[med-svn] [python-screed] 02/03: Merge tag 'upstream/0.9'

[Michael Crusoe]

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

commit 9621b0b315ed7ccf8ae1ad69a48cad24aa5c051e
Merge: 8269de4 3729975
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
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(-)

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