Steffen Möller pushed to branch master at Debian Med / snakemake
Commits: e5d06b9b by Steffen Moeller at 2021-10-19T15:23:19+02:00 More refinements for lintian - - - - - 4 changed files: - debian/TODO - debian/changelog - debian/rules - debian/source/lintian-overrides Changes: ===================================== debian/TODO ===================================== @@ -4,3 +4,7 @@ Tasks to do for next releases of snakemake * Prepare https://pypi.org/project/py-tes/ as a Debian pacakge - no need to re-activated cognate test in d/rules since this requires internet - add as recommendation to binary + + * Decide to remove obscure tests from source tree and have a +dfsg package + P: snakemake source: embedded-script-includes-copyright-statement tests/test_module_report/expected-results/report.html extract of copyright statement: (c) js foundation and other contributors | jquery.org/l + P: snakemake source: embedded-script-includes-copyright-statement tests/test_report/expected-results/report.html extract of copyright statement: (c) js foundation and other contributors | jquery.org/l ===================================== debian/changelog ===================================== @@ -20,7 +20,7 @@ snakemake (6.9.1-1) UNRELEASED; urgency=medium * fixing one calling pytest -> pytest-3 * d/rules: Allowing consecutive builds with better cleaning * Added d/TODO to remind about missing "tes" Python module - + -- Nilesh Patra <[email protected]> Sun, 17 Oct 2021 14:19:21 +0000 snakemake (5.24.1-2) unstable; urgency=medium ===================================== debian/rules ===================================== @@ -6,7 +6,7 @@ export PYBUILD_NAME=snakemake export PYBUILD_DESTDIR_python3=debian/snakemake export PYBUILD_BEFORE_TEST_python3=chmod +x {dir}/bin/snakemake; cp -r {dir}/bin {dir}/tests {build_dir} -export PYBUILD_TEST_ARGS=python{version} -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_ancient and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_github_issue1062 and not test_env_modules and not test_modules_meta_wrapper and not test_tes' +export PYBUILD_TEST_ARGS=python{version} -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_ancient and not test_module_complex and not test_module_complex2 and not test_module_with_script and not test_module_report and not test_github_issue1062 and not test_env_modules and not test_modules_meta_wrapper and not test_tes' # 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 @@ -40,9 +40,7 @@ override_dh_auto_build: override_dh_auto_install: dh_auto_install - find debian -name '__pycache__' | xargs rm -R - find debian -name '*.pyc' | xargs -r rm - find debian -name '.gitignore' | xargs -r rm + find debian/snakemake -name '.gitignore' | xargs -r rm # the modules.sh is a workaround for #928826; putting it in PYBUILD_BEFORE_TEST_python3 doesn't work override_dh_auto_test: ===================================== debian/source/lintian-overrides ===================================== @@ -3,3 +3,19 @@ snakemake source: source-is-missing tests/test_report/expected-results/report.ht snakemake source: source-is-missing tests/test_report/expected-results/report.html line length is * snakemake source: source-is-missing tests/test_module_report/expected-results/report.html snakemake source: mismatched-override source-is-missing tests/test_report/expected-results/report.html line length is * + +# Complaints about hand-written documentation / image +snakemake source: very-long-line-length-in-source-file docs/executing/cluster.rst line 68 is 809 characters long (>512) +snakemake source: very-long-line-length-in-source-file docs/project_info/faq.rst line 339 is 610 characters long (>512) +snakemake source: very-long-line-length-in-source-file docs/snakefiles/deployment.rst line 133 is 1046 characters long (>512) +snakemake source: very-long-line-length-in-source-file docs/snakefiles/remote_files.rst line 528 is 847 characters long (>512) +snakemake source: very-long-line-length-in-source-file docs/snakefiles/rules.rst line 976 is 1206 characters long (>512) +snakemake source: very-long-line-length-in-source-file docs/tutorial/advanced.rst line 254 is 666 characters long (>512) +snakemake source: very-long-line-length-in-source-file images/biglogo.svg line 68 is 906 characters long (>512) + +# We might want to discuss if these files + tests should be removed from the source tree that are deselected anyway +snakemake source: embedded-script-includes-copyright-statement tests/test_module_report/expected-results/report.html extract of copyright statement: (c) js foundation and other contributors | jquery.org/l +snakemake source: embedded-script-includes-copyright-statement tests/test_report/expected-results/report.html extract of copyright statement: (c) js foundation and other contributors | jquery.org/l + +# the long line is the test +snakemake source: very-long-line-length-in-source-file tests/tests.py line 1186 is 571 characters long (>512) View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/e5d06b9b525a49573053a94ebcc6e465ef2fbb10 -- View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/commit/e5d06b9b525a49573053a94ebcc6e465ef2fbb10 You're receiving this email because of your account on salsa.debian.org.
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