[Debian-med-packaging] Bug#1025022: python-bcbio-gff: (autopkgtest) needs update for python3.11: cannot import name '_aligners' from partially initialized module 'Bio.Align'

[Paul Gevers]

Source: python-bcbio-gff
Version: 0.6.9-1
Severity: serious
Tags: sid bookworm
User: debian-ci at lists.debian.org
Usertags: needs-update
User: debian-python at lists.debian.org
Usertags: python3.11
Control: affects -1 src:python3-defaults

Dear maintainer(s),

We are in the transition of adding python3.11 as a supported Python 
version [0]. With a recent upload of python3-defaults the autopkgtest of 
python-bcbio-gff fails in testing when that autopkgtest is run with the 
binary packages of python3-defaults from unstable. It passes when run 
with only packages from testing. In tabular form:

                        pass            fail
python3-defaults       from testing    3.10.6-3
python-bcbio-gff       from testing    0.6.9-1
all others             from testing    from testing

I copied some of the output at the bottom of this report.

Currently this regression is blocking the migration of python3-defaults 
to testing [1]. https://docs.python.org/3/whatsnew/3.11.html lists 
what's new in Python3.11, it may help to identify what needs to be updated.

More information about this bug and the reason for filing it can be found on
https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation

Paul

[0] https://bugs.debian.org/1021984
[1] https://qa.debian.org/excuses.php?package=python3-defaults

https://ci.debian.net/data/autopkgtest/testing/amd64/p/python-bcbio-gff/28728881/log.gz

Traceback (most recent call last):
   File 
"/tmp/autopkgtest-lxc.m7rgvaro/downtmp/autopkgtest_tmp/test_GFFSeqIOFeatureAdder.py", 
line 11, in <module>
     from Bio import SeqIO
   File "/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py", line 
374, in <module>
     from Bio.Align import MultipleSeqAlignment
   File "/usr/lib/python3/dist-packages/Bio/Align/__init__.py", line 18, 
in <module>
     from Bio.Align import _aligners
ImportError: cannot import name '_aligners' from partially initialized 
module 'Bio.Align' (most likely due to a circular import) 
(/usr/lib/python3/dist-packages/Bio/Align/__init__.py)
autopkgtest [23:01:48]: test run-unit-test

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