Rebecca N. Palmer pushed to branch debian-v7 at Debian Med / snakemake
Commits:
22bedfc9 by Rebecca N. Palmer at 2025-02-09T20:56:46+00:00
Tests: switch back to faulthandler_timeout.
This reverts commit cb1f185e0855dcc5f4a9166cda95ec6641fe32d3.
- - - - -
3 changed files:
- debian/changelog
- debian/tests/control
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,12 +1,11 @@
snakemake (7.32.4-7) unstable; urgency=medium
- * Tests: treat more tests as flaky (try 3 times),
- use pytest-timeout not faulthandler_timeout for flaky tests
- (together, these work around #1095394),
+ * Tests: treat more tests as flaky (try 3 times)
+ (workaround for #1095394),
use json not print for consistent formatting,
use svg not pdf for compatibility with graphviz 12.
- -- Rebecca N. Palmer <[email protected]> Sun, 09 Feb 2025 17:58:52
+0000
+ -- Rebecca N. Palmer <[email protected]> Sun, 09 Feb 2025 20:56:35
+0000
snakemake (7.32.4-6) unstable; urgency=medium
=====================================
debian/tests/control
=====================================
@@ -18,7 +18,6 @@ Depends: snakemake,
python3-requests-mock,
python3-retry,
python3-pytest-mock,
- python3-pytest-timeout,
python3-pygments,
stress
Restrictions: allow-stderr, needs-internet
=====================================
debian/tests/run-unit-test
=====================================
@@ -25,4 +25,4 @@ export HOME="${AUTOPKGTEST_TMP}"
python3 -m pytest -v tests/test*.py -k 'not test_cwl and not
test_cwl_singularity and not test_url_include and not test_wrapper and not
test_issue1083 and not test_github_issue78 and not test_container and not
test_singularity and not test_singularity_conda and not test_convert_to_cwl and
not test_report and not test_report_zip and not test_archive and not
test_jupyter_notebook and not test_conda and not test_upstream_conda and not
test_conda_custom_prefix and not test_script and not test_issue635 and not
test_issue1093 and not test_default_resources and not test_default_remote and
not test_remote and not test_output_file_cache_remote and not test_tibanna and
not test_module_complex and not test_module_complex2 and not
test_module_with_script and not test_module_report and not
test_modules_meta_wrapper and not test_tes and not test_deploy_script and not
test_deploy_hashing and not test_peppy and not test_modules_peppy and not
test_report_display_code and not test_wrapper_local_git_prefix and not
test_github_issue1396 and not test_az_batch_executor and not
test_modules_prefix and not test_env_modules and not test_github_issue1062 and
not test_ancient and not test_symlink_time_handling and not
test_github_issue1460 and not test_rule_inheritance_globals and not
test_prebuilt_conda_script and not test_pipes_fail and not test_pipes and not
test_multicomp_group_jobs and not test_group_job_resources_with_pipe'
#sometimes hangs, so use timeout and retry
-python3 -m pytest --timeout=60 --timeout_method=thread -v tests/test*.py -k
'test_pipes_fail or test_pipes or test_multicomp_group_jobs or
test_group_job_resources_with_pipe' || python3 -m pytest --timeout=60
--timeout_method=thread -v tests/test*.py -k 'test_pipes_fail or test_pipes or
test_multicomp_group_jobs or test_group_job_resources_with_pipe' || python3 -m
pytest --timeout=60 --timeout_method=thread -v tests/test*.py -k
'test_pipes_fail or test_pipes or test_multicomp_group_jobs or
test_group_job_resources_with_pipe'
+python3 -m pytest -o faulthandler_timeout=60 -v tests/test*.py -k
'test_pipes_fail or test_pipes or test_multicomp_group_jobs or
test_group_job_resources_with_pipe' || python3 -m pytest -o
faulthandler_timeout=60 -v tests/test*.py -k 'test_pipes_fail or test_pipes or
test_multicomp_group_jobs or test_group_job_resources_with_pipe' || python3 -m
pytest -o faulthandler_timeout=60 -v tests/test*.py -k 'test_pipes_fail or
test_pipes or test_multicomp_group_jobs or test_group_job_resources_with_pipe'
View it on GitLab:
https://salsa.debian.org/med-team/snakemake/-/commit/22bedfc9931ceecb66b507a96741ecceab7b7d4b
--
View it on GitLab:
https://salsa.debian.org/med-team/snakemake/-/commit/22bedfc9931ceecb66b507a96741ecceab7b7d4b
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