[med-svn] [Git][med-team/snakemake][main] 2 commits: skip newly-added tests we can't run

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

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


Commits:
921631cd by Rebecca N. Palmer at 2023-11-26T16:16:51+00:00
skip newly-added tests we can't run

- - - - -
86abbb88 by Rebecca N. Palmer at 2023-11-26T18:24:03+00:00
Fix crash in config handling.

- - - - -


5 changed files:

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


Changes:

=====================================
debian/changelog
=====================================
@@ -4,6 +4,7 @@ snakemake (7.32.4-1) UNRELEASED; urgency=medium
   * Skip newly added tests that we can't run.
   * Clean up after docs build.  (Closes: #1045316)
   * Depend on python3-yte.
+  * Fix crash in config handling.
 
  -- Rebecca N. Palmer <rebecca_palmer at zoho.com>  Mon, 12 Jun 2023 07:38:54 +0100
 


=====================================
debian/patches/remove_ccbysa_snippets.patch
=====================================
@@ -82,7 +82,7 @@ Forwarded: no - one part needs Python 3.6+
 +    def nestedupdate(old_d, new_d):
 +        for k, v in new_d.items():
 +            if isinstance(v, collections.abc.Mapping):
-+                if k not in old_d:
++                if k not in old_d or old_d[k] is None:
 +                    old_d[k] = {}
 +                nestedupdate(old_d[k], v)
              else:


=====================================
debian/patches/skip-tests-with-slurm.patch
=====================================
@@ -43,3 +43,12 @@ Author: Andreas Tille <tille at debian.org>, Rebecca N. Palmer
  def test_slurm_complex():
      os.environ["TESTVAR"] = "test"
      os.environ["TESTVAR2"] = "test"
+@@ -82,7 +82,7 @@ def test_slurm_complex():
+     )
+ 
+ 
+- at skip_on_windows
++ at pytest.mark.skip(reason="Slurm and Conda are not setup when building on Debian")
+ def test_slurm_extra_arguments():
+     """Make sure arguments to default resources
+     are allowed to contain = signs, which is needed


=====================================
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'
+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'
 
 # 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
@@ -18,6 +18,7 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -o faulthandler_timeout=60 -v
 # Modification to run without conda was previously attempted on test_issue635 (succeeded) and test_issue1093 (failed as current bwa gives a different ordering), but is not in current use
 
 # Skipped due to not-in-Debian dependencies
+# conda (but not downloading): test_prebuilt_conda_script
 # python3-moto (RFP #777089): test_default_resources, test_default_remote, test_remote, test_output_file_cache_remote
 # python3-retry: test_modules_prefix test_ancient
 # python3-peppy: test_peppy, test_modules_peppy


=====================================
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'
+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'
 
 #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'



View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/41b753fb55d5576ae58167fe376889f82653dd36...86abbb8809a73e2805d474e043fd15ed2244c6a5

-- 
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/41b753fb55d5576ae58167fe376889f82653dd36...86abbb8809a73e2805d474e043fd15ed2244c6a5
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