[Debian-med-packaging] Bug#944242: Test issues with BioPython 1.75

[Andreas Tille]

Hi Peter,

I'd like to give you credit as the fastest upstream answering a
question. ;-)  Thanks a lot for it!

On Tue, Nov 19, 2019 at 09:17:17AM +0000, Peter Cock wrote:
> Curious - do you have the Python 2.7 version and build details?

I've attached the full build log.
 
> Missing docstrings are unfortunate (and in this case they are in C
> code which is a bit different), but ultimately this is harmless. What
> puzzles me is what has triggered this, that we fail to see it on our
> own testing.

Hmmm, you say its harmless but its breaking the build of the Debian
package anyway.  So it would be good to have some means against it.
Since you are asking about the 2.7 version:  We need to get rid of
Python2 as soon as all reverse depends of biopython are ported to
Python3 (or removed from Debian).  This might take some time but if
we could move this kind of doc string generation to be done by Python3
this would be some step in the right direction.
 
> As an aside, for Python 3.8 you would ideally include this, it didn't
> get in the tag or tar-ball, but was in the Python 3.8 wheels:
> 
> https://github.com/biopython/biopython/commit/3b8e984e25bca84ea3cb56d8a1eb67006dcd26be

Pushed to the packaging git - thanks a lot for the hint.
 
Kind regards

      Andreas.
 
> On Tue, Nov 19, 2019 at 8:27 AM Andreas Tille <andreas at fam-tille.de> wrote:
> >
> > Hi,
> >
> > it seems that BioPython 1.75 has solved all issues with Python 3.8.
> > However, when trying to build the Debian package I get the following
> > issues in the Build-Time test suite:
> >
> > ...
> > ======================================================================
> > ERROR: Bio.KDTree._CKDTree
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "run_tests.py", line 367, in runTest
> >     optionflags=doctest.ELLIPSIS)
> >   File "/usr/lib/python2.7/doctest.py", line 2412, in DocTestSuite
> >     raise ValueError(module, "has no docstrings")
> > ValueError: (<module 'Bio.KDTree._CKDTree' from '/build/python-biopython-1.75+dfsg/.pybuild/cpython2_2.7/build/Bio/KDTree/_CKDTree.so'>, 'has no docstrings')
> > ======================================================================
> > ERROR: Bio.Nexus.cnexus
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "run_tests.py", line 367, in runTest
> >     optionflags=doctest.ELLIPSIS)
> >   File "/usr/lib/python2.7/doctest.py", line 2412, in DocTestSuite
> >     raise ValueError(module, "has no docstrings")
> > ValueError: (<module 'Bio.Nexus.cnexus' from '/build/python-biopython-1.75+dfsg/.pybuild/cpython2_2.7/build/Bio/Nexus/cnexus.so'>, 'has no docstrings')
> > ======================================================================
> > ERROR: Bio.PDB.QCPSuperimposer.qcprot
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "run_tests.py", line 367, in runTest
> >     optionflags=doctest.ELLIPSIS)
> >   File "/usr/lib/python2.7/doctest.py", line 2412, in DocTestSuite
> >     raise ValueError(module, "has no docstrings")
> > ValueError: (<module 'Bio.PDB.QCPSuperimposer.qcprotmodule' from '/build/python-biopython-1.75+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB/QCPSuperimposer/qcprotmodule.so'>, 'has no docstrings')
> > ======================================================================
> > ERROR: Bio.PDB.kdtrees
> > ----------------------------------------------------------------------
> > Traceback (most recent call last):
> >   File "run_tests.py", line 367, in runTest
> >     optionflags=doctest.ELLIPSIS)
> >   File "/usr/lib/python2.7/doctest.py", line 2412, in DocTestSuite
> >     raise ValueError(module, "has no docstrings")
> > ValueError: (<module 'Bio.PDB.kdtrees' from '/build/python-biopython-1.75+dfsg/.pybuild/cpython2_2.7/build/Bio/PDB/kdtrees.so'>, 'has no docstrings')
> > ----------------------------------------------------------------------
> > Ran 519 tests in 287.024 seconds
> >
> > FAILED (failures = 4)
> > Skipping any tests requiring internet access
> > Python version: 2.7.17 (default, Oct 19 2019, 23:36:22)
> > [GCC 9.2.1 20191008]
> > ...
> >
> >
> > Any hint how to solve this?
> >
> > Greetings from Biohackathon
> >
> >      Andreas.
> >
> > --
> > http://fam-tille.de
> 
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-- 
http://fam-tille.de
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