[Debian-med-packaging] Bug#1006002: pyparsing breaks cwltool autopkgtest: assert main(["--debug", "--print-dot", cwl_path], stdout=stdout) == 0
Paul Gevers
elbrus at debian.org
Fri Feb 18 20:02:16 GMT 2022
Source: pyparsing, cwltool
Control: found -1 pyparsing/3.0.7-1
Control: found -1 cwltool/3.1.20211104071347-3
Severity: serious
Tags: sid bookworm
X-Debbugs-CC: debian-ci at lists.debian.org
User: debian-ci at lists.debian.org
Usertags: breaks needs-update
Dear maintainer(s),
With a recent upload of pyparsing the autopkgtest of cwltool fails in
testing when that autopkgtest is run with the binary packages of
pyparsing from unstable. It passes when run with only packages from
testing. In tabular form:
pass fail
pyparsing from testing 3.0.7-1
cwltool from testing 3.1.20211104071347-3
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 pyparsing to
testing [1]. Due to the nature of this issue, I filed this bug report
against both packages. Can you please investigate the situation and
reassign the bug to the right package? I note that cwltool is newer in
unstable. I haven't tested if that "solves" the issue as the package is
blocked from migrating currently.
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=pyparsing
https://ci.debian.net/data/autopkgtest/testing/amd64/c/cwltool/19310147/log.gz
=================================== FAILURES
===================================
________________________________ test_print_dot
________________________________
[gw14] linux -- Python 3.9.10 /usr/bin/python3
def test_print_dot() -> None:
# print Workflow
cwl_path = get_data("tests/wf/revsort.cwl")
cwl_posix_path = Path(cwl_path).as_posix()
expected_dot = pydot.graph_from_dot_data(
"""
digraph {{
graph [bgcolor="#eeeeee",
clusterrank=local,
labeljust=right,
labelloc=bottom
];
subgraph cluster_inputs {{
graph [label="Workflow Inputs",
rank=same,
style=dashed
];
"file://{cwl_posix_path}#workflow_input"
[fillcolor="#94DDF4",
label=workflow_input,
style=filled];
"file://{cwl_posix_path}#reverse_sort"
[fillcolor="#94DDF4",
label=reverse_sort,
style=filled];
}}
subgraph cluster_outputs {{
graph [label="Workflow Outputs",
labelloc=b,
rank=same,
style=dashed
];
"file://{cwl_posix_path}#sorted_output"
[fillcolor="#94DDF4",
label=sorted_output,
style=filled];
}}
"file://{cwl_posix_path}#rev" [fillcolor=lightgoldenrodyellow,
label=rev,
style=filled];
"file://{cwl_posix_path}#sorted"
[fillcolor=lightgoldenrodyellow,
label=sorted,
style=filled];
"file://{cwl_posix_path}#rev" ->
"file://{cwl_posix_path}#sorted";
"file://{cwl_posix_path}#sorted" ->
"file://{cwl_posix_path}#sorted_output";
"file://{cwl_posix_path}#workflow_input" ->
"file://{cwl_posix_path}#rev";
"file://{cwl_posix_path}#reverse_sort" ->
"file://{cwl_posix_path}#sorted";
}}
""".format(
cwl_posix_path=cwl_posix_path
)
)[0]
stdout = StringIO()
> assert main(["--debug", "--print-dot", cwl_path], stdout=stdout) == 0
E AssertionError: assert 1 == 0
E + where 1 = main(['--debug', '--print-dot',
'/usr/lib/python3/dist-packages/cwltool/tests/wf/revsort.cwl'],
stdout=<_io.StringIO object at 0x7f634cc60550>)
/usr/lib/python3/dist-packages/cwltool/tests/test_examples.py:1083:
AssertionError
-------------- next part --------------
A non-text attachment was scrubbed...
Name: OpenPGP_signature
Type: application/pgp-signature
Size: 495 bytes
Desc: OpenPGP digital signature
URL: <http://alioth-lists.debian.net/pipermail/debian-med-packaging/attachments/20220218/0fdf3cc8/attachment.sig>
More information about the Debian-med-packaging
mailing list