttributeTrackingOF and ActivityAveragingOF moved from
	  topo/outputfns/homeostatic

2007-12-03  jbednar

	* [r7265] doc/Developer_Manual/coding_text.php:
	  Added minor clarification

2007-12-03  judelaw

	* [r7264] examples/lissom_oo_or_noshrinking.ty:
	  Replaced OutputFnDebugger with ValueTrackingOutputFn for
	  debugging

	* [r7263] topo/commands/pylabplots.py:
	  corrected errors in plot_values

	* [r7262] topo/outputfns/homeostatic.py:
	  minor change to documentation

	* [r7261] topo/commands/pylabplots.py:
	  changed plot_values to be compatible with new
	  ValueTrackingOutputFn

	* [r7260] topo/outputfns/homeostatic.py:
	  Made new ValueTrackingOutputFn which keeps track of parameter
	  values for debugging. Added AvgScalingOutputFn which keeps track
	  of average activities and calculates scaling factor for
	  homeostatic scaling

	* [r7259] topo/commands/pylabplots.py:
	  Added plot_values function for plotting or saving time series
	  data from output functions

2007-12-03  jbednar

	* [r7258] topo/outputfns/homeostatic.py:
	  Untested cleanup; should work the same as the previous revision

2007-12-03  judelaw

	* [r7257] topo/outputfns/homeostatic.py:
	  Cleaned up OutputFnDebugger, removed plotting imports

2007-12-02  ceball

	* [r7256] topo/base/simulation.py:
	  Added commented-out lines to set Dynamic's time_fn.

	* [r7255] topo/base/parameterclasses.py:
	  Demo code to allow us to try Dynamic parameters that only advance
	  once per simulation time. (Actually the time_fn can be any
	  function.) Needs pretty big cleanup if we decide to keep this.

	* [r7254] topo/base/parameterizedobject.py:
	  Removed code to look for a parameter object in a
	  ParameterizedObject instance's dict, since Dynamic parameters are
	  not longer stored that way (i.e. no more DynamicNumber inside a
	  Number).

	* [r7253] topo/base/parameterizedobject.py:
	  Moved ParameterizedObjectMetaclass.print_param_defaults() to
	  ParameterizedObject (as a classmethod).

	* [r7252] examples/hierarchical.ty:
	  classparams() is now just params().

	* [r7251] topo/tkgui/tkparameterizedobject.py:
	  No longer need to distinguish classparams() and params().

	* [r7250] topo/base/parameterizedobject.py:
	  Removed ParameterizedObjectMetaclass.classparams() and made
	  ParameterizedObject.params() be a classmethod.

	* [r7249] topo/tkgui/tkparameterizedobject.py:
	  Updates to match changes to Dynamic.

	* [r7248] topo/tests/testDynamicParameter.txt:
	  Tests use Dynamic rather than Number. Changed tests to reflect
	  possible instantiation of Dynamic parameters.

	* [r7247] topo/base/parameterizedobject.py:
	  Minor updates to match changes to Dynamic. Added some (unrelated)
	  comments.

	* [r7246] topo/base/parameterclasses.py:
	  (Intermediate checkin.) Dynamic parameters have instantiate set
	  to True if created with a dynamic default value. (No-effect
	  'update_fn' added, too, because some reorganization got mixed up
	  with fixing instantiation.)

2007-12-01  ceball

	* [r7245] Makefile:
	  Added gui-tests target.

	* [r7244] doc/buildbot/master.cfg:
	  Use make osx-patch on sake. Update basic-gui-tests to gui-tests.

	* [r7243] topo/tests/testDynamicParameter.txt:
	  Added test to show bug in current Dynamic parameter
	  implementation.

	* [r7242] topo/base/parameterclasses.py:
	  Added ERRORALERT about Dynamic's _dynamic slot.

	* [r7241] topo/tkgui/tkparameterizedobject.py:
	  Use EditableOptionMenu instead of OptionMenu (though not yet
	  taking advantage of the editable list). Added gui_set_param() and
	  gui_get_param() methods.

	* [r7240] topo/tkgui/testpattern.py:
	  Changed 'present' parameter to 'Present' for consistency. (I have
	  been naming ButtonParameters with a capital letter, but will
	  probably revert them all to lowercase sometime soon.)

	* [r7239] topo/tkgui/widgets.py:
	  Added get() and set() to EditableOptionMenu (for consistency with
	  other widgets).

	* [r7238] topo/tests/testparametersframe.py:
	  The OptionMenu we use now has get().

	* [r7237] topo/misc/commandline.py:
	  Added ALERT about topographica not staying open.

	* [r7236] Makefile:
	  Use gui_tests.py for running the GUI tests. Added
	  detailed-gui-tests target.

	* [r7235] topo/tests/gui_tests.py:
	  Initial version. run_detailed() fails right now because it shows
	  a test pattern bug.

2007-11-30  jbednar

	* [r7234] doc/Reference_Manual/index_text.php,
	  external/Makefile:
	  Added building instructions for Player

2007-11-30  judelaw

	* [r7233] topo/outputfns/homeostatic.py:
	  Removed plotting from OutputFnDebugger, changed so that
	  parameters are now stored in a values dictionary as a list of
	  (time, value) pairs which is extendable to any length

2007-11-30  jbednar

	* [r7232] topo/misc/playerrobot.py:
	  Minor clarification

	* [r7231] topo/misc/robotics.py:
	  Cleaned up comments and whitespace. Fixed syntax error in version
	  string.

	* [r7230] topo/misc/playerrobot.py:
	  Cleaned up docs and whitespace

	* [r7229] topo/outputfns/homeostatic.py:
	  Made OutputFnDebugger have a default function of None, so that
	  non-existing parameters will generate errors. Merged its
	  debug_dict and avg_dict, in preparation for defining a standard
	  interface and separating plotting out

	* [r7228] topo/outputfns/homeostatic.py:
	  Removed stray unused function

	* [r7227] topo/outputfns/homeostatic.py:
	  Merged save_debug_graphs into plot_debug_graphs, making
	  plot_debug_graphs save to disk if an optional filename parameter
	  is supplied

	* [r7226] topo/outputfns/homeostatic.py:
	  Simplified OutputFnDebugger by eliminating duplicate for loops

	* [r7225] topo/outputfns/homeostatic.py:
	  Fixed parameter default handling for OuputFnDebugger, and made
	  output files be saved in the appropriate directory

	* [r7224] topo/outputfns/homeostatic.py:
	  Restored penultimate version; had mistakenly removed some imports

2007-11-30  ceball

	* [r7223] topo/base/parameterclasses.py:
	  Minor change to comment.

	* [r7222] topo/tests/testplotgrouppanel.py:
	  Use startgui() function.

	* [r7221] topo/tests/__init__.py:
	  Added some documentation. Cleanup of run() and run_named().

	* [r7220] topo/tkgui/__init__.py:
	  Added option to suppress printing 'Launching GUI'.

	* [r7219] topo/tests/testsheet.py:
	  Reorganized so that tests no longer run identically twice (should
	  reduce 'make tests' time). Renamed 'slice' to 'slice_' where
	  'slice' was being used as a variable name. Added a little
	  documentation

2007-11-29  judelaw

	* [r7218] topo/outputfns/homeostatic.py:
	  examples/lissom_oo_or_scaling.ty

	* [r7217] topo/sheets/lissom.py:
	  removed SLISSOM sheet

	* [r7216] topo/projections/basic.py:
	  Removed DebugDFProjection

2007-11-29  jbednar

	* [r7215] topo/outputfns/homeostatic.py:
	  Cleaned up whitespace and comments

	* [r7214] topo/outputfns/basic.py:
	  Removed references to 'activity' and cleaned up PoissonSample
	  documentation

	* [r7213] topo/outputfns/basic.py:
	  Minor tweak

	* [r7212] topo/outputfns/basic.py:
	  Minor update to docstring

2007-11-29  ceball

	* [r7211] topo/base/parameterizedobject.py:
	  Tried to simplify and document inspect_value() and repr_value().
	  Should be no visible change.

	* [r7210]
	  topo/tests/testCompositeParameter.txt:
	  Added test that Composite is ok with Dynamic (test should really
	  be elsewhere).

	* [r7209] topo/base/parameterclasses.py:
	  Removed ERRORALERT (fixed elsewhere).

	* [r7208] topo/base/parameterizedobject.py:
	  Updated repr_value() and inspect_value() to handle
	  CompositeParameter.

	* [r7207] topo/base/parameterizedobject.py:
	  Simplified repr_value().

	* [r7206] topo/base/parameterizedobject.py:
	  In repr_value(), corrected how to find a Parameter object in the
	  ParameterizedObject class hierarchy.

	* [r7205] topo/tests/testDynamicParameter.txt:
	  Added test for repr_value().

	* [r7204] topo/tests/testDynamicParameter.txt:
	  Added test for Dynamic parameter shared by instances of a class.

	* [r7203] topo/base/parameterclasses.py:
	  Dynamic parameter not forced to instantiate.

	* [r7202] topo/base/parameterizedobject.py:
	  Cleaned up repr_value() so that it also works for Parameters set
	  on a class.

	* [r7201] topo/base/parameterclasses.py:
	  Added ERRORALERT.

	* [r7200] topo/base/parameterizedobject.py:
	  Fixed bug in repr_value() where dynamic values were being
	  advanced (dict.get default value is looked up even if not being
	  used). (Same bug existed in the past, but that was caused by
	  Parameter instances sharing last_value.)

	* [r7199] topo/tests/__init__.py:
	  Small cleanup of run_named().

	* [r7198] topo/tests/testcfsom.py,
	  topo/tests/testpatterngenerator.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testtemplateplotgrouppanel.py:
	  No longer uses DynamicNumber to wrap a number generator.

	* [r7197] topo/outputfns/basic.py,
	  topo/patterns/basic.py,
	  topo/tests/testDynamicParameter.txt:
	  Change from DynamicNumber to Number.

	* [r7196] topo/commands/basic.py:
	  Updated documentation regarding Dynamic parameters.

	* [r7195] topo/base/parameterclasses.py:
	  Turn of warnings about changed Dynamic parameters for the moment.

	* [r7194] topo/base/parameterclasses.py:
	  Fixed minor typo.

	* [r7193] examples/hierarchical.ty:
	  Updated to use dynamic Number rather than DynamicNumber (as first
	  example of how syntax changes).

	* [r7192] topo/patterns/image.py:
	  Removed unused import.

	* [r7191] topo/tests/testDynamicParameter.txt:
	  Suppress Dynamic warnings and show that DynamicNumber declared in
	  a class by adding doc string.

	* [r7190] topo/tkgui/parametersframe.py:
	  Some reorganization and support for regridding a parameter.
	  Intermediate checkin.

	* [r7189] topo/tkgui/tkparameterizedobject.py:
	  Updates for changes to Dynamic and DynamicNumber. Added
	  repack_param() (untested). Intermediate checkin, but Dynamic
	  parameters are working (not all features can be invoked
	  graphically yet).

	* [r7188] topo/plotting/palette.py:
	  Replaced lambda-in-a-parameter with a callable class. (Dynamic
	  parameters are always instantiated.)

	* [r7187] topo/base/parameterizedobject.py:
	  Updated inspect_value() with changes to Dynamic parameters. Added
	  repr_value() (name to be changed) to return the value of a
	  parameter in a form that allows the parameter to be recreated.
	  New Dynamic-support code not yet finished, but appears to be
	  working so far.

	* [r7186] topo/base/parameterclasses.py:
	  Updated Dynamic: has _dynamic and last_value slots. _dynamic is
	  set to True if the Dynamic's value is callable or is an iterator
	  (i.e. is dynamic). A Dynamic Parameter's last_value is stored
	  inside the Parameter itself when the Parameter is only set on the
	  class, but is stored as _X_param_value_last in the owning
	  *object* if the Parameter's value has been set on the object
	  (might not be final). Number now inherits from Dynamic. If Number
	  is set to a dynamic value, the bounds are checked at __get__ time
	  rather than at __set__ time (which is what happens for
	  non-dynamic values). Replaced DynamicNumber with a dummy that
	  fills the two previous (distinct) uses (i.e. it replaces class
	  Parameter declarations of DynamicNumber with Number, and it
	  replaces using DynamicNumber to wrap number generators as values
	  for Number parameters). New Dynamic code not yet finished, but
	  appears to be working so far.

2007-11-28  jprovost

	* [r7185] topo/outputfns/basic.py:
	  Added comment to PoissonSample OF class.

	* [r7184] topo/misc/traces.py:
	  Renamed TraceSpecification to Trace

2007-11-28  ceball

	* [r7183] topo/tests/testDynamicParameter.txt:
	  Initial version. Shows a current flaw (i.e. fails right now) and
	  has some checks for when new Dynamic parameter committed (yet to
	  happen).

2007-11-28  jbednar

	* [r7182] topo/base/simulation.py:
	  Added docstring

	* [r7181] doc/Tutorials/lissom_oo_or_text.php:
	  Fixed minor problems found by John Davey

2007-11-28  ceball

	* [r7180] topo/tests/__init__.py:
	  Added support for running a single named doctest file.

	* [r7179] topo/tests/testpatterngenerator.py:
	  Added test to show a bug (currently test fails).

2007-11-27  ceball

	* [r7178] doc/Downloads/index_text.php:
	  Update to Mac OS X build instructions.

	* [r7177] topo/tests/testsheet.py:
	  Updated Slice.tuple() to Slice.as_tuple().

	* [r7176] topo/base/sheet.py:
	  (Slice) Minor cleanup of documentation. Added __getitem__ method.
	  Made some methods private. Renamed tuple() to as_tuple(). Changed
	  'coordinate_transformer' to 'sheet_coordinate_system'.

	* [r7175] topo/base/sheetcoords.py:
	  Made some methods private.

	* [r7174] Makefile:
	  Undid part of previous commit - can't have the osx-patch file in
	  a different directory.

	* [r7173] Makefile:
	  Added target osx-patch-clean (in case someone wants to remove the
	  patch). Moved osx-patch file to external/ so it doesn't clutter
	  the topographica directory.

2007-11-26  jbednar

	* [r7172] topo/sheets/saccade.py:
	  Trivial cleanup of whitespace

	* [r7171] topo/base/parameterizedobject.py:
	  Clarified __is_abstract docstring

2007-11-26  ceball

	* [r7170] Makefile:
	  Added osx-patch target (for patching external/Makefile's python
	  building command.

	* [r7169] doc/Future_Work/current_text.php:
	  Minor additions.

	* [r7168] doc/buildbot/master.cfg:
	  4-hourly tests changed to be 8-hourly. xvfb-run gets display
	  automatically.

	* [r7167] doc/Future_Work/current_text.php:
	  Added first draft of procedure to convert from CVS to SVN.

	* [r7166] external/Python-2.5.1.tgz:
	  From python.org

2007-11-25  jbednar

	* [r7165] topo/patterns/teststimuli.py:
	  Fixed version control string

2007-11-25  ceball

	* [r7164] topo/base/simulation.py:
	  Cleaned up exception printing in CommandEvent.

	* [r7163] topo/base/simulation.py:
	  Added a comment.

	* [r7162] topo/base/simulation.py:
	  Altered some of SimSingleton's wrapper methods to call
	  actual_sim's methods directly.

	* [r7161] topo/base/simulation.py:
	  Allow 'x in topo.sim' syntax.

	* [r7160] doc/Future_Work/current_text.php:
	  IPython tasks moved to tracker.

	* [r7159] topo/base/parameterizedobject.py:
	  Added comment to __is_abstract().

2007-11-25  jbednar

	* [r7158] examples/lissom_photo_or.ty,
	  examples/saccade_demo.ty,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/tests/testimage.py,
	  topo/tests/testsheetview.py:
	  Changed users of FileImage to use the current name

	* [r7157] examples/lissom_oo_or_dy_photo.ty:
	  Fixed broken import

2007-11-25  ceball

	* [r7156] topo/base/parameterizedobject.py:
	  Fixed minor typo

	* [r7155] topo/commands/analysis.py,
	  topo/patterns/teststimuli.py,
	  topo/responsefns/projfns.py,
	  topo/sheets/generatorsheet.py:
	  Removed unused import.

	* [r7154] doc/buildbot/.pycheckrc:
	  Moved to pycheckrc.

2007-11-23  jbednar

	* [r7153] topo/base/parameterizedobject.py:
	  Simplified abstract property slightly

	* [r7152] topo/patterns/image.py:
	  Renamed Image to FileImage, keeping old name for compatibility.
	  Minor cleanup of whitespace and docs

	* [r7151] topo/base/arrayutils.py:
	  Minor fix to whitespace

	* [r7150] Makefile:
	  Added lint-base target, and disabled some spurious warnings for
	  lint

2007-11-23  ceball

	* [r7149] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Simplified denotion of an abstract class.

	* [r7148]
	  topo/tests/testparameterizedobject.py:
	  Simplified denotion of an abstract class and added test that
	  non-abstract class has abstract=False.

	* [r7147] topo/base/boundingregion.py,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/base/simulation.py,
	  topo/coordmapperfns/basic.py,
	  topo/learningfns/som.py,
	  topo/misc/numbergenerators.py,
	  topo/misc/traces.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/plotting/plotgroup.py:
	  Simplified denotion of an abstract class.

	* [r7146]
	  topo/tests/testparameterizedobject.py:
	  Added test for abstract class.

	* [r7145] topo/base/simulation.py:
	  Removed unused variable.

	* [r7144] topo/base/simulation.py:
	  Removed unused variable.

	* [r7143] Makefile:
	  Moved pychecker commandline options (except --config) to
	  pycheckrc.

	* [r7142] doc/buildbot/pycheckrc:
	  Moved pychecker commandline options from Makefile to pycheckrc.
	  Globally suppress warning about empty __slots__ and
	  __get__/__set__ not being special.

	* [r7141] topo/base/cf.py:
	  (CFPOF_Plugin) Removed unused variable, and out-of-date
	  documentation.

	* [r7140] doc/buildbot/pycheckrc:
	  Added a suppression (as a comment, because I'm not yet sure how
	  best to make suppressions work), and made the existing
	  suppression more specific.

	* [r7139] topo/base/simulation.py:
	  Renamed a variable that's the same as a builtin.

	* [r7138] topo/base/parameterclasses.py:
	  Renamed variable that had the same name as a built-in function.

	* [r7137] topo/base/arrayutils.py:
	  Renamed a variable that had the same name as a builtin function.

	* [r7136] Makefile,
	  doc/buildbot/pycheckrc:
	  Moved .pycheckrc to pycheckrc.

2007-11-22  judelaw

	* [r7135] topo/outputfns/homeostatic.py:
	  corrected bug in OutputFnDebugger

	* [r7134] topo/sheets/lissom.py:
	  added new SLISSOM sheet which allows scaling of projection
	  activities for use with lissom_oo_or_scaling.ty

2007-11-22  ceball

	* [r7133] topo/base/cf.py:
	  Removed unused variable (no visible change).

2007-11-21  jbednar

	* [r7132] doc/Tutorials/lissom_oo_or_text.php:
	  Fixed typo.

2007-11-21  judelaw

	* [r7131] topo/projections/basic.py:
	  added a new projection for debugging

2007-11-21  ceball

	* [r7130] doc/buildbot/master.cfg:
	  doozy tests now run with xvfb-run

2007-11-20  judelaw

	* [r7129] examples/lissom_oo_or_noshrinking.ty:
	  removed adapting homeostatic rule

	* [r7128] topo/outputfns/homeostatic.py:
	  added option for saving debugging graphs

2007-11-20  jbednar

	* [r7127] doc/Home/news_text.php:
	  Updated with news since 0.9.4

	* [r7126] topo/outputfns/basic.py:
	  Minor cleanup of docs

	* [r7125] topo/outputfns/basic.py:
	  Minor cleanup of docs

	* [r7124] ChangeLog.txt:
	  Added recent changes

	* [r7123] doc/Home/oldnews_text.php:
	  Moved 0.9.4 to old news

	* [r7122] doc/Makefile:
	  Fixed bug in previous checkin

	* [r7121] doc/Downloads,
	  doc/Downloads/.cvsignore,
	  doc/Home,
	  doc/Home/.cvsignore:
	  More to ignore

	* [r7120] doc/Future_Work/current_text.php:
	  More notes on how to specify real-world units

	* [r7119] doc/Home/news_text.php,
	  doc/Makefile,
	  doc/shared/index.php:
	  Made separate file for news

2007-11-20  ceball

	* [r7118] doc/Future_Work/current_text.php:
	  Removed all the pychecker output and restored general task
	  description.

	* [r7117] topo/base/sheet.py:
	  Added to comment.

	* [r7116] Makefile:
	  check-base: added --stdlib to ignore warnings from files in
	  standard library (I think that includes site-packages/)

	* [r7115] Makefile:
	  Added check-base section for running pychecker on topo.base.

	* [r7114] doc/buildbot/.pycheckrc:
	  Initial version.

	* [r7113] doc/Future_Work/current_text.php:
	  Removed bogus pychecker output: the Slice class implements
	  __iter__, which is enough for unpacking.

	* [r7112] topo/base/sheet.py:
	  Added note.

	* [r7111] topo/base/cf.py:
	  What should have happened in the previous commit.

	* [r7110] doc/Future_Work/current_text.php:
	  Fixed pychecker problem.

	* [r7109] topo/base/arrayutils.py:
	  Explicity pass 0,0 to complex() (at least currently,
	  complex()==complex(0,0)).

	* [r7108] topo/tkgui/parametersframe.py:
	  Altered a comment.

	* [r7107] doc/Future_Work/current_text.php:
	  Fixed pychecker problems.

	* [r7106] topo/base/parameterclasses.py:
	  Fixed comparisons with True and False.

	* [r7105] topo/base/cf.py:
	  Fixed comparison with True.

	* [r7104] doc/Future_Work/current_text.php:
	  Fixed a pychecker problem in parameterizedobject.py (v1.85).

	* [r7103] doc/Future_Work/current_text.php:
	  Added back revised pychecker task.

	* [r7102] topo/base/parameterizedobject.py:
	  Removed unused abtract_class argument from
	  ParameterizedObject.__init__.

	* [r7101] topo/base/parameterizedobject.py:
	  Changed parameter-deletion's string error to TypeError.

2007-11-19  jbednar

	* [r7100] topo/patterns/image.py:
	  Fixed copy-and-paste error; Image is called PIL in this file to
	  avoid name conflict. Loading a snapshot with an image should work
	  now.

2007-11-19  ceball

	* [r7099] doc/Future_Work/current_text.php:
	  Moved tasks to trackers on sf.net.

	* [r7098] doc/Future_Work/current_text.php:
	  Moved items to tracker. Added some notes.

2007-11-18  ceball

	* [r7097] topo/tkgui/widgets.py:
	  Added a comment.

	* [r7096] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/projectionpanel.py:
	  Use tag_set() rather than refresh() for TaggedSlider.

	* [r7095] topo/tkgui/tkparameterizedobject.py:
	  Corrected import.

	* [r7094] topo/tkgui/tkparameterizedobject.py,
	  topo/tkgui/topowidgets.py:
	  Removed TkPOTaggedSlider (does nothing more than TaggedSlider).

	* [r7093] topo/tkgui/plotgrouppanel.py:
	  Fixed bug with history mechanism: plotgroup now added to history
	  whenever refresh_plots() called, and is only added if there are
	  actually plots.

	* [r7092] topo/tkgui/parametersframe.py:
	  Added note for myself.

	* [r7091] topo/misc/commandline.py:
	  Simplification to gui starting.

	* [r7090] topo/tkgui/__init__.py:
	  start() prints 'Launching GUI' message.

	* [r7089] topo/misc/commandline.py:
	  Make sure IPython quits when topographica not started for
	  interactive use.

	* [r7088] Makefile:
	  (topographica script) When using IPython, Ctrl+D now quits
	  immediately (as for python).

	* [r7087] doc/Future_Work/current_text.php:
	  Added note.

	* [r7086] topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py:
	  Updates to match tkparameterizedobject 1.117.

	* [r7085] topo/tkgui/projectionpanel.py:
	  Renamed tk_vars to tkvars.

	* [r7084] topo/tkgui/parametersframe.py:
	  Updates to match tkparameterizedobject.py 1.117.

	* [r7083] topo/tkgui/tkparameterizedobject.py:
	  Improvements to Parameter-Tkinter linkage.
	  
	  Major:
	  - unapplied changes to parameter values are indicated with blue
	  labels
	  - parameters that are not set to class defaults have a green
	  label background
	  - an error in a parameter value is indicated with red labels
	  (note that the above indication styles are temporary)
	  
	  Minor:
	  - fixed _get_tk_val to return gui variable value
	  - no attempt to set Parameter if string-to-value translation
	  fails
	  
	  Internal:
	  - simplified handling of GUI editing of variables
	  - translation code moved from TkParameterizedObjectBase to
	  separate classes
	  - renamed tk_var to tkvar
	  - renamed object2string_ifrequired to _object2string
	  - renamed string2object_ifrequired to _string2object
	  (also added some debug messages)

	* [r7082] topo/patterns/image.py:
	  Added support for pickling GenericImage (PIL's Image cannot be
	  pickled).

	* [r7081] Makefile:
	  (topographica script) Start ipython as in bin/ipython.

	* [r7080] topo/misc/commandline.py:
	  Removed import of weave (was originally required for Windows
	  version, but seems no longer to be needed).

2007-11-16  jbednar

	* [r7079] doc/Links/index_text.php:
	  Added some info about NCS; not much info seems available.

2007-11-16  ceball

	* [r7078] topo/base/arrayutils.py:
	  Commented out code that I think is never being called.

2007-11-16  jbednar

	* [r7077] topo/sheets/generatorsheet.py:
	  Fixed longstanding typos in apparently never-used line of code

2007-11-15  jbednar

	* [r7076] topo/base/simulation.py:
	  Made eps_to_start backwards compatible with 0.9.4 so that 0.9.4
	  saved snapshots can be loaded.

	* [r7075] topo/misc/keyedlist.py:
	  Added values() method to match a regular dictionary

	* [r7074] topo/commands/pylabplots.py:
	  Added ability to specify the x values of a vectorplot

	* [r7073] topo/misc/commandline.py:
	  Minor simplification

	* [r7072] topo/misc/commandline.py:
	  Drastically simplified so that all options are processed as they
	  are encountered, without any list of commands to execute later

2007-11-15  ceball

	* [r7071] topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py:
	  Starting tkgui when this test is imported causes problems if
	  there's no DISPLAY. Only need to start tkgui if the test is run
	  alone, so having the code isn't important anyway (can just pass
	  -g).

2007-11-14  jbednar

	* [r7070] topo/commands/analysis.py:
	  Cleaned up decode_feature

	* [r7069] topo/base/simulation.py,
	  topo/sheets/lissom.py:
	  Removed Simulation.execute_next, and instead made EP.start() be
	  called just before the simulation begins processing events.

2007-11-14  rczhao

	* [r7068] topo/commands/analysis.py:
	  Fixed an indentation error.

	* [r7067] topo/commands/analysis.py:
	  Added a decode_feature function.

2007-11-14  jbednar

	* [r7066] topo/misc/commandline.py:
	  Added gui() and auto_import_commands() functions to allow -g and
	  -a options to be run explicitly even after Topographica has
	  started

2007-11-13  rczhao

	* [r7065] topo/patterns/image.py:
	  Fixed a boolean comparison problem caused by new version of
	  numpy.

2007-11-13  jbednar

	* [r7064] topo/tkgui/templateplotgrouppanel.py:
	  Trivial fix to typo in comment

	* [r7063] examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_dr.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_or_homeoscale.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_photo_or.ty,
	  examples/lissom_whisker_barrels.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty:
	  Removed now-unnecessary setting of topo.sim.name

	* [r7062] topo/misc/commandline.py:
	  Trivial doc cleanup

2007-11-13  ceball

	* [r7061] topo/base/simulation.py:
	  Removed unnecessary 'or' (no visible change).

2007-11-13  jbednar

	* [r7060] topo/misc/commandline.py:
	  Moved sim name setting to before the .ty file is executed, so
	  that the .ty file can override it.

2007-11-13  ceball

	* [r7059] Makefile:
	  (topographica script) Make IPython's user namespace be __main__.

	* [r7058] topo/base/simulation.py:
	  Do set Simulation name if one is passed to Simulation.__init__.
	  (Fixes failing tests that expect Simulations with specific
	  names.)

	* [r7057] topo/tests/__init__.py:
	  Added convenience function (for me): run a single test.

	* [r7056] examples/cfsom_or.ty,
	  examples/goodhill_network90.ty,
	  examples/hierarchical.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/tiny.ty:
	  Removed assignment of topo.sim.name.

	* [r7055] topo/misc/commandline.py:
	  Removed apparently out-of-date ALERT.

	* [r7054] topo/tkgui/topoconsole.py:
	  Renamed sim_title_from_filename to sim_name_from_filename.

	* [r7053] topo/misc/commandline.py:
	  Automatic simulation naming now takes account of filenames
	  supplied *before* the first commandline option. (Also: renamed
	  sim_title_from_filename to sim_name_from_filename; renamed
	  get_filenames to get_postoption_filenames.

	* [r7052] topo/misc/commandline.py:
	  Minor change to code style - no visible change.

	* [r7051] topo/misc/commandline.py:
	  Moved execution of startup file(s) into a function, and made two
	  changes: (1) 'Executing startup file...' message printed whether
	  option.interactive/gui or not (although if not interactive, print
	  statement will not show up anywhere); (2) if there is an error in
	  a startup file, execution stops at that point (and if
	  interactive, returns to a prompt).

	* [r7050] topo/misc/commandline.py:
	  Added comment to ALERT about weave on Windows.

	* [r7049] topo/misc/commandline.py:
	  Commented out print statement (otherwise, if you pass -g at the
	  end of the command used to start topographica it would be
	  printed).

	* [r7048] doc/Future_Work/current_text.php:
	  Removed erroneous example of not needing a Connection Fields
	  plot.

2007-11-12  jprovost

	* [r7047] topo/misc/robotics.py:
	  Robotics-related classes for topographica.

	* [r7046] topo/misc/playerrobot.py:
	  High-level interface to the Player client libraries. This is a
	  temporary home for this file until it finds a permanent home
	  (maybe in
	  the PlayerStage project or in PLASTK?)

	* [r7045] examples/saccade_demo.ty:
	  Updated to support image sequences in ShiftingGeneratorSheet.

	* [r7044] topo/patterns/image.py:
	  Refactored the Image class to allow images that are generated
	  through other means than reading a file. (e.g. from a camera)

	* [r7043] topo/outputfns/basic.py:
	  Moved Pipeline class to base/functionfamilies.py.
	  Added PoissonSample OF class.

	* [r7042] topo/base/functionfamilies.py:
	  Added operator support to OutputFn class to allow construction of
	  Pipelines using '+' operator. Moved Pipeline class in from
	  outputfns/basic.py, as PipelineOF.

	* [r7041] topo/base/simulation.py:
	  Minor refactoring to allow real-time (and other) simulation
	  subclasses.

2007-11-12  jbednar

	* [r7040] topo/base/simulation.py,
	  topo/misc/commandline.py,
	  topo/tkgui/topoconsole.py:
	  Change default Simulation name to be None, instead of
	  Simulation00001, but have it be set automatically based on the
	  first script run (from the command line or from Run Script).

2007-11-11  ceball

	* [r7039] doc/Future_Work/current_text.php:
	  Removed topoconsole title task.

	* [r7038] topo/tkgui/topoconsole.py:
	  Minor modification to title, plus remove set-title-on-run hack.

	* [r7037] topo/misc/commandline.py:
	  Set the console name if starting the gui.

	* [r7036] topo/tkgui/topoconsole.py:
	  Update the title after loading a script or snapshot.

	* [r7035] doc/Future_Work/current_text.php:
	  Moved some tasks out to the sf.net feature requests tracker.

	* [r7034] topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py:
	  Start tkgui before running the tests.

	* [r7033] Makefile:
	  (Topographica script) Added colors=NoColor for ipython.

	* [r7032] topo/tkgui/tkparameterizedobject.py:
	  Minor cleanup of mechanism for passing messages to the console.
	  Also, minor cleanup of some docstrings.

	* [r7031] topo/tkgui/__init__.py:
	  (1) Moved system_platform code to widgets.py because of circular
	  import problems (when trying to use topo.tkgui from several of
	  the files in topo/tkgui, get 'module does not contain tkgui'
	  attribute error). (2) Moved 'entry background hack to
	  topowidgets.py. (3) Made start() return immediately if a console
	  already exists.

	* [r7030] topo/tkgui/topoconsole.py,
	  topo/tkgui/widgets.py:
	  Moved system_platform from __init__ to widgets.

	* [r7029] topo/tkgui/topowidgets.py:
	  Moved entry background hack from __init__ to topowidgets.

	* [r7028] topo/tkgui/__init__.py:
	  Removed function that doesn't seem to be used in any existing
	  code.

	* [r7027] Makefile:
	  Added starting point to show how to change ipython's command
	  prompt. (Haven't figured out if it's possible to change the
	  prompt once ipython has started.)

	* [r7026] doc/Future_Work/current_text.php:
	  Added some notes.

	* [r7025]
	  topo/tests/testtkparameterizedobject.py:
	  Stop using the alias get_parameter (use get_parameter_object).

	* [r7024] external/Makefile:
	  Uninstall current gnosis before making it.

2007-11-10  ceball

	* [r7023] topo/tkgui/templateplotgrouppanel.py:
	  Fixed bug where labels were not being drawn when a panel was
	  first opened if the plot data came from e.g. a snapshot.

	* [r7022] topo/tkgui/testpattern.py:
	  TestPattern windows no longer all share the same PlotGroup (a
	  bug). Renamed TestPattern's PlotGroup to 'Test Pattern' (from
	  outdated 'Preview').

2007-11-09  ceball

	* [r7021] topo/tests/testsnapshots.py:
	  Added commented-out xml snapshot test.

	* [r7020] topo/tests/testsnapshots.py:
	  Refactor to allow tests to be duplicated for xml pickles.

	* [r7019] external/Makefile:
	  Switch to 1.3.0-alpha-7 version of Gnosis Utils.

	* [r7018] topo/commands/basic.py:
	  Updated commands to work with changed gnosis.xml.pickle module.

	* [r7017]
	  external/Gnosis_Utils-1.3.0-alpha-7.tar.gz:
	  Test version (for xml pickling problems with numpy) direct from
	  author.

	* [r7016] Makefile:
	  topographica script: try to use IPython shell if IPython has been
	  built.

2007-11-07  ceball

	* [r7015] doc/Downloads/cygwin_text.php:
	  Added link to packages list.

2007-11-06  ceball

	* [r7014] doc/Downloads/cygwin_text.php:
	  Added a note.

	* [r7013] doc/Downloads/cygwin_packages:
	  Cygwin packages present when I built pre-March 2007 topographica.
	  Needs to be pared down and updated. (Created with 'cygcheck -c'.)

	* [r7012] doc/Downloads/cygwin_text.php:
	  Updated information about GUI.

	* [r7011] external/Makefile:
	  Removed Numeric section.

	* [r7010] doc/Downloads/cygwin_text.php:
	  Initial version (originally produced in March 2007).

2007-11-05  ceball

	* [r7009] doc/Developer_Manual/gui_text.php,
	  doc/Future_Work/index_text.php:
	  Fixed typo.

2007-11-01  jbednar

	* [r7008] ChangeLog.txt:
	  Updated with recent changes

	* [r7007]
	  doc/Tutorials/images/activity_line_oo.png,
	  doc/Tutorials/images/activity_line_oo_or.png,
	  doc/Tutorials/images/lissom_oo_or_orpref_ft.png,
	  doc/Tutorials/images/natural_image_oo_or.png,
	  doc/Tutorials/images/natural_image_projact_oo_or.png,
	  doc/Tutorials/images/oo_or_map.png,
	  doc/Tutorials/images/projection_oo.png,
	  doc/Tutorials/images/test_pattern_oo.png,
	  doc/Tutorials/images/topographica_console.png,
	  doc/Tutorials/images/unit_weights_0_0_oo.png,
	  doc/Tutorials/images/unit_weights_0_0_oo_or.png,
	  doc/Tutorials/images/unit_weights_41_24_oo_or.png,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Updated lissom_oo_or tutorial images

2007-11-01  ceball

	* [r7006] topo/base/simulation.py:
	  Corrected test for None in timestr(). (Fix incorrect time in
	  plotgroups history.)

2007-10-31  jbednar

	* [r7005] /trunk/topographica-win/common/python_topo.tar.gz:
	  Added python24.dll from the .exe distribution

2007-10-30  ceball

	* [r7004] doc/buildbot/master.cfg:
	  Simplified file and added descriptions for web page.

	* [r7003] doc/buildbot/master.cfg:
	  Split builds into parts. Added email notifications.

	* [r7002] topo/tkgui/topoconsole.py:
	  Restored <Return> in run-for box to run simulation.

	* [r7001] topo/tkgui/widgets.py:
	  (TaggedSlider) Fixed test for something being a number; added
	  some documentation.

	* [r7000] topo/tkgui/parametersframe.py:
	  On pressing Apply, TaggedSliders have their sliders updated
	  (needs to move into TaggedSlider, but this problem only shows up
	  when changes are not applied immediately).

	* [r6999] topo/tkgui/topowidgets.py:
	  Removed useless methods from tkparameterizedobject-specialized
	  version of TaggedSlider. Will eventually remove the whole class.

2007-10-29  jbednar

	* [r6998] ChangeLog.txt:
	  Added recent changes

	* [r6997] topo/tkgui/plotgrouppanel.py:
	  Disable enlarge and reduce when there are no plots

	* [r6996] topo/plotting/plotgroup.py:
	  Minor cleanup, plus fixed bug in return value that was preventing
	  Reduce button from ever being disabled

2007-10-29  ceball

	* [r6995]
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat:
	  Added ALERT.

	* [r6994]
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat:
	  Corrections and updates to match Makefile.

	* [r6993] /trunk/topographica-win/create_python_topo/README.txt:
	  Added a note.

2007-10-28  ceball

	* [r6992] topo/tkgui/projectionpanel.py:
	  PlotMatrixPanels only redraw when the sheet changes (previously
	  only RFProjection panels did a redraw - the rest did a refresh).

	* [r6991] topo/plotting/plotgroup.py:
	  update_maximum_plot_height() handles the case where there are no
	  resizeable plots. Probably needs correcting.

	* [r6990] topo/commands/analysis.py:
	  Don't plot projection plots immediately.

	* [r6989] topo/tkgui/projectionpanel.py:
	  Override refresh(): additionally sets desired size from current
	  one each time. Removed unnecessary setup_plotgroup and __init__
	  methods.

	* [r6988] doc/Future_Work/current_text.php:
	  Removed completed buildbot task. (The part about automatic
	  restarting and xvfb is covered by the feature request on sf.net).

	* [r6987] doc/Tutorials/lissom_oo_or_text.php:
	  Change to punctuation.

	* [r6986] /trunk/topographica-win/create_installer/README.txt:
	  Clarified text.

	* [r6985] topo/tkgui/topowidgets.py:
	  Fixed bug: window wasn't closing (introduced when classes split).

	* [r6984] topo/tkgui/widgets.py:
	  Fixed Tkinter constants (command prompt was broken at the point
	  of entering a command).

	* [r6983] topo/tkgui/widgets.py:
	  Added missing import (command prompt was broken at the point of
	  entering a command.

	* [r6982] /trunk/topographica-win/create_python_topo/setup.bat:
	  Use matplotlib 0.90.1

2007-10-26  jbednar

	* [r6981] ChangeLog.txt:
	  Added recent updates

	* [r6980] topo/tkgui/topoconsole.py:
	  Removed initial directory for loading snapshots, now that they
	  may be
	  in Output instead

	* [r6979] doc/shared/index.php:
	  Updated announcement

	* [r6978] ChangeLog.txt:
	  Added recent updates

	* [r6977]
	  doc/Tutorials/images/som_activity_000000.png,
	  doc/Tutorials/images/som_activity_000001.png,
	  doc/Tutorials/images/som_activity_000005.png,
	  doc/Tutorials/images/som_activity_040000.png,
	  doc/Tutorials/images/som_cog_000000.png,
	  doc/Tutorials/images/som_cog_005000.png,
	  doc/Tutorials/images/som_cog_010000.png,
	  doc/Tutorials/images/som_cog_040000.png,
	  doc/Tutorials/images/som_grid_000000.png,
	  doc/Tutorials/images/som_grid_005000.png,
	  doc/Tutorials/images/som_grid_010000.png,
	  doc/Tutorials/images/som_grid_040000.png,
	  doc/Tutorials/images/som_network_diagram.png,
	  doc/Tutorials/images/som_projection_000000.png,
	  doc/Tutorials/images/som_projection_000001.png,
	  doc/Tutorials/images/som_projection_000005.png,
	  doc/Tutorials/images/som_projection_010000.png,
	  doc/Tutorials/images/som_projection_040000.png,
	  doc/Tutorials/images/som_projection_activity_000001.png,
	  doc/Tutorials/som_retinotopy_text.php:
	  Updated SOM tutorial, mainly to get new images

	* [r6976] doc/Future_Work/current_text.php:
	  Updated to show nearly completed tasks

	* [r6975] topo/commands/analysis.py:
	  Turned on situate by default

	* [r6974]
	  doc/Tutorials/images/lissom_oo_or_activity_rightclick.png:
	  Added transparency

	* [r6973]
	  doc/Tutorials/images/topographica_console.png,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Updated to match current version

	* [r6972] doc/FAQ/index_text.php:
	  Minor update

2007-10-26  ceball

	* [r6971] topo/tkgui/plotgrouppanel.py:
	  Removed ALERT that describes expected behavior.

	* [r6970] doc/Future_Work/current_text.php:
	  Removed completed scrollbar and projection history tasks.

	* [r6969] topo/tkgui/widgets.py:
	  Added EditableOptionMenu.

2007-10-25  ceball

	* [r6968] topo/tkgui/topoconsole.py:
	  Get plot_templates from the current plotgroups dictionary.

	* [r6967] topo/misc/utils.py:
	  Added ALERT.

	* [r6966] topo/tkgui/widgets.py:
	  Added note.

	* [r6965] topo/tkgui/plotgrouppanel.py:
	  Removed no-longer-necessary try/except (TaggedSlider support
	  'state' option).

	* [r6964] topo/tkgui/plotgrouppanel.py:
	  Removed unnecessary code to update widgetswhen navigating
	  history.

	* [r6963] topo/plotting/plotgroup.py:
	  Fixed error message.

2007-10-24  jbednar

	* [r6962] external,
	  external/.cvsignore,
	  external/Makefile:
	  Upgraded Matplotlib to 0.90.1 to fix problem on FC7

	* [r6961] doc/Future_Work/current_text.php:
	  Updated tasks

	* [r6960] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Fixed some bugs in plot scaling, hopefully without introducing
	  many more. Now plot histories should respect the current size
	  scaling options, rather than keeping their own sizes.

2007-10-24  ceball

	* [r6959] /trunk/topographica-win/common/python_topo.tar.gz:
	  Updated to matplotlib 0.90.1

	* [r6958] topo/commands/pylabplots.py:
	  Added needmain=False for wireframe plot.

	* [r6957] topo/tkgui/topoconsole.py:
	  Make plot_templates be shared across all instances of plotgroups
	  that same a name.

	* [r6956]
	  /trunk/topographica-win/create_python_topo/matplotlib-0.90.1.win32-py2.4.exe:
	  From sf.net

2007-10-23  jbednar

	* [r6955] topo/commands/analysis.py:
	  Removed alert

2007-10-23  ceball

	* [r6954] topo/commands/analysis.py:
	  Added question.

	* [r6953] doc/Future_Work/current_text.php:
	  Updates to tasks.

	* [r6952] topo/plotting/plotgroup.py:
	  Removed useless scaling hack.

	* [r6951] topo/plotting/plotgroup.py:
	  Fixed underscore error (forgot about name mangling).

	* [r6950] topo/tkgui/widgets.py:
	  Fixed recursion bug (update_idletasks() was being called inside
	  an after_idle()).

2007-10-22  jbednar

	* [r6949] doc/Future_Work/current_text.php:
	  Reordered remaining tasks

	* [r6948] external/matplotlib-0.90.1.tar.gz:
	  Version from SourceForge

	* [r6947] doc/Developer_Manual/gui_text.php:
	  Added missing newline

	* [r6946] topo/commands/basic.py:
	  Removed obsolete note

	* [r6945] topo/misc/patternfns.py:
	  Added fix from Jan; gabor was using incorrect sine grating
	  offset.

	* [r6944] doc/User_Manual/plotting_text.php:
	  Added example RF plots

	* [r6943]
	  doc/User_Manual/images/rf_matrixplot.png,
	  doc/User_Manual/images/rf_projection.png:
	  Screen grab from Topographica 0.9.4

2007-10-22  ceball

	* [r6942] topo/tkgui/plotgrouppanel.py:
	  Added ALERT about unbounded history.

	* [r6941] /trunk/topographica-win/common/python_topo.tar.gz:
	  Updated to current external packages.

	* [r6940] doc/Future_Work/current_text.php:
	  Added note to tutorial task.

2007-10-21  ceball

	* [r6939] doc/Future_Work/current_text.php:
	  Updated tasks (first bug temporarily fixed; second not too
	  serious so moved to after 0.9.4.

	* [r6938] topo/plotting/plotgroup.py:
	  Fixed plot sizes not sticking in the GUI with a hack (to get
	  things working for the release; see task in current tasks.

	* [r6937]
	  external/pybwidget-0.1.2_1.8.0.tar.gz:
	  Reverted to previous gzip'd version of tar now windows'
	  python_topo/ has been built. No idea why the gzip'd version is
	  incompatible between linux and Windows (linux gzip'd one won't
	  gunzip on Windows; Windows gzip'd one won't gunzip on linux).

	* [r6936]
	  external/pybwidget-0.1.2_1.8.0.tar.gz:
	  Same tar file as before, but gzip'd on Windows since I couldn't
	  get the original one to gunzip on Windows.

	* [r6935] doc/Future_Work/current_text.php:
	  Clarified 0.9.4 bugs. Moved tkgui cleanup task to after 0.9.4.

	* [r6934] topo/tkgui/topoconsole.py:
	  Corrected when to do the plotgroup copy (we want an independent
	  plotgroup for each panel, and made the copy be a deepcopy.

	* [r6933] doc/Developer_Manual/gui_text.php:
	  Finished brief introduction to tkgui programming.

	* [r6932] doc/shared/index.php:
	  Added commented-out link to relevant manual page for adding GUI
	  code. Commented out because I'm not sure we want to lead people
	  reading the news into the developer manual.

	* [r6931] topo/patterns/audio.py:
	  Print a warning when trying to import topo.patterns.audio if
	  pyaudiolab can't be imported.

	* [r6930] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/testpattern.py:
	  Minor update to doc.

	* [r6929] topo/tkgui/topowidgets.py,
	  topo/tkgui/widgets.py:
	  Some cleanup to comments (including warnings that will be visible
	  in the reference manual) about some things that aren't finished.

	* [r6928] doc/Future_Work/current_text.php:
	  Removed scrollbar and OSX/vnc tasks.

	* [r6927] topo/tkgui/topowidgets.py,
	  topo/tkgui/widgets.py:
	  Make scrollbars appear for manual resizing on linux.

	* [r6926] topo/tkgui/plotgrouppanel.py:
	  Added ALERT.

	* [r6925] topo/tkgui/widgets.py:
	  Restored missing 'auto' option for the scrollbars: seems to be
	  required for FC5 but not Ubuntu and OSX (should be required on
	  all...).

	* [r6924] doc/Downloads,
	  doc/Downloads/.cvsignore:
	  More to ignore.

	* [r6923] doc/Developer_Manual/gui_text.php:
	  Added links (unformatted).

	* [r6922] doc/Future_Work/current_text.php:
	  Updated tasks.

	* [r6921]
	  doc/Tutorials/som_retinotopy_text.php:
	  Mentioned translations for Windows.

	* [r6920] doc/Downloads/win32notes_text.php:
	  Added more conversions.

	* [r6919] doc/Downloads/index_text.php,
	  doc/Downloads/win32notes_text.php,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Added note about translating Unix commands to Windows.

	* [r6918] topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py:
	  Updated method names for ParametersFrame.

	* [r6917] topo/tkgui/parametersframe.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Cleanup.

2007-10-20  ceball

	* [r6916] doc/Downloads/index_text.php:
	  Try 'tool-tip' popup using title attribute for displaying Windows
	  equivalent of commands.

	* [r6915] doc/Future_Work/current_text.php:
	  Updated tasks.

	* [r6914] topo/tkgui/topoconsole.py,
	  topo/tkgui/topowidgets.py:
	  Hacked ProgressWindow in half to solve the problem with it
	  flickering on in Windows.

	* [r6913] topo/tkgui/widgets.py:
	  Stop buttons having black outline when mouse moves over them
	  (since it doesn't go away until another widget's clicked on).

	* [r6912] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/projectionpanel.py:
	  Ask that sheet/projection which is top after sorting is selected
	  by default.

	* [r6911] topo/tkgui/tkparameterizedobject.py:
	  Allow to request a new default value when packing a parameter.

	* [r6910] topo/tkgui/tkparameterizedobject.py:
	  Undo a previous change: gui should not change value of all
	  SelectorParameters to the item with the highest precedence. (Need
	  to alter so it's only done for GUI parameters.)

	* [r6909] topo/tkgui/widgets.py:
	  Added test for OSX to manual control of scrollbars (manual
	  control doesn't work on OSX and isn't needed).

	* [r6908] topo/tkgui/widgets.py:
	  Added commented-out line that (when uncommented) makes scrollbars
	  work properly on Ubuntu linux. Need to test platform is not mac
	  before calling.

	* [r6907] topo/tkgui/topoconsole.py,
	  topo/tkgui/topowidgets.py,
	  topo/tkgui/widgets.py:
	  Moved some methods from ScrolledTkguiWindow to
	  ResizeableScrollableFrame. Simplified resizing methods. Window
	  scrollbars work perfectly on OSX, but will need modification for
	  linux.

	* [r6906] topo/tkgui/plotgrouppanel.py:
	  PlotGroupPanel generates a <<SizeRight>> event whenever its
	  contents might have changed size.

	* [r6905] topo/tkgui/widgets.py:
	  TaggedSlider: make slider expand if necessary.

	* [r6904] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Simplified displaying no-plot note.

	* [r6903] topo/tkgui/plotgrouppanel.py:
	  Simplified calling display_plots() and display_labels().

	* [r6902] doc/Future_Work/current_text.php:
	  Removed plotgroup-saving task.

	* [r6901] topo/plotting/plotgroup.py:
	  Added ALERT.

	* [r6900] topo/plotting/plotgroup.py:
	  Images can be pickled, so plotgroup pickling should now be ok.

	* [r6899] topo/plotting/bitmap.py:
	  Allow pickling of any stored Image.

	* [r6898] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Simplified no-plot note.

	* [r6897] doc/Future_Work/current_text.php:
	  Added list of bugs to fix before 0.9.4, and moved around some
	  other tasks.

2007-10-19  ceball

	* [r6896] topo/tests/testplotfilesaver.py:
	  Removed unused import.

	* [r6895] topo/commands/analysis.py:
	  Don't copy the plotgroup in save_plotgroup() (at least until the
	  filesaver attribute is changed from an object to just the class,
	  for instantiation later - or some other correction is made).

	* [r6894] topo/plotting/plotgroup.py:
	  Disable plotgroups saving (still more problems pickling
	  plotgroup.

	* [r6893] topo/commands/analysis.py:
	  Removed unnecessary error raising (KeyedList raises an error
	  now).

	* [r6892] topo/plotting/plotgroup.py:
	  Store plotgroups with snapshots now problems have been fixed.

	* [r6891] topo/commands/analysis.py:
	  When saving a plotgroup, work on a copy of the original from
	  plotgroups.

	* [r6890] topo/tkgui/topoconsole.py:
	  Panels take a *copy* of a plotgroup from plotgroups, rather than
	  the original object.

	* [r6889] topo/plotting/plotgroup.py:
	  Temporarily disabled plotgroups saving (since plotgroups
	  themselves actually won't pickle).

	* [r6888] topo/tkgui/widgets.py:
	  Clarified ALERT.

	* [r6887] topo/tests/testparametersframe.py:
	  Simplified finding out whether or not a widget has a value which
	  we can get().

	* [r6886] topo/tkgui/tkparameterizedobject.py:
	  Removed unnecessary try/except.

	* [r6885] topo/tkgui/widgets.py:
	  Made TaggedSlider's config() method return the correct type (but
	  needs to return the correct thing eventually).

	* [r6884] topo/tkgui/tkparameterizedobject.py:
	  Use FocusTakingButton rather than Button so that any non-button
	  widget correctly receives <FocusOut> if a button is clicked.

	* [r6883] topo/tkgui/widgets.py:
	  Added FocusTakingButton.

	* [r6882] topo/tkgui/tkparameterizedobject.py:
	  Corrected error in previous checkin.

	* [r6881] topo/tkgui/tkparameterizedobject.py:
	  SelectorParameters defaults to displaying the first item in its
	  sorted lists.

	* [r6880] topo/plotting/plotgroup.py:
	  Save plotgroups when pickling.

	* [r6879] topo/commands/basic.py,
	  topo/misc/utils.py:
	  Added ExtraPickler to allow module-level attributes to be pickled
	  (specifically, lets us save plotgroups repository). Might not be
	  the best way to do this.

	* [r6878] topo/misc/keyedlist.py:
	  Fixed typo.

	* [r6877] topo/tkgui/featurecurvepanel.py:
	  Display a title when first opened.

2007-10-19  jbednar

	* [r6876] topo/misc/__init__.py:
	  Updated docs and list of packages

2007-10-18  jbednar

	* [r6875] doc/shared/index.php:
	  Updated announcement and added screenshots

	* [r6874] doc/Home/oldnews_text.php:
	  Tightened spacing

	* [r6873]
	  doc/images/071018_modeleditor_ubuntu.png,
	  doc/images/071018_plotting1_ubuntu.png,
	  doc/images/071018_plotting2_ubuntu.png:
	  Screenshots from 0.9.4 Ubuntu version

	* [r6872] topo/commands/analysis.py:
	  Disabled RF CoG plots pending study

	* [r6871] ChangeLog.txt:
	  Updated with recent changes

	* [r6870] topo/commands/basic.py:
	  Shortened analysis_times to times

	* [r6869] doc/User_Manual/batch_text.php:
	  Clarification

	* [r6868] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Tightened up parameter packing to make windows a bit smaller

	* [r6867] topo/plotting/plotgroup.py:
	  Fixed sheet coordinates for Connection Fields -- was failing to
	  find sizes of sheets that were being plotted but were not on the
	  list of sheets to consider

	* [r6866] topo/commands/pylabplots.py:
	  Fixed histogram plot -- had been getting mixed up with other
	  pylab plots if called after them

	* [r6865] topo/tkgui/projectionpanel.py:
	  Fixed problem with refresh instructions hanging around after RF
	  plotting

	* [r6864] topo/tkgui/projectionpanel.py:
	  Renamed TwoDThingPanel to PlotMatrixPanel

	* [r6863] doc/Future_Work/current_text.php:
	  Added minor task

	* [r6862] topo/commands/basic.py:
	  Generalized default_analysis_function to avoid assuming any
	  particular names of sheets or plots, so that it can be used as-is
	  in more cases

	* [r6861] Makefile:
	  More to clean up

	* [r6860] topo/commands/basic.py:
	  Removed now-unnecessary importing in run_batch; use -a instead

	* [r6859] doc/User_Manual/batch_text.php,
	  doc/User_Manual/commandline_text.php,
	  doc/shared/index.php:
	  Documented -a option

	* [r6858] doc/User_Manual/publishing_text.php:
	  Moved blurb about batch running to publishing.html

	* [r6857] topo/misc/commandline.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Added -a option to automatically import topo.commands.*.py for
	  convenience; now implied by -g

	* [r6856] doc/User_Manual/batch_text.php,
	  topo/commands/basic.py,
	  topo/misc/commandline.py:
	  Moved run_batch from topo.misc.commandline to topo.commands.basic

	* [r6855] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Added more parameters to control PlotGroup image scaling. Made
	  default be not to scale anything, for batch use, but now GUI
	  overrides the default.

	* [r6854] examples/tiny.ty:
	  Made projection name match other simulations

2007-10-17  ceball

	* [r6853] topo/tkgui/topowidgets.py:
	  Removed unnecessary calls to update_idletasks(); the first was
	  causing a recursion-depth problem when there were lots of
	  Configure events.

2007-10-16  jbednar

	* [r6852] topo/base/simulation.py:
	  Removed aliases for SomeTimer methods

	* [r6851] topo/commands/pylabplots.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Standardized time formatting

	* [r6850] topo/tkgui/plotgrouppanel.py:
	  Minor cleanup to unit coordinate formatting

	* [r6849] topo/tkgui/projectionpanel.py:
	  Removed extra copy of situate button

2007-10-16  ceball

	* [r6848] doc/Future_Work/current_text.php:
	  Added task.

	* [r6847] /trunk/topographica-win/create_python_topo/setup.bat:
	  Updated to use bwidget 1.8.0 from 1.7.0

	* [r6846] topo/tkgui/topowidgets.py:
	  Simplified scrollbar code by switching to after_idle(); needs to
	  be tested on all platforms.

	* [r6845] topo/tkgui/plotgrouppanel.py:
	  Use sheet's closest_cell_center() method rather than separate
	  calls to sheet2matrixidx and matrixidx2sheet.

	* [r6844] topo/tkgui/plotgrouppanel.py:
	  Change format of unit coordinates in rf plot so they show up as
	  more than (0,0).

	* [r6843] topo/tkgui/projectionpanel.py:
	  Added ALERT.

	* [r6842] doc/Future_Work/current_text.php:
	  Updated some tasks.

	* [r6841] topo/base/simulation.py:
	  topo.sim.timer respects SomeTimer's step. SomeTimer's step
	  defaults to 2.

	* [r6840] topo/commands/analysis.py:
	  Fixed error in previous checkin.

	* [r6839] topo/commands/analysis.py:
	  Fixed mistake introduced to measure_rfs() in the previous
	  checkin. Updated measure_rfs_noise().

	* [r6838] topo/plotting/plotgroup.py:
	  Added RF Projection (noise).

	* [r6837] topo/tkgui/topoconsole.py:
	  Added RF Projection (noise).

	* [r6836] topo/analysis/featureresponses.py,
	  topo/base/cf.py,
	  topo/base/sheet.py,
	  topo/base/sheetview.py,
	  topo/commands/analysis.py,
	  topo/commands/pylabplots.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplot.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testsheet.py,
	  topo/tests/testsheetview.py,
	  topo/tests/testtemplateplotgrouppanel.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Renamed sheet_view_dict to sheet_views.

	* [r6835] topo/commands/analysis.py:
	  Added in sheet and input_sheet arguments to RFCOG code.
	  measure_rfcof() prints a warning if measure_rfs() hasn't been
	  called before (i.e. if the right views don't exist).

	* [r6834] topo/commands/analysis.py:
	  Added RF CoG plot code: doesn't seem to crash, but untested other
	  than that.

	* [r6833] topo/base/sheetcoords.py:
	  Fixed error in closest_cell_center().

	* [r6832] topo/plotting/plotgroup.py:
	  Minor cleanup of hierarchy.

	* [r6831] topo/tkgui/projectionpanel.py:
	  Moved situate code to CFProjectionPanel, since ProjectionPanel
	  could eventually be displaying projections for which situate
	  makes no sense.

	* [r6830] topo/base/sheetcoords.py:
	  Added convenience method.

	* [r6829] topo/plotting/plotgroup.py:
	  Fixed comment.

	* [r6828] topo/plotting/plotgroup.py:
	  Fixed error in scale_images() for any case where list of sheets
	  has been overridden (e.g. test pattern window). Added commenta
	  about the sheets attribute.

	* [r6827] topo/tkgui/testpattern.py:
	  Removed unused attribute.

	* [r6826] topo/plotting/plotgroup.py:
	  Minor cleanup.

	* [r6825] topo/tkgui/projectionpanel.py:
	  Minor cleanup: removed outdated alerts (and those covered
	  elsewhere). Cleaned up imports.

	* [r6824] topo/tests/testplotgrouppanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py:
	  Removed 'PG' from xPGPanel names.

2007-10-15  jbednar

	* [r6823] doc/shared/index.php:
	  Added link to RF plot description

	* [r6822] doc/User_Manual/plotting_text.php:
	  Added stub of RF description

	* [r6821] topo/tkgui/projectionpanel.py:
	  Added no_plot_note_text to RF Projection

	* [r6820] topo/tkgui/plotgrouppanel.py:
	  Mostly fixed RF matrixplot titles

	* [r6819] topo/tkgui/projectionpanel.py:
	  Fixed time formatting on various PlotGroup types

	* [r6818] topo/plotting/plotgroup.py:
	  Fixed bizarre bug in Sheet coordinates; was reusing a value from
	  a previous loop and thus getting incorrect scaling values

	* [r6817] doc/Future_Work/current_text.php:
	  Added task

	* [r6816] topo/tkgui/plotgrouppanel.py:
	  Changed integer_scaling and sheet_coords to simply scale without
	  redrawing, to avoid popping up pylab plots whenever those buttons
	  are pressed on e.g. CoG plots

	* [r6815] topo/commands/analysis.py:
	  Minor updates to comments and error checking

	* [r6814] topo/tkgui/projectionpanel.py:
	  Added RFProjectionPanel's missing density parameter

	* [r6813] topo/tkgui/projectionpanel.py:
	  Restored Projection plot's missing situate button

	* [r6812] topo/analysis/featureresponses.py:
	  Added selectivity_multiplier parameter to replace the magical
	  number 17

	* [r6811] doc/User_Manual/plotting_text.php:
	  Added note about how to change the selectivity scaling.

	* [r6810] doc/Downloads/index_text.php:
	  Added note about xvfb-run when there is no DISPLAY

2007-10-15  ceball

	* [r6809] topo/commands/pylabplots.py:
	  Added RFHACK marker.

	* [r6808] topo/tkgui/plotgrouppanel.py:
	  Made the right-click RF plot option reasonable for the moment.
	  (Not there for generator sheets, warns about input sheets that
	  are missing RF data (might want to lose these warnings, though.)

2007-10-15  jbednar

	* [r6807] topo/base/projection.py,
	  topo/base/simulation.py,
	  topo/eps/basic.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py:
	  Removed now-redundant explicit printing of the simulation time

	* [r6806] topo/misc/commandline.py:
	  Cleaned up time formatting

	* [r6805] doc/User_Manual/commandline_text.php,
	  doc/User_Manual/time_text.php:
	  Added documentation for min_print_level

	* [r6804] topo/base/parameterizedobject.py:
	  Only calls dbprint_prefix if it's callable; somewhat of a hack

2007-10-15  ceball

	* [r6803] doc/Future_Work/current_text.php:
	  Clarified scrollbars task.

	* [r6802] topo/commands/analysis.py:
	  Added to comment.

	* [r6801] topo/tkgui/plotgrouppanel.py:
	  Temporarily disabled RF plots.

	* [r6800] topo/tkgui/topoconsole.py:
	  Added RFProjectionPanel.

	* [r6799] topo/tkgui/projectionpanel.py:
	  Some improvement of hierarchy (not at all finished); added
	  RFProjectionPlotGroupPanel.

	* [r6798] topo/plotting/plotgroup.py:
	  More class reorganization (still not at all finished). Added
	  RFProjectionPlotGroup.

	* [r6797] topo/analysis/featureresponses.py,
	  topo/commands/analysis.py:
	  First pass at integrating reverse-correlation RF measurement:
	  removed topo.analysis.featureresponses.grid dictionary, instead
	  storing data in the input_sheet's sheet_view_dict.

2007-10-15  jbednar

	* [r6796] topo/base/parameterizedobject.py,
	  topo/base/simulation.py:
	  Added parameterizedobject.dbprint_prefix parameter to simplify
	  message printing of times, and to allow it to be first on each
	  printed line for readability

	* [r6795] topo/base/simulation.py,
	  topo/eps/basic.py,
	  topo/misc/commandline.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topowidgets.py:
	  Made messages and labels use Simulator.timestr() so that they
	  will be formatted consistently

	* [r6794] topo/tkgui/testpattern.py:
	  Removed unused import

	* [r6793] topo/misc/keyedlist.py:
	  Made keys of None work for [] accessing, fixing problem with
	  'make
	  slow-tests'. Moved integer indexing code from get() to
	  __getitem__,
	  because that's presumably how it would be used (as in list[4]).
	  Added
	  a print statement to find out if that code is ever called; it
	  doesn't
	  seem necessary.

2007-10-15  ceball

	* [r6792] topo/base/simulation.py:
	  Made CommandEvent warning messages more helpful.

2007-10-15  jbednar

	* [r6791] topo/base/simulation.py:
	  Fixed broken error message

2007-10-15  ceball

	* [r6790] topo/misc/keyedlist.py:
	  Added note.

2007-10-14  jbednar

	* [r6789] topo/plotting/plotfilesaver.py:
	  Fixed mistake in previous checkin

	* [r6788] topo/plotting/plotfilesaver.py:
	  Added ability to substitute plotgroup name into filenames

	* [r6787] topo/misc/commandline.py:
	  Added to-do list for batch saving

	* [r6786] topo/misc/keyedlist.py:
	  Fixed alert for [] access of nonexistent keys, though there may
	  still be an issue for get()

	* [r6785] topo/base/projection.py:
	  Raise exception if there's nothing by that name for
	  projections(name), to avoid silent errors

	* [r6784] topo/misc/commandline.py:
	  Fixed broken import. Made output file have the full filename
	  prefix

2007-10-13  jbednar

	* [r6783] topo/misc/filepaths.py:
	  Clarified docstrings

	* [r6782] topo/misc/filepaths.py:
	  Clarified docstrings

2007-10-13  ceball

	* [r6781] doc/User_Manual/commandline_text.php:
	  Updated 'Saving Topographica bitmaps' section.

	* [r6780] doc/User_Manual/batch_text.php:
	  Minor update.

	* [r6779] topo/base/parameterclasses.py,
	  topo/commands/basic.py,
	  topo/misc/commandline.py,
	  topo/misc/filepaths.py,
	  topo/patterns/audio.py,
	  topo/patterns/image.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/test_script.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/tkparameterizedobject.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/topowidgets.py:
	  Moved file path code to topo.misc.filepaths. Renamed
	  resolve_filename to resolve_path.

	* [r6778] topo/misc/commandline.py:
	  Capture stdout from run_batch. Catch errors in what run_batch
	  executes, and write them to the output file (warning at the
	  console). Also stores command used to start topographica.

	* [r6777] topo/commands/analysis.py,
	  topo/tests/testplotfilesaver.py:
	  Hid projection plotgroup's 'sheet knowledge duplication' from
	  users of save_plotgroup.

	* [r6776] topo/plotting/plotgroup.py:
	  Removed duplicate ALERT.

	* [r6775] topo/tkgui/plotgrouppanel.py:
	  Fixed ALERT.

	* [r6774] topo/tkgui/plotgrouppanel.py:
	  Answered question.

	* [r6773] topo/commands/analysis.py:
	  Added to ALERT.

	* [r6772] doc/User_Manual/publishing_text.php:
	  Minor change to text. Removed ALERT.

2007-10-12  jbednar

	* [r6771] topo/plotting/plotfilesaver.py:
	  Fixed bug in previous checkin

	* [r6770] topo/commands/analysis.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Made Plotgroup.filesaver be an instance instead of a class

	* [r6769] topo/plotting/plotfilesaver.py:
	  Added **params to save_to_disk

	* [r6768] doc/Future_Work/index_text.php:
	  Updated to match current plans

	* [r6767] doc/shared/index.php:
	  Added new feature

	* [r6766] doc/Future_Work/current_text.php:
	  Removed completed task

	* [r6765] doc/User_Manual/publishing_text.php:
	  Updated for save_plotgroup and Save as PNG

	* [r6764] topo/commands/basic.py:
	  Changed default script_repr filename to be clearer

	* [r6763] topo/tkgui/editorwindow.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Cleaned up normalize_path usage so that the initial directory and
	  initial filename are set separately, which works more cleanly
	  with the GUI

	* [r6762] topo/base/parameterclasses.py:
	  Added default for normalize_path's path argument, to allow it to
	  simply return the current output directory

	* [r6761] topo/tkgui/templateplotgrouppanel.py:
	  Added Save image as PNG option

	* [r6760] topo/tkgui/plotgrouppanel.py:
	  Added question

	* [r6759] topo/tkgui/templateplotgrouppanel.py:
	  Added appropriate initial value for the filename for
	  right-clicking and saving as EPS

	* [r6758] topo/plotting/plotfilesaver.py:
	  Made filename() accept parameters to allow values to be
	  overridden temporarily

	* [r6757] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py:
	  Added label method to Plot to ensure that it is generated
	  consistently

	* [r6756] topo/plotting/plotfilesaver.py:
	  Removed plotsaving_classes

	* [r6755] topo/commands/analysis.py:
	  Removed dependence on plotsaving_classes

	* [r6754] topo/plotting/plotgroup.py:
	  Added filesaver attribute, to eliminate plotsaving_classes

	* [r6753] topo/tests/testplotfilesaver.py:
	  Removed unused import

2007-10-12  ceball

	* [r6752] topo/tkgui/topowidgets.py:
	  Previous checkin was an error: commented out code line by
	  mistake, and note was meant to refer to after_idle().

	* [r6751] topo/tkgui/topowidgets.py:
	  Added a note.

2007-10-12  jbednar

	* [r6750] topo/plotting/plotfilesaver.py:
	  Removed unused imports

2007-10-12  ceball

	* [r6749] doc/Future_Work/current_text.php:
	  Indicated some tasks I'll do.

2007-10-12  jbednar

	* [r6748] topo/tkgui/editorwindow.py:
	  Added missing normalize_path()

	* [r6747] topo/tkgui/editorwindow.py:
	  Added default for the model editor .ps file name.

2007-10-12  ceball

	* [r6746] topo/tkgui/topowidgets.py:
	  Improved scrollbar behavior now we can turn them on and off
	  ourselves: should be no stray bars.

2007-10-12  jbednar

	* [r6745] topo/tkgui/templateplotgrouppanel.py:
	  Added temporary guess for .ps filenames; can do better later

	* [r6744] topo/plotting/plotfilesaver.py:
	  Added docstring; minor reformatting

	* [r6743] topo/tkgui/topoconsole.py:
	  Made GUI default for script_repr and save_snapshot filenames use
	  the basename() instead of just the name.

	* [r6742] topo/commands/basic.py,
	  topo/misc/commandline.py:
	  Added default value for saved file names

	* [r6741] topo/base/simulation.py,
	  topo/plotting/plotfilesaver.py:
	  Added timestr(), basename(), time_printing_format, and
	  basename_format to standardize naming and printing, and allow the
	  user to override them

	* [r6740] topo/misc/commandline.py:
	  Removed : from run_batch filename to avoid problems on Windows

2007-10-12  ceball

	* [r6739] external,
	  external/.cvsignore:
	  Upgraded to BWidget 1.8.0.

	* [r6738] topo/tkgui/topowidgets.py:
	  After upgrading to BWidget 1.8.0, we can now manually turn on and
	  turn off the scrollbars. Also revert to previous size hack of 19.
	  (Intermediate checkin.)

	* [r6737] external/Makefile:
	  Upgraded pybwidget's BWidgets to 1.8.0.

	* [r6736]
	  external/pybwidget-0.1.2_1.8.0.tar.gz:
	  pybwidget-0.1.2, but with BWidget 1.8.0.

	* [r6735] topo/misc/commandline.py:
	  Minor change to text, and added an ALERT.

	* [r6734] topo/misc/keyedlist.py:
	  Added ALERT.

	* [r6733] topo/commands/analysis.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplotfilesaver.py:
	  Simplified PlotGroupSaver: removed generate_plotgroup() method.

	* [r6732] topo/tests,
	  topo/tests/.cvsignore:
	  Removed files that should no longer be present.

	* [r6731]
	  topo/tests/test_commands_analysis.txt:
	  Duplicates tests in testplotgroupsaver.py.

2007-10-11  jbednar

	* [r6730] doc/Future_Work/current_text.php:
	  Added publishing page task. Removed scheduled actions task.

	* [r6729] doc/User_Manual,
	  doc/User_Manual/.cvsignore,
	  doc/User_Manual/batch_text.php:
	  Added documentation for batch mode

	* [r6728] doc/User_Manual/index_text.php,
	  doc/shared/index.php:
	  Added documentation for batch mode

	* [r6727] topo/misc/commandline.py:
	  Removed trailing comma from options list

	* [r6726] topo/misc/commandline.py:
	  Renamed recording_times to analysis_times for clarity. Added
	  printing
	  of progress at each analysis_time.

	* [r6725] topo/misc/commandline.py:
	  Cleaned up run_batch and added time and date printing, simplified
	  simulation name, and more consistent usage of prefix

	* [r6724] topo/tests,
	  topo/tests/.cvsignore:
	  Fixed missing newline

2007-10-11  antolikjan

	* [r6723] topo/base/parameterclasses.py:
	  normalize_path now uses the output_path as a prefix unless it is
	  specified in the arguments

	* [r6722] topo/misc/commandline.py:
	  The run_batch function was completely rewritten, number of small
	  bugs corrected. The main change is that now it uses the
	  normalized_path interface to control the location where the
	  output of the simulation is being saved

	* [r6721] topo/commands/basic.py,
	  topo/plotting/plotfilesaver.py:
	  save routines in this now use normalize_path to obtain the final
	  path to which they save data

	* [r6720] topo/base/parameterclasses.py:
	  normalize_path now uses the output_path as a prefix unless it is
	  specified in the arguments

2007-10-11  jbednar

	* [r6719] doc/User_Manual/plotting_text.php:
	  Updated for Subplotting.set_subplots().

2007-10-11  ceball

	* [r6718] topo/tests,
	  topo/tests/.cvsignore:
	  Ignore more test images.

	* [r6717] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Removed unused attribute plotgroup_type.

	* [r6716]
	  topo/tests/test_commands_analysis.txt:
	  Initial version.

	* [r6715] topo/tests/testplotfilesaver.py:
	  Test that plots are actually written to disk.

	* [r6714] doc/Future_Work/current_text.php:
	  Update to scrollbars task.

	* [r6713] topo/tkgui/topowidgets.py:
	  Altered hack timing and sizes.

	* [r6712] topo/tkgui/topowidgets.py:
	  Distinguish x and y for scrollbar hacks.

	* [r6711] topo/tkgui/widgets.py:
	  Removed useless instruction.

	* [r6710] topo/tkgui/topowidgets.py:
	  When user resizes window, doesn't then automatically jump back to
	  ideal size straightaway.

	* [r6709] topo/tkgui/topowidgets.py:
	  Finally found how to determine if the scrollbars are really
	  needed, and to fake a click on the scrollbar. Scrollbars no
	  longer hang around on linux when not required. Need to check OS X
	  and Windows still work ok.

	* [r6708] topo/tests/testplotgrouppanel.py:
	  Don't start the gui unless there's a display. All subject to an
	  ALERT.

	* [r6707] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topowidgets.py:
	  Renamed ScrolledTkguiWindow.content.window_title() to title() so
	  that it matches Toplevel.

	* [r6706] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/topowidgets.py:
	  ScrolledTkguiWindow handles its own resizing.

2007-10-10  jbednar

	* [r6705] topo/base/parameterclasses.py:
	  Added alert

	* [r6704] topo/tkgui/topoconsole.py:
	  Display a message while waiting for a snapshot to save

	* [r6703] topo/commands/analysis.py:
	  Added OR subplot for measure_sf_pref as well

	* [r6702] examples/lissom_whisker_barrels.ty:
	  Updated to use Subplotting class

	* [r6701] topo/commands/analysis.py:
	  Added better handling of subplots; now just do
	  Subplotting.set_subplots('Direction') to set DirectionPreference
	  and DirectionSelectivity as the Hue and Confidence subplots for
	  most plots

	* [r6700] topo/coordmapperfns/basic.py:
	  Trivial space fix

	* [r6699] topo/base/parameterclasses.py:
	  Added output_path attribute, to allow the default to be changed
	  away
	  from application_path.

	* [r6698] topo/misc/commandline.py:
	  Added check for errors during startup -- skips command-line
	  arguments in that case

	* [r6697] examples/lissom_whisker_barrels.ty:
	  Updated now that plotgroup_templates is gone

	* [r6696] examples/Makefile:
	  Added sample command for lissom_whisker_barrels

	* [r6695] topo/base/parameterclasses.py:
	  Moved Filename to the end by its supporting functions

2007-10-10  ceball

	* [r6694] doc/Future_Work/current_text.php:
	  Removed bogus task.

	* [r6693] doc/User_Manual/publishing_text.php:
	  Added ALERT.

	* [r6692] doc/Future_Work/current_text.php:
	  Removed task. Also delayed windows testing problem task to after
	  0.9.4.

	* [r6691] doc/Developer_Manual/coding_text.php:
	  Added info about accessing files.

	* [r6690] topo/tkgui/testpattern.py:
	  make_plots() renamed to refresh_plots().

	* [r6689] doc/Future_Work/current_text.php:
	  Updates to tasks.

	* [r6688] topo/base/simulation.py:
	  Upgraded ALERT, since it could cause confusion.

	* [r6687] topo/tkgui/plotgrouppanel.py:
	  Connection Fields/Receptive Field in right-click unit menu
	  automatically enabled and disabled as appropriate.

	* [r6686] topo/tkgui/widgets.py:
	  Altered ALERT.

	* [r6685] topo/tkgui/widgets.py:
	  Altered ALERT.

2007-10-09  jbednar

	* [r6684] doc/Downloads/index_text.php:
	  Added note about Tcl/Tk on Mac

2007-10-09  ceball

	* [r6683] topo/tests/testparametersframe.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Search and replace: ParametersFrame->ParametersFrameWithApply,
	  LiveParametersFrame->ParametersFrame. (Documentation yet to be
	  checked and updated; it doesn't really exist yet anyway.)

	* [r6682] topo/tests/testplotfilesaver.py:
	  Removed unnecessary cmd_locations from PlotGroup.

	* [r6681] doc/Future_Work/current_text.php:
	  Removed two tasks and added one.

	* [r6680] topo/analysis/featureresponses.py,
	  topo/base/sheetview.py:
	  Added info to note.

	* [r6679] topo/tkgui/plotgrouppanel.py:
	  Added minor note.

	* [r6678] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py:
	  Made 'no plot note' text slightly less ugly.

	* [r6677] topo/plotting/plotgroup.py:
	  Removed documentation that's not useful.

	* [r6676] topo/plotting/plotgroup.py:
	  Removed unnecessary cmd_locations from PlotGroup.

	* [r6675] topo/plotting/plotgroup.py:
	  No visible changes: simple cleanup.

	* [r6674] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Removed plotgroup's redraw_plots because it's unnecessary.

	* [r6673] topo/plotting/plotgroup.py:
	  Added ALERT. Minor change to doc.

	* [r6672] topo/tkgui/templateplotgrouppanel.py:
	  Updated ALERT text.

	* [r6671] topo/tkgui/plotgrouppanel.py:
	  Normalize should only redraw the plots, not refresh them.

	* [r6670] doc/Future_Work/current_text.php:
	  More to do.

	* [r6669] doc/Future_Work/current_text.php:
	  Added to task.

	* [r6668] topo/tests/test_script.py:
	  Do not use resolve_filename() to create a path - use
	  normalize_path(). (Should fix make slow-tests bug.)

	* [r6667] topo/base/parameterclasses.py:
	  Added normalize_path(), and added some clarifications to
	  resolve_path().

	* [r6666] topo/base/parameterclasses.py:
	  Moved path-related code to the end of the file.

	* [r6665] topo/base/parameterclasses.py:
	  Renamed app_base_path to application_path.

	* [r6664] topo/plotting/plotgroup.py,
	  topo/tests/test_script.py,
	  topo/tkgui/tkparameterizedobject.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/topowidgets.py:
	  Renamed abs_app_path() to resolve_filename().

	* [r6663] topo/tkgui/topoconsole.py:
	  Revert previous version, but adding documentation for method.

	* [r6662] topo/tkgui/templateplotgrouppanel.py:
	  Give cyclic information to gradient plot.

	* [r6661] topo/base/sheetview.py:
	  Added cyclic and norm_factor parameters to SheetView.

	* [r6660] topo/analysis/featureresponses.py:
	  Store cyclic information with SheetView.

	* [r6659] doc/Future_Work/current_text.php:
	  Added task.

	* [r6658] topo/tkgui/topoconsole.py:
	  Removed unused method.

	* [r6657] topo/tkgui/topowidgets.py:
	  Fix bug in ProgressWindow where default argument was assumed to
	  be fresh each time, when in fact it remains the original value.

	* [r6656] topo/plotting/plotgroup.py:
	  Removed part of ALERT (same alert's in analysis.py).

2007-10-08  jbednar

	* [r6655] doc/Makefile:
	  Skipped removing the reference manual so that it will be in the
	  distribution

	* [r6654] Makefile:
	  Removed mistaken change

	* [r6653] Makefile,
	  examples/README.txt:
	  Keep direction map in release; document lissom_photo and
	  lissom_whisker

	* [r6652] external/Makefile:
	  More to clean

	* [r6651]
	  topo/plotting/default_plottingscript.py:
	  Removed; needs to be put somewhere else

	* [r6650] README.txt:
	  Updated to clarify that docs don't need to be built for released
	  versions

	* [r6649] topo/__init__.py:
	  Added coordmapperfns to docs and __all__

	* [r6648] doc/Downloads/index_text.php:
	  Updated hard-coded dates

	* [r6647] README.txt:
	  Updated requirements for making docs

	* [r6646]
	  doc/Developer_Manual/releases_text.php:
	  Added additional task

	* [r6645] /trunk/topographica-win/common/setup.py,
	  /trunk/topographica-win/create_installer/topographica.iss,
	  Makefile:
	  Updated version number in anticipation of 0.9.4 release

	* [r6644] doc/shared/index.php:
	  Fixed typos in new news; reorganized

	* [r6643] topo/coordmapperfns/__init__.py:
	  Fixed typos

	* [r6642] doc/Home/oldnews_text.php,
	  doc/shared/index.php:
	  Added preliminary news for the 0.9.4 release

	* [r6641] doc/User_Manual/parameters_text.php,
	  doc/User_Manual/patterns_text.php:
	  Fixed broken link

	* [r6640] doc/User_Manual/commandline_text.php:
	  Added link targets

	* [r6639] ChangeLog.txt:
	  Updated with changes since 0.9.3

	* [r6638] doc/Future_Work/current_text.php:
	  Updated task

2007-10-08  ceball

	* [r6637] topo/base/parameterclasses.py:
	  Filename warns if filename can't be found on __set__().

2007-10-08  jbednar

	* [r6636] topo/commands/pylabplots.py:
	  Clarified authorship

2007-10-08  ceball

	* [r6635] doc/Future_Work/current_text.php:
	  Added task.

	* [r6634] doc/Future_Work/current_text.php:
	  Updates to my tasks.

	* [r6633] topo/tests/test_script.py:
	  Use abs_app_path on filenames (for running these commands on
	  Windows).

	* [r6632] topo/tkgui/__init__.py:
	  Fixed typos. (I thought this fix had been committed weeks ago?).

	* [r6631] topo/tkgui/topowidgets.py:
	  Added missing import.

	* [r6630] topo/tkgui/widgets.py:
	  Fixed imports.

	* [r6629] topo/tkgui/topoconsole.py:
	  Added missing import.

	* [r6628] Makefile:
	  Added test of command prompt to basic-gui-tests.

2007-10-07  ceball

	* [r6627] topo/tkgui/topowidgets.py:
	  Minor cleanup to TkguiWindow.

	* [r6626] topo/base/parameterclasses.py:
	  Remove Filename's requirement that a path is valid on __set__().

	* [r6625] topo/tkgui/parametersframe.py:
	  Update method name to match change to tkparameterizedobject.

	* [r6624] topo/tkgui/tkparameterizedobject.py:
	  Cleanup (mainly to documentation, but also to order methods are
	  written in the file, and some _/__ changes) - should be no
	  visible change.

	* [r6623] doc/User_Manual/plotting_text.php,
	  examples/lissom_whisker_barrels.ty,
	  topo/commands/analysis.py,
	  topo/plotting/plotgroup.py:
	  Renamed new_pg() to create_plotgroup().

2007-10-06  ceball

	* [r6622] topo/misc/utils.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Moved inverse() from topo.tkgui.tkparameterizedobject to
	  topo.misc.utils.

	* [r6621] topo/tkgui/tkparameterizedobject.py:
	  Improved looking up key by value from a dictionary.

	* [r6620] doc/Future_Work/current_text.php,
	  topo/base/parameterclasses.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Cleaned up SelectorParameters.

	* [r6619] doc/Future_Work/current_text.php:
	  Removed task.

	* [r6618] topo/commands/basic.py:
	  Removed hack that's no longer necessary (Filename parameter now
	  returns the correct path (i.e. the path corrected for platform
	  and to be absolute) on __get__()).

	* [r6617] topo/tkgui/topoconsole.py:
	  Fixed previous commit so that help menu items work if local
	  documentation not already built.

	* [r6616] doc/Future_Work/current_text.php:
	  Added a task.

	* [r6615] topo/tkgui/topoconsole.py:
	  Cleanup: no visible changes.

	* [r6614] doc/Future_Work/current_text.php:
	  Removed file path task.

	* [r6613] topo/base/parameterclasses.py:
	  Cleanup to comment.

	* [r6612] topo/commands/analysis.py:
	  Reverted to version 1.109 after update to TemplatePlotGroup so
	  that it handles any necessary filepath correction.

	* [r6611] topo/plotting/plotgroup.py,
	  topo/tkgui/tkparameterizedobject.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/topowidgets.py:
	  Use abs_app_path.

	* [r6610] topo/misc/commandline.py:
	  Minor syntax adjustment.

	* [r6609] topo/base/parameterclasses.py:
	  Added abs_app_path(), which used to be __construct_path() in
	  Filename parameter. Filename parameter now uses abs_app_path().
	  Change to Filename parameter is that it now produces the correct
	  path on __get__(), allowing parameters where the paths were
	  created on Windows to be transferred to linux (in a snapshot).
	  This means calling abs_app_path() more often (every __get__())
	  instead of just on __set__().

2007-10-05  jprovost

	* [r6608] topo/sheets/saccade.py:
	  Fixed some problems with fixation jitter in
	  ShiftingGeneratorSheet.

	* [r6607] topo/misc/commandline.py:
	  Caught exceptions in startup files, so topographica will still
	  start.

	* [r6606] topo/commands/analysis.py:
	  Fixed relative paths problem.

2007-10-05  ceball

	* [r6605] topo/tests/testplotgrouppanel.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/tkguiwindow.py,
	  topo/tkgui/tkparameterizedobject.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/topowidgets.py,
	  topo/tkgui/widgets.py:
	  Some reorganization of tkgui classes; should be no visible
	  changes.

2007-10-05  jbednar

	* [r6604] topo/plotting/plotgroup.py:
	  Clarified docstring

2007-10-05  ceball

	* [r6603] topo/tkgui/plotgrouppanel.py:
	  Started to move things into more appropriate classes in the
	  PlotGroupPanel hierarchy.

	* [r6602] topo/tkgui/projectionpanel.py:
	  Don't display dynamic info for connection fields plot (dynamic
	  info not yet setup to handle projection plots). Removed separate
	  alerts about the same thing: see task in current task list.

	* [r6601] topo/tkgui/plotgrouppanel.py:
	  Added to window_master hack (it will all be removed eventually).

	* [r6600] topo/tests/testplotgrouppanel.py:
	  Started to implement tests for the new panel classes.

	* [r6599] doc/Future_Work/current_text.php:
	  Updated dynamic info task (probably will not implement dynamic
	  info for projection panels until after 0.9.4.

2007-10-04  jbednar

	* [r6598] doc/User_Manual/plotting_text.php:
	  Updated now that plotgroup_templates has disappeared; still needs
	  checking

	* [r6597] topo/commands/analysis.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Moved auto_refresh parameter up to the PlotGroup level to allow
	  it to be specified individually per PlotGroup type

2007-10-04  ceball

	* [r6596] doc/Future_Work/current_text.php,
	  topo/plotting/plotgroup.py:
	  Fixed mistake in ProjectionActivityPlotGroup (introduced at some
	  point during earlier cleanup).

	* [r6595] doc/Future_Work/current_text.php:
	  Added a task.

	* [r6594] doc/Future_Work/current_text.php:
	  Added a task.

	* [r6593] topo/base/parameterizedobject.py:
	  Minor corrections to docstring text.

2007-10-03  jbednar

	* [r6592] doc/User_Manual/commandline_text.php:
	  Minor fix to example, to use Numeric instead of numpy

	* [r6591] doc/User_Manual/commandline_text.php,
	  topo/commands/pylabplots.py:
	  Minor updates to text

	* [r6590] topo/commands/pylabplots.py:
	  Added workaround to allow empty bitmap plots

	* [r6589] topo/commands/pylabplots.py:
	  Enabled color bars by default for matrixplot

	* [r6588] topo/tkgui/templateplotgrouppanel.py:
	  Added 3D wireframe plots to right-click menu

	* [r6587] doc/Reference_Manual/index_text.php,
	  doc/User_Manual/commandline_text.php,
	  doc/User_Manual/images/matrixplot3d_matplotlib.png,
	  topo/commands/pylabplots.py:
	  Reimplemented matrixplot3d using undocumented matplotlib calls;
	  gnuplot implementation moved to matrixplot3d_gnuplot

	* [r6586] topo/tkgui/templateplotgrouppanel.py:
	  Removed duplication in right-click menu implementation

2007-10-03  ceball

	* [r6585] topo/tkgui/tkparameterizedobject.py:
	  Only add text if there's no image (otherwise text and image could
	  appear on some platforms).

	* [r6584] doc/Future_Work/current_text.php:
	  Updated my task organization.

	* [r6583] topo/plotting/plotgroup.py:
	  Indicated tasks to complete for 0.9.4.

	* [r6582] topo/tkgui/projectionpanel.py:
	  Removed stray comment.

	* [r6581] topo/plotting/plotgroup.py:
	  Collected some of the general ALERTs together.

	* [r6580] examples/hierarchical.ty:
	  Minor cleanup, and added commented-out code for a new projection
	  that's not a CFProjection.

	* [r6579] topo/tkgui/projectionpanel.py:
	  Added missing super() call (projection panel was not updating
	  when changing sheet).

	* [r6578] topo/plotting/plotgroup.py,
	  topo/plotting/templates.py:
	  More cleanup of TemplatePlotGroup, including moving in slightly
	  modified documentation from templates.py.

	* [r6577] topo/tkgui/__init__.py:
	  Added note to myself.

	* [r6576] doc/User_Manual/space_text.php:
	  Minor correction to text.

	* [r6575] doc/Future_Work/current_text.php:
	  Updates to my tasks.

	* [r6574] doc/Developer_Manual/gui_text.php:
	  Began adding section about programming with tkgui.

2007-10-02  jbednar

	* [r6573] external,
	  external/.cvsignore:
	  More to ignore

	* [r6572] doc/Reference_Manual/index_text.php,
	  doc/User_Manual/commandline_text.php:
	  Added mention of matrixplot3d

	* [r6571]
	  doc/User_Manual/images/matrixplot3d.png:
	  Added example 3D plot

	* [r6570] topo/commands/pylabplots.py:
	  Added note

	* [r6569] topo/commands/pylabplots.py:
	  Added matrixplot3d command

	* [r6568] external/gnuplot-py-1.7.tar.gz:
	  Version 1.7 from gnuplot-py.sourceforge.net

	* [r6567] external/Makefile:
	  Reverted to version 1.77; discovered workaround for gnuplot-py

	* [r6566] external/Makefile:
	  Reverted to version 1.76; gnuplot-py too buggy to use (converts
	  2D arrays to integers before plotting)

2007-10-02  ceball

	* [r6565] topo/tkgui/topoconsole.py:
	  Changed ProgressWindow's 'Remaining /s' to 'Remaining time'.

	* [r6564] topo/commands/analysis.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/topoconsole.py:
	  template_plot_type is not a Parameter of TemplatePlotGroup (but
	  is an argument ofnew_pg() ).

	* [r6563] topo/base/parameterclasses.py,
	  topo/tests/testparametersframe.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py:
	  Renamed ObjectSelectorParameter's 'Arange' attribute to
	  'objects'. (Also added checking that the value is within the
	  range.)

2007-10-02  jbednar

	* [r6562] external/Makefile:
	  Added optional gnuplot-py

2007-10-01  ceball

	* [r6561] topo/base/parameterclasses.py:
	  Began cleanup of SelectorParameters. Should be no effect on code
	  currently using SelectorParameters (ClassSelectorParameter now
	  checks its default value).

	* [r6560] topo/tkgui/parametersframe.py,
	  topo/tkgui/tkguiwindow.py,
	  topo/tkgui/tkparameterizedobject.py,
	  topo/tkgui/topoconsole.py:
	  Updates to documentation.

	* [r6559] topo/tkgui/plotgrouppanel.py:
	  Cleanup (should be no visible change).

	* [r6558] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py:
	  Cleanup of PlotGroupPanel: require a plotgroup to be specified;
	  simplified generate_plotgroup() and renamed to setup_plotgroup().

	* [r6557] topo/tkgui/plotgrouppanel.py:
	  Some cleanup of code formatting.

	* [r6556] topo/base/simulation.py:
	  Really minor cleanup of SomeTimer.

	* [r6555] doc/Future_Work/current_text.php:
	  Updates to my tasks.

	* [r6554] topo/tkgui/tkguiwindow.py:
	  Removed print statement accidentally left behind.

	* [r6553] topo/tkgui/tkguiwindow.py:
	  Hack to get the size for scrollbars, since the current
	  calculation works on Windows but not linux.

	* [r6552] topo/tkgui/tkguiwindow.py:
	  Scrolled frame's relief returned to flat.

	* [r6551] topo/tkgui/__init__.py:
	  Added note for myself.

	* [r6550] doc/Future_Work/current_text.php:
	  Updated my tasks + minor formatting change to icons task.

	* [r6549] topo/tkgui/topoconsole.py:
	  Closing ProgressWindow same as clicking stop.

	* [r6548] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/tkguiwindow.py,
	  topo/tkgui/topoconsole.py:
	  ResizableScrollableFrame moved from plotgrouppanel.py to
	  tkguiwindow.py. Rather than scrolling only plot frames, whole
	  windows now have scrollbars.

2007-09-29  ceball

	* [r6547] topo/tkgui/topoconsole.py:
	  Added more info to console when progress completed.

	* [r6546] topo/base/simulation.py:
	  Fixed error in previous checkin.

	* [r6545] topo/base/simulation.py:
	  Simplified timer object (now only one method for passing out
	  timing information).

	* [r6544] topo/analysis/featureresponses.py:
	  Open a progress window for map measurement if there's a gui.

	* [r6543] topo/tkgui/topoconsole.py:
	  Progress reporting all handled in progress window. ProgressWindow
	  supports any specified timer.

	* [r6542] topo/commands/basic.py:
	  Removed hack that's no longer necessary.

	* [r6541] topo/tkgui/topoconsole.py:
	  Moved progress window code into a new class. Try out Stop button
	  on the progress window rather than on the console.

	* [r6540] topo/base/simulation.py:
	  Added timing message for interruption.

	* [r6539] doc/Future_Work/current_text.php:
	  Fixed errors when asking for CFs of a sheet that doesn't have
	  any, but still need a more general solution. This task is now
	  less urgent (moved to after 0.9.4 release).

	* [r6538] topo/tkgui/plotgrouppanel.py:
	  Just warn if a connection fields plot is requested for a sheet
	  that doesn't have connection fields. (Also removed outdated part
	  of a comment.)

	* [r6537] topo/plotting/plotgroup.py:
	  Changed wrong sheet type/wrong projection type assertion errors
	  to TypeErrors.

	* [r6536] topo/tkgui/templateplotgrouppanel.py:
	  Removed outdated ALERT.

	* [r6535] doc/Future_Work/current_text.php:
	  Removed gui option menu sorting task.

	* [r6534] topo/tkgui/testpattern.py:
	  Removed commented-out code. Minor change to code formatting.

	* [r6533] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Added sorting options to widget_options (for SelectorParameters).

2007-09-28  jbednar

	* [r6532] examples/Makefile:
	  Fixed obermayer duration; added goodhill target

	* [r6531] examples/goodhill_network90.ty:
	  Updated now that plotgroup_templates has been eliminated

2007-09-28  ceball

	* [r6530] doc/Future_Work/current_text.php:
	  Removed some tasks that have already been finished.

2007-09-27  jbednar

	* [r6529] doc/Future_Work/current_text.php:
	  Prioritized tkgui tasks

	* [r6528] doc/Future_Work/current_text.php:
	  Prioritized tasks for upcoming release

2007-09-26  jbednar

	* [r6527] topo/plotting/plotgroup.py:
	  Fixed static images (like color keys); had been broken since
	  switch away from plot templates

	* [r6526] external/Makefile:
	  Minor fix to bluesphere

2007-09-25  ceball

	* [r6525] doc/buildbot/master.cfg:
	  Add sake (ppc_darwin8.10.0) + change to externally available port
	  + cleanup.

	* [r6524] doc/buildbot/doozy-buildbot.tac:
	  Initial version of doozy's buildslave configuration.

	* [r6523] topo/tkgui/__init__.py:
	  Hack to set topo.entry_background with the appropriate color
	  depending on the system.

	* [r6522] topo/tkgui/tkparameterizedobject.py:
	  Hack to set topo.entry_background with the appropriate color
	  depending on the system.

	* [r6521] topo/tkgui/testpattern.py:
	  Removed PlotGroupTemplate.

	* [r6520] topo/tkgui/tkparameterizedobject.py:
	  Set Button relief to FLAT when it's displaying and image.

	* [r6519] topo/tkgui/tkparameterizedobject.py:
	  Corrected mistake in previous commit.

	* [r6518] topo/tkgui/tkparameterizedobject.py:
	  Added temporary fix for systems where there are no button images.

2007-09-24  jbednar

	* [r6517] doc/Future_Work/current_text.php:
	  Updated the icons task

	* [r6516] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py:
	  Updated comments about the Refresh button

	* [r6515] external,
	  external/.cvsignore:
	  More to ignore

	* [r6514] topo/tkgui/icons/back-2.0.png,
	  topo/tkgui/icons/forward-2.0.png,
	  topo/tkgui/icons/redo-small.png,
	  topo/tkgui/icons/viewmag+_2.2.png,
	  topo/tkgui/icons/viewmag-_2.1.png:
	  20x20 versions created by make -C external bluesphere; edit
	  external/BlueSphere*_Makefile and rerun to change the size or
	  choice of icons

	* [r6513] topo/tkgui/plotgrouppanel.py:
	  Changed PlotGroupPanel to use icons for common buttons

	* [r6512]
	  external/BlueSphere-SVG-snapshot-Nov-29-2002.tar.gz,
	  external/BlueSphere-SVG-snapshot-Nov-29-2002_Makefile,
	  external/Makefile:
	  Added bluesphere icons for use with the Tk GUI

	* [r6511] topo/tkgui/icons,
	  topo/tkgui/icons/topo.xbm,
	  topo/tkgui/icons/topo.xpm,
	  topo/tkgui/tkguiwindow.py,
	  topo/tkgui/topo.xbm,
	  topo/tkgui/topo.xpm:
	  Moved topo.xbm and topo.xpm into an icons/ subdirectory

2007-09-24  ceball

	* [r6510] examples/lissom_whisker_barrels.ty,
	  topo/plotting/__init__.py,
	  topo/plotting/plotfilesaver.py,
	  topo/tests/testplotgroup.py,
	  topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Removed PlotGroupTemplate.

	* [r6509] topo/tkgui/templateplotgrouppanel.py:
	  Removed PlotGroupTemplate. Fixed strength-only button (ugly, but
	  it seems to work...).

	* [r6508] topo/tkgui/projectionpanel.py:
	  (Multiple changes) (1) Removed PlotGroupTemplate. (2) Removed
	  CFPGPanel; situate button code copied into classes that need it.

	* [r6507] topo/plotting/templates.py:
	  Commented out all code. Features moved to TemplatePlotGroup (but
	  need to adapt documentation).

	* [r6506] topo/plotting/plotgroup.py:
	  (Multiple changes) (1) Some tidying of PlotGroup classes (removed
	  some code duplication, began to modify to the hierarchy of
	  classes). (2) Removed PlotGroupTemplate: TemplatePlotGroup gets
	  PlotGroupTemplate's Parameters and methods, with minor
	  modifications.

	* [r6505] topo/commands/analysis.py:
	  Removed PlotGroupTemplate: new_pgt() is replaced with new_pg().

2007-09-23  ceball

	* [r6504] topo/tkgui/tkparameterizedobject.py:
	  Removed worst part of Entry background hack: Tkinter has
	  'systemWindowBody' background color.

	* [r6503] topo/tkgui/__init__.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Moved entry background color hack back to tkparameterizedobject
	  from __init__. Now the tests pass ok. There is a mysterious
	  import problem somewhere in tkgui (as noted in tkguiwindow.py).

2007-09-22  ceball

	* [r6502] doc/User_Manual/modeleditor_text.php:
	  Updated some text in ParametersFrame section.

	* [r6501] doc/User_Manual/commandline_text.php:
	  Added example of edit_parameters().

	* [r6500] doc/User_Manual/modeleditor_text.php:
	  Corrected anchor.

	* [r6499] topo/tkgui/tkparameterizedobject.py:
	  Updated comments related to ButtonParameter image size: presuming
	  different units for the button size depending on whether it's
	  showing text or an image is a Tkinter feature.

	* [r6498] topo/tkgui/tkparameterizedobject.py:
	  Change ButtonParameter to use size rather than image_size. Sizing
	  of ButtonParameters is not quite finished yet.

	* [r6497] topo/tkgui/tkparameterizedobject.py:
	  Added image support to ButtonParameter.

	* [r6496] topo/tkgui/__init__.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Made the entry highlighting hack at least blend in with the
	  background color.

	* [r6495] topo/tkgui/parametersframe.py:
	  Fixed bug where an old method name was not being overidden in a
	  subclass. Need to update all these old names in callers, once the
	  names are cleaned up. Removed some commented-out code.

	* [r6494] topo/base/parameterizedobject.py:
	  When instantiating a Parameter, if that Parameter is a PO, make
	  it uninitialized while a new name is set.

	* [r6493] topo/base/simulation.py:
	  Made EventProcessor's name be constant.

	* [r6492] topo/tests/testparametersframe.py:
	  Updates to match name changes in ParametersFrame.

	* [r6491] topo/tkgui/parametersframe.py:
	  Cleanup of some names.

	* [r6490] topo/tkgui/tkparameterizedobject.py:
	  (Multiple changes.) (1) Fixed bug (line 1087) where, on opening
	  the model editor or test pattern window, there was an error about
	  attempting to set a CallableParameter to a string. (2) Added
	  get_source_po() method to allow simplification of several others.
	  (3) Returned repr to the previous simple version, since the new
	  one still does not work properly.

2007-09-21  ceball

	* [r6489] topo/tkgui/testpattern.py:
	  Hide the Refresh button, since it's extremely unlikely anyone
	  will be editing the PatternGenerator on the commandline.

	* [r6488] topo/tkgui/parametersframe.py:
	  Corrected mistake with set_PO() method present in
	  LiveParametersFrame and ParametersFrame.

	* [r6487] topo/base/parameterclasses.py:
	  Added a basic repr method to InstanceMethodWrapper.

	* [r6486] doc/User_Manual/commandline_text.php:
	  Minor update to text.

	* [r6485] topo/tkgui/tkparameterizedobject.py:
	  Cleaned up ButtonParameter handling. Now the command of a button
	  of x named 'Button' can be invoked as x.Button(). Made a
	  reasonable (but not perfect) repr method. hide_param() and
	  unhide_param() just do nothing if the parameter is already hidden
	  or already displayed, respectively.

	* [r6484] topo/tkgui/parametersframe.py:
	  Minor cleanup.

	* [r6483] topo/tkgui/parametersframe.py:
	  Added some links discussing button order.

	* [r6482] topo/tkgui/parametersframe.py:
	  Clean up of Apply, Refresh, Close, and Defaults buttons.

	* [r6481] topo/tkgui/topoconsole.py:
	  Added a note.

	* [r6480] topo/tkgui/testpattern.py:
	  Defaults button now works in test pattern, so enable it.

	* [r6479] topo/tkgui/parametersframe.py:
	  Updated to use ParameterizedObject's defaults() method when
	  Defaults button is pressed.

	* [r6478] topo/tests/testparametersframe.py:
	  Added note.

	* [r6477] topo/base/parameterizedobject.py:
	  Replaced reset_params() with defaults(), which returns default
	  values for non-constant parameters.

2007-09-18  jprovost

	* [r6476] topo/tkgui/projectionpanel.py:
	  This change got the projections panel to stop raising exceptions
	  when encountering non-CF Projections, but it still doesn't really
	  work right.

	* [r6475] topo/sheets/saccade.py:
	  Added support for eye jitter in ShiftingGeneratorSheet

2007-09-18  ceball

	* [r6474] topo/tkgui/tkparameterizedobject.py:
	  Fix error: was not storing objects for ClassSelectorParameter.
	  (Still needs cleaning up.)

	* [r6473] topo/tests/testparametersframe.py:
	  Added another test.

	* [r6472] topo/tkgui/tkparameterizedobject.py:
	  Fixed mistake causing test failure in testparametersframe: was
	  converting to string twice.

	* [r6471] topo/tkgui/tkparameterizedobject.py:
	  Minor reorganization.

	* [r6470] topo/tkgui/tkparameterizedobject.py:
	  More cleanup: should be no visible change.

	* [r6469] topo/tkgui/tkparameterizedobject.py:
	  Cleanup: should be no visible change.

	* [r6468] topo/tkgui/tkparameterizedobject.py:
	  Cleanup - should be no visible change.

	* [r6467] topo/tkgui/tkparameterizedobject.py:
	  Minor cleanup: should be no visible change.

	* [r6466] topo/tkgui/parametersframe.py:
	  Added apply_button() method.

2007-09-17  jprovost

	* [r6465] topo/misc/traces.py:
	  Miscellaneous minor improvements.

	* [r6464] topo/misc/commandline.py:
	  Minor change to support using IDLE in Topographica. --still
	  doesn't work that great, though.

2007-09-16  ceball

	* [r6463] topo/tests/testparametersframe.py:
	  Added new test to expose bug. Renamed the other test method.

	* [r6462] topo/tkgui/tkparameterizedobject.py:
	  Added notes. Test for guimain (hack).

	* [r6461] topo/tests/testparametersframe.py:
	  Added test.

	* [r6460] topo/tkgui/tkguiwindow.py:
	  Added get() method to taggedslider (to match other widgets).

	* [r6459] topo/tests/testparametersframe.py:
	  Initial version.

	* [r6458] Makefile:
	  Added gui test: that connection fields window opens with x and y
	  as specified (i.e. test that right click opening of connection
	  fields window is working).

	* [r6457] topo/tkgui/topoconsole.py:
	  Switched run_for_var to DoubleVar. Get 'run for' value from
	  variable rather than widget.

	* [r6456] topo/tkgui/tkparameterizedobject.py:
	  Multiple improvements to behavior. Entry-style widgets do not
	  instantly apply their changes (waiting instead until <Return> or
	  equivalent). Corrected already noted instance of not using
	  object2string_ifrequired(). Added highlighting of entry boxes
	  with errors (experimental, unfinished). Fixed bug where only text
	  widgets were being disabled for constant parameters.

	* [r6455] topo/tkgui/tkguiwindow.py:
	  Improved TaggedSlider: removed a variable and its trace, and made
	  it generate events for use by callers. Added
	  TkPOTaggedSlider(TaggedSlider) for TkParameterizedObject-specific
	  features.

	* [r6454] topo/tkgui/projectionpanel.py:
	  Added missing method call.

	* [r6453]
	  topo/tests/testtkparameterizedobject.py:
	  Added more tests to simulate use in the GUI.

2007-09-16  jbednar

	* [r6452] doc/Links/index_text.php:
	  Added info on Emergent

2007-09-15  jbednar

	* [r6451] topo/misc/utils.py:
	  Added minor alert

	* [r6450] doc/Downloads/index_text.php:
	  Listed more packages that may be needed

2007-09-15  ceball

	* [r6449] topo/tkgui/tkguiwindow.py:
	  TaggedSlider: handle background and foreground options; don't try
	  to set the slider from a non-numeric value.

	* [r6448] topo/tkgui/__init__.py:
	  Added another reference.

	* [r6447] topo/tkgui/__init__.py:
	  Read options_database from topo/tkgui/options_database.

	* [r6446] topo/tkgui/__init__.py:
	  Added test support for reading option_database file (for setting
	  fonts etc).

2007-09-14  ceball

	* [r6445]
	  topo/tests/testtkparameterizedobject.py:
	  Commented out code that conditionally starts tkgui - still causes
	  problems with other tests.

	* [r6444]
	  topo/tests/testtkparameterizedobject.py:
	  Start()s tkgui if console not already present. Added more tests.
	  The tests in TestParameterTypeRepresentations define how we
	  expect the widgets to behave; they simulate user input to the
	  widgets.

2007-09-12  jbednar

	* [r6443] doc/Downloads/cvs_text.php:
	  Added tetex dependency

2007-09-12  ceball

	* [r6442] Makefile:
	  make tests returns an error code equal to the number of errors
	  plus the number of failures.

	* [r6441]
	  topo/tests/testtkparameterizedobject.py:
	  Cleaned up and added more tests (one of which fails because there
	  is currently an error in TkParameterizedObject).

	* [r6440]
	  topo/tests/testtkparameterizedobject.py:
	  Corrected comment; removed ERRORALERT.

	* [r6439]
	  topo/tests/testtkparameterizedobject.py:
	  Commented out line that start()s tkgui and added ERRORALERT.
	  (This test fails now.)

	* [r6438]
	  topo/tests/testtkparameterizedobject.py:
	  Explicitly start() tkgui for these tests.

	* [r6437]
	  topo/tests/testtkparameterizedobject.py:
	  Updated method names.

2007-09-12  jbednar

	* [r6436] doc/Downloads/index_text.php:
	  Minor rewriting

2007-09-10  jbednar

	* [r6435] doc/Downloads/index_text.php:
	  Added info about packages needed to get docs to compile

	* [r6434] doc/User_Manual/images/Makefile:
	  Added cleanup of generated PDF and PNG files, in case of errors

2007-09-08  ceball

	* [r6433] topo/tkgui/tkparameterizedobject.py:
	  Really minor cleanup.

2007-09-07  ceball

	* [r6432] topo/tkgui/parametersframe.py:
	  Added edit_parameters() function to allow inspection (and
	  editing) of ParameterizedObjects at the commandline (and
	  elsewhere).

	* [r6431] topo/tkgui/parametersframe.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Adjusted leading doc line for reference manual.

	* [r6430] topo/tkgui/tkparameterizedobject.py:
	  Added an introduction.

	* [r6429] topo/tkgui/parametersframe.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/tkparameterizedobject.py:
	  TkParameterizedObject/ParametersFrame cleanup.

	* [r6428] topo/tkgui/__init__.py:
	  Added note.

2007-09-06  ceball

	* [r6427] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Renamed XPGPanel to SheetPGPanel.

	* [r6426] topo/tkgui/parametersframe.py,
	  topo/tkgui/testpattern.py:
	  Renamed XParametersFrame to LiveParametersFrame.

	* [r6425] doc/Downloads/cvs_text.php:
	  Added ALERT about packages missing from the instructions for
	  building the docs on OS X.

	* [r6424]
	  doc/Developer_Manual/testing_text.php:
	  Updated buildbot note now we have an OSX buildslave.

	* [r6423] external/Makefile_OSX.diff:
	  Initial version.

	* [r6422] doc/Future_Work/current_text.php:
	  Added some references.

	* [r6421] doc/Future_Work/current_text.php:
	  Minor revision to text.

	* [r6420] topo/tkgui/__init__.py:
	  Slight cleanup to Tile stuff.

	* [r6419] doc/Future_Work/current_text.php:
	  Updated Tile task.

	* [r6418] doc/Downloads/cvs_text.php:
	  Updated Mac OS X instructions based on building topographica on
	  sake.csres.utexas.edu on 2007/09/05.

	* [r6417] doc/Downloads/cvs_text.php:
	  Changed OS X instructions: just get cvs, not cvsup+libraries.

	* [r6416] topo/base/simulation.py:
	  Changed delay to be a Number.

	* [r6415] topo/base/parameterclasses.py:
	  Changed is_number function to be operator.isNumberType.

2007-09-05  jbednar

	* [r6414] topo/misc/traces.py:
	  Updated comments, docstrings, and whitespace

	* [r6413] doc/Developer_Manual/coding_text.php:
	  Added note about whitespace convention

2007-09-05  ceball

	* [r6412] topo/tkgui/tkparameterizedobject.py:
	  More cleanup; should be no visible change.

2007-09-05  jprovost

	* [r6411] topo/misc/traces.py:
	  Added traces module for recording timeseries data.

2007-09-05  ceball

	* [r6410] topo/tkgui/tkparameterizedobject.py:
	  Removed unnecessary class attributes.

	* [r6409] topo/tkgui/tkparameterizedobject.py:
	  Fixed an ALERT.

	* [r6408] topo/tkgui/__init__.py:
	  Pasted in code for using Tile from an old copy of Topographica
	  (here for reference).

	* [r6407] doc/Downloads/cvs_text.php:
	  Updates to mac instructions (comments plus removed gcc_select
	  instruction).

	* [r6406] examples/lissom_oo_or.ty,
	  examples/lissom_or.ty:
	  Removed unused import.

	* [r6405] topo/tkgui/parametersframe.py:
	  Added ERRORALERT.

	* [r6404] doc/Future_Work/current_text.php:
	  Updates to tkgui task.

	* [r6403] Makefile:
	  Added ALERT.

	* [r6402] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Always use bwidget.

	* [r6401] external/Makefile:
	  bwidget is part of the default target.

	* [r6400] /trunk/topographica-win/create_python_topo/setup.bat:
	  Added bwidget.

	* [r6399] topo/tkgui/topoconsole.py:
	  Minor comment.

2007-09-04  ceball

	* [r6398] Makefile:
	  Combined gui tests into one command (because buildbot only seems
	  to run the first; for make-slow-tests, it runs lots of separate
	  topographica instances...is the problem the gui quit?).

	* [r6397] doc/buildbot/master.cfg:
	  Added basic-gui-tests. Updated URL. (Also messed up some of the
	  comments, but they still say the same things.)

	* [r6396] Makefile:
	  Removed more-gui-tests: just run those tests as part of
	  basic-gui-tests.

	* [r6395] Makefile:
	  Added some more gui tests.

	* [r6394] topo/tkgui/topoconsole.py:
	  Return the ModelEditor object from the open method.

	* [r6393] topo/tkgui/parametersframe.py:
	  Fixed ParametersFrame bug: return statement was missing.

2007-09-04  jprovost

	* [r6392] topo/tests/testsimulation.py:
	  Added a test to TestSimulation.test_event_cmp.

	* [r6391] topo/tests/testsimulation.py:
	  Added test to catch duplication of events in
	  Simulation.event_queue.

	* [r6390] topo/base/simulation.py:
	  Fixed bug in event queueing. Should fix 'make slow-tests'
	  failures.

2007-09-04  ceball

	* [r6389] topo/tkgui/tkparameterizedobject.py:
	  Began cleanup of documentation. (Plus some minor tidying of code:
	  should be no visible change.)

2007-09-03  jbednar

	* [r6388] topo/commands/analysis.py:
	  Fixed offset for single-lag case

	* [r6387] examples/lissom_whisker_barrels.ty:
	  Updated comment

	* [r6386] examples/whiskers/README.txt:
	  Added info from Stuart

	* [r6385] examples/whiskers/whiskerbot_frame.m:
	  Final MSc version from Stuart

	* [r6384] examples/whiskers/CoG_matrix_nf.m:
	  Removed unused file

2007-09-03  ceball

	* [r6383] doc/Future_Work/current_text.php:
	  More in tkgui task.

	* [r6382] doc/Future_Work/current_text.php:
	  Updated tkgui task.

2007-09-03  jbednar

	* [r6381] topo/tkgui/projectionpanel.py:
	  Removed outdated alert

	* [r6380] topo/tkgui/templateplotgrouppanel.py:
	  Fixed typo in comment

	* [r6379] topo/tkgui/plotgrouppanel.py:
	  Allowed sheet_coords and integer_scaling in plot history

	* [r6378] topo/tkgui/__init__.py:
	  Fixed typo

	* [r6377] doc/User_Manual/commandline_text.php:
	  Added instructions for turning off parameter pretty printing

	* [r6376] examples/lissom_whisker_barrels.ty,
	  topo/coordmapperfns/basic.py:
	  Moved Grid into coordmapperfns/

	* [r6375] examples/lissom_whisker_barrels.ty:
	  Generalized Grid (formerly called XYModulo and XYGrid) to be
	  suitable for general mapping use

	* [r6374] topo/base/functionfamilies.py:
	  Fixed minor error in docstring

	* [r6373] examples/tiny.ty:
	  Added command-line control over default_density

	* [r6372] examples/lissom_whisker_barrels.ty:
	  Cleaned up documentation, comments, some class names, parameter
	  types, unused parameters, etc.

	* [r6371] topo/sheets/generatorsheet.py:
	  Added alert

	* [r6370] topo/tkgui/topoconsole.py:
	  Added initial value for snapshot names

	* [r6369] examples/lissom_whisker_barrels.ty:
	  Fixed apparent bug in learning rates for afferent connections
	  when num_lags>1

	* [r6368] examples/lissom_whisker_barrels.ty,
	  topo/commands/analysis.py:
	  Removed hardcoded limitation on number of lags

	* [r6367]
	  examples/lissom_whisker_barrels_temporal.ty:
	  Obsolete; just call lissom_whisker_barrels.ty with the '-c
	  num_lags=4 option instead

	* [r6366] examples/lissom_whisker_barrels.ty:
	  Generalized to cover either the temporal or regular case from a
	  single .ty file

	* [r6365] examples/lissom_whisker_barrels.ty:
	  Changed to use arrow-based color key instead

	* [r6364]
	  examples/whiskers/dfl_key_white_vert.png:
	  Initial version; rotated and flipped copy of
	  dir_key_white_vert.png

	* [r6363] examples/lissom_whisker_barrels.ty:
	  Made specify_whisker_deflections() avoid declaring a measurement
	  time,
	  because the results are always the same, and to avoid staleness
	  warnings. It's now enabled by default.

2007-09-02  ceball

	* [r6362] doc/Future_Work/current_text.php:
	  Added to task.

	* [r6361] doc/Future_Work/current_text.php:
	  Updates to tasks.

	* [r6360] topo/tkgui/projectionpanel.py:
	  Removed outdated ERRORALERT.

	* [r6359] topo/tkgui/plotgrouppanel.py:
	  Removed outdated HACKALERTs; added ALERT about moving out
	  ResizableScrollableFrame.

	* [r6358] topo/tkgui/plotgrouppanel.py:
	  Added ALERT.

	* [r6357] topo/tkgui/plotgrouppanel.py:
	  Added missing calls to sizeright.

	* [r6356] topo/tkgui/plotgrouppanel.py:
	  Cleaned up calling of sizeright(). Should fix flickering on
	  bwidget version.

	* [r6355] doc/Future_Work/current_text.php:
	  Removed part of task.

	* [r6354] topo/tkgui/projectionpanel.py:
	  Removed outdated ERRORALERT.

	* [r6353] topo/tkgui/projectionpanel.py:
	  Changed an on_change to on_modify (which is what was really
	  meant). Also fixes history in projection window.

	* [r6352] topo/tkgui/projectionpanel.py:
	  Changed an on_change to on_modify (which is what was really
	  meant). Also fixes history in projection activity.

	* [r6351] topo/tkgui/plotgrouppanel.py:
	  Removed duplicate call to update_widgets() (should have no
	  visible effect).

	* [r6350] topo/tkgui/tkguiwindow.py:
	  Added fix to ensure slider matches tag when TaggedSlider is
	  created.

	* [r6349] topo/tkgui/testpattern.py:
	  Also hide plot_command, for consistency (already hidden from
	  display by pack_forget on its container).

	* [r6348] topo/tkgui/testpattern.py:
	  Override refresh() method (no history handling).

	* [r6347] topo/tkgui/plotgrouppanel.py:
	  Clean up.

	* [r6346] topo/commands/analysis.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py:
	  Updated after changes to plotgroup(panel).

	* [r6345] topo/tkgui/plotgrouppanel.py:
	  Cleanup of display_plots, update_plots etc.

	* [r6344] topo/plotting/plotgroup.py:
	  Cleanup of names of update_plots(), etc.

	* [r6343] topo/tkgui/plotgrouppanel.py:
	  Minor change to comment.

	* [r6342] topo/tkgui/plotgrouppanel.py:
	  Renamed variable for clarity.

	* [r6341] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Removed apparently unused bitmaps attribute.

	* [r6340] topo/tkgui/plotgrouppanel.py:
	  Fixed what I think was a bug: new canvases were being created
	  every time, even when the number of canvases and the size of each
	  did not change. This ought to reduce some flickering. Also added
	  unrelated ERRORALERT.

	* [r6339] topo/tkgui/testpattern.py:
	  Call correct method when changing sliders. (Names of the methods
	  in plotgrouppanel and plotgroup will be cleaned up.)

	* [r6338] topo/tkgui/plotgrouppanel.py:
	  In redraw_plots(), don't call display_plots() again. The methods
	  update_plots(), redraw_plots(), and refresh() all need to be
	  reviewed and cleaned up (finally, and simultaneously with
	  plotgroup).

	* [r6337] topo/tkgui/tkguiwindow.py:
	  Removed outdated alert.

	* [r6336] topo/tkgui/tkparameterizedobject.py:
	  Minor change to text.

	* [r6335] topo/tkgui/tkguiwindow.py:
	  Minor clarifications in TaggedSlider; should be no change.

	* [r6334] topo/tkgui/testpattern.py:
	  Removed duplicate call to change_pattern_generator().

	* [r6333] topo/base/patterngenerator.py:
	  Hid size from Constant pattern generator.

	* [r6332] topo/tkgui/tkguiwindow.py:
	  Added some comments and removed print statement.

	* [r6331] topo/tkgui/tkguiwindow.py:
	  Added adjustment of slider range based on tag value.

	* [r6330] topo/tkgui/tkguiwindow.py:
	  TaggedSlider: corrected some imports; cleaned up slightly.

	* [r6329] topo/tkgui/topoconsole.py:
	  Update to use new TaggedSlider class.

	* [r6328] topo/tkgui/tkparameterizedobject.py:
	  Don't apply changes to text variables immediately unless
	  requested.

	* [r6327] topo/tkgui/tkguiwindow.py:
	  Removed TaggedSlider and replaced with TaggedSlider3. Improved
	  TaggedSlider3 by having a separate variable for the slider.

	* [r6326] topo/tkgui/parametersframe.py:
	  Not-immediately-acting ParametersFrame needs to update all types
	  of Parameter when Apply is pressed.

	* [r6325] topo/tkgui/projectionpanel.py:
	  Removed outdated ALERT.

2007-09-01  jprovost

	* [r6324] topo/base/cf.py:
	  Reverted a change to CFProjection.input_buffer initialization

2007-09-01  ceball

	* [r6323] topo/tkgui/tkguiwindow.py:
	  Restored option accidentally removed from TaggedSlider and
	  removed it from TaggedSlider3, as originally intended.

	* [r6322] topo/tkgui/tkguiwindow.py:
	  Removed original TaggedSlider class. Makeshift TaggedSlider2
	  (what we are currently using) becomes TaggedSlider. Added
	  TaggedSlider3, a far simpler class which appears to perform the
	  same, but isn't quite finished.

	* [r6321] topo/tkgui/tkguiwindow.py,
	  topo/tkgui/tkparameterizedobject.py,
	  topo/tkgui/topoconsole.py:
	  Moved TaggedSliders into tkguiwindow from translatorwidgets.

	* [r6320] topo/tkgui/translatorwidgets.py:
	  Removed unused file.

	* [r6319] doc/Future_Work/current_text.php:
	  Demoted timing-code-cleanup task.

	* [r6318] topo/base/parameterclasses.py:
	  InstanceMethodWrapper.__name__ returns the function's name.

	* [r6317] topo/base/simulation.py:
	  SomeTimer: renamed methods.

	* [r6316] topo/base/simulation.py:
	  Simplification of SomeTimer. Note that timing messages are now
	  different, and are probably less clear than before.

2007-08-31  ceball

	* [r6315] topo/base/simulation.py:
	  Added some documentation to SomeTimer.

	* [r6314] topo/tkgui/testpattern.py:
	  Hid Defaults button; ParameterizedObject.reset_params() needs
	  some work.

2007-08-31  jbednar

	* [r6313]
	  examples/lissom_whisker_barrels_temporal.ty:
	  Made DeflectionPreference be the default subplot

	* [r6312] examples/lissom_whisker_barrels.ty:
	  Made DeflectionPreference be the default subplot

	* [r6311] doc/User_Manual/plotting_text.php:
	  Fixed bizarre example of how to turn off subplots

	* [r6310] topo/commands/analysis.py:
	  Added hard-coded whisker deflection support

	* [r6309] examples/lissom_whisker_barrels.ty,
	  examples/lissom_whisker_barrels_temporal.ty,
	  examples/whiskers,
	  examples/whiskers/CoG_matrix_nf.m,
	  examples/whiskers/README.txt,
	  examples/whiskers/cheque_data.mat,
	  examples/whiskers/ganglion_labels.m,
	  examples/whiskers/generate_barrelettes.m,
	  examples/whiskers/key.png,
	  examples/whiskers/pipe.m,
	  examples/whiskers/shuffle.m,
	  examples/whiskers/sweep.m,
	  examples/whiskers/sweep_anticor.m,
	  examples/whiskers/sweep_random.m,
	  examples/whiskers/sweep_uncor.m,
	  examples/whiskers/test_deflections.m,
	  examples/whiskers/wbot_data.mat,
	  examples/whiskers/wbot_data_new.mat,
	  examples/whiskers/wbot_object_data.mat:
	  Final MSc version from Stuart

	* [r6308] topo/plotting/plotgroup.py:
	  Added clarification

	* [r6307] topo/tkgui/__init__.py:
	  Made coordmapperfns available in the GUI

	* [r6306] topo/sheets/generatorsheet.py:
	  Minor cleanup; removed now-unused Trigger port

	* [r6305] topo/base/simulation.py:
	  Fixed typos

2007-08-31  jprovost

	* [r6304] topo/projections/basic.py:
	  Fixed small bug in OneToOneProjection.

	* [r6303] topo/sheets/saccade.py:
	  Rewrote ShiftingGeneratorSheet to inherit from newly rewritten
	  SequenceGeneratorSheet.

	* [r6302] topo/sheets/generatorsheet.py:
	  Rewrote GeneratorSheet and SequenceGeneratorSheet to use
	  PeriodicSequenceEvent.

	* [r6301] topo/tests/testsimulation.py:
	  added/fixed tests associated with simulation events

	* [r6300] topo/base/simulation.py:
	  Added several new event types and made some associated changes to
	  Events and how they're scheduled.
	  Schedulng semantics should be unchanged.

	* [r6299] topo/base/cf.py:
	  Added initialization of CFProjection.input_buffer to
	  self.src.activity.

	* [r6298] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  * Better reporting of param names in errors. (still not perfect)
	  * warnings_as_errors -> warnings_as_exceptions

2007-08-31  ceball

	* [r6297] topo/tkgui/testpattern.py:
	  Added note.

	* [r6296] doc/Future_Work/current_text.php:
	  Updated tkgui task; removed duplicate.

	* [r6295] topo/base/parameterizedobject.py:
	  reset_params(): tidied ALERTs and dealt with instantiated
	  Parameters. Still needs some work.

2007-08-31  jbednar

	* [r6294] topo/tkgui/plotgrouppanel.py:
	  Added note

	* [r6293] topo/plotting/plotgroup.py:
	  Fixed bug in sheet coordinate sizing

2007-08-31  ceball

	* [r6292] topo/tkgui/plotgrouppanel.py:
	  Moved conditional_refresh() from test pattern.

	* [r6291] topo/tkgui/testpattern.py,
	  topo/tkgui/testpattern2.py:
	  Replaced TestPattern with version from testpattern2.py.

2007-08-31  jbednar

	* [r6290] doc/Future_Work/current_text.php:
	  Fixed typo

	* [r6289] doc/Future_Work/current_text.php:
	  Added button icon task

2007-08-31  ceball

	* [r6288] topo/tkgui/parametersframe.py:
	  Fixed a bug with tracking displayed widgets. Rearranged some
	  ALERTs.

	* [r6287] topo/base/parameterizedobject.py:
	  Added and ALERT about reset_params().

2007-08-31  jbednar

	* [r6286] doc/Team_Members/index_text.php:
	  Reorganized and updated

2007-08-31  ceball

	* [r6285] topo/tkgui/testpattern2.py:
	  Addded some doc and softbounds.

	* [r6284] topo/tkgui/testpattern2.py:
	  Continued cleanup.

	* [r6283] topo/plotting/plotgroup.py:
	  Moved _sheets() method up to SheetPlotGroup, and allowed
	  specification of an arbitrary list of sheets on construction (not
	  definitely permanent changes).

2007-08-30  ceball

	* [r6282] topo/tkgui/testpattern2.py:
	  Updates for using XParametersFrame.

	* [r6281] topo/plotting/plotgroup.py:
	  Removed outdated comment and ALERT.

2007-08-29  ceball

	* [r6280] topo/tests/testplotfilesaver.py:
	  Updated after change to PlotGroup.

	* [r6279] topo/commands/analysis.py:
	  For save_plotgroup(): removed two ALERTS; added an ERRORALERT;
	  renamed a variable; added ability to pass Parameters to the
	  PlotFileSaver.

	* [r6278] topo/plotting/plotfilesaver.py:
	  generate_plotgroup() sets an attribute, rather than returning the
	  PlotGroup.

	* [r6277] topo/plotting/plotgroup.py:
	  Cleaned up type checking.

	* [r6276] topo/plotting/plotgroup.py:
	  Removed redundant command.

	* [r6275] topo/plotting/templates.py:
	  Changed 'command' Parameter to 'update_command'. Left 'command',
	  a copy of 'update_command', to allow current (possible
	  user-written) code to continue working.

	* [r6274] topo/plotting/plotgroup.py:
	  Removed old 'command' Parameter.

2007-08-29  jbednar

	* [r6273] topo/tests/testpropertiesframe.py,
	  topo/tkgui/propertiesframe.py:
	  Removed unused files

	* [r6272] topo/tkgui/translatorwidgets.py:
	  Removed outdated references to PropertiesFrame

2007-08-29  ceball

	* [r6271] topo/plotting/plotgroup.py:
	  Removed redundant code and ALERT about plot_list.

	* [r6270] topo/plotting/plotgroup.py:
	  Removed sheet_type from TemplatePlotGroup.

	* [r6269] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/testpattern2.py:
	  Renamed XPlotGroup to SheetPlotGroup.

	* [r6268] topo/plotting/plotgroup.py:
	  Minor cleanup.

	* [r6267] topo/base/parameterizedobject.py,
	  topo/base/simulation.py,
	  topo/misc/utils.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/propertiesframe.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/tkparameterizedobject.py,
	  topo/tkgui/translatorwidgets.py:
	  Merged in parametersframe_replacement_branch (version of that
	  branch as tagged with parametersframe_replacement_branch_FINAL).

	* [r6266] doc/Future_Work/current_text.php:
	  Added some links to think about putting somewhere.

2007-08-29  jbednar

	* [r6265] topo/plotting/plotgroup.py:
	  Added comments from phone meeting

	* [r6264] topo/plotting/plotgroup.py:
	  Fixed typos

	* [r6263] topo/plotting/plotgroup.py:
	  Fixed typos

	* [r6262] topo/plotting/plotgroup.py:
	  Added alert

	* [r6261] topo/plotting/plotgroup.py:
	  Simplified scale_images, fixing integer scaling in the process

	* [r6260] topo/plotting/plot.py:
	  Added set_scale option, to complement rescale

	* [r6259] topo/plotting/plotgroup.py:
	  Enforced bounds on sheet and matrix coordinate cases separately,
	  so that each will now be appropriate.

	* [r6258] topo/tkgui/testpattern2.py:
	  Removed stray import

	* [r6257] topo/tkgui/testpattern.py:
	  Removed outdated references to old PlotGroup code

2007-08-28  jbednar

	* [r6256] topo/plotting/plotgroup.py:
	  Localized minimum height computation in one spot so that it can
	  be fixed

	* [r6255] doc/Forums,
	  doc/Forums/.cvsignore:
	  More to ignore

	* [r6254] topo/plotting/plotgroup.py:
	  Removed obsolete initial_plot flag, making initial sizes be
	  computed automatically when the plots are first created

	* [r6253] topo/plotting/plotgroup.py:
	  Removed dependency on initial_plot for suppressing color-key-only
	  plots; this case can be deduced from other information

	* [r6252] topo/plotting/plot.py:
	  Clarified comment

	* [r6251] doc/Tutorials/lissom_oo_or_text.php,
	  doc/Tutorials/lissom_or_text.php,
	  topo/tkgui/topoconsole.py:
	  Made examples subdirectory be selected by default for loading
	  snapshots

2007-08-27  jbednar

	* [r6250] topo/plotting/plotgroup.py:
	  Removed redundant INITIAL_PLOT_HEIGHT attribute

	* [r6249] topo/plotting/plotgroup.py:
	  Removed code from ProjectionPlotGroup that was nearly duplicated
	  from XPlotGroup; no ill effects apparent

	* [r6248] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py:
	  Fixed Projection plots to rescale properly from the _orig_bitmap,
	  not the scaled one

	* [r6247] topo/tkgui/plotgrouppanel.py:
	  Moved enlarge and reduce implementation to the plotgroup

	* [r6246] topo/plotting/plotgroup.py:
	  Added zoom_factor option to scale_images, to allow code to be
	  eliminated in the GUI

	* [r6245] topo/tkgui/projectionpanel.py:
	  Simplified slightly and cleaned up

2007-08-27  ceball

	* [r6244] topo/plotting/plotgroup.py:
	  Added a docstring so I can see balloon help working in the GUI.

2007-08-27  jbednar

	* [r6243] topo/base/cf.py:
	  Minor clarification to comment

2007-08-27  ceball

	* [r6242] topo/tkgui/projectionpanel.py:
	  Remove label as well as widget before repacking projection param.
	  Updated ALERT about OptionMenu widget, and added ERRORALERT about
	  projection selector widget behavior.

	* [r6241] topo/tkgui/tkparameterizedobject.py:
	  Added hack to prevent 'bad window path error' for projection
	  panel.

2007-08-26  ceball

	* [r6240] doc/FAQ/index_text.php:
	  Minor change to text.

2007-08-25  jbednar

	* [r6239]
	  examples/sullivan_neurocomputing04.ty:
	  Fixed broken import

2007-08-25  ceball

	* [r6238] doc/Forums/index_text.php,
	  doc/Forums/problems_text.php,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/problems_text.php:
	  Moved problems.html to Forums/ from User_Manual/.

	* [r6237] doc/FAQ/index_text.php:
	  Added question about reporting problems.

	* [r6236] doc/Developer_Manual/alerts_text.php:
	  Changed HACKALERT to ERRORALERT because 'error' has a clearer
	  meaning than 'hack'. (Existing HACKALERTs in the code have not
	  yet been replaced with ERRORALERTs.)

2007-08-24  jbednar

	* [r6235] topo/plotting/plotgroup.py:
	  Added docstring

	* [r6234] topo/base/arrayutils.py,
	  topo/misc/distribution.py,
	  topo/misc/utils.py,
	  topo/patterns/basic.py,
	  topo/patterns/teststimuli.py,
	  topo/tests/testfeaturemap.py:
	  Moved wrap to arrayutils, making it work for arrays in the
	  process

	* [r6233] topo/commands/pylabplots.py:
	  Removed inexplicable cosine from gradient plots, replacing with
	  sqrt, plus wrapping of cyclic quantities

	* [r6232] topo/commands/analysis.py:
	  Removed unused old_name_support from save_group

2007-08-24  jprovost

	* [r6231] topo/coordmapperfns/basic.py:
	  minor fix to testing function

	* [r6230] topo/coordmapperfns/basic.py:
	  Improvements to Ottes inverse mapping.

2007-08-24  jbednar

	* [r6229] topo/commands/pylabplots.py:
	  Vastly simplified, correcting swapped axes and division by zero
	  problems

	* [r6228] topo/tkgui/topoconsole.py:
	  Added status message so that user knows that a snapshot is still
	  loading

	* [r6227] topo/analysis/featureresponses.py:
	  Restored HACKALERT mistakenly deleted

	* [r6226] doc/Forums/index_text.php,
	  doc/User_Manual/index_text.php:
	  Added link to problems.html

	* [r6225] doc/User_Manual/problems_text.php:
	  First complete version

	* [r6224] topo/coordmapperfns/basic.py:
	  Cleaned up whitespace and docstrings. Fixed OttesSCMapper
	  _abstract_class_name

	* [r6223] topo/base/parameterizedobject.py:
	  Fixed some comments

2007-08-22  jprovost

	* [r6222] topo/base/parameterclasses.py,
	  topo/base/patterngenerator.py:
	  Set PatternGenerator.position parameter to hidden.

	* [r6221]
	  topo/tests/testCompositeParameter.txt,
	  topo/tests/testCompoundParameter.txt:
	  Renamed CompoundParameter to CompositeParameter.

