galaxy-tool-refactor-registry 0.2.0__tar.gz

galaxy_tool_refactor_registry-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_registry-0.2.0/CLAUDE.md

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+# CLAUDE.md
+
+Guidance for Claude Code working in this repository.
+
+## Project
+
+`galaxy-tool-refactor-registry` is the **rule-registry facade** tier (tier 3.6)
+of the Galaxy tool refactoring framework: a unified, code-addressable view over
+every baked-in rule, named rulesets, per-rule enable/disable, and a library-first
+`run`/`upgrade`/`detect` API.
+
+| 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` *(this repo)* |
+| 4 | app / CLI | `galaxy-tool-refactor-cli` |
+| 4 | MCP server | `galaxy-tool-refactor-mcp` |
+
+It depends on the rule tiers (0.5 / 1 / 2 / 3 / 3.5); **the lower tiers do not
+depend on it**, and it is the only orchestration layer below the app CLI. Both
+the CLI and the MCP server (`galaxy-tool-refactor-mcp`) sit on top of it.
+
+## Key invariants
+
+- **Library-first.** No `click` / `sys.exit` / printing in the call path; inputs
+  are path / bytes / `ToolDocument`; outputs are structured (`FormatResult` /
+  `UpgradeResult` / `DetectResult`); files are written only when a `write_path`
+  is given. This is what lets the CLI and the MCP server be thin adapters.
+- **fmt is still the only serializer.** All XML bytes come out of
+  `format_tool_document_subset` / fmt's `to_bytes`; the facade never serialises
+  XML itself.
+- **One handle per code.** `RuleHandle` (`handle.py`) adapts each family's rule
+  to a uniform `meta` / `family` / `fixable` / `detect` / `apply` shape; the
+  registry asserts the GTR code namespace is collision-free.
+- **Selectable ≠ all.** `registry()` is the selectable set (canonical codemods +
+  cosmetic fmt + advisory checks). The non-selectable codemods — GTR007–GTR012 + GTR093
+  (validity-gated, internal to `UpgradeToLatest`), GTR014–GTR016 (runtime-gated,
+  applied by `upgrade`), and the opt-in-command-only GTR092/GTR094 (applied by
+  `convert-help` / `tokenize-version`; `adapters.OPT_IN_COMMAND_BY_CODE`) — appear only in
+  `all_handles()` / `list_rules(include_upgrade=True)`. `--select`/`--ignore`
+  on one of them raises `UnknownRuleCode` with a hint naming where it lives.
+- **Apply ordering reproduces `format`.** Codemods in `canonical_codemods()` order,
+  then cosmetic fmt in `meta.order`. The `default` ruleset reproduces the direct
+  `canonical_codemods()` + cosmetic pipeline (a regression test pins facade ==
+  pipeline). Note this tracks the *live* `canonical_codemods()`: when GTR020.1 joined
+  it, default-`format` output shifted vs the pre-partition historical bytes (codemod
+  `docs/decisions.md` §30) — the facade-vs-pipeline pin still holds.
+- **Rulesets and rules are developer-defined.** No user-defined rules/rulesets.
+
+## Coding standards
+
+Hand-written code follows **dignified-python** (vendored at the workspace root
+`.claude/skills/dignified-python/`): LBYL over try/except (the facade has no
+exception handling — it raises typed `UnknownRuleCode`/`UnknownRuleset` from
+`errors.py`, which the CLI catches at its boundary); `pathlib` with explicit
+`encoding` for text I/O; keyword-only args after the first; absolute imports, no
+re-exports, no `__all__`; no import-time side effects (`@cache` for the
+registry/ruleset tables). `optimized-python` is a secondary reference;
+dignified-python governs on conflict. New code lands tests-first.
+
+## Commands
+
+Run from the **workspace root** (`galaxy-tool-refactor/`):
+
+- `uv sync`
+- `uv run --package galaxy-tool-refactor-registry pytest galaxy-tool-refactor-registry/tests/`
+- `uv run ruff check galaxy-tool-refactor-registry/src galaxy-tool-refactor-registry/tests`
+- `uv run mypy --config-file galaxy-tool-refactor-registry/pyproject.toml galaxy-tool-refactor-registry/src`
+
+## Module map
+
+- `handle.py` — the `RuleHandle` adapter dataclass.
