[med-svn] [Git][med-team/snakemake][debian-v7] 2 commits: remove duplicate metadata

Wed Jul 1 19:46:10 BST 2026


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 <rebecca_palmer at zoho.com>  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. Manage all notifications: https://salsa.debian.org/-/profile/notifications | Help: https://salsa.debian.org/help


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20260701/f55eaba9/attachment-0001.htm>
