[med-svn] [python-cobra] branch debian/jessie-backports updated (c3cf874 -> 5046e5c)

[Afif Elghraoui]

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afif pushed a change to branch debian/jessie-backports
in repository python-cobra.

      from  c3cf874   python-cobra (0.4.0b6-1~bpo8+1) jessie-backports; urgency=medium
      adds  65201bd   Imported Upstream version 0.4.0b7
      adds  e930aef   Merge tag 'upstream/0.4.0b7'
      adds  71a4549   Add Suggests: qsopt-ex
      adds  d5d6837   Bump copyright year
      adds  743fbcf   Set up new revision
      adds  3fb39e8   Update standards version
      adds  55f9407   Add build-dependency on python-jsonschema to be able to run additional tests
      adds  6673d9f   Add scipy and numpy to build-depends
      adds  d7f3975   Backport patch from upstream to fix test skipping for unavailable utils
      adds  8e0e729   Clean up and fix autopkgtest
      adds  f3afb14   python-cobra (0.4.0b7-1) unstable; urgency=medium
       new  243c1a7   Merge tag 'debian/0.4.0b7-1' into debian/jessie-backports
       new  5046e5c   python-cobra (0.4.0b7-1~bpo8+1) jessie-backports; urgency=medium

The 2 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 +-
 debian/changelog                                  |  15 ++
 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, 595 insertions(+), 559 deletions(-)
 create mode 100644 debian/patches/fix-test-skips.patch
 create mode 100644 documentation_builder/plot_helper.py

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