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ChangeLog
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2014-07-22 Michael R. Crusoe <[email protected]>
* Makefile: combine pip invocation into single "install-dependencies"
target.
2014-07-22 Justin Lippi <[email protected]>
* 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 <[email protected]>
* scripts/filter-abund.py: no longer asks for parameters that are unused,
issue #524
2014-07-22 Justin Lippi <[email protected]>
* 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 <[email protected]>
* khmer/_khmermodule.cc: removed unused KhmerError, issue #503
2014-07-22 Rodney Picett <[email protected]>
* lib/scoringmatrix.{cc,hh}: removed assign function, issue #502
2014-07-22 Leonor Garcia-Gutierrez <[email protected]>
* tests/test_counting_single.py: reduced memory requirements
2014-07-21 Titus Brown <[email protected]>
* sandbox/saturate-by-median.py: introduce new sandbox script for
saturation analysis of low-coverage data sets.
2014-07-10 Joe Stein <[email protected]>
* sandbox/readstats.py: fixed divide-by-zero error, issue #458
2014-07-06 Titus Brown <[email protected]>
* doc/release.txt: fix formatting.
2014-06-20 Chuck Pepe-Ranney <[email protected]>
* scripts/extract-partitions.py: added epilog documentation for
<base>.dist columns.
2014-06-20 Michael R. Crusoe <[email protected]>
* doc/release.txt: Add Coverity Scan to release checklist
2014-06-19 Michael R. Crusoe <[email protected]>
* 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superceded by the above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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* MANIFEST.in: don't include docs/, data/, or examples/ in our PyPI
distribution. Saves 15MB.
2014-06-13 Michael R. Crusoe <[email protected]>
* Makefile: split coverity target in two: -build and -upload. Added
configuration target
2014-06-13 Titus Brown <[email protected]>
* doc/install.txt: updated virtualenv command to use python2 explicitly,
for arch support.
2014-06-13 Titus Brown <[email protected]>
* 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 <[email protected]>
* sandbox/load-into-hashbits: Deleted from sandbox. It is superseded
by load-graph.py --no-tagset.
2014-06-11 Michael Wright <[email protected]>
* scripts/load-into-counting: Fixed docstring misnomer to
load-into-counting.py
2014-06-10 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* lib/Makefile: do a distclean as the CFLAGS may have changed. Fixes #442
2014-06-03 Chuck Pepe-Ranney <[email protected]>
* scripts/abundance-dist.py: removed call to check_space on infiles.
2014-05-31 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* Makefile: add target for python test coverage plain-text report;
clarified where the HTML report is
2014-05-16 Michael R. Crusoe <[email protected]>
* docs/scripts.txt: include sweep-reads-buffered.py
2014-05-14 Adam Caldwell <[email protected]>
* Makefile: change pip to pip2. Fixes assorted make problems on systems
where pip links to pip3
2014-05-14 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* doc/release.txt: additional fixes
2014-05-09 Luiz Irber <[email protected]>
Version 1.0.1
2014-05-09 Michael R. Crusoe <[email protected]>
* doc/release.txt: update release instructions
2014-05-06 Michael R. Crusoe <[email protected]>
* lib/{subset,counting}.cc: fix cppcheck errors; astyle -A10
--max-code-length=80
2014-05-06 Titus Brown <[email protected]>
* sandbox/calc-best-assembly.py: added script to calculate best
assembly from a list of contig/scaffold files
2014-04-23 Titus Brown <[email protected]>
* 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 <[email protected]>
*.py: switch to explicit python2 invocation. Fixes #385.
2014-04-21 Titus Brown <[email protected]>
* doc/development.txt: added spellcheck to review checklist
2014-04-21 Titus Brown <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* scripts/*.py: fixed argument to check_space_for_hashtable to rely
on args.n_tables and not args.ksize.
2014-04-06 Titus Brown <[email protected]>
* scripts/normalize-by-median.py: added comment about table compatibility
with abundance-dist.
2014-04-05 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
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 <[email protected]>
* CITATION,khmer/khmer_args.py: Updated khmer software citation for
release.
2014-03-31 Titus Brown <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* Makefile,setup.py: demote nose & sphinx to extra dependencies.
