Your message dated Mon, 28 Nov 2022 22:20:39 +0000
with message-id <e1ozmur-004thz...@fasolo.debian.org>
and subject line Bug#1024858: fixed in python-biopython 1.80+dfsg-1
has caused the Debian Bug report #1024858,
regarding busco: (autopkgtest) needs update for python3.11: cannot import name
'_aligners' from partially initialized module 'Bio.Align'
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
1024858: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024858
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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.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
OpenPGP_signature
Description: OpenPGP digital signature
--- End Message ---
--- Begin Message ---
Source: python-biopython
Source-Version: 1.80+dfsg-1
Done: Étienne Mollier <emoll...@debian.org>
We believe that the bug you reported is fixed in the latest version of
python-biopython, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1024...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Étienne Mollier <emoll...@debian.org> (supplier of updated python-biopython
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Mon, 28 Nov 2022 22:19:25 +0100
Source: python-biopython
Architecture: source
Version: 1.80+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Étienne Mollier <emoll...@debian.org>
Closes: 1024855 1024858 1024986 1025014 1025022
Changes:
python-biopython (1.80+dfsg-1) unstable; urgency=medium
.
* Migrate biopython 1.80 from experimental to unstable.
Closes: #1024986, #1024858, #1024855, #1025014, #1025022
.
python-biopython (1.80+dfsg-1~0exp0) experimental; urgency=medium
.
* New upstream version
* Standards-Version: 4.6.1 (routine-update)
* Set upstream metadata fields: Security-Contact.
* privacy_breach_ie9.patch: refresh.
* adjust-test_GraphicsBitmaps.patch: delete; applied upstream.
* spelling.patch: delete; applied upstream.
* mkdssp4.patch: delete; fixed upstream.
* d/control: remove test dependency on problematic packages; muscle 5
wrapping is unsupported upstream, and t_coffee suffers from segmentation
faults documented in #1022570
* croak-on-muscle5.patch: add; raise RuntimeError with muscle 5.
* d/NEWS: describe incompatibility with muscle 5; also describe possible
workarounds.
* d/not-installed: add tree1 and other_trees.
* d/*.lintian-overrides: refresh override.
* debian/python3-biopython.lintian-overrides: override typo; the reported
spelling error does not seem to match anything meaningful on the side of
the source code.
* d/s/lintian-overrides: indicate location of Restriction.md, source of
Restriction.html.
* d/copyright: bump copyright years.
* muscle3.patch: add; default to use muscle3 command if available.
This is in preparation of the availability of a dedicated muscle3
package with the explicitly versioned command, since muscle 5 is a very
different program but can be installed in parallel.
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Checksums-Sha256:
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Files:
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python-biopython_1.80+dfsg-1.dsc
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