[med-svn] [python-cobra] 01/02: Merge tag 'debian/0.5.4-1' into debian/jessie-backports

[Afif Elghraoui]

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

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

commit 7374dc61b5a9464a87ff07b8214a92ae4f777db6
Merge: 282e80f 68d1946
Author: Afif Elghraoui <afif at debian.org>
Date:   Fri Nov 18 21:53:58 2016 -0800

    Merge tag 'debian/0.5.4-1' into debian/jessie-backports
    
    tagging package python-cobra version debian/0.5.4-1

 .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                             |  16 ++
 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, 1096 insertions(+), 519 deletions(-)

diff --cc debian/changelog
index 1932034,00d8e01..24f70ce
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,19 +1,25 @@@
+ python-cobra (0.5.4-1) unstable; urgency=medium
+ 
+   * Imported Upstream version 0.5.4
+   * Update upstream contact
+ 
+  -- Afif Elghraoui <afif at debian.org>  Mon, 07 Nov 2016 20:51:23 -0800
+ 
+ python-cobra (0.5.2-1) unstable; urgency=medium
+ 
+   * Drop patch applied upstream
+   * Imported Upstream version 0.5.2
+   * Update docs installation
+   * Remove unused lintian overrides
+ 
+  -- Afif Elghraoui <afif at debian.org>  Fri, 21 Oct 2016 22:57:41 -0700
+ 
 +python-cobra (0.4.2~b1-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Afif Elghraoui <afif at debian.org>  Sat, 23 Jul 2016 15:20:47 -0700
 +
  python-cobra (0.4.2~b1-1) unstable; urgency=medium
  
    * Imported Upstream version 0.4.2~b1

-- 
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