[med-svn] [python-cobra] branch upstream updated (191cd73 -> 9170c94)
Afif Elghraoui
afif at moszumanska.debian.org
Sat Oct 22 06:03:59 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch upstream
in repository python-cobra.
from 191cd73 Imported Upstream version 0.4.2~b1
new cfeed59 Imported Upstream version 0.5.0~b2
new 9170c94 Imported Upstream version 0.5.2
The 2 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:
.gitignore | 3 +
.travis.yml | 4 +-
CONTRIBUTING.md | 25 ---
CONTRIBUTING.rst | 165 +++++++++++++++
INSTALL.md | 104 ---------
INSTALL.rst | 115 ++++++++++
MANIFEST.in | 2 +-
README.md | 45 ----
README.rst | 102 +++++++++
appveyor.yml | 2 +-
cobra/VERSION | 2 +-
cobra/core/ArrayBasedModel.py | 21 +-
cobra/core/Metabolite.py | 11 +-
cobra/core/Model.py | 23 +-
cobra/core/Reaction.py | 14 ++
cobra/design/design_algorithms.py | 117 ++++++----
cobra/flux_analysis/parsimonious.py | 1 +
cobra/flux_analysis/phenotype_phase_plane.py | 31 +--
cobra/flux_analysis/reaction.py | 49 +++--
cobra/flux_analysis/summary.py | 305 ++++++++++++++++-----------
cobra/flux_analysis/variability.py | 23 +-
cobra/solvers/__init__.py | 1 +
cobra/test/data/textbook_solution.pickle | Bin 0 -> 5278 bytes
cobra/test/data/update_pickles.py | 5 +
cobra/test/flux_analysis.py | 133 +++++++-----
cobra/test/unit_tests.py | 21 +-
config.sh | 58 +++++
develop-requirements.txt | 15 ++
documentation_builder/faq.ipynb | 2 +-
documentation_builder/index.rst | 5 +-
make-mac-wheels.sh | 14 ++
manylinux_builder/Dockerfile | 6 +
manylinux_builder/README.md | 5 +
manylinux_builder/build_cobrapy.sh | 12 ++
manylinux_builder/run_cobrapy_builder.sh | 2 +
scripts/deploy-test.sh | 15 ++
scripts/deploy.sh | 6 +
setup.py | 14 +-
tox.ini | 12 ++
39 files changed, 1015 insertions(+), 475 deletions(-)
delete mode 100644 CONTRIBUTING.md
create mode 100644 CONTRIBUTING.rst
delete mode 100644 INSTALL.md
create mode 100644 INSTALL.rst
delete mode 100644 README.md
create mode 100644 README.rst
create mode 100644 cobra/test/data/textbook_solution.pickle
create mode 100644 config.sh
create mode 100644 develop-requirements.txt
create mode 100755 make-mac-wheels.sh
create mode 100644 manylinux_builder/Dockerfile
create mode 100644 manylinux_builder/README.md
create mode 100755 manylinux_builder/build_cobrapy.sh
create mode 100755 manylinux_builder/run_cobrapy_builder.sh
create mode 100755 scripts/deploy-test.sh
create mode 100755 scripts/deploy.sh
create mode 100644 tox.ini
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