galaxy-tool-refactor-cli 0.2.0__tar.gz

galaxy_tool_refactor_cli-0.2.0/.gitignore

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+# Machine-local scratch, never committed: the cloned corpus (.local/corpus,
+# seeded from corpus_sources.json) and external source clones for inspection
+# (e.g. .local/galaxy-src = a clone of galaxyproject/galaxy used to verify
+# Galaxy-internal behaviour locally).
+# No trailing slash: `.local/` matches only a directory, so an accidental
+# symlink at this path was committable (it happened once; removed in this branch).
+.local
+.venv/
+__pycache__/
+*.pyc
+*.pyo
+.pytest_cache/
+.mypy_cache/
+.ruff_cache/
+dist/
+*.egg-info/
+
+# Local-only draft of the GCC poster abstract.
+gcc2026-abstract.txt
+
+# Claude Code session scratch (the tracked .claude/ settings + skills stay; this
+# runtime lock for scheduled wakeups is machine-local).
+.claude/scheduled_tasks.lock
+.claude/worktrees/

galaxy_tool_refactor_cli-0.2.0/CLAUDE.md

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+# CLAUDE.md
+
+Guidance for Claude Code working in this repository.
+
+## Project
+
+`galaxy-tool-refactor-cli` is the **app tier** (tier 4) of the Galaxy tool
+refactoring framework: the user-facing CLI front-end over the rule-registry
+facade.
+
+| 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 repo)* |
+
+Rule orchestration lives in the tier-3.6 **registry facade**
+(`galaxy-tool-refactor-registry`); this package depends on it (plus fmt's
+`cli_support` engine and tier-1 parsing) and does CLI plumbing only — it no
+longer imports the codemod / check tiers directly. It exposes the
+`galaxy-tool-refactor` CLI with nine subcommands:
+
+- `format` — apply a ruleset's fixable rules then cosmetic formatting. The default
+  ruleset = `canonical_codemods()` (repair + attribute / element order + the
+  CDATA wraps + GTR020 command-var single-quoting) + cosmetic. Safe, idempotent,
+  never changes `profile=`. (GTR020 shifts default-`format` bytes vs the pre-GTR020
+  historical output — behaviour-preserving; codemod `docs/decisions.md` §30.)
+  Advisory rules in a selection are reported as notes, never applied. Also
+  cosmetically formats macro-library files (`<macros>` root) — kind-applicable
+  rules only (no codemods); selection governs tools (cli §D5).
+- `upgrade` — repair, then iterative profile upgrade, then cosmetic formatting.
+  Opt-in and semantic. No `--ruleset`; `--select`/`--ignore` adjust its rule set.
+  Also bumps an imported `@PROFILE@` token in place when every profile-using
+  importer in the run agrees on the target, else reports+skips (cli §D6); the
+  inline-token case is GTR007's job.
+- `check` — report-only linter (mutates nothing) over the selected rules' detect
+  phases: `file:line  CODE  message` per finding. The default ruleset reports only
+  *fixable* GTR findings; `--ruleset strict` adds the *advisory* checks (marked
+  `(advisory)`). Fixable findings exit non-zero; advisory are informational unless
+  `--strict`. Macro files are checked for cosmetic (fixable) drift too.
+- `find-references` — read-only query (mutates nothing, not a rule): print every
+  Cheetah `$NAME` reference site (`file:line  [section]  $ref`) across a tool **and its
+  imported macro files** (`galaxy_tool_source.cheetah_refs` + the bundle); see
+  `docs/decisions.md` §D8, §D10.
+- `rename-param` — the mutating sibling of `find-references` (not a rule): rename a
+  parameter OLD→NEW across every Cheetah section, by-name cross-ref attribute, and
+  `<tests>` mirror, plus the definition — across the tool **and its imported macros**
+  (the bundle), atomically. `--repo-root` proves a touched macro is sole-owned (a
+  shared macro is skipped + reported, or — with `--across-importers` — renamed across
+  every importer in lockstep when they all agree); `--check` previews; `--backup` keeps
+  `.bak`s. First Cheetah mutator (M5.3) over `cheetah_rename` / `bundle_rename`; see
+  `docs/decisions.md` §D9, §D10, §D11.
+- `rulesets` / `rules` — introspection of the baked-in rulesets and rules.
+- `convert-help` — opt-in: convert an RST `<help>` body to Markdown
+  (`format="markdown"`, GTR092) when provable — profile ≥ 24.2 (XSD gate; the skip
+  says "run `upgrade` first") + the tier-1 render-equivalence gate (needs the
+  `galaxy-tool-source[markdown]` extra). Behaviour-changing by construction (swaps the
+  rendering engine), so a deliberate, separate command — never part of
+  `format`/`upgrade` (cli §D12; codemod §38).
+- `normalize-macros` — opt-in, repo-scoped pass that lowercases literal
