Re: Fwd: [iva] - Python 3 code depends on pysam
Hi all, I am thinking to go about this in one of two ways: 1 - State python3-pip as a dependency and use pip3 to install pysam the python3 lib folder; 2 - Package python3-pysam. I really don't want to have to package another piece of software right now though. Do you see any other way to do this? Jorge On Mon, Nov 24, 2014 at 5:28 PM, Jorge Sebastião Soares j.s.soa...@gmail.com wrote: 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 ghisv...@gmail.com 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 j.s.soa...@gmail.com : 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 frozen importlib._bootstrap, line 1220, in load File frozen importlib._bootstrap, line 1200, in _load_unlocked File frozen importlib._bootstrap, line 1129, in _exec File frozen importlib._bootstrap, line 1471, in exec_module File frozen importlib._bootstrap, line 321, in _call_with_frames_removed File /tmp/buildd/iva-0.10.0/iva/__init__.py, line 20, in module from iva import * File /tmp/buildd/iva-0.10.0/iva/assembly.py, line 2, in module 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
[Jorge Sebastião Soares, 2014-11-25] Hi all, I am thinking to go about this in one of two ways: 1 - State python3-pip as a dependency and use pip3 to install pysam the python3 lib folder; 2 - Package python3-pysam. I really don't want to have to package another piece of software right now though. Do you see any other way to do this? you can add python3-pysam binary package yourself or ask someone else to add it (wishlist bug against src:python-pysam in both cases if you're not in Debian Med Packaging Team). There's no other way. You cannot use pip, you cannot disable tests (if you need this library runtime anyway) and you cannot bundle pysam in python3-iva package -- 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/20141125160051.gy4...@sts0.p1otr.com
Re: Fwd: [iva] - Python 3 code depends on pysam
Hi Piotr On Tue, Nov 25, 2014 at 4:00 PM, Piotr Ożarowski pi...@debian.org wrote: [Jorge Sebastião Soares, 2014-11-25] Hi all, I am thinking to go about this in one of two ways: 1 - State python3-pip as a dependency and use pip3 to install pysam the python3 lib folder; 2 - Package python3-pysam. I really don't want to have to package another piece of software right now though. Do you see any other way to do this? you can add python3-pysam binary package yourself or ask someone else to add it (wishlist bug against src:python-pysam in both cases if you're not in Debian Med Packaging Team). There's no other way. You cannot use pip, you cannot disable tests (if you need this library runtime anyway) That's what I thought. And yes, disabeling the tests was really just a proof of concept. and you cannot bundle pysam in python3-iva package Fine. I've had a chat with my team and there is room for me to package the python3-pysam. Regards, Jorge
Fwd: [iva] - Python 3 code depends on pysam
Forgot to CC debian python: -- Forwarded message -- From: Jorge Sebastião Soares j.s.soa...@gmail.com Date: Mon, Nov 24, 2014 at 11:31 AM Subject: Re: [iva] - Python 3 code depends on pysam To: Debian Med Project List debian-...@lists.debian.org Hi Bary, all On Fri, Nov 21, 2014 at 7:29 PM, Barry Warsaw ba...@python.org 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 pi...@debian.org 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 pi...@debian.org 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 frozen importlib._bootstrap, line 1220, in load File frozen importlib._bootstrap, line 1200, in _load_unlocked File frozen importlib._bootstrap, line 1129, in _exec File frozen importlib._bootstrap, line 1471, in exec_module File frozen importlib._bootstrap, line 321, in _call_with_frames_removed File /tmp/buildd/iva-0.10.0/iva/__init__.py, line 20, in module from iva import * File /tmp/buildd/iva-0.10.0/iva/assembly.py, line 2, in module 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 ghisv...@gmail.com 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 j.s.soa...@gmail.com: 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 frozen importlib._bootstrap, line 1220, in load File frozen importlib._bootstrap, line 1200, in _load_unlocked File frozen importlib._bootstrap, line 1129, in _exec File frozen importlib._bootstrap, line 1471, in exec_module File frozen importlib._bootstrap, line 321, in _call_with_frames_removed File /tmp/buildd/iva-0.10.0/iva/__init__.py, line 20, in module from iva import * File /tmp/buildd/iva-0.10.0/iva/assembly.py, line 2, in module 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 j.s.soa...@gmail.com: 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 frozen importlib._bootstrap, line 1220, in load File frozen importlib._bootstrap, line 1200, in _load_unlocked File frozen importlib._bootstrap, line 1129, in _exec File frozen importlib._bootstrap, line 1471, in exec_module File frozen importlib._bootstrap, line 321, in _call_with_frames_removed File /tmp/buildd/iva-0.10.0/iva/__init__.py, line 20, in module from iva import * File /tmp/buildd/iva-0.10.0/iva/assembly.py, line 2, in module 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 ghisv...@gmail.com 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 j.s.soa...@gmail.com: 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 frozen importlib._bootstrap, line 1220, in load File frozen importlib._bootstrap, line 1200, in _load_unlocked File frozen importlib._bootstrap, line 1129, in _exec File frozen importlib._bootstrap, line 1471, in exec_module File frozen importlib._bootstrap, line 321, in _call_with_frames_removed File /tmp/buildd/iva-0.10.0/iva/__init__.py, line 20, in module from iva import * File /tmp/buildd/iva-0.10.0/iva/assembly.py, line 2, in module 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