	* [r6220] topo/base/patterngenerator.py:
	  - Renamed CompoundParameter as CompositeParameter.
	  - Made PatternGenerator.position parameter hidden, to patch GUI
	  bug til more comprehensive solution is found.

	* [r6219] topo/base/parameterclasses.py:
	  Renamed CompoundParameter to CompositeParameter

	* [r6218] topo/base/parameterizedobject.py:
	  Added comments re CompositeParameter.

	* [r6217]
	  doc/Developer_Manual/testing_text.php:
	  Added doctest documentation.

2007-08-22  jbednar

	* [r6216] topo/base/patterngenerator.py:
	  Clarified docstring, hopefully correctly

	* [r6215] topo/tkgui/editorwindow.py:
	  Removed obsolete alert

	* [r6214] doc/Team_Members/index_text.php:
	  Updated Chris' role and Jeff's position

	* [r6213] topo/base/parameterclasses.py:
	  Fixed syntax error in assert statement

	* [r6212] topo/base/parameterclasses.py:
	  Made coordinate default be floating-point, just in case

	* [r6211] topo/commands/analysis.py:
	  Made more constants be floating-point to avoid problems with
	  integer
	  division, especially for measure_rfs().

	* [r6210] topo/tkgui/projectionpanel.py:
	  Minor clarification to label

2007-08-22  jprovost

	* [r6209] topo/tkgui/editorwindow.py:
	  Better warnings from model editor when not all EPs/connections
	  can be drawn.

	* [r6208] topo/tests/testCompoundParameter.txt:
	  Test for the CompoundParameter parameter type.

	* [r6207] topo/tests/__init__.py:
	  Added support for tests written as doctest files.

	* [r6206] topo/sheets/saccade.py:
	  Updated ShiftingGeneratorSheet to generate a new pattern every
	  time there is an eye movement. Added output port to send out the
	  bbox position if needed.

	* [r6205] topo/misc/commandline.py:
	  Tiny change to comments.

	* [r6204] topo/sheets/generatorsheet.py:
	  Improvements to SequenceGeneratorSheet.

	* [r6203] topo/base/patterngenerator.py:
	  Added compound 'position' parameter to patterngenerators.

	* [r6202] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  - Added warnings_as_errors flag in parameterizedobject module.
	  - Added CompoundParameter, including support in
	  ParameterizedObjectMetaClass.
	  - Added XYCoordinates parameter type.

2007-08-22  ceball

	* [r6201] topo/tkgui/plotgrouppanel.py:
	  Added HACKALERT.

	* [r6200] Makefile:
	  Added test pattern window to basic-gui-tests.

2007-08-21  ceball

	* [r6199] topo/tkgui/tkparameterizedobject.py:
	  Packing separated from widget creation in pack_param. Added
	  pack_params() to ParametersFrame2 to do what
	  ParametersFrame.__new_widgets() does (i.e. set the parameters out
	  on a grid, ordered by precedence).

	* [r6198] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/projectionpanel.py:
	  Update to match changes in tkparameterizedobject.py.

	* [r6197] topo/tkgui/tkparameterizedobject.py:
	  Cleaned up _widgets/_furames ALERT.

	* [r6196] topo/tkgui/plotgrouppanel.py:
	  Changed from widgets_in_history to params_in_history (simpler -
	  will be switching more things from referring to widgets to
	  referring to parameters). Updates to match changes in
	  tkparameterizedobject.

	* [r6195] topo/tkgui/projectionpanel.py:
	  Added HACKALERT.

	* [r6194] topo/tkgui/testpattern.py:
	  Switch to hide_param() from manual destruction of widgets.

	* [r6193] topo/tkgui/tkparameterizedobject.py:
	  Simplification to pack_param.

	* [r6192] topo/tkgui/tkparameterizedobject.py:
	  Correct version of 1.56-->1.57 checkin (i.e. this version is a
	  corrected 1.57).

	* [r6191] topo/tkgui/tkparameterizedobject.py:
	  Revert to version 1.56 (i.e. discard previous checkin) because of
	  bug that would stop everyone being able to open plots.

	* [r6190] topo/tkgui/tkparameterizedobject.py:
	  Simplify code to create button widgets.

	* [r6189] doc/Downloads/cvs_text.php:
	  Added note about checking buildbot.

	* [r6188] topo/tkgui/tkparameterizedobject.py:
	  Correct bug where help text was being displayed incorrectly for
	  buttons, and was being displayed at all for entry boxes.

	* [r6187] topo/tkgui/tkparameterizedobject.py:
	  Corrected typo in previous checkin.

	* [r6186] topo/tkgui/tkparameterizedobject.py:
	  ParametersFrame2: added show/hide parameter widget methods;
	  confirm close if unapplied changes; unimportant changes to
	  buttons docs (only for testing).

2007-08-20  ceball

	* [r6185] topo/tkgui/tkparameterizedobject.py:
	  ParametersFrame2: to match ParametersFrame, pack() itself and put
	  parameters into an inner frame.

	* [r6184] topo/tkgui/tkparameterizedobject.py:
	  Simplified AttributeError messages (don't print whole repr() of
	  objects - which led to pages of output - and cleaned up
	  internally).

	* [r6183] topo/tkgui/tkparameterizedobject.py:
	  ParametersFrame2: Added some compatibility with model editor.

	* [r6182]
	  topo/tests/testtkparameterizedobject.py:
	  Add a constant parameter among the test parameters.

	* [r6181]
	  doc/Developer_Manual/testing_text.php:
	  Added automatic testing section.

	* [r6180] doc/buildbot,
	  doc/buildbot/master.cfg:
	  Initial version for doozy, with only only slave (also on doozy).

2007-08-20  jbednar

	* [r6179] examples/lissom_oo_or.ty,
	  examples/lissom_or.ty:
	  Added command-line control over retinal density

	* [r6178]
	  topo/tests/testtkparameterizedobject.py:
	  Minor spelling fix in messages

2007-08-20  ceball

	* [r6177] doc/User_Manual/commandline_text.php:
	  Updated GUI scripting section. (Plus removed unnecessary
	  semi-colons from examples.)

2007-08-20  jbednar

	* [r6176] topo/tkgui/plotgrouppanel.py:
	  Added catch for right-clicking for an RF when Receptive Fields
	  plot
	  hasn't been run yet.

2007-08-20  ceball

	* [r6175] topo/tkgui/topoconsole.py:
	  Started to have menu commands return their objects, so that the
	  GUI can be scripted more. For instance:
	  act_win=topo.guimain['Plots']['Activity']();act_win.normalize=False.
	  At some point soon, should be able to script enough in the
	  activity window to - for instance - simulate a right click for
	  opening a connection fields window, allowing us to add a test to
	  ensure that the right-click opening of connection fields windows
	  does not get broken.

2007-08-20  jbednar

	* [r6174] doc/User_Manual/commandline_text.php,
	  doc/User_Manual/index_text.php:
	  Added instructions for controlling the GUI from the command line

	* [r6173] doc/Links/index_text.php:
	  Mentioned NEST interface

	* [r6172] topo/tkgui/editorwindow.py:
	  Removed apparently unused random_generator code

2007-08-20  ceball

	* [r6171] topo/tkgui/tkparameterizedobject.py:
	  Corrected mistake: need to convert object to string when checking
	  if current value is in range.

2007-08-19  ceball

	* [r6170] topo/tkgui/tkparameterizedobject.py:
	  Don't try to set constant parameters, unless they're in a
	  ParameterizedObjectMetaclass instance.

	* [r6169] Makefile:
	  Update to syntax for invoking GUI menu items.

	* [r6168] topo/tkgui/plotgrouppanel.py:
	  Update to accessing Connection Fields menu item.

	* [r6167] topo/tkgui/topoconsole.py:
	  Switch menus to tkguiwindow.ControllableMenu, and add
	  dictionary-style access to TopoConsole's menubar. Removed
	  plots_menu_entries, since the plot menu item 'EntryName' can now
	  be accessed by topo.guimain['Plots']['EntryName'].

	* [r6166] topo/tkgui/tkguiwindow.py:
	  Menu: take indexname to be label, if indexname not supplied.
	  Added comment about possibly removing indexname, though there is
	  probably some case where it would be necessary.

	* [r6165] topo/tkgui/tkguiwindow.py:
	  Menu class: renamed self.contents to self.indexname2index; made
	  actual item (if a menu or command) available to access. Added
	  ControllableMenu, which allows dictionary-style access to menu
	  items.

	* [r6164] topo/tkgui/tkguiwindow.py:
	  Addition to comment.

	* [r6163] topo/tkgui/tkguiwindow.py:
	  Corrected typo in previous checkin.

	* [r6162] topo/tkgui/tkguiwindow.py:
	  In Menu, override invoke() so that commands can be invoke()d by
	  name. (Plus cleanup: moved index conversion into a general method
	  so that it can be used by all methods.)

	* [r6161] topo/tkgui/tkparameterizedobject.py:
	  Switched order of two lines in __init__ (so we add the shadowed
	  PO before initializing Parameter values; previously it was in
	  this order, but got switched accidentally during a recent
	  cleanup). Not sure if anything we currently do would have been
	  affected by this.

2007-08-18  ceball

	* [r6160] Makefile:
	  Change syntax of command for basic GUI window opening.

	* [r6159] topo/tkgui/topoconsole.py:
	  Make PlotsMenuEntry call()able.

	* [r6158] topo/base/parameterizedobject.py:
	  Removed system for passing around warnings.

	* [r6157] topo/tkgui/topoconsole.py:
	  Warnings not displayed in the GUI.

2007-08-15  jbednar

	* [r6156] external/Imaging.diff:
	  Added patch for 64-bit ECDF machine, to get rid of 'encoder zip
	  not available' messages from tests that use PIL

	* [r6155] external/Makefile:
	  Added patch for 64-bit ECDF machine, to get rid of 'encoder zip
	  not available' messages from tests that use
	  PILexternal/Imaging.diff

2007-08-14  jprovost

	* [r6154] topo/tkgui/editorwindow.py:
	  Patched up a problem with connections to EPs that are not sheets.
	  Temporary fix only -- eventually such EPs should appear in the
	  editor.

2007-08-13  ceball

	* [r6153] topo/tkgui/tkparameterizedobject.py:
	  Removed mistaken if-test.

	* [r6152] doc/Forums/index_text.php:
	  Added link to the Windows forum.

	* [r6151] topo/tkgui/tkparameterizedobject.py:
	  Started to add ability to change the shadowed
	  ParameterizedObject, and methods to match calls meant for
	  parametersframe.ParametersFrame. Intermediate checkin, and
	  shouldn't affect existing code.

2007-08-12  ceball

	* [r6150] doc/Future_Work/current_text.php:
	  Added to task.

	* [r6149] doc/Future_Work/current_text.php:
	  Updates to various tasks.

	* [r6148] topo/tkgui/tkparameterizedobject.py:
	  Added to note.

	* [r6147] topo/tests/hierarchical.ty_DATA:
	  Data from 2007/04/25 03:53 GMT (i.e. after SOM changes).

	* [r6146] topo/tkgui/tkparameterizedobject.py:
	  All Parameters except Boolean are represented in the GUI by
	  StringVar (because the Parameters themselves take care of things
	  like checking types, so we don't want any restrictions from the
	  GUI variable). Added translation between __repr__ and objects so
	  that widgets can accept any valid Python expression, and
	  repr()esentations are displayed in the GUI for objects. Various
	  cleanup. Not yet finished, although I think ParametersFrame2 now
	  has at least all the features of ParametersFrame.

	* [r6145] topo/tkgui/translatorwidgets.py:
	  Added TaggedSlider2: TaggedSlider, but without some of the
	  translation stuff. (Not finished.)

	* [r6144] topo/tkgui/topoconsole.py:
	  Added trivial method to display a message on the status bar.

2007-08-11  ceball

	* [r6143] Makefile:
	  Added test to allow quick checking of GUI windows.

	* [r6142] topo/tkgui/topoconsole.py:
	  Added 'check' option to quit method, so quit can be invoked
	  without requiring someone to confirm.

	* [r6141] topo/tkgui/tkparameterizedobject.py:
	  Removed Refresh button since Reset does the same.

	* [r6140] topo/tkgui/tkparameterizedobject.py:
	  Uncommented section mistakenly commented-out in previous checkin.

	* [r6139] topo/tkgui/tkparameterizedobject.py:
	  Intermediate checkin (should still be no change to existing GUI).
	  Can reverse precedence of TkParameterizedObject and its extraPO
	  for finding parameters. Continued to work on ParametersFrame2.
	  General cleanup.

	* [r6138] topo/analysis/featureresponses.py:
	  Minor update to note.

2007-08-10  ceball

	* [r6137]
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/tkparameterizedobject.py:
	  TkParameterizedObject now only supports one ParameterizedObject
	  (previously it was any number, but that was too confusing and
	  probably unnecessary).

2007-08-10  jbednar

	* [r6136] doc/Reference_Manual,
	  doc/Reference_Manual/.cvsignore:
	  More to ignore

	* [r6135]
	  doc/Developer_Manual/refactoring_text.php:
	  Added more info on refactoring

2007-08-10  ceball

	* [r6134] topo/tkgui/tkparameterizedobject.py:
	  Intermediate checkin: began trying to adapt TkparameteredObject
	  to handle objects of type ParameterizedObjectMetaclass as well as
	  those of type ParameterizedObject in extra_pos.

2007-08-10  jbednar

	* [r6133] examples/lissom_oo_or.ty:
	  Minor tweak to get more info during training

2007-08-10  ceball

	* [r6132] topo/tkgui/tkparameterizedobject.py:
	  Added title to ParametersFrame2. Added support to
	  TkParameterizedObject for displaying constant parameters.

	* [r6131] topo/tkgui/testpattern2.py:
	  Replaced RangedParameter.

2007-08-10  jbednar

	* [r6130] topo/commands/analysis.py:
	  Split more plotting commands

	* [r6129] topo/commands/analysis.py:
	  Split commands to have a separate plot_command when appropriate

2007-08-10  ceball

	* [r6128] topo/tkgui/tkparameterizedobject.py:
	  ParametersFrame2: added right-click editing for OptionMenu.
	  TkParameterizedObject: added help text for current item in
	  OptionMenu.

2007-08-10  jbednar

	* [r6127] external/Makefile:
	  Moved psyco out of default make targets, as it is not available
	  on 64-bit platforms

	* [r6126] doc/User_Manual/plotting_text.php:
	  Small fix to documentation

	* [r6125] doc/Future_Work/current_text.php:
	  Various updates

2007-08-10  ceball

	* [r6124] topo/tkgui/tkparameterizedobject.py:
	  Replaced RangedParameter with ObjectSelectorParameter. Extended
	  TkParameterizedObject to handle ClassSelectorParameter. Updated
	  ParametersFrame2. Intermediate checkin (with everything still
	  working).

	* [r6123] topo/plotting/plotgroup.py,
	  topo/tests/testtkparameterizedobject.py,
	  topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/projectionpanel.py:
	  Replaced temporary RangedParameter with ObjectSelectorParameter.

	* [r6122] topo/base/parameterclasses.py:
	  Added ObjectSelectorParameter, with SelectorParameter as a parent
	  in common with ClassSelectorParameter. Intermediate checkin.

2007-08-09  ceball

	* [r6121] topo/tkgui/tkparameterizedobject.py:
	  Popup help bound to label (if present), rather than the whole
	  enclosing frame as before. If there's no label, help is bound to
	  the enclosing frame.

	* [r6120] topo/plotting/plotgroup.py:
	  Added doc string.

	* [r6119] topo/tkgui/templateplotgrouppanel.py:
	  Recovered doc for strength-only parameter.

	* [r6118] topo/commands/analysis.py:
	  Added input_sheet to the displayed command to make it more
	  obvious to users.

	* [r6117] topo/tkgui/projectionpanel.py:
	  Added command to size Projection windows (for bwidget version).

	* [r6116] topo/tkgui/topoconsole.py:
	  Expand panel frames in windows, so that contents expand when
	  window sizes are increased.

	* [r6115] topo/tkgui/featurecurvepanel.py:
	  Added note for users.

	* [r6114] topo/tkgui/topoconsole.py:
	  Try to improve appearance when opening panels with bwidget built
	  by keeping the window hidden until its construction is complete.
	  Still a small window appears just shortly before it's expanded to
	  full size, but it seems to be better.

	* [r6113] topo/tkgui/testpattern.py:
	  Removed update_command, plot_command, and redraw from Test
	  Pattern window. Left Refresh button, but it's not in a great
	  position. Removed Back and Fwd buttons.

	* [r6112] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/topoconsole.py:
	  Removed FullFieldFeatureCurvePanel, because with the 'redraw'
	  button on PlotGroupPanel it is now redundant.

	* [r6111] topo/commands/analysis.py:
	  Undo previous checkin, which was mistaken.

	* [r6110] topo/tkgui/featurecurvepanel.py:
	  Removed duplicate Redraw button.

	* [r6109] topo/tkgui/plotgrouppanel.py:
	  Moved Refresh button next to update_command, and added Redraw
	  button next to plot_command.

	* [r6108] topo/commands/analysis.py:
	  Separated plot_command from (update_)command.

	* [r6107] topo/tkgui/tkparameterizedobject.py:
	  Minor addition to doc.

	* [r6106] topo/tkgui/tkparameterizedobject.py:
	  Corrected method to match Parameter class to widget-creation
	  method (previously, could not match subclasses of the
	  widget_creators dictionary key). Renamed __update_param to
	  _update_param so that subclasses can acces it. Added sketch of a
	  replacement ParametersFrame (using TkParameterizedObject), and
	  temporarily modified TkParameterizedObjectBase methods to work
	  with ClassSelectorParameter; RangedParameter needs to be turned
	  into something permanent.

2007-08-08  ceball

	* [r6105] topo/plotting/plotgroup.py:
	  Added a comment.

	* [r6104] topo/tkgui/tkparameterizedobject.py:
	  Minor renaming and changes to documentation. Should be no visible
	  change.

	* [r6103] topo/commands/analysis.py,
	  topo/plotting/plotgroup.py,
	  topo/plotting/templates.py,
	  topo/tkgui/plotgrouppanel.py:
	  Renamed plotcommand Parameter to plot_command.

	* [r6102] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py:
	  Renamed updatecommand Parameter to update_command.

	* [r6101] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Renamed sheetcoords Parameter to sheet_coords.

	* [r6100] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Renamed integerscaling Parameter to integer_scaling.

	* [r6099] topo/tkgui/tkparameterizedobject.py:
	  Changed creation of widgets from Parameters to be more similar to
	  how that works in ParametersFrame; should be no visible change.

	* [r6098] topo/tkgui/translatorwidgets.py:
	  Added option to refresh the TaggedSlider widget when setting the
	  bounds.

2007-08-08  stuart_p_wilson

	* [r6097] examples/lissom_whisker_barrels.ty:
	  First version that seems to work well

2007-08-08  ceball

	* [r6096] topo/tkgui/tkparameterizedobject.py:
	  Removed provision for packing hidden parameters (not necessary,
	  since pack_param is called manually). Clarified code for trying
	  to set widget bounds.

	* [r6095] topo/tkgui/tkparameterizedobject.py:
	  Moved some Parameter name formatting into a method, and added
	  capitalization. Renamed variables in, and cleaned up,
	  pack_param() (should be no visible change from this).

2007-08-01  jbednar

	* [r6094] doc/Downloads/cvs_text.php:
	  Removed apparently unused and unrecognized option to checkout

2007-07-31  ceball

	* [r6093] topo/tkgui/testpattern.py:
	  Hack to make pattern generator change update the plot to the
	  right stage. (This TestPattern class will be replaced with one
	  from testpattern2.py.)

	* [r6092] topo/tkgui/projectionpanel.py:
	  Fixed ConnectionFields window: now opens with correct
	  coordinates, if coordinates were specified.

	* [r6091] topo/tkgui/tkparameterizedobject.py:
	  Try to set widget's bounds, if Parameter has bounds.

2007-07-31  jbednar

	* [r6090] doc/Tutorials/lissom_oo_or_text.php,
	  doc/Tutorials/lissom_or_text.php,
	  doc/Tutorials/som_retinotopy_text.php:
	  Put -g at the end of command lines for safety

	* [r6089] topo/misc/commandline.py:
	  Changed -g to work wherever it is specified, instead of being
	  reordered, to allow command-line commands and scripts to control
	  an open GUI. Added indication that startup files are being
	  processed, since that recently caused confusion regarding psyco

	* [r6088] topo/tkgui/topoconsole.py:
	  Removed apparently unnecessary check for topo.gui_cmdline_flag

2007-07-31  ceball

	* [r6087] topo/tkgui/projectionpanel.py:
	  Renamed a variable; should be no visible change.

2007-07-30  jbednar

	* [r6086] topo/tkgui/projectionpanel.py:
	  Minor cleanup; should be no change.

2007-07-28  jbednar

	* [r6085] topo/misc/__init__.py:
	  Removed obsolete file

2007-07-27  jbednar

	* [r6084] topo/misc/commandline.py:
	  Moved GUI code after all command-line arguments have been
	  processed, to allow scripts to add items that will be used in the
	  GUI, and to avoid hiding missing imports in the scripts

	* [r6083] doc/Future_Work/current_text.php:
	  Added potentially useful toolboxes

2007-07-26  jbednar

	* [r6082] doc/User_Manual/commandline_text.php:
	  Added info about save_plotgroup

2007-07-24  jbednar

	* [r6081] doc/User_Manual,
	  doc/User_Manual/.cvsignore:
	  More to ignore

2007-07-23  jbednar

	* [r6080] examples/lissom_whisker_barrels.ty:
	  Added minor note

	* [r6079] examples/lissom_whisker_barrels.ty:
	  Added sketch of matlab interface to external whisker code

2007-07-23  ceball

	* [r6078]
	  topo/tests/testtkparameterizedobject.py:
	  Requires DISPLAY.

2007-07-23  jbednar

	* [r6077] examples/lissom_whisker_barrels.ty:
	  Initial version, based on converting lissom_oo_dr.ty 1.2 to have
	  no on/off channels. Not yet tested at all.

	* [r6076] topo/patterns/basic.py:
	  Added Sweeper class for wiping patterns across a surface; not
	  well tested yet

	* [r6075] examples/lissom_oo_dr.ty:
	  Removed explicit delays and instead implemented exactly as in the
	  CMVC book

	* [r6074] examples/Makefile:
	  Added lissom_oo_dr targets

	* [r6073] examples/lissom_oo_dr.ty:
	  Initial version; parameters and architecture set up to match the
	  CMVC book, but untested and the input pattern does not actually
	  move

	* [r6072] doc/Future_Work/current_text.php:
	  Minor addition

2007-07-22  jbednar

	* [r6071] topo/commands/pylabplots.py:
	  Clarified documentation and simplified implementation

	* [r6070] topo/commands/pylabplots.py:
	  Clarified docstring

2007-07-20  yschoe

	* [r6069] topo/sheets/slissom.py:
	  Added matrixplot facility for visualizing
	  membrane_potential_trace.

	* [r6068] topo/commands/pylabplots.py:
	  Added named option "aspect" to matrixplot() so that y/x aspect
	  ratio
	  can be adjusted for certain plots like time series. Higher aspect
	  ratio means taller y axis relative to the x axis.

2007-07-19  ceball

	* [r6067]
	  topo/tests/testtkparameterizedobject.py:
	  Removed mistaken test. (I had forgotten that the default
	  representation of a Parameter (in the GUI) is by a string
	  variable.)

2007-07-19  yschoe

	* [r6066] examples/leaky_lissom_or.ty:
	  Added one more membrane potential trace to highlight withi-group
	  synchronization.

2007-07-18  yschoe

	* [r6065] examples/leaky_lissom_or.ty:
	  Learning rate and membrane potential trace locations changed a
	  bit.

	* [r6064] examples/leaky_lissom_or.ty:
	  First spiking LISSOM example that shows rudimentary sync/desync
	  behavior.
	  Much needs to be cleaned up though.

	* [r6063] topo/sheets/slissom.py:
	  Dynamic threshold and membrane potential calculation/plotting
	  facilities added.
	  Simply do, e.g.
	  
	  topo.sim["V1"].plot_trace()
	  
	  in the example script.
	  This the a first rudimentary version that showd
	  synchronization/desynchronization behavior.

	* [r6062] topo/commands/pylabplots.py:
	  Added "style" option in vectorplot() so that data points can be
	  plotted as
	  points rather than interpolated lines.

2007-07-15  ceball

	* [r6061] topo/plotting/plotgroup.py:
	  Instantiate RangedParameter (RangedParameter is temporary, I
	  hope). Added sheet_type to XPlotGroup.

	* [r6060]
	  topo/tests/testtkparameterizedobject.py:
	  Added test to show a bug (currently failing).

	* [r6059] topo/tkgui/tkparameterizedobject.py:
	  Mofidications to comments and docs. No visible changes.

2007-07-14  ceball

	* [r6058] doc/Future_Work/current_text.php:
	  Added note.

2007-07-13  ceball

	* [r6057]
	  topo/tests/testtkparameterizedobject.py:
	  Modified comment and added commented-out code.

	* [r6056] topo/tkgui/tkparameterizedobject.py:
	  Added commented-out method.

	* [r6055] topo/tkgui/tkparameterizedobject.py:
	  Added minor note.

	* [r6054] topo/tkgui/templateplotgrouppanel.py:
	  Added reminder.

	* [r6053]
	  topo/tests/testtkparameterizedobject.py:
	  No visible change - slight simplification.

	* [r6052] topo/tkgui/tkparameterizedobject.py:
	  Updated some documentation.

	* [r6051]
	  topo/tests/testtkparameterizedobject.py:
	  Added to range-handling test.

	* [r6050]
	  topo/tests/testtkparameterizedobject.py:
	  Test when a parameter has a range.

	* [r6049]
	  topo/tests/testtkparameterizedobject.py:
	  Tests direct get/set of Parameters.

	* [r6048]
	  topo/tests/testtkparameterizedobject.py:
	  Added test for __getattribute__ and __setattr__.

	* [r6047] topo/tkgui/tkparameterizedobject.py:
	  Removed commented-out testing code (now in a test file) and
	  modified check for Parameter having a range.

	* [r6046] doc/User_Manual/problems_text.php:
	  Minor addition to text.

	* [r6045]
	  topo/tests/testtkparameterizedobject.py:
	  Initial version.

	* [r6044] topo/tkgui/tkparameterizedobject.py:
	  Classes have empty name attribute, so just because 'name'
	  attribute exists doesn't mean it will be valid.

	* [r6043] topo/tkgui/testpattern2.py:
	  Commented out unused method. Added some debugging print
	  statements. Corrected some mistakes.

2007-07-12  ceball

	* [r6042] topo/tkgui/testpattern2.py:
	  Pattern generator is now a parameter (and deals with list of
	  objects rather than classes so that changes are kept - might
	  revert that).

	* [r6041] topo/tkgui/testpattern2.py:
	  Continued simplifying. 'Apply to' buttons temporarily not
	  functional.

	* [r6040] topo/tkgui/testpattern2.py:
	  Corrected some mistakes.

	* [r6039] doc/Future_Work/current_text.php:
	  Moved another task to the bug tracker.

	* [r6038] doc/Future_Work/current_text.php:
	  Moved some more tasks to trackers.

	* [r6037] topo/tkgui/testpattern2.py:
	  Continued cleaning. Temporarily removed disparity support.

	* [r6036] topo/tkgui/testpattern2.py:
	  Removed unused methods.

	* [r6035] topo/tkgui/testpattern2.py:
	  Continued cleanup.

	* [r6034] topo/tkgui/testpattern2.py:
	  Continued writing.

	* [r6033] doc/Future_Work/current_text.php:
	  Added note about SF trackers. Moved two tasks to SF trackers.

	* [r6032] topo/commands/analysis.py:
	  Call grid plot in measure_rfs*() rather than in
	  ReverseCorrelation. measure_rfs_noise() updated to accept
	  input_sheet.

	* [r6031] topo/analysis/featureresponses.py,
	  topo/commands/pylabplots.py:
	  Moved grid plotting from ReverseCorrelation.

2007-07-11  ceball

	* [r6030] topo/commands/analysis.py:
	  Minor modification to comment.

	* [r6029] topo/commands/analysis.py:
	  measure_rfs() requires an input_sheet argument (at least for the
	  moment).

	* [r6028] topo/tkgui/plotgrouppanel.py:
	  RF plot option displays plot for specific sheet.

	* [r6027] topo/analysis/featureresponses.py:
	  RFs are calculated for all sheets for which measure_maps=True.

	* [r6026] topo/commands/analysis.py:
	  Pass input sheet to ReverseCorrelation.

	* [r6025] topo/analysis/featureresponses.py:
	  Correction to FeatureResponses.__init__ to accept params. Added
	  input_sheet parameter to ReverseCorrelation. ReverseCorrelation's
	  grid is now an array of arrays rather than a list of lists.

	* [r6024] topo/analysis/featureresponses.py:
	  Cut out more duplicated code.

	* [r6023] topo/analysis/featureresponses.py:
	  Removed apparently outdated JABHACKALERT.

2007-06-27  ceball

	* [r6022] doc/User_Manual/problems_text.php:
	  Initial version.

	* [r6021] topo/tkgui/testpattern2.py:
	  Added some markers, reorganized, removed ALERTs, removed a
	  workaround (left note).

	* [r6020] topo/tkgui/testpattern2.py:
	  Version 1.71 of testpattern.py. Going to re-work the test pattern
	  window in this file (since the test pattern window is complex).

	* [r6019] topo/tkgui/testpattern.py:
	  Minor simplifications, plus removed a HACKALERT that was in the
	  wrong place.

	* [r6018] topo/tkgui/projectionpanel.py:
	  Minor simplifications, plus added a HACKALERT.

	* [r6017] topo/tkgui/projectionpanel.py:
	  All ProjectionSheetPGPanels call refresh on sheet_change.
	  Corrected bug in ConnectionFieldsPanel's sheet_change method (if
	  x and y not specified, were not being reset to 0).

	* [r6016] topo/commands/analysis.py:
	  Renamed some variables for easier understanding - no visible
	  change.

	* [r6015] topo/tests/testplotfilesaver.py:
	  Uncommented a test, which now works.

	* [r6014] topo/tests/testplotfilesaver.py:
	  Plot file saving only works for topo.sim (not some other
	  Simulation with register=False); removed ALERTs related to this.

	* [r6013] topo/tests/testsnapshots.py:
	  Use a new topo.sim for the tests.

	* [r6012] topo/tests/testsnapshots.py:
	  Altered confusing 'Sheet.nominal_density' line, because if
	  GeneratorSheet's nominal_density is set in another test, setting
	  Sheet's nominal_density makes no difference. Added some
	  commented-out code. Added a HACKALERT.

	* [r6011] topo/tests/testsnapshots.py:
	  Corrected bug introduced in previous checkin: was loading
	  different snapshot from that saved.

2007-06-26  ceball

	* [r6010] topo/tkgui/plotgrouppanel.py:
	  Added comment for cleanup.

	* [r6009] topo/base/simulation.py:
	  Added ALERT, and note about how to get timing messages at the
	  commandline.

	* [r6008] doc/Future_Work/current_text.php:
	  Added task.

	* [r6007] /trunk/topographica, .cvsignore:
	  No longer ignore testsnapshot.typ: moved to topo/tests/

	* [r6006] topo/tests,
	  topo/tests/.cvsignore:
	  More to ignore.

	* [r6005] Makefile:
	  Added more to clean: testplotfilesaver's output images.

	* [r6004] Makefile:
	  Changed location of testsnapshot.typ.

	* [r6003] topo/tests/testsnapshots.py:
	  Added comment and changed save location to be in tests directory.

	* [r6002] topo/analysis/featureresponses.py:
	  Removed now-unnecessary hack (since timer object's __getstate__
	  no longer removes contents of the timer's lists).

	* [r6001] topo/base/simulation.py,
	  topo/commands/basic.py:
	  Moved don't-pickle-receive*-lists hack from timer to
	  topo.commands.basic.save_snapshot().

2007-06-25  jprovost

	* [r6000] topo/tests/testsnapshots.py:
	  Added test to make sure that saving/loading snapshots doesn't
	  break the ability to construct a new simulaiton.

	* [r5999] topo/tests/__init__.py:
	  Sorted the list of tests, so the execute in the same order on all
	  machines.

	* [r5998] topo/tests/testcf.py:
	  Fixed a test interaction affecting testcf.py

2007-06-24  ceball

	* [r5997] topo/analysis/featureresponses.py:
	  Intermediate checkin. Made ReverseCorrelation be a subclass of
	  FeatureResponses to cut down on code duplication. Might need to
	  think about the proper class hierarchy.

	* [r5996] topo/commands/analysis.py:
	  display=False by default for measure_rfs().

	* [r5995] topo/tests/testplotfilesaver.py:
	  Added ALERT. Added better filename prefix.

	* [r5994] topo/base/simulation.py:
	  Added to ALERT.

	* [r5993] topo/analysis/featureresponses.py:
	  Use timer object rather than local timing code.

	* [r5992] topo/tests,
	  topo/tests/.cvsignore:
	  More to ignore.

	* [r5991] topo/tests/testplotfilesaver.py:
	  Named the simulation so test's saved files always have the same
	  name.

	* [r5990] topo/commands/pylabplots.py:
	  Minor modification to comment.

2007-06-23  ceball

	* [r5989] topo/analysis/featureresponses.py:
	  Restored an ALERT.

	* [r5988] topo/base/simulation.py:
	  Intermediate checkin: began to merge slighly different timing
	  methods.

	* [r5987] topo/tests/testplotfilesaver.py:
	  Modified ALERT.

	* [r5986] topo/tests/testplotfilesaver.py:
	  Re-wrote to match new PlotGroupSavers. Currently doesn't work
	  (see ALERT).

	* [r5985] topo/plotting/plotfilesaver.py:
	  Added a comment.

	* [r5984] topo/plotting/plotgroup.py:
	  Can control which dictionary plot and update commands get
	  executed in (might not want it to be __main__.__dict__ if the
	  commands are imported somewhere other than __main__.__dict__).

	* [r5983] topo/commands/analysis.py:
	  Removed stray print statement.

	* [r5982] topo/commands/analysis.py:
	  Support previous syntax of save_group command (i.e. requesting
	  sheets and projections by name).

	* [r5981] topo/plotting/plotfilesaver.py:
	  Corrected oversight during update of plotgroup classes
	  (preventing projection plotgroup saving).

	* [r5980] doc/Future_Work/current_text.php:
	  Added more comments to task.

2007-06-22  rczhao

	* [r5979] /trunk/facespace/face_space_patterns.py:
	  Changed the way parameter 'caricaturization' is defined.

2007-06-22  jprovost

	* [r5978] topo/tests/testcf.py:
	  Tests for CFs and CFIters.

	* [r5977] topo/plotting/plotgroup.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py:
	  Changes and ALERTs to dealing with sheets with very large bounds.

	* [r5976] topo/tkgui/topoconsole.py:
	  Added 'Step' button to console.

	* [r5975] topo/projections/basic.py:
	  Fixed bug with OneToOneProjection.learning_fn

	* [r5974] topo/misc/numbergenerators.py:
	  Changed time_fn of ExponentialDecay to a CallableParameter, now
	  that the pickling problem is seeminglyfixed.

	* [r5973] topo/coordmapperfns/basic.py:
	  Added Pipeline, Polar2Cartesian, and Cartesian2Polar mappings.
	  Fixed bugs with AffineTransform subclasses.

	* [r5972] topo/base/simulation.py:
	  Fixed bug with Simulator.run(until=...), added some ALERTs

2007-06-22  ceball

	* [r5971] topo/analysis/featureresponses.py:
	  Moved timing code to SomeTimer.

	* [r5970] topo/base/simulation.py:
	  Intermediate checkin. Added a second timing method to SomeTimer
	  that in order to support slightly different timing use in
	  featureresponses.

	* [r5969] topo/tkgui/topoconsole.py:
	  Added update() call in timing_message() in case it's used without
	  timing_progress().

	* [r5968] topo/tkgui/projectionpanel.py:
	  Added support to ConnectionFieldsPanel for specifying a sheet on
	  creation.

	* [r5967] topo/tkgui/plotgrouppanel.py:
	  Right-click opening of Connection Fields plot now includes the
	  sheet.

	* [r5966] topo/tkgui/projectionpanel.py:
	  Fixed bug in ConnectionFieldsPanel causing it to ignore any
	  requested x and y coordinates on creation.

	* [r5965] topo/tkgui/plotgrouppanel.py:
	  Update titles when updating plots.

	* [r5964] topo/plotting/plotgroup.py:
	  Corrected typos (supposed to have been checked in several days
	  ago).

	* [r5963] topo/tkgui/topoconsole.py:
	  Added ALERT.

	* [r5962] topo/tkgui/connectionfieldspanel.py:
	  Moved ConnectionFieldsPanel into projectionpanel.py.

	* [r5961] topo/tkgui/featurecurvepanel.py:
	  Updated titling.

	* [r5960] topo/tkgui/topoconsole.py:
	  Updated import locations.

	* [r5959] topo/tkgui/projectionpanel.py:
	  Moved ConnectionFieldsPanel into projectionpanel.py.

	* [r5958]
	  topo/tkgui/projectionactivitypanel.py,
	  topo/tkgui/projectionpanel.py:
	  Moved ProjectionActivityPanel into projectionpanel.py (and
	  corrected a mistake in the titling).

	* [r5957] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionactivitypanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Simplified titling.

2007-06-21  ceball

	* [r5956] topo/tkgui/__init__.py:
	  Added to comment.

2007-06-20  ceball

	* [r5955] topo/tkgui/topoconsole.py:
	  Added (test) option of having auto-refresh panels update once per
	  timing object iteration: allows one to see model in 'slow motion'
	  without having to press the 'Go' button over and over.

	* [r5954]
	  topo/tests/testtemplateplotgrouppanel.py:
	  Commented out test that isn't testing anything but did start
	  failing...

	* [r5953] doc/Future_Work/current_text.php:
	  Added to note.

	* [r5952] topo/base/parameterclasses.py:
	  Added ALERT.

	* [r5951] topo/base/parameterizedobject.py:
	  Added HACKALERT.

	* [r5950] topo/tkgui/topoconsole.py:
	  Use simulation's timing object rather than local timing code.
	  Only open progress window for durations of 10 or more. Added some
	  notes about progress window.

	* [r5949] topo/commands/basic.py:
	  Added hack for pickling of timer object.

	* [r5948] topo/base/simulation.py:
	  Integrated timing object with a 'run_and_time' method of
	  Simulation.

	* [r5947] topo/base/parameterizedobject.py:
	  Added some notes.

	* [r5946] topo/base/arrayutils.py:
	  Added HACKALERT.

	* [r5945] topo/tests/__init__.py:
	  Added to note.

	* [r5944] topo/base/simulation.py:
	  Added some ALERTs.

	* [r5943] doc/Future_Work/current_text.php:
	  Added note about decimal module.

	* [r5942] topo/base/simulation.py:
	  Added HACKALERT.

	* [r5941] topo/base/simulation.py:
	  Intermediate checkin. Made timing object a ParameterizedObject.

	* [r5940] doc/Future_Work/current_text.php:
	  Added note.

	* [r5939] doc/Future_Work/current_text.php:
	  Added some notes.

2007-06-19  rczhao

	* [r5938] /trunk/facespace/face_space.ty,
	  /trunk/facespace/perception.ty:
	  Modified parameters for experiments

2007-06-19  jbednar

	* [r5937] topo/projections/basic.py:
	  Cleaned up typos and formatting

2007-06-18  ceball

	* [r5936] topo/base/simulation.py:
	  Added first draft of a Timing object. Needs some more features
	  before using it to replace various bits of timing code around
	  topographica.

	* [r5935] topo/plotting/plotgroup.py,
	  topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Some more refactoring of GUI classes (still not finished).
	  Removed Parameters from FeatureCurvePlotGroup that are now
	  unnecessary.

	* [r5934] topo/tkgui/tkparameterizedobject.py:
	  Removed a stray print statement.

2007-06-17  ceball

	* [r5933] topo/tkgui/plotgrouppanel.py:
	  Added to comment.

	* [r5932] topo/plotting/plotgroup.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Removed stray print statements.

	* [r5931] topo/tkgui/topoconsole.py:
	  Updates for changes to PlotGroupPanel classes.

	* [r5930] topo/tkgui/tkparameterizedobject.py:
	  Multiple changes, but 2 significant ones: (1) Brought in changes
	  from tkgui_parameterization_branch; (2) RangedParameters get
	  translation between name and object for display in GUI. Whole
	  file now needs a review.

	* [r5929] topo/tkgui/testpattern.py:
	  Patchwork of updates to keep current TestPattern class working
	  with new plotgroups. (At least it opens without crashing and
	  seems to work as well as before.)

	* [r5928] topo/tkgui/projectionpanel.py:
	  Brought in changes from tkgui_parameterization_branch, with
	  additional changes to generate_plotgroup mechanism and
	  sheet+projection changing.

	* [r5927] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionactivitypanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Brought in changes from tkgui_parameterization_branch, with
	  additional changes to generate_plotgroup mechanism.

	* [r5926] topo/tkgui/plotgrouppanel.py:
	  Brought in changes from tkgui_parameterization_branch. Began to
	  simplify updating vs drawing plots.

	* [r5925] topo/tkgui/featurecurvepanel.py:
	  Brought in changes from tkgui_parameterization_branch. Trying
	  'redraw' button on full-field version.

	* [r5924] topo/plotting/plotgroup.py:
	  Brought in changes from tkgui_parameterization_branch. Further
	  improved separation of drawing and updating plots.

	* [r5923] topo/plotting/plotfilesaver.py:
	  Rather than having parameters on the *Saver objects shadowing
	  those on the underlying PlotGroups, just pass parameters to the
	  PlotGroups. Added Connection Fields saver.

	* [r5922] topo/commands/analysis.py:
	  Set parameters directly on PlotGroup rather than on
	  PlotFileSaver.

	* [r5921] topo/tkgui/translatorwidgets.py:
	  Added set_bounds() method to taggedslider.

	* [r5920] topo/base/boundingregion.py,
	  topo/base/parameterizedobject.py:
	  Added some comments about __getstate__ and friends.

2007-06-16  jbednar

	* [r5919] topo/base/projection.py:
	  Fixed typos in comments

2007-06-15  jprovost

	* [r5918] topo/base/parameterizedobject.py:
	  Removed deepcopy() of Parameters.

	* [r5917] topo/tkgui/editorobjects.py:
	  Fixed minor bug with doc strings.

	* [r5916] topo/projections/basic.py:
	  Added OneToOneProjection

	* [r5915] topo/patterns/basic.py:
	  Added Null pattern generator, a subclass of Constant

	* [r5914] topo/sheets/saccade.py:
	  Fixed activity_centroid() to handle the case where all activity
	  is zero.

	* [r5913] topo/sheets/generatorsheet.py:
	  Added SequenceGeneratorSheet for generating timed sequences of
	  inputs.

	* [r5912] topo/base/projection.py:
	  Updated ProjectionSheet.projections() to save a few keystrokes
	  when getting a single named projection.

	* [r5911] topo/base/parameterclasses.py:
	  Updated some error messages to better show the attribute name.

	* [r5910] topo/base/parameterizedobject.py:
	  Added Parameter.attrib_name() for generating error messages.

	* [r5909] topo/base/cf.py:
	  Added hack alert.

2007-06-15  ceball

	* [r5908] topo/tkgui/topoconsole.py:
	  Added HACKALERT.

2007-06-14  jbednar

	* [r5907] topo/base/cf.py:
	  Fixed bug since version 1.85: the projection's output_fn was
	  effectively being ignored because it was called not on the
	  Projection activity but on a stray throwaway object. I don't know
	  of any case where the Projection output_fn was being used, so it
	  hasn't been noticed

	* [r5906] topo/base/cf.py:
	  Removed mistaken alert

2007-06-13  jprovost

	* [r5905] topo/base/cf.py:
	  Added some ALERTs, and a typecheck.

2007-06-13  ceball

	* [r5904] topo/base/simulation.py:
	  Added more to an error message. Added an alert.

	* [r5903] topo/base/parameterclasses.py:
	  Added some comments.

	* [r5902] topo/base/parameterizedobject.py:
	  __setup_params() renamed to _setup_params() so it can be
	  overridden in subclasses. Added hack to allow some kind of a
	  system for passing warnings around (...to the gui).

2007-06-11  ceball

	* [r5901] doc/Future_Work/current_text.php:
	  Minor update to task.

	* [r5900]
	  topo/tests/testparameterizedobject.py:
	  Changes to some comments.

	* [r5899]
	  topo/tests/testparameterizedobject.py:
	  Added another test, plus an ALERT.

	* [r5898]
	  topo/tests/testparameterizedobject.py:
	  Initial version.

2007-06-10  ceball

	* [r5897] doc/Future_Work/current_text.php:
	  Update to task about test results on web.

	* [r5896] topo/tests/__init__.py:
	  Return the TestResult instance from run().

2007-06-08  antolikjan

	* [r5895]
	  topo/plotting/default_plottingscript.py:
	  This is the default plotting script that is used by run_batch
	  command

	* [r5894] topo/misc/commandline.py:
	  Added the new run_batch commands that allows running Topographica
	  simulation in batch mode

2007-06-07  rczhao

	* [r5893] /trunk/facespace/aam_fit_data.h5,
	  /trunk/facespace/aam_fit_setup.py,
	  /trunk/facespace/face_space.ty,
	  /trunk/facespace/face_space_patterns.py,
	  /trunk/facespace/perception.ty, /trunk/facespace/run_test.py:
	  Experimental face space simulation package for Topographica.

	* [r5892] /trunk/facespace, /trunk/facespace/.DS_Store,
	  /trunk/facespace/__init__.py, /trunk/facespace/aam_fit.pyx:
	  Experimental face space simulation package for Topographica.

2007-06-07  ceball

	* [r5891] doc/Future_Work/current_text.php:
	  Added notes to mac task.

	* [r5890] topo/tests/som_retinotopy.ty_DATA:
	  Data from 2007/05/05 06:00 GMT CVS version of topographica.
	  Updated because density of example was changed.

	* [r5889] doc/Future_Work/current_text.php:
	  Added some tasks, and updated others.

2007-06-06  jprovost

	* [r5888] topo/coordmapperfns/basic.py:
	  Added AffineTransform mapper.

	* [r5887] topo/base/projection.py:
	  Removed unnecessary reference to topo.sim

	* [r5886] topo/base/simulation.py:
	  - Removed redundant type checking on EPConnection src and dest.
	  - Allowed Simulation.grid_layout to take references to simulation
	  objects, not just names.

	* [r5885] topo/base/parameterclasses.py:
	  - Small change to instance method wrapping in CallableParameter
	  - Added DictParameter.

	* [r5884] topo/base/cf.py:
	  Added (optional) support for null CFs

	* [r5883] doc/Future_Work/current_text.php:
	  Added item for Mac GUI cleanup.

2007-06-06  chrispalmer

	* [r5882] topo/commands/analysis.py:
	  defaults at a high scale to allow mapping of rfs for
	  lissom_oo_or.ty, this model currently recieves very week input to
	  V1 and should probably be modified

2007-06-06  ceball

	* [r5881] topo/tkgui/templateplotgrouppanel.py:
	  Hack to get normalize from the template.

2007-06-05  ceball

	* [r5880] topo/tkgui/topoconsole.py:
	  Updated to use plotgroup_label, not plotgroup_key. Updated
	  open_test_pattern_window()

	* [r5879] topo/tkgui/testpattern.py:
	  Hacked to work with changes to PlotGroupPanel: needs major
	  overhaul. These changes don't need to copied to
	  tkgui_parameterization_branch (that's where the major overhaul
	  will occur.

2007-06-04  jbednar

	* [r5878] topo/analysis/featureresponses.py:
	  Cleaned up comments and added alerts

	* [r5877] topo/commands/pylabplots.py:
	  Minor space cleanup

	* [r5876] topo/analysis/featureresponses.py:
	  Minor improvement to docstring

	* [r5875] topo/commands/analysis.py:
	  Turned off display by default

	* [r5874] topo/analysis/featureresponses.py:
	  Cleaned up cruft left in previous checkin. Localized temporary
	  code for ReverseCorrelation into a small area so that it can be
	  moved later

	* [r5873] topo/commands/analysis.py:
	  Cleaned up cruft left in previous checkin

	* [r5872] topo/tkgui/plotgrouppanel.py:
	  Trivial change to title string

	* [r5871] topo/plotting/plotfilesaver.py:
	  Removed space and ampersand characters from filenames

	* [r5870] topo/plotting/plotfilesaver.py:
	  Added exception for common error condition

	* [r5869] topo/commands/analysis.py,
	  topo/commands/basic.py,
	  topo/plotting/plotfilesaver.py:
	  Moved save_plotgroup command from basic.py to analysis.py because
	  it only works if other things from analysis.py are loaded

	* [r5868] topo/plotting/plotfilesaver.py:
	  Added filename_format parameter and cleaned up

	* [r5867] topo/commands/basic.py,
	  topo/plotting/plotfilesaver.py:
	  Moved save_plotgroup command from topo/plotting/plotfilesaver.py
	  to topo/commands/basic.py; cleaned up formatting and organization

	* [r5866] topo/analysis/featureresponses.py:
	  Removed bogus spaces

2007-06-04  ceball

	* [r5865] topo/tkgui/plotgrouppanel.py:
	  Corrected bug in bwidget version: after changing PlotGroupPanel
	  back to being a Frame, forgot to set certain attributes on its
	  master (the window) rather than on itself.

2007-06-04  jbednar

	* [r5864] topo/commands/analysis.py:
	  Fixed defaults mistakenly changed.

	* [r5863] topo/tkgui/plotgrouppanel.py:
	  Fixed newline at end of file

2007-06-04  chrispalmer

	* [r5862] topo/analysis/featureresponses.py:
	  adds method for figuring out receptive fileds using reverse
	  correlation

	* [r5861] topo/commands/analysis.py:
	  adds options to map receptive fileds using reverse correlation

	* [r5860] topo/tkgui/plotgrouppanel.py:
	  adds option to view receptive fields for individual units

2007-06-03  ceball

	* [r5859] topo/tests/utils.py:
	  Added note to myself.

	* [r5858] topo/tkgui/topoconsole.py:
	  Panels are back to being Frames.

	* [r5857] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionactivitypanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Began switching to using new style Panel classes; users might
	  notice some problems until the updates are complete.

	* [r5856] topo/tkgui/plotgrouppanel.py:
	  Added comment.

2007-06-02  ceball

	* [r5855] topo/plotting/plotfilesaver.py:
	  Added assertion statements to catch misnamed projections/sheets.
	  (The errors raised by the PlotGroups are too cryptic to realize
	  what's going wrong if you specify a projection that doesn't exist
	  for a sheet.)

2007-05-31  jbednar

	* [r5854] topo/plotting/plotfilesaver.py:
	  Removed bogus print statement

	* [r5853] topo/plotting/plotfilesaver.py:
	  Added save_plotgroup command as a simple interface. Changed file
	  format from PNG to png.

2007-05-31  ceball

	* [r5852] topo/plotting/plotfilesaver.py:
	  Various changes that were not present in previous checkins but
	  should have been (i.e. were listed in the log messages). Started
	  ImageCompositor class.

	* [r5851] topo/plotting/plotfilesaver.py:
	  Added a comment.

	* [r5850] topo/plotting/plotfilesaver.py:
	  Continued writing. The projection saver now probably works for
	  projection plots where the images are different sizes.

2007-05-30  ceball

	* [r5849] topo/plotting/plotfilesaver.py:
	  Added some notes.

	* [r5848] topo/plotting/plotfilesaver.py:
	  Added beginning of CFProjectionPlotGroupSaver. Removed old,
	  commented-out code. This version isn't suitable for anyone to
	  use.

	* [r5847] topo/plotting/plotfilesaver.py:
	  Added temporary filename prefix parameter.

	* [r5846] topo/plotting/plotfilesaver.py:
	  Changes to comments.

	* [r5845] topo/plotting/plotfilesaver.py:
	  Commented out existing code. Added quick first implementation to
	  allow saving of templateplotgroups (e.g. activity, orientation
	  preference).

	* [r5844] topo/tkgui/templateplotgrouppanel.py:
	  (Re. new class.) Update command appears in the correct location.

	* [r5843] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  (Re. new classes.) Updated with changes to right-click menu.

	* [r5842] topo/tkgui/templateplotgrouppanel.py:
	  Added saving of any canvas (to postscript).

	* [r5841] topo/tkgui/tkguiwindow.py:
	  Change to comments and imports: no visible changes.

	* [r5840] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Use indexing-by-name Menu class.

	* [r5839] topo/tkgui/tkguiwindow.py:
	  Made a subclass of Tkinter.Menu that allows indexing by some
	  (fixed) name, rather than just by current position.

	* [r5838] topo/tkgui/plotgrouppanel.py:
	  (Re. new, unused class.) Continued matching behavior of current
	  panel.

2007-05-29  ceball

	* [r5837] topo/tkgui/plotgrouppanel.py:
	  (Re. new, unused classes.) Minor changes: some rearranging and
	  some fixes.

2007-05-27  ceball

	* [r5836] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/tkparameterizedobject.py:
	  Removed '_widgets2' and made _widgets a dictionary.

2007-05-26  ceball

	* [r5835] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  (Re. new, unused classes.) Changes to match alterations to
	  tkparameterizedobject (which has become a ParameterizedObject).

	* [r5834] topo/tkgui/tkparameterizedobject.py:
	  Renamed TkPO to TkParameterizedObjectBase, and WidgetDrawingTkPO
	  to TkParameterizedObject. TkParameterizedObjectBase is back to
	  being a ParamterizedObject that creates Tkinter.Variable shadows
	  of its Parameters, but now it also shadows Parameters of any
	  optional additional ParameterizedObjects it is given.

2007-05-24  ceball

	* [r5833] topo/tkgui/templateplotgrouppanel.py:
	  (re. new, unused class) Minor change to match plotgrouppanel
	  becoming a ParameterizedObject.

	* [r5832] topo/tkgui/plotgrouppanel.py:
	  (re. new, unused classes) Made PlotGroupPanel2 be a
	  ParameterizedObject and have parameters. Stores another
	  WidgetDrawingTkPO to edit those parameters (can't stay like
	  that).

	* [r5831] topo/tkgui/tkparameterizedobject.py:
	  Added (trial) ButtonParameter. WidgetDrawingTkPO is not a Frame
	  anymore (since it could be drawing its widgets on anything, so
	  there is no benefit that it's a Frame).

2007-05-23  ceball

	* [r5830] topo/tkgui/plotgrouppanel.py:
	  (Re. new, unused classes.) Added some notes. Removed special code
	  for integer scaling (there's an alert in plotgroup now about
	  that).

	* [r5829] topo/plotting/plotgroup.py:
	  Added strength-only parameter to TemplatePlotGroup, but it
	  currently does nothing. Added hackalerts about that and
	  PlotGroup's integerscaling parameter.

	* [r5828] topo/tkgui/plotgrouppanel.py:
	  (Re. new, unused classes.) Reduce/enlarge buttons work in
	  history. Removed alert that is covered by one in plotgroup
	  itself.

	* [r5827] topo/tkgui/plotgrouppanel.py:
	  (Re. new, unused classes.) Updated (and simplified a little) the
	  history code to work with new panel.

	* [r5826] topo/tkgui/tkparameterizedobject.py:
	  Added possibly temporary list for accessing widgets of
	  WidgetDrawingTkPO.

	* [r5825] topo/tkgui/tkparameterizedobject.py:
	  Added comment.

	* [r5824] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Made new panels look more like the old ones. Added some comments
	  to help my reading (temporary).

	* [r5823] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  (Re. new, unused classes.) Began to clean up some naming. Also
	  additional minor changes.

	* [r5822] topo/tkgui/tkparameterizedobject.py:
	  Added mechanism to allow a callback when a tk variable is set
	  (e.g. to allow a panel to have a function called when the
	  parameter is changed). Also, widget can optionally be drawn
	  inside a supplied frame (untested).

	* [r5821] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Continued working on new versions of PlotGroupPanel and
	  TemplatePlotGroupPanel; should be no change to code of existing
	  panels. (New versions are currently a mess.)

2007-05-22  jbednar

	* [r5820] topo/analysis/featureresponses.py:
	  Fixed bug introduced in revision 1.12 on 15 March 2007; as part
	  of timing code added to show progress on measuring maps, input
	  patterns were being presented twice instead of only once. This
	  did not affect the normal process of measuring maps, but for some
	  networks that keep track of activation counts or have some other
	  unusual architectures, there may have been some effect on the
	  results of map or curve measurement

2007-05-20  ceball

	* [r5819] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Working on making PlotGroupPanel and TemplatePlotGroupPanel
	  WidgetDrawingTkPOs. The existing classes are not changed (i.e. no
	  visible changes).

	* [r5818] topo/tkgui/tkparameterizedobject.py:
	  Labels are added by WidgetDrawingTkPO. Commented out demo code.

	* [r5817] topo/tkgui/tkparameterizedobject.py:
	  Use get_param and set_param methods to access TKPO's
	  parameterized_object's parameters (if that's even going to be
	  necessary...).

2007-05-19  ceball

	* [r5816] topo/tkgui/tkparameterizedobject.py:
	  t=TkPO() provides access to its parameterized_object's parameter
	  p via t.p__param, rather than as t.p (since t could also be
	  another type of object with its own attributes). This is just for
	  testing: might revert. Also, Tkinter Variables (shadows of
	  Parameters) are now guaranteed never to return out-of-date
	  values. Adding a refresh method that gets called e.g. on focus in
	  for a WidgetDrawingTkPO would keep the GUI pretty well in sync
	  with the underlying ParameterizedObject.

	* [r5815] topo/tkgui/connectionfieldspanel.py:
	  Added comment.

	* [r5814] topo/tkgui/tkparameterizedobject.py:
	  WidgetDrawingTkPO is a Frame, too. Added plotgroup template
	  example.

	* [r5813] topo/tkgui/tkparameterizedobject.py:
	  No longer pass through unused **params.

	* [r5812] topo/tkgui/tkparameterizedobject.py:
	  Commented out demo code, and added a docstring.

	* [r5811] topo/tkgui/tkparameterizedobject.py:
	  Change to comment.

	* [r5810] topo/tkgui/tkparameterizedobject.py:
	  Updates to documentation, some renaming, and some cleaning.

	* [r5809] topo/tkgui/propertiesframe.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/translatorwidgets.py:
	  Renamed TaggedSlider's 'tagvariable' to 'variable'.

2007-05-18  jbednar

	* [r5808]
	  doc/Developer_Manual/optimization_text.php:
	  Added notes about optimizing Python

2007-05-18  ceball

	* [r5807] topo/tkgui/tkparameterizedobject.py:
	  Removed some irrelevant docstrings. Corrected comment.

	* [r5806] topo/tkgui/tkparameterizedobject.py:
	  No visible change: altered variable name and added comment.

	* [r5805] topo/tkgui/tkparameterizedobject.py:
	  First pass at using a subobject to proxy Parameters.

2007-05-18  rczhao

	* [r5804] external,
	  external/.cvsignore,
	  external/Makefile:
	  Added pytables, which required adding pyrex and hdf5. hdf5
	  doesn't compile yet, but it's possible to get things working with
	  an external hdf5 library for now

2007-05-18  ceball

	* [r5803] topo/tkgui/tkparameterizedobject.py:
	  Minor change to have correct widget chosen automatically.

2007-05-18  jbednar

	* [r5802] topo/commands/analysis.py,
	  topo/patterns/image.py:
	  Changed location of imports; moved FaceSpace2Dfromfile into
	  face-space/face_space_patterns.py and Caricaturization Preference
	  maps into face-space/analysis.py

	* [r5801] doc/Future_Work/current_text.php:
	  Added to-do item

2007-05-18  ceball

	* [r5800] topo/tkgui/tkparameterizedobject.py:
	  Initial version; currently just to test out mechanisms for
	  Tkinter Variable/Topographica Parameter coupling (tkpo.py as sent
	  by e-mail to JAB 2006/05/17, slightly modified for Topographica).

2007-05-18  jbednar

	* [r5799] examples/face_space.ty,
	  facedb,
	  topo/patterns/face.py:
	  Moved examples/face_space.ty to face-space/face_space.ty,
	  facedb/aam_fit_data.h5 to face-space/aam_fit_data.h5, and
	  topo/patterns/face.py to face-space/face_space_patterns.ty

2007-05-18  ceball

	* [r5798] topo/tkgui/plotgrouppanel.py:
	  Removed auto-resize checkbutton. Window automatically resized
	  whenever a user does something to change the size (e.g. enlarges
	  the plots).

2007-05-18  rczhao

	* [r5797] external/Pyrex-0.9.5.1a.tar.gz:
	  A C extension for Python, required for PyTables compilation

	* [r5796] external/pytables-20070518.tar.gz:
	  A Python-HDF5 interface, enabling hierarchical dataset for
	  handling large amounts of datasets

	* [r5795] examples/face_space.ty:
	  Reverted to r 1.7 and modified codes based on r 1.7

	* [r5794] facedb,
	  facedb/aam_fit_data.h5:
	  IMM Face Database for use with examples/face_space.ty

	* [r5793] examples/face_space.ty:
	  Used a new class FaceSpace2D defined in patterns/face.py

	* [r5792] topo/patterns/face.py:
	  Face Generator based on shapes and textures stored in hdf5
	  database.

2007-05-16  ceball

	* [r5791] topo/tkgui/plotgrouppanel.py:
	  Using bwidget, scrollbars should no longer appear when reducing
	  the plot sizes in a fixed window (untested so far).

	* [r5790] topo/tkgui/plotgrouppanel.py:
	  Removed alert about message bar (since it matches topoconsole's).
	  Added question about button configuration when looking at
	  history.

	* [r5789] topo/tkgui/plotgrouppanel.py:
	  Removed borders from invisible sizing frames (left on by
	  mistake).

	* [r5788] topo/tkgui/plotgrouppanel.py:
	  Made ResizableScrollableFrame out of the scrollable frame code in
	  BasicPlotGroupPanel. Also fixed centering problem (i.e. plots are
	  centered now when using the bwidget version).

	* [r5787] topo/tkgui/testpattern.py:
	  Renamed auto_refresh to auto_refresh_var.

	* [r5786] topo/base/simulation.py:
	  Minor change to argument name for consistency.

	* [r5785] topo/base/parameterclasses.py:
	  Added question.

	* [r5784] topo/base/simulation.py:
	  Minor change to a docstring.

2007-05-13  ceball

	* [r5783] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionactivitypanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Renamed self.auto_resize to self.auto_resize_var, and
	  self.auto_refresh to self.auto_refresh_var.

	* [r5782] topo/tkgui/projectionpanel.py:
	  Intermediate (temporary) class hierarchy: the abstract
	  ProjectionRelatedPanel(TemplatePlotGroupPanel); the abstract
	  CFRelatedPanel(ProjectionRelatedPanel);
	  CFProjectionPanel(CFRelatedPanel);
	  ConnectionFieldsPanel(CFRelatedPanel);
	  ProjectionActivityPanel(ProjectionRelatedPanel).

	* [r5781]
	  topo/tkgui/projectionactivitypanel.py:
	  Use ProjectionRelatedPanel as the parent.

	* [r5780] topo/tkgui/connectionfieldspanel.py:
	  Use CFPRelatedPanel as the parent.

	* [r5779] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionpanel.py:
	  Moved history button updates up to parent of the projection
	  panels.

	* [r5778] topo/tkgui/templateplotgrouppanel.py:
	  Added a HACKALERT.

	* [r5777] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionpanel.py:
	  Moved restore_panel_environment() up to SomethingPanel (even
	  thought the classes are going to change, this reduces
	  duplication.

	* [r5776] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionpanel.py:
	  Don't set the situate status (temporary; avoids the
	  request-projection-views-from-non-cfsheets bug described in a
	  CEBHACKALERT in projectionpanel).

	* [r5775] topo/tkgui/projectionpanel.py,
	  topo/tkgui/topoconsole.py:
	  Renamed ProjectionPanel to CFProjectionPanel.

	* [r5774] topo/tkgui/projectionpanel.py:
	  Corrected a presumable indentation error. Updated comment.

	* [r5773] topo/tkgui/projectionpanel.py:
	  Removed stray print statement.

	* [r5772] topo/tkgui/projectionpanel.py:
	  Fix mistake in a previous checkin: display sheet names in the
	  sheet menu, rather than sheets themselves.

	* [r5771] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionactivitypanel.py,
	  topo/tkgui/projectionpanel.py:
	  Renamed self.situate to self.situate_var. Restored previous
	  default situate and auto-refresh states to various panels
	  (differences between them had been lost).

	* [r5770] topo/tkgui/projectionpanel.py:
	  valid_context() checks for CFProjections, not just Projections
	  (since the classes expect CFs).

	* [r5769] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionactivitypanel.py,
	  topo/tkgui/projectionpanel.py:
	  One valid_context() method for ConnectionFieldsPanel,
	  ProjectionPanel, ProjectionActivityPanel. (I assume that the
	  valid_context() methods were out of date for
	  ConnectionFieldsPanel and ProjectionActivityPanel; if that
	  assumption is wrong, then the differences should be restored.)

2007-05-12  ceball

	* [r5768] topo/tkgui/projectionpanel.py:
	  Added alert. Removed outdated docstring.

	* [r5767] topo/tkgui/plotgrouppanel.py:
	  Auto-refresh and auto-resize variables are traced, allowing the
	  corresponding methods to be called whenever the variables change
	  (rather than when a widget representing the variables changes).

	* [r5766] topo/tkgui/plotgrouppanel.py:
	  Removed unused import.

	* [r5765] topo/tkgui/connectionfieldspanel.py:
	  Simplification of update_plotgroup_variables().

	* [r5764] topo/tkgui/connectionfieldspanel.py:
	  Removed self.x, self.y. Renamed self.x_str to self.x_var.

	* [r5763] topo/tkgui/connectionfieldspanel.py:
	  Use float() to convert x,y rather than eval()ing in __main__.

	* [r5762] topo/tkgui/projectionpanel.py:
	  Commented out seemingly unused import.

	* [r5761] topo/tkgui/projectionpanel.py:
	  Just change density_var to float, rather than eval()ing in
	  __main__.

	* [r5760]
	  topo/tkgui/projectionactivitypanel.py:
	  Cleaned up imports.

	* [r5759]
	  topo/tkgui/projectionactivitypanel.py:
	  Intermediate checkin: started to move common code from
	  ConnectionFieldsPanel, ProjectionPanel, and
	  ProjectionActivityPanel into a shared parent class.

	* [r5758] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionpanel.py:
	  Intermediate checkin: started to move common code from
	  ConnectionFieldsPanel and ProjectionPanel into a shared parent
	  class.

	* [r5757] topo/tkgui/projectionpanel.py:
	  Mover super() call to the start of __init__.

	* [r5756] topo/tkgui/projectionpanel.py:
	  Removed individual alerts about things only being valid for CFs:
	  they are covered by the general JABALERT. Minor simplification to
	  _add_sheet_menu.

	* [r5755] topo/tkgui/projectionpanel.py:
	  More renaming: should be no visible change.

	* [r5754] topo/tkgui/projectionpanel.py:
	  Removed projection_refresh() method since it doesn't do anything.

	* [r5753] topo/tkgui/projectionpanel.py:
	  Replaced self.density with a method to return the float density
	  from its Tkinter string variable.

	* [r5752] topo/tkgui/projectionpanel.py:
	  More renaming and cleaning; should be no visible changes.

	* [r5751] topo/tkgui/projectionpanel.py:
	  More renaming: should be no visible change.

	* [r5750] topo/tkgui/projectionpanel.py:
	  Renamed 'region' to 'sheet' wherever it appeared. Removed unused
	  imports.

	* [r5749] topo/misc/keyedlist.py:
	  Added comment about alternatives to KeyedList.

	* [r5748] topo/base/projection.py:
	  Removed comment left in by mistake.

	* [r5747] topo/tkgui/projectionpanel.py:
	  Simplified _create_projection_dict(). Should be no visible
	  change.

2007-05-11  ceball

	* [r5746] topo/tkgui/projectionpanel.py:
	  Replaced HACKALERT with ALERT: ProjectionPanel now at least
	  checks that the Projections are CFProjections.

	* [r5745] topo/tkgui/projectionpanel.py:
	  Minor simplifications to _create_projection_dict() (should be no
	  visible change).

	* [r5744] topo/base/projection.py:
	  Minor modification to docstring.

	* [r5743] topo/plotting/plotgroup.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionactivitypanel.py,
	  topo/tkgui/projectionpanel.py:
	  Where we just want a list of the Projections into a
	  ProjectionSheet, use the sheet's list of in_connections (i.e.
	  replace projections().values() with in_connections).

	* [r5742] topo/base/projection.py:
	  Removed redundant assertion (connections are guaranteed to be
	  Projections at connection time).

	* [r5741] topo/base/simulation.py:
	  Minor change to comment.

	* [r5740] topo/base/projection.py:
	  Corrected mistake in previous checkin.

	* [r5739] topo/base/projection.py:
	  Updated numpy import statement (no visible change).

	* [r5738] topo/tkgui/plotgrouppanel.py:
	  Added a comment.

2007-05-09  ceball

	* [r5737] topo/tkgui/topoconsole.py:
	  Changed CommandPrompt to be a Tkinter.Frame.

	* [r5736] doc/Future_Work/current_text.php:
	  Rearranged some tasks and removed comment at the start.

	* [r5735] doc/Future_Work/current_text.php:
	  Updates to some tasks, plus some new ones.

2007-05-07  jbednar

	* [r5734]
	  doc/Tutorials/som_retinotopy_text.php,
	  examples/som_retinotopy.ty:
	  Made default size be more practical

	* [r5733] doc/Future_Work/current_text.php:
	  More to do

2007-05-07  ceball

	* [r5732] topo/tkgui/topoconsole.py:
	  Some renaming (no visible changes).

	* [r5731] topo/tkgui/plotgrouppanel.py:
	  Added comment.

	* [r5730] topo/tkgui/topoconsole.py:
	  Removed comment, changed relief of learning_frame, changed title
	  of progress bar.

	* [r5729] topo/tkgui/plotgrouppanel.py:
	  Uncommented maxsize (works on linux, at least), and reduced the
	  maximum size of the plot frame.

2007-05-06  ceball

	* [r5728] topo/tkgui/plotgrouppanel.py:
	  Initial scrolled frame size is now small (it can grow if
	  required).

	* [r5727] topo/tkgui/plotgrouppanel.py:
	  Replaced Pmw's scrollable frame with one from bwidget. If bwidget
	  is built, scrollbars are used - if not, then the behavior is as
	  before. The scrolling and resizing still isn't perfect, and it's
	  a bit complex. Restored auto-resize check button code.

	* [r5726] topo/tkgui/__init__.py:
	  Added a note.

	* [r5725] doc/Future_Work/current_text.php:
	  Minor updates.

	* [r5724] topo/tkgui/topoconsole.py:
	  Added demo progress bar for learning (for anyone who has done
	  'make -C external bwidget').

2007-05-05  ceball

	* [r5723] topo/plotting/templates.py:
	  Corrected variable name.

	* [r5722] topo/tkgui/templateplotgrouppanel.py:
	  Added 'Histogram' & 'Gradient' to plot titles.

	* [r5721] topo/tkgui/templateplotgrouppanel.py:
	  Added a comment.

	* [r5720] topo/tkgui/templateplotgrouppanel.py:
	  Added gradient plot to right-click menu.

	* [r5719] topo/commands/pylabplots.py:
	  Added gradient plot (from JB's octave code).

	* [r5718] topo/tkgui/topoconsole.py:
	  Took the command prompt off TopoConsole, which allowed a lot of
	  simplification of the code. (Unfortunately now TopoConsole looks
	  a little spartan.) The command prompt is now a class, and a
	  command prompt window can be opened from the simulation menu.

	* [r5717] topo/tkgui/topoconsole.py:
	  Removed messagebar's outer frame, and replaced learning_group's
	  with a Tkinter frame.

	* [r5716] topo/tkgui/topoconsole.py:
	  Added a comment about status bar.

	* [r5715] topo/tkgui/topoconsole.py:
	  Tried to document PlotsMenuEntry.

	* [r5714] topo/tkgui/topoconsole.py:
	  Minor cleanup - no visible change.

	* [r5713] topo/tkgui/topoconsole.py:
	  Clean up of PlotsMenuEntry. Minor cleanup elsewhere.

	* [r5712] topo/tkgui/topoconsole.py:
	  Removed code to track number of windows.

	* [r5711] topo/tests/testtopoconsole.py:
	  Added some notes.

	* [r5710] topo/tkgui/testpattern.py:
	  Added title, since I removed it from being set by topoconsole.

	* [r5709] topo/tkgui/topoconsole.py:
	  Corrected a previous oversight.

	* [r5708] topo/tkgui/topoconsole.py:
	  Renamed and tidied up things related to the test pattern window.
	  Renamed __plot_menu() to __plots_menu().

	* [r5707] topo/tkgui/topoconsole.py:
	  Removed unused variable. Removed reset_network() (which didn't do
	  anything).

	* [r5706] topo/tkgui/topoconsole.py:
	  Cleaned up the run_script method.

	* [r5705] topo/tkgui/topoconsole.py:
	  Corrected typos in simulation_menu. Renamed load_script to
	  run_script, and began to tidy that up.

	* [r5704] topo/tkgui/topoconsole.py:
	  Use Tkinter.Menu instead of Pmw.MainMenuBar. There should be no
	  visible change to the TopoConsole GUI.

	* [r5703] topo/tkgui/__init__.py:
	  Added some notes.

2007-05-04  ceball

	* [r5702] topo/tkgui/templateplotgrouppanel.py:
	  Added not-yet-configurable histogram plot to right-click menu.

	* [r5701] topo/commands/pylabplots.py:
	  Added histogramplot().

	* [r5700] topo/commands/pylabplots.py:
	  Fixed minor typo.

2007-05-03  rczhao

	* [r5699] examples/face_space.ty:
	  Removed PiecewiseLinear_debug class and replaced all
	  PiecewiseLinear_debug invokes with PiecewiseLinear.

2007-05-03  jbednar

	* [r5698] doc/Downloads/index_text.php:
	  Minor cleanup

	* [r5697] doc/Downloads/index_text.php:
	  Updated Mac instructions

2007-05-03  ceball

	* [r5696] topo/tkgui/topoconsole.py:
	  About window is a TkguiWindow rather than a Toplevel.

	* [r5695] doc/Future_Work/current_text.php:
	  Added 'cross normalization' and 'plot histograms' tasks.

	* [r5694] topo/tkgui/editorobjects.py,
	  topo/tkgui/parametersframe.py:
	  Parameter window opens in TkguiWindow rather than Toplevel.

	* [r5693] topo/tkgui/plotgrouppanel.py:
	  Corrected an earlier oversight: changed 'Toplevel' to
	  'TkguiWindow' in destroy().

	* [r5692] topo/tkgui/editortools.py:
	  Removed unused import.

	* [r5691] topo/tkgui/editorwindow.py:
	  Make the model editor use a TkguiWindow rather than a
	  Tkinter.Toplevel.

2007-05-02  judelaw

	* [r5690]
	  examples/lissom_oo_or_noshrinking_adapthomeo.ty:
	  no longer required, merged with lissom_oo_or_noshrinking.ty

	* [r5689] topo/outputfns/homeostatic.py:
	  removed piecewiselinear_debug functions and added averaging over
	  parameters to OutputFnDebugger

	* [r5688] examples/lissom_oo_or_noshrinking.ty:
	  changed OutputFnDebugger to include averaging over parameters

	* [r5687] examples/lissom_or_homeoscale.ty:
	  added PiecewiseLinear_debug2 function to this file so that it
	  could be removed from outputfns/homeostatic.py

	* [r5686] examples/face_space.ty:
	  added PiecewiseLinear_debug function to this file so that it
	  could be removed from outputfns/homeostatic.py

	* [r5685] examples/laminar_oo_or.ty:
	  changed strengths, changed output_fn back to HomeostaticMaxEnt,
	  best version so far but still work in progress

2007-04-30  jbednar

	* [r5684] doc/Downloads/index_text.php:
	  Updated with guess as to what to do on the Mac.

2007-04-28  ceball

	* [r5683] topo/tkgui/topoconsole.py:
	  Icon-setting code moved to TkguiWindow; TkguiWindow moved to
	  tkguiwindow.py.

	* [r5682] topo/tkgui/plotgrouppanel.py:
	  Plotgroup panels are TkguiWindows (so get an icon).

	* [r5681] topo/tkgui/tkguiwindow.py:
	  Initial version.

	* [r5680] topo/plotting/templates.py,
	  topo/tkgui/translatorwidgets.py:
	  Added ALERT.

	* [r5679] topo/tkgui/featurecurvepanel.py:
	  Removed unused import.

	* [r5678] topo/tkgui/connectionfieldspanel.py:
	  Removed unused import statement.

	* [r5677] topo/tkgui/topoconsole.py:
	  Minor updates to docstrings/comments.

	* [r5676] topo/tkgui/editortools.py:
	  Removed unused import.

	* [r5675] topo/tkgui/__init__.py:
	  Change to import statement.

	* [r5674] topo/tkgui/topoconsole.py:
	  Tidied imports, updated/added some comments.

	* [r5673] topo/tkgui/plotgrouppanel.py:
	  Added ALERT.

	* [r5672] topo/tkgui/topoconsole.py:
	  Added TkguiWindow class.

	* [r5671] topo/tkgui/__init__.py,
	  topo/tkgui/topoconsole.py:
	  TopoConsole is a subclass of Toplevel rather than Tk (so that we
	  can have a hierachy of windows with a common parent).

2007-04-27  judelaw

	* [r5670] examples/lissom_oo_or_noshrinking.ty:
	  further simplified file

2007-04-27  jbednar

	* [r5669]
	  doc/images/topographica-0.9.3_modeleditor_ubuntu.png,
	  doc/images/topographica-0.9.3_ubuntu.png,
	  doc/shared/index.php:
	  Added screenshots

2007-04-27  ceball_cvs2svn

	* [r5668] /tags/release_0_9_3,
	  /tags/release_0_9_3/topographica/doc,
	  /tags/release_0_9_3/topographica/topo/patterns/gratingpatches.py:
	  This commit was manufactured by cvs2svn to create tag
	  'release_0_9_3'.

2007-04-27  ceball

	* [r5667] doc/User_Manual/commandline_text.php:
	  Indicate where %APPDATA% is likely to be on Windows.

2007-04-26  judelaw

	* [r5666] examples/lissom_oo_or_noshrinking.ty:
	  Added options for Outputfn_type and num_inputs that can be read
	  in from command line, lissom_oo_or_noshrinking_adapthomeo.ty no
	  longer required

2007-04-26  ceball

	* [r5665] doc/Downloads/index_text.php:
	  Updated path info for compiled code on Windows.

	* [r5664] doc/User_Manual/commandline_text.php:
	  Updated site-specific customization with the various startup file
	  choices.

	* [r5663] topo/misc/commandline.py:
	  Try to execute commands in ~/.topographicarc, then
	  ~/Library/Application Support/Topographica/topographica.config,
	  then %APPDATA$\Topographica\topographica.ini.

	* [r5662] external/Makefile:
	  Added tilewrapper to uninstall and clean targets.

2007-04-25  jbednar

	* [r5661] doc/Downloads/index_text.php:
	  Minor improvement to Mac instructions

	* [r5660] doc/Future_Work/index_text.php:
	  Changed date

	* [r5659] doc/Future_Work/current_text.php:
	  Updated to-do list

	* [r5658] doc/User_Manual/commandline_text.php,
	  doc/User_Manual/plotting_text.php:
	  Updated to match change in search path for topographicarc

	* [r5657] doc/Downloads/index_text.php:
	  Removed change to space requirements

2007-04-25  judelaw

	* [r5656] examples/lissom_or_homeoscale.ty:
	  reverted back to previous version using PiecewiseLinear_debug2

	* [r5655] topo/outputfns/homeostatic.py:
	  re-added PeicewiseLinear_debug2 function for use with example
	  files

2007-04-25  ceball

	* [r5654] /trunk/topographica-win/create_installer/README.txt:
	  Minor clarification.

	* [r5653] /trunk/topographica-win/common/python_topo.tar.gz:
	  Added psyco.

	* [r5652]
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat:
	  Added hackalert.

	* [r5651]
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat:
	  Corrected syntax.

	* [r5650]
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat:
	  Updated what to delete (from Makefile).

	* [r5649] doc/Future_Work/current_text.php:
	  Removed psyco-on-win task.

	* [r5648] topo/tkgui/topoconsole.py:
	  Use tkgui's detection of platform.

	* [r5647] topo/tkgui/topoconsole.py:
	  Don't run 'stty sane' on Windows, since it causes an error
	  message (and isn't required on Windows anyway).

	* [r5646] topo/misc/commandline.py:
	  Changed method of finding user's home dir so that it works on
	  Windows (os.getenv('HOME') returns an empty string).

	* [r5645]
	  /trunk/topographica-win/create_python_topo/psyco-1.5.2.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/setup.bat:
	  Added psycho: http://psyco.sourceforge.net/

2007-04-25  jbednar

	* [r5644] doc/shared/index.php:
	  Minor fix

	* [r5643] Makefile:
	  More to delete

	* [r5642] doc/Downloads/index_text.php:
	  Added note for mac

	* [r5641] topo/tests/testfeaturemap.py:
	  Removed dependence on old SOM support

	* [r5640] doc/shared/index.php:
	  Updated for the release

	* [r5639] Makefile:
	  Minor change to list of distributed examples

	* [r5638] ChangeLog.txt:
	  Added recent changes

	* [r5637] topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testplotgrouppanel.py:
	  Converted tests to use CFSheet instead of CFSOM

	* [r5636] topo/learningfns/som.py,
	  topo/sheets/cfsom.py:
	  Added deprecation warning

	* [r5635] examples/hierarchical.ty:
	  Switched to CFSheet instead of obsolete CFSOM

	* [r5634] topo/tests/test_script.py:
	  Trivial cleanup to output

	* [r5633] topo/tests/som_retinotopy.ty_DATA,
	  topo/tests/sullivan_neurocomputing04.ty_DATA,
	  topo/tests/sullivan_nn06.ty_DATA:
	  Updated to match changes in SOM support

	* [r5632] topo/commands/analysis.py:
	  Fixed import

	* [r5631] external/Makefile:
	  Restored -Wl option to python's configure, so that Topographica
	  would compile under Ubuntu 6.10.

2007-04-25  ceball

	* [r5630] doc/shared/index.php:
	  Correct minor typo.

2007-04-24  jbednar

	* [r5629] topo/tests/cfsom_or.ty_DATA:
	  Updated to match changes to KernelMax

	* [r5628] topo/sheets/cfsom.py:
	  Updated comments

	* [r5627] examples/sullivan_nn06.ty:
	  Removed unimplemented variant of CFSOM

	* [r5626]
	  examples/sullivan_neurocomputing04.ty:
	  Added required density parameter to KernelMax

	* [r5625] examples/saccade_demo.ty:
	  Added version string

	* [r5624] examples/obermayer_pnas90.ty:
	  Fixed imports

	* [r5623] examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/lissom_or_noshrinking_latswitch.ty:
	  Cleaned up typos and formatting. Added version string.

	* [r5622] examples/joublin_bc96.ty:
	  Removed unused import

	* [r5621] examples/goodhill_network90.ty:
	  Fixed typo in version string

	* [r5620] examples/face_space.ty,
	  examples/lissom_or_homeoscale.ty:
	  Removed reference to obsolete class

	* [r5619] examples/cfsom_or.ty,
	  examples/som_retinotopy.ty,
	  topo/learningfns/projfns.py,
	  topo/learningfns/som.py:
	  Moved CFPLF_EuclideanHebbian to its final destination

	* [r5618] examples/obermayer_pnas90.ty:
	  Updated with new SOM support

	* [r5617] examples/som_retinotopy.ty:
	  Changed to use new SOM implementation now that it works

	* [r5616] topo/outputfns/basic.py:
	  Fixed KernelMax for when crop_radius was less than the input
	  sheet size

	* [r5615] doc/Team_Members/index_text.php:
	  Fixed name

2007-04-24  ceball

	* [r5614] doc/Team_Members/index_text.php:
	  Minor change to text and link.

	* [r5613] doc/Future_Work/current_text.php:
	  Added a link.

2007-04-24  jbednar

	* [r5612] topo/outputfns/homeostatic.py:
	  Reformatted, cleaning up comments and docstrings

2007-04-23  judelaw

	* [r5611] examples/lissom_or_noshrinking.ty:
	  fixed calculation of time constant for afferent learning rate
	  decrease

	* [r5610] topo/commands/pylabplots.py:
	  added label option to vectorplot

	* [r5609] topo/patterns/teststimuli.py:
	  changed name from gratingpatches.py

	* [r5608] topo/patterns/gratingpatches.py:
	  changed name to teststimuli.py

	* [r5607] topo/outputfns/homeostatic.py:
	  simplified to include a function for debugging and plotting debug
	  graphs

	* [r5606] examples/laminar_oo_or.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_adapthomeo.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty:
	  fixed calculation of time constant for afferent learning rate
	  decreaseexamples/lissom_or_noshrinking.ty

2007-04-23  ceball

	* [r5605] doc/Future_Work/current_text.php:
	  Updated tkinter problem (and merged note+task). Added psyco on
	  Windows task.

2007-04-23  jbednar

	* [r5604] doc/Downloads/index_text.php:
	  Updated disk space requirements

2007-04-23  judelaw

	* [r5603] topo/responsefns/projfns.py:
	  fixed documentation for CFPRF_ActivityBased

2007-04-23  jbednar

	* [r5602] topo/__init__.py:
	  Minor fix to revision control info

	* [r5601] topo/__init__.py:
	  Minor reformatting for epydoc

	* [r5600] topo/__init__.py:
	  Fixed epydoc formatting

	* [r5599]
	  doc/Developer_Manual/releases_text.php:
	  Minor fixes

	* [r5598]
	  doc/Developer_Manual/releases_text.php:
	  Fixed minor typo

	* [r5597] doc/shared/index.php:
	  Added caveat about the binaries

	* [r5596] doc/Future_Work/current_text.php:
	  Removed completed tasks

	* [r5595] ChangeLog.txt:
	  Updated with recent changes

	* [r5594] topo/outputfns/basic.py:
	  Fixed serious bug in KernelMax: the coordinates of the center of
	  the kernel function were incorrect, with y reversed.

	* [r5593] topo/learningfns/som.py:
	  Trivial reformatting to match new SOM support; no change in
	  function

	* [r5592] topo/analysis/featureresponses.py:
	  Trivial fix to comment

	* [r5591] doc/Links/index_text.php:
	  Minor fixes

	* [r5590] examples/lissom_oo_or.ty,
	  topo/base/simulation.py:
	  At Jeff's suggestion, changed grid_layout to be a method on
	  Simulation so that it can accept strings rather than paths to the
	  complete objects

	* [r5589]
	  doc/Developer_Manual/releases_text.php:
	  Minor addition

	* [r5588] doc/Links/index_text.php:
	  Added acknowledgement of DTC support

	* [r5587]
	  doc/Developer_Manual/releases_text.php:
	  Minor additions

	* [r5586] doc/Future_Work/current_text.php:
	  Removed completed task

	* [r5585] doc/Tutorials/lissom_oo_or_text.php:
	  Minor polishing

2007-04-22  jbednar

	* [r5584] examples/saccade_demo.ty:
	  Removed explicit grid layout now that the model editor defaults
	  work fine for this model

	* [r5583] examples/lissom_oo_or.ty:
	  Switched to grid_layout as an example of its usage

	* [r5582] topo/base/simulation.py,
	  topo/tkgui/editorwindow.py:
	  Moved modeleditor.setup_editor_grid to simulation.grid_layout to
	  avoid having examples be dependent on the GUI. Made the default
	  location of objects be computed from a similar grid rather than
	  random, so that at least simple models show up properly.

	* [r5581] topo/base/sheet.py:
	  Suppressed GUI display of layout_location, because the GUI
	  controls that separately using the Model Editor

	* [r5580] examples/face_space.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_adapthomeo.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/ohzawa_science90.ty,
	  topo/base/sheet.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py:
	  Replaced gui_x and gui_y attributes with new layout_location
	  parameter

	* [r5579] topo/base/parameterclasses.py:
	  Added a NumericTuple parameter type.

	* [r5578] doc/shared/topo.css:
	  Changed background color to match new screenshots

	* [r5577] doc/Developer_Manual,
	  doc/Developer_Manual/.cvsignore,
	  doc/Developer_Manual/index_text.php,
	  doc/Developer_Manual/releases_text.php:
	  Added Releases page to the Developer Manual

	* [r5576] topo/responsefns/projfns.py:
	  Cleaned up imports and formatting. Clarified documentation,
	  hopefully correctly

	* [r5575] topo/commands/analysis.py,
	  topo/patterns/image.py:
	  Cleaned up Caricaturization code. Deleted redundant Face
	  Preference map

	* [r5574] examples/laminar_oo_or.ty,
	  examples/lissom_oo_or_noshrinking_adapthomeo.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_or_noshrinking.ty:
	  Cleaned up formatting; should be no change in the code

	* [r5573] doc/Future_Work/current_text.php:
	  Removed messed-up terminal task

	* [r5572] topo/tkgui/topoconsole.py:
	  Added link to Chris's post about the bash problem

	* [r5571] topo/tkgui/topoconsole.py:
	  Added workaround for bash/Tkinter problem

	* [r5570] doc/Future_Work/current_text.php:
	  Fixed formatting bug

	* [r5569] examples/face_space.ty:
	  Fixed bogus Unicode file to be regular ASCII

2007-04-22  ceball

	* [r5568] doc/Tutorials/lissom_oo_or_text.php:
	  Minor change to text.

	* [r5567]
	  doc/Tutorials/images/lissom_oo_or_activity_rightclick.png,
	  doc/Tutorials/images/lissom_oo_or_orpref_ft.png,
	  doc/Tutorials/images/unit_weights_41_24_oo_or.png:
	  Initial version.

	* [r5566]
	  doc/Tutorials/images/activity_line_oo_or.png:
	  Shows dynamic info.

	* [r5565] doc/Tutorials/lissom_oo_or_text.php:
	  Added some right-click menu examples.

	* [r5564] doc/Tutorials/lissom_oo_or_text.php:
	  Added introduction to dynamic info.

	* [r5563]
	  doc/Tutorials/images/activity_line_oo.png:
	  Includes some info in status bar.

	* [r5562] doc/Tutorials/lissom_oo_or_text.php:
	  Minor corrections to text. Updated image sizes.

	* [r5561]
	  doc/Tutorials/images/activity_line_oo.png,
	  doc/Tutorials/images/activity_line_oo_or.png,
	  doc/Tutorials/images/natural_image_oo_or.png,
	  doc/Tutorials/images/oo_or_map.png,
	  doc/Tutorials/images/projection_oo.png,
	  doc/Tutorials/images/test_pattern_oo.png,
	  doc/Tutorials/images/topographica_console.png,
	  doc/Tutorials/images/unit_weights_0_0_oo.png,
	  doc/Tutorials/images/unit_weights_0_0_oo_or.png:
	  Updated to match current version of Topographica.

	* [r5560] doc/Reference_Manual/index_text.php:
	  Minor change to build command for scipy, and minor rewording.

	* [r5559] doc/Future_Work/index_text.php:
	  Added note about mlabwrap.

	* [r5558] doc/Reference_Manual/index_text.php:
	  Named the mlabwrap anchor so it can be linked to.

	* [r5557] doc/Tutorials/lissom_oo_or_text.php:
	  Minor updates.

	* [r5556] topo/commands/basic.py:
	  Added hack for not pickling Image's filename attribute.

2007-04-22  jbednar

	* [r5555] topo/misc/numbergenerators.py:
	  Replaced alert with note about base 2

	* [r5554] topo/base/boundingregion.py:
	  Made BoundingBox repr better

	* [r5553] external/Makefile:
	  Fixed psyco targets

	* [r5552] Makefile:
	  More to remove

2007-04-22  ceball

	* [r5551] topo/tkgui/parametersframe.py:
	  Defaults button positioned better on test pattern window.

2007-04-21  ceball

	* [r5550] doc/Tutorials/lissom_oo_or_text.php:
	  Added another note for updating.

	* [r5549] doc/Tutorials/lissom_oo_or_text.php:
	  Updated to use run.py for generating saved example. Added some
	  comments. Changed times to 10000.

	* [r5548] doc/Future_Work/current_text.php:
	  Added to task.

	* [r5547] doc/Future_Work/current_text.php:
	  Added small doc task.

	* [r5546] doc/Future_Work/current_text.php:
	  Updates to my tasks.

	* [r5545] topo/tkgui/topoconsole.py:
	  Modified an ALERT.

	* [r5544] topo/tkgui/topoconsole.py:
	  Added ALERT about tkMessageBox. In the quit() method, always call
	  sys.exit().

	* [r5543] examples/run.py:
	  Added ALERT for more to add from the Makefile.

	* [r5542] examples/run.py:
	  Changed syntax for running, so that arguments are processed as
	  for .ty files (eliminating an error at the end of the script.

	* [r5541] topo/tkgui/topoconsole.py:
	  Basic plots appear on the Plots menu itself, rather than in a
	  submenu.

	* [r5540] topo/tkgui/topoconsole.py:
	  Plot menu categories are now submenus.

2007-04-21  jbednar

	* [r5539] external/Makefile:
	  Added clean and uninstall targets for psyco

2007-04-20  jbednar

	* [r5538] examples/cfsom_or.ty,
	  examples/face_space.ty,
	  examples/hierarchical.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lgn_lateral.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_oo_or_noshrinking.ty,
	  examples/lissom_oo_or_noshrinking_adapthomeo.ty,
	  examples/lissom_oo_or_noshrinking_latswitch.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_or_homeoscale.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/lissom_photo_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty:
	  Replaced references to RandomArray with numpy.random

	* [r5537] examples/joublin_bc96.ty:
	  Replaced references to RandomArray with numpy.random. Changed
	  apparently obsolete get_center to centroid

	* [r5536] examples/Makefile:
	  Added basic tests to make sure that examples at least load and
	  run without errors

	* [r5535] examples/goodhill_network90.ty:
	  Fixed imports

2007-04-20  jprovost

	* [r5534] examples/saccade_demo.ty:
	  Fixed parameter bug with SaccadeController. Added GUI layout.

2007-04-20  jbednar

	* [r5533] topo/tkgui/templateplotgrouppanel.py:
	  Added alert

	* [r5532] external,
	  external/.cvsignore:
	  More to ignore

	* [r5531]
	  topo/tests/lissom_or_noshrinking.ty_DATA:
	  Updated to match changes in the source script

2007-04-20  ceball_cvs2svn

	* [r5530] /tags/april_2007_performance_testing,
	  /tags/april_2007_performance_testing/topographica/doc,
	  /tags/april_2007_performance_testing/topographica/topo/sheets/optimized.py:
	  This commit was manufactured by cvs2svn to create tag
	  'april_2007_performance_testing'.

2007-04-20  jbednar

	* [r5529] topo/sheets/optimized.py:
	  Updated docstring

	* [r5528] external/Makefile,
	  external/psyco-dist-svn42201.tar.gz:
	  Added psyco

	* [r5527] doc/Future_Work/current_text.php:
	  Added task

2007-04-20  ceball

	* [r5526] topo/tkgui/topoconsole.py:
	  Added Help item to Plots menu.

	* [r5525] topo/tkgui/topoconsole.py:
	  Plot menu entries are displayed in the order they are defined in
	  commands/analysis.py.

	* [r5524] topo/tkgui/topoconsole.py:
	  Sort plots by alphabet after category.

	* [r5523] /trunk/topographica-win/common/python_topo.tar.gz:
	  Patched numpy so scipy test warnings are not printed. Added
	  missing python24.dll.

	* [r5522] examples/run.py:
	  Clarified HACKALERT.

	* [r5521] doc/Future_Work/current_text.php:
	  Removed topographica-win task. Updated run.py task.

	* [r5520] examples/run.py:
	  Added a HACKALERT.

	* [r5519] /trunk/topographica-win/common/setup.py:
	  Make topographica.bat restore the user's path after it quits.

	* [r5518] /trunk/topographica-win/create_python_topo/setup.bat:
	  There was some problem during a previous commit, and some changes
	  were lost. This should be the correct version (numpy+python
	  installations not commented out, no syntax errors).

	* [r5517] /trunk/topographica-win/create_python_topo/setup.bat:
	  Corrected syntax again.

	* [r5516] /trunk/topographica-win/create_python_topo/setup.bat:
	  Corrected some syntax errors.

	* [r5515] /trunk/topographica-win/create_python_topo/setup.bat:
	  Added numpy patch and some comments.

	* [r5514] examples/run.py:
	  Added to docstring.

2007-04-19  ceball

	* [r5513] examples/run.py:
	  Minor simplification.

	* [r5512] examples/run.py:
	  Added default action of all_quick.

	* [r5511] examples/Makefile:
	  Added question.

	* [r5510] examples/run.py:
	  Simplifications, and setup running times to be the true values.

	* [r5509] examples/run.py,
	  examples/setup.py:
	  Moved from setup.py

	* [r5508] doc/Future_Work/current_text.php:
	  Removed plotting categories task. Added task about documenting
	  tkinter problems.

	* [r5507] topo/tkgui/topoconsole.py:
	  Plots menu has categories.

	* [r5506] doc/Future_Work/current_text.php:
	  Added task about problem with messed-up terminal when quitting
	  via tkgui.

2007-04-18  jprovost

	* [r5505] topo/tkgui/editorwindow.py:
	  Added function for simple user-specified grid layout of model
	  editor objects.

	* [r5504] topo/misc/numbergenerators.py:
	  Added ending_value parameter to ExponentialDecay generator. Decay
	  now decays exponentially toward the ending value.

	* [r5503] topo/base/boundingregion.py,
	  topo/base/cf.py:
	  Replaced redundant computation in BoundingRegion.get_center with
	  call to _aarect.centroid() and renamed get_center to centroid,
	  for consistency.

2007-04-18  jbednar

	* [r5502] topo/commands/analysis.py,
	  topo/plotting/templates.py:
	  Moved face space templates to topo.commands.analysis to be with
	  their commands

2007-04-18  rczhao

	* [r5501] topo/plotting/templates.py:
	  Added caricaturization and face preference plots

2007-04-18  judelaw

	* [r5500] topo/commands/analysis.py:
	  updated import for SineGratingDisk

	* [r5499] topo/patterns/gratingpatches.py:
	  pattern file for sine grating patch patterns to avoid having them
	  in test pattern list

2007-04-18  rczhao

	* [r5498] topo/patterns/image.py:
	  Added a missing import

2007-04-18  judelaw

	* [r5497] examples/laminar_oo_or.ty:
	  updated based on new lissom_oo_or_noshrinking.ty

	* [r5496] examples/lissom_or_noshrinking.ty:
	  updated with exponential decay of afferent learning rate

	* [r5495]
	  examples/lissom_oo_or_noshrinking_adapthomeo.ty:
	  lissom_oo_or_noshrinking with new AdaptingHomeostaticMaxEnt
	  output function - keeping old version as lissom_oo_or_noshrinking
	  for comparison for now

	* [r5494]
	  examples/lissom_oo_or_noshrinking_latswitch.ty:
	  Model with switching sign of long range lateral connections

	* [r5493] topo/responsefns/projfns.py:
	  Added activity based CFPResponseFn for latswitch model

2007-04-18  rczhao

	* [r5492] examples/face_space.ty:
	  2D Face Space demonstration

2007-04-18  judelaw

	* [r5491] topo/commands/analysis.py,
	  topo/patterns/image.py:
	  Added missing imports

	* [r5490] topo/outputfns/homeostatic.py:
	  added new AdaptingHomeostaticMaxEnt output functions which are
	  similar to HomeoMaxEnt except the learning rate (eta) also
	  changes depending on the current average activity.

2007-04-18  rczhao

	* [r5489] topo/commands/analysis.py:
	  Added measure_caricaturization and measure_face_pref for face
	  space

	* [r5488] topo/patterns/image.py:
	  Added a crude face space generator

2007-04-18  jbednar

	* [r5487] doc/Future_Work/current_text.php:
	  Removed completed task

	* [r5486] external/Makefile,
	  external/numpy.diff:
	  Added patch to numpy to silence bogus warnings about
	  SciPyTestCase

2007-04-18  ceball

	* [r5485] doc/Future_Work/current_text.php:
	  Added non-square tests task.

	* [r5484] doc/Future_Work/current_text.php:
	  Added information about icon and packaging on OS X.

	* [r5483] topo/tkgui/__init__.py:
	  Added to comment.

	* [r5482] topo/tkgui/topoconsole.py:
	  Removed an alert.

2007-04-17  jbednar

	* [r5481] topo/sheets/generatorsheet.py:
	  Added bounds on the period

	* [r5480] topo/tkgui/projectionpanel.py:
	  Added fix for strength-only() option, e.g. for lateral excitatory
	  weights

	* [r5479] topo/tkgui/topoconsole.py:
	  Put Help menu back on the right

	* [r5478] topo/tkgui/topoconsole.py:
	  Fixed TestPattern window -- did not have any console

2007-04-17  ceball

	* [r5477] examples/setup.py:
	  Added some comments.

	* [r5476] doc/Future_Work/current_text.php:
	  Added to right-click menus task.

2007-04-16  jbednar

	* [r5475] doc/Downloads/index_text.php,
	  doc/FAQ/index_text.php,
	  doc/Home/index_text.php,
	  doc/Links/index_text.php,
	  doc/Reference_Manual/index_text.php,
	  doc/Team_Members/index_text.php,
	  doc/User_Manual/about_text.php,
	  doc/User_Manual/introduction_text.php.m4:
	  Minor updates

	* [r5474]
	  doc/Developer_Manual/imports_text.php,
	  doc/Developer_Manual/optimization_text.php:
	  Changed Numeric to numpy

	* [r5473] Makefile:
	  More files to remove from distribution

	* [r5472] examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_or_homeoscale.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/ohzawa_science90.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty:
	  Removed unused oldnumeric imports; changed others to numpy

	* [r5471] examples/joublin_bc96.ty:
	  Partially updated to work with activity masks; may need more work

	* [r5470] examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_or_homeoscale.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_photo_or.ty,
	  examples/sullivan_nn06.ty:
	  Removed outdated references to Numeric

	* [r5469] /trunk/topographica, .cvsignore:
	  More to ignore

	* [r5468] /trunk/topographica-win/common/setup.py,
	  /trunk/topographica-win/create_installer/topographica.iss,
	  Makefile:
	  Changed version number in anticipation of release

	* [r5467] topo/outputfns/basic.py:
	  Corrected Numeric to numpy

	* [r5466] doc/Future_Work/current_text.php:
	  Removed completed task

	* [r5465] external,
	  external/.cvsignore:
	  Upgraded epydoc

	* [r5464] doc/Makefile:
	  Removed outdated comment

	* [r5463] topo/base/cf.py,
	  topo/learningfns/optimized.py,
	  topo/outputfns/optimized.py,
	  topo/sheets/optimized.py:
	  Made norm_total property implementation private where possible,
	  and discouraged otherwise

	* [r5462] external/Makefile,
	  external/epydoc-3.0alpha3.tar.gz,
	  external/epydoc-3.0beta1.tar.gz,
	  external/epydoc.diff:
	  Upgraded epydoc to version 3.0beta1

	* [r5461] doc/Reference_Manual,
	  doc/Reference_Manual/.cvsignore:
	  More to ignore

	* [r5460] Makefile:
	  More files to clean up

	* [r5459] Makefile:
	  More files to clean up

	* [r5458] topo/tests,
	  topo/tests/.cvsignore:
	  Speed tests should presumably be ignored

	* [r5457] topo/misc/utils.py:
	  Added alert

	* [r5456] topo/commands/analysis.py,
	  topo/plotting/templates.py:
	  Moved templates to be next to the commands that generate their
	  data, so that only one spot needs to be updated to add a new type
	  of plot

	* [r5455] doc/Future_Work/current_text.php:
	  Removed completed tasks

	* [r5454] external,
	  external/.cvsignore,
	  external/Makefile,
	  external/mlabwrap-1.0.tar.gz,
	  external/mlabwrap-1.0a3.tar.gz:
	  Upgraded mlabwrap to 1.0

	* [r5453] doc/Reference_Manual/index_text.php:
	  Added quotes for tcsh use

	* [r5452] doc/Tutorials/lissom_oo_or_text.php:
	  Added link targets

	* [r5451] doc/Future_Work/current_text.php:
	  Removed completed tasks

	* [r5450] doc/User_Manual,
	  doc/User_Manual/.cvsignore,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/plotting_text.php:
	  Added user manual page about plotting

	* [r5449] doc/User_Manual/commandline_text.php:
	  Added link target

	* [r5448]
	  doc/User_Manual/images/lissom_oo_or_10000_activity.png,
	  doc/User_Manual/images/lissom_oo_or_10000_activity_mono.png,
	  doc/User_Manual/images/lissom_oo_or_10000_activity_mono_pointer.png,
	  doc/User_Manual/images/or_tuning.png,
	  doc/User_Manual/images/pointer.png:
	  Added images needed by the new plotting.html page

	* [r5447] doc/Future_Work/current_text.php:
	  Removed completed tasks

	* [r5446] doc/User_Manual/patterns_text.php:
	  Minor fix

	* [r5445] examples/Makefile:
	  Fixed line mistakenly checked in for previous revision; had been
	  overriding density for lissom_oo_or.ty. Added ability to
	  specify density from the command line.

	* [r5444] topo/plotting/templates.py:
	  Reformatted and rearranged for clarity. Added docstring and
	  category for each plot.

	* [r5443] topo/base/parameterclasses.py,
	  topo/plotting/plotgroup.py:
	  Added StringParameter

	* [r5442] doc/User_Manual/index_text.php:
	  Changed description of user manual status

	* [r5441] doc/Future_Work/index_text.php:
	  Brought up to date

2007-04-16  ceball

	* [r5440] doc/Future_Work/current_text.php:
	  Added task about mistake with topographica-win.

2007-04-15  ceball

	* [r5439] doc/Future_Work/current_text.php:
	  Updates to my tasks.

	* [r5438]
	  topo/tkgui/projectionactivitypanel.py:
	  Disbaled dynamic info for projection activity window, and added
	  ALERT.

	* [r5437] topo/tkgui/plotgrouppanel.py:
	  update_dynamic_info() can be overridden by subclasses. Moved
	  HACKALERT to projectionactivitypanel.py.

	* [r5436]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Renamed autosizemask to autosize_mask.

	* [r5435] topo/base/cf.py:
	  Renamed autosizemask to autosize_mask. Clarified alert about
	  offering a scaling parameter so that users can set the mask size.

	* [r5434] doc/Future_Work/current_text.php:
	  Relegated testing of topographica-win until after the upcoming
	  release.

	* [r5433] doc/Future_Work/current_text.php:
	  Added task.

	* [r5432] doc/Future_Work/current_text.php:
	  Cleanup of introduction formatting (and a stray br tag).

2007-04-15  jbednar

	* [r5431] doc/Future_Work/current_text.php:
	  Changed task headings to be H4

	* [r5430] doc/Future_Work/current_text.php:
	  Restored linebreaks after headers

2007-04-15  ceball

	* [r5429] doc/Future_Work/current_text.php:
	  Updated topographica-win testing task.

	* [r5428] topo/tests/test_script.py:
	  The binary specifier is necessary under Windows (for reading
	  binary files).

	* [r5427] topo/tkgui/topoconsole.py:
	  Added platform test for window icon (since we could actually have
	  a small one on mac).

	* [r5426] topo/tkgui/topoconsole.py:
	  Removed Pmw.busycallback for running simulation. It didn't work
	  properly (on most window managers), and in any case the console
	  now remains active while running the simulation. Also removed the
	  busycallback for running commands from the GUI command prompt.

	* [r5425] topo/tkgui/topoconsole.py:
	  Removed commented-out code about menu --> status bar help.

	* [r5424] topo/tkgui/__init__.py,
	  topo/tkgui/topoconsole.py:
	  Collected together a couple of notes about tkgui.

2007-04-14  jbednar

	* [r5423] topo/base/cf.py:
	  Expanded docstring

	* [r5422] examples/Makefile:
	  Removed or_tuning and position_pref from default saved-examples
	  because they are very slow

	* [r5421] doc/shared/index.php:
	  Minor cleanup

	* [r5420] doc/User_Manual/overview_text.php:
	  Trivial whitespace fix

	* [r5419] doc/Future_Work/current_text.php:
	  Minor additions, plus changed from <pre> text to <p> paragraphs

	* [r5418] doc/Home/oldnews_text.php,
	  doc/shared/index.php:
	  Added preliminary news for 0.9.3

	* [r5417] doc/User_Manual/overview_text.php:
	  Added description of Pipeline and PatternCombine

	* [r5416] topo/tkgui/topoconsole.py:
	  Changed wording of Quit message to match other programs

	* [r5415] topo/tkgui/editorwindow.py:
	  Minor cleanup

	* [r5414] topo/tkgui/editorobjects.py:
	  Fixed longstanding bug -- was not cropping values before
	  displaying them

	* [r5413] topo/sheets/optimized.py:
	  Added NeighborhoodMask_Opt to LISSOM_Opt to enable neighborhood
	  optimizations

	* [r5412] topo/base/simulation.py,
	  topo/sheets/generatorsheet.py:
	  Added suppression of private connections (as in GeneratorSheet)
	  from script_repr

	* [r5411] ChangeLog.txt:
	  Removed changes associated with Numpy test branch, as those were
	  all
	  folded into the main branch.

	* [r5410] ChangeLog.txt:
	  Minor fixes

	* [r5409] ChangeLog.txt:
	  Added changes since 20 Feb 2007

2007-04-14  ceball

	* [r5408] topo/tkgui/topoconsole.py:
	  Corrected previous check-in.

	* [r5407] topo/tests/reference,
	  topo/tests/reference/.cvsignore:
	  Updated ignore list.

	* [r5406]
	  topo/tests/reference/or_map_topo.param:
	  No longer used - replaced by 010910_or_map_512MB.param

	* [r5405]
	  topo/tests/reference/:
	  Removed unused data files for lissom_or_reference.ty (mostly
	  these were added in error, since or_map_topo.params is no longer
	  used.)

	* [r5404] topo/tkgui/topoconsole.py:
	  Commented out trial code (unused) that imports bwidget (because
	  bwidget is not built by default yet).

2007-04-13  ceball

	* [r5403] topo/tkgui/topoconsole.py:
	  Cascade behavior alteration applies to linux only.

	* [r5402] topo/tkgui/__init__.py:
	  Test for the platform and store in system_platform for use by the
	  rest of tkgui.

	* [r5401] topo/tkgui/topoconsole.py:
	  Revert to tkinter default behavior on the main menu bar.

	* [r5400] doc/Future_Work/current_text.php:
	  Updates to my tasks.

	* [r5399] topo/tests/reference,
	  topo/tests/reference/.cvsignore:
	  Ignore all .matrix files.

	* [r5398] topo/tests/reference/:
	  Data from lodestar.

	* [r5397] topo/tests/reference/:
	  Data from lodestar.

	* [r5396] topo/tkgui/topoconsole.py:
	  Uncommented some code (calling code is commented out. Added
	  comment about window icon on OS X.

	* [r5395] topo/tkgui/topoconsole.py:
	  Added some commented-out code (ignore for the moment). Added a
	  comment for PlotsMenuEntry, and allow command() to accept an
	  event if necessary.

2007-04-12  jbednar

	* [r5394] topo/sheets/lissom.py:
	  Cleaned up docs. Removed unused imports

	* [r5393] topo/responsefns/optimized.py:
	  Minor code cleanup to match previous revisions

	* [r5392] topo/base/projection.py:
	  Cleaned up docs. Added alerts. Added parameters to replace
	  attributes, and slightly simplified code.

	* [r5391] topo/base/cf.py:
	  Cleaned up docs. Added alerts.

	* [r5390] topo/learningfns/optimized.py:
	  Restored bug introduced in recent revision; recent revisions
	  would have failed on non-square sheets.

2007-04-12  antolikjan

	* [r5389] topo/base/cf.py:
	  modified code to speed up the Iterators a bit

	* [r5388] topo/learningfns/projfns.py,
	  topo/responsefns/projfns.py:
	  modified code to _actually_ use the iterators

2007-04-12  judelaw

	* [r5387] topo/commands/analysis.py:
	  small changes to orientation tuning curve parameter so that
	  orientation values only plotted between 0 and pi

	* [r5386] topo/commands/pylabplots.py:
	  changed tuning curves, orientation tuning curves now plotted
	  differently as or_tuning_curve, values rotated to make maximum
	  more likely to be in the center

	* [r5385] topo/plotting/templates.py:
	  changed tuning curves, orientation tuning curves now plotted
	  differently, some template tuning curve parameters no longer
	  required

2007-04-12  ceball

	* [r5384] topo/tkgui/__init__.py:
	  Added comment.

	* [r5383] external,
	  external/.cvsignore:
	  Ignore scipy.

	* [r5382] external,
	  external/.cvsignore:
	  Ignore tile, tilewrapper, and bwidget.

	* [r5381] external/Makefile:
	  Added tilewrapper.

	* [r5380] external/Tile.py.gz:
	  http://tkinter.unpythonic.net/wiki/TileWrapper

	* [r5379] external/Makefile:
	  Corrected typo in ipython's uninstall.

	* [r5378] external/tile-0.7.8.tar.gz:
	  http://sourceforge.net/projects/tktable/

	* [r5377]
	  external/pybwidget-0.1.2_1.7.0.tar.gz:
	  http://tkinter.unpythonic.net/bwidget/

	* [r5376] external/Makefile:
	  Added tile and bwidget (not yet made by any targets).

	* [r5375] topo/tests/cfsom_or.ty_DATA,
	  topo/tests/hierarchical.ty_DATA,
	  topo/tests/lissom_oo_od.ty_DATA,
	  topo/tests/lissom_oo_or_dy.ty_DATA,
	  topo/tests/lissom_oo_or_homeomaxent.ty_DATA,
	  topo/tests/lissom_or.ty_DATA,
	  topo/tests/lissom_or_homeomaxent.ty_DATA,
	  topo/tests/lissom_or_homeoscale.ty_DATA,
	  topo/tests/lissom_or_noshrinking.ty_DATA,
	  topo/tests/sullivan_neurocomputing04.ty_DATA,
	  topo/tests/sullivan_nn06.ty_DATA:
	  Initial version.

	* [r5374] doc/Future_Work/current_text.php:
	  Added some tasks. Removed duplicate numpy deprecation warnings
	  task. Removed task about precision of slow-tests.

2007-04-11  jbednar

	* [r5373] topo/base/projection.py:
	  Updated docstrings

	* [r5372] topo/learningfns/projfns.py:
	  Fixed to work with recent Mask implementation

	* [r5371] topo/tkgui/editorobjects.py:
	  Turned on activity plotting by default

	* [r5370] doc/User_Manual/modeleditor_text.php:
	  Added information about saving the script_repr

	* [r5369] doc/User_Manual/modeleditor_text.php:
	  Reformatted to add line breaks for readability of the source
	  code; no visible changes

	* [r5368] topo/commands/basic.py,
	  topo/tkgui/topoconsole.py:
	  Added save_script_repr command and GUI option

	* [r5367] topo/base/boundingregion.py,
	  topo/base/parameterizedobject.py,
	  topo/base/simulation.py:
	  Changed imports list in script_repr to be a list for simplicity

	* [r5366] topo/base/simulation.py:
	  Fixed script_repr representation for cf_type parameter

	* [r5365] doc/Future_Work/current_text.php:
	  More to do

2007-04-11  antolikjan

	* [r5364] examples/joublin_bc96.ty,
	  examples/lissom_or_homeoscale.ty,
	  examples/lissom_or_noshrinking_latswitch.ty:
	  modified code to use the new iterators

	* [r5363] topo/learningfns/projfns.py,
	  topo/responsefns/projfns.py:
	  modified code to use the new iterators

	* [r5362] topo/learningfns/som.py:
	  modified code to use the new iterators

	* [r5361] topo/sheets/optimized.py:
	  A new class implementing a C optimized version of the
	  NeighbourhoodMask class was added

	* [r5360] topo/responsefns/optimized.py:
	  Changed the code to use the new iterators. Also the C code was
	  modified to use directly the new mask that is accessed through
	  the iterator to optimize code.

	* [r5359] topo/learningfns/optimized.py,
	  topo/outputfns/optimized.py:
	  Changed the code to use the new iterators

	* [r5358] topo/projections/basic.py:
	  The SharedWeightProjection was now changed to use the new
	  iterators

	* [r5357] topo/base/cf.py:
	  Two iterators were added to the code. Both of these iterate
	  through connection fields of given projection. The base iterator
	  iterates through all projections fields whereas the dervied Mask
	  iterator iterates only over connection fields corresponding to
	  the unmasked positions. All code in cf.py was changed to use
	  these iterators instead of directly accessing _cfs

	* [r5356] topo/sheets/lissom.py:
	  The code was modified to use the new mask optimization.
	  Particularly the initialization and the reset of the mask was
	  added to the timing logic of the LISSOM class

	* [r5355] topo/base/projection.py:
	  Two new classes were added SheetMask and derived NeighborhoodMask
	  that define the masking for the new optimization. The
	  ProjectionSheet mask now owns a new parameter that points to one
	  of these masks (the SheetMask by default)

2007-04-11  ceball

	* [r5354] topo/tkgui/__init__.py,
	  topo/tkgui/topoconsole.py:
	  Added alert.

	* [r5353] topo/base/cf.py:
	  Made autosize mask be a hidden parameter so it doesn't show up in
	  the GUI.

	* [r5352] topo/tkgui/topoconsole.py:
	  Added comment.

	* [r5351] Makefile:
	  Reduced precision of tests, so that results from one processor
	  (checked into CVS) can still be tested on another.

	* [r5350] /trunk/topographica-win/common/python_topo.tar.gz:
	  Upgraded to numpy 1.0.2.

2007-04-10  ceball

	* [r5349] topo/tkgui/topoconsole.py:
	  Updated comment.

	* [r5348] topo/tkgui/topoconsole.py:
	  Added HACKALERT.

	* [r5347] topo/tkgui/topoconsole.py:
	  Also make menubar cascades activate when the cursor is over them.

	* [r5346] topo/tkgui/__init__.py:
	  Moved code for making cascades open automatically to topoconsole.
	  Removed commented-out code. Console is already resizable -
	  doesn't need to be specified.

	* [r5345] topo/tkgui/topoconsole.py:
	  Main menu is Pmw.MainMenuBar, so is now a proper Toplevel menu
	  (should display as a native menu bar i.e. along the top for OS
	  X). Minor re-organization of methods. Context-sensitive help for
	  menus temporarily disabled. Asks for confirmatio?\004n before
	  quitting. Clicking 'x' on the window is like quitting from the
	  menu (rather than just closing the topoconsole window). Moved in
	  code for making cascades open automatically (from __init__.py).

	* [r5344] doc/Future_Work/current_text.php:
	  Update weave. Removed startup commands task (at least it works,
	  although it might need improving).

2007-04-09  jbednar

	* [r5343] topo/tkgui/topoconsole.py:
	  Enabled icon, to see if it is ok on other platforms

	* [r5342] topo/tkgui/topo.xbm,
	  topo/tkgui/topo.xpm:
	  Added icons

2007-04-08  ceball

	* [r5341] topo/tkgui/topoconsole.py:
	  Added more to comment about window icon.

	* [r5340] topo/tkgui/topoconsole.py:
	  Added commented-out example code to display an icon on the
	  console.

2007-04-07  ceball

	* [r5339] topo/tkgui/topoconsole.py:
	  Changed note into ALERT.

	* [r5338] topo/tkgui/topoconsole.py:
	  Added note: when did the status bar stop showing help text for
	  menu commands?

2007-04-05  ceball

	* [r5337] topo/tkgui/plotgrouppanel.py:
	  Added test that the console has not already been destroyed before
	  destroying a plotgrouppanel.

	* [r5336] topo/tkgui/topoconsole.py:
	  Added comment about help text for Stop button.

	* [r5335] doc/Future_Work/current_text.php:
	  Added task for before release.

	* [r5334] examples/setup.py:
	  Get topographica's location in a way that also works on Windows.

	* [r5333] topo/base/parameterclasses.py:
	  Moved alert.

	* [r5332]
	  /trunk/topographica-win/create_python_topo/numpy-1.0.1.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/numpy-1.0.2.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/setup.bat:
	  Upgraded to numpy 1.0.2.

	* [r5331] topo/tests/test_script.py:
	  Added alert & commented out speed assertion statement.

	* [r5330] topo/tkgui/parametersframe.py:
	  Added popup help to buttons on parameters frame. The buttons are
	  still likely to be confusing, though.

	* [r5329] doc/Future_Work/current_text.php:
	  Added task.

	* [r5328] Makefile:
	  Added comment.

	* [r5327] topo/sheets/lissom.py:
	  Minor change to comment.

	* [r5326] topo/base/simulation.py,
	  topo/sheets/lissom.py:
	  Added 'execute_next' parameter, which is a list of commands that
	  will be executed when the simulation is next run(), and which are
	  guaranteed only to run once. Might need to be reviewed (but fixes
	  repeated-normalization bug).

	* [r5325] doc/Future_Work/current_text.php:
	  Updates to various of my tasks.

2007-04-05  jbednar

	* [r5324] doc/Future_Work/current_text.php:
	  Added documentation notes

2007-04-05  ceball

	* [r5323] topo/tkgui/plotgrouppanel.py:
	  Commented out scrollbars, so behavior of all plotgrouppanels
	  should revert.

	* [r5322] doc/Future_Work/current_text.php:
	  Moved examples/Makefile task to complete before release.

	* [r5321] doc/Future_Work/current_text.php:
	  Added some tasks to complete for the release.

2007-04-04  ceball

	* [r5320] examples/setup.py:
	  Continued working on quickly translating the Makefile. Probably
	  finished, but needs simplifying.

	* [r5319] external/numpy-1.0.1.tar.gz:
	  Upgraded to 1.0.2.

	* [r5318] topo/tests/test_script.py:
	  Added assertion that speed hasn't increased by more than 5%.

	* [r5317] external,
	  external/.cvsignore,
	  external/Makefile:
	  Upgraded to numpy 1.0.2 (which, for us, primarily fixes the
	  subtract-reduce bug. All slow-tests pass, and make compare_oo_or
	  passes too. Some speeds appear to have improved:
	  lissom_or_homeoscale increased by 8%, and lissom_oo_od by 4.5%.
	  Other scripts did not change in speed by more than 1%. (Some of
	  the speed tests are still a little short to be completely
	  reliable.)

	* [r5316] external/numpy-1.0.2.tar.gz:
	  From numpy.scipy.org

	* [r5315] topo/tkgui/testpattern.py:
	  'Duration to present for' and 'Apply to pattern in' boxes no
	  longer expand.

	* [r5314] topo/tkgui/plotgrouppanel.py:
	  Renamed a variable.

	* [r5313] topo/tkgui/plotgrouppanel.py:
	  Use ParameterizedObject from topo.base.parameterizedobject.

	* [r5312] topo/analysis/featureresponses.py:
	  Added alert.

	* [r5311] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionactivitypanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py:
	  BasicPlotGroupPanel inherits from Toplevel instead of Frame
	  because it's a window, not a Frame.

	* [r5310] topo/tkgui/parametersframe.py,
	  topo/tkgui/plotgrouppanel.py:
	  Added comment.

	* [r5309] doc/Future_Work/current_text.php:
	  Added task to do before upcoming release.

	* [r5308] topo/tkgui/plotgrouppanel.py:
	  Added HACKALERT.

	* [r5307] topo/tkgui/templateplotgrouppanel.py:
	  Added alert.

	* [r5306] topo/tests/testplotgrouppanel.py,
	  topo/tests/testtemplateplotgrouppanel.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/topoconsole.py:
	  TopoConsole is the main application window, so it inherits from
	  Tkinter.Tk: this eliminates an extra frame.

	* [r5305] topo/tkgui/plotgrouppanel.py:
	  Removed some unused imports.

	* [r5304] topo/tkgui/plotgrouppanel.py:
	  Enabled scrollbars for plots. Scrolling needs to be
	  re-implemented after tkgui is cleaned up.

	* [r5303] topo/tkgui/templateplotgrouppanel.py:
	  Fixed some widget expansions.

2007-04-03  jbednar

	* [r5302] examples/cfsom_or.ty:
	  Removed unused imports

2007-04-03  judelaw

	* [r5301] examples/lissom_oo_or_noshrinking.ty:
	  Changed afferent scheduled learning rate to be exponential decay,
	  updated homeostatic parameters

2007-04-02  jbednar

	* [r5300] topo/sheets/optimized.py:
	  Cleaned up formatting, comments

	* [r5299] topo/tkgui/topoconsole.py:
	  Minor clarifications, plus help for the stop button

	* [r5298] topo/base/parameterizedobject.py:
	  Fixed representations of list parameters

2007-04-02  ceball

	* [r5297] topo/tkgui/editortools.py,
	  topo/tkgui/parametersframe.py:
	  Can reset new object frame to state when last opened.

	* [r5296] topo/tkgui/editortools.py:
	  Enabled Apply button for new objects: allows changing the class
	  defaults.

	* [r5295] topo/base/parameterizedobject.py:
	  Added comment.

	* [r5294] topo/tkgui/editortools.py,
	  topo/tkgui/testpattern.py:
	  Updated button names.

	* [r5293] topo/tkgui/parametersframe.py:
	  Have Apply, Reset, Close buttons, plus a Defaults one.

	* [r5292] doc/Future_Work/current_text.php:
	  Removed timing task.

	* [r5291] doc/Future_Work/current_text.php:
	  Removed script_repr task. Scheduled actions task for a later
	  release. Minor change to introductory text.

	* [r5290] topo/tkgui/topoconsole.py:
	  Removed currently unnecessary GUIToplevel class.

	* [r5289] topo/tkgui/plotgrouppanel.py:
	  Removed apparently unused frame.

2007-04-01  ceball

	* [r5288] topo/__init__.py:
	  Slightly improved script_repr's collection of import statements.
	  Should be no change to behavior.

	* [r5287] topo/base/boundingregion.py,
	  topo/base/parameterizedobject.py,
	  topo/base/simulation.py:
	  Slightly improved script_repr's collection of import statements.
	  Should be no change to behavior.

	* [r5286] topo/base/simulation.py:
	  Should have been present in previous checkin: generate import
	  statements for connections.

	* [r5285] topo/__init__.py:
	  Quick way to have script_repr() produce import statements. Needs
	  to be re-implemented more cleanly.

	* [r5284] topo/base/boundingregion.py,
	  topo/base/parameterizedobject.py,
	  topo/base/simulation.py:
	  Quick way to have script_repr() produce import statements. Needs
	  to be re-implemented more cleanly.

	* [r5283] topo/misc/inlinec.py:
	  Minor change to warning text.

2007-03-30  ceball

	* [r5282] doc/Future_Work/current_text.php:
	  Updated priorities of my tasks.

	* [r5281] doc/Future_Work/current_text.php:
	  Changed formatting so it's easier to write tasks that will be
	  formatted ok on the html version. Added introduction. Tidied a
	  couple of tasks.

2007-03-29  jbednar

	* [r5280] doc/Future_Work/index_text.php:
	  Minor updates

2007-03-29  ceball

	* [r5279] doc/Future_Work/current_text.php:
	  Reduced priority of lissom_oo_or_reference matching cleanup.
	  Merged some duplicate tasks. Added a new task.

2007-03-29  jprovost

	* [r5278] topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py:
	  Made EditorObjects inherit from ParameterizedObject and added
	  some parameters, so that the default view type (activity/normal)
	  can be set in a script or in the .topographicarc.

2007-03-29  ceball

	* [r5277] topo/base/cf.py:
	  Added some documentation for the autosizemask parameter.

2007-03-29  jprovost

	* [r5276] topo/tkgui/__init__.py:
	  Improved contextual menu support for Mac OS X.

	* [r5275] topo/coordmapperfns/basic.py:
	  Factored Ottes SC mapping.

	* [r5274] topo/commands/pylabplots.py:
	  Added 'actiivity' param to activityplot fn.

2007-03-29  ceball

	* [r5273]
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/oo_or_map_topo.param:
	  First go at matching scheduled actions, and running to 20000.

	* [r5272]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Updated to go to 200 iterations.

	* [r5271]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Added a note.

	* [r5270] topo/base/cf.py,
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Added back temporary parameter 'autosizemask' to CFProjection to
	  allow matching with c++.

	* [r5269] doc/Future_Work/current_text.php:
	  Added back task to document general advice for optimization.

	* [r5268]
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.Afferent01.023_023.matrix:
	  Added by mistake instead of gzipped version.

	* [r5267]
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.Afferent01.023_023.matrix,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.Afferent01.023_023.matrix.gz:
	  From c++ lissom.

	* [r5266]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Added note.

	* [r5265]
	  topo/tests/reference/oo_or_map_topo.000001p000.Eye0_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Ganglia00_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Ganglia01_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Primary_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Primary_InputResponse.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000050p000.Eye0_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000050p000.Ganglia00_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000050p000.Ganglia01_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000050p000.Primary_Activity.matrix.gz:
	  Removed potentially out of date and currently unused results.

	* [r5264] topo/tests/reference,
	  topo/tests/reference/.cvsignore:
	  Updated with current matrix files to ignore.

	* [r5263] topo/tests/reference,
	  topo/tests/reference/.cvsignore:
	  Ignore ref. sim. log file.

	* [r5262] topo/coordmapperfns,
	  topo/coordmapperfns/.cvsignore:
	  Initial version.

	* [r5261] /trunk/topographica-win/create_python_topo/jpeg-6b-3.exe:
	  Apparently no need to have jpeg package (PIL binary seems to have
	  it).

	* [r5260] /trunk/topographica-win/create_python_topo/setup.bat:
	  Apparently no need to add jpeg package (PIL binary seems to have
	  it).

	* [r5259] doc/Future_Work/current_text.php:
	  Jpeg support already exists in PIL (or in Windows, possibly - at
	  least I don't think it's possible for us to control where the
	  jpeg library is found when using the pre-built binary).

	* [r5258] doc/Future_Work/current_text.php:
	  Had already added gnosis utils.

	* [r5257] doc/Future_Work/current_text.php:
	  Updated topographica-win task. Demoted scrollbar task. Promoted
	  Makefile->python script task.

	* [r5256] topo/tests/test_script.py:
	  Minor modification to printing.

	* [r5255] Makefile:
	  Added comment.

2007-03-28  jbednar

	* [r5254] doc/Downloads/cvs_text.php:
	  Added note about x11SDK on Mac

2007-03-28  ceball_cvs2svn

	* [r5253] /tags/cnv_course_2007_2,
	  /tags/cnv_course_2007_2/topographica-win:
	  This commit was manufactured by cvs2svn to create tag
	  'cnv_course_2007_2'.

2007-03-28  rczhao

	* [r5252] topo/coordmapperfns/basic.py:
	  Fixed tailing "^ M" characters.

2007-03-28  ceball

	* [r5251]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Ganglia masks no longer set directly from r_L. Ganglia weights
	  back to not matching.

	* [r5250] topo/base/cf.py:
	  Reverted to version 1.79 (the only difference being modification
	  of one comment).

	* [r5249]
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.Afferent01.000_000.matrix.gz:
	  Temporary addition to cf.py: a parameter that allows the size of
	  the mask to be overridden. Eye-Ganglia initial weights match to 6
	  d.p. for c++ lissom and topographica (Primary afferents still
	  match to 8 d.p., as before; 6 d.p. is probably the best value
	  possible with Gaussian patterns, and is the same as for Gaussian
	  patterns on the Eye). The Eye-Ganglia matching happens because
	  Ganglia patterns are drawn with radius r_L (as in c++ lissom),
	  rather than with the radius of the actual connection field.
	  Additionally, there are some other minor changes that might be
	  reverted.

	* [r5248] topo/base/cf.py,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Ganglia00.Afferent0.000_000.matrix.gz:
	  Temporary addition to cf.py: a parameter that allows the size of
	  the mask to be overridden. Eye-Ganglia initial weights match to 6
	  d.p. for c++ lissom and topographica (Primary afferents still
	  match to 8 d.p., as before; 6 d.p. is probably the best value
	  possible with Gaussian patterns, and is the same as for Gaussian
	  patterns on the Eye). The Eye-Ganglia matching happens because
	  Ganglia patterns are drawn with radius r_L (as in c++ lissom),
	  rather than with the radius of the actual connection field.
	  Additionally, there are some other minor changes that might be
	  reverted.

	* [r5247]
	  topo/tests/reference/oo_or_map_topo.000000.wts.Ganglia00.Afferent0.012_012.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Ganglia01.Afferent0.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Ganglia01.Afferent0.012_012.matrix.gz:
	  Initial version.

	* [r5246] topo/tkgui/plotgrouppanel.py:
	  Made status bar look like topoconsole's. (Should it also have a
	  labeled frame round it?)

2007-03-28  jbednar

	* [r5245] doc/Future_Work/current_text.php:
	  Made first section be the actual tasks left for the 0.9.3 release

	* [r5244] topo/base/simulation.py:
	  Added startup commands to the list

2007-03-28  rczhao

	* [r5243] topo/coordmapperfns/basic.py:
	  Added ConstantMapper class

2007-03-28  jbednar

	* [r5242] topo/sheets/lissom.py:
	  Added note about repeated weight normalizations

2007-03-28  ceball

	* [r5241] topo/tkgui/testpattern.py:
	  Pressing return in the 'duration' box causes the pattern to be
	  presented.

	* [r5240] topo/tkgui/topoconsole.py:
	  Added to comments.

	* [r5239] topo/tkgui/plotgrouppanel.py:
	  Changed dynamic info to be displayed in a Pmw MessageBar. The
	  message bar expands to fill the window's width, so we see as much
	  of a message as possible in the current window. The message bar
	  does not expand automatically for long messages, so the window
	  size does not change rapidly when the message length changes
	  rapidly.

2007-03-28  jprovost

	* [r5238] topo/tkgui/editorwindow.py:
	  Removed some spurious code.

2007-03-27  jprovost

	* [r5237] topo/tkgui/__init__.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/plotgrouppanel.py:
	  Made context (right-click) menus work in Mac OS X.

2007-03-27  rczhao

	* [r5236] examples/lissom_fsa.ty:
	  Removed mask workaround for LGNOnToFSA and LGNOffToFSA such that
	  all connection fields' masks are now circular.

2007-03-27  jbednar

	* [r5235] topo/tkgui/templateplotgrouppanel.py:
	  Added abs to fft plots to make sure they are real valued. Flipped
	  axis to make the background white to match the CMVC book's plots

	* [r5234] doc/Future_Work/index_text.php,
	  doc/Tutorials/lissom_oo_or_text.php,
	  doc/Tutorials/lissom_or_text.php,
	  topo/analysis/featureresponses.py:
	  Added window updating and refreshing for map measurement commands

	* [r5233] doc/Future_Work/index_text.php:
	  Minor update

	* [r5232] topo/tkgui/topoconsole.py:
	  Made windows be updated during training. Added Stop button to
	  interrupt training.

2007-03-26  ceball

	* [r5231] doc/Future_Work/current_text.php:
	  Added task about abstract classes. Added info to
	  Makefile->setup.py task.

2007-03-26  jbednar

	* [r5230] doc/Future_Work/current_text.php:
	  Restored note about right-click menu expansibility

	* [r5229] topo/base/parameterizedobject.py:
	  Made lists of ParameterizedObjects format like a list of
	  ParameterizedObject.script_repr() instead of an unreadable
	  mishmash. Made script_repr_suppress_defaults into a module
	  attribute so that it wouldn't show up on script_repr output

	* [r5228] topo/base/simulation.py:
	  Added script_repr representations of schedule_command events and
	  topo.sim.name. Added section headings.

	* [r5227] examples/lissom_oo_or_noshrinking.ty:
	  Added another fix from Jude

	* [r5226] examples/lissom_oo_or_noshrinking.ty:
	  Added changes from Jude

2007-03-26  ceball

	* [r5225] doc/Future_Work/current_text.php:
	  Updated matching task. Removed combobox/ballon-help task. Removed
	  slow-tests/Makefile task. Updated build-on-windows task. Added
	  Makefile->setup.py task. Minor change to tkgui-cleanup task.
	  Added scrollbars-on-plotgrouppanel-windows task. Updated
	  right-click-menu task. Added task about notes for efficient array
	  computations.

2007-03-26  jbednar

	* [r5224] doc/Future_Work/current_text.php:
	  Added note about MDP

	* [r5223] examples/lissom_oo_or_noshrinking.ty:
	  Simplified by removing non-homeostatic option

	* [r5222] examples/lissom_oo_or_noshrinking.ty:
	  Created out of lissom_or_noshrinking.ty and lissom_oo_or.ty

	* [r5221] topo/base/simulation.py:
	  Added message when scheduled commands are running

	* [r5220] Makefile:
	  Removed laminar models from slow-tests because they have nothing
	  called V1

	* [r5219] examples/sullivan_nn06.ty:
	  Added missing imports; commented out broken code

	* [r5218]
	  examples/sullivan_neurocomputing04.ty:
	  Added missing imports

2007-03-25  jbednar

	* [r5217] examples/laminar_oo_or.ty,
	  examples/laminar_or.ty:
	  Added missing import

	* [r5216] Makefile:
	  Added all reasonable scripts to slow_tests. Temporarily made
	  som_retinotopy test pass, and added test-snapshots to slow-tests.

