ci: prek for lint/formatting, remove pre-commit(.ci)

.github/workflows/java.yml

@@ -41,6 +41,7 @@ jobs:
           filters: |
             src:
               - 'core/**'
+              - 'macros/**'
               - 'bindings/java/**'
               - 'Cargo.*'
               - '.github/workflows/java.yml'

.github/workflows/js-wasm.yml

@@ -41,6 +41,7 @@ jobs:
           filters: |
             src:
               - 'core/**'
+              - 'macros/**'
               - 'bindings/js/**'
               - 'Cargo.*'
               - '.github/workflows/js-wasm.yml'
@@ -51,29 +52,6 @@ jobs:
           echo "test=$test" >> "$GITHUB_OUTPUT"
           echo "gate=$gate" >> "$GITHUB_OUTPUT"
 
-  lint:
-    name: JS/WASM Lints
-    needs: [plan]
-    if: needs.plan.outputs.test == 'true'
-    runs-on: ubuntu-24.04
-    defaults:
-      run:
-        working-directory: bindings/js
-
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
-      - uses: actions/setup-node@53b83947a5a98c8d113130e565377fae1a50d02f # v6
-        with:
-          node-version: 24
-          cache: npm
-          cache-dependency-path: bindings/js/package-lock.json
-
-      - name: Install dependencies
-        run: npm ci
-
-      - name: Run linter
-        run: npm run lint
-
   test:
     name: JS/WASM Tests
     needs: [plan]

.github/workflows/prek.yml

@@ -0,0 +1,34 @@
+name: Prek (linting and formatting)
+
+on:
+  push:
+    branches: [main]
+    tags: ["*"]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
+      - uses: j178/prek-action@b0ae0c600be6176aa296014b4eab1974096ebd69 # v2
+
+  ci-gate:
+    name: Prek CI Gate
+    needs: [test]
+    if: github.event_name == 'pull_request' && !cancelled()
+    runs-on: ubuntu-slim
+    steps:
+      - run: |
+          if [[ "${{ contains(needs.*.result, 'failure') }}" == "true" ]]; then
+            exit 1
+          fi

.github/workflows/python.yml

@@ -48,6 +48,7 @@ jobs:
             src:
               - 'bindings/py/**'
               - 'core/**'
+              - 'macros/**'
               - 'sysand/**'
               - 'Cargo.*'
               - '.github/workflows/python.yml'
@@ -59,35 +60,6 @@ jobs:
           echo "test=$test" >> "$GITHUB_OUTPUT"
           echo "gate=$gate" >> "$GITHUB_OUTPUT"
 
-  lint:
-    needs: [plan]
-    if: needs.plan.outputs.test == 'true'
-    runs-on: ubuntu-24.04
-    defaults:
-      run:
-        working-directory: bindings/py
-
-    steps:
-      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
-      - uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6
-        with:
-          python-version: "3.14"
-      - uses: astral-sh/setup-uv@37802adc94f370d6bfd71619e3f0bf239e1f3b78 # v7
-
-      - name: Setup environment
-        run: |
-          uv sync --group linters --active --no-install-project --locked
-          echo "$(pwd)/.venv/bin" >> "$GITHUB_PATH"
-
-      - name: ruff format ...
-        run: ruff format --check python tests
-
-      - name: ruff check ...
-        run: ruff check python
-
-      - name: mypy ...
-        run: mypy --strict python
-
   windows:
     needs: [plan]
     if: needs.plan.outputs.test == 'true'
@@ -319,7 +291,7 @@ jobs:
 
   ci-gate:
     name: Python CI Gate
-    needs: [plan, lint, windows, linux, macos, sdist]
+    needs: [plan, windows, linux, macos, sdist]
     if: needs.plan.outputs.gate == 'true' && !cancelled()
     runs-on: ubuntu-slim
     steps:
@@ -331,7 +303,7 @@ jobs:
   release:
     name: Release to PyPI
     environment: pypi-publish
-    needs: [lint, linux, macos, windows, sdist]
+    needs: [linux, macos, windows, sdist]
     if: startsWith(github.ref, 'refs/tags/')
     runs-on: ubuntu-24.04
     permissions:

