[Debian-med-packaging] Bug#868927: python-pybedtools FTBFS with more than one supported Python3 version

[Andreas Tille]

Hi Adrian,

thanks for the patch.  I applied it in Git and also updated to the latest
upstream version.  However, when trying to build I'm running into

...
I: pybuild pybuild:219: cp /build/python-pybedtools-0.7.10/debian/mpl-expected.png /build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/test/
I: pybuild base:184: cd /build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose --attr '!url'
E
======================================================================
ERROR: Failure: ModuleNotFoundError (No module named 'pysam.libchtslib')
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/nose/failure.py", line 39, in runTest
    raise self.exc_val.with_traceback(self.tb)
  File "/usr/lib/python3/dist-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/lib/python3/dist-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/lib/python3/dist-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/usr/lib/python3.6/imp.py", line 244, in load_module
    return load_package(name, filename)
  File "/usr/lib/python3.6/imp.py", line 216, in load_package
    return _load(spec)
  File "<frozen importlib._bootstrap>", line 675, in _load
  File "<frozen importlib._bootstrap>", line 655, in _load_unlocked
  File "<frozen importlib._bootstrap_external>", line 678, in exec_module
  File "<frozen importlib._bootstrap>", line 205, in _call_with_frames_removed
  File "/build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/__init__.py", line 12, in <module>
    from . import contrib
  File "/build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/contrib/__init__.py", line 3, in <module>
    from . import venn_maker
  File "/build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/contrib/venn_maker.py", line 12, in <module>
    from pybedtools import helpers
  File "/build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build/pybedtools/helpers.py", line 13, in <module>
    import pysam
  File "/usr/lib/python3/dist-packages/pysam/__init__.py", line 5, in <module>
    from pysam.libchtslib import *
ModuleNotFoundError: No module named 'pysam.libchtslib'

----------------------------------------------------------------------
Ran 1 test in 0.011s

FAILED (errors=1)
E: pybuild pybuild:283: test: plugin distutils failed with: exit code=1: cd /build/python-pybedtools-0.7.10/.pybuild/pythonX.Y_3.6/build; python3.6 -m nose --attr '!url'
dh_auto_test: pybuild --test --test-nose -i python{version} -p 3.6 3.5 returned exit code 13
debian/rules:13: recipe for target 'build' failed
make: *** [build] Error 25
...


I guess python-pysam is not yet build for Python3 3.6.

Kind regards

      Andreas.

-- 
http://fam-tille.de