[med-svn] [python-cobra] 01/02: Merge branch 'master' into debian/jessie

[Afif Elghraoui]

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

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

commit cdfe131785275bd721f2d99cd4e4b44fb7a8dc26
Merge: fe42d7c 1f1cb07
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sat Aug 15 23:33:07 2015 -0700

    Merge branch 'master' into debian/jessie
    
    Conflicts:
    	debian/changelog
    Merge in new release to be backported.

 .travis.yml                                     |    15 +-
 INSTALL.md                                      |    10 +-
 appveyor.yml                                    |    14 +-
 cobra/VERSION                                   |     2 +-
 cobra/core/Gene.py                              |    39 +-
 cobra/core/Metabolite.py                        |     2 +-
 cobra/core/Model.py                             |    26 +-
 cobra/core/Object.py                            |    41 +-
 cobra/core/Reaction.py                          |    32 +-
 cobra/core/Species.py                           |    15 +-
 cobra/io/json.py                                |   203 +-
 cobra/io/mat.py                                 |    25 +-
 cobra/io/sbml.py                                |     4 +-
 cobra/io/sbml3.py                               |   390 +-
 cobra/manipulation/modify.py                    |    75 +-
 cobra/test/__init__.py                          |     2 +-
 cobra/test/data/mini.json                       |  1345 +-
 cobra/test/data/mini.mat                        |   Bin 14752 -> 14352 bytes
 cobra/test/data/mini.pickle                     |   Bin 10952 -> 25348 bytes
 cobra/test/data/mini_cobra.xml                  |   342 +-
 cobra/test/data/mini_fbc1.xml                   |   387 +-
 cobra/test/data/mini_fbc2.xml                   |  1416 +-
 cobra/test/data/mini_fbc2.xml.bz2               |   Bin 0 -> 4939 bytes
 cobra/test/data/mini_fbc2.xml.gz                |   Bin 0 -> 5637 bytes
 cobra/test/data/salmonella_fbc.xml              | 77257 ----------------------
 cobra/test/data/textbook.xml                    |  1562 -
 cobra/test/data/textbook.xml.gz                 |   Bin 0 -> 16329 bytes
 cobra/test/data/textbook_fva.json               |     1 +
 cobra/test/data/update_pickles.py               |   115 +-
 cobra/test/flux_analysis.py                     |    52 +-
 cobra/test/io_tests.py                          |    80 +-
 cobra/test/unit_tests.py                        |     3 +
 debian/changelog                                |    11 +
 debian/control                                  |    27 +-
 debian/copyright                                |     8 +-
 debian/patches/series                           |     2 +
 debian/patches/test-suite-return-code.patch     |    24 +
 debian/patches/testsuite-check-jsonschema.patch |    29 +
 debian/python-cobra-data.install                |     1 -
 debian/python-cobra-data.links                  |     2 -
 debian/python-cobra-data.lintian-overrides      |     4 +
 debian/tests/control                            |     7 +
 documentation_builder/io.ipynb                  |    37 +-
 setup.py                                        |     3 +-
 44 files changed, 3860 insertions(+), 79750 deletions(-)

diff --cc debian/changelog
index fcfa496,e6b318c..47c9822
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,14 +1,20 @@@
+ python-cobra (0.4.0b2-1) unstable; urgency=medium
+ 
+   * Adjust package relationships as requested by upstream
+   * Imported Upstream version 0.4.0b2 (Closes: 794978)
+   * Require matching version of the data package
+   * Configured autopkgtests
+   * Allowed tests to run without python-jsonschema
+   * Added lintian overrides for python-cobra-data
+ 
+  -- Afif Elghraoui <afif at ghraoui.name>  Tue, 04 Aug 2015 18:52:51 -0700
+ 
 +python-cobra (0.4.0b1-2~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Afif Elghraoui <afif at ghraoui.name>  Fri, 17 Jul 2015 00:10:40 -0700
 +
  python-cobra (0.4.0b1-2) unstable; urgency=medium
  
    * Add more recommended packages in d/control

-- 
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