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

[Andreas Tille]

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