[med-svn] [Git][med-team/snakemake][debian-v7] 2 commits: Tests: treat more tests as flaky (try 3 times).

[Rebecca N. Palmer (@rnpalmer-guest)]

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 <rebecca_palmer at zoho.com>  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
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