Bug#1024855: marked as done (augur: (autopkgtest) needs update for python3.11: cannot import name '_aligners' from partially)

Mon, 28 Nov 2022 14:21:34 -0800 

Your message dated Mon, 28 Nov 2022 22:20:39 +0000
with message-id <e1ozmur-004thw...@fasolo.debian.org>
and subject line Bug#1024855: fixed in python-biopython 1.80+dfsg-1
has caused the Debian Bug report #1024855,
regarding augur: (autopkgtest) needs update for python3.11: cannot import name 
'_aligners' from partially
to be marked as done.

This means that you claim that the problem has been dealt with.
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Bug report if necessary, and/or fix the problem forthwith.

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-- 
1024855: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024855
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message --- 
Source: augur
Version: 18.1.2-1
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 augur 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
augur                  from testing    18.1.2-1
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/a/augur/28706374/log.gz
============================= test session starts ============================== platform linux -- Python 3.11.0+, pytest-7.1.2, pluggy-1.0.0+repack -- /usr/bin/python3.11 
cachedir: .pytest_cache
rootdir: /tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src
plugins: mock-3.8.2
collecting ... collected 10 items / 21 errors
==================================== ERRORS ==================================== _____________________ ERROR collecting tests/test_align.py _____________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/test_align.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_align.py:10: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:374: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) ____________________ ERROR collecting tests/test_clades.py _____________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/test_clades.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_clades.py:6: in <module>
    from augur.clades import read_in_clade_definitions
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) _____________________ ERROR collecting tests/test_dates.py _____________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/test_dates.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_dates.py:4: in <module>
    from augur import dates
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) ____________________ ERROR collecting tests/test_filter.py _____________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/test_filter.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_filter.py:10: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:374: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) __________________ ERROR collecting tests/test_frequencies.py __________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/test_frequencies.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_frequencies.py:15: in <module>
from augur.frequency_estimators import get_pivots, TreeKdeFrequencies, AlignmentKdeFrequencies, TreeKdeFrequenciesError 
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) _____________________ ERROR collecting tests/test_mask.py ______________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/test_mask.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_mask.py:12: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:374: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) _____________________ ERROR collecting tests/test_parse.py _____________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/test_parse.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_parse.py:1: in <module>
    import Bio.SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:374: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) _________________ ERROR collecting tests/test_titer_models.py __________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/test_titer_models.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_titer_models.py:3: in <module>
    from augur.titer_model import TiterCollection
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) ___________________ ERROR collecting tests/test_translate.py ___________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/test_translate.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_translate.py:13: in <module>
    import treetime
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) _____________________ ERROR collecting tests/test_utils.py _____________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/test_utils.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_utils.py:6: in <module>
    from augur import utils
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) ___________________ ERROR collecting tests/test_validate.py ____________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/test_validate.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_validate.py:4: in <module>
    from augur.validate import (
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) ________________ ERROR collecting tests/test_validate_export.py ________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/test_validate_export.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_validate_export.py:1: in <module>
    import Bio.Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) ____________________ ERROR collecting tests/io/test_file.py ____________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/io/test_file.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/io/test_file.py:1: in <module>
    import augur.io.file