+- `adapters.py` — wrap each family (codemod / fmt / check) into a `RuleHandle`;
+  the family class enumerations.
+- `registry.py` — `@cache`d `code -> RuleHandle` index (duplicate-code guard);
+  `registry` / `all_handles` / `by_code` / `known_codes` / `advisory_codes`.
+- `rulesets.py` — derives ruleset code sets from per-rule `RuleMeta.rulesets`
+  membership, `DEFAULT_RULESET`.
+- `resolve.py` — `resolve_codes` / `resolve_upgrade_codes` (ignore ▸ select ▸
+  ruleset; select replaces; named rulesets union).
+- `apply.py` — `apply_selection` (phase-ordered apply).
+- `facade.py` — `run` / `upgrade` / `detect` / `find_references` / `rename_param`
+  (the mutating sibling of `find_references`; deep-copies + serialises on success, see
+  `docs/decisions.md` D11) / `convert_help` / `tokenize_version` / `list_rulesets` / `list_rules`.
+- `macro_profile.py` — Phase-3b imported-`@PROFILE@` upgrade: `profile_token_site`
+  (one tool → defining file + target), the pure `plan_from_sites` (per-file
+  importer agreement), and `apply_profile_token_plans` (bump the agreed files'
+  tokens via `format_macro_document`, skip the rest). See `docs/decisions.md` D5.
+- `version_token_share.py`: shared-macros version tokenization (`tokenize-version
+  --macros-file`) via `plan_shared_tokenization` (create / merge / consensus) behind a
+  proof-by-execution gate (every retargeted tool still expands to its original; a merge
+  is inert for every other importer of the file). The facade's `tokenize_version` (one
+  tool) and `tokenize_version_shared` (a directory group) sit on top. See
+  `docs/decisions.md` D20.
+- `results.py` — the structured result + introspection dataclasses.
+- `errors.py` — `UnknownRuleCode` / `UnknownRuleset`.
+
+## Useful references
+
+- `galaxy-tool-refactor-cli/src/galaxy_tool_refactor_cli/cli.py` — the CLI that
+  consumes this facade.
+- `galaxy-tool-refactor-mcp/src/.../service.py` — the facade->JSON adapter the MCP
+  server wraps (mcp `docs/decisions.md` D1); `docs/vision.md` — the agent-rules future.
+- `galaxy-tool-fmt/docs/decisions.md` §D15 — the per-rule subset seams.

galaxy_tool_refactor_registry-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: galaxy-tool-refactor-registry
+Version: 0.2.0
+Summary: Unified, code-addressable rule registry + named presets for the Galaxy tool refactoring tiers — tier 3.6, a library-first facade the CLI (and a future MCP server) compose.
+Author: Richard Burhans
+License-Expression: MIT
+Requires-Python: >=3.10
+Requires-Dist: galaxy-tool-codemod==0.2.0
+Requires-Dist: galaxy-tool-fmt==0.2.0
+Requires-Dist: galaxy-tool-lint==0.2.0
+Requires-Dist: galaxy-tool-refactor-rules==0.2.0
+Requires-Dist: galaxy-tool-source==0.2.0
+Description-Content-Type: text/markdown
+
+# galaxy-tool-refactor-registry
+
+The **rule-registry facade** (tier 3.6) of the Galaxy tool refactoring framework:
+a single, code-addressable view over every baked-in rule across the three rule
+families — codemod (tier 2, structural GTR), fmt (tier 3, cosmetic GTR), and
+check (tier 3.5, advisory) — plus **named rulesets** and **per-rule
+enable/disable**, behind a **library-first** API.
