[Debian-med-packaging] Bug#904317: python-biopython: autopkgtest fails: not ready for Python3.7

[Paul Gevers]

Source: python-biopython
Version: 1.71+dfsg-1
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: needs-update

Dear maintainers,

Currently the python3.7 transition¹ is going on, which means that
python3.7 is added to the supported python3 versions. However, since
python3-defaults added python3.7 support, your autopkgtest has been
failing. I copied the first error below, there are quite a few very
similar ones).

Could you please investigate? It looks like the source isn't ready for
Python3.7 yet, I suggest you pick this up with upstream and point
upstream at PEP-479². I think the right action right now is to claim
that the package doesn't support Python3.7 by adding the right
X-Python3-Version³ to debian/control. Don't forget to check if the
autopkgtest also needs updates to test with the right versions.

Paul
PS: it seems in unstable there is more regression as the test already
fails in the python2.7 part and doesn't even test any python3 code.

¹ https://release.debian.org/transitions/html/python3.7.html
² https://docs.python.org/3.7/whatsnew/3.7.html#changes-in-python-behavior
³
https://www.debian.org/doc/packaging-manuals/python-policy/ch-module_packages.html#s-specifying_versions

https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-biopython/657128/log.gz
======================================================================
ERROR: test_AlignIO
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/Bio/AlignIO/NexusIO.py", line 42,
in NexusIterator
    n = Nexus.Nexus(handle)
  File "/usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py", line 623, in
__init__
    self.read(input)
  File "/usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py", line 657, in
read
    commandlines = _get_command_lines(file_contents)
  File "/usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py", line 1898,
in _get_command_lines
    lines = _kill_comments_and_break_lines(file_contents)
  File "/usr/lib/python3/dist-packages/Bio/Nexus/Nexus.py", line 454, in
_kill_comments_and_break_lines
    t2 = next(contents)
StopIteration

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "run_tests.py", line 451, in runTest
    suite = loader.loadTestsFromName(name)
  File "/usr/lib/python3.7/unittest/loader.py", line 154, in
loadTestsFromName
    module = __import__(module_name)
  File
"/tmp/autopkgtest-lxc.rsofcney/downtmp/autopkgtest_tmp/Tests/test_AlignIO.py",
line 237, in <module>
    alignments = list(AlignIO.parse(handle, t_format))
  File "/usr/lib/python3/dist-packages/Bio/AlignIO/__init__.py", line
376, in parse
    for a in i:
RuntimeError: generator raised StopIteration

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