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commit 9621b0b315ed7ccf8ae1ad69a48cad24aa5c051e Merge: 8269de4 3729975 Author: Michael R. Crusoe <[email protected]> Date: Thu Jun 11 16:37:28 2015 -0700 Merge tag 'upstream/0.9' Upstream version 0.9 .travis.yml | 12 + ChangeLog | 80 +++ MANIFEST.in | 5 +- Makefile | 10 +- README.md | 4 +- bigtests/__init__.py | 4 +- doc/{CODE_OF_CONDUCT.txt => CODE_OF_CONDUCT.rst} | 0 doc/{LICENSE.txt => LICENSE.rst} | 0 doc/conf.py | 4 +- doc/dev/CODE_OF_CONDUCT.rst | 1 - ...review.txt => coding-guidelines-and-review.rst} | 0 doc/dev/{index.txt => index.rst} | 0 ...release-checklist.txt => release-checklist.rst} | 57 +- doc/{example.txt => example.rst} | 0 doc/{index.txt => index.rst} | 2 +- .../{RELEASE-0.5.txt => RELEASE-0.5.rst} | 0 doc/release-notes/RELEASE-0.8.md | 20 +- doc/release-notes/RELEASE-0.8.rst | 70 ++ doc/release-notes/RELEASE-0.9.md | 41 ++ doc/release-notes/RELEASE-0.9.rst | 72 ++ doc/release-notes/{index.txt => index.rst} | 1 + doc/screed.html | 743 --------------------- doc/{screed.txt => screed.rst} | 20 +- doc/user/known-issues.rst | 18 + doc/user/known-issues.txt | 26 - screed/__init__.py | 24 +- screed/_version.py | 102 ++- screed/conversion.py | 18 +- screed/createscreed.py | 3 +- screed/dna.py | 16 +- screed/dump_to_fasta.py | 5 +- screed/dump_to_fastq.py | 5 +- screed/fadbm.py | 2 +- screed/fasta.py | 17 +- screed/fastq.py | 26 +- screed/fqdbm.py | 8 +- screed/hava.py | 19 +- screed/openscreed.py | 181 +++-- screed/pygr_api.py | 6 +- screed/screedRecord.py | 34 +- screed/seqparse.py | 22 +- screed/tests/havaGen.py | 3 +- screed/tests/screed_tst_utils.py | 49 ++ screed/tests/{ => test-data}/empty.fa | 0 screed/tests/{ => test-data}/test-whitespace.fa | 0 screed/tests/{ => test-data}/test.fa | 0 screed/tests/{ => test-data}/test.fa.bz2 | Bin screed/tests/{ => test-data}/test.fa.gz | Bin screed/tests/{ => test-data}/test.fa.zip | Bin screed/tests/{ => test-data}/test.fastq | 0 screed/tests/{ => test-data}/test.fastq.bz2 | Bin screed/tests/{ => test-data}/test.fastq.gz | Bin screed/tests/{ => test-data}/test.hava | 0 screed/tests/test_convert.py | 14 +- screed/tests/test_dictionary.py | 23 +- screed/tests/test_fasta.py | 42 +- screed/tests/test_fasta_recover.py | 13 +- screed/tests/test_fastq.py | 50 +- screed/tests/test_fastq_recover.py | 13 +- screed/tests/test_hava_methods.py | 6 +- screed/tests/test_open.py | 54 +- screed/tests/test_open_cm.py | 96 +++ screed/tests/test_pygr_api.py | 4 +- screed/tests/test_shell.py | 16 +- screed/tests/test_streaming.py | 32 +- screed/utils.py | 7 + setup.py | 5 +- tox.ini | 9 +- versioneer.py | 295 +++++--- 69 files changed, 1268 insertions(+), 1141 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-screed.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
