2014-12-07  Michael R. Crusoe  <mcrusoe@msu.edu>

    * Makefile: add sandbox scripts to the pylint_report.txt target
    * doc/dev/coding-guidelines-and-review.txt: Add question about command
    line API to the checklist
    * doc/dev/release.txt: refresh release procedure

2014-12-05  Michael R. Crusoe  <mcrusoe@msu.edu>

    * CITATIONS,khmer/khmer_args.py: update citations for Qingpeng's paper

2014-12-01  Michael R. Crusoe  <mcrusoe@msu.edu>

    * doc/roadmap.txt: Explain the roadmap to v2 through v4

2014-12-01  Kevin Murray  <spam@kdmurray.id.au>

    * tests/test_scripts.py: Stop a test from making a temporary output file
    in the current dir by explictly specifying an output file.

2014-12-01  Kevin Murray  <spam@kdmurray.id.au>

    * load-into-counting.py: Add a CLI parameter to output a machine-readable
    summary of the run, including number of k-mers, FPR, input files etc in
    json or TSV format.

2014-12-01  Titus Brown  <t@idyll.org>

    * Update sandbox docs: some scripts now used in recipes

2014-11-23  Phillip Garland  <pgarland@gmail.com>

    * lib/khmer.hh (khmer): define KSIZE_MAX
    * khmer/_khmermodule.cc (forward_hash, forward_hash_no_rc) (reverse_hash):
    Use KSIZE_MAX to check whether the user-supplied k is larger than khmer
    supports.

2014-11-19  Michael R. Crusoe  <mcrusoe@msu.edu>

    * CODE_OF_CONDUT.RST,doc/dev/{index,CODE_OF_CONDUCT}.txt: added a code of
    conduct

2014-11-18  Jonathan Gluck  <jdg@cs.umd.edu>

    * tests/test_counting_hash.py: Fixed copy paste error in comments, True to
    False.

2014-11-15  Jacob Fenton  <bocajnotnef@gmail.com>

    * tests/test_scripts.py: added screed/read_parsers stream testing
    * khmer/file.py: modified file size checker to not break when fed
    a fifo/block device
    * tests/test-data/test-abund-read-2.fa.{bz2, gz}: new test files

2014-11-11  Jacob Fenton  <bocajnotnef@gmail.com>

    * do-partition.py: replaced threading args in scripts with things from 
    khmer_args
    * khmer/theading_args.py: removed as it has been deprecated

2014-11-06  Michael R. Crusoe  <mcrusoe@msu.edu>

    * lib/{counting,hashbits}.{cc,hh},lib/hashtable.hh: Moved the n_kmers()
    function into the parent Hashtable class as n_unique_kmers(), adding it to
    CountingHash along the way. Removed the unused start and stop parameters.
    * khmer/_khmermodule.cc: Added Python wrapping for CountingHash::
    n_unique_kmers(); adapted to the dropped start and stop parameters.
    * scripts/{load-graph,load-into-counting,normalize-by-median}.py: used the
    n_unique_kmers() function instead of the n_occupied() function to get the
    number of unique kmers in a table.
    * tests/test_{hashbits,hashbits_obj,labelhash,scripts}.py: updated the
    tests to reflect the above

2014-10-24  Camille Scott  <camille.scott.w@gmail.com>

    * do-partition.py: Add type=int to n_threads arg and assert to check
    number of active threads

2014-10-10  Brian Wyss  <wyssbria@msu.edu>

    * khmer/scripts/{abundance-dist, abundance-dist-single,
    annotate-partitions, count-median, count-overlap, do-partition,
    extract-paired-reads, extract-partitions, filter-abund, filter-abund-single,
    filter-stoptags, find-knots, load-graph, load-into-counting,
    make-initial-stoptags, merge-partitions, normalize-by-median, 
    partition-graph, sample-reads-randomly}.py:
    changed stdout output in scripts to go to stderr.

2014-10-06  Michael R. Crusoe  <mcrusoe@msu.edu>

    * Doxyfile.in: add links to the stdc++ docs

2014-10-01  Ben Taylor  <taylo886@msu.edu>

    * khmer/_khmermodule.cc, lib/hashtable.cc, lib/hashtable.hh,
    tests/test_counting_hash.py, tests/test_labelhash.py,
    tests/test_hashbits.py, tests/test_hashbits_obj.py:
    Removed Hashtable::consume_high_abund_kmers,
    Hashtable::count_kmers_within_depth, Hashtable::find_radius_for_volume,
    Hashtable::count_kmers_on_radius

2014-09-29  Michael R. Crusoe  <mcrusoe@msu.edu>

    * versioneer.py: upgrade versioneer 0.11->0.12

2014-09-29  Sherine Awad  <sherine.awad@gmail.com>

    * scripts/normalize-by-median.py: catch expections generated by wrong
    indentation for 'total'

2014-09-23  Jacob G. Fenton  <bocajnotnef@gmail.com>

    * scripts/{abundance-dist-single, abundance-dist, count-median,
    count-overlap, extract-paired-reads, filter-abund-single,
    load-graph, load-into-counting, make-initial-stoptags,
    partition-graph, split-paired-reads}.py: 
    added output file listing at end of file
    * scripts/extract-long-sequences.py: refactored to set write_out to
    sys.stdout by default; added output location listing.
    * scripts/{fastq-to-fasta, interleave-reads}.py: 
    added output file listing sensitive to optional -o argument
    * tests/test_scripts.py: added test for scripts/make-initial-stoptags.py

2014-09-19  Ben Taylor  <taylo886@msu.edu>

    * Makefile: added --inline-suppr to cppcheck, cppcheck-result.xml targets
    * khmer/_khmermodule.cc: Added comments to address cppcheck false positives
    * lib/hashtable.cc, lib/hashtable.hh: take args to filter_if_present by
    reference, address scope in destructor
    * lib/read_parsers.cc: Added comments to address cppcheck false positives
    * lib/subset.cc, lib/subset.hh: Adjusted output_partitioned_file,
    find_unpart to take args by reference, fix assign_partition_id to use
    .empty() instead of .size()

2014-09-19  Ben Taylor  <taylo886@msu.edu>
		
    * Makefile: Add astyle, format targets
    * doc/dev/coding-guidelines-and-review.txt: Add reference to `make format`
		target

2014-09-10  Titus Brown  <titus@idyll.org>

    * sandbox/calc-median-distribution.py: catch exceptions generated by reads
	shorter than k in length.
    * sandbox/collect-reads.py: added script to collect reads until specific
	average cutoff.
    * sandbox/slice-reads-by-coverage.py: added script to extract reads with
	a specific coverage slice (based on median k-mer abundance).
	
