[med-svn] [python-cobra] branch master updated (9ae4247 -> c0f9ecb)
Afif Elghraoui
afif at moszumanska.debian.org
Mon Feb 5 05:34:01 UTC 2018
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository python-cobra.
from 9ae4247 Drop obsolete patch
new ee24e38 TODO is to-done
new 362e088 New upstream version 0.11.0
new 030557f Merge tag 'upstream/0.11.0'
new 62492bd Update TODO
new 2e7e270 Update patch
new c0f9ecb Update changelog
The 6 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 | 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 ---
debian/TODO | 11 +-
debian/changelog | 9 +-
debian/patches/mathjax.patch | 2 +-
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 +-
98 files changed, 1613 insertions(+), 8132 deletions(-)
delete mode 100644 appveyor/build_glpk.py
delete mode 100644 appveyor/install.ps1
delete mode 100644 appveyor/run_with_env.cmd
delete mode 100644 cobra/core/arraybasedmodel.py
delete mode 100644 cobra/design/__init__.py
delete mode 100644 cobra/design/design_algorithms.py
create mode 100644 cobra/flux_analysis/deletion.py
delete mode 100644 cobra/flux_analysis/deletion_worker.py
delete mode 100644 cobra/flux_analysis/double_deletion.py
delete mode 100644 cobra/flux_analysis/single_deletion.py
delete mode 100644 cobra/solvers/__init__.py
delete mode 100644 cobra/solvers/cglpk.pyx
delete mode 100644 cobra/solvers/coin.py
delete mode 100644 cobra/solvers/cplex_solver.py
delete mode 100644 cobra/solvers/cplex_solver_java.py
delete mode 100644 cobra/solvers/esolver.py
delete mode 100644 cobra/solvers/glpk.pxd
delete mode 100644 cobra/solvers/glpk_solver.py
delete mode 100644 cobra/solvers/glpk_solver_java.py
delete mode 100644 cobra/solvers/gurobi_solver.py
delete mode 100644 cobra/solvers/gurobi_solver_java.py
delete mode 100644 cobra/solvers/mosek.py
delete mode 100644 cobra/solvers/parameters.py
delete mode 100644 cobra/solvers/wrappers.py
create mode 100644 cobra/test/test_io_order.py
delete mode 100644 cobra/test/test_solvers.py
delete mode 100644 cobra/topology/__init__.py
delete mode 100644 cobra/topology/reporter_metabolites.py
delete mode 100644 config.sh
create mode 100644 documentation_builder/.gitignore
delete mode 100755 documentation_builder/autodoc.sh
delete mode 100644 documentation_builder/cobra.core.rst
delete mode 100644 documentation_builder/cobra.design.rst
delete mode 100644 documentation_builder/cobra.flux_analysis.rst
delete mode 100644 documentation_builder/cobra.io.rst
delete mode 100644 documentation_builder/cobra.manipulation.rst
delete mode 100644 documentation_builder/cobra.rst
delete mode 100644 documentation_builder/cobra.topology.rst
delete mode 100644 documentation_builder/cobra.util.rst
delete mode 100755 make-mac-wheels.sh
delete mode 100644 manylinux_builder/Dockerfile
delete mode 100644 manylinux_builder/README.md
delete mode 100755 manylinux_builder/build_cobrapy.sh
delete mode 100755 manylinux_builder/run_cobrapy_builder.sh
create mode 100644 release-notes/0.10.0.md
create mode 100644 release-notes/0.10.1.md
create mode 100644 release-notes/0.11.0.md
create mode 100644 release-notes/0.9.1.md
delete mode 100755 scripts/deploy.sh
create mode 100755 scripts/deploy_website.sh
create mode 100755 scripts/prepare_notes.sh
create mode 100644 scripts/publish_release.py
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