+
+```
+                 galaxy-tool-refactor-registry   (this package, tier 3.6)
+                        ↑                       ↑
+   galaxy-tool-refactor-cli (tier 4)     galaxy-tool-refactor-mcp (tier 4, future)
+```
+
+It depends on the rule tiers (0.5 / 1 / 2 / 3 / 3.5); the lower tiers do **not**
+depend on it. It is the orchestration core the `galaxy-tool-refactor` CLI sits on
+top of, and the core the agent-facing MCP server sits on
+(`galaxy-tool-refactor-mcp`). All XML serialisation goes through fmt, preserving
+"fmt is the only tier that writes/serialises XML".
+
+## Why library-first
+
+No `click` / `sys.exit` / printing in the call path; functions take a path, raw
+`bytes`, or a `ToolDocument` and return **structured results**; files are written
+only when a `write_path` is given; and the rule/ruleset catalogs are
+introspectable (`list_rules()` / `list_rulesets()`). That shape lets both the CLI
+and a future agent-facing MCP server be thin adapters over the same core. See
+`../galaxy-tool-refactor-mcp/docs/vision.md`.
+
+## Rulesets
+
+| Ruleset | Contents | Notes |
+|---|---|---|
+| `cosmetic` | fmt cosmetic rules (GTR001/003/004) | whitespace / indent / shorthand only |
+| `default` *(default)* | canonical codemods (GTR006/002/005/013) + cosmetic | today's `format` — the opinionated formatter |
+| `iuc` | mirrors `default` (placeholder) | reserved for an IUC-specific divergence |
+| `strict` | `default` + advisory checks | format + flag everything IUC cares about (report-only) |
+
+Membership is declared **per rule** (`RuleMeta.rulesets`): the registry derives
+each ruleset's code set by grouping every registered rule by the names in its
+`meta.rulesets`. Adding or changing rules and rulesets is a **developer** task —
+there are no user-defined rules or rulesets.
+
+## Selection
+
+`resolve_codes(rulesets=…, select=…, ignore=…)` turns ruleset names plus
+`--select`/`--ignore` code lists into a concrete code set — the base is the
+**union** of the named rulesets (or the default ruleset when none are named).
+Precedence is ruff-style: `--ignore` ▸ `--select` ▸ `--ruleset` — an explicit
+`--select` *replaces* the rulesets' set, then `--ignore` subtracts. Unknown
+ruleset names / rule codes raise the typed `UnknownRuleset` / `UnknownRuleCode`.
+
+## Public API (by submodule import; no re-exports)
+
+```python
+from galaxy_tool_refactor_registry.facade import (
+    run, upgrade, detect, list_rulesets, list_rules,
+)
+from galaxy_tool_refactor_registry.resolve import resolve_codes, resolve_upgrade_codes
+from galaxy_tool_refactor_registry.registry import by_code, known_codes, advisory_codes
+```
+
+- `run(source, *, codes, write_path=None) -> FormatResult` — apply the fixable
+  rules in the selection (codemods in canonical order, then cosmetic fmt),
+  reporting advisory findings as notes.
+- `upgrade(source, *, codes, write_path=None) -> UpgradeResult` — profile-upgrade
+  plus the selected fixable rules.
+- `detect(source, *, codes) -> DetectResult` — report-only over the selection.
+- `by_code(code) -> RuleHandle` — the uniform, callable handle for one rule
+  (`meta`, `family`, `fixable`, `detect(document)`, `apply(document)` or `None`).
+
+## Develop
+
+Run from the workspace root (`galaxy-tool-refactor/`):
+
+```bash
+uv run --package galaxy-tool-refactor-registry pytest galaxy-tool-refactor-registry/tests/
+uv run ruff check galaxy-tool-refactor-registry/src galaxy-tool-refactor-registry/tests
+uv run mypy --config-file galaxy-tool-refactor-registry/pyproject.toml galaxy-tool-refactor-registry/src
+```

galaxy_tool_refactor_registry-0.2.0/README.md

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+# galaxy-tool-refactor-registry
+
+The **rule-registry facade** (tier 3.6) of the Galaxy tool refactoring framework:
+a single, code-addressable view over every baked-in rule across the three rule
+families — codemod (tier 2, structural GTR), fmt (tier 3, cosmetic GTR), and
+check (tier 3.5, advisory) — plus **named rulesets** and **per-rule
+enable/disable**, behind a **library-first** API.
