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commit 1ca60e88e8a120779b2fdad16796d665e585c369 Merge: 82e9edd 515cf06 Author: عفيف الغراوي <[email protected]> Date: Thu Jul 9 18:05:42 2015 -0700 Merge tag 'upstream/0.4.0b1' Upstream version 0.4.0b1 .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(-) -- 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
