Fwd: [iva] - Python 3 code depends on pysam
Forgot to CC debian python: -- Forwarded message -- From: Jorge Sebastião Soares Date: Mon, Nov 24, 2014 at 11:31 AM Subject: Re: [iva] - Python 3 code depends on pysam To: Debian Med Project List Hi Bary, all On Fri, Nov 21, 2014 at 7:29 PM, Barry Warsaw wrote: > On Nov 21, 2014, at 05:30 PM, Jorge Sebastião Soares wrote: > > >Does anyone know if python3-pysam will be available soon? > >Or if there are any plans to have it as a Debian package at all? > > I took a *very* quick look, but unfortunately don't have time to dig in > deeper. It seems that pysam is Python 3 compatible upstream, and the > Debian > packaging already uses pybuild. It might be as easy as adding --with > python3 > and then adding the appropriate additional binary packaging goodness. > > So, my rules file already has the '--with python3' statement. You can see this in [1] I think the problem is that when calling pysam, it looks inside '/usr/lib/python3/' and pysam is not deployed there. I'll have a look to see what I can find online. Any other suggestions are very welcome. Regards, Jorge [1] - http://anonscm.debian.org/cgit/debian-med/iva.git/tree/debian/rules
Re: Fwd: [iva] - Python 3 code depends on pysam
[Jorge Sebastião Soares, 2014-11-24] > [1] - http://anonscm.debian.org/cgit/debian-med/iva.git/tree/debian/rules just a quick look: * invoking dh_python3 before dh_auto_build doesn't make sense, remove this line * you'd not need "rm -rf build .pybuild" line if you re-enable dh_auto_clean -- Piotr Ożarowski Debian GNU/Linux Developer www.ozarowski.pl www.griffith.cc www.debian.org GPG Fingerprint: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645 -- To UNSUBSCRIBE, email to debian-python-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20141124115730.gr4...@sts0.p1otr.com
Re: Fwd: [iva] - Python 3 code depends on pysam
Hi Piotr, Thanks for having a look. On Mon, Nov 24, 2014 at 11:57 AM, Piotr Ożarowski wrote: > [Jorge Sebastião Soares, 2014-11-24] > > [1] - > http://anonscm.debian.org/cgit/debian-med/iva.git/tree/debian/rules > > just a quick look: > * invoking dh_python3 before dh_auto_build doesn't make sense, remove this > line > So I just let dh_auto_build cal dh_python3 automatically? > * you'd not need "rm -rf build .pybuild" line if you re-enable > dh_auto_clean > So I only override auto_clean to get rid of the man page directory? Best, Jorge
Re: Fwd: [iva] - Python 3 code depends on pysam
[Jorge Sebastião Soares, 2014-11-24] > > http://anonscm.debian.org/cgit/debian-med/iva.git/tree/debian/rules > > > > just a quick look: > > * invoking dh_python3 before dh_auto_build doesn't make sense, remove this > > line > > > > So I just let dh_auto_build cal dh_python3 automatically? dh_auto_build doesn't call it, --with python3 enables it at the right stage (after dh_auto_install) > > * you'd not need "rm -rf build .pybuild" line if you re-enable > > dh_auto_clean > > > > So I only override auto_clean to get rid of the man page directory? yes, if you don't want to disable dh_foo, use something like: override_dh_foo: whatever you want to call before dh_foo dh_foo whatever you want to call after dh_foo -- Piotr Ożarowski Debian GNU/Linux Developer www.ozarowski.pl www.griffith.cc www.debian.org GPG Fingerprint: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645 -- To UNSUBSCRIBE, email to debian-python-requ...@lists.debian.org with a subject of "unsubscribe". Trouble? Contact listmas...@lists.debian.org Archive: https://lists.debian.org/20141124122602.gs4...@sts0.p1otr.com
Re: Fwd: [iva] - Python 3 code depends on pysam
