[med-svn] [python-cobra] 02/08: Merge tag 'upstream/0.5.0_b2'

[Afif Elghraoui]

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

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

commit c4f4dd4e9e820a100e7703848a2c8ec1b176ad7e
Merge: 03e31a5 cfeed59
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Oct 9 12:49:39 2016 -0700

    Merge tag 'upstream/0.5.0_b2'
    
    Upstream version 0.5.0~b2

 .gitignore                                   |   3 +
 .travis.yml                                  |  96 ++++++---
 CONTRIBUTING.md                              |  25 ---
 CONTRIBUTING.rst                             |  26 +++
 INSTALL.md                                   | 104 ---------
 INSTALL.rst                                  | 134 ++++++++++++
 MANIFEST.in                                  |   2 +-
 README.md                                    |  45 ----
 README.rst                                   |  61 ++++++
 appveyor.yml                                 |   2 +-
 cobra/VERSION                                |   2 +-
 cobra/core/Metabolite.py                     |  11 +-
 cobra/core/Model.py                          |  23 +-
 cobra/core/Reaction.py                       |  14 ++
 cobra/design/design_algorithms.py            | 117 ++++++----
 cobra/flux_analysis/parsimonious.py          |   1 +
 cobra/flux_analysis/phenotype_phase_plane.py |  16 +-
 cobra/flux_analysis/reaction.py              |  49 +++--
 cobra/flux_analysis/summary.py               | 305 ++++++++++++++++-----------
 cobra/solvers/__init__.py                    |   1 +
 cobra/test/flux_analysis.py                  |  97 ++++-----
 cobra/test/unit_tests.py                     |   5 +-
 config.sh                                    |  57 +++++
 manylinux_builder/Dockerfile                 |   6 +
 manylinux_builder/README.md                  |   5 +
 manylinux_builder/build_cobrapy.sh           |  11 +
 manylinux_builder/run_cobrapy_builder.sh     |   2 +
 scripts/deploy-test.sh                       |  15 ++
 scripts/deploy.sh                            |   5 +
 setup.py                                     |  14 +-
 30 files changed, 794 insertions(+), 460 deletions(-)

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