[med-svn] [python-cobra] 02/02: Merge tag 'upstream/0.8.2'
Afif Elghraoui
afif at moszumanska.debian.org
Wed Oct 18 02:11:25 UTC 2017
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository python-cobra.
commit bc0100e281116ab785556b159190c49fe87e40b8
Merge: e463c21 6db8bde
Author: Afif Elghraoui <afif at debian.org>
Date: Fri Aug 11 17:00:19 2017 -0400
Merge tag 'upstream/0.8.2'
Upstream version 0.8.2
.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(-)
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