galaxy-tool-lint 0.2.0__tar.gz

galaxy_tool_lint-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_lint-0.2.0/CLAUDE.md

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+# CLAUDE.md
+
+Guidance for Claude Code working in this repository.
+
+## Project
+
+`galaxy-tool-lint` is the **advisory check** tier (tier 3.5) of the Galaxy
+tool refactoring framework: read-only IUC best-practice checks that report but
+never mutate.
+
+| 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` *(this repo)* |
+| 3.6 | rule registry / rulesets | `galaxy-tool-refactor-registry` |
+| 4 | app / CLI | `galaxy-tool-refactor-cli` |
+
+It owns the GTR-coded **detect-only** rules (`RuleMeta.detect_only=True`): a
+`CheckRule` ABC (`rules.py`), the concrete checks (the `checks/` sub-package,
+split by element/source area into `tool` / `partition` / `outputs` / `inputs` /
+`validators` / `tests` / `help` submodules + cross-module `_shared` helpers), and
+the registry + runner (`detect.py` — `all_checks()` is an explicit list, mirroring
+the codemod tier's `coded_codemods()` and fmt's `all_rules()`; `detect_violations()`).
+Each check is an LBYL tree query over a tier-1 `ToolDocument` that yields the shared
+tier-0.5 `Violation`.
+
+**Tier independence.** Depends ONLY on tier 1 + tier 0.5 — never on the mutating
+tiers (codemod/fmt) or the app. The advisory tier is a sibling the app composes,
+not a consumer of the fixers. Findings are advisory: the app's `check` command
+reports them but does not fail on them by default.
+
+**Scope.** Covers the mechanically-detectable IUC practices (presence /
+attribute / structure queries). The **flat** IUC advisories are `GTR021`,
+`GTR023`–`GTR029`, `GTR033` (package `<requirement>`s pin a version, D7) plus the
+`GTR032` (`&&`-vs-lone-`&`) — a real detector since D34 (the
+D3 no-op era ended): the `lone_amp.py` classifier flags only the genuine
+*joining* class.
+(unused `<param>`, D11). **Four are the advisory `.2` half of a partition
+practice** (D9/D31; registry D10): `GTR018.2` / `GTR019.2` (the `<command>` / `<help>`
+CDATA mixed-content residual), `GTR020.2` (the non-provable unquoted-`$var`
+residual, via the **read-only `command_text` lexer** in **tier 1**
+`galaxy_tool_source.command_text`), and `GTR089.2` (`HelpRstResidual` — the invalid
+`<help>` RST the repair can't safely fix, via the tier-1 `galaxy_tool_source.rst`
+predicate). Each `.2` reuses the same tier-1 predicate its fixable sibling
+(`GTR018.1` / `GTR019.1` / `GTR020.1` / `GTR089.1`, codemod tier) uses, so the
+partition is sound and the check never depends on the codemod tier.
+
+On top of those, the tier hosts the **planemo-parity wave `GTR038`–`GTR091`** (54
+rules) — a reimplementation of every mechanically-reimplementable
+`galaxy.tool_util.lint` linter, grouped by source area (citations/TODO, outputs,
+embedded expressions, the full `inputs.py` correctness surface, `tests.py`, and
+`<help>` RST validity via the tier-1 `galaxy_tool_source.rst` predicate — `GTR089`, now
+split into the `GTR089.1` repair + `GTR089.2` residual partition, so docutils is a
+tier-1 dep, not declared here — plus output reference integrity and data-param
+format, `GTR090`–`GTR091`; the `GTR035.2` name-whitespace residual, D33; and the
+`GTR095` id/name/version missing-or-empty trio — the half tier-1 `validate` can't
+see, D35). The tier is now **70 checks total**. Each
+wave check that a `<macro>` could spoof skips that tool via the tier-1 `has_macros`
+raw-tree guard (`detect()` reads the un-expanded tree). The authoritative
+planemo→GTR map is `../docs/planemo_linter_parity.md`; per-group rationale + corpus
+counts are in `docs/decisions.md` **D12–D32**. See `../docs/iuc_best_practices.md`
+for the IUC coverage map and D3–D11 for the command-text + requirement-pinning +
+partition-residual + unused-param decisions.
+
+## Coding standards
+
+Hand-written code follows **dignified-python** (vendored at the workspace root
+`.claude/skills/dignified-python/`): LBYL over try/except; `pathlib` with
+explicit `encoding`; keyword-only args after the first; absolute imports, no
+re-exports, no `__all__`; no import-time side effects (`@cache` for module
+state). `optimized-python` is a secondary reference; **dignified-python governs
+on conflict**. New checks land tests-first.
+
+## Commands
+
+Run from the **workspace root** (`galaxy-tool-refactor/`):
+
+- `uv sync` — install dependencies
+- `uv run --package galaxy-tool-lint pytest galaxy-tool-lint/tests/` — run tests
+- `uv run ruff check galaxy-tool-lint/src galaxy-tool-lint/tests` — lint
+- `uv run mypy --config-file galaxy-tool-lint/pyproject.toml galaxy-tool-lint/src` — type-check (strict)
+
+## Useful workspace references
+
+- `galaxy-tool-refactor-rules/src/galaxy_tool_refactor_rules/violation.py` — the
+  shared `Violation` these checks yield; `meta.py` — `RuleMeta` (the
+  `detect_only` flag this tier sets).
+- `galaxy-tool-source/README.md` — tier-1 public API (`ToolDocument`,
+  `newest_valid_profile`, the typed model) the checks query.
+- `galaxy-tool-refactor-cli/src/galaxy_tool_refactor_cli/cli.py` — the app
+  `check` command that runs these alongside the codemod + fmt detect phases.
+- `../docs/iuc_best_practices.md` — the cross-tier IUC coverage map.

