Simplify code formatting/linting

.github/workflows/tests.yml

@@ -13,43 +13,49 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.12']
-    
+
     steps:
       - name: Checkout
         uses: actions/checkout@v4
-      
+
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
-      
+
       - name: Install system dependencies
         run: |
           sudo apt-get update
           sudo apt-get install -y build-essential libffi-dev libssl-dev zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev libncurses5-dev libncursesw5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev libjpeg-dev libpng-dev libtiff-dev libwebp-dev libopenjp2-7-dev libharfbuzz-dev libfribidi-dev libfreetype6-dev libfontconfig1-dev libblas-dev liblapack-dev libatlas-base-dev gfortran libpoppler-cpp-dev libpoppler-dev libhdf5-dev libnetcdf-dev libgl1 libglib2.0-0 libsm6 libxext6 libxrender-dev libgomp1 libcairo2-dev libpango1.0-dev libpangocairo-1.0-0 libgdk-pixbuf2.0-dev libffi-dev shared-mime-info graphviz libgraphviz-dev
-      
+
       - name: Cache dependencies
         uses: actions/cache@v3
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ hashFiles('**/pyproject.toml') }}
-      
+
       - name: Cache SDK generation
         uses: actions/cache@v3
         with:
           path: src/tooluniverse/tools
           key: ${{ runner.os }}-sdk-${{ hashFiles('scripts/build_tools.py', 'src/tooluniverse/data/*.json') }}
-      
+
       - name: Install uv
         uses: astral-sh/setup-uv@v3
-      
+
       - name: Install project with dev extras
         run: |
           uv pip install -e .[dev] --system
-
+
+      - name: Check code formatting/linting requirements
+        uses: astral-sh/ruff-action@v3
+        with:
+          version: "latest"
+        run: ruff check
+
       - name: Generate SDK
         run: python scripts/build_tools.py
-      
+
       - name: Run fast tests (excluding tools, examples, and api)
         run: |
           pytest tests/ -v \
@@ -61,30 +67,28 @@ jobs:
             --ignore=tests/tools \
             --ignore=tests/examples \
             --ignore=tests/api
-      
+
       - name: Test doctor CLI tool
         run: |
           python -m src.tooluniverse.doctor
-      
+
       - name: Run tools, examples, and api tests (optional, requires network)
         if: github.event.inputs.run_tools_tests == 'true' || github.event_name == 'workflow_dispatch'
         run: |
           pytest tests/tools/ tests/examples/ tests/api/ -v \
             --tb=short \
             -m "not slow and not require_api_keys"
-      
+
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v3
         if: github.ref == 'refs/heads/main'
         with:
           file: ./coverage.xml
           fail_ci_if_error: false
-      
+
       - name: Upload test results
         if: always()
         uses: actions/upload-artifact@v4
         with:
           name: test-results-${{ matrix.python-version }}
-          path: coverage.xml
-
-
+          path: coverage.xml

.pre-commit-config.yaml

@@ -8,38 +8,19 @@ exclude: |
   )
 
 repos:
-
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v6.0.0
     hooks:
       - id: end-of-file-fixer
       - id: trailing-whitespace
-      - id: check-ast
       - id: check-yaml
       - id: check-toml
 
-  - repo: https://github.com/psf/black
-    rev: 25.9.0
-    hooks:
-      - id: black
-        args: ["--line-length=88"]
-        language_version: python3
-
-  - repo: https://github.com/PyCQA/autoflake
-    rev: v2.3.1
-    hooks:
-      - id: autoflake
-        args: ["--remove-all-unused-imports", "--remove-unused-variables", "--in-place"]
-
-  - repo: https://github.com/PyCQA/flake8
-    rev: 7.3.0
-    hooks:
-      - id: flake8
-        additional_dependencies: ["flake8-bugbear"]
-        args: ["--max-line-length=88", "--extend-ignore=E501,F401,F541,E203,W503"]
-
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.14.4
+    rev: v0.14.5
     hooks:
-      - id: ruff
-        args: ["--fix", "--line-length=88", "--ignore=E203"]
+      # Run the linter.
+      - id: ruff-check
+        args: [ --fix ] # automatically fix linting issues
+      # Run the formatter.
+      - id: ruff-format

pyproject.toml

@@ -12,7 +12,7 @@ authors = [
 dependencies = [
     "requests>=2.32.0",
     "numpy>=2.2.0",
-    "sympy>=1.12.0",  # Symbolic mathematics for Python executor
+    "sympy>=1.12.0", # Symbolic mathematics for Python executor
     "graphql-core>=3.2.0",
     "fastapi>=0.116.0",
     "uvicorn>=0.35.0",
@@ -31,7 +31,7 @@ dependencies = [
     "rcsb-api>=1.4.0",
     "fitz>=0.0.1.dev2",
     "pandas>=2.2.3",
-    "setuptools>=70.0.0,<81.0.0",  # Fix pkg_resources deprecation warnings
+    "setuptools>=70.0.0,<81.0.0", # Fix pkg_resources deprecation warnings
     "pdfplumber>=0.11.0",
     "playwright>=1.55.0",
     "faiss-cpu>=1.12.0",
@@ -58,12 +58,11 @@ dev = [
     "pytest-timeout>=2.3.1",
     "pytest-mock>=3.14.0",
     "pytest-asyncio>=0.21.0",
-    "requests-mock>=1.12.1",
-    "black>=22.0",
-    "flake8>=4.0",
     "pre-commit>=2.0",
     "pytest-xdist>=3.0",
     "pytest-html>=3.0",
+    "requests-mock>=1.12.1",
+    "ruff>=0.14.5",
 ]
 docs = [
     "sphinx>=4.0",
@@ -155,4 +154,16 @@ dev = [
 ]
 
 [tool.uv.sources]
-tooluniverse = { workspace = true }
+tooluniverse = { workspace = true }
+
+[tool.ruff]
+line-length = 88
+exclude = [
+    ".venv",
+    "docs",
+    "examples",
+]
+unsafe-fixes = true
+
+[tool.ruff.lint]
+ignore = ["E203", "E402", "E501", "F401", "F541"]