[med-svn] [python-cobra] branch master updated (e463c21 -> bc0100e)
Afif Elghraoui
afif at moszumanska.debian.org
Wed Oct 18 02:11:24 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch master
in repository python-cobra.
from e463c21 releasing package python-cobra version 0.5.9-1
new 6db8bde New upstream version 0.8.2
new bc0100e Merge tag 'upstream/0.8.2'
The 2 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:
.coveragerc | 10 +-
CONTRIBUTING.rst => .github/CONTRIBUTING.rst | 107 +-
.github/ISSUE_TEMPLATE.md | 28 +
.gitignore | 4 +-
.travis.yml | 55 +-
INSTALL.rst | 34 +-
MANIFEST.in | 2 +-
README.rst | 20 +-
appveyor.yml | 79 +-
appveyor/build_glpk.py | 1 +
...cobra-cameo-merge-benchmarks-before-merge.ipynb | 362 ++++
benchmarks/cobra-cameo-merge-benchmarks.ipynb | 548 +++++
cobra/VERSION | 1 -
cobra/__init__.py | 23 +-
cobra/config.py | 10 +
cobra/core/Metabolite.py | 285 ---
cobra/core/Model.py | 384 ----
cobra/core/Object.py | 26 -
cobra/core/Reaction.py | 708 -------
cobra/core/Solution.py | 39 -
cobra/core/__init__.py | 29 +-
.../{ArrayBasedModel.py => arraybasedmodel.py} | 20 +-
cobra/core/{DictList.py => dictlist.py} | 175 +-
cobra/core/{Formula.py => formula.py} | 31 +-
cobra/core/{Gene.py => gene.py} | 141 +-
cobra/core/metabolite.py | 264 +++
cobra/core/model.py | 1070 ++++++++++
cobra/core/object.py | 54 +
cobra/core/reaction.py | 1133 ++++++++++
cobra/core/solution.py | 322 +++
cobra/core/{Species.py => species.py} | 23 +-
cobra/design/__init__.py | 6 +-
cobra/design/design_algorithms.py | 432 +---
cobra/exceptions.py | 58 +
cobra/flux_analysis/__init__.py | 37 +-
cobra/flux_analysis/deletion_worker.py | 9 +-
cobra/flux_analysis/double_deletion.py | 30 +-
cobra/flux_analysis/essentiality.py | 70 -
cobra/flux_analysis/gapfilling.py | 468 +++--
cobra/flux_analysis/loopless.py | 252 ++-
cobra/flux_analysis/moma.py | 123 +-
cobra/flux_analysis/parsimonious.py | 334 ++-
cobra/flux_analysis/phenotype_phase_plane.py | 262 ++-
cobra/flux_analysis/reaction.py | 343 +--
cobra/flux_analysis/sampling.py | 826 ++++++++
cobra/flux_analysis/single_deletion.py | 442 ++--
cobra/flux_analysis/summary.py | 142 +-
cobra/flux_analysis/variability.py | 336 ++-
cobra/io/__init__.py | 40 +-
cobra/io/dict.py | 225 ++
cobra/io/json.py | 301 +--
cobra/io/mat.py | 94 +-
cobra/io/sbml.py | 541 ++---
cobra/io/sbml3.py | 150 +-
cobra/io/yaml.py | 114 +
cobra/manipulation/__init__.py | 22 +-
cobra/manipulation/annotate.py | 4 +-
cobra/manipulation/delete.py | 12 +-
cobra/manipulation/modify.py | 153 +-
cobra/manipulation/validate.py | 9 +-
cobra/oven/README | 30 -
cobra/oven/WARNING | 1 -
cobra/oven/__init__.py | 2 -
cobra/oven/aliebrahim/__init__.py | 0
cobra/oven/aliebrahim/designAnalysis.py | 143 --
cobra/oven/aliebrahim/gapAnalysis_MILP_figure.svg | 103 -
cobra/oven/aliebrahim/keggIO.py | 163 --
cobra/oven/aliebrahim/simphenyIO.py | 184 --
cobra/oven/danielhyduke/__init__.py | 0
cobra/oven/danielhyduke/construction/balance.py | 329 ---
.../oven/danielhyduke/construction/omics_guided.py | 18 -
cobra/oven/danielhyduke/general/__init__.py | 1 -
cobra/oven/danielhyduke/general/arrays.py | 32 -
cobra/oven/danielhyduke/jython/README | 1 -
