[med-svn] [python-cobra] branch debian/jessie-backports updated (4d742e2 -> c3cf874)

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

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

      from  4d742e2   python-cobra (0.4.0b4-1~bpo8+2) jessie-backports; urgency=medium
      adds  7839240   Run autopkgtests from outside the source tree
      adds  24c2285   Imported Upstream version 0.4.0b6
      adds  f5a3e7b   Merge tag 'upstream/0.4.0b6'
      adds  1a3d17f   Add lintian overrides for new data files
      adds  9768b71   python-cobra (0.4.0b6-1) unstable; urgency=medium
       new  42fc567   Merge branch 'master' into debian/jessie-backports
       new  c3cf874   python-cobra (0.4.0b6-1~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:
 .gitignore                                         |   1 +
 .travis.yml                                        |  16 +-
 CONTRIBUTING.md                                    |  25 ++
 INSTALL.md                                         |   3 +-
 README.md                                          |   2 +-
 appveyor.yml                                       |  23 +-
 appveyor/run_with_compiler.cmd                     |  47 ---
 appveyor/run_with_env.cmd                          |  88 +++++
 cobra/VERSION                                      |   2 +-
 cobra/__init__.py                                  |   2 +-
 cobra/core/DictList.py                             |   7 +-
 cobra/core/Gene.py                                 |   2 +-
 cobra/core/Metabolite.py                           |   2 +-
 cobra/core/Model.py                                |   1 +
 cobra/core/Object.py                               |   2 +-
 cobra/core/Reaction.py                             |  13 +-
 cobra/design/__init__.py                           |   1 +
 cobra/design/design_algorithms.py                  | 400 +++++++++++++++++++++
 cobra/flux_analysis/phenotype_phase_plane.py       |  15 +-
 cobra/flux_analysis/reaction.py                    |   5 +-
 cobra/io/json.py                                   |   4 +-
 cobra/io/mat.py                                    |  14 +-
 cobra/io/sbml.py                                   |  68 +++-
 cobra/io/sbml3.py                                  | 110 +++---
 cobra/manipulation/__init__.py                     |   9 +-
 cobra/manipulation/annotate.py                     |  24 ++
 cobra/manipulation/modify.py                       | 110 +++++-
 cobra/manipulation/validate.py                     |  54 +++
 cobra/solvers/__init__.py                          |   6 +-
 cobra/solvers/cglpk.pyx                            |  11 +-
 cobra/solvers/cplex_solver.py                      |   3 +-
 cobra/solvers/cplex_solver_java.py                 |  16 +-
 cobra/solvers/glpk_solver.py                       |  13 +-
 cobra/solvers/glpk_solver_java.py                  |  30 +-
 cobra/solvers/gurobi_solver.py                     |  36 +-
 cobra/solvers/gurobi_solver_java.py                |  14 +-
 cobra/solvers/mosek.py                             |   6 +
 cobra/test/__init__.py                             |   3 +-
 cobra/test/data/invalid0.xml                       |  47 +++
 cobra/test/data/invalid1.xml                       |  45 +++
 cobra/test/data/invalid2.xml                       |  68 ++++
 cobra/test/data/mini.json                          |  24 +-
 cobra/test/data/mini.mat                           | Bin 14352 -> 14600 bytes
 cobra/test/data/mini.pickle                        | Bin 25348 -> 25060 bytes
 cobra/test/data/mini_cobra.xml                     | 212 ++++++-----
 cobra/test/data/mini_fbc1.xml                      | 218 +++++------
 cobra/test/data/mini_fbc2.xml                      |  44 +--
 cobra/test/data/mini_fbc2.xml.bz2                  | Bin 4939 -> 4957 bytes
 cobra/test/data/mini_fbc2.xml.gz                   | Bin 5637 -> 5670 bytes
 cobra/test/data/textbook.xml.gz                    | Bin 16329 -> 16890 bytes
 cobra/test/design.py                               |  89 +++++
 cobra/test/flux_analysis.py                        | 157 +-------
 cobra/test/io_tests.py                             |  37 +-
 cobra/test/manipulation.py                         | 250 +++++++++++++
 cobra/test/unit_tests.py                           |  36 ++
 cobra/test_all.py                                  |   7 -
 cobra/topology/reporter_metabolites.py             |   4 +-
 debian/changelog                                   |  13 +
 debian/python-cobra-data.lintian-overrides         |   3 +
 debian/tests/control                               |   4 +-
 documentation_builder/io.ipynb                     |  12 +-
 documentation_builder/io.rst                       |  41 +--
 documentation_builder/loopless.ipynb               |   4 +-
 documentation_builder/loopless.rst                 |   4 +-
 documentation_builder/phenotype_phase_plane.ipynb  |  23 +-
 documentation_builder/phenotype_phase_plane.rst    |   7 +-
 .../phenotype_phase_plane_3_0.png                  | Bin 94579 -> 89909 bytes
 .../phenotype_phase_plane_5_0.png                  | Bin 106030 -> 100924 bytes
 .../phenotype_phase_plane_5_1.png                  | Bin 97694 -> 92540 bytes
 .../phenotype_phase_plane_7_0.png                  | Bin 68889 -> 63193 bytes
 documentation_builder/simulating.ipynb             |  80 ++++-
 documentation_builder/simulating.rst               |  43 ++-
 documentation_builder/solvers.ipynb                |   2 +-
 setup.py                                           |  20 +-
 74 files changed, 2004 insertions(+), 678 deletions(-)
 create mode 100644 CONTRIBUTING.md
 delete mode 100644 appveyor/run_with_compiler.cmd
 create mode 100644 appveyor/run_with_env.cmd
 create mode 100644 cobra/design/__init__.py
 create mode 100644 cobra/design/design_algorithms.py
 create mode 100644 cobra/manipulation/annotate.py
 create mode 100644 cobra/manipulation/validate.py
 create mode 100644 cobra/test/data/invalid0.xml
 create mode 100644 cobra/test/data/invalid1.xml
 create mode 100644 cobra/test/data/invalid2.xml
 create mode 100644 cobra/test/design.py
 create mode 100644 cobra/test/manipulation.py
 delete mode 100755 cobra/test_all.py

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