[med-svn] [Git][med-team/snakemake][master] 5 commits: Run the tests in a copy instead of trying to clean up after them.
Rebecca N. Palmer (@rnpalmer-guest)
gitlab at salsa.debian.org
Sun Jan 9 15:16:24 GMT 2022
Rebecca N. Palmer pushed to branch master at Debian Med / snakemake
Commits:
bd339a6c by Rebecca N. Palmer at 2022-01-08T21:20:04+00:00
Run the tests in a copy instead of trying to clean up after them.
- - - - -
bc37ef8f by Rebecca N. Palmer at 2022-01-09T14:07:36+00:00
Update Lintian overrides.
- - - - -
0e7f2f3f by Rebecca N. Palmer at 2022-01-09T14:14:05+00:00
Don't try to use local Javascript in GUI, as this is risky;
Fix possibly broken local Javascript in documentation.
- - - - -
312453af by Rebecca N. Palmer at 2022-01-09T14:25:23+00:00
Merge TODO into README.source and update.
- - - - -
5d087079 by Rebecca N. Palmer at 2022-01-09T15:16:05+00:00
Fix some broken tests, and document still needed test skips.
- - - - -
13 changed files:
- debian/README.source
- − debian/TODO
- debian/changelog
- debian/control
- debian/patches/local_javascript.patch
- debian/patches/series
- + debian/patches/test_from_any_directory.patch
- debian/rules
- + debian/snakemake.links
- debian/snakemake.lintian-overrides
- debian/source/lintian-overrides
- debian/tests/control
- debian/tests/run-unit-test
Changes:
=====================================
debian/README.source
=====================================
@@ -1,12 +1,15 @@
Use of external Javascript etc (privacy issue):
-- report.html, table.html: several
-- gui.html: mostly fixed but one remains,
- https://silviomoreto.github.io/bootstrap-select/
+- report.html, table.html, gui.html
+
+Intentionally left unfixed for the time being: there is a risk that
+using the version Debian has as libjs* instead of the version
+specified by upstream will break things, and also reports might be
+sent to people without snakemake installed.
Missing (optional) dependencies:
-- conda
+- conda (ITP #926416)
- gfal-copy and other gfal-* commands for gfal/gridftp (missing from gfal2?)
- setup.py-declared optional depends:
@@ -18,4 +21,5 @@ XRootD
aioeasywebdav
moto (RFP #777089)
pysftp
-tibanna
\ No newline at end of file
+tibanna
+tes
=====================================
debian/TODO deleted
=====================================
@@ -1,10 +0,0 @@
-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
- 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
=====================================
@@ -5,6 +5,12 @@ snakemake (6.12.3-1) UNRELEASED; urgency=medium
* Update d/copyright.
* Use python3-connection-pool instead of an embedded copy.
* Remove unsatisfiable Suggests. Update and sort build/test-Depends.
+ * Run the tests in a copy instead of trying to clean up after them.
+ * Update Lintian overrides.
+ * Don't try to use local Javascript in GUI, as this is risky.
+ * Fix possibly broken local Javascript in documentation.
+ * Merge TODO into README.source and update.
+ * Fix some broken tests, and document still needed test skips.
-- Rebecca N. Palmer <rebecca_palmer at zoho.com> Sat, 08 Jan 2022 19:33:41 +0000
=====================================
debian/control
=====================================
@@ -65,11 +65,7 @@ Depends: ${misc:Depends},
${python3:Depends},
${sphinxdoc:Depends},
ca-certificates,
- libjs-bootstrap,
- libjs-d3,
- libjs-jquery,
libjs-mathjax,
- node-dagre-d3-renderer,
python3-appdirs,
python3-configargparse,
python3-datrie,
=====================================
debian/patches/local_javascript.patch
=====================================
@@ -5,6 +5,10 @@ but this would appear to be a live status when it isn't
(or a per-version status that is easy to forget to update),
so use text links instead
+This intentionally doesn't cover gui.html, because it would be too
+easy to break it (by using the wrong versions) without noticing,
+and we can't do all of it anyway (no bootstrap-select)
+
Author: Kevin Murray <spam at kdmurray.id.au>, Andreas Tille <tille at debian.org>, Rebecca N. Palmer <rebecca_palmer at zoho.com>
Forwarded: no
@@ -15,31 +19,11 @@ Forwarded: no
autodoc_default_options = {'exclude-members': 'lazy_property'}
+# Use debian copy of mathjax, to avoid a lintian error
-+mathjax_path = "file:///usr/share/javascript/mathjax/MathJax.js"
++mathjax_path = "MathJax.js"
