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

[Peter Cock]

Curious - do you have the Python 2.7 version and build details?

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.

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

Regards,

Peter

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