[med-svn] [python-cobra] branch master updated (070affb -> 9768b71)

[Afif Elghraoui]

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

      from  070affb   prepare upload
       new  7839240   Run autopkgtests from outside the source tree
       new  24c2285   Imported Upstream version 0.4.0b6
       new  f5a3e7b   Merge tag 'upstream/0.4.0b6'
       new  1a3d17f   Add lintian overrides for new data files
       new  9768b71   python-cobra (0.4.0b6-1) unstable; urgency=medium

The 5 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
been added to this reference.


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                                   |   7 +
 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, 1998 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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