Michael R. Crusoe pushed to branch debian-v7 at Debian Med / snakemake
Commits: f5ee9a60 by Michael R. Crusoe at 2026-04-27T10:25:04+02:00 d/rules: skip the rpy2 using test. - - - - - 2 changed files: - debian/changelog - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +snakemake (7.32.4-11) unstable; urgency=medium + + * Team upload. + * d/rules: skip the rpy2 using test. + + -- Michael R. Crusoe <[email protected]> Mon, 27 Apr 2026 09:57:45 +0200 + snakemake (7.32.4-10) unstable; urgency=medium * Team upload. ===================================== debian/rules ===================================== @@ -8,7 +8,7 @@ export PYBUILD_DESTDIR=debian/snakemake # copy the tests and run them from there to avoid having to clean up after them export PYBUILD_BEFORE_TEST=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir} export PYBUILD_AFTER_TEST=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 and not test_prebuilt_conda_script and not test_persistent_dict and not test_issue328 and not test_pipes_fail and not test_pipes and not test_multicomp_group_jobs and not test_group_job_resources_with_pipe' +export PYBUILD_TEST_ARGS=python{version} -m pytest -o faulthandler_timeout=60 -v {build_dir}/tests/test*.py -k 'not (test_cwl or test_cwl_singularity or test_url_include or test_wrapper or test_issue1083 or test_github_issue78 or test_container or test_singularity or test_singularity_conda or test_convert_to_cwl or test_report or test_report_zip or test_archive or test_jupyter_notebook or test_conda or test_upstream_conda or test_conda_custom_prefix or test_script or test_issue635 or test_issue1093 or test_default_resources or test_default_remote or test_remote or test_output_file_cache_remote or test_tibanna or test_module_complex or test_module_complex2 or test_module_with_script or test_module_report or test_modules_meta_wrapper or test_tes or test_deploy_script or test_deploy_hashing or test_peppy or test_modules_peppy or test_report_display_code or test_wrapper_local_git_prefix or test_github_issue1396 or test_az_batch_executor or test_modules_prefix or test_ancient or test_github_issue1062 or test_symlink_time_handling or test_env_modules or test_github_issue1460 or test_rule_inheritance_globals or test_prebuilt_conda_script or test_persistent_dict or test_issue328 or test_pipes_fail or test_pipes or test_multicomp_group_jobs or test_group_job_resources_with_pipe or test_converting_path_for_r_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 @@ -38,6 +38,9 @@ export PYBUILD_TEST_ARGS=python{version} -m pytest -o faulthandler_timeout=60 -v # needs Azure credentials: test_az_batch_executor # flaky (these are run in autopkgtest but get 3 tries there) test_pipes_fail, test_pipes, test_multicomp_group_jobs, test_group_job_resources_with_pipe +# skipped to avoid R instability from removing the snakemake package +# test_converting_path_for_r_script + export PATH:=$(shell pybuild --print build_dir --interpreter python3 --name $(PYBUILD_NAME))/bin:$(PATH) # Force the use of python3's sphinx-build. View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/f5ee9a60b8086da55b118761fbe1b90761f534d2 -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/f5ee9a60b8086da55b118761fbe1b90761f534d2 You're receiving this email because of your account on salsa.debian.org. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help
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