2014-09-09  Titus Brown  <titus@idyll.org>

    * Added sandbox/README.rst to describe/reference removed files,
	 and document remaining sandbox files.

    * Removed many obsolete sandbox files, including:
      sandbox/abund-ablate-reads.py,
      sandbox/annotate-with-median-count.py,
      sandbox/assemble-individual-partitions.py,
      sandbox/assemstats.py,
      sandbox/assemstats2.py,
      sandbox/bench-graphsize-orig.py,
      sandbox/bench-graphsize-th.py,
      sandbox/bin-reads-by-abundance.py,
      sandbox/bowtie-parser.py,
      sandbox/calc-degree.py,
      sandbox/calc-kmer-partition-counts.py,
      sandbox/calc-kmer-read-abunds.py,
      sandbox/calc-kmer-read-stats.py,
      sandbox/calc-kmer-to-partition-ratio.py,
      sandbox/calc-sequence-entropy.py,
      sandbox/choose-largest-assembly.py,
      sandbox/consume-and-traverse.py,
      sandbox/contig-coverage.py,
      sandbox/count-circum-by-position.py,
      sandbox/count-density-by-position.py,
      sandbox/count-distance-to-volume.py,
      sandbox/count-median-abund-by-partition.py,
      sandbox/count-shared-kmers-btw-assemblies.py,
      sandbox/ctb-iterative-bench-2-old.py,
      sandbox/ctb-iterative-bench.py,
      sandbox/discard-high-abund.py,
      sandbox/discard-pre-high-abund.py,
      sandbox/do-intertable-part.py,
      sandbox/do-partition-2.py,
      sandbox/do-partition-stop.py,
      sandbox/do-partition.py,
      sandbox/do-subset-merge.py,
      sandbox/do-th-subset-calc.py,
      sandbox/do-th-subset-load.py,
      sandbox/do-th-subset-save.py,
      sandbox/extract-surrender.py,
      sandbox/extract-with-median-count.py,
      sandbox/fasta-to-fastq.py,
      sandbox/filter-above-median.py,
      sandbox/filter-abund-output-by-length.py,
      sandbox/filter-area.py,
      sandbox/filter-degree.py,
      sandbox/filter-density-explosion.py,
      sandbox/filter-if-present.py,
      sandbox/filter-max255.py,
      sandbox/filter-min2-multi.py,
      sandbox/filter-sodd.py,
      sandbox/filter-subsets-by-partsize.py,
      sandbox/get-occupancy.py,
      sandbox/get-occupancy2.py,
      sandbox/graph-partition-separate.py,
      sandbox/graph-size-circum-trim.py,
      sandbox/graph-size-degree-trim.py,
      sandbox/graph-size-py.py,
      sandbox/join_pe.py,
      sandbox/keep-stoptags.py,
      sandbox/label-pairs.py,
      sandbox/length-dist.py,
      sandbox/load-ht-and-tags.py,
      sandbox/make-coverage-by-position-for-node.py,
      sandbox/make-coverage-histogram.py,
      sandbox/make-coverage.py,
      sandbox/make-random.py,
      sandbox/make-read-stats.py,
      sandbox/multi-abyss.py,
      sandbox/multi-stats.py,
      sandbox/multi-velvet.py,
      sandbox/normalize-by-min.py,
      sandbox/occupy.py,
      sandbox/parse-bowtie-pe.py,
      sandbox/parse-stats.py,
      sandbox/partition-by-contig.py,
      sandbox/partition-by-contig2.py,
      sandbox/partition-size-dist-running.py,
      sandbox/partition-size-dist.py,
      sandbox/path-compare-to-vectors.py,
      sandbox/print-exact-abund-kmer.py,
      sandbox/print-high-density-kmers.py,
      sandbox/quality-trim-pe.py,
      sandbox/quality-trim.py,
      sandbox/reformat.py,
      sandbox/remove-N.py,
      sandbox/softmask-high-abund.py,
      sandbox/split-N.py,
      sandbox/split-fasta-on-circum.py,
      sandbox/split-fasta-on-circum2.py,
      sandbox/split-fasta-on-circum3.py,
      sandbox/split-fasta-on-circum4.py,
      sandbox/split-fasta-on-degree-th.py,
      sandbox/split-fasta-on-degree.py,
      sandbox/split-fasta-on-density.py,
      sandbox/split-reads-on-median-diff.py,
      sandbox/summarize.py,
      sandbox/sweep_perf.py,
      sandbox/test_scripts.py,
      sandbox/traverse-contigs.py,
      sandbox/traverse-from-reads.py,
      sandbox/validate-partitioning.py -- removed as obsolete.

2014-09-01  Michael R. Crusoe  <mcrusoe@msu.edu>

    * doc/dev/coding-guidelines-and-review.txt: Clarify pull request checklist
    * CONTRIBUTING.md: update URL to new dev docs

2014-08-30  Rhys Kidd  <rhyskidd@gmail.com>

    * khmer/_khmermodule.cc: fix table.get("wrong_length_string") gives core
    dump
    * lib/kmer_hash.cc: improve quality of exception error message
    * tests/{test_counting_hash,test_counting_single,test_hashbits,
        test_hashbits_obj}.py: add regression unit tests

2014-08-28  Titus Brown  <titus@idyll.org>

    * scripts/normalize-by-median.py: added reporting output after main loop
	exits, in case it hadn't been triggered.
    * sandbox/saturate-by-median.py: added flag to change reporting frequency,
	cleaned up leftover code from when it was copied from
	normalize-by-median.