.github/workflows/rust.yml

@@ -33,6 +33,7 @@ jobs:
     outputs:
       test: ${{ steps.decisions.outputs.test }}
       gate: ${{ steps.decisions.outputs.gate }}
+      lint_and_format: ${{ steps.decisions.outputs.lint_and_format }}
     steps:
       - uses: dorny/paths-filter@fbd0ab8f3e69293af611ebaee6363fc25e6d187d # v4
         if: github.event_name == 'pull_request'
@@ -41,19 +42,26 @@ jobs:
           filters: |
             src:
               - 'core/**'
+              - 'macros/**'
               - 'sysand/**'
               - 'Cargo.*'
               - '.github/workflows/rust.yml'
+            rs_src:
+              - '**/Cargo.*'
+              - '**/*.rs'
       - id: decisions
         run: |
           test=${{ steps.filter.outputs.src == 'true' || github.event_name == 'workflow_dispatch' || github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/') }}
           gate=${{ github.event_name == 'pull_request' }}
           echo "test=$test" >> "$GITHUB_OUTPUT"
           echo "gate=$gate" >> "$GITHUB_OUTPUT"
 
+          lint_and_format=${{ steps.filter.outputs.rs_src == 'true' || github.event_name == 'workflow_dispatch' || github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/') }}
+          echo "lint_and_format=$lint_and_format" >> "$GITHUB_OUTPUT"
+
   lint-and-format:
     needs: [plan]
-    if: needs.plan.outputs.test == 'true'
+    if: needs.plan.outputs.lint_and_format == 'true'
     runs-on: ubuntu-24.04
 
     steps:
@@ -62,14 +70,22 @@ jobs:
 
       - uses: taiki-e/install-action@6eec77b572d917fad00b2d3429df5ca9b6a0512c # cargo-hack
 
-      - name: cargo hack clippy ...
-        run: cargo hack clippy --each-feature --no-dev-deps --features std --ignore-unknown-features -- --deny warnings
+      # cargo clippy is run with variants of features enabled, where
+      # --all-features is done by prek so we don't do it here
 
-      - name: cargo clippy ...
-        run: cargo clippy --locked --all-targets --all-features -- --deny warnings
+      - name: cargo clippy ... (no features)
+        run: cargo clippy --workspace --locked --all-targets -- --deny warnings
 
-      - name: cargo fmt ...
-        run: cargo fmt --check
+      - name: cargo clippy --features std,filesystem,alltests ...  (specific feature set 1)
+        run: cargo clippy --workspace --locked --all-targets --no-default-features --features std,filesystem,alltests -- --deny warnings
+
+      - name: cargo clippy --features std,networking,alltests ... (specific feature set 2)
+        run: cargo clippy --workspace --locked --all-targets --no-default-features --features std,networking,alltests -- --deny warnings
+
+      # since we use --no-dev-deps below (as recommended), we don't do
+      # --all-targets to include tests with required development dependencies
+      - name: cargo hack clippy --each-feature ... (individual features)
+        run: cargo hack clippy --each-feature --no-dev-deps --features std --ignore-unknown-features -- --deny warnings
 
   test:
     needs: [plan]

.pre-commit-config.yaml

@@ -1,44 +1,31 @@
-# pre-commit is a tool to perform a predefined set of tasks manually and/or
-# automatically before git commits are made.
+# prek (Rust version of the Python based pre-commit) is a tool to perform a
+# predefined set of tasks manually and/or automatically before git commits are
+# made.
 #
-# Config reference: https://pre-commit.com/#pre-commit-configyaml---top-level
+# We require prek specifically, since we want support for rust based hooks.
+#
+# pre-commit reference: https://pre-commit.com/#pre-commit-configyaml---top-level
+# prek reference:       https://prek.j178.dev/configuration/
 #
 # Common tasks
 #
-# - Run once on all files: pre-commit run --all-files
-# - Register git hooks:    pre-commit install --install-hooks
+# - Run once on all files: prek run -a
+# - Register git hooks:    prek install
+#
+# FIXME: transition to a prek official config as we now require prek
+# FIXME: ensure hooks gets updated over time automatically
 #
 repos:
-  # Autoformat: python
-  - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.4
-    hooks:
-      - id: ruff-check
-        args: [--fix]
-      - id: ruff-format
-
   # Autoformat: markdown, yaml, json, js
   - repo: https://github.com/rbubley/mirrors-prettier
     rev: v3.8.1
     hooks:
       - id: prettier
-        exclude: |
-          (?x)^(
-              .*stdlib_assets/.*|
-              .*\.lock
-          )$
-
-  # Lint: javascript
-  - repo: https://github.com/pre-commit/mirrors-eslint
-    rev: v10.1.0
-    hooks:
-      - id: eslint
-        files: ^bindings/js/
-        types: [javascript]
-        additional_dependencies:
-          - eslint@^10.1.0
-          - "@eslint/js@^10.0.1"
-          - globals@^17.4.0
+        exclude: |-
+          (?x)(
+              stdlib_assets/|
+              \.lock
+          )
 