	* [r5215] examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_photo_or.ty:
	  Changed abbreviations to strings instead of startup commands, as
	  they didn't actually work for snapshots

	* [r5214] Makefile:
	  Added snapshot-tests target

	* [r5213] examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_photo_or.ty:
	  Fixed previous checkin; made sure that startup commands have all
	  been run at least once

	* [r5212] examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_photo_or.ty:
	  Moved convenience variables into startup commands so that
	  snapshots will work during training

	* [r5211] examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_photo_or.ty:
	  Removed local copies of n_units() in favor of the one now in
	  CFProjection, to avoid pickling warnings

	* [r5210] examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_photo_or.ty:
	  Added missing imports

	* [r5209] topo/learningfns/optimized.py,
	  topo/learningfns/projfns.py:
	  Changed constant_sum_connection_rate to call n_units from the
	  projection rather than the learning function

	* [r5208] topo/base/cf.py:
	  Changed constant_sum_connection_rate to call n_units from the
	  projection rather than the learning function

	* [r5207] topo/base/cf.py:
	  Fixed n_units function

	* [r5206] examples/joublin_bc96.ty,
	  examples/lissom_or_homeoscale.ty,
	  topo/base/cf.py,
	  topo/learningfns/optimized.py,
	  topo/learningfns/projfns.py,
	  topo/learningfns/som.py:
	  Changed CFPLearningFn to accept the full projection object,
	  rather than the _cfs array, so that it can access n_units

	* [r5205] examples/sullivan_nn06.ty,
	  topo/learningfns/basic.py:
	  Removed unused imports

	* [r5204] topo/base/cf.py:
	  Small cleanup in preparation for later changes; should not change
	  the behavior. Removed duplicate get_shape command, keeping the
	  tuple version (not the 2-element array version)

	* [r5203] examples/Makefile:
	  Added lissom_fsa target

	* [r5202] examples/lissom_or.ty:
	  Simplified by making variables for projections

	* [r5201] examples/lissom_fsa.ty:
	  Fixed typo in previous minus one checkin

	* [r5200] examples/lissom_fsa.ty:
	  Removed unnecessary precision on constants

	* [r5199] examples/lissom_fsa.ty:
	  Simplified by making variables for projections

	* [r5198] examples/lissom_oo_or.ty:
	  Simplified by making variables for projections

	* [r5197] examples/lissom_fsa.ty:
	  Changed scheduled actions to use round numbers and to use
	  standard timebase based on st

2007-03-25  ceball

	* [r5196] topo/tkgui/topoconsole.py:
	  Added reference.

	* [r5195] topo/tkgui/plotgrouppanel.py:
	  Added comment and reference.

	* [r5194] topo/tkgui/topoconsole.py:
	  Added some notes.

	* [r5193] topo/tkgui/plotgrouppanel.py:
	  Added auto-resize checkbutton, and tried to make window resizing
	  reasonable. If auto-resize is on, the window automatically fits
	  the widgets, and the user cannot resize it. If auto-resize is
	  off, the user can resize the window and it is never resized
	  automatically.

	* [r5192] external/Makefile:
	  Removed numeric target. Left the -uninstall and -clean targets
	  for the moment.

	* [r5191] external/Numeric-24.0.tar.gz:
	  No longer used (replaced by numpy).

	* [r5190] topo/tests/lissom_oo_or.ty_DATA,
	  topo/tests/som_retinotopy.ty_DATA:
	  Version from lodestar.

2007-03-25  jbednar

	* [r5189] examples/lissom_fsa_new.ty:
	  Removed this temporary file

	* [r5188] examples/lissom_fsa.ty:
	  Replaced with clean version based on lissom_oo_or.ty, but which
	  should not change the behavior

	* [r5187]
	  topo/tests/reference/lissom_fsa_reference.ty:
	  Moved from examples/lissom_fsa.ty

2007-03-25  ceball

	* [r5186]
	  topo/tests/reference/lissom_log_parser.py:
	  More info in assertion error.

	* [r5185] topo/tests/test_script.py:
	  Removed comment left in by mistake.

	* [r5184] topo/tests/test_script.py:
	  Corrected mistake in previous checkin.

	* [r5183] topo/tests/test_script.py:
	  Minor change to print statement formatting.

	* [r5182] topo/misc/utils.py:
	  Added comment.

	* [r5181] topo/tkgui/topoconsole.py:
	  Added comment about GUIToplevel.

2007-03-25  rczhao

	* [r5180] examples/lissom_fsa_new.ty:
	  Cleared version of lissom_fsa.ty. Tested and produced nearly
	  identical map with lissom_fsa.ty

2007-03-24  jbednar

	* [r5179] doc/User_Manual/commandline_text.php:
	  Added info about .topographicarc

2007-03-23  jbednar

	* [r5178] topo/patterns/random.py:
	  Made unused parameter be hidden

	* [r5177] topo/commands/pylabplots.py:
	  Fixed typo

2007-03-22  jprovost

	* [r5176] examples/saccade_demo.ty:
	  Fixed broken import line.

	* [r5175] topo/commands/pylabplots.py:
	  Added docstring to activityplot.

	* [r5174] topo/misc/commandline.py:
	  - Changed prompt behavior to more closely match Python,
	  especially for multi-line commands.
	  - Added loading of .topographicarc file in $HOME, if one exists.

	* [r5173] topo/misc/utils.py:
	  Added signabs function.

	* [r5172] topo/coordmapperfns/basic.py:
	  Minor code cleanup.

	* [r5171] topo/commands/pylabplots.py:
	  Added functions for plotting sheet activity and coordinate
	  mappings.

	* [r5170] topo/base/parameterclasses.py:
	  Added InstanceMethodWrapper and modified CallableParameter to
	  allow instance methods to be pickled.

	* [r5169] topo/sheets/saccade.py:
	  Moved saccade.py from examples into the library.

	* [r5168] examples/saccade.py,
	  examples/saccade_demo.ty:
	  - Cleaned up saccade_demo.ty
	  - Moved saccade.py into topo/sheets

2007-03-22  ceball

	* [r5167] topo/tests/test_script.py:
	  Turn on garbage collection during speed measurement.

	* [r5166] topo/tests/testsnapshots.py:
	  Removed alert.

2007-03-22  judelaw

	* [r5165] examples/lissom_or_noshrinking.ty:
	  changed radius of lateral excitatory connections to get better
	  organisation

	* [r5164] topo/patterns/basic.py:
	  made default smoothing for SineGratingDisk = 0, otherwise gives
	  strange results for tuning curves

2007-03-22  ceball

	* [r5163] topo/tests/__init__.py:
	  No longer disable pickle test. Corrected variable name error
	  introduced in previous checkin. Added comment.

	* [r5162] topo/tests/testplotgrouppanel.py:
	  Instead of a second input pattern, use the one created in
	  setUP().

	* [r5161] topo/tests/testpatternpresent.py,
	  topo/tests/testplotgrouppanel.py,
	  topo/tests/testtemplateplotgrouppanel.py:
	  Input parameters set on an instance, rather than a class.

	* [r5160] topo/tests/testcfsom.py:
	  Input parameters set on an instance of Gaussian, rather than the
	  class. Changed to a Gaussian pattern from a Line (since it looked
	  like Gaussian was originally intended...).

	* [r5159] topo/tests/test_script.py:
	  Added comment.

	* [r5158] topo/tests/__init__.py:
	  Unit test suite is not generated until run() is called, meaning
	  all the 'checking module x for test suite...found' lines are not
	  printed every time a file from topo/tests/ is used.

	* [r5157] Makefile:
	  Updated to match speed test changes.

	* [r5156] topo/tests/test_script.py:
	  Speed tests use Python's timeit module. Speed test data includes
	  number of iterations, so that the number of iterations will match
	  in the comparison.

2007-03-21  jbednar

	* [r5155] Makefile:
	  Fixed previous checkin; was regenerating each time

	* [r5154] topo/misc/commandline.py:
	  Added minor note

	* [r5153] topo/learningfns/optimized.py,
	  topo/responsefns/optimized.py:
	  Fixed apparently longstanding bug reported by Jeff -- optimized
	  response and learning functions would not have worked for
	  non-square input sheets

	* [r5152] topo/coordmapperfns/basic.py:
	  Minor updates and fixes to docstrings

	* [r5151] Makefile:
	  Generalized to accept any list of script files for the slow-tests
	  and speed-tests targets, and made generation of reference data be
	  automatic

2007-03-21  ceball

	* [r5150] Makefile,
	  topo/tests/test_script.py:
	  Added comment.

2007-03-21  jbednar

	* [r5149] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Removed tear-off menu entries

	* [r5148] topo/tests/test_script.py:
	  Cleaned up docstrings and messages

2007-03-21  ceball

	* [r5147] Makefile:
	  Added speed-tests target. Removed FORCE from slow-tests target (I
	  don't know what FORCE is).

	* [r5146] topo/tests/test_script.py:
	  Added drafts (currently a mess) of some timing functions.

	* [r5145] doc/Future_Work/current_text.php:
	  Correction to a task (testsnapshots.py is not a slow test).

	* [r5144] Makefile:
	  Added slow-tests target.

	* [r5143] topo/tests/test_script.py:
	  Added option to specify data file location.

	* [r5142] topo/tests/lissom_oo_or.ty_DATA,
	  topo/tests/som_retinotopy.ty_DATA:
	  Initial version.

	* [r5141] topo/tkgui/testpattern.py:
	  Added minor alert.

	* [r5140] topo/tkgui/templateplotgrouppanel.py:
	  Minor simplification - no visible change.

	* [r5139] topo/tkgui/templateplotgrouppanel.py:
	  _canvas_right_click() calls the super class's version first,
	  before adding extra information to the menu.

	* [r5138] topo/tkgui/plotgrouppanel.py:
	  Displaying the popup menu is optional for _canvas_right_click().

	* [r5137] topo/tkgui/templateplotgrouppanel.py:
	  Added some notes.

	* [r5136] topo/base/cf.py:
	  Added comment to ALERT about speed of access to norm_total
	  property.

2007-03-20  jbednar

	* [r5135] examples/lissom_photo_or.ty:
	  Added changes listed in CMVC appendix A.5.2; not yet tested

	* [r5134] examples/lissom_photo_or.ty:
	  Initial version identical to lissom_oo_or.ty

2007-03-20  ceball_cvs2svn

	* [r5133] /tags/before_basic_optims,
	  /tags/before_basic_optims/topographica-win,
	  /tags/before_basic_optims/topographica/topo/tests:
	  This commit was manufactured by cvs2svn to create tag
	  'before_basic_optims'.

	* [r5132] /tags/after_basic_optims,
	  /tags/after_basic_optims/topographica-win,
	  /tags/after_basic_optims/topographica/topo/tests:
	  This commit was manufactured by cvs2svn to create tag
	  'after_basic_optims'.

2007-03-20  antolikjan

	* [r5131] topo/tests/test_script.py:
	  The TestScript now takes second argument that forces only
	  approximate comparison within the decimal precission specified by
	  the additional argument. If this argument is set to None
	  (default) the script works as before

2007-03-20  jbednar

	* [r5130] topo/tkgui/templateplotgrouppanel.py:
	  Added workaround for Connection Field plot right-clicks

	* [r5129] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Added more info to the right-click menu to clarify what each item
	  represents

	* [r5128] doc/Tutorials/lissom_or_text.php:
	  Updated training time estimates

2007-03-20  ceball

	* [r5127] topo/tkgui/templateplotgrouppanel.py:
	  Begun adding channels to right-click menu and dynamic info line.
	  Parts are more complex than necessary (I hope), and should become
	  simpler.

	* [r5126] topo/tkgui/plotgrouppanel.py:
	  Minor tidy and __canvas_right_click is semi-private.

2007-03-19  ceball

	* [r5125] topo/tkgui/templateplotgrouppanel.py:
	  Updated to use _right_click_info. No need to catch IndexError now
	  r,c values will always be valid for the sheet.

	* [r5124] topo/tkgui/plotgrouppanel.py:
	  Distinguish between right-click event (which needs to persist for
	  submenu commands) and other events (which are no longer stored,
	  since they should be used immediately or discarded). Events that
	  do not occur on a plot of a sheet (or that occur on a plot of a
	  sheet, but not within the sheet bounds) are distinguishable from
	  those that do by the presence of 'plot' rather than 'coords'.

2007-03-19  jbednar

	* [r5123] doc/Future_Work/current_text.php:
	  Removed duplicate task

	* [r5122] topo/commands/analysis.py:
	  Fixed typo

	* [r5121] topo/tkgui/plotgrouppanel.py:
	  Changed dynamic info font back to the default

2007-03-19  ceball

	* [r5120] topo/tkgui/plotgrouppanel.py:
	  Update dynamic info after clicking off right-click menu. Update
	  dynamic info after leaving a plot, rather than just setting it to
	  an empty string.

2007-03-18  ceball

	* [r5119] topo/tkgui/plotgrouppanel.py:
	  Added an alert.

	* [r5118] topo/tkgui/plotgrouppanel.py:
	  Anything using __process_canvas_event_info() now gets the correct
	  information about a sheet at the edge of a plot (so e.g. the
	  dynamic info does not indicate the mouse is on a sheet unit when
	  in fact it is on the plot's border).

	* [r5117] topo/tkgui/plotgrouppanel.py:
	  Dynamic info. text is only present when mouse is inside a plot.

	* [r5116] topo/tkgui/__init__.py:
	  On linux, cascading menu options now show up when the mouse is
	  over the menu entry. However, there is now an extra partial menu
	  bar at the top of topoconsole.

	* [r5115] topo/tkgui/connectionfieldspanel.py:
	  Removed comment.

	* [r5114] topo/tkgui/templateplotgrouppanel.py:
	  'Update command' executed if return is pressed or an item is
	  selected from the ComboBox.

2007-03-18  jbednar

	* [r5113] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Fixed string format for unit and coord info to stay the same
	  length at all times

2007-03-18  ceball

	* [r5112] topo/tkgui/plotgrouppanel.py:
	  Use a fixed-width font for the dynamic label.

	* [r5111] topo/tkgui/__init__.py:
	  Added comment about fonts.

	* [r5110] topo/tkgui/plotgrouppanel.py:
	  Right-click submenus have correct master (previously, on linux,
	  the menu items could only be selected with the keyboard, not the
	  mouse).

	* [r5109] topo/tkgui/plotgrouppanel.py:
	  Added to a comment.

2007-03-17  ceball

	* [r5108] topo/tkgui/plotgrouppanel.py:
	  Uncommented connection fields-launching menu code, so connection
	  fields can be opened from the right-click menu.

	* [r5107] topo/tkgui/topoconsole.py:
	  PlotsMenuEntry's command() takes optional arguments, which are
	  passed onto the class (plot window, or whatever) that is created.

	* [r5106] topo/tkgui/connectionfieldspanel.py:
	  The ConnectionFieldsPanel's x any y values can optionally be
	  specified on creation.

	* [r5105] topo/tkgui/connectionfieldspanel.py:
	  Added some comments.

	* [r5104] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Right-click menu: updated commented-out 'connection fields
	  opening' code and moved definitions of right-click submenus up to
	  PlotGroupPanel. Intermediate checkin.

2007-03-16  antolikjan

	* [r5103] topo/sheets/optimized.py:
	  The c code optimized version of compute_joint_normalize in the
	  LISSOM_Opt class defined in this new file, overides the original
	  version of this function in the JointNormalizedSheet class

	* [r5102] topo/sheets/lissom.py:
	  Change the handling of mask for the apply_learn_output_fn and
	  compute_joint_norm_totals, now this mask is set to the activity
	  of neurons thus preventing of uneccessary recomputation of
	  weights of inactive neurons

	* [r5101] topo/outputfns/optimized.py:
	  Changed the optimized output fn to work with the new form of
	  norm_total property by directly accessing _norm_total and
	  has_norm_total

	* [r5100] topo/learningfns/optimized.py:
	  Changed the optimized learning fn to work with the new form of
	  norm_total property by directly accessing _norm_total and
	  has_norm_total

	* [r5099] topo/base/simulation.py:
	  Commented out a debug statement at line 745 that caused juge slow
	  down of program because of extremely frequent call to repr
	  function

	* [r5098] topo/base/cf.py:
	  Changed the norm_total property to rather than deleting the
	  _norm_total atribute to use has_norm_total flag to indicate the
	  validity of norm_total

2007-03-16  ceball

	* [r5097] topo/tkgui/templateplotgrouppanel.py:
	  Updated to use new canvas_event_info. Overrides
	  dynamic_info_string to add activity value.

	* [r5096] topo/tkgui/plotgrouppanel.py:
	  Added dynamic_info_string to allow subclasses to add more
	  information. Tried to simplify the processing of click and motion
	  events.

	* [r5095] topo/tkgui/plotgrouppanel.py:
	  Missed out from previous commit.

	* [r5094] topo/tkgui/plotgrouppanel.py:
	  If plot has no sheet, do not try to calculate sheet coordinates,
	  and do not display dynamic location information.

2007-03-16  jbednar

	* [r5093] topo/plotting/templates.py:
	  Minor cleanup

	* [r5092] topo/analysis/featureresponses.py,
	  topo/commands/analysis.py:
	  Changed reading parameter to weighted_average; added docs

2007-03-15  jbednar

	* [r5091] topo/tkgui/topoconsole.py:
	  Added note on fixing timing code

	* [r5090] topo/misc/commandline.py:
	  Suppressed banner when GUI starts up

	* [r5089] topo/coordmapperfns/basic.py:
	  Fixed typo and added citation info.

	* [r5088] topo/commands/analysis.py:
	  Removed some commented-out trash. Restored default duration of
	  measure_or_pref and measure_sf_pref to 0.175 instead of 1.0.

	* [r5087] topo/analysis/featureresponses.py:
	  Added alert

2007-03-15  jprovost

	* [r5086] topo/coordmapperfns/basic.py:
	  Fixed bug in Ottes et al colliculus efferent mapping fn

2007-03-15  jbednar

	* [r5085] topo/tkgui/templateplotgrouppanel.py:
	  Fixed capitalization

2007-03-15  r_primrose

	* [r5084]
	  examples/sullivan_neurocomputing04.ty,
	  topo/learningfns/projfns.py:
	  *** empty log message ***

2007-03-15  chrispalmer

	* [r5083] topo/commands/analysis.py:
	  adds measure_sf_pref, for spatial frequency map creation

	* [r5082] topo/plotting/templates.py:
	  adds spatial frequency map production to plot group templates

	* [r5081] topo/analysis/featureresponses.py:
	  allows spatial frequency map production using max_bin rather than
	  weighted_average

2007-03-15  jprovost

	* [r5080]
	  examples/sullivan_neurocomputing04.ty:
	  Updated to use XY coordinate mapper functions.

	* [r5079] examples/saccade_demo.ty:
	  Added nonlinear efferent mapping from SC.

	* [r5078] examples/saccade.py:
	  Fixed minor import error.

	* [r5077] topo/misc/commandline.py:
	  Changed command line processing to add a script file's directory
	  to sys.path, so extra modules can be loaded, if necessary.

	* [r5076] topo/coordmapperfns,
	  topo/coordmapperfns/__init__.py,
	  topo/coordmapperfns/basic.py:
	  Added topo.coordmapperfns subpackage and
	  topo.coordmapperfns.basic module with some mapper fns in it.

	* [r5075] topo/base/parameterizedobject.py:
	  Fixed some pychecker warnings

	* [r5074] topo/base/parameterclasses.py:
	  Added Boolean parameter class; plus minor changes to clean up
	  some pychecker warnings.

	* [r5073] topo/base/cf.py,
	  topo/base/functionfamilies.py:
	  Changed CF coordinate mapping to produce (x,y) intead of x and y
	  independently.

2007-03-15  fdemertzis

	* [r5072] examples/goodhill_network90.ty:
	  Fixed nominal_density=40 so that full ocular dominance maps can
	  be plotted.

2007-03-15  chrispalmer

	* [r5071] topo/analysis/featureresponses.py:
	  prints time remaining to screen, for feature map generation.
	  Uncomment print command for functionality.

	* [r5070] topo/analysis/featureresponses.py:
	  prints time remaining to screen, for feature map generation

2007-03-15  jbednar

	* [r5069] topo/tkgui/plotgrouppanel.py:
	  Formatted the dynamic display of coordinates

2007-03-15  ceball

	* [r5068] topo/tkgui/plotgrouppanel.py:
	  Added plot name to right-click menu.

	* [r5067] topo/tkgui/plotgrouppanel.py:
	  Minor alteration to menu label.

	* [r5066] topo/tkgui/templateplotgrouppanel.py:
	  Added back in right-click menu options. Might not be the final
	  way to do this, but it keeps the same features working as before.

	* [r5065] topo/tkgui/templateplotgrouppanel.py:
	  Beginning to implement cascading menu options.

	* [r5064] topo/tkgui/templateplotgrouppanel.py:
	  Temporarily removed right-click menu options.

	* [r5063] topo/tkgui/plotgrouppanel.py:
	  Beginning to implement cascading right-click menu.

	* [r5062] topo/tkgui/plotgrouppanel.py:
	  Minor reorganization to cut out some duplication.

	* [r5061] topo/tkgui/plotgrouppanel.py:
	  Added sheet coordinates and activity to 'live' display.

2007-03-14  jbednar

	* [r5060] examples/goodhill_network90.ty:
	  Updated for Numpy

2007-03-14  ceball

	* [r5059] topo/base/patterngenerator.py:
	  Addition to a comment.

	* [r5058] topo/tkgui/plotgrouppanel.py:
	  Added illustration that it's easy to print dynamically updated
	  coordinates, etc.

	* [r5057] doc/Future_Work/current_text.php:
	  Minor updates to tasks, plus removed pickling reorganization
	  task).

	* [r5056] topo/patterns/audio.py:
	  Minor changes to comments.

	* [r5055] topo/patterns/basic.py:
	  OneDPowerSpectrum: started to add some documentation, and cleaned
	  up a little.

	* [r5054]
	  topo/tests/reference/or_map_topo.log.gz:
	  Replaced by 010910_or_map_512MB.log.gz.

	* [r5053]
	  topo/tests/reference/010910_or_map_512MB.log.gz:
	  Initial version.

	* [r5052] external/Makefile:
	  No longer build numeric.

	* [r5051] external/Makefile:
	  Added libsndfile, ctypes, and pyaudiolab to 'clean:' and
	  'uninstall:'.

2007-03-13  ceball

	* [r5050] topo/misc/patternfns.py:
	  Added ALERT about possible nan values.

2007-03-12  judelaw

	* [r5049] examples/lissom_oo_or_homeomaxent.ty:
	  added missed line for SharedWeightCFProjection

	* [r5048] examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_or_noshrinking.ty:
	  updated parameters to match lissom_or.ty

2007-03-11  ceball

	* [r5047] topo/base/cf.py,
	  topo/base/patterngenerator.py,
	  topo/patterns/basic.py,
	  topo/patterns/random.py:
	  Added mask parameter to PatternGenerator. ConnectionField passes
	  its mask to the weights_generator, so that masking can occur
	  before any output_fn is applied.

2007-03-10  ceball

	* [r5046] topo/patterns/basic.py:
	  Added HACKALERT.

2007-03-09  jbednar

	* [r5045] external,
	  external/.cvsignore,
	  external/Makefile,
	  external/ipython-0.7.3.tar.gz,
	  external/ipython.el:
	  Added ipython; not yet configured

	* [r5044] examples/lissom_oo_or.ty:
	  Removed bogus line from recent checkin

	* [r5043] examples/lissom_oo_or.ty:
	  Fixed more problems with recent revisions, primarily for the
	  scheduled threshold changes

2007-03-08  jbednar

	* [r5042] topo/base/cf.py:
	  Removed unused property method

	* [r5041] examples/saccade.py,
	  examples/saccade_demo.ty:
	  Minor updates to match Topographica style

2007-03-08  jprovost

	* [r5040] examples/saccade.py,
	  examples/saccade_demo.ty:
	  Fixed a syntax error.

2007-03-08  rczhao

	* [r5039] examples/lissom_fsa.ty:
	  All the parameters have been adjusted according to the C++ LISSOM
	  parameter list and the book.

2007-03-08  jbednar

	* [r5038] examples/lissom_oo_or.ty,
	  examples/lissom_or.ty:
	  Added missing import

	* [r5037] examples/Makefile:
	  Updated to run for only 10000 iterations now that there are two
	  patterns per iteration

	* [r5036] examples/lissom_oo_or.ty,
	  examples/lissom_or.ty:
	  Cleaned up after recent checkins, restoring some lost features

2007-03-08  jprovost

	* [r5035] examples/saccade.py,
	  examples/saccade_demo.ty:
	  New sheet types for simulating eye movement, plus demo/example
	  script.

2007-03-08  judelaw

	* [r5034] examples/lissom_or_homeomaxent.ty:
	  Based parameters on new lissom_or which matched reduced lissom in
	  CMVC book

	* [r5033] examples/lissom_oo_or.ty:
	  based on lissom_or.ty matched with CMVC book parameters

2007-03-08  ceball

	* [r5032] topo/base/cf.py:
	  Added alert.

2007-03-07  jbednar

	* [r5031] topo/tkgui/templateplotgrouppanel.py:
	  Added print info and plot matrix commands

	* [r5030] examples/som_retinotopy.ty:
	  Changed variables to be set per object rather than per class, for
	  simplicity and to avoid problems when elminating RetinotopicSOM

	* [r5029] examples/cfsom_or.ty:
	  Switched to new SOM implementation

	* [r5028] topo/misc/numbergenerators.py:
	  Added BoundedNumber generator

	* [r5027] topo/misc/utils.py:
	  Cleaned up formatting and docstrings

	* [r5026] examples/cfsom_or.ty,
	  topo/misc/numbergenerators.py:
	  Removed timebase parameter from ExponentialDecay to allow it to
	  be pickled.

	* [r5025] topo/outputfns/basic.py:
	  Added cropping at a radius to KernelMax to avoid calculating
	  pattern over the entire matrix

	* [r5024] topo/__init__.py:
	  Updated list of programmers

	* [r5023] topo/patterns/basic.py:
	  Slight simplification

2007-03-07  judelaw

	* [r5022] examples/lissom_or.ty:
	  Changed sheet and projection names back to V1 and Retina

	* [r5021] examples/lissom_or.ty:
	  added seed for RandomArray

	* [r5020] examples/lissom_or.ty:
	  Changed so that parameters match
	  topo/tests/reference/lissom_or_reference.ty, added multiple
	  inputs and random gaussian initial weights

2007-03-07  ceball

	* [r5019] topo/commands/basic.py:
	  If gzip module is not present, uses Python's own open() function
	  rather than gzip.open().

2007-03-07  jprovost

	* [r5018] topo/plotting/templates.py:
	  Reformatted template list for (nominal) readability.

	* [r5017] topo/misc/utils.py:
	  Removed (non-working) local definition of enumerate, since Python
	  has it built-in now.

2007-03-07  jbednar

	* [r5016] topo/outputfns/basic.py:
	  Added Pipeline and PatternCombine classes, which provide
	  completely general support for adding noise to any calculation,
	  lesioning, using non-rectangular sheet shapes, and so on.

2007-03-06  jbednar

	* [r5015] examples/cfsom_or.ty:
	  Added commented-out implementation in terms of general
	  primitives, though the uncommented code still uses CFSOM

	* [r5014] topo/learningfns/som.py:
	  Added CFPLF_EuclideanHebbian, which (together with KernelMax)
	  should eventually replace CFPLF_HebbianSOM, CFPLF_SOM, and CFSOM

	* [r5013] topo/outputfns/basic.py:
	  Added a density parameter to allow radius to be
	  density-independent (currently as an option, since the default
	  density is 1.0). Should not change the result of existing users
	  of this class

	* [r5012] topo/misc/numbergenerators.py:
	  Added ExponentialDecay function for use for SOM parameters

	* [r5011] topo/base/parameterclasses.py:
	  Turned off instantiate by default for CallableParameter, to allow
	  regular functions to be used. Clarified docstring.

	* [r5010] doc/Home/index_text.php:
	  Updated release date

	* [r5009] README.txt:
	  Updated author list

	* [r5008] topo/tkgui/templateplotgrouppanel.py:
	  Added note

	* [r5007] topo/tests/reference/measure_or_pref:
	  Added OR map measurement script for use with LISSOM simulations

2007-03-06  judelaw

	* [r5006]
	  topo/tests/reference/010910_or_map_512MB.param,
	  topo/tests/reference/or_defs:
	  parameters for CMVC book simulation

	* [r5005]
	  topo/tests/reference/lissom_or_reference.ty:
	  now matches reduced simulation in CMVC book

	* [r5004] Makefile:
	  made new commands compare_or and compare_oo_or for lissom
	  reference comparison files

2007-03-06  jbednar

	* [r5003] examples/lissom_fsa.ty:
	  Replaced ManagedComposite with SeparatedComposite

	* [r5002] examples/cfsom_or.ty:
	  Minor cleanup

	* [r5001] examples/cfsom_or.ty:
	  Minor cleanup

	* [r5000] examples/cfsom_or.ty:
	  Updated to use SeparatedComposite as an example

	* [r4999] topo/patterns/basic.py:
	  Fixed apparent bug in Composite pattern -- was accessing the x
	  and y values of each pattern generator twice, presumably getting
	  different values each time. Probably so far undetected because
	  composites have not yet held patterns with variable orientations
	  and positions. Removed overlap with SeparatedComposite.

	* [r4998] doc/User_Manual/patterns_text.php:
	  Specified smoothing value for disks explicitly

	* [r4997] doc/User_Manual/patterns_text.php:
	  Updated for numpy

	* [r4996] doc/User_Manual/patterns_text.php:
	  Updated for numpy

2007-03-05  jbednar

	* [r4995] topo/tkgui/plotgrouppanel.py:
	  Added commented-out code for launching a Connection Fields panel
	  based on a location in a plot; needs work

	* [r4994] topo/tkgui/topoconsole.py:
	  Added plots_menu_entries list to allow plot windows to be started
	  explicitly (without a GUI action

	* [r4993] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Cleaned up right-click menu, adding option to print the array

	* [r4992] topo/patterns/basic.py:
	  Added first pass at ManagedComposite, plus ALERTs

	* [r4991] doc/Reference_Manual/index_text.php:
	  Added info about -k

2007-03-03  jbednar

	* [r4990] topo/base/patterngenerator.py:
	  Cleaned up docstring formatting

	* [r4989] topo/base/simulation.py:
	  Removed unused import

	* [r4988] doc/User_Manual/overview_text.php:
	  Removed duplicate line

2007-03-03  ceball

	* [r4987] topo/base/patterngenerator.py:
	  Added HACKALERT.

	* [r4986] /trunk/topographica-win/common/python_topo.tar.gz:
	  Previous version was missing a file, by accident.

	* [r4985] doc/Future_Work/current_text.php:
	  Added a task.

	* [r4984] /trunk/topographica-win/create_python_topo/setup.bat:
	  Added some comments.

	* [r4983] examples/hierarchical.ty:
	  Removed HACKALERT.

	* [r4982] external/Makefile:
	  Corrected typo in the 'clean:' line.

	* [r4981] topo/tests/testsnapshots.py:
	  Added comment.

2007-03-02  jbednar

	* [r4980] topo/base/projection.py:
	  Clarified docstring

	* [r4979]
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Remphasized that commits must have log messages

2007-03-02  ceball

	* [r4978] topo/commands/basic.py:
	  load_snapshot() works automatically with xml or normal pickle
	  snapshots.

	* [r4977] topo/commands/basic.py:
	  load_snapshot opens uncompressed or gzipped files.

	* [r4976] /trunk/topographica-win/common/python_topo.tar.gz:
	  Updated to include packages to match standard topographica (all
	  external default packages are present, but jpeg-6b is untested).

	* [r4975] doc/Future_Work/current_text.php:
	  Updated topographica-win task, and added a new task.

	* [r4974] /trunk/topographica-win/setup_cvs_copy/setup.bat:
	  Minor update to formatting.

	* [r4973] /trunk/topographica-win/create_python_topo/setup.bat,
	  /trunk/topographica-win/setup_cvs_copy/setup.bat:
	  Added some notes.

	* [r4972] /trunk/topographica-win/create_python_topo/setup.bat:
	  Added jpeg-6b.

	* [r4971] /trunk/topographica-win/create_python_topo/jpeg-6b-3.exe:
	  gnuwin32.sourceforge.net

	* [r4970] topo/tests/testsnapshots.py:
	  Added notes about testing xml pickling.

	* [r4969] topo/commands/basic.py:
	  Added experimental xml pickling. The xml pickling module needs
	  updating for numpy, so most users will be unable to use xml
	  pickling at present. Removed HACKALERT about pickling
	  topo.sim.actual_sim.

	* [r4968] topo/commands/basic.py:
	  Snapshots use gzip, compresslevel=5.

2007-03-01  ceball

	* [r4967] examples/setup.py:
	  Added ability to handle multiple targets with one label (not sure
	  of Makefile terminology). Still a draft.

	* [r4966] topo/commands/basic.py:
	  Added compresslevel=1 (minimum compression) to save_snapshot().

	* [r4965] topo/commands/basic.py:
	  Changed snapshots to use cPickle.

	* [r4964] topo/tests/testsnapshots.py:
	  Updated to be a reasonable test of snapshots.

	* [r4963] topo/commands/basic.py:
	  Changed snapshots to use bz2 compression. Added comment about
	  switching to cPickle.

	* [r4962] topo/commands/basic.py:
	  Added setting of topo.sim.RELEASE when saving snasphot.

	* [r4961] topo/__init__.py,
	  topo/base/parameterizedobject.py,
	  topo/commands/basic.py:
	  Moved PickleSupport class from topo.__init__ to
	  PicklableClassAttributes class in topo.base.parameterizedobject.
	  Instance of PicklableClassAttributes is created just before
	  pickling. This is an intermediate checkin.

2007-03-01  rczhao

	* [r4960] examples/lissom_fsa.ty:
	  The connection weights of RetinaTOLGNOn and RetinaTOLGNOff are
	  generally matched with C++ LISSOM. The retina activities, LGN
	  activities and learning rates need to be checked.

2007-02-28  ceball

	* [r4959] doc/Future_Work/current_text.php:
	  Updates to some tasks.

	* [r4958] topo/tkgui/testpattern.py:
	  Updated comment about OneDPowerSpectrum.

	* [r4957] doc/Reference_Manual/index_text.php:
	  Slight re-wording of optional packages section.

	* [r4956] doc/Reference_Manual/index_text.php:
	  Added pyaudiolab to optional packages.

	* [r4955] doc/Reference_Manual/index_text.php:
	  Moved SciPy information to the optional packages section.

	* [r4954] doc/Reference_Manual/index_text.php,
	  doc/User_Manual/externalpackages_text.php:
	  Moved information from UserManual/externalpackages_text.php to
	  ReferenceManual/index_text.php's external packages section.

	* [r4953]
	  doc/User_Manual/externalpackages_text.php:
	  Update to mlabwrap text.

	* [r4952] examples/hierarchical.ty:
	  Set default input_generator correctly. Also updated comment about
	  Windows (the Windows version works now).

	* [r4951] topo/sheets/generatorsheet.py:
	  Removed default_input_generator now that topo.tkgui.testpattern
	  has been fixed.

	* [r4950] topo/tkgui/testpattern.py:
	  Get default input_generator pattern correctly (i.e. version 1.57
	  ought to have done it this way).

2007-02-28  judelaw

	* [r4949] topo/tkgui/templateplotgrouppanel.py:
	  added fft plotting to right click menu on template plots

	* [r4948] topo/sheets/generatorsheet.py,
	  topo/tkgui/testpattern.py:
	  added default_input_generator for test pattern window

2007-02-28  jbednar

	* [r4947] doc/Future_Work/index_text.php:
	  Added link

	* [r4946] doc/Future_Work/current_text.php:
	  Reassigned some tasks; other minor cleanup

2007-02-27  jprovost

	* [r4945] topo/base/parameterclasses.py:
	  Changed DynamicNumber to accept iterable objects as well as
	  callable objects, to allow using generators to generate
	  parameters.

2007-02-27  ceball

	* [r4944] examples/setup.py:
	  Initial, totally incomplete version to replace the Makefile.

	* [r4943] /trunk/topographica-win/create_python_topo/setup.bat:
	  Added commented-out beginnings of installing pyaudiolab.

2007-02-27  jbednar

	* [r4942] examples/__init__.py,
	  topo/__init__.py,
	  topo/misc/tyimputil.py:
	  Removed tyimputil

	* [r4941] topo/__init__.py:
	  Temporarily added to get save_snapshot working; not yet sure what
	  the correct fix will be

	* [r4940] doc/Future_Work/current_text.php:
	  Minor addition

2007-02-27  ceball_cvs2svn

	* [r4939] /tags/cnv_course_2007,
	  /tags/cnv_course_2007/topographica-win,
	  /tags/cnv_course_2007/topographica/doc/Tutorials/lissom_oo_or_text.php:
	  This commit was manufactured by cvs2svn to create tag
	  'cnv_course_2007'.

2007-02-27  jbednar

	* [r4938] doc/Tutorials/lissom_oo_or_text.php:
	  Misc small bugfixes

2007-02-26  jbednar

	* [r4937] doc/Future_Work/current_text.php:
	  Added blurb about IPython

2007-02-26  ceball

	* [r4936]
	  /trunk/topographica-win/create_python_topo/ctypes-1.0.1.win32-py2.4.exe:
	  sourceforge.net/projects/ctypes/

	* [r4935] /trunk/topographica-win/create_python_topo/setup.bat:
	  Added Gnosis_Utils.

2007-02-26  judelaw

	* [r4934] topo/commands/analysis.py:
	  corrected for orientation normalization, changed contrast
	  definitions to get better range of values, made small changes to
	  default values

2007-02-26  ceball

	* [r4933] /trunk/topographica-win/README.txt:
	  Minor changes to text.

	* [r4932]
	  /trunk/topographica-win/create_python_topo/Numeric-24.2.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/matplotlib-0.81.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/python-2.4.2.msi,
	  /trunk/topographica-win/create_python_topo/scipy_test.tar.gz,
	  /trunk/topographica-win/create_python_topo/weave.tar.gz:
	  Upgraded to newer version.

	* [r4931]
	  /trunk/topographica-win/create_python_topo/libsndfile-1_0_17.zip:
	  From www.mega-nerd.com/libsndfile/

	* [r4930] /trunk/topographica-win/create_python_topo/README.txt:
	  Minor corrections

	* [r4929] /trunk/topographica-win/create_python_topo/setup.bat:
	  Updated external packages and clarified slightly.

2007-02-26  jbednar

	* [r4928] topo/__init__.py:
	  Disabled tyimputil to see if anything is affected

2007-02-26  ceball

	* [r4927]
	  /trunk/topographica-win/create_python_topo/python-2.4.4.msi:
	  From python.org

	* [r4926]
	  /trunk/topographica-win/create_python_topo/matplotlib-0.90.0.win32-py2.4.exe:
	  From matplotlib.sourceforge.net.

	* [r4925] topo/base/simulation.py,
	  topo/commands/basic.py:
	  Added __getstate__ and __setstate__ to SimSingleton.

	* [r4924] topo/commands/basic.py:
	  Removed unused import.

	* [r4923] topo/__init__.py,
	  topo/misc/utils.py:
	  Moved get_PO_class_attributes() from utils to be a method of
	  PickleSupport class.

	* [r4922] topo/__init__.py:
	  Updated to match function name change.

	* [r4921] topo/misc/utils.py:
	  Changed get_states_of_classes_from_module() to
	  get_PO_class_attributes() (trying to make its purpose more
	  obvious). Removed redundant setting of an argument (it now has a
	  default).

	* [r4920] topo/misc/utils.py:
	  Minor change to get_states_of_classes_from_module() documentation
	  and default arguments.

	* [r4919] topo/commands/basic.py:
	  load_snapshot and save_snapshot request that topo._picklesupport
	  be pickled.

	* [r4918] topo/__init__.py:
	  Added PickleSupport class.

	* [r4917] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r4916] examples/hierarchical.ty:
	  Set GeneratorSheet.input_generator.default to Line() (as an
	  example that the default can be set).

	* [r4915] topo/tkgui/testpattern.py:
	  Set default pattern from GeneratorSheet.input_generator.default.

	* [r4914] topo/tkgui/testpattern.py:
	  Clarified ALERTs.

2007-02-25  jbednar

	* [r4913] topo/base/parameterizedobject.py:
	  Fixed parameter that should not appear in menus

	* [r4912] examples/hierarchical.ty:
	  Added alert

	* [r4911] topo/sheets/cfsom.py:
	  Added SOM reimplementation plan

	* [r4910] doc/Downloads/index_text.php:
	  Updated with appropriate notes for OS X and machines with no
	  DISPLAY.

	* [r4909] doc/Reference_Manual/index_text.php:
	  Changed Numeric to NumPy; probably other references still around

	* [r4908] topo/base/boundingregion.py,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/base/sheetcoords.py,
	  topo/base/simulation.py,
	  topo/misc/distribution.py,
	  topo/misc/tyimputil.py,
	  topo/misc/utils.py,
	  topo/projections/basic.py,
	  topo/tests/test_script.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testdistribution.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testimage.py,
	  topo/tests/testplotgrouppanel.py,
	  topo/tests/testpropertiesframe.py,
	  topo/tests/testsheet.py,
	  topo/tests/testsheetview.py,
	  topo/tests/testsimulation.py,
	  topo/tests/testtemplateplotgrouppanel.py,
	  topo/tests/testtopoconsole.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/propertiesframe.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/translatorwidgets.py:
	  Downgraded most HACKALERTs to ALERTs, because they would not
	  actually affect the results seen by the user (or are otherwise
	  similarly serious). I think all HACKALERTs are now genuine, so
	  everyone should treat them as serious and/or downgrade them to
	  ALERTs if they are mislabeled. Also small fixes to other comments
	  and docs

	* [r4907] topo/base/arrayutils.py,
	  topo/tkgui/testpattern.py:
	  Downgraded most HACKALERTs to ALERTs, because they would not
	  actually affect the results seen by the user (or are otherwise
	  similarly serious). Renamed bogus variable.

2007-02-25  jprovost

	* [r4906] topo/tkgui/topoconsole.py:
	  Removed an unneeded comment.

2007-02-25  jbednar

	* [r4905] external/Makefile:
	  Changed order of 'all' targets so that the build in decreasing
	  likelihood of success

	* [r4904] doc/Future_Work/current_text.php,
	  topo/tkgui/topoconsole.py:
	  Updated to match Jeff's changes

2007-02-25  ceball

	* [r4903] topo/commands/basic.py:
	  Make snapshots be gzip'd.

	* [r4902]
	  doc/User_Manual/externalpackages_text.php:
	  Minor note.

	* [r4901] topo/commands/basic.py:
	  Simplify save_snapshot() and load_snapshot() by removing the
	  unnecessary double pickling of topo.sim (which had been done to
	  allow setting of class attributes and execution of startup
	  commands *before* the simulation was unpickled; that is not
	  required).

	* [r4900] doc/Future_Work/current_text.php:
	  Updated some tasks.

	* [r4899]
	  doc/User_Manual/externalpackages_text.php:
	  Beginning draft of page giving information about external
	  packages (that aren't built by default or are not obvious, etc).

	* [r4898] external,
	  external/.cvsignore:
	  Ignore mlabwrap.

	* [r4897] external/Makefile:
	  Added mlabwrap to target all.

	* [r4896] external/mlabwrap-1.0a3.tar.gz:
	  http://mlabwrap.sourceforge.net/

2007-02-25  jprovost

	* [r4895] topo/tkgui/topoconsole.py:
	  Fixed some .pack() command parameters to make console resizing
	  more sane. Fixed the command entry so that it prints the results
	  of statements and allows multi-line statements/commands, more
	  like a shell.

2007-02-24  ceball

	* [r4894] topo/tkgui/testpattern.py:
	  Remove OneDPowerSpectrum from the list of pattern generators.

	* [r4893] topo/patterns/audio.py:
	  Added an alert.

	* [r4892] topo/patterns/basic.py:
	  Made OneDPowerSpectrum's sample_spacing be a parameter. Added a
	  default for the signal.

	* [r4891] topo/patterns/audio.py:
	  Added missing import statement.

	* [r4890] topo/patterns/audio.py:
	  Audio(PatternGenerator) is now Audio(OneDPowerSpectrum).

	* [r4889] topo/patterns/basic.py:
	  Added draft of OneDPowerSpectrum class.

	* [r4888] external/Makefile:
	  Corrected typo.

	* [r4887] topo/patterns/audio.py:
	  Added some comments and pointed to an audio file that exists.

	* [r4886] doc/FAQ/index_text.php:
	  Added small notes.

	* [r4885] topo/patterns/__init__.py:
	  Hide the audio module.

	* [r4884] topo/patterns/audio.py:
	  Initial version, containing a sketch of Audio(OneDPowerSpectrum).

2007-02-23  jbednar

	* [r4883]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Removed outdated import

	* [r4882] external/Makefile:
	  Added build procedure for SciPy, though it doesn't work as-is on
	  DICE. Changed default target name to 'default', and added 'all'
	  target that includes things not built by default. Added scipy and
	  pyaudiolab to the 'all' target.

2007-02-23  ceball

	* [r4881] topo/tests/utils.py:
	  Added to a comment.

	* [r4880] doc/Future_Work/current_text.php:
	  Updated xml pickling task (and moved it out of tasks to be
	  completed before the next release).

2007-02-23  jbednar

	* [r4879]
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty:
	  Fixed typos

2007-02-23  ceball

	* [r4878] doc/Future_Work/current_text.php:
	  Various updates to tasks.

2007-02-23  ceball_cvs2svn

	* [r4877] /tags/first_numpy_version,
	  /tags/first_numpy_version/topographica-win,
	  /tags/first_numpy_version/topographica/topo,
	  /tags/first_numpy_version/topographica/topo/base/cf.py,
	  /tags/first_numpy_version/topographica/topo/projections,
	  /tags/first_numpy_version/topographica/topo/responsefns,
	  /tags/first_numpy_version/topographica/topo/sheets,
	  /tags/first_numpy_version/topographica/topo/tests/reference:
	  This commit was manufactured by cvs2svn to create tag
	  'first_numpy_version'.

2007-02-23  jbednar

	* [r4876] topo/base/arrayutils.py,
	  topo/base/functionfamilies.py,
	  topo/base/parameterclasses.py,
	  topo/commands/basic.py,
	  topo/patterns/basic.py,
	  topo/tests/utils.py:
	  Updated with changes from the numpy branch that were somehow
	  missed during the merge

2007-02-23  ceball

	* [r4875]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Updated SharedWeightCFProjection's response function.

	* [r4874] external,
	  external/.cvsignore:
	  Added more to ignore.

2007-02-23  jbednar

	* [r4873] topo/base/cf.py:
	  Fixed bug in previous revision; change_bounds was broken

2007-02-22  jbednar

	* [r4872] topo/responsefns/optimized.py:
	  Removed DotProduct_opt, which did not work for non-contiguous
	  arrays

	* [r4871] topo/patterns/basic.py:
	  Changed default Composite pattern to be blank, because two
	  Gaussians are quite arbitrary. Moved default valuefrom the
	  constructor into the generators parameter, so that defaults work
	  as expected. Added Jan's temporary GaussiansCorner class; needs
	  to be reimplemented or removed

	* [r4870] examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  topo/base/cf.py,
	  topo/projections/basic.py,
	  topo/responsefns/optimized.py,
	  topo/sheets/lissom.py:
	  SharedWeightCFProjection has been reimplemented by Jan Antolik to
	  have
	  a cfs data structure (now renamed _cfs to discourage direct
	  usage)
	  that is nearly entirely compatible with the one from
	  CFProjection.
	  The shared _cfs now contains a CF for every neuron, where the
	  weights
	  are all views (slices) of a single shared CF that stores the
	  actual
	  weights. Apart from the sharing, it works just like in
	  CFProjection.
	  
	  This allowed us to remove the special DummyCF and
	  CFPRF_SharedWeightDotProduct_opt classes entirely, replacing them
	  with
	  the standard ConnectionField and CFPRF_DotProduct_opt (modified
	  to
	  allow non-contiguous arrays).
	  
	  External code should now avoid using _cfs. To get the shape of
	  the
	  projection without accessing _cfs, a new property
	  CFProjection.cfs_shape has been added. The projections have also
	  been
	  simplified to store the bounds_template internally, rather than
	  sending it around as a parameter.
	  
	  The result should be much simpler to maintain, test, and
	  understand,
	  but at least on lissom_oo_or.ty the results are unchanged.

	* [r4869] examples/lissom_oo_od.ty:
	  Updated to use numpy instead of Numeric, on a separate CVS branch
	  named numpy_test_branch. First, ran the automatic conversion
	  code:
	  
	  import numpy.oldnumeric.alter_code1 as noa
	  noa.converttree('topo') noa.convertall('examples') # (After
	  temporarily renaming .ty to .py)
	  
	  The main automatic changes were:
	  
	  - Changed 'import Numeric' to 'import numpy.oldnumeric as
	  Numeric'
	  - Changed 'from Numeric import' to 'from numpy.oldnumeric import'
	  - Converted .flat to .ravel()
	  - Changed typecode= to dtype=
	  - Eliminated savespace() and spacesaver()
	  
	  Then cleaned up the results by hand:
	  
	  - Removed all traces of savespace
	  - Replaced custom ExtraPickler and ExtraUnpickler with
	  standard pickle.Pickler and pickle.Unpickler
	  - Used 'from numpy import inf' instead of the previous ad-hoc way
	  of
	  generating an infinite float. Cleaned up and simplified handling
	  of
	  division-by-zero and underflow errors for Gaussian-based
	  patterns.
	  - Updated weave version to work with numpy. Also adds full SciPy
	  distribution, although it is not yet unpacked and built
	  automatically
	  - Upgraded matplotlib to work with numpy.
	  - Patched numpy to fix bug in numpy.subtract.reduce.
	  - Removed the Wrapper class entirely, now that numpy's ufuncs
	  deepcopy without problems.
	  - Changed numpy array printing to show the actual data for any
	  array up
	  to 200*200 by default.
	  - Removed -Wl from LD_FLAGS for compiling Python, to make it
	  compile
	  on OS X 10.4.8 (intel and ppc) even though that platform does not
	  have or need the -rpath option

	* [r4868] 
	  examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar_oo_or.ty,
	  examples/laminar_or.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lissom_fsa.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_oo_or_dy_photo.ty,
	  examples/lissom_oo_or_homeomaxent.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_or_homeoscale.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  examples/ohzawa_science90.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_nn06.ty,
	  examples/tiny.ty,
	  external,
	  external/.cvsignore,
	  external/Makefile,
	  external/Scipy_core-0.3.0_108.1820.tar.gz,
	  external/matplotlib-0.81.tgz,
	  external/weave.diff,
	  topo/analysis/featureresponses.py,
	  topo/base/arrayutils.py,
	  topo/base/boundingregion.py,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/parameterclasses.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/base/sheetcoords.py,
	  topo/commands/analysis.py,
	  topo/commands/basic.py,
	  topo/commands/pylabplots.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/projfns.py,
	  topo/learningfns/som.py,
	  topo/misc/distribution.py,
	  topo/misc/patternfns.py,
	  topo/misc/utils.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/homeostatic.py,
	  topo/outputfns/optimized.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/patterns/rds.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/projections/basic.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/composer.py,
	  topo/sheets/lissom.py,
	  topo/sheets/slissom.py,
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/testbitmap.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testimage.py,
	  topo/tests/testoutputfnsbasic.py,
	  topo/tests/testoutputfnsoptimized.py,
	  topo/tests/testpalette.py,
	  topo/tests/testpatterngenerator.py,
	  topo/tests/testplot.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testsheet.py,
	  topo/tests/testsheetview.py,
	  topo/tests/testsimulation.py,
	  topo/tests/testtemplateplotgrouppanel.py,
	  topo/tests/utils.py,
	  topo/tkgui/editorobjects.py,
	  topo/tkgui/plotgrouppanel.py:
	  Updated to use numpy instead of Numeric, on a separate CVS branch
	  named numpy_test_branch. First, ran the automatic conversion
	  code:
	  
	  import numpy.oldnumeric.alter_code1 as noa
	  noa.converttree('topo') noa.convertall('examples') # (After
	  temporarily renaming .ty to .py)
	  
	  The main automatic changes were:
	  
	  - Changed 'import Numeric' to 'import numpy.oldnumeric as
	  Numeric'
	  - Changed 'from Numeric import' to 'from numpy.oldnumeric import'
	  - Converted .flat to .ravel()
	  - Changed typecode= to dtype=
	  - Eliminated savespace() and spacesaver()
	  
	  Then cleaned up the results by hand:
	  
	  - Removed all traces of savespace
	  - Replaced custom ExtraPickler and ExtraUnpickler with
	  standard pickle.Pickler and pickle.Unpickler
	  - Used 'from numpy import inf' instead of the previous ad-hoc way
	  of
	  generating an infinite float. Cleaned up and simplified handling
	  of
	  division-by-zero and underflow errors for Gaussian-based
	  patterns.
	  - Updated weave version to work with numpy. Also adds full SciPy
	  distribution, although it is not yet unpacked and built
	  automatically
	  - Upgraded matplotlib to work with numpy.
	  - Patched numpy to fix bug in numpy.subtract.reduce.
	  - Removed the Wrapper class entirely, now that numpy's ufuncs
	  deepcopy without problems.
	  - Changed numpy array printing to show the actual data for any
	  array up
	  to 200*200 by default.
	  - Removed -Wl from LD_FLAGS for compiling Python, to make it
	  compile
	  on OS X 10.4.8 (intel and ppc) even though that platform does not
	  have or need the -rpath option

2007-02-22  ceball_cvs2svn

	* [r4867] /tags/last_numeric_version,
	  /tags/last_numeric_version/topographica-win:
	  This commit was manufactured by cvs2svn to create tag
	  'last_numeric_version'.

2007-02-22  jbednar

	* [r4866] topo/misc/inlinec.py:
	  Changed error reporting to print only one error by default,
	  instead of one per optimized component; the old behavior can be
	  obtained by setting warn_for_each_unoptimized_component=True

	* [r4865] topo/__init__.py:
	  Enabled strict reporting of floating-point errors as exceptions
	  by default, to facilitate debugging of numpy, but disabled
	  underflow error reporting by default, because underflows are
	  expected in many normal cases

	* [r4864] external/numpy.diff:
	  Added patch to numpy to fix bug in numpy.subtract.reduce

	* [r4863] external/scipy-0.5.2.tar.gz:
	  Added full SciPy distribution to provide weave to numpy

	* [r4862] doc/User_Manual/commandline_text.php:
	  Added note about how to get numpy to display large arrays

	* [r4861] doc/Future_Work/current_text.php:
	  Updated Windows mingw task and removed a stray tag.

2007-02-21  jbednar

	* [r4860] ChangeLog.txt:
	  Brought up to date with changes

2007-02-21  ceball

	* [r4859]
	  doc/Developer_Manual/optimization_text.php:
	  Turned the bottlenecks section into prose.

2007-02-21  rczhao

	* [r4858] examples/lissom_fsa.ty:
	  *** empty log message ***

2007-02-21  ceball

	* [r4857] topo/responsefns/optimized.py:
	  Added comment.

	* [r4856]
	  doc/Developer_Manual/optimization_text.php:
	  Added information about when the timing results were from.

	* [r4855]
	  doc/Developer_Manual/optimization_text.php:
	  Minor update to text of bottlenecks section.

	* [r4854]
	  doc/Developer_Manual/optimization_text.php:
	  Updated bottlenecks section.

2007-02-21  jbednar

	* [r4853] doc/Future_Work/current_text.php:
	  Added task

	* [r4852]
	  doc/Developer_Manual/optimization_text.php:
	  Reformatted long <pre> lines to reduce the browser frame size.
	  Filled
	  new paragraphs to be within 80 columns for editing.

2007-02-21  ceball

	* [r4851] doc/Future_Work/current_text.php:
	  Some updates and tidying of tasks.

	* [r4850]
	  doc/Developer_Manual/optimization_text.php:
	  Updated bottleneck section examples, and made some changes to
	  text.

2007-02-20  jbednar

	* [r4849] topo/base/simulation.py:
	  Added note about script_repr

	* [r4848] topo/base/parameterizedobject.py:
	  Added suppression of default values to script_repr()

	* [r4847] topo/base/boundingregion.py:
	  Simplified str() representation of BoundingBox. Added
	  script_repr, because the relevant attributes of a BoundingBox are
	  not Parameters

2007-02-20  judelaw

	* [r4846] topo/tkgui/templateplotgrouppanel.py:
	  added refresh to set_strengthonly to avoid resizing error

2007-02-20  ceball

	* [r4845]
	  doc/Developer_Manual/optimization_text.php:
	  Added further part to bottleneck guide, regarding C code.

	* [r4844]
	  doc/Developer_Manual/optimization_text.php:
	  Minor change to wording.

	* [r4843]
	  doc/Developer_Manual/optimization_text.php:
	  Began to draft a guide to finding bottlenecks.

	* [r4842] topo/misc/utils.py:
	  Minor clarification of profile().

2007-02-20  jbednar

	* [r4841]
	  doc/Tutorials/som_retinotopy_text.php:
	  Added info on topological defects

	* [r4840]
	  doc/Tutorials/images/som_grid_kink.png:
	  Initial version, from ./topographica -g -c alpha_0=0.1 -c
	  radius_0=0.32 -c default_density=10 -c default_retina_density=10
	  examples/som_retinotopy.ty

	* [r4839] doc/Tutorials/lissom_oo_or_text.php:
	  Updated sizes and descriptions to match new images

2007-02-20  ceball

	* [r4838] topo/tkgui/editorobjects.py:
	  Re-classified some HACKALERTs as ALERTs (they were wrong before).

2007-02-20  jbednar

	* [r4837] doc/Tutorials/lissom_oo_or_text.php:
	  Updated sizes to match new images

	* [r4836]
	  doc/Tutorials/images/activity_line_oo.png,
	  doc/Tutorials/images/activity_line_oo_or.png,
	  doc/Tutorials/images/natural_image_oo_or.png,
	  doc/Tutorials/images/natural_image_projact_oo_or.png,
	  doc/Tutorials/images/oo_or_map.png,
	  doc/Tutorials/images/projection_oo.png,
	  doc/Tutorials/images/test_pattern_oo.png,
	  doc/Tutorials/images/unit_weights_0_0_oo.png,
	  doc/Tutorials/images/unit_weights_0_0_oo_or.png:
	  Updated for current CVS version

	* [r4835] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Extracted strength-only support into a method so that it can be
	  used in ConnectionField plots

2007-02-20  ceball

	* [r4834] doc/Downloads/index_text.php:
	  Removed commented-out note about pyaudiolab.

	* [r4833] doc/Future_Work/current_text.php:
	  Updated topographica-win task.

	* [r4832] external/Makefile:
	  Added libsndfile, and updated pyaudiolab's entry.

2007-02-20  jbednar

	* [r4831] topo/tkgui/testpattern.py:
	  Fixed missing time from Test Pattern window title

	* [r4830] topo/tkgui/templateplotgrouppanel.py:
	  Added Strength only button to allow orientation subplots to be
	  enabled or disabled on the fly

	* [r4829] topo/plotting/templates.py:
	  Removed orientation subplot from Projection Activity, because it
	  can be confusing with inhibitory weights

2007-02-20  ceball

	* [r4828] external/libsndfile-1.0.17.tar.gz:
	  http://www.mega-nerd.com/libsndfile/

2007-02-20  jbednar

	* [r4827] examples/som_retinotopy.ty:
	  Added mechanism for specifying seeds, retina density, radius_0,
	  and alpha_0 from the command line

	* [r4826]
	  doc/Tutorials/images/som_grid_000000.png:
	  Removed stray garbage from screenshot

	* [r4825]
	  doc/Tutorials/som_retinotopy_text.php:
	  Updated to match new screenshots

	* [r4824]
	  doc/Tutorials/images/som_activity_000006.png,
	  doc/Tutorials/images/som_cog_000100.png,
	  doc/Tutorials/images/som_grid_000100.png,
	  doc/Tutorials/images/som_projection_000006.png:
	  Removed now-unused plots

	* [r4823]
	  doc/Tutorials/images/som_activity_000000.png,
	  doc/Tutorials/images/som_activity_000001.png,
	  doc/Tutorials/images/som_activity_000005.png,
	  doc/Tutorials/images/som_activity_040000.png,
	  doc/Tutorials/images/som_cog_000000.png,
	  doc/Tutorials/images/som_cog_005000.png,
	  doc/Tutorials/images/som_cog_010000.png,
	  doc/Tutorials/images/som_cog_040000.png,
	  doc/Tutorials/images/som_grid_000000.png,
	  doc/Tutorials/images/som_grid_005000.png,
	  doc/Tutorials/images/som_grid_010000.png,
	  doc/Tutorials/images/som_grid_040000.png,
	  doc/Tutorials/images/som_projection_000000.png,
	  doc/Tutorials/images/som_projection_000001.png,
	  doc/Tutorials/images/som_projection_000005.png,
	  doc/Tutorials/images/som_projection_010000.png,
	  doc/Tutorials/images/som_projection_040000.png:
	  Updated for current CVS version of the simulator

2007-02-19  jbednar

	* [r4822]
	  doc/Tutorials/som_retinotopy_text.php:
	  General overhaul to work with recent Topographica versions,
	  with various other improvements and clarifications. The
	  screenshots still need to be updated.

2007-02-19  ceball

	* [r4821] doc/Future_Work/current_text.php:
	  Updated some tasks.

2007-02-19  jbednar

	* [r4820] doc/index.html:
	  Fixed typos

2007-02-19  ceball

	* [r4819] doc/Downloads/index_text.php:
	  Added commented-out note about libraries for pyaudiolab.

	* [r4818] external/Makefile:
	  Added ctypes and pyaudiolab (but they are not built by default).

	* [r4817] external/pyaudiolab-0.6.6.tar.gz:
	  http://www.ar.media.kyoto-u.ac.jp/members/david/softwares/pyaudiolab/

	* [r4816] external/ctypes-1.0.1.tar.gz:
	  http://sourceforge.net/projects/ctypes/

2007-02-19  jbednar

	* [r4815]
	  doc/Tutorials/som_retinotopy_text.php:
	  Minor update

2007-02-19  ceball

	* [r4814] topo/tkgui/propertiesframe.py:
	  Initial selection command performed inside ComboBoxTranslator
	  widget, rather than here.

	* [r4813] topo/tkgui/translatorwidgets.py:
	  Added balloon help text to currently selected item in a ComboBox.

2007-02-19  jbednar

	* [r4812]
	  doc/Tutorials/som_retinotopy_text.php:
	  Small updates

	* [r4811] doc/FAQ,
	  doc/FAQ/.cvsignore:
	  Initial version

	* [r4810] examples/Makefile:
	  Removed measure_contrast_response for now

	* [r4809] topo/plotting/plotgroup.py:
	  Cleaned up documentation

	* [r4808] examples/som_retinotopy.ty:
	  Increased radius to improve convergence. Removed now-redundant
	  change to learning rate. Changed random seeds to avoid
	  topological defect.

2007-02-19  ceball

	* [r4807] topo/misc/utils.py:
	  Clarified alerts.

	* [r4806] topo/misc/utils.py:
	  Added profile() function.

	* [r4805] topo/tests/test_script.py:
	  Added HACKALERT.

2007-02-17  judelaw

	* [r4804] topo/plotting/plotgroup.py:
	  added correct _create_plots command to
	  ProjectionActivityPlotGroup

	* [r4803] topo/commands/analysis.py:
	  changed update_projection activity so that values stored in
	  correct sheet_view_dict

2007-02-16  judelaw

	* [r4802] topo/base/cf.py:
	  Fixed bug in projection activity window - now uses correct bounds

2007-02-16  jbednar

	* [r4801] topo/tkgui/topoconsole.py:
	  Cleaned up progress report printing

	* [r4800] examples/som_retinotopy.ty:
	  Removed confusing random orientation

2007-02-15  antolikjan

	* [r4799] examples/lgn_lateral.ty:
	  Getting rid of CFPRF_SharedWeightDotProduct_opt and Wrapper

2007-02-15  judelaw

	* [r4798] topo/analysis/featureresponses.py:
	  fixed bug causing featurecurves to overwrite all previous data

2007-02-13  jbednar

	* [r4797] examples/Makefile:
	  Added alert from Jeff

	* [r4796] examples/lissom_oo_or.ty:
	  Updated to match lissom_oo_or_reference.ty

	* [r4795] examples/Makefile:
	  Added (now?) required argument for measure_contrast_response

2007-02-13  ceball

	* [r4794] Makefile:
	  Removed outdated plotting option for comparisons.

2007-02-12  jbednar

	* [r4793] examples/som_retinotopy.ty:
	  Significantly reduced alpha_0 to improve the convergence; not
	  clear why this is necessary. Changed random seeds (may or may not
	  be important).

	* [r4792] examples/Makefile:
	  Updated to match changes in topo/commands/analysis.py

	* [r4791] topo/base/parameterizedobject.py,
	  topo/base/simulation.py:
	  Added script_repr method for generating a concise, nearly
	  runnable representation of a simulation in memory

	* [r4790]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Fixed integer constants to be floats. Fixed apparent bug in
	  alpha_exc application at 499; was using alpha_input instead.
	  Fixed bug in 3999 and 19999 actions; Af01 was misspelled.

2007-02-11  jbednar

	* [r4789] topo/base/parameterizedobject.py:
	  Changed print_param_defaults to use repr() instead of str(), to
	  get closer to having a value that could be instantiated.
	  Simplified __repr__() implementation. Cleaned up docstrings and
	  spacing

2007-02-09  jbednar

	* [r4788] doc/FAQ,
	  doc/FAQ/index_text.php,
	  doc/shared/util.php:
	  Added FAQ

2007-02-09  ceball

	* [r4787] doc/Future_Work/current_text.php:
	  Updated my tasks.

2007-02-08  jbednar

	* [r4786] topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Added fix from Chris Ball for problem reported by Jan Antolik --
	  the initial contents of the scrolledlist_items in plot windows
	  were bogus, showing up as PY_VARXX, rather than as proper strings

2007-02-07  jbednar

	* [r4785] topo/learningfns/som.py:
	  Clarified alert

	* [r4784] examples/sullivan_nn06.ty:
	  Added hacks to do lateral weights; probably broken right now

2007-02-07  ceball

	* [r4783] topo/tests/test_script.py:
	  Minor updates.

	* [r4782] topo/tests/__init__.py,
	  topo/tests/test_script.py,
	  topo/tests/testlissom_oo_or.data,
	  topo/tests/testlissom_oo_or.py:
	  Replaced testlissom_oo_or.py with more general test_script.py.

	* [r4781] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r4780]
	  topo/tests/reference/lissom_or_reference.ty:
	  Added a comment.

	* [r4779] doc/Future_Work/current_text.php:
	  Removed some parts of a task.

	* [r4778]
	  topo/tests/reference/retina_lgn_match.000000.wts.Ganglia00.Afferent0.018_018.matrix.gz,
	  topo/tests/reference/retina_lgn_match.000001p000.Eye0_Activity.matrix.gz,
	  topo/tests/reference/retina_lgn_match.000001p000.Ganglia00_Activity.matrix.gz,
	  topo/tests/reference/retina_lgn_match.param,
	  topo/tests/reference/retina_lgn_match.ty:
	  Removed the retina_lgn_match simulation, since it's not really
	  nescessary but is probably confusing and creates extra work for
	  maintaining.

	* [r4777]
	  topo/tests/reference/oo_or_map_topo.param:
	  Updated some comments and orderings; shouldn't have affected
	  network behavior.

	* [r4776]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Updated to work with new comparison functions.

	* [r4775] doc/Future_Work/current_text.php:
	  Updated a task again.

	* [r4774] doc/Future_Work/current_text.php:
	  Updated a task.

	* [r4773]
	  topo/tests/reference/lissom_or_reference.ty:
	  Removed HACKALERT.

	* [r4772]
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/lissom_or_reference.ty:
	  Minor simplification to filename_base.

	* [r4771]
	  topo/tests/reference/lissom_log_parser.py:
	  Removed not-very-useful check from get_matrix(), so comparisons
	  don't have to specify the sheet size every time.

	* [r4770]
	  topo/tests/reference/lissom_or_reference.ty:
	  Minor change; no visible different.

	* [r4769]
	  topo/tests/reference/lissom_log_parser.py:
	  Updated documentation, plus minor change.

	* [r4768]
	  topo/tests/reference/lissom_log_parser.py:
	  Merged activity comparison functions.

	* [r4767]
	  topo/tests/reference/lissom_log_parser.py:
	  Merged weight comparison functions.

	* [r4766]
	  topo/tests/reference/lissom_log_parser.py:
	  Minor cleanup - should be no visible changes.

	* [r4765]
	  topo/tests/reference/lissom_or_reference.ty:
	  Removed outdated code related to plotting.

	* [r4764]
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/lissom_or_reference.ty:
	  Moved functions out of lissom_or to lissom_log_parser.

	* [r4763]
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/lissom_or_reference.ty:
	  compare_weights() and compare_activities() just print the results
	  immediately, and do not return anything.

	* [r4762]
	  topo/tests/reference/lissom_or_reference.ty:
	  Renamed Topographica sheets to match C++ lissom regions.

	* [r4761]
	  topo/tests/reference/lissom_or_reference.ty:
	  Cleanup: should be no visible change.

2007-02-06  ceball

	* [r4760] doc/Future_Work/current_text.php:
	  Updated my tasks.

2007-02-06  jbednar

	* [r4759]
	  doc/Tutorials/som_retinotopy_text.php:
	  Minor clarifications

2007-02-06  ceball

	* [r4758]
	  topo/tests/reference/lissom_log_parser.py:
	  Updated a comment.

	* [r4757]
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/reference/or_map_topo.param:
	  Reverted to a density of 24.

	* [r4756] doc/Future_Work/current_text.php:
	  Updated some of my tasks.

	* [r4755] topo/misc/utils.py:
	  Simplified Struct class.

2007-02-05  ceball

	* [r4754] topo/tests/utils.py:
	  Added comment.

	* [r4753]
	  topo/tests/reference/lissom_log_parser.py:
	  Converting both arrays to float seems to fix the comparisons
	  problems.

	* [r4752]
	  topo/tests/reference/lissom_log_parser.py:
	  Made error message slightly more helpful.

	* [r4751] topo/tests/utils.py:
	  Added HACKALERT.

	* [r4750]
	  topo/tests/reference/lissom_or_reference.ty:
	  Corrected timing and syntax of excitatory bounds change events.
	  Updated c++ weights slices now that the bounds are different
	  (plus corrected typo BaseRN for Base N, which didn't matter
	  before since they were equal).

	* [r4749] topo/base/simulation.py:
	  CommandEvent warns if an event is added that has faulty syntax.
	  Additionally, any CommandEvent that causes an error when it
	  executes is skipped, and a warning message is printed.

	* [r4748]
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/reference/or_map_topo.param:
	  Enlarged V1 density and added in an excitatory bounds change.

	* [r4747]
	  topo/tests/reference/lissom_log_parser.py:
	  compare_elements() no longer has a fixed maximum number of
	  decimal places at which to check for approximate equality.

	* [r4746]
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/retina_lgn_match.ty:
	  Added note that the comparisons in these files will not work
	  until they are updated.

	* [r4745]
	  topo/tests/reference/retina_lgn_match.000000.wts.Ganglia00.Afferent0.018_018.matrix,
	  topo/tests/reference/retina_lgn_match.000000.wts.Ganglia00.Afferent0.018_018.matrix.gz,
	  topo/tests/reference/retina_lgn_match.000001p000.Eye0_Activity.matrix,
	  topo/tests/reference/retina_lgn_match.000001p000.Eye0_Activity.matrix.gz,
	  topo/tests/reference/retina_lgn_match.000001p000.Ganglia00_Activity.matrix,
	  topo/tests/reference/retina_lgn_match.000001p000.Ganglia00_Activity.matrix.gz:
	  Gzipped to save space.

	* [r4744] topo/tests/reference/or_map_topo.log:
	  Now present as .gz file.

2007-02-05  jbednar

	* [r4743]
	  doc/Developer_Manual/imports_text.php,
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Minor tweak

	* [r4742] topo/patterns/basic.py:
	  Idea for a gradient pattern generator

	* [r4741] doc/Future_Work/current_text.php:
	  Added note on numpy.dot() performance

2007-02-04  jbednar

	* [r4740] topo/tests/utils.py:
	  Minor cleanup

2007-02-04  ceball

	* [r4739]
	  topo/tests/reference/lissom_or_reference.ty:
	  Now runs tests to 20000 iterations.

	* [r4738]
	  topo/tests/reference/lissom_or_reference.ty:
	  Now prints the smallest number of decimal places to which C++
	  LISSOM and Topographica match for various items.

	* [r4737]
	  topo/tests/reference/lissom_log_parser.py:
	  compare_elements() now returns the smallest number of decimal
	  places to which all corresponding elements of two arrays match.

	* [r4736] topo/tests/utils.py:
	  Added array_almost_equal() (based on
	  assert_array_almost_equal()), which tests whether or not two
	  arrays are equal to a specified number of decimal places. Added a
	  condition that assert_array_almost_equal is only valid if the
	  given number of decimal places is greater than 0.

	* [r4735]
	  topo/tests/reference/lissom_or_reference.ty:
	  Added some functions to cut down on typing, and updated lissom
	  command.

	* [r4734]
	  topo/tests/reference/lissom_log_parser.py:
	  Minor update to an error message.

	* [r4733] topo/misc/utils.py:
	  Added repr method to Struct class.

2007-02-03  ceball

	* [r4732]
	  topo/tests/reference/lissom_log_parser.py:
	  Minor simplifications.

	* [r4731]
	  topo/tests/reference/lissom_log_parser.py:
	  Removed unused code.

	* [r4730]
	  topo/tests/reference/or_map_topo.param:
	  Uncommented all the scheduled actions (except lat. exc. bounds
	  change).

	* [r4729]
	  topo/tests/reference/lissom_or_reference.ty:
	  Uncommented all the scheduled actions (except for lat. exc.
	  bounds change, since that starts off too small to shrink further.
	  Added commented-out code for comparisons up to t=14000.

2007-02-02  ceball

	* [r4728]
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/reference/or_map_topo.param:
	  Reverted times in topographica simulation. Uncommented scheduled
	  events for as far as I've checked (700 iterations, weights to 6
	  dp).

	* [r4727]
	  topo/tests/reference/lissom_or_reference.ty:
	  The previous commit happened by mistake, although the message was
	  partially correct (also commented out all scheduled actions in
	  the c++ and topographica simulations; topographica matches the
	  c++ lissom one to 6 decimal places in the weights of the central
	  unit after 700 iterations). Updated c++ lissom command this time.

	* [r4726]
	  topo/tests/reference/or_map_topo.param:
	  Commented out all scheduled actions.

	* [r4725]
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/lissom_or_reference.ty:
	  compare_elements returns more useful information (you can see how
	  what fraction of elements match at various numbers of decimal
	  places).

2007-02-02  judelaw

	* [r4724] topo/commands/analysis.py:
	  removed print statements from debugging

2007-02-02  ceball

	* [r4723]
	  topo/tests/reference/lissom_or_reference.ty:
	  Slight simplification (c++ lissom sheets will always be square).

	* [r4722]
	  topo/tests/reference/lissom_log_parser.py:
	  Slight simplification (c++ lissom sheets will always be square).
	  Added a comment and moved some import statements around.

	* [r4721]
	  topo/tests/reference/lissom_or_reference.ty:
	  Added comparison of retina activities.

	* [r4720]
	  topo/tests/reference/lissom_log_parser.py:
	  Records no. of d.p.

	* [r4719]
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/reference/or_map_topo.param:
	  The comparison simulations use a lower density. There are no
	  excitatory bounds changes.

	* [r4718]
	  topo/tests/reference/lissom_log_parser.py:
	  Corrected element comparison test (before it was sometimes saying
	  values didn't match to a certain number of decimal places, when
	  in fact they did (the numbers are floats).

2007-02-01  ceball

	* [r4717]
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/reference/or_map_topo.param:
	  Updated lissom_or_reference and or_map_topo at the same time,
	  checking they match the reference simulation in the book (except
	  with BaseN=72, and consequent changes). Currently radii are set
	  to specific values for testing; similarly, only some scheduled
	  events are present. These files can be made more general later
	  on. At this revision, the two simulations' weight values
	  consistently match to at least 4 d.p. over 550 iterations (I
	  haven't yet tested to more than 4 d.p. or 550 iterations). Both
	  files need to be tidied up.

	* [r4716]
	  topo/tests/reference/lissom_log_parser.py:
	  Added missing import.

2007-02-01  judelaw

	* [r4715] topo/commands/analysis.py:
	  fixed arror in contrast_response - added size to param_dict,
	  changed some default parameters

2007-02-01  ceball

	* [r4714]
	  topo/tests/reference/lissom_or_reference.ty:
	  Previous commit did not contain the real times (by mistake).

	* [r4713]
	  topo/tests/reference/lissom_or_reference.ty:
	  Corrected scheduled events.

	* [r4712]
	  topo/tests/reference/lissom_or_reference.ty:
	  Removed outdated alteration of scheduled-event timings.

	* [r4711]
	  topo/tests/reference/lissom_or_reference.ty:
	  Adjust learning rates by an amount that is now calculated when
	  the bounds change (and hence the number of units changes).

	* [r4710]
	  topo/tests/reference/lissom_or_reference.ty:
	  Updated some comments.

	* [r4709]
	  topo/tests/reference/lissom_or_reference.ty:
	  Updated to allow some automatic comparisons. Removed assertion
	  statements.

	* [r4708]
	  topo/tests/reference/or_map_topo.log.gz:
	  Compressed or_map_topo.log.

	* [r4707] topo/tests/reference,
	  topo/tests/reference/.cvsignore:
	  Ignore or_map_topo.log; might remove this line in the future but
	  for now it's the only way to make cvs diff feasible for me.

	* [r4706]
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Moved some functions to a more general location so I can use them
	  in lissom_or_reference.

	* [r4705]
	  topo/tests/reference/or_map_topo.param:
	  Version taken straight from the c++ lissom repository (the
	  current version, 1.15).

2007-01-31  fdemertzis

	* [r4704] examples/goodhill_network90.ty:
	  Fixed initialisation, and corrected the values for printing in
	  CoG.

2007-01-31  jbednar

	* [r4703]
	  /trunk/topographica-win/create_python_topo/numpy-1.0.1.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/scipy-0.5.2.win32-py2.4.exe:
	  Downloaded from sf.net

	* [r4702] examples/goodhill_network90.ty:
	  Forced update commands to be set properly for OD and CoG map
	  plotting

	* [r4701] examples/sullivan_nn06.ty:
	  Added optimized dot product activation function

	* [r4700] topo/commands/pylabplots.py:
	  Made axis parameter be user-controllable

2007-01-31  fdemertzis

	* [r4699] examples/goodhill_network90.ty:
	  Changed one value.

2007-01-31  antolikjan

	* [r4698] examples/lgn_lateral.ty:
	  The initial version of LGN with lateral connectivity

2007-01-31  jbednar

	* [r4697] topo/tkgui/topoconsole.py:
	  Changed 'Load script' menu option to 'Run script' to avoid
	  confusion
	  with 'Load snapshot'

	* [r4696] external,
	  external/.cvsignore:
	  More to ignore

2007-01-30  jbednar

	* [r4695] examples/goodhill_network90.ty:
	  Added update_elastic_net_maps to allow plotting in the GUI

	* [r4694] examples/Makefile:
	  Changed order of making examples

2007-01-30  fdemertzis

	* [r4693] examples/goodhill_network90.ty:
	  fixed documentation, made an array that stores the results for
	  printing.

2007-01-30  ceball

	* [r4692] external/Makefile:
	  Added gnosis utils.

	* [r4691] /trunk/topographica-win/create_python_topo/setup.bat:
	  Added note about what needs to be updated.

2007-01-30  fdemertzis

	* [r4690] examples/goodhill_network90.ty:
	  Complete implementation,fixed documentation, simplified some
	  code.

2007-01-29  jbednar

	* [r4689] doc/Downloads/index_text.php:
	  Added note about Mac system problems

2007-01-29  ceball

	* [r4688] doc/Downloads/cvs_text.php:
	  Minor update to Windows information.

2007-01-28  jbednar

	* [r4687] examples/goodhill_network90.ty:
	  Reformatted comments to match Topographica conventions. Changed
	  size parameters to be Integers. Made points be proper objects.

2007-01-28  fdemertzis

	* [r4686] examples/goodhill_network90.ty:
	  Implemented the second term of equation 1 of the paper, the
	  printing functionality is still missing.So now I the model must
	  be complete.

2007-01-28  jbednar

	* [r4685] external/Makefile:
	  Fixed typo in previous checkin

	* [r4684] external/Makefile:
	  Force removal of numpy weave version, for safety

	* [r4683] external/Makefile:
	  Fixed typo in previous checkin

	* [r4682] external/Makefile:
	  Added removal of previous installation for safety when switching
	  between the numpy and Numeric branches

2007-01-28  ceball

	* [r4681] topo/misc/numbergenerators.py:
	  Removed unused RandomWrapper class.

	* [r4680] topo/misc/utils.py:
	  Removed function that wrote an array to a file; there are now
	  functions to do this in arrayutils.

	* [r4679] topo/commands/analysis.py:
	  Removed unused import.

2007-01-27  fdemertzis

	* [r4678] examples/goodhill_network90.ty:
	  Complete overhaul. comment it heavily for future refernces.
	  Implemented further the learning function. Most of the heavy
	  parts are done. Missing the second term of equation 1 of the
	  paper, and the printing functionality.

2007-01-26  jbednar

	* [r4677] README.txt,
	  topo/__init__.py:
	  Updated copyright info

2007-01-25  judelaw

	* [r4676] topo/plotting/templates.py:
	  removed parameter inital_plot

	* [r4675] topo/plotting/templates.py:
	  removed contrast response full field

	* [r4674] topo/tkgui/topoconsole.py:
	  added ProjectionActivity window to refresh_activity_windows

2007-01-25  ceball

	* [r4673] doc/Future_Work/current_text.php:
	  Removed a task and updated another; added some notes for myself.

	* [r4672] topo/tkgui/editortools.py:
	  Made the new object parameters appear in the model editor, rather
	  than as a separate window. Needs some tidying up now.

	* [r4671] topo/tkgui/editorwindow.py:
	  The root of the editor window is not created by calling Tk(), but
	  is created by calling Toplevel(). Tk() - which initializes Tk -
	  'should only be called once per application'. This change
	  corrects some strange behavior (for example: having a
	  ParametersFrame inside a model editor window previously resulted
	  in a non-functional ParametersFrame).

2007-01-25  r_primrose

	* [r4670]
	  examples/sullivan_neurocomputing04.ty:
	  added orientation code for sweeping lines

2007-01-25  jbednar

	* [r4669] examples/lissom_oo_od.ty,
	  topo/base/arrayutils.py:
	  Removed previous bogus checkin

	* [r4668] examples/lissom_oo_od.ty,
	  topo/base/arrayutils.py,
	  topo/base/cf.py:
	  Fixed boolean comparison against array, to be compatible with
	  both Numeric and Numpy

	* [r4667] topo/sheets/generatorsheet.py:
	  Added assertion to catch confusing problem

	* [r4666] topo/commands/analysis.py:
	  Fixed longstanding bug -- if there were multiple input sheets
	  with different sizes (as in hierarchical.ty), patterns were being
	  presented by PatternPresenter with the same size in each sheet,
	  causing undefined behavior for values off the edge of the
	  ConnectionFields for each neuron.

2007-01-24  jbednar

	* [r4665] topo/commands/basic.py:
	  Changed default argument for pattern_present to present an empty
	  set of patterns, rather than give an error

	* [r4664] topo/misc/inlinec.py:
	  Fixed previous checkin -- was turning off optimization by default

	* [r4663] topo/learningfns/optimized.py,
	  topo/misc/inlinec.py,
	  topo/outputfns/optimized.py,
	  topo/responsefns/optimized.py:
	  Moved component substitution code into
	  provide_unoptimized_equivalent function for simplicity and to all
	  the messages to be disabled when necessary

	* [r4662] examples/goodhill_network90.ty:
	  Simplified and changed from a CFPLearningFn to a Sheet; no real
	  change
	  in capabilities (other than commenting out some code that was not
	  working).

	* [r4661] examples/goodhill_network90.ty:
	  Minor cleanup of docstrings and comments

2007-01-24  fdemertzis

	* [r4660] examples/goodhill_network90.ty:
	  Implemented further the learning function

2007-01-24  jbednar

	* [r4659] external,
	  external/.cvsignore,
	  external/Makefile,
	  external/numpy-1.0.1.tar.gz:
	  Added numpy to allow transition from Numeric

	* [r4658] topo/commands/basic.py:
	  Minor cleanup

	* [r4657] topo/outputfns/homeostatic.py:
	  Simplified docstring

	* [r4656] topo/outputfns/homeostatic.py:
	  Simplified docstring

2007-01-23  jbednar

	* [r4655] topo/tkgui/plotgrouppanel.py:
	  Removed duplicate code in enlarge() and reduce()

	* [r4654] topo/plotting/templates.py,
	  topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Changed PlotGroupTemplate.initial_plot to plot_immediately, to
	  avoid confusion with the entirely unrelated
	  PlotGroup.initial_plot. Made the default *not* to plot
	  immediately, because most user-added plots will need to be
	  measured somehow first, which is usually slow

	* [r4653] topo/tkgui/plotgrouppanel.py:
	  Changed right click to print plot name as well as the region name

	* [r4652] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py:
	  Changed to use plot's new rescale() method, and removed the
	  temporary hacks previously required for keeping track of the
	  scaling factors (using plot's new scale_factor instead).

	* [r4651] topo/plotting/plot.py:
	  Added method to rescale the images, keeping the original image
	  around for later rescaling, and storing the current scale_factor

2007-01-23  judelaw

	* [r4650] topo/commands/basic.py:
	  in pattern_present if any output_fn has a learning parameter then
	  set this to false during presentation of patterns

	* [r4649] topo/outputfns/homeostatic.py:
	  added learning parameter which can turn homeostatic learning off
	  during measurement of maps or curves

2007-01-23  jbednar

	* [r4648] topo/tkgui/plotgrouppanel.py:
	  Trivial reformatting of docstrings

2007-01-22  judelaw

	* [r4647] topo/plotting/templates.py,
	  topo/tkgui/featurecurvepanel.py,
	  topo/tkgui/topoconsole.py:
	  corrected Contrast Response Full field - should be replotted each
	  time unit is changed to avoid using wrong orientation

	* [r4646] topo/commands/analysis.py,
	  topo/commands/pylabplots.py,
	  topo/plotting/templates.py,
	  topo/tkgui/featurecurvepanel.py:
	  corrected error in prerequisite name, added sheet name to
	  warnings in feature curve measurement

	* [r4645] topo/commands/analysis.py:
	  corrected error in parameters for measure_or_tuning_fullfield

	* [r4644] topo/tkgui/featurecurvepanel.py:
	  added warnings for prerequisites

	* [r4643] topo/plotting/templates.py:
	  added a prerequisites paramleter for curves

	* [r4642] topo/plotting/plotgroup.py:
	  added a get_curve_time to FeatureCurvePlotGroup to get timestamps
	  from Curve SheetViews

	* [r4641] topo/commands/pylabplots.py:
	  changed tuning_curve_data to support getting data from SheetViews
	  rather than arrays

	* [r4640] topo/commands/analysis.py:
	  separated warnings for prerequisites in measure curves commands
	  so that defaults can be used separately

	* [r4639] topo/analysis/featureresponses.py:
	  changed curve_dict to contain SheetViews rather than activity
	  arrays in FeatureCurves

2007-01-22  ceball

	* [r4638] topo/tkgui/plotgrouppanel.py:
	  The row and col calculated for the matrix of a plot that is right
	  clicked on are integer row and column indexes.

	* [r4637] topo/tkgui/plotgrouppanel.py:
	  Added right click popup menu to PlotgroupPanel, showing the row
	  and column of the matrix corresponding to where was clicked on a
	  plot. Lots of the code is to illustrate how this could be used,
	  but does not currently do much.

	* [r4636] topo/plotting/plotgroup.py:
	  Added hack to store the original scaling factor. Might not be
	  required if that information is already available.

2007-01-21  jbednar

	* [r4635] topo/tkgui/templateplotgrouppanel.py:
	  Trivial cleanup

2007-01-21  ceball

	* [r4634] topo/tkgui/editortools.py:
	  Upgraded hack for 'new object properties' window: now clicking on
	  close does not destroy the window, but only hides it. This
	  prevents the error messages that used to appear if the window was
	  closed but then the user wanted to add another new object.

	* [r4633] topo/tkgui/topoconsole.py:
	  Added comment about clicking the window's 'X' to quit.

	* [r4632] topo/tkgui/editortools.py,
	  topo/tkgui/parametersframe.py:
	  Removed Reset button from the ParametersFrame for new objects,
	  because reset is not yet implemented for a class in a
	  ParametersFrame. Added reminder in parametersframe.

	* [r4631] topo/tkgui/editortools.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/testpattern.py:
	  Changed how to request which buttons a ParametersFrame should
	  display.

2007-01-20  judelaw

	* [r4630] topo/plotting/plotgroup.py:
	  call command and plot command separately

	* [r4629] topo/plotting/templates.py:
	  made command and plot command separate in full field curve
	  templates

	* [r4628] examples/laminar.ty:
	  corrected name, now laminar_or.ty

	* [r4627] examples/laminar_or.ty:
	  version with better self organisation

	* [r4626] examples/laminar_oo_or.ty:
	  *** empty log message ***

2007-01-20  jbednar

	* [r4625] examples/Makefile:
	  Added measure_cog and measure_position_pref

2007-01-19  jbednar

	* [r4624] topo/tkgui/featurecurvepanel.py:
	  Put commands side by side

	* [r4623] topo/commands/analysis.py:
	  Changed order of feature measurement so that the display option
	  is more meaningful

	* [r4622] topo/tkgui/plotgrouppanel.py:
	  Added help text for what to do when there is no plot on screen
	  yet

	* [r4621] doc/Tutorials/lissom_oo_or_text.php:
	  Updated to reflect the orientation map being saved with the file.

	* [r4620] examples/Makefile:
	  Added or maps and tuning curves to each snapshot

	* [r4619] topo/commands/analysis.py:
	  Turned display option off by default to allow usage in batch mode

	* [r4618] topo/plotting/plotgroup.py:
	  Set up to be a better starting point for using the timestamps
	  saved with curve data

2007-01-19  ceball

	* [r4617] topo/tkgui/parametersframe.py:
	  Added a HACKALERT.

	* [r4616] topo/tkgui/parametersframe.py:
	  Added Cancel button.

	* [r4615] topo/tkgui/testpattern.py:
	  ParametersFrame for PatternGenerator has only Reset button.

	* [r4614] topo/tkgui/editortools.py:
	  New object properties window has only Reset button. Also added
	  some notes to myself for coming changes.

	* [r4613] topo/tkgui/editorobjects.py:
	  ParametersFrame itself has Apply, Reset, and Ok buttons.

	* [r4612] topo/tkgui/parametersframe.py:
	  ParametersFrame itself has Apply, Reset, and Ok buttons (which
	  can be displayed or not). Removed buttons from right-click
	  editing method.

2007-01-19  jbednar

	* [r4611] topo/analysis/featureresponses.py:
	  Fixed curve_dict to be of type Float32 instead of Object to allow
	  it to be pickled

	* [r4610] topo/plotting/templates.py:
	  Added proj_name parameter to the measure_cog template so that
	  users can tell what to change when they don't get a plot

	* [r4609] examples/cfsom_or.ty:
	  Changed projection name to make measure_cog() work with no edits

	* [r4608] topo/base/cf.py,
	  topo/base/sheetview.py,
	  topo/commands/analysis.py:
	  Fixed Projection plots to use timestamps. Removed inappropriate
	  import of topo into cf.py

	* [r4607] topo/plotting/plotgroup.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Changed to use Plot's timestamps (created from the SheetView
	  timestamps) rather than the current time, to make it obvious when
	  old data is being plotted. Made various parts of the code work
	  when there were no plots (or only non-resizeable plots), to make
	  it possible to use any plots whose data *is* available while not
	  dying when there is no data available

	* [r4606] topo/tkgui/plotgrouppanel.py:
	  Removed code duplicated between PlotGroupPanel.refresh() and
	  BasicPlotGroupPanel.refresh()

	* [r4605] topo/analysis/featureresponses.py,
	  topo/base/cf.py,
	  topo/base/sheetview.py,
	  topo/commands/analysis.py:
	  Added timestamp to SheetViews

	* [r4604] topo/plotting/plot.py:
	  Added timestamp to Plots. Added warning for when the bitmaps used
	  in the plots become too stale, i.e. are too far out of sync in
	  their timestamps

2007-01-18  jbednar

	* [r4603] topo/commands/analysis.py:
	  Changed print statements into warnings

	* [r4602] topo/misc/numbergenerators.py:
	  Removed apparently stray print statement in RandomInt

2007-01-18  judelaw

	* [r4601] topo/tkgui/topoconsole.py:
	  added plotpanelclass for full field curves

	* [r4600] topo/plotting/templates.py:
	  added plotcommand for fullfield curves

	* [r4599] topo/plotting/plotgroup.py:
	  added support for fullfield feature curves ie. command to only
	  re-plot without re-measuring responses

	* [r4598] topo/tkgui/featurecurvepanel.py:
	  added a FullFieldFeatureCurvePanel for special case where full
	  field stimulus is used

	* [r4597] topo/tkgui/featurecurvepanel.py:
	  correction to update_plotgroup_variables to allow update command
	  to be changed before refresh

	* [r4596] topo/commands/analysis.py:
	  changes to allow for plotting curves for LGN, ie. using default
	  values for orientation

	* [r4595] topo/analysis/featureresponses.py:
	  added sheets_to_measure code to allow for plotting curves for LGN

	* [r4594] topo/tkgui/featurecurvepanel.py:
	  small changes to code determining wether or not to plot before
	  opening gui and adding all CFSheets to region list

	* [r4593] topo/tkgui/templateplotgrouppanel.py:
	  small change to code determining wether or not to plot before
	  opening gui

	* [r4592] topo/plotting/templates.py:
	  added flag for determining wether or not to plot before opening
	  gui window

	* [r4591] topo/tkgui/connectionfieldspanel.py:
	  minor change simplifying _add_region_menu

2007-01-17  jbednar

	* [r4590] topo/commands/pylabplots.py:
	  Cleaned up docstrings

	* [r4589] topo/tkgui/topoconsole.py:
	  Changed to allow specific override to FeatureCurvePanel if it is
	  ever
	  needed for a particular template

	* [r4588] topo/plotting/templates.py:
	  Cleaned up documentation and some comments

	* [r4587] examples/goodhill_network90.ty:
	  Cleaned up comments

2007-01-17  fdemertzis

	* [r4586] examples/goodhill_network90.ty:
	  Initial scetch of the Elastic net model

	* [r4585] examples/sullivan_nn06.ty:
	  Reviewed the parameters to be more precise but has error still..

2007-01-17  ceball

	* [r4584] topo/tkgui/editortools.py:
	  The little window for editing sheets/connections no longer
	  appears when the model editor is first opened.

	* [r4583] topo/tkgui/parametersframe.py:
	  Added reset method.

	* [r4582] topo/base/parameterizedobject.py:
	  Added reset_params() method, to return parameters to class
	  default values.

	* [r4581] doc/User_Manual/parameters_text.php:
	  Added a missing space.

	* [r4580] topo/tkgui/parametersframe.py:
	  Changes made while right-click editing a Parameter are saved for
	  all values of the Parameter, not just its initial value. (Also
	  corrected an accidental deletion of a 'self.__' I committed
	  previously.)

	* [r4579] topo/tkgui/parametersframe.py:
	  Clarified some of the code relating to right-click editing of
	  ParameterizedObjects. There should be no visible changes.

2007-01-15  judelaw

	* [r4578] topo/commands/analysis.py:
	  Various improvements to tuning curve measurements

	* [r4577] topo/tkgui/plotgrouppanel.py:
	  BasicPlotGroupPanel class added to plotgrouppanel.py

	* [r4576] topo/tkgui/basicplotgrouppanel.py:
	  no longer required, class added to plotgrouppanel.py

	* [r4575] topo/analysis/featureresponses.py:
	  updated gui refresh in measure_responses, removed
	  curve_param_dict

	* [r4574] topo/tkgui/featurecurvepanel.py:
	  now importing BasicPlotGroupPanel from plotgrouppanel

	* [r4573] topo/commands/pylabplots.py:
	  made changes to tuning_curve plotting

	* [r4572] topo/commands/pylabplots.py:
	  made changes to tuning_curve plotting

	* [r4571] topo/tkgui/topoconsole.py:
	  added if statement to decide on plotpanel class for
	  FeatureCurvePanel rather than making it a special case, also
	  added refresh_activity_windows function

	* [r4570] topo/plotting/templates.py:
	  made changes to tuning curve plotgroup templates, added
	  template_plot_type parameter for using in topoconcole to decide
	  on plotpanel class

	* [r4569] topo/patterns/basic.py:
	  changed name and fixed problems with SineGratingDisk

2007-01-15  antolikjan

	* [r4568] examples/laminar_oo.ty,
	  examples/laminar_oo_or.ty:
	  Moved laminar_oo.ty to laminar_oo_or.ty

2007-01-13  jbednar

	* [r4567] topo/analysis/featureresponses.py:
	  Cleaned up docstrings

2007-01-12  jbednar

	* [r4566] topo/commands/analysis.py:
	  Cleaned up docstrings and formatting

	* [r4565] topo/patterns/basic.py:
	  Added alert

	* [r4564] topo/patterns/basic.py:
	  Minor cleanup to docstring

	* [r4563] topo/plotting/templates.py:
	  Restored fixes to docstrings lost in previous revision

2007-01-11  judelaw

	* [r4562] topo/tkgui/plotgrouppanel.py:
	  Now a subclass of BasicPlotGroupPanel

	* [r4561] topo/tkgui/featurecurvepanel.py:
	  plot panel type for Feature curves - subclass of
	  BasicPlotGroupPanel

	* [r4560] topo/tkgui/basicplotgrouppanel.py:
	  Created superclass to PlotGroupPanel whcih implements only basic
	  refresh functions

	* [r4559] topo/commands/analysis.py:
	  Added new functions for measuring orientation tuning, contrast
	  response and size tuning curves

	* [r4558] topo/tkgui/topoconsole.py:
	  Specified plotpanel types for Feature Curves

	* [r4557] topo/patterns/basic.py:
	  Added GratingStimulus pattern for using as stimulus for plotting
	  curves

	* [r4556] topo/analysis/featureresponses.py:
	  Added FeatureCurve class for storing data for curve plotting

	* [r4555] topo/commands/pylabplots.py:
	  Added tuning_curve plots for curve plotting

	* [r4554] topo/plotting/plotgroup.py:
	  Added FeatureCurvePlotGroup for curve plotting

	* [r4553] topo/plotting/templates.py:
	  Added templates for new tuning curves

2007-01-06  jbednar

	* [r4552] doc/Makefile:
	  Now allows running even when the previous run was aborted,
	  leaving the tests directory in the wrong place

2007-01-05  jbednar

	* [r4551] topo/analysis/featureresponses.py:
	  Cleaned up documentation, variable names, and private routines;
	  should not have changed behavior (except if callers used keyword
	  rather than positional arguments)

	* [r4550] topo/tests/testfeaturemap.py:
	  Fixed to work with featureresponses.py; was only working on
	  systems with a .pyc file hanging around from earlier versions

	* [r4549] ChangeLog.txt:
	  Updated with recent changes

2007-01-04  jbednar

	* [r4548] doc/User_Manual/patterns_text.php:
	  Made link more explicit

	* [r4547] doc/Makefile,
	  external/Makefile,
	  external/epydoc.diff:
	  Major fix to reference manual to provide documentation for
	  Parameters in classes. Patched epydoc to show parsed Parameter
	  values in all cases, so that introspection can be used to get the
	  __doc__ values for Parameters

	* [r4546] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py,
	  topo/base/sheetcoords.py,
	  topo/base/sheetview.py,
	  topo/commands/analysis.py,
	  topo/misc/gendocs.py,
	  topo/misc/keyedlist.py,
	  topo/misc/numbergenerators.py,
	  topo/patterns/basic.py,
	  topo/plotting/palette.py,
	  topo/plotting/templates.py,
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testplotgrouppanel.py,
	  topo/tests/testtemplateplotgrouppanel.py:
	  Cleaned up docstrings to make epydoc happy. All of the remaining
	  problems (42 markup errors as of today) should be due to included
	  modules, mainly in TkInter and in the python pickle support.

	* [r4545] doc/Developer_Manual/coding_text.php:
	  Clarified what format the docstrings are in

	* [r4544] topo/base/sheet.py:
	  Minor fix to docstring

	* [r4543] topo/base/parameterizedobject.py:
	  Clarified documentation for ParameterizedObject

	* [r4542] topo/base/parameterizedobject.py,
	  topo/base/simulation.py,
	  topo/eps/basic.py,
	  topo/plotting/plotfilesaver.py,
	  topo/sheets/composer.py,
	  topo/tests/testsheetview.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionactivitypanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/translatorwidgets.py:
	  Changed **config to **params for a few ParameterizedObjects that
	  did not match the rest, for consistency. Should not have changed
	  any user-visible behavior in any way.

	* [r4541]
	  doc/User_Manual/images/centersurround.png,
	  doc/User_Manual/patterns_text.php:
	  Added example of center/surround pattern

	* [r4540] doc/Makefile:
	  Added more of reference manual to cleanup list

	* [r4539] doc/Reference_Manual/index_text.php:
	  Added notes on external packages

2006-12-21  jbednar

	* [r4538] doc/Future_Work/current_text.php:
	  Added more to do

2006-12-21  r_primrose

	* [r4537]
	  examples/sullivan_neurocomputing04.ty:
	  added pattern generator for moving lines

2006-12-20  jbednar

	* [r4536] examples/lissom_fsa.ty:
	  Initial sketch based on lissom_oo_or.ty

2006-12-19  judelaw

	* [r4535] topo/analysis/featuremap.py:
	  No longer required - has been replaced with featureresponses.py

	* [r4534] topo/analysis/featureresponses.py:
	  refactored file containing FeatureResponses and associated
	  classes which replaces featuremap.py

	* [r4533] topo/commands/analysis.py:
	  made changes so that functions now use the new
	  featureresponses.py which replaces featuremap.py

2006-12-16  ceball

	* [r4532] doc/Future_Work/current_text.php:
	  Transferred information from the existing task about upgrading
	  Numeric to the new one.

2006-12-15  antolikjan

	* [r4531] examples/laminar_oo.ty:
	  Initial version

2006-12-15  jbednar

	* [r4530] doc/Future_Work/current_text.php,
	  doc/User_Manual/commandline_text.php,
	  doc/images/ansiprompt.png,
	  topo/misc/commandline.py:
	  Documented new configurable command prompt

	* [r4529] doc/Future_Work/current_text.php:
	  Added tasks

2006-12-10  jbednar

	* [r4528] topo/misc/commandline.py:
	  Cleaned up new command prompt code

2006-12-10  ceball

	* [r4527] topo/misc/commandline.py:
	  Allows a dynamic prompt; might need some cleaning up.

2006-12-10  jbednar

	* [r4526] doc/shared/index.php:
	  Added news of PyCon 2007

2006-12-06  jbednar

	* [r4525]
	  examples/sullivan_neurocomputing04.ty:
	  Fixed simulation name. Moved KernelMax output_fn to the V1 sheet
	  instead of the connection weights

	* [r4524] topo/outputfns/basic.py:
	  Fixed KernelMax to return values in the original activity matrix
	  rather than returning a different-sized copy

	* [r4523] topo/learningfns/som.py:
	  Added alert -- the kernel_radius for a SOM is mistakenly still in
	  matrix coordinates

	* [r4522] topo/sheets/generatorsheet.py:
	  Added alert about memory allocation policies

2006-12-06  r_primrose

	* [r4521]
	  examples/sullivan_neurocomputing04.ty,
	  topo/outputfns/basic.py:
	  implemented kernel_max output_fn

2006-12-06  jbednar

	* [r4520] topo/patterns/basic.py:
	  Minor clarification to docstring

2006-12-06  fdemertzis

	* [r4519] examples/sullivan_nn06.ty:
	  Changed Gaussian size, bounding box, and general formatting.

2006-12-05  jbednar

	* [r4518] examples/sullivan_nn06.ty:
	  Simplified measure_topography and cleaned up its documentation

	* [r4517] doc/index.html:
	  Added better indexing information

2006-12-05  fdemertzis

	* [r4516] examples/sullivan_nn06.ty:
	  *** empty log message ***

2006-11-30  jbednar

	* [r4515] examples/sullivan_nn06.ty:
	  Fixed input region to be a 1-D array, with a 1-D Gaussian
	  pattern. Changed the measure_topography command to have a 1-pixel
	  pattern sweeping from the left

	* [r4514]
	  examples/sullivan_neurocomputing04.ty:
	  Fixed typos in previous checkin

	* [r4513] topo/learningfns/projfns.py:
	  Fixed bug in commented-out BCM rule; may work now. Updated
	  comments on Trace learning function. Changed to use
	  activity_type; shouldn't have any actual changes to behavior

	* [r4512]
	  examples/sullivan_neurocomputing04.ty:
	  Brought closer to what the paper seems to say, though there is
	  still a lot of work to do figuring it out

2006-11-30  r_primrose

	* [r4511]
	  examples/sullivan_neurocomputing04.ty,
	  topo/learningfns/projfns.py:
	  *** empty log message ***

2006-11-30  fdemertzis

	* [r4510] examples/sullivan_nn06.ty:
	  Almost complete, the learned map showing the winning outputs/
	  inputs.. not quite working properly... changed a bit the inputs..

	* [r4509] examples/sullivan_nn06.ty:
	  Almost complete, the learned map showing the winning outputs/
	  inputs.. not quite working properly...

2006-11-27  ceball_cvs2svn

	* [r4508] /tags/release_0_9_2,
	  /tags/release_0_9_2/topographica/examples/sullivan_neurocomputing06.ty:
	  This commit was manufactured by cvs2svn to create tag
	  'release_0_9_2'.

2006-11-27  jbednar

	* [r4507] Makefile:
	  Forced tags to be moved on topographica-win when needed

	* [r4506] Makefile:
	  Added more .cvsignores to remove

	* [r4505] doc/Reference_Manual/index_text.php:
	  Minor clarification

	* [r4504] doc/Makefile,
	  doc/Reference_Manual/index_text.php:
	  Fixed reference manual to have hand-coded index page, but added a
	  link to the auto-generated index.html

	* [r4503] Makefile:
	  Added removal of topographica-win from distribution, in case it
	  is
	  checked out in the local copy

2006-11-26  jbednar

	* [r4502] /trunk/topographica-win/create_installer/README.txt:
	  Added note for future builds

	* [r4501]
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat:
	  Put tiny.ty back into the distribution

	* [r4500] Makefile:
	  Added tagging for topographica-win

	* [r4499] doc/Downloads/cvs_text.php:
	  Added note about long pauses with CVS

	* [r4498] doc/Downloads/cvs_text.php:
	  Removed requirement for GCC 3.x under OS X

2006-11-24  jbednar

	* [r4497] topo/base/arrayutils.py:
	  Fixed obvious typos in previous checkin

	* [r4496] examples/sullivan_nn06.ty:
	  Added appropriate scaling for the learning rates

	* [r4495] topo/learningfns/projfns.py:
	  Added changes from Foivos. Changed default activity_target to
	  match sullivan:nn06. Removed hack for initializing the average
	  activities

	* [r4494] topo/base/arrayutils.py,
	  topo/learningfns/som.py:
	  Replaced special-purpose winner_coords function with general
	  array_argmax function

	* [r4493] examples/lissom_or_homeoscale.ty:
	  Added hack to initialize the average activities to those computed
	  during the initial period, rather than relying on that being done
	  within the HomeoSynaptic class. Changed outputfn from
	  PiecewiseLinear_debug to PiecewiseLinear_debug2 so that x_avg
	  would be available.

2006-11-24  ceball

	* [r4492] topo/misc/patternfns.py:
	  Removed unused import.

	* [r4491] topo/patterns/basic.py:
	  Updated Disk and Ring to transform the corresponding circular
	  patternfns.

	* [r4490] topo/misc/patternfns.py:
	  disk() and ring() functions changed to be circular only (and have
	  correct fall-off).

2006-11-24  jbednar

	* [r4489] examples/sullivan_nn06.ty:
	  Corrected citation

	* [r4488] Makefile,
	  examples/sullivan_neurocomputing06.ty,
	  examples/sullivan_nn06.ty:
	  Renamed sullivan_neurocomputing06.ty to sullivan_nn06.ty because
	  it's actually based on the longer journal paper version

	* [r4487]
	  examples/sullivan_neurocomputing06.ty:
	  Updated with changes from Foivos. Clarified comments, made
	  bounding boxes long and thin, removed disk weight shape, and
	  added plotting of average activities to compare against the
	  original paper

	* [r4486] topo/outputfns/homeostatic.py:
	  Minor cleanup of comments and spacing

	* [r4485] topo/learningfns/projfns.py:
	  Clarified documentation, and added normalizing term to the trace
	  learning rule

	* [r4484] topo/learningfns/basic.py:
	  Minor documentation update

	* [r4483]
	  examples/sullivan_neurocomputing04.ty:
	  Added scaling to make learning rates density-independent

	* [r4482] Makefile:
	  Keep tiny.ty in the distribution

2006-11-24  r_primrose

	* [r4481]
	  examples/sullivan_neurocomputing04.ty:
	  fixed connection field functions

2006-11-24  jbednar

	* [r4480] doc/Future_Work/current_text.php:
	  Merged identical categories

	* [r4479] ChangeLog.txt:
	  Added recent changes

	* [r4478] doc/Home/oldnews_text.php,
	  doc/shared/index.php:
	  Cleaned up news announcements

	* [r4477] doc/Makefile:
	  Fixed regeneration of ref manual after cleanup

	* [r4476] doc/Links/index_text.php:
	  Minor clarification

	* [r4475] doc/Team_Members/index_text.php:
	  Minor updates

	* [r4474] doc/User_Manual/index_text.php:
	  Removed outdated links

	* [r4473]
	  doc/User_Manual/background_text.php.m4,
	  doc/User_Manual/features_text.php.m4:
	  Removed unneeded files

	* [r4472]
	  doc/User_Manual/introduction_text.php.m4:
	  Added a few bits of text from the background and features files

2006-11-23  jbednar

	* [r4471] examples/lissom_or_homeoscale.ty,
	  examples/sullivan_neurocomputing06.ty,
	  topo/learningfns/projfns.py:
	  Moved HomeoSynaptic into main learningfns/projfns.py file

	* [r4470] topo/outputfns/homeostatic.py:
	  Fixed name of superclass

	* [r4469]
	  examples/sullivan_neurocomputing06.ty:
	  Cleaned up formatting to match lissom_or_homeoscale.ty for
	  merging them.

	* [r4468] examples/lissom_or_homeoscale.ty:
	  Commented out extra debugging operations

	* [r4467] examples/lissom_or_homeoscale.ty:
	  Cleaned up comments and formatting, and removed debugging
	  statements

	* [r4466]
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat:
	  Added more to delete; not entirely sure of Windows syntax

	* [r4465] topo/misc/utils.py:
	  Clarified comments

2006-11-23  ceball

	* [r4464] topo/tkgui/parametersframe.py:
	  Having made topo.misc.utils.atof() actually return only floats,
	  it no longer worked as a translator for non-float (Integer in
	  this case) quantities, so switched it for a different one.

2006-11-23  jbednar

	* [r4463] Makefile:
	  Removed -g from compare target to avoid popping up the GUI at the
	  end

	* [r4462] doc/Future_Work/current_text.php:
	  Fixed trivial typo

2006-11-23  ceball

	* [r4461] topo/misc/utils.py:
	  Minor change to comments.

	* [r4460] topo/tkgui/parametersframe.py:
	  Cleaned some comments.

	* [r4459] doc/Future_Work/current_text.php:
	  Updated ParametersFrame task; I cleaned it up as far as my
	  current knowledge of topo.tkgui goes...beyond the changes I made,
	  I'm no better able to clean it up than another developer.

	* [r4458] topo/tkgui/parametersframe.py:
	  Changed the location of the hack to avoid TaggedSlider being used
	  to represent Numeric types other than floats.

	* [r4457] topo/tkgui/parametersframe.py:
	  Clean-up: re-ordered two methods, made some methods be private.

	* [r4456] topo/tkgui/parametersframe.py:
	  Removed a hackalert. Made a method private.

	* [r4455] doc/Future_Work/current_text.php:
	  Updated tasks.

	* [r4454] topo/tkgui/parametersframe.py:
	  Added more information to a comment.

	* [r4453] topo/misc/utils.py:
	  Changed eval_atof() so that it produces a float from the string
	  it's given, unless that string is the name of a variable in
	  __main__, in which case it produces a float from the contents of
	  that variable. (I think that's what the original aim of the
	  method was.) If in_string, or the contents of the variable it
	  represents, does not contain something which can legitimately be
	  converted to a float, then string.atof() raises an error as it
	  would usually - before, illegitimate input resulted in a value of
	  0 or a non-float.

	* [r4452] topo/misc/utils.py,
	  topo/tkgui/translatorwidgets.py:
	  Moved an ALERT from topo/tkgui/translatorwidgets.py to
	  topo/misc/utils.py.

	* [r4451] topo/tkgui/translatorwidgets.py:
	  The 'optional_action()' method was not optional, but it is now.
	  (Fixes a bug where pressing return on e.g. test pattern window
	  leads to an error.)

	* [r4450]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Now advances the simulation time very slightly before comparing
	  weights, so that joint normalization has occurred before the
	  tests.

	* [r4449]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Changed calling syntax.

	* [r4448] Makefile:
	  Changed calling syntax of lissom_oo_or.ty.

2006-11-22  jbednar

	* [r4447] topo/tests/reference/Makefile:
	  Fixed typo in zcat definition; should run make clean to re-run
	  reference tests

	* [r4446] doc/Future_Work/current_text.php:
	  Clarified window title task

2006-11-22  ceball

	* [r4445]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Changed calling syntax from plots=True/False to plots=1/0 to make
	  it easy to specify from Makefile (might not have been necessary).

	* [r4444] Makefile:
	  make COMPARISON_PLOTS=1 compare shows plots for results that
	  don't match.

	* [r4443]
	  topo/tests/reference/lissom_log_parser.py:
	  compare_elements() returns True or False depending on result of
	  comparisons.

	* [r4442]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Continued simplification.

	* [r4441]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Simplified setting up a test.

	* [r4440] Makefile:
	  Disabled plotting for 'comparisons'.

	* [r4439]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Prints pass/fail information for tests. Plotting optional. Some
	  previous tests commented out (there for future use).

2006-11-21  jbednar

	* [r4438] Makefile:
	  Added more files to strip from public release

	* [r4437] /trunk/topographica-win/common/setup.py,
	  /trunk/topographica-win/create_installer/topographica.iss:
	  Updated Windows version number

	* [r4436] Makefile:
	  Updated release number in anticipation of release

	* [r4435] doc/Home/oldnews_text.php,
	  doc/shared/index.php:
	  Added news of upcoming 0.9.2 release

	* [r4434] ChangeLog.txt:
	  Added recent changes

	* [r4433] doc/User_Manual/basics_text.php.m4:
	  No longer needed

	* [r4432] doc/User_Manual/index_text.php,
	  doc/User_Manual/overview_text.php:
	  Minor updates

	* [r4431]
	  doc/User_Manual/introduction_text.php.m4:
	  Added some items to include later

	* [r4430] doc/Future_Work/current_text.php,
	  doc/Future_Work/index_text.php:
	  Added previously-commented-out sections of index_text.php to
	  current_text.php, plus other misc updates

	* [r4429] doc/Future_Work/current_text.php:
	  Removed completed tasks

2006-11-21  chrispalmer

	* [r4428] topo/tkgui/topoconsole.py:
	  script name will appear in console window title bar, after
	  running for one or more iterations

2006-11-21  jbednar

	* [r4427] topo/commands/basic.py:
	  Clarified warning message for pickling

	* [r4426] topo/misc/numbergenerators.py:
	  Minor fix to docs

2006-11-21  judelaw

	* [r4425] doc/Future_Work/current_text.php:
	  removed fixed bugs

	* [r4424] examples/laminar.ty,
	  examples/lissom_or_noshrinking_latswitch.ty:
	  added random Gaussian initial weights

	* [r4423] examples/lissom_or_noshrinking.ty:
	  changed parameters to previously calculated values that match C++
	  version, added random Gaussian initial weights

	* [r4422] topo/outputfns/basic.py:
	  Added sigmoid function and GeneralizedLogistic output functions

2006-11-20  jbednar

	* [r4421] examples/ohzawa_science90.ty:
	  Updated to match changes to rds.py. Added contents of Tikesh's
	  topo/analysis/testfeaturemap.py and topo/commands/test.py

	* [r4420] topo/base/parameterclasses.py:
	  Allowed Integers to be set to DynamicNumbers

	* [r4419] topo/misc/numbergenerators.py:
	  Added UniformRandomInt class

	* [r4418] topo/analysis/featuremap.py,
	  topo/commands/analysis.py,
	  topo/plotting/templates.py:
	  Changed name of disparity maps to phasedisparity, because
	  XDisparity and YDisparity are also likely to be needed

	* [r4417] topo/commands/analysis.py:
	  More documentation and comments for PatternPresenter

	* [r4416] topo/tkgui/testpattern.py:
	  Replaced several alerts with one that specifies what should be
	  done

	* [r4415] topo/patterns/rds.py:
	  Added alert

	* [r4414] topo/commands/analysis.py:
	  Added missing import command. Added alert for disparity and
	  ocularity changes. Added warnings for unsupported configurations
	  for those maps.

	* [r4413] topo/analysis/featuremap.py:
	  Fixed trivial typo

2006-11-20  judelaw

	* [r4412]
	  examples/lissom_or_noshrinking_latswitch.ty:
	  new model which switches sign of lateral connections based on
	  activity

2006-11-20  jbednar

	* [r4411] topo/tests/reference,
	  topo/tests/reference/.cvsignore:
	  Made auto-gunzipped files be ignored

	* [r4410] Makefile:
	  Added target for automatic comparisons with C++

	* [r4409] topo/tests/reference/Makefile:
	  Added support for gunzipping files automatically

2006-11-20  ceball

	* [r4408] topo/tkgui/parametersframe.py:
	  Removed an erroneous comment.

	* [r4407] topo/tkgui/parametersframe.py:
	  Minor simplification (removed an unnecessary variable).

	* [r4406] topo/tkgui/editortools.py:
	  Updated a method name to match changes in parametersframe.py.

	* [r4405] topo/tkgui/parametersframe.py:
	  Continued simplifying (by removing separate but near-identical
	  methods).

2006-11-19  ceball

	* [r4404] doc/Future_Work/current_text.php:
	  Removed a task. Any developer with a windows machine can recreate
	  the python_topo directory, so packages can be updated (e.g.
	  python 2.4.2 to python 2.4.4 to catch up with the main
	  repository).

	* [r4403] /trunk/topographica-win/create_python_topo/README.txt:
	  Updated now weave is present.

	* [r4402]
	  /trunk/topographica-win/create_python_topo/scipy_test.tar.gz,
	  /trunk/topographica-win/create_python_topo/weave.tar.gz:
	  Weave, I think from scipy 0.3.2, compiled with mingw. Seems to
	  have been running on several different computers fine for a while
	  now. When topographica switches to a newer scipy, we'll be able
	  to use the binary version of scipy (as we do for Numeric, etc).
	  We can't do that now because scipy has been reorganized, and
	  weave is in a different place (for example).

	* [r4401] /trunk/topographica-win/create_python_topo/setup.bat:
	  Adds weave and a c compiler.

	* [r4400] topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/testpattern.py:
	  Updated method names after changes to parametersframe.py.

	* [r4399] topo/tkgui/parametersframe.py:
	  Now there is only one method to have the ParametersFrame set
	  Parameters on its associated ParameterizedObject.

	* [r4398] topo/tkgui/editorobjects.py:
	  Update method name to match change to parametersframe.py.

	* [r4397] topo/tkgui/testpattern.py:
	  Update method name to match change to parametersframe.py.

	* [r4396] topo/tkgui/parametersframe.py:
	  Changed method name, tidied some documentation.

	* [r4395] topo/tkgui/testpattern.py:
	  Updated variable name to match ParametersFrame's.

	* [r4394] topo/tkgui/parametersframe.py:
	  Just one variable for the associated object (whether it's
	  ParameterizedObject object or metaclass, rather than two. Only
	  one or the other variable was used in the past, not both
	  together.

	* [r4393] topo/tkgui/parametersframe.py:
	  Changed variable name topo_class to PO_class since we have
	  ParameterizedObject now, not TopoObject. This variable name still
	  isn't good, but I hope this file can be reorganized further
	  anyway.

	* [r4392] topo/tkgui/testpattern.py:
	  Changed variable name topo_obj to PO_object.

	* [r4391] topo/tkgui/parametersframe.py:
	  Changed variable name topo_obj to PO_object since we have
	  ParameterizedObject now, not TopoObject. This variable name still
	  isn't good, but I hope this file can be reorganized further
	  anyway.

	* [r4390] topo/tkgui/parametersframe.py:
	  No visible change, just a minor reorganization of a method

	* [r4389] topo/tkgui/parametersframe.py:
	  Added a note.

	* [r4388] /trunk/topographica-win/README.txt:
	  Removed some accidentally left-over text.

	* [r4387] doc/Future_Work/current_text.php:
	  Minor update to a task.

	* [r4386]
	  topo/tests/reference/oo_or_map_topo.000050p000.Ganglia01_Activity.matrix.gz:
	  Data from c++ lissom.

	* [r4385]
	  topo/tests/reference/oo_or_map_topo.000050p000.Eye0_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000050p000.Ganglia00_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000050p000.Primary_Activity.matrix.gz:
	  Data from c++ lissom.

	* [r4384]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Updated the number of excitatory units after changing the radius.
	  Made the automatic comparisons optional (by commandline
	  parameter). Added more automatic tests.

	* [r4383]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Removed a comment.

	* [r4382]
	  topo/tests/reference/oo_or_map_topo.000000.wts.Ganglia00.Afferent0.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.Afferent00.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.Afferent00.023_023.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.LateralExcitatory.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.LateralExcitatory.023_023.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.LateralInhibitory.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.LateralInhibitory.023_023.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Eye0_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Ganglia00_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Ganglia01_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Primary_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Primary_InputResponse.matrix.gz:
	  New data after changing weights radii.

	* [r4381]
	  topo/tests/reference/oo_or_map_topo.param:
	  Tweaked the inh_rad and exc_rad so that they end in '.5'.

	* [r4380]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Changed the inh_rad and exc_rad parameters so that they end in .5
	  to help matching with c++ lissom. Commented out some assert
	  statements, which were useful for earlier debugging but are no
	  longer helpful.

2006-11-17  jbednar

	* [r4379] examples/joublin_bc96.ty,
	  topo/analysis/featuremap.py,
	  topo/commands/analysis.py:
	  Changed name of user_function to pattern_presenter and
	  display_projection to proj_name to more accurately reflect what
	  they do

	* [r4378] topo/commands/analysis.py:
	  Cleaned up comments, imports, and formatting, without altering
	  the function

	* [r4377] examples/som_retinotopy.ty:
	  Changed projection name to make CoG plots work unmodified

	* [r4376] examples/lissom_oo_or_dy_photo.ty:
	  Added alert

	* [r4375] topo/patterns/rds.py:
	  Added alert

	* [r4374] doc/Future_Work/current_text.php:
	  Added item

	* [r4373] topo/outputfns/basic.py:
	  Minor cleanup.

2006-11-17  ceball

	* [r4372] doc/Future_Work/current_text.php:
	  Removed 'press return to run simulation' task.

	* [r4371] topo/tests/reference/__init__.py:
	  Initial version. Seems to be required to allow importing from
	  files in this directory. Should have been added ages ago, but
	  existed as a .pyc file on my computer for a long time...

2006-11-16  judelaw

	* [r4370] topo/tkgui/plotgrouppanel.py:
	  fixed back/forward button bug - can now reduce and enlarge
	  without destroying history

	* [r4369] topo/outputfns/basic.py:
	  added sigmoidal output function

	* [r4368] topo/analysis/featuremap.py:
	  added state push and pop to present_input_patterns to ensure that
	  state rolls back after presentation of every pattern when
	  measuring maps

	* [r4367] examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/laminar_or_noshrinking.ty,
	  examples/lissom_or_noshrinking_latswitch.ty:
	  removed, no longer relevant

2006-11-15  judelaw

	* [r4366] topo/base/cf.py,
	  topo/commands/analysis.py,
	  topo/sheets/lissom.py:
	  Reversed changes - settling bug fix caused problems with
	  auto-refresh, kept fix for projection activity (really this time)

	* [r4365] topo/base/cf.py:
	  added new CFResponse_fn - Activity_dependent - for use with
	  lissom_or_noshrinking_latswitch.ty

	* [r4364]
	  examples/lissom_or_noshrinking_latswitch.ty:
	  version of lissom_or_noshrinking with long range lateral
	  connections with activity dependent strength - work in progress

	* [r4363] examples/laminar.ty:
	  current version of laminar - still a work in progress and also
	  need to change name

	* [r4362] topo/commands/analysis.py:
	  removed conditions on loop in update_projectionactivity which was
	  causing update of sheet_view_dict to be skipped, not sure why
	  they were necessary, hopefully this hasn't broken anything else

2006-11-15  jbednar

	* [r4361]
	  examples/sullivan_neurocomputing04.ty,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py:
	  Added support for mapping CF centers using CoordinateMapperFns

2006-11-15  judelaw

	* [r4360] topo/sheets/lissom.py:
	  changed activation count to include loop for when settling is
	  turned off when measuring maps

	* [r4359] topo/commands/analysis.py:
	  added a parameter which must be set to determine wether or not
	  settling is turned on when measuring maps (important for lissom
	  sheets)

2006-11-14  r_primrose

	* [r4358] topo/base/cf.py:
	  added commented out alternative receptive field code

2006-11-14  jbednar

	* [r4357] topo/patterns/rds.py:
	  Changed calculations to use array functions for speed and
	  robustness

2006-11-14  ceball

	* [r4356] topo/tkgui/topoconsole.py:
	  Updated name of method to match change to TaggedSlider's
	  refresh() and action() methods.

	* [r4355] topo/tkgui/translatorwidgets.py:
	  Pressing return in a TaggedSlider can cause more actions than
	  when it simply loses focus.

2006-11-14  jbednar

	* [r4354] topo/patterns/rds.py:
	  Removed special-purpose code for examples/ohzawa_science90.ty,
	  and simply set the default scale and offset so that the result
	  would be visible for most scripts

2006-11-14  ceball

	* [r4353] topo/tkgui/topoconsole.py:
	  Added a comment and moved line relating to pressing return for
	  running the simulation.

	* [r4352] topo/tkgui/translatorwidgets.py:
	  Added some comments.

2006-11-14  jbednar

	* [r4351] topo/patterns/rds.py:
	  Trivial cleanup

2006-11-14  ceball

	* [r4350] topo/tkgui/topoconsole.py:
	  Pressing return in 'run for' box makes the simulation run.

2006-11-14  jbednar

	* [r4349] examples/lissom_oo_od.ty:
	  Added warning that this file has not yet been tested

	* [r4348] topo/tkgui/parametersframe.py:
	  Fixed bug -- Integer parameters like rds.random_seed were
	  assigned TaggedSliders, but the TaggedSliders assume that the
	  result is floating-point, and so dragging the slider did not work
	  for such parameters

	* [r4347] topo/base/patterngenerator.py:
	  Made default orientation indicate that it is floating point

2006-11-14  ceball

	* [r4346] topo/tkgui/topoconsole.py:
	  Minor change to a comment.

	* [r4345]
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.Afferent00.023_023.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.LateralExcitatory.023_023.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.LateralInhibitory.023_023.matrix.gz:
	  Data from C++ lissom.

	* [r4344]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Added comparison for a central unit's LateralInhibitory CF, and
	  added a note.

	* [r4343]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Added comparison for a central unit's LateralExcitatory CF.

	* [r4342]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Removed a mistaken comment. Started to add a comparison for a
	  central unit as well as one on the edge.

2006-11-14  jbednar

	* [r4341] topo/patterns/rds.py:
	  Removed redundant initializations

	* [r4340] topo/patterns/rds.py:
	  Removed unused extra dimension on temporary vectors

2006-11-14  ceball

	* [r4339]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Removed stray line (should never have been introduced).

	* [r4338]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Minor change to notes.

2006-11-14  jbednar

	* [r4337] topo/patterns/rds.py:
	  Suppressed unused size parameter.

	* [r4336] topo/patterns/rds.py:
	  Fixed bug that would only appear if called with parameters
	  overriding in the __call_function

	* [r4335] topo/patterns/rds.py:
	  Combined __call__ and rds methods so that they can be simplified

2006-11-13  jbednar

	* [r4334] topo/patterns/rds.py:
	  Cleaned up parameters

	* [r4333] topo/patterns/rds.py:
	  Replaced fix() with floor() to use Numeric native functions

	* [r4332] examples/lissom_oo_or_dy.ty:
	  Further cleanup of position selection code

	* [r4331] examples/lissom_oo_or_dy.ty:
	  Further cleanup of position selection code

	* [r4330] examples/lissom_oo_or_dy.ty:
	  Renamed variables and classes to make their function clear

	* [r4329] topo/base/pickle.py:
	  Removed unneeded file; contents currently in
	  examples/lissom_oo_or_dy.ty

	* [r4328] examples/lissom_oo_or_dy.ty:
	  Moved input position pickling code here from Tikesh's
	  topo.base.pickle for working on it

	* [r4327] topo/misc/numbergenerators.py:
	  Specified a more universally valid set of defaults for Choice

	* [r4326] examples/lissom_oo_or_dy.ty:
	  Updated to state list of choices explicitly

	* [r4325] topo/misc/numbergenerators.py:
	  Cleaned up Choice class to allow any list of choices

	* [r4324] examples/README.txt:
	  Updated list of examples

	* [r4323] examples/read_visneuro02.ty:
	  Never completed; suppressed to avoid confusion

	* [r4322] examples/read_visneuro02.ty:
	  Minor tweak

	* [r4321] examples/ohzawa_science90.ty:
	  Updated documentation

	* [r4320] examples/odf_science90.ty,
	  examples/ohzawa_science90.ty:
	  Renamed odf_science90.ty to ohzawa_science90.ty

	* [r4319] examples,
	  examples/.cvsignore:
	  I decided that the .typ files should be ignored, even though they
	  might be something the user wants to keep, because they keep
	  clogging up the cvs diff output and obscuring more important
	  changes

	* [r4318] topo/outputfns/basic.py:
	  Clarified documentation, as suggested by Chris Ball

2006-11-13  ceball

	* [r4317]
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.Afferent00.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.LateralExcitatory.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000000.wts.Primary.LateralInhibitory.000_000.matrix.gz:
	  Data from c++ lissom.

	* [r4316]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Added some notes.

	* [r4315]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Added checks for more weights.

	* [r4314]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Added checking of Primary Afferent00 weights.

	* [r4313]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Fixed another typo, added another weight plot for comparison.

	* [r4312]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Fixed a typo.

	* [r4311]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Added some plots.

	* [r4310]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Minor addition to notes.

	* [r4309]
	  topo/tests/reference/or_map_topo.000001.wts.Primary.Afferent0.024_070.matrix,
	  topo/tests/reference/or_map_topo.000001.wts.Primary.LateralExcitatory.024_070.matrix,
	  topo/tests/reference/or_map_topo.000001p000.Eye0_Activity.matrix,
	  topo/tests/reference/or_map_topo.000001p000.Primary_Activity.matrix:
	  Removed unused data.

	* [r4308]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Corrected mistake in previous commit.

	* [r4307]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Updated notes.

	* [r4306]
	  topo/tests/reference/oo_or_map_topo.log.gz:
	  gzipped version of oo_or_map_topo.log.

	* [r4305]
	  topo/tests/reference/oo_or_map_topo.log:
	  Moved to oo_or_map_topo.log.gz

	* [r4304]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Minor clean-up.

	* [r4303]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Added some notes.

	* [r4302]
	  topo/tests/reference/oo_or_map_topo.000000.wts.Ganglia00.Afferent0.000_000.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Eye0_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Ganglia00_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Ganglia01_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Primary_Activity.matrix.gz,
	  topo/tests/reference/oo_or_map_topo.000001p000.Primary_InputResponse.matrix.gz:
	  Data from c++ lissom oo_or_map_topo

	* [r4301]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Added command to generate c++ lissom data.

	* [r4300]
	  topo/tests/reference/oo_or_map_topo.param:
	  Version from c++ lissom.

	* [r4299]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  Reverted some code that was previously committed by mistake
	  (several revisions ago).

	* [r4298]
	  topo/tests/reference/lissom_oo_or_reference.ty:
	  For the LGN ON and OFF weights, the ON Gaussian and OFF Gaussian
	  are now each normalized to 2.33 before being combined, and the
	  strength of the Retina-LGN connection is not multiplied by 2.33.
	  Added code to allow automatic comparison with equivalent c++
	  simulation.

2006-11-12  ceball

	* [r4297]
	  topo/tests/reference/retina_lgn_match.ty:
	  Minor change to allow easier specification of number of decimal
	  places for matching.

2006-11-11  jbednar

	* [r4296] topo/patterns/image.py:
	  Added code needed for lissom_oo_or_dy_photo.ty

	* [r4295] examples/lissom_oo_or_dy_photo.ty:
	  Cleaned up to match lissom_oo_or_dy.ty better

	* [r4294] examples/lissom_oo_or_dy_photo.ty:
	  Added Tikesh's lissom_oo_disparity_image.ty as
	  lissom_oo_or_dy_photo.ty ; not cleaned up at all yet

	* [r4293] examples/lissom_oo_or_dy.ty:
	  Verified identical code to yesterdays version of
	  lissom_oo_disparity_gauss_0.ty,
	  lissom_oo_disparity_gauss_2_pixel.ty,
	  lissom_oo_disparity_plus_minus_0.ty, and
	  lissom_oo_disparity_plus_minus_2_pixel.ty. Thus those files can
	  now all be ignored, and this one used in their place

	* [r4292] examples/lissom_oo_or_dy.ty:
	  Made declared name match filename

	* [r4291] examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/laminar_or_noshrinking.ty,
	  examples/lissom_oo_od.ty,
	  examples/lissom_oo_or_dy.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_homeomaxent.ty,
	  examples/lissom_or_homeoscale.ty,
	  examples/lissom_or_noshrinking.ty,
	  examples/odf_science90.ty,
	  examples/read_visneuro02.ty,
	  examples/som_retinotopy.ty,
	  examples/sullivan_neurocomputing04.ty,
	  examples/sullivan_neurocomputing06.ty,
	  examples/tiny.ty:
	  Cleaned up revision control information

	* [r4290]
	  examples/lissom_oo_disparity_plus_minus_0.ty:
	  Now obsolete; same simulation can be obtained by running
	  'topographica -c plusminus=True -c max_disparity=0
	  lissom_oo_or_dy.ty

	* [r4289]
	  examples/lissom_oo_disparity_plus_minus_2_pixel.ty:
	  Now obsolete; same simulation can be obtained by running
	  'topographica -c plusminus=True lissom_oo_or_dy.ty

	* [r4288] examples/lissom_oo_or_dy.ty:
	  Added plusminus option

	* [r4287] examples/lissom_oo_or_disparity.ty,
	  examples/lissom_oo_or_dy.ty:
	  Renamed lissom_oo_or_disparity.ty to lissom_oo_or_dy.ty to
	  establish naming convention

	* [r4286]
	  examples/lissom_oo_disparity_plus_minus_2_pixel.ty:
	  Minor cleanup

	* [r4285] examples/lissom_oo_or_disparity.ty:
	  Made the input scale and offset be parameters to help support
	  plus/minus inputs

	* [r4284]
	  examples/lissom_oo_disparity_plus_minus_2_pixel.ty:
	  Made the input scale and offset be parameters so that this file
	  can be merged with lissom_or_disparity.ty

	* [r4283]
	  examples/lissom_oo_disparity_plus_minus_2_pixel.ty,
	  examples/lissom_oo_or_disparity.ty:
	  Made LGN strength be a parameter to make it easier to match
	  simulations

	* [r4282]
	  examples/lissom_oo_disparity_plus_minus_2_pixel.ty,
	  examples/lissom_oo_or_disparity.ty:
	  Fixed typo

	* [r4281]
	  examples/lissom_oo_disparity_plus_minus_2_pixel.ty:
	  Added ability to control the amount of disparity externally

	* [r4280] examples/lissom_oo_or_disparity.ty:
	  Added parameter for position_bound, previously not matching the 0
	  pixel case properly. Changed disparity_range to be a
	  disparity_bound to match.

	* [r4279]
	  examples/lissom_oo_disparity_gauss_0.ty:
	  No longer needed; can be obtained as 'topographica -c
	  max_disparity=0 lissom_oo_or_disparity.ty' now instead

	* [r4278] examples/lissom_oo_or_disparity.ty:
	  Changed declared name to match filename

	* [r4277]
	  examples/lissom_oo_disparity_gauss_2_pixel.ty,
	  examples/lissom_oo_or_disparity.ty:
	  Renamed lissom_oo_disparity_gauss_2_pixel.ty to
	  lissom_oo_or_disparity.ty since it is no longer restricted to 2
	  pixel disparity, and should eventually allow different input
	  patterns

	* [r4276]
	  examples/lissom_oo_disparity_gauss_2_pixel.ty:
	  Added ability to control the amount of disparity externally

	* [r4275]
	  examples/lissom_oo_disparity_gauss_2_pixel.ty:
	  Cleaned up comments

2006-11-11  ceball

	* [r4274]
	  topo/tests/reference/retina_lgn_match.ty:
	  Updated c++ lissom command stored in this file.

