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afif pushed a change to branch upstream
in repository python-cobra.
from 5444318 New upstream version 0.9.0
new 362e088 New upstream version 0.11.0
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 | 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(-)
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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