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2016-11-14 Daniel Standage <daniel.standage@gmail.com>
* screed/{__init__.py,fasta.py,fastq.py,openscreed.py}: Remove implementation
(and related references) of Writer classes.
* screed/tests/{test_open.py,test_open_cm.py}: Remove Writer tests.
* screed/{screedRecord.py,{tests/test_{fasta,fastq}.py}}: New write_fastx
implementation and associated tests.
2016-11-14 Luiz Irber <khmer@luizirber.org>
* Makefile,doc/dev/release-checklist.rst,doc/screed.rst,jenkins-build.sh,
pytest.ini, setup.{cfg,py}, tox.ini, screed/tests/{__main__,havaGen,
screed_tst_utils,test_pygr_api, test_streaming}: Replace nose and adapt
for pytest.
2016-10-13 Daniel Standage <daniel.standage@gmail.com>
* .travis.yml: Reduce the size of the CI build.
2016-10-07 Luiz Irber <khmer@luizirber.org>
* screed/f{a,q}dbm.py: Fix import errors on Python 3.
* screed/tests/test_shell.py: check for return code and rewrite the test to
work more like the expected usage in the shell.
2016-10-06 Luiz Irber <khmer@luizirber.org>
* tox.ini: Use codecov for coverage reports, add Python 3.5 to builds.
* .travis.yml: Activate Python 3.5 build.
* .github/{CONTRIBUTING,PULL_REQUEST_TEMPLATE}.md: Add GitHub templates.
* Makefile: Throw an error If there are pep8 warnings.
* doc/dev/coding-guidelinbes-and-review.rst: Update checklist
* screed/{dna,openscreed,tests/test_attriberror}.py: Fix pep8 warnings.
2016-10-04 Luiz Irber <khmer@luizirber.org>
* screed/screedRecord.py: Implement comparison using total_ordering
decorator from functools.
* screed/tests/test_attriberror.py: Fix syntax errors for Python 3 and
remove tests for not implemented methods (they are implemented now).
2016-06-10 Titus Brown <titus@idyll.org>
* screed/dna.py: Fix reverse complement calculation for Python 2.7
2015-06-22 Jacob Fenton <bocajnotnef@gmail.com>
* screed/tests/test_attriberror.py: added tests to check screed db attribute
exception throwing
* screed/screedRecord.py: removed __cmp__ function, explicitly disallowed
all rich comparator functions that aren't == or !=
2015-06-10 Michael R. Crusoe <crusoe@ucdavis.edu>
* doc/user/known-issues.rst: removed two fixed issues
* doc/screed.rst: updated install & test instructions
* doc/screed.html: removed un-needed file
2015-06-05 Titus Brown <titus@idyll.org>
* screed/{fasta.py,fastq.py,seqparse.py}: Set parse_description default
to False.
* screed/tests/test*.py: updated tests appropriately.
2015-06-05 Luiz Irber <screed@luizirber.org>
* screed/screedRecord.py: Simplify implementation of record slicing.
* screed/tests/test_fast{a,q}.py: Loop over distinct slices during test.
2015-06-05 Michael Wright <wrigh517@msu.edu>
* screed/screedRecord.py: Allow slicing of screed records to fix issue #768
2015-06-05 en zyme <en_zyme@outlook.com>
* screed/tests/fastq.py: check for empty line in two places
2015-05-29 Luiz Irber <screed@luizirber.org>
* screed/openscreed.py: Add missing "close" method to context manager.
2015-05-27 Michael R. Crusoe <mcrusoe@msu.edu>
* MANIFEST.in: ship the recently relocated test data, fixed reference to
renamed LICENSE file
* doc/dev/CODE_OF_CONDUCT.rst: drop unused symlink
* doc/dev/release-checklist.rst: fix line wrap
2015-05-12 Luiz Irber <screed@luizirber.org>
* screed/openscreed.py: Implement open as a context manager, keep backward
compatibility.
* screed/tests/test_open_cm.py: Add same tests as test_open.py, but using
a context manager to make sure file is closed after being used.
