[med-svn] [Git][med-team/snakemake][master] Timeout and retry an intermittently hanging autopkgtest.

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

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 <rebecca_palmer at zoho.com>  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.


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20220204/65707430/attachment-0001.htm>