2014-08-24  Rhys Kidd  <rhyskidd@gmail.com>

    * khmer/thread_utils.py, sandbox/filter-below-abund.py,
	scripts/{extract-long-sequences,load-graph,load-into-counting,
	normalize-by-median,split-paired-reads}.py,
	scripts/galaxy/gedlab.py: fix minor PyLint issues 

2014-08-20  Michael R. Crusoe  <mcrusoe@msu.edu>

    * test/test_version.py: add Python2.6 compatibility.

2014-08-20  Rhys Kidd  <rhyskidd@gmail.com>

    * setup.py,README.rst,doc/user/install.txt: Test requirement for a 
    64-bit operating system, documentation changes. Fixes #529

2014-08-19  Michael R. Crusoe  <mcrusoe@msu.edu>

    * {setup,versioneer,khmer/_version}.py: upgrade versioneer from 0.10 to 0.11

2014-08-18  Michael R. Crusoe  <mcrusoe@msu.edu>

    * setup.py: Use the system bz2 and/or zlib libraries if specified in
    setup.cfg or overridden on the commandline

2014-08-06  Michael R. Crusoe  <mcrusoe@msu.edu>

    * CITATION: fixed formatting, added BibTeX
    * Makefile: Python code coverage targets will now compile khmer if needed
    * doc/dev/galaxy.txt: moved to doc/user/; updated & simplified
    * doc/{dev,user}/index.txt: galaxy.txt move
    * scripts/*.xml: moved to scripts/galaxy/; citations added; additional
    scripts wrapped
    * scripts/galaxy/README.txt: documented Galaxy codebase requirements
    * doc/citations.txt: symlink to CITATION
    * scripts/galaxy/test-data: added symlinks to files in tests/test-data or
    added short test files from scratch
    * scripts/galaxy/macros.xml: common configuration moved to central file
    * scripts/galaxy/gedlab.py: custom Galaxy datatypes for the counting
    tables and presence tables: it inherits from the Galaxy Binary type but
    isn't sniffable. Written with GalaxyTeam's Dave_B.
    * scripts/filter-abund.py: fix inaccurate parameter description
    * scripts/galaxy/tool_dependencies.xml: document install process
    * scripts/galaxy/filter-below-abund.py: symlink to
    sandbox/filter-below-abund.py for now.
    * khmer/khmer_args.py: point users to online citation file for details

2014-08-05  Michael R. Crusoe  <mcrusoe@msu.edu>

    * lib/read_parsers.{cc,hh}: close file handles. Fixes CID 1222793

2014-08-05  Justin Lippi  <jlippi@gmail.com>

    * khmer/__init__.py: import get_version_cpp method as __version_cpp__.
    * khmer/_khmermodule.cc: added get_version_cpp implementation
    * tests/test_version.py: check that version from C++ matches version from
    khmer.__version__
    * setup.cfg: don't run tests with 'jenkins' @attr with 'make test'

2014-08-04  Michael R. Crusoe  <mcrusoe@msu.edu>

    * khmer/_khmermodule.cc,lib/{kmer_hash.{cc,hh},read_aligner.cc,
    read_parsers.{cc,hh},trace_logger.cc: Replace remaining uses of assert()
    with khmer_exceptions. Fixes #215.
    * setup.py: simplify argparse conditional dependency

2014-08-03  Titus Brown & Michael R. Crusoe  <t@idyll.org>

    * doc/{artifact-removal,partitioning-workflow{.graffle,.png}},{biblio,
    blog-posts,guide,install,choosing-table-sizes,known-issues,scripts,
    partitioning-big-data.txt: moved to doc/user/
    * doc/{crazy-ideas,details,development,galaxy,release,examples}.txt: moved
    to doc/dev/
    * doc/dev/{a-quick-guide-to-testing,codebase-guide,
    coding-guidelines-and-review,for-khmer-developers,getting-started,
    hackathon,index}.txt,doc/user/index.txt: new content.
    * doc/design.txt: deleted
    The documentation has been split into user focused documentation and
    developer focused documentation. The new developer docs were field tested
    as part of the Mozilla Science Lab global sprint that we participated in;
    we are grateful to all the volunteers.

2014-07-24  Ivan Gonzalez  <iglpdc@gmail.com>

    * lib/khmer.hh, lib/khmer_exception.hh: All exceptions are now derived from
	a new base class exception, khmer::khmer_exception. Issue #508.
    * lib/counting.cc, lib/hashbits.cc, lib/hashtable.{cc,hh},lib/kmer_hash.cc,
	lib/labelhash.cc, lib/perf_metrics.hh, lib/read_parsers.{cc,hh},
	lib/subset.cc, lib/thread_id_map.hh: All exceptions thrown are now
	instances (or derived from) khmer::khmer_exception.

2014-07-24  Jiarong Guo  <guojiaro@gmail.com>

    * khmer/_khmermodule.cc: add python exception when thread = 0 for
    ReadParser.
    * tests/test_read_parsers.py: add test_with_zero_threads() to test Python
    exception when ReadParser has zero threads.

2014-07-23  Qingpeng Zhang  <qingpeng@gmail.com>

    * scripts/load-graph.py: write fp rate into *.info file with option 
    to switch on
    * tests/test_scripts.py: add test_load_graph_write_fp

2014-07-23  Ryan R. Boyce  <boycerya@msu.edu>

    * Makefile: fixed >80 character line wrap-around

2014-07-23  Leonor Garcia-Gutierrez  <l.garcia-gutierrez@warwick.ac.uk>

    * tests/test_hashbits.py, tests/test_graph.py, 
    tests/test_lump.py: reduced memory requirement
    
2014-07-23  Heather L. Wiencko  <wienckhl@tcd.ie>

    * khmer_tst_utils.py: added import traceback
    * test_scripts.py: added test for normalize_by_median.py for fpr rate

2014-07-22  Justin Lippi  <jlippi@gmail.com>
 
    * khmer/_khmermodule.cc: removed unused assignment
    * lib/read_aligner.cc,lib/read_aligner.hh: wrapped function declarations
    in the same compiler options that the only invocations are in to avoid
    unusedPrivateFunction violation.
    * lib/read_parsers.cc: fix redundantassignment error by assigning variable
    to its value directly

2014-07-22  Michael R. Crusoe  <mcrusoe@msu.edu>

    * Makefile: combine pip invocation into single "install-dependencies"
    target.

