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Planemo

Galaxy tool/workflow runtime testing CLI; used by run-workflow-test and friends.

draft cli/planemo
Revised
2026-09-13
Rev
6

planemo

Galaxy’s runtime testing and authoring CLI. Foundry Molds invoke planemo test, planemo lint, and friends for end-to-end workflow validation; the cast skill consumes structured JSON output from --test_output_json and validates it against planemo-test-report.

Pin

package_version pins to the released planemo==0.75.47 from PyPI — base upstream planemo, no fork. It is the single source of truth: the sync scripts carry no pin of their own and stamp whichever planemo they invoked, and make check-planemo-pin fails if any recorded copy of the version disagrees with this field.

galaxyproject/planemo#1636 merged 2026-05-14 and first shipped in released 0.75.42, so planemo cli_metadata and planemo output_schema are available in every release at or above this pin. Every Foundry consumer runs off this base pin: the workflow-test phases (run-workflow-test, implement-galaxy-workflow-test) which need only planemo test --test_output_json, the convergence loop in convert-nfcore-module-to-galaxy-tool, and the vendored-artifact regeneration story (packages/planemo-cli-meta/, packages/planemo-test-report-schema/). No fork pin is required.

The floor is now 0.75.46 for a packaging reason, not a feature one. galaxy-tool-util declares its galaxy-tool-util-models dependency unconstrained, so a fresh resolve of an older planemo pairs a 25.1.x galaxy-tool-util with a 26.x galaxy-tool-util-models and dies at import (cannot import name 'ToolOutputCollectionStructure'). galaxyproject/planemo#1674 constrains the transitive dependency and first shipped in 0.75.46. Any pin below that needs galaxy-tool-util-models<26 installed alongside it.

Install

uvx --from planemo==0.75.47 planemo --version

For a persistent install:

uv tool install planemo==0.75.47

Contributor laptops only need planemo when regenerating vendored artifacts (the schema JSON in packages/planemo-test-report-schema/, the planemo CLI manual pages under content/cli/planemo/). Normal Foundry development — npm run validate, npm run test, npm run packages-test — builds against the vendored JSON and does not invoke planemo.