[med-svn] [python-cobra] branch master updated (03e31a5 -> 5b737dc)

[Afif Elghraoui]

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

      from  03e31a5   releasing package python-cobra version 0.4.2~b1-1
       new  cfeed59   Imported Upstream version 0.5.0~b2
       new  c4f4dd4   Merge tag 'upstream/0.5.0_b2'
       new  268c4b2   Drop patch applied upstream
       new  9170c94   Imported Upstream version 0.5.2
       new  174522f   Merge tag 'upstream/0.5.2'
       new  3e31fed   Update docs installation
       new  5859e06   Remove unused lintian overrides
       new  5b737dc   releasing package python-cobra version 0.5.2-1

The 8 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
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Summary of changes:
 .gitignore                                   |   3 +
 .travis.yml                                  |   4 +-
 CONTRIBUTING.md                              |  25 ---
 CONTRIBUTING.rst                             | 165 +++++++++++++++
 INSTALL.md                                   | 104 ---------
 INSTALL.rst                                  | 115 ++++++++++
 MANIFEST.in                                  |   2 +-
 README.md                                    |  45 ----
 README.rst                                   | 102 +++++++++
 appveyor.yml                                 |   2 +-
 cobra/VERSION                                |   2 +-
 cobra/core/ArrayBasedModel.py                |  21 +-
 cobra/core/Metabolite.py                     |  11 +-
 cobra/core/Model.py                          |  23 +-
 cobra/core/Reaction.py                       |  14 ++
 cobra/design/design_algorithms.py            | 117 ++++++----
 cobra/flux_analysis/parsimonious.py          |   1 +
 cobra/flux_analysis/phenotype_phase_plane.py |  31 +--
 cobra/flux_analysis/reaction.py              |  49 +++--
 cobra/flux_analysis/summary.py               | 305 ++++++++++++++++-----------
 cobra/flux_analysis/variability.py           |  23 +-
 cobra/solvers/__init__.py                    |   1 +
 cobra/test/data/textbook_solution.pickle     | Bin 0 -> 5278 bytes
 cobra/test/data/update_pickles.py            |   5 +
 cobra/test/flux_analysis.py                  | 133 +++++++-----
 cobra/test/unit_tests.py                     |  21 +-
 config.sh                                    |  58 +++++
 debian/changelog                             |   9 +
 debian/docs                                  |   3 +-
 debian/patches/reproducible.patch            |  15 --
 debian/patches/series                        |   1 -
 debian/python-cobra-data.lintian-overrides   |   3 -
 debian/rules                                 |   3 -
 develop-requirements.txt                     |  15 ++
 documentation_builder/faq.ipynb              |   2 +-
 documentation_builder/index.rst              |   5 +-
 make-mac-wheels.sh                           |  14 ++
 manylinux_builder/Dockerfile                 |   6 +
 manylinux_builder/README.md                  |   5 +
 manylinux_builder/build_cobrapy.sh           |  12 ++
 manylinux_builder/run_cobrapy_builder.sh     |   2 +
 scripts/deploy-test.sh                       |  15 ++
 scripts/deploy.sh                            |   6 +
 setup.py                                     |  14 +-
 tox.ini                                      |  12 ++
 45 files changed, 1025 insertions(+), 499 deletions(-)
 delete mode 100644 CONTRIBUTING.md
 create mode 100644 CONTRIBUTING.rst
 delete mode 100644 INSTALL.md
 create mode 100644 INSTALL.rst
 delete mode 100644 README.md
 create mode 100644 README.rst
 create mode 100644 cobra/test/data/textbook_solution.pickle
 create mode 100644 config.sh
 delete mode 100644 debian/patches/reproducible.patch
 create mode 100644 develop-requirements.txt
 create mode 100755 make-mac-wheels.sh
 create mode 100644 manylinux_builder/Dockerfile
 create mode 100644 manylinux_builder/README.md
 create mode 100755 manylinux_builder/build_cobrapy.sh
 create mode 100755 manylinux_builder/run_cobrapy_builder.sh
 create mode 100755 scripts/deploy-test.sh
 create mode 100755 scripts/deploy.sh
 create mode 100644 tox.ini

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