Rebecca N. Palmer pushed to branch debian-v7 at Debian Med / snakemake
Commits: 3b95bb9a by Rebecca N. Palmer at 2026-07-01T19:42:00+01:00 remove duplicate metadata - - - - - da0b5f80 by Rebecca N. Palmer at 2026-07-01T19:45:40+01:00 Re-enable R/rpy2 tests. - - - - - 4 changed files: - debian/changelog - debian/control - debian/rules - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +snakemake (7.32.4-12) UNRELEASED; urgency=medium + + * Re-enable R/rpy2 tests. + + -- Rebecca N. Palmer <[email protected]> Wed, 01 Jul 2026 19:45:01 +0100 + snakemake (7.32.4-11) unstable; urgency=medium * Team upload. ===================================== debian/control ===================================== @@ -40,6 +40,7 @@ Build-Depends: python3-requests, python3-requests-mock <!nocheck>, python3-retry, + python3-rpy2 <!nocheck>, python3-pytest-mock <!nocheck>, python3-setuptools, python3-smart-open, @@ -54,6 +55,7 @@ Build-Depends: python3-wrapt, python3-yaml, python3-yte <!nocheck>, + r-cran-rmarkdown <!nocheck>, stress <!nocheck>, Vcs-Browser: https://salsa.debian.org/med-team/snakemake Vcs-Git: https://salsa.debian.org/med-team/snakemake.git @@ -87,7 +89,6 @@ Recommends: imagemagick, python3-pytz, python3-yappi, - python3-rpy2, # for the templating and reports features python3-jinja2, python3-pygments, ===================================== 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 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)' +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)' # 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 @@ -38,9 +38,6 @@ 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. ===================================== debian/upstream/metadata ===================================== @@ -18,5 +18,3 @@ Registry: Entry: SCR_003475 Repository: https://github.com/snakemake/snakemake.git Repository-Browse: https://github.com/snakemake/snakemake -Repository: https://github.com/snakemake/snakemake.git -Repository-Browse: https://github.com/snakemake/snakemake View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/f5ee9a60b8086da55b118761fbe1b90761f534d2...da0b5f80a6b0b865af2f714025b951917f4e3dee -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/f5ee9a60b8086da55b118761fbe1b90761f534d2...da0b5f80a6b0b865af2f714025b951917f4e3dee You're receiving this email because of your account on salsa.debian.org. 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