[med-svn] [python-pbh5tools] 02/02: Initial packaging
Afif Elghraoui
afif-guest at moszumanska.debian.org
Sun Jun 7 10:16:33 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository python-pbh5tools.
commit 3c639866fec2da9947e7dd2c5ceee8954b76001c
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sat Jun 6 23:25:31 2015 -0700
Initial packaging
---
debian/TODO | 12 ++++++++++++
debian/compat | 1 +
debian/control | 26 ++++++++++++++++++++++++++
debian/copyright | 36 ++++++++++++++++++++++++++++++++++++
debian/patches/remove-cram.patch | 11 +++++++++++
debian/patches/series | 2 ++
debian/patches/setup.patch | 11 +++++++++++
debian/rules | 16 ++++++++++++++++
debian/source/format | 1 +
9 files changed, 116 insertions(+)
diff --git a/debian/TODO b/debian/TODO
new file mode 100644
index 0000000..889560d
--- /dev/null
+++ b/debian/TODO
@@ -0,0 +1,12 @@
+* Package python-cram.
+ cram is required to run some of the tests.
+ cram's source is at <https://bitbucket.org/brodie/cram>.
+ It's also listed in the python package index.
+* Add python-cram as build-dependency and remove override_dh_auto_test.
+* Package python-pbcore.
+ It's a run-time dependency
+* Deal with architecture-dependent portions of the python module.
+ There's a C shared library that is compiled as part of the setup.py
+ build.
+* Create man-pages for the two python executables in this package.
+* Handle /usr/bin/env python vs /usr/bin/python issue.
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..7c3edae
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,26 @@
+Source: python-pbh5tools
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Afif Elghraoui <afif at ghraoui.name>
+Build-Depends: debhelper (>= 9),
+ python-setuptools,
+ python-sphinx,
+ python-nose,
+ pandoc
+Standards-Version: 3.9.6
+Homepage: https://github.com/PacificBiosciences/pbh5tools
+Vcs-Git: git://anonscm.debian.org/debian-med/python-pbh5tools.git
+Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/python-pbh5tools.git
+
+Package: python-pbh5tools
+Architecture: all
+Depends: ${misc:Depends},
+ ${python:Depends}
+Description: tools for manipulating HDF5 files produced by Pacific Biosciences
+ This package provides functionality for manipulating and extracting data
+ from cmp.h5 and bas.h5 files produced by the Pacific Biosciences sequencers.
+ cmp.h5 files contain alignment information while bas.h5 files contain
+ base-call information.
+ .
+ This package is part of the SMRTAnalysis suite.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 0000000..56ea30d
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,36 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: pbh5tools
+Source: https://github.com/PacificBiosciences/pbh5tools
+
+Files: *
+Copyright: 2011-2013 Pacific Biosciences of California, Inc.
+License: BSD-3-Clause
+
+Files: debian/*
+Copyright: 2015 Afif Elghraoui <afif at 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-cram.patch b/debian/patches/remove-cram.patch
new file mode 100644
index 0000000..1bc2542
--- /dev/null
+++ b/debian/patches/remove-cram.patch
@@ -0,0 +1,11 @@
+--- python-pbh5tools.orig/Makefile
++++ python-pbh5tools/Makefile
+@@ -23,7 +23,7 @@
+ sphinx-apidoc -T -f -o doc src/ && cd doc && make html
+
+ examples:
+- cram doc/examples.t
++# cram doc/examples.t
+ sed 's/^ / /' doc/examples.t > doc/examples.md
+
+ example-rendered: examples
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..38524b7
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,2 @@
+setup.patch
+remove-cram.patch
diff --git a/debian/patches/setup.patch b/debian/patches/setup.patch
new file mode 100644
index 0000000..b678e19
--- /dev/null
+++ b/debian/patches/setup.patch
@@ -0,0 +1,11 @@
+--- python-pbh5tools.orig/Makefile
++++ python-pbh5tools/Makefile
+@@ -11,7 +11,7 @@
+ python setup.py bdist --formats=egg
+
+ install:
+- python setup.py install
++ python setup.py install --root=$(DESTDIR) --install-layout=deb
+
+ develop:
+ python setup.py develop
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 0000000..0422a71
--- /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
+
+# cram is not in Debian, but required to run the tests.
+# This override skips building the tests to allow full package build in
+# the meantime.
+# cram's source is at https://bitbucket.org/brodie/cram
+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)
--
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