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Update workflows for Snakemake v9.17.0 #39
Description
Snakemake version 9.17.0 includes a breaking change for our usage.
Specifically, snakemake/snakemake@ffb19e7 moved Wildcards from snakemake.io to snakemake.io.container. This breaks all imports that rely on the old location – shared/snakemake/config.smk and all 14 copies of it.
Possible solutions
Short term
- Pin snakemake to <9.17.0 in managed runtimes (docker, conda)
Long term
- 🔴 Import from the new location.
- This would need a
try/except ImportErrorto be generally compatible across Snakemake versions.
- This would need a
- 🟢 Remove the import.
- This should be fine since the import is non-functional, for typing purposes only.
- Less reliance on Snakemake internals = less chance of future breakage
- Remove import of
snakemake.io.Wildcardsshared#72 - [bot] Update shared/vendored WNV#125
- [bot] Update shared/vendored avian-flu#167
- [bot] Update ingest/vendored chikv#15
- [bot] Update shared/vendored dengue#126
- [bot] Update shared/vendored ebola#51
- [bot] Update shared/vendored lassa#79
- [bot] Update shared/vendored measles#119
- [bot] Update shared/vendored mpox#359
- [bot] Update shared/vendored mumps#53
- [bot] Update shared/vendored nipah#26
- [bot] Update shared/vendored norovirus#49
- [bot] Update shared/vendored pathogen-repo-guide#104
- [bot] Update shared/vendored rsv#128
- [bot] Update shared/vendored zika#106
First noticed in nextstrain/conda-base#150 (comment).
Activity
joverlee521 commentedon Mar 26, 2026
Yeah, agree with option 2.
joverlee521 commentedon Mar 31, 2026
v9.18.0 (snakemake/snakemake@2ed2c23) moved
Wildcardsagain fromsnakemake.io.containerstosnakemake.iocontainers. Definitely going with option 2.Remove import of `snakemake.io.Wildcards`
victorlin commentedon Apr 6, 2026
@joverlee521 thanks for making the change in the shared repo.
The next step is to update all 14 downstream copies. This is inherently tedious. Half of the tedium could be removed with automated PRs of
git subrepo pullvia a central GitHub Actions workflow. We would still manually review/merge the PRs just like dependabot and pre-commit PRs. Any thoughts on this idea?joverlee521 commentedon Apr 7, 2026
Oh yeah, I like the idea of a central GH Action workflow that creates automated PRs. Most of the time this would be an easy review & merge and only a small number of PRs would require additional fixes.
joverlee521 commentedon Apr 11, 2026
Trying out the central GH Action workflow to update the vendored copies with nextstrain/shared@main...update-vendored. Test run failed with permission errors that I'll look into next week.
joverlee521 commentedon Apr 13, 2026
Latest test run completed successfully and created PRs for all of the vendored repos. I'll clean up the GH workflow a little and make a PR.
joverlee521 commentedon Apr 21, 2026
All relevant pathogen workflows have been updated to drop the
snakemake.io.Wildcardsimport and I've linked them in the main issue description.I did not merge the following PRs because they will require more fixes but they have an older copy of the vendored subrepo, so they do not have the import and should not block this issue.
Remove pin for Snakemake