[med-svn] [python-screed] branch master updated (203880a -> 8269de4)

[Michael Crusoe]

This is an automated email from the git hooks/post-receive script.

misterc-guest pushed a change to branch master
in repository python-screed.

      from  203880a   Add user advise how to test the package
       new  458072d   Imported Upstream version 0.8
       new  0004d7d   Merge tag 'upstream/0.8'
       new  b501c88   update to new release
       new  9b944a3   drop uneeded patches
       new  b0d9569   add dep on bz2file
       new  8269de4   skip failing tests

The 6 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:
 .gitattributes                           |    1 +
 .gitignore                               |   12 +
 .travis.yml                              |    6 -
 CODE_OF_CONDUCT.rst                      |   35 +
 ChangeLog                                |   61 +
 Doxyfile.in                              | 2303 ++++++++++++++++++++++++++++++
 MANIFEST.in                              |    4 +
 Makefile                                 |  117 ++
 README.md                                |    2 +-
 TODO                                     |    2 +
 benchmarks/fqGen.py                      |   10 +-
 benchmarks/fqToFaConvert.py              |    8 +-
 benchmarks/mysql/mysqlCreateTimeit.py    |    2 +-
 benchmarks/pgres/pgresCreateTimeit.py    |    2 +-
 benchmarks/screedCreateTimeit.py         |    2 +-
 bigtests/__init__.py                     |   30 +-
 debian/changelog                         |   10 +-
 debian/control                           |    3 +-
 debian/patches/add-nose-dep              |   14 -
 debian/patches/fix-tests                 |   17 -
 debian/patches/series                    |    2 -
 debian/rules                             |    3 +
 debian/tests/run-unit-test               |    2 +-
 doc/CODE_OF_CONDUCT.txt                  |    1 +
 doc/COPYRIGHT.txt                        |    2 -
 doc/LICENSE.txt                          |    6 +-
 doc/_static/labibi.css                   |   54 +
 doc/_static/labibi.js                    |   29 +
 doc/conf.py                              |   33 +-
 doc/dev/CODE_OF_CONDUCT.rst              |    1 +
 doc/dev/coding-guidelines-and-review.txt |   66 +
 doc/dev/index.txt                        |   20 +
 doc/dev/release-checklist.txt            |  142 ++
 doc/index.txt                            |    9 +-
 doc/{ => release-notes}/RELEASE-0.5.txt  |    4 +
 doc/release-notes/RELEASE-0.8.md         |   64 +
 doc/release-notes/index.txt              |   11 +
 doc/schema.txt                           |    5 -
 doc/screed.html                          |   14 +-
 doc/screed.txt                           |   45 +-
 doc/user/known-issues.txt                |   26 +
 get_version.py                           |   16 +
 jenkins-build.sh                         |   26 +
 screed/__init__.py                       |   68 +-
 screed/_version.py                       |  191 +++
 screed/conversion.py                     |   28 +-
 screed/createscreed.py                   |   12 +-
 screed/dna.py                            |    7 +-
 screed/dump_to_fasta.py                  |    5 +-
 screed/dump_to_fastq.py                  |    5 +-
 screed/fadbm.py                          |    3 +-
 screed/fasta.py                          |    9 +-
 screed/fastq.py                          |   25 +-
 screed/fqdbm.py                          |    2 +-
 screed/hava.py                           |    2 +-
 screed/openscreed.py                     |   98 +-
 screed/pygr_api.py                       |   33 +-
 screed/screedRecord.py                   |   33 +-
 screed/seqparse.py                       |    8 +-
 screed/tests/havaGen.py                  |   17 +-
 screed/tests/test.fa.zip                 |  Bin 0 -> 4237 bytes
 screed/tests/test.fastq.bz2              |  Bin 0 -> 3730 bytes
 screed/tests/test_convert.py             |    7 +-
 screed/tests/test_dictionary.py          |   13 +-
 screed/tests/test_dna.py                 |   28 +
 screed/tests/test_fasta.py               |   44 +-
 screed/tests/test_fasta_recover.py       |    5 +-
 screed/tests/test_fastq.py               |   35 +-
 screed/tests/test_fastq_recover.py       |    2 +
 screed/tests/test_hava_methods.py        |   35 +-
 screed/tests/test_nodb.py                |    6 +-
 screed/tests/test_open.py                |   26 +-
 screed/tests/test_pygr_api.py            |   39 +-
 screed/tests/test_shell.py               |    8 +-
 screed/tests/test_streaming.py           |   85 ++
 setup.py                                 |   22 +-
 versioneer.py                            |  913 ++++++++++++
 77 files changed, 4699 insertions(+), 337 deletions(-)
 create mode 100644 .gitattributes
 delete mode 100644 .travis.yml
 create mode 100644 CODE_OF_CONDUCT.rst
 create mode 100644 ChangeLog
 create mode 100644 Doxyfile.in
 create mode 100644 MANIFEST.in
 create mode 100644 Makefile
 delete mode 100644 debian/patches/add-nose-dep
 delete mode 100644 debian/patches/fix-tests
 delete mode 100644 debian/patches/series
 create mode 120000 doc/CODE_OF_CONDUCT.txt
 delete mode 100644 doc/COPYRIGHT.txt
 create mode 100644 doc/_static/labibi.css
 create mode 100644 doc/_static/labibi.js
 create mode 120000 doc/dev/CODE_OF_CONDUCT.rst
 create mode 100644 doc/dev/coding-guidelines-and-review.txt
 create mode 100644 doc/dev/index.txt
 create mode 100644 doc/dev/release-checklist.txt
 rename doc/{ => release-notes}/RELEASE-0.5.txt (95%)
 create mode 100644 doc/release-notes/RELEASE-0.8.md
 create mode 100644 doc/release-notes/index.txt
 delete mode 100644 doc/schema.txt
 create mode 100644 doc/user/known-issues.txt
 create mode 100755 get_version.py
 create mode 100755 jenkins-build.sh
 create mode 100644 screed/_version.py
 create mode 100644 screed/tests/test.fa.zip
 create mode 100644 screed/tests/test.fastq.bz2
 create mode 100644 screed/tests/test_dna.py
 create mode 100644 screed/tests/test_streaming.py
 mode change 100644 => 100755 setup.py
 create mode 100644 versioneer.py

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-screed.git