[med-svn] [python-cobra] branch master updated (53ba895 -> 4f620bb)
Afif Elghraoui
afif-guest at moszumanska.debian.org
Fri Jul 10 04:26:41 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a change to branch master
in repository python-cobra.
from 53ba895 Upload to unstable (new)
new 82e9edd Update watch file to pick up alpha and beta releases
new 515cf06 Imported Upstream version 0.4.0b1
new 1ca60e8 Merge tag 'upstream/0.4.0b1'
new be6efe5 Remove obsolete patches
new 7f923d9 Remove copyright statements for files removed upstream
new 9cf8ca0 Update d/copyright to reflect new upstream dual-licensing and correct gpl3 mistake
new 9ed63c6 Refine dh_install overrides to exclude jython code from python3 package
new c71ed43 Add build-dependencies on python(3)-six
new 9b76486 Disable building of documentation until Sphinx 1.3 is available
new 4f620bb Package ready for review
The 10 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 -
debian/README.source | 12 +-
debian/changelog | 14 +
debian/control | 2 +
debian/copyright | 77 +-
debian/patches/improve-python3-support.patch | 309 -
debian/patches/series | 1 -
debian/python-cobra-data.doc-base | 8 -
debian/python-cobra-data.install | 2 +-
debian/rules | 14 +-
debian/watch | 2 +-
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 +-
142 files changed, 53118 insertions(+), 95552 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 debian/patches/improve-python3-support.patch
delete mode 100644 debian/python-cobra-data.doc-base
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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