[Debian-med-packaging] Bug#1024858: busco: (autopkgtest) needs update for python3.11: cannot import name '_aligners' from partially initialized module 'Bio.Align'

[Paul Gevers]

Source: busco
Version: 5.4.3-2
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 
busco 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
busco                  from testing    5.4.3-2
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/b/busco/28706377/log.gz

File series fully applied, ends at patch 
debian/patches/find-bbmap-instead-of-bbtools.patch
Testing with python3.11 in 
/tmp/autopkgtest-lxc.firnv_xg/downtmp/autopkgtest_tmp:
unittest_runner (unittest.loader._FailedTest.unittest_runner) ... ERROR

======================================================================
ERROR: unittest_runner (unittest.loader._FailedTest.unittest_runner)
----------------------------------------------------------------------
ImportError: Failed to import test module: unittest_runner
Traceback (most recent call last):
   File "/usr/lib/python3.11/unittest/loader.py", line 154, in 
loadTestsFromName
     module = __import__(module_name)
              ^^^^^^^^^^^^^^^^^^^^^^^
   File 
"/tmp/autopkgtest-lxc.firnv_xg/downtmp/autopkgtest_tmp/tests/unittest_runner.py", 
line 2, in <module>
     from tests.unittests import run_BUSCO_unittests
   File 
"/tmp/autopkgtest-lxc.firnv_xg/downtmp/autopkgtest_tmp/tests/unittests/run_BUSCO_unittests.py", 
line 2, in <module>
     from busco import run_BUSCO
   File "/usr/lib/python3/dist-packages/busco/run_BUSCO.py", line 25, in 
<module>
     from busco.BuscoRunner import AnalysisRunner, BatchRunner, SingleRunner
   File "/usr/lib/python3/dist-packages/busco/BuscoRunner.py", line 2, 
in <module>
     from busco.analysis.BuscoAnalysis import BuscoAnalysis
   File 
"/usr/lib/python3/dist-packages/busco/analysis/BuscoAnalysis.py", line 
15, in <module>
     from busco.busco_tools.hmmer import HMMERRunner
   File "/usr/lib/python3/dist-packages/busco/busco_tools/hmmer.py", 
line 7, 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)


----------------------------------------------------------------------
Ran 1 test in 0.000s

FAILED (errors=1)
autopkgtest [14:14:42]: test run-unit-test

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