+
# Snakemake theme (made by SciAni).
html_css_files = ["theme.css"]
---- a/snakemake/gui.html
-+++ b/snakemake/gui.html
-@@ -2,12 +2,12 @@
- <html lang="en">
- <head>
- <title>Snakemake</title>
-- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/jquery/2.1.1/jquery.min.js"></script>
-- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.4.6/d3.min.js"></script>
-- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.1.1/js/bootstrap.min.js"></script>
-- <script type="text/javascript" src="https://cpettitt.github.io/project/dagre-d3/v0.1.5/dagre-d3.js"></script>
-+ <script type="text/javascript" src="file:///usr/share/javascript/jquery/jquery.min.js"></script>
-+ <script type="text/javascript" src="file:///usr/share/javascript/d3/d3.min.js"></script>
-+ <script type="text/javascript" src="file:///usr/share/javascript/bootstrap/js/bootstrap.min.js"></script>
-+ <script type="text/javascript" src="file:///usr/share/nodejs/dagre-d3/dist/dagre-d3.min.js"></script>
- <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.5.4/bootstrap-select.min.js"></script>
-- <link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.1.1/css/bootstrap.min.css"/>
-+ <link rel="stylesheet" type="text/css" href="file:///usr/share/javascript/bootstrap/css/bootstrap.min.css"/>
- <link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/bootstrap-select/1.5.4/bootstrap-select.min.css"/>
- <style>
- body {
--- a/docs/index.rst
+++ b/docs/index.rst
@@ -4,40 +4,15 @@
=====================================
debian/patches/series
=====================================
@@ -9,3 +9,4 @@ remove_ccbysa_snippets.patch
fix_test_pytest.patch
python2to3.patch
reproducible-build.patch
+test_from_any_directory.patch
=====================================
debian/patches/test_from_any_directory.patch
=====================================
@@ -0,0 +1,54 @@
+Description: Allow running the tests from any current directory
+
+Author: Rebecca N. Palmer <rebecca_palmer at zoho.com>
+Forwarded: no
+
+--- a/tests/tests.py
++++ b/tests/tests.py
+@@ -7,7 +7,6 @@ import os
+ import sys
+ import uuid
+ import subprocess as sp
+-from pathlib import Path
+
+ sys.path.insert(0, os.path.dirname(__file__))
+
+@@ -1217,29 +1216,29 @@ def test_generate_unit_tests():
+
+ @skip_on_windows
+ def test_metadata_migration():
+- outpath = Path(
+- "tests/test_metadata_migration/some/veryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryverylong"
++ outpath = dpath(
++ "test_metadata_migration/some/veryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryverylong"
+ )
+ os.makedirs(outpath, exist_ok=True)
+- metapath = Path(
+- "tests/test_metadata_migration/.snakemake/metadata/@c29tZS92ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5L3Zlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5L3Zlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcn/@l2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeS92ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnkvdmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnkvdmVyeXZlcnl2ZXJ5dmVy"
++ metapath = dpath(
++ "test_metadata_migration/.snakemake/metadata/@c29tZS92ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5L3Zlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5L3Zlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcn/@l2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeS92ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnkvdmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnkvdmVyeXZlcnl2ZXJ5dmVy"
+ )
+ os.makedirs(metapath, exist_ok=True)
+- exppath = Path(
+- "tests/test_metadata_migration/expected-results/some/veryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryverylong"
++ exppath = dpath(
++ "test_metadata_migration/expected-results/some/veryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryveryveryveryveryvery/veryveryveryveryveryveryveryveryveryveryveryveryverylong"
+ )
+ os.makedirs(exppath, exist_ok=True)
+- with open(outpath / "path.txt", "w"):
++ with open(outpath + "/path.txt", "w"):
+ # generate empty file
+ pass
+ # generate artificial incomplete metadata in v1 format for migration
+ with open(
+ metapath