2006-11-10  jbednar

	* [r4273]
	  topo/commands/disp_key_white_vert_small.png:
	  Replaced misleading orientation bars with squares to show the
	  color code more simply

	* [r4272] topo/patterns/basic.py,
	  topo/patterns/image.py:
	  Removed bogus outdated copy of PatternSampler from basic.py and
	  updated the correct version in image.py instead

	* [r4271] README.txt:
	  Added more developers to copyright statement

2006-11-09  jbednar

	* [r4270] doc/Future_Work/current_text.php:
	  Added tasks from the developers meeting, including plans for the
	  0.9.2 release

	* [r4269] doc/Future_Work/current_text.php:
	  Added tasks from the developers meeting, including plans for the
	  0.9.2 release

	* [r4268] external/Python-2.4.2.tgz:
	  Upgraded from Python 2.4.2 to 2.4.4 to fix libreadline problem

	* [r4267] external/Makefile:
	  Slight change to Python build commands; shouldn't have any
	  effect, but may work around a build problem

	* [r4266] external,
	  external/.cvsignore,
	  external/Makefile,
	  external/Python-2.4.4.tgz:
	  Upgraded from Python 2.4.2 to 2.4.4 to fix libreadline problem

2006-11-08  jbednar

	* [r4265] topo/learningfns/projfns.py:
	  Cleaned up whitespace

	* [r4264]
	  examples/sullivan_neurocomputing06.ty,
	  topo/outputfns/homeostatic.py:
	  Cleaned up sullivan_neurocomputing06.ty; moving TestFn to
	  topo.outputfns.homeostatic.PiecewiseLinear_debug2 and removing
	  the initial no-homeostatic plasticity phase

	* [r4263] doc/Links/index_text.php:
	  Added more info on NEST

	* [r4262]
	  examples/Sullivan_homeo_synaptic_SOM.ty,
	  examples/sullivan_neurocomputing06.ty:
	  Moved Sullivan_homeo_synaptic_SOM.ty to
	  sullivan_neurocomputing06.ty

2006-11-08  r_primrose

	* [r4261]
	  examples/sullivan_neurocomputing04.ty:
	  Added disclaimer

	* [r4260] examples/sullivan_nc04.ty,
	  examples/sullivan_neurocomputing04.ty:
	  Renamed sullivan_nc04.ty to sullivan_neurocomputing04.ty

2006-11-08  fdemertzis

	* [r4259]
	  examples/Sullivan_homeo_synaptic_SOM.ty:
	  Initial version, no date of publication

2006-11-08  r_primrose

	* [r4258] examples/sullivan_nc04.ty,
	  topo/learningfns/projfns.py:
	  *** empty log message ***

2006-11-07  jbednar

	* [r4257]
	  examples/homeo_intrinsic_lissom_or.ty,
	  examples/lissom_or_homeomaxent.ty:
	  Moved homeo_intrinsic_lissom_or.ty to lissom_or_homeomaxent.ty

	* [r4256] examples/lissom_or_homeoscale.ty:
	  Moved homeo_synaptic_lissom_or.ty to lissom_or_homeoscale.ty

	* [r4255] examples/homeo_synaptic_lissom_or.ty,
	  examples/lissom_or_homeoscale.ty:
	  Moved homeo_synaptic_lissom_or.ty to lissom_or_homeoscale.ty

	* [r4254]
	  examples/homeo_intrinsic_lissom_oo_or.ty,
	  examples/lissom_oo_or_homeomaxent.ty:
	  Moved homeo_intrinsic_lissom_oo_or.ty to
	  lissom_oo_or_homeomaxent.ty

	* [r4253]
	  examples/homeo_lissom_or_noshrinking.ty:
	  No longer needed; moved into lissom_or_noshrinking.ty

	* [r4252] examples/lissom_or_noshrinking.ty:
	  Made homeostatic by default; still usable as non-homeostatic by
	  adding '-c homeostatic=False' to the command line

	* [r4251]
	  examples/homeo_lissom_or_noshrinking.ty:
	  Cleaned up imports

	* [r4250] examples/lissom_oo_od.ty:
	  Trivial change to try to remove execute bit

	* [r4249] examples/lissom_oo_od.ty:
	  Trivial change to try to remove execute bit

	* [r4248] examples/laminar.ty,
	  examples/lissom_oo_od.ty:
	  Trivial change to try to remove execute bit

	* [r4247] examples/homeostatic.ty:
	  Removed unused file

	* [r4246]
	  examples/homeo_intrinsic_lissom_oo_or.ty,
	  examples/homeo_intrinsic_lissom_or.ty,
	  examples/homeo_synaptic_lissom_or.ty,
	  topo/outputfns/homeostatic.py:
	  Cleaned up homeostatic simulations -- moved OutputFns to
	  topo.outputfns.homeostatic, removed unused imports

	* [r4245] examples/joublin_bc96.ty:
	  Minor cleanup

2006-11-02  jbednar

	* [r4244] doc/shared/index.php:
	  Added blurb about weave

	* [r4243] external/Makefile:
	  Added re-make when weave.diff changes (or is newer than the weave
	  target) to force rebuild

	* [r4242] external/Makefile,
	  external/weave.diff:
	  Added patch to allow weave to work on GCC 4.1.x

	* [r4241] doc/Future_Work/current_text.php:
	  Added FFT plot to-do

2006-10-06  ceball

	* [r4240] topo/tests/testlissom_oo_or.py:
	  Corrected a HACKALERT; added note to myself on how to rnu the
	  test.

	* [r4239] doc,
	  doc/.cvsignore:
	  Ignore reference-manual.

	* [r4238] topo/tests/testlissom_oo_or.py:
	  Tests V1 activities at t=1, t=100, and t=210.

	* [r4237] topo/tests/testlissom_oo_or.data:
	  V1 activities from t=1,t=100,t=210 for examples/lissom_oo_or.ty
	  with Topographica updated just before the time of this commit.

	* [r4236] topo/tests/testlissom_oo_or.py:
	  Initial version.

	* [r4235] topo/tests/__init__.py:
	  Avoid running the slower testlissom_oo_or.py test file. (A future
	  task is to allow there to be a set of slower tests.)

	* [r4234] doc/Future_Work/current_text.php:
	  Added small clarification.

	* [r4233] topo/tests/testlissom.data,
	  topo/tests/testlissom.ty:
	  Removed unused and outdated test file, along with its data.

	* [r4232] topo/base/cf.py:
	  Tried to clarify some comments a little. Minor corrections to
	  docstrings.

2006-10-05  ceball

	* [r4231] topo/tests/reference,
	  topo/tests/reference/.cvsignore:
	  Initial version.

	* [r4230]
	  topo/tests/reference/retina_lgn_match.ty:
	  Checks LGN weights.

	* [r4229]
	  topo/tests/reference/lissom_log_parser.py:
	  get_matrix() (which reads a c++ lissom matrix) always returns an
	  array. compare_elements() first checks that the two arrays are
	  the same shape.

	* [r4228]
	  topo/tests/reference/retina_lgn_match.000000.wts.Ganglia00.Afferent0.018_018.matrix:
	  Initial version

2006-10-04  ceball

	* [r4227] topo/tests/reference/lissom5.gz:
	  Gzip'd lissom5 binary, for generation of reference results.

	* [r4226] topo/tests/reference/lissom5:
	  Adding gzip'd version to repository.

	* [r4225]
	  topo/tests/reference/retina_lgn_match.ty:
	  Added comment.

	* [r4224]
	  topo/tests/reference/retina_lgn_match.param,
	  topo/tests/reference/set_thresholds.command:
	  Initial version.

	* [r4223] topo/tests/reference/lissom5:
	  C++ LISSOM 5 binary, for generation of C++ data.

	* [r4222]
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty:
	  Updated location of lissom_log_parser module to the correct one
	  (was working before because of pyc file left behind).

	* [r4221]
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty:
	  Removed outdated automatic testing code; the current code is in
	  retina_lgn_match.ty.

	* [r4220]
	  topo/tests/reference/retina_lgn_match.ty:
	  Added commented-out code from one of the other reference files.

	* [r4219]
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/retina_lgn_match.ty:
	  Moved compare_elements() function from retina_lgn_match.ty to
	  lissom_log_parser.py.

	* [r4218]
	  topo/tests/reference/retina_lgn_match.000001p000.Eye0_Activity.matrix,
	  topo/tests/reference/retina_lgn_match.000001p000.Ganglia00_Activity.matrix:
	  Values from C++ LISSOM.

	* [r4217]
	  topo/tests/reference/retina_lgn_match.ty:
	  Compares retina and cfsheet activities with those from c++.

	* [r4216]
	  topo/tests/reference/lissom_log_parser.py:
	  Minor clarifications.

	* [r4215]
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/reference/retina_lgn_match.ty:
	  Updated path after moving.

	* [r4214] doc/Future_Work/current_text.php:
	  Removed task.

	* [r4213] topo/tests/reference/README.txt:
	  Removed ALERT.

	* [r4212]
	  topo/tests/reference/lissom_log_parser.py,
	  topo/tests/reference/lissom_oo_or_reference.ty,
	  topo/tests/reference/lissom_or_reference.ty,
	  topo/tests/reference/oo_or_map_topo.log,
	  topo/tests/reference/or_map_topo.000001.wts.Primary.Afferent0.024_070.matrix,
	  topo/tests/reference/or_map_topo.000001.wts.Primary.LateralExcitatory.024_070.matrix,
	  topo/tests/reference/or_map_topo.000001p000.Eye0_Activity.matrix,
	  topo/tests/reference/or_map_topo.000001p000.Primary_Activity.matrix,
	  topo/tests/reference/or_map_topo.log:
	  Moved here from tests/ directory.

	* [r4211] topo/tests/lissom_log_parser.py,
	  topo/tests/lissom_oo_or_reference.ty,
	  topo/tests/lissom_or_reference.ty,
	  topo/tests/oo_or_map_topo.log,
	  topo/tests/or_map_topo.000001.wts.Primary.Afferent0.024_070.matrix,
	  topo/tests/or_map_topo.000001.wts.Primary.LateralExcitatory.024_070.matrix,
	  topo/tests/or_map_topo.000001p000.Eye0_Activity.matrix,
	  topo/tests/or_map_topo.000001p000.Primary_Activity.matrix,
	  topo/tests/or_map_topo.log:
	  Moved to reference/ subdirectory.

	* [r4210]
	  topo/tests/reference/retina_lgn_match.ty:
	  Some clarifications.

	* [r4209] doc/Future_Work/current_text.php:
	  Minor clean-up.

2006-10-02  jbednar

	* [r4208] topo/learningfns/basic.py:
	  Fixed typos found by Brad Bowman

2006-09-18  jbednar

	* [r4207] doc/Makefile:
	  Added skipping of reference-manual creation if no files have
	  changed

2006-09-17  jbednar

	* [r4206] topo/base/simulation.py:
	  Cleaned up documentation strings and spacing. Removed unused
	  state_len().

	* [r4205] topo/analysis/featuremap.py,
	  topo/base/sheet.py,
	  topo/sheets/lissom.py:
	  Cleaned up documentation strings and spacing

	* [r4204] topo/tests/testsimulation.py:
	  Removed use of state_len() so that it can be deleted

2006-09-16  jbednar

	* [r4203] topo/base/sheet.py:
	  Clarified state_push and state_pop, and removed apparently unused
	  functionality from state_pop

	* [r4202] topo/base/parameterclasses.py:
	  Fixed minor typo

2006-09-15  judelaw

	* [r4201] topo/base/sheet.py:
	  changed name of activity_push to state_push

2006-09-14  judelaw

	* [r4200] topo/sheets/lissom.py:
	  added state_push and pop which also ensure the correct iteration
	  and settling step are saved

	* [r4199] topo/base/simulation.py:
	  rewrote state_push and pop to save state of all event processors
	  and added event_push and pop which save only the event as before

	* [r4198] topo/commands/basic.py:
	  renamed state_push and pop to event_push and pop in
	  pattern_present - where these new functions save and reset the
	  anly the simulation events as before (rather than the state), to
	  ensure that a map can be calculated

	* [r4197] topo/analysis/featuremap.py:
	  now saves state before and re-instates after
	  present_input_patterns inMeasureFeatureMap.measure_maps in order
	  to reset settling count and simulation time properly during map
	  measurment

	* [r4196] topo/tkgui/testpattern.py:
	  now saves state before and re-instates after pattern_present to
	  reset activity after a presentation

	* [r4195] topo/outputfns/projfns.py:
	  Added CFPOF_Identity function

2006-09-12  jbednar

	* [r4194] topo/patterns/rds.py:
	  Minor formatting cleanup

	* [r4193] topo/misc/patternfns.py,
	  topo/patterns/rds.py:
	  Collected RandomDotStereogram code into rds.py for easier
	  understanding and debugging

	* [r4192] doc/Future_Work/current_text.php,
	  topo/tkgui/testpattern.py:
	  Fixed bug in Test Pattern window for cases where there are
	  multiple GeneratorSheets of different sizes or densities -- was
	  using a single shared test PatternGenerator object for all cases.
	  Added Sheet Coordinate support to Test Pattern window

2006-09-10  jbednar

	* [r4191] doc/Downloads/index_text.php:
	  Fixed markup errors in previous commit

	* [r4190] README.txt,
	  doc/Downloads/index_text.php:
	  Added suggestions from Brad Bowman

2006-09-01  chrispalmer

	* [r4189] topo/commands/analysis.py:
	  Corrected so OD, disparity and postion all use the new Feature
	  class when calling MeasureFeatureMap

	* [r4188] topo/tests/testfeaturemap.py:
	  Altered to test MeasureFeatureMap using newly implemented Feature
	  class

2006-09-01  jbednar

	* [r4187] doc/Reference_Manual/index_text.php:
	  Fixed links for epydoc; should provide a PHP function for this

	* [r4186] topo/base/arrayutils.py,
	  topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py,
	  topo/misc/keyedlist.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/sheets/composer.py:
	  Trivial tweak to docs to make epydoc happy

	* [r4185] topo/analysis/featuremap.py:
	  Removed outdated comments

	* [r4184] doc/User_Manual/overview_text.php:
	  First complete version; fixed many broken links and filled out
	  basic descriptions

	* [r4183] Makefile,
	  doc/Makefile:
	  Changed order of making to avoid clobbering reference manual
	  first page

2006-08-31  chrispalmer

	* [r4182] topo/commands/analysis.py:
	  Creation of Feature class, whish stores the parameters needed for
	  generating one map, this polulates empty values and/or range
	  fields if neccessary

	* [r4181] topo/analysis/featuremap.py:
	  Simplification of MeasureFeatureMap. Determines
	  __sheets_to_measure_maps_for in more straight forward manner. In
	  __present_input_patterns determines permutations for presentation
	  in easier fashion.

2006-08-31  jbednar

	* [r4180] topo/misc/patternfns.py:
	  Fixed the fix() function to work without pylab imported

	* [r4179] Makefile:
	  Changed default targets to avoid rebuilding the Reference_Manual
	  each time

	* [r4178] topo/misc/patternfns.py:
	  Removed usage of pylab, since that is not available when there is
	  no GUI

	* [r4177]
	  topo/commands/disp_key_white_vert_small.PNG,
	  topo/commands/disp_key_white_vert_small.png:
	  Fixed bogus filename

	* [r4176] doc/Reference_Manual,
	  doc/Reference_Manual/.cvsignore:
	  Added epydoc outputs to ignore

	* [r4175] topo/responsefns/optimized.py:
	  Minor cleanup of imports

	* [r4174] topo/base/patterngenerator.py:
	  Minor tweaks to documentation

	* [r4173] Makefile,
	  doc/Makefile,
	  doc/shared/util.php:
	  Changed Reference_Manual to use epydoc

	* [r4172] external,
	  external/.cvsignore,
	  external/Makefile,
	  external/docutils-0.4.tar.gz,
	  external/epydoc-3.0alpha3.tar.gz,
	  external/epydoc.diff:
	  Added Epydoc

2006-08-31  tikesh

	* [r4171] topo/patterns/basic.py:
	  added a small method used in one of the scripts for disparity
	  project

	* [r4170] topo/base/pickle.py,
	  topo/misc/numbergenerators.py,
	  topo/misc/patternfns.py,
	  topo/patterns/basic.py:
	  *** empty log message ***

	* [r4169] examples/disparity_energy.ty,
	  examples/lissom_oo_disparity_gauss_0.ty,
	  examples/lissom_oo_disparity_gauss_2_pixel.ty,
	  examples/lissom_oo_disparity_plus_minus_0.ty,
	  examples/lissom_oo_disparity_plus_minus_2_pixel.ty,
	  examples/lissom_oo_phase_disparity.ty,
	  examples/lissom_oo_position_disparity.ty,
	  examples/odf_science90.ty,
	  examples/ohzawa_science90.ty,
	  topo/analysis/featuremap.py,
	  topo/commands/analysis.py,
	  topo/commands/disp_key_white_vert_small.PNG,
	  topo/patterns/rds.py,
	  topo/plotting/templates.py,
	  topo/tkgui/testpattern.py:
	  *** empty log message ***

2006-08-30  jbednar

	* [r4168] doc/User_Manual/overview_text.php:
	  Minor formatting fix

2006-08-29  vldkr

	* [r4167] examples/homeo_synaptic_lissom_or.ty:
	  Updated version

	* [r4166] topo/outputfns/homeostatic.py:
	  Output functions based on homeostatic plasticity

	* [r4165] examples/homeo_lissom_oo_or_image.ty:
	  *** empty log message ***

	* [r4164]
	  examples/homeo_lissom_or_noshrinking.ty:
	  Updated version

	* [r4163]
	  examples/homeo_intrinsic_lissom_oo_or.ty,
	  examples/homeo_intrinsic_lissom_or.ty:
	  Updated version

2006-08-29  jbednar

	* [r4162] external/Makefile:
	  Made DISPLAY hack for matplotlib be a bit more robust, in case
	  DISPLAY is already set to something other than :0

2006-08-28  ceball

	* [r4161] topo/tests/lissom_oo_or_reference.ty:
	  Corrected afferent connection strength.

2006-08-28  jbednar

	* [r4160] doc/User_Manual/basics_text.php.m4:
	  Added partially completed Overview section

	* [r4159] topo/base/sheet.py:
	  Minor clarification

	* [r4158] doc/User_Manual/parameters_text.php:
	  Made class links uniform

	* [r4157]
	  doc/User_Manual/introduction_text.php.m4:
	  Minor clarifications

	* [r4156] doc/User_Manual,
	  doc/User_Manual/.cvsignore,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/overview_text.php:
	  Added partially completed Overview section

2006-08-26  ceball

	* [r4155] topo/tests/lissom_oo_or_reference.ty:
	  Corrected mistake introduced in some previous commit.

2006-08-25  ceball

	* [r4154] topo/tests/lissom_oo_or_reference.ty:
	  CompositePatternGenerator renamed to Composite.

2006-08-24  jbednar

	* [r4153] doc/User_Manual/basics_text.php.m4:
	  Cleaned up and reformatted

	* [r4152] doc/User_Manual/basics_text.php.m4:
	  Added sketch of list of what Topographica supports

2006-08-21  jbednar

	* [r4151]
	  doc/User_Manual/background_text.php.m4:
	  Minor cleanup

	* [r4150] doc/User_Manual/basics_text.php.m4,
	  doc/User_Manual/images/060220_topographica_screen_shot_small.png,
	  doc/User_Manual/images/gaussianrandomweights_dense.png,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/introduction_text.php.m4,
	  doc/shared/topographica.bib:
	  Added Introduction section to user manual based on text of paper
	  that had been in background_text.php.m4

	* [r4149] doc/Reference_Manual/index_text.php:
	  Added targets for intro section to use

	* [r4148] doc/User_Manual,
	  doc/User_Manual/.cvsignore:
	  More to ignore

	* [r4147] topo/tests/testbitmap.py,
	  topo/tests/testplotgrouppanel.py:
	  Reduced size of array to speed up tests

	* [r4146]
	  doc/User_Manual/images/fourclassweights.png,
	  doc/User_Manual/images/gaussian_0.3.png,
	  doc/User_Manual/images/gaussian_0.5.png,
	  doc/User_Manual/images/or_gaussian_1.png,
	  doc/User_Manual/images/or_gaussian_2.png,
	  doc/User_Manual/images/patterntypes_small.png,
	  doc/User_Manual/patterns_text.php:
	  Updated Patterns section images for better resolution

2006-08-19  jbednar

	* [r4145] topo/patterns/basic.py:
	  Minor updates to documentation

2006-08-18  jbednar

	* [r4144] doc/User_Manual/images/face.png,
	  doc/User_Manual/images/patterntypes.png,
	  doc/User_Manual/images/patterntypes_small.png,
	  doc/User_Manual/patterns_text.php:
	  Added more documentation

	* [r4143] topo/patterns/basic.py:
	  Added scale and offset for Composite and Selector patterns, and
	  fixed x and y positions for rotations.

	* [r4142] doc/User_Manual/publishing_text.php:
	  Minor tweak

	* [r4141]
	  doc/User_Manual/images/fourclassweights.png,
	  doc/User_Manual/images/gaussian_0.3.png,
	  doc/User_Manual/images/gaussian_0.5.png,
	  doc/User_Manual/images/gaussianrandomweights.png,
	  doc/User_Manual/images/or_gaussian_1.png,
	  doc/User_Manual/images/or_gaussian_2.png,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/patterns_text.php:
	  Added section on patterns

	* [r4140] doc/User_Manual,
	  doc/User_Manual/.cvsignore:
	  More to ignore

	* [r4139] doc/Future_Work/current_text.php:
	  Removed completed tasks

	* [r4138] topo/base/patterngenerator.py,
	  topo/patterns/basic.py:
	  Added size parameter for all PatternGenerators so that all can be
	  used with Composite

	* [r4137] topo/patterns/basic.py:
	  Changed lists of PatternGenerators to be ListParameters to
	  provide better error checking

	* [r4136] topo/base/parameterclasses.py:
	  Added ListParameter

	* [r4135] topo/base/parameterclasses.py,
	  topo/base/patterngenerator.py,
	  topo/misc/distribution.py:
	  Removed previous change for now, to avoid breaking existing saved
	  .typ files

	* [r4134] topo/base/parameterclasses.py,
	  topo/base/patterngenerator.py:
	  Clarified parameter name

	* [r4133] topo/patterns/basic.py:
	  Added Selector pattern (equivalent to C++ LISSOM's Accum_OneHot)

	* [r4132] topo/patterns/basic.py:
	  Minor clarifications

	* [r4131] topo/patterns/basic.py:
	  Added more extensive documentation for Composite

2006-08-17  jbednar

	* [r4130] topo/patterns/basic.py:
	  Fixed x and y position of Composite patterns so that they don't
	  depend on the size

	* [r4129] topo/patterns/basic.py,
	  topo/patterns/image.py:
	  Moved PatternSampler from basic.py to image.py, where it is used

	* [r4128] topo/tests/testpatterngenerator.py:
	  Minor cleanup

	* [r4127] examples/lissom_oo_or.ty,
	  examples/lissom_or_sf.ty,
	  topo/patterns/basic.py,
	  topo/tests/testpatterngenerator.py:
	  Changed name of CompositePatternGenerator to Composite for
	  consistency

	* [r4126] topo/patterns/basic.py:
	  Added support for scaling size of Composite patterns

	* [r4125] topo/patterns/basic.py:
	  Added support for rotating Composite patterns

	* [r4124] topo/patterns/basic.py,
	  topo/tests/testpatterngenerator.py:
	  Added support for Composite pattern displacement, and enabled the
	  corresponding test

2006-08-17  judelaw

	* [r4123] topo/commands/analysis.py:
	  changed cog to take projection as argument instead of sheet

2006-08-17  jbednar

	* [r4122] topo/patterns/basic.py:
	  Removed obsolete comment

	* [r4121] topo/patterns/basic.py:
	  Simplified implementation of Composite by removing
	  PatternSampler. It does not currently support translation,
	  rotation, etc. of the whole Composite, but those weren't working
	  properly before either, and are easier to do without
	  PatternSampler

2006-08-16  judelaw

	* [r4120] topo/commands/analysis.py:
	  added argument to measure_cog function so that projections from a
	  chosen sheet can be plotted

2006-08-16  jbednar

	* [r4119] doc/User_Manual/about_text.php,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/publishing_text.php:
	  Added page on how to publish using Topographica

2006-08-15  vldkr

	* [r4118]
	  examples/homeo_lissom_or_noshrinking.ty:
	  initial version

2006-08-15  judelaw

	* [r4117] topo/commands/analysis.py:
	  Made changes to centre of gravity plotting

2006-08-14  jbednar

	* [r4116] topo/base/cf.py,
	  topo/outputfns/optimized.py:
	  Changed output_activity argument name to mask to clarify what the
	  data will be used for. Made all CFPOFs respect the mask, for
	  consistency.

	* [r4115] topo/tests/testpatterngenerator.py:
	  Enabled some tests of composite patterns

	* [r4114] topo/patterns/basic.py:
	  Cleaned up comments and documentation

	* [r4113] topo/outputfns/optimized.py:
	  Re-enabled optimization that should now be safe again

	* [r4112] topo/base/cf.py,
	  topo/base/projection.py,
	  topo/sheets/lissom.py:
	  Changed name of apply_output_fn() to apply_learn_output_fn() to
	  clarify that it is different from the activity output_fn. (It's
	  called learn_output_fn instead of weights_output_fn because the
	  interface is specified at the ProjectionSheet level, and there is
	  no concept of weights at that level, only learning.) Made
	  apply_learn_output_fn() accept an explicit mask so that it can be
	  forced to apply to all units, and made all ones be passed in for
	  the intial iteration for joint normalization.

	* [r4111] topo/base/sheet.py:
	  Added typedef for activity matrices, to encourage consistency.

	* [r4110] examples/lissom_oo_od.ty:
	  Changed input pattern definition to be a class so that it can be
	  pickled. Temporarily changed learning rates to match
	  lissom_oo_or.ty.

2006-08-12  jbednar

	* [r4109] examples/lissom_oo_or.ty:
	  Changed ON and OFF channels to have a single DoG projection,
	  instead of separate Center/Surround. Switched to joint
	  normalization. Changed default size of Gaussian for Test Pattern
	  window. Still needs parameter matching with the book simulations.

2006-08-11  jbednar

	* [r4108] topo/outputfns/optimized.py:
	  Deleted an optimization that was causing problems for joint
	  normalization

	* [r4107] topo/base/cf.py:
	  Changed __norm_total to _norm_total because hasattr() fails for
	  names starting with a __ (due to name mangling)

	* [r4106] topo/sheets/lissom.py:
	  Trivial improvement to comment

	* [r4105] topo/misc/utils.py:
	  Added handing for case where an array shape is an empty list; not
	  sure why this would ever occur, but unpickling was failing until
	  this was added

	* [r4104] topo/sheets/lissom.py:
	  Removed division by length of joint normalization group

	* [r4103] topo/sheets/lissom.py:
	  Added joint normalization for the first iteration

	* [r4102] topo/base/projection.py:
	  Added default learning method for all ProjectionSheets, to
	  replace the one no longer in CFSheet

	* [r4101] topo/base/cf.py,
	  topo/sheets/lissom.py:
	  Moved methods related to joint normalization out of CFSheet and
	  into JointNormalizingCFSheet (in lissom.py), so that only models
	  using it will have to deal with that complexity.

	* [r4100] topo/outputfns/optimized.py:
	  Minor clarification

	* [r4099] topo/base/cf.py:
	  Replaced __normalize_joint_projections with
	  __compute_joint_norm_totals, which only updates the norm_total
	  property values, without actually doing any normalization

	* [r4098] topo/base/cf.py,
	  topo/learningfns/optimized.py,
	  topo/outputfns/optimized.py:
	  Renamed ConnectionField.sum to ConnectionField.norm_total to
	  emphasize that it is not necessarily always the sum.

	* [r4097] examples/joublin_bc96.ty:
	  Fixed missing import

	* [r4096] examples/joublin_bc96.ty:
	  Removed duplicate specification of weight_type, to ensure that it
	  is consistent with cf.py

	* [r4095] examples/joublin_bc96.ty:
	  Removed duplicate specification of weight_type, to ensure that it
	  is consistent with cf.py

2006-08-07  ceball

	* [r4094]
	  topo/tests/reference/retina_lgn_match.ty:
	  Initial version should have been like this.

	* [r4093] topo/tests/reference/README.txt:
	  Initial version.

	* [r4092] topo/tests/reference,
	  topo/tests/reference/retina_lgn_match.ty:
	  Script to help matching between c++ lissom and topographica.

2006-08-07  jbednar

	* [r4091] doc/Downloads/win32_text.php:
	  No longer in use

2006-08-04  jbednar

	* [r4090] topo/outputfns/optimized.py:
	  Finished up the code for CFPOF_DivisiveNormalizeL1; mistakenly
	  checked in earlier

	* [r4089] topo/outputfns/basic.py:
	  Removed outdated comment

	* [r4088] topo/outputfns/optimized.py:
	  Added patch to get old pickled files to work

	* [r4087] topo/base/cf.py,
	  topo/learningfns/optimized.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/optimized.py,
	  topo/tests/testoutputfnsoptimized.py:
	  Renamed _sum to __sum to make it private, and made all external
	  code use sum instead. This should prevent various problems found
	  when _sum did not exist, due to mixing optimized and
	  non-optimized components. Removed use of cached values in
	  DivisiveNormalizeL1, and instead supported that only in
	  CFPOF_DivisiveNormalizeL1 to avoid problems when CFPOF_Plugin was
	  used with anything but DivisiveNormalizeL1. Removed unused
	  DivisiveNormalizeL1_opt. The changes will affect the numerical
	  value of each activation pattern, at the six or seventh decimal
	  place total, due to using Numeric.sum in some cases and other sum
	  routines in others. This should also fix the various segfaults
	  that were possible when mixing and matching optimized and
	  non-optimized components.

	* [r4086] doc/User_Manual/parameters_text.php:
	  Fixed example

	* [r4085] doc/Links/index_text.php:
	  Fixed link

	* [r4084] examples/lissom_oo_or.ty:
	  Made some parameters match those in miikkulainen:book05 better;
	  not yet tested

2006-08-02  ceball

	* [r4083] topo/tests/lissom_oo_or_reference.ty:
	  Back to Composite for LGN weights, rather than separate
	  projections.

	* [r4082] topo/base/cf.py:
	  Take the number of connections into account during joint
	  normalization.

	* [r4081] topo/base/cf.py:
	  Fixed incorrect handling of cf.sum by CFPOF_Plugin; the problem
	  ultimately comes from elsewhere, probably.

	* [r4080] topo/tests/lissom_oo_or_reference.ty:
	  Changed size parameter of Gaussians for projections to LGN (to
	  match the different definition of Gaussian in c++ lissom; c++
	  lissom divides by pi in the argument of exp in
	  RadialFunction::Gaussian but not in retinalobjs).

	* [r4079] topo/tests/lissom_oo_or_reference.ty:
	  Reverted to separate center and surround projections for
	  debugging.

2006-08-01  judelaw

	* [r4078] examples/lissom_or.ty:
	  changed mistake in name etc.

2006-08-01  vldkr

	* [r4077] examples/homeo_lissom_oo_or_image.ty:
	  update 2

2006-07-31  judelaw

	* [r4076] examples/lissom_or.ty:
	  matched to C++ version

2006-07-28  ceball

	* [r4075] topo/misc/utils.py:
	  Added function to output an array in a format suitable for Matlab
	  to read.

2006-07-26  vldkr

	* [r4074]
	  examples/homeo_intrinsic_lissom_oo_or.ty,
	  examples/homeo_intrinsic_lissom_or.ty,
	  examples/homeo_lissom_oo_or_image.ty:
	  Initial version

	* [r4073] examples/homeo_synaptic_lissom_or.ty:
	  *** empty log message ***

2006-07-26  jbednar

	* [r4072] examples/joublin_bc96.ty:
	  Minor cleanup; probably no user-visible effect other than
	  changing the name of HindpawGaussian to HindpawGaussian2

2006-07-26  cmnglewis

	* [r4071] examples/joublin_bc96.ty:
	  Completed most parts of the implementation

2006-07-24  ceball

	* [r4070] doc/Future_Work/current_text.php:
	  Removed task about display problem on Windows; I'd messed up one
	  of my copies (by upgrading Python...P.S. good luck for that...)

	* [r4069] /trunk/topographica-win/create_python_topo/setup.bat:
	  Added HACKALERT.

	* [r4068] /trunk/topographica-win/util/Y_OR_N.COM:
	  Removed unused file.

	* [r4067] doc/Downloads/cvs_text.php,
	  doc/Downloads/index_text.php:
	  Updated instructions for new topographica-win module.

	* [r4066] doc/Downloads/cvs_text.php:
	  No need to download PuTTY since it comes with TortoiseCVS.
	  Changed note about testing date, and version to current stable
	  TortoiseCVS.

	* [r4065] /trunk/topographica, .cvsignore:
	  Added back topographica.ico to ignore, since it's present on
	  windows.

2006-07-23  jbednar

	* [r4064] Makefile:
	  Restored version 1.67 for new post-0.91 changes

2006-07-23  ceball_cvs2svn

	* [r4063] /tags/release_0_9_1,
	  /tags/release_0_9_1/topographica-win,
	  /tags/release_0_9_1/topographica-win/README.txt,
	  /tags/release_0_9_1/topographica-win/common/python_topo.tar.gz,
	  /tags/release_0_9_1/topographica-win/common/topographica.ico,
	  /tags/release_0_9_1/topographica-win/create_installer/README.txt,
	  /tags/release_0_9_1/topographica-win/create_installer/prepare_for_installer.bat,
	  /tags/release_0_9_1/topographica-win/create_python_topo,
	  /tags/release_0_9_1/topographica-win/setup_cvs_copy,
	  /tags/release_0_9_1/topographica-win/util,
	  /tags/release_0_9_1/topographica/Makefile,
	  /tags/release_0_9_1/topographica/doc/shared,
	  /tags/release_0_9_1/topographica/external/.cvsignore,
	  /tags/release_0_9_1/topographica/external/Makefile,
	  /tags/release_0_9_1/topographica/external/mswin/util,
	  /tags/release_0_9_1/topographica/external/tcl8.4.13-src.tar.gz,
	  /tags/release_0_9_1/topographica/external/tcl8.4.9.tgz,
	  /tags/release_0_9_1/topographica/external/tk8.4.13-src.tar.gz,
	  /tags/release_0_9_1/topographica/external/tk8.4.9.tgz,
	  /tags/release_0_9_1/topographica/external/win32/util:
	  This commit was manufactured by cvs2svn to create tag
	  'release_0_9_1'.

2006-07-23  jbednar

	* [r4062] doc/shared/index.php:
	  Added 0.9.0 announcement

	* [r4061] Makefile:
	  Temporary checkin for 0.9.1 release only

	* [r4060] /trunk/topographica-win/common/setup.py,
	  /trunk/topographica-win/create_installer/topographica.iss,
	  Makefile:
	  Changed version number to 0.9.1 for bugfix release

	* [r4059] external,
	  external/.cvsignore,
	  external/Makefile,
	  external/tcl8.4.13-src.tar.gz,
	  external/tcl8.4.9.tgz,
	  external/tk8.4.13-src.tar.gz,
	  external/tk8.4.9.tgz:
	  Updated tcl/tk to 8.4.13 to fix bug in their configure script for
	  some platforms. Added DISPLAY variable for matplotlib so that it
	  builds even in a remote session

2006-07-22  ceball

	* [r4058] /trunk/topographica-win/create_python_topo/README.txt:
	  Added note about weave.

	* [r4057] /trunk/topographica-win/create_python_topo/setup.bat:
	  Removed debugging pause.

	* [r4056] /trunk/topographica-win/create_python_topo/setup.bat:
	  Corrected mistake.

	* [r4055] /trunk/topographica-win/create_python_topo/setup.bat:
	  Initial version.

	* [r4054] /trunk/topographica-win/create_python_topo/README.txt:
	  Updated instructions.

	* [r4053]
	  /trunk/topographica-win/create_python_topo/fixedpoint-0.1.2_patched.py,
	  /trunk/topographica-win/create_python_topo/fixedpoint-0.1.2_patched.tgz:
	  Removed confusing archive: replaced with single file (patched in
	  unix).

	* [r4052] /trunk/topographica-win/create_python_topo/setup.py:
	  Removed unused file.

	* [r4051] /trunk/topographica-win/create_python_topo/jpeg-6b-3.exe:
	  Removed unused package.

	* [r4050] /trunk/topographica-win/setup_cvs_copy/setup.bat:
	  Added HACKALERT.

	* [r4049] /trunk/topographica-win/create_installer/README.txt:
	  Minor update.

	* [r4048] /trunk/topographica-win/create_installer/README.txt:
	  Updates to procedure.

	* [r4047]
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat:
	  Corrected slash direction.

	* [r4046]
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat:
	  Remove external/ subdirectory.

	* [r4045] /trunk/topographica-win/setup_cvs_copy/setup.bat:
	  Removed some testing lines.

	* [r4044] /trunk/topographica-win/setup_cvs_copy/setup.bat:
	  Minor update.

	* [r4043] /trunk/topographica-win/create_installer/README.txt,
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat:
	  Updated for topographica-win

	* [r4042] Makefile:
	  Updated file locations.

	* [r4041] Makefile:
	  Files no longer exist to delete.

	* [r4040] /trunk/topographica-win/create_installer/README.txt:
	  Updated

	* [r4039] /trunk/topographica-win/create_python_topo/README.txt:
	  Added warning that the setup script in this directory does not
	  yet work.

	* [r4038] doc/Future_Work/current_text.php:
	  Added a task.

	* [r4037] /trunk/topographica-win/setup_cvs_copy/setup.bat:
	  More correction and cleaning.

	* [r4036] /trunk/topographica-win/setup_cvs_copy/setup.bat:
	  Corrected paths.

	* [r4035] /trunk/topographica-win/create_python_topo/mingw,
	  /trunk/topographica-win/create_python_topo/mingw/binutils-2.15.91-20040904-1.tar.gz,
	  /trunk/topographica-win/create_python_topo/mingw/gcc-core-3.4.2-20040916-1.tar.gz,
	  /trunk/topographica-win/create_python_topo/mingw/gcc-g++-3.4.2-20040916-1.tar.gz,
	  /trunk/topographica-win/create_python_topo/mingw/gcc-g77-3.4.2-20040916-1.tar.gz,
	  /trunk/topographica-win/create_python_topo/mingw/mingw-runtime-3.9.tar.gz,
	  /trunk/topographica-win/create_python_topo/mingw/w32api-3.6.tar.gz:
	  Packages currently used for topographica's c compiler. Might not
	  all be necessary.
	  Added for my convenience, for the moment.

	* [r4034] /trunk/topographica-win/setup_cvs_copy/setup.bat:
	  Corrected minor mistake with line echoing.

	* [r4033] /trunk/topographica-win/README.txt,
	  /trunk/topographica-win/common/setup.py:
	  Updated for new topographica-win module.

	* [r4032]
	  /trunk/topographica-win/setup_cvs_copy/create_shortcut.vbs,
	  /trunk/topographica-win/setup_cvs_copy/setup.bat:
	  Updated directory locations.

2006-07-21  ceball

	* [r4031] doc/Future_Work/current_text.php:
	  Updated topographica-win task.

	* [r4030] /trunk/topographica-win/common/python_topo.tar.gz:
	  From topographica module.

	* [r4029] setup.bat,
	  topographica.ico:
	  Moved to topographica-win module or deleted if unused.

	* [r4028] external/mswin:
	  Moved to topographica-win module.

	* [r4027] /trunk/topographica-win/create_python_topo,
	  /trunk/topographica-win/create_python_topo/Numeric-24.2.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/PIL-1.1.5.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/README.txt,
	  /trunk/topographica-win/create_python_topo/fixedpoint-0.1.2_patched.tgz,
	  /trunk/topographica-win/create_python_topo/jpeg-6b-3.exe,
	  /trunk/topographica-win/create_python_topo/matplotlib-0.81.win32-py2.4.exe,
	  /trunk/topographica-win/create_python_topo/python-2.4.2.msi,
	  /trunk/topographica-win/create_python_topo/setup.py:
	  From the original topographica module, external/win32

	* [r4026] /trunk/topographica-win/common,
	  /trunk/topographica-win/common/setup.py,
	  /trunk/topographica-win/common/topographica.ico,
	  /trunk/topographica-win/util/Y_OR_N.COM,
	  /trunk/topographica-win/util/patch.exe:
	  From topographica module.

	* [r4025] external/win32:
	  Moved to topographica-win module.

	* [r4024] external/win32/util:
	  Moved to topographica-win module or deleted if no longer
	  required.

	* [r4023] /trunk/topographica-win/README.txt:
	  Initial version

	* [r4022] /trunk/topographica-win/setup_cvs_copy,
	  /trunk/topographica-win/setup_cvs_copy/README.txt,
	  /trunk/topographica-win/setup_cvs_copy/create_shortcut.vbs,
	  /trunk/topographica-win/setup_cvs_copy/setup.bat:
	  *** empty log message ***

	* [r4021] /trunk/topographica-win/create_installer,
	  /trunk/topographica-win/create_installer/README.txt,
	  /trunk/topographica-win/create_installer/prepare_for_installer.bat,
	  /trunk/topographica-win/create_installer/topographica.iss:
	  From the original topographica module, external/mswin/

	* [r4020] /trunk/topographica-win, /trunk/topographica-win/util,
	  /trunk/topographica-win/util/README.txt,
	  /trunk/topographica-win/util/gunzip.exe,
	  /trunk/topographica-win/util/tar.exe:
	  *** empty log message ***

2006-07-18  jbednar

	* [r4019] topo/tests/README.txt:
	  Fixed outdated info about running tests

2006-07-18  tikesh

	* [r4018]
	  examples/lissom_oo_position_disparity.py,
	  examples/lissom_oo_position_disparity.ty:
	  Moved lissom_oo_position_disparity.py to
	  lissom_oo_position_disparity.ty

	* [r4017]
	  examples/lissom_oo_phase_disparity.py,
	  examples/lissom_oo_phase_disparity.ty:
	  Moved lissom_oo_phase_disparity.py to
	  lissom_oo_phase_disparity.ty

	* [r4016] examples/lissom_oo_od.py,
	  examples/lissom_oo_od.ty:
	  Moved lissom_oo_od.py to lissom_oo_od.ty

	* [r4015] examples/read_visneuro02.py,
	  examples/read_visneuro02.ty:
	  Moved read_visneuro02.py to read_visneuro02.ty

	* [r4014] examples/ohzawa_science90.py,
	  examples/ohzawa_science90.ty:
	  Moved ohzawa_science90.py to ohzawa_science90.ty

2006-07-11  ceball

	* [r4013] topo/tests/lissom_oo_or_reference.ty:
	  Afferents are jointly normalized; removed strength=0.75 hack.

2006-07-10  tikesh

	* [r4012] examples/disparity_energy_Read.py,
	  examples/lissom_oo_od.ty,
	  examples/read_visneuro02.py,
	  examples/read_visneuro02.ty:
	  *** empty log message ***

	* [r4011] examples/disparity_energy_Read.py:
	  *** empty log message ***

	* [r4010] examples/lissom_oo_od.py,
	  examples/lissom_oo_phase_disparity.py,
	  examples/lissom_oo_position_disparity.py,
	  examples/ohzawa_science90.py,
	  topo/commands/analysis.py,
	  topo/plotting/templates.py:
	  *** empty log message ***

2006-07-08  jbednar

	* [r4009] topo/base/cf.py:
	  Added alert

	* [r4008] doc/Future_Work/current_text.php:
	  Added current work

2006-07-07  ceball

	* [r4007] topo/tests/lissom_oo_or_reference.ty:
	  Trivial change: removed names of projections to LGN.

	* [r4006] topo/tests/lissom_oo_or_reference.ty:
	  Uses CompositePatternGenerator for the shared weights, rather
	  than having two projections.

	* [r4005] topo/tests/lissom_oo_or_reference.ty:
	  Updated out-of-date syntax.

	* [r4004] topo/patterns/basic.py:
	  Corrected typo in the code for CompositePatternGenerator that led
	  to a bug in the handling of xdensity and ydensity for composite
	  patterns.

2006-07-04  jbednar

	* [r4003] examples/lissom_oo_or.ty:
	  Added example of joint normalization

	* [r4002] topo/base/cf.py:
	  Replaced commented-out joint normalization code with enabled
	  version using ports; still needs more cleanup

	* [r4001] topo/base/simulation.py:
	  Added _port_match method to allow the matching rule to be
	  overridden by subclasses; should not have changed the behavior at
	  all

2006-07-03  yschoe

	* [r4000] examples/leaky_lissom_or.ty,
	  topo/base/cf.py,
	  topo/learningfns/projfns.py:
	  Moved CFPLF_OutstarHebbian from base/cf.py to
	  learningfns/projfns.py, and
	  made appropriate changes in leaky_lissom_or.ty.

2006-07-03  jbednar

	* [r3999] etc/topographica.el:
	  Fixed Emacs code for selecting Topographica-mode

2006-07-01  jbednar

	* [r3998] doc/Downloads/cvs_text.php:
	  Added info from Yoonsuck about SSH agent

	* [r3997] doc/shared/index.php:
	  Added news link to the book

2006-06-29  ceball

	* [r3996] topo/patterns/basic.py:
	  The composite pattern generators for a CPG are called with the
	  same bounds, xdensity, and ydensity as the CPG itself.

	* [r3995] topo/tests/testpatterngenerator.py:
	  Added new test for CompositePatternGenerator. Commented out at
	  the moment because it fails.

	* [r3994] topo/tests/testpatterngenerator.py:
	  Commented out a test. The test passes when run in isolation, but
	  I didn't check it also passes when part of the test suite. Added
	  note about this (should be simple to fix).

2006-06-28  ceball

	* [r3993] topo/tests/testpatterngenerator.py:
	  Added basic test for CompositePatternGenerator.

2006-06-26  ceball

	* [r3992] doc/Future_Work/current_text.php:
	  Added a task.

	* [r3991] doc/Future_Work/current_text.php:
	  Added task about test pattern window.

	* [r3990] topo/tkgui/testpattern.py:
	  Added note of bug.

	* [r3989] topo/tests/lissom_oo_or_reference.ty:
	  Removed unnecessary port specifications.

	* [r3988] topo/tests/lissom_or_reference.ty:
	  Removed unnecessary port specifications.

	* [r3987] topo/tkgui/parametersframe.py:
	  Change to comments.

2006-06-24  yschoe

	* [r3986] topo/base/cf.py:
	  In the process of adding outstar normalization (implementation
	  is still incomplete). Needs a lot of work.

	* [r3985] examples/leaky_lissom_or.ty:
	  In the process of adding outstar normalization (implementation
	  is still incomplete).

2006-06-23  jbednar

	* [r3984] topo/base/cf.py,
	  topo/base/simulation.py:
	  Slight cleanup to documentation

2006-06-23  tikesh

	* [r3983] topo/outputfns/basic.py:
	  topo/outputfns/basic.py

	* [r3982] examples/disparity_energy.ty,
	  examples/lissom_oo_od.ty,
	  examples/read_visneuro02.ty:
	  Initial version

2006-06-23  jbednar

	* [r3981] examples/Makefile:
	  Added target for obermayer_pnas90

2006-06-22  jbednar

	* [r3980] topo/base/projection.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/slissom.py:
	  Made the default src_port and dest_port for Projections be
	  'Activity' so that incorrect connections can be detected

	* [r3979] topo/base/simulation.py:
	  Added src_ports attribute to provide a roster of what src_ports
	  are provided

	* [r3978] topo/base/projection.py,
	  topo/base/simulation.py,
	  topo/sheets/composer.py:
	  Changed EventProcessor._connect_from to _dest_connect, and
	  _connect_to to _src_connect, so that it is more obvious at which
	  end they will be executed

	* [r3977] etc/toporename:
	  Fixed example usage

	* [r3976] topo/sheets/generatorsheet.py:
	  Changed to use a special 'Trigger' port for the self-connection,
	  to allow error-checking.

	* [r3975] topo/tkgui/editortools.py:
	  Made error message more informative

	* [r3974] topo/base/simulation.py,
	  topo/eps/basic.py,
	  topo/sheets/composer.py:
	  Added dest_ports attribute to EventProcessor, and made it accept
	  connections only those ports

	* [r3973] topo/tkgui/editorobjects.py:
	  Removed duplicate entries in Connections lists

	* [r3972] examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  topo/patterns/basic.py:
	  Set default scale for Line in example files instead of pattern
	  definition

	* [r3971] topo/commands/basic.py:
	  Added handling for case where the class name or location has
	  changed since a snapshot was created, so that a saved snapshot
	  can still be loaded

	* [r3970] topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py:
	  Replaced CFPRF_DotProduct with simpler one based on CFPRF_Plugin;
	  for some reason it's also much faster.

	* [r3969] topo/misc/inlinec.py:
	  Clarified comment

	* [r3968] topo/sheets/generatorsheet.py:
	  Changed default phase to be nonzero so that it will be useful

2006-06-22  ceball

	* [r3967] topo/tkgui/parametersframe.py:
	  Added hackalert plus a break to stop unnecessary looping.

	* [r3966] topo/tkgui/parametersframe.py:
	  Some more simplification and restored an accidentally removed
	  feature (right clicking on an object allows you to set parameters
	  for the object being right clicked on).

	* [r3965] topo/misc/utils.py:
	  Changed dict_translator to eval in __main__.__dict__ rather than
	  calling eval_atof(), which happens (wrongly) just to eval in
	  __main__.__dict__. (Aiming at being able to make eval_atof() act
	  as would be expected.

	* [r3964] topo/tkgui/parametersframe.py:
	  Cleaning up (should be no change)...

	* [r3963] topo/tkgui/parametersframe.py:
	  Cleaning up show_parameter_properties()...

	* [r3962] topo/tkgui/parametersframe.py:
	  Removed code that currently never runs. If it were ever to run,
	  it wouldn't work anyway. Replaced with a NotImplementedError for
	  the time being.

	* [r3961] topo/tkgui/parametersframe.py:
	  Removed 'object_dictionary' attribute.

	* [r3960] topo/misc/utils.py:
	  Added note.

	* [r3959] topo/misc/utils.py:
	  Renamed dict_sort() to values_sorted_by_key(), plus minor
	  tidy-up.

2006-06-21  jbednar

	* [r3958] topo/tkgui/translatorwidgets.py:
	  Changed TranslatorWidget to WidgetTranslator to clarify that it
	  is not itself a Widget. Made get() abstract so that it can be
	  tested for easily

	* [r3957] topo/misc/utils.py,
	  topo/plotting/templates.py,
	  topo/tkgui/topoconsole.py:
	  Cleaned up comments, documentation, imports ordering, alerts, and
	  spacing.

	* [r3956] topo/base/cf.py,
	  topo/eps/basic.py,
	  topo/learningfns/__init__.py,
	  topo/learningfns/optimized.py,
	  topo/learningfns/som.py,
	  topo/outputfns/__init__.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/optimized.py,
	  topo/outputfns/projfns.py,
	  topo/patterns/__init__.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/projections/__init__.py,
	  topo/projections/basic.py,
	  topo/responsefns/__init__.py,
	  topo/responsefns/projfns.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py,
	  topo/sheets/slissom.py:
	  Cleaned up comments, documentation, imports ordering, alerts, and
	  spacing.

	* [r3955] topo/responsefns/basic.py:
	  Added example ResponseFn

	* [r3954] topo/responsefns/optimized.py:
	  Fixed minor alert

2006-06-20  jbednar

	* [r3953] topo/analysis/__init__.py,
	  topo/base/patterngenerator.py,
	  topo/commands/__init__.py,
	  topo/learningfns/__init__.py,
	  topo/misc/commandline.py,
	  topo/misc/gendocs.py,
	  topo/misc/inlinec.py,
	  topo/misc/keyedlist.py,
	  topo/plotting/__init__.py,
	  topo/sheets/generatorsheet.py:
	  Minor cleanup of documentation and comments

	* [r3952] topo/misc/patternfns.py:
	  Clarified what the problem is for disks and rings

2006-06-20  judelaw

	* [r3951] topo/plotting/templates.py:
	  Changed back unnecessary fix

2006-06-20  jbednar

	* [r3950] topo/misc/__init__.py:
	  Added missing files

	* [r3949] topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py:
	  Cleaned up trailing colon formatting

	* [r3948] topo/tkgui/editorobjects.py:
	  Cleaned up documentation and comments to be closer to
	  Topographica conventions elsewhere

	* [r3947] topo/tkgui/editortools.py:
	  Cleaned up documentation and comments to be closer to
	  Topographica conventions elsewhere

	* [r3946] topo/tkgui/editorwindow.py:
	  Cleaned up documentation and comments to be closer to
	  Topographica conventions elsewhere

	* [r3945] topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py:
	  Fixed error when connections have no target object

	* [r3944] topo/plotting/bitmap.py:
	  Clarified documentation

	* [r3943] topo/base/parameterizedobject.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/simulation.py,
	  topo/eps/basic.py,
	  topo/sheets/generatorsheet.py:
	  Cleaned up verbose messages so that they will be useful; more
	  esoteric ones are now visible only with a debugging print level

	* [r3942] topo/base/cf.py:
	  Added debugging messages when unsuitable Projection types are
	  encountered. Simplified update_unit_view

	* [r3941] topo/commands/analysis.py:
	  Fixed trivial typo

	* [r3940] external/Makefile:
	  Removed outdated alert

2006-06-20  judelaw

	* [r3939] topo/plotting/templates.py:
	  Corrected bug in projection activity

	* [r3938] examples/laminar.ty:
	  Most recent version - lots of changes

	* [r3937] examples/laminar_or_noshrinking.ty:
	  Initial version - work in progress

	* [r3936] examples/lissom_or_noshrinking.ty:
	  Initial version - work in progress

2006-06-19  ceball

	* [r3935] doc/Future_Work/current_text.php:
	  Added task about not pickling certain things.

	* [r3934] doc/Future_Work/current_text.php:
	  Added note to a task.

2006-06-17  jbednar

	* [r3933] topo/base/cf.py:
	  Removed unneeded update_projection_view

	* [r3932] topo/commands/analysis.py:
	  Changed update_projectionactivity() to be simpler and
	  self-contained. Updated doc strings. Made commands check for
	  appropriate subclasses of Sheet and Projection

2006-06-17  ceball

	* [r3931] doc/Downloads/cvs_text.php:
	  Minor correction.

2006-06-17  jbednar

	* [r3930]
	  topo/tkgui/projectionactivitypanel.py:
	  Added warning

	* [r3929] topo/plotting/plotgroup.py:
	  Slight cleanup and additional merging into parent class

	* [r3928] topo/plotting/plotgroup.py:
	  Made ConnectionFieldsPlotGroup and ProjectionPlotGroup inherit
	  shared code from ProjectionSheetPlotGroup

	* [r3927] topo/plotting/plotgroup.py:
	  Pulled out common code from ProjectionActivityPlotGroup to make a
	  new base class to be used in ConnectionFieldPlotGroup and
	  ProjectionPlotGroup

2006-06-16  judelaw

	* [r3926]
	  topo/tkgui/projectionactivitypanel.py:
	  Added Projection Activity Window

	* [r3925] topo/base/cf.py,
	  topo/base/sheetview.py,
	  topo/commands/analysis.py,
	  topo/plotting/plotgroup.py,
	  topo/plotting/templates.py,
	  topo/tkgui/topoconsole.py:
	  Added Projection Activity window

2006-06-15  jbednar

	* [r3924] doc/Downloads,
	  doc/Downloads/.cvsignore,
	  doc/Downloads/cvs_text.php,
	  doc/Downloads/index_text.php,
	  doc/shared/index.php:
	  Revamped Download instructions to simplify instructions for
	  non-CVS installs

2006-06-13  ceball

	* [r3923] doc/Future_Work/current_text.php:
	  Added task about the command prompt. (Also removed a comment.)

2006-06-12  ceball

	* [r3922] doc/shared/index.php:
	  Added Windows screenshot to 0.9.0 news.

	* [r3921]
	  doc/images/060607_topographica_win_screenshot.png:
	  Added Windows screenshot.

2006-06-10  ceball_cvs2svn

	* [r3920] /tags/release_0_9_0:
	  This commit was manufactured by cvs2svn to create tag
	  'release_0_9_0'.

2006-06-10  jbednar

	* [r3919] doc/shared/index.php:
	  Noted that binaries are available

	* [r3918] doc/shared/index.php:
	  Added link to downloads page

2006-06-10  ceball

	* [r3917] doc/Downloads/index_text.php:
	  Minor update to examples for Windows users.

2006-06-08  ceball

	* [r3916] doc/Downloads/index_text.php:
	  Removed duplicate updates mailing list note.

	* [r3915] doc/Downloads/index_text.php:
	  Updated suggested startup example to lissom_oo_or, and the link
	  to the tutorial.

	* [r3914] doc/Downloads/index_text.php:
	  Slightly altered the 'updating' section to distinguish between
	  CVS and binary users.

	* [r3913] doc/Downloads/index_text.php:
	  Updated instructions to link to Sourceforge's files section.

	* [r3912]
	  external/mswin/for_binaries/prepare_for_binaries.bat:
	  Corrected another backslash error.

	* [r3911]
	  external/mswin/for_binaries/prepare_for_binaries.bat:
	  Corrected a backslash mistake.

	* [r3910]
	  external/mswin/for_binaries/prepare_for_binaries.bat:
	  Corrections to previous two commits.

	* [r3909]
	  external/mswin/for_binaries/prepare_for_binaries.bat:
	  Deletes CVS subdirectories.

	* [r3908]
	  external/mswin/for_binaries/prepare_for_binaries.bat:
	  Updated now I know how to delete files recursively from windows
	  command prompt.

	* [r3907]
	  doc/Tutorials/images/or_key_horiz_transparent.png:
	  Updated key.

2006-06-08  jbednar

	* [r3906] doc/images/cmvc-cover-icon.jpg:
	  Copied from computationalmaps.org

	* [r3905] ChangeLog.txt:
	  Updated with current changes

	* [r3904] doc/shared/index.php:
	  Added news item for 0.9.0

	* [r3903]
	  doc/Tutorials/images/som_activity_000000.png,
	  doc/Tutorials/images/som_activity_000001.png,
	  doc/Tutorials/images/som_activity_000006.png,
	  doc/Tutorials/images/som_cog_000000.png,
	  doc/Tutorials/images/som_cog_000100.png,
	  doc/Tutorials/images/som_grid_000000.png,
	  doc/Tutorials/images/som_grid_000100.png,
	  doc/Tutorials/images/som_grid_010000.png,
	  doc/Tutorials/images/som_grid_040000.png,
	  doc/Tutorials/images/som_network_diagram.png,
	  doc/Tutorials/images/som_projection_000000.png,
	  doc/Tutorials/images/som_projection_000001.png,
	  doc/Tutorials/images/som_projection_000006.png,
	  doc/Tutorials/images/som_projection_040000.png,
	  doc/Tutorials/som_retinotopy_text.php:
	  Reverted to full-density simulation; reduced-density version
	  needs work

	* [r3902] doc/Tutorials/lissom_oo_or_text.php:
	  Fixed the text to match the new simulation

	* [r3901] doc/User_Manual/commandline_text.php:
	  Updated to current syntax

	* [r3900] topo/tkgui/plotgrouppanel.py:
	  Disabled sheet coordinates by default, because it makes V1 be too
	  tiny to see with any reasonable plot size

2006-06-07  ceball

	* [r3899] topo/responsefns/optimized.py:
	  Added comment to an ALERT.

	* [r3898] doc/Future_Work/index_text.php:
	  Really minor change to wording.

	* [r3897] topo/patterns/basic.py:
	  Changed default scale of Line, for the tutorial.

	* [r3896] doc/Tutorials/lissom_oo_or_text.php:
	  Resized images.

	* [r3895]
	  doc/Tutorials/images/activity_line_oo.png,
	  doc/Tutorials/images/activity_line_oo_or.png,
	  doc/Tutorials/images/lissom_network_diagram_oo.png,
	  doc/Tutorials/images/natural_image_oo_or.png,
	  doc/Tutorials/images/oo_or_map.png,
	  doc/Tutorials/images/projection_oo.png,
	  doc/Tutorials/images/test_pattern_oo.png,
	  doc/Tutorials/images/topographica_console.png,
	  doc/Tutorials/images/unit_weights_0_0_oo.png,
	  doc/Tutorials/images/unit_weights_0_0_oo_or.png:
	  Updated to match current simulation.

2006-06-07  jbednar

	* [r3894] topo/tests/testsheetview.ppm:
	  Removed unused image

	* [r3893] doc/Home,
	  doc/Home/.cvsignore,
	  doc/Home/oldnews_text.php:
	  Added oldnews page

	* [r3892] Makefile,
	  external/mswin/for_binaries/topographica.iss,
	  external/mswin/setup.py:
	  Updated to 0.9.0 release

	* [r3891] doc/Developer_Manual/index_text.php:
	  Uncommented Chris's addition

	* [r3890] ChangeLog.txt:
	  Fixed typos

2006-06-07  ceball

	* [r3889] topo/base/cf.py:
	  Mask size set to be that of the weights matrix, rather than the
	  nominal (user-specified) bounds.

	* [r3888] examples/lissom_oo_or.ty:
	  LGNOnAfferent strength reverted to 0.5 (i.e. removed a hack).

2006-06-07  jbednar

	* [r3887] topo/tkgui/testpattern.py:
	  Restored auto-refresh=True in the Test Pattern window, to make
	  sure that the preview updates when the PatternGenerator is
	  changed

	* [r3886] README.txt:
	  Added stronger warnings

	* [r3885] ChangeLog.txt:
	  Updated with recent changes

	* [r3884] doc/Future_Work/current_text.php:
	  Added task

	* [r3883] examples/hierarchical.ty:
	  Changed aspect ratio and density of sheets as an example of doing
	  so

	* [r3882]
	  doc/Developer_Manual/optimization_text.php:
	  Updated to match recent changes

	* [r3881] doc/Future_Work/current_text.php,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/modeleditor_text.php,
	  doc/User_Manual/parameters_text.php:
	  Cleaned up to match recent changes

	* [r3880] doc/Tutorials/index_text.php,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Commented out lissom_or.ty tutorial so that I don't have to keep
	  updating it.

	* [r3879] topo/tkgui/topoconsole.py:
	  Removed unnecessary command prompting. Reordered command output
	  box to look more like a shell

	* [r3878] topo/tkgui/plotgrouppanel.py:
	  Set plots to Sheet coordinates by default. Removed unnecessary
	  command prompting

	* [r3877] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Changed Boolean Checkbutton variables to use an automatically
	  updated BooleanVar to avoid gratuitous complexity such as the
	  various toggle_ functions, to allow the default value to be set
	  easily.

	* [r3876] topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/base/patterngenerator.py:
	  Removed unneeded packages lists for ClassSelectorParameters

2006-06-06  jbednar

	* [r3875] topo/base/parameterclasses.py,
	  topo/tkgui/__init__.py:
	  Removed requirement that ClassSelectorParameters define a
	  packages attribute now that they use concrete_descendents instead

	* [r3874] doc/Reference_Manual/index_text.php,
	  topo/base/parameterclasses.py,
	  topo/tkgui/editortools.py:
	  Replaced find_classes_in_package with concrete_descendents, to
	  allow classes defined anywhere to be found

	* [r3873] examples/joublin_bc96.ty:
	  Added HindpawGaussian

	* [r3872] topo/base/parameterizedobject.py:
	  Added temporary function for getting access to a parameter
	  without changing its value

	* [r3871] doc/Tutorials/lissom_oo_or_text.php,
	  doc/Tutorials/lissom_or_text.php:
	  Updated to match current code

2006-06-05  jbednar

	* [r3870] doc/User_Manual/space_text.php:
	  Updated to match recent changes

2006-06-04  jbednar

	* [r3869] doc/Downloads/index_text.php,
	  doc/Future_Work/current_text.php,
	  doc/Future_Work/index_text.php,
	  doc/Home/index_text.php,
	  doc/Reference_Manual/index_text.php,
	  doc/Team_Members/index_text.php,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Updated with recent changes

	* [r3868] topo/tkgui/topoconsole.py:
	  Moved implementation notes here from Future_Work

2006-06-04  yschoe

	* [r3867] examples/leaky_lissom_or.ty:
	  Tweaking parameters.

2006-06-04  jbednar

	* [r3866] topo/base/cf.py:
	  Added alert

2006-06-04  ceball

	* [r3865] topo/tests/lissom_oo_or_reference.ty:
	  Updated class names.

	* [r3864] topo/tests/lissom_or_reference.ty:
	  Updated class names.

2006-06-04  yschoe

	* [r3863] topo/patterns/basic.py:
	  Added TwoRectangles class. This is really a hack, so it needs to
	  be replaced
	  later with a more general version.

	* [r3862] examples/leaky_lissom_or.ty:
	  Testing new pattern generator. Tuning learning rate and decay
	  parameters.

2006-06-03  ceball

	* [r3861] doc/Future_Work/current_text.php:
	  Added task about allowing min_matrix_rad to be zero; altered task
	  about problem with examples/joublin_bc96.ty.

	* [r3860] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3859] topo/outputfns/optimized.py:
	  PyFloat_FromDouble() returns a new reference, so after using it
	  the reference count should be decremented.

	* [r3858] topo/learningfns/optimized.py:
	  PyFloat_FromDouble() returns a new reference, so after using it
	  the reference count should be decremented.

	* [r3857] examples/lissom_or.ty:
	  Removed unused import.

	* [r3856] examples/lissom_or.ty:
	  Removed unused imports.

	* [r3855] topo/base/cf.py:
	  Added back line to update the CF's sum (that had been
	  accidentally removed in the past). If CFPOF_Plugin was being used
	  in combination with a CFPLF that selectively sets the _sum
	  attribute (as CFPLF_Hebbian_opt does, setting it only where the
	  output activity is not 0), then the sum could be out of date
	  while this line was missing.

	* [r3854] topo/outputfns/optimized.py:
	  Removed unnecessary call to super's init from
	  CPOF_DivisiveNormalizeL1_opt.

2006-06-02  jbednar

	* [r3853] Makefile:
	  Moved info about specific targets into examples/Makefile

	* [r3852] examples/Makefile:
	  Added more full targets. Added more dependencies.

	* [r3851] topo/responsefns/optimized.py:
	  Cleaned up C variable declarations for
	  CFPRF_EuclideanDistance_opt

2006-06-02  ceball

	* [r3850] topo/outputfns/optimized.py:
	  No visible change. Removed unnecessary __init__() method and
	  simplified code in DivisiveNormalizeL1_opt.

2006-06-02  jbednar

	* [r3849] topo/learningfns/optimized.py,
	  topo/outputfns/optimized.py,
	  topo/responsefns/optimized.py:
	  Cleaned up memory handling for PyObject calls from C code;
	  reference counts were increasing with each call, possibly leading
	  to memory leaks.

2006-06-01  jbednar

	* [r3848] topo/tkgui/editorwindow.py:
	  Fixed Model Editor, broken since
	  topo.tkgui.topoconsole.dict_console['console'] changed to
	  topo.guimain

	* [r3847] topo/base/arrayutils.py:
	  Removed confusing return values

	* [r3846] topo/outputfns/optimized.py:
	  Removed now-unnecessary C++ version of PiecewiseLinear

	* [r3845] topo/outputfns/basic.py:
	  Removed outdated alert.

	* [r3844] topo/base/sheet.py:
	  Added explanation from Chris Ball

	* [r3843] doc/Future_Work/current_text.php:
	  Rearranged and reassigned tasks now that Chris Ball is leaving

2006-06-01  judelaw

	* [r3842] examples/lissom_or.ty:
	  corrected errors in naming

2006-06-01  yschoe

	* [r3841] examples/leaky_lissom_or.ty:
	  Changed lateral connections to have LeakyCFProjection. Run this
	  example, and
	  use the test pattern generator (gaussian) to observe spiking.

	* [r3840] topo/sheets/slissom.py:
	  Added absolute refractory period to SLISSOM class. Use test
	  pattern generator
	  (gaussian) and repeatedly present the input to see the spiking.

2006-06-01  jbednar

	* [r3839] topo/base/functionfamilies.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/optimized.py:
	  Removed now-unused OutputFn return value

	* [r3838] topo/tests/testoutputfnsbasic.py,
	  topo/tests/testoutputfnsoptimized.py:
	  Removed tests of OuputFns as functions, in anticipation of
	  removing the return values

	* [r3837] topo/outputfns/basic.py:
	  Removed unused Spike OutputFn

	* [r3836] topo/base/cf.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/patterns/basic.py,
	  topo/patterns/random.py,
	  topo/projections/basic.py,
	  topo/sheets/slissom.py:
	  Made calls to output_fns consistently use them in place rather
	  than as functions, which will allow the return value to be
	  removed

	* [r3835] topo/tkgui/parametersframe.py:
	  Minor documentation cleanup

	* [r3834] examples/Makefile:
	  Added som_retinotopy to standard examples to test with 'make all'

	* [r3833]
	  doc/Tutorials/som_retinotopy_text.php,
	  examples/som_retinotopy.ty:
	  Made density be overridable from command line

	* [r3832] topo/base/arrayutils.py,
	  topo/outputfns/basic.py:
	  At long last, fixed clip_in_place and related functions to use
	  matrix operations for speed and so that they operate cleanly in
	  place.

	* [r3831] examples/lissom_or.ty:
	  Fixed typo in commented-out code

2006-05-31  yschoe

	* [r3830] topo/responsefns/basic.py,
	  topo/responsefns/optimized.py:
	  Removed DynamicThreshold_CFPRF_DotProduct_opt class from
	  responsefn.basic.
	  See sheets.slissom for the implementation of spiking.

	* [r3829] topo/responsefns/basic.py:
	  Added hack alert. The stuff here needs to be removed or moved to
	  optimized.py

	* [r3828] examples/leaky_lissom_or.ty:
	  Moved spiking mechanism from responsefn to sheet (new class
	  SLISSOM).

	* [r3827] topo/sheets/slissom.py:
	  Spiking LISSOM sheet class, implementing dynamic thresholding.
	  For leaky
	  synapses, it needs the LeakyCFProjection class.

2006-05-31  jbednar

	* [r3826] topo/tkgui/topoconsole.py:
	  Made auto-refresh update the actual windows also, so that it
	  takes effect immediately even when called from a script. Also
	  made load_snapshot do an auto_refresh() to update any windows
	  that have auto-refresh enabled.

	* [r3825] topo/analysis/featuremap.py,
	  topo/tkgui/topoconsole.py:
	  Greatly simplified display of the activity patterns during map
	  measurement, and now left it uncommented by default.

	* [r3824] topo/commands/analysis.py:
	  Increased size of default pattern for position preference
	  measurement so that it would be more likely to activate all
	  neurons; typically improves quality of position preference map.

2006-05-30  jbednar

	* [r3823] topo/responsefns/optimized.py:
	  Removed redundant class

	* [r3822] examples/homeostatic.ty:
	  Fixed thresholds to be applied even on the first call, used
	  Numeric.sum() for averaging, and allowed bounds to be controlled
	  by parameters.

	* [r3821] examples/homeostatic.ty:
	  Updated with Veldri's changes: simple example of adjusting
	  threshold based on the average value in a rectangular window.
	  Reduced LGNOn density to make debugging easier. Fixed output_fn
	  for SharedWeightCFProjection.

	* [r3820] topo/outputfns/basic.py:
	  Added BinaryThreshold

	* [r3819] topo/base/arrayutils.py:
	  Clarified alerts

	* [r3818] topo/outputfns/basic.py:
	  Cleaned up spacing

2006-05-30  yschoe

	* [r3817] examples/leaky_lissom_or.ty:
	  Fixed small bug (renamed primitive).

	* [r3816] examples/leaky_lissom_or.ty:
	  Modified a bit to make tsettle=1 and generate spikes using the
	  dynamic
	  threshold CFP function.

	* [r3815] topo/responsefns/basic.py:
	  Added DynamicThreshold_CFPRF_DotProduct_opt, a
	  CFPRF_DotProduct_opt with
	  dynamic thresholding. Right now, it only has a fixed threshold.
	  It uses
	  the optimized __call__ in its parent, while the thresholding part
	  is plain
	  Python code.

	* [r3814] topo/outputfns/basic.py:
	  Added a "primitive" Spike output function.

2006-05-29  jbednar

	* [r3813] Makefile:
	  Made examples directory be cleaned up for distributions

	* [r3812] examples/README.txt:
	  Initial version

	* [r3811] examples/cfsom_or.ty,
	  examples/disparity_energy.ty,
	  examples/hierarchical.ty,
	  examples/homeostatic.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty:
	  Removed unnecessary run(0) command from examples

	* [r3810] examples/disparity_energy.ty,
	  examples/homeostatic.ty,
	  examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  topo/learningfns/optimized.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/optimized.py,
	  topo/tests/testoutputfnsbasic.py,
	  topo/tests/testoutputfnsoptimized.py:
	  Changed DivisiveSumNormalize to DivisiveNormalizeL1

	* [r3809] examples/cfsom_or.ty,
	  examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/leaky_lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/tiny.ty:
	  Made all examples use a standard delay from retina to V1 so that
	  the same default would work for measuring orientation maps

	* [r3808] examples/laminar.ty:
	  Trivial change to remove execute bit

	* [r3807] examples/lissom_or.ty:
	  Changed retina->V1 delay so that orientation map can be measured
	  at the same time as lissom_oo_or_map.ty

	* [r3806] topo/commands/analysis.py:
	  Changed default duration of orientation map measurement to avoid
	  settling in LISSOM

	* [r3805] topo/tkgui/propertiesframe.py:
	  Reduced width slightly

	* [r3804] topo/outputfns/basic.py:
	  Added HalfRectifyAndSquare output_fn

	* [r3803] topo/base/arrayutils.py:
	  Added (slow) clip_lower function

	* [r3802] examples/disparity_energy.ty:
	  Initial version

	* [r3801] topo/learningfns/basic.py:
	  Added note about original author

	* [r3800] doc/Links/index_text.php:
	  Minor cleanup

	* [r3799] doc/Links/index_text.php:
	  Cleaned up formatting and expanded a bit

	* [r3798] doc/shared/util.php:
	  Added Links to toolbar

2006-05-28  jbednar

	* [r3797] doc/Links,
	  doc/Links/.cvsignore,
	  doc/Links/index_text.php:
	  Initial version

2006-05-26  ceball

	* [r3796] topo/tkgui/propertiesframe.py:
	  Set Entry widths.

	* [r3795] topo/tkgui/topoconsole.py:
	  Commented out balloon help binding for 'Go' button because it
	  prevents simulation time from being printed in the messagebar.

2006-05-26  jbednar

	* [r3794] topo/learningfns/projfns.py:
	  Updated commented code that had gotten stale

2006-05-25  jbednar

	* [r3793] topo/tkgui/editorobjects.py:
	  Fixed bug with help balloons

2006-05-25  ceball

	* [r3792] topo/outputfns/basic.py:
	  Minor change to docstring.

	* [r3791] topo/outputfns/basic.py,
	  topo/patterns/image.py,
	  topo/tests/testoutputfnsbasic.py:
	  Changed DivisiveMaxNormalize to DivisiveNormalizeLinf

	* [r3790] topo/outputfns/basic.py,
	  topo/tests/testoutputfnsbasic.py:
	  Changed DivisiveLpNormalize to DivisiveNormalizeLp

	* [r3789] topo/outputfns/optimized.py,
	  topo/tests/testoutputfnsoptimized.py:
	  Changed DivisiveSumNormalize_opt1 to DivisiveSumNormalize_opt

	* [r3788] topo/outputfns/basic.py,
	  topo/tests/testoutputfnsbasic.py:
	  Changed DivisiveLengthNormalize to DivisiveNormalizeL2

	* [r3787] examples/tiny.ty,
	  topo/outputfns/basic.py:
	  Changed DivisiveL1Normalize to DivisiveNormalizeL1

	* [r3786] topo/outputfns/basic.py,
	  topo/outputfns/optimized.py:
	  Clarified some alerts.

	* [r3785] topo/projections/basic.py:
	  Minor alteration to comments.

	* [r3784] topo/projections/basic.py:
	  Changed \bSharedWeightCFPOutputFn\b to CFPOF_SharedWeight

	* [r3783] external/win32/README.txt:
	  Added note.

	* [r3782] topo/base/cf.py,
	  topo/projections/basic.py:
	  Changed IdentityCFPOutputFn to CFPOF_Identity

	* [r3781] doc/Future_Work/current_text.php,
	  examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  topo/outputfns/optimized.py:
	  Changed CFPDivisiveSumNormalize_opt1 to
	  CFPOF_DivisiveSumNormalize_opt

	* [r3780] examples/tiny.ty,
	  topo/base/cf.py,
	  topo/outputfns/optimized.py,
	  topo/outputfns/projfns.py:
	  Changed GenericCFPOutputFn to CFPOF_Plugin

	* [r3779] topo/outputfns/optimized.py:
	  Changed CFPDivisiveSumNormalize to CFPOF_DivisiveSumNormalize

	* [r3778] topo/responsefns/optimized.py:
	  Changed \bDotProduct_opt1\b to DotProduct_opt

	* [r3777] examples/lissom_oo_or.ty,
	  examples/lissom_or_sf.ty,
	  topo/responsefns/optimized.py:
	  Changed \bSharedWeightCFPDotProduct_opt1\b to
	  CFPRF_SharedWeightDotProduct_opt

	* [r3776] topo/responsefns/optimized.py:
	  Changed \bSharedWeightCFPDotProduct\b to
	  CFPRF_SharedWeightDotProduct

	* [r3775] topo/misc/inlinec.py:
	  Added comment.

	* [r3774] topo/projections/basic.py,
	  topo/responsefns/optimized.py:
	  Changed SharedWeightCFPResponseFn to CFPRF_SharedWeight

	* [r3773] topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py:
	  Changed GenericCFPResponseFn to CFPRF_Plugin

	* [r3772] examples/som_retinotopy.ty,
	  topo/responsefns/optimized.py:
	  Changed \bCFPEuclideanDistance_opt1\b to
	  CFPRF_EuclideanDistance_opt

	* [r3771] topo/responsefns/optimized.py:
	  Minor change to docstrings.

	* [r3770] topo/misc/utils.py:
	  Changes to comments.

	* [r3769] doc/Future_Work/current_text.php:
	  Update to task.

	* [r3768] topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py:
	  Changed \bCFPEuclideanDistance\b to CFPRF_EuclideanDistance

	* [r3767] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  examples/tiny.ty,
	  topo/misc/utils.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py,
	  topo/tests/testplotgroup.py:
	  Changed \bCFPDotProduct_opt1\b to CFPRF_DotProduct_opt

	* [r3766] topo/misc/utils.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py:
	  Changed CFPDotProduct to CFPRF_DotProduct

	* [r3765] topo/learningfns/som.py,
	  topo/sheets/cfsom.py:
	  Changed SOMLF to CFPLF_SOM

	* [r3764] examples/tiny.ty,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/learningfns/__init__.py,
	  topo/learningfns/optimized.py,
	  topo/learningfns/projfns.py:
	  Changed \bGenericCFPLearningFn\b to CFPLF_Plugin

	* [r3763] topo/base/cf.py,
	  topo/learningfns/projfns.py,
	  topo/projections/basic.py:
	  Changed IdentityCFPLearningFn to CFPLF_Identity

	* [r3762] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/joublin_bc96.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  topo/learningfns/som.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py:
	  Changed \bHebbianSOMLF\b to CFPLF_HebbianSOM

	* [r3761] etc/toporename:
	  Changed example use and added a note.

	* [r3760] topo/learningfns/optimized.py:
	  Changed \bCFPHebbian\b to CFPLF_Hebbian

2006-05-24  jbednar

	* [r3759] topo/tkgui/editorobjects.py:
	  Added class documentation to balloon help for editor objects

	* [r3758] topo/misc/utils.py:
	  Added shortclassname function

2006-05-24  ceball

	* [r3757] doc/Future_Work/current_text.php,
	  examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/leaky_lissom_or.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  topo/learningfns/optimized.py:
	  Changed CFPHebbian_opt1 to CFPLF_Hebbian_opt

	* [r3756] etc/toporename:
	  Corrected location of replaceall.

	* [r3755] etc/toporename:
	  Correction to code for whether or not to continue.

2006-05-24  jbednar

	* [r3754] doc/Future_Work/current_text.php:
	  Added task

	* [r3753] examples/joublin_bc96.ty:
	  Initial sketch

	* [r3752] topo/base/cf.py,
	  topo/sheets/lissom.py:
	  Minor doc cleanup

	* [r3751] doc/Future_Work/current_text.php:
	  Minor addition

2006-05-23  ceball

	* [r3750] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3749] topo/tests/testoutputfnsoptimized.py:
	  Reduced precision of a test because Numeric sticks with the
	  Float32s.

	* [r3748] topo/projections/basic.py:
	  The sharedcf has its weights pattern centered on the src sheet,
	  not the dest shee.

	* [r3747] topo/base/cf.py:
	  Just save the center unit's xcenter and ycenter as attributes
	  that can be used later. This will be cleaned up.

	* [r3746] topo/tkgui/editorobjects.py,
	  topo/tkgui/parametersframe.py:
	  Shows balloon help for object over the title.

	* [r3745] topo/tkgui/editortools.py:
	  Added more text to HACKALERT.

	* [r3744] doc/Future_Work/current_text.php:
	  Added some tasks.

	* [r3743] topo/tkgui/parametersframe.py:
	  Checkbuttons are aligned on the left. Removed unused width
	  specification.

	* [r3742] topo/tkgui/propertiesframe.py:
	  Readonly properties have a readonly Entry.

	* [r3741] topo/tkgui/propertiesframe.py:
	  Removed font specification for read-only entry text.

2006-05-23  jbednar

	* [r3740] topo/tkgui/parametersframe.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Changed balloon help to use inspect.getdoc(x) instead of
	  x.__doc__ so that leading whitespace would be removed

2006-05-23  ceball

	* [r3739] topo/base/parameterizedobject.py:
	  Added doc string to name Parameter.

2006-05-23  jbednar

	* [r3738] topo/base/sheet.py:
	  Trivial space change

	* [r3737] topo/sheets/cfsom.py:
	  Added docstrings and removed apparently unused rmin and rmax
	  parameters

	* [r3736] topo/base/cf.py,
	  topo/base/projection.py,
	  topo/sheets/lissom.py:
	  Added docstrings

	* [r3735] topo/base/cf.py,
	  topo/sheets/generatorsheet.py:
	  Added help text

2006-05-23  yschoe

	* [r3734] topo/projections/basic.py:
	  Cleaned up LeakyCFProjection.__init__(), following Jim's
	  suggestions.

2006-05-22  jbednar

	* [r3733] topo/plotting/plotgroup.py,
	  topo/tkgui/topoconsole.py:
	  Cleaned up help text

	* [r3732] topo/tkgui/connectionfieldspanel.py:
	  Fixed longstanding bug in error message

	* [r3731] topo/projections/basic.py:
	  Minor cleanup and suggestions

	* [r3730] topo/tkgui/plotgrouppanel.py:
	  Fixed typo that crept into previous version somehow

	* [r3729] topo/plotting/plotgroup.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Added parameters for normalize, sheetcoords, integerscaling, and
	  updatecommand so that they can have documentation. Added balloon
	  help.

	* [r3728] etc/replaceall:
	  Minor note

2006-05-22  ceball

	* [r3727] topo/base/cf.py:
	  CFProjection creates a slice_template and passes it to each CF,
	  rather than each CF creating its own slice. Reduces
	  lissom_or.ty's startup time to about 80% of its previous value.

	* [r3726] topo/projections/basic.py:
	  SharedWeightCFProjection initializes its sharedcf to have x and y
	  'on the grid' - previously it just set them both to 0.

2006-05-22  yschoe

	* [r3725] examples/leaky_lissom_or.ty:
	  Added leaky_lissom_or.ty to the source tree. This is a copy of
	  lissom_or.ty
	  with the afferent connections turned into LeakyCFProjection. The
	  lissom_or.ty
	  file will be periodically copied to leaky_lissom_or.ty and minor
	  edits made,
	  to keep future developments in lissom_or.ty independent of
	  leaky_lissom_or.ty.

	* [r3724] topo/tkgui/plotgrouppanel.py:
	  Added "kill" hotkey for plot windows (Control-q).

2006-05-22  jbednar

	* [r3723] etc/toporename:
	  Initial version

2006-05-22  yschoe

	* [r3722] topo/projections/basic.py:
	  Fixed bug in LeakyCFProjection, and initialized
	  leaky_input_activity to a zero matrix.

	* [r3721] topo/projections/basic.py:
	  Added activate() for LeakyCFProjection. A finer time-scale needs
	  to be
	  implemented.

2006-05-22  ceball

	* [r3720] topo/outputfns/basic.py:
	  Uses Numeric's sum().

	* [r3719] topo/outputfns/optimized.py:
	  Uses Numeric's sum instead of Python's. This has a big impact on
	  the performance. Starting lissom_or (which uses
	  DivisiveSumNormalize_opt1 many times), this gives a the startup
	  time 65% of the previous time.

	* [r3718] topo/tkgui/topoconsole.py:
	  Shell prints new prompt everytime there simulation is run, as it
	  did before. Otherwise the prompt does not appear again after
	  messages are printed.

2006-05-21  ceball

	* [r3717] topo/tests/testtopoconsole.py:
	  Removed test that didn't have much use.

	* [r3716] topo/tkgui/topoconsole.py:
	  Added some sample help messages.

	* [r3715] topo/tkgui/topoconsole.py:
	  Changed layout of 'status' section to match the others.

	* [r3714] topo/tkgui/topoconsole.py:
	  Reduced width of the console. Added HACKALERT.

	* [r3713] topo/base/simulation.py:
	  Corrected typo.

	* [r3712] topo/base/parameterclasses.py:
	  Added ALERT.

	* [r3711] topo/tkgui/topoconsole.py:
	  Changed 'run for' slider.

	* [r3710] topo/tkgui/translatorwidgets.py:
	  Added facility to set slider_width to TaggedSlider.

	* [r3709] topo/tkgui/topoconsole.py:
	  Stopped shell printing a new prompt after every run command from
	  the GUI.

	* [r3708] topo/tkgui/topoconsole.py:
	  Added '>>>' label to command prompt.

	* [r3707] topo/tkgui/topoconsole.py:
	  'run for' displays 1.0 initially. 'commands' not displayed by
	  default.

	* [r3706] topo/tkgui/topoconsole.py:
	  'Run for' is a TaggedSlider. String format needs to be adjusted,
	  and pressing enter should make the simulation run too.

	* [r3705] topo/tkgui/translatorwidgets.py:
	  TaggedSlider seems to assume a method optional_refresh() will
	  always exist on its parent; I put in a try/catch but the whole
	  thing (still) needs to be reviewed.

	* [r3704] topo/tkgui/topoconsole.py:
	  Corrected variable name.

	* [r3703] topo/tkgui/topoconsole.py:
	  Altered 'run simulation for group'. Changed how 'commands' group
	  is hidden. There are still some problems: width changes, not
	  enough padding in places.

2006-05-21  jbednar

	* [r3702] topo/tkgui/editorwindow.py:
	  Removed debugging print statement

2006-05-21  yschoe

	* [r3701] topo/projections/basic.py:
	  LeakyCFProjection class added (just a place holder, for now).

2006-05-21  ceball

	* [r3700] topo/tkgui/topoconsole.py:
	  Added code to demonstrate showing/hiding the commands box.

2006-05-21  jbednar

	* [r3699] etc/pipecap,
	  etc/replaceall:
	  Initial version

	* [r3698] topo/outputfns/projfns.py,
	  topo/responsefns/projfns.py:
	  Added missing imports

	* [r3697] topo/base/boundingregion.py,
	  topo/base/cf.py,
	  topo/base/simulation.py,
	  topo/learningfns/som.py,
	  topo/misc/numbergenerators.py:
	  Declared abstract classes abstract

	* [r3696] topo/learningfns/basic.py,
	  topo/learningfns/projfns.py:
	  Moved CFPLearningFns from basic.py to projfns.py

2006-05-20  jbednar

	* [r3695] topo/learningfns/basic.py:
	  Partially debugged BCMCFP; commented it out until fully debugged

	* [r3694] topo/learningfns/basic.py:
	  Added new learning functions; need more testing still

2006-05-20  ceball

	* [r3693] topo/tkgui/topoconsole.py:
	  Minor change: command output box is inside the "Command" frame.

	* [r3692] doc/Future_Work/index_text.php:
	  Added a comment.

	* [r3691] topo/tkgui/topoconsole.py:
	  Added scrollbars to command output textbox.

	* [r3690] topo/tkgui/topoconsole.py:
	  Made command output 10 lines long.

	* [r3689] topo/tkgui/topoconsole.py:
	  'Run simulation for' moved to top of console.

	* [r3688] topo/tkgui/topoconsole.py:
	  Corrected mistake.

	* [r3687] topo/tkgui/topoconsole.py:
	  Command output text is not editable.

	* [r3686] topo/tkgui/topoconsole.py:
	  Output window echos the command.

	* [r3685] topo/tkgui/topoconsole.py:
	  Command output text box scrolls with new text. Added HACKALERT.

	* [r3684] topo/tkgui/topoconsole.py:
	  Updated documentation.

	* [r3683] topo/tkgui/topoconsole.py:
	  Removed unused do_command().

	* [r3682] topo/tkgui/topoconsole.py:
	  Added a Text window to display results of commands.

	* [r3681] doc/Future_Work/index_text.php:
	  Added some notes.

	* [r3680] doc/Future_Work/index_text.php:
	  Updated pickling section.

2006-05-19  ceball

	* [r3679] doc/Future_Work/current_text.php:
	  Added pycheck task and some updates.

	* [r3678] doc/Future_Work/index_text.php:
	  Minor change to wording.

	* [r3677] topo/base/cf.py:
	  Can specify minimum matrix radius for weights of CFProjection;
	  defaults to 1 for a 3x3 matrix minimum.

	* [r3676] doc/Future_Work/current_text.php:
	  Updated a task.

	* [r3675] doc/Future_Work/current_text.php:
	  Added task about memory usage growing.

	* [r3674] doc/Future_Work/current_text.php:
	  Removed task that was finished recently.

	* [r3673] doc/Future_Work/current_text.php:
	  Removed duplicate task.

	* [r3672] doc/Future_Work/current_text.php:
	  Removed the task about updating documentation before the release,
	  since it would never be finished and I try to do it continuously
	  anyway.

	* [r3671] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3670] doc/Tutorials/lissom_oo_or_text.php:
	  No need to re-run the script when loading a network. Added note
	  about updating the time estimate for initial training.

	* [r3669] doc/Tutorials/lissom_or_text.php:
	  Don't need to run script before loading snapshot.

	* [r3668] doc/Future_Work/current_text.php:
	  Removed a task. The text I added to the user manual about
	  xdensity and ydensity should be reviewed.

	* [r3667] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3666] topo/outputfns/optimized.py:
	  Added comment about the relative performance of all-c vs python/c
	  vs python/python CFP learning functions.

	* [r3665] topo/responsefns/optimized.py:
	  Added comment about the relative performance of all-c vs python/c
	  vs python/python CFP response functions.

	* [r3664] topo/outputfns/basic.py,
	  topo/outputfns/optimized.py:
	  Clarified some hackalerts.

	* [r3663] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3662] topo/base/cf.py:
	  Added enforce_min_rad BooleanParameter to CFProjection (defaults
	  to true), which means the weights matrix resulting from the
	  supplied nominal_bounds_template will be at least 3x3.

	* [r3661] topo/tkgui/taggedslider.py:
	  Renamed to translatorwidgets (was removed in the past but appears
	  to have resurrected itself.)

	* [r3660]
	  external/mswin/for_binaries/README.txt:
	  Updated instructions.

	* [r3659]
	  external/mswin/for_binaries/topographica.iss:
	  Added comments.

	* [r3658]
	  external/mswin/for_binaries/topographica.iss:
	  Added a HACKALERT.

	* [r3657]
	  external/mswin/for_binaries/topographica.iss:
	  Corrected syntax.

	* [r3656] external/mswin/setup.py:
	  Corrected mistake in earlier checkin.

	* [r3655]
	  external/mswin/for_binaries/topographica.iss:
	  Doesn't use batch file to execute setup.py.

	* [r3654]
	  external/mswin/for_binaries/prepare_for_binaries.bat:
	  Update after removing setup.bat.

	* [r3653] external/mswin/setup.py:
	  Updates to documentation.

	* [r3652]
	  external/mswin/for_binaries/setup.bat:
	  Removed unnecessary file.

2006-05-19  jbednar

	* [r3651] Makefile,
	  external/mswin/for_binaries/topographica.iss,
	  external/mswin/setup.py:
	  Added new-version target and updated the corresponding files

2006-05-19  ceball

	* [r3650] topo/base/cf.py:
	  Corrected a comment.

	* [r3649] doc/Future_Work/current_text.php:
	  Updated.

	* [r3648]
	  external/mswin/for_binaries/setup.bat:
	  Updated with changes to setup.py.

	* [r3647] external/mswin/setup.bat:
	  Updated with change to setup.py.

	* [r3646] external/mswin/setup.py:
	  Tidied up.

	* [r3645]
	  external/mswin/for_binaries/README.txt:
	  Updated.

	* [r3644]
	  external/mswin/for_binaries/prepare_for_binaries.bat:
	  Added comment.

2006-05-18  ceball

	* [r3643]
	  external/mswin/for_binaries/topographica.iss:
	  Added back in something that got removed by accident.

	* [r3642]
	  external/mswin/for_binaries/topographica.iss:
	  Removed changing the setup icon file, which didn't seem to work.
	  Not important.

	* [r3641]
	  external/mswin/for_binaries/topographica.iss:
	  Shortcuts get topographica.ico

	* [r3640]
	  external/mswin/for_binaries/topographica.iss:
	  Correction

	* [r3639]
	  external/mswin/for_binaries/topographica.iss:
	  Minor update (desktop icon's optional).

	* [r3638]
	  external/mswin/for_binaries/topographica.iss:
	  Added a tip.

	* [r3637]
	  external/mswin/for_binaries/topographica.iss:
	  Makes desktop shortcut, start menu shortcut, associates ty files
	  (properly, doesn't
	  use a vbs script).

	* [r3636]
	  external/mswin/for_binaries/prepare_for_binaries.bat:
	  Not using create_shortcut.vbs.

	* [r3635]
	  external/mswin/for_binaries/setup.bat,
	  external/mswin/setup.bat,
	  external/mswin/setup.py:
	  Added "cvs" commandline option to setup.py.

2006-05-18  jbednar

	* [r3634] topo/base/simulation.py:
	  Clarified warning

	* [r3633] topo/base/patterngenerator.py:
	  Minor cleanup of documentation and comments

	* [r3632] topo/base/parameterizedobject.py:
	  Cleaned up comments and formatting of warning messages and class
	  defaults listing

	* [r3631] topo/base/functionfamilies.py:
	  Cleaned up comment

	* [r3630] topo/base/__init__.py:
	  Sorted list in order

2006-05-18  ceball

	* [r3629] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3628] topo/tkgui/editorobjects.py:
	  Deleting connection actually deletes it from the the simulation.

	* [r3627] topo/base/simulation.py:
	  EPConnection has a remove() method.

2006-05-18  jbednar

	* [r3626] topo/base/projection.py:
	  Minor cleanup of documentation

	* [r3625] doc/Downloads/index_text.php:
	  Updated CVS download instructions

	* [r3624] topo/tkgui/editorobjects.py:
	  Changed default color for Projections from purple to blue to be
	  more visible. Added alert.

2006-05-18  ceball

	* [r3623] topo/base/sheet.py:
	  Updates to Parameter docstrings.

	* [r3622] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3621] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/homeostatic.ty,
	  examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/tiny.ty,
	  topo/base/sheet.py,
	  topo/base/sheetcoords.py,
	  topo/patterns/basic.py,
	  topo/plotting/plotgroup.py,
	  topo/sheets/cfsom.py,
	  topo/tests/lissom_oo_or_reference.ty,
	  topo/tests/lissom_or_reference.ty,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testlissom.ty,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testplotgrouppanel.py,
	  topo/tests/testsheet.py,
	  topo/tests/testsheetview.py,
	  topo/tests/testsnapshots.py,
	  topo/tests/testtemplateplotgrouppanel.py,
	  topo/tkgui/editorobjects.py:
	  SheetCoordinateSystem stores the bounds in its bounds attribute,
	  not a true_bounds attribute. Sheet has Parameters nominal_density
	  and nominal_bounds; these are what gets set by users of Sheet.
	  Because Sheet is a SheetCoordinateSystem, it has its true bounds
	  in its bounds attribute, and its true density in its xdensity or
	  ydensity attributes (because for a Sheet xdensity=ydensity).

	* [r3620] topo/tests/testlissom_cpointer.ty:
	  Removed test of non-existent classes.

	* [r3619] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py:
	  Removed TopoConsole's active_sim.

	* [r3618] topo/tkgui/editorobjects.py:
	  Simplified getting a connection's bounds.

2006-05-17  ceball

	* [r3617] doc/Future_Work/current_text.php:
	  Added tasks. Fixed typos.

	* [r3616] topo/base/simulation.py:
	  added commented-out code for ensuring all out_connections have a
	  unique name.

	* [r3615] topo/sheets/composer.py:
	  Made call to EP's _connect_from in a more obvious way.

	* [r3614] topo/base/simulation.py:
	  Corrected a docstring.

	* [r3613] topo/base/projection.py:
	  Removed a HACKALERT: corrected call to EP's _connect_from.

	* [r3612] doc/Future_Work/current_text.php:
	  Updates to tasks.

	* [r3611] topo/base/simulation.py:
	  Modified HACKALERT.

	* [r3610] topo/tkgui/editorobjects.py:
	  Choosing to 'Delete' a sheet actually deletes the sheet from the
	  simulation.

	* [r3609] topo/base/simulation.py:
	  When adding an EP to the simulation, if one with the same name
	  already exists, it's overwritten.

	* [r3608] topo/base/simulation.py:
	  EPs can be deleted from the simulation.

	* [r3607] topo/tkgui/editorwindow.py:
	  Removed my HACKALERT about indentation - seems I was wrong. I
	  don't see how it's working, but it is.

	* [r3606] topo/tkgui/editorwindow.py:
	  Corrected my previous-but-one checkin for iterating through
	  out_connections.

	* [r3605] topo/tkgui/editorwindow.py:
	  Added HACKALERT.

	* [r3604] topo/commands/analysis.py:
	  Removed HACKALERT that no longer applies (cog plot for
	  SharedWeightCFProjection is a regular grid).

	* [r3603] topo/commands/analysis.py:
	  Made measure_cog only be called for CFSheets, rather than for all
	  ProjectionSheets.

	* [r3602] topo/commands/analysis.py:
	  Removed hackalert that doesn't apply since the previous commit.

	* [r3601] topo/commands/analysis.py:
	  Changed how ProjectionSheets are detected by measure_cog().

	* [r3600] topo/base/cf.py,
	  topo/base/projection.py,
	  topo/base/simulation.py,
	  topo/commands/analysis.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/lissom.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/projectionpanel.py:
	  EventProcessor.out_connections is now a plain list, like
	  in_connections. A ProjectionSheet does not store a separate
	  dictionary of in_projections, but it only permits Projections in
	  its list of in_connections.

	* [r3599] doc/Future_Work/current_text.php:
	  Updates to tasks.

	* [r3598] doc/Future_Work/current_text.php:
	  Updates to tasks. Removed windows binary task.

	* [r3597]
	  external/mswin/for_binaries/topographica.iss:
	  Minor updates.

	* [r3596]
	  external/mswin/for_binaries/prepare_for_binaries.bat,
	  external/mswin/for_binaries/setup.bat:
	  Corrections

2006-05-16  ceball

	* [r3595]
	  external/mswin/for_binaries/prepare_for_binaries.bat:
	  Uncommented line I commented out by mistake.

	* [r3594]
	  external/mswin/for_binaries/README.txt:
	  Added note about getting html doc.

	* [r3593]
	  external/mswin/for_binaries/topographica.iss:
	  Minor updates.

	* [r3592]
	  external/mswin/for_binaries/topographica.iss:
	  Changed a comment to a HACKALERT.

	* [r3591]
	  external/mswin/for_binaries/prepare_for_binaries.bat:
	  Forgot to copy a file...

	* [r3590]
	  external/mswin/for_binaries/README.txt:
	  Further clarifications.

	* [r3589]
	  external/mswin/for_binaries/README.txt:
	  Clarifications.

	* [r3588]
	  external/mswin/for_binaries/topographica.iss:
	  Minor updates.

	* [r3587] external/mswin/setup.py:
	  Minot update to comments.

	* [r3586]
	  external/mswin/for_binaries/topographica.iss:
	  Minor updates.

	* [r3585]
	  external/mswin/for_binaries/prepare_for_binaries.bat:
	  Corrected initial version.

	* [r3584] external/mswin/for_binaries,
	  external/mswin/for_binaries/README.txt,
	  external/mswin/for_binaries/prepare_for_binaries.bat,
	  external/mswin/for_binaries/setup.bat,
	  external/mswin/for_binaries/topographica.iss:
	  Initial version.

	* [r3583] external/mswin/README.txt:
	  Initial version to describe files in this directory.

	* [r3582] setup.bat:
	  Added a comment.

2006-05-16  jbednar

	* [r3581] etc/toporoot:
	  Fixed usage info

2006-05-16  ceball

	* [r3580] topo/base/simulation.py:
	  Changed time to a 4 d.p. (FixedPoint) number.

	* [r3579] topo/tests/lissom_or_reference.ty:
	  Made input pattern properties be set on an object, rather than on
	  the whole Gaussian class.

	* [r3578] topo/base/simulation.py:
	  Re-enabled the repr method of EPConnectionEvent, now that
	  ParameterizedObject's get_param_values() does not generate a new
	  DynamicNumber.

	* [r3577] topo/base/parameterizedobject.py:
	  Added a hack to get_param_values to avoid generating new
	  DynamicNumbers.

	* [r3576] topo/base/parameterclasses.py:
	  Added 'last_value' to DynamicNumber, for storing the last value
	  that was generated.

	* [r3575] topo/base/parameterizedobject.py:
	  Simplified get_param_values(); I think it still does the same
	  thing.

	* [r3574] topo/base/simulation.py:
	  Commented out EPConnectionEvent's repr method, because it was
	  causing new DynamicNumbers to be generated. Added HACKALERT.

2006-05-15  ceball

	* [r3573] topo/tests/lissom_oo_or_reference.ty,
	  topo/tests/lissom_or_reference.ty:
	  Set GeneratorSheet.phase after changes to Simulation.run().

	* [r3572] topo/base/simulation.py:
	  Added repr() methods to CommandEvent and EPConnectionEvent so
	  that printing for debugging is easier.

2006-05-15  jbednar

	* [r3571] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/homeostatic.ty,
	  examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/tiny.ty,
	  topo/base/simulation.py:
	  Changed Simulation.run() to complete all events at the stop time,
	  rather than stopping before the stop time. Shouldn't affect any
	  long-term simulation results, but scripts have to change
	  GeneratorSheet.phase to be nonzero so that the plots make sense
	  at even multiples of the period

2006-05-15  ceball

	* [r3570] topo/base/projection.py,
	  topo/base/simulation.py,
	  topo/eps/basic.py,
	  topo/sheets/composer.py,
	  topo/sheets/lissom.py:
	  Renamed pre_sleep() to process_current_time().

	* [r3569] topo/base/simulation.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testsimulation.py:
	  Removed unimplemented step_mode.

	* [r3568] topo/base/simulator.py:
	  Renamed to simulation.py

	* [r3567] topo/base/simulation.py:
	  Updated some ALERTs.

	* [r3566] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3565] examples/laminar.ty,
	  examples/laminar_nolearning.ty,
	  examples/som_retinotopy.ty,
	  examples/tiny.ty:
	  Uses UniformRandom instead of RandomWrapper.

	* [r3564] examples/homeostatic.ty,
	  examples/laminar_lissom.ty,
	  examples/obermayer_pnas90.ty:
	  Uses UniformRandom instead of RandomWrapper.

	* [r3563] examples/lissom_or_sf.ty:
	  Uses UniformRandom instead of RandomWrapper.

	* [r3562] examples/hierarchical.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty:
	  Reverted orientation's seed to previous value (changed
	  accidentally in previous commit.

	* [r3561] examples/cfsom_or.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty:
	  Uses UniformRandom instead of RandomWrapper.

	* [r3560] topo/base/simulation.py,
	  topo/base/simulator.py,
	  topo/eps/basic.py,
	  topo/sheets/generatorsheet.py:
	  Renamed enqueue_event_abs() to enqueue_event().

	* [r3559] topo/base/simulation.py,
	  topo/eps/basic.py,
	  topo/sheets/generatorsheet.py:
	  Events are first created, and then are passed to Simulation's
	  enqueue_event_abs().

	* [r3558] topo/base/simulation.py:
	  schedule_command() is always for an absolute time.

	* [r3557] topo/base/simulation.py:
	  Removed sleep(), sleep_window, and sleep_window_violation.

	* [r3556] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3555] topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/projections/basic.py,
	  topo/responsefns/basic.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py:
	  Renamed Mdot to DotProduct.

	* [r3554] topo/base/connectionfield.py:
	  Renamed to cf.py

	* [r3553] doc/Future_Work/current_text.php:
	  Updated tasks.

	* [r3552] topo/tkgui/propertiesframe.py:
	  Added HACKALERT about binding return key to combobox widget.

	* [r3551] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3550] examples/hierarchical.ty:
	  Uses UniformRandom rather than RandomWrapper.

	* [r3549] topo/tkgui/editortools.py:
	  Missing code from previous commit.

	* [r3548] topo/tkgui/editortools.py,
	  topo/tkgui/parametersframe.py:
	  Allow name to be set on the class but not on an existing object.

	* [r3547] topo/base/parameterizedobject.py:
	  'name' parameter is no longer hidden.

2006-05-15  jbednar

	* [r3546] topo/tests/testsimulator.py:
	  Removed old filename of testsimulation.py

2006-05-14  ceball

	* [r3545] topo/base/parameterizedobject.py:
	  Removed unnecessary deletion of 'initialized' attribute.

	* [r3544] topo/misc/numbergenerators.py:
	  Corrected mistake.

2006-05-14  jbednar

	* [r3543] topo/commands/basic.py,
	  topo/commands/pylabplots.py:
	  Fixed broken topographic grid plots; had not been updated fully
	  for topo.sim

	* [r3542] examples/lissom_oo_or.ty:
	  Fixed typo

	* [r3541] examples/cfsom_or.ty:
	  Added missing simulation name

	* [r3540] doc/Downloads/index_text.php:
	  Enabled note about CVS status page

	* [r3539] topo/base/boundingregion.py,
	  topo/base/cf.py:
	  Added inclusive comparison for bounding boxes to prevent bogus
	  warning for change_bounds

	* [r3538] doc/Future_Work/current_text.php:
	  Added task for Chris

2006-05-14  ceball

	* [r3537] topo/tkgui/parametersframe.py:
	  Added a HACKALERT.

	* [r3536] topo/tests/testsimulation.py:
	  Made the test slightly more realistic to allow stronger argument
	  checking in EPConnectionEvent. [jbednar]

	* [r3535] topo/tests/testsimulation.py:
	  Renamed EPEvent to EPConnectionEvent.

	* [r3534] topo/sheets/generatorsheet.py:
	  Removed Simulator's enqueue_epevent_rel(); an EPConnectionEvent
	  can be created first then passed to Simulator's
	  enqueue_event_rel().

	* [r3533] topo/sheets/composer.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testsimulation.py:
	  EPEvent stores conn so no need to pass all of conn's attributes
	  too.

	* [r3532] topo/sheets/composer.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testsimulation.py:
	  Intermediate checkin (further cleaning to follow). EPEvent stores
	  the connection. This allows ProjectionSheet to activate the
	  correct connection. The performance of a LISSOM sheet is now back
	  to 19 February speed (i.e. approximately twice as fast as it has
	  been recently).

	* [r3531] topo/base/simulation.py:
	  Cleaned up comments, documentation, and alerts. Changed to
	  require that input_event is implemented by any subclass.
	  [jbednar]

	* [r3530] topo/base/simulation.py:
	  Simplified Simulator.connection().

	* [r3529] topo/base/simulation.py:
	  EventProcessor's in_connections must each have a unique name.

	* [r3528] topo/base/simulation.py:
	  Removed a HACKALERT.

	* [r3527] topo/base/projection.py:
	  Fixed typo in commennt

	* [r3526] topo/base/projection.py:
	  No longer check for unique names of Projections because
	  EventProcessor checks all connections have unique names. Added
	  HACKALERT about having separate list of in_projections.

	* [r3525] topo/base/cf.py:
	  Minor fix to comment

	* [r3524] examples/lissom_or_sf.ty:
	  Switched to use optimized response function for
	  SharedWeightCFProjection.

	* [r3523] topo/base/simulation.py:
	  Removed Simulator's enqueue_epevent_rel(); an EPConnectionEvent
	  can be created first then passed to Simulator's
	  enqueue_event_rel().

	* [r3522] topo/base/simulation.py:
	  Renamed EPEvent to EPConnectionEvent.

	* [r3521] topo/base/projection.py,
	  topo/base/simulation.py:
	  EPEvent stores conn so no need to pass all of conn's attributes
	  too.

	* [r3520] topo/base/projection.py,
	  topo/base/simulation.py:
	  Intermediate checkin (further cleaning to follow). EPEvent stores
	  the connection. This allows ProjectionSheet to activate the
	  correct connection. The performance of a LISSOM sheet is now back
	  to 19 February speed (i.e. approximately twice as fast as it has
	  been recently).

	* [r3519] topo/eps/basic.py:
	  Removed Simulator's enqueue_epevent_rel(); an EPConnectionEvent
	  can be created first then passed to Simulator's
	  enqueue_event_rel().

	* [r3518] topo/eps/basic.py:
	  PulseGenerator must have period>0. EPEvent stores conn so no need
	  to pass all of conn's attributes too.

	* [r3517] topo/eps/basic.py:
	  Intermediate checkin (further cleaning to follow). EPEvent stores
	  the connection. This allows ProjectionSheet to activate the
	  correct connection. The performance of a LISSOM sheet is now back
	  to 19 February speed (i.e. approximately twice as fast as it has
	  been recently).

	* [r3516] topo/base/simulation.py:
	  Fixed typo in SimSingleton.__str__; couldn't have been working.
	  Cleaned up docs and comments, and added ALERTs. [jbednar]

	* [r3515] topo/base/utils.py:
	  Removed empty file.

	* [r3514] topo/base/utils.py:
	  Moved find_classes_in_package() to parameterclasses.py.

2006-05-12  jbednar

	* [r3513] etc/toporoot:
	  Initial version

	* [r3512] Makefile:
	  Updated in preparation for new release

	* [r3511] doc/Tutorials/index_text.php:
	  Trivial update to test CVS

2006-05-07  ceball

	* [r3510] doc/Future_Work/current_text.php:
	  Added another task.

	* [r3509] doc/Future_Work/current_text.php:
	  Added a task.

	* [r3508] doc/Future_Work/current_text.php:
	  Made corrections to previous commit.

	* [r3507] doc/Future_Work/current_text.php:
	  Updated tasks.

2006-05-06  ceball

	* [r3506] examples/lissom_oo_or.ty:
	  Uses c++ response function. Now runs 3.5 times faster than
	  before.

	* [r3505] topo/tests/lissom_oo_or_reference.ty:
	  Uses c++ shared weight response function.

	* [r3504] topo/responsefns/optimized.py:
	  Added SharedWeightCFPDotProduct_opt1, as a speedier replacement
	  for SharedWeightCFPResponseFn(single_cf_fn=Mdot()). Also added
	  untested DotProduct_op1, Mdot in C++; it's not used anywhere, we
	  might just remove it.

	* [r3503] topo/projections/basic.py:
	  SharedWeightCFProjection needs to wrap its cfs list in a better
	  way, so we don't need separate response fns etc. But for now,
	  I've done this enough to allow a C++ replacement of the shared
	  weight response fn, which we badly need to improve performance.

	* [r3502] doc/Future_Work/current_text.php:
	  Updated tasks.

	* [r3501] topo/base/sheet.py:
	  Altered HACKALERT.

	* [r3500] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/homeostatic.ty,
	  examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/tiny.ty,
	  topo/base/cf.py,
	  topo/projections/basic.py,
	  topo/tests/lissom_oo_or_reference.ty,
	  topo/tests/lissom_or_reference.ty,
	  topo/tests/testlissom.ty,
	  topo/tkgui/editorobjects.py:
	  CFProjection has nominal_bounds_template parameter, and
	  bounds_template attribute.

2006-05-06  jbednar

	* [r3499] ChangeLog.txt:
	  Updated with recent changes

2006-05-05  ceball

	* [r3498] topo/base/sheetcoords.py:
	  Added comment (from JAB) about 'bounds-master' vs
	  'density-master' approaches.

	* [r3497] doc/User_Manual/space_text.php:
	  Initial attempt at describing 'bounds-master' approach to Sheet
	  bounds/density.

	* [r3496] topo/base/simulation.py:
	  Made the saved_commands Simulation Parameter be instantiated
	  (it's specific to one Simulation object); this isn't very
	  important since most users will not have more than one
	  Simulation. Removed two HACKALERTs.

	* [r3495] topo/base/simulation.py,
	  topo/eps/basic.py,
	  topo/sheets/generatorsheet.py:
	  Cleaned up enqueue_event* methods. This could probably be
	  simplified further. Events must have a time.

	* [r3494] topo/base/simulation.py:
	  Cleaned up a little.

	* [r3493] topo/base/simulation.py,
	  topo/commands/pylabplots.py:
	  Removed get_active_sim().

	* [r3492] topo/base/sheet.py:
	  Updates to docstrings and comments.

	* [r3491] topo/base/sheet.py,
	  topo/base/sheetcoords.py:
	  Simplified creation of SheetCoordinateSystem.

	* [r3490] topo/base/sheetcoords.py:
	  Updated file's docstring.

	* [r3489] topo/base/cf.py:
	  Removed outdated HACKALERT.

	* [r3488] topo/base/parameterclasses.py,
	  topo/tkgui/editortools.py:
	  Moved find_classes_in_package() to parameterclasses.py.

	* [r3487] topo/base/__init__.py:
	  Updated __all__.

	* [r3486] topo/misc/tyimputil.py:
	  Corrected HACKALERT.

	* [r3485] topo/base/arrayutils.py:
	  Added HACKALERT about savespace and .flat/ravel(), with a note
	  about upgrading Numeric and a link to Numeric's convertcode.py.

	* [r3484] topo/base/arrayutils.py,
	  topo/base/functionfamilies.py:
	  Removed mdot() function - there is the Mdot ResponseFn in
	  topo.responsefns.basic. Moved comment about weave.blitz from mdot
	  to Mdot.

	* [r3483] topo/base/arrayutils.py:
	  Removed unused and potentially misleading msum() function.

2006-05-04  ceball

	* [r3482] topo/patterns/basic.py:
	  PatternSampler (and hence CompositePatternGenerator and Image) is
	  based on SheetCoordinateSystem with an activity matrix, rather
	  than on Sheet.

	* [r3481] topo/tests/lissom_or_reference.ty:
	  Corrected learning rates, added missing scheduled action, and
	  commented out final weights bounds change.

	* [r3480] topo/tests/lissom_oo_or_reference.ty:
	  Updated for recent changes to code.

	* [r3479] doc/Downloads/index_text.php:
	  Added commented-out section (for JAB to decide whether or not
	  it's worthwhile to include) about problems with cvs, with a link
	  to SourceForge's status page.

	* [r3478] topo/tests/lissom_or_reference.ty:
	  Adjusted times which I'd changed by mistake earlier. Altered some
	  comments. Appears to match c++ lissom after 201 iterations (i.e.
	  after the first set of scheduled actions).

	* [r3477] topo/tests/lissom_or_reference.ty:
	  Corrected mistake left in previous version by mistake.

	* [r3476] topo/tests/lissom_or_reference.ty:
	  Forget to divide min_exc_rad by BaseN.

	* [r3475] topo/base/sheet.py:
	  Update to a comment.

	* [r3474] topo/base/sheet.py,
	  topo/base/sheetcoords.py:
	  Moved HACKALERT from sheetcoords to sheet.

	* [r3473] topo/base/sheetcoords.py:
	  Updated HACKALERT.

	* [r3472] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/homeostatic.ty,
	  examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/tiny.ty,
	  topo/base/cf.py,
	  topo/projections/basic.py,
	  topo/tests/lissom_oo_or_reference.ty,
	  topo/tests/lissom_or_reference.ty,
	  topo/tests/testlissom.ty:
	  For a CFProjection, users specify the BoundingRegionParameter
	  user_weights_bounds. The actual weights_bounds are stored in the
	  attribute weights_bounds.

	* [r3471] topo/tests/lissom_or_reference.ty:
	  Added min_exc_rad.

	* [r3470] topo/misc/tyimputil.py:
	  Updated HACKALERT (ty files no longer get compiled to typ).

	* [r3469] topo/tests/lissom_or_reference.ty:
	  Updated learning rates.

2006-05-04  jbednar

	* [r3468] topo/base/simulation.py:
	  Added alert

	* [r3467] topo/base/projection.py:
	  Fixed trivial typo on doc

	* [r3466] doc/shared/trailer.php:
	  Fixed web pages to show the date the page was generated, not a
	  fixed date from 2005

2006-05-04  ceball

	* [r3465] topo/tests/lissom_oo_or_reference.ty:
	  Corrected mistake in previous commit.

2006-05-04  jbednar

	* [r3464] topo/tkgui/parametersframe.py:
	  Added titles for ParametersFrame windows

2006-05-04  ceball

	* [r3463] topo/tests/lissom_or_reference.ty:
	  Finished previous update.

2006-05-04  jbednar

	* [r3462] topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py:
	  Added titles for ParametersFrame windows

2006-05-04  ceball

	* [r3461] topo/tests/lissom_or_reference.ty:
	  Updated for recent changes to code.

	* [r3460] doc/Future_Work/current_text.php:
	  Updated tasks.

	* [r3459] topo/tkgui/editortools.py:
	  For editing sheet and projection classes, a new window opens.
	  This at least makes the model editor ok for creating sheets and
	  projections.

	* [r3458] doc/Future_Work/current_text.php:
	  Updates to tasks.

	* [r3457] topo/tkgui/parametersframe.py:
	  Removed unused method.

	* [r3456] topo/tkgui/parametersframe.py:
	  Change to variable name.

	* [r3455] topo/tkgui/parametersframe.py:
	  Added back a modified version of dict_translator use for
	  add_text_property().

	* [r3454] topo/misc/utils.py:
	  Added comment.

	* [r3453] topo/tkgui/translatorwidgets.py:
	  Minor change to comment.

2006-05-03  ceball

	* [r3452] topo/tkgui/parametersframe.py:
	  Minor changes to notes.

	* [r3451] topo/tkgui/parametersframe.py:
	  Removed some commented-out code about DynamicNumber. If
	  DynamicNumbers display strangely in ParametersFrames, then it
	  might be because I commented out this code before - so it may be
	  necessary to restore it. For now, though, I don't remember what
	  it was for.

	* [r3450] topo/tkgui/parametersframe.py:
	  Tidied imports.

	* [r3449] topo/tkgui/parametersframe.py:
	  Minor cleanup, with some reminders for myself.

	* [r3448] topo/tkgui/parametersframe.py:
	  Still cleaning: simplified widget creation, corrected some
	  mistakes.

	* [r3447] topo/tkgui/parametersframe.py:
	  Continued cleaning...

	* [r3446] topo/tkgui/editortools.py:
	  Only ask ParametersFrame to make widgets if something has been
	  selected.

	* [r3445] topo/tkgui/editorobjects.py,
	  topo/tkgui/parametersframe.py:
	  Intermediate checkin. Model editor can now set all parameters on
	  sheet and projection classes before they're instantiated. Not
	  fully tested, not finished, and might be a regression in some
	  areas.

	* [r3444] topo/misc/utils.py:
	  Removed some string translation functions.

	* [r3443] topo/tkgui/propertiesframe.py,
	  topo/tkgui/translatorwidgets.py:
	  Renamed taggedslider.py to translatorwidgets.py.

	* [r3442] examples/homeostatic.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or_sf.ty,
	  topo/base/cf.py,
	  topo/commands/analysis.py,
	  topo/projections/basic.py,
	  topo/tests/lissom_oo_or_reference.ty:
	  Renamed SharedWeightProjection to SharedWeightCFProjection, as
	  well as the corresponding response and output functions.

	* [r3441] examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  topo/learningfns/optimized.py,
	  topo/tests/lissom_oo_or_reference.ty,
	  topo/tests/lissom_or_reference.ty:
	  Renamed CFProjectionHebbian to CFPHebbian (along with _opt1
	  version).

	* [r3440] examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  topo/outputfns/optimized.py,
	  topo/tests/lissom_oo_or_reference.ty,
	  topo/tests/lissom_or_reference.ty:
	  Renamed CFProjectionDivisiveSumNormalize to
	  CFPDivisiveSumNormalize (along with _opt1 version).

	* [r3439] examples/som_retinotopy.ty,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py:
	  Renamed CFProjectionEuclideanDistance to CFPEuclideanDistance
	  (along with _opt1 version).

	* [r3438] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/laminar.ty,
	  examples/laminar_lissom.ty,
	  examples/laminar_nolearning.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  examples/tiny.ty,
	  topo/misc/utils.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py,
	  topo/tests/lissom_oo_or_reference.ty,
	  topo/tests/lissom_or_reference.ty,
	  topo/tests/testplotgroup.py:
	  Renamed CFProjectionDotProduct to CFPDotProduct (and the _opt1
	  version).

2006-05-03  jbednar

	* [r3437] topo/tests/testsimulation.py:
	  Moved testsimulator.py to testsimulation.py

	* [r3436] topo/__init__.py,
	  topo/base/__init__.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/commands/pylabplots.py,
	  topo/eps/basic.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testplotgrouppanel.py,
	  topo/tests/testsheetview.py,
	  topo/tests/testsnapshots.py,
	  topo/tests/testtemplateplotgrouppanel.py,
	  topo/tests/testtopoconsole.py,
	  topo/tkgui/topoconsole.py:
	  Moved topo.base.simulator to topo.base.simulation

	* [r3435] topo/base/simulation.py:
	  Moved topo/base/simulator.py to topo/base/simulation.py

	* [r3434] topo/tkgui/testpattern.py:
	  Added missing import

	* [r3433] topo/plotting/plotgroup.py:
	  Added hack to work around problem with reducing integer
	  coordinates in the Test Pattern window

	* [r3432] topo/base/arrayutils.py:
	  Removed apparently outdated comments

	* [r3431] ChangeLog.txt:
	  Updated with recent changes

2006-05-03  julienciroux

	* [r3430] topo/plotting/plotgroup.py,
	  topo/tkgui/testpattern.py:
	  Improved TestPattern so that the reduce, enlarge and sheetcoords
	  button ar working. There is still a problem remaining for
	  integerscaling button: when it is on, and that we try to reduce,
	  we obtain a Division by Zero error.

2006-05-03  ceball

	* [r3429] topo/base/parameterizedobject.py:
	  Removed unused function and the HACKALERT about it.

	* [r3428] topo/base/parameterizedobject.py:
	  Added method to return parameters of a
	  ParameterizedObjectMetaClass. The object method now just calls
	  this method.

2006-05-03  jbednar

	* [r3427] topo/misc/utils.py:
	  Added alert

2006-05-03  ceball

	* [r3426] topo/tkgui/parametersframe.py:
	  Added HACKALERT.

2006-05-02  ceball

	* [r3425] topo/base/sheet.py:
	  Set density back to being a Number; it should only ever be a
	  number.

	* [r3424] topo/base/sheetcoords.py:
	  No visible change - removed duplicate brackets.

	* [r3423] examples/cfsom_or.ty,
	  examples/homeostatic.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/tiny.ty:
	  Removed unused import statement.

	* [r3422] examples/hierarchical.ty:
	  Removed an import statement that's not currently used.

	* [r3421] topo/learningfns/__init__.py,
	  topo/outputfns/__init__.py,
	  topo/patterns/__init__.py,
	  topo/responsefns/__init__.py,
	  topo/tkgui/__init__.py:
	  Now the GUI imports all outputfns, patterns, and responsefns
	  (rather than having a function to allow this in all the separate
	  packages). Also populates the appropriate ClassSelectorParameter
	  lists.

2006-05-02  jbednar

	* [r3420] topo/tkgui/topoconsole.py:
	  Removed unused variable

	* [r3419] topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py:
	  Renamed self.canvas.simulator to self.canvas.simulation

	* [r3418] topo/base/simulator.py,
	  topo/commands/__init__.py,
	  topo/commands/analysis.py,
	  topo/commands/basic.py,
	  topo/eps/__init__.py,
	  topo/eps/basic.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/generatorsheet.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testsheetview.py,
	  topo/tests/testsimulator.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py:
	  Renamed self.simulator link for EPs to self.simulation, plus
	  other instances of the word simulator in documentation and
	  comments

	* [r3417] examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  topo/__init__.py,
	  topo/base/projection.py,
	  topo/base/simulator.py:
	  Renamed self.simulator link for EPs to self.simulation, plus
	  other instances of the word simulator in documentation and
	  comments

2006-05-02  judelaw

	* [r3416] examples/laminar.ty:
	  Work in progress - Changed Lateral Excitatory projection to be
	  one single projection with initial gaussian weights

	* [r3415] examples/laminar_nolearning.ty:
	  Work in progress - contains 2 separate, initially random lateral
	  excitatory projections - only works for case with afferent
	  learning or excitatory learning only

	* [r3414] examples/laminar_lissom.ty:
	  Version of Lissom_or with separate excitatory and inhibitory
	  layers

2006-05-02  ceball

	* [r3413] topo/patterns/__init__.py:
	  Removed outdated HACKALERT.

	* [r3412] doc/Future_Work/current_text.php:
	  Added long-term task of upgrading Numeric.

	* [r3411] topo/base/boundingregion.py:
	  Override __str__() so that the bounds are displayed when printing
	  a BoundingBox.

2006-05-02  jbednar

	* [r3410] topo/base/simulator.py:
	  Renamed Simulator to Simulation

	* [r3409] topo/analysis/featuremap.py,
	  topo/commands/__init__.py,
	  topo/eps/__init__.py,
	  topo/plotting/templates.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testplotgrouppanel.py,
	  topo/tests/testsimulator.py,
	  topo/tests/testsnapshots.py,
	  topo/tests/testtemplateplotgrouppanel.py,
	  topo/tests/testtopoconsole.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py:
	  Renamed Simulator to Simulation

	* [r3408] topo/base/simulator.py:
	  Temporary: Simulation is an alias for Simulator

2006-05-02  ceball

	* [r3407] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionpanel.py:
	  Renamed topo/base/connectionfield.py to topo/base/cf.py.

2006-05-02  jbednar

	* [r3406] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/obermayer_pnas90.ty,
	  examples/tiny.ty:
	  Removed unused import

2006-05-02  ceball

	* [r3405] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3404] topo/base/cf.py:
	  IdentityCFLearningFn has single_cf_fn=IdentityLF.

	* [r3403] topo/base/functionfamilies.py:
	  Added IdentityLF.

	* [r3402] doc/Future_Work/current_text.php:
	  Removed a task, and split up another.

	* [r3401] topo/projections/basic.py:
	  Renamed SharedWeightOutputFn and SharedWeightResponseFn to
	  SWPOutputFn and SWPResponseFn. These names might be a bit
	  cryptic, but for now they are only used in this file.

	* [r3400] examples/homeostatic.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or_sf.ty,
	  topo/projections/basic.py,
	  topo/tests/lissom_oo_or_reference.ty:
	  Renamed SharedCFProjection to SharedWeightProjection.

	* [r3399] topo/base/patterngenerator.py,
	  topo/base/sheet.py,
	  topo/patterns/random.py,
	  topo/plotting/plot.py,
	  topo/tests/testsheet.py:
	  Moved SheetCoordinateSystem to sheetcoords.py.

	* [r3398] topo/base/sheetcoords.py:
	  Initial version. SheetCoordinateSystem from sheet.py.

	* [r3397] topo/base/cf.py,
	  topo/base/patterngenerator.py,
	  topo/base/sheet.py,
	  topo/patterns/random.py,
	  topo/plotting/plot.py,
	  topo/tests/testsheet.py:
	  Renamed CoordinateTransformer to SheetCoordinateSystem.

	* [r3396] topo/tests/testimage.py:
	  Commented out a test (with an explanation).

	* [r3395] doc/Future_Work/current_text.php:
	  Update to tasks.

	* [r3394] doc/Future_Work/current_text.php:
	  Moved a task.

	* [r3393] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3392] topo/tkgui/editortools.py:
	  Updated how sheet is added to simulator.

	* [r3391] examples/lissom_or_sf.ty:
	  Import BoundingBox as a Simulator startup action.

2006-05-01  ceball

	* [r3390] doc/Future_Work/current_text.php:
	  Removed a stub. I hope it wasn't about to become an important
	  task because I've forgotten what it was...

	* [r3389] doc/Future_Work/current_text.php:
	  Restored some text I cut by mistake.

	* [r3388] doc/Future_Work/current_text.php:
	  Updated the task orderings and split some of them up.

	* [r3387] doc/Future_Work/current_text.php:
	  Updated a task.

	* [r3386] topo/base/cf.py,
	  topo/projections/basic.py:
	  Renamed CFProjectionIdentityOutputFn to IdentityCFPOutputFn.

	* [r3385] examples/tiny.ty,
	  topo/base/cf.py,
	  topo/outputfns/optimized.py,
	  topo/outputfns/projfns.py:
	  Renamed CFProjectionGenericOutputFn to GenericCFPOutputFn.

	* [r3384] topo/base/cf.py,
	  topo/outputfns/optimized.py,
	  topo/projections/basic.py:
	  Renamed CFProjectionOutputFn to CFPOutputFn.

	* [r3383] examples/tiny.ty,
	  topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/learningfns/optimized.py,
	  topo/learningfns/projfns.py:
	  Renamed CFProjectionGenericLearningFn to GenericCFPLearningFn.

	* [r3382] topo/base/cf.py,
	  topo/projections/basic.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py:
	  Renamed CFProjectionResponseFn to CFPResponseFn.

	* [r3381] topo/base/cf.py,
	  topo/learningfns/projfns.py,
	  topo/projections/basic.py:
	  Renamed CFProjectionIdentityLearningFn to IdentityCFPLearningFn.

	* [r3380] topo/base/cf.py,
	  topo/learningfns/__init__.py,
	  topo/learningfns/optimized.py,
	  topo/learningfns/som.py,
	  topo/projections/basic.py:
	  Renamed CFProjectionLearningFn and
	  CFProjectionLearningFnParameter to CFPLearningFn and
	  CFPLearningFnParameter, respectively.

	* [r3379] topo/base/cf.py,
	  topo/base/functionfamilies.py,
	  topo/projections/basic.py,
	  topo/responsefns/__init__.py,
	  topo/responsefns/projfns.py:
	  Renamed CFProjectionGenericResponseFn to GenericCFPResponseFn.
	  Renamed CFProjectionResponseFnParameter to
	  CFPResponseFnParameter.

	* [r3378] doc/Future_Work/current_text.php:
	  Updated a task.

	* [r3377] topo/base/cf.py:
	  Renamed connectionfield.py to cf.py.

	* [r3376] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/homeostatic.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/tiny.ty,
	  topo/commands/analysis.py,
	  topo/learningfns/__init__.py,
	  topo/learningfns/optimized.py,
	  topo/learningfns/projfns.py,
	  topo/learningfns/som.py,
	  topo/misc/utils.py,
	  topo/outputfns/optimized.py,
	  topo/outputfns/projfns.py,
	  topo/plotting/plotgroup.py,
	  topo/projections/basic.py,
	  topo/responsefns/__init__.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/lissom.py,
	  topo/tests/lissom_oo_or_reference.ty,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testsnapshots.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionpanel.py:
	  Renamed connectionfield.py to cf.py

	* [r3375] doc/Future_Work/current_text.php:
	  Updated a task.

	* [r3374] topo/base/functionfamilies.py,
	  topo/responsefns/basic.py,
	  topo/responsefns/optimized.py,
	  topo/responsefns/projfns.py:
	  Moved ResponseFnParameter, Mdot, and ResponseFn to
	  functionfamilies.

	* [r3373] topo/learningfns/optimized.py:
	  Removed imports of unused classes - the optimized module just has
	  the optimized classes, and any it needs to use as fall-backs.

	* [r3372] topo/base/functionfamilies.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py:
	  Moved LearningFn, LearningFnParameter, and Hebbian to
	  functionfamilies.py.

	* [r3371] doc/Future_Work/current_text.php:
	  Removed a task.

	* [r3370] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/homeostatic.ty,
	  examples/laminar.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/tiny.ty,
	  topo/base/simulator.py,
	  topo/eps/basic.py,
	  topo/sheets/composer.py,
	  topo/sheets/generatorsheet.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotgrouppanel.py,
	  topo/tests/testsimulator.py,
	  topo/tests/testsnapshots.py,
	  topo/tkgui/editortools.py:
	  Renamed Simulator's connect2() to connect().

	* [r3369]
	  topo/tests/testtemplateplotgrouppanel.py:
	  Added a HACKALERT and commented some code.

	* [r3368] topo/base/simulator.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotgrouppanel.py,
	  topo/tests/testsimulator.py:
	  Uses Simulator's connect2() instead of connect().

	* [r3367] topo/tests/testcfsom.py:
	  Uses Simulator's connect2() instead of connect().

	* [r3366] topo/tests/lissom_oo_or_reference.ty,
	  topo/tests/lissom_or_reference.ty:
	  Uses Simulator's connect2() instead of connect().

	* [r3365] topo/sheets/composer.py:
	  Update to doc string.

	* [r3364] topo/eps/basic.py,
	  topo/sheets/generatorsheet.py:
	  Uses Simulator's connect2() instead of connect().

	* [r3363] topo/tkgui/editortools.py:
	  Uses Simulator.connect2() rather than .connect(). Before this
	  change there was an error when making a connection.

	* [r3362] doc/Future_Work/current_text.php:
	  Added task about model editor. Removed schedule_action task.

	* [r3361] topo/base/simulator.py:
	  Removed schedule_action().

	* [r3360] examples/lissom_or_sf.ty:
	  Updated with changes to code, including topo.sim-style access,
	  and using schedule_command().

2006-05-01  jbednar

	* [r3359] examples/hierarchical.ty,
	  examples/homeostatic.ty,
	  examples/laminar.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/tiny.ty:
	  Added names for the simulations

	* [r3358] topo/commands/pylabplots.py:
	  Added control over window titles

2006-05-01  ceball

	* [r3357] examples/laminar.ty:
	  Changed to use topo.sim-style access to simulator. Tidied up.

	* [r3356] examples/homeostatic.ty:
	  Minor updates, including to use topo.sim rather than s.

	* [r3355] examples/som_retinotopy.ty:
	  Minor tidy.

	* [r3354] examples/cfsom_or.ty:
	  Minor clean up.

	* [r3353] examples/obermayer_pnas90.ty:
	  Tidied up file; uses 'topo.sim' rather than 's'.

	* [r3352] topo/base/simulator.py:
	  If a connection wasn't given a name, it defaults to 'srcTodest'
	  (e.g. 'RetinaToV1')

	* [r3351] doc/Future_Work/current_text.php:
	  Removed a task; added one to more long-term work.

	* [r3350] topo/base/connectionfield.py:
	  Corrected index order for accessing a list.

	* [r3349] topo/misc/tyimputil.py:
	  Added HACKALERT.

	* [r3348] examples/obermayer_pnas90.ty:
	  Added import of pi; minor reformating of comments.

	* [r3347] topo/commands/basic.py:
	  Minor update to comment.

	* [r3346] topo/commands/basic.py:
	  Warns if there are classes or functions around that were defined
	  in __main__, since the source won't be found on unpickling.

2006-04-30  ceball

	* [r3345] doc/Future_Work/current_text.php:
	  Updated a task.

	* [r3344] examples/obermayer_pnas90.ty:
	  Input pattern parameters are set on a Gaussian object rather than
	  on the Gaussian class.

	* [r3343] topo/sheets/generatorsheet.py:
	  Added a HACKALERT about the input_generator bounds.

	* [r3342] examples/tiny.ty:
	  Uses RandomWrapper with separate seed for each stream of number.
	  Minor tidy.

	* [r3341] examples/lissom_or.ty:
	  Changed to use topo.sim['V1']-style access to simulator.
	  Scheduled actions changed to strings.

	* [r3340] examples/lissom_or.ty:
	  Finished previous minor cleanup.

	* [r3339] examples/lissom_or.ty:
	  Minor cleanup. Removed commented-out code (it was confusing).

	* [r3338] doc/Future_Work/current_text.php:
	  Corrected date.

	* [r3337] doc/Future_Work/current_text.php:
	  Added task.

	* [r3336] examples/hierarchical.ty:
	  Updated input pattern to use RandomWrapper and have a separate
	  seed for each stream of random numbers.

	* [r3335] examples/cfsom_or.ty:
	  Updated input pattern to use RandomWrapper, have a separate seed
	  for each stream of random number, and not set softbounds.

