galaxy-tool-refactor-cli

The app tier of the Galaxy tool refactoring framework — the user-facing galaxy-tool-refactor CLI, a thin front-end over the tier-3.6 rule-registry facade (galaxy-tool-refactor-registry).

Rule orchestration lives in the registry facade; this package depends on it (plus fmt's cli_support engine and tier-1 parsing) and exposes twelve commands (format, upgrade, check, find-references, rename-param, rulesets, rules, normalize-macros, convert-help, tokenize-version, bump-version-suffix, lint-skip):

# Safe, idempotent: apply a ruleset's fixable rules + cosmetic formatting.
# Default ruleset = structural canonicalisation + cosmetic; never profile=.
galaxy-tool-refactor format tool.xml
galaxy-tool-refactor format --ruleset cosmetic tool.xml  # whitespace only
galaxy-tool-refactor format --ignore GTR002 tool.xml     # all but param-reorder
galaxy-tool-refactor format tools/                       # also formats <macros> files

# Opt-in, semantic: repair typos, then place profile=, then format.
# Minimal-bump by default: profile= moves only when strictly needed for
# validity (kept when the repaired tool validates at its baseline, undeclared
# stays undeclared, else the minimum valid profile at or above the baseline).
# --modernize opts into the behavior-preserving walk: upgrade profile= as far
# as behaviour provably stays the same, stopping at the behaviour ceiling
# (report naming the blocking code(s), pointing at docs/profile_boundaries.md)
# and never past the deployment ceiling (the newest profile every major
# public Galaxy server runs). Only an explicit --target-profile exceeds the
# deployment ceiling. No --ruleset; --select/--ignore tune it.
galaxy-tool-refactor upgrade tool.xml
galaxy-tool-refactor upgrade --modernize tool.xml              # gated walk to the ceilings
galaxy-tool-refactor upgrade --modernize --allow-behavior-change tool.xml  # lift the behaviour gate
galaxy-tool-refactor upgrade --target-profile 23.0 tool.xml    # explicit cap (implies the walk)

# Report-only linter: one `file:line  CODE  message` per finding, mutating
# nothing. The default ruleset reports the fixable GTR rules; `--ruleset strict` adds
# the advisory checks (marked `(advisory)`). Exits non-zero on any fixable
# finding; advisory findings are informational unless --strict.
galaxy-tool-refactor check tool.xml
galaxy-tool-refactor check --ruleset strict tool.xml

# Introspection.
galaxy-tool-refactor rulesets
galaxy-tool-refactor rules

# Opt-in, repo-scoped: lowercase literal format/ftype in <macros>-root files (the
# macro-library fix the per-tool `upgrade` can't reach). Rewrites files other than
# the one named, so it is a separate command — never part of format/upgrade.
galaxy-tool-refactor normalize-macros macros/            # --check to preview

# Opt-in convenience: prune planemo .lint_skip suppressions we can prove are
# resolved (apply the fixes, remove a line only when its linter is completely
# covered and clean on every tool in the dir). Leaves what it can't prove
# untouched and unmentioned. See docs/lint_skip.md.
galaxy-tool-refactor lint-skip tools/                    # --check to preview

format/upgrade/check share rule selection — --ruleset NAME (repeatable / comma-separated — the union of the named sets), --select CODE…, --ignore CODE… (ruff-style precedence: --ignore ▸ --select ▸ --ruleset; --select replaces the rulesets' set; upgrade takes no --ruleset). format/upgrade also honour --check (detect drift, exit non-zero, don't write — distinct from the check command), --diff, and --quiet; check honours --quiet and --strict. The typical modernization flow is upgrade then format.

Why a separate tier

Profile upgrade is semantic, fallible, and reports outcomes; canonicalisation + formatting is safe and idempotent. Keeping them in separate, explicit commands (rather than auto-upgrading inside "format my tool") lets users opt into modernization deliberately. Rule orchestration sits below the CLI in the registry facade — both because output is written via fmt's serializer (so the orchestrator must sit above fmt) and so the MCP server reuses the same core. See docs/decisions.md §D1 (the app tier), §D2 (check), §D3 (advisory findings), §D4 (the registry facade + rule selection).

Install / test

End-user install (the metapackage is the front door; it pulls this CLI):

pip install galaxy-tool-refactor          # provides the `galaxy-tool-refactor` command
pip install galaxy-tool-refactor-cli      # or this package directly

For development, from the workspace root:

uv sync
uv run --package galaxy-tool-refactor-cli pytest galaxy-tool-refactor-cli/tests/