+- / "eXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeWxvbmcvcGF0aC50eHQ=",
++ + "/eXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeXZlcnl2ZXJ5dmVyeWxvbmcvcGF0aC50eHQ=",
+ "w",
+ ) as meta:
+ print('{"incomplete": true, "external_jobid": null}', file=meta)
+- with open(exppath / "path.txt", "w") as out:
++ with open(exppath + "/path.txt", "w") as out:
+ print("updated", file=out)
+
+ # run workflow, incomplete v1 metadata should be migrated and trigger rerun of the rule,
=====================================
debian/rules
=====================================
@@ -5,8 +5,10 @@
export PYBUILD_NAME=snakemake
export PYBUILD_DESTDIR_python3=debian/snakemake
+# copy the tests and run them from there to avoid having to clean up after them
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_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests
+export PYBUILD_TEST_ARGS=python{version} -m pytest -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_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_modules_meta_wrapper and not test_tes and not test_github_issue1062 and not test_env_modules'
# Avoiding new queue and leaving all in one big package for now
#DOCPACKAGE=snakemake-doc
@@ -15,20 +17,21 @@ DOCPACKAGE=snakemake
TESTPACKAGE=snakemake
# 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
-# Docker images: test_issue1083, test_github_issue78, test_container, test_singularity, test_singularity_conda, test_cwl_singularity, test_convert_to_cwl, test_report, test_report_zip
+# Snakefile/snakemake-wrapper/CWL scripts: test_cwl, test_cwl_singularity, test_url_include, test_wrapper, test_module_with_script, test_module_report, test_module_complex(2), test_modules_meta_wrapper
+# Docker images: test_issue1083, test_github_issue78, test_container, test_singularity, test_singularity_conda, test_cwl_singularity, test_convert_to_cwl, test_report, test_report_zip, test_module_complex(2)
# Conda packages: test_archive, test_jupyter_notebook, test_conda, test_upstream_conda, test_conda_custom_prefix, test_wrapper, test_script, test_issue635, test_issue1093, test_singularity_conda, test_report, test_report_zip
# Note that even if conda were added to Debian (ITP #926416), using it normally would still be downloading executables = forbidden
# Modification to run without conda was previously attempted on test_issue635 (succeeded) and test_issue1093 (failed as current bwa gives a different ordering), but is not in current use
# Skipped due to not-in-Debian dependencies
# python3-moto (RFP #777089): test_default_resources, test_default_remote, test_remote, test_output_file_cache_remote
-# python3-tibanna: test_tibanna
+# python3-tibanna: test_tibanna (possibly also specific to one cloud provider?)
+# python3-tes: test_tes
-# Skipped in build due to network use, but run in autopkgtest: test_ancient
+# Skipped in build due to network use, but run in autopkgtest: test_ancient test_github_issue1062
# Tests marked @connected skip themselves in this case
-export PYBUILD_AFTER_TEST_python3=rm -fr {build_dir}/bin {build_dir}/tests {dir}/tests/test_filegraph/.snakemake/ {dir}/tests/linting/*/.snakemake/ {dir}/tests/test_filegraph/fg.pdf
+# possibly an actual bug: test_env_modules
export PATH:=$(shell pybuild --print build_dir --interpreter python3 --name $(PYBUILD_NAME))/bin:$(PATH)
@@ -44,11 +47,8 @@ override_dh_auto_build:
PYTHONPATH=$(shell pybuild --print build_dir --interpreter python3) \
python3 setup.py build_sphinx
-execute_after_dh_install:
- find debian/snakemake -name '.gitignore' | xargs -r rm
-
execute_after_dh_installdocs:
- find debian/ -name '__pycache__' -o -name '\.snakemake' | xargs rm -rf
+ find debian -name '__pycache__' -o name '.gitignore' | xargs rm -rf
# the modules.sh is a workaround for #928826; putting it in PYBUILD_BEFORE_TEST_python3 doesn't work
override_dh_auto_test:
@@ -64,10 +64,6 @@ override_dh_installdocs:
mkdir -p debian/$(DOCPACKAGE)/usr/share/doc/snakemake/examples
cp -r build/sphinx/html/* debian/$(DOCPACKAGE)/usr/share/doc/snakemake/html/
cp -r examples/* debian/$(DOCPACKAGE)/usr/share/doc/snakemake/examples
- find debian -name .snakemake | xargs -r rm -r
