[med-svn] [python-cobra] branch debian/jessie-backports updated (282e80f -> 51a5ae5)

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a change to branch debian/jessie-backports
in repository python-cobra.

      from  282e80f   releasing package python-cobra version 0.4.2~b1-1~bpo8+1
      adds  cfeed59   Imported Upstream version 0.5.0~b2
      adds  c4f4dd4   Merge tag 'upstream/0.5.0_b2'
      adds  268c4b2   Drop patch applied upstream
      adds  9170c94   Imported Upstream version 0.5.2
      adds  174522f   Merge tag 'upstream/0.5.2'
      adds  3e31fed   Update docs installation
      adds  5859e06   Remove unused lintian overrides
      adds  5b737dc   releasing package python-cobra version 0.5.2-1
      adds  1ac926f   Imported Upstream version 0.5.4
      adds  05be2a8   Merge tag 'upstream/0.5.4'
      adds  b222520   Update upstream contact
      adds  68d1946   releasing package python-cobra version 0.5.4-1
       new  7374dc6   Merge tag 'debian/0.5.4-1' into debian/jessie-backports
       new  51a5ae5   releasing package python-cobra version 0.5.4-1~bpo8+1

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/io/sbml3.py                            |  66 ++++--
 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/io_tests.py                       |  10 +-
 cobra/test/unit_tests.py                     |  21 +-
 config.sh                                    |  58 +++++
 debian/changelog                             |  22 ++
 debian/copyright                             |   8 +-
 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 ++
 48 files changed, 1102 insertions(+), 519 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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