Enhancement/ruff updates

.env.example

@@ -3,7 +3,7 @@
 
 # API Configuration
 API_VERSION=v2.0
-ENVIRONMENT=development
+ENVIRONMENT=dev
 
 # Beacon Information
 BEACON_ID=org.example.beacon

.github/workflows/ci.yml

@@ -29,10 +29,10 @@ jobs:
         run: |
           uv pip install -e ".[dev]"
 
-      - name: Check formatting with black
+      - name: Check formatting with ruff
         run: |
           source .venv/bin/activate
-          black --check src/ tests/
+          ruff format --check src/ tests/
 
       - name: Lint with ruff
         run: |
@@ -85,25 +85,38 @@ jobs:
   docker:
     name: Build Docker Image
     runs-on: ubuntu-latest
+    services:
+      registry:
+        image: registry:3
+        ports:
+          - 5000:5000
 
     steps:
       - uses: actions/checkout@v4
 
       - name: Set up Docker Buildx
         uses: docker/setup-buildx-action@v3
+        with:
+          driver-opts: network=host
 
       - name: Build Docker image
         uses: docker/build-push-action@v5
         with:
+          push: true
           context: .
-          push: false
-          tags: beacon-api:latest
+          tags: localhost:5000/beacon-api:latest
           cache-from: type=gha
           cache-to: type=gha,mode=max
 
       - name: Test Docker image
         run: |
-          docker run -d -p 8000:8000 --name beacon-test beacon-api:latest
-          sleep 5
-          curl --fail http://localhost:8000/health || exit 1
+          docker run -d -p 8000:8000 --name beacon-test localhost:5000/beacon-api:latest
+          echo "Waiting for container to be ready..."
+          sleep 10
+          echo "Testing health endpoint..."
+          curl --fail --retry 3 --retry-delay 2 --retry-all-errors http://localhost:8000/api/monitor/health || {
+            echo "Health check failed. Container logs:"
+            docker logs beacon-test
+            exit 1
+          }
           docker stop beacon-test

Dockerfile

@@ -9,13 +9,15 @@ COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
 # Set working directory
 WORKDIR /app
 
-# Copy dependency files
-COPY pyproject.toml ./
+# Copy dependency files and source code
+COPY pyproject.toml README.md ./
+COPY src/ ./src/
 
 # Create virtual environment and install dependencies
 RUN uv venv /opt/venv && \
     . /opt/venv/bin/activate && \
-    uv pip install --no-cache -e .
+    uv pip install --no-cache . && \
+    rm -rf /app/src /app/pyproject.toml /app/README.md
 
 # Stage 2: Runtime
 FROM python:3.12-slim
@@ -36,9 +38,6 @@ COPY --from=builder --chown=beacon:beacon /opt/venv /opt/venv
 # Set working directory
 WORKDIR /app
 
-# Copy application code
-COPY --chown=beacon:beacon src/ ./src/
-
 # Switch to non-root user
 USER beacon
 
@@ -47,7 +46,7 @@ EXPOSE 8000
 
 # Health check
 HEALTHCHECK --interval=30s --timeout=10s --start-period=5s --retries=3 \
-    CMD python -c "import urllib.request; urllib.request.urlopen('http://localhost:8000/health')"
+    CMD python -c "import urllib.request; urllib.request.urlopen('http://localhost:8000/api/monitor/health')"
 
 # Run the application
 CMD ["uvicorn", "beacon_api.main:app", "--host", "0.0.0.0", "--port", "8000"]

README.md

@@ -11,7 +11,7 @@ A production-ready implementation of the [GA4GH Beacon v2 API](https://github.co
 - ✅ **Production-ready** with Docker support and health checks
 - ✅ **CI/CD** with GitHub Actions (linting, testing, Docker builds)
 - ✅ **Configuration** using Pydantic Settings with environment variables
-- ✅ **Modern tooling** - uv, ruff, black, mypy
+- ✅ **Modern tooling** - uv, ruff, mypy
 
 ## Architecture
 
@@ -215,9 +215,9 @@ services:
 
 ### Code Quality
 
-Format code with black:
+Format code with ruff:
 ```bash
-black src/ tests/
+ruff format src/ tests/
 ```
 
 Lint with ruff:

pyproject.toml

@@ -33,7 +33,6 @@ dev = [
     "pytest-asyncio>=0.24.0",
     "httpx>=0.27.0",
     "ruff>=0.7.0",
-    "black>=24.10.0",
     "mypy>=1.13.0",
 ]
 
@@ -44,7 +43,6 @@ dev = [
     "pytest-asyncio>=0.24.0",
     "httpx>=0.27.0",
     "ruff>=0.7.0",
-    "black>=24.10.0",
     "mypy>=1.13.0",
 ]
 
@@ -55,24 +53,6 @@ build-backend = "hatchling.build"
 [tool.hatch.build.targets.wheel]
 packages = ["src/beacon_api"]
 
-[tool.black]
-line-length = 88
-target-version = ["py311", "py312"]
-include = '\.pyi?$'
-extend-exclude = '''
-/(
-  # directories
-  \.eggs
-  | \.git
-  | \.hg
-  | \.mypy_cache
-  | \.tox
-  | \.venv
-  | build
-  | dist
-)/
-'''
-
 [tool.ruff]
 line-length = 88
 target-version = "py311"
@@ -109,7 +89,7 @@ select = [
     "UP",  # pyupgrade
 ]
 ignore = [
-    "E501",  # line too long, handled by black
+    "E501",  # line too long, handled by ruff formatter
     "B008",  # do not perform function calls in argument defaults
     "C901",  # too complex
 ]
@@ -120,12 +100,15 @@ ignore = [
 [tool.ruff.lint.isort]
 known-third-party = ["fastapi", "pydantic", "uvicorn"]
 
+[tool.ruff.format]
+quote-style = "double"
+indent-style = "space"
+skip-magic-trailing-comma = false
+line-ending = "auto"
+
 [tool.pytest.ini_options]
-minversion = "8.0"
-addopts = "-ra -q --strict-markers --cov=src/beacon_api --cov-report=term-missing --cov-report=html"
 testpaths = ["tests"]
 pythonpath = ["src"]
-asyncio_mode = "auto"
 
 [tool.mypy]
 python_version = "3.11"

src/beacon_api/api/__init__.py

@@ -1,14 +1,14 @@
 """FastAPI routers for Beacon v2 API endpoints."""
 
-from beacon_api.api.info import router as info_router
-from beacon_api.api.individuals import router as individuals_router
-from beacon_api.api.biosamples import router as biosamples_router
-from beacon_api.api.genomic_variations import router as g_variations_router
 from beacon_api.api.analyses import router as analyses_router
+from beacon_api.api.biosamples import router as biosamples_router
 from beacon_api.api.cohorts import router as cohorts_router
 from beacon_api.api.datasets import router as datasets_router
-from beacon_api.api.runs import router as runs_router
+from beacon_api.api.genomic_variations import router as g_variations_router
+from beacon_api.api.individuals import router as individuals_router
+from beacon_api.api.info import router as info_router
 from beacon_api.api.monitor import router as monitor_router
+from beacon_api.api.runs import router as runs_router
 
 __all__ = [
     "info_router",
@@ -19,5 +19,5 @@
     "cohorts_router",
     "datasets_router",
     "runs_router",
-    "monitor_router"
+    "monitor_router",
 ]