[med-svn] [fast5] 03/03: New binary packages: python-fast5 and python3-fast5

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif pushed a commit to branch master
in repository fast5.

commit ac2611e6c91667a5f17e8c339fb7f48ce8cff489
Author: Afif Elghraoui <afif at debian.org>
Date:   Thu Oct 20 01:25:56 2016 -0700

    New binary packages: python-fast5 and python3-fast5
---
 debian/control             | 33 +++++++++++++++++++++++++++++++++
 debian/patches/rpath.patch | 17 +++++++++++++++++
 debian/patches/series      |  1 +
 debian/rules               | 22 ++++++++++++++++++++--
 4 files changed, 71 insertions(+), 2 deletions(-)

diff --git a/debian/control b/debian/control
index 2e4f8ad..1bbc454 100644
--- a/debian/control
+++ b/debian/control
@@ -5,6 +5,13 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
 Uploaders: Afif Elghraoui <afif at debian.org>
 Build-Depends:
 	debhelper (>= 9),
+	dh-python,
+	libhdf5-dev,
+	libboost-python-dev,
+	python-all-dev,
+	python-setuptools,
+	python3-all-dev,
+	python3-setuptools,
 Standards-Version: 3.9.8
 Homepage: https://github.com/mateidavid/fast5
 Vcs-Git: https://anonscm.debian.org/git/debian-med/fast5.git
@@ -21,3 +28,29 @@ Description: library for reading Oxford Nanopore Fast5 files -- headers
  Nanopore's FAST5 files.
  .
  This package provides the header files for development with fast5.
+
+Package: python-fast5
+Section: python
+Architecture: any
+Depends:
+	${shlibs:Depends},
+	${misc:Depends},
+	${python:Depends},
+Description: library for reading Oxford Nanopore Fast5 files -- Python 2
+ A lightweight C++11 library to read raw signal data from Oxford
+ Nanopore's FAST5 files.
+ .
+ This package provides the Python 2 library
+
+Package: python3-fast5
+Section: python
+Architecture: any
+Depends:
+	${shlibs:Depends},
+	${misc:Depends},
+	${python3:Depends},
+Description: library for reading Oxford Nanopore Fast5 files -- Python 3
+ A lightweight C++11 library to read raw signal data from Oxford
+ Nanopore's FAST5 files.
+ .
+ This package provides the Python 3 library
diff --git a/debian/patches/rpath.patch b/debian/patches/rpath.patch
new file mode 100644
index 0000000..94fe9e7
--- /dev/null
+++ b/debian/patches/rpath.patch
@@ -0,0 +1,17 @@
+Description: Don't set RPATH for compiled Python extensions
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: not-needed
+Last-Update: 2016-10-20
+--- fast5.orig/python/setup.py
++++ fast5/python/setup.py
+@@ -69,10 +69,6 @@
+             hdf5_lib_dir,
+             boost_lib_dir,
+         ],
+-        runtime_library_dirs=[
+-            hdf5_lib_dir,
+-            boost_lib_dir,
+-        ],
+         libraries=[
+             hdf5_lib,
+             boost_python_lib,
diff --git a/debian/patches/series b/debian/patches/series
index 1b20762..35f09db 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
 relative-paths.patch
+rpath.patch
diff --git a/debian/rules b/debian/rules
index 3d2f40f..856e07e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,7 +1,25 @@
 #!/usr/bin/make -f
 
 #DH_VERBOSE = 1
-#include /usr/share/dpkg/default.mk
+export LC_ALL=C.UTF-8
+include /usr/share/dpkg/default.mk
+
+export PYBUILD_NAME=fast5
+
+export HDF5_INCLUDE_DIR=/usr/include/hdf5/serial
+export HDF5_LIB_DIR=/usr/lib/$(DEB_HOST_MULTIARCH)/hdf5/serial
+export BOOST_LIB_DIR=/usr/lib/$(DEB_HOST_MULTIARCH)
 
 %:
-	dh $@ 
+	dh $@ --with python2,python3 --buildsystem=pybuild \
+	--sourcedirectory=python
+
+override_dh_auto_build:
+	mkdir -p src/fast5
+	ln -sf ../hdf5_tools.hpp src/fast5/hdf5_tools.hpp
+	dh_auto_build
+
+override_dh_auto_clean:
+	cd src && $(MAKE) clean
+	$(RM) -r src/fast5
+	dh_auto_clean

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