[med-svn] [python-screed] branch upstream updated (3729975 -> 2d03733)

[Michael Crusoe]

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  3729975   Imported Upstream version 0.9
       new  2d03733   New upstream version 1.0

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:
 .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(-)
 create mode 100644 .coveragerc
 create mode 100644 .github/CONTRIBUTING.md
 create mode 100644 .github/PULL_REQUEST_TEMPLATE.md
 create mode 100644 CHANGELOG.md
 delete mode 100644 TODO
 create mode 100644 doc/dev/parsers.rst
 create mode 100644 doc/release-notes/RELEASE-1.0.md
 create mode 100644 doc/requirements.txt
 rename ChangeLog => legacy/ChangeLog (70%)
 rename jenkins-build.sh => legacy/jenkins-build.sh (96%)
 create mode 100644 screed/__main__.py
 create mode 100644 screed/dump_fasta.py
 create mode 100644 screed/dump_fastq.py
 delete mode 100644 screed/dump_to_fasta.py
 delete mode 100644 screed/dump_to_fastq.py
 delete mode 100755 screed/fadbm.py
 delete mode 100755 screed/fqdbm.py
 create mode 100644 screed/tests/test_attriberror.py
 create mode 100644 screed/tests/test_db.py
 delete mode 100644 screed/tests/test_nodb.py
 create mode 100644 screed/tests/test_record.py
 create mode 100644 setup.cfg

-- 
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