Retire the jmchilton/planemo fork: source everything from released planemo 0.75.44#326
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Fork SHA pin rendered an invalid install command in casts (`uv tool install planemo==git+https://...`). Base released pin renders valid `uv tool install planemo==0.75.44`. Workflow-test phases only need `planemo test --test_output_json`, which base has. - content/cli/planemo: pin/fallback/Install -> 0.75.44; Pin section notes fork-only cli_metadata/output_schema (+ convert-nfcore + vendored artifacts) still need a #1636 release before moving off the fork. - regen run-workflow-test (also un-stubs its Procedure), implement- galaxy-workflow-test, and 6 assembled pipeline harnesses. - convert-nfcore cast left fork-pinned: needs separate re-condense. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
… released 0.75.44
#1636 merged (2026-05-14) and shipped in released planemo 0.75.44
(PyPI 2026-05-26; tag is 27 commits ahead of the merge, ships
cmd_cli_metadata.py + cmd_output_schema.py). No Foundry consumer needs
the fork anymore.
- content/cli/planemo: rewrite Pin section — 0.75.44 carries #1636; drop
the "subcommands absent / needs a release" claim. Regen CLI manual pages
(upstream URL fork SHA -> 0.75.44 tag).
- content/schemas/planemo-test-report: #1636 merged+released, not OPEN;
upstream URL -> 0.75.44; provenance is a release, not a SHA.
- vendored artifacts: re-sync cli-meta + test-report schema vs released
0.75.44 (content identical to fork; only planemo_version + provenance
shape change). sync-from-planemo.mjs PIN now records {repo,release}; tests
assert release pin. sync-planemo-cli.ts PIN -> release ref.
- planemo-drift.yml: read package_version (now a release, no SHA) and
pip-install planemo==<version>; the SHA-grep step was broken by the
0.75.44 pin. AGENTS.md + Makefile install hints -> uvx --from planemo==<version>.
- re-cast run-workflow-test + implement-galaxy-workflow-test reference copies.
convert-nfcore cast still fork-pinned: re-casting it pulls in an unrelated
research-note re-condense backlog (patterns/ -> notes/). Deferred.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Jun 19, 2026
Retire planemo fork in convert-nfcore cast (last holdout, follow-up to #326)
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What
Move Foundry's planemo dependency fully onto the released
planemo==0.75.44(PyPI) and retire thejmchilton/planemofork.PR #1636 merged 2026-05-14 and shipped in
0.75.44(released 2026-05-26 — the tag is 27 commits ahead of the merge and shipscmd_cli_metadata.py+cmd_output_schema.py). So the fork is no longer needed anywhere.Commits
run-workflow-test,implement-galaxy-workflow-test, 6 pipeline harnesses). Recovered from the rebased, now-mergedinterview-galaxy-scenario-referencesbranch.Fork retirement (commit 2)
content/cli/planemo: rewrite the Pin section — 0.75.44 carries #1636, so every consumer runs off the base pin. Regenerate the CLI manual pages (upstream:fork SHA →0.75.44tag).content/schemas/planemo-test-report: #1636 is merged + released (was labeled "OPEN");upstream:→0.75.44; provenance is a release, not a SHA.packages/planemo-cli-meta,packages/planemo-test-report-schema): re-synced against released 0.75.44. Content is identical to the fork output — onlyplanemo_versionand the provenance shape ({repo, release}instead of{repo, branch, sha}) changed. Sync-scriptPINs and package tests updated to assert the release pin..github/workflows/planemo-drift.yml: was extracting a SHA frompackage_versionand pip-installing the fork — broken oncepackage_versionbecame0.75.44. Now reads the version and installsplanemo==<version>from PyPI.AGENTS.md/Makefileinstall hints →uvx --from planemo==<version>.Verification
npm run validate(0 errors),npm run typecheck,npm run packages-test/-typecheck/-lint/-format,make check-assemble-pipelines,make check-planemo-cli— all clean. Vendored artifacts regenerated against a locally-installedplanemo==0.75.44.Deferred
The
convert-nfcore-module-to-galaxy-toolcast bundle still carries the fork pin. Re-casting it cleanly is blocked on an unrelated pre-existing re-condense backlog (its research-note references migratedpatterns/→notes/and need an LLM condense step). Retiring its fork pin will ride along with that re-cast in a separate change.🤖 Generated with Claude Code