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

Sat, 26 Nov 2022 13:03:26 -0800 

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

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