[med-svn] [python-screed] branch upstream updated (458072d -> 3729975)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sun Jun 14 08:15:15 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream
in repository python-screed.
from 458072d Imported Upstream version 0.8
new 3729975 Imported Upstream version 0.9
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
.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(-)
create mode 100644 .travis.yml
rename doc/{CODE_OF_CONDUCT.txt => CODE_OF_CONDUCT.rst} (100%)
rename doc/{LICENSE.txt => LICENSE.rst} (100%)
delete mode 120000 doc/dev/CODE_OF_CONDUCT.rst
rename doc/dev/{coding-guidelines-and-review.txt => coding-guidelines-and-review.rst} (100%)
rename doc/dev/{index.txt => index.rst} (100%)
rename doc/dev/{release-checklist.txt => release-checklist.rst} (67%)
rename doc/{example.txt => example.rst} (100%)
rename doc/{index.txt => index.rst} (96%)
rename doc/release-notes/{RELEASE-0.5.txt => RELEASE-0.5.rst} (100%)
create mode 100644 doc/release-notes/RELEASE-0.8.rst
create mode 100644 doc/release-notes/RELEASE-0.9.md
create mode 100644 doc/release-notes/RELEASE-0.9.rst
rename doc/release-notes/{index.txt => index.rst} (91%)
delete mode 100644 doc/screed.html
rename doc/{screed.txt => screed.rst} (97%)
create mode 100644 doc/user/known-issues.rst
delete mode 100644 doc/user/known-issues.txt
create mode 100644 screed/tests/screed_tst_utils.py
rename screed/tests/{ => test-data}/empty.fa (100%)
rename screed/tests/{ => test-data}/test-whitespace.fa (100%)
rename screed/tests/{ => test-data}/test.fa (100%)
rename screed/tests/{ => test-data}/test.fa.bz2 (100%)
rename screed/tests/{ => test-data}/test.fa.gz (100%)
rename screed/tests/{ => test-data}/test.fa.zip (100%)
rename screed/tests/{ => test-data}/test.fastq (100%)
rename screed/tests/{ => test-data}/test.fastq.bz2 (100%)
rename screed/tests/{ => test-data}/test.fastq.gz (100%)
rename screed/tests/{ => test-data}/test.hava (100%)
create mode 100644 screed/tests/test_open_cm.py
create mode 100644 screed/utils.py
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