Re: Enabling Python bindings for jellyfish
On Tuesday, December 29, 2015 12:30:14 AM Andreas Tille wrote:
> Hi,
>
> I realised that for jellyfish[1] Python bindings can be activated. I
> tried to do so and configuring and building works fine - but I have no
> idea how to sensibly install the files into the python-jellyfish
> package. Any idea how to call swig/python/setup.py or do something else
> to install the files into the right location.
>
> Any help?
>
> Kind regards
>
> Andreas.
>
> [1] git://anonscm.debian.org/debian-med/jellyfish.git
I haven't been able to actually test this since when I try to build it, I get
this error:
jellyfish_wrap.cxx:3104:33: fatal error: jellyfish/mer_dna.hpp: No such file or
directory
I think it should ~work. Note that these bindings are for python3, not
python. I've adjusted things accordingly. The configure changes I made (so
that configure wouldn't fail) mean perl bindings don't get built either. I
didn't check if that was working before.
Scott K
>From 72a9b63d0d8bf4d64614966aed79025c7c7d0fdf Mon Sep 17 00:00:00 2001
From: Scott Kitterman <scott@kitterman.com>
Date: Tue, 29 Dec 2015 10:45:11 -0500
Subject: [PATCH] python binding fixups
---
debian/changelog | 11 ++++++++++-
debian/control | 9 +++++----
debian/rules | 9 ++++++++-
3 files changed, 23 insertions(+), 6 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 1af4381..17e56d4 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,17 @@
jellyfish (2.2.4-3) UNRELEASED; urgency=medium
+ [ Andreas Tille ]
* Enable Python and Perl bindings
- -- Andreas Tille <tille@debian.org> Mon, 28 Dec 2015 22:42:59 +0100
+ [ Scott Kitterman ]
+ * Rename python-jellyfish to python3-jellyfish
+ * Change python-dev build-dep to python3-all-dev (since this is a python3
+ extension)
+ * Add dh-python to build-depends
+ * Add building with python3
+ * Add call to setup.py in dh_autobuild override
+
+ -- Scott Kitterman <scott@kitterman.com> Tue, 29 Dec 2015 10:43:40 -0500
jellyfish (2.2.4-2) unstable; urgency=medium
diff --git a/debian/control b/debian/control
index 63e1bec..3c3d15f 100644
--- a/debian/control
+++ b/debian/control
@@ -14,7 +14,8 @@ Build-Depends: debhelper (>= 9),
procps,
valgrind,
swig,
- python-dev
+ python3-all-dev,
+ dh-python
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/jellyfish.git
Vcs-Git: git://anonscm.debian.org/debian-med/jellyfish.git
@@ -87,10 +88,10 @@ Description: count k-mers in DNA sequences (development files of jellyfish)
This package contains the development files (static library and
header files)
-Package: python-jellyfish
-Architecture: all
+Package: python3-jellyfish
+Architecture: any
Section: python
-Depends: ${python:Depends},
+Depends: ${python3:Depends},
${misc:Depends}
Description: count k-mers in DNA sequences (Python bindings of jellyfish)
JELLYFISH is a tool for fast, memory-efficient counting of k-mers in
diff --git a/debian/rules b/debian/rules
index 1d1f78a..960a128 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,14 +1,21 @@
#!/usr/bin/make -f
DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}')
+build3vers := $(shell py3versions -sv)
export DH_OPTIONS
%:
- dh $@ --with autoreconf
+ dh $@ --with autoreconf,python3
override_dh_install:
# dh_install -X*.a -X*.la -Xpkgconfig
+ dh_install -ppython3-jellyfish
+ set -e && for i in $(build3vers); do \
+ cd swig/python \
+ python$$i ./setup.py install --install-layout=deb --root ../../debian/python3-jellyfish; \
+ done
+
dh_install
d-shlibmove --commit \
--multiarch \
--
1.9.1
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