	* [r3334] topo/base/sheet.py:
	  Sheet cannot be created with unequal densities.

	* [r3333] doc/Future_Work/current_text.php:
	  Removed and updated some tasks.

2006-04-28  ceball

	* [r3332] topo/tests/lissom_oo_or_reference.ty:
	  Minor updates to commented-out code. Also set afferent
	  connections strengths to 0.5 each.

	* [r3331] topo/tests/lissom_oo_or_reference.ty:
	  Removed some commented-out code.

	* [r3330] topo/tests/lissom_oo_or_reference.ty:
	  Added commented-out code for using Composite for center/surround,
	  rather than two projections.

	* [r3329] topo/tests/lissom_oo_or_reference.ty:
	  Updated to work with current classes.

	* [r3328] topo/base/boundingregion.py:
	  Added reminder that someone should make BoundingRegion display
	  something useful (like the bounds...) when it's printed.

	* [r3327] doc/Future_Work/current_text.php:
	  Added task.

	* [r3326] topo/patterns/basic.py:
	  Corrected mistake in Composite; now works again for weights
	  generation.

	* [r3325] doc/Future_Work/current_text.php:
	  Removed erroneous statement in one of the tasks.

	* [r3324] topo/base/connectionfield.py:
	  Changed CFProjection.initialize_bounds() so that it avoids
	  floating-point representation difficulties. Specifically, it uses
	  bounds2slice() to get the right and bottom values of the slice,
	  then mirrors these about the center of the slice to get the left
	  and top values - ensuring the slice is odd. Updated
	  CF.offset_bounds() so that it does not assume the bounds it
	  receives are centered at (0,0) on the Sheet. These alterations
	  could affect the behaviour of existing networks; the reference
	  simulations show no change.

	* [r3323] topo/base/sheet.py:
	  Made set_slice be available outside the Slice class, temporarily.

	* [r3322] topo/base/boundingregion.py:
	  Added method to BoundingBox that results the coordinates of the
	  center of the bounds.

	* [r3321] topo/tests/testsheet.py:
	  Commented out test of bounds2slice() that fails because of the
	  floating point representation of these particular bounds.

	* [r3320] topo/base/connectionfield.py:
	  Raises a ValueError if the weights matrix ends up with a
	  zero-sized dimension.

	* [r3319] topo/base/connectionfield.py:
	  Added assert statement (assert that the weights matrix is odd).

2006-04-28  jbednar

	* [r3318] topo/tkgui/testpattern.py:
	  Added ALERTs

	* [r3317] topo/tkgui/plotgrouppanel.py:
	  Minor clarification

	* [r3316] topo/tkgui/plotgrouppanel.py:
	  Added serious HACKALERT

2006-04-28  ceball

	* [r3315] topo/tests/testsheet.py:
	  Updated test.

2006-04-28  jbednar

	* [r3314] topo/tkgui/templateplotgrouppanel.py:
	  Fixed normalize option for ConnectionFieldPanel and
	  ProjectionPanel -- the button was on, but the plots weren't
	  normalized

	* [r3313] topo/tkgui/projectionpanel.py:
	  Fixed typo

	* [r3312] topo/tkgui/connectionfieldspanel.py:
	  Removed outdated ALERT

	* [r3311] topo/plotting/plotgroup.py:
	  Improved plot size calculation for projections; still needs work.
	  Cleaned up comments and documentation.

2006-04-27  ceball

	* [r3310] topo/tests/testsheet.py:
	  Added comment.

	* [r3309] topo/tests/testsheet.py:
	  Added another test of bounds2slice(), currenly failing.

	* [r3308] topo/base/connectionfield.py:
	  Removed the HACKALERT I just added; I was confused.

	* [r3307] topo/base/connectionfield.py:
	  Added HACKALERT about initialize_bounds().

	* [r3306] doc/Future_Work/current_text.php:
	  Updated a task.

	* [r3305] examples/lissom_oo_or.ty:
	  Changed to use 'topo.sim'-style access; tidied up a little.

	* [r3304] examples/lissom_oo_or.ty:
	  Switced to using RandomWrapper.

	* [r3303] topo/misc/numbergenerators.py:
	  Renamed RandomDistributionWrapper to RandomDistribution. Removed
	  a HACKALERT.

2006-04-27  jbednar

	* [r3302] topo/tkgui/testpattern.py:
	  Minor typo fixed

	* [r3301] topo/tkgui/editorobjects.py:
	  Made default CF representation be more useful

	* [r3300] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py:
	  Enforced minimum size on plots, so that no pixels are lost

2006-04-27  ceball

	* [r3299] topo/misc/numbergenerators.py:
	  Added hack to save state of random generators in RandomWrapper.

	* [r3298] examples/lissom_or.ty:
	  Moved RandomWrapper to topo.misc.numbergenerators.

	* [r3297] topo/base/parameterclasses.py:
	  Moved RandomWrapper to topo/misc/numbergenerators.py

	* [r3296] topo/misc/numbergenerators.py:
	  Renamed RandomWrapper to RandomDistributionWrapper. Moved
	  parameterclasses.py's RandomWrapper into this file.

	* [r3295] topo/misc/numbergenerators.py:
	  Initial version.

	* [r3294] topo/tkgui/testpattern.py:
	  Updated with changes to xdensity and ydensity for
	  PatternGenerator and Sheet.

	* [r3293] doc/Future_Work/current_text.php:
	  Added some tasks (including one for before release).

2006-04-26  ceball

	* [r3292] doc/Future_Work/current_text.php:
	  Re-inserted a task that got deleted some time back by accident
	  while rearranging the file.

	* [r3291] topo/tests/lissom_or_reference.ty:
	  Minor update to comment.

	* [r3290] topo/tests/lissom_or_reference.ty:
	  Updated learning rates (before bounds change).

	* [r3289] topo/base/connectionfield.py:
	  Changed CFProjection's initialize_bounds() to move the bounds to
	  the center of a unit before converting to a slice, thereby
	  guaranteeing an odd size for the slice.

	* [r3288] doc/Future_Work/current_text.php:
	  Updated a task.

	* [r3287] topo/base/parameterclasses.py:
	  Added note that random streams don't appear to be pickled such
	  that they resume where they left off.

	* [r3286] topo/base/connectionfield.py:
	  Added HACKALERT.

	* [r3285] topo/tests/lissom_or_reference.ty:
	  Updates to match changes to equivalen C++ lissom example.

	* [r3284] doc/Future_Work/current_text.php:
	  Removed a task! About pickling!

	* [r3283] examples/lissom_oo_or.ty:
	  Added startup command to allow V1 still to be referred to.

	* [r3282] topo/commands/basic.py:
	  Instead of pickle.Pickler and pickle.Unpickler, use our custom
	  Pickler and Unpickler.

	* [r3281] topo/misc/utils.py:
	  Added new Pickler and Unpickler, used at the moment to save array
	  savespace setting.

	* [r3280] topo/commands/basic.py:
	  No visible change: switched from using pickle's load() and dump()
	  functions to using pickle.Pickler and pickle.Unpickler objects
	  explicitly.

	* [r3279] topo/base/patterngenerator.py:
	  Removed unused import.

2006-04-25  ceball

	* [r3278] topo/misc/patternfns.py:
	  Added deliberate conversion of input to float, in case user
	  passes an int (for divisions)

2006-04-25  jbednar

	* [r3277] doc/Future_Work/current_text.php:
	  Updated slightly

2006-04-25  ceball

	* [r3276] doc/Future_Work/current_text.php:
	  Finished part of a task.

	* [r3275] topo/commands/basic.py:
	  Removed hack from load_snapshot().

	* [r3274] topo/misc/utils.py:
	  Set class attributes on true class rather than on the name we
	  might be using for a class.

2006-04-25  jbednar

	* [r3273] doc/Developer_Manual/coding_text.php,
	  doc/Developer_Manual/optimization_text.php,
	  doc/Reference_Manual/index_text.php:
	  Minor fixes and clarifications

	* [r3272] doc/User_Manual/images,
	  doc/User_Manual/images/.cvsignore:
	  Minor fix

2006-04-24  ceball

	* [r3271] doc/Future_Work/current_text.php:
	  Updated a task.

	* [r3270] topo/commands/basic.py:
	  Added a hack to avoid a problem with unpickling when Topographica
	  was pickled after falling back to non-optimized components.

	* [r3269] doc/Future_Work/current_text.php:
	  Added a task.

	* [r3268] topo/tests/testsimulator.py:
	  Updated test with new class name.

	* [r3267] examples/hierarchical.ty,
	  examples/lissom_oo_or.ty:
	  Adds a command to the simulator's startup_commands.

	* [r3266] topo/base/simulator.py,
	  topo/commands/basic.py:
	  Added startup_commands Parameter to Simulator. Altered
	  topo.commands.basic's save_snapshot() and load_snapshot() so that
	  these commands are executed before the simulator is unpickled.
	  Now scheduled actions can be pickled and unpickled without
	  difficulty.

	* [r3265] doc/Future_Work/current_text.php:
	  Added a task about correcting things causing pickling to fail.
	  Added task about adding a set of more in-depth tests, distinct
	  from the quick-to-run tests.

	* [r3264] doc/Future_Work/current_text.php:
	  Updated my tasks.

	* [r3263] doc/Future_Work/index_text.php:
	  Added commented-out optimistic update for pickling section.

	* [r3262] topo/commands/basic.py:
	  Added note for improvement to pickling.

	* [r3261] doc/Future_Work/index_text.php:
	  Updated section about different platforms.

	* [r3260] doc/Future_Work/current_text.php:
	  Updated my tasks, including marking those that need to be
	  completed before the next release.

	* [r3259] examples/lissom_oo_or.ty:
	  Changed to use schedule_command() instead of schedule_action().

	* [r3258] topo/base/simulator.py:
	  Added more helpful printing in the case of a SyntaxError for
	  CommandEvent.

	* [r3257] topo/base/simulator.py:
	  Added Event class, and EPEvent and CommandEvent subclasses (as
	  well as SAEVent class which will be removed when all uses of
	  schedule_action() in the examples are removed). There is one
	  change to the logic in Simulator.run(): now did_event is set to
	  True no matter what type of Event is called (rather than just for
	  SimulatorEvents without 'fn' attribute, as before). I don't think
	  this affects the behaviour.

2006-04-24  jbednar

	* [r3256] doc/User_Manual,
	  doc/User_Manual/.cvsignore,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/modeleditor_text.php:
	  Moved model_editor.html to modeleditor.php and added TOC link

	* [r3255] doc/User_Manual/model_editor.html:
	  Moved to model_editor_text.php

	* [r3254] doc/Future_Work/index_text.php:
	  Fixed stray comment ender that was giving garbage text at the end
	  of the page

	* [r3253] topo/base/connectionfield.py:
	  Clarified documentation

	* [r3252] doc/shared/index.php:
	  Added more keywords to title

2006-04-24  ceball

	* [r3251] examples/hierarchical.ty:
	  Changed scheduled action example to use schedule_command(), which
	  allows the network to be pickled before all the scheduled actions
	  have occurred.

	* [r3250] topo/base/simulator.py:
	  Added ScheduledCommand class and schedule_command() for exec'ing
	  an arbitrary string in __main__.__dict__ at a specified time.
	  Added some HACKALERTs (about scheduling commands).

	* [r3249] examples/hierarchical.ty:
	  Added an example scheduled action.

	* [r3248] topo/base/simulator.py:
	  Added comment. Added HACKALERT.

	* [r3247] topo/base/simulator.py:
	  Clarified a HACKALERT.

	* [r3246] topo/base/simulator.py:
	  Added HACKALERT about SimulatorEvent.

	* [r3245] topo/tests/lissom_or_reference.ty:
	  Removed erroneous cropping of rf_radius to an integer.

	* [r3244] topo/base/connectionfield.py:
	  Mask size set from the original, user-specified weights_bounds,
	  rather than the weights_bounds that may have been adjusted to be
	  odd-sized. Still need to change to have user-specified
	  weights_bounds as the Parameter user_weights_bounds.

2006-04-23  jbednar

	* [r3243] Makefile:
	  Added automatic ChangeLog creation

	* [r3242] ChangeLog.txt:
	  Updated with recent changes

2006-04-23  ceball

	* [r3241] topo/tests/lissom_or_reference.ty:
	  Minor clean-up.

	* [r3240] topo/tests/lissom_or_reference.ty:
	  Updated to work with current code, and made some minor
	  simplifications.

	* [r3239]
	  doc/Developer_Manual/imports_text.php:
	  Fixed minor typo.

2006-04-22  ceball

	* [r3238] topo/base/connectionfield.py,
	  topo/base/sheet.py:
	  Added translate() method to Slice.

2006-04-21  ceball

	* [r3237] topo/responsefns/optimized.py:
	  Corrected typo in the code that was stopping Topographica running
	  without weave.

	* [r3236] doc/Future_Work/current_text.php:
	  Removed a task!

	* [r3235] topo/base/connectionfield.py:
	  Removed a HACKALERT and the corresponding HACK.

	* [r3234] topo/base/connectionfield.py:
	  Removed an assert statement from get_view().

	* [r3233] topo/base/connectionfield.py:
	  get_view() asks for cf's slice directly, rather than getting
	  bounds and calculating the slice.

	* [r3232] topo/projections/basic.py:
	  Removed get_view() because there is no longer any need to
	  override the superclass's version.

	* [r3231] topo/base/connectionfield.py:
	  Removed another print statement that I left in by mistake.

	* [r3230] topo/projections/basic.py:
	  SharedWeight's cf(r,c) method now returns the cf with the
	  appropriate bounds.

	* [r3229] topo/base/connectionfield.py:
	  Removed commented-out print statements left in by mistake.

	* [r3228] topo/base/sheet.py:
	  Corrected typo.

	* [r3227] doc/Future_Work/current_text.php:
	  Updated my tasks; started to put them in some kind of order (in
	  which I'm doing them).

2006-04-20  ceball

	* [r3226] topo/base/sheet.py:
	  Added HACKALERT about location of CoordinateTransformer.

	* [r3225] topo/base/parameterizedobject.py,
	  topo/base/patterngenerator.py:
	  Moved _check_params to ParameterizedObject, where I meant to put
	  it originally.

	* [r3224] topo/patterns/random.py:
	  __call__() checks that its arguments are Parameters.

	* [r3223] topo/base/patterngenerator.py:
	  Moved code that checks arguments of __call__() are Parameters to
	  its own method; added call to that method to Constant.

	* [r3222] topo/base/patterngenerator.py:
	  PatternGenerator uses a CoordinateTransformer method to get
	  pattern sampling vectors.

	* [r3221] topo/base/sheet.py:
	  Added method to return the sheet coordinate x-centers and
	  y-centers of the underlying matrix cells of a
	  CoordinateTransformer.

2006-04-20  julienciroux

	* [r3220] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionpanel.py:
	  Fixed projectionpanel and corrected errors in connectionfield
	  panel. There is still a warning when opening the connectionfield
	  panel, it has to be sorted.

	* [r3219] topo/tkgui/connectionfieldspanel.py:
	  Corrected display of the sheet_name while looking into history.

2006-04-20  ceball

	* [r3218] topo/tests/testsheet.py:
	  Minor update after change to Sheet.

	* [r3217] topo/base/sheet.py:
	  Continued to update recent work CoordinateTransformer. Equalizing
	  the densities by adjusting bounds is now an option on creating a
	  CoordinateTransformer, and is True by default for Sheets.

2006-04-20  julienciroux

	* [r3216] topo/tkgui/connectionfieldspanel.py:
	  Corrected the double call to refresh in the __init__, and got rid
	  of the FocusOut action for the xy boxes.

	* [r3215] topo/tkgui/connectionfieldspanel.py:
	  Got rid of now unuseful chain import.

2006-04-20  ceball

	* [r3214] topo/base/sheet.py:
	  Minor updates to use of Slice and CoordinateTransformer.

2006-04-20  julienciroux

	* [r3213] topo/tkgui/plotgrouppanel.py:
	  Corrected handling of integerscaling.

	* [r3212] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Added a parameter looking_in_history that indicates if we are
	  currently looking back in time. Fixed the handling of the
	  checkbuttons when hitting back and forward.

2006-04-20  ceball

	* [r3211] topo/patterns/random.py:
	  Random generators get shape from CoordinateTransformer, rather
	  than from a Slice. Removed Slice from imports.

	* [r3210] topo/base/patterngenerator.py:
	  Constant gets shape from CoordinateTransformer, rather than from
	  a Slice. Removed Slice from imports.

	* [r3209] doc/Future_Work/current_text.php:
	  Updated my tasks.

	* [r3208] topo/base/patterngenerator.py:
	  PatternGenerator uses matrixidx2sheet_array()

	* [r3207] topo/tests/testsheet.py:
	  Added some comments.

	* [r3206] topo/base/sheet.py:
	  Added matrixidx2sheet_array() and updated some comments.

2006-04-20  julienciroux

	* [r3205] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py:
	  Added a method restaure_environment in PlotGroup panel to
	  re-instate the state of the buttons when re-loading a Plotgroup
	  from the history.

	* [r3204] topo/tkgui/plotgrouppanel.py:
	  Corrected the handling of the history so that it act properly
	  when hitting refresh or auto-refresh.

	* [r3203] topo/tkgui/plotgrouppanel.py:
	  Corrected the saving of the history so that we do not update a
	  PlotGroup in the past.

	* [r3202] topo/plotting/plotgroup.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Changed the handling of the history: now a copy of the plotgroup
	  is kept in history instead of bitmaps. It still needs more work.

2006-04-20  ceball

	* [r3201] topo/base/sheet.py:
	  Simplified code committed in the last version.

	* [r3200] topo/tests/testsheet.py:
	  Where xdensity==ydensity, CoordinateTransformers are created by
	  passing just one density.

	* [r3199] topo/base/sheet.py:
	  Can create a CoordinateTransformer by specifying only one density
	  if xdensity==ydensity.

	* [r3198] doc/Future_Work/current_text.php:
	  Updated my tasks.

	* [r3197] doc/Future_Work/current_text.php:
	  Updated my tasks.

	* [r3196] topo/tests/testimage.py,
	  topo/tests/testpatterngenerator.py:
	  Uses xdensity and ydensity in the tests, rather than just
	  density. Only tests cases where they're equal, though.

	* [r3195] topo/tests/testcfsom.py,
	  topo/tests/testsheetview.py:
	  Commented out the ImageGenerator class. Tests using it will be
	  resurrected in an equivalent form using the Image class.

	* [r3194] topo/tests/testsheet.py:
	  Updated after changes to sheet.py (introduction of
	  CoordinateTransformer). Some further changes will be required
	  when CoordinateTransformer is changed some more...

	* [r3193] topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py:
	  Removed unused import statement.

	* [r3192] topo/sheets/generatorsheet.py:
	  The image generator is passed xdensity and ydensity (both equal,
	  since for a sheet these are equal).

	* [r3191] topo/plotting/plot.py:
	  Uses Slice and CoordinateTransformer.

	* [r3190] topo/patterns/random.py:
	  Uses xdensity and ydensity, and the Slice object.

	* [r3189] topo/patterns/image.py:
	  Uses xdensity and ydensity.

	* [r3188] topo/patterns/basic.py:
	  PatternSampler uses xdensity and ydensity. This is an
	  intermediate checkin - needs to be cleaned up.

	* [r3187] topo/learningfns/som.py:
	  Uses xdensity and ydensity in call to pattern generator.

	* [r3186] topo/commands/analysis.py:
	  Calls matrix2sheet() as a method of the sheet being considered.

	* [r3185] topo/base/patterngenerator.py:
	  Part-way checkin. Uses the Slice object, but more of the
	  calculations in PatternGenerator will move to the Slice object.

	* [r3184] topo/base/connectionfield.py:
	  Uses the Slice and CoordinateTransformer classes. Some of the
	  calculations in here will move to the Slice object (e.g.
	  translation of a slice).

	* [r3183] topo/base/sheet.py:
	  Part-way checkin. Created CoordinateTransformer class, which
	  contains methods that were previously coordinate-transforming
	  functions in this file. Updated the Slice object. Still have to
	  move some methods from CoordinateTransformer to Slice, and
	  finalize other aspects.

2006-04-19  julienciroux

	* [r3182] topo/plotting/plotgroup.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionpanel.py:
	  Deleted the attribute sheet_filter_lam of a PlotGroup in order to
	  be able to deep copy a PlotGroup.

	* [r3181] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Corrected the _set_height_of_tallest_plot and the scale_images
	  method for a ProjectionPlotGroup.

2006-04-19  ceball

	* [r3180] topo/patterns/basic.py:
	  Replaced the untested CompositePatternGenerator with a new,
	  untested CompositePatternGenerator. This one is simpler.

2006-04-19  julienciroux

	* [r3179] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Added a parameter update when calling display_plots (decide
	  wether re-generating the Sheetviews or not.

	* [r3178] topo/plotting/plotgroup.py:
	  Minor change in doc and comment.

2006-04-19  ceball

	* [r3177] topo/commands/analysis.py:
	  Get cf.slice_array rather than calling cf.slice_tuple(). (This
	  was part of an earlier change, but does not seem to have been
	  committed.)

2006-04-18  ceball

	* [r3176] topo/sheets/generatorsheet.py:
	  Removed unnecessary setting of bounds and density. Removed out of
	  date HACKALERT.

2006-04-15  ceball

	* [r3175] topo/tests/testpatterngenerator.py:
	  File is now a reasonable test of PatternGenerator.

	* [r3174] topo/tests/testpatterngenerator.py:
	  Added more tests.

	* [r3173] topo/tests/testpatterngenerator.py:
	  Updated test.

	* [r3172] topo/tests/testpatterngenerator.py:
	  Changed the test so that it actually does what was intended
	  (previously the 'assert' statement was not testing anything about
	  the arrays). Currently it fails but this might be because the
	  test itself is wrong.

2006-04-14  ceball

	* [r3171] topo/base/connectionfield.py,
	  topo/projections/basic.py,
	  topo/responsefns/projfns.py:
	  Removed cf's slice_tuple() method. Going to rename slice_array to
	  slice_. slice_ being an array does not make it awkward to access
	  the elements since Python automatically unpacks array values
	  anyway.

	* [r3170] topo/base/sheet.py:
	  Removed an outdated HACKALERT.

2006-04-14  julienciroux

	* [r3169] topo/plotting/plotgroup.py:
	  Minor re-organization; deleted self.bitmaps.

	* [r3168] topo/plotting/bitmap.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Delete the attribute plot_src_name and name for a Bitmap (Not
	  needed anymore). Delete the PlotGroup load_images method, now we
	  explicitly built the bitmap list in PlotGroupPanel
	  display_plots().

	* [r3167] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/plotgrouppanel.py:
	  Moved the generation of the plot labels to PlotGroup; it will
	  enable getting rid of the copy of plot_src_name and name from
	  Plot to Bitmap, and eventually getting rid of the direct use of
	  Bitmaps objects.

	* [r3166] topo/tkgui/plotgrouppanel.py:
	  Re-organized order in the file, added alert.

	* [r3165] topo/tkgui/plotgrouppanel.py:
	  Deleted unused import statements.

	* [r3164] topo/tkgui/plotgrouppanel.py:
	  Temporary hack to fix back and forward buttons.

	* [r3163] topo/tkgui/plotgrouppanel.py:
	  Minor re-organization of the __init__ method.

	* [r3162] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Added a second control frame for Back, Forward, Sheetcoordinates
	  and Integerscaling Buttons. Moved the Sheetcoords button from
	  templateplotgrouppanel to plotgrouppanel. Deleted old comments.

	* [r3161] topo/tkgui/plotgrouppanel.py:
	  Deleted the scale_images() method in PlotGroupPanel. Now the
	  scaling is done within PlotGroup. Also deleted unused import
	  statements and old alerts and update doc.

2006-04-13  julienciroux

	* [r3160] topo/plotting/plotgroup.py:
	  Added two ALERTS.

2006-04-13  ceball

	* [r3159] topo/base/patterngenerator.py:
	  No visible change - minor alteration to the code.

2006-04-13  julienciroux

	* [r3158] topo/plotting/plotgroup.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Deleted the attribute plotgroup_key of a PlotGroup.

2006-04-13  ceball

	* [r3157] topo/base/connectionfield.py:
	  Get sheet's shape from sheet's activity matrix shape.

	* [r3156] topo/base/connectionfield.py:
	  Use sheet methods bounds2slice() and slice2bounds().

	* [r3155] topo/base/sheet.py:
	  Added sheet methods bounds2slice() and slice2bounds().

	* [r3154] topo/base/sheet.py:
	  Minor changes to documentation.

	* [r3153] topo/base/sheet.py:
	  Enforce minimum number of units in each direction to be 1; rename
	  slice variable to slice_; changes to documentation.

2006-04-13  julienciroux

	* [r3152] topo/plotting/plotgroup.py:
	  Deleted two unused import statement.

	* [r3151] topo/plotting/plotgroup.py:
	  Got rid of the use of dict_sort. Now the ordering of the plot is
	  performed differently.

	* [r3150] topo/plotting/plotgroup.py:
	  Deleted the import statement for flatten and change the code that
	  was using it.

2006-04-13  ceball

	* [r3149] topo/base/sheet.py:
	  Small change to documentation.

	* [r3148] topo/base/sheet.py:
	  No visible change - small tidy up.

	* [r3147] topo/base/boundingregion.py:
	  Minor change to documentation.

	* [r3146] topo/base/parameterizedobject.py:
	  Moved __doc__ definition higher up in the Parameter class so it
	  is a bit more obvious. Added check that subclasses of Parameter
	  define __slots__.

	* [r3145] topo/base/simulator.py:
	  Added __slots__ and __doc__ to EventProcessorParameter.

	* [r3144] topo/base/boundingregion.py:
	  Added __slots__ and __doc__ to BoundingRegionParameter.

	* [r3143] topo/base/sheet.py:
	  Updated Sheet documentation a bit.

2006-04-13  julienciroux

	* [r3142] topo/plotting/plotgroup.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Replaced the import statement for the commands within
	  templateplotgrouppanel, and import them in __main__.__dict__.
	  They laso are executed in __main__.__dict__ from the PlotGroups.

2006-04-13  ceball

	* [r3141] topo/base/sheet.py:
	  Removed unused functions slicearray2bounds() and
	  bounds2slicearray(). All slices will be arrays eventually, but
	  for now they are Python tuples.

2006-04-13  julienciroux

	* [r3140] topo/plotting/plotgroup.py:
	  Deleted unused import statements.

2006-04-13  ceball

	* [r3139] topo/patterns/basic.py:
	  Removed xdensity and ydensity from current Composite class (which
	  will be replaced anyway).

2006-04-13  julienciroux

	* [r3138] topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Deleted the plotgroup_dict variable: now each panel create and
	  store its own plotgroup attribute and uses it accordingly. Added
	  a method generate_sheet_views to the PlotGroups: now the command
	  to update the sheet view is contained in PlotGroups (and still
	  can be modified from the panel). It is the first version without
	  plotgroup_dict, it needs some cleaning and improving (in
	  particular for the projectionpanel and testpattern).

2006-04-13  ceball

	* [r3137] topo/base/sheet.py,
	  topo/tests/testsheet.py:
	  Removed xdensity and ydensity. Except in the documentation.

	* [r3136] topo/base/sheet.py,
	  topo/tests/testsheet.py:
	  slice2bounds() does not use xdensity and ydensity.

	* [r3135] topo/base/sheet.py,
	  topo/commands/analysis.py,
	  topo/tests/testsheet.py:
	  matrix2sheet() does not use xdensity and ydensity.

	* [r3134] topo/base/sheet.py,
	  topo/tests/testsheet.py:
	  sheet2matrix() and sheet2matrixidx() don't use xdensity and
	  ydensity.

	* [r3133] topo/tests/testsheet.py:
	  Altered a test; no visible change.

	* [r3132] topo/tests/testsheet.py:
	  Uncommented a test case that I'd previously left commented out by
	  mistake.

2006-04-12  ceball

	* [r3131] topo/base/sheet.py:
	  crop_slice_to_sheet() doesn't use xdensity and ydensity.

	* [r3130] topo/plotting/plot.py:
	  Removed unused import.

	* [r3129] topo/base/sheet.py:
	  submatrix() just takes density.

	* [r3128] topo/base/sheet.py,
	  topo/tests/testsheet.py:
	  bounds2slice() just uses density, not xdensity and ydensity.

	* [r3127] topo/tests/testplotfilesaver.py:
	  Only one line was in the test, so I commented that one too.

	* [r3126] topo/plotting/plot.py:
	  Removed xdensity and ydensity. Adjusted the corresponding
	  HACKALERT.

	* [r3125] topo/base/functionfamilies.py:
	  Initial version.

	* [r3124] topo/base/connectionfield.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/learningfns/som.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/optimized.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/projections/basic.py,
	  topo/tests/testimage.py:
	  Moved OutputFn, OutputFnParameter, and Identity to
	  functionfamilies (from projection). Renamed Identity to
	  IdentityOF.

	* [r3123] topo/responsefns/basic.py:
	  Import the basic response functions.

	* [r3122] topo/responsefns/projfns.py:
	  Removed unnecessary __init__()s. Use ResponseFnParameter for
	  single_cf_fn.

	* [r3121] topo/responsefns/optimized.py:
	  Removed unnecessary __init__(). Use ResponseFnParameter.

	* [r3120] topo/projections/basic.py:
	  Use ResponseFnParameter.

	* [r3119] topo/base/arrayutils.py,
	  topo/base/connectionfield.py:
	  Moved Mdot() to connectionfield.py and made it a LearningFn. Made
	  ResponseFnParameter.

	* [r3118] topo/base/connectionfield.py:
	  Changed a sum() of the weights to Numeric.sum(). Numeric.sum() is
	  faster. (Python's sum() and Numeric's sum() appear to give
	  slightly different results in general, though this particular
	  change makes no difference at the moment.)

2006-04-12  julienciroux

	* [r3117] topo/plotting/plotgroup.py:
	  Minor re-organization of the __init__.

	* [r3116] topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Renamed plot_group_key to plotgroup_key for consistency.

	* [r3115] topo/plotting/plotgroup.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Added arguments sheetcoords and integersaling to the PlotGroup
	  constructor. Renamed plotgroup() to refresh_plotgroup() in
	  PlotGroupPanel and subclasses. Now, refresh_plotgroup() is only
	  called from the refresh method, and I added an attribute
	  self.plotgroup that stores the current PlotGroup. Also deleted
	  old code in PlotGroupPanel.

	* [r3114] topo/plotting/plotgroup.py:
	  Deleted old comments; improved two lines of code.

2006-04-12  ceball

	* [r3113] doc/Future_Work/current_text.php:
	  Updated a task.

	* [r3112] doc/Future_Work/current_text.php:
	  Updated my tasks.

	* [r3111] topo/base/connectionfield.py:
	  Removed xdensity and ydensity, just using density now.

	* [r3110] topo/base/sheet.py:
	  Intermediate checkin. Removing xdensity and ydensity gradually.

	* [r3109] topo/base/patterngenerator.py,
	  topo/patterns/random.py:
	  PatternGenerators only accept density as a single number.

	* [r3108] topo/sheets/generatorsheet.py:
	  Only passes density, not xdensity and ydensity, to
	  PatternGenerator for creating the input pattern.

	* [r3107] topo/tests/testsheet.py:
	  Removed test of bounds2slice() that deliberately uses different x
	  and y densities.

	* [r3106] topo/tests/testsheet.py:
	  Added a test for Sheet creation where the specified bounds and
	  density would not give a sheet with the same density along x as
	  along y.

2006-04-11  ceball

	* [r3105] topo/plotting/plot.py:
	  Changed a HACKALERT.

2006-04-11  julienciroux

	* [r3104] topo/plotting/bitmap.py,
	  topo/plotting/plot.py:
	  Got rid of the attribute resize for the bitmap, and added it to
	  Plot objects.

	* [r3103] topo/plotting/plotgroup.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Moved everything not special to the GUI from PlotGroupPanel to
	  PlotGroup (e.g. sale_images, _set_height_of_tallest_plot). Also
	  deleted the old do_plot_cmd, by a plotgroup() method that
	  regenrates the PlotGroup anytime from the panels. It is a first
	  version that have been committed in order to be further
	  simplified. Note also that there is a slight bug for the
	  ProjectionPanel and for the handling of the SheetCoordinates
	  check_button, but they will be fixed very soon.

2006-04-11  ceball

	* [r3102] topo/base/sheet.py:
	  Sheet has same density in x and y directions (by adjusting height
	  of BoundingBox if necessary. Intermediate checkin: still have to
	  removed xdensity and ydensity from the code, and update the
	  documentation.

	* [r3101] examples/Makefile:
	  Sets default_density to be smaller before running each example.

	* [r3100] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty:
	  Allowed cortical density to be set externally via default_density
	  variable (otherwise uses the value set in the file).

2006-04-11  alan_lindsay

	* [r3099] topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py:
	  Colours of sheets changed (together) by setting the canvas' mode.
	  No lateral button in sheet's property panel, just a list of
	  connections (opens their properties). Auto refresh and normalize
	  options in the canvas.

	* [r3098]
	  doc/User_Manual/images/editorconnectiondrag.png,
	  doc/User_Manual/images/editorproperties.png,
	  doc/User_Manual/images/editorrepresentations.png,
	  doc/User_Manual/images/editortoolbaritems.png,
	  doc/User_Manual/model_editor.html:
	  First draft user guide for the model editor. Does not link to
	  other sections and does not conform to the style of the other
	  pages.

2006-04-11  jbednar

	* [r3097] topo/tests/testsheet.py:
	  Fix by Chris -- override default Sheet bounds and density to be
	  sure it's the ones we expect

	* [r3096] /trunk/topographica, .cvsignore:
	  Added missing newline

2006-04-11  ceball

	* [r3095] topo/responsefns/basic.py:
	  Removed projection-level response functions (they are in
	  projfns.py.

	* [r3094] topo/responsefns/optimized.py:
	  Updated CFProjectionResponseFn imports to be from projfns.

	* [r3093] topo/responsefns/projfns.py:
	  Renamed basic.py to projfns.py since it contains only
	  projection-level response functions.

2006-04-10  ceball

	* [r3092] topo/tests/testsheet.py:
	  Re-enabled a test that I disabled. This version, revision 1.25,
	  is identical to revision 1.23. I disabled the test when I changed
	  how the tests are run, because it began failing with no change
	  other than the test-running mechanism (and had not been failing
	  before). As far as I could tell, the test was running properly
	  and not failing before I changed the testing mechanism, so I
	  decided to comment out the test and investigate later on. I am
	  re-enabling the test because it is legitimately failing. I'm not
	  sure what is going on: was it not running before? How could it
	  not have been failing? The functions it is testing have not
	  changed throughout this process, so I am confused. Maybe we all
	  had *.pyc files left that were not updated, though that seems
	  unlikely.

	* [r3091] topo/patterns/basic.py:
	  Added commented-out new version of CompositePatternGenerator.
	  Corrected import statements (including for when new
	  CompositePatternGenerator is uncommented.

2006-04-08  ceball

	* [r3090] doc/Future_Work/current_text.php:
	  Updated my tasks.

	* [r3089] examples/tiny.ty,
	  topo/learningfns/__init__.py,
	  topo/learningfns/basic.py:
	  Sorted LearningFns into basic and projfns.

	* [r3088] topo/learningfns/projfns.py:
	  Initial version.

	* [r3087] topo/base/connectionfield.py:
	  Removed HACKALERT.

	* [r3086] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/homeostatic.ty,
	  examples/laminar.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/lissom_or_sf.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  examples/tiny.ty,
	  topo/base/connectionfield.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/learningfns/__init__.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py,
	  topo/learningfns/som.py,
	  topo/outputfns/__init__.py,
	  topo/outputfns/basic.py,
	  topo/outputfns/optimized.py,
	  topo/outputfns/projfns.py,
	  topo/patterns/image.py,
	  topo/projections/basic.py,
	  topo/responsefns/__init__.py,
	  topo/responsefns/basic.py,
	  topo/responsefns/optimized.py,
	  topo/sheets/lissom.py,
	  topo/tests/lissom_oo_or_reference.ty,
	  topo/tests/testplotgroup.py:
	  Attempting to organize functions that iterate over the CFs of a
	  CFProjection and those that act on a single array.
	  
	  (As part of the more general idea that there are e.g. output
	  functions
	  which apply to a Projection.)
	  
	  For output functions, we have the single-array (normal
	  mathematical) output
	  functions, e.g.:
	  OutputFn
	  Identity
	  DivisiveSumNormalize
	  We also have the functions that iterate through a CFProjection's
	  CFs,
	  applying an OutputFn to each:
	  CFProjectionOuputFn
	  CFProjectionIdentityOutputFn(single_cf_fn=Identity())
	  CFProjectionDivisiveSumNormalize(single_cf_fn=DivisiveSumNormalize())
	  
	  OutputFns are in topo.outputfns.basic, and CFProjectionOutputFns
	  are
	  in topo.outputfns.projfns. Other Projection-level output
	  functions
	  would also go in the projfns module.
	  
	  The same applies to LearningFns and
	  CFProjectionLearningFns. ResponseFunctions have been renamed
	  CFProjectionResponseFunctions where they apply to a CFProjection.
	  The
	  reorganization of LearningFns and ResponseFns is not complete
	  yet.
	  
	  Along with this reorganization, CFProjectionOutputFnParameter (as
	  distinct from OutputFnParameter) has been introduced (and
	  similarly
	  for LearningFns). Implementation of these is not complete yet;
	  notably
	  the __init__.py files in the outputfns, learningfns, and
	  responsefns
	  packages need to be cleaned up.
	  
	  In addition to this, minor cleanups may also have occurred,
	  including:
	  skipping calls to __init__() methods if all they do is call the
	  superclass' __init__()s; documentation strings.

	* [r3085] topo/base/parameterclasses.py:
	  Updated documentation for ClassSelectorParameter.

	* [r3084] topo/base/connectionfield.py:
	  Added CFOutputFunctionParameter class; made weights_output_fn be
	  a CFOutputFunctionParameter.

	* [r3083] topo/base/connectionfield.py:
	  GenericCFOF: removed __init__() method, since it does nothing but
	  call the superclass'. Made single_cf_fn parameter be an
	  OutputFunctionParameter.

	* [r3082] topo/base/projection.py:
	  Minor clean-up of comments.

	* [r3081] topo/base/connectionfield.py:
	  CFOutputFunction is abstract.

	* [r3080] topo/outputfns/optimized.py:
	  Updated docstring.

	* [r3079] topo/outputfns/projfns.py:
	  Initial version.

	* [r3078] doc/Future_Work/current_text.php:
	  Updated my tasks.

	* [r3077] topo/misc/utils.py:
	  No visible change, altered syntax.

	* [r3076] topo/commands/basic.py,
	  topo/misc/utils.py:
	  Minor changes to pickling - should be no visible change.

	* [r3075] topo/tests/__init__.py:
	  Allowed a test to be ignored easily. Removed testsnapshots from
	  the automatic tests.

	* [r3074] topo/tests/testsnapshots.py:
	  Initial version.

	* [r3073] topo/tests/__init__.py:
	  Added ability to run a specific list of test modules.

	* [r3072] topo/commands/basic.py:
	  Updated docstrings for save_ and load_snapshot

	* [r3071] topo/commands/basic.py:
	  When being pickled, the simulator has its RELEASE attribute set
	  to topo.release.

	* [r3070]
	  topo/tests/testtemplateplotgrouppanel.py:
	  Added missing import statement.

	* [r3069] topo/tests/tkgui:
	  Removing directory.

	* [r3068] topo/tests/__init__.py:
	  Updated doc string, added ALERT about structure of tests/
	  directory that we might consider in the future.

	* [r3067] topo/tests/__init__.py,
	  topo/tests/testmatplotlibtk.py,
	  topo/tests/testplotgrouppanel.py,
	  topo/tests/testpropertiesframe.py,
	  topo/tests/testtemplateplotgrouppanel.py,
	  topo/tests/testtopoconsole.py,
	  topo/tests/tkgui/__init__.py,
	  topo/tests/tkgui/testmatplotlibtk.py,
	  topo/tests/tkgui/testplotgrouppanel.py,
	  topo/tests/tkgui/testpropertiesframe.py,
	  topo/tests/tkgui/testtemplateplotgrouppanel.py,
	  topo/tests/tkgui/testtopoconsole.py:
	  Moved tkgui tests into main test directory.

	* [r3066] topo/tests/testcfsom.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotfilesaver.py:
	  Reduced sheet densities.

	* [r3065]
	  topo/tests/tkgui/testplotgrouppanel.py:
	  Spelt 'density' correctly this time.

	* [r3064]
	  topo/tests/tkgui/testplotgrouppanel.py:
	  Reduced sheet densities to speed up tests.

	* [r3063] topo/analysis/featuremap.py,
	  topo/commands/analysis.py:
	  Removed calls to active_sim() and some passing round of
	  simulators.

	* [r3062] topo/analysis/featuremap.py:
	  Removed a HACKALERT and the corresponding call to active_sim().

	* [r3061] topo/tests/testfeaturemap.py:
	  Reduced density of sheets in test_measurefeaturemap(). It runs a
	  lot faster now.

2006-04-07  julienciroux

	* [r3060] topo/tkgui/cfsheetplotpanel.py:
	  Deleted cfsheetplotpanel.py: the code is now in both
	  connectionfield and projection panels.

	* [r3059] topo/tkgui/projectionpanel.py:
	  Added the code of cfsheetplotpanel in projectionpanel and made it
	  inherit from TemplatePlotGroupPanel instead

	* [r3058] topo/tkgui/templateplotgrouppanel.py:
	  Modified the __init__ method: call refresh only if it is an
	  instance of TemplatePlotGroupPanel. Allow calling the constructor
	  for subclasses.

	* [r3057] topo/tkgui/connectionfieldspanel.py:
	  Added the code of cfsheetplotpanel in connectionfieldpanel and
	  made it inherit from TemplatePlotGroupPanel instead

2006-04-07  ceball

	* [r3056] doc/Future_Work/current_text.php:
	  Updated my tasks.

	* [r3055] topo/patterns/image.py:
	  Removed TopoImage, which I forgot to do on the previous commit.

	* [r3054] topo/patterns/image.py:
	  Removed the TopoImage class and a related HACKALERT. Images are
	  now loaded only once, rather than every time Image's function()
	  is called.

2006-04-07  julienciroux

	* [r3053] topo/tkgui/cfsheetplotpanel.py:
	  temporary hack to get the normalize button set properly for a
	  connectionfieldspanel and a projectionpanel. It will be properly
	  sorted when getting rid of CFSheetPlotPanel and correcting the
	  hierarchy of the panels.

2006-04-07  ceball

	* [r3052] topo/patterns/image.py:
	  Added HACKALERT.

	* [r3051] topo/patterns/basic.py,
	  topo/patterns/image.py:
	  Corrected mistake in PatternSampler where background value was
	  being calculated before array was normalized.

2006-04-07  julienciroux

	* [r3050] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Renamed _set_initial_master_zoom to _set_eight_of_tallest_plot.

	* [r3049] topo/tkgui/projectionpanel.py:
	  Corrected self.zoom_factor to be self.height_of_tallest_plot and
	  INITIAL_PLOT_WIDTH to INITIAL_PLOT_HEIGHT. Added a
	  re-implementation of the _set_initial_naster_zoom for the
	  projectionpanel (that needs more work).

2006-04-07  ceball

	* [r3048] topo/patterns/basic.py,
	  topo/patterns/image.py:
	  Moved PatternSampler class from topo/patterns/image.py to
	  topo/patterns/basic.py in anticipation of using it for Composite.
	  This might not be the correct final location for PatternSampler.

	* [r3047] topo/patterns/image.py:
	  Created a new class, PatternSampler, which does the sampling of a
	  pattern that TopoImage did previously. TopoImage is now a
	  subclass of PatternSampler.

2006-04-07  julienciroux

	* [r3046] topo/tkgui/cfsheetplotpanel.py:
	  Corrected error in cfsheetplotpanel (forgot to change the name of
	  self.zoom_factor to self.height_of_tallest_plot and
	  self.min_zoom_factor to self.min_master_zoom); that should fix
	  the connectionfieldpanel.

	* [r3045] topo/tkgui/plotgrouppanel.py:
	  Replaced self.master_zoom by self.height_of_tallest_plot.

2006-04-07  ceball

	* [r3044] topo/tests/__init__.py,
	  topo/tests/tkgui/__init__.py:
	  Any file named test*.py that defines the 'suite' attribute will
	  be included when the tests are run.

	* [r3043] topo/tests/testsheet.py:
	  Commented out a test which is out of date. Will be updated when
	  sheet.py and connectionfield.py are reviewed.

2006-04-06  julienciroux

	* [r3042] topo/tkgui/plotgrouppanel.py:
	  simplified the function _set_initial_plot_zoom; now there is only
	  one master_zoom. Deleted the function _compute_max_height.

	* [r3041] topo/tkgui/plotgrouppanel.py:
	  Corrected the function scale image; renamed self.min_zoom_factor
	  to self.min_master_zoom.

2006-04-06  ceball

	* [r3040] /trunk/topographica, .cvsignore:
	  Added 'topographica.bat' (which exists after installation on
	  Windows).

	* [r3039] topo/tests/testimage.py:
	  Added more tests.

2006-04-06  julienciroux

	* [r3038] topo/tkgui/plotgrouppanel.py:
	  Implement a master_zoom for both sheet coordinates and matrix
	  coordinates.

2006-04-06  ceball

	* [r3037] topo/patterns/image.py:
	  User-specified numbers involved in divisions are first turned to
	  floats in case integer
	  values are specified.

	* [r3036] topo/tests/testimage.py:
	  Altered HACKALERT.

2006-04-05  ceball

	* [r3035] topo/tests/__init__.py:
	  testimage.py added to the list of tests. Currently one test is
	  failing, because of a mistake in image.py version 1.40; this will
	  be corrected in the next version of image.py.

	* [r3034] topo/tests/testimage.py:
	  Continued writing.

	* [r3033] topo/patterns/basic.py:
	  Removed an out-of-date HACKALERT.

	* [r3032] topo/patterns/basic.py:
	  Altered a HACKALERT.

	* [r3031] topo/patterns/image.py:
	  Size scaling of each of the image dimensions is done relative to
	  the default retinal dimension of 1.0, rather than the current
	  sheet's dimension.

	* [r3030] topo/patterns/image.py:
	  Corrected typo in documentation.

	* [r3029] topo/patterns/image.py:
	  Changed previous output_fn to 'whole_image_output_fn (needs a
	  better name), so that there can also be an output_fn to apply to
	  the section of image that is actually displayed (i.e. the meaning
	  of output_fn for other PatternGenerators).

	* [r3028] topo/patterns/random.py:
	  Added output_fn to PatternGenerators in random.py. Switched order
	  of import statements.

	* [r3027] topo/base/patterngenerator.py:
	  Added output_fn to Constant.

	* [r3026] topo/base/patterngenerator.py:
	  PatternGenerators have an OutputFunctionParameter.

	* [r3025] topo/base/projection.py:
	  OutputFunction is an abstract class.

	* [r3024] topo/base/patterngenerator.py:
	  Corrected test for whether or not an argument supplied to
	  __call__() is a Parameter. Added commented-out code for an
	  output_fn on PatternGenerator (so this change is separate from
	  the first one).

	* [r3023] topo/base/patterngenerator.py:
	  Updated some documentation.

	* [r3022] topo/base/patterngenerator.py:
	  Added a warning to __call__() of PatternGenerator if a value is
	  passed for something that does not exist as a Parameter.

	* [r3021] topo/base/patterngenerator.py:
	  No visible change, just switched order of import statements.

	* [r3020] topo/base/patterngenerator.py:
	  Allowed to specifiy scale and offset when calling
	  PatternGenerator (altered ConstantGenerator in the same way).

	* [r3019] topo/tests/testimage.pgm:
	  Changed to have one even dimension and one odd dimension.

	* [r3018] topo/patterns/image.py:
	  Simplified the TopoImage class by using a Sheet as the container
	  for an image. That way, coordinate transforms can work using the
	  standard sheet.py functions. Also, altered how the initial image
	  scaling works (it remains to make the initial
	  scaling relative to the default 1.0 retinal area, rather than the
	  current retina).

	* [r3017] topo/base/sheet.py:
	  Added a version of sheet2matrixidx() that works for arrays. (All
	  these functions still
	  have to be cleaned up into the Slice class.)

	* [r3016] topo/base/boundingregion.py:
	  Added contains_exclusive(), which is the same as contains()
	  except the right and bottom boundaries of the BoundingBox are
	  considered exclusive.

2006-04-05  jbednar

	* [r3015] ChangeLog.txt:
	  Updated with recent changes

	* [r3014]
	  topo/tests/tkgui/testplotgrouppanel.py:
	  Fixed broken test uncovered by better error messages

2006-04-05  ceball

	* [r3013] topo/base/projection.py:
	  Added 'sum' argument to Identity.

	* [r3012] topo/tests/testimage.py,
	  topo/tests/utils.py:
	  Initial version.

	* [r3011] topo/tests/testimage.pgm:
	  An image to use for testing the image generator in image.py.

2006-03-29  julienciroux

	* [r3010] topo/tkgui/plotgrouppanel.py:
	  Started to re-write scale_images: got rid of the arbitrary factor
	  10 in the case of sheet coordinate scaling; now the largest
	  bitmap is scaled to INITIAL_PLOT_HEIGHT in any cases. It remains
	  to implement a master zoom for each case.

	* [r3009] topo/plotting/plotgroup.py,
	  topo/tkgui/connectionfieldspanel.py:
	  Corrected label display for connection field panel accordingly to
	  the new changes in the UnitView plot_src_name attribute.

	* [r3008] topo/base/sheetview.py:
	  Made the plot_src_name attribute beeing set to the src sheet name
	  for a UnitView as well, (it is a necessary step in order to
	  implement the sheet coordinates button for the connection field
	  panel).

2006-03-29  ceball

	* [r3007] topo/projections/basic.py:
	  Removed a line (unused) that I left in by accident one time.

2006-03-29  jbednar

	* [r3006] topo/tkgui/plotgrouppanel.py:
	  Made Integer scaling button refresh automatically

	* [r3005] topo/plotting/plotgroup.py:
	  Fixed typo in comment

2006-03-28  julienciroux

	* [r3004] topo/tkgui/plotgrouppanel.py:
	  Corrected mistake in toogle_normalize (without a call to
	  scale_images, the Plot are not regenerated.)

	* [r3003] topo/tkgui/templateplotgrouppanel.py:
	  Set the attribute normalize according to the value for the
	  template (for a TemplatePlotGroupPanel).

	* [r3002] topo/tkgui/testpattern.py:
	  Corrected Plot creation in the TestPattern, according to the new
	  changes in Plot.

	* [r3001] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py:
	  Got rid of the situate argument for plot: now it is all
	  determined by the plot_bounding_box.

	* [r3000] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplot.py:
	  Changed Plot: now that UnitViews shared the same bounds as the
	  SheetViews, there is no need to slice anymore when combining
	  SheetViews with UnitViews. Now, a plot_bounding_box is specified,
	  in which the plot is drawn, or the bounds of the Sheet are taken
	  if no plot_bounding_box are specified. There is still some
	  problems for some plot_bounding_box and density values
	  combinations that will have to be adressed, but no current used
	  feature is broken.

	* [r2999] topo/base/connectionfield.py:
	  Made UnitView bounds the same as the source Sheet bounds of the
	  connectionfield; therefore, all SheetViews from a Sheet have the
	  same bounds.

2006-03-27  jbednar

	* [r2998] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Changed PlotGroupPanel to keep track of the plot_time of the
	  current plot, which may differ from the current simulator time;
	  this makes the back and forward buttons work with all
	  PlotGroupPanels. Cleaned up implementation of back and forward in
	  general.

	* [r2997] examples/tiny.ty:
	  Made it more obvious that the learning_rate is a float

2006-03-27  judelaw

	* [r2996] topo/tkgui/plotgrouppanel.py:
	  Added back and forward buttons - only really currently working
	  well for activity window

2006-03-27  jbednar

	* [r2995] topo/base/connectionfield.py:
	  Fixed bug -- if users specified the learning rate as an integer,
	  it was being truncated to an even multiple of the size of the CF,
	  with surprising results. Now effectively promotes the rate to a
	  float.

2006-03-27  ceball

	* [r2994] topo/base/projection.py:
	  Removed print statements accidentally left in the previous
	  version.

	* [r2993] topo/base/projection.py:
	  Altered wording of an error message.

	* [r2992] topo/base/projection.py:
	  Updated documentation for present_input(). Also renamed uses of
	  the 'dest_port' variable name to just 'port' within the
	  ProjectionSheet code; before it was confusing. The Projection has
	  the dest_port and src_port concept (referring to src and dest
	  EPs), but for a ProjectionSheet should it be more like 'in_port'
	  and 'out_port'?

2006-03-27  jbednar

	* [r2991] topo/tkgui/topoconsole.py:
	  Added ALERT

	* [r2990] topo/tkgui/topoconsole.py:
	  Improved error message and removed stray unused code

2006-03-27  ceball

	* [r2989] topo/base/projection.py:
	  Removed an outdated HACKALERT.

	* [r2988] topo/base/projection.py:
	  ProjectionSheet raises a TypeError if an attempt is made to
	  connect anything other than a Projection.

2006-03-27  julienciroux

	* [r2987] topo/tkgui/taggedslider.py:
	  Corrected error in previous commit.

2006-03-27  jbednar

	* [r2986] topo/tkgui/topoconsole.py:
	  Better error message; added ALERT

	* [r2985] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Added better checks for whether various plots will be successful
	  for the current simulation

	* [r2984] doc/Future_Work/index_text.php:
	  More work

2006-03-27  ceball

	* [r2983] doc/Future_Work/current_text.php:
	  Updated my tasks

2006-03-27  chrispalmer

	* [r2982] examples/lissom_or_sf.ty:
	  initial spatial frequency work

2006-03-27  ceball

	* [r2981] topo/tests/lissom_oo_or_reference.ty:
	  Set V1 afferents to normalize together. Set afferent connection
	  strengths to have
	  strength 1.

	* [r2980] topo/base/connectionfield.py:
	  Added delattr for _sum attribute. Altered commented-out code.

2006-03-25  jbednar

	* [r2979] doc/Tutorials/lissom_oo_or_text.php,
	  doc/Tutorials/lissom_or_text.php:
	  Updated estimates of training times based on an actual run!

	* [r2978] examples/Makefile:
	  Changed to put .typ files in this directory

2006-03-23  jbednar

	* [r2977] topo/tkgui/plotgrouppanel.py:
	  Intermediate checkin; still messy. Added integer scaling option,
	  and sketched eventual cleaned up code for resizing. Turned off
	  sheetcoords by default so that ConnectionField would work

	* [r2976]
	  topo/commands/or_key_white_vert_small.png,
	  topo/plotting/templates.py:
	  Changed default size of OR key to be a smaller image

	* [r2975] topo/tkgui/templateplotgrouppanel.py:
	  Turned off sheetcoords by default so that ConnectionField would
	  work

2006-03-23  julienciroux

	* [r2974] topo/plotting/templates.py:
	  Corrected mistype.

	* [r2973] topo/plotting/plot.py:
	  Corrected the doc.

	* [r2972] topo/tkgui/plotgrouppanel.py:
	  Started an implementation of the scrollbar that is commented out.
	  Deleted unused import statement. Cleaned up doc and comments.
	  Corrected the use of **config by the use of **param in the
	  __init__ method.

2006-03-23  jbednar

	* [r2971] topo/tkgui/plotgrouppanel.py:
	  Added alert

	* [r2970] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Changed actualsize to sheetcoords for clarity; made on by default

	* [r2969] topo/tkgui/topoconsole.py:
	  Renamed Learning iterations to indicate that it's not necessarily
	  learning anything and it's not in terms of iterations (!).
	  Cleaned up time remaining text.

2006-03-22  chrispalmer

	* [r2968] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Added actualsize button; name not yet decided

	* [r2967] topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Added the simulator name to window titles to help users keep
	  multiple simulations straight

2006-03-22  julienciroux

	* [r2966] topo/tkgui/plotgrouppanel.py:
	  Deleted unused attribute self.plots in PlotGroupPanel.Added doc
	  and comment.

2006-03-22  chrispalmer

	* [r2965] topo/tkgui/topoconsole.py:
	  Added estimate of time remaining

2006-03-22  julienciroux

	* [r2964] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Changed the argument pgt_name to name for a PlotGroupPanel. There
	  is no references to template in the PlotGroup class.

	* [r2963] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/testpattern.py:
	  Cleaned up reference to a template from PlotGroupPanel. At the
	  same time, enabled the normalize button for the testpattern. It
	  recquired to re-implement the toggle_normalize in the
	  testpattern, but it is only a temporary solution while
	  re-organizing the panel hierarchy.

2006-03-22  jbednar

	* [r2962] topo/base/simulator.py:
	  Fixed bug in recent checking; scheduled events were failing due
	  to lack of a src or dest for which to print information

	* [r2961] Makefile,
	  doc/Makefile:
	  Cleaned up dist package generation

2006-03-22  julienciroux

	* [r2960] topo/base/projection.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testcfsom.py:
	  Deleted the get_in_projection_by_name in ProjectionSheet.
	  Replaced by using the projections() method now that we ensure a
	  unique name for projections to the same ProjectionSheet.

	* [r2959] topo/plotting/plotgroup.py:
	  Replaced the use of get_in_projection_by_name() by the use of
	  projections(). Now that the problem of having a unique name is
	  solved, we do not need to return a list of projections for a
	  given name. Deeleted correponding Aletrt. Cleaned up the doc.

2006-03-22  jbednar

	* [r2958] Makefile:
	  More files to clean up for distribution

	* [r2957] doc/Future_Work/current_text.php:
	  Removed completed item

	* [r2956] doc/Downloads/win32_text.php:
	  Added note

	* [r2955] Makefile:
	  First pass at creating dist archive

2006-03-21  julienciroux

	* [r2954] topo/misc/commandline.py,
	  topo/tkgui/taggedslider.py:
	  Removed global constants Pi and PI. The only syntax is now pi.

	* [r2953] topo/misc/commandline.py:
	  Removed unnecessary exec statements.

	* [r2952] topo/misc/commandline.py:
	  Removed unnecessary in __main__.__dict__ statements.

2006-03-20  julienciroux

	* [r2951] topo/misc/commandline.py:
	  Removed the start function and moved the corresponding code
	  within process_argv.

2006-03-18  ceball

	* [r2950] topo/outputfns/optimized.py:
	  Corrected DivisiveSumNormalize's test of the current_norm_value.

	* [r2949] topo/outputfns/basic.py:
	  Corrected DivisiveSumNormalize's test of the current_norm_value.

	* [r2948] /trunk/topographica, .cvsignore:
	  Added python_topo directory (which exists on Windows).

	* [r2947] topo/plotting/plotfilesaver.py:
	  Started changing to get simulator from topo.sim.

2006-03-18  ceball_cvs2svn

	* [r2946] /tags/CNV_COURSE:
	  This commit was manufactured by cvs2svn to create tag
	  'CNV_COURSE'.

2006-03-18  jbednar

	* [r2945] topo/tkgui/plotgrouppanel.py:
	  Hopefully fixed longstanding issues about minimum and initial
	  plot widths. Plots should now default properly to around 150
	  pixels wide, or larger if the Sheet has more pixels than that.
	  The Reduce button will now allow plots to be reduced down to one
	  pixel per unit, but no further (at the moment)

2006-03-18  ceball

	* [r2944] topo/plotting/plotgroup.py,
	  topo/tkgui/cfsheetplotpanel.py,
	  topo/tkgui/connectionfieldspanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Started changing to get simulator from topo.sim.

2006-03-18  jbednar

	* [r2943] examples/tiny.ty:
	  Added explanatory note

2006-03-18  ceball

	* [r2942] topo/tkgui/connectionfieldspanel.py:
	  Removed outdated alert.

	* [r2941] topo/base/simulator.py:
	  Altered a comment - no visible change.

	* [r2940] topo/base/connectionfield.py:
	  Altered commented-out code: no visible change.

2006-03-18  jbednar

	* [r2939] examples/tiny.ty,
	  topo/outputfns/basic.py:
	  Added abs()-using DivisiveL1Normalize

	* [r2938] examples/tiny.ty:
	  Added more example parameters

	* [r2937] examples/tiny.ty:
	  Initial version

	* [r2936] topo/learningfns/som.py:
	  Moved from basic.py

	* [r2935] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  topo/learningfns/basic.py,
	  topo/sheets/cfsom.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py:
	  Moved SOM learning functions to topo/learningfns/som

	* [r2934] topo/base/connectionfield.py:
	  Added LearningFunction abstract class to establish a family of
	  objects for use with GenericCFLF

	* [r2933] topo/responsefns/basic.py,
	  topo/responsefns/optimized.py:
	  Fixed docstrings

	* [r2932] topo/outputfns/basic.py:
	  Added alert

	* [r2931] topo/outputfns/basic.py:
	  Added alert. Removed redundant constructors

	* [r2930] topo/base/simulator.py:
	  Added debugging messages

	* [r2929] topo/base/connectionfield.py:
	  Added alert

	* [r2928] topo/learningfns/optimized.py,
	  topo/projections/optimized.py,
	  topo/responsefns/optimized.py,
	  topo/sheets/lissom.py:
	  Removed out-of-date LISSOM_CPointer, CFDotProduct_CPointer,
	  CFProjection_CPointer, and DivisiveHebbian_CPointer; may
	  eventually be resurrected

2006-03-17  jbednar

	* [r2927] examples/cfsom_or.ty:
	  Cleaned up and simplified

	* [r2926] examples/cfsom_or.ty:
	  Changed to Chris's new topo.sim format

	* [r2925] examples/hierarchical.ty:
	  Fixed typo

	* [r2924] examples/hierarchical.ty:
	  Sorted imports

2006-03-17  ceball

	* [r2923] doc/Future_Work/current_text.php:
	  Updates to my tasks.

	* [r2922] examples/hierarchical.ty:
	  Set the simulator name.

	* [r2921] topo/base/simulator.py:
	  Corrected an error in SimSingleton's __setattribute__() method.

	* [r2920] topo/base/simulator.py:
	  Removed a HACKALERT from SimSingleton.

	* [r2919] topo/base/simulator.py:
	  Corrected logic error in SimSingleton.init() that was creating
	  two Simulators (though it left only one behind).

2006-03-17  jbednar

	* [r2918] examples/main.ppm,
	  topo/tests/testcfsom.py:
	  Removed unnecessary image

2006-03-17  ceball

	* [r2917] topo/base/simulator.py:
	  Cleaned up code for dictionary-style access to simulator objects.
	  Doing topo.sim['V1']=EP where EP already exists in the simulator
	  results in a warning and the object not being added. Doing
	  topo.sim['V1']=EP2 where topo.sim['V1'] already exists results in
	  the EP already in topo.sim['V1'] being overwritten with EP2 (as
	  for dictionaries). Simulator's _event_processors is now a dict
	  rather than a list to make things simpler.

2006-03-17  jbednar

	* [r2916] doc/User_Manual/time_text.php:
	  Fixed image sizes

2006-03-17  ceball

	* [r2915] examples/hierarchical.ty:
	  Changed to use newer simulator syntax: topo.sim['V1'], etc.

	* [r2914] topo/base/simulator.py:
	  SimSingleton uses the simulator's repr and str methods.

2006-03-17  jbednar

	* [r2913]
	  doc/Developer_Manual/optimization_text.php:
	  Edited Chris's text slightly

2006-03-17  ceball

	* [r2912] doc/Future_Work/current_text.php:
	  Updated my tasks.

	* [r2911] examples/som_retinotopy.ty:
	  Reduced SOM radius slightly (and random seeds are different).

	* [r2910] doc/Developer_Manual/index_text.php,
	  doc/Developer_Manual/optimization_text.php:
	  Added some information about how we provide optimized components.
	  It's commented out for the moment so JAB can review it.

2006-03-16  ceball

	* [r2909] examples/som_retinotopy.ty,
	  topo/responsefns/basic.py,
	  topo/responsefns/optimized.py:
	  CFEuclideanDistance is the basic Python version,
	  CFEuclideanDistance_opt1 is the optimized C version.

	* [r2908] examples/som_retinotopy.ty:
	  Removed unused line of imports.

	* [r2907] topo/base/connectionfield.py:
	  No visible change. Changed commented-out code so it's simpler
	  (still behaves the
	  same).

	* [r2906] topo/base/connectionfield.py:
	  Changed sum property's documentation. Apart from that, no visible
	  change - altered commented-out code.

2006-03-15  ceball

	* [r2905] topo/tests/lissom_oo_or_reference.ty:
	  Update after recent class changes.

	* [r2904] topo/base/connectionfield.py:
	  Removed duplicate import statement.

	* [r2903] topo/base/connectionfield.py:
	  Removed optimization from GenericCFOF.

	* [r2902] topo/learningfns/basic.py:
	  Removed unused references to output_fn.

	* [r2901] topo/outputfns/optimized.py:
	  DivisiveSumNormalizeCFOF sets the cfs' sum attribute after
	  normalizing. (Currently has no visible effect.)

	* [r2900] topo/learningfns/optimized.py,
	  topo/outputfns/optimized.py:
	  Modified documentation.

	* [r2899] examples/lissom_oo_or.ty:
	  Reverted names of projections - changes which I accidentally left
	  in.

	* [r2898] examples/laminar.ty,
	  examples/lissom_oo_or.ty:
	  Uses DivisiveSumNormalizeCFOF_opt1 instead of GenericCFOF with
	  single_cf_fn=DivisiveSumNormalize_opt1.

	* [r2897] topo/projections/basic.py:
	  Corrected location of single_cf_fn for weight initialization.

	* [r2896] topo/base/connectionfield.py:
	  Removed output_fn Parameter accidentally left behind in
	  CFLearningFunction.

	* [r2895] examples/lissom_or.ty:
	  Uses DivisiveSumNormalizeCFOF_opt1 instead of GenericCFOF with
	  single_cf_fn=DivisiveSumNormalize_opt1.

	* [r2894] topo/outputfns/optimized.py:
	  Corrected mistake in non-optimized wrapper for
	  DivisiveSumNormalizeCFOF.

	* [r2893] topo/responsefns/basic.py:
	  Corrected call to super(), must have been missed from a previous
	  set of commits.

	* [r2892] topo/outputfns/optimized.py:
	  Corrected typo (in the code).

	* [r2891] topo/outputfns/optimized.py:
	  Uncommented code for DivisiveSumNormalizeCFOF and added
	  non-optimized fallback to
	  GenericCFOF(single_cf_fn=DivisiveSumNormalize).

	* [r2890] topo/tkgui/topoconsole.py:
	  Added return statement so all the possible locations aren't
	  opened in open_location().

	* [r2889] topo/tkgui/topoconsole.py:
	  Windows users are unlikely to have the locally built
	  documentation. Therefore, locations on the web are tried if the
	  local copies fail. Also, fixed 'about' text,
	  since the ABOUT_TEXT variable in topo/__init__ had been moved
	  into a function.

	* [r2888] topo/__init__.py:
	  'About' text can be returned or printed. Default is to print, as
	  before.

2006-03-14  ceball

	* [r2887] doc/Future_Work/current_text.php:
	  Update to a task.

	* [r2886] topo/base/connectionfield.py:
	  learn() split tp learn() and apply_output_fn(). No visible
	  change. Also committed commented-out code in CFSheet's learn().

	* [r2885] topo/misc/inlinec.py:
	  Reverted to previous version (mistakenly committed).

	* [r2884] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/laminar.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  topo/misc/inlinec.py,
	  topo/responsefns/basic.py,
	  topo/responsefns/optimized.py,
	  topo/tests/testplotgroup.py:
	  Changed response_fns.optimized.CFDotProduct to CFDotProduct_opt1.
	  If inline-optimized components aren't available, falls back to
	  basic's CFDotProduct.

	* [r2883] examples/laminar.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  topo/learningfns/optimized.py:
	  Changed learningfns.optimized.Hebbian to Hebbian_opt1. If
	  inline-optimized components aren't available, falls back to
	  Hebbian.

	* [r2882] topo/base/projection.py:
	  Added 'norm_value' Parameter to OutputFunction(). This is a hack
	  while ConnectionField assumes all OutputFunctions have a
	  norm_value.

	* [r2881] examples/laminar.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  topo/outputfns/optimized.py,
	  topo/tests/testoutputfnsoptimized.py:
	  Changed ouputfns.optimized.DivisiveSumNormalize to
	  DivisiveSumNormalize_opt1. If inline-optimized components aren't
	  available, falls back to DivisiveSumNormalize.

	* [r2880] examples/laminar.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty:
	  Removed cache_sum attribute from CFProjection.

	* [r2879] topo/learningfns/optimized.py:
	  Hebbian sets cf._sum, allowing the sum of the weights to be
	  cached without using the slower Python property.

	* [r2878] topo/base/connectionfield.py:
	  Removed cache_sum; if _sum attribute exists, it is assumed that
	  the value is always current.

	* [r2877] examples/laminar.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  topo/base/connectionfield.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py,
	  topo/projections/basic.py:
	  Split output_fns from learning_fns. Introduced CFOuputFunction
	  class to apply the output_fn to all CFs. Some ways things have
	  been done are a little confusing and could be simplified (notably
	  caching the sum of a CF's weights), but at the moment the example
	  networks should all behave the same.

	* [r2876] topo/outputfns/optimized.py:
	  Committed some commented-out classes (the CF output function
	  doesn't belong here).

	* [r2875] examples/homeostatic.ty:
	  Removed apparently unused code.

2006-03-13  ceball

	* [r2874] topo/tests/__init__.py:
	  Test of optimized output functions runs automatically.

	* [r2873] topo/outputfns/optimized.py:
	  Added return statements to match other output functions.

	* [r2872] topo/outputfns/optimized.py:
	  Corrected DivisiveSumNormalize for when the desired norm_value is
	  not 1.

2006-03-12  ceball

	* [r2871] topo/outputfns/basic.py:
	  Changed DivisiveSumNormalize so that it can accept a
	  pre-calculated norm_value for the array, if one is known. If the
	  pre-calculated value is equal to the current value, no
	  normalization operation need occur.

2006-03-11  ceball

	* [r2870] topo/outputfns/optimized.py:
	  Initial version. DivisiveSumNormalize intended to be equivalent
	  but faster version of that in outputfns/basic.py

	* [r2869] topo/learningfns/optimized.py:
	  The previous commit was a mistake (it was supposed to be
	  outputfns/optimized that I committed, not learningfns/optimized).
	  This is the code from version 1.39.

	* [r2868] topo/learningfns/optimized.py,
	  topo/tests/testoutputfnsoptimized.py:
	  Initial version. DivisiveSumNormalize intended to be equivalent
	  but faster version of that in outputfns/basic.py

2006-03-10  ceball

	* [r2867] topo/learningfns/optimized.py:
	  DivisiveHebbian's normalization happens every time, whether or
	  not the output activity is zero.

	* [r2866] topo/base/connectionfield.py:
	  Added sum of cf's initial weights.

2006-03-09  ceball

	* [r2865] external/mswin/setup.bat,
	  external/mswin/setup.py:
	  Installation creates a desktop shortcut with the Topographica
	  icon.

	* [r2864] external/mswin/create_shortcut.vbs:
	  Creates a desktop shortcut.

2006-03-08  ceball

	* [r2863] external/mswin/setup.py:
	  Fixed typo.

	* [r2862] external/mswin/setup.py:
	  Removed comment left in by accident.

	* [r2861] topo/misc/commandline.py:
	  Filename arguments are enclosed in repr() so that bits of Windows
	  paths that look like control characters don't turn into control
	  characters. (Note: I don't know that the slashes around the
	  string were for originally.)

	* [r2860] external/mswin/setup.py:
	  Batch file: changes to Topographica path before running, so that
	  the current path variable is correct.

	* [r2859] topo/responsefns/optimized.py:
	  Changed syntax in CFDotProduct: no visible change.

	* [r2858] topo/learningfns/optimized.py:
	  Moving to c++ syntax for clarity...no visible change.

	* [r2857] topo/learningfns/optimized.py:
	  Moving to c++ syntax for clarity...no visible change.

	* [r2856] topo/learningfns/optimized.py:
	  Moving to c++ syntax for clarity...no visible change.

	* [r2855] topo/misc/inlinec.py:
	  Added verbose=0 to the inline() arguments. I'm not sure it
	  actually makes any difference. Developers can set it to 2 to see
	  more output for debugging; 0 should result in less garbage output
	  for users. See the weave documentation (but good luck finding
	  it...try old.scipy.org).

	* [r2854] topo/misc/commandline.py:
	  Removed apparently redundant try/catch block (there is already
	  one in inlinec.py; in any case, if something other than an
	  ImportError occurs I think a user should see it).

	* [r2853] topo/learningfns/optimized.py:
	  Cleanup in DivisiveHebbian - no visible change.

	* [r2852] topo/learningfns/optimized.py:
	  Intermediate checkin: DivisiveHebbian has learning in one chunk
	  of C, and normalization in another. No visible change.

	* [r2851] topo/learningfns/optimized.py:
	  Intermediate checkin: store sum of cf's weights in cf.sum, and
	  retrieve. No visible change.

	* [r2850] topo/base/connectionfield.py:
	  Intermediate checkin: added sum attribute to connectionfield.

	* [r2849] topo/learningfns/optimized.py:
	  Normalization factor is calculated as the sum of the weights each
	  time, rather than accumulating the differences and assuming they
	  summed to 1 in the previous iteration. This has a very small
	  effect; after 20000 iterations, the weights are different in
	  about the 6th decimal place, and a sum over the activity in V1
	  differs in about the fifth decimal place.

2006-03-07  ceball

	* [r2848] topo/misc/commandline.py:
	  No visible change: minor change to import statement.

	* [r2847] doc/Downloads/index_text.php:
	  Minor correction to text.

	* [r2846] doc/Future_Work/current_text.php:
	  Updated with my current tasks.

	* [r2845] doc/Downloads/index_text.php:
	  Changed Windows installation instructions.

	* [r2844] setup.bat:
	  Just calls external\mswin\setup.bat

	* [r2843] external/mswin/setup.bat,
	  external/mswin/setup.py:
	  Minor changes, plus associates '.ty' files with Topographica.

	* [r2842] external/mswin/setup.bat:
	  Minor change - pauses at the end in case launched by double
	  clicking.

	* [r2841] external/mswin/setup.py:
	  Now generates a script that looks more like the one on unix.
	  Fixed a problem with quotation marks.

	* [r2840] topo/__init__.py:
	  Added 'release' attribute, which is set by the topographica
	  script. Moved ABOUT_TEXT into the about() function so that the
	  release value is filled in once it's been set, rather than
	  before.

	* [r2839] Makefile:
	  Removed setting of TOPORELEASE environment variable, and replaced
	  it by setting topo.release.

	* [r2838] Makefile:
	  Removed PYTHONPATH.

	* [r2837] Makefile:
	  Removed TOPOGRAPHICAPATH.

2006-03-07  jbednar

	* [r2836] external/mswin/setup.py:
	  Hopefully fixes the backslash problem for the generated
	  topographica.py script

2006-03-07  ceball

	* [r2835] topo/learningfns/optimized.py,
	  topo/projections/optimized.py,
	  topo/responsefns/optimized.py,
	  topo/sheets/lissom.py:
	  Commented out cpointer code.

2006-03-06  ceball

	* [r2834] external/mswin/setup.py:
	  Corrected another mistake.

	* [r2833] external/mswin/setup.py:
	  Corrected an error with quotation marks.

	* [r2832] external/mswin/setup.bat,
	  external/mswin/setup.py,
	  external/mswin/topographica.bat:
	  Various changes to the scripts.

	* [r2831] Makefile,
	  topo/base/parameterclasses.py:
	  Filename parameter gets the path by going up a level from the
	  directory of the binary, which works on Windows and unix. There
	  might be a better way.

2006-03-06  jbednar

	* [r2830] topo/tkgui/editorwindow.py:
	  Clarified what the snapshot is, to distinguish it from the
	  network snapshot

2006-03-06  ceball

	* [r2829] external/mswin/python242_topo.tar.gz,
	  external/mswin/python242_topo_weave.tar.gz,
	  external/mswin/python_topo.tar.gz:
	  Removed previous versions of Python directories and added one
	  back. The new one has weave and the mingw c compiler, and is
	  configured to use this c compiler by default so it will work on
	  windows without any extra work.

	* [r2828] external/mswin/setup.bat,
	  external/mswin/setup.py,
	  external/mswin/topographica.bat:
	  Updated to work with new python_topo.tar.gz

	* [r2827] Makefile,
	  external/Makefile:
	  Instead of setting the LD_LIBRARY_PATH environment variable after
	  python has started, we hard-code the lib/ as the path when we
	  make the python binary.

2006-03-04  ceball

	* [r2826] topo/base/parameterclasses.py:
	  Added a HACKALERT and corrected a typo in the code.

	* [r2825]
	  external/mswin/python242_topo_weave.tar.gz:
	  Python with weave from scipy. Unfortunately includes other things
	  for the moment that take up space and could be removed.

	* [r2824] external/mswin/setup.bat:
	  Added note on how to get weave.

	* [r2823] topo/base/parameterclasses.py:
	  Removed a HACKALERT.

	* [r2822] external/mswin/python242_topo.tar.gz:
	  Python 2.4.2 with Numeric, PIL, matplotlib, Pmw, Fixedpoint

	* [r2821] external/mswin/topographica.bat:
	  Starts python with the topographica.py script. INitial version.

	* [r2820] external/mswin/setup.py:
	  Creates topographica.py script. Initial version.

	* [r2819] external/mswin/setup.bat:
	  Simple windows batch file to install ready-made python. Initial
	  version.

	* [r2818] external/mswin,
	  external/mswin/util,
	  external/mswin/util/gunzip.exe,
	  external/mswin/util/tar.exe:
	  Utilities for extracting archives.

	* [r2817] Makefile,
	  topo/base/parameterclasses.py:
	  Added TOPOGRAPHICAPATH to environment variables.

2006-03-03  ceball

	* [r2816]
	  external/win32/Numeric-24.2.win32-py2.4.exe:
	  New version (added binary)

	* [r2815]
	  external/win32/Numeric-24.2.win32-py2.4.exe:
	  Removed apparently-corrupt file. It wasn't added as binary and
	  isn;t the same size as the original.

	* [r2814] doc/Future_Work/current_text.php:
	  Updated my tasks.

	* [r2813] external/win32/python-2.4.2.msi:
	  Added as a binary file.

	* [r2812] external/win32/python-2.4.2.msi:
	  Not in binary format. Two Windows machines I tried it on said it
	  is invalid; it worked on another.

	* [r2811] external/win32/python-2.4.msi:
	  Removed Python 2.4 since it's not used any more (we have 2.4.2).

	* [r2810] Makefile:
	  Topograpgica script: no longer uses os.getenv() - instead
	  accesses the os.environ dictionary itself.

	* [r2809] Makefile:
	  For topographica script: ignore PYTHONPATH environment variable
	  and just use our own Python's path.

2006-03-03  jbednar

	* [r2808] examples/lissom_or_20000.typ:
	  Removed saved .typ files, to speed up CVS downloads

	* [r2807] examples/lissom_oo_or_20000.typ:
	  Removed saved .typ files, to speed up CVS downloads

	* [r2806] doc/Tutorials/lissom_oo_or_text.php,
	  doc/Tutorials/lissom_or_text.php:
	  Changed tututorial instructions to ask users to build a map
	  rather than assuming it is in CVS

	* [r2805] Makefile,
	  examples/Makefile:
	  Added code to generate saved example files

	* [r2804] doc/Future_Work/index_text.php:
	  Added note about filenames as window titles

	* [r2803] ChangeLog.txt:
	  Updated with recent changes

	* [r2802] examples/Makefile:
	  Added one iteration of execution

	* [r2801] Makefile:
	  Changed exec_argv to process_argv to match change in
	  commandline.py

	* [r2800] Makefile:
	  Changed exec_argv to process_argv to match change in
	  commandline.py

	* [r2799] topo/misc/commandline.py:
	  Cleaned up and simplified

	* [r2798] Makefile:
	  Minor cleanup to topographica script

2006-03-02  ceball

	* [r2797] Makefile:
	  Removed 'rm topographica' and put back '> topographica' instead
	  of '>> topographica' on first line. (I didn't realize there was a
	  difference...)

	* [r2796] Makefile:
	  Removed TOPO variable from generated topographica script code.

	* [r2795] Makefile:
	  Changed generated code for topographica script. (1) Environment
	  variables are set before any imports of Topographica things. (2)
	  Environment variables are not set with putenv() (see
	  http://www.python.org/doc/2.4.2/lib/os-procinfo.html). (3)
	  Removed extra slash in first line. (4) Sorted out ':' between
	  paths. (3) and (4) might be wrong and need to be checked.

	* [r2794] topo/__init__.py:
	  No visible change - moved import statemtements to the top.

	* [r2793] topo/misc/commandline.py:
	  If topographica is started with no scripts or commands to run, it
	  opens interactively (i.e. './topographica' is the same as
	  './topographica -i').

	* [r2792] topo/base/parameterclasses.py,
	  topo/plotting/templates.py:
	  Simplified Filename Parameter, so it has just one search list.

2006-03-02  jbednar

	* [r2791] topo/base/patterngenerator.py:
	  Moved an alert here from learningfns/basic.py. (Chris)

	* [r2790] topo/learningfns/basic.py:
	  Removed an irrelevant alert and moved another to
	  patterngenerator. (Chris)

	* [r2789] topo/learningfns/basic.py:
	  Modified commented-out print statement to include simulation
	  time. (Chris)

	* [r2788] Makefile:
	  Added control over test verbosity

	* [r2787] topo/misc/commandline.py:
	  Fixed scripts to run in main (e.g. to get the value of pi
	  defined); not sure why the previous syntax was not signalling an
	  error

2006-03-02  ceball

	* [r2786] runtests:
	  No longer required: tests can be run like this:\n./topographica
	  -c 'import topo.tests; topo.tests.run()'

	* [r2785] Makefile:
	  Changed how tests are run (no longer uses runtests script).

	* [r2784] topo/tests/__init__.py:
	  Added run() function to allow tests to be run like
	  this:\n./topographica -c 'import topo.tests; topo.tests.run()'

	* [r2783] topo/base/parameterclasses.py:
	  Added HACKALERT: think about Parameter class attributes,
	  remembering they won't pickle because Parameter isn't a
	  TopoObject (in most cases that's likely to be fine, but some
	  class attributes are designed to be set by the user). Moved
	  Filename's topographica_path to be an instance attribute for the
	  moment, because trying to set it on unpickling wasn't possible
	  since it's read-only. This will be investigated at the same time
	  as the alert.

	* [r2782] topo/tkgui/topoconsole.py:
	  Removed a line that should have been removed in the previous
	  version.

	* [r2781] topo/base/simulator.py,
	  topo/tkgui/topoconsole.py:
	  Got rid of some uses of 'active_sim', and got rid of
	  'objects_to_notify_of_active_sim' concept, since the current
	  simulator is always in topo.sim.

2006-03-01  jbednar

	* [r2780] topo/__init__.py:
	  Reduced amount imported

	* [r2779] topo/learningfns/basic.py:
	  Moved aspect_ratio into the default Gaussian neighborhood,
	  because it's conceivable to use a non-unity aspect ratio

	* [r2778] topo/commands/analysis.py:
	  Fixed bogus assumption that all projections will have a cfs
	  variable, and made it respect the measure_maps declaration. It
	  should now work with lissom_oo_or.ty, but it still needs work
	  because it doesn't seem to measure any useful map for a
	  SharedWeightProjection

	* [r2777] topo/misc/commandline.py:
	  Clarified help message

	* [r2776] runtests:
	  Added ALERT

	* [r2775] topo/tkgui/editorwindow.py:
	  Added alert

2006-03-01  ceball

	* [r2774] topo/tkgui/topoconsole.py:
	  Removed uses of get_active_sim().

	* [r2773] topo/commands/basic.py:
	  Replaced get_active_sim() with topo.sim

	* [r2772] topo/base/parameterclasses.py:
	  No visible change - changed a variable name.

	* [r2771] topo/base/simulator.py,
	  topo/tests/tkgui/testtopoconsole.py:
	  Removed topo.base.simulator.set_active_sim().

	* [r2770] topo/tkgui/editorwindow.py:
	  Just uses topo.sim to get the simulator.

	* [r2769] examples/hierarchical.ty:
	  Added some temporary demonstration lines for how access to the
	  simulator might work.

	* [r2768] topo/base/simulator.py:
	  Simulator supports dictionary-like assignment. Temporary method
	  connect2() added to work with this.

	* [r2767] topo/tkgui/topoconsole.py:
	  On initialization, gets self.simulator from topo.sim. There is
	  always a simulator now. Some plotting menu options need to be
	  updated to check there are sheets of the right type to do
	  whatever it is they're supposed to do.

	* [r2766] topo/__init__.py,
	  topo/base/simulator.py,
	  topo/commands/basic.py,
	  topo/tkgui/topoconsole.py:
	  Added SimSingleton class. Added variable topo.sim=SimSingleton(),
	  so there is simulator (empty) on startup. SimSingleton() keeps
	  one Simulator() object and allows almost-transparent access to
	  it, so topo.sim['V1'] etc is possible. Begun changing calls to
	  get_active_sim etc.

2006-03-01  jbednar

	* [r2765] examples/homeostatic.ty:
	  Initial version for Veldri to work with

2006-02-28  ceball

	* [r2764] runtests:
	  Commented out argument-processing to allow runtests (and 'make
	  all') to work.

	* [r2763] examples/som_retinotopy.ty:
	  Uses indepedent streams for input pattern parameters.

	* [r2762] topo/plotting/templates.py:
	  Made image_path be a parameter; a path can be 'put through' this
	  to ensure it's valid for the OS and that the correct locations
	  are searched.

	* [r2761] topo/base/parameterclasses.py:
	  Filename searches prefixes specified for this particular
	  parameter first, then common ones.

	* [r2760] topo/base/parameterclasses.py:
	  Filename can be declared with None as the path (i.e. no default
	  path). Changed path searching method, to allow relative and
	  absolute prefix paths.

	* [r2759] topo/patterns/image.py:
	  Removed path left in by mistake, updated doc string.

	* [r2758] topo/base/parameterclasses.py,
	  topo/patterns/image.py:
	  For relative paths, Filename now searches both the
	  Filename.common_search_paths list and any specific list of
	  search_paths an instance is given. Currently common_search_paths
	  includes sys.exec_prefix (Topographica base directory.

	* [r2757] doc/Future_Work/current_text.php:
	  Updated with current work.

2006-02-28  julienciroux

	* [r2756] Makefile,
	  topo/misc/commandline.py:
	  Changed the generate_params and generate_prefixes so that they
	  execute commands as they find them instead of creating a string.
	  They have been re-named exec_argv and exec_prefixes.

2006-02-28  ceball

	* [r2755] examples/lissom_or.ty:
	  Uses RandomWrapper, so x, y, and orientation are independent
	  random streams, and resume where they left off on pickling.

	* [r2754] topo/base/parameterclasses.py:
	  Added RandomWrapper, a modified version of Wrapper, that creates
	  a new Random() instance. Gives independent random streams, and
	  allows the state of the stream to be saved when pickling.

2006-02-28  julienciroux

	* [r2753] Makefile,
	  topo/misc/commandline.py:
	  Modified the generate_params and generate_prefixes function in
	  commandline.py so that to work with the first copy of python,
	  instead of having to re-open a new one. Python options are now
	  directly set on the corresponding environment variable, and the
	  string of command is then executed with the exec command. There
	  is one problem for the verbose option: the variable PYTHONVERBOSE
	  is only read during startup, and cannot be re-set afterwards.
	  Therefore, the verbose option is currently disabled.

2006-02-28  jbednar

	* [r2752] topo/misc/commandline.py:
	  Added alert

2006-02-27  julienciroux

	* [r2751] topo/misc/commandline.py:
	  Replaced old topographica_script code by the new version that
	  uses Optparse.

	* [r2750] topographica_script.py:
	  Deleted the topographica_script.py file; the code has been moved
	  to topo.misc.commandline.py.

	* [r2749] Makefile:
	  Modified the Makefile to take into account that the code of
	  topographica_script has been moved to topo/misc/commandline.py;
	  also inserted the variable TOPO into the environment. People will
	  have to do a make after the update to get a version that works.

	* [r2748] topo/misc/commandline.py:
	  Moved the topographica_script code to topo/misc/commandline.py.

	* [r2747] topo/learningfns/basic.py:
	  Set the x and y to 0 when creating the Gaussian instead of when
	  calling it. That allows more flexibility for the user.

2006-02-27  ceball

	* [r2746] topo/base/simulator.py:
	  Added more helpful error to __getattribute__(), for if a string
	  is not given.

	* [r2745] topo/base/simulator.py:
	  Added dictionary-like object access for Simulator: for a
	  Simulator s, s['V1'] does s.objects()['V1'].

2006-02-27  jbednar

	* [r2744] topo/base/simulator.py:
	  Fixed typo

	* [r2743] topo/base/parameterizedobject.py:
	  Minor comment cleanup

	* [r2742] doc/Future_Work,
	  doc/Future_Work/.cvsignore:
	  Added current page

2006-02-26  ceball

	* [r2741] examples/hierarchical.ty:
	  Input pattern parameters set on objects, rather than the class. I
	  use two independent objects here, though for the moment they
	  aren't really independent because everything shares one stream of
	  random numbers.

	* [r2740] doc/Future_Work/current_text.php:
	  Updated my tasks.

	* [r2739] examples/laminar.ty,
	  examples/lissom_or.ty:
	  Input pattern parameters set on a Gaussian object rather than the
	  Gaussian class.

	* [r2738] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/laminar.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  topo/base/connectionfield.py,
	  topo/base/parameterclasses.py,
	  topo/patterns/basic.py:
	  Some things will not deepcopy, such as Numeric's ufuncs. Added a
	  Wrapper class (which will be renamed and will probably be changed
	  to operate differently) that allows these things to be
	  deepcopied. CompositePatternGenerator used a ufunc, so is changed
	  to use a Wrapper. Lambdas will also not deepcopy; Wrapper does
	  not support them, but does offer an alternative. Examples files
	  that used lambdas are changed accordingly.

	* [r2737] topo/commands/basic.py:
	  save_snapshot and load_snapshot are changed to include pickling
	  of class attributes.

	* [r2736] topo/misc/utils.py:
	  Added a function (which could be simplified) to search modules
	  and retrieve class' states.

	* [r2735] topo/base/parameterizedobject.py:
	  ParameterizedObject has __getstate__() that only returns instance
	  data (before it also returned class data). Also, it deep copies
	  any instance attribute that is a Parameter. Parameter has support
	  for deepcopy and pickle with its own __getstate__ and
	  __setstate__ (required because Parameter uses __slots__, and does
	  not have a __dict__).

2006-02-25  jbednar

	* [r2734] doc/Future_Work/index_text.php:
	  More to do

	* [r2733] topo/tkgui/topoconsole.py:
	  Added indication of why the GUI is exiting

2006-02-24  ceball

	* [r2732] topo/base/parameterizedobject.py:
	  No visible change: commented-out code for new __getstate__().

	* [r2731] topo/commands/basic.py:
	  No visible change: new commented-out code for replacement
	  snapshot functions.

	* [r2730] topo/misc/utils.py:
	  No visible change: new commented-out code for a recursive module
	  search. Might not belong here.

	* [r2729] topo/base/parameterclasses.py:
	  No visible change: a commented-out Wrapper class.

	* [r2728] topo/base/parameterizedobject.py:
	  No visible change: commented-out code for __getstate__() and
	  __setstate__() of Parameter.

	* [r2727] doc/Future_Work/current_text.php:
	  Updated what I'm working on.

	* [r2726] topo/__init__.py:
	  ABOUT text includes the Topographica release number.

2006-02-24  julienciroux

	* [r2725] topo/plotting/templates.py:
	  Made normalize be a BooleanParameter, and corrected the templates
	  where it was passed in as a string. Cleaned up ALERTS.

	* [r2724] topo/plotting/bitmap.py:
	  Cleaned up doc and ALERTS.

2006-02-24  ceball

	* [r2723] topo/tkgui/topoconsole.py:
	  Updates to 'Help' menu options.

	* [r2722] doc/Future_Work/current_text.php:
	  Added a task.

2006-02-23  julienciroux

	* [r2721] examples/som_retinotopy.ty:
	  Corrected to the right density (which has been changed by mistake
	  in the previous commit.

	* [r2720] topo/learningfns/basic.py:
	  Ensured that the neighborhood matrix is defined with x=0 and y=0.

	* [r2719] examples/som_retinotopy.ty:
	  Corrected the som_retinotopy example such as not setting x,y and
	  orientation directly on the Gaussian class, but rather creating a
	  Gaussian object and assigning it to the GeneratorSheet.

2006-02-23  ceball

	* [r2718] doc/Future_Work/current_text.php:
	  Added task, moved another to current work section.

	* [r2717] topo/projections/basic.py:
	  Projection imported to projections/basic.py so that it's part of
	  the projections package.

	* [r2716] topo/base/projection.py:
	  Projection is an abstract class.

	* [r2715] doc/Future_Work/current_text.php:
	  Added a task, changed some others round.

2006-02-23  alan_lindsay

	* [r2714] topo/tkgui/editorobjects.py:
	  Fixed a wee typo(Ta Chris).

2006-02-23  ceball

	* [r2713] topo/base/parameterclasses.py,
	  topo/base/utils.py:
	  find_classes_in_package() returns the base class, but does not
	  return any abstract classes.

	* [r2712] topo/base/sheet.py:
	  Sheet is declared to be an abstract class.

	* [r2711] topo/base/sheet.py:
	  Continued to write Slice class. Added methods sheet2matrix() and
	  matrix2sheet() to Sheet. This is still a work in progress - there
	  won't be so many functions by the end.

	* [r2710] topo/patterns/image.py:
	  Tidied up import statements.

2006-02-23  jbednar

	* [r2709] topo/base/parameterizedobject.py:
	  Changed ParameterizedObject.__repr__ to use __repr__ for
	  attribute values also, to get closer to a valid Python expression

2006-02-23  ceball

	* [r2708] doc/Future_Work/current_text.php:
	  Corrected html tag error.

	* [r2707] doc/Future_Work/current_text.php:
	  Removed a task and added another to the doing next section.

	* [r2706] topo/base/connectionfield.py,
	  topo/base/parameterclasses.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py:
	  ClassSelectorParameter subclasses have packages attribute that
	  works properly.

	* [r2705] topo/base/parameterclasses.py:
	  Corrected mistake introduced in the previous-but-one version.

	* [r2704] topo/base/parameterclasses.py:
	  Minor updates

	* [r2703] topo/base/connectionfield.py,
	  topo/base/parameterclasses.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py:
	  ClassSelectorParameter and subclasses use __slots__.

	* [r2702] topo/tkgui/editortools.py:
	  Removed duplicate import statement.

	* [r2701] topo/base/parameterclasses.py:
	  Tidying ClassSelectorParameter; no visible change.

2006-02-23  jbednar

	* [r2700] examples/Makefile:
	  Made default LISSOM test be oo_or instead of or to test more code

	* [r2699] doc/Future_Work/current_text.php:
	  Cleaned up and reworded

2006-02-22  ceball

	* [r2698] topo/base/parameterizedobject.py:
	  __repr__() returns almost-runnable expression.

	* [r2697] doc/Future_Work/current_text.php:
	  Removed a task; moved another to currently-working-on section.

	* [r2696] topo/base/sheet.py,
	  topo/base/simulator.py:
	  No longer overrides __repr__().

	* [r2695] topo/base/parameterizedobject.py:
	  ParameterizedObject's __repr__() returns <classname name> and a
	  list of all Parameters. __str__() returns <classname name>.

	* [r2694] topo/base/parameterclasses.py:
	  ClassSelectorParameter's suffix_to_lose defaults to empty string
	  rather than None (which it did before I accidentally changed it).

	* [r2693] topo/base/parameterclasses.py,
	  topo/tkgui/testpattern.py:
	  ClassSelectorParameter doesn't list abstract_classes.

	* [r2692] topo/patterns/random.py:
	  RandomGenerator declared to be an abstract class.

	* [r2691] topo/tkgui/parametersframe.py:
	  Moved topo/base/utils.py to topo/misc/utils.py

	* [r2690] topo/base/parameterizedobject.py,
	  topo/base/patterngenerator.py:
	  Classes now have an 'abstract' attribute which is True if the
	  class declares an _abstract_class_name equal to its name and
	  False otherwise (i.e. if it doesn't declare _abstract_class_name,
	  or it's set to False. Abstract classes can be instantiated.

2006-02-22  julienciroux

	* [r2689] topo/base/parameterclasses.py:
	  Added the possibility to change the default value for instantiate
	  when creating a ClassSelectorParameter.

2006-02-22  ceball

	* [r2688] topo/analysis/featuremap.py,
	  topo/base/utils.py,
	  topo/commands/pylabplots.py,
	  topo/misc/distribution.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/sheets/composer.py,
	  topo/sheets/generatorsheet.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testsheetview.py,
	  topo/tkgui/parametersframe.py:
	  Moved contents of topo/base/utils.py to topo/misc/utils.py

	* [r2687] topo/misc/utils.py:
	  Moved topo/base/utils.py to topo/misc/utils.py.

2006-02-22  jbednar

	* [r2686] examples/laminar.ty:
	  Made afferent learning match over the first few iterations. Fixed
	  bug in tsettle. Removed cortical edge buffers.

2006-02-22  ceball

	* [r2685] topo/base/arrayutils.py,
	  topo/base/utils.py,
	  topo/outputfns/basic.py:
	  Moved clip_in_place() from utils.py to arrayutils.py

	* [r2684] topo/base/parameterizedobject.py:
	  Minor edit of comments.

	* [r2683] topo/base/parameterizedobject.py:
	  Removed HACKALERT

	* [r2682] topo/base/parameterclasses.py,
	  topo/base/utils.py:
	  classname_repr() moved to be a method of ClassSelectorParameter.

	* [r2681] topo/base/parameterclasses.py,
	  topo/base/patterngenerator.py,
	  topo/tkgui/testpattern.py:
	  Added suffix_to_lose to ClassSelectorParameter, allowing that
	  siffix to be removed when the class name is displayed.
	  PatternGeneratorParameter removes 'Generator' by default.

	* [r2680] topo/base/utils.py:
	  Cleaned up documentation and removed unused import for
	  classname_repr().

	* [r2679] topo/base/sheet.py,
	  topo/base/simulator.py:
	  __repr__() is overridden to print more useful information.

	* [r2678] topo/base/utils.py:
	  classname_repr() no longer inserts spaces before capital letters.

	* [r2677] topo/base/parameterizedobject.py:
	  Made __str__() use __repr__() (both previously contained the same
	  code).

	* [r2676] topo/base/parameterizedobject.py:
	  Removed HACKALERT about name-sharing; added a HACKALERT about
	  printing more useful info at the commandline.

	* [r2675] doc/Future_Work/current_text.php:
	  Added task (CB).

	* [r2674] doc/Future_Work/current_text.php:
	  Initial version, biased towards my work.

2006-02-21  jbednar

	* [r2673] topo/sheets/lissom.py:
	  Changed tsettle into a positive Integer parameter instead of a
	  plain attribute

	* [r2672] topo/sheets/lissom.py:
	  Fixed for cases where there are multiple sheets in the model --
	  it had been counting the number of times pre_sleep was called,
	  which happens whenever any input event occurs. Now it counts the
	  number of actual activations for this sheet instead. Should not
	  change the results for lissom_or.ty, but should change the
	  results for lissom_oo_or.ty (which should do one less settling
	  step now)

2006-02-21  ceball

	* [r2671] topo/patterns/basic.py:
	  Minor alterations to CompositePatternGenerator.

	* [r2670] topo/patterns/basic.py:
	  Composite is now in a state where it can be tried out usefully in
	  the test pattern window (to see better how it should finally
	  work). But the implementation is temporary.

2006-02-20  ceball

	* [r2669] topo/base/parameterizedobject.py,
	  topo/base/patterngenerator.py:
	  Example of how we could prevent instantiation of abstract
	  classes, PatternGenerator in this case. Since the super() call
	  requires the class itself inside the call anyway, putting it in
	  there again is not too much trouble...

	* [r2668] topo/base/parameterclasses.py:
	  Change to a HACKALERT.

	* [r2667] topo/base/utils.py:
	  Added to documentation.

2006-02-20  ceball_cvs2svn

	* [r2666] /tags/release_0_8_2:
	  This commit was manufactured by cvs2svn to create tag
	  'release_0_8_2'.

2006-02-20  ceball

	* [r2665] topo/base/parameterizedobject.py:
	  Changed __param_inheritance() to look up the classlist
	  (superclasses) itself, rather than having it passed in. Renamed
	  uses of 'base_classes' to 'superclasses'; previously there was
	  confusion between 'bases' returned from classlist() and bases as
	  passed to the metaclass' __init__() method.

	* [r2664] topo/base/parameterizedobject.py:
	  __param_inheritance() changed to look at all slots, not just
	  those in the immediate class (so e.g. a Number parameter does
	  inheritance for bounds,softbounds and all the slots of its
	  superclasses (Parameter in this case)).

	* [r2663] topo/base/parameterizedobject.py:
	  Moved classlist() and descendents() to beginning of file.

2006-02-20  julienciroux

	* [r2662] topo/plotting/plot.py:
	  Cleaned up the doc.

	* [r2661] topo/plotting/plot.py:
	  Corrected mistake in Plot.

	* [r2660] topo/analysis/featuremap.py:
	  Deleted old Alert in FeatureMap.

2006-02-20  jbednar

	* [r2659] doc/shared/index.php:
	  Updated release date

	* [r2658] topo/patterns/basic.py,
	  topo/patterns/image.py:
	  Updated doc strings

2006-02-20  ceball

	* [r2657] doc/Team_Members/index_text.php:
	  Updated link.

	* [r2656] topo/base/parameterclasses.py:
	  Cleaned up ClassSelectorParameter a little.

	* [r2655] topo/base/connectionfield.py:
	  Cleaned up ResponseFunctionParameter and
	  LearningFunctionParameter.

	* [r2654] topo/base/patterngenerator.py:
	  Cleaned up PatternGeneratorParameter a little.

	* [r2653] topo/base/projection.py:
	  Cleaned up OutputFunctionParameter a little.

	* [r2652] topo/patterns/basic.py,
	  topo/patterns/image.py:
	  Added some doc strings

	* [r2651] topo/tkgui/parametersframe.py:
	  Removed out-of-date hackalert.

2006-02-20  jbednar

	* [r2650] doc/User_Manual/parameters_text.php:
	  Changed get_paramobj_dict to params

	* [r2649]
	  doc/images/060220_model_editor_screen_shot.png,
	  doc/images/060220_topographica_screen_shot.png,
	  doc/shared/index.php:
	  Added screenshots

2006-02-20  ceball

	* [r2648] topo/base/parameterizedobject.py:
	  Removed unused argument from params().

	* [r2647] topo/base/parameterizedobject.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/testpattern.py:
	  Re-named get_paramobj_dict() to params().

2006-02-20  jbednar

	* [r2646] doc/shared/index.php:
	  Updated release date

	* [r2645] examples/lissom_or_20000.typ:
	  Retrained map

	* [r2644] examples/lissom_oo_or_20000.typ:
	  Retrained map

	* [r2643] doc/User_Manual,
	  doc/User_Manual/.cvsignore,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/parameter_text.php,
	  doc/User_Manual/parameters_text.php:
	  Added link to Parameters documentation

	* [r2642] doc/User_Manual/parameter_text.php:
	  Cleaned up

2006-02-19  jbednar

	* [r2641] topo/base/simulator.py:
	  Changed schedule_action to accept only callable values. Changed
	  step_mode and register to be BooleanParameters, and added ALERT
	  about step_mode.

	* [r2640] topo/tests/testcfsom.py,
	  topo/tests/testsimulator.py:
	  Fixed step_mode to be Boolean to allow that parameter to be a
	  BooleanParameter

	* [r2639] topo/base/parameterclasses.py:
	  Added CallableParameter

	* [r2638] topo/plotting/templates.py:
	  Added OrientationSelectivity subplot to avoid confusion for
	  Sheets that are not orientation selective but still sometimes
	  have a map measured

	* [r2637] topo/plotting/bitmap.py:
	  Removed unused normalize parameter

	* [r2636] topo/learningfns/basic.py:
	  Made SOM neighborhood function into a PatternGeneratorParameter

	* [r2635] topo/eps/basic.py:
	  Replaced Parameters with Numbers

	* [r2634] topo/base/patterngenerator.py:
	  Changed density into a Number with a lower bound

	* [r2633] topo/base/parameterizedobject.py:
	  Added ALERT

2006-02-19  alan_lindsay

	* [r2632] topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py:
	  Activity toggle for all now too.

	* [r2631] topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py:
	  Right click in the canvas to bring up menu, allows save snapshot
	  of canvas (saved to postscript) and all sheet densities to be
	  toggled on/off.

2006-02-19  jbednar

	* [r2630] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py,
	  topo/base/sheet.py,
	  topo/learningfns/optimized.py:
	  Removed Constant Parameter, since it is the same as
	  Parameter(constant=True).

	* [r2629] topo/projections/basic.py:
	  Changed Constant to a LearningFunctionParameter(constant=True)

2006-02-19  julienciroux

	* [r2628] topo/sheets/generatorsheet.py:
	  Made period and phase parameter be Number instead of Parameter.

	* [r2627] topo/base/connectionfield.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py:
	  Moved the declaration of the ouput_fn parameter in the superclass
	  CFLearningFunction, instead of re-declaring it in all
	  sub-classes.

	* [r2626] topo/learningfns/optimized.py:
	  Cleaned up parameter doc string, changed output_fn for for
	  DivisiveHebbian and DivisiveHebbian_Cpointer to be
	  OutputFunctionParameter rather than Constant.

	* [r2625] topo/learningfns/basic.py:
	  Cleaned up parameters doc string.

	* [r2624] topo/base/connectionfield.py:
	  Added period to doc strings.

	* [r2623] topo/base/simulator.py:
	  Added alert about not being able to decalrestep_mode and register
	  Parameter as BooleanParameter.

	* [r2622] topo/base/patterngenerator.py:
	  Declared BoundingBox parameters as BoundingRegionParameter rather
	  than Parameter.

	* [r2621] topo/base/connectionfield.py:
	  Declared BoundingBox parameters as BoundingRegionParameter rather
	  than Parameter. Added some parameter doc string. Transformed
	  CFProjection learning_rate parameter to be a Number. Transformed
	  CF x and y parameters to be Numbers as well.

	* [r2620] examples/lissom_or.ty:
	  Deleted ommitted code added for testing purpose.

2006-02-19  jbednar

	* [r2619] topo/base/connectionfield.py:
	  Cleaned up doc strings

2006-02-19  julienciroux

	* [r2618] topo/base/connectionfield.py:
	  Added a doc string for the learning_fn parameter of a
	  CFProjection.

	* [r2617] topo/projections/optimized.py:
	  Declared the CFProjection_Cpointer learning_fn parameter as a
	  LearningFunctionParameter rather than a Parameter.

	* [r2616] topo/projections/optimized.py:
	  Declared the CFProjection_Cpointer response_fn parameter as a
	  ResponseFunctionParameter rather than a Parameter.

	* [r2615] topo/base/connectionfield.py:
	  Added a doc string for the response_fn parameter of a
	  CFProjection.

	* [r2614] topo/base/connectionfield.py,
	  topo/base/projection.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py,
	  topo/projections/basic.py:
	  Changed the output_fn declared as Parameters to be declared as
	  OutputFunctionParameter. I added a doc string when needed, that
	  might need to be reviewed. I tried to see in which case this doc
	  string was already inherited, and not added it ?\004in such case.

2006-02-19  jbednar

	* [r2613] topo/base/boundingregion.py:
	  Made BoundingRegionParameter instantiate by default

2006-02-19  julienciroux

	* [r2612] examples/lissom_oo_or.ty,
	  examples/lissom_or.ty:
	  Deleted the dest_port setting when creating a CFProjection. Now,
	  it is possible for different projections to the same sheet to
	  share the same dest_port (as soon as they are named differently).

	* [r2611] topo/base/projection.py:
	  Solved the problem of the port for Projection: first, ensure that
	  all the projection to the same ProjectionSheet are named
	  differently by raising an error if intenting to do so; second,
	  allow all the projection sharing the same ports to be?\004
	  activated (by removing the break in the activate method).

2006-02-19  jbednar

	* [r2610] topo/base/sheet.py:
	  Made bounds be a BoundingRegionParameter, and density be a
	  constant Parameter

2006-02-19  julienciroux

	* [r2609] topo/base/connectionfield.py,
	  topo/base/sheet.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotgroup.py:
	  Replaced the old bounds.aarect().lbrt() syntax by bounds.lbrt().

2006-02-19  jbednar

	* [r2608] topo/base/boundingregion.py:
	  Added BoundingRegionParameter

	* [r2607] topo/base/simulator.py:
	  Added EventProcessorParameter for src and dest of an EPConnection

	* [r2606] topo/base/projection.py:
	  Added docstring

	* [r2605] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  Added ALERT

2006-02-19  julienciroux

	* [r2604] topo/base/boundingregion.py:
	  Added a lbrt() method to the BoundingBox. It should make Chris
	  happy by allowing him to to do bounds.lbrt().

	* [r2603] examples/lissom_or.ty:
	  Corrected the Retina edge buffer.

2006-02-19  jbednar

	* [r2602] topo/base/parameterclasses.py:
	  Fixed exceptions to be classes

	* [r2601] topo/base/boundingregion.py:
	  Added Cartesian2DPoint parameter, and changed BoundingCircle to
	  use it and Number instead of Parameter

	* [r2600] ChangeLog.txt:
	  Added new entries

2006-02-18  jbednar

	* [r2599] topo/base/connectionfield.py,
	  topo/base/simulator.py:
	  Made a few more parameters constant

2006-02-18  julienciroux

	* [r2598] topo/base/parameterizedobject.py:
	  Corrected a doc referring to topo.base.parameter.

	* [r2597] topo/tkgui/parametersframe.py:
	  Corrected a doc referring to topo.base.parameter.

2006-02-18  alan_lindsay

	* [r2596] topo/tkgui/editorobjects.py:
	  Line view bounds check sorted.

	* [r2595] topo/tkgui/editortools.py:
	  Updates class parameters without update button

2006-02-18  ceball

	* [r2594] doc/User_Manual/parameter_text.php:
	  Tried to break text up a little.

	* [r2593] doc/User_Manual/parameter_text.php:
	  Continued writing...

2006-02-18  alan_lindsay

	* [r2592] topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py:
	  Added Refresh, Enlarge, Reduce buttons and an error message for
	  when connections don't happen.

2006-02-18  ceball

	* [r2591] doc/User_Manual/parameter_text.php:
	  Continued writing; still incomplete.

2006-02-18  jbednar

	* [r2590] doc/User_Manual/commandline_text.php,
	  doc/User_Manual/images/matrixvectorplot.png,
	  doc/User_Manual/images/sine_plot.png:
	  Added plot screenshots

	* [r2589] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  Cleaned up and generalized the documentation. Renamed methods and
	  variables that referred to Topographica, since the classes are
	  now fully general

	* [r2588] doc/Downloads/index_text.php:
	  Added note about make -k

2006-02-18  ceball

	* [r2587] topo/base/parameterizedobject.py:
	  Removed get_param_dict() because it simply returns attributes of
	  the TopoObject (and its superclasses) that are Parameters.

	* [r2586] topo/base/parameterizedobject.py:
	  Tidied comments.

	* [r2585] topo/base/parameterizedobject.py:
	  Moved two functions to the end of the file.

	* [r2584] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  Moved a HACKALERT

	* [r2583] topo/tkgui/parametersframe.py:
	  Parameters with attribute constant==True are set non-editable for
	  an object, and editable for a class (i.e. no visible change, just
	  updated for constant attribute of Parameter).

	* [r2582] topo/base/connectionfield.py:
	  weights_shape is set to be a constant Parameter.

	* [r2581] topo/tkgui/parametersframe.py:
	  Corrected import for classlist. There might be other files with
	  this mistake?

	* [r2580] topo/base/parameterclasses.py:
	  Removed HACKALERT.

	* [r2579] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  Moved Constant to parameterclasses.py

	* [r2578] topo/base/parameterizedobject.py:
	  Parameters can have a 'constant' attribute. If this is True, they
	  cannot be set on an initialized TopoObject (and they are also
	  instantiated). The Constant Parameter is now simply a Parameter
	  with constant=True. Constant parameters are now no longer
	  excluded from pickling - they are pickled like everything else.
	  Such changes go together because deepcopy uses __getstate__ and
	  __setstate__, as does pickling.

2006-02-17  ceball

	* [r2577] topo/projections/basic.py:
	  All SharedWeightCFProjections were sharing the same
	  cf_slice_and_bounds list because it was declared as a class
	  attribute.

	* [r2576] topo/base/parameterizedobject.py:
	  Removed print statement accidentally left behind.

	* [r2575] topo/base/parameterizedobject.py:
	  Corrected mistake in previous commit.

	* [r2574] topo/base/parameterizedobject.py:
	  get_name() doesn't just look in the immediate class for the
	  parameter, but in the whole class hierarchy. Before, None was
	  being returned sometimes. That had broken pickling.

2006-02-17  julienciroux

	* [r2573] topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py:
	  Moved Parameter (and associated functions class_list() and
	  descendents()) in parameterizedobject.py. I also momentarily
	  moved Constant, until the use of this class in Parameter is
	  deleted (Chris should fix that). Parameter and Constant are?\004
	  still imported in parameterclasses.py, so that we can still
	  import any Parameter class from parameterclasses.py.

	* [r2572] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  topo/base/__init__.py,
	  topo/base/boundingregion.py,
	  topo/base/connectionfield.py,
	  topo/base/parameter.py,
	  topo/base/parameterclasses.py,
	  topo/base/parameterizedobject.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/base/simulator.py,
	  topo/eps/basic.py,
	  topo/learningfns/__init__.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py,
	  topo/outputfns/__init__.py,
	  topo/outputfns/basic.py,
	  topo/patterns/__init__.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/plotting/templates.py,
	  topo/projections/basic.py,
	  topo/projections/optimized.py,
	  topo/responsefns/__init__.py,
	  topo/responsefns/basic.py,
	  topo/responsefns/optimized.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py,
	  topo/tests/lissom_oo_or_reference.ty,
	  topo/tests/lissom_or_reference.ty,
	  topo/tests/testcfsom.py,
	  topo/tests/testlissom.ty,
	  topo/tests/testlissom_cpointer.ty,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testsheetview.py,
	  topo/tests/tkgui/testplotgrouppanel.py,
	  topo/tkgui/parametersframe.py:
	  Renamed parameter.py to parameterclasses.py.

	* [r2571] topo/base/parameter.py:
	  Re-implemented the __get__ method for Number, so that not having
	  to know about DynamicNumber from the Parameter class (will
	  eventually allow to move the Parameter class to
	  parameterizedobject.py.

2006-02-17  alan_lindsay

	* [r2570] topo/tkgui/editorobjects.py:
	  Added density grid view for sheets

2006-02-17  julienciroux

	* [r2569] examples/hierarchical.ty,
	  topo/analysis/featuremap.py,
	  topo/base/__init__.py,
	  topo/base/boundingregion.py,
	  topo/base/connectionfield.py,
	  topo/base/parameterizedobject.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheetview.py,
	  topo/base/simulator.py,
	  topo/base/topoobject.py,
	  topo/base/utils.py,
	  topo/commands/basic.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py,
	  topo/outputfns/basic.py,
	  topo/patterns/image.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/plotting/templates.py,
	  topo/projections/basic.py,
	  topo/projections/optimized.py,
	  topo/responsefns/basic.py,
	  topo/responsefns/optimized.py,
	  topo/sheets/lissom.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplot.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testsheet.py,
	  topo/tests/tkgui/testplotgrouppanel.py,
	  topo/tests/tkgui/testtemplateplotgrouppanel.py,
	  topo/tests/tkgui/testtopoconsole.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Re-named topoobject.py to parameterizedobject.py.

	* [r2568] topo/base/parameter.py,
	  topo/base/topoobject.py:
	  Renamed TopoMetaclass to ParameterizedObjectMetaclass.

	* [r2567] topo/analysis/featuremap.py,
	  topo/base/arrayutils.py,
	  topo/base/boundingregion.py,
	  topo/base/connectionfield.py,
	  topo/base/parameter.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheetview.py,
	  topo/base/simulator.py,
	  topo/base/topoobject.py,
	  topo/base/utils.py,
	  topo/commands/basic.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py,
	  topo/outputfns/basic.py,
	  topo/patterns/image.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/plotting/templates.py,
	  topo/projections/basic.py,
	  topo/projections/optimized.py,
	  topo/responsefns/basic.py,
	  topo/responsefns/optimized.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py,
	  topo/tests/testplot.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Renamed TopoObject to ParameterizedObject.

2006-02-17  ceball

	* [r2566] topo/tkgui/parametersframe.py:
	  Added HACKALERT.

2006-02-17  julienciroux

	* [r2565] topo/base/connectionfield.py:
	  Added comment and ALERT.

2006-02-17  ceball

	* [r2564] topo/base/parameter.py,
	  topo/base/topoobject.py:
	  bounds and softbounds are None when not set so that parameter
	  inheritance works.

2006-02-17  julienciroux

	* [r2563] topo/base/connectionfield.py,
	  topo/sheets/cfsom.py:
	  Moved the test on the input_buffer from CFSheet learn() to
	  CFProjection learn().

2006-02-17  ceball

	* [r2562] topo/tkgui/parametersframe.py:
	  set_obj_params() only sets the value on an object if the value is
	  different from the one already in the object.

2006-02-17  jbednar

	* [r2561] topo/sheets/cfsom.py:
	  Moved alert here from som_retinotopy.ty

	* [r2560] examples/som_retinotopy.ty:
	  Simplified slightly

2006-02-17  ceball

	* [r2559] topo/base/connectionfield.py:
	  Added wrapper around hebbian() so deepcopy works. TopoObject
	  needs to have its support for deepcopy corrected.

	* [r2558] topo/base/topoobject.py:
	  Renamed __set_name() to __generate_name().

	* [r2557] topo/base/topoobject.py:
	  If a Parameter is a TopoObject, and it's deepcopied for a new
	  TopoObject, it's renamed.

	* [r2556] topo/base/topoobject.py:
	  No visible change: created a simple __set_name() method from the
	  original line of code in topoobject. (Done because it will be
	  used when Parameters are deepcopied to new objects.)

	* [r2555] topo/base/topoobject.py:
	  Added HACKALERT about the possibility of TopoObjects sharing the
	  same name.

	* [r2554] topo/base/connectionfield.py,
	  topo/base/topoobject.py,
	  topo/projections/basic.py:
	  Added wrapper around mdot so deepcopy works. TopoObject needs to
	  have its support for deepcopy corrected.

	* [r2553] topo/base/arrayutils.py:
	  Added temporary wrapper class around mdot.

2006-02-16  ceball

	* [r2552] topo/base/topoobject.py:
	  Had to add a HACK - some things don't seem to deepcopy.

	* [r2551] topo/sheets/lissom.py:
	  A Parameter has an 'instantiate' attribute (previously
	  'value_semantics') that indicates whether or not a TopoObject
	  should copy the Parameter into its own __dict__. instantiate
	  defaults to False for Parameter, but True for certain subclasses
	  (e.g. ClassSelectorParameter, Constant).

	* [r2550] topo/base/sheet.py:
	  topo/sheets/lissom.py

	* [r2549] topo/base/parameter.py,
	  topo/base/topoobject.py:
	  topo/sheets/lissom.py

2006-02-15  jbednar

	* [r2548] examples/laminar.ty:
	  Initial version from Judith

2006-02-15  julienciroux

	* [r2547] topo/base/connectionfield.py,
	  topo/sheets/cfsom.py:
	  Added a mysterious test (if proj.input_buffer), that I previously
	  deleted in CFSheet abd CFSOM learn() function, but that happens
	  to be needed. This will be solved tomorrow.

	* [r2546] topo/sheets/cfsom.py:
	  Modified the CFSOM learning function so that it calls the learn()
	  function on the projections, instead of re-implementing it.

	* [r2545] topo/base/connectionfield.py,
	  topo/base/projection.py:
	  Added a learn() function for Projections, which is called from
	  the CFSheet learn() function.

2006-02-15  ceball

	* [r2544] examples/lissom_oo_or.ty,
	  examples/lissom_oo_or_20000.typ:
	  Increased ON connection strength to 0.75. C++ LISSOM normalizes
	  all its afferent weights to 1 so the ON and OFF channel can have
	  different effects; topographica doesn't so we compensate by
	  increasing the ON connection strength until we sup?\004port joint
	  normalization.

	* [r2543] topo/tests/lissom_oo_or_reference.ty:
	  density and output_fn set on V1 rather than on LISSOM.

	* [r2542] topo/tests/lissom_oo_or_reference.ty:
	  Various changes to help match c++ lissom (adding edge buffers)
	  and to make the file clearer.

2006-02-14  ceball

	* [r2541] topo/base/boundingregion.py:
	  min_radius is deleted from the args if it's passed in, so that
	  it's not passed to the superclass. Removed a hackalert.

	* [r2540] topo/tests/lissom_oo_or_reference.ty:
	  SharedWeightCFProjection.learning_fn.output_fn set to
	  DivisiveSumNormalize, rather than being set on the Projections
	  separately.

2006-02-14  jbednar

	* [r2539] topo/commands/or_key_white_vert.png:
	  Flipped to fix

2006-02-14  julienciroux

	* [r2538] topo/plotting/plotgroup.py:
	  Added the possibility of passing SheetView plot_template to a
	  ConnectionField PlotGroupTemplate. If the plot_template uses the
	  keyword 'Weights' for the Strength, we request a UnitView,
	  otherwise we create a normal plot with Strength specifying a
	  SheetView. This not at all effective so far, because no such
	  template are declared (also the displaying of labels is not
	  exactly consistent between a connection field plot, and a normal
	  SheetView plot, but still it looks alright).

	* [r2537] topo/tkgui/connectionfieldspanel.py:
	  Corrected a typo mistake in the label display.

2006-02-14  ceball

	* [r2536] doc/User_Manual/parameter_text.php:
	  Beginnings of Parameter documentation. Committed while I change
	  locations...

	* [r2535] topo/base/topoobject.py:
	  Added HACKALERT about parameter inheritance.

	* [r2534] examples/lissom_oo_or.ty:
	  SharedWeightCFProjection.learning_fn.output_fn set to
	  DivisiveSumNormalize, instead of setting the projections'
	  learning_fn.output_fns separately.

2006-02-14  alan_lindsay

	* [r2533] topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py:
	  Changed the way you change the view of connectioons and sheets.
	  Radius' are represented, though, it seems like connections might
	  not be reporting the truth..

2006-02-13  jbednar

	* [r2532]
	  doc/Tutorials/som_retinotopy_text.php:
	  Minor cleanup

2006-02-13  julienciroux

	* [r2531] topo/plotting/plotgroup.py:
	  Deleted the added_list attribute and the add() function in
	  PlotGroup. It was an unused concept, and we can still add Plots
	  to a PlotGroup since its plot_list attribute is public.

	* [r2530] topo/plotting/plotgroup.py:
	  Added a function _ordering_plots in PlotGroup. It is called by
	  plots() before returning the plot_list. It allows to only have to
	  re-implement this simple function in ProjectionPlotGroup, instead
	  of the whole plots() function.

2006-02-13  ceball

	* [r2529] doc/User_Manual/space_text.php:
	  Minor changes.

2006-02-13  julienciroux

	* [r2528] topo/plotting/plotgroup.py:
	  Deleted a unused attribute self.all_plots.

2006-02-13  ceball

	* [r2527] doc/Tutorials/lissom_oo_or_text.php:
	  Changed Afferent0 that was left over to LGNOnAfferent.

2006-02-13  julienciroux

	* [r2526] topo/tkgui/projectionpanel.py:
	  Modified the sorting of the projections in the projection_menu:
	  now they are first sorted with the precedence number of there
	  source Sheet and then by alphabetical order. Also added a comment
	  about re-writing the function _create_projection_dict(), which is
	  quite messy.

	* [r2525] topo/base/sheetview.py:
	  Made the UnitView precedence parameter to be set to the value of
	  the projection.src.precedence parameter (the precedence number of
	  the source Sheet). That allows the plot in the
	  connectionfieldpanel to be sorted accordingly.

2006-02-13  ceball

	* [r2524] examples/lissom_oo_or_20000.typ:
	  Same map, but with updates to code in the pickle.

	* [r2523] topo/base/parameter.py,
	  topo/base/sheet.py,
	  topo/base/topoobject.py:
	  Parameter has a 'value_semantics' attribute. TopoObject copies
	  the Parameter into its own dictionary if this is set True. This
	  is just a demonstration of how we could do explicit value
	  semantics: setting value_semantics=True on any paramet?\004er
	  means a copy of its default value is always given to a new
	  TopoObject. So for a Constant parameter, setting
	  value_semantics=True makes the Constant truly constant. There is
	  one example of this for demonstration: Sheet's bounds. Presumably
	  the attribut?\004e shouldn't actually be called value_semantics.

2006-02-13  jbednar

	* [r2522] doc/Tutorials/lissom_oo_or_text.php:
	  Fixes and cleanup

	* [r2521]
	  doc/Tutorials/images/natural_image_oo_or.png,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Fixes and cleanup

2006-02-13  ceball

	* [r2520] topo/patterns/image.py:
	  Updated to take account of patterngenerator being passed the true
	  xdensity and ydensity rather than just the density. Added
	  hackalert.

2006-02-13  jbednar

	* [r2519]
	  doc/Tutorials/images/or_key_vert_transparent_topo.png:
	  Unused

	* [r2518] topo/commands/or_key_white_vert.png,
	  topo/plotting/templates.py:
	  Updated color key

	* [r2517]
	  doc/Tutorials/images/activity_line_oo.png,
	  doc/Tutorials/images/activity_line_oo_or.png,
	  doc/Tutorials/images/lissom_network_diagram_oo.png,
	  doc/Tutorials/images/oo_or_map.png,
	  doc/Tutorials/images/or_key_horiz_transparent.png,
	  doc/Tutorials/images/projection_oo.png,
	  doc/Tutorials/images/test_pattern_oo.png,
	  doc/Tutorials/images/unit_weights_0_0_oo.png,
	  doc/Tutorials/images/unit_weights_0_0_oo_or.png,
	  doc/Tutorials/lissom_oo_or_text.php:
	  Updated lissom_oo_or tutorial

	* [r2516] examples/lissom_oo_or.ty:
	  Adjusted model editor coordinates due to edge buffer change

	* [r2515] doc/Reference_Manual/index_text.php:
	  Added caveat

	* [r2514] doc/Downloads/index_text.php:
	  Updated Mac and Windows instructions

	* [r2513] doc/Tutorials/index_text.php:
	  Added link to lissom_oo_or tutorial

	* [r2512] doc/User_Manual/commandline_text.php:
	  Reorganized

	* [r2511] doc/shared/index.php:
	  Added news item

	* [r2510] README.txt:
	  Minor bugfix

	* [r2509] doc/User_Manual/commandline_text.php,
	  doc/User_Manual/index_text.php:
	  Added command line examples

	* [r2508] doc/User_Manual,
	  doc/User_Manual/.cvsignore:
	  More to ignore

	* [r2507] doc/Future_Work/index_text.php:
	  Updates; some items actually completed!

	* [r2506] Makefile:
	  Bumped version number in anticipation of release

	* [r2505] doc/Downloads/index_text.php:
	  Added Windows disclaimer

	* [r2504]
	  external/win32/Numeric-23.7.win32-py2.4.exe,
	  external/win32/Numeric-24.2.win32-py2.4.exe,
	  external/win32/setup.py:
	  Upgraded to Numeric 24

2006-02-13  ceball

	* [r2503] topo/base/connectionfield.py:
	  Minor change to hackalert.

	* [r2502] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty:
	  BoundingBox can be created by specifying a radius.

2006-02-13  jbednar

	* [r2501] doc/Developer_Manual,
	  doc/Developer_Manual/.cvsignore,
	  doc/Developer_Manual/parameters_text.php,
	  doc/Developer_Manual/python_text.php:
	  Reorganized developer manual to be grouped more reasonably

2006-02-13  ceball

	* [r2500] examples/lissom_oo_or.ty,
	  topo/base/boundingregion.py,
	  topo/base/connectionfield.py,
	  topo/tests/lissom_oo_or_reference.ty:
	  BoundingBox can be created by passing a radius or points. This
	  takes the place of the previous radial_bounds() function.

2006-02-13  jbednar

	* [r2499] doc/Tutorials,
	  doc/Tutorials/.cvsignore:
	  More to ignore

2006-02-12  jbednar

	* [r2498] doc/Developer_Manual/alerts_text.php,
	  doc/Developer_Manual/coding_text.php,
	  doc/Developer_Manual/communication_text.php,
	  doc/Developer_Manual/gui_text.php,
	  doc/Developer_Manual/imports_text.php,
	  doc/Developer_Manual/index_text.php,
	  doc/Developer_Manual/naming_text.php,
	  doc/Developer_Manual/ood_text.php,
	  doc/Developer_Manual/optimization_text.php,
	  doc/Developer_Manual/revisioncontrol_text.php:
	  Reorganized developer manual to be grouped more reasonably

2006-02-12  ceball

	* [r2497] topo/base/parameter.py:
	  Changed variable name in Constant to make the code clearer. The
	  previous version does appear to work - I appear to have been
	  confusing myself while testing it.

	* [r2496] topo/base/parameter.py:
	  Simple version of Constant that ought to work, but appears not
	  to.

2006-02-12  jbednar

	* [r2495] topo/responsefns/optimized.py:
	  Simplified CFDotProduct C++ code by moving declarations to where
	  they are needed

2006-02-12  ceball

	* [r2494] topo/base/parameter.py:
	  Changed Constant's attepted set error to a TypeError.

	* [r2493] topo/base/parameter.py:
	  Removed a HACKALERT that should have been removed a while back.

	* [r2492] topo/base/parameter.py:
	  Constant parameter is now constant (i.e. doesn't inherit changes
	  once it's been created).

	* [r2491] topo/base/sheet.py:
	  Removed 'default=' from Constant declarations.

	* [r2490] topo/sheets/lissom.py:
	  The LISSOM sheet output_fn Parameter is set in the constructor,
	  rather than being re-declared at the class level. This means that
	  each LISSOM sheet object has its own output_fn by default, rather
	  than all LISSOM sheets sharing one object.?\004

2006-02-12  julienciroux

	* [r2489] topo/tkgui/cfsheetplotpanel.py:
	  Changed the sorting of the region_menu, so that to start by high
	  area instead of low area.

	* [r2488] topo/tkgui/cfsheetplotpanel.py:
	  Sorted the region_menu for a CFSheetPlotPanel, according to the
	  precedence parameter of the sheets.

	* [r2487] topo/plotting/plotgroup.py:
	  Changed the sort_plots function (and introduced a new cmp_plot
	  function) to sort according to bith the precedence and the
	  alphabetical order.

	* [r2486] topo/base/connectionfield.py:
	  Forgotten CFSheet precedence default value in previous commit.

	* [r2485] topo/plotting/plot.py:
	  Added an attribute precedence to a Plot, that is 0.0 by default,
	  and a copy of the SheetViews used for making the plot (set at the
	  same time as the src_name).

	* [r2484] topo/analysis/featuremap.py,
	  topo/base/sheetview.py,
	  topo/commands/analysis.py:
	  Added a precedence attribute to the SheetView, which is a copy of
	  the sheet precedence parameter, passed when creating a SheetView.

	* [r2483] topo/base/sheet.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/lissom.py:
	  Added a parameter precedence to the Sheet objects. It gives a
	  sorting information for plot display.

2006-02-12  jbednar

	* [r2482] topo/plotting/bitmap.py:
	  Fixed bug when plotting selectivities higher than 1.0; now crops
	  h,s,v before calling hsv2rgb. Silenced warning from PIL.

	* [r2481] doc/Downloads/index_text.php:
	  Cleanup of Windows instructions in progress

	* [r2480]
	  doc/Developer_Manual/testing_text.php:
	  Minor clarification

	* [r2479] examples/lissom_oo_or_20000.typ:
	  Retrained the map

2006-02-12  ceball

	* [r2478] topo/base/sheet.py:
	  Initializes activity matrix correctly. Added HACKALERT: here and
	  elsewhere there is duplication of code.

	* [r2477] topo/sheets/generatorsheet.py:
	  Now uses PatternGenerator correctly.

2006-02-12  jbednar

	* [r2476] README.txt:
	  Simplified so that it will stay up to date; just points to doc/

2006-02-12  ceball

	* [r2475] topo/patterns/basic.py,
	  topo/patterns/image.py:
	  Removed 'precedence constants' since we have decided on an
	  ordering for the parameters.

2006-02-12  julienciroux

	* [r2474] topo/tkgui/plotgrouppanel.py:
	  Corrected an error in load_image.

2006-02-12  ceball

	* [r2473] topo/base/connectionfield.py,
	  topo/projections/basic.py:
	  Initialization of the cfs in CFProjection.__init__() can be
	  disabled. SharedWeightCFProjection uses this to avoid
	  initializing the cfs (since it only requires a single, shared cf
	  - that it was previously initializing all the cfs was an error,
	  causing its initialization time to be much longer than
	  necessary).

2006-02-12  jbednar

	* [r2472] ChangeLog,
	  ChangeLog.txt:
	  Moved ChangeLog to ChangeLog.txt to make it readable under
	  Windows

	* [r2471] models:
	  Not used anymore

2006-02-12  alan_lindsay

	* [r2470] topo/tkgui/editorobjects.py:
	  Fixed a rounding error

	* [r2469] topo/tkgui/editorobjects.py:
	  Fixed a delete update bug

2006-02-12  jbednar

	* [r2468] topo/tkgui/topoconsole.py:
	  Fixed error in percentage calculation

	* [r2467] examples/lissom_oo_or.ty:
	  Changed Retina's edge buffer to match wt_bounds

2006-02-12  julienciroux

	* [r2466] examples/lissom_oo_or.ty:
	  Set the retina and LGN edge buffer.

2006-02-12  jbednar

	* [r2465] ChangeLog:
	  Added recent changes

	* [r2464] examples/lissom_oo_or.ty:
	  Updated gui attribute names to match Alan's recent changes

2006-02-12  alan_lindsay

	* [r2463] topo/tkgui/parametersframe.py:
	  Allows class constants to be set, crudely. A dictionary of
	  dictionaries, holding only the objects changed by the user is
	  used to allow values to be mainained after closing the
	  parameterframe.

	* [r2462] topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py:
	  Changed method and variable names to coincide with the rest of
	  Topographica. Activity plots are now mapped correctly onto sheets
	  and the shape and size of a sheets bounding box is represented by
	  the editor sheet.

	* [r2461] topo/base/utils.py:
	  Added extra translator functions for features in ParameterFrame.

	* [r2460] examples/hierarchical.ty:
	  ModelEditor uses gui_x instead of guiX, same fory.

2006-02-12  jbednar

	* [r2459] examples/lissom_oo_or_20000.typ:
	  New version from Chris

2006-02-11  jbednar

	* [r2458] topo/tkgui/topoconsole.py:
	  Added simple progress reporting (just a sketch)

2006-02-10  ceball

	* [r2457] examples/lissom_oo_or_20000.typ:
	  Removed - something went wrong with the previous commit. Will
	  replace.

	* [r2456] examples/lissom_oo_or_20000.typ:
	  Slied in measure_maps code and change to input_generator.

	* [r2455] doc/Tutorials/lissom_oo_or_text.php:
	  Initial version - unchecked.

	* [r2454]
	  doc/Tutorials/images/activity_line_oo.png,
	  doc/Tutorials/images/activity_line_oo_or.png,
	  doc/Tutorials/images/lissom_network_diagram_oo.png,
	  doc/Tutorials/images/natural_image_oo_or.png,
	  doc/Tutorials/images/oo_or_map.png,
	  doc/Tutorials/images/projection_oo.png,
	  doc/Tutorials/images/test_pattern_oo.png,
	  doc/Tutorials/images/unit_weights_0_0_oo.png,
	  doc/Tutorials/images/unit_weights_0_0_oo_or.png,
	  doc/Tutorials/images/unit_weights_0_0_or.png:
	  New image for oo_or tutorial.

	* [r2453] examples/lissom_oo_or.ty:
	  Positioned network for model editor. Replaced lambda functions
	  for getting random.uniform value with a class (to allow
	  pickling); this class will be moved.

	* [r2452] examples/lissom_oo_or.ty:
	  LGN declared with measure_maps=False.

	* [r2451] topo/analysis/featuremap.py:
	  Sheets with a measure_maps attribute, and with it set True, get
	  their maps measured - others do not.

	* [r2450] topo/base/connectionfield.py:
	  Added a 'measure_maps' attribute to CFSheet.

	* [r2449] examples/lissom_oo_or.ty:
	  No longer have afferent_weight_bounds, lgn_weight_bounds, and
	  input_bounds. Instead, bounds are just created by
	  radial_bounds().

2006-02-10  jbednar

	* [r2448] doc/User_Manual/space_text.php:
	  Minor clarification

2006-02-10  ceball

	* [r2447] examples/lissom_oo_or.ty:
	  Eliminated inhibitory_ and excitatory_weight_bounds variables,
	  instead just creating the bounds where the projection is defined.

	* [r2446] examples/lissom_oo_or.ty,
	  topo/base/connectionfield.py:
	  Renamed wt_bounds() to radial_bounds().

	* [r2445] examples/lissom_oo_or.ty:
	  Gaussian class' parameters are not now set; instead, parameters
	  on the Retina's input_generator are set.

