[Debian-med-packaging] Bug#1008635: atropos: ImportError: cannot import name 'Iterable' from 'collections' (/usr/lib/python3.10/collections/__init__.py)

[Sebastian Ramacher]

Source: atropos
Version: 1.1.31+dfsg-1
Severity: serious
Tags: ftbfs sid bookworm
Justification: fails to build from source (but built successfully in the past)

atropos FTBFS with python 3.10

E   ImportError: cannot import name 'Iterable' from 'collections' (/usr/lib/python3.10/collections/__init__.py)
_______ ERROR collecting .pybuild/cpython3_3.10/build/tests/test_trim.py _______
ImportError while importing test module '/<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/tests/test_trim.py'.
Hint: make sure your test modules/packages have valid Python names.
Traceback:
/usr/lib/python3.10/importlib/__init__.py:126: in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
tests/test_trim.py:2: in <module>
    from atropos.adapters import Adapter, ColorspaceAdapter, PREFIX, BACK
atropos/adapters/__init__.py:13: in <module>
    from atropos import align
atropos/align/__init__.py:7: in <module>
    from atropos.util import RandomMatchProbability, reverse_complement
atropos/util/__init__.py:3: in <module>
    from collections import OrderedDict, Iterable, Sequence
E   ImportError: cannot import name 'Iterable' from 'collections' (/usr/lib/python3.10/collections/__init__.py)
=============================== warnings summary ===============================
tests/test_paired.py:612
  /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build/tests/test_paired.py:612: PytestUnknownMarkWarning: Unknown pytest.mark.timeout - is this a typo?  You can register custom marks to avoid this warning - for details, see https://docs.pytest.org/en/stable/mark.html
    @pytest.mark.timeout(10)

-- Docs: https://docs.pytest.org/en/stable/warnings.html
=========================== short test summary info ============================
ERROR tests/test_adapters.py
ERROR tests/test_align.py
ERROR tests/test_colorspace.py
ERROR tests/test_commands.py
ERROR tests/test_filters.py
ERROR tests/test_modifiers.py
ERROR tests/test_multicore.py
ERROR tests/test_qualtrim.py
ERROR tests/test_seqio.py
ERROR tests/test_trim.py
!!!!!!!!!!!!!!!!!!! Interrupted: 10 errors during collection !!!!!!!!!!!!!!!!!!!
======================== 1 warning, 10 errors in 1.05s =========================
E: pybuild pybuild:367: test: plugin distutils failed with: exit code=2: cd /<<PKGBUILDDIR>>/.pybuild/cpython3_3.10/build; python3.10 -m pytest tests
dh_auto_test: error: pybuild --test --test-pytest -i python{version} -p 3.10 "--before-test=ln -s /<<PKGBUILDDIR>>/tests/cut {build_dir}/tests && ln -s /<<PKGBUILDDIR>>/tests/data {build_dir}/tests" returned exit code 13

See
https://buildd.debian.org/status/fetch.php?pkg=atropos&arch=amd64&ver=1.1.31%2Bdfsg-1%2Bb1&stamp=1648449686&raw=0

Cheers
-- 
Sebastian Ramacher