[med-svn] [Git][med-team/snakemake][master] 2 commits: Tests: skip peppy tests (not in Debian).

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

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


Commits:
da1a9e8d by Rebecca N. Palmer at 2022-02-20T14:41:54+00:00
Tests: skip peppy tests (not in Debian).

- - - - -
1d9c1c81 by Rebecca N. Palmer at 2022-02-20T14:53:22+00:00
Tests: use Python 3 subprocesses.

- - - - -


4 changed files:

- debian/changelog
- debian/patches/python3.patch
- debian/rules
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -2,8 +2,9 @@ snakemake (6.15.5-1) unstable; urgency=medium
 
   * Upstream bugfix release.
   * Remove drmaa Recommends, as that package is broken (see #951704).
+  * Tests: skip peppy tests (not in Debian), use Python 3 subprocesses.
 
- -- Rebecca N. Palmer <rebecca_palmer at zoho.com>  Sun, 20 Feb 2022 13:39:00 +0000
+ -- Rebecca N. Palmer <rebecca_palmer at zoho.com>  Sun, 20 Feb 2022 14:53:05 +0000
 
 snakemake (6.15.1-2) unstable; urgency=medium
 


=====================================
debian/patches/python3.patch
=====================================
@@ -58,6 +58,17 @@ Forwarded: no
  
      # make sure the output can be interpreted by dot
      with open(dot_path, "rb") as dot_file, open(pdf_path, "wb") as pdf_file:
+@@ -1426,8 +1426,8 @@ def test_github_issue1384():
+         shell(
+             """
+             cd {tmpdir}
+-            python -m snakemake --generate-unit-tests
+-            pytest -v .tests/unit
++            python3 -m snakemake --generate-unit-tests
++            python3 -m pytest -v .tests/unit
+             """
+         )
+     finally:
 --- a/tests/test_profile/Snakefile
 +++ b/tests/test_profile/Snakefile
 @@ -1,3 +1,3 @@


=====================================
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_ancient and not test_github_issue1062 and not test_symlink_time_handling and not test_env_modules'
+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_ancient and not test_github_issue1062 and not test_symlink_time_handling and not test_env_modules'
 
 # 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_module_with_script, test_module_report, test_module_complex(2), test_modules_meta_wrapper
@@ -19,6 +19,7 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -v {build_dir}/tests/test*.py
 
 # Skipped due to not-in-Debian dependencies
 # python3-moto (RFP #777089): test_default_resources, test_default_remote, test_remote, test_output_file_cache_remote
+# python3-peppy: test_peppy, test_modules_peppy
 # python3-tibanna: test_tibanna (possibly also specific to one cloud provider?)
 # python3-tes: test_tes
 


=====================================
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_env_modules and not test_github_issue1062 and not test_pipes_fail'
+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_env_modules and not test_github_issue1062 and not test_pipes_fail'



View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/3e2242a4166b3e2a9b5b490e61bff0c2d7b5ea80...1d9c1c81932b2b0a48a08aba2581c86ca3b0db4c

-- 
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/3e2242a4166b3e2a9b5b490e61bff0c2d7b5ea80...1d9c1c81932b2b0a48a08aba2581c86ca3b0db4c
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