Bump Versions

Bump Versions

versions.yml at the repo root is the single source of truth for the pipeline version (bactopia) and the plugin pin (nf-bactopia). It is edited by hand — this skill never touches it. Its job is the mechanical, error-prone part: copying those two values into every hand-maintained file that repeats them, so bactopia-lint's V001 (version-bearing files must equal versions.yml) goes green.

Two classes of version-bearing files exist, and only one is this skill's concern:

• Hand-maintained (this skill fixes these): conf/test_base.config (bactopia_version + the nf-bactopia@ plugin pin, inherited by all ~183 module/subworkflow test configs), CITATION.cff, bin/bactopia, data/conda/meta.yaml.
• Generated (this skill does NOT touch these): nextflow.config, every workflows/*/nextflow.config, catalog.json, llms.txt. These are rendered from versions.yml by bactopia-merge-schemas / bactopia-catalog, so the fix is to regenerate them — a follow-up, not an edit. Slash commands cannot invoke other slash commands, so you recommend those to the user rather than running them.

Steps

1. Dry-run first. Show the user exactly what will change before writing anything:

   python3 .agents/skills/bump-versions/scripts/bump_versions.py \
       --bactopia-path /home/rpetit3/repos/bactopia/bactopia --check
   

   The script reads versions.yml, then reports each hand-maintained literal as would update <old> -> <new>, already <value>, or a WARN (file missing or the literal moved). If everything is already ok, tell the user the hand-maintained files are in sync and skip to step 4 (they may still need a regen if a generated artifact lagged).

2. Confirm, then apply. Once the user is happy with the dry-run, drop --check to write the changes:

   python3 .agents/skills/bump-versions/scripts/bump_versions.py \
       --bactopia-path /home/rpetit3/repos/bactopia/bactopia
   

   Only the version token inside each match is rewritten; runs are idempotent.

3. Recommend the regeneration follow-ups. If anything changed (or a generated artifact is suspected stale), tell the user to run, in order:

   • /merge-schemas all — re-renders nextflow.config + workflow configs + schemas from versions.yml.
   • /update-catalog — rebuilds catalog.json + llms.txt. Do not attempt to run these from here.

4. Verify V001–V003. Confirm the version gate is actually green:

   bash .agents/skills/review-groovydoc/scripts/run-bactopia-lint.sh \
       --bactopia-path /home/rpetit3/repos/bactopia/bactopia --json --silent
   

   Read the repo component's results. A clean run lists no V0xx failures (PASS results are suppressed). If V001 still fails, report the offending files verbatim — most often a generated artifact whose regen (step 3) hasn't run yet, or a version-bearing file this skill doesn't own.

5. Flag downstream checks (report, don't fix):

   • V002 compares versions.yml to the top ## vX.Y.Z CHANGELOG heading. If they disagree, the CHANGELOG needs a section for the new version — that's human-authored content, so surface it, don't invent it.
   • Bumping bactopia_version changes the test container tag (bactopia/bactopia:<version>) used by every module/subworkflow test. Recommend a smoke test (/run-tests on a quick component) once the matching image exists, since a nonexistent tag will fail tests even with a green lint.

Notes

• The script needs only Python stdlib + read access to versions.yml; no conda env or bactopia-* CLI. There is deliberately no bactopia-versions CLI — versions.yml is hand-edited and this propagation is the whole story.
• The four hand-maintained targets and their literal formats are encoded in the script's TARGETS map, matching V001's own regexes so the skill fixes exactly what the linter checks. If V001 ever grows a new hand-maintained file, add it there.

Sibling skills

• /merge-schemas, /update-catalog — the regeneration follow-ups (step 3).
• /review-groovydoc — backs the bactopia-lint verification run (step 4).
• /release-checklist — its check 1 delegates the version gate to these same V-rules.