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from 35beca5 Imported Upstream version 0.3.2 new 515cf06 Imported Upstream version 0.4.0b1 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: .coveragerc | 54 + .travis.yml | 7 +- INSTALL.md | 31 +- LICENSE | 1344 +- README.md | 45 +- appveyor.yml | 46 + appveyor/install.ps1 | 85 + appveyor/run_with_compiler.cmd | 47 + cobra/VERSION | 2 +- cobra/__init__.py | 2 +- cobra/core/ArrayBasedModel.py | 4 +- cobra/core/DictList.py | 10 +- cobra/core/Gene.py | 143 +- cobra/core/Metabolite.py | 183 +- cobra/core/Model.py | 106 +- cobra/core/Object.py | 2 +- cobra/core/Reaction.py | 134 +- cobra/core/Species.py | 46 +- cobra/core/__init__.py | 1 - cobra/external/__init__.py | 0 cobra/external/ppmap.py | 151 - cobra/external/six.py | 747 - cobra/flux_analysis/__init__.py | 12 +- cobra/flux_analysis/deletion_worker.py | 2 +- cobra/flux_analysis/double_deletion.py | 890 +- cobra/flux_analysis/essentiality.py | 31 +- cobra/flux_analysis/gapfilling.py | 165 + cobra/flux_analysis/loopless.py | 2 +- cobra/flux_analysis/moma.py | 353 +- cobra/flux_analysis/objective.py | 45 - cobra/flux_analysis/parsimonious.py | 2 - cobra/flux_analysis/single_deletion.py | 416 +- cobra/flux_analysis/variability.py | 60 +- cobra/io/__init__.py | 4 +- cobra/io/json.py | 8 +- cobra/io/mat.py | 56 +- cobra/io/sbml.py | 29 +- cobra/io/sbml3.py | 429 + cobra/manipulation/__init__.py | 4 +- cobra/manipulation/delete.py | 124 +- cobra/manipulation/modify.py | 47 + cobra/mlab/__init__.py | 15 - cobra/mlab/matlab_scripts/cell_to_string.m | 3 - cobra/mlab/matlab_scripts/create_container.m | 2 - cobra/mlab/matlab_scripts/load_mat.m | 3 - cobra/mlab/matlab_scripts/save_from_python.m | 3 - cobra/mlab/mlab.py | 405 - cobra/oven/aliebrahim/gapAnalysis.py | 209 - cobra/solvers/__init__.py | 4 +- cobra/solvers/cglpk.pyx | 72 +- cobra/solvers/coin.py | 136 + cobra/solvers/cplex_solver.py | 20 +- cobra/solvers/esolver.py | 2 +- cobra/solvers/glpk.pxd | 11 + cobra/solvers/gurobi_solver.py | 2 +- cobra/solvers/mosek.py | 4 +- cobra/test/__init__.py | 87 +- cobra/test/data/iJO1366.json | 1 - cobra/test/data/iJO1366.mat | Bin 1549400 -> 0 bytes cobra/test/data/iJO1366.xml | 124980 ++++++------------ cobra/test/data/mini.json | 1 + cobra/test/data/mini.mat | Bin 0 -> 14752 bytes cobra/test/data/mini.pickle | Bin 0 -> 10952 bytes cobra/test/data/mini_cobra.xml | 634 + cobra/test/data/mini_fbc1.xml | 561 + cobra/test/data/mini_fbc2.xml | 337 + cobra/test/data/textbook.xml | 1562 + cobra/test/data/update_pickles.py | 2 +- cobra/test/flux_analysis.py | 361 +- cobra/test/io_tests.py | 54 +- cobra/test/solvers.py | 23 +- cobra/test/unit_tests.py | 129 +- cobra/topology/reporter_metabolites.py | 29 - documentation_builder/autodoc.bat | 4 - documentation_builder/autodoc.sh | 5 +- documentation_builder/building_model.ipynb | 521 +- documentation_builder/building_model.rst | 77 +- documentation_builder/cobra.flux_analysis.rst | 16 +- documentation_builder/cobra.io.rst | 8 + documentation_builder/cobra.mlab.rst | 22 - documentation_builder/cobra.rst | 2 - documentation_builder/cobra.solvers.rst | 54 - documentation_builder/conf.py | 16 +- documentation_builder/deletions.ipynb | 1223 +- documentation_builder/deletions.rst | 703 +- documentation_builder/faq.ipynb | 634 +- documentation_builder/faq.rst | 7 + documentation_builder/gapfilling.ipynb | 185 + documentation_builder/gapfilling.rst | 104 + documentation_builder/getting_started.ipynb | 1715 +- documentation_builder/getting_started.rst | 117 +- documentation_builder/index.rst | 7 + documentation_builder/io.ipynb | 592 +- documentation_builder/io.rst | 146 +- documentation_builder/loopless.ipynb | 521 +- documentation_builder/loopless.rst | 23 +- .../loopless_files/loopless_3_0.png | Bin 0 -> 10699 bytes .../loopless_files/loopless_4_0.png | Bin 10776 -> 0 bytes documentation_builder/milp.ipynb | 809 +- documentation_builder/milp.rst | 25 +- documentation_builder/phenotype_phase_plane.ipynb | 356 +- documentation_builder/phenotype_phase_plane.rst | 56 +- .../phenotype_phase_plane_3_0.png | Bin 0 -> 94579 bytes .../phenotype_phase_plane_5_0.png | Bin 91579 -> 106030 bytes .../phenotype_phase_plane_5_1.png | Bin 0 -> 97694 bytes .../phenotype_phase_plane_7_0.png | Bin 101786 -> 68889 bytes .../phenotype_phase_plane_7_1.png | Bin 93758 -> 0 bytes .../phenotype_phase_plane_9_0.png | Bin 64219 -> 0 bytes documentation_builder/pymatbridge.ipynb | 235 + documentation_builder/pymatbridge.rst | 124 + documentation_builder/pyscript.tpl | 29 - documentation_builder/qp.ipynb | 586 +- documentation_builder/qp.rst | 15 +- documentation_builder/qp_files/qp_12_0.png | Bin 0 -> 14601 bytes documentation_builder/qp_files/qp_14_0.png | Bin 16893 -> 0 bytes documentation_builder/qp_files/qp_1_0.png | Bin 0 -> 18553 bytes documentation_builder/qp_files/qp_3_0.png | Bin 21854 -> 0 bytes documentation_builder/simulating.ipynb | 797 +- documentation_builder/simulating.rst | 308 +- documentation_builder/solvers.ipynb | 723 + documentation_builder/solvers.rst | 451 + examples/building_model.py | 126 - examples/deletions.py | 92 - examples/getting_started.py | 250 - examples/io.py | 117 - examples/loopless.py | 141 - examples/milp.py | 217 - examples/phenotype_phase_plane.py | 53 - examples/qp.py | 133 - examples/simulating.py | 81 - ez_setup.py | 185 +- setup.py | 97 +- 132 files changed, 53056 insertions(+), 95173 deletions(-) create mode 100644 .coveragerc create mode 100644 appveyor.yml create mode 100644 appveyor/install.ps1 create mode 100644 appveyor/run_with_compiler.cmd delete mode 100644 cobra/external/__init__.py delete mode 100644 cobra/external/ppmap.py delete mode 100644 cobra/external/six.py create mode 100644 cobra/flux_analysis/gapfilling.py delete mode 100644 cobra/flux_analysis/objective.py create mode 100644 cobra/io/sbml3.py delete mode 100644 cobra/mlab/__init__.py delete mode 100644 cobra/mlab/matlab_scripts/cell_to_string.m delete mode 100644 cobra/mlab/matlab_scripts/create_container.m delete mode 100644 cobra/mlab/matlab_scripts/load_mat.m delete mode 100644 cobra/mlab/matlab_scripts/save_from_python.m delete mode 100644 cobra/mlab/mlab.py delete mode 100644 cobra/oven/aliebrahim/gapAnalysis.py create mode 100644 cobra/solvers/coin.py delete mode 100644 cobra/test/data/iJO1366.json delete mode 100644 cobra/test/data/iJO1366.mat create mode 100644 cobra/test/data/mini.json create mode 100644 cobra/test/data/mini.mat create mode 100644 cobra/test/data/mini.pickle create mode 100644 cobra/test/data/mini_cobra.xml create mode 100644 cobra/test/data/mini_fbc1.xml create mode 100644 cobra/test/data/mini_fbc2.xml create mode 100644 cobra/test/data/textbook.xml delete mode 100644 documentation_builder/autodoc.bat delete mode 100644 documentation_builder/cobra.mlab.rst delete mode 100644 documentation_builder/cobra.solvers.rst create mode 100644 documentation_builder/gapfilling.ipynb create mode 100644 documentation_builder/gapfilling.rst create mode 100644 documentation_builder/loopless_files/loopless_3_0.png delete mode 100644 documentation_builder/loopless_files/loopless_4_0.png create mode 100644 documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_3_0.png create mode 100644 documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_5_1.png delete mode 100644 documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_7_1.png delete mode 100644 documentation_builder/phenotype_phase_plane_files/phenotype_phase_plane_9_0.png create mode 100644 documentation_builder/pymatbridge.ipynb create mode 100644 documentation_builder/pymatbridge.rst delete mode 100644 documentation_builder/pyscript.tpl create mode 100644 documentation_builder/qp_files/qp_12_0.png delete mode 100644 documentation_builder/qp_files/qp_14_0.png create mode 100644 documentation_builder/qp_files/qp_1_0.png delete mode 100644 documentation_builder/qp_files/qp_3_0.png create mode 100644 documentation_builder/solvers.ipynb create mode 100644 documentation_builder/solvers.rst delete mode 100644 examples/building_model.py delete mode 100644 examples/deletions.py delete mode 100644 examples/getting_started.py delete mode 100644 examples/io.py delete mode 100644 examples/loopless.py delete mode 100644 examples/milp.py delete mode 100644 examples/phenotype_phase_plane.py delete mode 100644 examples/qp.py delete mode 100644 examples/simulating.py -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-cobra.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit