[med-svn] [python-cobra] 02/11: Merge tag 'upstream/0.4.0b7'

[Afif Elghraoui]

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

commit e930aef4463c8eff65cc47bfbf7fabd5b42f9e9a
Merge: 9768b71 65201bd
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Feb 19 20:48:41 2016 -0800

    Merge tag 'upstream/0.4.0b7'
    
    Upstream version 0.4.0b7

 .travis.yml                                       |   3 +-
 cobra/VERSION                                     |   2 +-
 cobra/core/ArrayBasedModel.py                     |   7 +-
 cobra/core/DictList.py                            |   3 +-
 cobra/core/Formula.py                             |   3 +-
 cobra/core/Gene.py                                |   4 +-
 cobra/core/Metabolite.py                          |   1 -
 cobra/core/Object.py                              |   3 -
 cobra/core/Reaction.py                            |  66 +++--
 cobra/core/Solution.py                            |   2 +-
 cobra/design/design_algorithms.py                 |   6 +-
 cobra/flux_analysis/phenotype_phase_plane.py      |   7 +-
 cobra/io/sbml.py                                  |   4 +
 cobra/manipulation/annotate.py                    |   2 +-
 cobra/test/data/mini.json                         |   2 +
 cobra/test/data/mini.mat                          | Bin 14600 -> 14600 bytes
 cobra/test/data/mini.pickle                       | Bin 25060 -> 25128 bytes
 cobra/test/data/mini_fbc1.xml                     |  20 +-
 cobra/test/data/mini_fbc2.xml                     |   5 +-
 cobra/test/data/mini_fbc2.xml.bz2                 | Bin 4957 -> 5008 bytes
 cobra/test/data/mini_fbc2.xml.gz                  | Bin 5670 -> 5719 bytes
 cobra/test/unit_tests.py                          |  25 +-
 cobra/topology/__init__.py                        |   2 +-
 documentation_builder/building_model.ipynb        | 107 ++++----
 documentation_builder/deletions.ipynb             | 306 ++++------------------
 documentation_builder/gapfilling.ipynb            |   3 +-
 documentation_builder/getting_started.ipynb       |  74 ++++--
 documentation_builder/io.ipynb                    |  33 ++-
 documentation_builder/loopless.ipynb              |  40 +--
 documentation_builder/milp.ipynb                  |  21 +-
 documentation_builder/phenotype_phase_plane.ipynb |  48 ++--
 documentation_builder/plot_helper.py              |  81 ++++++
 documentation_builder/pymatbridge.ipynb           |   2 +-
 documentation_builder/qp.ipynb                    |  48 +---
 documentation_builder/simulating.ipynb            |  77 ++++--
 documentation_builder/solvers.ipynb               |  46 ++--
 36 files changed, 509 insertions(+), 544 deletions(-)

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