Piotr, On Mon, Nov 24, 2014 at 12:26 PM, Piotr Ożarowski wrote: > [Jorge Sebastião Soares, 2014-11-24] > > > http://anonscm.debian.org/cgit/debian-med/iva.git/tree/debian/rules > > > > > > just a quick look: > > > * invoking dh_python3 before dh_auto_build doesn't make sense, remove > this > > > line > > > > > > > So I just let dh_auto_build cal dh_python3 automatically? > > dh_auto_build doesn't call it, --with python3 enables it at the right > stage (after dh_auto_install) > I see. Thanks for the tip. > > > > * you'd not need "rm -rf build .pybuild" line if you re-enable > > > dh_auto_clean > > > > > > > So I only override auto_clean to get rid of the man page directory? > > yes, if you don't want to disable dh_foo, use something like: > > override_dh_foo: > whatever you want to call before dh_foo > dh_foo > whatever you want to call after dh_foo > Cool. I've implemented both things. Pushed it. > -- > Piotr Ożarowski Debian GNU/Linux Developer > www.ozarowski.pl www.griffith.cc www.debian.org > GPG Fingerprint: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645 > > > -- > To UNSUBSCRIBE, email to debian-python-requ...@lists.debian.org > with a subject of "unsubscribe". Trouble? Contact > listmas...@lists.debian.org > Archive: https://lists.debian.org/20141124122602.gs4...@sts0.p1otr.com > >
Re: Fwd: [iva] - Python 3 code depends on pysam
Hi guys, So essentially the package build halts when it tries to run the test suite: This is the error I'm getting when the pysam module is being imported: root@debian:~/iva-0.10.0# python3.4 setup.py test running test running egg_info writing top-level names to iva.egg-info/top_level.txt writing iva.egg-info/PKG-INFO writing dependency_links to iva.egg-info/dependency_links.txt reading manifest file 'iva.egg-info/SOURCES.txt' writing manifest file 'iva.egg-info/SOURCES.txt' running build_ext Failure: ImportError (No module named 'pysam') ... ERROR == ERROR: Failure: ImportError (No module named 'pysam') -- Traceback (most recent call last): File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/usr/lib/python3/dist-packages/nose/loader.py", line 414, in loadTestsFromName addr.filename, addr.module) File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/usr/lib/python3.4/imp.py", line 245, in load_module return load_package(name, filename) File "/usr/lib/python3.4/imp.py", line 217, in load_package return methods.load() File "", line 1220, in load File "", line 1200, in _load_unlocked File "", line 1129, in _exec File "", line 1471, in exec_module File "", line 321, in _call_with_frames_removed File "/tmp/buildd/iva-0.10.0/iva/__init__.py", line 20, in from iva import * File "/tmp/buildd/iva-0.10.0/iva/assembly.py", line 2, in import pysam ImportError: No module named 'pysam' -- Ran 1 test in 0.016s FAILED (errors=1) If pysam is python 3 compliant, I'm tempted to create the needed symlinks in python3.4 pointing to pysam in python2.7, eg. ln -s /usr/lib/python2.7/dist-packages/pysam /usr/lib/python3.4/dist-packages/pysam I'm sure that this is not the proper way of doing things, so is there any other way I can get pysam to be installed under python3.4 rather than python2.7? Regards, Jorge
Re: Fwd: [iva] - Python 3 code depends on pysam
Hi Ghis On Mon, Nov 24, 2014 at 4:58 PM, Ghislain Vaillant wrote: > At worst, can't you just disable the test suite for the Python 3 builds ? > Pybuild should allow to do that easily. > Trying that now. But I would still need to link pysam to the iva package at some point, no? Regards, Jorge > 2014-11-24 16:36 GMT+00:00 Jorge Sebastião Soares : > >> Hi guys, >> >> So essentially the package build halts when it tries to run the test >> suite: >> >> This is the error I'm getting when the pysam module is being imported: >> >> root@debian:~/iva-0.10.0# python3.4 setup.py test >> running test >> running egg_info >> writing top-level names to iva.egg-info/top_level.txt >> writing iva.egg-info/PKG-INFO >> writing dependency_links to iva.egg-info/dependency_links.txt >> reading manifest file 'iva.egg-info/SOURCES.txt' >> writing manifest file 'iva.egg-info/SOURCES.txt' >> running build_ext >> Failure: ImportError (No module named 'pysam') ... ERROR >> >> == >> ERROR: Failure: ImportError (No module named 'pysam') >> -- >> Traceback (most recent call last): >> File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in >> runTest >> raise self.exc_val.with_traceback(self.tb) >> File "/usr/lib/python3/dist-packages/nose/loader.py", line 414, in >> loadTestsFromName >> addr.filename, addr.module) >> File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in >> importFromPath >> return self.importFromDir(dir_path, fqname) >> File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in >> importFromDir >> mod = load_module(part_fqname, fh, filename, desc) >> File "/usr/lib/python3.4/imp.py", line 245, in load_module >> return load_package(name, filename) >> File "/usr/lib/python3.4/imp.py", line 217, in load_package >> return methods.load() >> File "", line 1220, in load >> File "", line 1200, in _load_unlocked >> File "", line 1129, in _exec >> File "", line 1471, in exec_module >> File "", line 321, in >> _call_with_frames_removed >> File "/tmp/buildd/iva-0.10.0/iva/__init__.py", line 20, in >> from iva import * >> File "/tmp/buildd/iva-0.10.0/iva/assembly.py", line 2, in >> import pysam >> ImportError: No module named 'pysam' >> >> -- >> Ran 1 test in 0.016s >> >> FAILED (errors=1) >> >> >> If pysam is python 3 compliant, I'm tempted to create the needed symlinks >> in python3.4 pointing to pysam in python2.7, eg. >> >> ln -s /usr/lib/python2.7/dist-packages/pysam >> /usr/lib/python3.4/dist-packages/pysam >> >> I'm sure that this is not the proper way of doing things, so is there any >> other way I can get pysam to be installed under python3.4 rather than >> python2.7? >> >> Regards, >> >> Jorge >> > >
Re: Fwd: [iva] - Python 3 code depends on pysam
At worst, can't you just disable the test suite for the Python 3 builds ? Pybuild should allow to do that easily. Ghis 2014-11-24 16:36 GMT+00:00 Jorge Sebastião Soares : > Hi guys, > > So essentially the package build halts when it tries to run the test suite: > > This is the error I'm getting when the pysam module is being imported: > > root@debian:~/iva-0.10.0# python3.4 setup.py test > running test > running egg_info > writing top-level names to iva.egg-info/top_level.txt > writing iva.egg-info/PKG-INFO > writing dependency_links to iva.egg-info/dependency_links.txt > reading manifest file 'iva.egg-info/SOURCES.txt' > writing manifest file 'iva.egg-info/SOURCES.txt' > running build_ext > Failure: ImportError (No module named 'pysam') ... ERROR > > == > ERROR: Failure: ImportError (No module named 'pysam') > -- > Traceback (most recent call last): > File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in > runTest > raise self.exc_val.with_traceback(self.tb) > File "/usr/lib/python3/dist-packages/nose/loader.py", line 414, in > loadTestsFromName > addr.filename, addr.module) > File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in > importFromPath > return self.importFromDir(dir_path, fqname) > File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in > importFromDir > mod = load_module(part_fqname, fh, filename, desc) > File "/usr/lib/python3.4/imp.py", line 245, in load_module > return load_package(name, filename) > File "/usr/lib/python3.4/imp.py", line 217, in load_package > return methods.load() > File "", line 1220, in load > File "", line 1200, in _load_unlocked > File "", line 1129, in _exec > File "", line 1471, in