[med-svn] [python-cobra] 01/02: Merge branch 'master' into debian/jessie-backports

[Afif Elghraoui]

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

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

commit 42fc5676fb7478c2116c997996cae6b223a92407
Merge: 4d742e2 9768b71
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sat Dec 26 22:20:32 2015 -0800

    Merge branch 'master' into debian/jessie-backports

 .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(-)

diff --cc debian/changelog
index 5aaca13,2a02489..827ea8b
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,15 -1,10 +1,22 @@@
+ python-cobra (0.4.0b6-1) unstable; urgency=medium
+ 
+   * Run autopkgtests from outside the source tree
+   * Imported Upstream version 0.4.0b6
+ 
+  -- Afif Elghraoui <afif at ghraoui.name>  Mon, 21 Dec 2015 21:29:51 -0800
+ 
 +python-cobra (0.4.0b4-1~bpo8+2) jessie-backports; urgency=medium
 +
 +  * Fix Python3 package.
 +
 + -- Afif Elghraoui <afif at ghraoui.name>  Wed, 07 Oct 2015 20:59:22 -0700
 +
 +python-cobra (0.4.0b4-1~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Rebuild for jessie-backports.
 +
 + -- Afif Elghraoui <afif at ghraoui.name>  Sat, 19 Sep 2015 12:45:29 -0700
 +
  python-cobra (0.4.0b4-1) unstable; urgency=medium
  
    * Imported Upstream version 0.4.0b4

-- 
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