2014-07-22  Justin Lippi  <jlippi@gmail.com>

    * tests/test_subset_graph.py: decrease the amount of memory that is being
    requested for the hash tables in test.

2014-07-22  Jim Stapleton  <jas@msu.edu>

     * scripts/filter-abund.py: no longer asks for parameters that are unused,
     issue #524

2014-07-22  Justin Lippi  <jlippi@gmail.com> 

    * tests/khmer_tst_utils.py: put runscript here
    * tests/test_sandbox_scripts.py: remove 'runsandbox', renamed to runscript
      and placed in khmer_tst_utils
    * tests/test_scripts.py: removed 'runscript' and placed in khmer_tst_utils

2014-07-22  Jeramia Ory  <jeramia.ory@gmail.com>

    * khmer/_khmermodule.cc: removed unused KhmerError, issue #503

2014-07-22  Rodney Picett  <pickett.rodney@gmail.com>

    * lib/scoringmatrix.{cc,hh}: removed assign function, issue #502
 
2014-07-22  Leonor Garcia-Gutierrez  <l.garcia-gutierrez@warwick.ac.uk>

    * tests/test_counting_single.py: reduced memory requirements
    
2014-07-21  Titus Brown  <t@idyll.org>

    * sandbox/saturate-by-median.py: introduce new sandbox script for
	saturation analysis of low-coverage data sets.

2014-07-10  Joe Stein  <joeaarons@gmail.com>

    * sandbox/readstats.py: fixed divide-by-zero error, issue #458

2014-07-06  Titus Brown  <t@idyll.org>

    * doc/release.txt: fix formatting.

2014-06-25  Michael R. Crusoe <mcrusoe@msu.edu>

    * scripts/load-graph.py: fix #507. Threading doesn't give any advantages
    to this script right now; the threading parameter is ignored for now.

2014-06-20  Chuck Pepe-Ranney  <chuck.peperanney@gmail.com>

    * scripts/extract-partitions.py: added epilog documentation for 
	<base>.dist columns.

2014-06-20  Michael R. Crusoe  <mcrusoe@msu.edu>

    * doc/release.txt: Add Coverity Scan to release checklist

2014-06-19  Michael R. Crusoe  <mcrusoe@msu.edu>

    * lib/read_aligner.{cc,hh},khmer/_khmermodule.cc,setup.py,
    tests/test_read_aligner.py,sandbox/{normalize-by-align,read-aligner}.py:
    Update of @fishjord's graph alignment work
    * lib/{aligner,kmer,node}.{cc,hh},tests/test_align.py: removed as they are
    superceded by the above
    * Makefile: fixed wildcards
    * tests/read_parsers.py: tests that are too complicated to run with
    Valgrind's memcheck are now marked @attr('multithread')

2014-06-16  Titus Brown  <t@idyll.org>

    * doc/release.txt: updated release process.
    * doc/known-issues.txt: updated known-issues for v1.1 release
    * doc/release-notes/: added release notes for 1.0, 1.0.1, and 1.1

2014-06-16  Michael R. Crusoe  <mcrusoe@msu.edu>

    * scripts/{abundance-dist-single,filter-abund-single,load-into-counting,
    normalize-by-median,load-graph}.py: restore Python 2.6 compatability for
    Debian 6, RedHat 6, SL6, and Ubuntu 10.04 LTS users.

2014-06-15  Titus Brown  <t@idyll.org>

    * doc/scripts.txt: removed sweep-reads.py from script documentation.
    * scripts/sweep-reads.py, scripts/sweep-files.py: moved sweep-reads.py
	and sweep-files.py over to sandbox.
    * tests/test_sandbox_scripts.py: created a test file for scripts in
	sandbox/; skip when not in developer mode (e.g. installed egg).
    * tests/test_script_arguments.py: capture file.py output to stderr
	so that it is not displayed during tests.
    * sandbox/calc-median-distribution.py: updates to print cumulative
	distribution for calc-median-distribution.

2014-06-14  Michael R. Crusoe  <mcrusoe@msu.edu>

    * scripts/{abundance-dist-single,filter-abund-single,load-into-counting,
    normalize-by-median,load-graph}.py,tests/test_scripts.py: added
    '--report-total-kmers' option to all scripts that create k-mer tables.

2014-06-14  Titus Brown  <t@idyll.org>

    * doc/scripts.txt, tests/test_scripts.py, scripts/sweep-reads.py:
	renamed sweep-reads-buffered to sweep-reads; added FASTQ output to
	sweep-reads.
    * doc/scripts.txt: added extract-long-sequences.py doc reference.
    * scripts/extract-long-sequences.py: set default sequence length to
	extract to 200 bp.

2014-06-13  Michael R. Crusoe  <mcrusoe@msu.edu>

    * MANIFEST.in: don't include docs/, data/, or examples/ in our PyPI
    distribution. Saves 15MB.

2014-06-13  Michael R. Crusoe  <mcrusoe@msu.edu>

    * Makefile: split coverity target in two: -build and -upload. Added
    configuration target

2014-06-13  Titus Brown  <t@idyll.org>

    * doc/install.txt: updated virtualenv command to use python2 explicitly,
	for arch support.

2014-06-13  Titus Brown  <t@idyll.org>

    * khmer/__init__.py, khmer/file_args.py: Moved copyright message to a
	comment.
    * khmer/file.py: updated error messages for disk-space checking functions;
	added test hooks.
    * tests/test_script_arguments.py: added tests for several functions in
	khmer/file.py.
    * sandbox/assemstats3.py: handle missing input files.

2014-06-12  Michael Wright <wrigh517@msu.edu>

    * sandbox/load-into-hashbits: Deleted from sandbox. It is superseded
    by load-graph.py --no-tagset.