cobra/oven/danielhyduke/jython/__init__.py | 0
cobra/oven/danielhyduke/jython/numpy/README | 1 -
cobra/oven/danielhyduke/jython/numpy/__init__.py | 5 -
.../oven/danielhyduke/jython/numpy/core/Matrix.py | 211 --
.../danielhyduke/jython/numpy/core/__init__.py | 3 -
cobra/oven/danielhyduke/jython/numpy/core/core.py | 582 -----
.../danielhyduke/jython/numpy/core/multiarray.py | 312 ---
.../oven/danielhyduke/jython/numpy/core/numeric.py | 2217 --------------------
.../danielhyduke/jython/numpy/core/numerictypes.py | 734 -------
cobra/oven/danielhyduke/jython/scipy/README | 1 -
cobra/oven/danielhyduke/jython/scipy/__init__.py | 0
.../danielhyduke/jython/scipy/sparse/__init__.py | 22 -
.../oven/danielhyduke/jython/scipy/sparse/base.py | 615 ------
.../danielhyduke/jython/scipy/sparse/compressed.py | 708 -------
.../danielhyduke/jython/scipy/sparse/construct.py | 535 -----
cobra/oven/danielhyduke/jython/scipy/sparse/csr.py | 652 ------
cobra/oven/danielhyduke/jython/scipy/sparse/lil.py | 454 ----
.../danielhyduke/jython/scipy/sparse/sputils.py | 133 --
cobra/oven/danielhyduke/query/__init__.py | 1 -
cobra/oven/danielhyduke/query/query.py | 63 -
cobra/solvers/__init__.py | 16 +-
cobra/solvers/cglpk.pyx | 19 +-
cobra/solvers/coin.py | 12 +-
cobra/solvers/cplex_solver.py | 15 +-
cobra/solvers/cplex_solver_java.py | 27 +-
cobra/solvers/esolver.py | 18 +-
cobra/solvers/glpk_solver.py | 23 +-
cobra/solvers/glpk_solver_java.py | 29 +-
cobra/solvers/gurobi_solver.py | 20 +-
cobra/solvers/gurobi_solver_java.py | 27 +-
cobra/solvers/mosek.py | 10 +-
cobra/solvers/parameters.py | 4 +
cobra/solvers/wrappers.py | 4 +
cobra/test/__init__.py | 18 +-
cobra/test/conftest.py | 98 +-
cobra/test/data/iJO1366.pickle | Bin 1354269 -> 1810497 bytes
cobra/test/data/mini.json | 3 +-
cobra/test/data/mini.mat | Bin 14600 -> 17688 bytes
cobra/test/data/mini.pickle | Bin 25128 -> 32825 bytes
cobra/test/data/mini.yml | 1148 ++++++++++
cobra/test/data/mini_cobra.xml | 104 +-
cobra/test/data/mini_fbc1.xml | 35 +-
cobra/test/data/mini_fbc2.xml | 1 +
cobra/test/data/mini_fbc2.xml.bz2 | Bin 5008 -> 5016 bytes
cobra/test/data/mini_fbc2.xml.gz | Bin 5719 -> 5729 bytes
cobra/test/data/raven.pickle | Bin 11233 -> 13758 bytes
cobra/test/data/salmonella.pickle | Bin 1475508 -> 2151196 bytes
cobra/test/data/textbook_fva.json | 2 +-
cobra/test/data/textbook_pfba_fva.json | 1 +
cobra/test/data/textbook_solution.pickle | Bin 5278 -> 143584 bytes
cobra/test/data/update_pickles.py | 38 +-
cobra/test/test_design.py | 60 -
cobra/test/test_flux_analysis.py | 910 +++++---
cobra/test/test_io.py | 54 +-
cobra/test/test_manipulation.py | 51 +-
cobra/test/test_model.py | 542 ++++-
cobra/test/test_solver_model.py | 800 +++++++
cobra/test/test_solver_utils.py | 133 ++
cobra/test/test_solvers.py | 17 +-
cobra/test/{test_dictlist.py => test_util.py} | 111 +-
cobra/topology/__init__.py | 12 +-
cobra/topology/reporter_metabolites.py | 137 +-
cobra/util/__init__.py | 8 +
cobra/util/array.py | 198 ++
cobra/util/context.py | 71 +
cobra/util/solver.py | 444 ++++
cobra/util/util.py | 15 +
cobra/util/version_info.py | 79 +
cobra/version.py | 133 --
config.sh | 45 +-
develop-requirements.txt | 5 +-
