[med-svn] [python-cobra] 02/05: Merge tag 'upstream/0.4.0b2'

[Afif Elghraoui]

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

commit 68334d95a9223519586f1e9614d25f7187f6218e
Merge: 4aa43cd eb3fb84
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Tue Aug 4 18:52:36 2015 -0700

    Merge tag 'upstream/0.4.0b2'
    
    Upstream version 0.4.0b2

 .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 +
 documentation_builder/io.ipynb     |    37 +-
 setup.py                           |     3 +-
 34 files changed, 3767 insertions(+), 79728 deletions(-)

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