[Debian-med-packaging] Bug#937177: obitools: Python2 removal in sid/bullseye

Sat Mar 7 06:50:37 GMT 2020

Le sam. 7 mars 2020 à 06:12, Sergio Durigan Junior <sergiodj at 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 at 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 at energija:/# cd build/obitools-1.2.13+dfsg/
> > root at 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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