[med-svn] [python-cobra] branch upstream updated (35beca5 -> 515cf06)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Fri Jul 10 04:26:45 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a change to branch upstream
in repository python-cobra.
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
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