Update workflows for Snakemake v9.17.0

[victorlin]

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

1. 🔴 Import from the new location.
   • This would need a try/except ImportError to be generally compatible across Snakemake versions.
2. 🟢 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.Wildcards shared#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).

[joverlee521]

Yeah, agree with option 2.

[joverlee521]

v9.18.0 (snakemake/snakemake@2ed2c23) moved Wildcards again from snakemake.io.containers to snakemake.iocontainers. Definitely going with option 2.

[victorlin]

@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 pull via 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]

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]

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]

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.