documentation_builder/autodoc.sh | 6 +-
documentation_builder/building_model.ipynb | 238 ++-
documentation_builder/cobra.core.rst | 40 +-
documentation_builder/cobra.flux_analysis.rst | 16 +-
documentation_builder/cobra.rst | 21 +
documentation_builder/cobra.util.rst | 46 +
documentation_builder/conf.py | 52 +-
documentation_builder/constraints_objectives.ipynb | 484 +++++
documentation_builder/deletions.ipynb | 361 ++--
documentation_builder/faq.ipynb | 149 +-
documentation_builder/gapfilling.ipynb | 174 +-
documentation_builder/getting_started.ipynb | 542 +++--
documentation_builder/index.rst | 4 +-
documentation_builder/io.ipynb | 290 ++-
documentation_builder/loopless.ipynb | 399 ++--
documentation_builder/milp.ipynb | 423 ----
documentation_builder/phenotype_phase_plane.ipynb | 309 ++-
documentation_builder/plot_helper.py | 8 +-
documentation_builder/pymatbridge.ipynb | 2 +-
documentation_builder/qp.ipynb | 287 ---
documentation_builder/sampling.ipynb | 576 +++++
documentation_builder/simulating.ipynb | 811 +++----
documentation_builder/solvers.ipynb | 676 +-----
ez_setup.py | 426 ----
manylinux_builder/Dockerfile | 2 +-
manylinux_builder/build_cobrapy.sh | 1 -
release-notes/0.6.0.md | 206 ++
release-notes/0.6.1.md | 9 +
release-notes/0.6.2.md | 29 +
release-notes/0.7.0.md | 23 +
release-notes/0.8.0.md | 27 +
release-notes/0.8.1.md | 14 +
release-notes/0.8.2.md | 17 +
release-notes/next-release.md | 7 +
scripts/compare-benchmark.py | 35 +
scripts/deploy.sh | 12 +-
setup.cfg | 54 +
setup.py | 65 +-
tox.ini | 24 +-
184 files changed, 16764 insertions(+), 15677 deletions(-)
rename CONTRIBUTING.rst => .github/CONTRIBUTING.rst (68%)
create mode 100644 .github/ISSUE_TEMPLATE.md
create mode 100644 benchmarks/cobra-cameo-merge-benchmarks-before-merge.ipynb
create mode 100644 benchmarks/cobra-cameo-merge-benchmarks.ipynb
delete mode 100644 cobra/VERSION
create mode 100644 cobra/config.py
delete mode 100644 cobra/core/Metabolite.py
delete mode 100644 cobra/core/Model.py
delete mode 100644 cobra/core/Object.py
delete mode 100644 cobra/core/Reaction.py
delete mode 100644 cobra/core/Solution.py
rename cobra/core/{ArrayBasedModel.py => arraybasedmodel.py} (96%)
rename cobra/core/{DictList.py => dictlist.py} (72%)
rename cobra/core/{Formula.py => formula.py} (88%)
rename cobra/core/{Gene.py => gene.py} (63%)
create mode 100644 cobra/core/metabolite.py
create mode 100644 cobra/core/model.py
create mode 100644 cobra/core/object.py
create mode 100644 cobra/core/reaction.py
create mode 100644 cobra/core/solution.py
rename cobra/core/{Species.py => species.py} (77%)
create mode 100644 cobra/exceptions.py
delete mode 100644 cobra/flux_analysis/essentiality.py
create mode 100644 cobra/flux_analysis/sampling.py
create mode 100644 cobra/io/dict.py
create mode 100644 cobra/io/yaml.py
delete mode 100644 cobra/oven/README
delete mode 100644 cobra/oven/WARNING
delete mode 100644 cobra/oven/__init__.py
delete mode 100644 cobra/oven/aliebrahim/__init__.py
delete mode 100644 cobra/oven/aliebrahim/designAnalysis.py
delete mode 100644 cobra/oven/aliebrahim/gapAnalysis_MILP_figure.svg
delete mode 100644 cobra/oven/aliebrahim/keggIO.py
