galaxy-tool-refactor-cli 0.2.0

Top-level CLI app that composes the Galaxy tool refactoring tiers (format + upgrade).

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).

Tier	Layer	Package
0.5	rule metadata	galaxy-tool-refactor-rules
1	parsing & validation	galaxy-tool-source
2	structure	galaxy-tool-codemod
3	formatting	galaxy-tool-fmt
3.5	advisory checks	galaxy-tool-lint
3.6	rule registry / rulesets	galaxy-tool-refactor-registry
4	app / CLI	galaxy-tool-refactor-cli (this package)

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

# 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 upgrade profile= to the latest reachable
# version (applying each step's structural migration), then format. Reports the
# steps applied and warns if a tool stalls. No --ruleset; --select/--ignore tune it.
galaxy-tool-refactor upgrade tool.xml

# 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

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

uv sync   # from the workspace root
uv run --package galaxy-tool-refactor-cli pytest galaxy-tool-refactor-cli/tests/