+
+```
+                 galaxy-tool-refactor-registry   (this package, tier 3.6)
+                        ↑                       ↑
+   galaxy-tool-refactor-cli (tier 4)     galaxy-tool-refactor-mcp (tier 4, future)
+```
+
+It depends on the rule tiers (0.5 / 1 / 2 / 3 / 3.5); the lower tiers do **not**
+depend on it. It is the orchestration core the `galaxy-tool-refactor` CLI sits on
+top of, and the core the agent-facing MCP server sits on
+(`galaxy-tool-refactor-mcp`). All XML serialisation goes through fmt, preserving
+"fmt is the only tier that writes/serialises XML".
+
+## Why library-first
+
+No `click` / `sys.exit` / printing in the call path; functions take a path, raw
+`bytes`, or a `ToolDocument` and return **structured results**; files are written
+only when a `write_path` is given; and the rule/ruleset catalogs are
+introspectable (`list_rules()` / `list_rulesets()`). That shape lets both the CLI
+and a future agent-facing MCP server be thin adapters over the same core. See
+`../galaxy-tool-refactor-mcp/docs/vision.md`.
+
+## Rulesets
+
+| Ruleset | Contents | Notes |
+|---|---|---|
+| `cosmetic` | fmt cosmetic rules (GTR001/003/004) | whitespace / indent / shorthand only |
+| `default` *(default)* | canonical codemods (GTR006/002/005/013) + cosmetic | today's `format` — the opinionated formatter |
+| `iuc` | mirrors `default` (placeholder) | reserved for an IUC-specific divergence |
+| `strict` | `default` + advisory checks | format + flag everything IUC cares about (report-only) |
+
+Membership is declared **per rule** (`RuleMeta.rulesets`): the registry derives
+each ruleset's code set by grouping every registered rule by the names in its
+`meta.rulesets`. Adding or changing rules and rulesets is a **developer** task —
+there are no user-defined rules or rulesets.
+
+## Selection
+
+`resolve_codes(rulesets=…, select=…, ignore=…)` turns ruleset names plus
+`--select`/`--ignore` code lists into a concrete code set — the base is the
+**union** of the named rulesets (or the default ruleset when none are named).
+Precedence is ruff-style: `--ignore` ▸ `--select` ▸ `--ruleset` — an explicit
+`--select` *replaces* the rulesets' set, then `--ignore` subtracts. Unknown
+ruleset names / rule codes raise the typed `UnknownRuleset` / `UnknownRuleCode`.
+
+## Public API (by submodule import; no re-exports)
+
+```python
+from galaxy_tool_refactor_registry.facade import (
+    run, upgrade, detect, list_rulesets, list_rules,
+)
+from galaxy_tool_refactor_registry.resolve import resolve_codes, resolve_upgrade_codes
+from galaxy_tool_refactor_registry.registry import by_code, known_codes, advisory_codes
+```
+
+- `run(source, *, codes, write_path=None) -> FormatResult` — apply the fixable
+  rules in the selection (codemods in canonical order, then cosmetic fmt),
+  reporting advisory findings as notes.
+- `upgrade(source, *, codes, write_path=None) -> UpgradeResult` — profile-upgrade
+  plus the selected fixable rules.
+- `detect(source, *, codes) -> DetectResult` — report-only over the selection.
+- `by_code(code) -> RuleHandle` — the uniform, callable handle for one rule
+  (`meta`, `family`, `fixable`, `detect(document)`, `apply(document)` or `None`).
+
+## Develop
+
+Run from the workspace root (`galaxy-tool-refactor/`):
+
+```bash
+uv run --package galaxy-tool-refactor-registry pytest galaxy-tool-refactor-registry/tests/
+uv run ruff check galaxy-tool-refactor-registry/src galaxy-tool-refactor-registry/tests
+uv run mypy --config-file galaxy-tool-refactor-registry/pyproject.toml galaxy-tool-refactor-registry/src
+```