[med-svn] [python-cobra] branch upstream updated (1ac926f -> 2a0a196)

[Afif Elghraoui]

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afif pushed a change to branch upstream
in repository python-cobra.

      from  1ac926f   Imported Upstream version 0.5.4
       new  2a0a196   Imported Upstream version 0.5.6

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:
 .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(-)
 create mode 100644 cobra/test/conftest.py
 delete mode 100644 cobra/test/design.py
 delete mode 100644 cobra/test/io_tests.py
 delete mode 100644 cobra/test/solvers.py
 create mode 100644 cobra/test/test_design.py
 create mode 100644 cobra/test/test_dictlist.py
 rename cobra/test/{flux_analysis.py => test_flux_analysis.py} (50%)
 create mode 100644 cobra/test/test_io.py
 rename cobra/test/{manipulation.py => test_manipulation.py} (52%)
 create mode 100644 cobra/test/test_model.py
 create mode 100644 cobra/test/test_solvers.py
 delete mode 100644 cobra/test/unit_tests.py
 delete mode 100755 scripts/deploy-test.sh

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