	* [r2444] topo/base/parameter.py:
	  Added a hack to allow DynamicNumbers to work when they are set on
	  an object.

	* [r2443] topo/commands/basic.py:
	  Hacked the hack in load_snapshot to allow
	  examples/lissom_oo_or_20000.typ to keep its dynamic input pattern
	  numbers. Because the unpickleable lambda functions for generating
	  random numbers are used in two different ways now, there are two
	  different hacks here. Once we eliminate those lambda functions,
	  it should all be ok.

2006-02-10  jbednar

	* [r2442] topo/base/sheet.py,
	  topo/base/simulator.py:
	  Added ALERTs

2006-02-10  ceball

	* [r2441] examples/lissom_oo_or_20000.typ:
	  Initial version.

2006-02-09  ceball

	* [r2440] examples/lissom_oo_or.ty:
	  Updates to match lissom_oo_or_reference.ty.

	* [r2439] examples/lissom_oo_or.ty:
	  Updates to match lissom_oo_or_reference.ty.

	* [r2438] topo/tests/lissom_oo_or_reference.ty:
	  delta and beta values corrected.

2006-02-09  julienciroux

	* [r2437] topo/plotting/templates.py:
	  Added the color_key to the Orientation Preference
	  PlotGroupTemplate.

	* [r2436] topo/tkgui/plotgrouppanel.py:
	  Changed the function load_image; now, all topographica plot are
	  resized to be the close as possible to the height of the biggest
	  topographica plot; then, the static_images are resized to be of
	  this height. There is still a warning about using the
	  image.resize function with floats that we need to take care
	  about.

	* [r2435] topo/plotting/plotgroup.py:
	  Set the resize parameter to False when creating static image
	  plot.

	* [r2434] topo/plotting/bitmap.py:
	  Added a resize attribute for a bitmap; it is set to True by
	  default. It is a flag that allows distinguishing between
	  topographica plot and static external images when resizing them.

	* [r2433] doc/images/color_key.png:
	  Added the color_key png file in doc/images.

2006-02-09  ceball

	* [r2432] topo/tests/lissom_oo_or_reference.ty:
	  Corrected setting LGN's density - I probably re-introduced
	  accidentally setting it on the CFSheet class.

	* [r2431] topo/tests/lissom_oo_or_reference.ty:
	  Removed bounds change that has no effect at this density. Updated
	  learning rates.

	* [r2430] examples/lissom_oo_or.ty:
	  Updated parameters to match the ones in
	  lissom_oo_or_reference.ty. There are more to go...

	* [r2429] examples/lissom_oo_or.ty:
	  Simplified weights bounds specification with wt_bounds().

	* [r2428] topo/tests/lissom_oo_or_reference.ty:
	  Removed last change_bounds for lateral excitatory connection
	  because it wouldn't occur anyway for this density.

	* [r2427] topo/tests/lissom_or_reference.ty:
	  Added note to myself.

	* [r2426] examples/lissom_or.ty:
	  Added a HACAKLERT about missing scheduled events.

	* [r2425] topo/tests/lissom_oo_or_reference.ty:
	  Use wt_bounds() function to set weight bounds. Included
	  min_exc_rad parameter.

	* [r2424] topo/base/connectionfield.py:
	  Removed print statement accidentally left in previous commit.

	* [r2423] topo/base/connectionfield.py:
	  Added wt_bounds(), which allows a bounding box to be created with
	  simple syntax from a radius. Also allows specification of a
	  minimum radius. Added a HACKALERT about the change_bounds
	  warning.

	* [r2422] topo/tests/oo_or_map_topo.log:
	  About 20000 iterations from the equivalent c++ lissom simulation.

	* [r2421] topo/tests/lissom_oo_or_reference.ty:
	  Learning rates set on correct projections.

2006-02-09  jbednar

	* [r2420] doc/User_Manual/images,
	  doc/User_Manual/images/.cvsignore:
	  More to ignore

	* [r2419]
	  doc/User_Manual/images/connection_field.fig,
	  doc/User_Manual/images/matrix_coords.fig,
	  doc/User_Manual/images/matrix_coords_hidensity.fig,
	  doc/User_Manual/images/sheet_coords.fig,
	  doc/User_Manual/images/sheet_coords_-0.275_-0.0125_0.025_0.2885.fig,
	  doc/User_Manual/images/sheet_coords_-0.2_0.4.fig:
	  Made images line up; added some missing elements and removed some
	  stray ones, and added markings for similar features in different
	  plots

	* [r2418]
	  doc/User_Manual/background_text.php.m4,
	  doc/User_Manual/basics_text.php.m4,
	  doc/User_Manual/features_text.php.m4,
	  doc/User_Manual/images/Makefile,
	  doc/User_Manual/space_text.php,
	  doc/User_Manual/time_text.php:
	  Reduced image sizes to allow two side by side, and added such
	  plots where appropriate

	* [r2417] doc/Future_Work/index_text.php:
	  More work

2006-02-08  jbednar

	* [r2416] topo/tests/lissom_oo_or_reference.ty:
	  LGNOn and LGNOff to V1 connection strengths halved. LGNOn and
	  LGNOff sheet bounds adjusted. (Chris)

2006-02-08  julienciroux

	* [r2415] topo/plotting/plotgroup.py:
	  Added a function _add_static_images() in TemplatePlotGroup. It
	  creates the Plot specified by the static_images attribute of the
	  PlotGroupTemplate, and add them to the added_list of Plot (This
	  will still need some clean up).

	* [r2414] topo/plotting/templates.py:
	  Added an attribute static_images to the PlotGroupTemplate and a
	  method add_static_image; static_images is a KeyedList of tuple
	  (name,file_path) specifying a Plot from an image file. It will
	  enable specifying additional static plots to a
	  Pl?\004otGroupTemplate (e.g. color key for Orientation
	  Preference). There is no images added to a template yet, because
	  the re-sizing needs to be fixed in PlotGroupPanel; therefore, the
	  line is commented out for the moment.

	* [r2413] topo/plotting/plot.py:
	  Added a missing import statement; added a call to the super class
	  in the Plot __init__.

	* [r2412] topo/plotting/bitmap.py,
	  topo/plotting/plot.py:
	  Deleted the unuseful FileBitmap class.

	* [r2411] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplot.py,
	  topo/tkgui/testpattern.py:
	  Renamed make_plot() to make_template_plot().

	* [r2410] topo/plotting/plot.py:
	  Changed the Plot hierarchy: now the Plot class is really simple
	  and just creates its bitmap from an image; the former Plot class
	  has been renamed TemplatePlot, and others sub-classes inherit
	  from it. It remains to re-name the make_plot fun?\004ction to
	  make_template_plot. Also deleted the BitmapPlot class which is
	  now replaced by the simple Plot class.

2006-02-08  ceball

	* [r2409] topo/tests/lissom_or_reference.ty:
	  Change to a comment.

	* [r2408] topo/tests/lissom_oo_or_reference.ty:
	  Updates to parameters and learning rates.

	* [r2407] topo/tests/lissom_oo_or_reference.ty:
	  Initial version; parameters don't yet match the equivalent c++
	  simulation.

	* [r2406] topo/tests/oo_or_map_topo.log:
	  log file from oo_or_map_topo.param c++ simulation.

	* [r2405] topo/tests/lissom_or_reference.ty:
	  Added some comments.

	* [r2404] examples/lissom_oo_or.ty:
	  Corrected typo in afferent_weight_bounds.

2006-02-07  julienciroux

	* [r2403] topo/responsefns/optimized.py:
	  Simplified the CFEuclideanDistance function; got rid of the
	  optimization in the code.

2006-02-07  ceball

	* [r2402] examples/lissom_oo_or.ty:
	  Updated alpha and beta (V1.outputfn bounds).

2006-02-07  julienciroux

	* [r2401] topo/responsefns/optimized.py:
	  Continued to clean up the CFDotProduct() code, using C++ syntax.

2006-02-07  ceball

	* [r2400] examples/lissom_oo_or.ty:
	  Changed bounding boxes for circular rfs.

2006-02-07  julienciroux

	* [r2399] topo/responsefns/optimized.py:
	  Simplified version of CFDotProduct().It still needs some clean up
	  (e.g using C++ syntax). It seems to perform a bit better than the
	  previous optimized version; in any case it does not do worse
	  (most of the times, the profiling statistics are better for the
	  new version).

2006-02-07  ceball

	* [r2398] examples/lissom_or.ty:
	  Last commit contained an error - switched commented
	  afferent_weights_bounds with uncommented.

	* [r2397] examples/lissom_or.ty:
	  No visible change. Committed commented-out code for circular
	  connection fields (including adjustments to input_bounds.

	* [r2396] topo/tests/lissom_or_reference.ty:
	  Undid previous changes. I didn't notice that in c++ lissom the
	  changes to e.g. exc_radius were accumulating.

	* [r2395] topo/tests/lissom_or_reference.ty:
	  Altered to match equivalent c++ lissom simulation: scheduled
	  lateral excitatory bounds changes, scheduled lateral excitatory
	  learning rates, scheduled afferent learning rates.

	* [r2394] topo/tests/or_map_topo.log:
	  20001 iterations from c++ lissom's or_map_topo.param

	* [r2393] examples/lissom_oo_or.ty:
	  Added learning rates and scheduled changes to them for LGN ON/OFF
	  afferents. Added some comments.

2006-02-06  jbednar

	* [r2392] doc/User_Manual/simulator.html:
	  Not sure why this was checked in

	* [r2391] doc/User_Manual,
	  doc/User_Manual/.cvsignore:
	  More to ignore

	* [r2390] doc/User_Manual/coordinates_text.php,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/simulator_text.php,
	  doc/User_Manual/space_text.php,
	  doc/User_Manual/time_text.php:
	  Renamed files to reflect their contents

	* [r2389] doc/User_Manual/coordinates_text.php,
	  doc/User_Manual/index_text.php,
	  doc/User_Manual/simulator_text.php:
	  Clarified distinction between time and space topics

	* [r2388] doc/User_Manual/coordinates_text.php:
	  Fixed Sheet coordinate errors found by Julien

2006-02-06  ceball

	* [r2387] topo/tests/lissom_or_reference.ty:
	  Removed a HACKALERT - clarified why scheduled events are at one
	  time-step less than the equivalent or_map_topo's.

2006-02-06  jbednar

	* [r2386]
	  doc/Tutorials/som_retinotopy_text.php:
	  Fixed typos; clarified SOM algorithm

2006-02-06  ceball

	* [r2385] topo/responsefns/optimized.py:
	  Same change to CFEuclideanDistance as to CFProjection (i.e. same
	  changes as were made to CFProjection in the previous two
	  commits).

	* [r2384] topo/responsefns/optimized.py:
	  Removed the variables or and oc (that were having no effect and
	  should have been removed in the previous version).

	* [r2383] topo/responsefns/optimized.py:
	  Removed an apparently problematicoptimization from CFProjection,
	  but it needs to be done properly. Julien is going to do this, and
	  make the same change to CFEuclideanDistance.

2006-02-06  jbednar

	* [r2382] doc/User_Manual/simulator_text.php:
	  Minor clarification

	* [r2381] doc/User_Manual/coordinates.html:
	  Not sure why this generated file was ever checked in

2006-02-06  julienciroux

	* [r2380] topo/plotting/plot.py:
	  New class BitmapPlot that is just a Plot constructed by
	  specifying a file path.

	* [r2379] topo/plotting/bitmap.py:
	  New class FileBitmap that just creates a Bitmap from a file path.

2006-02-06  jbednar

	* [r2378] doc/User_Manual/simulator.html:
	  Clarification

	* [r2377] doc/User_Manual/coordinates.html,
	  doc/User_Manual/simulator.html,
	  doc/User_Manual/simulator_text.php:
	  Initial version

	* [r2376] doc/User_Manual/basics_text.php.m4:
	  Removed items now implemented elsewhere

	* [r2375] doc/User_Manual/images,
	  doc/User_Manual/images/.cvsignore:
	  More to ignore

	* [r2374] doc/User_Manual/index_text.php:
	  Added link to simulator.html

	* [r2373]
	  doc/User_Manual/images/clocked-timeline.fig,
	  doc/User_Manual/images/connection_field.fig,
	  doc/User_Manual/images/connection_field_master.fig,
	  doc/User_Manual/images/event-driven-timeline.fig,
	  doc/User_Manual/images/matrix_coords.fig,
	  doc/User_Manual/images/matrix_coords_hidensity.fig,
	  doc/User_Manual/images/sheet_coords.fig,
	  doc/User_Manual/images/sheet_matrix_master.fig,
	  doc/User_Manual/images/sheet_matrix_master_hidensity.fig:
	  Sorted labels in order for easier editing

	* [r2372] doc/User_Manual/coordinates_text.php,
	  doc/shared/util.php:
	  Moved classref function to shared utils file

	* [r2371] doc/User_Manual/coordinates_text.php,
	  doc/User_Manual/index_text.php:
	  Added coordinates page

	* [r2370]
	  doc/User_Manual/images/connection_field.fig,
	  doc/User_Manual/images/matrix_coords.fig,
	  doc/User_Manual/images/sheet_matrix_master.fig,
	  doc/User_Manual/images/sheet_matrix_master_hidensity.fig:
	  Fixed bogus labels

	* [r2369] doc/Makefile:
	  Added automatic making of images

	* [r2368] doc/User_Manual/features_text.php.m4:
	  Fixed path

	* [r2367] doc/User_Manual/background_text.php,
	  doc/User_Manual/background_text.php.m4,
	  doc/User_Manual/basics_text.php,
	  doc/User_Manual/basics_text.php.m4,
	  doc/User_Manual/features_text.php,
	  doc/User_Manual/features_text.php.m4:
	  Moved .php files to .m4 files for now

	* [r2366] doc,
	  doc/.cvsignore,
	  doc/Makefile,
	  doc/shared/topographica.bib:
	  Added m4 preprocessing and bib2html support for .php.m4 files

2006-02-05  jbednar

	* [r2365] doc/shared/bib2html.m4:
	  Copied from lib/nn/tex/bib2html/bib2html.m4

	* [r2364] doc/shared/bib2html,
	  doc/shared/bib2html/.cvsignore,
	  doc/shared/bib2html/README,
	  doc/shared/bib2html/bib2html,
	  doc/shared/bib2html/bib2html.m4,
	  doc/shared/bib2html/bib2html.man,
	  doc/shared/bib2html/bibsearch,
	  doc/shared/bib2html/gen-bst,
	  doc/shared/bib2html/html-btxbst.doc,
	  doc/shared/bib2html/makefile:
	  Initial version

2006-02-05  alan_lindsay

	* [r2363] topo/tkgui/parametersframe.py:
	  Allows the current value to belong to a class that is not one of
	  the usual classes for a given parameter. This allows
	  CFProjections to be manipulated.

	* [r2362] topo/tkgui/parametersframe.py:
	  Seems to allow updating of connections and sheets and selected
	  classes within fields of these.

	* [r2361] topo/tkgui/parametersframe.py:
	  Allows a dictionary, with a list entry for fields of the object,
	  to be passed in; these lists are searched for object covers for
	  each of the possible classes of a class selector item. Works for
	  sheets.

2006-02-05  ceball

	* [r2360] topo/tests/or_map_topo.log:
	  About 200 iterations from current c++ reference.

	* [r2359] topo/tests/lissom_or_reference.ty:
	  Use only integer part of rf_radius, as c++ LISSOM does.

	* [r2358] topo/responsefns/optimized.py:
	  Added missing import statement.

2006-02-04  alan_lindsay

	* [r2357] topo/base/utils.py:
	  a method that takes a dictionary and a key and returns
	  dictionary[key] or key if it doesn't exist.

	* [r2356] topo/tkgui/parametersframe.py:
	  First attempt at allowing a translator dictionary to be passed to
	  parameter frame, has broken embedded class property windows
	  though.

	* [r2355] topo/tkgui/editorwindow.py:
	  Displays activity as soon as you set it. Does not need refreshed
	  anymore.

	* [r2354] topo/tkgui/parametersframe.py:
	  Class selector fields can have there properties modified. These
	  are lost as soon as the original object is updated. Works for
	  TestPatterns.

2006-02-03  jbednar

	* [r2353]
	  doc/Tutorials/som_retinotopy_text.php:
	  Fixed paths

2006-02-03  alan_lindsay

	* [r2352] topo/tkgui/parametersframe.py:
	  The object's current value is now selected in ComboBox.

2006-02-03  jbednar

	* [r2351] examples/som_retinotopy.ty:
	  Fixed typo in last checkin

	* [r2350] doc/Downloads/index_text.php:
	  Clarified issue found by Yoonsuck

2006-02-03  chrispalmer

	* [r2349] topo/patterns/basic.py:
	  Added initial version of CompositePatternGenerator. There seems
	  to be a problem with Parameter, which needs to be investigated.

2006-02-03  julienciroux

	* [r2348] topo/tkgui/connectionfieldspanel.py:
	  Renamed unitweightspanel to connectionfieldspanel.

	* [r2347] topo/tkgui/topoconsole.py,
	  topo/tkgui/unitweightspanel.py:
	  topo/tkgui/connectionfieldspanel.py

	* [r2346]
	  topo/tests/tkgui/testtemplateplotgrouppanel.py:
	  Forgotten assert line in previous commit.

	* [r2345] topo/tests/tkgui/__init__.py,
	  topo/tests/tkgui/testtemplateplotgrouppanel.py:
	  Corrected a strange bug in testtemplateplotgrouppanel.py. The
	  'case' notation was not working there.. maybe because the
	  tests/tkgui/ directory is a sub-directory?

2006-02-03  ceball

	* [r2344] topo/tests/tkgui/__init__.py:
	  Commented out import of test that doesn't seem to run properly.
	  It's not clear why it doesn't run.

2006-02-03  julienciroux

	* [r2343] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/unitweightspanel.py:
	  Renamed the class UnitWeightsPanel to ConnectionFieldsPanel.

2006-02-03  jbednar

	* [r2342] doc/User_Manual/about_text.php,
	  doc/User_Manual/background_text.php,
	  doc/User_Manual/basics_text.php,
	  doc/User_Manual/features_text.php,
	  doc/User_Manual/index_text.php:
	  Moved material in comments into other unlinked files

	* [r2341] doc/User_Manual,
	  doc/User_Manual/.cvsignore:
	  More to ignore

	* [r2340] doc/User_Manual/images/Makefile:
	  Added special handling for one PDF->PNG conversion

2006-02-03  ceball

	* [r2339] examples/lissom_oo_or.ty:
	  Still not tested. Changed LGN connections.

2006-02-03  jbednar

	* [r2338] doc/User_Manual/images,
	  doc/User_Manual/images/.cvsignore:
	  More to ignore

	* [r2337] doc/User_Manual/images,
	  doc/User_Manual/images/.cvsignore:
	  Ignore PNG too

	* [r2336] doc/User_Manual/images,
	  doc/User_Manual/images/.cvsignore,
	  doc/User_Manual/images/Makefile,
	  doc/User_Manual/images/connection_field.fig,
	  doc/User_Manual/images/connection_field_master.fig,
	  doc/User_Manual/images/epstopdf,
	  doc/User_Manual/images/generic-cortical-hierarchy-model.fig,
	  doc/User_Manual/images/matrix_coords.fig,
	  doc/User_Manual/images/retina_edge_buffer.fig,
	  doc/User_Manual/images/sheet_coords.fig,
	  doc/User_Manual/images/sheet_matrix_master.fig,
	  doc/User_Manual/images/sheet_matrix_master_hidensity.fig,
	  doc/User_Manual/images/toplevel.fig,
	  doc/User_Manual/images/toplevel_bare.fig:
	  Initial version

	* [r2335] doc/User_Manual/images,
	  doc/User_Manual/images/face-blurred-off-stretched-sheared.gif,
	  doc/User_Manual/images/face-blurred-on-stretched-sheared.gif,
	  doc/User_Manual/images/face-blurred-stretched-sheared.gif,
	  doc/User_Manual/images/measuring-map.v3.pdf:
	  Version from book

2006-02-03  ceball

	* [r2334] topo/tests/or_map_topo.log:
	  Updated for changes to c++ lissom's params file.

	* [r2333] topo/tests/lissom_or_reference.ty:
	  Changed rf_radius, inh_rad, and exc_rad. Changed
	  retina_edge_buffer and RN. Altered layout at start of file to
	  look more like equivalent c++ lissom params file. The input
	  pattern is identical to C++ lissom, but the activity in V1 has
	  not y?\004et been matched (the parameters aren't all being used
	  correctly).

2006-02-03  jbednar

	* [r2332] topo/commands/pylabplots.py:
	  Added simple vector and matrix plots for the command line

	* [r2331] topo/commands/lineplotting.py,
	  topo/commands/pylabplots.py,
	  topo/tkgui/templateplotgrouppanel.py:
	  Renamed lineplotting.py to pylabplots.py in anticipation of new
	  non-line-based plot

	* [r2330] doc/Downloads/index_text.php,
	  doc/Home/index_text.php,
	  doc/Reference_Manual/index_text.php,
	  doc/shared/index.php,
	  doc/shared/util.php:
	  Moved Tutorial to Tutorials now that there are more than one

	* [r2329] doc/Tutorial,
	  doc/Tutorials,
	  doc/Tutorials/.cvsignore,
	  doc/Tutorials/images,
	  doc/Tutorials/images/activity_gaussian.png,
	  doc/Tutorials/images/activity_gaussian_or.png,
	  doc/Tutorials/images/activity_line.png,
	  doc/Tutorials/images/activity_line_or.png,
	  doc/Tutorials/images/lissom_network_diagram.png,
	  doc/Tutorials/images/or_key_horiz_transparent.png,
	  doc/Tutorials/images/or_key_vert_transparent_topo.png,
	  doc/Tutorials/images/or_map.png,
	  doc/Tutorials/images/projection.png,
	  doc/Tutorials/images/som_activity_000000.png,
	  doc/Tutorials/images/som_activity_000001.png,
	  doc/Tutorials/images/som_activity_000006.png,
	  doc/Tutorials/images/som_cog_000000.png,
	  doc/Tutorials/images/som_cog_000100.png,
	  doc/Tutorials/images/som_grid_000000.png,
	  doc/Tutorials/images/som_grid_000100.png,
	  doc/Tutorials/images/som_grid_010000.png,
	  doc/Tutorials/images/som_grid_040000.png,
	  doc/Tutorials/images/som_network_diagram.png,
	  doc/Tutorials/images/som_projection_000000.png,
	  doc/Tutorials/images/som_projection_000001.png,
	  doc/Tutorials/images/som_projection_000006.png,
	  doc/Tutorials/images/som_projection_040000.png,
	  doc/Tutorials/images/test_pattern.png,
	  doc/Tutorials/images/topographica_console.png,
	  doc/Tutorials/images/unit_weights_0.2_0.0.png,
	  doc/Tutorials/images/unit_weights_0.2_0.0_or.png,
	  doc/Tutorials/images/unit_weights_0_0.png,
	  doc/Tutorials/images/unit_weights_0_0_or.png,
	  doc/Tutorials/index_text.php,
	  doc/Tutorials/lissom_or_text.php,
	  doc/Tutorials/som_retinotopy_text.php:
	  Moved Tutorial to Tutorials now that there are more than one

2006-02-02  julienciroux

	* [r2328] examples/obermayer_pnas90.ty:
	  Corrected the initial and final learning rate value, according to
	  the new changes in learning rate computation in HebbianSOMLF().

	* [r2327] topo/plotting/plotgroup.py:
	  Fixed sort_plot() according to the new changes in Plot. Cleaned
	  up comments and doc.

	* [r2326] topo/tests/tkgui/__init__.py,
	  topo/tests/tkgui/testactivitypanel.py,
	  topo/tests/tkgui/testbasicplotgrouppanel.py,
	  topo/tests/tkgui/testtemplateplotgrouppanel.py:
	  Renamed testbasicplotgrouppanel.py to
	  testtemplateplotgrouppanel.py. Also deleted testactivitypanel.py
	  and put the code that was in it into
	  testtemplateplotgrouppanel.py.

	* [r2325]
	  topo/tests/tkgui/testbasicplotgrouppanel.py:
	  Forgotten in previous commit.

	* [r2324]
	  topo/tests/tkgui/testactivitypanel.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/templateplotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Renamed basicplotgrouppanel.py to templateplotgrouppanel.py.

2006-02-02  ceball

	* [r2323] examples/lissom_oo_or.ty:
	  Rearranged file to make more sense - no visible change.

	* [r2322] topo/learningfns/optimized.py:
	  Added HACKALERT about C pointer version of DivisiveHebbian.

	* [r2321] topo/tests/testlissom_cpointer.ty:
	  Cleaned up connecitions (removed connection_params, but also
	  sharedweight projection code). Added a HACKALERT.

	* [r2320] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_oo_or.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  topo/base/simulator.py,
	  topo/tests/lissom_or_reference.ty,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testlissom.ty,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py:
	  Made syntax to specificy connections simpler by removing
	  'connection_params' and using a dictionary of keywords. Left a
	  note by Simulator.connect() about adding a dictionary back in for
	  extra parameters should they later be required.

2006-02-02  jbednar

	* [r2319] doc/Tutorial,
	  doc/Tutorial/.cvsignore:
	  More to ignore

	* [r2318] topo/commands/lineplotting.py:
	  Reduced default topographic grid figure size

	* [r2317]
	  doc/Tutorial/images/som_activity_000000.png,
	  doc/Tutorial/images/som_activity_000001.png,
	  doc/Tutorial/images/som_activity_000006.png,
	  doc/Tutorial/images/som_cog_000000.png,
	  doc/Tutorial/images/som_cog_000100.png,
	  doc/Tutorial/images/som_grid_000000.png,
	  doc/Tutorial/images/som_grid_000100.png,
	  doc/Tutorial/images/som_grid_010000.png,
	  doc/Tutorial/images/som_grid_040000.png,
	  doc/Tutorial/images/som_network_diagram.png,
	  doc/Tutorial/images/som_projection_000000.png,
	  doc/Tutorial/images/som_projection_000001.png,
	  doc/Tutorial/images/som_projection_000006.png,
	  doc/Tutorial/images/som_projection_040000.png,
	  doc/Tutorial/som_retinotopy_text.php:
	  Initial version

	* [r2316] doc/shared/util.php:
	  Added alert

	* [r2315] topo/plotting/plot.py,
	  topo/tkgui/projectionpanel.py:
	  Added an alert

	* [r2314] topo/base/sheet.py:
	  Fixed typo

	* [r2313] doc/Reference_Manual/index_text.php:
	  Added explanation of why to read or avoid this manual

	* [r2312] doc/Future_Work/index_text.php:
	  Added notes from meetings, etc.

	* [r2311] doc/Downloads/index_text.php:
	  Added note about CVS

2006-02-01  julienciroux

	* [r2310] topo/tests/testplotgroup.py,
	  topo/tests/tkgui/testactivitypanel.py,
	  topo/tests/tkgui/testbasicplotgrouppanel.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/cfsheetplotpanel.py,
	  topo/tkgui/topoconsole.py:
	  Renamed BasicPlotGroupPanel to TemplatePlotGroupPanel.

2006-02-01  alan_lindsay

	* [r2309] topo/tkgui/editorwindow.py:
	  Tidied and some of the methods written a little nicer.

2006-02-01  julienciroux

	* [r2308] topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/unitweightspanel.py:
	  Renamed UnitWeightsPlotGroup to ConnectionFieldsPlotGroup, for
	  consistency with the template name. Nevertheless, I realised that
	  it might be confusing from a developper point of view: the
	  concept of CF is different that the weights of a unit, i.e. we
	  can have sheets with no CF and still vizualize the weights of a
	  unit.

	* [r2307] topo/plotting/templates.py,
	  topo/tkgui/topoconsole.py:
	  Renamed the Connection Field template to Connection Fields
	  (plural).

	* [r2306] topo/tkgui/testpattern.py:
	  Deleted two old ALERTS and wrote a new one.

	* [r2305] topo/plotting/bitmap.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Replaced the Bitmap's view_info attribute by a name and
	  plot_src_name attributes; they are copies of the plot's
	  attributes of the same name. Now, the string that has to be
	  displayed is built from these two attributes in PlotGroupPanel's
	  display_labels(). The UnitWeightPanel() display_labels method has
	  to be modified: connection fields panel and projection's panel do
	  not handle labels as a normal BasicPlotGroupPanel.

2006-02-01  ceball

	* [r2304] examples/lissom_oo_or.ty:
	  Changed V1's density to 48. Changed CFSheet's density to 24.
	  Connected on and off LGN sheets to V1, though not properly.

	* [r2303] topo/projections/basic.py:
	  If a unit is near the sheet edge, the shared weights matrix will
	  not necessarily be the right matrix - the correct submatrix is
	  needed. Added code to do that.

	* [r2302] topo/base/connectionfield.py:
	  Changed the function that was for slicing the mask matrix to one
	  that returns the slice.

2006-02-01  julienciroux

	* [r2301] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py:
	  Replaced the Plot attribute view_info (a dict) by a single
	  plot_src_name. It has still to be changed in future commit.

	* [r2300] topo/base/connectionfield.py,
	  topo/base/sheetview.py,
	  topo/commands/analysis.py,
	  topo/plotting/plot.py,
	  topo/projections/basic.py,
	  topo/tests/testplot.py,
	  topo/tests/testsheet.py,
	  topo/tests/testsheetview.py:
	  Deleted the attribute view_info of a SheetView, replaced by a
	  single src_name attribute. Deleted the parameter view_type that
	  wasn't of any use. Also added two ALERT in sheetview.py that will
	  have to be examined.

2006-02-01  ceball

	* [r2299] topo/tests/lissom_or_reference.ty:
	  Added performance profiling code examples back in (they're
	  commented out).

2006-02-01  julienciroux

	* [r2298] examples/cfsom_or.ty,
	  examples/hierarchical.ty:
	  Corrected the learning rate now that the HebbianSOMLF function
	  does not use the constant_sum_connection_rate() anymore.

	* [r2297] examples/som_retinotopy.ty:
	  Adapted the min radius to be set like in the book (0.5/40 in
	  sheet coordinates), now that there is a crop_radius. It gives a
	  good result (with the same parameters than in the book: 40 units
	  and so on...), but I did not compared it with our previous result
	  with a radius of 1.25/40.

	* [r2296] examples/som_retinotopy.ty:
	  Made the simulation use the new C coded CFEuclideanDistance()
	  function; also corrected the generator sheet density to be 24 (it
	  has been committed with a value of 40, by mistake). Also got rid
	  of unused commented out code.

	* [r2295] topo/responsefns/optimized.py:
	  C version of the CFEuclideanDistance reponse function. It is
	  mostly based on the C version of CFDotProduct().It does seem to
	  be about 1.5 times faster (when it took 1mn it now takes 40s). It
	  could probably be even faster (as well as the CFDotProduct() C
	  version, I think) but would need more work.

2006-01-31  julienciroux

	* [r2294] topo/plotting/palette.py:
	  Started an implementation of the String-Based Palette class. It
	  is just committed for my convenience, but there is nothing
	  finished at all; it shouldn't affect anything to commit it
	  though.

	* [r2293] examples/som_retinotopy.ty,
	  topo/learningfns/basic.py:
	  Fixed afferent learning rate scaling for SOMs; i.e, don't need
	  scaling at all for this learning function. Changed the
	  crop_radius for the neighborhood function to have a minimum
	  radius, to ensure that it covers at least a neighboring unit in
	  each direction

2006-01-31  ceball

	* [r2292] examples/lissom_oo_or.ty:
	  Initial version - incomplete. Based on lissom_or.ty, but with
	  circular connectionfields.

	* [r2291] topo/projections/basic.py:
	  Updated SharedWeightCFProjection to match changes in
	  connectionfield and cfprojection. Not yet tested.

	* [r2290] topo/tests/or_map_topo.log:
	  20009 iterations from c++ lissom.

	* [r2289] topo/tests/lissom_or_reference.ty:
	  Updated learning rates to correct ones from lissom_or.ty before
	  it was split into lissom_or.ty and lissom_or_reference.ty. THey
	  were lost when lissom_or_reference was reverted to 21st December
	  2005 code.

2006-01-30  ceball

	* [r2288] topo/tests/lissom_or_reference.ty:
	  Back to the previous network size (BaseN=72).

	* [r2287] topo/tests/or_map_topo.log:
	  200 iterations from c++ lissom

	* [r2286] topo/tests/lissom_or_reference.ty:
	  Using a smaller network.

	* [r2285] topo/base/connectionfield.py,
	  topo/tests/lissom_or_reference.ty:
	  Altered some hackalerts.

	* [r2284] topo/base/connectionfield.py:
	  Mask centered on matrixidx center.

	* [r2283] topo/tkgui/testpattern.py:
	  Added hack to remove Random Generator from the list of
	  PatternGenerators in the test pattern window. But it will still
	  appear in other menus.

2006-01-30  jbednar

	* [r2282] ChangeLog:
	  Updated with recent changes

2006-01-30  julienciroux

	* [r2281] topo/base/connectionfield.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py:
	  Renamed the single_connection_learning_rate() to
	  constant_sum_connection_rate(); it indicates that the learning
	  rate is scaled based on keeping the sum constant,which leaving it
	  open for adding other types of connection_rate() functions.

	* [r2280] topo/analysis/featuremap.py,
	  topo/plotting/bitmap.py:
	  Modified featuremap so that in the case of a cyclic value the
	  preference matrix is normalized, but not in the case of a
	  non-cyclic value. It solves the problem of the position
	  preference plot shrinking when increasing the range of values.
	  Though it might be an alright reasoning, an hack alert has been
	  added in FeatureMap and in bitmap.py, because it made me realised
	  that if this normalization is not performed for a sheetview that
	  will be used as the hue key in an HSV plot, an error will occur
	  in bitmap. Therefore, we should think about this case, and decide
	  what to do to avoid unexpected errors in the future.

	* [r2279] topo/commands/analysis.py:
	  Corrected a mistyped parenthesis.

2006-01-30  ceball

	* [r2278] topo/base/connectionfield.py:
	  Mask is resized by change_bounds() in a way that is consistent
	  with how it's generated in the first place. Not sure if it's the
	  right way though - these changes have not yet been verified (but
	  the resizing is better than before, in any cas?\004e).

	* [r2277] topo/base/connectionfield.py:
	  ConnectionField.__init__()'s mask creation code is moved to a
	  subroutine.

	* [r2276] topo/base/connectionfield.py:
	  Moved CFProjection's mask creation code to a subroutine.

	* [r2275] topo/base/connectionfield.py:
	  weight_type no longer an attribute of CFProjection (and no longer
	  passed to ConnectionField). Instead, it's a global variable.

	* [r2274] topo/base/connectionfield.py:
	  Corrected variable name error in previous commit. Updated a
	  HACKALERT.

	* [r2273] topo/tests/lissom_or_reference.ty:
	  Changed to circular ConnectionFields.

	* [r2272] topo/base/connectionfield.py:
	  Mask pattern is generated in CFProjection and passed to each
	  ConnectionField. A ConnectionField takes the correct submatrix of
	  this mask (which is all of the mask, unless it is near an edge.
	  The way this is done needs to be simplified, but?\004 is
	  currently working. The size calculated for a mask that is e.g. a
	  Disk does not appear to be correct.

2006-01-30  jbednar

	* [r2271] topo/patterns/random.py:
	  Made RandomGenerator base class to make it simpler to add other
	  Random classes. Added GaussianRandom

2006-01-29  jbednar

	* [r2270] examples/som_retinotopy.ty:
	  Cleaned up comments

	* [r2269] examples/som_retinotopy.ty:
	  Changed density to match lissombook

	* [r2268] topo/learningfns/basic.py:
	  Changed crop_radius_multiplier to match fm2d; will make
	  simulations much slower but much more likely to work. Also added
	  commented-out print function printing parameters in the format of
	  fm2d

	* [r2267] topo/learningfns/basic.py:
	  Added radius_crop_multiplier. Shouldn't have changed the behavior
	  at all yet.

2006-01-29  ceball

	* [r2266] topo/base/connectionfield.py:
	  Corrected mistake in previous version.

	* [r2265] examples/hierarchical.ty,
	  topo/base/connectionfield.py:
	  Masks are setup with the size of the weights_bounds_template.
	  This is an intermediate checkin for how it will work, but the
	  specification of the weights_shape at the user level code won't
	  change. hierarchical contains a commented-out example.

2006-01-29  jbednar

	* [r2264] examples/som_retinotopy.ty:
	  Cleaned up comments and documentation

	* [r2263] topo/learningfns/basic.py:
	  Fixed to match recent change in definition of Gaussian
	  PatternGenerator size

	* [r2262] topo/plotting/templates.py:
	  Added CoG plot

	* [r2261] topo/commands/lineplotting.py:
	  Added user-controllable sheet_view names for x and y preferences
	  in topographic_grid. Suppressed annoying plotting display glitch.

	* [r2260] topo/commands/analysis.py:
	  Added measure_cog function. Added user-controllable x_range and
	  y_range parameters to measure_position_pref.

	* [r2259] topo/base/arrayutils.py:
	  Added centroid function written by Julien

	* [r2258] topo/responsefns/basic.py:
	  Improved CFEuclideanDistance_Py

	* [r2257] topo/base/sheet.py:
	  Added alert

2006-01-29  ceball

	* [r2256] topo/base/connectionfield.py:
	  initialize_slice_array() changed to initialize_bounds().
	  initialize_bounds() takes the centered bounds, converts them to a
	  slice at the origin of the sheet, then translates that slice to
	  the cf's location, and finally stores the correspond?\004ing
	  bounding box (and slice_array for access by C). Removed
	  set_slice_array().

	* [r2255] topo/base/patterngenerator.py:
	  Removed a CEBHACKALERT, which was out of date.

2006-01-29  jbednar

	* [r2254] topo/misc/patternfns.py,
	  topo/patterns/basic.py:
	  Changed name of height and width for gaussian and gabor to xsigma
	  and ysigma, to avoid confusion (since they are radii and not
	  actual widths and heights)

	* [r2253] doc/Reference_Manual/index_text.php:
	  Minor updates

2006-01-29  julienciroux

	* [r2252] topo/plotting/plotfilesaver.py:
	  Added a class TemplateFile to plotfilesaver. It is just a first
	  try for implementing plotfilesaver. Just committed for my
	  convenience (i.e. beeing able to work on it at the office.)

2006-01-28  ceball

	* [r2251] doc/Downloads/win32_text.php:
	  Corrected scipy install command.

2006-01-28  julienciroux

	* [r2250] topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplotgroup.py,
	  topo/tkgui/basicplotgrouppanel.py:
	  Renamed BasicPlotGroup to TemplatePlotGroup.

	* [r2249] topo/patterns/basic.py:
	  Changed the default size value for the Gaussian to be 0.5 (to
	  match recent changes in Gaussian size definition).

	* [r2248] topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/unitweightspanel.py:
	  Changed the hierarchy of the PlotGroup classes: now PlotGroup is
	  a simpler class that works by passing it a plot_list of plots,
	  while BasicPlotGroup (soon to be renamed TemplatePlotGroup)
	  implements the generation of the plot_list according to a
	  template specification; others PlotGroup classes now inherit from
	  BasicPlotGroup.

	* [r2247] examples/cfsom_or.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  topo/patterns/basic.py,
	  topo/tests/lissom_or_reference.ty,
	  topo/tests/testlissom.ty,
	  topo/tests/testlissom_cpointer.ty:
	  Modified the size parameter for a Gaussian so that it corresponds
	  to the real size (and it is consistent with the definition of the
	  size for,e.g. a disk or rectangle). The width of the Gaussian
	  (sigma) corresponds to half the size.

	* [r2246] topo/base/sheet.py:
	  Updated doc for slice2bounds().

	* [r2245] examples/som_retinotopy.ty:
	  Added some commentary; working version for switching from
	  CFDotProduct to CFEuclideanDistance_Py response function. Left
	  with a density of 10, used during testing.

	* [r2244] topo/responsefns/basic.py:
	  First version of an euclidean-distance response function. This is
	  supposed to be used by the som_retinotopy example, but did not
	  allow to achieve the expected result yet.

2006-01-28  ceball

	* [r2243] topo/base/connectionfield.py:
	  Removed line left in by mistake in the previous commit.

2006-01-28  jdepaula

	* [r2242] doc/Downloads/index_text.php:
	  Changed line about Windows install to use CVS

	* [r2241] doc/Downloads/win32_text.php:
	  added that scipy_core is already in external

2006-01-28  ceball

	* [r2240] topo/plotting/plot.py:
	  Restored situate, but haven't checked it's correct.

	* [r2239] topo/base/sheet.py:
	  Added initial version of Slice object; currently unused and
	  untested.

	* [r2238] topo/patterns/basic.py:
	  Simplified a little - nobody would be passing in pattern_x and
	  pattern_y as parameters.

	* [r2237] topo/base/parameter.py,
	  topo/base/topoobject.py:
	  A TopoObject is 'uninitialized' until its __init__() method
	  completes. A Constant Parameter can be set on an uninitialized
	  TopoObject.

2006-01-27  ceball

	* [r2236] topo/plotting/plot.py:
	  slice2matrixshape() removed and replaced with current functions
	  from sheet (bounds2slice() with crop_slice_to_sheet_bounds),

	* [r2235] topo/base/connectionfield.py,
	  topo/base/patterngenerator.py,
	  topo/base/sheet.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/tests/testsheet.py:
	  PatternGenerator no longer takes slice_array from
	  ConnectionField. Now, it is passed the ConnectionField's bounds
	  and x and y location. PatternGenerator still evaluates the
	  pattern in the center rather than at the ConnectionField's
	  location. bounds2slice()-type functions are tidied up a bit in
	  sheet. lissom_or_reference behavior is unchanged.

	* [r2234] topo/tests/lissom_or_reference.ty:
	  Updated to current Topographica code (had been setup for
	  2005/12/21 code). Actual tests commented out.

	* [r2233] topo/plotting/plot.py:
	  Accidentally checked in a half-finished version previously.

	* [r2232] topo/plotting/plot.py:
	  Changed to work with different functions in sheet.py. The changes
	  will probably need updating after work on sheet.py is finished.

	* [r2231] topo/base/connectionfield.py,
	  topo/base/sheet.py:
	  No visible changes. Removed bounds2shape(). Temporary
	  modification to bounds2slice() allowing it to skip cropping the
	  slice to the sheet. Temporarily added slice2matrixshape().
	  ConnectionField temporarily modified so its behavior is
	  unchanged.

	* [r2230] topo/patterns/image.py:
	  Removed use of bounds2shape() function. Image is now broken, but
	  does not cause errors. To be fixed after modification of sheet.py
	  is finished.

	* [r2229] topo/tests/testsheet.py:
	  Commented-out bounds2shape() tests. They will be replaced with an
	  equivalent test.

	* [r2228] topo/tests/testlissom.ty:
	  CFDotProduct moved to topo/responsefns/optimized.py

2006-01-27  jbednar

	* [r2227] doc/Downloads/win32_text.php:
	  Added Id tag

	* [r2226] doc/Downloads/win32_text.php:
	  Minor updates

2006-01-26  ceball

	* [r2225] topo/tkgui/editorwindow.py:
	  Removed an import that was preventing the tests from running.

	* [r2224] topo/base/sheet.py:
	  Temporary hack (I'm sorry) in bounds2shape() to get round a
	  problem (which only occurs for some bounds and densities) in
	  bounds2slice() - I think it's a floating point issue.

2006-01-26  jdepaula

	* [r2223] doc/Downloads/win32_text.php:
	  Extensive revision to directions, turned into steps, and Weave is
	  now more of a natural part of the installation process.

2006-01-26  ceball

	* [r2222] topo/tests/testsheet.py:
	  Added a test that involves the kind of situation that exists in
	  creating a connection field. The test fails because
	  bounds2shape() returns the wrong shape. Is the problem a floating
	  point issue?

2006-01-26  alan_lindsay

	* [r2221] topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py:
	  Activity of a sheet can be displayed in the Editor, upsidedown..

2006-01-26  jbednar

	* [r2220] topo/commands/lineplotting.py:
	  Added ALERT

	* [r2219] examples/lissom_or_20000.typ:
	  This version was self-organized again, instead of just editing
	  the file to change the path (though that seemed to work fine)

	* [r2218] examples/lissom_or_20000.typ:
	  Moved inlinec-dependent functions from responsefns/basic.py to
	  responsefns/optimized.py

2006-01-26  julienciroux

	* [r2217] topo/plotting/plot.py:
	  Added doc for _normalize() and _situate_plot().

	* [r2216] topo/plotting/plot.py:
	  Corrected normalize again: in case of a negative or zero
	  constant, a zero matrix is returned; in case of a positive value,
	  a one matrix is returned.

2006-01-26  jbednar

	* [r2215] topo/commands/analysis.py:
	  Fixed docstring

2006-01-26  julienciroux

	* [r2214] topo/plotting/plot.py:
	  Corrected _normalize() so that it returns a one matrix in case of
	  a constant.

2006-01-26  jbednar

	* [r2213] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  examples/som_retinotopy.ty,
	  topo/projections/optimized.py,
	  topo/responsefns/basic.py,
	  topo/responsefns/optimized.py,
	  topo/tests/testplotgroup.py:
	  Moved inlinec-dependent functions from basic.py to optimized.py

	* [r2212] topo/learningfns/optimized.py:
	  Minor documentation cleanup

2006-01-25  jbednar

	* [r2211] ChangeLog:
	  Updated with recent changes

	* [r2210] topo/commands/lineplotting.py:
	  Enforced minimum size of topographic map plots

2006-01-25  julienciroux

	* [r2209] topo/commands/analysis.py,
	  topo/plotting/templates.py:
	  Changed the name of the template CoG Preference to be Position
	  Preference. Also changed measure_cog() to be named
	  measure_position_pref().

2006-01-25  jbednar

	* [r2208] topo/learningfns/basic.py:
	  Added question about proper scaling for a SOM learning rate

	* [r2207] topo/sheets/lissom.py:
	  Added tsettle alert

	* [r2206] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_or.ty,
	  examples/som_retinotopy.ty:
	  Changed all parameter files to remove initial iteration so that
	  the user can inspect an untrained network

	* [r2205] topo/base/parameter.py:
	  Added alert

	* [r2204] doc/shared/util.php:
	  Minor tweak

2006-01-25  ceball

	* [r2203] topo/base/sheet.py:
	  bounds2shape() uses bounds2slice() to get the matrix shape.

	* [r2202] topo/base/connectionfield.py,
	  topo/base/patterngenerator.py,
	  topo/patterns/random.py:
	  PatternGenerator no longer uses bounds2shape(); instead, it uses
	  bounds2slice(). If the slice is already known, it can be passed
	  in (as an optimization, like rows and cols could be passed in
	  before). There should be no visible changes.

2006-01-25  julienciroux

	* [r2201] examples/som_retinotopy.ty:
	  Corrected an error in last commit.

	* [r2200] examples/som_retinotopy.ty:
	  Version that appears to match the parameter in the book, but
	  still does not give the expected results with Topographica.

	* [r2199] topo/commands/analysis.py:
	  Improved the code in PatternPresenter: now use the __setattr__
	  method rather than an exec to update the pattern generator
	  attributes.

	* [r2198] examples/som_retinotopy.ty:
	  Adjusted the parameters to match the simulation in the book.

	* [r2197] topo/plotting/plotgroup.py:
	  Minor cleaning.

2006-01-24  jdepaula

	* [r2196] doc/Downloads/index_text.php,
	  doc/Downloads/win32_text.php:
	  Updated documentation for Windows port

2006-01-24  julienciroux

	* [r2195] topo/plotting/__init__.py:
	  Deleted plotengine from the plotting/__init__.py file.

	* [r2194] topo/plotting/templates.py:
	  Cleaned up old alerts.

	* [r2193] topo/tkgui/plotgrouppanel.py:
	  Cleaned up comments and old alerts.

2006-01-24  jdepaula

	* [r2192] external/win32/setup.py:
	  Added header information about the different steps within
	  setup.py

	* [r2191] external/win32/README.txt:
	  Moved what the code in setup.py does, into setup.py

2006-01-24  julienciroux

	* [r2190] topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/cfsheetplotpanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/unitweightspanel.py:
	  Deleted the parameter plotgroup_type and plotgroup_key when
	  creating a PlotGroupPanel.

2006-01-24  jdepaula

	* [r2189] topo/misc/inlinec.py,
	  topographica_script.py:
	  Changed direction of importing. Lowercased variable.

2006-01-24  julienciroux

	* [r2188] topo/tkgui/plotgrouppanel.py:
	  Re-organized import statements.

	* [r2187] topo/plotting/plot.py:
	  Added the normalizing for the RGBPlot.

	* [r2186] topo/tkgui/cfsheetplotpanel.py:
	  Got rid of unused default value.

	* [r2185] topo/plotting/templates.py:
	  Deleted the normalize field in the plot_templates. Now, normalize
	  is only specified for a PlotGroupTemplate.

	* [r2184] topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/unitweightspanel.py:
	  Added a parameter normalize to be passed to a PlotGroup. Now the
	  information normalize is no longer passed through the template
	  but rather by modifying the PlotGroup.normalize attribute.

2006-01-24  ceball

	* [r2183] topo/base/sheet.py:
	  bounds2slice() always returns int values.

2006-01-24  julienciroux

	* [r2182] topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Renamed the PlotGroupPanel attribute plot_group to
	  plot_group_title.

	* [r2181] topo/tkgui/plotgrouppanel.py:
	  Started a re-organization of the file. Moved code around to made
	  it clearer. Added alert about how to improve the file, and take
	  the normalize information from the template rather than the first
	  plot_template. (This has been tested with version 1.42 of
	  sheet.py because the new version 1.43 has introduced an error in
	  the slicing of the sheetviews.)

2006-01-24  ceball

	* [r2180] topo/base/sheet.py:
	  bounds2slice() returns the slice that includes all units whose
	  centres are within the specified bounds (and within the sheet's
	  bounds).

2006-01-24  julienciroux

	* [r2179] topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/plotting/templates.py,
	  topo/tkgui/projectionpanel.py:
	  Got rid of the now un-used Density and Projection_name fields in
	  the Projection PlotGroupTemplate.

	* [r2178] topo/commands/analysis.py:
	  Omitted in previous commit: changed the name of update_weights()
	  to update_connectionfields().

	* [r2177] topo/plotting/templates.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/unitweightspanel.py:
	  Renamed the Unit Weights template to Connection Field; made the
	  corresponding change in topoconsole. Also modified the way labels
	  is display from the UnitWeightsPanel to display the name of the
	  template (as it is defined in templates.py). I think we might
	  renamed UnitWeightsPanel to ConnectionFieldPanel, it has to be
	  decided.

	* [r2176] topo/plotting/templates.py:
	  Added a function new_plotgroup_template to create and store a
	  PlotGroupTemplate. Renamed add_plot_template() to add_plot(), and
	  re-write all the template creation using new_plotgroup_template()
	  and add_plot().

2006-01-23  ceball

	* [r2175] examples/lissom_or.ty:
	  Added a note about the input_bounds.

2006-01-23  julienciroux

	* [r2174] examples/cfsom_or.ty:
	  Added a comment to explain how to find the learning rate.

	* [r2173] examples/som_retinotopy.ty:
	  Added the skeleton for the retinotopic map simulation. It has to
	  be modifiedf
	  so that the parameters exactly match the simulation published in
	  the book.

2006-01-23  alan_lindsay

	* [r2172] topo/tkgui/editorobjects.py:
	  1st receptive field in centre and labels are closer to middle.

2006-01-23  ceball

	* [r2171] topo/tests/testlissom.ty:
	  Added test for activity matrix size.

	* [r2170] topo/base/connectionfield.py:
	  No visible change for networks that use weight generators like
	  COnstat() or UniformRandom(): weights patterns drawn at the
	  center of the sheet rather than at the ConnectionField's x and y
	  location (as used to be the case).

	* [r2169] topo/base/sheet.py:
	  No visible change. Removed redundant 'maxrow+1', clarified
	  'toprow+1'. Cleaned up docstring.

	* [r2168] topo/base/sheet.py:
	  No visible change. Altered variable names in bounds2slice().

2006-01-22  jbednar

	* [r2167] examples/obermayer_pnas90.ty:
	  Made initial state be clean

	* [r2166] topo/commands/lineplotting.py:
	  Minor tweaks

	* [r2165] topo/commands/analysis.py:
	  Removed temporary plot_cog() command

	* [r2164] topo/commands/lineplotting.py,
	  topo/plotting/templates.py,
	  topo/tkgui/basicplotgrouppanel.py:
	  Added topographic_grid plot

	* [r2163] topo/commands/analysis.py:
	  Temporary commit to preserve octave-based topographic-grid
	  plotting; requires external command topogrid in ./external/

	* [r2162] topo/analysis/updatecommands.py,
	  topo/commands/analysis.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Moved topo/analysis/updatecommands to topo/commands/analysis

	* [r2161]
	  doc/Developer_Manual/imports_text.php:
	  Minor tweak

	* [r2160] topo/base/arrayutils.py:
	  Added octave_str and octave_output commands

	* [r2159] doc/Future_Work/index_text.php:
	  Added link to pymat

	* [r2158] topo/plotting/templates.py:
	  Added a few notes

2006-01-20  julienciroux

	* [r2157] topo/base/sheet.py:
	  Added a comment about a JABALERT./topographica -g
	  examples/cfsom_or.ty I need Jim's advise before getting rid of
	  it.

	* [r2156] topo/plotting/templates.py:
	  Wrote an add_plot_template() function in PlotGroupTemplate in
	  order to create them more conveniently. I did not change the
	  current way templates are defined because I am waiting for Jim
	  reviewing the function and confirming it is OK.

	* [r2155] topo/base/sheet.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testsheet.py,
	  topo/tests/testsheetview.py,
	  topo/tests/tkgui/testactivitypanel.py:
	  Got rid of add_sheet_view() in Sheet now that the sheet_view_dict
	  is public.

	* [r2154] topo/tests/testsheet.py:
	  Wrote a slice2bounds test. Now there is a pretty heavy testing
	  of: bounds2slice,slice2bounds and also
	  slice2bounds_to_bounds2slice (that test that both function
	  combined together provide an identity function).

2006-01-20  alan_lindsay

	* [r2153] topo/tkgui/editorwindow.py:
	  Fixed a few wee bugs in the popup menu.

	* [r2152] topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py:
	  Add order to objects drawn in the canvas. Allow for order to be
	  changed, in popup menu.

2006-01-20  julienciroux

	* [r2151] topo/tests/testsheet.py:
	  Finished to write the test for bounds2slice. I think it is enough
	  testing for this function now.

	* [r2150] topo/base/connectionfield.py,
	  topo/base/sheet.py:
	  Modified slice2bounds and bounds2slice so that the bounds
	  returned by slice2bounds do not have any additional margins; the
	  margin is now built internally to bounds2slice, and therefore
	  slice2bounds return the exact bounds. I had to slightly (and
	  temporarily, because Chris is still working on it) modified
	  connectionfield.py.

2006-01-19  alan_lindsay

	* [r2149] topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py:
	  All possible import * occurrences omitted

	* [r2148] topo/tkgui/editorobjects.py:
	  Ok button added to objects properties window. Updates and closes.

2006-01-19  ceball

	* [r2147] topo/base/connectionfield.py:
	  No visible change. Altered call to ConnectionField.__init__().

2006-01-18  alan_lindsay

	* [r2146] topo/tkgui/editorobjects.py:
	  Lateral Connections colour when they have the focus.

	* [r2145] topo/tkgui/editorobjects.py:
	  Connections from a sheet from one neuron. Lateral connection
	  ovals can be selected and their properties obtained. Labels
	  highlight when their object is selected and they sit (right
	  justified) on the left of their object.

	* [r2144] topo/tkgui/editorwindow.py:
	  Order of boundary search changed to allow lateral connections to
	  be selected.

	* [r2143] topo/tkgui/editortools.py:
	  More distinct display of focus

2006-01-18  jdepaula

	* [r2142] topo/misc/inlinec.py,
	  topographica_script.py:
	  Make loading weave on Windows non-default

	* [r2141] external/win32/setup.py:
	  Now uses Python 2.4.2

	* [r2140] external/win32/python-2.4.2.msi:
	  Upgrade Python 2.4 to 2.4.2

	* [r2139] setup.bat:
	  Upgrade Python 2.4.2 for Windows

2006-01-18  jbednar

	* [r2138] topo/tkgui/parametersframe.py:
	  Added ALERT

	* [r2137] CONVENTIONS,
	  doc/Developer_Manual,
	  doc/Developer_Manual/.cvsignore,
	  doc/Developer_Manual/communication_text.php,
	  doc/Developer_Manual/gui_text.php,
	  doc/Developer_Manual/imports_text.php,
	  doc/Developer_Manual/index_text.php,
	  doc/Developer_Manual/naming_text.php,
	  doc/Developer_Manual/ood_text.php,
	  doc/Developer_Manual/optimization_text.php,
	  doc/Developer_Manual/parameters_text.php,
	  doc/Developer_Manual/python_text.php,
	  doc/Developer_Manual/refactoring_text.php,
	  doc/Developer_Manual/revisioncontrol_text.php,
	  doc/Developer_Manual/testing_text.php,
	  doc/shared/util.php:
	  Converted CONVENTIONS into a developer manual

	* [r2136] doc/Future_Work/index_text.php:
	  Added Judith's suggestion

2006-01-18  julienciroux

	* [r2135] topo/tkgui/plotgrouppanel.py:
	  Changed the code for toggle normalize so that it just regenerate
	  the normalized plots but not re-run the do_plot command.

	* [r2134] topo/plotting/plot.py:
	  Changed the code for normalizing, introduced an offset so that
	  the minimum value of the matirx is zero.

2006-01-18  ceball

	* [r2133] topo/base/connectionfield.py:
	  Weight (and mask) patterns are setup using the bounds as
	  calculated by initialize_slice_array(). This corrects the weights
	  near the edges of sheets. There should be no visible change to
	  simulations that were using a weights_generator or
	  w?\004eights_shape that was a pattern such as UniformRandom() or
	  Constant() (as opposed to a Disk() or Gaussian(), which were
	  being incorrectly calculated at the edge of Sheets).

2006-01-18  louisem

	* [r2132] examples/obermayer_pnas90.ty:
	  Cleaned up alpha and radius; might work now. Enabled
	  DivisiveSumNormalize

2006-01-18  ceball

	* [r2131] topographica_script.py:
	  Undid previous change - commandline.py is in topo/misc/, not
	  topo/base/.

2006-01-18  jdepaula

	* [r2130] topographica_script.py:
	  Someone missed this file when they moved commandline.py

2006-01-17  ceball

	* [r2129] topo/tests/testsheet.py:
	  Added a partial test of bounds2slice(). I think bounds2slice()
	  might be incorrect - needs to be investigated (I might be
	  confused).

2006-01-17  jbednar

	* [r2128] topo/plotting/templates.py:
	  Replaced testing version of RGB plot with a real RGB CoG plot

	* [r2127] topo/analysis/featuremap.py:
	  Cleaned up imports and minor spelling errors. Cleaned up
	  commented-out display functions, and Julien made them work with
	  the current version of the GUI (though they still aren't clean
	  enough to leave uncommented). Fixed non-cyclic features to use an
	  inclusive frange.

	* [r2126] topo/analysis/updatecommands.py:
	  Added measure_cog command

	* [r2125] topo/base/utils.py:
	  Added inclusive option to frange

	* [r2124] topo/tkgui/topoconsole.py:
	  Added hack useful for MeasureFeatureMap

	* [r2123] topo/analysis/updatecommands.py:
	  Expanded HACKALERT description

	* [r2122] topo/analysis/updatecommands.py:
	  Changed SineGratingPresenter to be a general PatternPresenter
	  class that accepts any PatternGenerator

	* [r2121] topo/analysis/updatecommands.py:
	  Changed measure_or_pref to accept a presenter object instead of a
	  presenter class

	* [r2120] topo/analysis/featuremap.py,
	  topo/analysis/updatecommands.py:
	  Moved sim argument out of SineGratingPresenter __init__ and put
	  it in __call__ instead

	* [r2119] external/Makefile:
	  Fixed bug in previous commit

	* [r2118] topo/analysis/updatecommands.py,
	  topo/commands/basic.py,
	  topo/tkgui/testpattern.py:
	  Removed unused sim argument in pattern_present

	* [r2117] external/Makefile:
	  Forced matplotlib to be remade when Python changes, because it
	  seems to require that

	* [r2116] ChangeLog:
	  Up-to-date version of changes

2006-01-17  ceball

	* [r2115] topo/tests/lissom_or_reference.ty:
	  Minor correction plus put back RN=32.0 in case that's the
	  problem.

2006-01-16  julienciroux

	* [r2114]
	  topo/tests/tkgui/testplotgrouppanel.py:
	  Directly access the Sheet.sheet_view_dict, instead of the
	  add_sheet_view function the SheetViews. The function
	  add_sheet_view will be soon deleted when all similar calls (in
	  other files) will have been replaced.

	* [r2113] topo/analysis/updatecommands.py:
	  Directly access the Sheet.sheet_view_dict, instead of the
	  add_sheet_view function to store the Activity sheetviews. The
	  function add_sheet_view will be soon deleted when all similar
	  calls (in other files) will have been replaced.

	* [r2112] topo/analysis/featuremap.py:
	  Directly access the Sheet.sheet_view_dict, instead of the
	  add_sheet_view function to store the feature preference and
	  selectivity sheetviews. The function add_sheet_view will be soon
	  deleted when all similar calls (in other files) will hav?\004e
	  been replaced.

2006-01-16  ceball

	* [r2111] topo/tests/lissom_or_reference.ty:
	  Added test for weights.

	* [r2110]
	  topo/tests/or_map_topo.000001p000.Eye0_Activity.matrix,
	  topo/tests/or_map_topo.000001p000.Primary_Activity.matrix:
	  For or_map_topo.param v.1.6

	* [r2109]
	  topo/tests/or_map_topo.000001.wts.Primary.Afferent0.024_070.matrix,
	  topo/tests/or_map_topo.000001.wts.Primary.LateralExcitatory.024_070.matrix:
	  C++ LISSOM values from or_map_topo.param version 1.6

2006-01-16  julienciroux

	* [r2108] topo/analysis/updatecommands.py,
	  topo/tkgui/projectionpanel.py:
	  Added a parameter proj_name to set before calling
	  update_projection(), so that we only request UnitView for a given
	  projection.

	* [r2107] topo/base/connectionfield.py:
	  Corrected Unit_View in CFSheet so that it only installs UnitView
	  in the sheet_view_dict but does not do any look_up or does not
	  return any UnitView object. Also added a test for making sure
	  that we request UnitView from CFProjections only,?\004 and added
	  the possibility to pass a projection name to only request
	  UnitViews from the requested projection (or for all of them if
	  projection_name == None).

	* [r2106] topo/plotting/plotfilesaver.py:
	  Got rid of the call to PlotGroup do_plot_cmd that no longer
	  exists. It has to be replaced by a call to update_projection, but
	  it will be done when re-writing entirely PlotFileSaver.

	* [r2105] topo/tkgui/projectionpanel.py:
	  Got rid of the now un-used attribute shape and corresponding
	  ALERT! (It has been forgotten in the last commit.)

	* [r2104] topo/plotting/plotgroup.py:
	  Cleaned up old ALERTS: got rid of the unused FLAT constant and
	  PlotGroup shape attribute, deleted PlotGroup do_plot_cmd() that
	  is now unused.

	* [r2103] topo/plotting/plotgroup.py,
	  topo/tkgui/projectionpanel.py:
	  Replaced generate_coords() in ProjectionPlotGroup and made it
	  non-private so that it is callable from the projectionpanel.py.
	  It enables to keep executing the
	  updatecommands.update_projection() from the projectionpanel.

2006-01-16  jbednar

	* [r2102] doc/Future_Work/index_text.php:
	  Minor clarifications, plus added Eyal notes

	* [r2101] doc/Downloads/index_text.php:
	  Fixed the explanation of upgrading to the very latest release

	* [r2100] CONVENTIONS:
	  Added section about ALERTs

2006-01-15  ceball

	* [r2099] topo/tests/lissom_or_reference.ty:
	  To match C++ LISSOM's samples/or_map_topo.param version 1.6. This
	  version is for Topographica as of 2005/12/21 00:00. It will be
	  updated for the current version of Topographica as testing
	  proceeds from that date in December.

	* [r2098]
	  topo/tests/or_map_topo.000001p000.Eye0_Activity.matrix,
	  topo/tests/or_map_topo.000001p000.Primary_Activity.matrix:
	  From C++ LISSOM's samples/or_map_topo.param version 1.6

	* [r2097] topo/tests/lissom_log_parser.py:
	  Added function to read in C++ LISSOM .matrix file.

	* [r2096] topo/tests/or_map_topo.log:
	  Values from C++ LISSOM's or_map_topo.param version 1.6

2006-01-14  julienciroux

	* [r2095] examples/lissom_or.ty:
	  Added a scheduled action deleted by mistake on a previous commit.

2006-01-14  jbednar

	* [r2094] examples/lissom_or.ty:
	  Minor cleanup; shouldn't have affected results

2006-01-14  julienciroux

	* [r2093] examples/lissom_or.ty:
	  Rounded the value assigned to the input learning rate for the
	  scheduled actions (left temporary comments with original values).

	* [r2092] examples/lissom_or.ty:
	  Rounded the value assigned to the excitatory learning rate for
	  the scheduled action (left temporary comment with original
	  values).

	* [r2091] examples/lissom_or.ty:
	  Rounded the initial values of the three learning rates (input,
	  exc, inh).

	* [r2090] examples/lissom_or.ty:
	  Got rid of a scheduled action that had no effect on the
	  simulation.

	* [r2089] examples/lissom_or.ty:
	  Rounded the numerical value for declaring the inhibitory weights
	  bounding box.

	* [r2088] examples/lissom_or.ty:
	  Rounded the numerical value for declaring the afferent weights
	  bounding box.

	* [r2087] examples/lissom_or.ty:
	  Rounded the numerical value for declaring the Gaussian size
	  parameter.

	* [r2086] examples/lissom_or.ty:
	  Rounded the value for declaring the input_bounds. Also replaced
	  the fraction for declaring the Gaussian size by its numerical
	  expression.

	* [r2085] examples/lissom_or.ty:
	  Changed expression written as fraction to replace them by the
	  numerical expression as they are calculated by Python. Next step
	  is to round these values and still have a valid simulation.

2006-01-13  ceball

	* [r2084] topo/tests/lissom_or_reference.ty:
	  Skips first C++ LISSOM input pattern...which C++ LISSOM skips
	  also?

	* [r2083] topo/tests/lissom_or_reference.ty:
	  Corrected conversion from C++ LISSOM's cx and cy.
	  retina_edge_buffer set to match C++ LISSOM's - might not be
	  correct.

2006-01-13  alan_lindsay

	* [r2082] topo/tkgui/editorobjects.py:
	  Lateral projections represented as dotted circles; labels appear
	  when hovered over and properties set through the projection's
	  sheet. In bounds calculations are determined using full extent of
	  parallelogram or receptive field. Multiple connections have a
	  representation, however labels need sorted.

	* [r2081] topo/tkgui/editorwindow.py:
	  Correction to the import code (doesn't connect connections
	  twice).

2006-01-13  ceball

	* [r2080] topo/tests/lissom_or_reference.ty:
	  weights_generator is Constant().

	* [r2079] topo/tests/lissom_or_reference.ty:
	  Takes input pattern parameters from a C++ lissom log file.

	* [r2078] topo/tests/lissom_log_parser.py:
	  Used to parse .log files from lissom and return input parameters.

	* [r2077] topo/tests/or_map_topo.log:
	  Initial verison of log file from C++ LISSOM's or_map_topo.params.
	  This initial version is just to setup the testing.

	* [r2076] examples/lissom_or_reference.ty,
	  topo/tests/lissom_or_reference.ty:
	  Moved from examples/ to topo/tests/

2006-01-12  ceball

	* [r2075] topo/tests/testlissom.data:
	  Data from 2006/01/09 1315

	* [r2074] topo/tests/testlissom.ty:
	  Added comment about changing the reference data.

	* [r2073] topo/tests/testlissom.data:
	  Added as binary

	* [r2072] topo/tests/testlissom.data:
	  Removed - file should have been added as binary.

	* [r2071] topo/tests/testlissom.ty:
	  Made afferent_weights_bounds larger. Test cases bound to fail
	  right now until the test activities are updated.

2006-01-12  julienciroux

	* [r2070] examples/lissom_or_reference.ty:
	  Commented what are the number added to match the old simulation
	  now that the learning rate is divided by the number of unit of
	  the CF at the center.

	* [r2069] topo/base/connectionfield.py:
	  Deleted old JCALERT.

	* [r2068] topo/base/connectionfield.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py:
	  Delered the parameter rows and cols that were passed to
	  CFLearningFunction.single_connection_learning_rate(), they are
	  now retrieved from the cfs parameter instead of being passed.

	* [r2067] topo/base/connectionfield.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py:
	  Changed the name of set_learning_rate() to
	  single_connection_learning_rate() in CFLearningFunction, and
	  wrote the documentation for this function. Also changed the
	  parameter single_cf_learning_rate to be
	  single_connection_learning_rate in all sub-classes of
	  CFLearningFunction. Got rid of old JABALERT about the learning
	  rate handling.

2006-01-12  ceball

	* [r2066] topo/tests/testlissom.ty:
	  Updated to use pickled data file testlissom.data.

	* [r2065] topo/tests/testlissom.data:
	  Pickled data for use with the test file. Data from release_0_8_1.

	* [r2064] topo/tests/testlissom.ty:
	  Was running with slightly different results each time. I have no
	  idea why - the random and RandomArray seeds were set. I replaced
	  all the lissom code again and it seems to run with the same
	  results every time now. Test values to follow...?\004

2006-01-12  julienciroux

	* [r2063] examples/lissom_or.ty:
	  Cleaned up the new lissom_or.ty.

2006-01-12  ceball

	* [r2062] topo/tests/testlissom.ty:
	  The previous commit contained incorrect activity arrays.

	* [r2061] topo/tests/testlissom.ty:
	  Test values come from release_0_8_1.

2006-01-12  julienciroux

	* [r2060] examples/lissom_or.ty:
	  New version of lissom_or.ty without any old Lissom parameters
	  explicilty declared. This version matches exactly the old one
	  (which is now saved as lissom_or_reference.ty.

	* [r2059] examples/lissom_or_reference.ty:
	  The former lissom_or.ty file has been renamed
	  lissom_or_reference.ty.The former lissom_or.ty will be replaced
	  by a simpler version that won't declare any of the old Lissom
	  parameters.

2006-01-12  ceball

	* [r2058] topo/tests/testlissom.ty:
	  Rough initial version.

	* [r2057] topo/learningfns/optimized.py:
	  Had to add a hack for detection of zero in the mask values.
	  Removed a stray '*' (that was having no effect).

	* [r2056] topo/learningfns/optimized.py:
	  Corrected a mistake in the previous version of DivisiveHebbian
	  where even unmasked values were used to calculate the total
	  weight change. Made application of the mask simpler and more
	  efficient by doing it in the same loop as the weight
	  mo?\004dification. Added HACKALERT about how to make the code
	  clearer.

2006-01-12  jbednar

	* [r2055] topo/tests/tkgui/testmatplotlibtk.py:
	  Tried to make the test be skipped when there is no display, but
	  without any apparent effect

	* [r2054] doc/User_Manual/index_text.php:
	  Added note about citations

	* [r2053] doc/Downloads/index_text.php:
	  Cleaned up Mac instructions

	* [r2052] topo/base/connectionfield.py:
	  Cleaned up comments

2006-01-11  ceball

	* [r2051] topo/base/connectionfield.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py:
	  Added HACKALERT; changed order of output_fn and mask as a
	  temporary solution.

	* [r2050] topo/outputfns/basic.py:
	  Added HACKALERT

	* [r2049] topo/learningfns/optimized.py:
	  Removed code accidentally left behind.

	* [r2048] topo/learningfns/optimized.py:
	  Minor change to DivisiveHebbian_CPointer C code to improve speed.

	* [r2047] topo/tests/testlissom_cpointer.ty:
	  Initial version, based on examples/lissom_or.ty version 1.42.

	* [r2046] topo/learningfns/optimized.py,
	  topo/projections/optimized.py,
	  topo/sheets/lissom.py:
	  LISSOM_CPointer and its various optimized functions now respects
	  the mask of the weights.

	* [r2045] topo/learningfns/optimized.py:
	  Corrected learning_rate setting in DivisiveHebbian_CPointer.

	* [r2044] topo/learningfns/optimized.py:
	  Minor alteration to DivisiveHebbian C code to improve speed.

	* [r2043] topo/learningfns/optimized.py:
	  The DivisiveHebbian C code now respects the mask. Added a
	  hackalert about the name, and slightly changed 1 another
	  hackalert.

	* [r2042] topo/base/connectionfield.py:
	  Made cf's mask array be the same type as the weights array, and
	  made it savespace(1). Had to do the same on change_bounds because
	  it appears that using Numeric.where() causes these attributes to
	  be lost.

	* [r2041] topo/base/connectionfield.py:
	  Removed apparently redundant use of savespace(). The savespace
	  and typecode attributes of the weights matrix appear to be kept
	  anyway. If they weren't, typecode would need to be set again
	  anyway.

2006-01-11  julienciroux

	* [r2040] external,
	  external/.cvsignore:
	  Ignore Python-2.4.2 directory.

2006-01-11  ceball

	* [r2039] topo/projections/basic.py:
	  Added missing import statement.

2006-01-10  julienciroux

	* [r2038] topo/analysis/updatecommands.py,
	  topo/plotting/plotgroup.py,
	  topo/plotting/templates.py,
	  topo/tkgui/projectionpanel.py:
	  Moved the function _generate_coords() from ProjectionPlotGroup to
	  ProjectionPanel. Wrote the function update_projections in
	  analysis/updatecommands.py. Now this command is executed instead
	  of do_plot_cmd() in ProjectionPlotGroup (that has been deleted).

	* [r2037] topo/plotting/plotengine.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/__init__.py,
	  topo/tests/testplotengine.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/tkgui/testactivitypanel.py,
	  topo/tests/tkgui/testbasicplotgrouppanel.py,
	  topo/tests/tkgui/testplotgrouppanel.py,
	  topo/tests/tkgui/testtopoconsole.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/cfsheetplotpanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/testpattern.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/unitweightspanel.py:
	  Deleted plotengine.py (and testplotengine.py). Now, the PlotGroup
	  objects are stored in a variable plotgroup_dict declared in
	  plotgroup.py. From the panel, the plotgroup_dict is accessed, and
	  if the requested PlotGroup is not found, it is directly created
	  from the panel. Corresponding changes have been made in some test
	  files and in PlotFileSaver.

2006-01-10  ceball

	* [r2036] topo/base/connectionfield.py:
	  Removed line I left in by accident at some time in the past.

2006-01-10  julienciroux

	* [r2035] topo/plotting/plotgroup.py:
	  Got rid of now unused do_plot_cmd() function in
	  UnitWeightPlotGroup() (replaced by update_weights in
	  analysis/updatecommands.py). Simplified the do_plot_cmd in
	  ProjectionPlotGroup: the goal is too soon replace it by an
	  update_projection command in analysis/updatecommands.py.

2006-01-10  ceball

	* [r2034] topo/base/connectionfield.py:
	  Removed unused import statement.

	* [r2033] examples/lissom_or.ty,
	  topo/base/connectionfield.py,
	  topo/projections/basic.py:
	  Moved SharedWeightProjection and SharedWeightCFResponseFunction
	  from topo/base/connectionfield.py to topo/projections/basic.py.
	  Renamed SharedWeightProjection to SharedWeightCFProjection.

	* [r2032] examples/lissom_or.ty:
	  No visible changes (only changed commented-out code). LGNOn
	  projections' output_fns set to DivisiveSumNormalize(). Added
	  LGNOff. Called DivisiveSumNormalize() with norm_value=-1.0 where
	  projections' strengths are -1.0 so that activities' signs aren't
	  reversed. On and Off channels appear to work (which you can see
	  if you normalize the activity in the GUI).

	* [r2031] topo/outputfns/basic.py:
	  Added HACKALERT to DivisiveSumNormalize.

	* [r2030] topo/outputfns/basic.py:
	  Removed HACKALERT. I realize now that although the syntax for
	  Numeric.clip() implies it is an in-place operation, the array
	  must really be copied.

	* [r2029] topo/outputfns/basic.py:
	  Undid change in previous commit. Why doesn't Numeric.clip() work
	  here?

	* [r2028] topo/learningfns/basic.py:
	  No visible changes. Changed use of output_fn() so the syntax
	  matches the in-place operation.

	* [r2027] topo/outputfns/basic.py:
	  Used Numeric's clip() rather than utils.clip_in_place(). See the
	  hackalert.

	* [r2026] topo/base/connectionfield.py:
	  No visible changes. Used xrange() to generate a loop instead of
	  range(), and inside large loops that will run often avoided some
	  evaluations.

2006-01-09  ceball

	* [r2025] topo/base/connectionfield.py:
	  Added HACKALERT about already-known masking problem.

	* [r2024] examples/lissom_or.ty:
	  Added dest_port to connections for LGNOn (change is to
	  commented-out code, so no visible effect).

	* [r2023] topo/base/projection.py:
	  Added HACKALERT about ports.

2006-01-09  julienciroux

	* [r2022] doc/Downloads/index_text.php:
	  Added instructions for building Topographica on Mac OS X 10.4
	  (Tiger), in the Downloads section of the /doc/ directory. It may
	  have to reviewed by a native english speaker.

	* [r2021] external/Python-2.4.tgz:
	  remove Python-2.4.tgz from external/.

	* [r2020] external/Makefile,
	  external/Python-2.4.2.tgz:
	  Replaced Python-2.4 by Python-2.4.2 in the external packages, and
	  made the corresponding changes to the external/Makefile. This
	  upgrade allows to get rid of a warning appearing in the Mac
	  version of Python-2.4.

	* [r2019] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  topo/base/connectionfield.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py:
	  Changed the handling of the learning rate: now the learning rate
	  (as it is applied when passing to connectionfield.hebbian()) has
	  been divided by the number of unit in the receptive field of the
	  unit at the center of the sheet. The learning rate is set by a
	  function set_learning_rate in CFLearningFunction, and has to be
	  called by the subclasses of CFLearningFunction. Changes have been
	  made to the simulation scripts in order to match the former
	  situation, these changes have been heavily tested.

2006-01-08  jbednar

	* [r2018] topo/base/connectionfield.py:
	  Removed apparently unneeded set_cfs function. Changed base class
	  of SharedWeightProjection to be CFProjection instead of
	  Projection. Added ALERTs.

	* [r2017] examples/lissom_or.ty:
	  Fixed radius/diameter confusion for circular RF masks

	* [r2016] topo/base/simulator.py,
	  topo/tkgui/unitweightspanel.py:
	  Added ALERTs

	* [r2015] topo/tkgui/editorobjects.py:
	  Changed Update to Apply, and added ALERT

	* [r2014] examples/lissom_or.ty:
	  Changed commented-out example SharedWeightProjection to a
	  prototype of an ON channel

2006-01-07  jbednar

	* [r2013] topo/base/connectionfield.py:
	  Corrections to messages and documentation

	* [r2012] topo/analysis/updatecommands.py:
	  Added ALERTs

	* [r2011] topo/__init__.py:
	  Updated list for import *

2006-01-07  julienciroux

	* [r2010] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty:
	  Added control of the input stream seed and weight stream seed for
	  all the examples currently implemented. That way, the simulation
	  are always similar, which enables easy testing.

	* [r2009] topo/tests/testplotengine.py:
	  Got rid of old commented out code in testplotengine.

2006-01-07  ceball

	* [r2008] examples/lissom_or.ty:
	  Added note about the radius of the afferent projection's
	  connecttionfields.

	* [r2007] examples/cfsom_or.ty:
	  No visible change - removed some commented-out code.

	* [r2006] examples/lissom_or.ty:
	  No visible change: checked in commented-out code. The code is an
	  example SharedWeightProjection. (Also added another note.)

	* [r2005] topo/base/connectionfield.py:
	  SharedWeightProjection stores the slice indexes and bounds of
	  units (and still just the single set of weights). This allows
	  shared weight response functions to use the correct
	  activity_matrix slice, and SharedWeightProjection.get_view() to
	  get the correct bounds for a unit. The slices and bounds are
	  stored to avoid having to calculate them each time e.g. a
	  response function is called. Also added some hackalerts
	  (including minor ones about code unrelated to that being
	  committed here).

2006-01-06  julienciroux

	* [r2004] topo/plotting/templates.py,
	  topo/tkgui/cfsheetplotpanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Changed templates.py, unitweightpanel.py and cfsheetpanel.py so
	  that now it executes the command update_weight defines in
	  updatecommands.py and declared in the UnitWeight template,
	  instead of using the do_plot_cmd in UnitWeightPlotGroup.

	* [r2003] topo/analysis/featuremap.py,
	  topo/analysis/updatecommands.py,
	  topo/tkgui/basicplotgrouppanel.py:
	  Moved the updatecommands (e.g. update_activity), from
	  featuremap.py to a new file updatecommands.py in the analysis
	  directory. Made the corresponding change in the import in
	  BasicPlotGroupPanel.

2006-01-06  jbednar

	* [r2002] topo/projections/basic.py:
	  Cleaned up documentation

	* [r2001] topo/base/connectionfield.py,
	  topo/base/sheet.py,
	  topo/plotting/plotgroup.py:
	  Added alerts

2006-01-06  ceball

	* [r2000] examples/lissom_or.ty:
	  No visible change. Added commented-out code to allow the shape of
	  the weights to be specified.

	* [r1999] topo/base/connectionfield.py:
	  ConnectionField's mask (for weights) has a threshold (temporarily
	  hard-coded rather than being user-definable).

2006-01-06  julienciroux

	* [r1998] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py:
	  Got rid of the unused function release_sheetviews both in Plot
	  and PlotGroup. It has ot be re-defined if we want to re-implement
	  this functionnality.

2006-01-06  ceball

	* [r1997] topo/base/connectionfield.py:
	  Corrected a mistake (changed Int to Numeric.Int32).

2006-01-05  ceball

	* [r1996] topo/base/parameter.py:
	  Added HACKALERT about inheritance of default values for
	  Parameters.

	* [r1995] topo/base/connectionfield.py:
	  Added weights_shape to SharedWeightProjection.

	* [r1994] examples/obermayer_pnas90.ty:
	  Temporarily commented line that sets default
	  PatternGeneratorParameter.

	* [r1993] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_or.ty,
	  topo/base/connectionfield.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py:
	  No visible change (I hope) (except the example files temporarily
	  do not default to a particular PatternGenerator for e.g. the test
	  pattern window) , although simulations will run a little slower.
	  Added code to allow ConnectionFields to have a shape
	  (CFProjection has a weights_shape Parameter). The default shape
	  is Constant (i.e. the same rectangular shape as before).

	* [r1992] topo/base/connectionfield.py:
	  Changed references to topo.base.patterngenerator to
	  patterngenerator.

	* [r1991] topo/base/connectionfield.py:
	  No visible change - small alteration to code.

2006-01-04  ceball

	* [r1990] topo/tkgui/__init__.py:
	  Imported all LearningFunctions and ResponseFunctions for the GUI.

	* [r1989] topo/responsefns/__init__.py:
	  Code to populate ResponseFunctionParameter's range().

	* [r1988] topo/learningfns/__init__.py:
	  Code to populate LearningFunctionParameter's range().

	* [r1987] topo/base/utils.py:
	  Added HACKALERT about classname_repr().

	* [r1986] topo/base/connectionfield.py:
	  Added LearningFunctionParameter and ResponseFunctionParameter.
	  Made response_fn and learning_fn attributes into
	  ResponseFunctionParameters and LearningFunctionParameters.

	* [r1985] topo/learningfns/optimized.py:
	  Added a comment about using xrange() instead of range().

	* [r1984] topo/learningfns/basic.py:
	  Changed height and width to size and aspect ratio (I missed when
	  I made the change from height and width to size and aspect_ratio.
	  Added notes about (1) specifying size and aspect_ratio here in
	  the first place and (2) there being no warnin?\004g when the
	  non-parameter attributes height and width were being set (I spent
	  a long, long time finding this bug).

2006-01-02  ceball

	* [r1983] topo/base/patterngenerator.py,
	  topo/base/sheet.py:
	  Added a HACKALERT noting problems in the unlikely case of
	  zero-sized or very small density matrices being specified.

	* [r1982] topo/tkgui/parametersframe.py:
	  Added HACKALERT.

	* [r1981] topo/base/projection.py:
	  Changed output_fn to be an OutputFunctionParameter.

2005-12-31  ceball

	* [r1980] topo/sheets/lissom.py:
	  Made the output_fn be an OutputFunctionParameter.

	* [r1979] topo/__init__.py:
	  Added HACKALERT.

	* [r1978] topo/base/parameter.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/outputfns/__init__.py,
	  topo/patterns/__init__.py,
	  topo/sheets/generatorsheet.py,
	  topo/tkgui/__init__.py:
	  Part-way checkin. ClassSelectorParameters (such as
	  PatternGeneratorParameter) can now be declared in the correct
	  file (topo.base.patterngenerator in this example) because the
	  list of available classes (PatternGenerators in this case) is
	  added to in the relevant __init__.py file
	  (topo/patterns/__init__.py in this case). The list of available
	  classes comes from the imported modules in the package, so the
	  GUI does e.g. 'from topo.patterns import *' to make all options
	  available. There are other ClassSelectorParameters still to add,
	  and the documentation is incomplete.

	* [r1977] topo/outputfns/__init__.py,
	  topo/patterns/__init__.py,
	  topo/patterns/basic.py,
	  topo/tkgui/parametersframe.py:
	  Changed name of PackageParameter to ClassSelectorParameter.

	* [r1976] topo/base/parameter.py:
	  Changed name of PackageParameter to ClassSelectorParameter. Made
	  DynamicNumber's setting error message slightly more informative.

	* [r1975] topo/tkgui/parametersframe.py:
	  Commented out some currently unused code.

2005-12-30  ceball

	* [r1974] topo/tkgui/parametersframe.py:
	  Continued cleaning - no visible change.

	* [r1973] topo/tkgui/parametersframe.py,
	  topo/tkgui/propertiesframe.py:
	  Cleaned method arguments.

	* [r1972] topo/tkgui/taggedslider.py:
	  Added ALERT about TaggedSlider widths.

	* [r1971] topo/tkgui/propertiesframe.py,
	  topo/tkgui/taggedslider.py:
	  Some simplifications.

	* [r1970] topo/tkgui/parametersframe.py:
	  Now uses a dictionary to map parameters to widgets.

2005-12-29  ceball

	* [r1969] topo/tkgui/taggedslider.py:
	  Cleaned up TaggedSlider (no visible change).

	* [r1968] topo/tkgui/parametersframe.py,
	  topo/tkgui/propertiesframe.py,
	  topo/tkgui/taggedslider.py:
	  Continued to cleaned up widgets in taggedslider.py (not yet
	  finished). Gave the idea of 'string_translator' widgets an
	  existence with a TranslatorWidget base class. We might want to
	  change the name.

2005-12-28  ceball

	* [r1967] topo/tkgui/parametersframe.py,
	  topo/tkgui/propertiesframe.py,
	  topo/tkgui/taggedslider.py:
	  Read-only properties are displayed with a label rather than a
	  read-only entry box. The label text needs to be fixed - there's
	  an alert about that.

2005-12-22  jbednar

	* [r1966] doc/Downloads/index_text.php:
	  Clarified updating

	* [r1965] doc/Downloads/index_text.php:
	  Clarified updating

	* [r1964] doc/shared/trailer.php:
	  Updated web site date; not sure why it is not set up to update
	  automatically

2005-12-22  ceball_cvs2svn

	* [r1963] /tags/release_0_8_1:
	  This commit was manufactured by cvs2svn to create tag
	  'release_0_8_1'.

2005-12-22  jbednar

	* [r1962] Makefile,
	  doc/Downloads/index_text.php:
	  Fixed problem with LATEST_STABLE tagging

	* [r1961] doc/Downloads/index_text.php,
	  doc/Future_Work/index_text.php,
	  doc/Home/index_text.php,
	  doc/Reference_Manual/index_text.php,
	  doc/Team_Members/index_text.php,
	  doc/Tutorial/index_text.php,
	  doc/User_Manual/index_text.php,
	  doc/shared/index.php,
	  topo/misc/__init__.py:
	  Updated documentation to match latest release

	* [r1960] Makefile:
	  Minor fix

	* [r1959] Makefile:
	  Made web site depend on doc

	* [r1958] Makefile:
	  Updated release to 0.8.1

	* [r1957] Makefile:
	  Added releasing and versioning commands

	* [r1956] topo/tkgui/editortools.py:
	  Clarified toolbar labels

	* [r1955] examples/hierarchical.ty:
	  Set default locations for the Model Editor

2005-12-22  ceball

	* [r1954] doc/Tutorial/index_text.php:
	  Changed 'layout' to 'architecture'.

	* [r1953] doc/Tutorial/index_text.php:
	  Added picture of network from model editor. Removed text about
	  edge-effects now there's a buffer round the retina.

	* [r1952]
	  doc/Tutorial/images/lissom_network_diagram.png:
	  Picture of network from the model editor window.

	* [r1951] topo/patterns/image.py:
	  Image as the new name for ImageGenerator caused a clash...with
	  Image. So temporarily Python's Image library is imported as
	  pImage.

	* [r1950] examples/cfsom_or.ty,
	  examples/obermayer_pnas90.ty:
	  Default test pattern is a Gaussian.

	* [r1949] topo/patterns/basic.py:
	  Adjusted default Parameter settings.

	* [r1948] topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testsheetview.py:
	  Sheet's bounds and density cannot be set on an object now they
	  are Constant parameters. Uses of ImageGenerator(Sheet) were
	  setting them on an object.

	* [r1947]
	  doc/Tutorial/images/unit_weights_0.2_0.0.png,
	  doc/Tutorial/images/unit_weights_0.2_0.0_or.png:
	  Added unit weights plots for unit at (0.2,0.0) since it's clearly
	  orientation selective.

	* [r1946] doc/Tutorial/index_text.php:
	  Added color key underneath colorized weights plot.

	* [r1945] doc/Tutorial/index_text.php:
	  Updated horizontal orientation key.

2005-12-21  ceball

	* [r1944]
	  doc/Tutorial/images/or_key_horiz_transparent.png:
	  Corrected to match topographica's orientation coloring scheme.

2005-12-21  jbednar

	* [r1943] topo/tkgui/unitweightspanel.py:
	  Set situate on by default for UnitWeightsPanel

2005-12-21  ceball

	* [r1942]
	  doc/Tutorial/images/activity_line.png,
	  doc/Tutorial/images/activity_line_or.png,
	  doc/Tutorial/images/or_map.png,
	  doc/Tutorial/images/projection.png,
	  doc/Tutorial/images/test_pattern.png,
	  doc/Tutorial/index_text.php:
	  Update to tutorial now that weights can be colorized, and with
	  most recent map.

	* [r1941] examples/lissom_or_20000.typ:
	  Updated the snapshot to have the model set out better in the
	  model editor.

	* [r1940] doc/Team_Members/index_text.php:
	  Added a link to a soon-to-be-realized page about motion
	  after-effects to Chris' section.

	* [r1939] examples/lissom_or_20000.typ:
	  I trained another map. I like training maps. This one was for
	  changes to the PatternGenerator subclass names.

	* [r1938] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty,
	  topo/analysis/featuremap.py,
	  topo/base/connectionfield.py,
	  topo/base/patterngenerator.py,
	  topo/base/utils.py,
	  topo/commands/basic.py,
	  topo/learningfns/basic.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/sheets/generatorsheet.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testpatterngenerator.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotengine.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/tkgui/testactivitypanel.py,
	  topo/tests/tkgui/testplotgrouppanel.py:
	  The PatternGenerator subclasses lose the 'Generator' suffix.
	  
	  For example:
	  "
	  from topo.patterns.basic import LineGenerator
	  ...
	  LineGenerator()
	  "
	  
	  has changed to:
	  "
	  import topo.patterns.basic
	  ...
	  topo.patterns.basic.Line()
	  "
	  
	  This checkin was part of an approximately 10-kilometre diff, so
	  the chance of a mistake somewhere is quite high.

	* [r1937] examples/lissom_or_20000.typ:
	  I trained another map. I like training maps. This one was for
	  changes to the way Sheet computes density.

	* [r1936] topo/tkgui/testpattern.py:
	  Added hack to reverse the order of the 'present in:' buttons.

	* [r1935] topo/tkgui/parametersframe.py:
	  'Install as class defaults' button hidden for the moment.

	* [r1934] examples/lissom_or.ty:
	  GeneratorSheet bounds are set on the class, as in the other
	  examples. This makes more sense than setting them on the specific
	  Retina used in this example, I think.

	* [r1933] topo/tkgui/parametersframe.py,
	  topo/tkgui/propertiesframe.py,
	  topo/tkgui/taggedslider.py:
	  Constant parameters are displayed but cannot be edited (EntryEval
	  gets a 'readonly' config option...please feel free to change the
	  background color). How to deal with Constants for a class is left
	  for another day...

	* [r1932] topo/patterns/__init__.py:
	  Added HACKALERT.

	* [r1931] topo/base/sheet.py:
	  density and bounds are Constant parameters.

	* [r1930] topo/base/parameter.py:
	  Changed Constant so that its value can be set on a class, but not
	  on an object.

	* [r1929] topo/learningfns/basic.py:
	  Removed unused import of Constant

	* [r1928] topo/patterns/__init__.py:
	  PatternGenerators don't have 'Generator' cut off their name in
	  menus. Either we rename PatternGenerator to Pattern (so
	  LineGenerator to Line, and all the rest), or we do something like
	  alter the name attribute of the PatternGenerator c?\004lass. Or
	  someone has a better idea...

	* [r1927] topo/tkgui/parametersframe.py:
	  Removed print statement left in by accident.

	* [r1926] topo/tkgui/parametersframe.py,
	  topo/tkgui/propertiesframe.py,
	  topo/tkgui/taggedslider.py:
	  PropertiesFrame gets a checkbutton property, which is
	  CheckbuttonEval (added to taggedslider.py). ParametersFrame now
	  deals with Boolean Parameters.

2005-12-21  alan_lindsay

	* [r1925] topo/tkgui/editorobjects.py,
	  topo/tkgui/editorwindow.py:
	  Creates a window holding a ParametersFrame, when properties is
	  selected from popup, or EditorObject is double clicked.

2005-12-21  ceball

	* [r1924] topo/commands/basic.py:
	  Uncommented a line that was accidentally left commented in the
	  previous update.

2005-12-20  yfsit

	* [r1923] topo/base/connectionfield.py,
	  topo/base/patterngenerator.py,
	  topo/base/sheet.py,
	  topo/patterns/image.py,
	  topo/patterns/random.py,
	  topo/plotting/plot.py,
	  topo/tests/testsheet.py:
	  - Added xdensity and ydensity that stores the true densities
	  along x
	  and y to the class Sheet. These densities are different from the
	  density
	  parameter when the width or height of the sheet bounds multiplied
	  by
	  density is not a integer. The size of the sheet matrix will be
	  the
	  integer part of that product and therefore the real density is
	  less than
	  the parameter by no more than 1. These real densities are
	  important for
	  computing the conversion between sheet and matrix coordinates,
	  which
	  were computed in these conversion functions.
	  
	  There are two reasons for moving them into the sheet:
	  1) more efficient because the true densities are cached in Sheet
	  2) It ensure the same densities are used across all conversion
	  functions and different bounds.
	  
	  - All conversion functions between matrix and sheet coordinates
	  now
	  require BOTH the true x and y densities.

2005-12-20  jbednar

	* [r1922] topo/plotting/templates.py:
	  Removed TestingPanel_for_RGB_Activity for now

	* [r1921] topo/base/boundingregion.py,
	  topo/base/sheetview.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/unitweightspanel.py:
	  Cleaned up documentation and comments

2005-12-20  alan_lindsay

	* [r1920] topo/tkgui/editorwindow.py:
	  Allow the editor to import models from the simulator. If the topo
	  Sheets don't have gui coords strored, uses random numbers to
	  position them.

	* [r1919] topo/tkgui/editortools.py:
	  Add topo sheets as they are made, rather than when they are
	  connected.

	* [r1918] topo/tkgui/editorobjects.py:
	  Small refinements; nicer.

2005-12-20  ceball

	* [r1917] topo/base/patterngenerator.py:
	  Added a HACKALERT (which is a question, really).

	* [r1916] examples/lissom_or_20000.typ:
	  Updated trained network after changes to lissom_or.ty's
	  parameters.

2005-12-20  yfsit

	* [r1915] examples/lissom_or.ty:
	  Changed the definition of gaussian's width and height, also the
	  afferent
	  weights.

2005-12-19  alan_lindsay

	* [r1914] topo/tkgui/editortools.py:
	  First attempt solution of Pmw/Tkinter Menu item clash

2005-12-19  ceball

	* [r1913] topo/commands/basic.py:
	  After loading a saved network, GaussianGenerators are only
	  installed in the GeneratorSheets if GaussianGenerator has already
	  been imported. This is a hack of a hack so that a
	  GaussianGenerator is restored to the GeneratorSheets in the
	  liss?\004om_or.ty example (but does not raise an error for other
	  cases).

2005-12-19  jbednar

	* [r1912] topo/tkgui/editorobjects.py:
	  Removed filling of CF oval, to eventually allow activity pattern
	  to show through.

2005-12-19  ceball

	* [r1911] examples/hierarchical.ty,
	  examples/lissom_or.ty,
	  topo/tkgui/testpattern.py:
	  PatternGeneratorParameter.default should be a
	  PatternGeneratorParameter instance, not a class.

	* [r1910] examples/cfsom_or.ty:
	  Corrected previous commit: BoundingBox is now imported from
	  topo.base.boundingregion, which is what I meant to type.

	* [r1909] examples/cfsom_or.ty:
	  BoundingBox is now imported from topo.base.sheet instead of
	  topo.base.patterngenerator.

	* [r1908] topo/tkgui/parametersframe.py:
	  Added a hack to have a DynamicNumber not display as a
	  DynamicNumber in a ParametersFrame while we figure out how to do
	  deal with DynamicNumbers properly.

2005-12-18  julienciroux

	* [r1907] topo/plotting/plot.py:
	  Got rid of old code commented out.

	* [r1906] topo/plotting/plotgroup.py:
	  Cleaned up comments.

2005-12-18  yfsit

	* [r1905] topo/base/connectionfield.py,
	  topo/responsefns/basic.py:
	  added ConnectionField.slice_tuple() and set_slice_array() to
	  simplify the code.

2005-12-18  ceball

	* [r1904] topo/tkgui/testpattern.py:
	  Edited HACKALERT

	* [r1903] examples/hierarchical.ty,
	  examples/lissom_or.ty:
	  Added a default for PatternGeneratorParameter for e.g. the GUI.

	* [r1902] topo/base/utils.py:
	  Altered a comment

2005-12-18  julienciroux

	* [r1901] topo/plotting/plotgroup.py:
	  Cleaned up the comments. Made initialize_plot_list (semi)
	  private.

2005-12-18  ceball

	* [r1900] topo/tkgui/parametersframe.py,
	  topo/tkgui/propertiesframe.py,
	  topo/tkgui/taggedslider.py,
	  topo/tkgui/testpattern.py:
	  Continued reorganizing parametersframe and testpattern. This is
	  an intermediate checkin.

2005-12-18  julienciroux

	* [r1899] topo/plotting/plotgroup.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Got rid of now unused got for handling static plot_list in
	  PlotGroup; plot_list is always a dynamic list. Fixed an hack in
	  the plotgrouppanel subclasses that was relating to that.

	* [r1898] topo/plotting/plotgroup.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Changed initialize_plot_list so that to only have dynamic list
	  and still have the possibility to pass an already built plot_list
	  when creating a PlotGroup. Made corresponding changes in the
	  plotgrouppanel classes.

	* [r1897] topo/plotting/plotengine.py,
	  topo/plotting/plotgroup.py:
	  Got rid of the possibility of passing lambda function as a filter
	  in PlotGroup; instead always pass a string (sheet_name) or None,
	  and build the corresponding lambda function in the PlotGroup
	  constructor. Simplified PlotEngine accordingly.

	* [r1896] topo/plotting/templates.py:
	  Changed the name of the temporary test template for RGBPlot.

	* [r1895] topo/plotting/plotgroup.py:
	  Cleaned up the file by getting rid of old comments and alerts.

	* [r1894] topo/plotting/templates.py:
	  Corrected a minor error on last commit.

2005-12-18  alan_lindsay

	* [r1893] topo/tkgui/editorobjects.py:
	  Added optional receptive fields

2005-12-18  julienciroux

	* [r1892] topo/plotting/templates.py:
	  Cleaned up templates.py from unused part of the code.

	* [r1891] topo/plotting/plot.py,
	  topo/plotting/templates.py:
	  Implemented RGBPlot. Added a temporary PlotGroupTemplate in
	  templates.py used for testing RGBPlot.

2005-12-18  alan_lindsay

	* [r1890] topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py:
	  Restructured classes and used default topo naming

2005-12-18  julienciroux

	* [r1889] topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/plotting/templates.py,
	  topo/tests/testplotengine.py,
	  topo/tests/testplotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/topoconsole.py:
	  Got rid of the PlotTemplate class in template. Now, a
	  plot_template is simply a dictionary associated to a name in the
	  KeyedList() plot_templates attribute of a PlotGroupTemplate.
	  Coresponding changes have been made in some tests files, and in
	  PlotGroup, PlotFileSaver and the PlotGroupPanels. I also got rid
	  of the attribute description of a PlotGroupTemplate, that was a
	  simple copy of the name attribute, and made the correponding
	  changes in TopoConsole.

	* [r1888] topo/plotting/plot.py:
	  Changed the name of HSVPlot to SHCPlot and of ColormapPlot to
	  PalettePlot.

2005-12-18  jbednar

	* [r1887] topo/plotting/plot.py:
	  Cleaned up documentation and comments

	* [r1886] topo/plotting/bitmap.py:
	  Cleaned up comments and documentation

	* [r1885] topo/plotting/bitmap.py:
	  Added counting of bad pixels

2005-12-17  julienciroux

	* [r1884] topo/plotting/bitmap.py:
	  Added a TO DO list.

	* [r1883] topo/plotting/bitmap.py,
	  topo/plotting/plotfilesaver.py:
	  Changed the attribute Bitmap.bitmap to be Bitmap.image. Made
	  corresponding changes on plotfilesaver.

	* [r1882] topo/plotting/bitmap.py,
	  topo/plotting/plot.py,
	  topo/tests/testbitmap.py,
	  topo/tests/testplot.py,
	  topo/tests/testplotengine.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testsheetview.py:
	  Got rid of an unused part of the code in RGBBitmap. Changed the
	  name from HSVMap, RGBMap and ColorMap to HSVBitmap, RGBBitmap and
	  PaletteBitmap. Made corresponding changes in plot and testfiles.

	* [r1881] topo/plotting/plot.py:
	  Modified __slice_matrices() and moved it from HSVPlot to Plot. It
	  is now a simple routine that only works on one matrix.

	* [r1880] topo/plotting/plot.py:
	  Cleaned up doc and comments.

2005-12-16  ceball

	* [r1879] topo/base/parameter.py,
	  topo/patterns/__init__.py,
	  topo/tests/tkgui/testpropertiesframe.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/propertiesframe.py,
	  topo/tkgui/taggedslider.py,
	  topo/tkgui/testpattern.py:
	  Continued modification of parametersframe and propertiesframe,
	  and associated files. Particularly, the way testpattern works is
	  changing. Some changes are here so that things carry on working
	  during the reorganization; nevertheless, the ability to choose
	  whether or not a generatorsheet's preview window is updated in
	  the test pattern window is temporarily gone. Most of the methods
	  involved in presenting patterns in the test pattern window are
	  already subject to JABHACKALERTS.

2005-12-16  julienciroux

	* [r1878] topo/plotting/plot.py:
	  Added the call to TopoObject __init__ from Plot. Allowed to get
	  rid of the parameter name in Plot and passing it as a TopoObject
	  param. Also get rid of default value for Plot subclasses RGBPlot
	  and ColormapPlot.

	* [r1877] topo/plotting/bitmap.py,
	  topo/plotting/plot.py:
	  Eliminated redundant clipping. Now it only clips in
	  Bitmap._arrayToImage() if the value are over 255. No other
	  clipping is performed before. Also eliminated unused part of the
	  code (e.G. attribute cropped in Plot, normalizing in
	  _arrayToImage).

	* [r1876] topo/plotting/plot.py:
	  Cleaned up the doc. Got rid of the matrix_hsv_to_rgb() (it was
	  supposed to be done on my last commit... it is now). Got rid of
	  unused default value in Plot.__init__. Changed the name of a
	  parameter from resu to plot.

	* [r1875] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplot.py:
	  Changed Plot so that it has an attribute Bitmap, rather than a
	  three tuple of rgb_matrices. From PlotGroup, the bitmap is
	  directly taken, without having to worry about which kind of
	  Bitmap it is (i.e. HSV,RGB or Pallette), the different case
	  beeing handled within Plot without anyone having to know about it
	  from outside. The TestPlot file has been temporary commented out
	  and has to be re-written so that to work with Bitmaps rather than
	  Matrices. The function matrix_hsv_to_rgb is no longer used by
	  Plot, but have been moved to testplot, in case we need it for
	  testing purpose in the future.

	* [r1874] topo/plotting/bitmap.py:
	  New version of HSVMap. It is a copy of the code of the soon to be
	  unused matrix_hsv_to_rgb() function.

	* [r1873] topo/plotting/plotgroup.py:
	  Simplified the function load_images() in PlotGroup: got rid of
	  unused tests and clipping. Intermediary step before directly
	  returning a bitmap from Plot.

2005-12-16  jbednar

	* [r1872] topo/plotting/plot.py:
	  Cleaned up documentation and comments

	* [r1871] topo/plotting/plotfilesaver.py,
	  topo/tests/testcfsom.py:
	  Cleaned up documentation, and moved ImageSaver to
	  topo/tests/testcfsom.py

	* [r1870] topo/plotting/templates.py:
	  Cleaned up documentation and added ALERTs

	* [r1869] topo/plotting/palette.py:
	  Cleaned up documentation, added ALERTs, including the plan for
	  the future

	* [r1868] topo/plotting/__init__.py:
	  Removed Histogram for now

2005-12-16  ceball

	* [r1867] topo/base/patterngenerator.py:
	  Changed default density from 10000 to 10.

2005-12-16  jbednar

	* [r1866] topo/plotting/bitmap.py:
	  Added alerts and cleaned up documentation and interface

	* [r1865] topo/plotting/bitmap.py,
	  topo/tests/testcfsom.py:
	  Cleaned up imports

	* [r1864] topo/plotting/bitmap.py,
	  topo/plotting/palette.py,
	  topo/tests/testpalette.py:
	  Moved mostly-unused BLACK_BACKGROUND and WHITE_BACKGROUND options
	  to the only place they are used, in palette.py. Removed unused
	  MONITOR_BASED_PLOTS and PAPER_BASED_PLOTS.

	* [r1863] topo/plotting/plot.py:
	  Cleaned up imports

	* [r1862] doc/Future_Work/index_text.php:
	  Added more to do

	* [r1861] topo/tests/__init__.py:
	  Removed Histogram class

	* [r1860] topo/plotting/histogram.py,
	  topo/tests/testhistogram.py:
	  Removed for now; may reinstate later if it is implemented

2005-12-16  julienciroux

	* [r1859] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplot.py,
	  topo/tkgui/testpattern.py:
	  New version of Plot that now works with subclasses
	  HSVPlot,RGBPlot and ColormapPlot. It is the first version for
	  this code: only HSVPlot is implemented, and there is still things
	  to change (e.g. using the Bitmap class from Plot instead of the
	  matrix_hsv_to_rgb). Corresponding changes have been made in
	  plotgroup.py, testpattern.py and testplot.py.

2005-12-16  ceball

	* [r1858] topo/base/parameter.py,
	  topo/tests/tkgui/testpropertiesframe.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/propertiesframe.py,
	  topo/tkgui/taggedslider.py,
	  topo/tkgui/testpattern.py:
	  Reorganization of ParametersFrame, PropertiesFrame, and
	  TestPattern. This is an intermediate checkin.

2005-12-15  jbednar

	* [r1857] doc/Team_Members/index_text.php:
	  Added Risto to Team Members

	* [r1856] topo/plotting/plotgroup.py:
	  Partial cleanup of documentation and imports

	* [r1855] topo/plotting/bitmap.py:
	  Removed unused BWMap

	* [r1854] CONVENTIONS:
	  Added convention for lists of imports

	* [r1853] topo/plotting/bitmap.py,
	  topo/tests/testbitmap.py,
	  topo/tests/testsheetview.py:
	  Removed unused BWMap

	* [r1852] topo/plotting/plot.py:
	  Added and removed ALERTs

	* [r1851] topo/plotting/bitmap.py:
	  Removed unused class

2005-12-15  julienciroux

	* [r1850] topo/plotting/plotgroup.py,
	  topo/tkgui/cfsheetplotpanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Simplified the situated button mechanisms. I realised I had wrote
	  unnecessary code for implementing it, and then simplified the
	  code of my last commit about that.

	* [r1849] topo/plotting/plotgroup.py,
	  topo/tkgui/cfsheetplotpanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Added the situated button in UnitWeightPanel and ProjectionPanel,
	  from the super-class CFSheetPlotPanel.Made the necessary changes
	  in UnitWeightPlotGroup and ProjectionPlotGroup.

	* [r1848] topo/tkgui/testpattern.py:
	  Forgotten file from the last commit concerning the deletion of
	  the template and plot_group_key default value in PlotGroup. I
	  should have committed this file at the same time.

2005-12-15  jbednar

	* [r1847] topo/base/connectionfield.py,
	  topo/projections/basic.py:
	  Added a draft of a SharedWeightProjection, which runs without
	  errors but doesn't yet do what one would expect.

	* [r1846] examples/lissom_or.ty:
	  Cleaned up retina_edge_buffer calculation; still needs more work
	  to make sure that it matches C++ LISSOM

2005-12-15  julienciroux

	* [r1845] topo/plotting/plotgroup.py:
	  Just got rid of the default value for template and plot_group_key
	  in the __init__ of PlotGroup. Modified testpattern accordingly.

2005-12-15  ceball

	* [r1844] topo/tkgui/propertiesframe.py:
	  Commented out unused set_values() method.

	* [r1843] topo/tkgui/propertiesframe.py:
	  Removed unused get_value() method.

	* [r1842] topo/tkgui/propertiesframe.py:
	  Removed set_value() method. Only used inside this class to access
	  a dictionary element.

	* [r1841] topo/tkgui/parametersframe.py,
	  topo/tkgui/testpattern.py:
	  Removed non-functioning reset_to_defaults() method from
	  ParametersFrame. Added HACKALERT about 'reset to defaults' in
	  testpattern.py and parametersframe.py for future implementation.

2005-12-15  jbednar

	* [r1840] topo/tkgui/editorwindow.py:
	  Fixed problem with ModelEditor stealing the Tkinter mainloop,
	  which was causing the command prompt to stop working immediately,
	  and all remaining windows to stop working if the Model Editor
	  window was closed

	* [r1839] topo/base/connectionfield.py:
	  Fixed typo

2005-12-15  ceball

	* [r1838] topo/tkgui/parametersframe.py:
	  No visible change. Cleaned up code in create_widgets().

2005-12-15  julienciroux

	* [r1837] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplot.py:
	  Changed the Plot.matrices attribute to be named
	  Plot.rgb_matrices. Made the corresponding changes in testplot.py
	  and plotgroup.py. Also, write a new version of __situate_plot()
	  in Plot, that now return and works with a three-tuple.

	* [r1836] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplot.py:
	  Made the Plot.matrices attribute beeing a three-tuple instead of
	  a list. Made corresponding changes in PlotGroup and TestPlot.

	* [r1835] topo/plotting/bitmap.py,
	  topo/plotting/plot.py,
	  topo/tests/testbitmap.py,
	  topo/tests/testplot.py:
	  Moved the function matrix_hsv_to_rgb() from bitmap.py to
	  plot.py.Made the corresponding changes in testplot.py and
	  bitmap.py.

2005-12-15  alan_lindsay

	* [r1834] topo/tkgui/topoconsole.py:
	  Added ModelEditor to simulation menu items.

2005-12-15  julienciroux

	* [r1833] topo/plotting/plot.py:
	  Cleaned up the code: got rid of attribute normalize and situated,
	  they are now passed as a parameter only. Rename situated to
	  situate.

2005-12-15  ceball

	* [r1832] topo/tkgui/topoconsole.py:
	  Removed menu separator that is no longer required.

2005-12-14  jbednar

	* [r1831] examples/lissom_or.ty:
	  Added retina edge buffer

	* [r1830] topo/plotting/plotgroup.py:
	  Added ALERT

	* [r1829] topo/plotting/plot.py:
	  Fixed typos

2005-12-14  ceball

	* [r1828] topo/tkgui/parametersframe.py:
	  Two separate changes (sorry). (1) class_parameters() returns a
	  dict. (2) Holding the mouse over a Parameter's name brings up the
	  Parameter's __doc__.

	* [r1827] topo/base/topoobject.py,
	  topo/tkgui/testpattern.py:
	  class_parameters() returns a dict.

	* [r1826] topo/tkgui/taggedslider.py:
	  Minor change - no visible changes.

	* [r1825] topo/tkgui/taggedslider.py:
	  Updated a comment that I forgot on the previous update.

	* [r1824] topo/tkgui/taggedslider.py:
	  Slider only updates after 'return' is pressed in the tag box.
	  This prevents the tag limits changing to really big values after
	  accidental inclusion of e.g. an extra 0 while typing. More
	  importantly, expressions for max,min,and val won't be evaluated
	  until the user presses 'return'. This stops evaluation of partial
	  expressions, and is important because now expressions are
	  evaluated in __main__, variables etc. are available.

	* [r1823] topo/tkgui/parametersframe.py:
	  TaggedSlider no longer has need_to_refresh_sliders attribute.

	* [r1822]
	  topo/tests/tkgui/testpropertiesframe.py,
	  topo/tkgui/taggedslider.py:
	  TaggedSlider uses utils.eval_atof() to evaluate strings in
	  __main__, rather than using string.atof(). Removed redundant
	  attribute need_to_refresh_slider. Tidied code a little and added
	  small bits of documentation. In anticipation of slider max and
	  min values being set from e.g. evaluated functions (for example
	  when the value is a function and the upper bound must be
	  extended), max and min slider variables are reverted to strings.

2005-12-14  jbednar

	* [r1821] topo/tkgui/editorwindow.py:
	  Fixed ALERT that was holding up the tests

2005-12-14  julienciroux

	* [r1820] topo/plotting/plot.py:
	  Cleaned up Plot. Made some sub-function return results rather
	  than modifying Plot attributes. Got rid of now unused attribute.
	  Changed _get_matrices_from_view_dict to __extract_view_dict_info.
	  Made other sub-function private.

	* [r1819] topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Added a temporary add to re-initialize the plot_list of a
	  PlotGroup from a panel. It was done before by the function plot()
	  in Plot, but we need now to re-create a new plot_list anytime
	  (i.e. because the code previously in Plot.plot() is now in
	  Plot.__init__()). This has to implemented in a better way and is
	  only a temporary solution.

2005-12-14  ceball

	* [r1818] topo/tkgui/propertiesframe.py:
	  Text boxes update when 'return' is pressed. (This message does
	  not apply to TaggedSliders' text boxes.)

	* [r1817] topo/tkgui/taggedslider.py:
	  TaggedSlider only updates from textbox if 'return' is pressed or
	  the box loses focus. Previously input was passed through to the
	  simulator the second it was typed.

2005-12-14  jbednar

	* [r1816] topo/base/simulator.py:
	  Made connect() return the connection created

2005-12-14  alan_lindsay

	* [r1815] topo/tkgui/editorobjects.py,
	  topo/tkgui/editortools.py,
	  topo/tkgui/editorwindow.py:
	  Initial CVS version

2005-12-14  julienciroux

	* [r1814] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplot.py:
	  Moved the code of plot() in __init__(): plot() no longer exists
	  in Plot, and the matrices bitmap are now created when the Plot()
	  object is created. I made the corresponding changes in PlotGroup
	  and TestPlot.

	* [r1813] topo/plotting/plotengine.py,
	  topo/tests/testplotengine.py:
	  Got rid of the unuseful add_plot_group() in PlotEngine; instead
	  it is simpler to directly access the plot_group_dict when adding
	  a PlotGroup. Made the corresponding changes in testplotengine.

2005-12-14  ceball

	* [r1812] topo/base/parameter.py:
	  Corrected code accidentally committed in revision 1.33.

	* [r1811] topo/base/parameter.py:
	  Subclasses of Parameter now define __slots__ as appropriate.

	* [r1810] topo/base/topoobject.py:
	  Moved classlist() and descendents from() utils.py to parameter.py
	  because it's unlikely for any user not using Parameters to want
	  them.

	* [r1809] topo/base/parameter.py,
	  topo/base/utils.py:
	  Moved classlist() and descendents() from utils.py to parameter.py
	  because it's unlikely for any user not using Parameters to want
	  them.

	* [r1808] topo/base/connectionfield.py,
	  topo/base/utils.py:
	  Moved hebbian() from utils.py to connectionfield.py, where it is
	  used.

	* [r1807] topo/base/boundingregion.py:
	  Removed unused import

	* [r1806] topo/base/topoobject.py,
	  topo/base/utils.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/testpattern.py:
	  Moved class_parameters() from utils.py to topoobject.py.

	* [r1805] topo/tkgui/inputparamspanel.py:
	  Renamed inputparamspanel.py to testpattern.py

	* [r1804] topo/tests/tkgui/__init__.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Renamed inputparamspanel.py to testpattern.py, and
	  InputParamsPanel to TestPattern.

	* [r1803] topo/tkgui/testpattern.py:
	  Renamed inputparamspanel.py to testpattern.py

	* [r1802] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/topoconsole.py:
	  Removed auto-refresh menu item. Topoconsole's list of panels to
	  refresh automatically is no longer accessed through functions.

2005-12-14  jbednar

	* [r1801] topo/learningfns/optimized.py:
	  Changed DivisiveHebbian_Fallback to DivisiveHebbian_Py

	* [r1800] topo/__init__.py:
	  Removed nonexistent directory

2005-12-14  yfsit

	* [r1799] topo/base/connectionfield.py,
	  topo/base/sheet.py,
	  topo/responsefns/basic.py:
	  - merged the slice tuple in ConnectionField into slice_array.

2005-12-14  jdepaula

	* [r1798] topo/learningfns/optimized.py:
	  Added wrapper classes for optimization Fallback to set the
	  correct output_fn for GenericCFLF

2005-12-14  julienciroux

	* [r1797] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplot.py,
	  topo/tkgui/inputparamspanel.py:
	  Changed Plot class so that it takes a dictionary specifying the
	  different channels, instead of a three-tuple. That way, it will
	  be easier to extend the code for passing more information to a
	  Plot object. This new change will also enable a better version of
	  the current code of Plot. The call to Plot() has been modified
	  accordingly in plotgroup.py, inputsparampanel.py and testplot.py.

2005-12-13  ceball

	* [r1796] topo/tkgui/__init__.py,
	  topo/tkgui/topoconsole.py:
	  Changed the import of all patterngenerators to be in
	  tkgui/__init__.py instead of tkgui/topoconsole.py

2005-12-13  alan_lindsay

	* [r1795] topo/__init__.py:
	  topo/tkgui/modeleditor

2005-12-13  ceball

	* [r1794] topo/tkgui/topoconsole.py:
	  Updated some HACKALERTs.

2005-12-13  jbednar

	* [r1793] topo/tkgui/plotgrouppanel.py:
	  Fixed typo

	* [r1792] topo/tkgui/plotgrouppanel.py:
	  Removed ALERT

2005-12-13  ceball

	* [r1791] topo/tests/__init__.py,
	  topo/tests/testsimulator.py:
	  Added HACKALERT.

	* [r1790] doc/Tutorial/index_text.php,
	  topo/tests/testdistribution.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testpatterngenerator.py,
	  topo/tests/tkgui/__init__.py,
	  topo/tests/tkgui/testpropertiesframe.py,
	  topo/tests/tkgui/testtopoconsole.py:
	  Added HACKALERT.

2005-12-13  jdepaula

	* [r1789] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Gave up on Tkinter Border mechanism, and I now draw a rectangle
	  around the plot instead.

	* [r1788] topo/tkgui/projectionpanel.py:
	  Added CANVASBUFFER.

	* [r1787] topo/tkgui/plotgrouppanel.py:
	  Added CANVASBUFFER. Fixed flicker that was introduced by adding
	  borders.

2005-12-13  julienciroux

	* [r1786] topo/plotting/plot.py:
	  Switched from using MLab.clip() to using Numeric.clip().

2005-12-13  ceball

	* [r1785] examples/lissom_or_20000.typ:
	  New version for current classes.

2005-12-13  julienciroux

	* [r1784] topo/plotting/plot.py:
	  Added a comment.

2005-12-13  jbednar

	* [r1783] topo/base/sheetview.py,
	  topo/plotting/plot.py,
	  topo/tkgui/plotgrouppanel.py:
	  Cleaned up imports, comments, alerts, and documentation

2005-12-13  ceball

	* [r1782] topo/tkgui/topoconsole.py:
	  When topoconsole loads a new Simulator, it needs to tell itself
	  that the active_sim will have changed.

	* [r1781] topo/base/patterngenerator.py:
	  Increasing y was moving the pattern downwards, an error
	  introduced in revision 1.37.

2005-12-13  julienciroux

	* [r1780] topo/plotting/plotengine.py:
	  Cleaned up the doc.

	* [r1779] topo/plotting/templates.py:
	  Updated the plotgrouptemplate of UnitWeightPlotGroup and
	  ProjectionPlotGroup according to the new changes in plotgroup.py
	  and plot.py.

	* [r1778] topo/tkgui/unitweightspanel.py:
	  Got rid of an old part of the code that is no longer used. Now,
	  no information is passed by the UnitWeight template, all is done
	  with the plot_group_key. The template should also be changed in
	  template.py.

2005-12-13  jbednar

	* [r1777] topo/responsefns/basic.py:
	  Added ALERT

	* [r1776] topo/responsefns/basic.py:
	  Added ALERT

2005-12-13  julienciroux

	* [r1775] topo/plotting/plotgroup.py:
	  Got rid of old comments.

2005-12-13  jdepaula

	* [r1774] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Added comment information about BORDERWIDTH and canvas offsets.

	* [r1773] topo/learningfns/optimized.py:
	  Added a Hebbian_Py to allow optimized fallback support for
	  Hebbian

	* [r1772] topo/base/connectionfield.py:
	  Added output_fn, since CFProjection needed it.

	* [r1771] topo/responsefns/basic.py:
	  Added TopoObject import

	* [r1770] topo/responsefns/basic.py:
	  Forgot to import optimized

	* [r1769] topo/responsefns/basic.py:
	  Added fallback for optimized functions.

	* [r1768] topo/sheets/lissom.py:
	  Changed incorrect comment, expanded warning message.

	* [r1767] topo/projections/optimized.py:
	  Changed incorrect comment, expanded warning message.

	* [r1766] topo/learningfns/optimized.py:
	  Changed incorrect comment, expanded warning message.

	* [r1765] topo/base/connectionfield.py:
	  Removed unneeded import

2005-12-13  julienciroux

	* [r1764] topo/plotting/plot.py:
	  Added the possibility to get situated plot. The code is working,
	  but is not in use for the moment (it would require to create
	  Plot() with the option situated=True when creating a plot from
	  the plotgroup class).

2005-12-12  julienciroux

	* [r1763] topo/plotting/plot.py:
	  Minor change in the code: the self.plot_bounding_box passed as a
	  parameter is no longer use for passing the sheet bounding_box to
	  submatrix(). Instead, this bounds comes from the bigger matrix in
	  self.matrices in the case where slicing is required. This will
	  enable to pass whatever plot_bounding_box for situating the plot
	  if required. Added a comment and an alert about that, because I
	  might not have thought of some special cases (though not yet
	  implemented) where that would not work.

	* [r1762] topo/plotting/plot.py:
	  Added comments and TO DO notes, updated the doc.

	* [r1761] topo/plotting/plot.py:
	  Added a function _get_slice() as a subfunction of plot. It
	  consists of the code that deals with slicing the different
	  matrices to the size of the smallest view; it was previously in
	  _make_hsv_matrix.

2005-12-12  yfsit

	* [r1760] topo/base/parameter.py:
	  - Replaced _NumberBoundsException with the buit-in ValueError.

2005-12-12  ceball

	* [r1759] topo/commands/basic.py:
	  Updated load_snapshot() to reflect changes to active_sim().

2005-12-12  julienciroux

	* [r1758] topo/plotting/plot.py:
	  Minor cleaning of the code in _make_hsv_matrix.

	* [r1757] topo/plotting/plot.py:
	  Cleaned up the code: now the empty plot exception is caught from
	  plot() instead to be caught in the sub-function
	  _make_hsv_matrices() (I think it is clearer); also minor
	  correction to comments.

2005-12-12  jbednar

	* [r1756] examples/lissom_or.ty:
	  Removed apparently outdated comment

2005-12-12  julienciroux

	* [r1755] topo/plotting/plot.py:
	  Minor correction of the code in the cropping case. Got rid of
	  some old comments and added new one.

2005-12-12  ceball

	* [r1754] topo/patterns/image.py:
	  Altered a hackalert.

	* [r1753] topo/base/parameter.py:
	  Added HACKALERT.

	* [r1752] topo/patterns/basic.py:
	  Reverted accidentally committed change in previous version (where
	  Rectangle's softbounds were removed.

	* [r1751] topo/outputfns/__init__.py,
	  topo/patterns/__init__.py,
	  topo/patterns/basic.py,
	  topo/patterns/image.py,
	  topo/sheets/generatorsheet.py,
	  topo/tkgui/inputparamspanel.py,
	  topo/tkgui/parametersframe.py:
	  PatternGeneratorParameter and OutputFunctionParameter now exist
	  in the __init__ file for their respective packages. They are
	  subclasses of PackageParameter.

	* [r1750] topo/base/parameter.py:
	  Added PackageParameter(Parameter) to parameter.py. This is the
	  base class for a Parameter such as an OutputFunctionParameter,
	  which can be set to an OutputFunction and and return a list of
	  available OutputFunctions.

2005-12-12  julienciroux

	* [r1749] topo/projections/optimized.py:
	  Corrected the call to CFProjection.change_bounds to only take two
	  parameters. he optimized.change_bounds method also take two
	  parameters now, as the output_fn is an attribute of CFProjection;
	  that solves the problem that occured when running the optimized
	  version of LISSOM.

2005-12-12  ceball

	* [r1748] topo/base/parameter.py,
	  topo/patterns/basic.py,
	  topo/tkgui/inputparamspanel.py:
	  Added PackageParameter to topo/base/parameter.py. This is the
	  base class for Parameters such as PatternGeneratorParameter,
	  which do things like return the list of all types of a class in a
	  package.

	* [r1747] topo/tkgui/parametersframe.py,
	  topo/tkgui/propertiesframe.py:
	  Continued cleaning. Added documentation. ParametersFrame doesn't
	  convert Parameter values to strings - that was already being done
	  by PropertiesFrame. PropertiesFrame defaults to a
	  string_translator of topo.base.utils.eval_atof() instead of
	  string.atof() so that any expression valid at the command line
	  can be entered in the test patterns window (e.g. 'cos(pi/2)', if
	  cos has been imported from math into __main__.__dict__ - that is,
	  if 'from math import cos' has been done at the command line).

	* [r1746]
	  topo/tests/tkgui/testpropertiesframe.py:
	  Number bounds stay as floats (rather than float->string->float).

	* [r1745] topo/base/utils.py:
	  Moved an import statement and added a HACKALERT about it.

	* [r1744] topo/tkgui/parametersframe.py,
	  topo/tkgui/taggedslider.py:
	  Number bounds stay as floats (rather than float->string->float).

2005-12-12  jdepaula

	* [r1743] topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Added borders to Canvas images

2005-12-12  ceball

	* [r1742] topo/tkgui/inputparamspanel.py,
	  topo/tkgui/parametersframe.py:
	  ^D &

	* [r1741] topo/base/utils.py:
	  Removed HACKALERT from class_parameters()

	* [r1740] topo/base/parameter.py:
	  Moved some documentation to circumvent hidden class docstrings;
	  added HACKALERT about it.

2005-12-12  jdepaula

	* [r1739] topo/misc/inlinec.py:
	  Updated comment

	* [r1738] topo/learningfns/optimized.py,
	  topo/projections/optimized.py,
	  topo/sheets/lissom.py:
	  Added Python-only fallback function definition.

	* [r1737] topo/base/connectionfield.py:
	  Restored GenericCFResponseFcn as default response_fn to restore
	  topo.base requirement to not point to outside functions.

	* [r1736] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty:
	  Remove default option for response_fn

	* [r1735] topo/base/connectionfield.py:
	  Removed optimized switch in CFProjection.

2005-12-11  julienciroux

	* [r1734] topo/plotting/templates.py:
	  Changed the Projection and UnitWeight PlotGroupTemplate so that
	  it colors the plot with OrientationPreference (the Confidence key
	  hasn't been added even though it works).

	* [r1733] topo/plotting/plotgroup.py:
	  Minor correction.

2005-12-11  ceball

	* [r1732] topo/tests/testcfsom.py,
	  topo/tests/testpatterngenerator.py,
	  topo/tests/tkgui/testactivitypanel.py,
	  topo/tests/tkgui/testplotgrouppanel.py:
	  PatternGenerators use aspect_ratio and size rather than height
	  and width.

	* [r1731] examples/cfsom_or.ty:
	  Uses size and aspect_ratio rather than height and width.

	* [r1730] examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty:
	  Uses size and aspect_ratio rather than height and width. Since
	  height and width of the GaussianGenerator are important
	  parameters of the model (for matching other work), they are shown
	  explicitly.

2005-12-11  julienciroux

	* [r1729] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py:
	  New version of plot.py that support coloring the weights and
	  projection by passing the 'Hue' and 'Confidence' plot keys define
	  by the UnitWeight or the Projection plotgroup template. The code
	  in plot.py is working but remains to be clarified and simplified.
	  Changes in plotgroup.py are only related to the changes in
	  plot.py.

2005-12-11  ceball

	* [r1728] topo/patterns/basic.py,
	  topo/patterns/image.py:
	  Use size and aspect_ratio rather than height and width.

2005-12-11  julienciroux

	* [r1727] topo/base/connectionfield.py:
	  Corrected an error that I made with CVS. Basically, I had got rid
	  of the changes made by version 1.39 to 1.41 because checking a
	  non-updated code. I re-added these changes and this version is
	  correct.

2005-12-11  ceball

	* [r1726] topo/patterns/image.py:
	  Uses same sheet2matrixidx() as is in topo.base.sheet, except this
	  works for scalars and arrays.

	* [r1725] topo/tests/testsheet.py:
	  Added a comment and some commented-out code so my changes don't
	  get left behind. No visible change.

2005-12-11  julienciroux

	* [r1724] topo/base/connectionfield.py:
	  Replaced the code to build the bounds by a call to the new
	  slice2bounds function in sheet. The same code is performed, but
	  it has been moved in slice2bounds so that to have the two
	  function slice2bounds and bounds2slice both in sheet.py.

	* [r1723] topo/tests/testsheet.py:
	  Added a test slice2bounds_bounds2slice that test the
	  transformation from slice to bounds and bounds to slice using the
	  bounds2slice and slice2bounds function.

	* [r1722] topo/base/sheet.py:
	  Added a function slice2bounds that returns the bounds
	  corresponding to a given slice. This function is the e
	  xact transformation of bounds2slice, i.e. when creating bounds
	  with slice2bounds and convert tham back with bounds2slice, you
	  are sure to have the same slice than at the begining.Also, I got
	  rid of the former old version of bounds2slice that was commented
	  out.

	* [r1721] topo/base/connectionfield.py:
	  Clarified the doc and change bounds_to_slice to its new name
	  bounds2slice in a debug print.

	* [r1720] topo/base/sheet.py:
	  Got rid of the function input_slice(). It was previously used to
	  generate the slice for a given ConnectionField, which is now done
	  in the function __initialize_slice in ConnectionField. Also,
	  changed the name of bounds_to_slice to be bounds2slice.

	* [r1719] topo/base/connectionfield.py:
	  Inserted the code that was previously in input_slice from
	  sheet.py to the function __initialize_slice of
	  connectionfield.py. input_slice is no longer used and will be
	  deleted from sheet. Also, modified the bounding box for a weight
	  so that to add a small margin around the bounds (i.e. for solving
	  the problem of getting the right sloces from the bounding box
	  afterwards).

2005-12-11  jbednar

	* [r1718] doc/User_Manual/index_text.php:
	  Added some notes for the manual

2005-12-11  julienciroux

	* [r1717] topo/base/sheet.py:
	  New version of bounds_to_slice (the former one is still there but
	  commented out). This function is not used for the moment, so
	  changing it does not change the way topographica works. Also, I
	  changed bounds2shape to an equivalent version, and updated the
	  comment about that. Both solutions would be reasonnable, and give
	  the appropriate results in the cases where we should use this
	  function (i.E. in patterngenerator and for generating the
	  weights); nevertheless, it is not possible to use this function
	  for implementing the functions that need to transform a slice to
	  bounds and then convert them back, that is why bounds2shape is no
	  longer used by the bounds_to_slice function.

2005-12-11  ceball

	* [r1716] topo/base/sheet.py:
	  Added some documentation about density to sheet2matrix().

	* [r1715] topo/tests/testsheet.py:
	  Added test that sheet2matrixidx() is the inverse of
	  matrixidx2sheet(). Renamed several functions.

	* [r1714] topo/base/sheet.py:
	  Removed a HACKALERT; rearranged some comments.

2005-12-11  jbednar

	* [r1713] topo/base/sheet.py:
	  Cleaned up comments and documentation

2005-12-11  yfsit

	* [r1712] topo/base/connectionfield.py:
	  - checked GenericCFLF() and uncommented the unchecked comment.

	* [r1711] examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty:
	  - updated the comment to reflect the name change from
	  DivisiveL1Normalize to DivisiveSumNormlaize

	* [r1710] examples/lissom_or.ty,
	  topo/eps/basic.py,
	  topo/learningfns/basic.py,
	  topo/learningfns/optimized.py,
	  topo/projections/optimized.py:
	  - Added learningfns/optimized.py and move all the learning
	  functions that need weave into it.

2005-12-11  ceball

	* [r1709] topo/tests/testsheet.py:
	  Begun adding in full tests of Sheet defined by non-integer
	  (right-left) and (top-bottom).

	* [r1708] topo/tests/testsheet.py:
	  Added bounds2shape() test. Updated HACKALERT - the tests are not
	  all being run for the awkward case.

	* [r1707] topo/tests/testsheet.py:
	  Continued cleaning tests.

2005-12-10  ceball

	* [r1706] topo/tests/testsheet.py:
	  Continued adding tests for the functions in topo.base.sheet.

	* [r1705] topo/tests/testsheet.py:
	  Tidied up a bit and added some matrix2sheet() tests.
	  matrixidx2sheet() tests haven't been reviewed yet.

	* [r1704] topo/base/sheet.py:
	  Removed some documentation I left in by accident.

	* [r1703] topo/base/sheet.py:
	  Changed sheet2matrixidx()

	* [r1702] topo/base/sheet.py:
	  Added HACKALERT to sheet2matrixidx because I think it returns the
	  wrong matrix row or column for some points outside the
	  BoundingBox.

	* [r1701] topo/tests/testsheet.py:
	  Included sheet2matrix tests, and increased testing of
	  sheet2matrixidx. Note that some of the new sheet2matrixidx tests
	  fail. This is because I think sheet2matrixidx is incorrect for
	  points just outside the left bound and points just outside the
	  top bound.

	* [r1700] topo/base/sheet.py:
	  Corrected a mistake in my previous comment. No visible change.

	* [r1699] topo/base/sheet.py:
	  Added a comment about sheet2matrix(). Changed some documentation
	  and a variable name to better describe its use. No visible
	  change.

2005-12-10  jbednar

	* [r1698] topo/base/boundingregion.py:
	  Clarified alerts, and changed the name of Intersection to clarify
	  that it works only for BoundingBoxes

2005-12-10  jdepaula

	* [r1697] topo/base/connectionfield.py:
	  Changed GenericCF response_fn to CFDotProduct_Py.
	  GenericCFResponseFn() is the same as CFDotProduct_Py. We want to
	  call CFDotProduct_Py instead of GenericCFResponseFn, because the
	  exact behavior of GenericCFResponseFn is controlled?\004 by the
	  single_cf_fn parameter.

2005-12-10  yfsit

	* [r1696] topo/learningfns/basic.py:
	  - tested Hebbian() and uncommented it.

2005-12-10  jdepaula

	* [r1695] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty:
	  Removed the CFDotProduct assignment since it's now the default
	  for CFProjection

2005-12-09  jdepaula

	* [r1694] topo/base/connectionfield.py:
	  Added inlinec.optimized switch for response_fn

2005-12-09  yfsit

	* [r1693] topo/base/simulator.py,
	  topo/tests/testsimulator.py:
	  - Simulator.objects(baseclass) has the default argument
	  baseclass=EventProcessor
	  - Removed Simulator.get_event_processors(), which is essentially
	  the same as Simulator.objects() now
	  - Updated the tests accordingly.

