[med-svn] [python-pyfaidx] 02/02: Initial packaging
Andreas Tille
tille at debian.org
Mon Oct 19 19:55:00 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository python-pyfaidx.
commit 4668bb52b98cf8f277f24b22fcf7408dd5f08c10
Author: Andreas Tille <tille at debian.org>
Date: Mon Oct 19 21:48:32 2015 +0200
Initial packaging
---
debian/changelog | 5 +++++
debian/clean | 1 +
debian/compat | 1 +
debian/control | 56 ++++++++++++++++++++++++++++++++++++++++++++++++
debian/copyright | 44 +++++++++++++++++++++++++++++++++++++
debian/rules | 14 ++++++++++++
debian/source/format | 1 +
debian/upstream/metadata | 9 ++++++++
debian/watch | 2 ++
9 files changed, 133 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..e941075
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+python-pyfaidx (0.4.2-1) UNRELEASED; urgency=medium
+
+ * Initial upload (Closes: #801721)
+
+ -- Andreas Tille <tille at debian.org> Tue, 13 Oct 2015 17:02:08 +0200
diff --git a/debian/clean b/debian/clean
new file mode 100644
index 0000000..f2db7ea
--- /dev/null
+++ b/debian/clean
@@ -0,0 +1 @@
+tests/data/genes.fasta.lower.fai
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..e9253d8
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,56 @@
+Source: python-pyfaidx
+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,
+ python-all (>= 2.7),
+ python-coverage,
+ python-setuptools,
+ python-nose,
+ python-numpy,
+ python-six,
+ python3-all,
+ python3-setuptools,
+ python3-nose,
+ python3-numpy,
+ python3-six
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/python-pyfaidx.git
+Vcs-Git: git://anonscm.debian.org/debian-med/python-pyfaidx.git
+Homepage: https://github.com/mdshw5/pyfaidx
+
+Package: python-pyfaidx
+Architecture: all
+Depends: ${misc:Depends},
+ ${python:Depends}
+Description: efficient random access to fasta subsequences for Python
+ Samtools provides a function "faidx" (FAsta InDeX), which creates a
+ small flat index file ".fai" allowing for fast random access to any
+ subsequence in the indexed FASTA file, while loading a minimal amount of
+ the file in to memory. This python module implements pure Python classes
+ for indexing, retrieval, and in-place modification of FASTA files using
+ a samtools compatible index. The pyfaidx module is API compatible with
+ the pygr seqdb module. A command-line script "faidx" is installed
+ alongside the pyfaidx module, and facilitates complex manipulation of
+ FASTA files without any programming knowledge.
+ .
+ This package provides the Python 2 modules to access fasta files.
+
+Package: python3-pyfaidx
+Architecture: all
+Depends: ${misc:Depends},
+ ${python3:Depends}
+Description: efficient random access to fasta subsequences for Python 3
+ Samtools provides a function "faidx" (FAsta InDeX), which creates a
+ small flat index file ".fai" allowing for fast random access to any
+ subsequence in the indexed FASTA file, while loading a minimal amount of
+ the file in to memory. This python module implements pure Python classes
+ for indexing, retrieval, and in-place modification of FASTA files using
+ a samtools compatible index. The pyfaidx module is API compatible with
+ the pygr seqdb module. A command-line script "faidx" is installed
+ alongside the pyfaidx module, and facilitates complex manipulation of
+ FASTA files without any programming knowledge.
+ .
+ This package provides the Python 3 modules to access fasta files.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..01a211f
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,44 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pyfaidx
+Upstream-Contact: Matthew Shirley <mdshw5 at gmail.com>
+Source: https://github.com/mdshw5/pyfaidx
+
+Files: *
+Copyright: 2013-2015 The Johns Hopkins University
+ Matthew Shirley <mdshw5 at gmail.com>
+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 Johns Hopkins University, or the name of any
+ affiliate of the Johns Hopkins University, including but not limited to The
+ Johns Hopkins Health System Corporation, or any of its hospitals or
+ affiliates, or the names of any of their respective faculty, employees, or
+ students 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 JOHNS HOPKINS UNIVERSITY NOR ANY OF
+ ITS AFFILIATES, FACULTY, EMPLOYEES OR STUDENTS 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/rules b/debian/rules
new file mode 100755
index 0000000..4a80baf
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,14 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+export PYBUILD_NAME=pyfaidx
+
+%:
+ 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; \
+ nosetests --with-coverage --cover-package=pyfaidx'
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..95428b9
--- /dev/null
+++ b/debian/upstream/metadata
@@ -0,0 +1,9 @@
+Reference:
+ Author: Matthew D. Shirley and Zhaorong Ma and Brent S. Pedersen and Sarah J. Wheelan
+ Title: Efficient "pythonic" access to FASTA files using pyfaidx
+ Journal: PeerJ PrePrints
+ Year: 2015
+ Volume: 3
+ Pages: e1196
+ DOI: 10.7287/peerj.preprints.970v1
+ URL: https://peerj.com/preprints/970/
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 0000000..5fff922
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,2 @@
+version=3
+https://github.com/mdshw5/pyfaidx/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
\ No newline at end of file
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