[Debian-med-packaging] Bug#1001535: busco: (autopkgtest) needs update for python3.10

[Graham Inggs]

Source: busco
Version: 5.2.2-1
Severity: serious
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: needs-update
User: debian-python at lists.debian.org
Usertags: python3.10
Control: affects -1 src:python3-defaults

Hi Maintainer

As can be seen [1], the autopkgtests of busco fail when python3.10 is
a supported version.
This currently blocks the migration of python3-defaults to testing [2].

I've copied what I hope is the relevant part of the log below.

Regards
Graham


[1] https://ci.debian.net/packages/b/busco/unstable/amd64/
[2] https://qa.debian.org/excuses.php?package=python3-defaults


======================================================================
ERROR: test_init_tools_eukaryota_metaeuk
(tests.unittests.GenomeAnalysis_unittests.TestConfigManager)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3.10/unittest/mock.py", line 1366, in patched
    with self.decoration_helper(patched,
  File "/usr/lib/python3.10/contextlib.py", line 135, in __enter__
    return next(self.gen)
  File "/usr/lib/python3.10/unittest/mock.py", line 1348, in decoration_helper
    arg = exit_stack.enter_context(patching)
  File "/usr/lib/python3.10/contextlib.py", line 492, in enter_context
    result = _cm_type.__enter__(cm)
  File "/usr/lib/python3.10/unittest/mock.py", line 1528, in __enter__
    raise InvalidSpecError(
unittest.mock.InvalidSpecError: Cannot autospec attr 'config' from
target 'BuscoAnalysis' as it has already been mocked out.
[target=<class 'busco.analysis.BuscoAnalysis.BuscoAnalysis'>,
attr=<Mock id='140560674098768'>]

======================================================================
ERROR: test_init_tools_prokaryota
(tests.unittests.GenomeAnalysis_unittests.TestConfigManager)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3.10/unittest/mock.py", line 1366, in patched
    with self.decoration_helper(patched,
  File "/usr/lib/python3.10/contextlib.py", line 135, in __enter__
    return next(self.gen)
  File "/usr/lib/python3.10/unittest/mock.py", line 1348, in decoration_helper
    arg = exit_stack.enter_context(patching)
  File "/usr/lib/python3.10/contextlib.py", line 492, in enter_context
    result = _cm_type.__enter__(cm)
  File "/usr/lib/python3.10/unittest/mock.py", line 1528, in __enter__
    raise InvalidSpecError(
unittest.mock.InvalidSpecError: Cannot autospec attr 'config' from
target 'BuscoAnalysis' as it has already been mocked out.
[target=<class 'busco.analysis.BuscoAnalysis.BuscoAnalysis'>,
attr=<Mock id='140560674098768'>]

======================================================================
ERROR: test_run_analysis_metaeuk
(tests.unittests.GenomeAnalysis_unittests.TestConfigManager)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python3.10/unittest/mock.py", line 1366, in patched
    with self.decoration_helper(patched,
  File "/usr/lib/python3.10/contextlib.py", line 135, in __enter__
    return next(self.gen)
  File "/usr/lib/python3.10/unittest/mock.py", line 1348, in decoration_helper
    arg = exit_stack.enter_context(patching)
  File "/usr/lib/python3.10/contextlib.py", line 492, in enter_context
    result = _cm_type.__enter__(cm)
  File "/usr/lib/python3.10/unittest/mock.py", line 1528, in __enter__
    raise InvalidSpecError(
unittest.mock.InvalidSpecError: Cannot autospec attr 'config' from
target 'BuscoAnalysis' as it has already been mocked out.
[target=<class 'busco.analysis.BuscoAnalysis.BuscoAnalysis'>,
attr=<Mock id='140560674098768'>]

----------------------------------------------------------------------
Ran 99 tests in 2.065s

FAILED (errors=3, skipped=1)
autopkgtest [19:49:27]: test run-unit-test: -----------------------]
autopkgtest [19:49:28]: test run-unit-test:  - - - - - - - - - -
results - - - - - - - - - -
run-unit-test        FAIL non-zero exit status 1