2005-12-09  jdepaula

	* [r1692] topo/learningfns/basic.py:
	  Commented out Hebbian, comment said it's untested, so may as well
	  make explicit that it's not being used.

	* [r1691] examples/lissom_or.ty:
	  Adjusted comment

2005-12-09  julienciroux

	* [r1690] topo/base/sheet.py:
	  Re-wrote bounds2shape so that it uses sheet2matixidx. This has be
	  done so that all methods that transform sheet information to
	  matrix information do it in a consistent way.

2005-12-09  ceball

	* [r1689] topo/patterns/image.py:
	  Tidied documentation a bit and changed some variable names. No
	  visible change.

2005-12-09  jbednar

	* [r1688] topo/base/topoobject.py:
	  Cleaned up imports and comments

	* [r1687] topo/base/parameter.py,
	  topo/base/topoobject.py:
	  Made __doc__ return the doc slot properly when called on a
	  TopoObject, even for subclasses of Parameter, allowing us to
	  remove a hack from TopoMetaclass

2005-12-09  julienciroux

	* [r1686] topo/base/sheet.py:
	  Minor change in the doc. Deleted a line of code that were
	  overwritten in bounds_to_slice.

2005-12-09  jbednar

	* [r1685] examples/Makefile,
	  examples/image_example.py,
	  examples/test.ppm:
	  Removed outdated image_example.py and associated image

2005-12-09  ceball

	* [r1684] topo/patterns/image.py,
	  topo/tkgui/parametersframe.py:
	  Changed name of EnumeratedParameter to Enumeration.

	* [r1683] topo/base/parameter.py:
	  Changed the name of EnumeratedParameter to Enumeration. Updated
	  Parameter documentation.

2005-12-09  julienciroux

	* [r1682] topo/base/sheet.py:
	  Deleted a comment that I had wrongly added to the last commit.

	* [r1681] topo/base/sheet.py:
	  Changed the name of one of the two functions input_slice to be
	  bounds_to_slice (I picked the one that is used by submatrix and
	  only takes three parameters: real bounds, sheet bounds and
	  density. This function, as well as submatrix, is not used for the
	  moment). I also added two ALERTS concerning problem with the
	  future version of plot.

	* [r1680] topo/base/connectionfield.py:
	  Now we pass the real bounds of the weight instead of the sheet
	  bounds when creating a UnitView (in get_view() in CFProjection).
	  Corrected the call to matrix2sheet for creating the bounds in
	  ConnectionField (now the bounding box is really the boundaries of
	  the weight submatrix). Added temporary debug print and deleted a
	  JABHACKALERT.

2005-12-09  yfsit

	* [r1679] topo/base/boundingregion.py:
	  - removed the unnecssary import * from Numeric

2005-12-08  ceball

	* [r1678] topo/patterns/image.py,
	  topo/tests/tkgui/testpropertiesframe.py,
	  topo/tkgui/inputparamspanel.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/propertiesframe.py:
	  Using EnumeratedParameter to allow different types of size
	  normalization for images (i.e. initial scaling of image).
	  Adjusted things in the GUI to allow this. These changes are again
	  intermediate - there will be more to come.

	* [r1677] topo/base/parameter.py:
	  Added EnumeratedParameter. It's not finished and not documented
	  but is committed.

2005-12-08  jbednar

	* [r1676] topo/base/connectionfield.py:
	  Added real bounds for this ConnectionField

	* [r1675] topo/base/sheet.py:
	  Fixed bogus matrix2sheet definition -- was accepting mx, my
	  instead of float_row, float_col (i.e., in the wrong order, though
	  it didn't matter because the function was being called with the
	  order swapped.

	* [r1674] topo/tests/testsheet.py:
	  Added ALERT about missing tests

	* [r1673] topo/base/connectionfield.py:
	  Added a function __initialize_slice in ConnectionField,
	  containing code shared between __init__ and change_bounds. Made
	  it clearer that the ConnectionField weight_bounds parameter is
	  actually only a weights_bounds_template, and that x and y are
	  locations in the input sheet, not the sheet owning this
	  ConnectionField.

	* [r1672] topo/base/sheet.py:
	  Clarified by changing name and arguments of activity_submatrix to
	  reflect their generality. Removed unused activity_submatrix
	  method of Sheet.

	* [r1671] topo/base/connectionfield.py:
	  Removed unused self.bounds and contains() of ConnectionField

2005-12-08  ceball

	* [r1670] topo/base/patterngenerator.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testplot.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testsheetview.py:
	  Removed ImageGenerator class from patterngenerator.py. It wasn't
	  being used any more by Topographica (there is already one in
	  patterns/image.py), but it is being used by test files - so now
	  it's in testsheetview.py.

2005-12-08  jbednar

	* [r1669] topo/misc,
	  topo/misc/.cvsignore:
	  Copied from base

2005-12-08  julienciroux

	* [r1668] topo/plotting/plotgroup.py,
	  topo/tests/testplotengine.py,
	  topo/tests/testplotfilesaver.py:
	  Fixed broken tests.

	* [r1667] topo/plotting/plotfilesaver.py:
	  Changed the call to get_plot_group() accordingly to the change
	  made in PlotEngine.

2005-12-08  jbednar

	* [r1666] Makefile:
	  Moved gendocs.py from base to misc

2005-12-08  ceball

	* [r1665] topo/base/topoobject.py:
	  Minor tidy.

	* [r1664] topo/plotting/templates.py,
	  topo/tests/tkgui/testtopoconsole.py:
	  Moved commandline.py distribution.py gendocs.py inlinec.py
	  keyedlist.py patternfns.py tyimputil.py from topo/base/ to
	  topo/misc.

	* [r1663] topo/__init__.py,
	  topo/analysis/featuremap.py,
	  topo/base/__init__.py,
	  topo/learningfns/basic.py,
	  topo/patterns/basic.py,
	  topo/projections/optimized.py,
	  topo/responsefns/basic.py,
	  topo/tests/testdistribution.py,
	  topo/tkgui/projectionpanel.py,
	  topographica_script.py:
	  Moved commandline.py distribution.py gendocs.py inlinec.py
	  keyedlist.py patternfns.py tyimputil.py from topo/base/ to
	  topo/misc.

	* [r1662] topo/base/commandline.py,
	  topo/base/distribution.py,
	  topo/base/gendocs.py,
	  topo/base/inlinec.py,
	  topo/base/keyedlist.py,
	  topo/base/patternfns.py,
	  topo/base/tyimputil.py:
	  Moved to topo/misc/

	* [r1661] topo/misc/__init__.py:
	  Initial version.

	* [r1660] topo/misc,
	  topo/misc/commandline.py,
	  topo/misc/distribution.py,
	  topo/misc/gendocs.py,
	  topo/misc/inlinec.py,
	  topo/misc/keyedlist.py,
	  topo/misc/patternfns.py,
	  topo/misc/tyimputil.py:
	  Moved from topo/base/

2005-12-08  jbednar

	* [r1659] topo/analysis/featuremap.py,
	  topo/plotting/__init__.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgrouptemplate.py,
	  topo/plotting/templates.py,
	  topo/tests/testplotengine.py,
	  topo/tests/testplotgroup.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/unitweightspanel.py:
	  Moved plotgrouptemplate.py to templates.py

	* [r1658] topo/base/__init__.py,
	  topo/base/registry.py:
	  Removed registry.py

	* [r1657] topo/tkgui/topoconsole.py:
	  Moved plotpanel_classes from registry.py to topoconsole.py

	* [r1656] topo/analysis/featuremap.py,
	  topo/commands/basic.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgrouptemplate.py,
	  topo/tests/testplotengine.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/unitweightspanel.py:
	  Moved plotgroup_templates from registry into
	  plotting/plotgrouptemplates.py

	* [r1655] CONVENTIONS:
	  Added note about naming conventions

	* [r1654] topo/base/patterngenerator.py,
	  topo/tkgui/inputparamspanel.py:
	  Cleaned up comments

2005-12-07  ceball

	* [r1653] topo/base/parameter.py:
	  Updated documentation about slots. Added HACKALERT about using
	  slots in subclasses of Parameter.

	* [r1652] topo/base/parameter.py:
	  Removed HACKALERT.

	* [r1651] topo/base/simulator.py:
	  Changed documentation about active_sim.

2005-12-07  louisem

	* [r1650] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_or.ty,
	  examples/obermayer_pnas90.ty:
	  Changed confusing bit -- had been specifying weights bounding box
	  as a parameter to the weights_generator, but this was ignored.
	  Now uses the CFProjection.weights_bounds parameter, which has the
	  desired effect.

2005-12-07  ceball

	* [r1649] topo/analysis/featuremap.py,
	  topo/base/registry.py,
	  topo/base/simulator.py,
	  topo/tests/tkgui/testactivitypanel.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/topoconsole.py:
	  topo.base.simulator stores a list of objects that have asked to
	  be notified when the active_sim changes. These objects must have
	  a notify_of_active_sim() method, and this will be called when the
	  active_sim changes. The objects can do whate?\004ver they need to
	  once they receive this call, including changing their simulator.
	  This means there is no need to store the 'active gui'
	  (topoconsole) in the registry. TopoConsole is also only
	  associated with one PlotEngine, so it is clarified. Added
	  some?\004 HACKALERTs about further changes that are required.

	* [r1648] topo/tkgui/topoconsole.py:
	  Added hackalert about loading a script.

	* [r1647] topo/tkgui/topoconsole.py:
	  Minor update to 'help' variable names. Added hackalert about help
	  items.

	* [r1646] topo/tkgui/topoconsole.py:
	  Removed refresh_title() method. The simulator name used to be
	  printed in the titlebar. Ever since that was removed, the title
	  of the window has stayed constant, so now it's set in the
	  TopoConsole constructor. Also removed some stray comments I left
	  behind a while ago.

	* [r1645] topo/plotting/plotgroup.py:
	  Removed unused import.

2005-12-07  jbednar

	* [r1644] topo/learningfns/basic.py:
	  Added comments

2005-12-07  yfsit

	* [r1643] topo/learningfns/basic.py:
	  - use neighborhood_kernel_generator as a callable object instead
	  of a class.

2005-12-07  ceball

	* [r1642] topo/base/topoobject.py:
	  Parameters that are class attributes of a TopoObject class
	  inherit from Parameters with the same name in super classes of
	  that TopoObject class - now including when the class attribute is
	  set to be a new Parameter. Updated the documentation.

2005-12-06  ceball

	* [r1641] topo/base/topoobject.py:
	  Some clarification of TopoMetaclass. No visible changes.

2005-12-06  julienciroux

	* [r1640] topo/plotting/plotengine.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Changed the name and the order of the parameter for get_plot_cmd.
	  Made the required change in the panel classes (changed the call
	  to get_plot_cmd).

2005-12-06  ceball

	* [r1639] topo/base/topoobject.py:
	  Added a comment (and some code temporarily in a comment).

	* [r1638] topo/base/topoobject.py:
	  Made a method that does the inheritance for a Parameter, given
	  the list of base classes of the TopoObject that owns the
	  Parameter.

	* [r1637] topo/patterns/basic.py:
	  Precedence constants for scale is no longer required since
	  Parameters can inherit from those in the owning TopoObject's
	  superclasses.

	* [r1636] topo/base/utils.py:
	  Added a note to myself.

	* [r1635] topo/base/patterngenerator.py:
	  'precedence' constants are no longer required since Parameters
	  can inherit from those in the owning TopoObject's superclasses.

	* [r1634] topo/base/parameter.py:
	  A Parameter's slots all default to None so that the TopoMetaclass
	  knows when to try inheriting from the superclasses of the
	  TopoObject that owns the Parameter.

	* [r1633] topo/base/topoobject.py:
	  Code to allow Parameters inside a TopoObject to inherit from
	  Parameters with the same name in super classes of the TopoObject
	  (just on creation of the TopoObject, for the moment).

2005-12-06  jbednar

	* [r1632] topo/base/topoobject.py:
	  Added documentation (some of it prospective) for metaclass
	  members

2005-12-06  julienciroux

	* [r1631] topo/tkgui/basicplotgrouppanel.py:
	  Added an alert and deleted an unnecessary line of code in
	  do_plot_cmd().

	* [r1630] topo/plotting/plot.py:
	  Minor correction in the doc.

	* [r1629] topo/plotting/plotengine.py:
	  Minor changes: erased old comments, corrected the doc.

	* [r1628] topo/tkgui/plotgrouppanel.py:
	  Minor re-organization of the file: moved a function around,
	  corrected doc, added alerts.

2005-12-06  yfsit

	* [r1627] topo/learningfns/basic.py:
	  use PatternGenerator to compute a matrix of neighborhood value
	  instead of calling a pattern_fn every we need such value.

2005-12-06  jdepaula

	* [r1626] doc/Downloads/win32_text.php:
	  Added information about how to install to non-default locations.

	* [r1625] external/win32/setup.py,
	  setup.bat:
	  Added a BASE_INSTALL_PATH to the setup for a non-default install
	  path.

	* [r1624] topographica_script.py:
	  Updated comment

	* [r1623] external/win32/setup.py:
	  Added the -g option to the topographica.bat startup script.

2005-12-05  jdepaula

	* [r1622] topographica_script.py:
	  importing inlinec causes the same system fault that not importing
	  weave causes. Do a test, so that Windows users do not have to
	  change the code.

	* [r1621] topographica_script.py:
	  Added source comment about need to import inlinec.

	* [r1620] doc/Downloads/win32_text.php:
	  Removed import weave ordering comment. Changed the compiler='gcc'
	  reference to directions on how to use MSVC instead if desired.

	* [r1619] topographica_script.py:
	  Added inlinec import to test for weave immediately.

2005-12-05  julienciroux

	* [r1618] topo/base/connectionfield.py,
	  topo/base/sheet.py,
	  topo/base/sheetview.py,
	  topo/tests/testsheet.py,
	  topo/tests/testsheetview.py:
	  Got rid of the function sheet_view() in Sheet (sheet.py) and in
	  CFSheet (connectionfield.py). Now, the sheet_view() is always
	  created explicitly, as well by get_view in CFProjection (for a
	  UnitWeight view), or by specific function such as measure_or_pref
	  or measure_activity;(eventually, we might want to make this
	  process more uniform by creating measure_weight() and
	  measure_projection() functions). Then, we access the sheet_view
	  by directly looking for it in a sheet_view_dict. Changes have
	  been made accordingly in sheetview.py,testsheet.py and
	  testsheetview.py.

	* [r1617] topo/plotting/plotengine.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplotengine.py,
	  topo/tkgui/inputparamspanel.py:
	  Added a parameter simulator in the __init__ fucntion for
	  PlotGroups. The simulator has to be passed when creating the
	  PlotGroup (generally from the plotengine, but also from
	  InputParamsPanel). It allows to get rid of the call to
	  active_sim() in PlotGroup. Corrected the calls in plotengine.py,
	  inputparamspanel and testplotengine.py.

2005-12-05  jbednar

	* [r1616] topo/base/patterngenerator.py:
	  Added a bit of documentation to Parameters, and reformatted other
	  documentation

	* [r1615] topo/base/parameter.py:
	  Made __doc__ work a little more like it does for normal objects

2005-12-05  ceball

	* [r1614] topo/base/parameter.py:
	  Passing doc='' to the __init__() methods of subclasses of
	  Parameter isn't necessary.

	* [r1613] topo/base/parameter.py:
	  Removed a HACKALERT.

	* [r1612] topo/analysis/featuremap.py:
	  Expanded a HACKALERT.

	* [r1611] topo/commands/basic.py:
	  Removed CEBHACKALERT.

	* [r1610] topo/commands/__init__.py:
	  Added documentation about commands printing warnings and avoiding
	  raising errors so that batch runs etc. aren't interrupted.

	* [r1609] topo/plotting/plotgroup.py:
	  Expanded an alert about looking up active_sim.

	* [r1608] topo/analysis/featuremap.py,
	  topo/tests/testfeaturemap.py:
	  topo.base.simulator tests if there is an active_sim and prints a
	  warning if not, so callers don't need to do that. No longer
	  passing a Simulator back and forth between methods.

	* [r1607] topo/analysis/featuremap.py,
	  topo/commands/basic.py:
	  topo.base.simulator tests if there is an active_sim and prints a
	  warning if not, so callers don't need to do that. No longer
	  passing a Simulator to methods in topo/commands/basic.py as we
	  intend not to have more than one at a time.

	* [r1606] topo/analysis/featuremap.py,
	  topo/base/simulator.py,
	  topo/commands/basic.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/tkgui/testtopoconsole.py,
	  topo/tkgui/topoconsole.py:
	  topo.base.simulator now contains the methods get_active_sim() and
	  set_active_sim(). get_active_sim() will print a warning if there
	  is no active_sim, meaning callers do not have to do the test
	  themselves.

2005-12-05  jbednar

	* [r1605] topo/learningfns/basic.py,
	  topo/sheets/cfsom.py:
	  Cleaned up comments and docstrings. Removed unused functions from
	  CFSOM

	* [r1604] doc/images/T-bg.png,
	  doc/images/Topologo.xcf,
	  doc/images/logo_jb.png:
	  No longer used

	* [r1603] doc/images/topo-banner7.xcf:
	  Version from Yoonsuck

	* [r1602] topo/responsefns/basic.py,
	  topo/tests/__init__.py,
	  topo/tests/testbitmap.py,
	  topo/tests/testboundingregion.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testdistribution.py,
	  topo/tests/testdummy.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testhistogram.py,
	  topo/tests/testmatplotlib.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/propertiesframe.py,
	  topo/tkgui/taggedslider.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/unitweightspanel.py:
	  Fixed broken CVS version strings

2005-12-05  yfsit

	* [r1601] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/obermayer_pnas90.ty,
	  topo/learningfns/basic.py,
	  topo/sheets/cfsom.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotengine.py,
	  topo/tests/testplotfilesaver.py:
	  Added an abstract class SOMLF that contains learning_radius for
	  SOMs in learning_fn/basic.py. The old HebbianSOM is renamed to
	  HebbianSOMLF and is a subclass of SOMLF. other files are changed
	  accordingly.

2005-12-05  yschoe

	* [r1600] doc/shared/config.php:
	  Edited button color scheme.

	* [r1599] doc/images/topo-banner7.png:
	  Edited banner subtitle.

2005-12-05  julienciroux

	* [r1598] topo/tests/testplotengine.py:
	  Started re-writing testplotengine according to the changes in the
	  file. The test is not truly working yet and cannot be use for
	  testing (it does not crash though, but is not relevant).

	* [r1597] topo/plotting/plotgroup.py:
	  Added the possibility to pass a string as a sheet_filter (instead
	  of the only possibilities being to pass None or a function).

	* [r1596] topo/plotting/plotengine.py:
	  Clarified the doc, added some alerts, get rid of unused import.

2005-12-04  julienciroux

	* [r1595] topo/tests/__init__.py:
	  Added testoutputfnsbasic to the list of the import statement in
	  tests/__init__.py. Now the test is performed when running make
	  all topo/tests.

	* [r1594] topo/tests/testplot.py:
	  Continued to write testplot.py. The tests for plot.py are
	  complete, except for catching the exeption of an empty plot.

2005-12-04  jbednar

	* [r1593] topo/patterns/basic.py:
	  Fixed indentation

	* [r1592] topo/base/boundingregion.py:
	  Minor fix

	* [r1591] topo/base/utils.py:
	  Minor update to comment

	* [r1590] topo/learningfns/basic.py:
	  Updated documentation and comments slightly, added some alerts,
	  and removed some outdated ones.

2005-12-04  yfsit

	* [r1589] examples/hierarchical.ty:
	  - used output function PiecewiseLinear for V1, V2, and V3 so that
	  the activations satuates at 1.0.

2005-12-04  ceball

	* [r1588] topo/analysis/featuremap.py,
	  topo/base/registry.py,
	  topo/base/simulator.py,
	  topo/commands/basic.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/tkgui/testactivitypanel.py,
	  topo/tests/tkgui/testtopoconsole.py,
	  topo/tkgui/__init__.py,
	  topo/tkgui/cfsheetplotpanel.py,
	  topo/tkgui/inputparamspanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/unitweightspanel.py:
	  Whenever a Simulator is created, topo.base.simulator.active_sim
	  is set to be that Simulator. Rather than going through the
	  registry, this is now the place to find the active simulator.
	  Files in tkgui use topo.tkgui.topoconsole.active_sim() to access
	  this variable. The change-over from the previous ways of finding
	  active_sim is not complete yet.

2005-12-04  jbednar

	* [r1587] topo/tkgui/parametersframe.py:
	  Trivial space change

2005-12-04  julienciroux

	* [r1586] topo/tests/testplot.py:
	  Started to re-write testplot.py according to the changes made in
	  plot.py. The test is no longer entirely disabled.

	* [r1585] topo/plotting/plot.py:
	  Continued simplified plot.py: re-organized the code in
	  _make_hsv_matrices(). Added some comments, got rid of unused
	  import statement, clarified the doc.

2005-12-04  yfsit

	* [r1584] examples/hierarchical.ty,
	  examples/obermayer_pnas90.ty,
	  topo/base/connectionfield.py:
	  - examples/obermayer_pnas90.ty and examples/hierarchical.ty use
	  HebbianSOM as the learning_fn, which wat not specified before.
	  - moved the declaration of output_fn() in GenericCFLF() to
	  IndentityCFLF().

	* [r1583] topo/learningfns/basic.py:
	  - Added a neighborhood_fn paramter (defaulted to gaussian) in
	  HebbianSOM.

	* [r1582] topo/learningfns/basic.py,
	  topo/sheets/cfsom.py:
	  - copied CFSOM.winner_coord() into HebbianSOM so that the winner
	  can be found within the learning function.
	  - radius in HebbianSOM is renamed to learning_radius and is now a
	  parameter of HebbianSOM instead of an argument in __call__().
	  - used patternfns.gaussian() instead of a hard-coded exponential
	  function to compute the neighbour radius.

2005-12-03  ceball

	* [r1581] topo/tkgui/parametersframe.py,
	  topo/tkgui/taggedslider.py:
	  Changed a HACKALERT.

	* [r1580] topo/base/patterngenerator.py:
	  Added HACKALERT about using constants for the precedences - it's
	  pretty ugly.

	* [r1579] topo/patterns/image.py:
	  Made use of Parameter ordering constants defined in
	  topo/patterns/basic.py.

	* [r1578] topo/base/patterngenerator.py,
	  topo/patterns/basic.py:
	  Changed Parameter ordering.

	* [r1577] topo/base/patterngenerator.py:
	  The previous commit was a mistake - I forgot the save my changes.

	* [r1576] topo/base/patterngenerator.py,
	  topo/patterns/basic.py:
	  Made it easier to specify an ordering of PatternGenerator
	  Parameters by defining constant values for precedences of
	  standard and typical PatternGenerator Parameters.

	* [r1575] topo/base/parameter.py:
	  Added note about pickling in the Parameter class docstring.

	* [r1574] topo/tkgui/parametersframe.py,
	  topo/tkgui/taggedslider.py:
	  Altered some comments.

	* [r1573] CONVENTIONS:
	  Really minor edit. Added a missing word.

	* [r1572] topo/tkgui/inputparamspanel.py,
	  topo/tkgui/parametersframe.py:
	  Continued reorganization.

	* [r1571] topo/base/utils.py:
	  Updated class_parameters(). Removed exp() (it's in
	  arrayutils.py). Should clip_in_place() be in arrayutils.py
	  instead?

	* [r1570] topo/patterns/basic.py:
	  Removed an alert - it should have been in patterngenerator.py.

	* [r1569] topo/base/patterngenerator.py:
	  Changed a local variable name for clarity. Changed some comments
	  and removed JABHACKALERT about generation of x and y vectors.

2005-12-03  yfsit

	* [r1568] topo/base/arrayutils.py,
	  topo/base/boundingregion.py,
	  topo/base/connectionfield.py,
	  topo/base/distribution.py,
	  topo/base/patternfns.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/utils.py,
	  topo/learningfns/basic.py,
	  topo/outputfns/basic.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/generatorsheet.py,
	  topo/tests/testdistribution.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testoutputfnsbasic.py:
	  Fixed some ALERTS:
	  - removed the redundant paramter theta and comments about
	  input_event() in generatorsheet.py
	  - renamed DivisiveL1Normalize to DivisiveSumNormalize
	  - renamed DivisiveL2Normalize to DivisiveLengthNormalize
	  - replaced error message with real exception in boundingregion.py
	  - removed the useless __init__ in IdentityCFLF in
	  connectionfield.py and Identit
	  y in projection.py
	  - Added some comments and answers to questions about
	  __produce_sampling_vectorsin patterngenerator.py
	  - Move the functions in utils.py that depends on Numeric into a
	  new file calledarrayutils.py
	  - updated the tests

2005-12-02  ceball

	* [r1567] topo/base/parameter.py:
	  Added another hack alert.

	* [r1566] topo/base/parameter.py:
	  Added comment and made slight cleanup to space.

	* [r1565] topo/base/patterngenerator.py:
	  Made Parameter definitions make use of precedence to offer an
	  order to e.g. the GUI. The precedence attribute in Parameter
	  (revision 1.15) does not quite work yet...

	* [r1564] topo/patterns/basic.py,
	  topo/patterns/image.py:
	  Made Parameter definitions make use of precedence to offer an
	  order to e.g. the GUI. The precedence attribute in Parameter
	  (revision 1.15) does not quite work yet...

	* [r1563] topo/tkgui/inputparamspanel.py,
	  topo/tkgui/parametersframe.py:
	  Continued reorganization to make ParametersFrame general for
	  TopoObjects. Some clarifications in the code. Also made Parameter
	  widgets be added in order of Parameter precedence (well, reverse
	  order).

	* [r1562] topo/base/utils.py:
	  Added function keys_sorted_by_value() to return the keys of a
	  dictionary sorted by value. Added a comment about the function
	  name 'dict_sort()', which I think should be changed.

	* [r1561] topo/base/parameter.py:
	  Added 'precedence' attribute to Parameters. Precedence can be
	  used to specify an ordering for Parameters within a TopoObject,
	  which could be useful e.g. to order them in the GUI.

2005-12-02  yfsit

	* [r1560] examples/cfsom_or.ty,
	  topo/base/connectionfield.py,
	  topo/learningfns/basic.py,
	  topo/sheets/cfsom.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplotfilesaver.py:
	  fixed the ALERTS in cfsom.py.
	  Moved most part of CFSOM.learn() into a new method HebbianSOM()
	  in learningfns.py. CFSOM.learn() calls HebbianSOM() for each
	  projection. Examples and test cases are updated accordingly.

2005-12-01  julienciroux

	* [r1559] topo/plotting/plotgrouptemplate.py:
	  Minor change to doc and comment.

	* [r1558] topo/plotting/plotengine.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/cfsheetplotpanel.py,
	  topo/tkgui/inputparamspanel.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/unitweightspanel.py:
	  Changed the attribute and parameter name plot_key to be
	  plot_group_key in PlotGroup and all the sub-classes. Changed the
	  call accordingly in the PlotGroupPanel classes and PlotsMenuEntry
	  in topoconsole.py.

	* [r1557] topo/plotting/plot.py:
	  Minor re-organization of the file, just moved the code for
	  release_sheetviews to another place.

	* [r1556] topo/plotting/plot.py:
	  Continued to simplified plot.py. I created one more sub-function
	  called _make_hsv_matrices in order to cut plot() in more
	  comprehensive part. I also simplified the code by deleting unused
	  tests unused plot attribute (channel_views does not exist anymore
	  as we only need to keep a list of matrices but not the
	  sheet_views itself, therefore
	  _get_channel_views_from_sheet_view() is now
	  _get_matrices_from_sheet_view()). Added some doc and comments,
	  deleted some old alerts.

	* [r1555] topo/plotting/plot.py:
	  Corrected an error on the last commit.

	* [r1554] topo/analysis/featuremap.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/inputparamspanel.py:
	  Continued cleaning up plot.py. Added comments erased old ones.
	  Reorganized the function _get_channel_views_from_view_dict(). I
	  also made change to the way name are handled, and so made
	  corresponding changes in featuremap.py, plotgroup.py and
	  inputsparampanel.py; it is still not really good the way name are
	  handled for the display and I left an Alert about it.

	* [r1553] topo/plotting/plot.py:
	  Continued to clean up the file. Added some alerts and deleted
	  some old ones, reviewed the doc and renamed and made private the
	  function _get_channel_views_from_view_dict().

2005-12-01  ceball

	* [r1552] topo/patterns/image.py:
	  Removed HACKALERT - filename can now be visible on
	  inputparamspanel.

	* [r1551] topo/base/parameter.py:
	  Uses os.path.normpath() to convert UNIX-style paths to the style
	  of the user's operating system.

	* [r1550] topo/patterns/image.py:
	  Changed image filename's variable name to 'filename' - it's
	  clearer.

	* [r1549] topo/tkgui/inputparamspanel.py,
	  topo/tkgui/parametersframe.py:
	  Intermediate commit during reorganization. Filename Parameters
	  now work (in that the image can be changed - the behaviour of the
	  text box will be improved). There is more reorganization to come.

2005-11-30  julienciroux

	* [r1548] topo/tests/testplot.py,
	  topo/tests/testplotengine.py,
	  topo/tests/testplotgroup.py:
	  Temporarily commented out some tests while re-organizing plot.py,
	  plotgroup.py and plotengine.py. They will be re-written very
	  soon.

	* [r1547] topo/base/sheet.py:
	  Got rid of the function look_up_dict. The method get will be used
	  instead when passing None as a second parameter that is returned
	  if the key is not in the dictionnary.

	* [r1546] topo/plotting/plotengine.py,
	  topo/tests/testplotengine.py,
	  topo/tests/testplotgroup.py,
	  topo/tkgui/topoconsole.py:
	  Corrected the import statement for PlotTemplate and
	  PlotGroupTemplate, now that they have been moved in
	  plotgrouptemplate.py.

	* [r1545] topo/plotting/plot.py:
	  Got rid of PlotTemplate that is now in plotgrouptemplate.py.
	  Reviewed the doc and corrected the import statement.

	* [r1544] topo/plotting/plotgroup.py:
	  Got rid of PlotGroupTemplate and template definitions that are
	  now in plotgrouptemplate.py. Reviewed the doc and corrected the
	  import statement.

	* [r1543] topo/plotting/plotgrouptemplate.py:
	  Added a new file plotgrouptemplate.py that contains: the
	  PlotTemplate class (that was previously in plot.py) and the
	  PlotGroup class (previously in plotgroup.py), as well as the
	  definitions of the PlotGroupTemplate objects and their
	  record?\004ing in the registry (previously in plotgroup.py, too).
	  This way, there is a relatively short and clean file for the user
	  to add PlotGroupTemplate definition in, while benifiting at the
	  same time from the doc and the code contain in the PlotTemplate
	  and P?\004lotGroupTemplate class.

2005-11-30  ceball

	* [r1542] topo/base/parameter.py,
	  topo/patterns/image.py:
	  Added a Parameter called Filename. This takes a string specifying
	  the path to the file, but when asked for its value, returns the
	  path in the correct format for the operating system. Or at least,
	  it will but probably doesn't at the moment - see the HACKALERT.

	* [r1541] topo/base/patterngenerator.py:
	  Removed unused import statements.

	* [r1540] topo/base/patterngenerator.py:
	  Had been receiving the GeneratorSheet's x and y bounds switched
	  around (because of 'x/y hack patch' in GeneratorSheet, so it was
	  itself flipping x and y again. Now that GeneratorSheet passes the
	  actual bounds, this doesn't flip x and y anymore. Also simplified
	  the functions a bit.

	* [r1539] examples/hierarchical.ty:
	  Corrected LineGenerator's bounds.

2005-11-30  jdepaula

	* [r1538] topo/learningfns/basic.py,
	  topo/projections/optimized.py,
	  topo/responsefns/basic.py:
	  Changed import of weave to import of inlinec wrapper.

	* [r1537] topo/base/inlinec.py:
	  Added named_parameters for inline to make remote reference calls
	  easier to handle

	* [r1536] topo/projections/optimized.py:
	  Removed an import star

	* [r1535] topo/base/inlinec.py:
	  Added named value dictionary parameter to functions

2005-11-29  jbednar

	* [r1534] examples/obermayer_pnas90.ty:
	  Clarified how constant was calculated

2005-11-29  julienciroux

	* [r1533] topo/analysis/featuremap.py:
	  Changed the sheet_view.view_info['src_name'] so that it displays
	  nicely in the GUI.

	* [r1532] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py,
	  topo/tkgui/inputparamspanel.py:
	  Changed plot so that it takes a sheet view dictionnary as a
	  calling parameter instead of a sheet. There is not the
	  possibility anymore to pass directly a sheet_view to Plot() but
	  only a sheet_view_dict and the three channels that are defined by
	  the template (e.g (plot_key,None,None) for UnitWeight.
	  plotgroup.py and inputparampanel have been changed accordingly.

2005-11-29  ceball

	* [r1531] examples/hierarchical.ty:
	  Made previous change less extreme - GeneratorSheets'
	  BoundingBoxes are now centered on (0,0). Before, it might have
	  looked like a bug to a new user.

2005-11-29  julienciroux

	* [r1530] topo/plotting/plotengine.py:
	  Very minor changes to comment.

	* [r1529] topo/plotting/plotgroup.py:
	  Continued clarifying plotgroup.py. Now, it creates the plot for a
	  projection by calling plot with a plot_key, and no more list of
	  UnitViews is stored in the sheet_view_dict. Instead, when
	  creating the plots, a ProjectionPlotGroup will catch each unit
	  view with the corresponding Weights plot_key.

	* [r1528] topo/plotting/plotgroup.py:
	  Continued to clean up and simplify the file. In particular, the
	  create_plots function for the UnitWeightPlotGroup does get the
	  location of the unit from the template anymore, but from the
	  plot_key passed when creating the PlotGroup. Also, in the same
	  function, made the call to Plot more general by adding the
	  possibility to have a hue and confidence parameter (it still does
	  not work though when adding 'Hue'='OrientationPreference') to the
	  UnitWeight template). Added comments and clarified others.

2005-11-29  jbednar

	* [r1527] topo/sheets/cfsom.py:
	  Changed Parameters to Numbers for clarity; should also get at
	  least lower bounds

	* [r1526] examples/cfsom_or.ty:
	  Fixed typo

	* [r1525] examples/obermayer_pnas90.ty:
	  Fixed density

	* [r1524] examples/obermayer_pnas90.ty:
	  Initial version based on cfsom_or.py

2005-11-29  julienciroux

	* [r1523] topo/base/sheet.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotgroup.py:
	  Fixed a little bug caused momentarily because I forgot to use
	  look_up_dict when requested a sheet_view from the
	  sheet_view_dict. Finally, I used sheet_view_dict.get(key,None),
	  and I think we could get rid of look_up_dict. I added some
	  comments about that. Also, modified some comments in
	  plotgorup.py.

2005-11-29  ceball

	* [r1522] topo/sheets/generatorsheet.py:
	  Removed 'patterngenerator hack patch to get x/y right outside of
	  kfs' because I think it was incorrectly swapping the x and y axes
	  of GeneratorSheets.

2005-11-29  julienciroux

	* [r1521] topo/base/connectionfield.py,
	  topo/plotting/plot.py:
	  Got rid of an hack that were dealing with the list of UnitView
	  that were added to the sheet_view_dict for a UnitViewPlotGroup.
	  Now, a given UnitWeight plot_key correspond to a single UnitView
	  in the sheet_view_dict. Some comments have been added in CFSheet
	  in connectionfield.py for some more future changes.

2005-11-29  ceball

	* [r1520] examples/hierarchical.ty:
	  Now uses a rectangular retina: no more hiding from flipped x and
	  y coordinates. (The box is also not centered about (0,0).)
	  Updated the LineGenerator's BoundingBox - not sure if it's the
	  right kind of size. Should LineGenerator.x's Boundin?\004gBox etc
	  also be changed slightly?

2005-11-29  julienciroux

	* [r1519] topo/base/connectionfield.py:
	  Changed unit_view in ConnectionField so that it inserts UnitView
	  in the sheet_view_dict instead of one element list of UnitView.
	  Also modified the doc of unit_view.

2005-11-29  ceball

	* [r1518] topo/sheets/generatorsheet.py:
	  Moved PatternGeneratorParameter from topo.base.patterngenerator
	  to topo.patterns.base.

	* [r1517] topo/base/utils.py:
	  classname_repr() doesn't default to chopping off the suffix
	  'Generator'.

	* [r1516] topo/base/utils.py:
	  Added comment to find_classes_in_package().

	* [r1515] topo/base/patterngenerator.py,
	  topo/patterns/basic.py:
	  Moved PatternGeneratorParameter from topo.base.patterngenerator
	  to topo.patterns.base.

	* [r1514] topo/tkgui/topoconsole.py:
	  Added statement to import all patterns, and a note to update the
	  comment.

	* [r1513] topo/base/patterngenerator.py,
	  topo/sheets/generatorsheet.py,
	  topo/tkgui/parametersframe.py:
	  Moved PatternGeneratorParameter from
	  topo/tkgui/parametersframe.py to topo/base/patterngenerator.py

	* [r1512] topo/base/utils.py:
	  Added comment for myself.

	* [r1511] topo/base/patterngenerator.py:
	  Added note to myself about reorganization of parametersframe.py

	* [r1510] topo/base/registry.py,
	  topo/sheets/generatorsheet.py,
	  topo/tkgui/inputparamspanel.py,
	  topo/tkgui/parametersframe.py:
	  The registry no longer holds a list of PatternGenerators.
	  Instead, there is a class PatternGeneratorParameter that has a
	  method to perform the same function. PatternGeneratorParameter is
	  not finished, and is not in its final location.

2005-11-29  jbednar

	* [r1509] topo/base/inlinec.py:
	  Added optimized flag and made use exceptions

2005-11-29  ceball

	* [r1508] topo/sheets/generatorsheet.py:
	  Added comment about 'patch to get x/y right outside of
	  kernelfactories': I think it should be removed.

2005-11-29  julienciroux

	* [r1507] topo/base/connectionfield.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotgroup.py:
	  Re-organization of plot.py and corresponding changes in
	  plotgroup.py. Mostly, plot has been simplified and unused part of
	  the code have been erased. Now, to create a Plot you pass the
	  sheet and three channels, that will be set for each PlotGroup as
	  it is described in the template (it is planed that in the future,
	  the sheet_view_dict will be passed instead of the sheet). There
	  is still some issues for a ProjectionPlotGroup because of the way
	  the sheet_view_dict is constructed in this case (accepting a list
	  of sheet_views). There is also a similar problem for
	  UnitViewPlotGroup that is fixed by an hack in plot.py; that has
	  to be changed in unit_view in connectionfield.py. Finally,
	  handling of the label display is now wrong, which leads to a
	  double label in the activity panel. All this (relatively minor)
	  problems should be fixed quickly, and have a corresponding
	  JCALERT.

	* [r1506] topo/analysis/featuremap.py:
	  Got rid of an unused debug print.

2005-11-28  jdepaula

	* [r1505] topo/base/inlinec.py:
	  Changed the comments to not reference the dictionary.

	* [r1504] topo/base/inlinec.py:
	  Initial version. Using this package inline function is the same
	  as the Weave inline, except that it prints a failure warning if
	  Weave was not able to be imported.

	* [r1503] topo/base/utils.py:
	  Updated comment

2005-11-28  ceball

	* [r1502] topo/tkgui/inputparamspanel.py:
	  Changed a variable name to improve clarity.

	* [r1501] topo/base/utils.py,
	  topo/tkgui/inputparamspanel.py:
	  Made a function classname_repr() out of part of the
	  patterngenerator_names() function. classname_repr() is available
	  in topo.base.utils.

2005-11-28  julienciroux

	* [r1500] topo/analysis/featuremap.py,
	  topo/base/sheet.py:
	  Added the function measure_activity in featuremap.py; this
	  function just load up the activity sheet view for all the Sheets
	  in the simulator. t will eventually allow to get rid of the
	  sheet_view function in sheet, instead directly working ?\004on
	  the sheet_view_dict sheet attribute (I added an alert for that in
	  sheet.py). It remains to add measure_activity() instead of pass
	  in the command field of the activity PlotGroupTemplate; I have
	  done it and it works, but I could not commit plotgroup.py
	  ?\004since I am in the middle of some re-organization of the file
	  that will take some more time.

2005-11-28  ceball

	* [r1499] topo/patterns/basic.py:
	  Changed note to myself.

	* [r1498] topo/tkgui/inputparamspanel.py,
	  topo/tkgui/parametersframe.py:
	  Moved create_patterns() from ParameterFrame to InputParamsPanel
	  since it's not in general useful to ParameterFrame objects.

2005-11-28  jbednar

	* [r1497] doc/Downloads/index_text.php:
	  Fixed typo

2005-11-28  ceball

	* [r1496] topo/tkgui/parametersframe.py:
	  Changes to make the file easier to read (removed any unused
	  attributes, made functions private if they aren't used outside
	  the class).

	* [r1495] topo/patterns/image.py:
	  Now uses sheet2matrixidx() from Sheet. This is an intermediate
	  check-in because there is no automatic scaling.

2005-11-28  julienciroux

	* [r1494] topo/plotting/plot.py:
	  Added temporary comments and alert for future file
	  re-organization.

	* [r1493] topo/plotting/plotengine.py:
	  Added a minor alert.

	* [r1492] topo/plotting/plotgroup.py,
	  topo/tkgui/plotgrouppanel.py,
	  topo/tkgui/projectionpanel.py:
	  Added an alert about a PlotGroup.plots() being called for nothing
	  in the PlotGroupPanels.

2005-11-28  ceball

	* [r1491] topo/patterns/image.py:
	  Made edge_average() more like the C++ version.

2005-11-27  jbednar

	* [r1490] topo/tkgui/projectionpanel.py:
	  Cleaned up docstring

2005-11-27  yfsit

	* [r1489] topo/base/connectionfield.py,
	  topo/base/patterngenerator.py,
	  topo/base/sheet.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/composer.py,
	  topo/tests/testsheet.py:
	  Fixed the ALERTS on matrix2sheet and sheet2matrix.
	  Any transformation between matrix indices and sheet coordinates
	  should now be done through matrixidx2sheet and sheet2matrixidx.
	  The test cases are updated accodringly.

2005-11-26  julienciroux

	* [r1488] topo/plotting/plotgroup.py,
	  topo/tkgui/projectionpanel.py:
	  Added the sheet name for the plot_key of a ProjectionPlotGroup,
	  so that the connection can have the same name for two different
	  sheets, and still the plot_key will differentiate them. That
	  fixes a bug that was occuring with hierarchical.ty: when
	  switching form V1 to V2 the AfferentLeft and AfferentRight were
	  the same. It was because both ProjectionPlotGroup had the same
	  plot_key, without the sheet differentiating them. Also modified
	  some comments in plotgroup.py.

	* [r1487] topo/plotting/plotgroup.py:
	  Got rid of the initialize_plot_list function for
	  ProjectionPlotGroup by adding some code in its create_plots
	  function. Now, initialize_plot_list is only implemented in the
	  superclass PlotGroup, and no sub-class have to re-implement it.
	  Also, minor changes in the comments.

	* [r1486] topo/plotting/plotengine.py:
	  Changed the default value of group_type to be None instead of
	  'BasicPlotGroup', because the case of a string was unused (it is
	  always a template that should be passed) in the function
	  get_plot_group; I also changed the comment about get_plot_group
	  and the possible changes still to be done on it.

	* [r1485] topo/plotting/plotengine.py,
	  topo/plotting/plotgroup.py,
	  topo/tests/testplotengine.py,
	  topo/tests/testplotgroup.py:
	  Continued clarifying PlotEngine and PlotGroup. I got rid of the
	  function sheet_filter that wasn't really useful (in both
	  plotengine and plotgroup), I got rid of the default values in the
	  make_plot_group function of PlotEngine to avoid confusion, got
	  rid of the corresponding JCALERT and modified some comments. I
	  changed the testplotengine and tesplotgroup accordingly.

2005-11-26  jdepaula

	* [r1484] doc/Downloads/win32_text.php:
	  Updated the formatting.

2005-11-26  julienciroux

	* [r1483] topo/plotting/plotgroup.py:
	  Minor change to comment; also put the simulator to be an
	  attribute of the super-class PlotGroup, becasue it was re-defined
	  in every sub-classes anyway.

	* [r1482] topo/tkgui/inputparamspanel.py:
	  Changed the call to PlotGroup in InputParamPanel to match the
	  changes that have been done in PlotGroup.

2005-11-25  jbednar

	* [r1481] doc/User_Manual/index_text.php,
	  doc/shared/util.php:
	  Added note about missing user manual

	* [r1480] doc/Downloads/index_text.php:
	  Removed bogus option

	* [r1479] doc/Downloads,
	  doc/Downloads/.cvsignore:
	  More to ignore

	* [r1478] doc/Downloads/win32_text.php:
	  Added road map

	* [r1477] README.txt,
	  WIN32_INSTALL.txt,
	  doc/Downloads/index_text.php,
	  doc/Downloads/win32_text.php:
	  Moved ../WIN32_INSTALL.txt to Downloads/win32_text.php

	* [r1476] doc/Downloads/index_text.php,
	  doc/Downloads/text.php:
	  Moved */text.php to */index_text.php

	* [r1475] doc/Forums/text.php,
	  doc/Future_Work/text.php,
	  doc/Home/text.php,
	  doc/Reference_Manual/text.php,
	  doc/Team_Members/text.php,
	  doc/Tutorial/text.php,
	  doc/User_Manual/text.php:
	  Moved */text.php to */index_text.php

	* [r1474] doc/Makefile,
	  doc/shared/index.php:
	  Make PHP generation work for any source file named *_text.php,
	  generating *.html. For this to work, had to rename */text.php to
	  */index_text.php, so that index.html is just a special case of
	  the general rule.

	* [r1473] doc/Forums/index_text.php,
	  doc/Future_Work/index_text.php,
	  doc/Home/index_text.php,
	  doc/Reference_Manual/index_text.php,
	  doc/Team_Members/index_text.php,
	  doc/Tutorial/index_text.php,
	  doc/User_Manual/index_text.php:
	  Moved */text.php to */index_text.php

2005-11-25  julienciroux

	* [r1472] topo/tkgui/parametersframe.py:
	  Minor change to comment.

	* [r1471] topo/tkgui/basicplotgrouppanel.py:
	  Minor change in prevision of future changes in PlotEngine (i.e. I
	  will get rid of most of the default parameter value in
	  get_plot_group and also re-order them)

	* [r1470] topo/plotting/plotengine.py,
	  topo/plotting/plotgroup.py:
	  Re-arranged the organization of both PlotEngine and PlotGroup.
	  Now, the PlotEngine only creates the PlotGroups when first
	  requested, and stores it in a dictionnary for later reuse; all
	  the plots generation is now done in each subclasses of PlotGroup,
	  instead of being done in the PlotEngine (i.e. the attribute
	  plot_list is now generated when the PlotGroup is created instead
	  of being passed as a parameter when creating the PlotGroup from
	  the PlotEngine). It makes the organization of the plotting
	  directory clearer, and solves some former bugs or limitations
	  (e.g. it is now possible to add whatever parameter in the
	  PlotGroupTemplates, like Hue or Confidence in the UnitWeights
	  PlotTemplate). Nevertheless, it is the first checked-in version,
	  but a lot remains to be done for cleaning up the file and
	  improving its clarity; a lot of JCALERT have been written for
	  this purpose. Also, the next step is to re-write the plot.py file
	  and then improve again plotgroup.py accordingly.

	* [r1469] topo/tkgui/plotgrouppanel.py:
	  Minor changes to the comments (again).

	* [r1468] topo/tkgui/plotgrouppanel.py:
	  Minor changes to the comments.

2005-11-24  julienciroux

	* [r1467]
	  topo/tests/tkgui/testpreferencemappanel.py:
	  Got rid of the testpreferencemappanel.py file that have been
	  replaced by testbasicplotgrouppanel.

	* [r1466] topo/tests/tkgui/testplotpanel.py:
	  Got rid of the plotpanel.py file that have been replaced by
	  plotgrouppanel.

	* [r1465] topo/tests/tkgui/__init__.py:
	  Changed the __init__.py file in the topo/tests/tkgui/ directory
	  to replace testplotpanel by testplotgrouppanel and
	  testpreferencemappanel by testbasicplotgrouppanel.

	* [r1464]
	  topo/tests/tkgui/testbasicplotgrouppanel.py:
	  Changed the name of testpreferencemappanel.py to be
	  testbasicplotgrouppanel.py.

	* [r1463]
	  topo/tests/tkgui/testplotgrouppanel.py:
	  Changed the name of testplotpanel.py to be testplotgrouppanel.py.

	* [r1462] topo/tkgui/preferencemappanel.py:
	  Got rid of the file preferencemappanel.py that have been replaced
	  by basicplotgrouppanel.py.

	* [r1461] topo/tkgui/plotpanel.py:
	  Got rid of the file plotpanel.py that have been replaced by
	  plotgrouppanel.py.

	* [r1460] topo/plotting/plotengine.py,
	  topo/tests/tkgui/testactivitypanel.py,
	  topo/tests/tkgui/testpreferencemappanel.py,
	  topo/tkgui/topoconsole.py:
	  Changed references to the module preferencemappanel to be
	  basicplotgrouppanel in any files that used it.

	* [r1459] topo/tests/tkgui/testplotpanel.py,
	  topo/tkgui/basicplotgrouppanel.py,
	  topo/tkgui/cfsheetplotpanel.py,
	  topo/tkgui/inputparamspanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Changed references to the module plotpanel to be plotgrouppanel
	  in any files that used it.

	* [r1458] topo/tkgui/basicplotgrouppanel.py:
	  Renamed preferencemappanel.py to be basicplotgrouppanel.py
	  (because PreferenceMapPanel and BasicPlotPanel are now merged
	  into BasicPlotGroupPanel).

	* [r1457] topo/plotting/plotengine.py,
	  topo/tkgui/plotgrouppanel.py:
	  Renamed plotpanel.py to be plotgrouppanel.py

2005-11-24  jbednar

	* [r1456] topo/tkgui/plotpanel.py:
	  Clarified comment

2005-11-23  julienciroux

	* [r1455] topo/tkgui/plotpanel.py:
	  Minor change to the comments.

2005-11-23  ceball

	* [r1454] examples/ellen_arthur_square.pgm:
	  Removed square version of Ellen Arthur.

	* [r1453] topo/patterns/image.py:
	  Updated to use new ellen_arthur.pgm. Added some comments.

2005-11-23  jbednar

	* [r1452] examples/ellen_arthur.pgm:
	  Added full-resolution non-square version

2005-11-23  ceball

	* [r1451] topo/patterns/image.py:
	  Background value is now an edge average. Also changed range to
	  xrange in the sampling for loop because xrange is slightly faster
	  for looping.

2005-11-22  ceball

	* [r1450] topo/patterns/image.py:
	  Changed to use normalization function from outputfns/basic.py,
	  and made the normalization function be a Parameter. Removed
	  unused import statement.

	* [r1449] topo/tests/testoutputfnsbasic.py:
	  Removed the duplicated docstring.

	* [r1448] topo/base/utils.py:
	  Just added a reference about infinity and NaN in Python.

	* [r1447] topo/tests/testfeaturemap.py:
	  Initial docstring was duplicated.

	* [r1446] topo/base/distribution.py:
	  Added reminder that we planned to refine the definition of
	  selectivity for non-cyclic distributions.

	* [r1445] topo/patterns/image.py:
	  Changed how parts of retina with no image get an activity (no
	  change to behavior yet.

	* [r1444] topo/patterns/image.py:
	  Image no longer wraps when it's made smaller than the retina.

	* [r1443] topo/patterns/image.py:
	  Image's methods are no longer used for resizing.

2005-11-22  jdepaula

	* [r1442] WIN32_INSTALL.txt:
	  Removed two steps for Weave integration, since they are now part
	  of the CVS distribution.

	* [r1441] topo/learningfns/basic.py,
	  topo/projections/optimized.py:
	  Split multi-arg inline string into individual entries in list.

	* [r1440] topo/base/utils.py:
	  Changed float('inf') reference to the inf variable.

2005-11-21  jdepaula

	* [r1439] topo/responsefns/basic.py:
	  Changed bzero in inlines to memset

2005-11-21  ceball

	* [r1438] topo/patterns/image.py:
	  Initial version. Added so that I can track changes - the file
	  will probably by split up and/or moved.

	* [r1437] examples/ellen_arthur_square.pgm:
	  Added as a sample image to use as retinal input.

2005-11-21  jdepaula

	* [r1436] WIN32_INSTALL.txt:
	  Added painful process to get Weave to work with Topographica
	  under Windows

2005-11-21  yfsit

	* [r1435] topo/base/utils.py:
	  a little faster crop_in_place

2005-11-20  yfsit

	* [r1434] topo/base/connectionfield.py,
	  topo/base/utils.py:
	  - a more efficient clip_in_place()
	  - documentation of ConnectionField.change_bounds().

2005-11-16  julienciroux

	* [r1433] topo/tests/testoutputfnsbasic.py:
	  Error on the last commit; correction of this error in the test
	  file for outputfnsbasic.

	* [r1432] topo/outputfns/basic.py,
	  topo/tests/testoutputfnsbasic.py:
	  Fixed the JCALERT about DivisiveLpNormalize; all the
	  function/procedure in the file /outputfns/basic.py are now
	  working; the testoutpufns has been fixed too. Nevertheless, the
	  return x statement have still to be removed and the calls to be
	  changed in any files using these procedures (though it seems to
	  work fine when creating no intermediate copy and yet keeping a
	  return statement); also note that for the moment the test file
	  test both cases: procedure and function calls.

	* [r1431] topo/plotting/plotengine.py,
	  topo/tests/tkgui/testactivitypanel.py,
	  topo/tests/tkgui/testpreferencemappanel.py,
	  topo/tkgui/plotpanel.py,
	  topo/tkgui/preferencemappanel.py,
	  topo/tkgui/topoconsole.py:
	  Merged PreferenceMapPanel and BasicPlotPanel in a unique class
	  BasicPlotGroupPanel (currently still in the file
	  preferencemap.py), and got rid of the associated JABHACKALERT;
	  changed the name accordingly in any file that used them;it
	  remains to change the name of the file preferencemappanel.py to
	  basicplotgrouppanel.py (and also plotpanel.py to
	  plotgrouppanel.py), also to write a function measure_activity()
	  to pass to the Activity PlotGroupTemplate instead of pass for the
	  moment; added a JCALERT for that in preferencemappanel.py.

	* [r1430] topo/plotting/plotengine.py,
	  topo/tests/tkgui/testplotpanel.py,
	  topo/tkgui/cfsheetplotpanel.py,
	  topo/tkgui/inputparamspanel.py,
	  topo/tkgui/plotpanel.py,
	  topo/tkgui/preferencemappanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Changed the name of the PlotPanel class to be PlotGroupPanel, and
	  got rid of a JABHACKALERT on this occasion. I added a JCALERT
	  though, because I think we should change the name of the file
	  plotpanel.py to plotgrouppanel.py, and also the name of the
	  PlotGroupPanel sub-classes (e.g. BasicPlotPanel).

	* [r1429] topo/tkgui/plotpanel.py:
	  Got rid of an unused function (enum) and its associated JABALERT.

	* [r1428] topo/plotting/plotengine.py:
	  Forgot to copy a comment.

	* [r1427] topo/plotting/plotengine.py:
	  Continued to add comment for future re-organization of the file;
	  re-wrote a part of the code and commented out the former one: now
	  it is possible to add more things in Projection and Unit Weights
	  PlotTemplate without being stopped at the PlotEngine level
	  because the choice of plot is done according to the name of the
	  PlotTemplates rather than what are their channels. The next step
	  is to re-write plot.py so that to obtain colored plot in all the
	  cases if we wish to.

	* [r1426] topo/plotting/plotengine.py:
	  Added some JCALERT and comment for preparing the re-organization
	  of the file; also commented out some part of the code that seems
	  not to be used (It has been left in comment to help re-writing
	  the file later).

2005-11-16  yfsit

	* [r1425] examples/lissom_or.ty:
	  import CFProjection from topo.projections.basic instead of
	  topo.base.connectionfield.

	* [r1424] topo/projections/basic.py:
	  added topo.projection.basic so that CFProjection can be imported
	  from topo.projections.

2005-11-16  ceball

	* [r1423] topo/patterns/basic.py:
	  Removed another unused import statement.

	* [r1422] topo/patterns/basic.py:
	  Removed unused import statement. Folded functions within
	  SquareGratingGenerator and SineGratingGenerator. Corrected error
	  that was having no effect: I don't understand why params.get()
	  statements are present (so I added a note about that).

	* [r1421] topo/patterns/basic.py:
	  Missed an update on the last commit. For a SquareGrating to have
	  horizontal bars at orientation=0, the sin() function must depend
	  on the y coordinate rather than the x coordinate (see previous
	  log message).

2005-11-15  ceball

	* [r1420] topo/base/patterngenerator.py:
	  Sorted out import statements.

2005-11-15  jdepaula

	* [r1419] WIN32_INSTALL.txt:
	  Added directions to the lissom_or.ty file for cutting Weave out
	  of the Windows port.

2005-11-15  julienciroux

	* [r1418] topo/plotting/plotengine.py:
	  Started to clean up plotengine.py in the perspective of
	  simplifying it a lot in the future: added comments to help, added
	  JCALERT.

	* [r1417] topo/analysis/featuremap.py:
	  Got rid of an irrelevant CEBALERT.

2005-11-15  ceball

	* [r1416] topo/base/patterngenerator.py:
	  Made setup_xy be a private method of PatternGenerator.

	* [r1415] topo/base/patterngenerator.py:
	  Made transform_coordinates() be a private function of
	  PatternGenerator.

	* [r1414] topo/base/patterngenerator.py:
	  Made produce_pattern_matrices() be a private function of
	  PatternGenerator.

	* [r1413] topo/base/patterngenerator.py:
	  Removed an item under a JABHACKALERT. Functions from sheet.py are
	  already used.

	* [r1412] examples/cfsom_or.ty:
	  Made the default Gaussian more like lissom_or.ty's by having it
	  wider than it is high.

	* [r1411] topo/base/patternfns.py:
	  Changed gabor() also to vary sinusoidally with the y coordinate
	  (see previous log message).

	* [r1410] topo/base/patternfns.py,
	  topo/base/patterngenerator.py,
	  topo/patterns/basic.py:
	  The previous commit of patterngenerator.py caused the x and y
	  values to be swapped: it turns out the rotations were not so
	  mysterious! However, I think the x matrix was being setup
	  incorrectly; it should have been rotated in the opposite sense.
	  Now that the matrices are setup correctly, it makes sense to
	  refer correctly to x and y in the various functions that use the
	  x and y matrices. For example, for a SineGrating to have
	  horizontal bars at orientation=0, the sin() function must depend
	  on the y coordinate rather than the x coordinate.

2005-11-15  julienciroux

	* [r1409] topo/tests/testoutputfnsbasic.py:
	  Corrected the test file for the outputfns so that it test both
	  the procedure and the function call; also added some comments to
	  clarify the situation.

	* [r1408] topo/outputfns/basic.py:
	  Got rid of the clip_in_place function that have been put in
	  utils.py; got rid of the JABALERT! about the x.savespace(1);
	  added some JCALERT about the fact that we kept the return
	  statement for the moment and also about DivisiveLpNormalize that
	  could not have been made to work as a procedure.

	* [r1407] topo/base/utils.py:
	  Moved the function clip_in_place from outputfns/basic.py to
	  utils.py; also add some comment about the fact that I did not
	  find any convenient matrix function to use for replacing the for
	  loop

	* [r1406] topo/tkgui/preferencemappanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/unitweightspanel.py:
	  Got rid of the unused call to get_event_processor in the
	  subclasses of PlotPanel; this function is almost not used
	  anywhere now, and we might be able to get rid of it.

	* [r1405] topo/plotting/plotengine.py:
	  Got rid of unused lines in plotengine.py

2005-11-15  ceball

	* [r1404] topo/base/patternfns.py,
	  topo/base/patterngenerator.py,
	  topo/patterns/basic.py:
	  Removed a mysterious 90-degree rotation from patterngenerator.
	  Patterns now seem to be drawn at the conventional orientation.
	  Updated line(), which had been changed to be horizontal for the
	  tutorial. 'height' and 'width' are still probably confusing
	  labels.

2005-11-15  jbednar

	* [r1403] doc/Downloads/text.php:
	  Broke long line to fix formatting. Added instructions on
	  updating.

	* [r1402] README.txt:
	  Added note

2005-11-14  yfsit

	* [r1401] examples/lissom_or.ty:
	  updated instructions on running a pure python implementation.

	* [r1400] examples/lissom_or.ty:
	  corrected the description on how to use the _CPointer classes.

2005-11-14  jdepaula

	* [r1399] WIN32_INSTALL.txt:
	  Changed tag which was not being replaced, with date line.

	* [r1398] external/win32/setup.py:
	  Added more comments to FixedPoint section

	* [r1397] WIN32_INSTALL.txt:
	  Removed references to Dislin. Added references to MatPlotLib and
	  FixedPoint

	* [r1396] external/win32/setup.py:
	  Install FixedPoint package.

	* [r1395] external/win32,
	  external/win32/.cvsignore:
	  Added fixedpoint files

	* [r1394] external,
	  external/.cvsignore:
	  Added Pmw.tar

	* [r1393]
	  external/win32/fixedpoint-0.1.2_patched.tgz:
	  Typo in directory. Added wait and B flag to setup.bat

	* [r1392]
	  external/win32/fixedpoint-0.1.2_patched.tgz:
	  Changed bat startup directory to avoid infinite loop of calling
	  setu.py

	* [r1391]
	  external/win32/fixedpoint-0.1.2_patched.tgz:
	  Added a setup.bat file to allow changing directories for the
	  setup.py file

	* [r1390]
	  external/win32/fixedpoint-0.1.2_patched.tgz:
	  Changed permissions of setup file so it would run. Changed name
	  of setup file to setup.py

	* [r1389]
	  external/win32/fixedpoint-0.1.2_patched.tgz:
	  Same as in the external dir, but already patched to make the
	  Windows install easier.

2005-11-11  jbednar

	* [r1388] topo/sheets/lissom.py:
	  Removed unneeded imports

	* [r1387] topo/base/connectionfield.py,
	  topo/plotting/plotengine.py:
	  Cleaned up comments

2005-11-11  yfsit

	* [r1386] examples/lissom_or.ty:
	  changed the instruction on how to run the _CPointer classes.

	* [r1385] topo/base/connectionfield.py,
	  topo/projections/optimized.py:
	  - change response_fn and learning_fn of CFProjection_CPointer
	  into Parameter.
	  - remove the storing of normlaize_fn in ConnectionField. The
	  function to normalize the weights are passed into __init__ and
	  change_bound instead.

2005-11-10  jdepaula

	* [r1384] topo/plotting/plotengine.py:
	  Fixed error with UnitView plotting, sheet_view. Was requesting
	  sheet_view of the src instead of the target. Also removed
	  commented and deprecated code. Warning still left in.

2005-11-10  jbednar

	* [r1383] examples/lissom_or.ty:
	  Simplified switching between CPointer and non- versions

	* [r1382] topo/base/connectionfield.py:
	  Fixed typo in warning

2005-11-10  jdepaula

	* [r1381] external/win32/util/patch.exe:
	  For fixedpoint patch file.

	* [r1380] external/win32/README.txt:
	  Removed dislin reference, added comment about MatPlotLib.

	* [r1379] external/win32/setup.py:
	  Removed dislin

	* [r1378] external/win32/dl_83_py.tar.gz:
	  Now using MatPlotLib instead.

2005-11-10  jbednar

	* [r1377] topo/base/__init__.py:
	  Updated __all__ list

2005-11-09  ceball

	* [r1376] examples/lissom_or.ty:
	  Added instructions for using Python-only code.

2005-11-09  yfsit

	* [r1375] examples/lissom_or.ty,
	  topo/base/connectionfield.py,
	  topo/base/patterngenerator.py,
	  topo/projections/optimized.py,
	  topo/sheets/lissom.py:
	  learning_fn is now a parameter of CFProjection, instead of a
	  Sheet.

2005-11-09  jbednar

	* [r1374] doc/Forums/text.php:
	  Added bug and feature trackers

2005-11-09  ceball_cvs2svn

	* [r1373] /tags/release_0_8_0,
	  /tags/release_0_8_0/topographica/doc/Downloads,
	  /tags/release_0_8_0/topographica/doc/Forums,
	  /tags/release_0_8_0/topographica/doc/Tutorial/images,
	  /tags/release_0_8_0/topographica/doc/Tutorial/images/activity_line.png,
	  /tags/release_0_8_0/topographica/doc/Tutorial/images/activity_line_or.png,
	  /tags/release_0_8_0/topographica/doc/images,
	  /tags/release_0_8_0/topographica/examples/lissom_or_20000.typ,
	  /tags/release_0_8_0/topographica/topo/projections/optimized.py,
	  /tags/release_0_8_0/topographica/topo/tests,
	  /tags/release_0_8_0/topographica/topo/tkgui:
	  This commit was manufactured by cvs2svn to create tag
	  'release_0_8_0'.

2005-11-09  jbednar

	* [r1372]
	  doc/images/051107_topographica_screen_shot_white.png:
	  Initial version

	* [r1371] doc/shared/index.php:
	  New news

	* [r1370] doc/Home/text.php:
	  Minor cleanup

	* [r1369] doc/index.html:
	  Changed main page to redirect instead of frame for simplicity

	* [r1368] doc/Tutorial/text.php:
	  Added note suggested by Chris

	* [r1367] doc/Tutorial/text.php:
	  Minor clarifications

	* [r1366] doc/Future_Work/text.php:
	  Added blurb on state saving

	* [r1365] doc/Downloads/text.php:
	  Added Win32 notes

2005-11-09  ceball

	* [r1364]
	  doc/Tutorial/images/activity_line.png,
	  doc/Tutorial/images/activity_line_or.png,
	  doc/Tutorial/images/test_pattern.png,
	  doc/Tutorial/text.php:
	  Updated images to use line with a thickness that stops the retina
	  appearing monochrome.

	* [r1363] topo/patterns/basic.py:
	  Changed default thickness and smoothing of LineGenerator, and
	  added a default scale parameter. This allows users of the
	  tutorial to see reasonable responses without having to adjust the
	  scale themselves.

2005-11-08  ceball

	* [r1362]
	  doc/Tutorial/images/activity_line.png,
	  doc/Tutorial/images/activity_line_or.png:
	  Added line plot images, which I forgot on the last update.

2005-11-08  jbednar

	* [r1361] Makefile,
	  doc/Downloads/text.php:
	  Added tests and examples to 'all' target; it's what I'm always
	  doing...

2005-11-08  ceball

	* [r1360] doc/Tutorial/text.php:
	  Fixed mistake introduced by JAB. You'd think after all these
	  years around LISSOM that he'd understand it.

	* [r1359] doc/Tutorial/images/or_map.png,
	  doc/Tutorial/images/projection.png,
	  doc/Tutorial/images/test_pattern.png,
	  doc/Tutorial/images/unit_weights_0_0.png,
	  doc/Tutorial/text.php:
	  Updated tutorial with screenshots from the new saved network
	  (v.1.3), and using a line as the demonstration pattern.

	* [r1358] examples/lissom_or_20000.typ:
	  Resaved the network so that first activity pattern viewed by a
	  user is not some crazy-ass wiggly line. (I was messing with the
	  input patterns before I saved the network.

	* [r1357] topo/patterns/basic.py:
	  Adjusted default properties of LineGenerator() to give a
	  reasonable response on lissom_or.ty.

	* [r1356] topo/base/patternfns.py:
	  Changed variable name x to y in line() as it better describes the
	  idea.

	* [r1355] examples/lissom_or_20000.typ:
	  New pickled network that was trained to 20000 with corrected
	  LateralExcitatory bounds (see log message for examples/lissom.ty
	  v.1.9).

	* [r1354] examples/lissom_or.ty:
	  Changed BoundingBox dimensions for final LateralExcitatory change
	  of bounds at 2000 iterations. Previously it was trying to enlarge
	  the bounds for a 48x48 V1.

	* [r1353] topo/patterns/basic.py:
	  Corrected LineGenerator so that an orientation of zero is
	  horizontal.

2005-11-08  jbednar

	* [r1352] topo/__init__.py:
	  Made warning less severe

	* [r1351]
	  doc/Tutorial/images/unit_weights_0_0.png,
	  doc/Tutorial/text.php:
	  Minor edits -- first complete version!

2005-11-08  julienciroux

	* [r1350] topo/plotting/plotgroup.py:
	  Added a function sort_plots() that sort a list of plots according
	  to their src_name (in plot.view_info['src_name']); it is then
	  applied in the plots() method of PlotGroup to sort the bitmap
	  list in alphabetical order; the function plots() ?\004is
	  overwritten in the ProjectionPlotGroup so that it does not sort
	  in this case (because it would otherwise sort the UnitView
	  constituting the projection plot)

	* [r1349] topo/plotting/plot.py:
	  Erased an unused comment

	* [r1348] topo/plotting/plotengine.py:
	  Minor change in comment

	* [r1347] topo/tests/testplotengine.py:
	  Changed the test for plotengine so that it does not call the
	  function _sheet anymore (because it has been erased)

2005-11-08  ceball

	* [r1346]
	  doc/Tutorial/images/activity_gaussian.png,
	  doc/Tutorial/images/activity_gaussian_or.png,
	  doc/Tutorial/images/or_map.png,
	  doc/Tutorial/images/projection.png,
	  doc/Tutorial/images/unit_weights_0_0.png,
	  doc/Tutorial/text.php:
	  Updated tutorial screenshots and recorded time to measure an OR
	  map as about 30 sec.

	* [r1345] topo/commands/basic.py:
	  Added hack to restore random properties of gaussian generators to
	  make cfsom_or and lissom_or work after unpickling.

	* [r1344] topo/base/topoobject.py:
	  Now when being pickled, TopoObjects save their class attributes.
	  Currently this only gets attributes from the object's class, not
	  from any superclasses (see hackalert). There is a problem with
	  this implementation: e.g. in the lissom_or.ty example, the random
	  x,y,orientation parameters are not pickled correctly.

	* [r1343] examples/lissom_or.ty:
	  Changed BaseN to 48.0.

	* [r1342] examples/lissom_or_20000.typ:
	  Saved network for lissom_or.ty with a 48x48 V1

2005-11-08  jbednar

	* [r1341] MILESTONES,
	  doc/Future_Work/text.php:
	  Moved MILESTONES into doc/Future_Work

2005-11-08  ceball

	* [r1340] doc/Tutorial/text.php,
	  doc/Tutorial/tutorial.css,
	  doc/shared/topo.css:
	  Moved Tutorial/tutorial.css code into shared/topo.css

	* [r1339] doc/Tutorial/text.php:
	  Updated tutorial. Pictures are still for a 72x72 V1. No map yet
	  available in the stated location.

2005-11-08  jbednar

	* [r1338] doc/Reference_Manual/text.php:
	  Moved tk to tkgui

	* [r1337] topo/tests/testbitmap.py,
	  topo/tests/testplot.py,
	  topo/tests/testplotengine.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testsheetview.py,
	  topo/tests/tkgui/testactivitypanel.py,
	  topo/tests/tkgui/testplotpanel.py:
	  Moved tests to topo/tests

	* [r1336] doc/Forums,
	  doc/Forums/.cvsignore,
	  doc/Forums/text.php,
	  doc/Lists,_Forums,
	  doc/shared/util.php:
	  Moved Lists, Forums to Forums

	* [r1335] runtests, tests,
	  topo/tests,
	  topo/tests/.cvsignore,
	  topo/tests/README.txt,
	  topo/tests/__init__.py,
	  topo/tests/testbitmap.jpg,
	  topo/tests/testbitmap.py,
	  topo/tests/testboundingregion.py,
	  topo/tests/testcfsom.py,
	  topo/tests/testdistribution.py,
	  topo/tests/testdummy.py,
	  topo/tests/testfeaturemap.py,
	  topo/tests/testhistogram.py,
	  topo/tests/testmatplotlib.py,
	  topo/tests/testoutputfnsbasic.py,
	  topo/tests/testpalette.py,
	  topo/tests/testpatterngenerator.py,
	  topo/tests/testpatternpresent.py,
	  topo/tests/testplot.py,
	  topo/tests/testplotengine.py,
	  topo/tests/testplotfilesaver.py,
	  topo/tests/testplotgroup.py,
	  topo/tests/testsheet.py,
	  topo/tests/testsheetview.ppm,
	  topo/tests/testsheetview.py,
	  topo/tests/testsimulator.py,
	  topo/tests/tkgui,
	  topo/tests/tkgui/.cvsignore,
	  topo/tests/tkgui/__init__.py,
	  topo/tests/tkgui/testactivitypanel.py,
	  topo/tests/tkgui/testmatplotlibtk.py,
	  topo/tests/tkgui/testplotpanel.py,
	  topo/tests/tkgui/testpreferencemappanel.py,
	  topo/tests/tkgui/testpropertiesframe.py,
	  topo/tests/tkgui/testtopoconsole.py:
	  Moved tests to topo/tests

	* [r1334] tests/tk,
	  tests/tkgui,
	  tests/tkgui/.cvsignore,
	  tests/tkgui/__init__.py,
	  tests/tkgui/testactivitypanel.py,
	  tests/tkgui/testmatplotlibtk.py,
	  tests/tkgui/testplotpanel.py,
	  tests/tkgui/testpreferencemappanel.py,
	  tests/tkgui/testpropertiesframe.py,
	  tests/tkgui/testtopoconsole.py,
	  topo/tk:
	  Moved tk to tkgui

	* [r1333] topo/tkgui,
	  topo/tkgui/.cvsignore,
	  topo/tkgui/__init__.py,
	  topo/tkgui/cfsheetplotpanel.py,
	  topo/tkgui/inputparamspanel.py,
	  topo/tkgui/parametersframe.py,
	  topo/tkgui/plotpanel.py,
	  topo/tkgui/preferencemappanel.py,
	  topo/tkgui/projectionpanel.py,
	  topo/tkgui/propertiesframe.py,
	  topo/tkgui/taggedslider.py,
	  topo/tkgui/topoconsole.py,
	  topo/tkgui/unitweightspanel.py:
	  Moved from tk/

	* [r1332] Makefile:
	  Restored library support broken by previous checkin

	* [r1331] tests/__init__.py,
	  tests/tk/__init__.py,
	  tests/tk/testactivitypanel.py,
	  tests/tk/testmatplotlibtk.py,
	  tests/tk/testplotpanel.py,
	  tests/tk/testpreferencemappanel.py,
	  tests/tk/testtopoconsole.py,
	  topo/__init__.py,
	  topo/analysis/featuremap.py,
	  topo/tk/plotpanel.py,
	  topo/tk/topoconsole.py,
	  topographica_script.py:
	  Changes required when renaming tk to tkgui

	* [r1330] Makefile:
	  Removed unused DISLIN commands

2005-11-08  yfsit

	* [r1329] topo/projections/kernelprojection.py:
	  removing projections/kernelprojection.py

	* [r1328] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/lissom_or.ty,
	  tests/testcfsom.py,
	  tests/testfeaturemap.py,
	  tests/testpatternpresent.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  topo/base/connectionfield.py,
	  topo/base/projection.py,
	  topo/learningfns/basic.py,
	  topo/projections/kernelprojection.py,
	  topo/projections/optimized.py,
	  topo/responsefns/basic.py,
	  topo/sheets/lissom.py:
	  Merged KernelProjection into CFProjection. That means there is no
	  longer a KernelProjection class. The old KernelPointerProjection
	  that uses the C pointer functions is renamed as
	  CFProjection_CPointer and moved into a new file
	  projections/optimized.py.
	  
	  projections/kernelprojection.py will be removed.

2005-11-08  jbednar

	* [r1327] tests/tk/testpropertiesframe.py:
	  Fixed syntax error in previous checkin

2005-11-08  ceball

	* [r1326]
	  doc/Tutorial/images/activity_gaussian.png,
	  doc/Tutorial/images/activity_gaussian_or.png,
	  doc/Tutorial/images/or_map.png,
	  doc/Tutorial/images/projection.png,
	  doc/Tutorial/images/test_pattern.png,
	  doc/Tutorial/images/topographica_console.png,
	  doc/Tutorial/images/unit_weights_0_0.png,
	  doc/Tutorial/images/unit_weights_0_0_or.png:
	  Image from window manager with a border.

2005-11-07  jdepaula

	* [r1325] topo/plotting/bitmap.py:
	  No longer exits Topographica when a NaN received. Prints warning
	  and uses Zero matrix.

	* [r1324] topo/plotting/plotgroup.py:
	  Print a warning if the plot bitmap has NaNs.

2005-11-07  ceball

	* [r1323] topo/tk/topoconsole.py:
	  Updated 'Help' menu with 'reference manual', 'tutorial', and so
	  on. These should launch a browser (unless one is already open),
	  and load the correct page. If a browser was open, it should bring
	  it to the front - but I am skeptical about that. I have only
	  tested this on DICE so far, where it works. If it doesn't work
	  for you, please let me know. If you think the list should be
	  different, you're welcome to change it. Should we include the
	  python documentation locally? It would have to be made - that
	  seems to take a while.

2005-11-07  julienciroux

	* [r1322] topo/tk/projectionpanel.py:
	  Added an hack so that the projections are displayed in
	  alphabetical order within the projection panel (and the
	  scrolled-list menu corresponding to it).

2005-11-07  ceball

	* [r1321] examples/lissom_or.ty:
	  Set the random seed for pattern generators to a specific value so
	  that runs of the lissom_or.ty example are identical (except for
	  the initial weights, which are still random).

2005-11-07  jbednar

	* [r1320] doc/Future_Work/text.php:
	  Added note about needing more tests

2005-11-07  julienciroux

	* [r1319] topo/plotting/plotengine.py:
	  Corrected minor typing error

2005-11-07  jbednar

	* [r1318]
	  doc/Tutorial/images/or_key_vert_transparent_topo.png,
	  doc/Tutorial/text.php:
	  Added color key for Topographica

	* [r1317] README.txt:
	  Added note about make -k

2005-11-07  julienciroux

	* [r1316] topo/plotting/plotengine.py:
	  Added an hack so that the unit weights are plotted in the right
	  order (afferent, lat.Excitatory and Lat.Inhibitory) in the
	  unitweight panel

	* [r1315] topo/commands/basic.py,
	  topo/plotting/plotengine.py,
	  topo/plotting/plotgroup.py,
	  topo/tk/cfsheetplotpanel.py,
	  topo/tk/unitweightspanel.py:
	  Changed calls to get_event_processors() for obtaining the list of
	  Sheet by calls to objects(Sheet).values().

	* [r1314] tests/tk/testpreferencemappanel.py:
	  Added the __name__='__main__' line at the end of the
	  preferencemap test file so that it can be executed form the
	  topographica directory.

	* [r1313] tests/tk/testplotpanel.py,
	  tests/tk/testtopoconsole.py:
	  Added the __name__='__main__' line at the end of both test files
	  so that it can be executed form the topographica directory.

	* [r1312] tests/testplotgroup.py:
	  Added the __main__ line at the end of the test file so that it
	  runs from the command line in /topographica

	* [r1311] tests/testplotengine.py:
	  Added the __main__ line at the end of the test file so that it
	  can be run from the command line

	* [r1310] topo/base/utils.py:
	  Added a simple and fast routine dict_sort to sort a dictionary on
	  key

	* [r1309] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/image_example.py,
	  examples/lissom_or.ty:
	  Added the __version__='$' line to the file in the /examples
	  directory

	* [r1308] tests/tk/__init__.py,
	  tests/tk/testactivitypanel.py,
	  tests/tk/testmatplotlibtk.py,
	  tests/tk/testplotpanel.py,
	  tests/tk/testpreferencemappanel.py,
	  tests/tk/testpropertiesframe.py,
	  tests/tk/testtopoconsole.py:
	  Added the __version__='$' line and the $ line to the file in the
	  /tests/tk directory

	* [r1307] tests/__init__.py,
	  tests/testbitmap.py,
	  tests/testboundingregion.py,
	  tests/testcfsom.py,
	  tests/testdistribution.py,
	  tests/testdummy.py,
	  tests/testfeaturemap.py,
	  tests/testhistogram.py,
	  tests/testmatplotlib.py,
	  tests/testoutputfnsbasic.py,
	  tests/testpalette.py,
	  tests/testpatterngenerator.py,
	  tests/testpatternpresent.py,
	  tests/testplot.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/testplotgroup.py,
	  tests/testsheet.py,
	  tests/testsheetview.py,
	  tests/testsimulator.py:
	  Added the __version__='$' line and the $ line to the file in the
	  /tests directory

2005-11-07  jbednar

	* [r1306] doc/User_Manual/text.php:
	  Added notes in progress

	* [r1305] README.txt:
	  Updated to remove text moved to web site

	* [r1304] doc/Makefile:
	  Added comments

	* [r1303] Makefile:
	  Renamed doc targets for clarity

2005-11-07  julienciroux

	* [r1302] topo/__init__.py:
	  Added the __version__='$' line to the __init__.py file in the
	  topo/ directory

	* [r1301] topo/tk/__init__.py,
	  topo/tk/cfsheetplotpanel.py,
	  topo/tk/inputparamspanel.py,
	  topo/tk/parametersframe.py,
	  topo/tk/plotpanel.py,
	  topo/tk/preferencemappanel.py,
	  topo/tk/projectionpanel.py,
	  topo/tk/propertiesframe.py,
	  topo/tk/taggedslider.py,
	  topo/tk/topoconsole.py,
	  topo/tk/unitweightspanel.py:
	  Added the __version__='$' line to the files in the topo/tk
	  directory

	* [r1300] topo/sheets/__init__.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/composer.py,
	  topo/sheets/generatorsheet.py,
	  topo/sheets/lissom.py:
	  Added the __version__='$' line to the files in the topo/sheets
	  directory

	* [r1299] topo/responsefns/__init__.py,
	  topo/responsefns/basic.py:
	  Added the __version__='$' line to the files in the
	  topo/responsefns directory

	* [r1298] topo/projections/__init__.py,
	  topo/projections/kernelprojection.py:
	  Added the __version__='$' line to the files in the
	  topo/projections directory

	* [r1297] topo/plotting/__init__.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/histogram.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotengine.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py:
	  Added the __version__='$' line to the files in the topo/plotting
	  directory

2005-11-07  jbednar

	* [r1296] doc/Downloads,
	  doc/Downloads/.cvsignore,
	  doc/Downloads/text.php:
	  Initial version

	* [r1295] topo/tk/inputparamspanel.py:
	  Added ALERT

	* [r1294] doc/shared/config.php:
	  Removed unused code

	* [r1293] doc/index.html,
	  doc/shared/index.php:
	  Moved meta information to main site frame only

	* [r1292] WIN32_INSTALL.txt:
	  Added caveat

	* [r1291] doc/shared/util.php:
	  Added Downloads page

2005-11-07  julienciroux

	* [r1290] topo/patterns/__init__.py,
	  topo/patterns/basic.py,
	  topo/patterns/random.py:
	  Added the __version__='$' line to the files in the topo/patterns
	  directory

	* [r1289] topo/outputfns/__init__.py,
	  topo/outputfns/basic.py:
	  Added the __version__='$' line to the files in the topo/outputfns
	  directory

	* [r1288] topo/learningfns/__init__.py:
	  Added the __version__='$' line to the __init__.py file in the
	  topo/learningfns directory

	* [r1287] topo/eps/__init__.py,
	  topo/eps/basic.py:
	  Added the __version__='$' line to the files in the topo/eps
	  directory

	* [r1286] topo/commands/__init__.py,
	  topo/commands/basic.py:
	  Added the __version__='$' line to the files in the topo/commands
	  directory

	* [r1285] topo/base/__init__.py,
	  topo/base/boundingregion.py,
	  topo/base/commandline.py,
	  topo/base/distribution.py,
	  topo/base/gendocs.py,
	  topo/base/keyedlist.py,
	  topo/base/parameter.py,
	  topo/base/patternfns.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/registry.py,
	  topo/base/sheetview.py,
	  topo/base/simulator.py,
	  topo/base/topoobject.py,
	  topo/base/tyimputil.py,
	  topo/base/utils.py:
	  Added the __version__='$' line to the files in the topo/base
	  directory

	* [r1284] topo/analysis/__init__.py,
	  topo/analysis/featuremap.py:
	  Added the __version__='$' line to the files in the topo/analysis
	  directory

2005-11-07  jbednar

	* [r1283] doc/Future_Work/text.php:
	  More to do...

	* [r1282] Makefile:
	  Added making of PHP documenation to 'make all'

	* [r1281] doc/Makefile:
	  Removed outdated hack

	* [r1280] doc/shared/index.php,
	  doc/shared/util.php:
	  Corrections needed for PHP 4.3.11

	* [r1279] doc/Future_Work/text.php:
	  Added notes from checked-out copy of TODO.txt on lodestar

	* [r1278] doc/Tutorial,
	  doc/Tutorial/.cvsignore,
	  doc/User_Manual,
	  doc/User_Manual/.cvsignore,
	  doc/User_Manual/text.php:
	  Initial version

	* [r1277] doc/Lists,_Forums/text.php:
	  Added note to self.

	* [r1276] doc/Tutorial/index.html,
	  doc/Tutorial/text.php:
	  Moved Tutorial/index.html to Tutorial/text.php to work with rest
	  of web site

	* [r1275] doc/shared/util.php:
	  Moved subpage titles down slightly

2005-11-07  yschoe

	* [r1274] doc/shared/util.php:
	  Fixed subdir banner text position -- yschoe

2005-11-07  jbednar

	* [r1273] doc/Makefile:
	  Minor target name change

	* [r1272] doc/Future_Work/text.php:
	  Expanded with other plans

	* [r1271] TODO.txt:
	  Moved to doc/Future_Work

	* [r1270] topographica_script.py:
	  Added details from TODO.txt

	* [r1269] topo/base/utils.py:
	  Added note from TODO.txt

2005-11-07  yschoe

	* [r1268] doc/images/topo-subbanner-bg.png,
	  doc/shared/util.php:
	  updated subdir banner and util.php -- yschoe

	* [r1267] doc/images/topo-subbanner-bg.png:
	  Fixed subdir banner -- yschoe

	* [r1266] doc/images/topo-banner7.png,
	  doc/images/topo-subbanner-bg.png,
	  doc/shared/util.php:
	  edited banner images (both home and blank) and util.php -- yschoe

2005-11-07  ceball

	* [r1265] topo/analysis/featuremap.py:
	  Added HACKALERT about duration of presentation for
	  measure_or_pref(). It needs to be different for LISSOM (0.06) and
	  CFSOM (1.0), so ought to read a variable set in lissom_or.ty (but
	  otherwise default to 1.0).

2005-11-07  jbednar

	* [r1264] doc/Future_Work,
	  doc/Future_Work/.cvsignore,
	  doc/Future_Work/text.php,
	  doc/shared/util.php:
	  Added Future Work page

	* [r1263] doc/Reference_Manual/text.php:
	  Cleaned up and added list of external packages

2005-11-07  ceball

	* [r1262] topo/patterns/basic.py:
	  More reasonable default frequency (in fact the same as
	  lissom_or.ty uses to measure its maps...

	* [r1261] topo/commands/basic.py:
	  Switched to most recent pickling protocol (2).

	* [r1260] topo/base/commandline.py:
	  Removed repeated word from intro text.

2005-11-06  yschoe

	* [r1259] doc/images/topo-banner7.png,
	  doc/shared/config.php,
	  doc/shared/util.php:
	  edited color scheme and banner image -- yschoe

2005-11-06  jbednar

	* [r1258] doc/shared/util.php:
	  Added links to new subdirectories

	* [r1257] doc/Team_Members/text.php:
	  Updated Yoonsuck's duties

	* [r1256] doc/Lists,_Forums,
	  doc/Lists,_Forums/.cvsignore,
	  doc/Lists,_Forums/text.php:
	  Added info about mailing lists and web forums

2005-11-06  ceball

	* [r1255] doc/Tutorial,
	  doc/Tutorial/images,
	  doc/Tutorial/images/activity_gaussian.png,
	  doc/Tutorial/images/activity_gaussian_or.png,
	  doc/Tutorial/images/or_key_horiz_transparent.png,
	  doc/Tutorial/images/or_map.png,
	  doc/Tutorial/images/projection.png,
	  doc/Tutorial/images/test_pattern.png,
	  doc/Tutorial/images/topographica_console.png,
	  doc/Tutorial/images/unit_weights_0_0.png,
	  doc/Tutorial/images/unit_weights_0_0_or.png,
	  doc/Tutorial/index.html,
	  doc/Tutorial/tutorial.css:
	  Capitalized tutorial/ --> Tutorial/

	* [r1254] doc/tutorial:
	  Capitalizing tutorial/ directory --> Tutorial/

2005-11-06  yschoe

	* [r1253] doc/Home/text.php,
	  doc/images/topo-banner7.png,
	  doc/shared/config.php,
	  doc/shared/index.php,
	  doc/shared/topo.css,
	  doc/shared/util.php:
	  Home page edits by yschoe.

2005-11-06  jbednar

	* [r1252] Makefile:
	  Added dependency to force re-make of documentation after a clean

	* [r1251] doc/Makefile:
	  Changed to remove pydoc-generated documentation only, since that
	  can always be regenerated. Kept PHP documentation around by
	  default, since not everyone will have PHP, and it will rarely
	  need updating anyway

	* [r1250] doc/Reference_Manual,
	  doc/Reference_Manual/.cvsignore:
	  More to ignore

	* [r1249] topo/sheets/lissom.py:
	  Trivial fix to whitespace

	* [r1248] topo/__init__.py:
	  Updated with new directories

	* [r1247] /trunk/topographica, .cvsignore,
	  Makefile,
	  topo/base/gendocs.py:
	  Move reference manual from docs/ to doc/Reference_Manual

	* [r1246] doc/Reference_Manual,
	  doc/Reference_Manual/.cvsignore,
	  doc/Reference_Manual/text.php,
	  doc/shared/util.php:
	  Added local copy of reference manual

	* [r1245] doc/images/Topologo.xcf:
	  Imported existing version

	* [r1244] doc/Home,
	  doc/Home/.cvsignore,
	  doc/Team_Members,
	  doc/Team_Members/.cvsignore:
	  Initial version

	* [r1243] doc/Home,
	  doc/Home/text.php,
	  doc/Makefile,
	  doc/Team_Members,
	  doc/Team_Members/text.php,
	  doc/images,
	  doc/images/T-bg.png,
	  doc/images/Topo-arch-white.jpg,
	  doc/images/logo_jb.png,
	  doc/images/topo-banner7.png,
	  doc/images/topo-subbanner-bg.png,
	  doc/index.html,
	  doc/shared,
	  doc/shared/config.php,
	  doc/shared/index.php,
	  doc/shared/topo.css,
	  doc/shared/trailer.php,
	  doc/shared/util.php:
	  Initial version, based on Yoonsuck's prototype of the web site

	* [r1242] doc/tutorial/index.html:
	  Changed to use images/ directory

	* [r1241] doc/tutorial/images,
	  doc/tutorial/images/activity_gaussian.png,
	  doc/tutorial/images/activity_gaussian_or.png,
	  doc/tutorial/images/or_key_horiz_transparent.png,
	  doc/tutorial/images/or_map.png,
	  doc/tutorial/images/projection.png,
	  doc/tutorial/images/test_pattern.png,
	  doc/tutorial/images/topographica_console.png,
	  doc/tutorial/images/unit_weights_0_0.png,
	  doc/tutorial/images/unit_weights_0_0_or.png:
	  Moved from topographica/tutorial/

2005-11-06  ceball

	* [r1240] doc,
	  doc/tutorial,
	  doc/tutorial/index.html,
	  doc/tutorial/tutorial.css:
	  Moved from tutorial/

	* [r1239] tutorial:
	  Moving tutorial/ to doc/tutorial/.

	* [r1238] tutorial/screen_shots:
	  Moving tutorial/ to doc/tutorial/

2005-11-05  ceball

	* [r1237] tutorial/index.html:
	  Minor fix.

	* [r1236] tutorial,
	  tutorial/index.html,
	  tutorial/screen_shots,
	  tutorial/screen_shots/activity_gaussian.png,
	  tutorial/screen_shots/activity_gaussian_or.png,
	  tutorial/screen_shots/or_key_horiz_transparent.png,
	  tutorial/screen_shots/or_map.png,
	  tutorial/screen_shots/projection.png,
	  tutorial/screen_shots/test_pattern.png,
	  tutorial/screen_shots/topographica_console.png,
	  tutorial/screen_shots/unit_weights_0_0.png,
	  tutorial/screen_shots/unit_weights_0_0_or.png,
	  tutorial/tutorial.css:
	  Initial version.

	* [r1235] topo/analysis/featuremap.py:
	  Changed the default parameters so that all match those of the
	  equivalent LISSOM's measure_or_pref command.

	* [r1234] topo/analysis/featuremap.py:
	  measure_or_pref() now takes a list of frequencies. The default is
	  the list [2.4].

2005-11-05  jbednar

	* [r1233] examples/cfsom_or.ty,
	  examples/hierarchical.ty,
	  examples/image_example.py,
	  examples/lissom_or.ty,
	  topo/analysis/featuremap.py:
	  Cleaned up comments

2005-11-05  ceball

	* [r1232] examples/lissom_or.ty,
	  topo/base/patternfns.py:
	  patternfns.py is back to using the conventional definition of a
	  Gaussian. lissom_or.ty adjusted so that it continues to match
	  LISSOM, which does not use the same definition (doesn't use the
	  factor of 0.5 in the exp's argument.

	* [r1231] topo/analysis/featuremap.py:
	  Changed use of deprecated uses of String.capitalize() to
	  string_itself.capitalize(). Added HACKALERT about names of maps
	  and what the GUI does with them.

	* [r1230] topo/commands/basic.py,
	  topo/tk/topoconsole.py:
	  Moved save_snapshot() and load_snapshot() to topo.commands.basic.
	  topoconsole now asks for the filenames, and uses an extension
	  .typ for saved networks. That obviously stands for 'topographica
	  pickled network'. save_ and load_snapshot() in?\004
	  topo.commands.basic do nothing to the filenames. Maybe
	  topoconsole shouldn't either? Currently, whatever the user types
	  in the filename box will have .typ added to it.

2005-11-05  jbednar

	* [r1229] examples/hierarchical.ty:
	  Added extra areas and connections as examples of a hierarchy

	* [r1228] topo/base/patterngenerator.py:
	  Fixed typo in previous commit

	* [r1227] README.txt:
	  Updated to match filename in examples

	* [r1226] topo/plotting/plot.py:
	  Removed debugging statement

	* [r1225] topo/base/patterngenerator.py:
	  Fixed bug in normalizing images

	* [r1224] tests/testsimulator.py:
	  Updated to match changes in simulator.py

	* [r1223] examples/Makefile:
	  Updated filenames to match recent changes

2005-11-05  yfsit

	* [r1222] topo/plotting/bitmap.py,
	  topo/plotting/plot.py:
	  change max(max(array)) to max(array.flat). max(array), where
	  array is a 2D matrix is ill-defined and gives unexpected resulted
	  sometimes.

2005-11-04  yfsit

	* [r1221] topo/sheets/lissom.py:
	  fixed the counting of tsettle when learning is turned off.

2005-11-04  jbednar

	* [r1220] examples/lissom_or.ty:
	  Changed to match changes in lissom/samples/or_map_topo.param

	* [r1219] examples/cfsom-or.ty,
	  examples/lissom-or.ty:
	  Moved cfsom_example.py to cfsom_or.ty and lissom.ty to
	  lissom_or.ty

	* [r1218] examples/cfsom_or.ty,
	  examples/lissom_or.ty:
	  Slight name change

2005-11-04  julienciroux

	* [r1217] examples/gui_example.py,
	  examples/hierarchical.ty:
	  Changed the name of gui_example.py to be hierarchical.ty; also
	  changed the way the gui example connected V1, V2 and the Retinas
	  to something more realistic.

	* [r1216] examples/cfsom-or.ty,
	  examples/cfsom_example.py:
	  Changed the name of cfsom_example.py to be cfsom-or.ty

	* [r1215] examples/lissom-or.ty,
	  examples/lissom.ty:
	  Changed the name of lissom.ty to be lissom-or.ty

	* [r1214] topo/plotting/plot.py:
	  Added an hack so that a plot display the name from the
	  PlotTemplate instead of the name of the SheetView; it would need
	  more restructuring work to make sure this does not raise problems
	  in the future.

	* [r1213] topo/plotting/plotgroup.py:
	  Added space in the PlotTemplate's name so that the display is
	  nice when using them in the GUI.

2005-11-04  jbednar

	* [r1212] topo/base/simulator.py:
	  Fixed apparent serious bug: SimulatorEvents were storing a
	  reference to the data, not the actual data, which means that the
	  data they provide when the event is delivered might be stale (or
	  the opposite of stale? too fresh?). Now that the data is
	  deepcopy-ed, can remove the __copy__ routine, which is good,
	  because it was skipping copying of the fn field, which could have
	  been causing some recent problems involving switching back and
	  forth between pattern_present and s.run()

	* [r1211] examples/lissom.ty:
	  Minor cleanup

	* [r1210] topo/base/connectionfield.py,
	  topo/learningfns/basic.py,
	  topo/sheets/lissom.py:
	  Changed argument order for CFResponseFunctions and
	  CFLearningFunctions

	* [r1209] topo/sheets/cfsom.py:
	  Minor cleanup

	* [r1208] topo/base/connectionfield.py,
	  topo/base/utils.py,
	  topo/learningfns/basic.py,
	  topo/sheets/lissom.py:
	  Renamed arguments to CFLearningFunctions

2005-11-04  julienciroux

	* [r1207] topo/tk/plotpanel.py,
	  topo/tk/preferencemappanel.py,
	  topo/tk/projectionpanel.py,
	  topo/tk/unitweightspanel.py:
	  Changed all the PlotPanel's subclasses in the plots menu to
	  display the simulator time both at the top of the window and in
	  the label; got rid of the variable num_panel and of the number
	  that was printed at the top and was not incremented anyway

2005-11-04  jbednar

	* [r1206] external/Imaging-1.1.4jp.tgz:
	  Removed outdated library

	* [r1205] external/Makefile,
	  external/darwin,
	  external/dislin-8.2.linux.tgz,
	  tests/testdislinplot:
	  Removed DISLIN, at least for now, since we aren't using it

	* [r1204] external,
	  external/.cvsignore,
	  external/Makefile,
	  tests/__init__.py,
	  tests/testdislinplot.py,
	  topo/plotting/dislindriver.py,
	  topo/plotting/dislinplot.py:
	  Removed DISLIN, at least for now, since we aren't using it

	* [r1203] topo/tk/plotpanel.py:
	  Moved standard set of buttons to the top so that too-large plots
	  can always be reduced

2005-11-04  yfsit

	* [r1202] tests/testfeaturemap.py:
	  removed importing the unused _sinegrating_present that does not
	  exist.

	* [r1201] topo/base/connectionfield.py,
	  topo/base/projection.py,
	  topo/learningfns/basic.py,
	  topo/projections/kernelprojection.py,
	  topo/responsefns/basic.py,
	  topo/sheets/lissom.py:
	  reduced the complexity in the argument list of CFResponseFunction
	  and CFLearningFunction.

	* [r1200] topo/sheets/lissom.py:
	  Changed input_event() so that it does not depend on the name of
	  the projection to detect a new iteration.

2005-11-03  jbednar

	* [r1199] topo/analysis/featuremap.py:
	  Reorganized to allow duration to be specified

2005-11-03  ceball

	* [r1198] topo/base/patternfns.py:
	  Reverted definition of gaussian to match LISSOM (factor of 0.5 in
	  the exponential).

2005-11-03  julienciroux

	* [r1197] topo/tk/projectionpanel.py,
	  topo/tk/unitweightspanel.py:
	  Fixed the titles for the unitweightspanel and the projectionpanel
	  (added a , instead of a . and added the Region in the Unit
	  Weights title

2005-11-03  jbednar

	* [r1196] topo/tk/topoconsole.py:
	  Added note on possible thing to get working: window icons

2005-11-03  julienciroux

	* [r1195] topo/tk/topoconsole.py:
	  Got rid of 'Active Simulator=' in the title of the topographica
	  console

	* [r1194] topo/tk/projectionpanel.py:
	  Changed the title of the window for the projection panel: now
	  density is no more specified in the title, there is no period in
	  the middle and it fits in when opening the window.

	* [r1193] topo/tk/preferencemappanel.py:
	  Got rid of the period at the end of the title in the Preference
	  Map panel.

	* [r1192] topo/plotting/plotengine.py:
	  Commented out unused function; add commentary for helping future
	  cleaning up of the file.

	* [r1191] topo/tk/plotpanel.py:
	  Got rid of an unused comment

	* [r1190] topo/tk/cfsheetplotpanel.py,
	  topo/tk/inputparamspanel.py,
	  topo/tk/preferencemappanel.py,
	  topo/tk/projectionpanel.py,
	  topo/tk/unitweightspanel.py:
	  Changed the call to the PlotPanel constructor so that it is
	  consistent with the change made to plotpanel; also got rid of
	  unused and confusing default values.

	* [r1189] topo/tk/topoconsole.py:
	  Changed the call to PlotPanel (or one of its subclasses) so that
	  it does not rely on default values in the constructor but rather
	  on information contained in the PlotGroupTemplate. It was working
	  before only because the parameters were set?\004 to a default
	  value in each subclasses, but wouldn't work otherwise.

	* [r1188] topo/tk/plotpanel.py:
	  Cleaned up PlotPanel so that there is no need to pass any default
	  arguments (which was confusing); re-aranged the order of these
	  arguments; added documentation; added slight change so that to
	  reach consistency between all subclasses of Plo?\004tPanel.
	  Modified the call to PlotPanel _init_ in BasicPlotPanel.

2005-11-03  ceball

	* [r1187] topo/base/projection.py,
	  topo/sheets/lissom.py:
	  Moved projections() from LISSOM to ProjectionSheet.

	* [r1186] topo/base/patternfns.py:
	  Corrected two syntax mistakes introduced by accident. Added
	  hackalert about use of the word 'ellipse'

	* [r1185] examples/lissom.ty,
	  topo/sheets/lissom.py:
	  Updated lissom.ty to use LISSOM.projections() method to access
	  projections (for changing projection learning rates and bounds),
	  rather than LISSOM.change_learning_rate() and .change_bounds().
	  Removed change_learning_rate() and change_bounds() from LISSOM.
	  LISSOM.projections() will be moved to projections.py.

2005-11-03  jbednar

	* [r1184] topo/base/connectionfield.py:
	  Removed illegal use of topo.learningfns

2005-11-03  ceball

	* [r1183] examples/lissom.ty:
	  Removed stray line I left by mistake.

	* [r1182] examples/lissom.ty:
	  Added hackalert detailing changes to make. I didn't make them
	  because I know this file is currently being edited and the
	  changes will clash.

	* [r1181] topo/sheets/lissom.py:
	  Created a function projections() that returns a dictionary
	  {projection.name: projection}. Removed lateral_projections() and
	  afferent_projections(). Added hackalert to indicate that
	  change_learning_rate() and change_bounds() should be removed when
	  lissom.ty is updated.

	* [r1180] topo/base/patternfns.py:
	  Made __elipse() be a public function; updated other functions
	  accordingly and changed some ring() and disk() internal variable
	  names.

2005-11-03  jbednar

	* [r1179] topo/sheets/lissom.py:
	  Added alert and removed apparently redundant code

2005-11-03  ceball

	* [r1178] topo/tk/topoconsole.py:
	  Added another note to myself for saving and loading.

	* [r1177] topo/tk/topoconsole.py:
	  Added further notes to myself for saving and loading.

2005-11-03  jdepaula

	* [r1176] topo/tk/plotpanel.py,
	  topo/tk/projectionpanel.py,
	  topo/tk/unitweightspanel.py:
	  Text fields now update when entered.

2005-11-03  yfsit

	* [r1175] topo/base/connectionfield.py,
	  topo/base/projection.py,
	  topo/sheets/lissom.py:
	  - Changed pre_sleep() in lissom.py such that the last iteration
	  is a pure learning phase without computing the new activity.
	  - pre_sleep() in lissom.py now calls activate(), which is a
	  method in the superclass ProjectionSheet.
	  - learn() moved into CFSheet.

2005-11-03  jbednar

	* [r1174] topo/tk/preferencemappanel.py:
	  Added label for update command widget

	* [r1173] Makefile:
	  Made docs depend on all Python files

	* [r1172] topo/tk/inputparamspanel.py:
	  Clarified documentation

2005-11-02  jbednar

	* [r1171] topo/tk/plotpanel.py:
	  Fixed comment

	* [r1170] topo/tk/topoconsole.py:
	  Moved BasicPlotPanel to plotpanel.py

	* [r1169] tests/tk/testactivitypanel.py,
	  topo/tk/basicplotpanel.py,
	  topo/tk/plotpanel.py:
	  Moved BasicPlotPanel to plotpanel.py

	* [r1168] topo/tk/preferencemappanel.py:
	  Cleaned up comments and removed unused items

	* [r1167] topo/outputfns/basic.py:
	  Added alerts and cleaned up documentation. Changed clip to
	  clip_in_place

2005-11-02  jdepaula

	* [r1166] topo/tk/cfsheetplotpanel.py,
	  topo/tk/plotpanel.py,
	  topo/tk/projectionpanel.py:
	  Change so widgets refresh independent of auto-refresh.

	* [r1165] topo/tk/projectionpanel.py:
	  Removed MakeStaticFunction import

	* [r1164] topo/tk/inputparamspanel.py,
	  topo/tk/plotpanel.py,
	  topo/tk/projectionpanel.py,
	  topo/tk/unitweightspanel.py:
	  Changed MakeStaticFunction to the @staticmethod operator.

	* [r1163] topo/base/utils.py:
	  Removed MakeStaticFunction. Found the @staticmethod operator

	* [r1162] topo/tk/plotpanel.py:
	  Oversight, need to check height as well as width for canvas
	  resizing

2005-11-02  ceball

	* [r1161] topo/base/patternfns.py:
	  Forgot to save all my changes last time.

2005-11-02  julienciroux

	* [r1160] tests/testoutputfnsbasic.py,
	  topo/outputfns/basic.py:
	  Transformed the output functions so that they don't create
	  intermediate copies of the array; rewrote a clip function for
	  this purpose; left the return statement so that I did not have to
	  change all the call to output functions in the rest ?\004of the
	  code. Modified the test file so that it calls procedures instead
	  of function.

	* [r1159] topo/tk/preferencemappanel.py:
	  Got rid of unused comments; added some comments about
	  JABHACKALERTs that I believe are obsolete.

2005-11-02  ceball

	* [r1158] topo/base/patterngenerator.py:
	  Removed comment after renaming user-visible variables.

	* [r1157] examples/gui_example.py,
	  tests/testpatternpresent.py,
	  tests/testplotfilesaver.py,
	  tests/tk/testplotpanel.py:
	  Changed LineGenerator's 'width' parameter to 'thickness'.

	* [r1156] topo/patterns/basic.py:
	  Changed disk() and ring() to be elliptical, so changed the
	  parameters of DiskGenerator and RingGenerator to match (e.g. they
	  have orientation now, radius has been replaced with height and
	  width... Changed LineGenerator's 'width' parameter to 'thickness'
	  (sorry this is in the same commit).

	* [r1155] topo/base/patternfns.py:
	  Changed disk() and ring() to be elliptical.

2005-11-02  julienciroux

	* [r1154] topo/base/simulator.py:
	  Removed the call to start() in the run() method: an
	  EventProcessor is now start()ed when it is add()ed to the
	  simulator. Merged _continue() into run() since run() only called
	  continue after no longer starting the EventProcessors.

2005-11-02  jbednar

	* [r1153] examples/lissom.ty:
	  Restored training of one iteration, due to strange bug with the
	  event queue that's being addressed separately

	* [r1152] topo/projections/kernelprojection.py:
	  Removed strange Constant response_fns

	* [r1151] topo/tk/inputparamspanel.py:
	  Trivial reorganization for clarity

2005-11-02  ceball

	* [r1150] topo/plotting/plotgroup.py:
	  Activity is now colored by OrientationPreference, if it has been
	  measured. This is ok while we're only talking about orientation
	  maps.

2005-11-02  jbednar

	* [r1149] topo/sheets/lissom.py:
	  Added ALERTs

	* [r1148] topo/tk/projectionpanel.py:
	  Increased padding slightly

2005-11-02  jdepaula

	* [r1147] topo/tk/topoconsole.py:
	  Added test before trying to open a panel.

	* [r1146] topo/tk/inputparamspanel.py,
	  topo/tk/plotpanel.py,
	  topo/tk/projectionpanel.py,
	  topo/tk/unitweightspanel.py:
	  Added valid_context()

	* [r1145] topo/base/utils.py:
	  Added a wrapper that allows Static class functions.

	* [r1144] topo/tk/projectionpanel.py:
	  Reduced space between projection plots.

	* [r1143] topo/tk/plotpanel.py:
	  Patch so that if any plot size changes, the canvases are
	  recreated.

2005-11-02  yfsit

	* [r1142] examples/lissom.ty,
	  topo/projections/kernelprojection.py,
	  topo/sheets/lissom.py:
	  LISSOM does not use the pointer implementation and so does
	  lissom.ty.
	  A new subclass, LISSOMPointer, is added which uses the pointer
	  implementation.

2005-11-01  julienciroux

	* [r1141] topo/analysis/featuremap.py:
	  Modified the measure_or_pref function so that we can pass some
	  parameter such as: scale, offset, freq of the SineGrating used
	  for measuring the map; user_function which by default is
	  '_sinegrating_present' (but gives the possibility to als?\004o
	  write _gaussian_present and change it when calling
	  measure_or_pref); display which enables to see the patterns
	  presented during the map measurement (display=True, False by
	  default); apply_output_fn that enables to disable the output
	  function (True by d?\004efault). All this parameters can now be
	  set from the command line in the Orientation Preference panel.

2005-11-01  jbednar

	* [r1140] topo/base/projection.py,
	  topo/commands/basic.py,
	  topo/sheets/lissom.py:
	  Added apply_output_fn option to ProjectionSheet, for use with
	  e.g. pattern_present and measure_or_pref

2005-11-01  jdepaula

	* [r1139] topo/base/gendocs.py:
	  Made more powerful so that source code can be in subdirectories.

	* [r1138] Makefile:
	  Updated to use new gendocs.py revision that handles directories
	  in source code.

2005-10-31  julienciroux

	* [r1137] topo/tk/preferencemappanel.py:
	  Changed PreferenceMapPanel so that it works by passing the name
	  of a group template and all the parameter are initialized by
	  looking into the specified template; eventually we would like to
	  have the same file for other panel types

	* [r1136] topo/plotting/plotgroup.py:
	  Added a command parameter to the PlotGroupTemplates; this is the
	  default command to execute when opening or refreshing the panel
	  corresponding to this template

	* [r1135] topo/analysis/featuremap.py:
	  Added some debugging lines that enable to display the pattern
	  that have been presented when measuring the map; they are
	  currently commented out

	* [r1134] topo/tk/topoconsole.py:
	  Changed the command() method in PlotsMenuEntry so that it returns
	  a panel instead of nothing

2005-10-30  ceball

	* [r1133] topo/base/patternfns.py:
	  Simplified functions involving exp() after switching to
	  Numeric-24.0. The functions should be as robust as they were in
	  the previous version but the code is much clearer.

	* [r1132] topo/base/utils.py:
	  Clarified documentation string in exp().

	* [r1131] topo/base/utils.py:
	  Added an alternative to Numeric's exp() function; this one still
	  uses Numeric's, but works for any magnitude of argument.

	* [r1130] external,
	  external/.cvsignore,
	  external/Makefile,
	  external/Numeric-23.0.tgz,
	  external/Numeric-24.0.tar.gz:
	  Substituted Numeric-23.0.tgz with Numeric-24.0.tar.gz.
	  Numeric-24.0 handles nans and infs properly in arrays (rather
	  than raising errors).

	* [r1129] topo/patterns/basic.py:
	  Changed 'fringe' to 'smoothing'

2005-10-30  yfsit

	* [r1128] topo/base/connectionfield.py,
	  topo/learningfns/basic.py,
	  topo/projections/kernelprojection.py,
	  topo/responsefns/basic.py,
	  topo/sheets/lissom.py:
	  minor performance enhancement in CFDotProductP. Learning function
	  DivisiveHebbianP uses pointers to get the weight array instead of
	  using
	  C API.

2005-10-30  ceball

	* [r1127] topo/patterns/basic.py:
	  Renamed gaussian_width to fringe (I bet it gets changed before
	  you even read this). Changed names of parameters for ring to try
	  to make it match disk more obviously. Altered some default
	  parameter values.

	* [r1126] topo/base/patternfns.py:
	  Main change is to make all functions involving exp() behave more
	  as would be expected by a user, although the changes do not
	  affect current use of patternfns (e.g. as used by various
	  PatternGenerators); these changes are hacks. Corrected mistake in
	  previous commit made line() have same hack as ring() and disk().
	  Redefined gaussian fall-off to be exp(-0.5*(x/sigma)^2) rather
	  than exp(-(x/sigma)^2) (can easily be reverted - the change was
	  made for comparison). Slightly altered ring() to try to make it
	  match disk() more obviously.

2005-10-29  ceball

	* [r1125] topo/base/utils.py:
	  Added comment about how inf is created in here as 1/0 rather than
	  e.g. float('inf').

	* [r1124] topo/base/patternfns.py:
	  Fixed bug in Disk and Ring where there could be an attempt to
	  work with 0*inf. The fix is a hack, though. This file might be
	  better for using e.g. SciPy.

	* [r1123] topo/patterns/basic.py:
	  Renamed FuzzyRing to Ring and fuzzy_ring to ring; updated
	  comments for Disk to reflect earlier change from FuzzyDisk

	* [r1122] topo/base/patternfns.py:
	  Renamed FuzzyRing to Ring and fuzzy_ring to ring

	* [r1121] topo/base/patternfns.py,
	  topo/patterns/basic.py:
	  Renamed FuzzyDisk to Disk and fuzzy_disk() to disk().

	* [r1120] examples/gui_example.py,
	  tests/testpatternpresent.py,
	  tests/testplotfilesaver.py,
	  tests/tk/testplotpanel.py,
	  topo/base/patternfns.py,
	  topo/patterns/basic.py:
	  Changed name of FuzzyLine to Line; fuzzy_line() changed to line()

	* [r1119] topo/plotting/plotgroup.py:
	  Renamed user-visible instances of the variable 'theta' to
	  'orientation'

	* [r1118] tests/testcfsom.py,
	  tests/testfeaturemap.py,
	  tests/testpatternpresent.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/tk/testactivitypanel.py,
	  tests/tk/testplotpanel.py:
	  Renamed user-visible instances of the variable 'theta' to
	  'orientation'

	* [r1117] topo/analysis/featuremap.py:
	  Now at least one frequency, phase, and orientation must be
	  specified for measuring the map (instead of 'not zero' of them).

	* [r1116] examples/cfsom_example.py,
	  examples/gui_example.py,
	  examples/lissom.ty,
	  topo/analysis/featuremap.py,
	  topo/base/patterngenerator.py,
	  topo/patterns/basic.py,
	  topo/patterns/random.py:
	  Renamed user-visible instances of the variable 'theta' to
	  'orientation'

	* [r1115] topo/tk/inputparamspanel.py:
	  The function use_for_learning() (and so the button 'Use for
	  future learning') now works as it did originally; the
	  JABHACKALERT still applies.

2005-10-29  jbednar

	* [r1114] CONVENTIONS:
	  Minor clarification

	* [r1113] topo/base/sheet.py:
	  Clarified previous ALERT

	* [r1112] README.txt:
	  Clarified what is not yet done

	* [r1111] MILESTONES:
	  Updated to reflect recent progress

2005-10-27  julienciroux

	* [r1110] topo/analysis/featuremap.py:
	  Get rid of an unused commentary

2005-10-27  ceball

	* [r1109] topo/base/patternfns.py,
	  topo/base/patterngenerator.py,
	  topo/patterns/basic.py:
	  Made theta be a hidden parameter for fuzzy disk and ring since
	  they are currently symmetric; removed variable y from fuzzyline()
	  since it's not used; added comment about problem with fuzzyline.

2005-10-27  julienciroux

	* [r1108] topo/analysis/featuremap.py:
	  Added a raise error when trying to use 0 feature value in
	  measure_or_pref; added some debugging statement in an attempt to
	  display the pattern presented when measuring the map

2005-10-27  ceball

	* [r1107] topo/base/patterngenerator.py:
	  Removed comment about scale-0 error; the problem wasn't here.

2005-10-27  julienciroux

	* [r1106] topo/base/utils.py:
	  Changed the norm function so that it works with the abs of the
	  elements; necessary in the case of the Lp norm

2005-10-27  ceball

	* [r1105] topo/base/patternfns.py:
	  Temporary fix to avoid 0/0 error.
	  Numeric.where(test,pass_expression,fail_expression) calculates
	  both pass_expression and fail_expression no matter what the
	  result of test. test cannot therefore be used, for instance, to
	  avoid divide-by-zero errors.

2005-10-26  ceball

	* [r1104] topo/base/patternfns.py:
	  Explicitly used Numeric's divide function to avoid divide-by-zero
	  errors.

2005-10-26  jbednar

	* [r1103] tests/tk/testtopoconsole.py:
	  Fixed broken tests, caused by eliminating topoconsole's copy of
	  the simulator

2005-10-26  julienciroux

	* [r1102] tests/testoutputfnsbasic.py:
	  Finished to write the test file for the output functions defined
	  in topo/outputfns/basic.py

2005-10-26  jbednar

	* [r1101] README.txt:
	  Updated to match current state of the code

2005-10-26  ceball

	* [r1100] topo/base/patternfns.py,
	  topo/base/utils.py,
	  topo/plotting/plotgroup.py,
	  topo/sheets/cfsom.py:
	  Changed randomly worded notes about hacks to CEBHACKALERTs so JAB
	  can find them when searching for 'ALERT'

	* [r1099] topo/plotting/plotgroup.py:
	  Hack so that when scale is zero the GUI does not cause an
	  exception. Presentation of scale-0 patterns to the network works.

2005-10-26  jbednar

	* [r1098] topo/tk/preferencemappanel.py:
	  Cleaned up comments

	* [r1097] topo/plotting/plotgroup.py,
	  topo/tk/topoconsole.py:
	  Removed unused plot

2005-10-26  ceball

	* [r1096] topo/base/parameter.py:
	  Added comment about pickling.

	* [r1095] topo/plotting/plot.py:
	  Changed some warnings and messages to debugs so that users don't
	  see warnings every time they measure orientation maps (warnings
	  about no plots in the retina)

2005-10-26  julienciroux

	* [r1094] topo/plotting/plotgroup.py:
	  Added the PlotGroupTemplate for Preference Map

	* [r1093] topo/tk/preferencemappanel.py:
	  Removed Ocular Preference from the scrolled list; made the
	  associated measure_or_pref() command executed when entering or
	  refreshing the Orientation Preference plot

2005-10-26  ceball

	* [r1092] topo/tk/inputparamspanel.py:
	  Added note that 'use for future learning' button doesn't work
	  (and didn't before these most recent pickling modifications.

	* [r1091] topo/tk/topoconsole.py:
	  Added menu items to allow loading and saving a snapshot.
	  TopoConsole no longer stores the active simulator itself, it
	  instead gets it from the registry.

	* [r1090] topo/base/boundingregion.py,
	  topo/sheets/cfsom.py:
	  Basic support for pickling added; might not be required but as it
	  is a snapshot of the simulator's state can be saved and then
	  reloaded if topographica is started with the example in both
	  cases. Some of the changes will not be permananent ?\004but these
	  are noted.

2005-10-26  jbednar

	* [r1089] topo/tk/topoconsole.py:
	  Declare that orientation maps should use PreferenceMapPanel

2005-10-26  julienciroux

	* [r1088] topo/tk/preferencemappanel.py:
	  Changed so that in the GUI preference map menu, there is actually
	  the preference maps instead of the activity; works only for
	  Orientation Preference so far

	* [r1087] tests/testmeasurefeaturemap.py,
	  topo/analysis/featuremap.py,
	  topo/base/featuremap.py,
	  topo/base/measurefeaturemap.py:
	  Created new file topo/analysis/featuremap.py from
	  topo/base/featuremap.py and topo/base/measurefeaturemap.py

	* [r1086] tests/testfeaturemap.py:
	  Merged tests for featuremap and measurefeaturemap

	* [r1085] topo/base/measurefeaturemap.py:
	  Added the command measure_or_pref() for measuring an orientation
	  map; improved the user function sinegrating_present and made it
	  private

	* [r1084] topo/outputfns/basic.py:
	  Improved some comments

2005-10-26  jbednar

	* [r1083] topo/__init__.py:
	  Added analysis directory

	* [r1082] topo/analysis,
	  topo/analysis/.cvsignore,
	  topo/analysis/__init__.py:
	  Initial version

2005-10-25  ceball

	* [r1081] topo/base/measurefeaturemap.py:
	  Made measuring maps clearer (changed no functionality). Still
	  have to move sinegrating_present out

2005-10-25  julienciroux

	* [r1080] tests/testoutputfnsbasic.py:
	  First version of the test file for the output functions in
	  topo/outputfns/basic.py

	* [r1079] tests/testfeaturemap.py:
	  First complete version of the test file for featuremap; need to
	  clarify the definition of selectivity to actually finishing the
	  test file

2005-10-25  jbednar

	* [r1078] topo/base/parameter.py:
	  Removed pickle support; doesn't seem to work yet

	* [r1077] topo/base/boundingregion.py:
	  Changed AARectangle to new-style class so that __slots__ is
	  meaningful; not necessarily completed. Made slots be weakly
	  private instead of fully private; this appears (?) to be
	  necessary for deepcopy

	* [r1076] topo/base/parameter.py:
	  Changed indentation to match 4-space convention used elsewhere

	* [r1075] topo/base/parameter.py:
	  Removed unused code saving the __dict__ for pickling, because a
	  Parameter has no __dict__

	* [r1074] tests/testsimulator.py,
	  topo/base/simulator.py:
	  Changed Simulator.Event to non-nested SimulatorEvent to avoid
	  problems with pickle

	* [r1073] examples/lissom.ty:
	  Added running of one iteration, to ensure that it is tested

	* [r1072] topo/base/parameter.py:
	  Added pickle support from Jeff and Chris

	* [r1071] topo/base/topoobject.py,
	  topo/base/utils.py:
	  Moved classlist and descendents to utils.py for all to use

	* [r1070] tests/testpatternpresent.py:
	  Moved pattern_present to topo.commands

	* [r1069] external/fixedpoint.diff:
	  Added pickling support

	* [r1068] external/Makefile:
	  Made FixedPoint update more cleanly

	* [r1067] topo/commands/basic.py:
	  Made pattern_present not modify the simulation clock

	* [r1066] topo/base/connectionfield.py:
	  Trivial documentation change

2005-10-24  julienciroux

	* [r1065] topo/base/measurefeaturemap.py,
	  topo/base/utils.py:
	  Moved functions cross_product and frange from
	  topo/base/measurefeaturemap.py to topo/base/utils.py; changed
	  MeasureFeatureMap so that it works with a user-defined function
	  rather than a string command; get rid of debugging statements and
	  u?\004seless commentaries in measurefeaturemap

2005-10-24  jbednar

	* [r1064] topo/base/measurefeaturemap.py,
	  topo/commands/basic.py,
	  topo/patterns/patternpresent.py,
	  topo/tk/inputparamspanel.py:
	  Moved pattern_present to commands/ directory

	* [r1063] topo/__init__.py:
	  Added commands directory to default imports

	* [r1062] topo/commands,
	  topo/commands/.cvsignore,
	  topo/commands/__init__.py:
	  Initial version

	* [r1061] topo/tk/parametersframe.py:
	  Removed stray print statements

	* [r1060] topo/patterns/patternpresent.py,
	  topo/tk/inputparamspanel.py:
	  Made pattern_present save the input_generator by default

	* [r1059] topo/base/measurefeaturemap.py:
	  Minor cleanup

	* [r1058] topo/tk/inputparamspanel.py:
	  Fixed bug in previous checkin

	* [r1057] topo/base/measurefeaturemap.py,
	  topo/patterns/patternpresent.py,
	  topo/sheets/generatorsheet.py,
	  topo/tk/inputparamspanel.py:
	  Renamed commands to save and restore input_generators. Removed
	  _register_inputsheet_patterns; didn't seem to have any reason to
	  be a separate function

2005-10-24  julienciroux

	* [r1056] topo/base/distribution.py,
	  topo/base/featuremap.py:
	  Modified the JABHACKALERT commentaries about the use of __add__
	  with the Numeric arrays

2005-10-24  jbednar

	* [r1055] examples/lissom.ty,
	  topo/base/connectionfield.py,
	  topo/projections/kernelprojection.py,
	  topo/sheets/lissom.py:
	  Made response_fn be declared Constant when it cannot be modified.
	  Changed name of reduce_cfsize to change_bounds. Added
	  change_density stub for future implementation.

	* [r1054] topo/learningfns/basic.py:
	  Simplified Constant declaration; it was confusing to say default

	* [r1053] topo/base/parameter.py:
	  Trivial whitespace cleanup

	* [r1052] CONVENTIONS:
	  Minor rewording

2005-10-24  julienciroux

	* [r1051] tests/testfeaturemap.py,
	  topo/base/featuremap.py:
	  Changed FeatureMap to work with a sheet instead of the activity
	  matrix dimension; changed the test file accordingly

2005-10-24  jbednar

	* [r1050] topo/base/simulator.py:
	  Removed unused sched.scheduler import and variable to make pickle
	  work

2005-10-24  yfsit

	* [r1049] examples/lissom.ty,
	  topo/base/connectionfield.py,
	  topo/base/simulator.py,
	  topo/projections/kernelprojection.py,
	  topo/responsefns/basic.py:
	  An enhanced implementation of CFDotProduct, called CFDotProductP,
	  that uses arrays of pointers to access the weights instead of
	  through the C API. This response function should only be used by
	  KernelPointerProjection, which is a new subclass of
	  KernelProjection that contains the extra data structure to store
	  the pointers array.

2005-10-24  ceball

	* [r1048] topo/base/patterngenerator.py:
	  Added a comment to note error that occurs when scale is set to 0.

	* [r1047] topo/patterns/patternpresent.py:
	  Removed accidental tab in the previous update.

	* [r1046] topo/tk/inputparamspanel.py:
	  Updated to work with altered pattern_present

	* [r1045] topo/base/measurefeaturemap.py:
	  Correction for when there are multiple sheets to measure maps on;
	  updates to some comments; changed to work with altered
	  pattern_present

	* [r1044] topo/patterns/patternpresent.py:
	  Changed pattern_present so that saving/restoring previous input
	  patterns is done with a separate function; changed
	  pattern_present so that presentations where learning==False no
	  longer use a copy of the simulator's event list - this might be
	  the wrong thing to have done.

	* [r1043] topo/sheets/generatorsheet.py:
	  Added a stack onto which the current input_generator can be
	  placed, and from which previous input_generators can be restored
	  .

2005-10-22  jbednar

	* [r1042] topo/projections/kernelprojection.py:
	  Fixed major bug: reduce_cfsize() was having no effect because
	  three lines were omitted when it was moved from topo/cfsheet.py

2005-10-21  jbednar

	* [r1041] topo/base/measurefeaturemap.py:
	  Cleaned up; removed useless loop; changed to use SineGrating;
	  added debugging statements

	* [r1040] topo/tk/parametersframe.py:
	  Removed debugging prints

	* [r1039] topo/base/measurefeaturemap.py:
	  Removed outdated hack

	* [r1038] topo/plotting/plotgroup.py:
	  Added selectivity and preference/selectivity plots for
	  OrientationPreference

2005-10-21  julienciroux

	* [r1037] topo/base/measurefeaturemap.py:
	  Normalized the preference map according to the feature range

2005-10-21  jbednar

	* [r1036] topo/base/sheet.py:
	  Fixed default density

2005-10-21  julienciroux

	* [r1035] tests/testmeasurefeaturemap.py:
	  Changed delay to be 0.5; added debugging statement

2005-10-21  jbednar

	* [r1034] topo/tk/plotpanel.py:
	  Added JABHACKALERT

2005-10-21  ceball

	* [r1033] tests/testdistribution.py,
	  tests/testfeaturemap.py,
	  topo/base/distribution.py:
	  Distribution now wraps vector directions back into the axis
	  range. Directions used to come back as principal values from
	  arctan2 - now any tests that were expecting the principal value
	  rather than one within the axis range would fail, so they were
	  corrected.

2005-10-21  jbednar

	* [r1032] topo/plotting/plot.py,
	  topo/plotting/plotgroup.py:
	  Made it legal for a plot to be empty for some (or even all)
	  sheets

	* [r1031] topo/plotting/plot.py:
	  Fixed bogus behavior when no strength or no color was supplied;
	  was preventing orientation maps from being visible

	* [r1030] topo/base/topoobject.py:
	  Added Jeff's changes to help pickle()

	* [r1029] topo/base/parameter.py:
	  Added Jeff's changes that should help pickling

2005-10-21  julienciroux

	* [r1028] examples/cfsom_example.py:
	  Corrected the mistake introduced in the last version.

	* [r1027] examples/cfsom_example.py:
	  Changed FuzzyLineGenerator to GaussianGenerator for training

2005-10-21  jbednar

	* [r1026] examples/cfsom_example.py:
	  Made Retina names match between object and __main__, to avoid
	  confusion. Changed delay to 0.5 so that the behavior in the GUI
	  is more reasonable

	* [r1025] CONVENTIONS:
	  Added section on docstrings and comments

2005-10-21  ceball

	* [r1024] topo/base/patterngenerator.py:
	  Removed JABHACKALERT that I forgot to take out when I fixed it
	  yesterday.

2005-10-21  jbednar

	* [r1023] topo/base/patterngenerator.py,
	  topo/patterns/random.py:
	  Simplified Constant and Random PatternGenerators

	* [r1022] topo/tk/parametersframe.py:
	  Added ALERTs. Removed unused code.

	* [r1021] topo/patterns/random.py,
	  topo/tk/propertiesframe.py:
	  Added trivial comment

	* [r1020] topo/patterns/basic.py:
	  Made all parameters go through params() to allow user-specified
	  x,y

	* [r1019] topo/base/patterngenerator.py:
	  Added function abstract base class to emphasize what we expect to
	  be implemented

	* [r1018] examples/cfsom_example.py,
	  examples/gui_example.py,
	  examples/lissom.ty:
	  Made default bounds match those in other files

2005-10-20  jbednar

	* [r1017] examples/cfsom_example.py,
	  examples/gui_example.py,
	  examples/lissom.ty:
	  Made use DynamicNumber so that the GUI works again

	* [r1016] examples/cfsom_example.py:
	  Changed to use a DynamicNumber so that the GUI still works

	* [r1015] topo/base/parameter.py:
	  Added DynamicParameter class

	* [r1014] topo/plotting/plot.py:
	  Changed missing SheetView into a warning instead of a crash

	* [r1013] examples/gui_example.py:
	  Made __main__ name match the one inside the Retinas

2005-10-20  julienciroux

	* [r1012] topo/base/measurefeaturemap.py:
	  Added the SheetView object correctly; temporarily including
	  GeneratorSheets in the preference and selectivity map

2005-10-20  ceball

	* [r1011] topo/tk/parametersframe.py:
	  made the list of parameters be sorted alphabetically

	* [r1010] topo/base/patterngenerator.py,
	  topo/patterns/basic.py,
	  topo/patterns/random.py:
	  Added scale and offset; moved definitions of x and y from
	  individual PatternGenerator classes into the PatternGenerator
	  class

	* [r1009] topo/base/measurefeaturemap.py:
	  Corrected presentation loop...making available to Julien

	* [r1008] topo/base/measurefeaturemap.py:
	  The patterns are now presented as expected rather than not at
	  all. "Lord only knows what idiot coded it that way!"

2005-10-20  jdepaula

	* [r1007] topo/tk/parametersframe.py:
	  Sliders created based upon the Parameters in the
	  PatternGenerator! Problem with Dynamics in Fuzzy Line

	* [r1006] topo/base/patterngenerator.py:
	  theta is defined for everyone. It needs to be a Number to have
	  soft bounds.

2005-10-19  ceball

	* [r1005] tests/testdistribution.py:
	  Added code to allow test to be run independently of runtests
	  script

	* [r1004] tests/testmeasurefeaturemap.py,
	  topo/base/measurefeaturemap.py:
	  Continued writing this file. At this stage, with the
	  default_input command, the preference and selectivity maps are
	  added to the relevant Sheets for whatever features are specified.

2005-10-19  jbednar

	* [r1003] topo/patterns/patternpresent.py,
	  topo/plotting/plotengine.py,
	  topo/tk/inputparamspanel.py:
	  Removed unnecessary generator_eps() command

	* [r1002] tests/testfeaturemap.py,
	  topo/base/featuremap.py:
	  Assumed that keep_peak will always be true. Cleaned up argument
	  lists, documentation, and comments.

	* [r1001] CONVENTIONS:
	  Added section with suggestions for getting started in Python

2005-10-19  ceball

	* [r1000] tests/testmeasurefeaturemap.py:
	  Initial, incomplete version (not yet added to list of tests to
	  run automatically)

	* [r999] tests/testdistribution.py:
	  Corrected some uses of Histogram (changed to Distribution)

2005-10-19  yfsit

	* [r998] topo/base/projection.py:
	  ProjectionSheet inserts a connection into in_projection in
	  connection_from() only if the connection is a Projection.

	* [r997] topo/responsefns/basic.py:
	  A further optimized version of CFDotProduct().

2005-10-19  jdepaula

	* [r996] topo/tk/inputparamspanel.py,
	  topo/tk/parametersframe.py:
	  Moved create_pattern from inputparamspanel.py

	* [r995] topo/tk/topoconsole.py:
	  Now allow multiple InputParamPanels

	* [r994] topo/tk/parametersframe.py:
	  Added refresh function

	* [r993] topo/tk/inputparamspanel.py:
	  Moved learning state saving to within pattern_present. Removed
	  specialized window destroy function hook. Changed
	  _create_inputsheet_pattern to not use self.in_ep_dict global in
	  preparation for moving

	* [r992] topo/patterns/patternpresent.py:
	  Added a learning option to pattern_present. Should be replaced
	  with a function call that does more checking.

2005-10-18  jdepaula

	* [r991] topo/tk/inputparamspanel.py:
	  Removed _learning_toggle

	* [r990] topo/tk/parametersframe.py:
	  Changed class name to ParametersFrame

	* [r989] topo/tk/inputparamspanel.py:
	  self.learning can now start in on or off mode

	* [r988] topo/tk/parametersframe.py:
	  Renamed from parameterframe.py

	* [r987] topo/tk/parameterframe.py:
	  Moved to parametersframe.py

2005-10-18  jbednar

	* [r986] topo/tk/__init__.py:
	  Removed long list of unneeded imports

	* [r985] topo/base/projection.py:
	  Removed comments that seemed like they were in the wrong class
	  now

	* [r984] README.txt:
	  Added help for CVS

2005-10-18  jdepaula

	* [r983] topo/tk/inputparamspanel.py:
	  Moved out relevant_parameters(), refresh_sliders(), and
	  reset_to_defaults()

	* [r982] topo/tk/parameterframe.py:
	  Added relevant_parameters(), refresh_sliders(), and
	  reset_to_defaults()

	* [r981] topo/tk/inputparamspanel.py:
	  Moved tparams to ParameterFrame, and moved add_slider too.

	* [r980] topo/tk/propertiesframe.py:
	  Uncommented gridding code.

	* [r979] topo/tk/__init__.py:
	  Added parameterframe.py

	* [r978] topo/tk/parameterframe.py:
	  Moving Parameter adjustment code from inputparamspanel.py

2005-10-18  ceball

	* [r977] topo/base/featuremap.py,
	  topo/base/measurefeaturemap.py:
	  Minor addition of comments

	* [r976] topo/base/measurefeaturemap.py:
	  Updated some comments

2005-10-18  julienciroux

	* [r975] topo/base/measuredimensionmap.py,
	  topo/base/measurefeaturemap.py:
	  renamed measuredimensionmap to measurefeaturemap; continued
	  implementation of MeasureFeatureMap in that file

2005-10-18  yfsit

	* [r974] examples/cfsom_example.py,
	  examples/gui_example.py,
	  examples/lissom.ty,
	  tests/testcfsom.py,
	  tests/testpatternpresent.py,
	  tests/testplotfilesaver.py,
	  topo/base/connectionfield.py,
	  topo/base/projection.py,
	  topo/base/simulator.py,
	  topo/plotting/plotengine.py,
	  topo/plotting/plotgroup.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/lissom.py,
	  topo/tk/projectionpanel.py:
	  EventProcessor now has 2 separate data stuctures (in_connections
	  and out_connections) to store the incoming and outgoing
	  connections.
	  
	  ProjectinSheet, a subclass of EventProcessor, has it own storage
	  for incoming connection (in_projections) that are indexed by the
	  source name of the projection to optimize projection lookup.

2005-10-17  ceball

	* [r973] topo/base/measuredimensionmap.py:
	  initial and incomplete version, probably with the wrong name.
	  Just here so that Julien and Chris can both work on it

	* [r972] topo/base/featuremap.py:
	  Changed type of preference matrices to Float

	* [r971] tests/testdistribution.py:
	  values() and counts() no longer return bins as well as
	  values/counts; added tests for selectivity

	* [r970] topo/base/distribution.py:
	  Attended to some JABALERTS - mainly values() and counts() return
	  no longer return bins as well.