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) _________________ ERROR collecting tests/io/test_sequences.py __________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/io/test_sequences.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/io/test_sequences.py:2: in <module>
    from Bio import SeqIO
/usr/lib/python3/dist-packages/Bio/SeqIO/__init__.py:374: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) ____________ ERROR collecting tests/io/test_shell_command_runner.py ____________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/io/test_shell_command_runner.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/io/test_shell_command_runner.py:5: in <module>
    from augur.io.shell_command_runner import ShellCommandRunner
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) ____________________ ERROR collecting tests/io/test_vcf.py _____________________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/io/test_vcf.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/io/test_vcf.py:2: in <module>
    import augur.io.vcf
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) ___________ ERROR collecting tests/util_support/test_color_parser.py ___________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/util_support/test_color_parser.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/util_support/test_color_parser.py:1: in <module>
    from augur.util_support.color_parser import ColorParser
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) ________ ERROR collecting tests/util_support/test_date_disambiguator.py ________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/util_support/test_date_disambiguator.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/util_support/test_date_disambiguator.py:3: in <module>
    from augur.util_support import date_disambiguator
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) ____________ ERROR collecting tests/util_support/test_node_data.py _____________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/util_support/test_node_data.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/util_support/test_node_data.py:1: in <module>
from augur.util_support.node_data import DuplicatedNonDictAttributeError 
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) __________ ERROR collecting tests/util_support/test_node_data_file.py __________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/util_support/test_node_data_file.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/util_support/test_node_data_file.py:3: in <module>
    from augur.__version__ import __version__
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) _________ ERROR collecting tests/util_support/test_node_data_reader.py _________ ImportError while importing test module '/tmp/autopkgtest-lxc.cskdmo0l/downtmp/build.nDH/src/tests/util_support/test_node_data_reader.py'. 
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.11/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/util_support/test_node_data_reader.py:1: in <module>
    from augur.util_support.node_data_reader import NodeDataReader
augur/__init__.py:12: in <module>
    from treetime import TreeTimeError, TreeTimeUnknownError
/usr/lib/python3/dist-packages/treetime/__init__.py:32: in <module>
    from .treeanc import TreeAnc
/usr/lib/python3/dist-packages/treetime/treeanc.py:4: in <module>
    from Bio import Phylo
/usr/lib/python3/dist-packages/Bio/Phylo/__init__.py:14: in <module>
    from Bio.Phylo._io import parse, read, write, convert
/usr/lib/python3/dist-packages/Bio/Phylo/_io.py:16: in <module>
    from Bio.Phylo import BaseTree, NewickIO, NexusIO, PhyloXMLIO, NeXMLIO
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXMLIO.py:24: in <module>
    from Bio.Phylo import PhyloXML as PX
/usr/lib/python3/dist-packages/Bio/Phylo/PhyloXML.py:22: in <module>
    from Bio.Align import MultipleSeqAlignment
/usr/lib/python3/dist-packages/Bio/Align/__init__.py:18: in <module>
    from Bio.Align import _aligners
E 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) =========================== short test summary info ============================ 
ERROR tests/test_align.py
ERROR tests/test_clades.py
ERROR tests/test_dates.py
ERROR tests/test_filter.py
ERROR tests/test_frequencies.py
ERROR tests/test_mask.py
ERROR tests/test_parse.py
ERROR tests/test_titer_models.py
ERROR tests/test_translate.py
ERROR tests/test_utils.py
ERROR tests/test_validate.py
ERROR tests/test_validate_export.py
ERROR tests/io/test_file.py
ERROR tests/io/test_sequences.py
ERROR tests/io/test_shell_command_runner.py
ERROR tests/io/test_vcf.py
ERROR tests/util_support/test_color_parser.py
ERROR tests/util_support/test_date_disambiguator.py
ERROR tests/util_support/test_node_data.py
ERROR tests/util_support/test_node_data_file.py
ERROR tests/util_support/test_node_data_reader.py
!!!!!!!!!!!!!!!!!!! Interrupted: 21 errors during collection !!!!!!!!!!!!!!!!!!! ============================== 21 errors in 2.28s ============================== 
autopkgtest [14:15:35]: test run-unit-test

Attachment: 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.
Checksums-Sha1:
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 29f76812a17c6cc658f45bf743f077d0af2a7376 19244 
python-biopython_1.80+dfsg-1.debian.tar.xz
Checksums-Sha256:
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python-biopython_1.80+dfsg-1.dsc
 16edd6ce4bacb06a51b46210a6adde40080fcc4fc4b35c7cb29c5c36945e3745 19244 
python-biopython_1.80+dfsg-1.debian.tar.xz
Files:
 0b4bd816b0c210822949af3fcbbb03ff 3346 python optional 
python-biopython_1.80+dfsg-1.dsc
 af1a971c80ba03e3a693fa161695ea00 19244 python optional 
python-biopython_1.80+dfsg-1.debian.tar.xz

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