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Groups > linux.debian.maint.python > #12204 > unrolled thread
| Started by | Andreas Tille <andreas@fam-tille.de> |
|---|---|
| First post | 2020-01-12 18:30 +0100 |
| Last post | 2020-03-07 08:00 +0100 |
| Articles | 4 — 4 participants |
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Bug#937177: obitools: Python2 removal in sid/bullseye Andreas Tille <andreas@fam-tille.de> - 2020-01-12 18:30 +0100
Bug#937177: obitools: Python2 removal in sid/bullseye Sandro Tosi <morph@debian.org> - 2020-03-06 03:30 +0100
Bug#937177: obitools: Python2 removal in sid/bullseye Sergio Durigan Junior <sergiodj@debian.org> - 2020-03-07 07:10 +0100
Bug#937177: obitools: Python2 removal in sid/bullseye olivier sallou <osallou@debian.org> - 2020-03-07 08:00 +0100
| From | Andreas Tille <andreas@fam-tille.de> |
|---|---|
| Date | 2020-01-12 18:30 +0100 |
| Subject | Bug#937177: obitools: Python2 removal in sid/bullseye |
| Message-ID | <znPdL-5RR-1@gated-at.bofh.it> |
Control: tags -1 help
Hi Scott,
On Sun, Jan 12, 2020 at 07:27:59AM -0500, Scott Kitterman wrote:
> On Fri, 30 Aug 2019 07:28:59 +0000 Matthias Klose <doko@debian.org> wrote:
> ...
>
> I don't see any evidence of upstream progress on converting to python3.
This seems to be correct.
> This
> package is blocking several others. Would it be best to remove it? It can
> always be re-introduced if a python3 port appears.
Since some time I've pushed a 2to3 based port to Git. I've now fixed
some issues of this and I wonder whether we might give it a try to do
the port inside Debian. For the moment I'm running into the following
issue:
dh_auto_test -O--buildsystem=pybuild
I: pybuild base:217: cd /build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build; python3.7 -m unittest discover -v
obitools (unittest.loader._FailedTest) ... ERROR
======================================================================
ERROR: obitools (unittest.loader._FailedTest)
----------------------------------------------------------------------
ImportError: Failed to import test module: obitools
Traceback (most recent call last):
File "/usr/lib/python3.7/unittest/loader.py", line 470, in _find_test_path
package = self._get_module_from_name(name)
File "/usr/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name
__import__(name)
File "/build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build/obitools/__init__.py", line 23, in <module>
from _obitools import BioSequence,NucSequence,AASequence, \
ModuleNotFoundError: No module named '_obitools'
----------------------------------------------------------------------
Ran 1 test in 0.000s
FAILED (errors=1)
E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1: cd /build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build; python3.7 -m unittest discover -v
dh_auto_test: pybuild --test -i python{version} -p 3.7 returned exit code 13
make: *** [debian/rules:15: build] Error 255
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
I: copying local configuration
E: Failed autobuilding of package
I: user script /var/cache/pbuilder/build/cow.1543005/tmp/hooks/C99_failed_build starting
Installing convenience apps: mc less bash-completion
root@energija:/# cd build/obitools-1.2.13+dfsg/
root@energija:/build/obitools-1.2.13+dfsg# find . -name "*.so"
./.pybuild/cpython3_3.7_obitools/build/obitools/options/_options.cpython-37m-x86_64-linux-gnu.so =
./.pybuild/cpython3_3.7_obitools/build/obitools/options/_bioseqfilter.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/profile/_profile.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/utils/_utils.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/_obitools.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/tools/_solexapairend.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/fasta/_fasta.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_upperbond.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_rassemble.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_freeendgapfm.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_nwsdnabyprot.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_assemble.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_freeendgap.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_qsrassemble.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_gprofilenws.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_dynamic.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_nws.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_lcs.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_qsassemble.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_profilenws.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/align/_codonnws.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/format/_format.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/format/genericparser/_genericparser.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/fastq/_fastq.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/word/_binary.cpython-37m-x86_64-linux-gnu.so
./.pybuild/cpython3_3.7_obitools/build/obitools/word/_readindex.cpython-37m-x86_64-linux-gnu.so
The problem is that the former build system using python2.7 and cython had created
obitools: /usr/lib/python2.7/dist-packages/obitools/_obitools.x86_64-linux-gnu.so
But now with python3.7 and cython3 the result are single dynamic libs.
I'd love to give at least the test suite a try so if I get some hint how
to create that single _obitools.x86_64-linux-gnu.so instead of those
many *.so libs I could possibly run the test and see how it performs.
Kind regards
Andreas.
