[med-svn] [python-screed] 02/05: Updated version 1.0 from 'upstream/1.0'

[Michael Crusoe]

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

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

commit 1220e87255a97f50626e82e847ae4f579d1db571
Merge: e1fe381 2d03733
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date:   Fri Jun 23 06:25:44 2017 -0700

    Updated version 1.0 from 'upstream/1.0'
    
    with Debian dir cd5c9fa9fb846f8f3c30c6b6d25c9fd369435c32

 .coveragerc                                 |    2 +
 .github/CONTRIBUTING.md                     |    3 +
 .github/PULL_REQUEST_TEMPLATE.md            |    9 +
 .travis.yml                                 |    3 +-
 CHANGELOG.md                                |   15 +
 Makefile                                    |   21 +-
 README.md                                   |    2 +-
 TODO                                        |   16 -
 benchmarks/faGen.py                         |    1 +
 benchmarks/fqGen.py                         |    1 +
 benchmarks/fqToFaConvert.py                 |    1 +
 benchmarks/screedCreateTimeit.py            |    1 +
 benchmarks/screedTimeit.py                  |    1 +
 benchmarks/screedTimeit1M.py                |    1 +
 bigtests/__init__.py                        |  269 ++--
 doc/LICENSE.rst                             |   28 +-
 doc/conf.py                                 |  158 ++-
 doc/dev/coding-guidelines-and-review.rst    |   12 +-
 doc/dev/index.rst                           |    3 +-
 doc/dev/parsers.rst                         |  167 +++
 doc/dev/release-checklist.rst               |   36 +-
 doc/index.rst                               |   10 +-
 doc/release-notes/RELEASE-1.0.md            |   52 +
 doc/release-notes/index.rst                 |    4 +-
 doc/requirements.txt                        |    1 +
 doc/screed.rst                              |  473 ++-----
 get_version.py                              |    1 +
 ChangeLog => legacy/ChangeLog               |   56 +-
 jenkins-build.sh => legacy/jenkins-build.sh |    2 +-
 screed/DBConstants.py                       |    2 +-
 screed/__init__.py                          |   12 +-
 screed/__main__.py                          |   52 +
 screed/_version.py                          |  489 +++++--
 screed/conversion.py                        |   12 +-
 screed/createscreed.py                      |   51 +-
 screed/dna.py                               |    9 +-
 screed/dump_fasta.py                        |   33 +
 screed/dump_fastq.py                        |   31 +
 screed/dump_to_fasta.py                     |   25 -
 screed/dump_to_fastq.py                     |   25 -
 screed/fadbm.py                             |   19 -
 screed/fasta.py                             |   17 +-
 screed/fastq.py                             |   17 +-
 screed/fqdbm.py                             |   22 -
 screed/hava.py                              |    3 +-
 screed/openscreed.py                        |   42 +-
 screed/pygr_api.py                          |    2 +-
 screed/screedRecord.py                      |  118 +-
 screed/seqparse.py                          |    6 +-
 screed/tests/__main__.py                    |   17 +-
 screed/tests/havaGen.py                     |    2 +-
 screed/tests/screed_tst_utils.py            |    1 -
 screed/tests/test_attriberror.py            |   63 +
 screed/tests/test_db.py                     |   76 ++
 screed/tests/test_fasta.py                  |   46 +-
 screed/tests/test_fastq.py                  |   55 +-
 screed/tests/test_nodb.py                   |   33 -
 screed/tests/test_open.py                   |   13 +-
 screed/tests/test_open_cm.py                |   13 +-
 screed/tests/test_pygr_api.py               |   25 +-
 screed/tests/test_record.py                 |   34 +
 screed/tests/test_shell.py                  |  108 +-
 screed/tests/test_streaming.py              |    6 +-
 screed/utils.py                             |    3 +
 setup.cfg                                   |   16 +
 setup.py                                    |   37 +-
 tox.ini                                     |   16 +-
 versioneer.py                               | 1904 +++++++++++++++++++--------
 68 files changed, 3163 insertions(+), 1641 deletions(-)

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