Auto-install Python developer tools as needed.
2013-03-27 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* Makefile: update cppcheck command to match new version of Jenkins
plugin. Now ignores the lib/test*.cc files.
2013-03-20 Michael R. Crusoe <[email protected]>
* lib/storage.hh,khmer/_khmermodule.cc,lib/{readtable,read_parsers}.hh:
remove unused storage.hh
2014-03-19 Qingpeng Zhang <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]> and Luiz Irber
* 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 <[email protected]>
* extract-partitions.py: pylint warnings addressed
* test_scripts.py: tests added to cover extract-partitions completely
2014-03-16 Michael R. Crusoe <[email protected]>
* lib/read_parsers.cc: fix for Coverity CID 1054789: Unititialized scalar
field II: fill_id is never zeroed out.
2014-03-16 Ram RS <[email protected]>
* Project email in copyright headers updated
2014-03-14 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* Bug fix: tests.test_normalize_by_median_no_bigcount() now runs within
temp directory
2014-03-11 Michael R. Crusoe <[email protected]>
* lib/read_parsers.hh: fix for Coverity CID 1054789: Uninitialized scalar
field
2014-03-10 Michael R. Crusoe <[email protected]>
* doc/development.txt: document fork/tag policy + formatting fixes
2014-03-03 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* Fixed output_partitioned_file, sweep-reads3.py, and extract-partitions.py
to retain FASTQ format in output.
2013-12-11 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* doc/install.txt Add setup instructions for RHEL6 & fix invocation to get
master branch to work for non-developers
2013-12-18 Titus Brown <[email protected]>
* Added a test to ensure that normalize-by-median.py has bigcount set to
False.
2013-11-22 Camille Scott <[email protected]>
* Makefile: Added debug target for profiling.
2013-11-22 Michael R. Crusoe <[email protected]>
* Documented release process
2013-10-21 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* Version 0.6.1
* No code changes, just build fixes
2013-10-10 Michael R. Crusoe <[email protected]>
* 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 [email protected]
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* Makefile,setup.py: demote nose & sphinx to extra dependencies.
Auto-install Python developer tools as needed.
2013-03-27 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* Makefile: update cppcheck command to match new version of Jenkins
plugin. Now ignores the lib/test*.cc files.
2013-03-20 Michael R. Crusoe <[email protected]>
* lib/storage.hh,khmer/_khmermodule.cc,lib/{readtable,read_parsers}.hh:
remove unused storage.hh
2014-03-19 Qingpeng Zhang <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]> and Luiz Irber
* 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 <[email protected]>
* extract-partitions.py: pylint warnings addressed
* test_scripts.py: tests added to cover extract-partitions completely
2014-03-16 Michael R. Crusoe <[email protected]>
* lib/read_parsers.cc: fix for Coverity CID 1054789: Unititialized scalar
field II: fill_id is never zeroed out.
2014-03-16 Ram RS <[email protected]>
* Project email in copyright headers updated
2014-03-14 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* Bug fix: tests.test_normalize_by_median_no_bigcount() now runs within
temp directory
2014-03-11 Michael R. Crusoe <[email protected]>
* lib/read_parsers.hh: fix for Coverity CID 1054789: Uninitialized scalar
field
2014-03-10 Michael R. Crusoe <[email protected]>
* doc/development.txt: document fork/tag policy + formatting fixes
2014-03-03 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* 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 <[email protected]>
* Fixed output_partitioned_file, sweep-reads3.py, and extract-partitions.py
to retain FASTQ format in output.
2013-12-11 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* doc/install.txt Add setup instructions for RHEL6 & fix invocation to get
master branch to work for non-developers
2013-12-18 Titus Brown <[email protected]>
* Added a test to ensure that normalize-by-median.py has bigcount set to
False.
2013-11-22 Camille Scott <[email protected]>
* Makefile: Added debug target for profiling.
2013-11-22 Michael R. Crusoe <[email protected]>
* Documented release process
2013-10-21 Michael R. Crusoe <[email protected]>
* 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 <[email protected]>
* Version 0.6.1
* No code changes, just build fixes
2013-10-10 Michael R. Crusoe <[email protected]>
* 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 [email protected]
* 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