Debian Patches

Status for snakemake/7.32.4-3

Patch Description Author Forwarded Bugs Origin Last update
local_javascript.patch Use local Javascript etc for privacy
Some of the badge images legally could be replaced with local copies,
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)
Kevin Murray <>, Andreas Tille <>, Rebecca N. Palmer <> no
0003-Compat-fix.patch Compat fix Kevin Murray <> no 2016-12-02
0006-restore-bin.patch Version 3.9.1 is lacking snakemake executable - using the binary that results from build process as quilt patch at the former location Andreas Tille <> no 2017-01-09
0008-remove_sphinx.ext.patch Remove sphinxext which spoils doc generation Andreas Tille <> no 2017-12-06
0009-skip-test-without-google-cloud-sdk.patch Skip tests that depend on google-cloud-sdk if not installed
This is not currently in Debian - see RFP #759578.
chrysn <>, Rebecca N. Palmer <> not-needed
python3.patch Use Python 3 in subprocess calls
TODO - are any of the ones in snakemake/ a problem?
Michael R. Crusoe <>, Rebecca N. Palmer <> no
workaround_sphinx_issue.patch Exclude from documentation
Needed as Sphinx 2 can't process it

This is obviously not an ideal fix, but it's an internal class with little
documentation to begin with:

Also exclude Flask.request due to
Rebecca N. Palmer <> yes debian
remove_ccbysa_snippets.patch Remove code from Stack Overflow
Stack Overflow content is CC-BY-SA licensed,
which this package is not supposed to be. These snippets may be
too small to be copyrightable, but removing them to be safe.
Rebecca N. Palmer <> invalid
fix_test_pytest.patch pytest has the -3 suffix on Debian Steffen Moeller <> invalid
python2to3.patch Tests have a series of invocations of the former python executable. Steffen Moeller not-needed
reproducible-build.patch Make the build reproducible Chris Lamb <> no 2021-10-22
test_from_any_directory.patch Allow running the tests from any current directory Rebecca N. Palmer <> no
cirumvent-retry.patch Debian has original retry, not reretry Nilesh Patra <>, Rebecca N. Palmer <> not-needed
skip-tests-with-internet.patch no
skip-tests-with-slurm.patch Skip slurm tests since slurm is not setup at build time Andreas Tille <>, Rebecca N. Palmer no
skip-test-lint_long_run.patch Skip lint test that is known to fail Andreas Tille <> no 2023-01-11
skip-test_workflow_calling.patch Skip lint test that is known to fail Andreas Tille <> no 2023-01-11
no_mix_tabs_spaces.patch Don't mix tabs and spaces
This is no longer allowed in Python 3.12
Rebecca N. Palmer <> no debian upstream
fstring.patch Adapt to Python 3.12 tokenizing f-strings Hocnonsense, Rebecca N. Palmer <> no upstream 2a50dc02bb709161d62d6f7dc5d6f2733e534c09 + 87c06c0f5745f577c12db39852c6f763a2d41954 + f2c761320a5a73d6027ae3649843e6bf6a24f324
1068010_appdirs_to_platformdirs.patch Use platformdirs not appdirs
(I suspect it's an (unrelated) bug that it appears twice
in test-environment.yml)
Rebecca N. Palmer <> no debian

All known versions for source package 'snakemake'