galaxy_tool_lint-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: galaxy-tool-lint
+Version: 0.2.0
+Summary: Advisory (detect-only) IUC best-practice checks for Galaxy tool XML — tier 3.5 of the galaxy-tool-source ecosystem.
+Author: Richard Burhans
+License-Expression: MIT
+Requires-Python: >=3.10
+Requires-Dist: galaxy-tool-refactor-rules==0.2.0
+Requires-Dist: galaxy-tool-source==0.2.0
+Requires-Dist: lxml>=5
+Requires-Dist: packaging>=23
+Description-Content-Type: text/markdown
+
+# galaxy-tool-lint
+
+The **advisory check** tier (tier 3.5) of the Galaxy tool refactoring framework:
+read-only IUC best-practice checks that *report* but never mutate.
+
+Where the codemod (tier 2) and fmt (tier 3) tiers *fix* a tool (their detect
+phases report what their fix would change), this tier covers the
+[IUC `tool_xml` best-practices][iuc] that are **not** safely auto-fixable — they
+need a content or semantic decision (add tests, declare requirements, write
+help). Each check is a `RuleMeta`-coded, `detect_only=True` rule that yields the
+shared tier-0.5 `Violation`. The findings are **advisory**: the
+`galaxy-tool-refactor check` command shows them but, by default, does not fail on
+them (use `--strict` to gate on them too).
+
+[iuc]: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html
+
+## Scope
+
+Depends only on tier 1 (`galaxy-tool-source`, the parsed `ToolDocument` and
+profile helpers) and tier 0.5 (`galaxy-tool-refactor-rules`, `RuleMeta` /
+`Violation`). It does **not** depend on the mutating tiers — the app
+(`galaxy-tool-refactor-cli`) composes this alongside them.
+
+```python
+from galaxy_tool_source.binding import load_tool
+from galaxy_tool_lint.detect import detect_violations
+
+for violation in detect_violations(load_tool("my_tool.xml")):
+    print(violation.code, violation.message)
+```
+
+## Checks
+
+See `galaxy_tool_lint.checks` and the IUC coverage map at
+`../docs/iuc_best_practices.md`. **`GTR020.2`** (single-quote Cheetah `$var`) is
+implemented — it reads `<command>` text through the read-only `command_text.py`
+lexer (quote/directive-aware, across newlines; the lexer lives in tier 1,
+`galaxy_tool_source.command_text`, so the GTR020.1 codemod shares it) and reports one
+advisory per fully-unquoted shell-line `$var`. Its *provable* subset is now
+auto-fixed by the GTR020.1 codemod (`docs/decisions.md` D8). **`GTR089.2`**
+(`HelpRstResidual`) is the advisory half of the GTR089 partition: it reports the
+invalid `<help>` reStructuredText the `GTR089.1` repair codemod can't safely fix,
+through the same tier-1 predicate (`galaxy_tool_source.rst`; `docs/decisions.md`
+D31). **`GTR032`** (`&&`-vs-lone-`&`) is a real detector since `docs/decisions.md`
+D34 (the data-backed D3 deferral ended when the CT3 lexer landed): the
+`lone_amp.py` classifier flags only genuine command-joining lone `&`s.

