[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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