2014-06-11  Michael Wright <wrigh517@msu.edu>

    * scripts/load-into-counting: Fixed docstring misnomer to 
	load-into-counting.py

2014-06-10  Michael R. Crusoe  <mcrusoe@msu.edu>

    * setup.py,tests/{__init__,khmer_tst_utils,test_scripts,
    khmer_test_counting_single}.py: made tests runnable after installation.
    * lib/{khmer.hh,hashtable.hh,read_parsers.cc,read_parsers.hh}: restructure
    exception hierarchy.
    * khmer/_khmermodule.cc: Nicer error checking for hash_consume_fasta,
    hash_abundance_distribution, hashbits_consume_{fasta,fasta_and_tag
    {,with_stoptags},partitioned_fasta}, hashbits_output_partitions, and
    labelhash_consume_{,partitioned_}fasta_and_tag_with_labels.

2014-06-10  Titus Brown  <t@idyll.org>

    * Makefile: remove SHELL setting so that 'make doc' works in virtualenvs.
    * scripts/sample-reads-randomly.py: extend to take multiple subsamples
	with -S.
    * tests/test_scripts.py: added test for multiple subsamples from
	sample-reads-randomly.py

2014-06-10  Michael Wright <wrigh517@msu.edu>

    * scripts/extract-long-sequences: Moved from sandbox, added argparse and 
    FASTQ support.
    * scripts/fastq-to-fasta: Fixed outdated argparse oversight.
    * tests/test_scripts.py: Added tests for extract-long-sequences.py

2014-06-08  Titus Brown  <t@idyll.org>

    * doc/conf.py: set google_analytics_id and disqus_shortname properly;
	disable "editme" popup.
    * doc/_templates/page.html: take google_analytics_id and disqus_shortname
	from doc/conf.py.

2014-06-04  Michael R. Crusoe <mcrusoe@msu.edu>

    * lib/Makefile: do a distclean as the CFLAGS may have changed. Fixes #442

2014-06-03 Chuck Pepe-Ranney <chuck.peperanney@gmail.com>

    * scripts/abundance-dist.py: removed call to check_space on infiles.  

2014-05-31  Michael R. Crusoe  <mcrusoe@msu.edu>

    * khmer/_khmermodule.cc,lib/counting.{cc,hh},
    sandbox/{stoptag-abundance-ham1-hist.py,off-by-one.py,filter-ham1.py}:
    Remove CountingHash get_kmer_abund_mean, get_kmer_abund_abs_deviation, and
    max_hamming1_count along with Python glue code and sandbox scripts. They
    are no longer useful.

2014-05-30  Titus Brown  <t@idyll.org>

    * khmer/_khmermodule.cc: remove merge2* functions: unused, untested.
    * lib/counting.cc, lib/hashbits.cc, lib/hashtable.cc: made file loading
	exceptions more verbose and informative.
    * tests/test_subset_graph.py: added tests for SubsetPartition::
	load_partitionmap.
    * khmer/_khmermodule.cc, lib/subset.cc, wrapped SubsetPartition::
	load_partitionmap to catch, propagate exceptions
    * tests/test_hashbits.py, tests/test_counting_hash.py: added tests
	for fail-on-load of bad file format versions; print exception messages.
    * .gitignore: added various temporary pip & build files
    * lib/counting.cc: added I/O exception handling to CountingHashFileReader
	and CountingHashGzFileReader.
    * lib/hashbits.cc: added I/O exception handling to Hashbits::load.
    * lib/subset.cc: added I/O exception handling to merge_from_disk.
    * lib/hashtable.cc: added I/O exception handling to load_tagset and
	load_stop_tags
    * khmer/_khmermodule.cc: added I/O exception propagation from C++ to
	Python, for all loading functions.

2014-05-22  Michael Wright  <wrigh517@msu.edu>

    * scripts/fastq-to-fasta: Moved and improved fastq-to-fasta.py into scripts 
    from sandbox
    * tests/test_scripts.py: Added tests for fastq-to-fasta.py
    * tests/test-data: Added test-fastq-n-to-fasta.py file with N's in 
    sequence for testing

2014-05-19  Michael R. Crusoe  <mcrusoe@msu.edu>

    * Makefile: add target for python test coverage plain-text report;
    clarified where the HTML report is

2014-05-16  Michael R. Crusoe  <mcrusoe@msu.edu>

    * docs/scripts.txt: include sweep-reads-buffered.py

2014-05-14  Adam Caldwell  <adam.caldwell@gmail.com>

    * Makefile: change pip to pip2. Fixes assorted make problems on systems
    where pip links to pip3

2014-05-14  Michael R. Crusoe  <mcrusoe@msu.edu>

    * lib/{zlib,bzip2} -> third-party/
    * setup.{cfg,py}: Move third party libraries to their own directory
    * Makefile: add sloccount target for humans and the sloccount.sc target for
   Jenkins

2014-05-13  Michael Wright  <wrigh517@msu.edu>

    * sandbox/fastq-to-fasta.py: now reports number of reads dropped due to
    'N's in sequence. close 395

2014-05-13  Michael R. Crusoe  <mcrusoe@msu.edu>

    * doc/release.txt: additional fixes

2014-05-09  Luiz Irber  <irberlui@msu.edu>

    Version 1.0.1

2014-05-09  Michael R. Crusoe  <mcrusoe@msu.edu>

    * doc/release.txt: update release instructions

2014-05-06  Michael R. Crusoe  <mcrusoe@msu.edu>

    * lib/{subset,counting}.cc: fix cppcheck errors; astyle -A10
    --max-code-length=80

2014-05-06  Titus Brown  <titus@idyll.org>

    * sandbox/calc-best-assembly.py: added script to calculate best
    assembly from a list of contig/scaffold files
	
2014-04-23  Titus Brown  <titus@idyll.org>

    * scripts/abundance-dist-single.py: fixed problem where ReadParser was
    being created anew for each thread; regression introduced in 4b823fc.

2014-04-22  Michael R. Crusoe  <mcrusoe@msu.edu>

    *.py: switch to explicit python2 invocation. Fixes #385.

2014-04-21  Titus Brown  <t@idyll.org>

    * doc/development.txt: added spellcheck to review checklist

2014-04-21  Titus Brown  <titus@idyll.org>

    * scripts/normalize-by-median.py: updated FP rate to match latest info from
      Qingpeng's paper; corrected spelling error.

