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commit bc0100e281116ab785556b159190c49fe87e40b8 Merge: e463c21 6db8bde Author: Afif Elghraoui <[email protected]> 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-cobra.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