galaxy_tool_lint-0.2.0/README.md

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+# galaxy-tool-lint
+
+The **advisory check** tier (tier 3.5) of the Galaxy tool refactoring framework:
+read-only IUC best-practice checks that *report* but never mutate.
+
+Where the codemod (tier 2) and fmt (tier 3) tiers *fix* a tool (their detect
+phases report what their fix would change), this tier covers the
+[IUC `tool_xml` best-practices][iuc] that are **not** safely auto-fixable — they
+need a content or semantic decision (add tests, declare requirements, write
+help). Each check is a `RuleMeta`-coded, `detect_only=True` rule that yields the
+shared tier-0.5 `Violation`. The findings are **advisory**: the
+`galaxy-tool-refactor check` command shows them but, by default, does not fail on
+them (use `--strict` to gate on them too).
+
+[iuc]: https://galaxy-iuc-standards.readthedocs.io/en/latest/best_practices/tool_xml.html
+
+## Scope
+
+Depends only on tier 1 (`galaxy-tool-source`, the parsed `ToolDocument` and
+profile helpers) and tier 0.5 (`galaxy-tool-refactor-rules`, `RuleMeta` /
+`Violation`). It does **not** depend on the mutating tiers — the app
+(`galaxy-tool-refactor-cli`) composes this alongside them.
+
+```python
+from galaxy_tool_source.binding import load_tool
+from galaxy_tool_lint.detect import detect_violations
+
+for violation in detect_violations(load_tool("my_tool.xml")):
+    print(violation.code, violation.message)
+```
+
+## Checks
+
+See `galaxy_tool_lint.checks` and the IUC coverage map at
+`../docs/iuc_best_practices.md`. **`GTR020.2`** (single-quote Cheetah `$var`) is
+implemented — it reads `<command>` text through the read-only `command_text.py`
+lexer (quote/directive-aware, across newlines; the lexer lives in tier 1,
+`galaxy_tool_source.command_text`, so the GTR020.1 codemod shares it) and reports one
+advisory per fully-unquoted shell-line `$var`. Its *provable* subset is now
+auto-fixed by the GTR020.1 codemod (`docs/decisions.md` D8). **`GTR089.2`**
+(`HelpRstResidual`) is the advisory half of the GTR089 partition: it reports the
+invalid `<help>` reStructuredText the `GTR089.1` repair codemod can't safely fix,
+through the same tier-1 predicate (`galaxy_tool_source.rst`; `docs/decisions.md`
+D31). **`GTR032`** (`&&`-vs-lone-`&`) is a real detector since `docs/decisions.md`
+D34 (the data-backed D3 deferral ended when the CT3 lexer landed): the
+`lone_amp.py` classifier flags only genuine command-joining lone `&`s.