Updates based on repo-review report

.github/dependabot.yml

@@ -0,0 +1,27 @@
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
+
+version: 2
+updates:
+  # Enable version updates for GitHub Actions
+  - package-ecosystem: "github-actions"
+    groups:
+      actions:
+        patterns:
+          - "*"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every week
+      interval: "weekly"
+
+  # Enable version updates for pre-commit hooks
+  - package-ecosystem: "pre-commit"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      pre-commit:
+        patterns:
+          - "*"

.github/workflows/check.yml

@@ -6,6 +6,10 @@ on:
 permissions:
   contents: read
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   check:
     runs-on: ubuntu-latest
@@ -16,23 +20,27 @@ jobs:
 
     steps:
       - uses: actions/checkout@v5
-      - name: Set up Python 3.12
-        uses: actions/setup-python@v6
-        with:
-          python-version: "3.12"
 
       - name: Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v8.1.0
         with:
+          python-version: "3.12"
           enable-cache: true
           cache-dependency-glob: "pyproject.toml"
 
       - name: Install package with check dependencies
-        run: uv sync --extra check
+        run: uv sync --group check
+
+      - name: Run Ruff linter
+        uses: astral-sh/ruff-action@v3
+        with:
+          args: "check --output-format=github"
 
-      # check with ruff
-      - name: Run ruff
-        run: uv run ruff check
+      - name: Run Ruff formatter
+        # NOTE: ruff format does not currently support github output format
+        run: ruff format --check --diff  src tests
+        # Check formatting even if the previous step failed
+        if: always()
 
       # check docs build
       - name: Check that documentation builds with no errors or warnings

.github/workflows/python-publish.yml

@@ -11,6 +11,8 @@ name: Upload Python Package
 on:
   release:
     types: [published]
+  # allow manually running on main
+  workflow_dispatch:
 
 permissions:
   contents: read

.github/workflows/unit_tests.yml

@@ -4,6 +4,10 @@ permissions:
   contents: read
   id-token: write
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 on:
   push:
     branches:
@@ -34,23 +38,23 @@ jobs:
 
       # use github python action instead of uv to take advantage of caching
       - name: Set up Python ${{ matrix.python }}
-        uses: actions/setup-python@v6
+        uses: astral-sh/setup-uv@v8.1.0
         with:
           python-version: ${{ matrix.python }}
           cache: 'pip'
           cache-dependency-path: '**/pyproject.toml'
 
-      - name: Install package with dependencies
-        run: pip install -e ".[test]"
+      - name: Install package with check dependencies
+        run: uv sync --group test
 
       # for all versions but the one we use for code coverage, run normally
       - name: Run unit tests without code coverage
-        run: pytest
+        run: uv run pytest
         if: ${{ matrix.python != env.COV_PYTHON_VERSION }}
 
       # run code coverage in one version only
       - name: Run unit tests with code coverage reporting
-        run: pytest --cov=.
+        run: uv run pytest --cov=.
         if: ${{ matrix.python == env.COV_PYTHON_VERSION }}
 
       - name: Upload coverage to Codecov

.pre-commit-config.yaml

@@ -1,22 +1,46 @@
 files: \.py
 repos:
+  # ruff for linting and formatting python
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.4
+    rev: v0.15.12
     hooks:
-      - id: ruff
-        args: [ --fix, --exit-non-zero-on-fix ]
+      - id: ruff-check
+        args: [ --fix, --show-fixes, --exit-non-zero-on-fix ]
       - id: ruff-format
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v6.0.0
     hooks:
       - id: check-case-conflict
+      - id: check-merge-conflict
       - id: check-executables-have-shebangs
       - id: debug-statements
       - id: end-of-file-fixer
       - id: mixed-line-ending
       - id: trailing-whitespace
+      - id: check-yaml
+      - id: name-tests-test
+        args: [--pytest-test-first]
+
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v2.0.0
     hooks:
       - id: mypy
         additional_dependencies: [numpy]
+  # yamlfmt for formatting YAML files
+  - repo: https://github.com/google/yamlfmt
+    rev: v0.21.0
+    hooks:
+      - id: yamlfmt
+  # Codespell for spell checking
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.4.2
+    hooks:
+      - id: codespell
+        additional_dependencies:
+          - tomli
+        exclude_types: ["css", "html", "javascript", "json"]
+  # Validate GitHub Actions workflow files
+  - repo: https://github.com/mpalmer/action-validator
+    rev: v0.9.0
+    hooks:
+      - id: action-validator

.readthedocs.yaml

@@ -11,8 +11,8 @@ sphinx:
   configuration: docs/conf.py
 
 python:
-  install:
-    - method: pip
-      path: .
-      extra_requirements:
-        - docs
+   install:
+      - method: uv
+        command: sync
+        groups:
+          - docs

DEVELOPER_NOTES.md

@@ -44,9 +44,15 @@ source .venv/bin/activate
 Install an editable version of the local package along with python dependencies needed for testing and development.
 
 ```sh
-pip install -e ".[dev]"
+pip install -e . --group=dev
 ```
 
+If using `uv`, use 
+
+```sh
+ uv sync --group test
+ ```
+
 ### Install pre-commit hooks
 
 We use [pre-commit](https://pre-commit.com/) for automated checks and consistent formatting.  If you're planning to contribute, please install these when you set up your local development.