Further cleanup with repo-review

.github/copilot-instructions.md

@@ -7,18 +7,24 @@ Standard Knowledge is a multi-language library for programmatically augmenting C
 ## Working Effectively
 
 ### Bootstrap, build, and test the repository
+
 - `cargo build --verbose` -- builds all Rust components. Takes ~55 seconds. NEVER CANCEL. Set timeout to 120+ seconds.
 - `cargo test --verbose` -- runs all Rust tests. Takes ~25 seconds. NEVER CANCEL. Set timeout to 60+ seconds.
 - `cd py && uv run pytest` -- runs Python tests. Takes ~25 seconds. NEVER CANCEL. Set timeout to 60+ seconds.
 
 ### Install CLI tool
+
 - `cargo install --path cli` -- installs the standard_knowledge CLI tool. Takes ~32 seconds. NEVER CANCEL. Set timeout to 90+ seconds.
 
 ### Run applications
+
 Python library (interactive testing):
+
 - `cd py && uv run python`
+
 ```python
 import standard_knowledge
+
 library = standard_knowledge.StandardsLibrary()
 library.load_cf_standards()
 library.load_knowledge()
@@ -27,13 +33,15 @@ print(standard.attrs())  # Note: use standard.unit, not standard.units
 ```
 
 CLI usage:
+
 - `standard_knowledge --help` -- show CLI help
 - `standard_knowledge get air_pressure_at_mean_sea_level` -- get standard details
 - `standard_knowledge get -f xarray air_pressure_at_mean_sea_level` -- get xarray format
 - `standard_knowledge filter --search temp` -- search for standards
 - `standard_knowledge filter --ioos-category Meteorology` -- filter by category
 
 ### Linting and formatting
+
 - `cargo fmt --check` -- check Rust formatting (~0.6 seconds)
 - `cargo fmt --all` -- apply Rust formatting
 - `cargo clippy --all-targets --all-features` -- run Rust linting. Takes ~12 seconds. NEVER CANCEL. Set timeout to 30+ seconds.
@@ -42,16 +50,19 @@ CLI usage:
 ## Validation
 
 Always manually validate changes by:
+
 1. **Build and test**: Run both Rust and Python test suites after making changes
-2. **CLI functionality**: Test CLI commands with real examples from the README
-3. **Python library**: Test Python library functionality interactively
-4. **Standards data**: Verify standards can be loaded and queried correctly
+1. **CLI functionality**: Test CLI commands with real examples from the README
+1. **Python library**: Test Python library functionality interactively
+1. **Standards data**: Verify standards can be loaded and queried correctly
 
 ### Test CLI changes
+
 - Update CLI tests: `TRYCMD=overwrite cargo test --package standard_knowledge_cli --test cmd` -- Takes ~11 seconds. NEVER CANCEL. Set timeout to 30+ seconds.
 - For new CLI features, copy existing test files in `cli/tests/cmd/` and run the TRYCMD command
 
 ### Update standards
+
 - Run `uv run --script utils/update_standards.py` to refresh CF Standards from official sources. Takes ~10 seconds.
 
 ## Repository Structure
@@ -62,14 +73,17 @@ Always manually validate changes by:
 - **utils/**: Python utility scripts for maintaining standards data
 
 ### Key files and directories
+
 - `core/standards/`: YAML files containing community knowledge for each standard
 - `core/src/lib.rs`: Main Rust library entry point
 - `cli/src/main.rs`: CLI application entry point
 - `py/src/lib.rs`: Python bindings entry point
 - `.pre-commit-config.yaml`: Pre-commit hooks configuration
 
 ### Standards Knowledge Structure
+
 Each standard has a YAML file in `core/standards/<standard_name>.yaml` with:
+
 - `ioos_category`: IOOS measurement category
 - `long_name`: Human readable name
 - `common_variable_names`: Alternative column/variable names
@@ -82,6 +96,7 @@ Each standard has a YAML file in `core/standards/<standard_name>.yaml` with:
 ## Common Tasks
 
 ### Build times (with 50% buffer for timeout recommendations)
+
 - Rust build: ~55 seconds → Use 120+ second timeout
 - Rust tests: ~25 seconds → Use 60+ second timeout
 - CLI install: ~32 seconds → Use 90+ second timeout
@@ -90,18 +105,22 @@ Each standard has a YAML file in `core/standards/<standard_name>.yaml` with:
 - CLI test updates: ~11 seconds → Use 30+ second timeout
 
 ### Project Workspace Structure
+
 This is a Cargo workspace with three members:
+
 - `core` (standard_knowledge): Core Rust library
 - `cli` (standard_knowledge_cli): CLI application
 - `py` (standard_knowledge_py): Python bindings
 