2005-10-17  jbednar

	* [r969] tests/testsimulator.py,
	  topo/eps/basic.py,
	  topo/eps/scalarep.py:
	  Moved scalarep.py to basic.py to match other library directories

	* [r968] CONVENTIONS:
	  Added section on object-oriented design and a few other notes

2005-10-16  jbednar

	* [r967] topo/base/connectionfield.py,
	  topo/base/projection.py:
	  Corrected comments to say projection or connection as appropriate

2005-10-15  ceball

	* [r966] examples/gui_example.py,
	  examples/image_example.py,
	  tests/testcfsom.py,
	  tests/testpatternpresent.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/testsheet.py,
	  tests/tk/testactivitypanel.py,
	  tests/tk/testplotpanel.py,
	  tests/tk/testtopoconsole.py,
	  topo/base/boundingregion.py,
	  topo/base/connectionfield.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheetview.py,
	  topo/base/simulator.py,
	  topo/learningfns/basic.py,
	  topo/outputfns/basic.py,
	  topo/patterns/patternpresent.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/histogram.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotengine.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py,
	  topo/tk/__init__.py,
	  topo/tk/plotpanel.py,
	  topo/tk/topoconsole.py:
	  Renamed topo.base.object to topo.base.topoobject, so updated
	  imports etc.

	* [r965] topo/base/object.py,
	  topo/base/topoobject.py:
	  Renamed object.py to topoobject.py

	* [r964] tests/__init__.py:
	  Added testfeaturemap to list of tests

	* [r963] tests/testfeaturemap.py:
	  Corrected some of the tests

2005-10-15  jbednar

	* [r962] topo/base/connectionfield.py,
	  topo/base/learningrules.py,
	  topo/base/utils.py:
	  Moved divisive_normalization to utils

	* [r961] topo/sheets/cfsom.py:
	  Trivial comment fix

	* [r960] topo/sheets/lissom.py:
	  Changed to use CFLearningFunction classes

	* [r959] topo/base/connectionfield.py,
	  topo/learningfns/basic.py:
	  Added CFLearningFunction classes

	* [r958] topo/sheets/lissom.py:
	  Added ALERTs

	* [r957] topo/base/utils.py:
	  Clarified documentation

	* [r956] topo/base/projection.py,
	  topo/outputfns/basic.py:
	  Clarified output_fn semantics

	* [r955] topo/base/projection.py,
	  topo/outputfns/basic.py:
	  Clarified calling semantics for OutputFunctions

	* [r954] topo/base/parameter.py:
	  Added Constant Parameter class

	* [r953] topo/base/sheet.py:
	  Minor comment clarification

2005-10-15  yfsit

	* [r952] topo/base/connectionfield.py,
	  topo/base/projection.py,
	  topo/base/simulator.py,
	  topo/plotting/plotengine.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/lissom.py,
	  topo/tk/projectionpanel.py:
	  Fixed alert:
	  - EventProcessors now have only one unified list (connections)
	  that contains all the incoming and outgoing projections.

	* [r951] topo/base/learningrules.py,
	  topo/responsefns/basic.py:
	  add -lstdc++ when weave links the compiled C codes. This solves
	  the problem when "undefined symbol" is reported during link time
	  of the C code in distribution like Ubuntu 5.10.

2005-10-14  jbednar

	* [r950] topo/base/projection.py:
	  Added clarification to comment

	* [r949] topo/base/utils.py:
	  Added simple learning rule example

	* [r948] topo/projections/kernelprojection.py:
	  Removed unneeded import

	* [r947] topo/learningfns,
	  topo/learningfns/.cvsignore,
	  topo/learningfns/__init__.py:
	  Initial version

	* [r946] topo/responsefns/__init__.py:
	  Fixed documentation

	* [r945] topo/base/utils.py:
	  Removed unused compute_response functions

	* [r944] examples/lissom.ty:
	  Removed unneeded import

	* [r943] examples/lissom.ty,
	  topo/base/connectionfield.py,
	  topo/projections/kernelprojection.py:
	  Changed activation functions to use CFResponseFunction classes

	* [r942] topo/responsefns,
	  topo/responsefns/.cvsignore,
	  topo/responsefns/__init__.py,
	  topo/responsefns/basic.py:
	  Initial version; copied implementation from utils.py

	* [r941] topo/base/connectionfield.py:
	  Added CFResponseFunction classes

	* [r940] topo/base/utils.py:
	  Minor cleanup

	* [r939] topo/base/distribution.py:
	  Minor comment cleanup

	* [r938] examples/lissom.ty:
	  Fixed output_fn name

	* [r937] topo/projections/kernelprojection.py:
	  Added output_fn for Projections

	* [r936] topo/base/projection.py,
	  topo/base/utils.py,
	  topo/outputfns/basic.py:
	  Moved OutputFunction and Identity here, the first place they are
	  used, though I may have to break down and make a new file for
	  them because they don't fit here all that well

2005-10-14  ceball

	* [r935] tests/testfeaturemap.py,
	  topo/base/featuremap.py:
	  continued producing initial version

	* [r934] tests/testdistribution.py,
	  topo/base/distribution.py:
	  Changed weighted_average() to return angle of vector_sum if
	  distribution is cyclic

2005-10-14  jbednar

	* [r933] topo/transferfns:
	  Removed transferfns

	* [r932] topo/base/projection.py,
	  topo/base/utils.py,
	  topo/outputfns,
	  topo/outputfns/.cvsignore,
	  topo/outputfns/__init__.py,
	  topo/outputfns/basic.py,
	  topo/sheets/lissom.py:
	  Changed TransferFunction to OutputFunction

2005-10-14  ceball

	* [r931] tests/testdistribution.py:
	  updated some comments

	* [r930] topo/base/distribution.py:
	  updated some comments; prepared for using wrap() function

2005-10-14  jbednar

	* [r929] topo/base/simulator.py:
	  Fixed errors in warning message

	* [r928] examples/lissom.ty,
	  topo/base/projection.py,
	  topo/sheets/lissom.py:
	  Made all transfer_fns work with uniform set of objects in
	  transferfns; still need to change names

2005-10-14  ceball

	* [r927] tests/testdistribution.py,
	  topo/base/distribution.py:
	  Since distribution knows whether or not it's cyclic, a call to
	  weighted_average() returns the vector or non-vector average
	  depending on cyclic.

2005-10-14  jbednar

	* [r926] topo/base/projection.py,
	  topo/patterns/basic.py,
	  topo/transferfns/basic.py:
	  Minor changes to comments and documentation

	* [r925] topo/transferfns/basic.py:
	  Added L1, L2, Linf, and Lp norms

	* [r924] examples/cfsom_example.py,
	  examples/gui_example.py:
	  Cleaned up

	* [r923] topo/base/distribution.py:
	  Cleaned up documentation, comments, and some variable names. Made
	  undefined_vals be a class variable, though that may not be enough
	  to make it track all values for any instances. Added a few
	  ALERTs.

2005-10-14  ceball

	* [r922] topo/base/featuremap.py:
	  initial version

2005-10-14  jbednar

	* [r921] topo/base/utils.py:
	  Added wrap() function

2005-10-14  ceball

	* [r920] topo/base/utils.py:
	  Added import statement to get TopoObject

2005-10-13  jbednar

	* [r919] topo/transferfns/basic.py:
	  Made parameter name more obvious

	* [r918] topo/transferfns,
	  topo/transferfns/.cvsignore:
	  Initial version

	* [r917] topo/base/utils.py,
	  topo/transferfns,
	  topo/transferfns/__init__.py,
	  topo/transferfns/basic.py:
	  Added TransferFunction classes

	* [r916] topo/base/utils.py:
	  Fixed bug for activations exactly equallying 1.0 (were being set
	  to zero!)

2005-10-13  jdepaula

	* [r915] topo/tk/inputparamspanel.py:
	  Removed some code, changed the access to Sheet.learning.

	* [r914] topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/sheets/lissom.py:
	  Removed enable_learning and disable_learning in lieu of direct
	  access of the learning parameter.

2005-10-13  ceball

	* [r913] tests/testdistribution.py,
	  topo/base/distribution.py:
	  made keep_peak an attribute of the distribution instead of an
	  argument in distribution.add()

	* [r912] tests/testdistribution.py,
	  topo/base/distribution.py:
	  implemented raises a ValueError if trying to add a bin outside
	  bounds

2005-10-13  jbednar

	* [r911] topo/base/projection.py:
	  Removed apparently unused learning_fn

	* [r910] topo/base/patterngenerator.py:
	  Removed registration of ConstantGenerator; that's already taken
	  care of by having it be imported into topo.patterns.basic

2005-10-13  yfsit

	* [r909] examples/cfsom_example.py,
	  examples/gui_example.py,
	  examples/image_example.py,
	  examples/lissom.ty,
	  tests/testcfsom.py,
	  tests/testpatterngenerator.py,
	  tests/testpatternpresent.py,
	  tests/testplot.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/testplotgroup.py,
	  tests/testsheet.py,
	  tests/testsheetview.py,
	  tests/tk/testactivitypanel.py,
	  tests/tk/testplotpanel.py,
	  topo/base/sheet.py,
	  topo/sheets/cfsom.py:
	  density of Sheet now means "linear density".

2005-10-13  ceball

	* [r908] tests/__init__.py:
	  Added testdistribution.py to list of tests to import

	* [r907] tests/testdistribution.py:
	  distribution's values() and counts() now return bins as well so
	  updated tests

	* [r906] topo/base/distribution.py:
	  values() and counts() now return bins as well; cleaned up file

2005-10-12  ceball

	* [r905] tests/testplotfilesaver.py,
	  topo/tk/cfsheetplotpanel.py:
	  topo.base.cfsheet -> topo.base.connectionfield

2005-10-12  jbednar

	* [r904] topo/base/connectionfield.py:
	  Added missing import

	* [r903] CONVENTIONS:
	  Added sections on terminology and optimization

	* [r902] topo/base/connectionfield.py,
	  topo/base/projection.py:
	  Cleaned up documentation

	* [r901] topo/base/cfsheet.py,
	  topo/base/connectionfield.py,
	  topo/plotting/plotengine.py,
	  topo/projections/kernelprojection.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/lissom.py:
	  Moved cfsheet.py to connectionfield.py

	* [r900] topo/base/cfsheet.py,
	  topo/base/projection.py:
	  Removed extra imports

2005-10-12  ceball

	* [r899] tests/testdistribution.py,
	  topo/base/distribution.py:
	  initial version: not yet complete

2005-10-12  yfsit

	* [r898] topo/base/patterngenerator.py,
	  topo/patterns/random.py,
	  topo/sheets/generatorsheet.py:
	  fixed a bug which generates a zero-sized array when rows and cols
	  are not passed into the UniformRandomGenerator and
	  ConstantGenerator

2005-10-12  jbednar

	* [r897] topo/base/cfsheet.py,
	  topo/base/projection.py,
	  topo/projections/kernelprojection.py:
	  Moved all CF-related items to cfsheet.py, and all
	  Projection-related-but-not-CF-related items to projection.py

	* [r896] topo/base/__init__.py:
	  Added comment

	* [r895] topo/tk/projectionpanel.py:
	  Added JABHACKALERT

	* [r894] topo/base/cfsheet.py,
	  topo/base/projection.py:
	  Split CFSheet into ProjectionSheet and CFSheet. ProjectionSheet
	  has all the features of CFSheet except that it doesn't know
	  ConnectionFields exist; most CFSheet operations have moved to
	  ProjectionSheet.

2005-10-11  yfsit

	* [r893] topo/base/cfsheet.py,
	  topo/sheets/lissom.py:
	  Alert fix:
	  - removed activity_buffer (used in computing the sheet
	  activation) in cfsheet and lissom.

2005-10-11  jdepaula

	* [r892] topo/patterns/patternpresent.py:
	  Added comment

	* [r891] topo/base/registry.py:
	  Removed a JAB, turned pattern_generators into a KeyedList. This
	  required additional functions added to KeyedList.

	* [r890] topo/base/patterngenerator.py:
	  Hide bounds and density.

	* [r889] topo/base/parameter.py:
	  Added hidden attribute to base Parameter, and added unnamed
	  params constructor passing to Parameter subclasses.

	* [r888] topo/base/object.py:
	  Added get_paramobj_dict() and made name and print_level hidden by
	  default.

	* [r887] topo/base/keyedlist.py:
	  Added keys() and update()

2005-10-11  yfsit

	* [r886] examples/lissom.ty:
	  commented back s.run(), which was uncommented in previous
	  version.

2005-10-11  jbednar

	* [r885] topo/base/patterngenerator.py,
	  topo/patterns/random.py:
	  Trivial change to comments, and removed extra print statement

2005-10-11  yfsit

	* [r884] topo/base/patterngenerator.py,
	  topo/patterns/random.py:
	  eliminated calling unnecessary setup_xy() in
	  UniformRandomGenerator and ConstantGenerator.

2005-10-10  jbednar

	* [r883] topo/base/sheet.py,
	  topo/plotting/plotgroup.py:
	  Added JABHACKALERTs

	* [r882] topo/base/projection.py,
	  topo/plotting/plotfilesaver.py:
	  Made abstract classes explicit

	* [r881] Makefile:
	  Added checking targets

	* [r880] topo/base/cfsheet.py:
	  Moved activate() function outside of pre_sleep() for clarity.

	* [r879] Makefile:
	  Removed old sh version of script; allowed generation of
	  topographica script to be skipped

	* [r878] examples/lissom.ty:
	  Added one iteration of training to make testing easier; will
	  eventually need to be removed

	* [r877] examples/cfsom_example.py,
	  examples/gui_example.py:
	  Removed extra print statements

	* [r876] topo/base/projection.py,
	  topo/projections/kernelprojection.py,
	  topo/tk/projectionpanel.py:
	  Changed Projection to CFProjection (a Projection based on
	  ConnectionFields), and changed BaseProjection to Projection (any
	  sort of Projection between Sheets)

	* [r875] topo/base/cfsheet.py:
	  Added JABHACKALERT

	* [r874] topo/base/projection.py:
	  Temporarily added BaseProjection superclass to Projection; will
	  be changing the names

	* [r873] topo/base/cfsheet.py,
	  topo/base/projection.py,
	  topo/base/utils.py,
	  topo/projections/kernelprojection.py:
	  Changed Projection.compute_response to Projection.activate

	* [r872] topo/base/projection.py:
	  Added comment

	* [r871] topo/patterns/patternpresent.py:
	  Added JABHACKALERT and fixed outdated comment.

	* [r870] topo/base/simulator.py:
	  Added objects() function. Made it clear how an EP gets its
	  simulator link.

2005-10-10  jdepaula

	* [r869] topo/tk/inputparamspanel.py:
	  present function now uses patternpresent package.

	* [r868] topo/patterns/patternpresent.py:
	  Added a restore option for the pattern_present function.

2005-10-09  ceball

	* [r867] topo/base/utils.py:
	  Changed arg(z) so that it works for arrays, too.

2005-10-09  jbednar

	* [r866] topo/base/sheet.py:
	  Fixed typo

2005-10-08  jbednar

	* [r865] tests/__init__.py:
	  Added JABALERT

2005-10-08  yfsit

	* [r864] topo/base/cfsheet.py,
	  topo/base/projection.py,
	  topo/base/utils.py,
	  topo/projections/kernelprojection.py,
	  topo/sheets/lissom.py:
	  temp_activity in Sheet and its subclasses is now changed to
	  activity_buffer.
	  
	  temp_activity in Projection and its subclasses is now changed to
	  activity.

2005-10-07  jdepaula

	* [r863] topo/tk/inputparamspanel.py:
	  Moved out input_eps(), in prep for larger code exodus.

	* [r862] tests/__init__.py:
	  Added testpatternpresent.py

	* [r861] topo/patterns/patternpresent.py:
	  Moving out some of the useful code in inputparamspanel.py to be
	  more general for measuring maps, etc.

	* [r860] tests/testpatternpresent.py:
	  Test patternpresent.py

2005-10-07  ceball

	* [r859] topo/base/utils.py:
	  Added arg(z) function to find the complex argument of z - I
	  couldn't find it in Python. Maybe it does exist?

2005-10-07  jbednar

	* [r858] topo/base/commandline.py:
	  Minor clarification

	* [r857] topo/base/learningrules.py:
	  Minor fix to comment

	* [r856] topo/base/cfsheet.py:
	  Minor clarification to comment

	* [r855] topo/__init__.py:
	  Added clarification

	* [r854] topo/base/sheet.py:
	  Fixed comment colorizing for emacs

	* [r853] topo/base/projection.py,
	  topo/patterns/basic.py:
	  Cleaned up comments

	* [r852] topo/__init__.py,
	  topo/eps/__init__.py,
	  topo/patterns/__init__.py,
	  topo/plotting/__init__.py,
	  topo/projections/__init__.py,
	  topo/sheets/__init__.py,
	  topo/tk/__init__.py:
	  Added basic documentation for each package

2005-10-07  yfsit

	* [r851] topo/base/cfsheet.py:
	  Removed the parameter weight_type in ConnectionField and made it
	  an optional argument.
	  
	  Added explanation on the Numeric.Int32 type of
	  ConnectionField.slice_array.

2005-10-07  jbednar

	* [r850] topo/base/projection.py:
	  Removed unused parameters

	* [r849] topo/base/cfsheet.py:
	  Removed outdated comments, unneeded imports

	* [r848] Makefile,
	  examples/Makefile:
	  Added examples makefile

	* [r847] topo/base/projection.py:
	  Removed some ALERTs, cleaned up some comments, and removed unused
	  plot_cfs

	* [r846] examples/cfsom_example.py,
	  examples/gui_example.py:
	  Removed outdated comments

	* [r845] examples/lissom.ty,
	  topo/sheets/lissom.py:
	  Moved LISSOM class to the topo.sheets package, and cleaned up
	  lissom.ty

	* [r844] topo/base/patterngenerator.py,
	  topo/patterns/basic.py,
	  topo/sheets/generatorsheet.py:
	  Changed SolidGenerator to ConstantGenerator

2005-10-06  yfsit

	* [r843] examples/lissom.ty,
	  topo/base/cfsheet.py,
	  topo/base/learningrules.py,
	  topo/base/projection.py,
	  topo/patterns/basic.py,
	  topo/projections/kernelprojection.py:
	  /tmp/cvshoNVMD

2005-10-06  ceball

	* [r842] topo/tk/__init__.py,
	  topo/tk/plotpanel.py,
	  topo/tk/projectionpanel.py,
	  topo/tk/topoconsole.py,
	  topo/tk/unitweightspanel.py:
	  Simplified intra-package references

2005-10-06  jbednar

	* [r841] topo/__init__.py,
	  topo/base/commandline.py,
	  topo/base/object.py,
	  topo/tk/topoconsole.py:
	  Moved about() to topo namespace

2005-10-06  ceball

	* [r840] topo/plotting/dislindriver.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotengine.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py:
	  Simplified intra-package references

	* [r839] topo/base/boundingregion.py,
	  topo/base/cfsheet.py,
	  topo/base/commandline.py,
	  topo/base/object.py,
	  topo/base/patternfns.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/sheet.py,
	  topo/base/sheetview.py,
	  topo/base/simulator.py:
	  Simplified intra-package references (e.g. 'topo.base.object' to
	  'object')

2005-10-06  jbednar

	* [r838] topo/base/keyedlist.py:
	  Removed comments and variable names specific to topographica

	* [r837] /trunk/topographica, .cvsignore:
	  More to ignore

	* [r836] topo/base/__init__.py,
	  topo/plotting/__init__.py:
	  Added support for 'from topo import *'.

	* [r835] topo/__init__.py:
	  Removed nearly everything, so that users can choose which
	  packages they want to import. Added support for 'from topo import
	  *'.

	* [r834] examples/lissom.ty:
	  Fixed missing import

	* [r833] examples/image_example.py:
	  Fixed missing import and added missing full path

	* [r832] topo/base/registry.py,
	  topo/plotting/plotgroup.py:
	  Moved definition of standard plots from registry.py into
	  plotting/ directory so that the code can run without importing
	  plotting/

	* [r831] topo/base/keyedlist.py:
	  Moved from plotting/plotgroup.py

	* [r830] topo/base/gendocs.py,
	  topo/base/patternfns.py,
	  topo/base/patterngenerator.py,
	  topo/base/sheetview.py,
	  topo/base/simulator.py:
	  Removed some bits of cruft found by pychecker; there are many
	  more to do

	* [r829] CONVENTIONS:
	  Added guidelines for using Parameters and their bounds

	* [r828] topo/base/patterngenerator.py:
	  Used Sit's implementation of UniformGenerator for SolidGenerator

	* [r827] topo/patterns/basic.py:
	  Made SolidGenerator also show up in topo.patterns namespace, for
	  uniformity

	* [r826] topo/base/cfsheet.py:
	  Removed outdated imports

2005-10-06  ceball

	* [r825] Makefile:
	  Updated after moving topo.gendocs to topo.base.gendocs

	* [r824] topo/base,
	  topo/base/.cvsignore,
	  topo/eps,
	  topo/eps/.cvsignore,
	  topo/plotting,
	  topo/plotting/.cvsignore:
	  added .cvsignore

	* [r823] examples/lissom.ty:
	  Missed an update after reorganization (topo.utils ->
	  topo.base.utils)

	* [r822] examples/cfsom_example.py,
	  examples/gui_example.py,
	  examples/image_example.py,
	  examples/lissom.ty,
	  tests/testbitmap.py,
	  tests/testboundingregion.py,
	  tests/testcfsom.py,
	  tests/testdislinplot.py,
	  tests/testhistogram.py,
	  tests/testpalette.py,
	  tests/testpatterngenerator.py,
	  tests/testplot.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/testplotgroup.py,
	  tests/testsheet.py,
	  tests/testsheetview.py,
	  tests/testsimulator.py,
	  tests/tk/testactivitypanel.py,
	  tests/tk/testplotpanel.py,
	  tests/tk/testpreferencemappanel.py,
	  tests/tk/testtopoconsole.py,
	  topo/base/registry.py:
	  Updated after reorganization of plotting into topo.plotting

	* [r821] topo/patterns/basic.py,
	  topo/patterns/random.py,
	  topo/projections/kernelprojection.py,
	  topo/sheets/cfsom.py,
	  topo/sheets/composer.py,
	  topo/sheets/generatorsheet.py,
	  topo/tk/__init__.py,
	  topo/tk/cfsheetplotpanel.py,
	  topo/tk/inputparamspanel.py,
	  topo/tk/plotpanel.py,
	  topo/tk/preferencemappanel.py,
	  topo/tk/projectionpanel.py,
	  topo/tk/topoconsole.py,
	  topo/tk/unitweightspanel.py:
	  Updated after reorganization into topo.base and topo.plotting

	* [r820] topo/__init__.py:
	  updated after reorganization into topo.base, topo.plotting, and
	  topo.eps

	* [r819] topographica_script.py:
	  Updated because commandline.py moved from topo/ to
	  topo/base/commandline.py

	* [r818] topo/base.py,
	  topo/bitmap.py,
	  topo/boundingregion.py,
	  topo/cfsheet.py,
	  topo/commandline.py,
	  topo/dislindriver.py,
	  topo/dislinplot.py,
	  topo/gendocs.py,
	  topo/histogram.py,
	  topo/learningrules.py,
	  topo/palette.py,
	  topo/parameter.py,
	  topo/patternfns.py,
	  topo/patterngenerator.py,
	  topo/plot.py,
	  topo/plotengine.py,
	  topo/plotfilesaver.py,
	  topo/plotgroup.py,
	  topo/projection.py,
	  topo/registry.py,
	  topo/scalarep.py,
	  topo/sheet.py,
	  topo/sheetview.py,
	  topo/simulator.py,
	  topo/tyimputil.py,
	  topo/utils.py:
	  Moved core code to topo.base, plotting code to topo.plotting

	* [r817] topo/eps,
	  topo/eps/__init__.py,
	  topo/eps/scalarep.py:
	  Moved scalar some event processors code into topo.eps

	* [r816] topo/plotting,
	  topo/plotting/__init__.py,
	  topo/plotting/bitmap.py,
	  topo/plotting/dislindriver.py,
	  topo/plotting/dislinplot.py,
	  topo/plotting/histogram.py,
	  topo/plotting/palette.py,
	  topo/plotting/plot.py,
	  topo/plotting/plotengine.py,
	  topo/plotting/plotfilesaver.py,
	  topo/plotting/plotgroup.py:
	  Moved plotting code into topo.plotting

	* [r815] topo/base,
	  topo/base/__init__.py,
	  topo/base/boundingregion.py,
	  topo/base/cfsheet.py,
	  topo/base/commandline.py,
	  topo/base/gendocs.py,
	  topo/base/learningrules.py,
	  topo/base/object.py,
	  topo/base/parameter.py,
	  topo/base/patternfns.py,
	  topo/base/patterngenerator.py,
	  topo/base/projection.py,
	  topo/base/registry.py,
	  topo/base/sheet.py,
	  topo/base/sheetview.py,
	  topo/base/simulator.py,
	  topo/base/tyimputil.py,
	  topo/base/utils.py:
	  Moved main code base from topo to topo.base

2005-10-05  yfsit

	* [r814] examples/lissom.ty,
	  topo/cfsheet.py:
	  Alerts fixed:
	  - default learning_fn of CFSheet is no-op. The specific learning
	  function now needs to be specified, as in lissom.ty.
	  - added more comments to pre_sleep()

2005-10-05  jbednar

	* [r813] topo/palette.py:
	  Minor documentation tweak to fix emacs colorization

	* [r812] external,
	  external/.cvsignore,
	  external/Makefile:
	  Added pylint

	* [r811] external/common-0.12.0.tar.gz,
	  external/pylint-0.7.0.tar.gz:
	  Downloaded from http://www.logilab.org/projects/pylint/

	* [r810] external,
	  external/.cvsignore,
	  external/Makefile:
	  Added pychecker

2005-10-05  yfsit

	* [r809] topo/sheets/composer.py:
	  fixed a bug in calling Sheet._connect_from.

	* [r808] examples/lissom.ty,
	  topo/cfsheet.py,
	  topo/learningrules.py,
	  topo/patterns/basic.py,
	  topo/projection.py,
	  topo/projections/kernelprojection.py:
	  Fixed some of the ALERTs in cfsheet.py:
	  - removed the special case for UniformRandomGenerator
	  - normalization of connection field weights is handled by
	  user-define normalize_fn. This same function is called after
	  weights initialization, learning, and change of connection field
	  radius.
	  - type of connection weight, e.g. Numeric.Float32, is a parameter
	  of Projection.
	  
	  Fixed the divisive normalization code in learningrules.py.
	  
	  Added UniformGenerator in patterns/basic.py.

2005-10-05  ceball

	* [r807] examples/image_example.py:
	  Added comment about it appearing not to work.

	* [r806] examples/cfsom_example.py,
	  examples/gui_example.py:
	  Updated to use the new interface of simulator.connect().

2005-10-05  yfsit

	* [r805] tests/testcfsom.py,
	  tests/testplotfilesaver.py:
	  updated to use the new interface of simulator.connect().

2005-10-04  yfsit

	* [r804] examples/lissom.ty:
	  updated for the modified Simulator.connect(). The named parameter
	  projection_type is now needed if the projection is not
	  EPConnection, e.g. KernelProjection.

2005-10-04  ceball

	* [r803] topo/patternfns.py:
	  Corrected my earlier alteration of exp() hack

2005-10-04  yfsit

	* [r802] topo/cfsheet.py,
	  topo/projection.py,
	  topo/projections/kernelprojection.py,
	  topo/sheets/composer.py,
	  topo/simulator.py:
	  New class: EPConnection (in simulator.py)
	  Connections between two EventProcessors are now instances of
	  EPConnection, which was a tuple.
	  Projection is now a subclass of EPConnection.
	  
	  The interface of _connect_to and _connect_from of EventProcessors
	  are changed to
	  _connect_to(self, proj, **args) (similarly for _connect_from).
	  
	  All the subclasses of EventProcessor that invoke these methods
	  are updated accordingly.

2005-10-04  jdepaula

	* [r801] topo/plot.py:
	  Fixed error with normalizing B channel of RGB instead of V of HSV

	* [r800] topo/tk/plotpanel.py:
	  Removed print statement

2005-10-04  ceball

	* [r799] topo/patternfns.py:
	  Changed EXP_CUTOFF hack for Numeric.exp() so that it's in one
	  place.

2005-10-04  jbednar

	* [r798] examples/image_example.py:
	  Fixed to work from parent directory, and added usage info

	* [r797] topo/sheets/composer.py:
	  Added missing import statement

2005-10-04  jdepaula

	* [r796] topo/registry.py:
	  Turn on normalization by default for Projection plots

2005-10-04  yfsit

	* [r795] external/Makefile:
	  fixed uninstallation so that the empty files fixedpoint, weave,
	  and
	  matplotlib are removed when they are uninstalled.

2005-10-04  jdepaula

	* [r794] topo/plot.py:
	  Fix divide by 0 error.

	* [r793] topo/tk/basicplotpanel.py,
	  topo/tk/preferencemappanel.py,
	  topo/tk/projectionpanel.py,
	  topo/tk/unitweightspanel.py:
	  Added plot group template name variable.

	* [r792] topo/tk/plotpanel.py:
	  Added normalization check box.

	* [r791] topo/registry.py:
	  Added default normalization to Unit plots

	* [r790] topo/plotgroup.py:
	  KeyedList allows integer indexing now.

	* [r789] topo/plotengine.py:
	  Added ability to normalize plots if templates set Normalization.

2005-10-04  yfsit

	* [r788] examples/lissom.ty,
	  topo/simulator.py:
	  fixed JABALERT in simulator.ty:
	  - removed base.simulator class and moved the essential methods
	  into simulator.
	  - removed the redundant flag execfn.
	  - renamed sched_execfn to schedule_action.
	  
	  examples/lissom.ty is changed accordingly.

2005-10-04  jdepaula

	* [r787] topo/plot.py:
	  Added normalization to color maps and HSV.

2005-10-04  yfsit

	* [r786] external/Makefile:
	  fixed the installation of fixedpoint

2005-10-03  jbednar

	* [r785] topo/patterns/random.py,
	  topo/projection.py,
	  topo/projections/kernelprojection.py,
	  topo/sheets/cfsom.py:
	  Cleaned up comments

	* [r784] topo/patterngenerator.py:
	  Cleaned up comments, alerts, and imports

	* [r783] topo/patternfns.py,
	  topo/patterns/basic.py:
	  Cleaned up comments, alerts, and imports. Moved not-very-useful
	  functions from patternfuns.py into patterns/basic.py

	* [r782] external/Makefile:
	  Fixed cleanup commands

	* [r781] external,
	  external/.cvsignore:
	  Removed outdated file, so that is clear it should be deleted now

	* [r780] README.txt:
	  Updated estimated time

2005-10-03  ceball

	* [r779] tests/testkernelfactory.py:
	  After renaming kernelfactory.py patterngenerator.py, renamed this
	  to testpatterngenerator.py

	* [r778] tests/testpatterngenerator.py:
	  After renaming kernelfactory.py patterngenerator.py, renamed this
	  from testkernelfactory.py

	* [r777] topo/patterns/basic.py:
	  Re-implemented FuzzyLine

	* [r776] topo/patternfns.py:
	  Changed pattern_x and pattern_y to x and y respectively;
	  re-implemented FuzzyLine

2005-10-03  jbednar

	* [r775] topo/sheets/generatorsheet.py,
	  topo/tk/inputparamspanel.py:
	  Fixed comments

2005-10-03  ceball

	* [r774] examples/cfsom_example.py,
	  examples/gui_example.py,
	  examples/image_example.py,
	  examples/lissom.ty,
	  tests/__init__.py,
	  tests/testcfsom.py,
	  tests/testkernelfactory.py,
	  tests/testplot.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/testplotgroup.py,
	  tests/testsheetview.py,
	  tests/tk/testactivitypanel.py,
	  tests/tk/testplotpanel.py,
	  tests/tk/testpreferencemappanel.py,
	  topo/__init__.py,
	  topo/cfsheet.py,
	  topo/patternfns.py,
	  topo/patterns/basic.py,
	  topo/patterns/random.py,
	  topo/projections/kernelprojection.py,
	  topo/registry.py,
	  topo/sheets/generatorsheet.py,
	  topo/tk/inputparamspanel.py:
	  Renamed kernelfactory.py to patterngenerator.py. Renamed
	  KernelFactory to PatternGenerator, along with all subclasses
	  (e.g. SineGratingFactory to SineGratingGenerator).

	* [r773] topo/kernelfactory.py,
	  topo/patterngenerator.py:
	  Renamed kernelfactory.py to patterngenerator.py

2005-10-03  jbednar

	* [r772] topo/utils.py:
	  Minor tweak suggested by Jeff

2005-10-02  jbednar

	* [r771] topo/utils.py:
	  Clarified documentation

	* [r770] topo/sheets/composer.py,
	  topo/sheets/generatorsheet.py:
	  Updated comments

2005-10-02  ceball

	* [r769] topo/projections/kernelprojection.py:
	  imported topo.utils, which got accidentally removed

2005-10-02  jbednar

	* [r768] topo/sheets/generatorsheet.py:
	  Removed now-obsolete JABALERT

2005-10-02  ceball

	* [r767] examples/lissom.ty:
	  Removed import topo.gui

	* [r766] topo/inputsheet.py:
	  Moved inputsheet.py to sheets/generatorsheet.py, also renaming
	  the class InputSheet to GeneratorSheet

	* [r765] examples/cfsom_example.py,
	  examples/gui_example.py,
	  examples/lissom.ty,
	  tests/testcfsom.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/tk/testactivitypanel.py,
	  tests/tk/testplotpanel.py,
	  tests/tk/testpreferencemappanel.py,
	  topo/tk/inputparamspanel.py:
	  Changed import statements after moving topo.inputsheet to
	  topo.sheets.generatorsheet, and uses of InputSheet to
	  GeneratorSheet

	* [r764] topo/kernelfactory.py,
	  topo/tk/plotpanel.py:
	  Changed comments after moving topo.inputsheet to
	  topo.sheets.generatorsheet

	* [r763] topo/__init__.py:
	  Changed import statement after moving topo.inputsheet to
	  topo.sheets.generatorsheet

	* [r762] topo/sheets/generatorsheet.py:
	  Renamed from inputsheet.py and moved from topo/ to topo/sheets/

	* [r761] topo/projection.py:
	  Corrected import of UnitView

	* [r760] topo/projections/kernelprojection.py:
	  Updated import of Projection after moving projection.py

	* [r759] topo/projection.py,
	  topo/projections/projection.py:
	  Moved from topo/projections (mistaken) to topo/

2005-10-02  jbednar

	* [r758] examples/lissom.ty:
	  Fixed name of activity arrays

2005-10-02  ceball

	* [r757] examples/image_example.py,
	  examples/lissom.ty:
	  Corrected import statement for ImageSaver

	* [r756] topo/projections,
	  topo/projections/.cvsignore,
	  topo/sheets,
	  topo/sheets/.cvsignore:
	  *** empty log message ***

	* [r755] tests/testplotfilesaver.py:
	  Updated use of KernelProjection after having moved it to a
	  separate module

	* [r754] examples/cfsom_example.py,
	  examples/gui_example.py:
	  Changed import statements for KernelProjection after moving it to
	  a separate module

	* [r753] topo/cfsheet.py:
	  Moved Projection and KernelProjection into separate modules,
	  topo.projections.projection and topo.projections.kernelprojection

	* [r752] topo/projections/kernelprojection.py:
	  Moved KernelProjection from topo/cfsheet.py into its own module,
	  at topo/projections/kernelprojection.py

	* [r751] topo/projections/projection.py:
	  Moved Projection from topo/cfsheet into its own module, at
	  topo/projections/projection.py

	* [r750] topo/projections,
	  topo/projections/__init__.py:
	  Initial version

	* [r749] topo/plotfilesaver.py:
	  Changed a comment about cfsom after moving cfsom.py from models/
	  to topo/sheets

	* [r748] examples/cfsom_example.py,
	  examples/gui_example.py,
	  tests/testcfsom.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/tk/testplotpanel.py:
	  Updated CFSOM import statement after moving cfsom.py from models/
	  to topo/sheets

	* [r747] models/__init__.py:
	  Removed cfsom import statement after moving cfsom.py from models/
	  to topo/sheets

	* [r746] examples/image_example.py:
	  Updated Composer import statement after moving composer.py from
	  topo/ to topo/sheets

	* [r745] models/cfsom.py,
	  topo/composer.py:
	  Moved into topo/sheets/ directory

	* [r744] topo/sheets/cfsom.py:
	  Moved from models/ directory

	* [r743] topo/sheets/composer.py:
	  Moved from topo/ directory

	* [r742] topo/sheets,
	  topo/sheets/__init__.py:
	  Initial version

2005-10-02  jbednar

	* [r741] topo/utils.py:
	  Used Jeff's implementation of find_classes_in_package

	* [r740] topo/tk/inputparamspanel.py,
	  topo/utils.py:
	  Changed submodule_classes name to be clearer

2005-10-01  jbednar

	* [r739] topo/patterns,
	  topo/patterns/.cvsignore:
	  Removed unneeded ignores

	* [r738] topo/patterns,
	  topo/patterns/.cvsignore:
	  Initial version

	* [r737] topo/patterns/basic.py:
	  Simplified the rectangle pattern

2005-10-01  yfsit

	* [r736] external/Makefile,
	  external/fixedpoint-0.1.2.tgz,
	  external/fixedpoint.diff,
	  external/fixedpoint_setup.py:
	  The tar archive is reverted to the original distribution.
	  Added the patch file and fixedpoint_setup.py in external/.
	  Makefile is changed accordingly.

2005-10-01  jbednar

	* [r735] topo/patterns/random.py:
	  Simplified by eliminating extra function

2005-09-30  jbednar

	* [r734] topo/patternfns.py:
	  Deleted now-unused copies of functions

	* [r733] topo/kernelfactory.py,
	  topo/tk/inputparamspanel.py:
	  Deleted KernelFactory classes now in patterns/, and moved
	  populating the registry from kernelfactory.py to
	  inputparamspanel.py

	* [r732] tests/testcfsom.py,
	  tests/testkernelfactory.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/tk/testactivitypanel.py,
	  tests/tk/testplotpanel.py:
	  Changed to use KernelFactory classes in patterns/

	* [r731] examples/cfsom_example.py,
	  examples/gui_example.py,
	  examples/lissom.ty,
	  topo/cfsheet.py:
	  Changed to use KernelFactory classes in patterns/

	* [r730] topo/inputsheet.py:
	  Selected a simpler KernelFactory by default

	* [r729] topo/kernelfactory.py:
	  Added SolidFactory. Cleaned up some comments.

	* [r728] topo/patterns,
	  topo/patterns/__init__.py,
	  topo/patterns/basic.py,
	  topo/patterns/random.py:
	  Moved from kernelfactory.py

	* [r727] topo/__init__.py:
	  Updated comment

	* [r726] topo/utils.py:
	  Added submodule_classes function

	* [r725] topo/tk/inputparamspanel.py:
	  Fixed bug in looking up KernelFactory classes by name; had been
	  looking in the contents of topo.kernelfactory instead of in the
	  registry

	* [r724] topo/kernelfactory.py,
	  topo/patternfns.py:
	  Moved kernel functions into patternfns.py

	* [r723] topo/parameter.py:
	  Cleaned up comments, and made Number setting raise exceptions for
	  violated bounds, by default

	* [r722] topo/tk/inputparamspanel.py:
	  Added JABHACKALERT

	* [r721] README.txt:
	  Pointed people to the CONVENTIONS file

	* [r720] MILESTONES:
	  Marked items done

2005-09-30  yfsit

	* [r719] external/Makefile,
	  external/fixedpoint-0.1.2.tgz:
	  added a patch file to fixedpoint-0.1.2.tgz. The Makefile will
	  apply the
	  patch before installation.

2005-09-29  ceball

	* [r718] topo/kernelfactory.py:
	  Added two comments (notes to update fuzzyline() and KernelFactory
	  + subclasses).

	* [r717] topo/kernelfactory.py:
	  Individual KernelFactory parameters are now declared as Numbers,
	  with bounds.

	* [r716] topo/parameter.py:
	  Number now does not take exception when an attempt is made to set
	  a parameter outside its hard bounds: it sets the parameter to the
	  nearest hard bound. An exception is generated on attempting to
	  create a Number with a default value outside the bounds.

2005-09-29  jbednar

	* [r715] topo/parameter.py:
	  Made default documentation be empty

2005-09-29  yfsit

	* [r714] topo/cfsheet.py:
	  name change: activity_fn to activation_fn

2005-09-29  jbednar

	* [r713] topo/bitmap.py,
	  topo/palette.py,
	  topo/plot.py,
	  topo/plotengine.py,
	  topo/plotfilesaver.py,
	  topo/plotgroup.py:
	  Added JABHACKALERTs

	* [r712] topo/simulator.py:
	  Added JABHACKALERTs and clarified comments and documentation

	* [r711] topo/inputsheet.py:
	  Added JABALERT

	* [r710] MILESTONES:
	  Marked more things as done

	* [r709] topo/histogram.py:
	  Added JABHACKALERT

	* [r708] CONVENTIONS:
	  Added guidelines for modifying external packages

2005-09-29  ceball

	* [r707] topo/parameter.py:
	  Added soft bounds and a bounds-check on the default value

2005-09-29  yfsit

	* [r706] topo/simulator.py:
	  name change: InfinteTime to Forever

2005-09-28  jdepaula

	* [r705] topo/plot.py:
	  Plot class now crops before sending to bitmap.py

	* [r704] topo/bitmap.py:
	  Updated warning messages

	* [r703] topo/tk/inputparamspanel.py:
	  Changed string replace with regular expression replace.

2005-09-28  yfsit

	* [r702] examples/lissom.ty:
	  used the time_precision paramter for simulator (set to 2).
	  delays of connections are now 0.05.

	* [r701] topo/simulator.py:
	  precision of FixedPoint time changed into a paremeter of
	  simulator.
	  defined InfiniteTime to -1.

2005-09-28  jdepaula

	* [r700] models/cfsom.py,
	  tests/testplotengine.py,
	  tests/tk/testactivitypanel.py,
	  tests/tk/testplotpanel.py,
	  topo/bitmap.py,
	  topo/cfsheet.py,
	  topo/composer.py,
	  topo/inputsheet.py,
	  topo/kernelfactory.py,
	  topo/learningrules.py,
	  topo/plotgroup.py,
	  topo/sheet.py,
	  topo/tk/inputparamspanel.py,
	  topo/utils.py:
	  Changed code references of activitaion to activity

	* [r699] external,
	  external/.cvsignore:
	  ignore fixedpoint secondary files

2005-09-28  jbednar

	* [r698] topo/cfsheet.py:
	  Added JABHACKALERTs and clarified documentation

2005-09-28  yfsit

	* [r697] models/cfsom.py:
	  The FixedPoint time used in computing the decay of alpha and
	  radius is
	  converted to float so that the decayed value will still be a
	  float.

	* [r696] examples/lissom.ty:
	  dealys of connections are specified in FixedPoint.

	* [r695] topo/simulator.py:
	  Time is now of type FixedPoint.

	* [r694] external/Makefile:
	  Added fixed point package

	* [r693] external/fixedpoint-0.1.2.tgz:
	  Fixed point package used by timing in simulator.

2005-09-27  ceball

	* [r692] topo/kernelfactory.py:
	  Corrected fuzzyline() and rectangle() function headers, which I'd
	  forgotten to change.

	* [r691] topo/kernelfactory.py:
	  Changed FuzzyLine so that there is a real line in the center, and
	  with Gaussian fall-off from its edges.

2005-09-27  jbednar

	* [r690] MILESTONES:
	  Updated some completed items

2005-09-27  ceball

	* [r689] topo/kernelfactory.py:
	  Changed rectangle() so that rectangles translate and rotate
	  correctly

2005-09-27  jdepaula

	* [r688] topo/registry.py,
	  topo/tk/topoconsole.py:
	  Created a registry for special classes to call for Plot Group
	  Templates

	* [r687] topo/tk/inputparamspanel.py:
	  Changed method of removing Factory from the name so it is more
	  flexible for future use.

2005-09-26  jbednar

	* [r686] topo/boundingregion.py,
	  topo/inputsheet.py,
	  topo/kernelfactory.py,
	  topo/registry.py,
	  topo/tk/inputparamspanel.py:
	  Added JABHACKALERTs and clarified comments

2005-09-23  jbednar

	* [r685] topo/plotgroup.py:
	  Added JABHACKALERT for KeyedList

2005-09-23  ceball

	* [r684] topo/kernelfactory.py:
	  Added SquareGratingFactory

2005-09-22  jbednar

	* [r683] topo/registry.py:
	  Clarified comments and added a JABHACKALERT

2005-09-20  jdepaula

	* [r682] tests/testplotengine.py,
	  tests/testplotgroup.py,
	  topo/__init__.py,
	  topo/plotengine.py,
	  topo/plotfilesaver.py,
	  topo/plotgroup.py,
	  topo/registry.py,
	  topo/sheet.py,
	  topo/tk/projectionpanel.py,
	  topo/tk/topoconsole.py,
	  topo/tk/unitweightspanel.py:
	  Moved plot template dictionary to the registry.

2005-09-19  jdepaula

	* [r681] topo/kernelfactory.py,
	  topo/registry.py,
	  topo/tk/inputparamspanel.py:
	  Moved kernel_factories dictionary to registry

	* [r680] tests/tk/testtopoconsole.py,
	  topo/__init__.py,
	  topo/plotfilesaver.py,
	  topo/plotgroup.py,
	  topo/simulator.py,
	  topo/tk/__init__.py,
	  topo/tk/topoconsole.py:
	  Moved active_sim() to the new registry class.

	* [r679] topo/registry.py:
	  Variables that the user may want to change.

	* [r678] topo/tk/inputparamspanel.py,
	  topo/tk/propertiesframe.py,
	  topo/tk/taggedslider.py:
	  Removed references to Topographica from taggedslider.py and
	  passthrough for propertiesframe.py

2005-09-17  yfsit

	* [r677] topo/cfsheet.py:
	  fixed a wrong statement in setting up the random weight array in
	  the
	  previous version.

	* [r676] topo/cfsheet.py,
	  topo/learningrules.py,
	  topo/utils.py:
	  All the weight arrays are now of type Float32.
	  
	  The learn method is largely moved to learningrules.py

2005-09-14  yfsit

	* [r675] examples/lissom.ty:
	  some bug fixes. The V1 map now does not call send_output at the
	  last
	  activation of an iteration. This should speed things up a bit.

2005-09-13  jbednar

	* [r674] models,
	  models/.cvsignore:
	  Copied from examples

	* [r673] topo/kernelfactory.py,
	  topo/plotfilesaver.py:
	  Added JABHACKALERT so we don't lose track of the to-do items

	* [r672] topo/commandline.py:
	  Removed bogus pI

2005-09-12  jdepaula

	* [r671] tests/testgui.py,
	  topo/gui.py:
	  Moved code to simulator.py and to topographica_script.py

	* [r670] tests/__init__.py,
	  topo/__init__.py,
	  topo/plotengine.py,
	  topo/plotfilesaver.py,
	  topo/simulator.py,
	  topo/tk/__init__.py,
	  topo/tk/basicplotpanel.py,
	  topo/tk/topoconsole.py:
	  Removed gui.py, moved console registration back to simulator.py

	* [r669] topo/tk/inputparamspanel.py:
	  Pull down Kernels menu now has spaces and no longer displays the
	  word Factory.

	* [r668] topo/gui.py:
	  Removed reference to now missing function

	* [r667] topo/gui.py:
	  Removed all code references to topo.tk

	* [r666] topographica_script.py:
	  topographica_script now knows about topo.tk to start GUI

	* [r665] topo/tk/topoconsole.py:
	  GUI now quits Topographica when exiting if GUI started from
	  commandline. Also removed commented code that is no longer
	  necessary.

	* [r664] topographica_script.py:
	  Added topo.gui_cmdline_flag

2005-09-12  jbednar

	* [r663] topo/tk/topoconsole.py:
	  Clarified comment

	* [r662] topo/plotengine.py:
	  Fixed typo

2005-09-12  jdepaula

	* [r661] topo/tk/taggedslider.py:
	  Changed import to reflect eval_atof move.

	* [r660] topo/tk/inputparamspanel.py:
	  Moved out eval_atof

	* [r659] topo/utils.py:
	  Added eval_atof

	* [r658] topo/commandline.py:
	  Added dictionary of constants to add to the __main__ namespace.

	* [r657] topo/image.py:
	  Temporarily split between kernelfactory and plotfilesaver until
	  the code is absorbed.

	* [r656] examples/cfsom_example.py,
	  examples/gui_example.py,
	  examples/image_example.py,
	  tests/testcfsom.py,
	  tests/testplot.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/testplotgroup.py,
	  tests/testsheetview.py,
	  tests/tk/testplotpanel.py,
	  topo/__init__.py,
	  topo/kernelfactory.py,
	  topo/plotfilesaver.py:
	  Removed image.py. Classes now split between kernelfactory.py and
	  plotfilesaver.py

	* [r655] topo/sheet.py,
	  topo/tk/topoconsole.py:
	  Added comments

2005-09-11  jdepaula

	* [r654] topo/tk/topoconsole.py:
	  Added comments, removed two JABs.

2005-09-10  yfsit

	* [r653] topo/cfsheet.py:
	  normalization_fn is added as a parameter. Ther are some minor
	  fixes as well.

	* [r652] topo/learningrules.py:
	  Added divisive normalization.

	* [r651] topo/simulator.py:
	  pre_sleep() of the event processors now will not be called if
	  only exec_fn is
	  evoked at that particular time. exec_fn (or hook in the c++
	  simulator) is not
	  an event to those event processor and therefore they should not
	  care.

2005-09-09  jdepaula

	* [r650] topo/tk/__init__.py,
	  topo/tk/cfsheetplotpanel.py,
	  topo/tk/projectionpanel.py,
	  topo/tk/unitweightspanel.py:
	  Changed regionplotpanel to cfsheetplotpanel.py

	* [r649] topo/tk/regionplotpanel.py:
	  Changed filename to cfsheetplotpanel.py

	* [r648] tests/testgui.py,
	  tests/testplot.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/testplotgroup.py,
	  tests/testsheet.py,
	  tests/testsheetview.py,
	  tests/tk/testactivitypanel.py,
	  tests/tk/testplotpanel.py,
	  topo/cfsheet.py,
	  topo/plot.py,
	  topo/plotengine.py,
	  topo/plotfilesaver.py,
	  topo/plotgroup.py,
	  topo/sheet.py,
	  topo/tk/basicplotpanel.py,
	  topo/tk/inputparamspanel.py,
	  topo/tk/preferencemappanel.py:
	  All references to Activation or Activity have now been
	  standardized to Activity

	* [r647] topo/sheet.py:
	  Fixed two JAB comments

	* [r646] topo/parameter.py,
	  topo/scalarep.py:
	  Updated comments

	* [r645] topo/params.py:
	  file changed to parameter.py

	* [r644] examples/cfsom_example.py,
	  examples/gui_example.py,
	  models/cfsom.py,
	  tests/testcfsom.py,
	  tests/testplotengine.py,
	  tests/tk/testplotpanel.py,
	  topo/__init__.py,
	  topo/base.py,
	  topo/boundingregion.py,
	  topo/cfsheet.py,
	  topo/image.py,
	  topo/inputsheet.py,
	  topo/kernelfactory.py,
	  topo/palette.py,
	  topo/parameter.py,
	  topo/plot.py,
	  topo/scalarep.py,
	  topo/sheet.py,
	  topo/simulator.py:
	  Renamed params.py to parameter.py

	* [r643] topo/kernelfactory.py:
	  Updated JAB comment

	* [r642] topo/inputsheet.py:
	  Removed import star

	* [r641] topo/gui.py:
	  Listed the three purposes of file in comment.

	* [r640] topo/composer.py:
	  Updated comment

	* [r639] topo/image.py,
	  topo/kernelfactory.py,
	  topo/plotfilesaver.py:
	  Added comments about moving evenually moving image.py and moving
	  functionality.

	* [r638] topo/cfsom.py:
	  Moved to /models/

	* [r637] models/cfsom.py,
	  tests/testcfsom.py:
	  Moved sample code in __main__ block of cfsom.py to testcfsom.py

	* [r636] examples/cfsom_example.py,
	  examples/gui_example.py,
	  models,
	  models/__init__.py,
	  models/cfsom.py,
	  tests/testcfsom.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/tk/testplotpanel.py,
	  topo/__init__.py:
	  Moved cfsom.py into a /models/ module. This required changes to
	  files that used it, and test cases.

	* [r635] topo/base.py:
	  Removed an import star

2005-09-02  jdepaula

	* [r634] tests/testgui.py,
	  tests/testplotengine.py,
	  tests/testplotfilesaver.py,
	  tests/testplotgroup.py:
	  Updated function call parameters to work with PlotTemplate-Only
	  PlotEngine class

	* [r633] topo/plotgroup.py:
	  Changed class names to match UnitWeights and Projection

	* [r632] topo/plotfilesaver.py:
	  Updated file saving classes to use the PlotTemplates instead of
	  the original mechanism.

	* [r631] topo/plotengine.py:
	  Removed an unused lambda. Commented out old PlotGroup creation
	  mechanism in preperation for complete deletion.

	* [r630] topo/tk/unitweightspanel.py:
	  Changed reference to WeightsPlotGroup to UnitWeights....

	* [r629] topo/tk/topoconsole.py:
	  Commented out old static Plot menu code, in preperation of
	  complete removal

	* [r628] tests/tk/testactivitypanel.py,
	  tests/tk/testplotpanel.py:
	  Functions no longer exist

	* [r627] tests/tk/__init__.py:
	  Removed weights files

	* [r626] tests/tk/testweightsarraypanel.py,
	  tests/tk/testweightspanel.py:
	  These files no longer exist

	* [r625] topo/tk/weightsarraypanel.py,
	  topo/tk/weightspanel.py:
	  Changed filenames, and functional interface

2005-09-01  yfsit

	* [r624] examples/lissom.ty:
	  Orientation-selective receptive fields can now be learned.

2005-08-31  yfsit

	* [r623] topo/cfsheet.py:
	  added reduce_cfsize to class Projection and reduce_radius in
	  ConnectionField.

	* [r622] topo/simulator.py:
	  added sched_execfn() to the Simulator class that schedules the
	  execution of
	  of passed function at the given time. These events are marked
	  with the execfn
	  flag.

	* [r621] topo/utils.py:
	  changed PLTF so that lower and upper thresholds can be set. The
	  old PLTF is nowcalled PLTF01.

	* [r620] topo/boundingregion.py:
	  bug fix of containsbb_exclusive().

2005-08-31  jbednar

	* [r619] topo/tk/projectionpanel.py,
	  topo/tk/unitweightspanel.py:
	  Removed outdated JABHACKALERTs

	* [r618] topo/bitmap.py:
	  Changed warning to notice, and clarified JABHACKALERT

2005-08-30  jdepaula

	* [r617] topo/plotgroup.py:
	  Created a new PlotGroup named ProjectionPlotGroup that is from
	  WeightsArrayPlotGroup but used with the PlotTemplates.
	  WeightsArrayPlotGroup needs to be phased out now.

	* [r616] topo/plotengine.py:
	  Added PlotTemplate support for Unit Weights and Projection plots.
	  Still has the old mechanism to be removed.

	* [r615] topo/tk/plotpanel.py:
	  Changed an if so broken code sometimes fails safely.

	* [r614] topo/plot.py:
	  Added comments for new PlotTemplate options, adjusted __init__
	  parameters

	* [r613] topo/cfsheet.py:
	  Added get_projection_by_name()

	* [r612] topo/tk/topoconsole.py:
	  Added dynamic Plots menu generation. Removed old entries, but the
	  code is still there for now to avoid name problems.

	* [r611] tests/testplotgroup.py:
	  Additional test of .append to verify fixed bug in KeyedList

	* [r610] tests/testcfsom.py:
	  Added test for get_projection_by_name()

	* [r609] topo/tk/__init__.py:
	  Added projectionpanel.py and unitweightspanel.py

	* [r608] topo/tk/projectionpanel.py,
	  topo/tk/unitweightspanel.py:
	  Changed filenames and included PlotTemplate mechanism

2005-08-30  jbednar

	* [r607] topo/base.py:
	  Fixed comment

2005-08-28  jbednar

	* [r606] examples/gui_example.py:
	  Made densities easier to edit

2005-08-25  jdepaula

	* [r605] topo/tk/topoconsole.py:
	  Moved the PlotGroupTemplate definitions out of this class.

	* [r604] topo/plotengine.py,
	  topo/tk/topoconsole.py:
	  Moved the PlotGroupTemplate definitions into PlotEngine, for now
	  Activity and a Activity HSV

	* [r603] tests/testbitmap.py:
	  Added tests for matrix_hsv_to_rgb

	* [r602] topo/plot.py:
	  Potential bug fixed so now new empty matrices will be Floats.

	* [r601] topo/bitmap.py:
	  Fixed error with matrix_hsv_to_rgb where the return matrices were
	  not taking on the correct values and side-effects were making it
	  hard to detect.

2005-08-23  yfsit

	* [r600] examples/lissom.ty:
	  every projection now has a different learning rate.

	* [r599] topo/cfsheet.py:
	  learning_rate is now an attribute of KernelProjection

	* [r598] topo/boundingregion.py:
	  Added method containsbb_exclusive() that finds is a region is
	  contained in the
	  boundingbox.

2005-08-23  jdepaula

	* [r597] topo/tk/topoconsole.py:
	  Two sample dynamic plots added, will be replaced shortly with
	  properly named plots; this done to guarantee Topo running for
	  other developers.

	* [r596] topo/sheetview.py:
	  Changed comment

	* [r595] topo/plotengine.py:
	  Removed background attributes from PlotGroup Templates at Jim's
	  request

	* [r594] topo/bitmap.py:
	  Patched matrix_hsv_to_rgb so it does not raise exceptions, but it
	  must be fixed so that reasonable things take place such as
	  cropping and warnings.

2005-08-20  yfsit

	* [r593] examples/lissom.ty:
	  moved the inline C learning code into learningrules.py.

2005-08-19  yfsit

	* [r592] topo/cfsheet.py:
	  added a learning_fn parameter in CFSheet.

	* [r591] topo/learningrules.py:
	  A new file that contains different learning rules.

	* [r590] topo/cfsheet.py:
	  moved compute_response_mdot_c and comput_response_mdot_py into
	  utils.py

	* [r589] topo/utils.py:
	  The inline C function compute_response_mdot_c is moved into
	  utils.py from
	  cfsheet.py.

2005-08-18  jbednar

	* [r588] topo/inputsheet.py:
	  Made message more useful

2005-08-17  jbednar

	* [r587] topo/boundingregion.py:
	  Cleaned up comments; added upperexclusive_contains

	* [r586] topo/inputsheet.py:
	  Added JABHACKALERTs

	* [r585] topo/sheet.py,
	  topo/sheetview.py:
	  Added JABHACKALERTs and cleaned up documentation

2005-08-17  yfsit

	* [r584] examples/lissom.ty:
	  The learn() function is rewritten in C.

2005-08-17  jdepaula

	* [r583] topo/tk/topoconsole.py:
	  Initial creation of dynamic Plots entries based upon
	  plotgroup_templates dictionary. Additional cleanup needed, but
	  core classes and functionality now exists.

	* [r582] topo/plotgroup.py:
	  Added self.description to PlotGroups

	* [r581] topo/plotengine.py:
	  Moved plotgroup_templates out of the PlotEngine class so that
	  there is one static list per Topographica run.

2005-08-16  jbednar

	* [r580] topo/base.py,
	  topo/composer.py,
	  topo/params.py,
	  topo/sheetview.py:
	  Added JABHACKALERTs and cleaned up documentation

	* [r579] CONVENTIONS:
	  Added note about filenames

2005-08-15  jbednar

	* [r578] topo/cfsom.py,
	  topo/scalarep.py,
	  topo/utils.py:
	  Added JABHACKALERTs and cleaned up some documentation

	* [r577] CONVENTIONS:
	  Added note about .ty vs. .py.

	* [r576] topo/composer.py,
	  topo/dislindriver.py,
	  topo/dislinplot.py:
	  Added note about not being used

	* [r575] topo/bitmap.py:
	  Fixed typo

	* [r574] topo/base.py:
	  Moved documentation of TopoObject directly into that class

	* [r573] topo/__init__.py,
	  topo/gui.py,
	  topo/inputsheet.py,
	  topo/tyimputil.py,
	  topographica_script.py:
	  Added JABHACKALERTs

	* [r572] topo/tk/inputparamspanel.py,
	  topo/tk/plotpanel.py,
	  topo/tk/preferencemappanel.py,
	  topo/tk/topoconsole.py:
	  Minor cleanup, and added more JABHACKALERTs

	* [r571] topo/bitmap.py,
	  topo/kernelfactory.py,
	  topo/tk/basicplotpanel.py,
	  topo/tk/propertiesframe.py,
	  topo/tk/taggedslider.py,
	  topo/tk/weightspanel.py:
	  Minor cleanup

	* [r570] CONVENTIONS:
	  Added note about how to name UI items

	* [r569] topo/bitmap.py,
	  topo/kernelfactory.py,
	  topo/tk/basicplotpanel.py,
	  topo/tk/inputparamspanel.py,
	  topo/tk/plotpanel.py,
	  topo/tk/preferencemappanel.py,
	  topo/tk/regionplotpanel.py,
	  topo/tk/topoconsole.py,
	  topo/tk/weightsarraypanel.py,
	  topo/tk/weightspanel.py:
	  Added JABHACKALERTs and cleaned up text labels and some class
	  names

2005-08-14  yfsit

	* [r568] topo/bitmap.py,
	  topo/cfsheet.py:
	  fixed the array dimension get passed into the bitmap constructor.

2005-08-12  jbednar

	* [r567] external,
	  external/.cvsignore:
	  Added weave files to ignore

2005-08-11  jdepaula

	* [r566] topo/cfsheet.py,
	  topo/plotengine.py,
	  topo/plotfilesaver.py,
	  topo/plotgroup.py,
	  topo/tk/preferencemappanel.py,
	  topo/tk/weightspanel.py:
	  Moved the storage of UnitViews from the destination of the
	  Projections, to the Source of the projections. This means weights
	  views for a unit on a Sheet is now distributed.

2005-08-11  yfsit

	* [r565] topo/cfsheet.py,
	  topo/kernelfactory.py,
	  topo/sheet.py:
	  - Improved performance by changing the mdot function into C code.
	  - A better fix using kernels other than uniform for connection
	  field.

	* [r564] external/Makefile:
	  added entry for weave (Scipy)

	* [r563]
	  external/Scipy_core-0.3.0_108.1820.tar.gz:
	  add the weave package

2005-08-10  jbednar

	* [r562] topo/tk/inputparamspanel.py:
	  Added JABHACKALERT warning

	* [r561] MILESTONES:
	  Updated with progress

	* [r560] topo/tk/taggedslider.py:
	  Added JABHACKALERT

2005-07-30  jdepaula

	* [r559] topo/tk/preferencemappanel.py:
	  Removed SCCPlot reference and old code

	* [r558] topo/plotengine.py:
	  Templates now store background info

	* [r557] topo/plot.py:
	  Removed class that is no longer used.

	* [r556] topo/bitmap.py:
	  Comment typo

	* [r555] topo/tk/preferencemappanel.py:
	  Preference panel stub now uses a PlotGroupTemplate

	* [r554] topo/plotengine.py:
	  PlotGroupTemplates are now accepted when creating PlotGroups

	* [r553] topo/plotgroup.py:
	  Removed DictPlotGroup since templates are now implemented.

	* [r552] topo/plot.py:
	  Added SHC plot type. For now it's just an alias for an HSV map,
	  with the channels realigned.

	* [r551] tests/testplotengine.py:
	  Test new template format

	* [r550] topo/plot.py:
	  Added TODO comment about needing to allow multiple sheets in the
	  SheetView sources

	* [r549] topo/plotgroup.py:
	  Added fix for PlotGroups started with no PlotTemplates in
	  constructor

	* [r548] tests/testplotgroup.py:
	  Added tests for PlotGroupTemplate

	* [r547] tests/testplot.py:
	  Added tests for PlotTemplate

	* [r546] topo/plotgroup.py:
	  Added PlotGroupTemplate and KeyedList

	* [r545] topo/plot.py:
	  Added PlotTemplate

	* [r544] tests/tk/testpreferencemappanel.py,
	  tests/tk/testweightspanel.py:
	  Cut some dead lines

	* [r543] tests/testplotengine.py,
	  tests/testplotgroup.py:
	  Starting to add Plot Templates

2005-07-23  jdepaula

	* [r542] topo/tk/preferencemappanel.py:
	  Removed some dead commands

2005-07-21  yfsit

	* [r541] topo/cfsheet.py,
	  topo/sheet.py:
	  fixed cfsheet.py and sheet.py so that the all the unit tests are
	  passed.
	  
	  The way that the weights in a connection field are initialized
	  was changed
	  quite significantly in the previous version of cfsheet (1.11).
	  This breaks one
	  test because the weights were assumed to be uniform in that
	  version. Now the
	  code first checks if the initial weight distribution is uniform
	  random. If yes,
	  then the code will follow the same flow as version 1.11. If no,
	  the flow will
	  fall back to 1.10. The main difference between these two version
	  is that 1.11
	  implements find the set of connection field boundary that matched
	  the C++
	  simulator and should be correct. In 1.10, the size seems to be
	  off by one
	  in some cases.
	  
	  To fix the code so that all kinds of initial weight distributions
	  will have the
	  correct connection field boundary may require some significant
	  changes in
	  kernelfactory.py.

2005-07-17  jdepaula

	* [r540] topo/tk/plotpanel.py:
	  Removed the old code Preference Map code from LISSOM into a new
	  class file. All old windows have now been removed from this file.

	* [r539] topo/tk/topoconsole.py:
	  Preference Map option is now active, and no longer grayed out.

	* [r538] topo/plotgroup.py:
	  Added PreferenceMapPlotGroup

	* [r537] topo/plotengine.py:
	  Uncommented try/except catch for a bad PlotGroup subclass type

	* [r536] topo/plot.py:
	  Added SCCPlot

	* [r535] tests/testplot.py:
	  Added test for SCC Plots

	* [r534] tests/tk/__init__.py,
	  topo/tk/__init__.py:
	  Added preferencemappanel.py

	* [r533] tests/tk/testpreferencemappanel.py,
	  topo/tk/preferencemappanel.py:
	  For new GUI window

2005-07-16  jdepaula

	* [r532] tests/README.txt:
	  Added run examples

2005-07-11  yfsit

	* [r531] topo/cfsheet.py:
	  restores the changes made in 1.11 that were overwritten in 1.12.

2005-07-09  yfsit

	* [r530] examples/lissom.ty,
	  topo/cfsheet.py,
	  topo/sheet.py,
	  topo/utils.py:
	  changed cfsheet.py, sheet.py, and utils.py so that the new
	  lissom.ty now
	  matches the c++ simulator.
	  
	  The computation of response of each connection field is now moved
	  into
	  the Projection class. The response is stored in temp_activation
	  of each
	  Projection so that it does not have to be computed every time.
	  There are
	  some simple optimizations to decrease the number of function
	  calls as well.

2005-06-21  jbednar

	* [r529] topo/cfsheet.py:
	  Added some notes

2005-06-18  jdepaula

	* [r528] topo/tk/inputparamspanel.py,
	  topo/tk/regionplotpanel.py,
	  topo/tk/weightsarraypanel.py,
	  topo/tk/weightspanel.py:
	  Patched for new files with no wildcard imports

	* [r527] tests/tk/testactivitypanel.py:
	  Added new import

	* [r526] topo/plotfilesaver.py:
	  Updated to save PNGs instead of JPGs

	* [r525] topo/tk/basicplotpanel.py,
	  topo/tk/inputparamspanel.py,
	  topo/tk/plotpanel.py,
	  topo/tk/propertiesframe.py,
	  topo/tk/regionplotpanel.py,
	  topo/tk/taggedslider.py,
	  topo/tk/topoconsole.py,
	  topo/tk/weightsarraypanel.py,
	  topo/tk/weightspanel.py:
	  Removed wildcard imports to clean up namespaces

2005-06-17  jdepaula

	* [r524] topo/tk/basicplotpanel.py:
	  plot_key is now part of constructor, so users do not have to
	  subclass.

2005-06-15  jdepaula

	* [r523] topo/tk/activitypanel.py:
	  *** empty log message ***

	* [r522] tests/testplotgroup.py,
	  tests/tk/testactivitypanel.py,
	  tests/tk/testweightsarraypanel.py,
	  tests/tk/testweightspanel.py,
	  topo/plotengine.py,
	  topo/plotfilesaver.py,
	  topo/plotgroup.py,
	  topo/tk/__init__.py,
	  topo/tk/plotpanel.py,
	  topo/tk/topoconsole.py:
	  Necessary name changes to go from ActivityPanel to BasicPlotPanel

	* [r521] topo/tk/basicplotpanel.py:
	  Originally ActivityPanel

2005-06-12  jdepaula

	* [r520] external/win32,
	  external/win32/.cvsignore:
	  Init

	* [r519] external/win32/setup.py:
	  Added matplotlib

	* [r518]
	  external/win32/PIL-1.1.5.win32-py2.4.exe,
	  external/win32/matplotlib-0.81.win32-py2.4.exe:
	  For file permissions under windows

	* [r517]
	  external/win32/PIL-1.1.5.win32-py2.4.exe,
	  external/win32/matplotlib-0.81.win32-py2.4.exe:
	  For file permissions

	* [r516] TODO.txt:
	  Added suggestion for normalization/clipping buttons in GUI.

	* [r515] tests/__init__.py,
	  tests/tk/__init__.py:
	  Added testmatplotlib.py

	* [r514] tests/testmatplotlib.py,
	  tests/tk/testmatplotlibtk.py:
	  Initial version

	* [r513] external/Makefile:
	  Added MatPlotLib

	* [r512] /trunk/topographica, .cvsignore,
	  external,
	  external/.cvsignore:
	  Ignore PyPlotLib assoc files

	* [r511] external/matplotlib-0.81.tgz,
	  external/win32/matplotlib-0.81.win32-py2.4.exe:
	  June 7, 2005 release

2005-06-11  jdepaula

	* [r510] topo/tk/taggedslider.py:
	  Preview will now update when the user enters text and clicks
	  somewhere else, even without hitting enter.

2005-06-05  jdepaula

	* [r509] topo/tk/weightspanel.py:
	  Removed some whitespace

	* [r508] topo/cfsheet.py:
	  Important bug fix: corrected r/c unit view swap, and transpose
	  weights so they will be in x/y, width/height orientation.

	* [r507] topo/tk/weightsarraypanel.py:
	  Fixed WeightArray unit display order to match order generated by
	  plotgroup.py

	* [r506] topo/plotgroup.py:
	  Removed filenames, changed WeightsArray coordinate generation.

	* [r505] topo/tk/taggedslider.py:
	  Bug fix: Refresh the sliders on creation

2005-06-04  jdepaula

	* [r504] topo/tk/activitypanel.py,
	  topo/tk/plotpanel.py:
	  Decreased amount of code in ActivityPanel

	* [r503] topo/tk/inputparamspanel.py,
	  topo/tk/taggedslider.py:
	  Tags now only update preview on CR or Refresh

	* [r502] topo/tk/topoconsole.py:
	  Made title smaller, so active sim is shown.

	* [r501] topo/tk/activitypanel.py:
	  Changed comment

	* [r500] TODO.txt:
	  Added two todos about extending GUI kernels

	* [r499] tests/testplotfilesaver.py:
	  Forgot to uncomment the file-deletion loop.

2005-06-03  jdepaula

	* [r498]
	  external/win32/PIL-1.1.5.win32-py2.4.exe,
	  external/win32/setup.py:
	  Upgraded to 1.1.5

	* [r497]
	  external/win32/PIL-1.1.5b3.win32-py2.4.exe:
	  Upgraded

	* [r496] external,
	  external/.cvsignore,
	  external/Imaging-1.1.5.tgz,
	  external/Makefile:
	  Updated to PIL 1.1.5

	* [r495] tests/testplotfilesaver.py,
	  topo/plotfilesaver.py:
	  Added skeleton functionality for plot file saving.

2005-06-02  jdepaula

	* [r494] topo/sheet.py,
	  topo/tk/inputparamspanel.py:
	  Separated learning and activation saving.

2005-05-18  jbednar

	* [r493] TODO.txt:
	  Fixed typo

2005-05-18  jdepaula

	* [r492] tests/testplotengine.py,
	  tests/testplotgroup.py,
	  topo/plotengine.py,
	  topo/plotgroup.py,
	  topo/tk/activitypanel.py,
	  topo/tk/inputparamspanel.py,
	  topo/tk/plotpanel.py,
	  topo/tk/regionplotpanel.py,
	  topo/tk/weightsarraypanel.py,
	  topo/tk/weightspanel.py:
	  Refactored so PlotGroups now create plots using
	  self.do_plot_cmd(), and GUI now uses this instead of generating
	  working with the sheets directly.

	* [r491] tests/__init__.py:
	  Added testplotfilesaver.py

	* [r490] tests/testplotfilesaver.py:
	  Init.

	* [r489] topo/__init__.py:
	  Added plotfilesaver.py

	* [r488] topo/plotfilesaver.py:
	  Initial. Single class, mostly stub.

	* [r487] topo/plot.py:
	  Patched plot() so that multiple calls to the same object works.

2005-05-14  jbednar

	* [r486] topo/sheet.py:
	  Fixed typo

	* [r485] topo/sheet.py:
	  Cleaned up comments

	* [r484] Makefile:
	  Added test target

	* [r483] CONVENTIONS,
	  topo/kernelfactory.py:
	  Fixed conflict with lissom.ty, and wrote section on how to avoid
	  future such problems

2005-05-14  jdepaula

	* [r482] topo/simulator.py:
	  Bug when sleeping, but no events yet. Just deleted a debug
	  statement that used the offending variable.

	* [r481] tests/__init__.py,
	  tests/testplot.py,
	  tests/testplotengine.py,
	  tests/testplotgroup.py,
	  topo/__init__.py,
	  topo/plot.py,
	  topo/plotengine.py,
	  topo/plotgroup.py:
	  Refactored to move PlotGroup into its own file.

	* [r480] topo/kernelfactory.py:
	  Changed return of rectangle value back to rev 1.39 version

	* [r479] external,
	  external/.cvsignore:
	  Added topographica flag

	* [r478] topo/kernelfactory.py:
	  Commented code, attempt to resolve the rotation problem with
	  rectangle()

	* [r477] topo/tk/inputparamspanel.py,
	  topo/tk/plotpanel.py:
	  Cleaned up comments

2005-05-13  jdepaula

	* [r476] tests/testkernelfactory.py:
	  Added orientation test

	* [r475] topo/tk/weightspanel.py:
	  Updated labels so it stays correct

	* [r474] topo/sheet.py:
	  Changed comment

	* [r473] tests/tk/testweightspanel.py:
	  Added an orientation test for kernels.

2005-05-09  jdepaula

	* [r472] topo/sheet.py:
	  Condition where bounds is less than a density slice required a
	  default single array element inside bounds2shape()

2005-05-08  jdepaula

	* [r471] topo/tk/plotpanel.py:
	  Changed normalisation to cliping. No warning, or reporting if
	  cliped.

	* [r470] tests/testsheet.py,
	  topo/sheet.py:
	  Changed matrix2sheet and sheet2matrix to have the coordinates
	  centered on the middle of the matrix units. Updated unit tests to
	  reflect this

	* [r469] topo/kernelfactory.py:
	  Added comments to header.

2005-05-06  jdepaula

	* [r468] topo/kernelfactory.py:
	  Removed forgotten print statement

2005-05-05  jdepaula

	* [r467] topo/cfsheet.py,
	  topo/inputsheet.py,
	  topo/kernelfactory.py,
	  topo/tk/inputparamspanel.py:
	  Fixed internal KernelFactory matrix representaiton so it's
	  cartesian orientation.

	* [r466] topo/simulator.py:
	  Updated comments to reflect Simulator class renaming

	* [r465] topo/tk/plotpanel.py:
	  Disable normalization default, for Preview Panel

	* [r464] topo/bitmap.py:
	  Extended normalization warning

	* [r463] TODO.txt:
	  Added user entry eval to GUI

2005-05-04  jdepaula

	* [r462] topo/tk/weightspanel.py:
	  x/y outside of the bounding box is now caught.

	* [r461] topo/tk/inputparamspanel.py:
	  All kernelfactories now give proper bounds matching their
	  InputSheets.

	* [r460] topo/kernelfactory.py:
	  Cleaned up white-out limit effects of 4 kernels.

2005-05-02  jbednar

	* [r459] topo/tk/inputparamspanel.py:
	  Made default values more useful

	* [r458] topo/sheet.py:
	  Removed apparently unused code

	* [r457] tests/testcfsom.py:
	  Trivial fix

2005-05-01  jdepaula

	* [r456] topo/tk/inputparamspanel.py:
	  Fix Reset to Defaults to maintain learning state.

	* [r455] topo/tk/inputparamspanel.py:
	  Input Params panel now is destroyed, not minimized.

	* [r454] topo/tk/plotpanel.py:
	  Flicker free preview plots and labels

	* [r453] topo/tk/inputparamspanel.py:
	  Enabled 'Learning' checkbox. non-learning simulation state now
	  possible.

	* [r452] examples/cfsom_example.py:
	  Changed SimpleSimulator to the Simulator. Functionality should
	  not have changed.

	* [r451] tests/testsimulator.py:
	  Added additional tests for state_push and state_pop

	* [r450] topo/simulator.py:
	  Changed SimpleSimulator to Simulator. Added state_push and pop,
	  so restore previous Simulator states.

	* [r449] topo/sheet.py:
	  Name fix, incorrect variable name.

2005-04-30  jdepaula

	* [r448] topo/tk/weightspanel.py:
	  Changed projection plot to connection field plot

	* [r447] topo/kernelfactory.py:
	  Removed some dead code

	* [r446] tests/testkernelfactory.py:
	  For kernelfactory.py

	* [r445] tests/__init__.py:
	  Added unit test for kernelfactory

2005-04-27  jdepaula

	* [r444] tests/testcfsom.py,
	  tests/tk/testplotpanel.py,
	  tests/tk/testtopoconsole.py:
	  Updated to reflect RF to CF change in core code

2005-04-26  jprovost

	* [r443] topo/cfsheet.py:
	  Small optimization in getting CF matrix slice bounds.

2005-04-25  jdepaula

	* [r442] examples/lissom.ty:
	  Change train() to learn()

	* [r441] topo/tk/topoconsole.py:
	  Changed train to learn

	* [r440] topo/tk/inputparamspanel.py:
	  Removed text message when InputParamsPanel withdrawn.

	* [r439] topo/tk/inputparamspanel.py:
	  Tweaked default values of Sliders

	* [r438] topo/kernelfactory.py:
	  Fixed FuzzyDisk, and FuzzyRing

2005-04-24  jdepaula

	* [r437] topo/cfsheet.py:
	  Patch to unit_view

	* [r436] topo/cfsheet.py:
	  Patch to unit_view

2005-04-23  jdepaula

	* [r435] topo/kernelfactory.py:
	  Changed X/Y vectors so they'll be symmetric with Topographica
	  standards.

	* [r434] topo/tk/inputparamspanel.py:
	  Changed message strings; User Kernels now presented even to
	  unselected input sheets; Hack to rotate and flip off-axis
	  KernelFactories; Make Kernels have same density as InputSheets.

	* [r433] topo/cfsheet.py,
	  topo/inputsheet.py:
	  Dirty hack using flipud(rot90(.)) to get X/Y working right with
	  KernelFactories and the rest of the simulator.

2005-04-22  jbednar

	* [r432] examples/lissom.ty:
	  Changed to match lissom/samples/or_map_topo.param

2005-04-22  jdepaula

	* [r431] topo/tk/inputparamspanel.py,
	  topo/tk/topoconsole.py:
	  Changed bounds on some kernels; changed window deletion manager
	  to inside InputParamsPanel; separated activation saving and
	  learning disabling.

	* [r430] topo/kernelfactory.py:
	  Changed comment; code to swap x/y tried, then commented out.
	  Future work will be necessary.

2005-04-21  jdepaula

	* [r429] examples/cfsom_example.py,
	  examples/gui_example.py:
	  Added ID CVS tags

	* [r428] examples/cfsom_example.py,
	  examples/gui_example.py:
	  Changed class attribute training_length to leaning_length

	* [r427] topo/cfsheet.py:
	  Changed learning to _learning

	* [r426] topo/sheet.py:
	  Added activation_push and activation_pop

2005-04-21  jbednar

	* [r425] etc/topographica.el:
	  Fixed emacs code; wouldn't have worked on other people's systems

	* [r424] README.txt:
	  Made ready for public consumption

	* [r423] etc/topographica.el:
	  Made auto-select the right mode for .ty files

2005-04-21  jdepaula

	* [r422] topo/tk/weightsarraypanel.py,
	  topo/tk/weightspanel.py:
	  Turned off auto-refresh

	* [r421] topo/cfsheet.py,
	  topo/cfsom.py,
	  topo/sheet.py:
	  Changed training to learning

2005-04-20  jdepaula

	* [r420] topo/tk/inputparamspanel.py:
	  Added real value field for length of time to present stimulus to
	  network.

	* [r419] topo/tk/activitypanel.py,
	  topo/tk/plotpanel.py,
	  topo/tk/weightspanel.py:
	  Made auto-refresh the default for plot panels. Removed toggles in
	  derived classes

	* [r418] topo/cfsheet.py,
	  topo/sheet.py:
	  Added training Parameter, stores activation, and does not train
	  if flag not set

	* [r417] topo/params.py:
	  Added a BooleanParameter

2005-04-20  jbednar

	* [r416] topo/tk/activitypanel.py,
	  topo/tk/weightsarraypanel.py,
	  topo/tk/weightspanel.py:
	  Made initial plot sizes be more usable; not sure why weightspanel
	  can't get smaller

	* [r415] topo/simulator.py:
	  Fixed some comments

	* [r414] topo/kernelfactory.py:
	  Removed debugging message

	* [r413] MILESTONES:
	  Marked some items as done

2005-04-19  jdepaula

	* [r412] topo/inputsheet.py,
	  topo/tk/inputparamspanel.py:
	  Linked input presentation kernel to simulators, so that Presents
	  now run the Simulatior 1 time step with the input presentation.

	* [r411] examples/cfsom_example.py,
	  examples/gui_example.py:
	  Patched for RF to CF

2005-04-15  jbednar

	* [r410] topo/rfsheet.py:
	  Moved to cfsheet.py

	* [r409] topo/tk/regionplotpanel.py:
	  Changed to use CFSheet instead of RFSheet

	* [r408] examples/lissom.ty:
	  Fixed old typo

	* [r407] examples/rfsom_example.py,
	  tests/testrfsom.py,
	  topo/rfsom.py:
	  Moved to CFSOM equivalent

	* [r406] examples/gui_example.py,
	  tests/__init__.py,
	  tests/testplotengine.py,
	  topo/__init__.py:
	  Changed RFSOM to CFSOM

	* [r405] examples/cfsom_example.py,
	  tests/testcfsom.py,
	  topo/cfsom.py:
	  Initial version copied from RFSOM equivalent

	* [r404] examples,
	  examples/.cvsignore:
	  Initial version

	* [r403] etc/topographica.el:
	  Added usage notes

	* [r402] etc,
	  etc/.cvsignore,
	  etc/topographica.el:
	  Initial version

	* [r401] external/README.txt:
	  Minor fix

	* [r400] examples/gui_example.py,
	  examples/lissom.ty,
	  examples/rfsom_example.py,
	  topo/rfsom.py,
	  topo/simulator.py:
	  Changed to use CFSheet instead of RFSheet

	* [r399] topo/cfsheet.py:
	  Initial version copied from topo/rfsheet.py 1.22

2005-04-11  jdepaula

	* [r398] topo/tk/inputparamspanel.py:
	  Lots of good stuff added: A Preview window, dynamic slider list,
	  and dynamic list of KernelFactory types for input presentation.
	  Buttons now allow choice of which input sheets to present to. Now
	  a subclass of PlotPanel so Enlarge/Re?\004duce/Auto-refresh are
	  all now included. Still does not connect to the simulation, since
	  the input sheet mechanism is not yet ready.

	* [r397] topo/tk/propertiesframe.py:
	  Added new function to refresh only if the auto-refresh is set.

	* [r396] topo/tk/topoconsole.py:
	  Added plot engine parameter to ImputParamsPanel

	* [r395] topo/tk/taggedslider.py:
	  Added optional refresh after a slider movement

	* [r394] topo/kernelfactory.py:
	  Patched FuzzyDisk, Rectangle. Added registry for KernelFactory
	  types that the GUI can use

	* [r393] topo/inputsheet.py:
	  Added accessor and mutator for input_generator

	* [r392] topo/params.py:
	  Fixed grammar in comment.

2005-04-11  jbednar

	* [r391] examples/lissom.ty:
	  Made delays be fractions so that LISSOM matches the standard time
	  base of 1.0 time steps per input presentation

	* [r390] topo/rfsheet.py:
	  Fixed typo

2005-04-08  jbednar

	* [r389] JP-NOTES.txt:
	  Moved to TODO.txt

	* [r388] CONVENTIONS:
	  Small clarification

2005-04-08  jdepaula

	* [r387] topo/tk/inputparamspanel.py,
	  topo/tk/propertiesframe.py,
	  topo/tk/taggedslider.py,
	  topo/tk/weightsarraypanel.py:
	  Added dynamic generation of KernelFactory types. Doesn't load all
	  of the Params fields properly, but CVSed to show Jim what it
	  looks like

2005-04-08  jbednar

	* [r386] /trunk/topographica, .cvsignore:
	  Added generated directories and scripts

	* [r385] external,
	  external/.cvsignore,
	  tests, tests/.cvsignore,
	  tests/tk,
	  tests/tk/.cvsignore:
	  Initial version

	* [r384] topo/tk/weightsarraypanel.py:
	  Allowed smaller plots, and made intial size smaller

	* [r383] examples/gui_example.py:
	  Reduced the densities to speed up debugging

	* [r382] topo/tk/weightsarraypanel.py:
	  Fixed the default density

	* [r381] topo/tk/plotpanel.py:
	  Removed unneeded LISSOM interface functions. Allowed small plots

	* [r380] topo/plot.py,
	  topo/plotengine.py,
	  topo/sheet.py,
	  topo/tk/__init__.py,
	  topo/tk/activitypanel.py:
	  Cleaned up comments

	* [r379] runtests:
	  Tried to make runnable, but doesn't work for some reason

2005-04-07  jdepaula

	* [r378] topo/tk/inputparamspanel.py:
	  Pulled from plotpanel

2005-04-06  jdepaula

	* [r377] topo/tk/__init__.py,
	  topo/tk/plotpanel.py,
	  topo/tk/taggedslider.py,
	  topo/tk/topoconsole.py:
	  Added the input presentation window. Doesn't do anything to the
	  back end.

	* [r376] TODO.txt:
	  Added two points on GUI and Cmdline

2005-04-05  jdepaula

	* [r375] tests/testgui.py,
	  tests/testplot.py,
	  tests/testplotengine.py,
	  tests/testsheet.py:
	  Patched to work with changes to GUI for new label name storage

	* [r374] topo/bitmap.py,
	  topo/plot.py,
	  topo/plotengine.py,
	  topo/sheetview.py,
	  topo/tk/activitypanel.py,
	  topo/tk/plotpanel.py,
	  topo/tk/regionplotpanel.py,
	  topo/tk/weightsarraypanel.py:
	  Completed transition of GUI labels generated from view_info
	  dictionaries

2005-04-04  jdepaula

	* [r373] topo/plot.py,
	  topo/rfsheet.py,
	  topo/sheet.py,
	  topo/sheetview.py:
	  Added view_info dictionaries

	* [r372] topo/tk/plotpanel.py,
	  topo/tk/weightsarraypanel.py,
	  topo/tk/weightspanel.py:
	  Added self.baloon

2005-04-03  jbednar

	* [r371] TODO.txt:
	  Initial version

2005-04-01  jdepaula

	* [r370] examples/gui_example.py:
	  Added names to the projections

	* [r369] topo/tk/plotpanel.py,
	  topo/tk/weightsarraypanel.py:
	  Changed canvas x,y pad, made space smaller.

2005-03-30  jdepaula

	* [r368] topo/tk/regionplotpanel.py:
	  do_plot_cmd() now takes in a tuple from PlotGroup.plots()

	* [r367] topo/tk/weightspanel.py:
	  Redefines display_labels() to change grid label.

	* [r366] topo/tk/activitypanel.py:
	  Now redefines display_labels() to show different label. Takes is
	  a tuple from PlotEngine.plots() now.

	* [r365] topo/tk/weightsarraypanel.py:
	  The UnitViews are now shown in a 2D grid, and the source
	  projection sheet is now named

	* [r364] topo/tk/plotpanel.py:
	  Main plot window now has a label

	* [r363] topo/sheetview.py:
	  UnitViews now require the projection they came from

	* [r362] topo/sheet.py:
	  SheetViews now include Sheet names

	* [r361] topo/rfsheet.py:
	  Removed bad function. UnitView names now include the sheetname.

	* [r360] topo/plot.py:
	  Now makes Plots match SheetView names

	* [r359] topo/plotengine.py:
	  Makes Plot names match the SheetView names.

2005-03-28  jdepaula

	* [r358] topo/tk/weightsarraypanel.py:
	  Mid-development cycle: Checked in so current CVS version will
	  build. TopoConsole now requires a refresh_title() function, that
	  is in this file. This class has been cleaned up further, and now
	  just needs the 2D plots put it the grid

	* [r357] topo/tk/topoconsole.py:
	  Moved title maintenance from TopoConsole to the Frame classes

	* [r356] topo/tk/weightspanel.py:
	  Added refresh_title()

	* [r355] topo/tk/regionplotpanel.py:
	  Moved in do_plot_cmd()

	* [r354] topo/tk/plotpanel.py:
	  Added refresh_title() and generate_plot_key(), plus some class
	  header comments

	* [r353] topo/tk/activitypanel.py:
	  Added refresh_title() and generate_plot_key()

	* [r352] topo/plot.py,
	  topo/sheet.py,
	  topo/sheetview.py:
	  Added a dictionary entry release function to clean up memory when
	  doing UnitView plots

	* [r351] tests/tk/testplotpanel.py:
	  Removed some tests to put in other files

	* [r350] tests/tk/testactivitypanel.py,
	  tests/tk/testweightsarraypanel.py,
	  tests/tk/testweightspanel.py:
	  Pulled from testplotpanel.py, since the classes were pulled from
	  plotpanel.py recently.

	* [r349] tests/tk/__init__.py:
	  Added testactivitypanel, testweightspanel, testweightsarraypanel

	* [r348] tests/testplot.py,
	  tests/testsheet.py,
	  tests/testsheetview.py:
	  Updated for release() functions in plots

2005-03-28  jbednar

	* [r347] COPYING.txt,
	  README.txt:
	  Initial version

	* [r346] topo/base.py,
	  topo/commandline.py,
	  topo/tk/topoconsole.py:
	  Added About dialog box and function

2005-03-28  jprovost

	* [r345] topo/scalarep.py:
	  Added topo/scalarep.py

2005-03-27  jdepaula

	* [r344] topo/tk/regionplotpanel.py:
	  New virtual class for RFSheet plots

	* [r343] topo/tk/activitypanel.py:
	  Pulled from plotpanel.py

	* [r342] topo/tk/weightsarraypanel.py:
	  Pulled from plotpanel.py. Half-operational, and not yet clean.

	* [r341] topo/tk/weightspanel.py:
	  Pulled from plotpanel.py and cleaned up

	* [r340] topo/tk/topoconsole.py:
	  Package name changes

	* [r339] topo/tk/plotpanel.py:
	  Extremely cleaned up. Removed many subclasses

	* [r338] topo/tk/__init__.py:
	  Added extra class files

	* [r337] tests/testsheetview.py:
	  Updated

	* [r336] topo/rfsheet.py,
	  topo/sheet.py,
	  topo/sheetview.py:
	  Updated to work with topo.tk.WeightsPanel

	* [r335] examples/gui_example.py:
	  Added some extra sheets and projections to make the network more
	  complicated.

2005-03-26  jbednar

	* [r334] CONVENTIONS:
	  Added CVS and refactoring info

	* [r333] topo/tk,
	  topo/tk/.cvsignore:
	  Initial version

	* [r332] MILESTONES:
	  Fixed minor typo

2005-03-26  jprovost

	* [r331] examples/lissom.ty,
	  topo/rfsheet.py,
	  topo/utils.py:
	  Code documentation and cleanup.

2005-03-25  jprovost

	* [r330] topo/composer.py:
	  Moved Composer class to separate module

2005-03-25  jbednar

	* [r329] CONVENTIONS:
	  Minor clarifications

	* [r328] CONVENTIONS:
	  Added bit about GUI-related code

	* [r327] JP-NOTES.txt:
	  Added note

2005-03-25  jprovost

	* [r326] JP-NOTES.txt:
	  Implementation notes and future perspectives.

	* [r325] examples/image_example.py,
	  examples/image_example2.py,
	  topo/rfsheet.py,
	  topo/sheet.py,
	  topo/simulator.py:
	  Code cleanup and documentation

2005-03-25  jbednar

	* [r324] CONVENTIONS:
	  Initial version

2005-03-24  jbednar

	* [r323] MILESTONES:
	  Added dates

	* [r322] topo/simulator.py:
	  Added note from Jeff

	* [r321] topo/rfsheet.py,
	  topo/simulator.py:
	  Trivial typo fixes

2005-03-24  jprovost

	* [r320] topo/base.py,
	  topo/simulator.py:
	  minor doc updates

2005-03-24  jdepaula

	* [r319] topographica_script.py:
	  Added -g flag for commandline GUI startup.

	* [r318] topo/plotengine.py:
	  Location of flatten has been moved.

2005-03-24  jprovost

	* [r317] topo/base.py,
	  topo/plot.py,
	  topo/rfsheet.py:
	  Minor fixes.

2005-03-23  jprovost

	* [r316] topo/simulator.py:
	  Minor bugfix

	* [r315] topo/rfsheet.py,
	  topo/simulator.py:
	  Documentation.

	* [r314] tests/testplotengine.py,
	  tests/testrfsom.py,
	  tests/testsimulator.py,
	  topo/__init__.py,
	  topo/base.py,
	  topo/commandline.py,
	  topo/convolve2d.py,
	  topo/dislinplot.py,
	  topo/histogram.py,
	  topo/image.py,
	  topo/kernelfactory.py,
	  topo/rfsom.py,
	  topo/simulator.py,
	  topo/utils.py:
	  Code cleanup and documentation.

2005-03-15  jdepaula

	* [r313] topo/rfsheet.py:
	  Patched r/c to y/x bug

2005-03-14  jdepaula

	* [r312] external/win32/setup.py:
	  Updated so that Windows now runs with the extensive changes made
	  to the startup scripts made this semester.

	* [r311] WIN32_INSTALL.txt:
	  Updated the documentation notes.

2005-03-13  jprovost

	* [r310] examples/lissom.ty,
	  topo/base.py,
	  topo/rfsheet.py,
	  topo/rfsom.py:
	  LISSOM cleanup

2005-03-12  jdepaula

	* [r309] topographica_script.py:
	  Windows patch patched to work again under Linux

	* [r308] topographica_script.py:
	  Added different double-quote management for running under Windows

2005-03-11  jprovost

	* [r307] examples/lissom.ty,
	  topo/rfsheet.py,
	  topo/utils.py:
	  - Fixed LISSOM learning for inhibitory connections.

	* [r306] examples/gui_example.py,
	  examples/lissom.ty,
	  examples/rfsom_example.py,
	  tests/testrfsom.py,
	  tests/tk/testplotpanel.py,
	  topo/base.py,
	  topo/boundingregion.py,
	  topo/kernelfactory.py,
	  topo/params.py,
	  topo/rfsheet.py,
	  topo/rfsom.py,
	  topo/simulator.py:
	  - RFSheet changes to support LISSOM, and corresponding updates to
	  test
	  cases and scripts.
	  - Better parameter handling and new parameter types.

2005-03-10  jdepaula

	* [r305] WIN32_INSTALL.txt:
	  Added an info block on an error with Python 2.3

2005-03-09  jprovost

	* [r304] Makefile,
	  examples/gui_example.py,
	  examples/lissom.ty,
	  examples/rfsom_example.py,
	  topo/inputsheet.py,
	  topo/rfsheet.py,
	  topo/rfsom.py,
	  topo/simulator.py:
	  - Various changes to support LISSOM.
	  - SimpleSimulator class for Simulator event stream debugging
	  - added topographica dir to PYTHONPATH in topo startup script

2005-03-09  jbednar

	* [r303] examples/gui_example.py:
	  Reduced connection delay so that Sheet activity values will be
	  synchronized when they are plotted

2005-03-07  jdepaula

	* [r302] tests/tk/testplotpanel.py:
	  Added RFSOM simulation to test WeightsPanel

	* [r301] topo/gui.py,
	  topo/simulator.py,
	  topo/tk/__init__.py,
	  topo/tk/topoconsole.py:
	  Added Simulator.active_sim(), and adjusted files that make use of
	  it.

	* [r300] examples/gui_example.py:
	  Removed the now superfluous topo.gui.link_to_sim() call

	* [r299] tests/tk/testtopoconsole.py:
	  Patched to handle Simulator's new active_sim()

	* [r298] topo/plot.py,
	  topo/plotengine.py,
	  topo/rfsheet.py,
	  topo/sheetview.py,
	  topo/tk/plotpanel.py,
	  topo/tk/topoconsole.py:
	  Matured WeightsPanel: Added StringVar to r,c input; added r,c to
	  tititle; autoscale initial plot

	* [r297] topo/simulator.py:
	  Changed PyDoc for run()

	* [r296] topo/simulator.py:
	  Patched run() so it can be called more than once without breaking

	* [r295] topo/plot.py,
	  topo/plotengine.py,
	  topo/rfsheet.py,
	  topo/sheet.py,
	  topo/sheetview.py,
	  topo/tk/plotpanel.py,
	  topo/tk/topoconsole.py:
	  Added support for UnitViews

	* [r294] topo/base.py:
	  Added a flatten() function

2005-02-26  jdepaula

	* [r293] tests/tk/testplotpanel.py:
	  Removed a mainloop() so it will not display plots

	* [r292] topo/tk/plotpanel.py:
	  Now normalizes activation plots.

	* [r291] topo/bitmap.py:
	  Added additional range assertions

	* [r290] examples/lissom.ty:
	  Added fully-qualified package names

	* [r289] topo/tk/__init__.py:
	  Moved mainloop() so works from shell.

	* [r288] examples/gui_example.py:
	  Reduced run to 2

2005-02-25  jdepaula

	* [r287] examples/gui_example.py:
	  Copy of rfsom_example.py except with 200 steps instead of 10000,
	  and a topo.gui.link_to_sim() call

	* [r286] topo/tk/__init__.py,
	  topo/tk/topoconsole.py:
	  Added topo.gui import

	* [r285] topo/gui.py:
	  Added

	* [r284] topo/__init__.py:
	  Added gui.py

2005-02-24  jdepaula

	* [r283] examples/rfsom_example.py:
	  Added import command to load Simulator

2005-02-19  jdepaula

	* [r282] WIN32_INSTALL.txt,
	  setup.bat:
	  Updated for Python 2.4

	* [r281] external/win32/README.txt:
	  Changed for Python 2.4

	* [r280] external/win32/setup.py:
	  Installs the Python 2.4 packages, but does not properly automate
	  startup of Topographica from the batch files

	* [r279]
	  external/win32/Numeric-23.1.win32-py2.3.exe,
	  external/win32/PIL-1.1.4.win32-py2.3.exe,
	  external/win32/Python-2.3.4.exe,
	  external/win32/dl_82_p2.tar.gz:
	  Upgraded to Python 2.4

	* [r278]
	  external/win32/Numeric-23.7.win32-py2.4.exe,
	  external/win32/PIL-1.1.5b3.win32-py2.4.exe,
	  external/win32/dl_83_py.tar.gz,
	  external/win32/python-2.4.msi:
	  Upgrade to Python 2.4

2005-02-18  jdepaula

	* [r277] topo/tk/topoconsole.py:
	  Added two catches for if Simulator is Null

	* [r276] topo/tk/__init__.py:
	  Cut down on number of imports

	* [r275] tests/testgui.py,
	  tests/tk/testplotpanel.py,
	  tests/tk/testtopoconsole.py:
	  Changed package access because of tk/__init__.py

	* [r274] tests/testdummy.py:
	  Changed comment

	* [r273] topo/tk/plotpanel.py:
	  Added plot-labels

	* [r272] external/Imaging-1.1.4jp.tgz:
	  Added a blind TCLTK install to create _imagingtk.so . Needs
	  cleanup.

	* [r271] topo/tk/plotpanel.py,
	  topo/tk/topoconsole.py:
	  Added working Activity Plot

	* [r270] topo/tk/__init__.py:
	  Added comment

	* [r269] topo/bitmap.py:
	  Added bitmap accessors

	* [r268] tests/tk/testplotpanel.py:
	  Added mainlooped Activation window test

	* [r267] tests/testgui.py,
	  tests/tk/testtopoconsole.py:
	  Added .quit() to extra TopoConsoles

2005-02-17  jbednar

	* [r266] topo/tk/plotpanel.py,
	  topo/tk/propertiesframe.py,
	  topo/tk/taggedslider.py,
	  topo/tk/topoconsole.py:
	  Cleaned up file and class comments

2005-02-17  jdepaula

	* [r265] topo/tk/__init__.py:
	  Added gui.py functions

	* [r264] topo/gui.py:
	  Moved contents to tk/__init__.py

	* [r263] topo/__init__.py:
	  Removed auto-load of gui

	* [r262] tests/testgui.py,
	  tests/tk/testpropertiesframe.py,
	  tests/tk/testtopoconsole.py:
	  Changed location of gui start function

2005-02-13  jdepaula

	* [r261] topo/tk/plotpanel.py,
	  topo/tk/topoconsole.py:
	  Pulled from gui.py

	* [r260] topo/tk/__init__.py:
	  Added plotpanel and topoconsole

	* [r259] topo/gui.py:
	  Removed classes into new files

	* [r258] tests/README.txt:
	  Added reference to testdummy.py

	* [r257] tests/__init__.py:
	  Added tk directory, and requires_display test

	* [r256] tests/testdummy.py:
	  Added suite.requires_display example

	* [r255] tests/testgui.py:
	  Moved test to testtopoconsole.py

	* [r254] tests/tk,
	  tests/tk/__init__.py,
	  tests/tk/testplotpanel.py,
	  tests/tk/testpropertiesframe.py,
	  tests/tk/testtopoconsole.py:
	  For GUI

	* [r253] tests/testpropertiesframe.py:
	  Moved

2005-02-12  jdepaula

	* [r252] topo/commandline.py:
	  Removed one more

	* [r251] topo/commandline.py:
	  Cut some unused imports

	* [r250] tests/testgui.py:
	  Added test_tk

	* [r249] topo/gui.py:
	  To work with latest testgui.py file.

	* [r248] tests/testgui.py,
	  tests/testplotengine.py,
	  tests/testrfsom.py:
	  Reduced message levels to WARNINGs only.

	* [r247] topo/__init__.py:
	  Added commandline.py

	* [r246] topo/simulator.py:
	  Changed 4 prints to self.message

2005-02-11  jdepaula

	* [r245] topographica_script.py:
	  No longer sets up interactive prompt variables. Now strictly a
	  support file for ./topographica

	* [r244] topo/commandline.py:
	  Initial version

	* [r243] topographica-script.py:
	  Name changed to topographica_script.py

	* [r242] Makefile:
	  Change startup script to exec with generate_params()

	* [r241] topographica_script.py:
	  Filename change

2005-02-10  jdepaula

	* [r240] tests/testpropertiesframe.py:
	  Moved location of propertiesframe

	* [r239] topo/gui.py:
	  Removed import 'if/else', added root return, moved location of
	  propertiesframe.

	* [r238] topo/__init__.py:
	  Moved propertiesframe and taggedslider

	* [r237] topo/tk,
	  topo/tk/__init__.py,
	  topo/tk/propertiesframe.py,
	  topo/tk/taggedslider.py:
	  Moved to topo/tk to separate gui from base

	* [r236] topo/propertiesframe.py,
	  topo/taggedslider.py:
	  Moved to topo/tk

	* [r235] tests/testgui.py:
	  Initial file to create some bitmaps but not display them. Will be
	  expanded in the future.

	* [r234] tests/testplotengine.py:
	  Removed dependency on rfsom.py.

2005-02-04  jprovost

	* [r233] topo/rfsheet.py:
	  Little RFSheet fix.

	* [r232] Makefile,
	  examples/lissom.ty,
	  examples/rfsom_example.py,
	  topo/boundingregion.py,
	  topo/inputsheet.py,
	  topo/kernelfactory.py,
	  topo/rfsheet.py,
	  topo/sheet.py,
	  topographica-script.py:
	  -Various generic bugfixes in Makefile, topo-script.
	  -Fixed various RF-size inconsistencies when computing o
	  velap/boundary conditions.

2005-02-03  jdepaula

	* [r231] tests/__init__.py:
	  Added testrfsom

	* [r230] tests/testrfsom.py:
	  Raised level of debug code to verbose()

	* [r229] topo/kernelfactory.py:
	  Changed two .message() to .verbose()

2005-02-02  jdepaula

	* [r228] topographica-script.py:
	  Added clean exit for Ctrl-D

	* [r227] topo/gui.py,
	  topo/simulator.py:
	  Changed GUI to run commands in __main__

	* [r226] topographica-script.py:
	  Added new command-line interpreter

2005-02-02  jprovost

	* [r225] Makefile,
	  external/Imaging-1.1.4jp.tgz,
	  external/Makefile:
	  Got Python-based startup script working.

	* [r224] Makefile,
	  external/Makefile:
	  Fixed Makefile target for the topographica startup script

2005-01-31  jdepaula

	* [r223] topo/gui.py:
	  Updated to open empty Activity and Weights plots

	* [r222] tests/testplotengine.py:
	  Latest changes according to Jeff

2005-01-26  jdepaula

	* [r221] topo/gui.py,
	  topo/simulator.py:
	  Commands now execute in topo.simulator

2005-01-25  jdepaula

	* [r220] topo/dislinplot.py:
	  Fixed Deprication error; Eliminated Dislin file generation
	  messages.

	* [r219] external/Makefile:
	  Python version startscript does not import dislin! (???)

	* [r218] tests/testplotengine.py:
	  Changed to match kernelfactory changes.

	* [r217] external/Makefile:
	  Changed startscript make from using sh to using python

	* [r216] topographica-script.py:
	  Added conditional to not display banner if not running
	  topographica-script.py

2005-01-25  jprovost

	* [r215] topo/kernelfactory.py:
	  Updated kernel factories to work as stand-alone function objects.

2005-01-24  jbednar

	* [r214] topo/image.py:
	  Turned off unneeded message

	* [r213] topo,
	  topo/.cvsignore:
	  Added files to ignore

2005-01-22  jdepaula

	* [r212] external/Python-2.3.3.tgz,
	  external/tcl8.4.6.tgz,
	  external/tk8.4.6.tgz:
	  Old versions

	* [r211] external/Makefile:
	  Added Dislin-Python interface compile

	* [r210] Makefile,
	  external/Makefile:
	  Changed startup script ./topographica

	* [r209] external/Makefile:
	  Upgraded versions of tcl, tk, and Python. Patched python make.

	* [r208] external/Python-2.4.tgz:
	  Initial

	* [r207] external/Imaging-1.1.4jp.tgz:
	  Added two lines to setup.py (see '-judah') to compile under
	  Python 2.4

	* [r206] external/tcl8.4.9.tgz,
	  external/tk8.4.9.tgz:
	  Version 8.4.9.

	* [r205] tests/testdislinplot,
	  tests/testdislinplot/.cvsignore:
	  Ignore generated test files

	* [r204] topo/dislinplot.py:
	  Added function to change output filename

	* [r203] tests/testdislinplot.py:
	  Initial check-in

	* [r202] tests/__init__.py:
	  Added testdislinplot.py

	* [r201] tests/testdislinplot,
	  tests/testdislinplot/testdislin_od_noselect_bw.bmp,
	  tests/testdislinplot/testdislin_or_Eye1_noselect.bmp,
	  tests/testdislinplot/testdislin_or_od_select.bmp,
	  tests/testdislinplot/testdislin_target.tiff,
	  tests/testdislinplot/testdislin_wts.056_085_s.bmp:
	  Test cases

	* [r200] topo/gendocs.py:
	  Patched so gendocs.py now shows up in the documentation

	* [r199] topo/__init__.py:
	  Added gendocs.py, so autogenerated documentation includes the
	  file

2005-01-20  jprovost

	* [r198] topo/base.py,
	  topo/boundingregion.py,
	  topo/inputsheet.py,
	  topo/kernelfactory.py,
	  topo/rfsheet.py:
	  Changes to support LISSOM.

2005-01-20  jbednar

	* [r197] topographica-script.py:
	  Added help info to the prompt

	* [r196] runtests:
	  Minor clarification

	* [r195] MILESTONES,
	  WIN32_INSTALL.txt:
	  Trivial fixes

2005-01-20  jdepaula

	* [r194] topo/gui.py:
	  Latest version for Jim. Cleaned up stubs. Fixed Quit. Added Load
	  and Reload.

2005-01-19  jdepaula

	* [r193] external/Makefile:
	  Added dislin to the build

	* [r192] external/dislin-8.2.linux.tgz:
	  Initial

2005-01-18  jdepaula

	* [r191] topo/propertiesframe.py,
	  topo/taggedslider.py:
	  Added Pydoc comment headers

	* [r190] tests/__init__.py:
	  Added testpropertiesframe.py

	* [r189] tests/testpropertiesframe.py:
	  Initial tests pulled from .py source

	* [r188] tests/__init__.py:
	  Added testgui.py

	* [r187] tests/testgui.py:
	  Initial check-in. Stub only.

	* [r186] topo/__init__.py,
	  topo/gui.py,
	  topo/propertiesframe.py:
	  Adjusted import names to match Topographica naming convention

	* [r185] topo/__init__.py:
	  Added PropertiesFrame, TaggedSlider, gui

	* [r184] topo/propertiesframe.py,
	  topo/taggedslider.py:
	  Support file for gui.py. Taken straight from LISSOM 5.0. No
	  Pydocs have been added yet

	* [r183] topo/gui.py:
	  Copied from LISSOM 5.0 python/. All LISSOM calls commented out so
	  the file is a driver with a lot of stubs and junk lines. Only
	  changes in this version include necessary fixes to get the window
	  to open under Topographica. Found that PMW 1.2 MUST be installed
	  to work with Python 2.3 and get this file to run.

	* [r182] external/Pmw.tgz:
	  Pmw version 1.2. Upgraded because Python 2.3 required a patch to
	  PmwMenuBar._addHotkeyToOptions that could not be worked around.

	* [r181] topo/dislindriver.py:
	  Changed the three test cases so they'll only run if the file is
	  Main--in other words the driver is now ignored, but left here as
	  an example of how to use the dislinplot file.

2005-01-14  jprovost

	* [r180] examples/lissom.ty:
	  Intermediate save for backup purposes. Things are probably still
	  broken.

2005-01-14  jbednar

	* [r179] MILESTONES:
	  Initial version

2005-01-10  jbednar

	* [r178] topo/boundingregion.py:
	  Trivial whitespace fix

2005-01-09  jbednar

	* [r177] runtests:
	  Added note

	* [r176] tests/README.txt:
	  Fixed typos and added note about large-scale tests

2004-11-08  jprovost

	* [r175] examples/lissom.ty,
	  examples/rfsom_example.py,
	  topo/boundingregion.py,
	  topo/inputsheet.py,
	  topo/kernelfactory.py,
	  topo/rfsheet.py,
	  topo/rfsom.py:
	  Changes allow LISSOM implementation.

2004-09-28  jprovost

	* [r174] external/Imaging-1.1.4jp.tgz,
	  topographica-script.py:
	  external package build improvements

	* [r173] Makefile,
	  external/Imaging-1.1.4jp.tgz,
	  external/Makefile,
	  external/Python-2.3.3.tgz,
	  external/darwin/tcl8.4.6-src.tar.gz,
	  external/darwin/tk8.4.6-src.tar.gz,
	  external/tcl8.4.6.tgz,
	  external/tk8.4.6.tgz,
	  topographica-script.py:
	  Updates to ext-packages and Makefiles to get 'make' to work.

2004-09-01  jbednar

	* [r172] topo/plot.py:
	  Fixed typo

2004-08-31  jprovost

	* [r171] topo/params.py:
	  Modified documentation for Dynamic params.

2004-08-30  jp

	* [r170] runtests:
	  Test commit...

2004-08-28  judah

	* [r169] tests/testbitmap.py:
	  Changed rgb_to_hsv to hsv_to_rgb

	* [r168] tests/testpalette.py:
	  Initial ci

	* [r167] tests/__init__.py:
	  Added testpalette.py

	* [r166] topo/plot.py:
	  Changed comments, added Dynamics

	* [r165] topo/bitmap.py:
	  Added background constants

	* [r164] topo/__init__.py:
	  Added palette

	* [r163] topo/palette.py:
	  Initial ci, with comments

2004-08-24  jp

	* [r162] topo/heap.py,
	  topo/som.py,
	  topo/toolbar.py:
	  Removing deadwood.

2004-08-24  judah

	* [r161] tests/testplotengine.py:
	  Extensive additions. First Example of how to use PlotEngine

	* [r160] tests/testplot.py,
	  tests/testsheetview.py:
	  Added more tests

	* [r159] tests/testsheetview.ppm:
	  Initial version

	* [r158] topo/plotengine.py:
	  Debugged at end of Summer

	* [r157] topo/bitmap.py,
	  topo/histogram.py,
	  topo/plot.py,
	  topo/sheet.py,
	  topo/sheetview.py:
	  Cleaned up version for end of Summer

2004-08-23  jp

	* [r156] examples/rfsom_example.py,
	  topo/rfsheet.py,
	  topo/simulator.py:
	  *** empty log message ***

2004-08-17  judah

	* [r155] tests/testsimulator.py:
	  name change

2004-08-16  judah

	* [r154] topo/plotengine.py:
	  End of work day

	* [r153] topo/plot.py:
	  Worked on PlotGroup

	* [r152] topo/simulator.py:
	  Changed find_EP to get_event_processors

	* [r151] topo/plotengine.py:
	  Initial version. Constructor only, no testing.

	* [r150] topo/__init__.py:
	  added plotengine.py

	* [r149] tests/testplotengine.py:
	  Stub

	* [r148] tests/__init__.py:
	  Added testplotengine.py

2004-08-15  jbednar

	* [r147] topo/sheetview.py:
	  Clarified comments

2004-08-14  judah

	* [r146] topo/histogram.py:
	  Stub version

	* [r145] topo/plot.py:
	  Completed. No testing yet.

	* [r144] tests/testbitmap.py,
	  topo/bitmap.py:
	  Added matrix_rgb_to_hsv for use in other classes

	* [r143] tests/testplot.py:
	  Changed constructor parameters to compile

	* [r142] topo/__init__.py:
	  Added histogram.py

	* [r141] tests/__init__.py:
	  Added testhistogram.py

	* [r140] tests/testhistogram.py:
	  Starting version

	* [r139] topo/sheetview.py:
	  First pass of testing done, no integration

	* [r138] tests/__init__.py:
	  Added testsheetview

	* [r137] tests/testsheetview.py:
	  Complete initial testing done

2004-08-13  judah

	* [r136] tests/testsimulator.py:
	  To match changes in simulator.py

	* [r135] topo/plot.py:
	  Still broken

	* [r134] topo/simulator.py:
	  went with Jeff's suggestions

	* [r133] tests/testsheetview.py:
	  Initial checkin

	* [r132] topo/sheetview.py:
	  Completed base, but no testing whatsoever yet.

2004-08-11  judah

	* [r131] topo/sheet.py:
	  Changed call to SheetView

	* [r130] topo/simulator.py:
	  Added find_EP

	* [r129] tests/testsimulator.py:
	  Initial version

	* [r128] tests/testsheet.py:
	  Took out comment

	* [r127] tests/__init__.py:
	  Added testsimulator.py

2004-08-10  judah

	* [r126] topo/plot.py:
	  Two small fixes

	* [r125] topo/plot.py:
	  Initial check-in. gererate_plot not complete

	* [r124] topo/sheetview.py:
	  Has Sheetview and UnitView

	* [r123] topo/sheet.py:
	  Added sheet_view, add_sheet_view, sheet_view_dict

	* [r122] topo/bitmap.py:
	  Added CVS ID tag

	* [r121] topo/__init__.py:
	  Added plot, sheetview

	* [r120] tests/testplot.py:
	  Stub at this point

	* [r119] tests/__init__.py,
	  tests/testsheet.py:
	  Added testplot

	* [r118] topo/params.py:
	  Fix comment typo

2004-08-08  judah

	* [r117] topo/gendocs.py:
	  Added sentence to header comment

2004-08-03  jp

	* [r116] topo/rfsheet.py,
	  topo/rfsom.py:
	  Added RFSheet, abstract class for RFSOM and other RF-based
	  sheets.

2004-07-16  judah

	* [r115] tests/__init__.py:
	  Added testbitmap

2004-07-15  judah

	* [r114] tests/testbitmap.py:
	  Init

	* [r113] tests/testbitmap.jpg:
	  Init

	* [r112] runtests:
	  Changed header commment to proper execution string

2004-07-14  judah

	* [r111] topo/gendocs.py:
	  No longer uses os.system to call pydocs

	* [r110] Makefile:
	  Tweaked docs tag

	* [r109] topo/gendocs.py:
	  Changed make comment

	* [r108] Makefile:
	  Changed source for docs index.html

	* [r107] topo/gendocs.py:
	  Doesn't change filenames anymore

	* [r106] Makefile:
	  Added stub of clean

	* [r105] topo/gendocs.py:
	  Init

	* [r104] Makefile:
	  Added docs and cleandocs tags

	* [r103] topo/__init__.py:
	  Changed header string

2004-07-13  judah

	* [r102] topo/bitmap.py:
	  Added header comments

2004-07-12  judah

	* [r101] WIN32_INSTALL.txt:
	  Be sure to have DOS EOLs

	* [r100] external/win32/setup.py:
	  Fix output line

2004-07-09  judah

	* [r99] topo/bitmap.py:
	  Added BWMap, and further testing

	* [r98] topo/__init__.py:
	  Added bitmap.py

	* [r97] topo/bitmap.py:
	  Init

2004-07-08  judah

	* [r96] topo/dislindriver.py:
	  Added pydoc strings

	* [r95] external/win32/setup.py:
	  Move dislin to the end of the script

2004-07-07  judah

	* [r94] setup.bat:
	  This needed backslashes for Win2K, and binary mode to stop
	  messing
	  with the end-of-lines.

2004-07-04  judah

	* [r93] topo/__init__.py:
	  Moved the TY importer to the top

	* [r92] topo/tyimputil.py:
	  Added entire imputil.py when encountering trouble

2004-07-03  judah

	* [r91] topo/tyimputil.py:
	  Changed install type

	* [r90] topo/__init__.py:
	  Changed comment

	* [r89] topo/tyimputil.py:
	  Changed so it auto-loads

	* [r88] topo/__init__.py:
	  Added tyimputil.py

2004-07-02  judah

	* [r87] topo/tyimputil.py:
	  Changed commenting format

2004-07-01  judah

	* [r86] topo/tyimputil.py:
	  Init

2004-06-30  judah

	* [r85] external/win32/README.txt:
	  Init

	* [r84] external/win32/setup.py:
	  Missed a slash

	* [r83] setup.bat:
	  No longer creates the topographica.py file.

	* [r82] external/win32/setup.py:
	  This creates the topographica.py file now.

	* [r81] external/win32/setup.py:
	  Had it right the first time.

	* [r80] external/win32/setup.py:
	  Another

	* [r79] external/win32/setup.py:
	  Fix xcopy

	* [r78] setup.bat:
	  Remove pause

	* [r77] external/win32/util/noinstall.txt:
	  Init

	* [r76] external/win32/setup.py:
	  All components complete

	* [r75] setup.bat:
	  Changed setup.py parameter call

	* [r74] topographica.ico:
	  Init

2004-06-28  judah

	* [r73] external/win32/dl_82_p2:
	  Don't need them

	* [r72] external/win32/dl_82_p2.tar.gz:
	  Init

	* [r71] external/win32/setup.py:
	  Pale unstable

	* [r70] setup.bat:
	  Misc

2004-06-27  judah

	* [r69] external/win32/Y_OR_N.COM,
	  external/win32/dl_82_p2.zip:
	  Moved and changed compression

	* [r68] external/win32/setup.py:
	  New locations

	* [r67] external/win32/util,
	  external/win32/util/Y_OR_N.COM,
	  external/win32/util/gunzip.exe,
	  external/win32/util/gzip.exe,
	  external/win32/util/tar.exe:
	  Init

	* [r66] external/win32/jpeg-6b-3.exe:
	  Init

2004-06-26  judah

	* [r65] setup.bat:
	  Added script copy

	* [r64] external/win32/Y_OR_N.COM:
	  For setup.bat

	* [r63] external/win32/setup.py:
	  Init

	* [r62] external/win32/Python-2.3.4.exe:
	  Init

	* [r61]
	  external/win32/ActivePython-2.3.2-232-win32-ix86.msi:
	  done with Active state

	* [r60] external/win32/dl_82_p2,
	  external/win32/dl_82_p2/appa.txt,
	  external/win32/dl_82_p2/appb.txt,
	  external/win32/dl_82_p2/appc.txt,
	  external/win32/dl_82_p2/areaf.py,
	  external/win32/dl_82_p2/color3d.py,
	  external/win32/dl_82_p2/complx10.bdf,
	  external/win32/dl_82_p2/complx12.bdf,
	  external/win32/dl_82_p2/complx14.bdf,
	  external/win32/dl_82_p2/complx18.bdf,
	  external/win32/dl_82_p2/conshd.py,
	  external/win32/dl_82_p2/contents.txt,
	  external/win32/dl_82_p2/contour.py,
	  external/win32/dl_82_p2/curve.py,
	  external/win32/dl_82_p2/disdrv.bat,
	  external/win32/dl_82_p2/disdrv_w.exe,
	  external/win32/dl_82_p2/disdrv_x.exe,
	  external/win32/dl_82_p2/disgdi_x.exe,
	  external/win32/dl_82_p2/dishlp.exe,
	  external/win32/dl_82_p2/dishpj_x.exe,
	  external/win32/dl_82_p2/disimg.bat,
	  external/win32/dl_82_p2/disimg_w.exe,
	  external/win32/dl_82_p2/disimg_x.exe,
	  external/win32/dl_82_p2/dislin.inf,
	  external/win32/dl_82_p2/dislin23.dll,
	  external/win32/dl_82_p2/disman.exe,
	  external/win32/dl_82_p2/dismov.bat,
	  external/win32/dl_82_p2/dismov_w.exe,
	  external/win32/dl_82_p2/dismov_x.exe,
	  external/win32/dl_82_p2/distif.bat,
	  external/win32/dl_82_p2/distif_w.exe,
	  external/win32/dl_82_p2/distif_x.exe,
	  external/win32/dl_82_p2/helve10.bdf,
	  external/win32/dl_82_p2/helve12.bdf,
	  external/win32/dl_82_p2/helve14.bdf,
	  external/win32/dl_82_p2/helve18.bdf,
	  external/win32/dl_82_p2/hlp0.txt,
	  external/win32/dl_82_p2/hlp10.txt,
	  external/win32/dl_82_p2/hlp11.txt,
	  external/win32/dl_82_p2/hlp12.txt,
	  external/win32/dl_82_p2/hlp13.txt,
	  external/win32/dl_82_p2/hlp14.txt,
	  external/win32/dl_82_p2/hlp15.txt,
	  external/win32/dl_82_p2/hlp16.txt,
	  external/win32/dl_82_p2/hlp17.txt,
	  external/win32/dl_82_p2/hlp3.txt,
	  external/win32/dl_82_p2/hlp4.txt,
	  external/win32/dl_82_p2/hlp5.txt,
	  external/win32/dl_82_p2/hlp6.txt,
	  external/win32/dl_82_p2/hlp6_1.txt,
	  external/win32/dl_82_p2/hlp6_2.txt,
	  external/win32/dl_82_p2/hlp7.txt,
	  external/win32/dl_82_p2/hlp8.txt,
	  external/win32/dl_82_p2/hlp9.txt,
	  external/win32/dl_82_p2/intpol.py,
	  external/win32/dl_82_p2/kap0.txt,
	  external/win32/dl_82_p2/kap1.txt,
	  external/win32/dl_82_p2/kap10.txt,
	  external/win32/dl_82_p2/kap11.txt,
	  external/win32/dl_82_p2/kap12.txt,
	  external/win32/dl_82_p2/kap13.txt,
	  external/win32/dl_82_p2/kap14.txt,
	  external/win32/dl_82_p2/kap15.txt,
	  external/win32/dl_82_p2/kap16.txt,
	  external/win32/dl_82_p2/kap2.txt,
	  external/win32/dl_82_p2/kap3.txt,
	  external/win32/dl_82_p2/kap4.txt,
	  external/win32/dl_82_p2/kap5.txt,
	  external/win32/dl_82_p2/kap6.txt,
	  external/win32/dl_82_p2/kap6_1.txt,
	  external/win32/dl_82_p2/kap6_2.txt,
	  external/win32/dl_82_p2/kap6_3.txt,
	  external/win32/dl_82_p2/kap7.txt,
	  external/win32/dl_82_p2/kap8.txt,
	  external/win32/dl_82_p2/kap9.txt,
	  external/win32/dl_82_p2/legend.py,
	  external/win32/dl_82_p2/logscl.py,
	  external/win32/dl_82_p2/map.py,
	  external/win32/dl_82_p2/map1.dat,
	  external/win32/dl_82_p2/map2.dat,
	  external/win32/dl_82_p2/map3.dat,
	  external/win32/dl_82_p2/piegrf.py,
	  external/win32/dl_82_p2/polar.py,
	  external/win32/dl_82_p2/python.inf,
	  external/win32/dl_82_p2/readme.exe,
	  external/win32/dl_82_p2/setup.exe,
	  external/win32/dl_82_p2/simplx10.bdf,
	  external/win32/dl_82_p2/simplx12.bdf,
	  external/win32/dl_82_p2/simplx14.bdf,
	  external/win32/dl_82_p2/simplx8.bdf,
	  external/win32/dl_82_p2/styles.py,
	  external/win32/dl_82_p2/surface.py,
	  external/win32/dl_82_p2/surfcp.py,
	  external/win32/dl_82_p2/symbols.py,
	  external/win32/dl_82_p2/tex.py,
	  external/win32/dl_82_p2/triang.py,
	  external/win32/dl_82_p2/vectors.py,
	  external/win32/dl_82_p2/widgets.py,
	  external/win32/dl_82_p2/world.py:
	  Init

	* [r59] setup.bat:
	  Windows Install front end

2004-06-21  judah

	* [r58]
	  external/darwin/dislin-8.2.darwin.tar.gz:
	  Init

	* [r57] external/darwin,
	  external/darwin/tcl8.4.6-src.tar.gz,
	  external/darwin/tk8.4.6-src.tar.gz:
	  Init

2004-06-15  jp

	* [r56] Makefile:
	  Fixed topographica script for Mac OS X

2004-06-14  judah

	* [r55] external/win32,
	  external/win32/ActivePython-2.3.2-232-win32-ix86.msi,
	  external/win32/Numeric-23.1.win32-py2.3.exe,
	  external/win32/PIL-1.1.4.win32-py2.3.exe,
	  external/win32/dl_82_p2.zip:
	  Creation of the Windows 32 files

2004-06-11  jp

	* [r54] external/Imaging-1.1.4jp.tgz,
	  external/jpeg-6b.tgz:
	  Mac support update.

2004-06-08  jp

	* [r53] examples/rfsom_example.py:
	  More minor changes.

	* [r52] examples/rfsom_example.py,
	  runtests:
	  Minor changes.

2004-05-31  joeraii

	* [r51] topo/inputsheet.py,
	  topo/kernelfactory.py:
	  Preliminary changes for a more general kernel factory model. Now
	  the kernel
	  factor functions are stand-alone and can be used arbitrarily on
	  matrix input or
	  single value input. There are a few kinks to work out, and
	  uniform random is
	  completely non-working as an input sheet.

2004-05-07  jbednar

	* [r50] topo/kernelfactory.py:
	  Minor update to comment

	* [r49] topo/gaussiansheet.py:
	  Obsolete

2004-05-06  joeraii

	* [r48] topo/kernelfactory.py:
	  Update to fix some problems with sine_grating. The function sin()
	  returns
	  between -1 and 1, we need to scale this between 0 and 1.

2004-04-29  joeraii

	* [r47] topo/kernelfactory.py:
	  Added a fuzzy ring function. Needs testing.

2004-04-23  jp

	* [r46] topo/inputsheet.py:
	  Made InputSheet class objects callable.

2004-04-22  jp

	* [r45] examples/rfsom_example.py,
	  topo/boundingregion.py,
	  topo/params.py:
	  Some optimizations to speed up rfsom_example.py.

2004-04-11  joeraii

	* [r44] topo/inputsheet.py,
	  topo/kernelfactory.py:
	  Added FuzzyDisk and Rectangle kernels.

	* [r43] topo/inputsheet.py,
	  topo/kernelfactory.py:
	  Cleaned up version of input sheet. Parameters are correctly
	  passed to the
	  generator functions. Also Gabor is enhanced with more parameters.

2004-04-09  joeraii

	* [r42] topo/kernelfactory.py:
	  Added a preliminary version of fuzzy line, also cleaned up the
	  remaining kernel
	  factory definitions.

	* [r41] topo/inputsheet.py,
	  topo/kernelfactory.py:
	  New kernel factory without classes, and input sheet to reflect
	  these changes.
	  Some problems: Gabor probably doesn't work correctly, also there
	  may be an issue
	  with how parameters are being passed.

2004-04-02  joeraii

	* [r40] topo/inputsheet.py,
	  topo/kernelfactory.py:
	  Fixed the 90 degree rotation problem, also added a simple
	  generator for doing
	  translations. I'm not sure if it works like it should (i.e. if
	  each instance of
	  the generator is independent), however it does create the effect
	  of moving a
	  gaussian across the input area.

2004-03-31  joeraii

	* [r39] topo/kernelfactory.py:
	  Fixed a minor bug with the generic kernel factory.

2004-03-29  jp

	* [r38] examples/rfsom_example.py,
	  topo/rfsom.py,
	  topo/utils.py:
	  Add borders to RFSOM rf plot output.

	* [r37] Makefile,
	  topographica,
	  topographica-script.py:
	  Changed Makefile to generate main topographica script, so it
	  properly calls bin/python for each installation.

2004-03-26  joeraii

	* [r36] topo/inputsheet.py:
	  Little bug regarding TopoMetaClass resolved.

	* [r35] topo/inputsheet.py:
	  Merged two different versions. Better testing functions.

2004-03-26  jp

	* [r34] examples/rfsom_example.py,
	  topo/__init__.py,
	  topo/base.py,
	  topo/inputsheet.py,
	  topo/kernelfactory.py,
	  topo/rfsom.py,
	  topo/sheet.py:
	  Added rfsom_example.py. Fixes to RFSOM support. Some parameter
	  fixes. Minor changes to inputsheet and kernelfactory.

2004-03-26  joeraii

	* [r33] topo/kernelfactory.py:
	  Kernel factory cleanups .

	* [r32] topo/inputsheet.py,
	  topo/kernelfactory.py:
	  Updated to work with the TopoMetaClass, however I'm currently not
	  able to set
	  the default class attributes... Also added Sheet versions of Sine
	  Grating and
	  Gabor. More functions to come.

2004-03-25  jp

	* [r31] topo/base.py:
	  Added TopoMetaclass, to handle class-wide Parameter setting.

2004-03-18  joeraii

	* [r30] topo/inputsheet.py,
	  topo/kernelfactory.py,
	  topo/params.py:
	  Changed the kernel factory and input sheet to use the Parameter
	  model. Also
	  created some mix-in classes for input sheets.

2004-03-13  jp

	* [r29] topo/base.py:
	  added the base module

	* [r28] examples/image_example2.py,
	  topo/params.py,
	  topo/sheet.py,
	  topo/simulator.py:
	  Added the .pre_sleep() EP method.

	* [r27] topo/rfsom.py,
	  topo/simulator.py:
	  RFSOM cleanup + minor simulator changes

2004-03-12  jp

	* [r26] examples/image_example2.py,
	  topo/__init__.py,
	  topo/boundingregion.py,
	  topo/convolve2d.py,
	  topo/debug.py,
	  topo/gaussiansheet.py,
	  topo/image.py,
	  topo/inputsheet.py,
	  topo/kernelfactory.py,
	  topo/params.py,
	  topo/rfsom.py,
	  topo/sheet.py,
	  topo/simulator.py,
	  topo/som.py:
	  Removed the debug module and Debuggable class, and added the base
	  module and TopoObject global base class.

	* [r25] topo/boundingregion.py,
	  topo/convolve2d.py,
	  topo/debug.py,
	  topo/image.py,
	  topo/params.py,
	  topo/sheet.py,
	  topo/simulator.py:
	  New parameter model using attribute descriptors.

2004-03-05  nn

	* [r24] topo/inputsheet.py,
	  topo/kernelfactory.py:
	  New kernel functions. Not completely integrated with the kernel
	  sheet yet;
	  wating for the new parameters model.

2004-02-24  nn

	* [r23] topo/inputsheet.py,
	  topo/kernelfactory.py:
	  Cleaned up code and made the kernelfactory and inputsheet code
	  more generic.
	  Should now be trivial to begin adding other types of input sheet
	  functions
	  (other than gaussian).

2004-02-22  nn

	* [r22] topo/params.py:
	  Change params back to the original.

	* [r21] topo/inputsheet.py:
	  More generic version of gaussiansheet.py. However it only
	  supports gaussian
	  kernels.

	* [r20] topo/kernelfactory.py:
	  New version of kernelfactory that is faster, and does not crash.
	  However it may
	  be inconsistent in the ouput matrix size. This will be fixed
	  later.

2004-02-20  jp

	* [r19] examples/image_example2.py,
	  topo/gaussiansheet.py,
	  topo/sheet.py,
	  topographica:
	  Composer sheet fixes.

2004-02-15  nn

	* [r18] topo/gaussiansheet.py,
	  topo/kernelfactory.py,
	  topo/params.py:
	  Pass parameters as either tuples representing functions to be
	  applied, or as
	  constants.

2004-02-08  nn

	* [r17] topo/gaussiansheet.py:
	  Bug fix.

2004-02-08  joeraii

	* [r16] topo/gaussiansheet.py,
	  topo/kernelfactory.py:
	  Added width and height parameters to the gaussian, and also
	  cleaned up the generation function.

2004-02-04  jp

	* [r15] topo/gaussiansheet.py:
	  Gaussian sheet update.

2004-02-04  joeraii

	* [r14] topo/gaussiansheet.py:
	  Just added a comment

	* [r13] topo/gaussiansheet.py,
	  topo/kernelfactory.py:
	  First commit of the gaussian sheet, generator for random
	  gaussians.

2004-01-30  jp

	* [r12] external/Imaging-1.1.4jp.tgz:
	  Finally (I hope) fixed PIL's setup.py

	* [r11] external/Imaging-1.1.4jp.tgz,
	  external/Makefile:
	  Fixed config bug in PIL. Added 'make uninstall' to
	  external/Makefile.

	* [r10] external/Makefile:
	  Added Pmw to external packages makefile.

	* [r9] Makefile, external,
	  external/Imaging-1.1.4jp.tgz,
	  external/Makefile,
	  external/Numeric-23.0.tgz,
	  external/Pmw.tgz,
	  external/Python-2.3.3.tgz,
	  external/README.txt,
	  external/jpeg-6b.tgz:
	  Added external source packages for development.

2004-01-23  jp

	* [r8] examples/image_example2.py,
	  examples/main.ppm,
	  examples/test.ppm,
	  topo/rfsom.py,
	  topo/sheet.py,
	  topo/simulator.py,
	  topographica:
	  Minor improvements to topographica script & image_example2"

	* [r7] examples/__init__.py:
	  Made examples dir into a package.

	* [r6] topographica:
	  minor bugfix

	* [r5] topographica:
	  Fixed error for machines with no readline module.

	* [r4] examples,
	  examples/image_example.py,
	  examples/image_example2.py,
	  topo/image_example.py,
	  topo/image_example2.py:
	  Created examples dir.

	* [r3] topographica:
	  Readine support at topographica prompt.

	* [r2] /trunk/topographica, .cvsignore,
	  runtests, tests,
	  tests/README.txt,
	  tests/__init__.py,
	  tests/testboundingregion.py,
	  tests/testdummy.py,
	  tests/testsheet.py, topo,
	  topo/__init__.py,
	  topo/boundingregion.py,
	  topo/convolve2d.py,
	  topo/debug.py,
	  topo/dislindriver.py,
	  topo/dislinplot.py,
	  topo/heap.py,
	  topo/image.py,
	  topo/image_example.py,
	  topo/image_example2.py,
	  topo/kernelfactory.py,
	  topo/params.py,
	  topo/rfsom.py,
	  topo/sheet.py,
	  topo/simulator.py,
	  topo/som.py,
	  topo/toolbar.py,
	  topo/utils.py,
	  topographica:
	  Start

2004-01-23  ceball_cvs2svn

	* [r1] /branches, /tags, /trunk:
	  New repository initialized by cvs2svn.
