Rebecca N. Palmer pushed to branch master at Debian Med / snakemake
Commits: 5b3400fa by Rebecca N. Palmer at 2022-02-04T22:36:43+00:00 Timeout and retry an intermittently hanging autopkgtest. - - - - - 3 changed files: - debian/changelog - debian/rules - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +snakemake (6.15.1-2) unstable; urgency=medium + + * Timeout and retry an intermittently hanging autopkgtest. + * Upload to unstable. + + -- Rebecca N. Palmer <[email protected]> Fri, 04 Feb 2022 22:35:19 +0000 + snakemake (6.15.1-1~exp1) experimental; urgency=medium * New upstream release. Refresh patches, d/copyright. ===================================== debian/rules ===================================== @@ -30,6 +30,7 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -v {build_dir}/tests/test*.py # Skipped in build to let reproducibility tests pass (it fails under faketime, with what looks like the outer script but not the rules running under it), but run in autopkgtest: test_symlink_time_handling # possibly an actual bug: test_env_modules +# test_pipes_fail is done outside the main run in autopkgtest because it sometimes hangs export PATH:=$(shell pybuild --print build_dir --interpreter python3 --name $(PYBUILD_NAME))/bin:$(PATH) ===================================== debian/tests/run-unit-test ===================================== @@ -21,5 +21,8 @@ export HOME="${AUTOPKGTEST_TMP}" # workaround for #928826 . /etc/profile.d/modules.sh +#sometimes hangs, so use timeout and retry +python3 -m pytest -o faulthandler_timeeout=60 -v tests/test*.py -k 'test_pipes_fail' || python3 -m pytest -o faulthandler_timeeout=60 -v tests/test*.py -k 'test_pipes_fail' || python3 -m pytest -o faulthandler_timeeout=60 -v tests/test*.py -k 'test_pipes_fail' + #See debian/rules for why these are excluded -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_env_modules and not test_github_issue1062' +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_env_modules and not test_github_issue1062 and not test_pipes_fail' View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/5b3400faa42ed4871e062695a4e177b5122f93be -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/5b3400faa42ed4871e062695a4e177b5122f93be You're receiving this email because of your account on salsa.debian.org.
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