[med-svn] [python-cobra] branch upstream updated (24c2285 -> 65201bd)

[Afif Elghraoui]

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

      from  24c2285   Imported Upstream version 0.4.0b6
       new  65201bd   Imported Upstream version 0.4.0b7

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
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Summary of changes:
 .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(-)
 create mode 100644 documentation_builder/plot_helper.py

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