| 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 <spam@kdmurray.id.au>, Andreas Tille <tille@debian.org>, Rebecca N. Palmer <rebecca_palmer@zoho.com> | no | |||
| 0003-Compat-fix.patch | Compat fix | Kevin Murray <kdmfoss@gmail.com> | 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 <tille@debian.org> | no | 2017-01-09 | ||
| 0008-remove_sphinx.ext.patch | Remove sphinxext which spoils doc generation | Andreas Tille <tille@debian.org> | 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 <chrysn@fsfe.org>, Rebecca N. Palmer <rebecca_palmer@zoho.com> | not-needed | |||
| python3.patch | Use Python 3 in subprocess calls TODO - are any of the ones in snakemake/script.py:execute_script a problem? |
Michael R. Crusoe <michael.crusoe@gmail.com>, Rebecca N. Palmer <rebecca_palmer@zoho.com> | no | |||
| workaround_sphinx_issue.patch | Exclude common.py:lazy_property 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: https://snakemake.readthedocs.io/en/stable/api_reference/internal/snakemake.html#snakemake.common.lazy_property Also exclude Flask.request due to https://github.com/sphinx-doc/sphinx/issues/7516 |
Rebecca N. Palmer <rebecca_palmer@zoho.com> | 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 <rebecca_palmer@zoho.com> | invalid | |||
| fix_test_pytest.patch | pytest has the -3 suffix on Debian | Steffen Moeller <moeller@debian.org> | 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 <lamby@debian.org> | no | 2021-10-22 | ||
| test_from_any_directory.patch | Allow running the tests from any current directory | Rebecca N. Palmer <rebecca_palmer@zoho.com> | no | |||
| cirumvent-retry.patch | Debian has original retry, not reretry | Nilesh Patra <nilesh@debian.org>, Rebecca N. Palmer <rebecca_palmer@zoho.com> | 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 <tille@debian.org>, Rebecca N. Palmer | no | |||
| skip-test-lint_long_run.patch | Skip lint test that is known to fail | Andreas Tille <tille@debian.org> | no | 2023-01-11 | ||
| skip-test_workflow_calling.patch | Skip lint test that is known to fail | Andreas Tille <tille@debian.org> | 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 <rebecca_palmer@zoho.com> | no | debian upstream | ||
| fstring.patch | Adapt to Python 3.12 tokenizing f-strings | Hocnonsense, Rebecca N. Palmer <rebecca_palmer@zoho.com> | 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 <rebecca_palmer@zoho.com> | no | debian | ||
| test_solver.patch | Make test_solver actually call the solver (i.e. have more than 1 job that could be run first) Related to (but not a fix for) https://launchpad.net/bugs/1928940 |
Rebecca N. Palmer <rebecca_palmer@zoho.com> | no | |||
| test_extra_time.patch | Allow more time for test*_cancelscript* They were failing on riscv64 because the SIGINT was before they'd finished loading (the different times for the two tests are to get more information if this fails, I expect them to load in similar amounts of time) |
Rebecca N. Palmer <rebecca_palmer@zoho.com> | no | |||
| no_pkg_resources.patch | Stop using pkg_resources | Rebecca N. Palmer <rebecca_palmer@zoho.com> | no | debian |