[med-svn] [python-pyvcf] 02/03: Add initial packaging
Andreas Tille
tille at debian.org
Wed Oct 14 09:46:29 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-pyvcf.
commit 8ca401a58d4177d2b8fbc5716035f5c36b914057
Author: Andreas Tille <tille at debian.org>
Date: Wed Oct 14 11:44:16 2015 +0200
Add initial packaging
---
debian/changelog | 5 +++
debian/compat | 1 +
debian/control | 61 +++++++++++++++++++++++++++++++++++++
debian/copyright | 38 +++++++++++++++++++++++
debian/get-orig-source | 32 +++++++++++++++++++
debian/patches/series | 1 +
debian/patches/use_setuptools.patch | 11 +++++++
debian/rules | 20 ++++++++++++
debian/source/format | 1 +
debian/watch | 5 +++
10 files changed, 175 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..01ba828
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+python-pyvcf (0.6.7-1) UNRELEASED; urgency=medium
+
+ * Initial upload (Closes: #??)
+
+ -- Andreas Tille <tille at debian.org> Tue, 13 Oct 2015 17:02:08 +0200
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..781979f
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,61 @@
+Source: python-pyvcf
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Andreas Tille <tille at debian.org>
+Section: python
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ dh-python,
+ cython,
+ python-dev (>= 2.7),
+ python-setuptools,
+ cython3,
+ python3-dev,
+ python3-setuptools
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-pyvcf/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/python-pyvcf/trunk/
+Homepage: https://pypi.python.org/pypi/PyVCF
+
+Package: python-pyvcf
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ${python:Depends}
+Description: Variant Call Format (VCF) parser for Python
+ The Variant Call Format (VCF) specifies the format of a text file used
+ in bioinformatics for storing gene sequence variations. The format has
+ been developed with the advent of large-scale genotyping and DNA
+ sequencing projects, such as the 1000 Genomes Project.
+ .
+ The intent of this module is to mimic the ``csv`` module in the Python
+ stdlib, as opposed to more flexible serialization formats like JSON or
+ YAML. ``vcf`` will attempt to parse the content of each record based on
+ the data types specified in the meta-information lines -- specifically
+ the ##INFO and
+ ##FORMAT lines. If these lines are missing or incomplete, it will check
+ against the reserved types mentioned in the spec. Failing that, it will
+ just return strings.
+ .
+ This package provides the Python 2 modules.
+
+Package: python3-pyvcf
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ${python3:Depends}
+Description: Variant Call Format (VCF) parser for Python 3
+ The Variant Call Format (VCF) specifies the format of a text file used
+ in bioinformatics for storing gene sequence variations. The format has
+ been developed with the advent of large-scale genotyping and DNA
+ sequencing projects, such as the 1000 Genomes Project.
+ .
+ The intent of this module is to mimic the ``csv`` module in the Python
+ stdlib, as opposed to more flexible serialization formats like JSON or
+ YAML. ``vcf`` will attempt to parse the content of each record based on
+ the data types specified in the meta-information lines -- specifically
+ the ##INFO and
+ ##FORMAT lines. If these lines are missing or incomplete, it will check
+ against the reserved types mentioned in the spec. Failing that, it will
+ just return strings.
+ .
+ This package provides the Python 3 modules.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..b9b84eb
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,38 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: PyVCF
+Upstream-Contact: James Casbon <casbon at gmail.com>
+Source: https://pypi.python.org/pypi/PyVCF
+
+Files: *
+Copyright: 2011-2015, Population Genetics Technologies Ltd, All rights reserved.
+License: BSD-3-clause
+
+Files: debian/*
+Copyright: 2015 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:
+ .
+ 1. Redistributions of source code must retain the above copyright notice, this
+ list of conditions and the following disclaimer.
+ .
+ 2. 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.
+ .
+ 3. Neither the name of the Population Genetics Technologies Ltd 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/get-orig-source b/debian/get-orig-source
new file mode 100755
index 0000000..46986b2
--- /dev/null
+++ b/debian/get-orig-source
@@ -0,0 +1,32 @@
+#!/bin/sh
+# Test-Data needs to be fetched separately from Git
+
+set -e
+set -x
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+
+if ! echo $@ | grep -q upstream-version ; then
+ VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'`
+ uscan --verbose --force-download
+else
+ VERSION=`echo $@ | sed 's?^.*--upstream-version \([0-9.]\+\) .*?\1?'`
+ if echo "$VERSION" | grep -q "upstream-version" ; then
+ echo "Unable to parse version number"
+ exit
+ fi
+fi
+
+TARDIR="$PKG"-"$VERSION"
+cd ..
+mkdir -p tarballs
+cd tarballs
+
+tar xaf ../PyVCF-${VERSION}.tar.gz
+mv PyVCF-${VERSION} ${TARDIR}
+find . -name "*.egg-info" -type d | xargs rm -rf
+git clone https://github.com/jamescasbon/PyVCF.git
+rsync -a --exclude '*.py' PyVCF/vcf/test ${TARDIR}/vcf
+
+GZIP="--best --no-name" tar --owner=root --group=root --mode=a+rX --exclude-vcs -caf "$PKG"_"$VERSION".orig.tar.xz ${TARDIR}
+rm -rf ${TARDIR} PyVCF
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..7b64906
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+use_setuptools.patch
diff --git a/debian/patches/use_setuptools.patch b/debian/patches/use_setuptools.patch
new file mode 100644
index 0000000..552bf01
--- /dev/null
+++ b/debian/patches/use_setuptools.patch
@@ -0,0 +1,11 @@
+--- a/setup.py
++++ b/setup.py
+@@ -53,7 +53,7 @@ setup(
+ description='Variant Call Format (VCF) parser for Python',
+ long_description=DOC,
+ test_suite='vcf.test.test_vcf.suite',
+- install_requires=['distribute'],
++ install_requires=['setuptools'],
+ requires=requires,
+ entry_points = {
+ 'vcf.filters': [
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..b6aa909
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,20 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export PYBUILD_NAME=pyvcf
+
+%:
+ dh $@ --with python2,python3 --buildsystem=pybuild
+
+override_dh_auto_test____:
+ LC_ALL=C.UTF-8 dh_auto_test -- --test --system=custom \
+ --test-args='set -e; \
+ cp -a Tests {build_dir}; \
+ cd {build_dir}/Tests; \
+ {interpreter} run_tests.py'
+
+get-orig-source:
+ . debian/get-orig-source
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..6644ec8
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,5 @@
+# Test-Data needs to be fetched separately from Git so wee need to call get-orig-source
+
+version=3
+https://pypi.python.org/pypi/PyVCF .*/PyVCF-([0-9.]+).tar.[xgb]z2? \
+ debian debian/get-orig-source
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/python-pyvcf.git
More information about the debian-med-commit
mailing list