+  `format`/`ftype` in `<macros>`-root files (the macro-library analog of 24.2
+  normalization the per-tool `upgrade` cannot reach). Rewrites files other than the
+  one named (a shared macro file affects every importer), so it is a deliberate,
+  separate command — never part of `format`/`upgrade` (cli §D7;
+  `galaxy-tool-codemod/docs/macro-aware-normalization.md`).
+
+Macro handling is **cosmetic-only and bundle-free for `format`/`check`** (macro
+files are formatted/checked standalone as encountered — cosmetic formatting is safe
+regardless of sharing; cli §D5). But `rename-param` / `find-references` **are
+bundle-aware** (cli §D10): they operate over a tool *and its imported macro files*,
+with a sole-owned `--repo-root` gate for the macro edits a rename makes (registry D12;
+`galaxy-tool-source/docs/decisions.md` §21). All five mutating commands accept `--backup`
+(`<file>.bak` before overwrite).
+
+Selection (`--ruleset` / `--select` / `--ignore`) is shared by
+`format`/`upgrade`/`check` (upgrade takes no `--ruleset`); precedence is ruff-style
+(`--ignore` ▸ `--select` ▸ `--ruleset`, where `--select` replaces the ruleset set;
+`--ruleset` is repeatable / comma-separated and takes the union of the named sets).
+`format`/`upgrade` reuse fmt's `cli_support` engine (file walking,
+`--check`/`--diff`/`--quiet`, drift detection, summary), wrapping `facade.run` /
+`facade.upgrade` in the per-file transform; `check` runs its own report-only loop
+(`cli_support.iter_targets`/`is_tool_root` + `facade.detect`). The facade — not
+this package — composes the lower tiers, which is *why* the orchestration sits
+below the CLI (so the MCP server reuses it). See `docs/decisions.md` §D1
+(app tier), §D2 (`check`), §D3 (advisory findings), §D4 (registry facade +
+selection); `galaxy-tool-refactor-registry/docs/decisions.md` D1–D4;
+`galaxy-tool-fmt/docs/decisions.md` §D12.
+
+## Coding standards
+
+Hand-written code follows **dignified-python** (vendored at the workspace root
+`.claude/skills/dignified-python/`): LBYL over try/except; exceptions only at
+the CLI error boundary; `pathlib.Path` with explicit `encoding="utf-8"`;
+keyword-only args after the first; absolute imports, no re-exports, no
+`__all__`; no import-time side effects. `optimized-python` is a secondary
+reference; **dignified-python governs on conflict**.
+
+## Commands
+
+Run from the **workspace root** (`galaxy-tool-refactor/`):
+
+- `uv sync` — install dependencies
+- `uv run --package galaxy-tool-refactor-cli pytest galaxy-tool-refactor-cli/tests/` — run tests
+- `uv run ruff check galaxy-tool-refactor-cli/src galaxy-tool-refactor-cli/tests` — lint
+- `uv run mypy --config-file galaxy-tool-refactor-cli/pyproject.toml galaxy-tool-refactor-cli/src` — type-check (strict)
+- `uv run galaxy-tool-refactor format <file>` / `uv run galaxy-tool-refactor upgrade <file>` — run the CLI
+
+## Useful workspace references
+
+- `galaxy-tool-refactor-registry/src/galaxy_tool_refactor_registry/facade.py` —
+  the `run` / `upgrade` / `detect` / `list_rulesets` / `list_rules` entry points
+  this CLI wraps; `resolve.py` for `resolve_codes` / `resolve_upgrade_codes`.
+- `galaxy-tool-fmt/src/galaxy_tool_fmt/cli_support.py` — the shared
+  file-processing engine (`run`, `iter_targets`, `is_tool_root`,
+  `TransformOutcome`).
+- `galaxy-tool-codemod/src/galaxy_tool_codemod/canonical.py` — the
+  `canonical_codemods()` / `AUTO_UPGRADE_CODEMODS` contracts the facade consumes.

galaxy_tool_refactor_cli-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: galaxy-tool-refactor-cli
+Version: 0.2.0
+Summary: Top-level CLI app that composes the Galaxy tool refactoring tiers (format + upgrade).
+Author: Richard Burhans
+License-Expression: MIT
+Requires-Python: >=3.10
+Requires-Dist: click>=8
+Requires-Dist: galaxy-tool-fmt==0.2.0
+Requires-Dist: galaxy-tool-refactor-registry==0.2.0
+Requires-Dist: galaxy-tool-source==0.2.0
+Description-Content-Type: text/markdown
+
+# 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`):
+
+```bash
+# 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
+
+```bash
+uv sync   # from the workspace root
+uv run --package galaxy-tool-refactor-cli pytest galaxy-tool-refactor-cli/tests/
+```

galaxy_tool_refactor_cli-0.2.0/README.md

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+# 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`):
+
+```bash
+# 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
+
+```bash
+uv sync   # from the workspace root
+uv run --package galaxy-tool-refactor-cli pytest galaxy-tool-refactor-cli/tests/
+```