 ### Common CI/CD commands that must pass
+
 - All pre-commit hooks (rustfmt, clippy, ruff, codespell, actionlint)
 - `cargo build --verbose`
 - `cargo test --verbose`
 - `cd py && uv run pytest`
 
 ### Example repository root listing
+
 ```
 .
 ├── .github/
@@ -117,7 +136,9 @@ This is a Cargo workspace with three members:
 ```
 
 ### Standards Library Usage Patterns
+
 **Rust:**
+
 ```rust
 use standard_knowledge::StandardsLibrary;
 let mut library = StandardsLibrary::new();
@@ -126,28 +147,34 @@ library.load_knowledge();
 ```
 
 **Python:**
+
 ```python
 import standard_knowledge
+
 library = standard_knowledge.StandardsLibrary()
 library.load_cf_standards()
 library.load_knowledge()
 ```
 
 **CLI:**
+
 ```bash
 standard_knowledge get <standard_name>
 standard_knowledge filter --var <variable_name>
 standard_knowledge qc config <standard> <region> <params>
 ```
 
 ### Adding new standards knowledge
+
 1. Create or edit YAML file in `core/standards/<standard_name>.yaml`
-2. Run tests to validate: `cargo test`
-3. Update CLI tests if needed: `TRYCMD=overwrite cargo test --package standard_knowledge_cli --test cmd`
-4. Always run linting before committing: `cargo fmt --all && cargo clippy`
+1. Run tests to validate: `cargo test`
+1. Update CLI tests if needed: `TRYCMD=overwrite cargo test --package standard_knowledge_cli --test cmd`
+1. Always run linting before committing: `cargo fmt --all && cargo clippy`
 
 ### Building Pyodide/WASM wheels locally
+
 Pyodide wheels require specific Rust and Pyodide versions due to Emscripten compatibility:
+
 ```bash
 # Install the compatible Rust version
 rustup install nightly-2025-01-20
@@ -156,11 +183,14 @@ rustup target add wasm32-unknown-emscripten --toolchain nightly-2025-01-20
 # Build pyodide wheels with pinned Rust toolchain and Pyodide 0.27.7
 RUSTUP_TOOLCHAIN=nightly-2025-01-20 CIBW_PYODIDE_VERSION=0.27.7 uvx cibuildwheel --platform pyodide py
 ```
+
 **Why these version pins?**
+
 1. **Rust nightly-2025-01-20**: Rust 1.87+ generates WASM code requiring `--enable-bulk-memory-opt` which older wasm-opt (bundled with Emscripten 3.1.58) doesn't support. See: https://github.com/PyO3/maturin/issues/2549
-2. **Pyodide 0.27.7**: Pyodide 0.28+ uses Emscripten 4.0.9 which has a bug with Rust-mangled symbol exports. The fix is in Emscripten 4.0.22+ but Pyodide hasn't updated yet. See: https://github.com/emscripten-core/emscripten/issues/24825
+1. **Pyodide 0.27.7**: Pyodide 0.28+ uses Emscripten 4.0.9 which has a bug with Rust-mangled symbol exports. The fix is in Emscripten 4.0.22+ but Pyodide hasn't updated yet. See: https://github.com/emscripten-core/emscripten/issues/24825
 
 ### Important Notes
+
 - Python bindings automatically rebuild when Rust code changes
 - CLI tests use trycmd for snapshot testing - update with `TRYCMD=overwrite`
 - Standards data is embedded into binaries at compile time via `build.rs`

.github/dependabot.yml

@@ -11,10 +11,6 @@ updates:
       - "/py"
     schedule:
       interval: "weekly"
-    groups:
-      cargo:
-        patterns:
-          - "*"
     cooldown:
       default-days: 7
 

.github/workflows/javascript.yml

@@ -9,6 +9,9 @@ on:
     branches: [ main ]
   workflow_dispatch:
 
+env:
+  FORCE_COLOR: 3
+
 permissions:
   contents: read
 

.github/workflows/python.yml

@@ -14,6 +14,9 @@ on:
   pull_request:
   workflow_dispatch:
 
+env:
+  FORCE_COLOR: 3
+
 permissions:
   contents: read
 
@@ -114,6 +117,11 @@ jobs:
         if: matrix.os == 'windows-intel'
         run: rustup target add i686-pc-windows-msvc
 
+      - name: Install uv
+        uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
+        with:
+          enable-cache: true
+
       - name: Build wheels
         uses: pypa/cibuildwheel@a0a973acdc9e7b7f8b04ac5c80e6883a5a102615 # v4.1.0
         env:

