[med-svn] [python-cobra] branch master updated (68d1946 -> 6f42cc5)

[Afif Elghraoui]

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

      from  68d1946   releasing package python-cobra version 0.5.4-1
       new  2a0a196   Imported Upstream version 0.5.6
       new  cf4c7a3   Merge tag 'upstream/0.5.6'
       new  c9ccb36   Update packaging to accomodate change in test suite framework
       new  0a10ae2   Work around #846045 (in pytest-benchmark) to be able to run tests
       new  1ec0fba   d/tests/Makefile: update test script to accomodate return code change
       new  6f42cc5   releasing package python-cobra version 0.5.6-1

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repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
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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 +-
 debian/changelog                                   |  10 +
 debian/control                                     |   2 +
 debian/patches/exclude-pytest-benchmark.patch      | 248 +++++++
 debian/patches/series                              |   1 +
 debian/tests/Makefile                              |   2 +-
 debian/tests/control                               |   2 +
 develop-requirements.txt                           |   1 +
 documentation_builder/conf.py                      |   2 +-
 scripts/deploy-test.sh                             |  15 -
 scripts/deploy.sh                                  |   9 +-
 tox.ini                                            |   2 +-
 36 files changed, 2254 insertions(+), 1979 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
 create mode 100644 debian/patches/exclude-pytest-benchmark.patch
 delete mode 100755 scripts/deploy-test.sh

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