[med-svn] [python-cobra] 02/06: Merge tag 'upstream/0.5.6'

[Afif Elghraoui]

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afif pushed a commit to branch master
in repository python-cobra.

commit cf4c7a3fb994eca61a3657d039069e8161a2ad97
Merge: 68d1946 2a0a196
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Nov 27 13:01:42 2016 -0800

    Merge tag 'upstream/0.5.6'
    
    Upstream version 0.5.6

 .gitignore                                         |   3 +
 .travis.yml                                        |  96 ++-
 CONTRIBUTING.rst                                   |  44 +-
 appveyor.yml                                       |   5 +-
 cobra/VERSION                                      |   2 +-
 cobra/core/DictList.py                             |   2 +-
 cobra/core/Model.py                                |  17 +-
 cobra/core/Reaction.py                             |   3 +
 cobra/flux_analysis/parsimonious.py                |   4 +-
 cobra/io/__init__.py                               |  12 +-
 cobra/io/json.py                                   | 129 ++--
 cobra/test/__init__.py                             |  54 +-
 cobra/test/conftest.py                             |  48 ++
 cobra/test/design.py                               |  89 ---
 cobra/test/io_tests.py                             | 261 -------
 cobra/test/solvers.py                              | 292 --------
 cobra/test/test_design.py                          |  60 ++
 cobra/test/test_dictlist.py                        | 257 +++++++
 .../{flux_analysis.py => test_flux_analysis.py}    | 415 ++++++-----
 cobra/test/test_io.py                              | 213 ++++++
 .../test/{manipulation.py => test_manipulation.py} | 231 +++---
 cobra/test/test_model.py                           | 597 +++++++++++++++
 cobra/test/test_solvers.py                         | 266 +++++++
 cobra/test/unit_tests.py                           | 806 ---------------------
 config.sh                                          |  33 +-
 develop-requirements.txt                           |   1 +
 documentation_builder/conf.py                      |   2 +-
 scripts/deploy-test.sh                             |  15 -
 scripts/deploy.sh                                  |   9 +-
 tox.ini                                            |   2 +-
 30 files changed, 1990 insertions(+), 1978 deletions(-)

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