.pre-commit-config.yaml

@@ -8,30 +8,49 @@ repos:
         exclude: docs/mkdocs.yml
       - id: debug-statements
       - id: mixed-line-ending
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: 4b2e70d08cb2ccd26d1fba73588de41c7a5d50b7  # frozen: v0.25
+    hooks:
+      - id: validate-pyproject
+        # The package lives in py/, not at the repo root
+        files: 'pyproject\.toml$'
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
+
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: f805888065fdb6162e1f800e50bb9460cbd223d6  # frozen: 0.37.2
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
     rev: '3b3f7c3f57fe9925356faf5fe6230835138be230'  # frozen: v0.15.17
     hooks:
       - id: ruff-format
       - id: ruff-check
         args: ["--fix", "--show-fixes"]
+
   - repo: https://github.com/rhysd/actionlint
     rev: 914e7df21a07ef503a81201c76d2b11c789d3fca  # frozen: v1.7.12
     hooks:
       - id: actionlint
         files: ".github/workflows/"
         args: ["-ignore", "SC1090", "-ignore", "SC2046", "-ignore", "SC2086", "-ignore", "SC2129", "-ignore", "SC2155"]
+
   - repo: https://github.com/zizmorcore/zizmor-pre-commit
     rev: 9257c6050c0261b8c57e712f632dc4a8010109a9  # frozen: v1.25.2
     hooks:
       - id: zizmor
         files: "^\\.github"
         args: [--persona=pedantic]
+
   - repo: https://github.com/codespell-project/codespell
     # Configuration for codespell is in .codespellrc
     rev: 2ccb47ff45ad361a21071a7eedda4c37e6ae8c5a  # frozen: v2.4.2
     hooks:
       - id: codespell
+
   - repo: local
     hooks:
       - id: rustfmt
@@ -47,8 +66,32 @@ repos:
         language: system
         pass_filenames: false
 
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "fda77690955e9b63c6687d8806bafd56a526e45f"  # frozen: 1.20.0
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
+
+  - repo: https://github.com/hukkin/mdformat
+    rev: 82912cdaea4fb830f751504486a7879c70526547  # frozen: 1.0.0
+    hooks:
+    - id: mdformat
+
   - repo: https://github.com/biomejs/pre-commit
     rev: "5e270eb5db26a98324ef2f4b96135fc342c5d197"  # frozen: v2.4.16
     hooks:
     -   id: biome-check
         additional_dependencies: ["@biomejs/biome@2.1.1"]
+
+  - repo: https://github.com/scientific-python/cookie
+    rev: "8f0581cc50b14023b14a9c77e9b358738ba637e7" # frozen: 2026.06.18
+    hooks:
+      - id: sp-repo-review
+        name: repo-review (root)
+        entry: repo-review --ignore PY001,PY004,PY005,PP301,GH212,PC140,PC170
+      - id: sp-repo-review
+        name: repo-review (py)
+        entry: repo-review py
+
+auto_update:
+  cooldown_days: 7

README.md

@@ -1,4 +1,5 @@
 # standard_knowledge
+
 Programmatically augmenting CF Standards with IOOS operational knowledge.
 
 ```py
@@ -237,9 +238,10 @@ Best run with `./noxfile -s test_js`, but individual tests are listed in the [Ja
 Unless a session is specified, Nox will run all but `update_standards`, `install_cli`, `release`, and `test_wasm_env` sessions.
 
 Sessions (use `-s`):
+
 - `update_standards` - Updates the CF standards.
 - `install_cli` - Install the Rust CLI.
-- `release` -- <patch|minor|major> - Bumps the version of the all the packages for a release.
+- `release` -- \<patch|minor|major> - Bumps the version of the all the packages for a release.
 - `py_test-<version>` - Test a Python version as specified in the Github actions matrix.
 - `py_wheel` - Build Linux wheels for currently supported Python versions.
 - `py_wheel_wasm` - Build 3.14 WASM wheel.

py/Cargo.toml

@@ -3,7 +3,7 @@ name = "standard_knowledge_py"
 version.workspace = true
 license.workspace = true
 repository.workspace = true
-readme = "Readme.md"
+readme = "README.md"
 description.workspace = true
 edition.workspace = true
 rust-version.workspace = true

py/Readme.md → py/README.md

@@ -44,7 +44,9 @@ Note: [cibuildwheel only uses official builds](https://github.com/pypa/cibuildwh
 `../noxfile.py -s wheel` should run that as well.
 
 ### Building Pyodide/WASM wheels locally
+
 Pyodide wheels require specific Rust and Pyodide versions due to Emscripten compatibility:
+
 ```bash
 # Install the compatible Rust version
 rustup install nightly-2025-01-20