[med-svn] [python-bx] 02/04: Check-in initial draft packaging
Afif Elghraoui
afif at moszumanska.debian.org
Thu Jun 30 08:38:06 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository python-bx.
commit f11d4b44c67a8c8cdc56e71d93a70151acf6a33d
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Thu Jun 30 01:23:14 2016 -0700
Check-in initial draft packaging
---
debian/changelog | 5 +++
debian/compat | 1 +
debian/control | 74 ++++++++++++++++++++++++++++++++++++++++
debian/copyright | 31 +++++++++++++++++
debian/docs | 0
debian/patches/no-download.patch | 17 +++++++++
debian/patches/series | 1 +
debian/rules | 16 +++++++++
debian/source/format | 1 +
9 files changed, 146 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..a257941
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+python-bx (0.7.2+20150623-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #nnnn)
+
+ -- Afif Elghraoui <afif at debian.org> Thu, 14 Jan 2016 20:15:15 -0800
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..aa5a818
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,74 @@
+Source: python-bx
+Section: python
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Build-Depends:
+ debhelper (>= 9),
+ dh-python,
+ zlib1g-dev,
+# Python2
+ python-setuptools,
+ python-all-dev,
+ python-nose,
+ python-numpy,
+ cython,
+# Python3
+ python3-setuptools,
+ python3-all-dev,
+ python3-nose,
+ python3-numpy,
+ cython3,
+Standards-Version: 3.9.7
+Homepage: https://bitbucket.org/james_taylor/bx-python/wiki/Home
+Vcs-Git: https://anonscm.debian.org/git/debian-med/python-bx.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-bx.git
+
+Package: python-bx
+Architecture: any
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ ${python:Depends},
+Description: manipulating multiple sequence alignments and other biological data -- Python 2
+ The bx-python project is a python library and associated set of scripts to
+ allow for rapid implementation of genome scale analyses. The library contains
+ a variety of useful modules, but the particular strengths are:
+ * Classes for reading and working with genome-scale multiple local
+ alignments (in MAF, AXT, and LAV formats)
+ * Generic data structure for indexing on disk files that contain blocks of
+ data associated with intervals on various sequences (used, for example, to
+ provide random access to individual alignments in huge files; optimized for
+ use over network filesystems)
+ * Data structures for working with intervals on sequences
+ * "Binned bitsets" which act just like chromosome sized bit arrays, but
+ lazily allocate regions and allow large blocks of all set or all unset bits
+ to be stored compactly
+ * "Intersecter" for performing fast intersection tests that preserve both
+ query and target intervals and associated annotation
+ .
+ This package provides the Python 2 library.
+
+Package: python3-bx
+Architecture: any
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ ${python3:Depends},
+Description: manipulating multiple sequence alignments and other biological data -- Python 3
+ The bx-python project is a python library and associated set of scripts to
+ allow for rapid implementation of genome scale analyses. The library contains
+ a variety of useful modules, but the particular strengths are:
+ * Classes for reading and working with genome-scale multiple local
+ alignments (in MAF, AXT, and LAV formats)
+ * Generic data structure for indexing on disk files that contain blocks of
+ data associated with intervals on various sequences (used, for example, to
+ provide random access to individual alignments in huge files; optimized for
+ use over network filesystems)
+ * Data structures for working with intervals on sequences
+ * "Binned bitsets" which act just like chromosome sized bit arrays, but
+ lazily allocate regions and allow large blocks of all set or all unset bits
+ to be stored compactly
+ * "Intersecter" for performing fast intersection tests that preserve both
+ query and target intervals and associated annotation
+ .
+ This package provides the Python 3 library.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..99cdf72
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,31 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: bx-python
+Source: https://pypi.python.org/pypi/bx-python
+
+Files: *
+Copyright: 2005-2015 The Pennsylvania State University
+ 2013-2015 The Johns Hopkins University
+License: MIT
+
+Files: debian/*
+Copyright: 2016 Afif Elghraoui <afif at debian.org>
+License: MIT
+
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a
+ copy of this software and associated documentation files (the "Software"),
+ to deal in the Software without restriction, including without limitation
+ the rights to use, copy, modify, merge, publish, distribute, sublicense,
+ and/or sell copies of the Software, and to permit persons to whom the
+ Software is furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included
+ in all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
+ OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+ IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY
+ CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+ TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+ SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/debian/docs b/debian/docs
new file mode 100644
index 0000000..e69de29
diff --git a/debian/patches/no-download.patch b/debian/patches/no-download.patch
new file mode 100644
index 0000000..c50e6ea
--- /dev/null
+++ b/debian/patches/no-download.patch
@@ -0,0 +1,17 @@
+Description: Don't download setuptools
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: not-needed
+Last-Update: 2016-04-23
+--- python-bx.orig/setup.py
++++ python-bx/setup.py
+@@ -4,10 +4,6 @@
+ print >> sys.stderr, "ERROR: bx-python requires python 2.4 or greater"
+ sys.exit()
+
+-# Automatically download setuptools if not available
+-from distribute_setup import use_setuptools
+-use_setuptools()
+-
+ from setuptools import *
+ from glob import glob
+
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..3db461d
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+no-download.patch
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..b2a7b24
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+
+#DH_VERBOSE = 1
+#include /usr/share/dpkg/default.mk
+
+export LC_ALL=C.UTF-8
+
+export NOSE_VERBOSE=2
+
+%:
+ dh $@ --with python2,python3 --buildsystem=pybuild
+
+override_dh_auto_clean:
+ dh_auto_clean
+# C files are generated by Cython
+ find -name "*.pyx" | sed 's/pyx$$/c/' | xargs $(RM)
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)
--
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