[med-svn] [python-cobra] branch upstream updated (191cd73 -> 9170c94)

[Afif Elghraoui]

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

      from  191cd73   Imported Upstream version 0.4.2~b1
       new  cfeed59   Imported Upstream version 0.5.0~b2
       new  9170c94   Imported Upstream version 0.5.2

The 2 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                                  |   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 +++++
 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 ++
 39 files changed, 1015 insertions(+), 475 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
 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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