2014-04-21  Michael R. Crusoe  <mcrusoe@msu.edu>

    * setup.py,doc/installing.txt: Remove argparse from the requirements
    unless it isn't available. Argparse is bundled with Python 2.7+. This
    simplifies the installation instructions.

2014-04-17  Ram RS  <ramrs@nyu.edu>

    * scripts/make-initial-stoptags.py: fixed bug that threw error on
     missing .ht input file while actual expected input file is .pt

2014-04-11  Titus Brown  <t@idyll.org>

    * scripts/*.py: fixed argument to check_space_for_hashtable to rely
    on args.n_tables and not args.ksize.

2014-04-06  Titus Brown  <titus@idyll.org>

    * scripts/normalize-by-median.py: added comment about table compatibility
    with abundance-dist.

2014-04-05  Michael R. Crusoe  <mcrusoe@msu.edu>

    * MANIFEST.in,setup.py: fix to correct zlib packaging for #365
    * ChangeLog: fix date for 1.0 release, email addresses

2014-04-01  Michael R. Crusoe  <mcrusoe@msu.edu>

    Version 1.0
    * Makefile: run 'build' command before install; ignore _version.py for
    coverage purposes.
    * bink.ipynb: deleted
    * doc/choosing-hash-sizes.txt -> choosing-table-sizes.txt
    * setup.py,doc/{conf.py,index.txt}: update lists of authors
    * doc/development.txt: typo
    * doc/{galaxy,guide,index,introduction,scripts}.txt: remove some
    references to implementation details of the k-mer tables
    * doc/{known-issues,release}.txt: updated
    * khmer/*.cc,lib/*.{cc,hh}: astyle -A10 formatted
    * lib/read_parsers.cc: fixed case statement fall through
    * lib/subset.cc: removed unnecessary NULL check (CID 1054804 & 1195088)
    * scripts/*.py: additional documentation updates
    * tests/test-data/test-overlap1.ht,data/MSB2-surrender.fa &
    data/1m-filtered.fa: removed from repository history, .git is now 36M!

2014-04-01  Titus Brown  <t@idyll.org>

    * CITATION,khmer/khmer_args.py: Updated khmer software citation for
    release.

2014-03-31  Titus Brown  <t@idyll.org>

    * scripts/normalize-by-median.py: Fixed unbound variable bug introduced in
    20a433c2.

    * khmer/file.py: Fixed incorrect use of __file__ dirname instead of
    os.getcwd(); also fixed bug where statvfs would choke on an empty
    dirname resulting from input files being in the cwd.

2014-03-31  Michael R. Crusoe  <mcrusoe@msu.edu>

    * versioneer.py,ez_setup.py: updated to version 0.10 and 3.4.1
    respectively.
    * docs/release.txt,khmer/_version.py,MANIFEST.in: update ancillary
    versioneer files

2014-03-31  Titus Brown  <t@idyll.org>

    * scripts/*.py,khmer/khmer_args.py: added 'info' function to khmer_args,
    and added citation information to each script.
    * CITATION: added basic citation information for khmer functionality.

2013-03-31  Michael R. Crusoe  <mcrusoe@msu.edu>

    * docs/scripts.txt,scripts/*.py,khmer/*.py: overhaul the documentation of
    the scripts. Uses sphinxcontrib.autoprogram to leverage the existing
    argparse objects. Moved the documentation into each script + misc cleanups.
    All scripts support the --version option. Migrated the last scripts to use
    khmer_args
    * docs/blog-posts.txt: removed outdated reference to filter-exact.py; its
    replacement filter-abund.py is better documented in the eel-pond protocol
    * figuregen/,novelty/,plots/,templatem/,scripts/do-partition.sh: removed
    outdated code not part of core project

2013-03-30  Michael R. Crusoe  <mcrusoe@msu.edu>

    * setup.py: monkeypatched distutils.Distribution.reinitialize_command() so
    that it matches the behavior of Distribution.get_command_obj(). This fixes
    issues with 'pip install -e' and './setup.py nosetests' not respecting the
    setup.cfg configuration directives for the build_ext command. Also
    enhanced our build_ext command to respect the dry_run mode.

    * .ycm_extra_conf.py: Update our custom YouCompleteMe configuration to
    query the package configuration for the proper compilation flags.

2014-03-28  Michael R. Crusoe  <mcrusoe@msu.edu>

    * Makefile,setup.py: demote nose & sphinx to extra dependencies.
    Auto-install Python developer tools as needed.

2013-03-27  Michael R. Crusoe  <mcrusoe@msu.edu>

    * The system zlib and bzip2 libraries are now used instead of the bundled
    versions if specified in setup.cfg or the command line.

2014-03-25  Michael R. Crusoe  <mcrusoe@msu.edu>

    * Makefile: update cppcheck command to match new version of Jenkins
    plugin. Now ignores the lib/test*.cc files.

2013-03-20  Michael R. Crusoe  <mcrusoe@msu.edu>

    * lib/storage.hh,khmer/_khmermodule.cc,lib/{readtable,read_parsers}.hh:
    remove unused storage.hh

2014-03-19  Qingpeng Zhang  <qingpeng@msu.edu>

    * hashbits.cc: fix a bug of 'Division or modulo by zero' described in #182
    * test_scripts.py: add test code for count-overlap.py
    * count-overlap.py: (fix a bug because of a typo and hashsize was replaced
    by min_hashsize)
    * count-overlap.py: needs hashbits table generated by load-graph.py. 
    This information is added to the "usage:" line.
    * count-overlap.py: fix minor PyLint issues

2014-03-19  Michael R. Crusoe  <mcrusoe@msu.edu>

    * Update bundled zlib version to 1.2.8 from 1.2.3. Changes of note:
    "Wholesale replacement of gz* functions with faster versions"
    "Added LFS (Large File Summit) support for 64-bit file offsets"
    "Fix serious but very rare decompression bug"

2014-03-19  Michael R. Crusoe <mcrusoe@msu.edu>

    * lib/counting.hh: include hashtable.hh
    * lib/{counting,aligner,hashbits,hashtable,labelhash,node,subset}.{cc,hh},
    kmer.cc,khmer/_khmermodule.cc: removed downcast, replaced non-functional
    asserts() with exception throws.
    * khmer/_khmermodule.cc: fixed parsing of PyLists
    * setup.py: force 64bit only builds on OS X.

