[med-svn] [python-cobra] 03/05: Merge tag 'upstream/0.4.0b6'

[Afif Elghraoui]

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

commit f5a3e7b50bf186ff908d9c62d5303dad0978223a
Merge: 7839240 24c2285
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Mon Dec 21 20:10:28 2015 -0800

    Merge tag 'upstream/0.4.0b6'
    
    Upstream version 0.4.0b6

 .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 +-
 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 +-
 71 files changed, 1986 insertions(+), 676 deletions(-)

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