[med-svn] [Git][med-team/snakemake][master] More refinements for lintian

[Steffen Möller (@moeller)]

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 <nilesh at debian.org>  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
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