Add quality checks and pre-commit & editor configs

.editorconfig

@@ -0,0 +1,22 @@
+# Check http://editorconfig.org for more information
+# This is the main config file for this project:
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+indent_style = space
+indent_size = 2
+trim_trailing_whitespace = true
+
+[*.py]
+indent_style = space
+indent_size = 4
+
+[*.py.jinja]
+indent_style = space
+indent_size = 4
+
+[*.md]
+trim_trailing_whitespace = false

.github/workflows/check-dependencies.yaml

@@ -8,7 +8,29 @@ on:
     types: trigger-run-check-dependencies
 
 jobs:
+  quality-checks:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/[email protected]
+      - name: Install Poetry
+        run: |
+          pipx install poetry
+          pipx inject poetry poetry-dynamic-versioning
+      - uses: actions/[email protected]
+        with:
+          python-version: 3.13
+      - name: Check pyproject.toml and poetry.lock
+        run: poetry check
+      - name: Install tox
+        run: python -m pip install tox
+      - name: Run codespell
+        run: tox -e codespell
+      - name: Run code quality checks
+        run: tox -e lint
+
   test:
+    needs:
+      - quality-checks
     strategy:
       fail-fast: false
       matrix:
@@ -35,7 +57,7 @@ jobs:
         with:
           # Fetch all history for all branches and all tags.
           # The tags are required for dynamic versioning.
-          fetch-depth: 0  
+          fetch-depth: 0
 
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/[email protected]

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+default_language_version:
+  python: python3
+# Specify files to exclude - pre-commit hook doesn't parse pyproject.toml
+exclude: tests/data/hp.ttl|tests/data/hp_f.ttl|.*\.svg|jsonschema_value_constraints.yaml
+repos:
+- repo: https://github.com/pre-commit/pre-commit-hooks
+  rev: v4.4.0
+  hooks:
+  - id: end-of-file-fixer
+    exclude: __snapshots__
+  - id: check-yaml
+    exclude: (__snapshots__|test_utils/input)
+  - id: check-toml
+  - id: trailing-whitespace
+    # TODO: This is temporary while bioliank is being fixed upstream.
+    # TODO: Should look at snapshot exclusion to find upstream problems
+    exclude: (__snapshots__|biolink-model.yaml)
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  # Ensure this version stays in sync with tox.ini
+  rev: v0.11.13
+  hooks:
+  # Run the linter.
+  - id: ruff-check
+    args: [--fix, --exit-non-zero-on-fix]
+  # Run the formatter.
+  - id: ruff-format
+- repo: https://github.com/codespell-project/codespell
+  rev: v2.4.1
+  hooks:
+  - id: codespell
+    additional_dependencies:
+      - tomli