Rebecca N. Palmer pushed to branch master at Debian Med / snakemake
Commits:
2d75b16c by Rebecca N. Palmer at 2022-02-01T21:53:58+00:00
Tests: skip another new conda-using test.
- - - - -
3 changed files:
- debian/changelog
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,8 +1,8 @@
-snakemake (6.15.1-1) UNRELEASED; urgency=medium
+snakemake (6.15.1-1) unstable; urgency=medium
* New upstream release. Refresh patches, d/copyright.
* Split up the binary package (main, -doc) to save space.
- * Tests: skip an FTP-using test and a new conda-using test,
+ * Tests: skip an FTP-using test and 2 new conda-using tests,
mark as needs-internet, copy the test tree to avoid writing to it.
* Don't ship the test suite, as some of it doesn't work from a
non-writable directory.
@@ -10,7 +10,7 @@ snakemake (6.15.1-1) UNRELEASED; urgency=medium
skip a test that fails under faketime.
* salsa-ci: ignore expected Lintian error, enable diffoscope.
- -- Rebecca N. Palmer <[email protected]> Tue, 01 Feb 2022 20:23:02
+0000
+ -- Rebecca N. Palmer <[email protected]> Tue, 01 Feb 2022 21:53:02
+0000
snakemake (6.12.3-1) unstable; urgency=medium
=====================================
debian/rules
=====================================
@@ -8,12 +8,12 @@ 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_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_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
# Docker images: test_issue1083, test_github_issue78, test_container,
test_singularity, test_singularity_conda, test_cwl_singularity,
test_convert_to_cwl, test_report, test_report_zip, test_module_complex(2)
-# Conda packages: test_archive, test_jupyter_notebook, test_conda,
test_upstream_conda, test_conda_custom_prefix, test_wrapper, test_script,
test_issue635, test_issue1093, test_singularity_conda, test_report,
test_report_zip, test_deploy_script
+# Conda packages: test_archive, test_jupyter_notebook, test_conda,
test_upstream_conda, test_conda_custom_prefix, test_wrapper, test_script,
test_issue635, test_issue1093, test_singularity_conda, test_report,
test_report_zip, test_deploy_script, test_deploy_hashing
# Note that even if conda were added to Debian (ITP #926416), using it
normally would still be downloading executables = forbidden
# 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
=====================================
debian/tests/run-unit-test
=====================================
@@ -22,4 +22,4 @@ 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_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'
View it on GitLab:
https://salsa.debian.org/med-team/snakemake/-/commit/2d75b16ccb4a6b8eda406583612716774b3ed377
--
View it on GitLab:
https://salsa.debian.org/med-team/snakemake/-/commit/2d75b16ccb4a6b8eda406583612716774b3ed377
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