   # Autoformat: rust
   - repo: local
@@ -47,35 +34,57 @@ repos:
         name: cargo fmt
         entry: cargo fmt
         description: Formats all bin and lib files of the current workspace using rustfmt.
-        language: system
+        language: rust
         types: [rust]
         args: ["--"]
+
       - id: cargo-clippy
         name: cargo clippy
         entry: cargo clippy
         description: Checks all packages in the workspace to catch common mistakes and improve your Rust code.
-        language: system
+        language: rust
         types: [rust]
         args:
-          [
-            "--workspace",
-            "--all-targets",
-            "--all-features",
-            "--",
-            "--deny",
-            "warnings",
-          ]
+          - --workspace
+          - --all-targets
+          - --all-features
+          - --allow-dirty
+          - --fix
+          - --
+          - --deny
+          - warnings
         pass_filenames: false
 
-# pre-commit.ci is a free automation service that can both run a validation job
-# and push commits with fixes to PRs, and keep the versions of configured
-# pre-commit hooks up to date by creating version bumping PRs.
-#
-# pre-commit.ci config reference: https://pre-commit.ci/#configuration
-ci:
-  autoupdate_schedule: monthly
-  skip:
-    # The hooks rely on cargo being available, which it won't be in
-    # pre-commit.ci's runners, so we skip them from running there.
-    - cargo-fmt
-    - cargo-clippy
+  # Autoformat: python
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.4
+    hooks:
+      - id: ruff-check
+        args: [--fix]
+      - id: ruff-format
+
+  # Lint: python type checking
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.20.0
+    hooks:
+      - id: mypy
+        args:
+          - --strict
+        # lint only what is known to use typings
+        files: |-
+          (?x)^(
+              bindings/py/python/|
+              bindings/java/scripts/
+          )
+
+  # Lint: javascript
+  - repo: https://github.com/pre-commit/mirrors-eslint
+    rev: v10.1.0
+    hooks:
+      - id: eslint
+        files: ^bindings/js/
+        types: [javascript]
+        additional_dependencies:
+          - eslint@^10.1.0
+          - "@eslint/js@^10.0.1"
+          - globals@^17.4.0

DEVELOPMENT.md

@@ -127,21 +127,8 @@ Run tests for all crates and language bindings (requires bindings dependencies):
 
 ## Formatting and linting
 
-Format Rust code in core crates:
-
-```sh
-cargo fmt -p sysand-core -p sysand
-```
-
-Format and lint all Rust and bindings code (requires bindings dependencies):
-
-```sh
-./scripts/run_chores.sh
-```
-
-Format and lint all other code based on configuration in
-`.pre-commit-config.yaml`, either with prek or pre-commit, available to install
-via uv or pip.
+Format and lint all code based on configuration in `.pre-commit-config.yaml`
+with `prek` ([installation options]).
 
 ```sh
 prek run -a
@@ -150,6 +137,8 @@ prek run -a
 prek install
 ```
 
+[installation options]: https://github.com/j178/prek?tab=readme-ov-file#installation
+
 ## Commits and pull requests
 
 Committing your changes:

bindings/java/README.md

@@ -67,3 +67,7 @@ Only run tests:
 ```sh
 ./scripts/java-builder.py test
 ```
+
+## Formatting and linting
+
+Refer to the main [DEVELOPMENT.md](../../DEVELOPMENT.md).

bindings/java/scripts/java-builder.py

@@ -109,7 +109,7 @@ def parse_version() -> str:
     metadata = json.loads(output)
     for package in metadata["packages"]:
         if package["name"] == "sysand-java":
-            version = package["version"]
+            version: str = package["version"]
             return version
     raise ValueError("sysand-java not found in Cargo.toml")