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

[Andreas Tille]

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 at 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 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.

Kind regards

       Andreas.

-- 
http://fam-tille.de