exec_module > File "", line 321, in > _call_with_frames_removed > File "/tmp/buildd/iva-0.10.0/iva/__init__.py", line 20, in > from iva import * > File "/tmp/buildd/iva-0.10.0/iva/assembly.py", line 2, in > import pysam > ImportError: No module named 'pysam' > > -- > Ran 1 test in 0.016s > > FAILED (errors=1) > > > If pysam is python 3 compliant, I'm tempted to create the needed symlinks > in python3.4 pointing to pysam in python2.7, eg. > > ln -s /usr/lib/python2.7/dist-packages/pysam > /usr/lib/python3.4/dist-packages/pysam > > I'm sure that this is not the proper way of doing things, so is there any > other way I can get pysam to be installed under python3.4 rather than > python2.7? > > Regards, > > Jorge >
Re: Fwd: [iva] - Python 3 code depends on pysam
Hi Ghis, Disabling the tests worked. The package builds at least, but not lintian clean . I'll cary on tomorrow. Regards, Jorge On Mon, Nov 24, 2014 at 5:02 PM, Jorge Sebastião Soares < j.s.soa...@gmail.com> wrote: > Hi Ghis > > On Mon, Nov 24, 2014 at 4:58 PM, Ghislain Vaillant > wrote: > >> At worst, can't you just disable the test suite for the Python 3 builds ? >> Pybuild should allow to do that easily. >> > > Trying that now. > > But I would still need to link pysam to the iva package at some point, no? > > Regards, > > Jorge > > > >> 2014-11-24 16:36 GMT+00:00 Jorge Sebastião Soares : >> >>> Hi guys, >>> >>> So essentially the package build halts when it tries to run the test >>> suite: >>> >>> This is the error I'm getting when the pysam module is being imported: >>> >>> root@debian:~/iva-0.10.0# python3.4 setup.py test >>> running test >>> running egg_info >>> writing top-level names to iva.egg-info/top_level.txt >>> writing iva.egg-info/PKG-INFO >>> writing dependency_links to iva.egg-info/dependency_links.txt >>> reading manifest file 'iva.egg-info/SOURCES.txt' >>> writing manifest file 'iva.egg-info/SOURCES.txt' >>> running build_ext >>> Failure: ImportError (No module named 'pysam') ... ERROR >>> >>> == >>> ERROR: Failure: ImportError (No module named 'pysam') >>> -- >>> Traceback (most recent call last): >>> File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in >>> runTest >>> raise self.exc_val.with_traceback(self.tb) >>> File "/usr/lib/python3/dist-packages/nose/loader.py", line 414, in >>> loadTestsFromName >>> addr.filename, addr.module) >>> File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in >>> importFromPath >>> return self.importFromDir(dir_path, fqname) >>> File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in >>> importFromDir >>> mod = load_module(part_fqname, fh, filename, desc) >>> File "/usr/lib/python3.4/imp.py", line 245, in load_module >>> return load_package(name, filename) >>> File "/usr/lib/python3.4/imp.py", line 217, in load_package >>> return methods.load() >>> File "", line 1220, in load >>> File "", line 1200, in _load_unlocked >>> File "", line 1129, in _exec >>> File "", line 1471, in exec_module >>> File "", line 321, in >>> _call_with_frames_removed >>> File "/tmp/buildd/iva-0.10.0/iva/__init__.py", line 20, in >>> from iva import * >>> File "/tmp/buildd/iva-0.10.0/iva/assembly.py", line 2, in >>> import pysam >>> ImportError: No module named 'pysam' >>> >>> -- >>> Ran 1 test in 0.016s >>> >>> FAILED (errors=1) >>> >>> >>> If pysam is python 3 compliant, I'm tempted to create the needed >>> symlinks in python3.4 pointing to pysam in python2.7, eg. >>> >>> ln -s /usr/lib/python2.7/dist-packages/pysam >>> /usr/lib/python3.4/dist-packages/pysam >>> >>> I'm sure that this is not the proper way of doing things, so is there >>> any other way I can get pysam to be installed under python3.4 rather than >>> python2.7? >>> >>> Regards, >>> >>> Jorge >>> >> >> >
