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in repository python-pbcore.
commit 6b3abfb4d8a80a8e3f02c2291171f057d31fbd07
Author: Afif Elghraoui <a...@ghraoui.name>
Date: Sun Jun 7 03:12:10 2015 -0700
initial packaging
---
debian/TODO | 3 +++
debian/changelog | 5 ++++
debian/compat | 1 +
debian/control | 32 +++++++++++++++++++++++
debian/copyright | 36 ++++++++++++++++++++++++++
debian/patches/remove-convenience-script.patch | 19 ++++++++++++++
debian/patches/series | 2 ++
debian/patches/setup.patch | 16 ++++++++++++
debian/rules | 16 ++++++++++++
debian/source/format | 1 +
debian/watch | 7 +++++
11 files changed, 138 insertions(+)
diff --git a/debian/TODO b/debian/TODO
new file mode 100644
index 0000000..3694c45
--- /dev/null
+++ b/debian/TODO
@@ -0,0 +1,3 @@
+* The python-pysam package needs to be updated to version 0.8.1.
+
+* Put documentation in the correct place so that it gets installed.
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 0000000..788ae2f
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+python-pbcore (1.0.0-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #nnnn)
+
+ -- Afif Elghraoui <a...@ghraoui.name> Sat, 06 Jun 2015 23:35:12 -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..49bce38
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,32 @@
+Source: python-pbcore
+Section: python
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-...@lists.debian.org>
+Uploaders: Afif Elghraoui <a...@ghraoui.name>
+Build-Depends: debhelper (>= 9),
+ dh-python,
+ python,
+ python-setuptools,
+ python-sphinx,
+ python-nose
+# # Required for tests
+# ,
+# python-numpy,
+# python-h5py
+Standards-Version: 3.9.6
+Homepage: https://github.com/PacificBiosciences/pbcore
+Vcs-Git: git://anonscm.debian.org/debian-med/python-pbcore.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-pbcore.git
+
+Package: python-pbcore
+Architecture: all
+Depends: ${misc:Depends},
+ ${python:Depends}
+Description: Python library for processing PacBio data files
+ The pbcore package provides Python modules for processing Pacific Biosciences
+ data files and building PacBio bioinformatics applications. These modules
+ include tools to read/write PacBio data formats, sample data files for
+ testing and debugging, base classes, and utilities for building bioinformatics
+ applications.
+ .
+ This package is part of the SMRTAnalysis suite.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..fc0e34d
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,36 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pbcore
+Source: https://github.com/PacificBiosciences/pbcore
+
+Files: *
+Copyright: 2011-2015 Pacific Biosciences of California, Inc.
+License: BSD-3-Clause
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <a...@ghraoui.name>
+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 University 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 HOLDERS 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/patches/remove-convenience-script.patch
b/debian/patches/remove-convenience-script.patch
new file mode 100644
index 0000000..6b39f09
--- /dev/null
+++ b/debian/patches/remove-convenience-script.patch
@@ -0,0 +1,19 @@
+Description: Remove convenience script ".open"
+ I am not quite sure what this script does, but it puts a file named
+ ".open" in /usr/bin, which is quite strange. The upstream changelog
+ indicates that this script is for convenience, so I am removing it
+ for the time being.
+Author: Afif Elghraoui <a...@ghraoui.name>
+Last-Update: 2015-06-07
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pbcore.orig/setup.py
++++ python-pbcore/setup.py
+@@ -24,7 +24,6 @@
+ 'chemistry/resources/*.xml']
+ },
+ zip_safe = False,
+- entry_points = { "console_scripts" : [ ".open =
pbcore.io.opener:entryPoint" ] },
+ install_requires=[
+ 'h5py >= 2.0.1',
+ 'numpy >= 1.6.0',
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..2c62e7f
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+remove-convenience-script.patch
+setup.patch
diff --git a/debian/patches/setup.patch b/debian/patches/setup.patch
new file mode 100644
index 0000000..91c8b46
--- /dev/null
+++ b/debian/patches/setup.patch
@@ -0,0 +1,16 @@
+Description: Change destination directory for python install
+Author: Afif Elghraoui <a...@ghraoui.name>
+Last-Update: 2015-06-06
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- python-pbcore.orig/Makefile
++++ python-pbcore/Makefile
+@@ -8,7 +8,7 @@
+ python setup.py bdist --formats=egg
+
+ install:
+- python setup.py install
++ python setup.py install --root=$(DESTDIR) --install-layout=deb
+
+ clean: doc-clean
+ rm -rf build/;\
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..43e5ef9
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,16 @@
+#!/usr/bin/make -f
+
+DPKG_EXPORT_BUILDFLAGS = 1
+include /usr/share/dpkg/default.mk
+
+DESTDIR=`pwd`/debian/tmp/
+export DESTDIR
+
+%:
+ dh $@ --with python2
+
+#get-orig-source:
+# uscan
+
+# test requires the package itself to be installed...
+override_dh_auto_test:
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..24796a8
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,7 @@
+version=3
+
+# For GitHub projects you can use the tags or releases page. Since the archive
+# URLs use only the version as the name, it is recommended to use a
+# filenamemangle to adjust the name of the downloaded file:
+opts="filenamemangle=s/(?:.*)?v?(\d[\d\.]*)\.tar\.gz/pbcore-$1.tar.gz/" \
+ https://github.com/PacificBiosciences/pbcore/tags
(?:.*/)?v?(\d[\d\.]*)\.tar\.gz
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