[Debian-med-packaging] Bug#1014100: We should do an update of all qiime2 modules as soon as possible (Was: Bug#1014100: qiime: autopkgtest needs update for new version of python-decorator)
Andreas Tille
andreas at an3as.eu
Thu Jun 30 10:51:50 BST 2022
Hi,
I'd like to point out to this serious bug. Steffen, would you mind
koordinating (not doing alone) an upgrade of the qiime infrastructure to
make sure everything will go smoothly?
Kind regards
Andreas.
Am Thu, Jun 30, 2022 at 11:30:21AM +0200 schrieb Paul Gevers:
> Source: qiime
> Version: 2021.8.0-2
> Severity: serious
> X-Debbugs-CC: python-decorator at packages.debian.org
> Tags: sid bookworm
> User: debian-ci at lists.debian.org
> Usertags: needs-update
> Control: affects -1 src:python-decorator
>
> Dear maintainer(s),
>
> With a recent upload of python-decorator the autopkgtest of qiime fails in
> testing when that autopkgtest is run with the binary packages of
> python-decorator from unstable. It passes when run with only packages from
> testing. In tabular form:
>
> pass fail
> python-decorator from testing 5.1.1-2
> qiime from testing 2021.8.0-2
> 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 python-decorator to
> testing [1]. Of course, python-decorator shouldn't just break your
> autopkgtest (or even worse, your package), but it seems to me that the
> change in python-decorator was intended and your package needs to update to
> the new situation. To me it looks like the references need updating for the
> new version but I might be wrong.
>
> If this is a real problem in your package (and not only in your
> autopkgtest), the right binary package(s) from python-decorator should
> really add a versioned Breaks on the unfixed version of (one of your)
> package(s). Note: the Breaks is nice even if the issue is only in the
> autopkgtest as it helps the migration software to figure out the right
> versions to combine in the tests.
>
> More information about this bug and the reason for filing it can be found on
> https://wiki.debian.org/ContinuousIntegration/RegressionEmailInformation
>
> Paul
>
> [1] https://qa.debian.org/excuses.php?package=python-decorator
>
> https://ci.debian.net/data/autopkgtest/testing/amd64/q/qiime/23173367/log.gz
>
> ................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................FF.........F....................................................................................................................................FF..........................................
> ======================================================================
> FAIL: test_callable_and_async_signature_with_artifacts_and_parameters
> (qiime2.sdk.tests.test_method.TestMethod)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/tmp/autopkgtest-lxc.t_q3d0jx/downtmp/autopkgtest_tmp/qiime2/sdk/tests/test_method.py",
> line 223, in test_callable_and_async_signature_with_artifacts_and_parameters
> self.assertEqual(parameters, exp_parameters)
> AssertionError: Lists differ: [('in[20 chars]ts1: list">), ('ints2',
> <Parameter "ints2: lis[108 chars]t">)] != [('in[20 chars]ts1: IntSequence1 |
> IntSequence2">), ('ints2',[147 chars]t">)]
>
> First differing element 0:
> ('ints1', <Parameter "ints1: list">)
> ('ints1', <Parameter "ints1: IntSequence1 | IntSequence2">)
>
> Diff is 735 characters long. Set self.maxDiff to None to see it.
