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

Sat Mar 7 05:12:19 GMT 2020

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.

> 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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