[med-svn] [python-cobra] branch upstream updated (c887cfb -> e296849)

[Afif Elghraoui]

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

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

      from  c887cfb   Imported Upstream version 0.4.0+0
       new  e296849   Imported Upstream version 0.4.1

The 1 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                                         |  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(-)
 create mode 100644 cobra/flux_analysis/summary.py
 delete mode 100644 documentation_builder/building_model.rst
 create mode 100644 documentation_builder/cobra.design.rst
 delete mode 100644 documentation_builder/deletions.rst
 delete mode 100644 documentation_builder/faq.rst
 delete mode 100644 documentation_builder/gapfilling.rst
 delete mode 100644 documentation_builder/getting_started.rst
 delete mode 100644 documentation_builder/io.rst
 delete mode 100644 documentation_builder/loopless.rst
 delete mode 100644 documentation_builder/loopless_files/loopless_3_0.png
 delete mode 100644 documentation_builder/milp.rst
 delete mode 100644 documentation_builder/phenotype_phase_plane.rst
 delete mode 100644 documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_3_0.png
 delete mode 100644 documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_5_0.png
 delete mode 100644 documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_5_1.png
 delete mode 100644 documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_7_0.png
 delete mode 100644 documentation_builder/pymatbridge.rst
 delete mode 100644 documentation_builder/qp.rst
 delete mode 100644 documentation_builder/qp_files/qp_12_0.png
 delete mode 100644 documentation_builder/qp_files/qp_1_0.png
 create mode 100644 documentation_builder/requirements.txt
 delete mode 100644 documentation_builder/simulating.rst
 delete mode 100644 documentation_builder/solvers.rst

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-cobra.git