2014-02-27  Michael R. Crusoe <mcrusoe@msu.edu>

    * tagged: version 0.8
    * setup.py: Specify a known working version of setuptools so we don't
    force an unneeded and awkward upgrade.
    * setup.py: We aren't zipsafe, mark as such

2014-02-18  Michael R. Crusoe <mcrusoe@msu.edu>

* Normalized C++ namespace usage to fix CID 1054792
* Updated install instructions. We recommend OS X users and those Linux
users without root access to install virtualenv instead of pip.
* New documentation: doc/known-issues.txt
* Added code review checklist & other guidance: doc/development.txt

2014-02-03  Camille Scott <camille.scott.w@gmail.com>

* Standardized command line arguments in khmer_args; added version flag

* Added support for sparse graph labeling

* Added script to reinflate partitions from read files using the 
  labeling system, called sweep-reads-by-partition-buffered.py

* Implemented __new__ methods for Hashbits, enforced inheritance
  hierarchy between it and the new LabelHash class both in C++
  and CPython API

2013-12-20  Titus Brown  <titus@idyll.org>

* Fixed output_partitioned_file, sweep-reads3.py, and extract-partitions.py
  to retain FASTQ format in output.

2013-12-11  Michael R. Crusoe <mcrusoe@msu.edu>

* normalize-by-median.py: new optional argument: --record-filenames to specify
a path where a list of all the output filenames will be written to. Will
be used to better integrate with Galaxy.

* All commands that use the counting args now support the --version switch

* abundance-dist-single.py, abundance-dist.py, do-partition.py,
interleave-reads.py, load-graph.py, load-into-counting.py
normalize-by-median.py now exit with return code 1 instead of 255 as is
standard.

2013-12-19  Michael R. Crusoe  <mcrusoe@msu.edu>

* doc/install.txt Add setup instructions for RHEL6 & fix invocation to get
master branch to work for non-developers

2013-12-18  Titus Brown  <titus@idyll.org>

* Added a test to ensure that normalize-by-median.py has bigcount set to
  False.

2013-11-22  Camille Scott  <camille.scott.w@gmail.com>

* Makefile: Added debug target for profiling.

2013-11-22  Michael R. Crusoe  <mcrusoe@msu.edu>

* Documented release process

2013-10-21  Michael R. Crusoe  <mcrusoe@msu.edu>

* Version 0.7

* New script: sample-reads-randomly.py which does a single pass random
subsample using reservoir sampling.

* the version number is now only stored in one place

* Makefile: new dist, cppcheck, pep8, and autopep8 targets for developers.
VERSION is now set by versioneer and exported to C/C++ code.

* README switched from MarkDown to ReStructuredText format to clean up PyPI
listing. Install count badge added.

* doc/: updates to how the scripts are called. Sphinx now pulls version
number from versioneer. C/Python integration is now partially documented.
Reference to bleeding-edge has been removed. Release instructions have been
clarified and simplified.

* all python code in khmer/, scripts/, and tests/ should be PEP8 compliant now.

* khmer/_khmermodule.cc has gotten a once-over with cpychecker. Type errors
were eliminated and the error checking has improved.

* Several fixes motivated by the results of a Coverity C/C++ scan. 

* Tests that require greater than 0.5 gigabytes of memory are now annotated as
being 'highmem' and be skipped by changing two lines in setup.cfg

* warnings about -Wstrict-prototypes will no longer appear

* contributors to this release are: ctb, mr-c and camillescott. 

2013-10-15  Michael R. Crusoe  <mcrusoe@msu.edu>

* Version 0.6.1

* No code changes, just build fixes

2013-10-10  Michael R. Crusoe  <mcrusoe@msu.edu>

* Version 0.6

* Switch to setuptools to run the entire build

* The various Makefiles have been merged into one inside lib for posterity

* A new top-level Makefile wraps "python setup.py"

* argparse.py has been removed and is installed automatically by setuptools/pip

* setup.py and the python/khmer directory have been moved to the root of the
project to conform to the standard layout

* The project contact address is now khmer-project@idyll.org

* Due to the new build system the project now easily builds under OS X + XCode

* In light of the above the installation instructions have been rewritten

* Sphinx now builds the documentation without warnings or errors

* It is now easy to calculate code coverage.

* setup.py is now PEP8 compliant
