[med-svn] [Git][med-team/snakemake][main] Skip failing tests.

Mon Jun 12 20:09:31 BST 2023


Rebecca N. Palmer pushed to branch main at Debian Med / snakemake


Commits:
920796d1 by Rebecca N. Palmer at 2023-06-12T20:08:51+01:00
Skip failing tests.

- - - - -


4 changed files:

- debian/changelog
- debian/patches/skip-tests-with-slurm.patch
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,6 +1,9 @@
 snakemake (7.28.1-1) UNRELEASED; urgency=medium
 
   * New upstream release.  Update d/copyright and patches.
+  * Skip newly added tests that we can't run.
+  * Skip yte-using tests.  (Don't upload without discussion -
+this version needs yte for enough functionality that we might not want it without packaging that.)
 
  -- Rebecca N. Palmer <rebecca_palmer at zoho.com>  Mon, 12 Jun 2023 07:38:54 +0100
 


=====================================
debian/patches/skip-tests-with-slurm.patch
=====================================
@@ -1,7 +1,7 @@
-Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 11 Jan 2023 07:29:29 +0100
 Description: Skip slurm tests since slurm is not setup at build time
 
+Author: Andreas Tille <tille at debian.org>, Rebecca N. Palmer
+
 --- a/tests/test_slurm.py
 +++ b/tests/test_slurm.py
 @@ -10,9 +10,9 @@ sys.path.insert(0, os.path.dirname(__fil
@@ -25,6 +25,15 @@ Description: Skip slurm tests since slurm is not setup at build time
  def test_slurm_group_job():
      """
      same test as test_group_job(),
+@@ -43,7 +43,7 @@ def test_slurm_group_job():
+     )
+ 
+ 
+- at skip_on_windows
++ at pytest.mark.skip(reason="Slurm is not setup when building on Debian")
+ def test_slurm_group_parallel():
+     """
+     same test as test_group_job(),
 @@ -61,7 +61,7 @@ def test_slurm_group_parallel():
      )
  


=====================================
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 -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_template_engine and not test_github_issue1396 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'
+export PYBUILD_TEST_ARGS=python{version} -m pytest -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_template_engine 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_config and not test_config_ref and not test_dataframe and not test_subworkflows and not test_update_config and not test_config_merging and not test_yaml_config and not test_profile and not test_validate and not test_validate_fail and not test_modules_all and not test_modules_all_exclude_2 and not test_module_worfklow_namespacing and not test_github_issue1500 and not test_config_yte'
 
 # 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
@@ -23,7 +23,7 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -v {build_dir}/tests/test*.py
 # python3-peppy: test_peppy, test_modules_peppy
 # python3-tibanna: test_tibanna (possibly also specific to one cloud provider?)
 # python3-tes: test_tes
-# python3-yte: test_template_engine
+# python3-yte: test_template_engine,test_config,test_config_ref,test_dataframe,test_subworkflows,test_update_config,test_config_merging,test_yaml_config,test_profile,test_validate,test_validate_fail,test_modules_all,test_modules_all_exclude_2,test_module_worfklow_namespacing,test_github_issue1500,test_config_yte
 
 # Skipped due to network use
 # skipped in build, but run in autopkgtest: test_ancient
@@ -34,6 +34,7 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -v {build_dir}/tests/test*.py
 
 # possibly an actual bug: test_env_modules
 # should be marked google_credentials: test_github_issue1396
+# needs Azure credentials: test_az_batch_executor
 # 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
=====================================
@@ -25,4 +25,4 @@ export HOME="${AUTOPKGTEST_TMP}"
 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_peppy and not test_modules_peppy and not test_report_display_code and not test_wrapper_local_git_prefix and not test_template_engine and not test_github_issue1396 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'
+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_template_engine 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_config and not test_config_ref and not test_dataframe and not test_subworkflows and not test_update_config and not test_config_merging and not test_yaml_config and not test_profile and not test_validate and not test_validate_fail and not test_modules_all and not test_modules_all_exclude_2 and not test_module_worfklow_namespacing and not test_github_issue1500 and not test_config_yte'



View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/920796d19af0ed166a119fe47e01e4271e874825

-- 
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/920796d19af0ed166a119fe47e01e4271e874825
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