[med-svn] [python-cobra] 02/02: Initial Packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Tue Jun 9 15:06:32 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-cobra.
commit b5e221040bad59201d886590d6660263c892ab1a
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Tue Jun 9 08:04:31 2015 -0700
Initial Packaging
---
debian/changelog | 5 +++++
debian/compat | 1 +
debian/control | 55 ++++++++++++++++++++++++++++++++++++++++++++++++
debian/copyright | 30 ++++++++++++++++++++++++++
debian/rules | 13 ++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 10 +++++++++
debian/watch | 4 ++++
8 files changed, 119 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..ffb5b8e
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+python-cobra (0.3.2-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #788224)
+
+ -- Afif Elghraoui <afif at ghraoui.name> Tue, 09 Jun 2015 06:20:48 -0700
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 0000000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 0000000..eebd991
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,55 @@
+Source: python-cobra
+Section: python
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med at lists.debian.org>
+Uploaders: Afif Elghraoui <afif at ghraoui.name>
+Build-Depends: debhelper (>= 9),
+ dh-python,
+ python-all,
+ python-all-dev,
+ python-setuptools,
+ cython,
+ python3-all,
+ python3-all-dev,
+ python3-setuptools,
+ cython3,
+ libglpk-dev
+X-Python-Version: >= 2.7
+X-Python3-Version: >= 3.4
+Standards-Version: 3.9.6
+Homepage: http://opencobra.github.io/cobrapy/
+Vcs-Git: git://anonscm.debian.org/debian-med/python-cobra.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-cobra.git
+
+
+Package: python-cobra
+Architecture: all
+Depends: ${misc:Depends},
+ ${python:Depends}
+Recommends: libglpk36
+Description: constraint-based modeling of biological networks (Python 2)
+ COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely
+ used for genome-scale modeling of metabolic networks in both prokaryotes
+ and eukaryotes. COBRApy is a constraint-based modeling package that is
+ designed to accommodate the biological complexity of the next generation
+ of COBRA models and provides access to commonly used COBRA methods, such
+ as flux balance analysis, flux variability analysis, and gene deletion
+ analyses.
+ .
+ This package provides the Python 2 module.
+
+Package: python3-cobra
+Architecture: all
+Depends: ${misc:Depends},
+ ${python3:Depends}
+Recommends: libglpk36
+Description: constraint-based modeling of biological networks (Python 3)
+ COnstraint-Based Reconstruction and Analysis (COBRA) methods are widely
+ used for genome-scale modeling of metabolic networks in both prokaryotes
+ and eukaryotes. COBRApy is a constraint-based modeling package that is
+ designed to accommodate the biological complexity of the next generation
+ of COBRA models and provides access to commonly used COBRA methods, such
+ as flux balance analysis, flux variability analysis, and gene deletion
+ analyses.
+ .
+ This package provides the Python 3 module.
\ No newline at end of file
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..6dd7ee0
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,30 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: cobrapy
+Upstream-Contact: Ali Ebrahim <aebrahim at ucsd.edu>
+Source: http://opencobra.github.io/cobrapy/
+
+Files: *
+Copyright: 2012-2014 Daniel R. Hyduke <danielhyduke at gmail.com>
+ 2012-2015 Ali Ebrahim <aebrahim at ucsd.edu>
+License: GPL-3.0+
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <afif at ghraoui.name>
+License: GPL-3.0+
+
+License: GPL-3.0+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation, either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>.
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..40e1d04
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,13 @@
+#!/usr/bin/make -f
+#DH_VERBOSE = 1
+export PYBUILD_NAME=cobra
+
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+%:
+ LC_ALL=C.UTF-8 dh $@ --with python2,python3 --buildsystem=pybuild
+
+override_dh_auto_clean:
+ dh_auto_clean
+ rm -f cobra/solvers/cglpk.c
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 0000000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
new file mode 100644
index 0000000..caaf543
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,10 @@
+Reference:
+ Author: Ali Ebrahim and Joshua A Lerman and Bernhard O Palsson and Daniel R Hyduke
+ Title: COBRApy: COnstraints-Based Reconstruction and Analysis for Python
+ Journal: BMC Systems Biology
+ Year: 2013
+ Volume: 7
+ Number: 74
+ DOI: 10.1186/1752-0509-7-74
+ PMID: 23927696
+ URL: http://www.biomedcentral.com/1752-0509/7/74
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..25cc295
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,4 @@
+version=3
+
+opts="filenamemangle=s/(?:.*)?v?(\d[\d\.]*)\.tar\.gz/python-cobra-$1.tar.gz/" \
+ https://github.com/opencobra/cobrapy/releases (?:.*/)?v?(\d[\d\.]*)\.tar\.gz
--
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