[med-svn] [python-cobra] branch master updated (9768b71 -> f3afb14)

[Afif Elghraoui]

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

      from  9768b71   python-cobra (0.4.0b6-1) unstable; urgency=medium
       new  65201bd   Imported Upstream version 0.4.0b7
       new  e930aef   Merge tag 'upstream/0.4.0b7'
       new  71a4549   Add Suggests: qsopt-ex
       new  d5d6837   Bump copyright year
       new  743fbcf   Set up new revision
       new  3fb39e8   Update standards version
       new  55f9407   Add build-dependency on python-jsonschema to be able to run additional tests
       new  6673d9f   Add scipy and numpy to build-depends
       new  d7f3975   Backport patch from upstream to fix test skipping for unavailable utils
       new  8e0e729   Clean up and fix autopkgtest
       new  f3afb14   python-cobra (0.4.0b7-1) unstable; urgency=medium

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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 +-
 debian/changelog                                  |   9 +
 debian/control                                    |  21 +-
 debian/copyright                                  |   4 +-
 debian/patches/fix-test-skips.patch               |  40 +++
 debian/patches/series                             |   2 +-
 debian/tests/control                              |  19 +-
 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 ++--
 42 files changed, 589 insertions(+), 559 deletions(-)
 create mode 100644 debian/patches/fix-test-skips.patch
 create mode 100644 documentation_builder/plot_helper.py

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