--
http://fam-tille.de
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| From | Sandro Tosi <morph@debian.org> |
|---|---|
| Date | 2020-03-06 03:30 +0100 |
| Message-ID | <zHaUp-1KO-1@gated-at.bofh.it> |
| In reply to | #12204 |
> > This > > package is blocking several others. Would it be best to remove it? It can > > always be re-introduced if a python3 port appears. > > Since some time I've pushed a 2to3 based port to Git. I've now fixed > some issues of this and I wonder whether we might give it a try to do > the port inside Debian. It looks like Olivier committed a py3k port on debmed almost a month ago: Olivier, do you have any plan to complete (if necessary) and upload this package soon? it would help with the py2removal effort. Regards, -- Sandro "morph" Tosi My website: http://sandrotosi.me/ Me at Debian: http://wiki.debian.org/SandroTosi Twitter: https://twitter.com/sandrotosi
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| From | Sergio Durigan Junior <sergiodj@debian.org> |
|---|---|
| Date | 2020-03-07 07:10 +0100 |
| Message-ID | <zHA2t-yU-7@gated-at.bofh.it> |
| In reply to | #12204 |
[Multipart message — attachments visible in raw view] — view raw
On Sunday, January 12 2020, Andreas Tille wrote:
> On Sun, Jan 12, 2020 at 07:27:59AM -0500, Scott Kitterman wrote:
>> On Fri, 30 Aug 2019 07:28:59 +0000 Matthias Klose <doko@debian.org> wrote:
>> This
>> package is blocking several others. Would it be best to remove it? It can
>> always be re-introduced if a python3 port appears.
>
> Since some time I've pushed a 2to3 based port to Git. I've now fixed
> some issues of this and I wonder whether we might give it a try to do
> the port inside Debian. For the moment I'm running into the following
> issue:
>
> dh_auto_test -O--buildsystem=pybuild
> I: pybuild base:217: cd /build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build; python3.7 -m unittest discover -v
> obitools (unittest.loader._FailedTest) ... ERROR
>
> ======================================================================
> ERROR: obitools (unittest.loader._FailedTest)
> ----------------------------------------------------------------------
> ImportError: Failed to import test module: obitools
> Traceback (most recent call last):
> File "/usr/lib/python3.7/unittest/loader.py", line 470, in _find_test_path
> package = self._get_module_from_name(name)
> File "/usr/lib/python3.7/unittest/loader.py", line 377, in _get_module_from_name
> __import__(name)
> File "/build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build/obitools/__init__.py", line 23, in <module>
> from _obitools import BioSequence,NucSequence,AASequence, \
> ModuleNotFoundError: No module named '_obitools'
>
>
> ----------------------------------------------------------------------
> Ran 1 test in 0.000s
Hey Andreas,
I cannot reproduce this bug when building inside a clean schroot
(unstable). I don't know if the reason is because I don't have
python3.7 installed in the schroot anymore (it was removed recently, and
python3.8 is the default), or because there's something else different.
> FAILED (errors=1)
> E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1: cd /build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build; python3.7 -m unittest discover -v
> dh_auto_test: pybuild --test -i python{version} -p 3.7 returned exit code 13
> make: *** [debian/rules:15: build] Error 255
> dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
> I: copying local configuration
> E: Failed autobuilding of package
> I: user script /var/cache/pbuilder/build/cow.1543005/tmp/hooks/C99_failed_build starting
> Installing convenience apps: mc less bash-completion
> root@energija:/# cd build/obitools-1.2.13+dfsg/
> root@energija:/build/obitools-1.2.13+dfsg# find . -name "*.so"
> ./.pybuild/cpython3_3.7_obitools/build/obitools/options/_options.cpython-37m-x86_64-linux-gnu.so =
> ./.pybuild/cpython3_3.7_obitools/build/obitools/options/_bioseqfilter.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/profile/_profile.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/utils/_utils.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/_obitools.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/tools/_solexapairend.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/fasta/_fasta.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_upperbond.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_rassemble.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_freeendgapfm.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_nwsdnabyprot.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_assemble.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_freeendgap.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_qsrassemble.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_gprofilenws.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_dynamic.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_nws.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_lcs.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_qsassemble.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_profilenws.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_codonnws.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/format/_format.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/format/genericparser/_genericparser.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/fastq/_fastq.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/word/_binary.cpython-37m-x86_64-linux-gnu.so
> ./.pybuild/cpython3_3.7_obitools/build/obitools/word/_readindex.cpython-37m-x86_64-linux-gnu.so
>
>
> The problem is that the former build system using python2.7 and cython had created
>
> obitools: /usr/lib/python2.7/dist-packages/obitools/_obitools.x86_64-linux-gnu.so
>
>
> But now with python3.7 and cython3 the result are single dynamic libs.
> I'd love to give at least the test suite a try so if I get some hint how
> to create that single _obitools.x86_64-linux-gnu.so instead of those
> many *.so libs I could possibly run the test and see how it performs.
FWIW, I have the same list of .so files.