>
> ======================================================================
> FAIL: test_callable_and_async_signature_with_no_parameters
> (qiime2.sdk.tests.test_method.TestMethod)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/tmp/autopkgtest-lxc.t_q3d0jx/downtmp/autopkgtest_tmp/qiime2/sdk/tests/test_method.py",
> line 242, in test_callable_and_async_signature_with_no_parameters
> self.assertEqual(parameters, exp_parameters)
> AssertionError: Lists differ: [('ma[26 chars]ng1: dict">), ('mapping2',
> <Parameter "mapping2: dict">)] != [('ma[26 chars]ng1: Mapping">),
> ('mapping2', <Parameter "mapping2: Mapping">)]
>
> First differing element 0:
> ('mapping1', <Parameter "mapping1: dict">)
> ('mapping1', <Parameter "mapping1: Mapping">)
>
> - [('mapping1', <Parameter "mapping1: dict">),
> ? ^ ^^
>
> + [('mapping1', <Parameter "mapping1: Mapping">),
> ? ^^^^ ^^
>
> - ('mapping2', <Parameter "mapping2: dict">)]
> ? ^ ^^
>
> + ('mapping2', <Parameter "mapping2: Mapping">)]
> ? ^^^^ ^^
>
>
> ======================================================================
> FAIL: test_callable_and_async_signature
> (qiime2.sdk.tests.test_pipeline.TestPipeline)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/tmp/autopkgtest-lxc.t_q3d0jx/downtmp/autopkgtest_tmp/qiime2/sdk/tests/test_pipeline.py",
> line 78, in test_callable_and_async_signature
> self.assertEqual(parameters, exp_parameters)
> AssertionError: Lists differ: [('in[32 chars]uence">), ('mapping',
> <Parameter "mapping">), [74 chars]1">)] != [('in[32 chars]uence:
> IntSequence1">), ('mapping', <Parameter[110 chars]1">)]
>
> First differing element 0:
> ('int_sequence', <Parameter "int_sequence">)
> ('int_sequence', <Parameter "int_sequence: IntSequence1">)
>
> - [('int_sequence', <Parameter "int_sequence">),
> + [('int_sequence', <Parameter "int_sequence: IntSequence1">),
> ? ++++++++++++++
>
> - ('mapping', <Parameter "mapping">),
> + ('mapping', <Parameter "mapping: Mapping">),
> ? +++++++++
>
> - ('do_extra_thing', <Parameter "do_extra_thing">),
> + ('do_extra_thing', <Parameter "do_extra_thing: Bool">),
> ? ++++++
>
> - ('add', <Parameter "add=1">)]
> + ('add', <Parameter "add: Int = 1">)]
> ? ++++++ +
>
>
> ======================================================================
> FAIL: test_callable_and_async_different_signature
> (qiime2.sdk.tests.test_visualizer.TestVisualizer)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/tmp/autopkgtest-lxc.t_q3d0jx/downtmp/autopkgtest_tmp/qiime2/sdk/tests/test_visualizer.py",
> line 211, in test_callable_and_async_different_signature
> self.assertEqual(parameters, exp_parameters)
> AssertionError: Lists differ: [('ints', <Parameter "ints:
> collections.Counter">)] != [('ints', <Parameter "ints: IntSequence1 |
> IntSequence2">)]
>
> First differing element 0:
> ('ints', <Parameter "ints: collections.Counter">)
> ('ints', <Parameter "ints: IntSequence1 | IntSequence2">)
>
> - [('ints', <Parameter "ints: collections.Counter">)]
> + [('ints', <Parameter "ints: IntSequence1 | IntSequence2">)]
>
> ======================================================================
> FAIL: test_callable_and_async_signature
> (qiime2.sdk.tests.test_visualizer.TestVisualizer)
> ----------------------------------------------------------------------
> Traceback (most recent call last):
> File "/tmp/autopkgtest-lxc.t_q3d0jx/downtmp/autopkgtest_tmp/qiime2/sdk/tests/test_visualizer.py",
> line 193, in test_callable_and_async_signature
> self.assertEqual(parameters, exp_parameters)
> AssertionError: Lists differ: [('ma[26 chars]ng1: dict">), ('mapping2',
> <Parameter "mapping[100 chars]r">)] != [('ma[26 chars]ng1: Mapping">),
> ('mapping2', <Parameter "mapp[106 chars]r">)]
>
> First differing element 0:
> ('mapping1', <Parameter "mapping1: dict">)
> ('mapping1', <Parameter "mapping1: Mapping">)
>
> Diff is 756 characters long. Set self.maxDiff to None to see it.
>
> ----------------------------------------------------------------------
> Ran 940 tests in 10.542s
>
> FAILED (failures=5)
> autopkgtest [01:12:37]: test run-unit-test
>
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