Source: busco Version: 5.4.3-2 Severity: serious Tags: sid bookworm User: debian...@lists.debian.org Usertags: needs-update User: debian-pyt...@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.gzFile 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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