Rebecca N. Palmer pushed to branch debian-v7 at Debian Med / snakemake
Commits: 9fc27d2d by Rebecca N. Palmer at 2025-02-09T16:50:26+00:00 Tests: treat more tests as flaky (try 3 times). - - - - - cb1f185e by Rebecca N. Palmer at 2025-02-09T16:53:11+00:00 Tests: use pytest-timeout not faulthandler_timeout for flaky tests. (in the hope that it will be better at actually terminating the hung test, instead of reporting a timeout then staying hung) - - - - - 4 changed files: - debian/changelog - debian/rules - debian/tests/control - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +snakemake (7.32.4-7) UNRELEASED; urgency=medium + + * Tests: treat more tests as flaky (try 3 times), + use pytest-timeout not faulthandler_timeout for flaky tests. + + -- Rebecca N. Palmer <[email protected]> Sun, 09 Feb 2025 16:43:24 +0000 + snakemake (7.32.4-6) unstable; urgency=medium * Stop using pkg_resources. (Closes: #1083775) ===================================== debian/rules ===================================== @@ -8,7 +8,7 @@ export PYBUILD_DESTDIR_python3=debian/snakemake # copy the tests and run them from there to avoid having to clean up after them export PYBUILD_BEFORE_TEST_python3=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir} export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests -export PYBUILD_TEST_ARGS=python{version} -m pytest -o faulthandler_timeout=60 -v {build_dir}/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_ancient and not test_github_issue1062 and not test_symlink_time_handling and not test_env_modules and not test_github_issue1460 and not test_rule_inheritance_globals and not test_prebuilt_conda_script and not test_persistent_dict and not test_issue328' +export PYBUILD_TEST_ARGS=python{version} -m pytest -o faulthandler_timeout=60 -v {build_dir}/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_ancient and not test_github_issue1062 and not test_symlink_time_handling and not test_env_modules and not test_github_issue1460 and not test_rule_inheritance_globals and not test_prebuilt_conda_script and not test_persistent_dict and not test_issue328 and not test_pipes_fail and not test_pipes and not test_multicomp_group_jobs and not test_group_job_resources_with_pipe' # Skipped because they download executables (which is forbidden in Debian buildd and debci) # Snakefile/snakemake-wrapper/CWL scripts: test_cwl, test_cwl_singularity, test_url_include, test_wrapper, test_wrapper_local_git_prefix, test_module_with_script, test_module_report, test_module_complex(2), test_modules_meta_wrapper @@ -36,7 +36,7 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -o faulthandler_timeout=60 -v # pytools too old, #1076925, only fail in build and not autopkgtest: test_persistent_dict test_issue328 # should be marked google_credentials: test_github_issue1396 # needs Azure credentials: test_az_batch_executor -# the -o faulthandler_timeout=60 is because test_pipes_fail sometimes hangs +# flaky (these are run in autopkgtest but get 3 tries there) test_pipes_fail, test_pipes, test_multicomp_group_jobs, test_group_job_resources_with_pipe export PATH:=$(shell pybuild --print build_dir --interpreter python3 --name $(PYBUILD_NAME))/bin:$(PATH) ===================================== debian/tests/control ===================================== @@ -18,6 +18,7 @@ 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 ===================================== @@ -22,7 +22,7 @@ export HOME="${AUTOPKGTEST_TMP}" . /etc/profile.d/modules.sh #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_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_pipes_fail 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' +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 -o faulthandler_timeout=60 -v tests/test*.py -k 'test_pipes_fail' || python3 -m pytest -o faulthandler_timeout=60 -v tests/test*.py -k 'test_pipes_fail' || python3 -m pytest -o faulthandler_timeout=60 -v tests/test*.py -k 'test_pipes_fail' +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' View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/95c52c0780451a7daf9b08a45db22d95b73c0fbd...cb1f185e0855dcc5f4a9166cda95ec6641fe32d3 -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/95c52c0780451a7daf9b08a45db22d95b73c0fbd...cb1f185e0855dcc5f4a9166cda95ec6641fe32d3 You're receiving this email because of your account on salsa.debian.org.
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