Cheers,
--
Sergio
GPG key ID: 237A 54B1 0287 28BF 00EF 31F4 D0EB 7628 65FC 5E36
Please send encrypted e-mail if possible
http://sergiodj.net/
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| From | olivier sallou <osallou@debian.org> |
|---|---|
| Date | 2020-03-07 08:00 +0100 |
| Message-ID | <zHBBf-1pM-1@gated-at.bofh.it> |
| In reply to | #12352 |
[Multipart message — attachments visible in raw view] — view raw
Le sam. 7 mars 2020 à 06:12, Sergio Durigan Junior <sergiodj@debian.org> a
écrit :
> On Sunday, January 12 2020, Andreas Tille wrote:
>
> > On Sun, Jan 12, 2020 at 07:27:59AM -0500, Scott Kitterman wrote:
> >> On Fri, 30 Aug 2019 07:28:59 +0000 Matthias Klose <doko@debian.org>
> wrote:
> >> This
> >> package is blocking several others. Would it be best to remove it? It
> can
> >> always be re-introduced if a python3 port appears.
> >
> > Since some time I've pushed a 2to3 based port to Git. I've now fixed
> > some issues of this and I wonder whether we might give it a try to do
> > the port inside Debian. For the moment I'm running into the following
> > issue:
> >
> > dh_auto_test -O--buildsystem=pybuild
> > I: pybuild base:217: cd
> /build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build; python3.7
> -m unittest discover -v
> > obitools (unittest.loader._FailedTest) ... ERROR
> >
> > ======================================================================
> > ERROR: obitools (unittest.loader._FailedTest)
> > ----------------------------------------------------------------------
> > ImportError: Failed to import test module: obitools
> > Traceback (most recent call last):
> > File "/usr/lib/python3.7/unittest/loader.py", line 470, in
> _find_test_path
> > package = self._get_module_from_name(name)
> > File "/usr/lib/python3.7/unittest/loader.py", line 377, in
> _get_module_from_name
> > __import__(name)
> > File
> "/build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build/obitools/__init__.py",
> line 23, in <module>
> > from _obitools import BioSequence,NucSequence,AASequence, \
> > ModuleNotFoundError: No module named '_obitools'
> >
> >
> > ----------------------------------------------------------------------
> > Ran 1 test in 0.000s
>
> Hey Andreas,
>
> I cannot reproduce this bug when building inside a clean schroot
> (unstable). I don't know if the reason is because I don't have
> python3.7 installed in the schroot anymore (it was removed recently, and
> python3.8 is the default), or because there's something else different.
>
I pushed in february during our sprint some updates in git fixing the
issue. However it implied lots of modification that may impact software as
it implied to do some choices on types (bytes vs str for example with c
binding), without really knowing the impact....
We may push the package but other packages using might be broken....
On other side, package will be removed.
So either we push an update, knowing that it may not be fully fonctional,
or let it go.....
Olivier
> > FAILED (errors=1)
> > E: pybuild pybuild:341: test: plugin distutils failed with: exit code=1:
> cd /build/obitools-1.2.13+dfsg/.pybuild/cpython3_3.7_obitools/build;
> python3.7 -m unittest discover -v
> > dh_auto_test: pybuild --test -i python{version} -p 3.7 returned exit
> code 13
> > make: *** [debian/rules:15: build] Error 255
> > dpkg-buildpackage: error: debian/rules build subprocess returned exit
> status 2
> > I: copying local configuration
> > E: Failed autobuilding of package
> > I: user script
> /var/cache/pbuilder/build/cow.1543005/tmp/hooks/C99_failed_build starting
> > Installing convenience apps: mc less bash-completion
> > root@energija:/# cd build/obitools-1.2.13+dfsg/
> > root@energija:/build/obitools-1.2.13+dfsg# find . -name "*.so"
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/options/_
> options.cpython-37m-x86_64-linux-gnu.so
> =
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/options/_
> bioseqfilter.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/profile/_
> profile.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/utils/_
> utils.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/_
> obitools.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/tools/_
> solexapairend.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/fasta/_
> fasta.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> upperbond.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> rassemble.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> freeendgapfm.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> nwsdnabyprot.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> assemble.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> freeendgap.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> qsrassemble.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> gprofilenws.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> dynamic.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> nws.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> lcs.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> qsassemble.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> profilenws.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/align/_
> codonnws.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/format/_
> format.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/format/genericparser/_
> genericparser.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/fastq/_
> fastq.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/word/_
> binary.cpython-37m-x86_64-linux-gnu.so
> > ./.pybuild/cpython3_3.7_obitools/build/obitools/word/_
> readindex.cpython-37m-x86_64-linux-gnu.so
> >
> >
> > The problem is that the former build system using python2.7 and cython
> had created
> >
> > obitools: /usr/lib/python2.7/dist-packages/obitools/_
> obitools.x86_64-linux-gnu.so
> >
> >
> > But now with python3.7 and cython3 the result are single dynamic libs.
> > I'd love to give at least the test suite a try so if I get some hint how
> > to create that single _obitools.x86_64-linux-gnu.so instead of those
> > many *.so libs I could possibly run the test and see how it performs.
>
> FWIW, I have the same list of .so files.
>
> Cheers,
>
> --
> Sergio
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> Please send encrypted e-mail if possible
> http://sergiodj.net/
>
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