[med-svn] [python-screed] 02/06: Merge tag 'upstream/0.8'

[Michael Crusoe]

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

commit 0004d7d89e70edac27fda76b4930556269265af3
Merge: 203880a 458072d
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date:   Wed May 27 21:27:51 2015 -0400

    Merge tag 'upstream/0.8'
    
    Upstream version 0.8

 .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 +-
 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 ++++++++++++
 70 files changed, 4685 insertions(+), 300 deletions(-)

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