[med-svn] [python-cobra] 03/06: Merge tag 'upstream/0.11.0'

[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 030557f2cd3de31bb3a8c3f0e33058f2130fac28
Merge: ee24e38 362e088
Author: Afif Elghraoui <afif at debian.org>
Date:   Sun Feb 4 22:10:08 2018 -0500

    Merge tag 'upstream/0.11.0'
    
    Upstream version 0.11.0

 .gitignore                                        |   1 +
 .travis.yml                                       | 128 +++--
 MANIFEST.in                                       |   2 +-
 README.rst                                        |  17 +-
 appveyor.yml                                      |  83 +---
 appveyor/build_glpk.py                            |  60 ---
 appveyor/install.ps1                              |  85 ----
 appveyor/run_with_env.cmd                         |  88 ----
 cobra/__init__.py                                 |   4 +-
 cobra/core/arraybasedmodel.py                     | 435 ----------------
 cobra/core/dictlist.py                            |  17 +-
 cobra/core/model.py                               | 149 ++----
 cobra/core/reaction.py                            |  21 +-
 cobra/design/__init__.py                          |   5 -
 cobra/design/design_algorithms.py                 |  17 -
 cobra/exceptions.py                               |  33 +-
 cobra/flux_analysis/__init__.py                   |  14 +-
 cobra/flux_analysis/deletion.py                   | 362 ++++++++++++++
 cobra/flux_analysis/deletion_worker.py            | 177 -------
 cobra/flux_analysis/double_deletion.py            | 580 ----------------------
 cobra/flux_analysis/gapfilling.py                 |  35 +-
 cobra/flux_analysis/loopless.py                   |  44 +-
 cobra/flux_analysis/moma.py                       | 128 +----
 cobra/flux_analysis/parsimonious.py               | 173 +------
 cobra/flux_analysis/phenotype_phase_plane.py      | 303 +----------
 cobra/flux_analysis/reaction.py                   |   8 +-
 cobra/flux_analysis/sampling.py                   |  17 +-
 cobra/flux_analysis/single_deletion.py            | 383 --------------
 cobra/flux_analysis/variability.py                | 175 ++-----
 cobra/io/dict.py                                  |  25 +-
 cobra/io/json.py                                  |  16 +-
 cobra/io/sbml3.py                                 |   2 +-
 cobra/io/yaml.py                                  |  14 +-
 cobra/manipulation/__init__.py                    |   4 +-
 cobra/manipulation/modify.py                      |  75 +--
 cobra/solvers/__init__.py                         | 134 -----
 cobra/solvers/cglpk.pyx                           | 566 ---------------------
 cobra/solvers/coin.py                             | 140 ------
 cobra/solvers/cplex_solver.py                     | 347 -------------
 cobra/solvers/cplex_solver_java.py                | 326 ------------
 cobra/solvers/esolver.py                          | 161 ------
 cobra/solvers/glpk.pxd                            | 218 --------
 cobra/solvers/glpk_solver.py                      | 276 ----------
 cobra/solvers/glpk_solver_java.py                 | 372 --------------
 cobra/solvers/gurobi_solver.py                    | 305 ------------
 cobra/solvers/gurobi_solver_java.py               | 285 -----------
 cobra/solvers/mosek.py                            | 245 ---------
 cobra/solvers/parameters.py                       | 158 ------
 cobra/solvers/wrappers.py                         |  49 --
 cobra/test/conftest.py                            |  31 +-
 cobra/test/test_flux_analysis.py                  | 416 ++++++++--------
 cobra/test/test_io.py                             |  12 +-
 cobra/test/test_io_order.py                       |  92 ++++
 cobra/test/test_manipulation.py                   |  44 +-
 cobra/test/test_model.py                          |  82 +--
 cobra/test/test_solver_model.py                   | 133 ++---
 cobra/test/test_solver_utils.py                   |  18 +-
 cobra/test/test_solvers.py                        | 271 ----------
 cobra/test/test_util.py                           |   2 -
 cobra/topology/__init__.py                        |   5 -
 cobra/topology/reporter_metabolites.py            |   9 -
 cobra/util/solver.py                              |  45 +-
 config.sh                                         |  68 ---
 develop-requirements.txt                          |  20 +-
 documentation_builder/.gitignore                  |   1 +
 documentation_builder/autodoc.sh                  |   5 -
 documentation_builder/cobra.core.rst              |  94 ----
 documentation_builder/cobra.design.rst            |  22 -
 documentation_builder/cobra.flux_analysis.rst     | 110 ----
 documentation_builder/cobra.io.rst                |  46 --
 documentation_builder/cobra.manipulation.rst      |  46 --
 documentation_builder/cobra.rst                   |  43 --
 documentation_builder/cobra.topology.rst          |  22 -
 documentation_builder/cobra.util.rst              |  46 --
 documentation_builder/conf.py                     |  54 +-
 documentation_builder/index.rst                   |   3 +-
 documentation_builder/phenotype_phase_plane.ipynb | 251 ++++++----
 documentation_builder/requirements.txt            |   2 +
 make-mac-wheels.sh                                |  14 -
 manylinux_builder/Dockerfile                      |   6 -
 manylinux_builder/README.md                       |   5 -
 manylinux_builder/build_cobrapy.sh                |  11 -
 manylinux_builder/run_cobrapy_builder.sh          |   2 -
 release-notes/0.10.0.md                           |  19 +
 release-notes/0.10.1.md                           |   9 +
 release-notes/0.11.0.md                           |  14 +
 release-notes/0.9.1.md                            |  19 +
 release-notes/next-release.md                     |   1 +
 scripts/deploy.sh                                 |   7 -
 scripts/deploy_website.sh                         |  21 +
 scripts/prepare_notes.sh                          |  10 +
 scripts/publish_release.py                        | 138 +++++
 setup.cfg                                         |   2 +-
 setup.py                                          | 173 ++-----
 tox.ini                                           |  17 +-
 95 files changed, 1598 insertions(+), 8125 deletions(-)

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