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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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 _alignersE 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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