[med-svn] [python-cobra] 02/05: Merge tag 'upstream/0.4.1'

[Afif Elghraoui]

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afif pushed a commit to branch master
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commit 302c9584dc7be4bee6aa5285b601a35fd1932eee
Merge: fb2b5f1 e296849
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Thu Mar 24 20:00:46 2016 -0700

    Merge tag 'upstream/0.4.1'
    
    Upstream version 0.4.1

 .gitignore                                         |  89 ++-
 .travis.yml                                        |   4 +-
 appveyor.yml                                       |   5 +-
 appveyor/build_glpk.py                             |   4 +-
 cobra/VERSION                                      |   2 +-
 cobra/__init__.py                                  |  26 +-
 cobra/core/Metabolite.py                           |  35 +-
 cobra/core/Model.py                                |  20 +
 cobra/core/Reaction.py                             | 118 ++--
 cobra/design/design_algorithms.py                  |   4 +-
 cobra/flux_analysis/deletion_worker.py             |   7 +-
 cobra/flux_analysis/double_deletion.py             |   6 +-
 cobra/flux_analysis/essentiality.py                |  49 +-
 cobra/flux_analysis/gapfilling.py                  |   3 +-
 cobra/flux_analysis/loopless.py                    |   2 +-
 cobra/flux_analysis/moma.py                        |   3 +-
 cobra/flux_analysis/parsimonious.py                | 114 ++--
 cobra/flux_analysis/phenotype_phase_plane.py       |   5 +-
 cobra/flux_analysis/reaction.py                    | 167 +++---
 cobra/flux_analysis/single_deletion.py             |   6 +-
 cobra/flux_analysis/summary.py                     | 191 ++++++
 cobra/flux_analysis/variability.py                 |   7 +-
 cobra/io/mat.py                                    |   2 +-
 cobra/solvers/cglpk.pyx                            |  24 +-
 cobra/solvers/coin.py                              |   2 +-
 cobra/test/flux_analysis.py                        | 162 +++++-
 cobra/test/io_tests.py                             |   4 +
 cobra/test/unit_tests.py                           |  86 +++
 cobra/topology/__init__.py                         |   2 +-
 cobra/topology/reporter_metabolites.py             | 114 ++--
 documentation_builder/autodoc.sh                   |   2 -
 documentation_builder/building_model.ipynb         |  22 +-
 documentation_builder/building_model.rst           | 179 ------
 documentation_builder/cobra.design.rst             |  22 +
 documentation_builder/cobra.flux_analysis.rst      |   8 +
 documentation_builder/cobra.manipulation.rst       |  16 +
 documentation_builder/cobra.rst                    |   1 +
 documentation_builder/conf.py                      | 171 +-----
 documentation_builder/deletions.ipynb              | 230 ++++----
 documentation_builder/deletions.rst                | 640 ---------------------
 documentation_builder/faq.ipynb                    |  32 +-
 documentation_builder/faq.rst                      | 178 ------
 documentation_builder/gapfilling.ipynb             |  92 ++-
 documentation_builder/gapfilling.rst               | 104 ----
 documentation_builder/getting_started.ipynb        |  64 +--
 documentation_builder/getting_started.rst          | 489 ----------------
 documentation_builder/io.ipynb                     |  20 +-
 documentation_builder/io.rst                       | 170 ------
 documentation_builder/loopless.ipynb               |  24 +-
 documentation_builder/loopless.rst                 | 194 -------
 .../loopless_files/loopless_3_0.png                | Bin 10699 -> 0 bytes
 documentation_builder/milp.ipynb                   |  10 +-
 documentation_builder/milp.rst                     | 283 ---------
 documentation_builder/phenotype_phase_plane.ipynb  |  38 +-
 documentation_builder/phenotype_phase_plane.rst    |  85 ---
 .../phenotype_phase_plane_3_0.png                  | Bin 89909 -> 0 bytes
 .../phenotype_phase_plane_5_0.png                  | Bin 100924 -> 0 bytes
 .../phenotype_phase_plane_5_1.png                  | Bin 92540 -> 0 bytes
 .../phenotype_phase_plane_7_0.png                  | Bin 63193 -> 0 bytes
 documentation_builder/pymatbridge.ipynb            |  23 +-
 documentation_builder/pymatbridge.rst              | 124 ----
 documentation_builder/qp.ipynb                     |  26 +-
 documentation_builder/qp.rst                       | 190 ------
 documentation_builder/qp_files/qp_12_0.png         | Bin 14601 -> 0 bytes
 documentation_builder/qp_files/qp_1_0.png          | Bin 18553 -> 0 bytes
 documentation_builder/requirements.txt             |   2 +
 documentation_builder/simulating.ipynb             | 489 +++++++++++-----
 documentation_builder/simulating.rst               | 436 --------------
 documentation_builder/solvers.ipynb                |  34 +-
 documentation_builder/solvers.rst                  | 451 ---------------
 70 files changed, 1662 insertions(+), 4450 deletions(-)

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