2014-03-19  Titus Brown  <t@idyll.org>

    * Makefile: update documentation on targets at top; clean autopep8 output.
    * test_counting_single.py: fixed pep8 violations in spacing
    * test_scripts.py: eliminate popenscript in favor of proper SystemExit
	handling in runscript; fix pep8 violations.

2014-03-19  Michael R. Crusoe <mcrusoe@msu.edu> and Luiz Irber
<luiz.irber@gmail.com>

    * lib/ktable.{cc,hh},khmer/{__init__.py},{_khmermodule.cc}, tests/
    test_{counting_{hash,single},ktable}.py: remove the unused KTable object
    * doc/{index,ktable}.txt: remove references to KTable
    * lib/{ktable.{hh,cc} → kmer_hash.{hh,cc}}: rename remaining ktable files
    to kmer_hash
    * lib/{hashtable,kmer}.hh: replace ktable headers with kmer_hash

2014-03-17  Ram RS  <ramrs@nyu.edu>

    * extract-partitions.py: pylint warnings addressed
    * test_scripts.py: tests added to cover extract-partitions completely

2014-03-16  Michael R. Crusoe <mcrusoe@msu.edu>

    * lib/read_parsers.cc: fix for Coverity CID 1054789: Unititialized scalar
    field II: fill_id is never zeroed out.

2014-03-16  Ram RS  <ramrs@nyu.edu>

    * Project email in copyright headers updated

2014-03-14  Michael R. Crusoe <mcrusoe@msu.edu>

    * khmer/_khmermodule.cc, lib/{khmer.hh, hashtable.{cc,hh}},
    tests/test_{hashbits,hashbits_obj,labelhash}.py: don't implicitly downcast
    tagset_size(). Changes fileformat version for saved tagsets.

2014-03-13  Ram RS  <ramrs@nyu.edu>

    * added: khmer/file.py - script to check disk space, check input file
    status and check space before hashtable writing
    * modified: scripts/*.py - all scripts now use khmer.file for above-mentioned
    functionality.
    * modified: scripts/*.py - pylint violations addressed in all scripts
    under scripts/

2014-03-13  Ram RS  <ramrs@nyu.edu>

    * Bug fix: tests.test_normalize_by_median_no_bigcount() now runs within
    temp directory

2014-03-11  Michael R. Crusoe  <mcrusoe@mcrusoe.edu>

    * lib/read_parsers.hh: fix for Coverity CID 1054789: Uninitialized scalar
    field

2014-03-10  Michael R. Crusoe  <mcrusoe@msu.edu>

    * doc/development.txt: document fork/tag policy + formatting fixes

2014-03-03  Michael R. Crusoe  <mcrusoe@msu.edu>

    * lib/trace_logger.{cc,hh}: fix for Coverity CID 1063852: Uninitialized
    scalar field (UNINIT_CTOR) 
    * lib/node.cc: fix for Coverity CID 1173035:  Uninitialized scalar field
    (UNINIT_CTOR)
    * lib/hashbits.hh: fix for Coverity CID 1153101:  Resource leak in object
    (CTOR_DTOR_LEAK)
    * lib/{perf_metrics.{cc,hh},hashtable.{cc,hh}
    ,read_parsers.{cc,hh},trace_logger.{cc,hh}}: ifndef WITH_INTERNAL_METRICS
    then lets not + astyle -A10

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
2014-04-10  Michael R. Crusoe  <mcrusoe@msu.edu>

    * Makefile: run 'build' command before install; ignore _version.py for
    coverage purposes.
    * bink.ipynb: deleted
    * doc/choosing-hash-sizes.txt -> choosing-table-sizes.txt
    * setup.py,doc/{conf.py,index.txt}: update lists of authors
    * doc/development.txt: typo
    * doc/{galaxy,guide,index,introduction,scripts}.txt: remove some
    references to implementation details of the k-mer tables
    * doc/{known-issues,release}.txt: updated
    * khmer/*.cc,lib/*.{cc,hh}: astyle -A10 formatted
    * lib/read_parsers.cc: fixed case statement fall through
    * lib/subset.cc: removed unnecessary NULL check (CID 1054804 & 1195088)
    * scripts/*.py: additional documentation updates
    * tests/test-data/test-overlap1.ht,data/MSB2-surrender.fa &
    data/1m-filtered.fa: removed from repository history, .git is now 36M!

2014-03-31  Titus Brown  <ctb@msu.edu>

    * scripts/normalize-by-median.py: Fixed unbound variable bug introduced in
    20a433c2.

    * khmer/file.py: Fixed incorrect use of __file__ dirname instead of
    os.getcwd(); also fixed bug where statvfs would choke on an empty
    dirname resulting from input files being in the cwd.

2014-03-31  Michael R. Crusoe  <mcrusoe@msu.edu>

    * versioneer.py,ez_setup.py: updated to version 0.10 and 3.4.1
    respectively.
    * docs/release.txt,khmer/_version.py,MANIFEST.in: update ancillary
    versioneer files

2014-03-31  Titus Brown  <ctb@msu.edu>

    * scripts/*.py,khmer/khmer_args.py: added 'info' function to khmer_args,
    and added citation information to each script.
    * CITATION: added basic citation information for khmer functionality.

2013-03-31  Michael R. Crusoe  <mcrusoe@msu.edu>

    * docs/scripts.txt,scripts/*.py,khmer/*.py: overhaul the documentation of
    the scripts. Uses sphinxcontrib.autoprogram to leverage the existing
    argparse objects. Moved the documentation into each script + misc cleanups.
    All scripts support the --version option. Migrated the last scripts to use
    khmer_args
    * docs/blog-posts.txt: removed outdated reference to filter-exact.py; its
    replacement filter-abund.py is better documented in the eel-pond protocol
    * figuregen/,novelty/,plots/,templatem/,scripts/do-partition.sh: removed
    outdated code not part of core project

2013-03-30  Michael R. Crusoe  <mcrusoe@msu.edu>

    * setup.py: monkeypatched distutils.Distribution.reinitialize_command() so
    that it matches the behavior of Distribution.get_command_obj(). This fixes
    issues with 'pip install -e' and './setup.py nosetests' not respecting the
    setup.cfg configuration directives for the build_ext command. Also
    enhanced our build_ext command to respect the dry_run mode.

