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commit 030557f2cd3de31bb3a8c3f0e33058f2130fac28 Merge: ee24e38 362e088 Author: Afif Elghraoui <a...@debian.org> Date: Sun Feb 4 22:10:08 2018 -0500 Merge tag 'upstream/0.11.0' Upstream version 0.11.0 .gitignore | 1 + .travis.yml | 128 +++-- MANIFEST.in | 2 +- README.rst | 17 +- appveyor.yml | 83 +--- appveyor/build_glpk.py | 60 --- appveyor/install.ps1 | 85 ---- appveyor/run_with_env.cmd | 88 ---- cobra/__init__.py | 4 +- cobra/core/arraybasedmodel.py | 435 ---------------- cobra/core/dictlist.py | 17 +- cobra/core/model.py | 149 ++---- cobra/core/reaction.py | 21 +- cobra/design/__init__.py | 5 - cobra/design/design_algorithms.py | 17 - cobra/exceptions.py | 33 +- cobra/flux_analysis/__init__.py | 14 +- cobra/flux_analysis/deletion.py | 362 ++++++++++++++ cobra/flux_analysis/deletion_worker.py | 177 ------- cobra/flux_analysis/double_deletion.py | 580 ---------------------- cobra/flux_analysis/gapfilling.py | 35 +- cobra/flux_analysis/loopless.py | 44 +- cobra/flux_analysis/moma.py | 128 +---- cobra/flux_analysis/parsimonious.py | 173 +------ cobra/flux_analysis/phenotype_phase_plane.py | 303 +---------- cobra/flux_analysis/reaction.py | 8 +- cobra/flux_analysis/sampling.py | 17 +- cobra/flux_analysis/single_deletion.py | 383 -------------- cobra/flux_analysis/variability.py | 175 ++----- cobra/io/dict.py | 25 +- cobra/io/json.py | 16 +- cobra/io/sbml3.py | 2 +- cobra/io/yaml.py | 14 +- cobra/manipulation/__init__.py | 4 +- cobra/manipulation/modify.py | 75 +-- cobra/solvers/__init__.py | 134 ----- cobra/solvers/cglpk.pyx | 566 --------------------- cobra/solvers/coin.py | 140 ------ cobra/solvers/cplex_solver.py | 347 ------------- cobra/solvers/cplex_solver_java.py | 326 ------------ cobra/solvers/esolver.py | 161 ------ cobra/solvers/glpk.pxd | 218 -------- cobra/solvers/glpk_solver.py | 276 ---------- cobra/solvers/glpk_solver_java.py | 372 -------------- cobra/solvers/gurobi_solver.py | 305 ------------ cobra/solvers/gurobi_solver_java.py | 285 ----------- cobra/solvers/mosek.py | 245 --------- cobra/solvers/parameters.py | 158 ------ cobra/solvers/wrappers.py | 49 -- cobra/test/conftest.py | 31 +- cobra/test/test_flux_analysis.py | 416 ++++++++-------- cobra/test/test_io.py | 12 +- cobra/test/test_io_order.py | 92 ++++ cobra/test/test_manipulation.py | 44 +- cobra/test/test_model.py | 82 +-- cobra/test/test_solver_model.py | 133 ++--- cobra/test/test_solver_utils.py | 18 +- cobra/test/test_solvers.py | 271 ---------- cobra/test/test_util.py | 2 - cobra/topology/__init__.py | 5 - cobra/topology/reporter_metabolites.py | 9 - cobra/util/solver.py | 45 +- config.sh | 68 --- develop-requirements.txt | 20 +- documentation_builder/.gitignore | 1 + documentation_builder/autodoc.sh | 5 - documentation_builder/cobra.core.rst | 94 ---- documentation_builder/cobra.design.rst | 22 - documentation_builder/cobra.flux_analysis.rst | 110 ---- documentation_builder/cobra.io.rst | 46 -- documentation_builder/cobra.manipulation.rst | 46 -- documentation_builder/cobra.rst | 43 -- documentation_builder/cobra.topology.rst | 22 - documentation_builder/cobra.util.rst | 46 -- documentation_builder/conf.py | 54 +- documentation_builder/index.rst | 3 +- documentation_builder/phenotype_phase_plane.ipynb | 251 ++++++---- documentation_builder/requirements.txt | 2 + make-mac-wheels.sh | 14 - manylinux_builder/Dockerfile | 6 - manylinux_builder/README.md | 5 - manylinux_builder/build_cobrapy.sh | 11 - manylinux_builder/run_cobrapy_builder.sh | 2 - release-notes/0.10.0.md | 19 + release-notes/0.10.1.md | 9 + release-notes/0.11.0.md | 14 + release-notes/0.9.1.md | 19 + release-notes/next-release.md | 1 + scripts/deploy.sh | 7 - scripts/deploy_website.sh | 21 + scripts/prepare_notes.sh | 10 + scripts/publish_release.py | 138 +++++ setup.cfg | 2 +- setup.py | 173 ++----- tox.ini | 17 +- 95 files changed, 1598 insertions(+), 8125 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 debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit