[Debian-med-packaging] Bug#1024855: augur: (autopkgtest) needs update for python3.11: cannot import name '_aligners' from partially

Paul Gevers elbrus at debian.org
Sat Nov 26 20:59:18 GMT 2022 

Source: augur
Version: 18.1.2-1
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 
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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