delete mode 100644 cobra/oven/aliebrahim/simphenyIO.py
delete mode 100644 cobra/oven/danielhyduke/__init__.py
delete mode 100644 cobra/oven/danielhyduke/construction/balance.py
delete mode 100644 cobra/oven/danielhyduke/construction/omics_guided.py
delete mode 100644 cobra/oven/danielhyduke/general/__init__.py
delete mode 100644 cobra/oven/danielhyduke/general/arrays.py
delete mode 100644 cobra/oven/danielhyduke/jython/README
delete mode 100644 cobra/oven/danielhyduke/jython/__init__.py
delete mode 100644 cobra/oven/danielhyduke/jython/numpy/README
delete mode 100644 cobra/oven/danielhyduke/jython/numpy/__init__.py
delete mode 100644 cobra/oven/danielhyduke/jython/numpy/core/Matrix.py
delete mode 100644 cobra/oven/danielhyduke/jython/numpy/core/__init__.py
delete mode 100755 cobra/oven/danielhyduke/jython/numpy/core/core.py
delete mode 100644 cobra/oven/danielhyduke/jython/numpy/core/multiarray.py
delete mode 100755 cobra/oven/danielhyduke/jython/numpy/core/numeric.py
delete mode 100755 cobra/oven/danielhyduke/jython/numpy/core/numerictypes.py
delete mode 100644 cobra/oven/danielhyduke/jython/scipy/README
delete mode 100644 cobra/oven/danielhyduke/jython/scipy/__init__.py
delete mode 100644 cobra/oven/danielhyduke/jython/scipy/sparse/__init__.py
delete mode 100644 cobra/oven/danielhyduke/jython/scipy/sparse/base.py
delete mode 100644 cobra/oven/danielhyduke/jython/scipy/sparse/compressed.py
delete mode 100644 cobra/oven/danielhyduke/jython/scipy/sparse/construct.py
delete mode 100644 cobra/oven/danielhyduke/jython/scipy/sparse/csr.py
delete mode 100644 cobra/oven/danielhyduke/jython/scipy/sparse/lil.py
delete mode 100644 cobra/oven/danielhyduke/jython/scipy/sparse/sputils.py
delete mode 100644 cobra/oven/danielhyduke/query/__init__.py
delete mode 100644 cobra/oven/danielhyduke/query/query.py
create mode 100644 cobra/test/data/mini.yml
create mode 100644 cobra/test/data/textbook_pfba_fva.json
delete mode 100644 cobra/test/test_design.py
create mode 100644 cobra/test/test_solver_model.py
create mode 100644 cobra/test/test_solver_utils.py
rename cobra/test/{test_dictlist.py => test_util.py} (73%)
create mode 100644 cobra/util/__init__.py
create mode 100644 cobra/util/array.py
create mode 100644 cobra/util/context.py
create mode 100644 cobra/util/solver.py
create mode 100644 cobra/util/util.py
create mode 100644 cobra/util/version_info.py
delete mode 100644 cobra/version.py
create mode 100644 documentation_builder/cobra.util.rst
create mode 100644 documentation_builder/constraints_objectives.ipynb
delete mode 100644 documentation_builder/milp.ipynb
delete mode 100644 documentation_builder/qp.ipynb
create mode 100644 documentation_builder/sampling.ipynb
delete mode 100644 ez_setup.py
create mode 100644 release-notes/0.6.0.md
create mode 100644 release-notes/0.6.1.md
create mode 100644 release-notes/0.6.2.md
create mode 100644 release-notes/0.7.0.md
create mode 100644 release-notes/0.8.0.md
create mode 100644 release-notes/0.8.1.md
create mode 100644 release-notes/0.8.2.md
create mode 100644 release-notes/next-release.md
create mode 100644 scripts/compare-benchmark.py
create mode 100644 setup.cfg
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