[med-svn] [python-skbio] 01/13: Inject python-skbio as per BioLinux + some enhancements (including renaming source package from skbio to python-skbio)

Andreas Tille tille at debian.org
Thu Jul 30 15:46:24 UTC 2015 

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tille pushed a commit to branch master
in repository python-skbio.

commit 60db584714364ff2060b9b744b3ef008459e4b8c
Author: Andreas Tille <tille at debian.org>
Date:   Wed Jul 29 15:06:40 2015 +0000

    Inject python-skbio as per BioLinux + some enhancements (including renaming source package from skbio to python-skbio)
---
 debian/changelog             | 12 +++++++++++
 debian/compat                |  1 +
 debian/control               | 51 ++++++++++++++++++++++++++++++++++++++++++++
 debian/copyright             | 39 +++++++++++++++++++++++++++++++++
 debian/python-skbio.install  |  1 +
 debian/python3-skbio.install |  1 +
 debian/rules                 | 24 +++++++++++++++++++++
 debian/source/format         |  1 +
 debian/watch                 |  2 ++
 9 files changed, 132 insertions(+)

diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..7e014fe
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,12 @@
+python-skbio (0.2.3-1) UNRELEASED; urgency=medium
+
+  * Initial upload to Debian (Closes: #???)
+
+ -- Andreas Tille <tille at debian.org>  Wed, 29 Jul 2015 17:02:03 +0200
+
+skbio (0.2.3-0biolinux2) trusty; urgency=medium
+
+  * Initial release for QIIME 1.9.0
+  * Note that this build does include compiled code and so must be arch=any
+
+ -- Tim Booth <tbooth at ceh.ac.uk>  Mon, 23 Feb 2015 17:46:31 +0000
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..fd7af36
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,51 @@
+Source: python-skbio
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Tim Booth <tbooth at ceh.ac.uk>,
+           Andreas Tille <tille at debian.org>
+Section: python
+Priority: optional
+Build-Depends: debhelper (>= 9),
+               python-all (>= 2.7),
+               python-support,
+               python3,
+               dh-python,
+               python-dev,
+               python3-dev,
+               python-setuptools,
+               python3-setuptools,
+               python-numpy,
+               python3-numpy,
+               python-natsort,
+               python3-natsort,
+               python-pandas,
+               python3-pandas,
+               python-matplotlib,
+               python3-matplotlib,
+               python-scipy,
+               python3-scipy
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-skbio/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-skbio/trunk/
+Homepage: https://github.com/biocore/scikit-bio
+
+Package: python-skbio
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         ${python:Depends}
+Description: Python data structures, algorithms, educational resources for bioinformatics
+ scikit-bio is an open-source, BSD-licensed, python package providing data
+ structures, algorithms, and educational resources for bioinformatics.
+ .
+ It is used as a dependency by various projects including QIIME
+
+Package: python3-skbio
+Architecture: any
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         ${python3:Depends}
+Description: Python3 data structures, algorithms, educational resources for bioinformatic
+ scikit-bio is an open-source, BSD-licensed, python package providing data
+ structures, algorithms, and educational resources for bioinformatics.
+ .
+ This is the package for Python3
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..e601bbd
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,39 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: scikit-bio
+Upstream-Contact: gregcaporaso at gmail.com
+Source: https://github.com/biocore/scikit-bio
+
+Files: *
+Copyright: 2013-2015 scikit-bio development team.
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: 2015 Tim Booth <tbooth at ceh.ac.uk>
+                Andreas Tille <tille at debian.org>
+License: BSD-3-clause
+
+License: BSD-3-clause
+ Redistribution and use in source and binary forms, with or without modification,
+ are permitted provided that the following conditions are met:
+ .
+ * Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+ .
+ * Redistributions in binary form must reproduce the above copyright notice, this
+   list of conditions and the following disclaimer in the documentation and/or
+   other materials provided with the distribution.
+ .
+ * Neither the names scikit-bio, skbio, or biocore nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/debian/python-skbio.install b/debian/python-skbio.install
new file mode 100644
index 0000000..dbdb301
--- /dev/null
+++ b/debian/python-skbio.install
@@ -0,0 +1 @@
+/usr/lib/python2*
diff --git a/debian/python3-skbio.install b/debian/python3-skbio.install
new file mode 100644
index 0000000..fef6392
--- /dev/null
+++ b/debian/python3-skbio.install
@@ -0,0 +1 @@
+/usr/lib/python3*
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..e5d7206
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,24 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+PKG := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+
+%:
+	dh $@ --with python2,python3 --buildsystem=pybuild
+
+override_dh_auto_test:
+	#Loads of failures at this point.
+	dh_auto_test || true
+
+override_dh_install:
+	# Do this after running the tests
+	find debian/tmp/usr -name tests -prune -exec rm -rf '{}' ';'
+	dh_install
+
+override_dh_clean:
+	dh_clean
+	rm -f .t* .c*
+	find ./skbio -name '*.so' -delete
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/watch b/debian/watch
new file mode 100644
index 0000000..89280e3
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+https://github.com/biocore/scikit-bio/releases .*/scikit-bio/archive/([.0-9]+)\.tar\.gz

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