- find debian/snakemake -name '.gitignore' -o -name '.gitkeep' | xargs -r rm
- find debian/$(DOCPACKAGE) -name '.gitignore' -o -name '.gitkeep' | xargs -r rm
- rm -rf debian/*/usr/share/doc/snakemake/tests/__pycache__
ifneq (snakemake,$(TESTPACKAGE))
if [ -d debian/snakemake/usr/share/doc/snakemake/tests/ ]; then \
mv debian/snakemake/usr/share/doc/snakemake/tests debian/$(TESTPACKAGE)/usr/share/doc/snakemake/ ; \
@@ -76,18 +72,5 @@ endif
override_dh_auto_clean:
dh_auto_clean
- # eaasing transition between all-in-one and separate packages
- rm -rf debian/snakemake-doc debian/snakemake-test
- # cleaning up after build
find . -name '__pycache__' | xargs -r rm -r
- find . -name '*.pyc' | xargs -r rm
- rm -f tests/test_filegraph/fg.pdf
- rm -f tests/test_filegraph/fg.dot
- rm -rf tests/test_github_issue413/.snakemake
- rm -f tests/test_github_issue413/stats.txt
- find tests/test_metadata_migration -name "path.txt" -delete
- find tests -name "*.log" | grep -v expected-results | xargs -r rm -f
- rm -rf .snakemake
- rm -rf tests/test_metadata_migration/.snakemake
- rm -rf snakemake.egg-info
- if [ ! -r bin/snakemake ]; then rm -rf bin; fi
+ rm -rf .snakemake snakemake.egg-info
=====================================
debian/snakemake.links
=====================================
@@ -0,0 +1 @@
+usr/share/javascript/mathjax/MathJax.js usr/share/doc/snakemake/html/_static/MathJax.js
=====================================
debian/snakemake.lintian-overrides
=====================================
@@ -1,3 +1,2 @@
snakemake: no-manual-page usr/bin/snakemake-bash-completion
-snakemake: script-not-executable usr/lib/python3/dist-packages/snakemake/executors/jobscript.sh
snakemake: extra-license-file usr/share/doc/snakemake/html/_sources/project_info/license.rst.txt
=====================================
debian/source/lintian-overrides
=====================================
@@ -1,21 +1,18 @@
# This is just pure test data we need to compare with
snakemake source: source-is-missing tests/test_report/expected-results/report.html
-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)
+# using long lines is not always a bug
+snakemake source: very-long-line-length-in-source-file docs/executing/cluster.rst *
+snakemake source: very-long-line-length-in-source-file docs/project_info/faq.rst *
+snakemake source: very-long-line-length-in-source-file docs/snakefiles/deployment.rst *
+snakemake source: very-long-line-length-in-source-file docs/snakefiles/remote_files.rst *
+snakemake source: very-long-line-length-in-source-file docs/snakefiles/rules.rst *
+snakemake source: very-long-line-length-in-source-file docs/tutorial/advanced.rst *
+snakemake source: very-long-line-length-in-source-file tests/tests.py *
+snakemake source: very-long-line-length-in-source-file tests/test_*/.snakemake/metadata/* *
+snakemake source: very-long-line-length-in-source-file tests/test_*/expected-results/* *
+snakemake source: very-long-line-length-in-source-file tests/test_*report*/test.csv *
+snakemake source: very-long-line-length-in-source-file tests/test_*report*/custom-stylesheet.css *
=====================================
debian/tests/control
=====================================
@@ -7,7 +7,9 @@ Restrictions: allow-stderr
Tests: run-unit-test
Depends: snakemake,
environment-modules,
+ r-base-core,
python3-connection-pool,
+ python3-ftputil,
python3-jinja2,
python3-pandas,
python3-pygraphviz,
=====================================
debian/tests/run-unit-test
=====================================
@@ -21,4 +21,4 @@ export HOME="${AUTOPKGTEST_TMP}"
. /etc/profile.d/modules.sh
#See debian/rules for why these are excluded
-python3 -m pytest -v ${ROOT}/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 and not test_metadata_migration'
+python3 -m pytest -v ${ROOT}/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_env_modules'
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/f115a157ed922d936e014909173055421421b5cc...5d0870799bd68980e62704141418ff7e2b0be443
--
View it on GitLab: https://salsa.debian.org/med-team/snakemake/-/compare/f115a157ed922d936e014909173055421421b5cc...5d0870799bd68980e62704141418ff7e2b0be443
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