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 <[email protected]> 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
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