2015-04-15 Thomas Fenzl <thomas.fenzl@gmx.net>
* screed/tests/screed_tst_utils.py: removed unnecessary import
* screed/tests/test_streaming.py: changed execution order to handle
missing import files better
* screed/openscreed.py: pylint-ified
2015-04-15 Thomas Fenzl <thomas.fenzl@gmx.net>
* Makefile: added setup.py develop to test goal
* screed/openscreed.py,screed/tests/test_open.py: added handling of '-'
2015-04-09 Sarah Guermond <sarah.guermond@gmail.com>
* screed/screedRecord.py: renamed _screed_record_dict() to Rename()
* screed/__init__.py: added import for Record
* screed/fasta.py: changed _screed_record_dict() to Rename()
* screed/fastq.py: changed _screed_record_dict() to Rename()
2015-04-09 Jacob Fenton <bocajnotnef@gmail.com>
* doc/dev/release-checklist.txt: added "making final release" notes
* Makefile: copied over @mr-c's md-to-rst release notes conversion target
* doc/dev/release-notes/RELEASE-0.8.txt: added rst version of release notes
for sphinx
* doc/dev/release-notes/index.txt: added rst version of 0.8 release notes to
toctree
2015-04-07 Jacob Fenton <bocajnotnef@gmail.com>
* screed/tests/test_{dictionary, fasta, fasta_recover, fastq, fastq_recover,
hava_methods, shell}.py: changed tests to use tempdirs
* screed/tests/screed_tst_utils.py: copied in khmer test utils
* screed/tests/{empty.fa, test-whitespace.fa, test.fa, test.fa.bz2,
test.fa.gz, test.fa.zip, test.fastq, test.fastq.bz2, test.hava}: moved test
data to screed/tests/test-data/ directory
2015-04-04 Jacob Fenton <bocajnotnef@gmail.com>
* doc/dev/release{.txt,-checklist.txt}: renamed/restored release.txt to
release-checklist.txt
2015-03-06 Kevin Murray <spam@kdmurray.id.au>
* screed/screedRecord.py: Fix a typo in a try: except: block.
s/AttributError/AttributeError/
2015-02-23 Gabriel Pratt <gpratt@ucsd.edu>
* Fixed Issue 705 len(read) != len(read.sequence)
2015-02-23 Michael R. Crusoe <mcrusoe@msu.edu>
* Doxyfile.in: make documentation generation reproducible; removed
timestamp
2015-02-23 Michael R. Crusoe <mcrusoe@msu.edu>
* doc/dev/release.txt: Fix formatting
* MANIFEST.in: include the MANIFEST.in template, the license and other
files
* versioneer.py,screed/{__init__,_version}.py: upgrade versioneer to 0.13
2015-02-23 Michael R. Crusoe <mcrusoe@msu.edu>
* setup.py: work around versioneer bug:
https://github.com/warner/python-versioneer/issues/52
2014-12-07 Michael R. Crusoe <mcrusoe@msu.edu>
* Initial jenkins-build.sh
2014-12-03 Jacob Fenton <bocajnotnef@gmail.com>
* ChangeLog: updated to include major revisions since 0.7.1
* CODE_OF_CONDUCT: copied in code of conduct from khmer project
* docs/dev/{CODE_OF_CONDUCT, coding-guidelines-and-review, index,
releases}.txt, docs/index.txt: added screed dev docs
* setup.py, .gitattributes, __init__.py, _version.py, versioneer.py:
installed versioneer version naming system
* MANIFEST.in: now includes versioneer files and empty testing file
2014-11-02 Michael R. Crusoe <mcrusoe@msu.edu>
* Doxyfile, Makefile: added Doxygen support, coverage & pylint make targets
2014-10-27 Ben Taylor <taylo886@msu.edu>
* benchmarks/fqGen.py, benchmarks/fqToFaConvert.py,
benchmarks/mysql/mysqlCreateTimeit.py, benchmarks/screedCreateTimeit.py,
benchmarks/pgres/pgresCreateTimeit.py, gibtests/__init__.py,
doc/screed.html, doc/screed.txt, screed/conversion.py, screed/fastq.py,
screed/tests/test_fastq.py: Changed all uses of "accuracy" to "quality"
* screed/tests/test_dna.py: Added basic test coverage for screed/dna.py
2014-05-16 Michael R. Crusoe <mcrusoe@msu.edu>
* screed/openscreed.py: added sniffing of compression types, including zip
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