    * .ycm_extra_conf.py: Update our custom YouCompleteMe configuration to
    query the package configuration for the proper compilation flags.

2014-03-28  Michael R. Crusoe  <mcrusoe@msu.edu>

    * Makefile,setup.py: demote nose & sphinx to extra dependencies.
    Auto-install Python developer tools as needed.

2013-03-27  Michael R. Crusoe  <mcrusoe@msu.edu>

    * The system zlib and bzip2 libraries are now used instead of the bundled
    versions if specified in setup.cfg or the command line.

2014-03-25  Michael R. Crusoe  <mcrusoe@msu.edu>

    * Makefile: update cppcheck command to match new version of Jenkins
    plugin. Now ignores the lib/test*.cc files.

2013-03-20  Michael R. Crusoe  <mcrusoe@msu.edu>

    * lib/storage.hh,khmer/_khmermodule.cc,lib/{readtable,read_parsers}.hh:
    remove unused storage.hh

2014-03-19  Qingpeng Zhang  <qingpeng@msu.edu>

    * hashbits.cc: fix a bug of 'Division or modulo by zero' described in #182
    * test_scripts.py: add test code for count-overlap.py
    * count-overlap.py: (fix a bug because of a typo and hashsize was replaced
    by min_hashsize)
    * count-overlap.py: needs hashbits table generated by load-graph.py. 
    This information is added to the "usage:" line.
    * count-overlap.py: fix minor PyLint issues

2014-03-19  Michael R. Crusoe  <mcrusoe@msu.edu>

    * Update bundled zlib version to 1.2.8 from 1.2.3. Changes of note:
    "Wholesale replacement of gz* functions with faster versions"
    "Added LFS (Large File Summit) support for 64-bit file offsets"
    "Fix serious but very rare decompression bug"

2014-03-19  Michael R. Crusoe <mcrusoe@msu.edu>

    * lib/counting.hh: include hashtable.hh
    * lib/{counting,aligner,hashbits,hashtable,labelhash,node,subset}.{cc,hh},
    kmer.cc,khmer/_khmermodule.cc: removed downcast, replaced non-functional
    asserts() with exception throws.
    * khmer/_khmermodule.cc: fixed parsing of PyLists
    * setup.py: force 64bit only builds on OS X.

2014-03-19  Titus Brown  <t@idyll.org>

    * Makefile: update documentation on targets at top; clean autopep8 output.
    * test_counting_single.py: fixed pep8 violations in spacing
    * test_scripts.py: eliminate popenscript in favor of proper SystemExit
	handling in runscript; fix pep8 violations.

2014-03-19  Michael R. Crusoe <mcrusoe@msu.edu> and Luiz Irber
<luiz.irber@gmail.com>

    * lib/ktable.{cc,hh},khmer/{__init__.py},{_khmermodule.cc}, tests/
    test_{counting_{hash,single},ktable}.py: remove the unused KTable object
    * doc/{index,ktable}.txt: remove references to KTable
    * lib/{ktable.{hh,cc} → kmer_hash.{hh,cc}}: rename remaining ktable files
    to kmer_hash
    * lib/{hashtable,kmer}.hh: replace ktable headers with kmer_hash

2014-03-17  Ram RS  <ramrs@nyu.edu>

    * extract-partitions.py: pylint warnings addressed
    * test_scripts.py: tests added to cover extract-partitions completely

2014-03-16  Michael R. Crusoe <mcrusoe@msu.edu>

    * lib/read_parsers.cc: fix for Coverity CID 1054789: Unititialized scalar
    field II: fill_id is never zeroed out.

2014-03-16  Ram RS  <ramrs@nyu.edu>

    * Project email in copyright headers updated

2014-03-14  Michael R. Crusoe <mcrusoe@msu.edu>

    * khmer/_khmermodule.cc, lib/{khmer.hh, hashtable.{cc,hh}},
    tests/test_{hashbits,hashbits_obj,labelhash}.py: don't implicitly downcast
    tagset_size(). Changes fileformat version for saved tagsets.

2014-03-13  Ram RS  <ramrs@nyu.edu>

    * added: khmer/file.py - script to check disk space, check input file
    status and check space before hashtable writing
    * modified: scripts/*.py - all scripts now use khmer.file for above-mentioned
    functionality.
    * modified: scripts/*.py - pylint violations addressed in all scripts
    under scripts/

2014-03-13  Ram RS  <ramrs@nyu.edu>

    * Bug fix: tests.test_normalize_by_median_no_bigcount() now runs within
    temp directory

2014-03-11  Michael R. Crusoe  <mcrusoe@mcrusoe.edu>

    * lib/read_parsers.hh: fix for Coverity CID 1054789: Uninitialized scalar
    field

2014-03-10  Michael R. Crusoe  <mcrusoe@msu.edu>

    * doc/development.txt: document fork/tag policy + formatting fixes

2014-03-03  Michael R. Crusoe  <mcrusoe@msu.edu>

    * lib/trace_logger.{cc,hh}: fix for Coverity CID 1063852: Uninitialized
    scalar field (UNINIT_CTOR) 
    * lib/node.cc: fix for Coverity CID 1173035:  Uninitialized scalar field
    (UNINIT_CTOR)
    * lib/hashbits.hh: fix for Coverity CID 1153101:  Resource leak in object
    (CTOR_DTOR_LEAK)
    * lib/{perf_metrics.{cc,hh},hashtable.{cc,hh}
    ,read_parsers.{cc,hh},trace_logger.{cc,hh}}: ifndef WITH_INTERNAL_METRICS
    then lets not + astyle -A10

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
