[med-svn] [python-cobra] branch upstream updated (515cf06 -> eb3fb84)

[Afif Elghraoui]

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

      from  515cf06   Imported Upstream version 0.4.0b1
       new  eb3fb84   Imported Upstream version 0.4.0b2

The 1 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:
 .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(-)
 create mode 100644 cobra/test/data/mini_fbc2.xml.bz2
 create mode 100644 cobra/test/data/mini_fbc2.xml.gz
 delete mode 100644 cobra/test/data/salmonella_fbc.xml
 delete mode 100644 cobra/test/data/textbook.xml
 create mode 100644 cobra/test/data/textbook.xml.gz
 create mode 100644 cobra/test/data/textbook_fva.json

-- 
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