[med-svn] [python-cobra] 03/10: Merge tag 'upstream/0.4.0b1'
Afif Elghraoui
afif-guest at moszumanska.debian.org
Fri Jul 10 04:26:44 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-cobra.
commit 1ca60e88e8a120779b2fdad16796d665e585c369
Merge: 82e9edd 515cf06
Author: عفيف الغراوي <afif at ghraoui.name>
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(-)
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