Migrate to UV and Update Dependencies

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "daily"

.github/workflows/ci.yml

@@ -18,34 +18,29 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: actions/setup-python@v5
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
       with:
-        python-version: ${{ env.PYTHON_VERSION }}
-        cache: 'pip'
+        version: "latest"
+
+    - name: Set up Python
+      run: uv python install ${{ env.PYTHON_VERSION }}
 
     - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install -r requirements-dev.txt
+      run: uv sync --all-extras
 
     - name: Run Black (Code Formatting Check)
-      run: |
-        black --check --diff app/ domains/ tests/ scripts/
+      run: uv run black --check --diff app/ domains/ tests/ scripts/
 
     - name: Run Ruff (Linting)
-      run: |
-        ruff check app/ domains/ tests/ scripts/
+      run: uv run ruff check app/ domains/ tests/ scripts/
 
     - name: Run mypy (Type Checking)
-      run: |
-        mypy app/ domains/ scripts/
+      run: uv run mypy app/ domains/ scripts/
       continue-on-error: true  # Allow failures initially during migration
 
     - name: Check import sorting (isort)
-      run: |
-        isort --check-only --diff app/ domains/ tests/ scripts/
+      run: uv run isort --check-only --diff app/ domains/ tests/ scripts/
 
   test:
     name: Run Tests
@@ -71,22 +66,21 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v4
 
-    - name: Set up Python
-      uses: actions/setup-python@v5
+    - name: Install uv
+      uses: astral-sh/setup-uv@v4
       with:
-        python-version: ${{ env.PYTHON_VERSION }}
-        cache: 'pip'
+        version: "latest"
+
+    - name: Set up Python
+      run: uv python install ${{ env.PYTHON_VERSION }}
 
     - name: Install system dependencies
       run: |
         sudo apt-get update
         sudo apt-get install -y tesseract-ocr tesseract-ocr-eng
 
     - name: Install Python dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install -r requirements.txt
-        pip install -r requirements-dev.txt
+      run: uv sync --all-extras
 
     - name: Wait for Neo4j
       run: |
@@ -100,16 +94,14 @@ jobs:
         done
 
     - name: Run unit tests
-      run: |
-        pytest tests/unit -v --cov=app --cov=domains --cov-report=xml --cov-report=term
+      run: uv run pytest tests/unit -v --cov=app --cov=domains --cov-report=xml --cov-report=term
       env:
         NEO4J_URI: bolt://localhost:7687
         NEO4J_USER: neo4j
         NEO4J_PASSWORD: testpassword
 
     - name: Run service tests
-      run: |
-        pytest tests/service -v --cov=app --cov=domains --cov-append --cov-report=xml --cov-report=term
+      run: uv run pytest tests/service -v --cov=app --cov=domains --cov-append --cov-report=xml --cov-report=term
       env:
         NEO4J_URI: bolt://localhost:7687
         NEO4J_USER: neo4j

.gitignore

@@ -61,6 +61,7 @@ neo4j_logs/
 .pytest_cache/
 .coverage
 htmlcov/
+coverage.xml
 .tox/
 
 # Temporary files

Dockerfile

@@ -21,15 +21,21 @@ RUN apt-get update && apt-get install -y \
 # Set working directory
 WORKDIR /app
 
-# Copy requirements first for layer caching
-COPY requirements.txt .
-COPY requirements-dev.txt .
+# Install uv
+RUN pip install uv
 
-# Install Python dependencies
-RUN pip install --no-cache-dir -r requirements.txt
-RUN pip install --no-cache-dir -r requirements-dev.txt
+# Copy project configuration and lock file first for better layer caching
+COPY pyproject.toml uv.lock ./
 
-# Copy application code
+# Copy source directories needed for package installation
+COPY app/ app/
+COPY domains/ domains/
+COPY schemas/ schemas/
+
+# Install Python dependencies using uv sync for reproducible builds
+RUN uv sync --no-dev --frozen --no-cache
+
+# Copy remaining application code
 COPY . .
 
 # Create data directories

app/api/admin.py

@@ -8,18 +8,18 @@
 """
 
 from fastapi import APIRouter, BackgroundTasks
-from pydantic import BaseModel
-from typing import Optional
 from loguru import logger
+from pydantic import BaseModel
 
 router = APIRouter()
 
 
 class ScanResponse(BaseModel):
     """Scan operation response."""
+
     status: str
     message: str
-    job_id: Optional[str] = None
+    job_id: str | None = None
 
 
 @router.post("/scan", response_model=ScanResponse)
@@ -45,7 +45,7 @@ async def trigger_system_scan(background_tasks: BackgroundTasks, full: bool = Fa
     return ScanResponse(
         status="queued",
         message=f"{'Full' if full else 'Incremental'} system scan queued",
-        job_id=None
+        job_id=None,
     )
 
 
@@ -61,10 +61,7 @@ async def trigger_screenshot():
 
     # TODO: Implement in Phase 1 (Visual Timeline)
 
-    return {
-        "status": "captured",
-        "message": "Screenshot captured successfully"
-    }
+    return {"status": "captured", "message": "Screenshot captured successfully"}
 
 
 @router.delete("/cleanup")
@@ -88,7 +85,7 @@ async def cleanup_old_data(days: int = 90):
     return {
         "status": "completed",
         "message": f"Cleaned up data older than {days} days",
-        "deleted_count": 0
+        "deleted_count": 0,
     }
 
 
@@ -107,16 +104,7 @@ async def get_system_stats():
     # - Recent activity
 
     return {
-        "nodes": {
-            "total": 0,
-            "by_type": {}
-        },
-        "relationships": {
-            "total": 0
-        },
-        "storage": {
-            "screenshots": "0 MB",
-            "ocr_data": "0 MB",
-            "database": "0 MB"
-        }
+        "nodes": {"total": 0, "by_type": {}},
+        "relationships": {"total": 0},
+        "storage": {"screenshots": "0 MB", "ocr_data": "0 MB", "database": "0 MB"},
     }

app/api/ask.py

@@ -8,36 +8,37 @@
 - Status: MCP/container/service status
 """
 
-from fastapi import APIRouter, HTTPException
-from pydantic import BaseModel
-from typing import List, Dict, Any, Optional
-
+from fastapi import APIRouter
 from loguru import logger
+from pydantic import BaseModel
 
 router = APIRouter()
 
 
 class AskRequest(BaseModel):
     """Ask endpoint request model."""
+
     query: str
-    context: Optional[str] = None
+    context: str | None = None
     limit: int = 10
 
 
 class Source(BaseModel):
     """Source reference in response."""
+
     type: str
-    path: Optional[str] = None
-    timestamp: Optional[str] = None
-    entity_id: Optional[str] = None
+    path: str | None = None
+    timestamp: str | None = None
+    entity_id: str | None = None
 
 
 class AskResponse(BaseModel):
     """Ask endpoint response model."""
+
     answer: str
-    sources: List[Source]
+    sources: list[Source]
     query_type: str
-    cypher_query: Optional[str] = None
+    cypher_query: str | None = None
 
 
 @router.post("/", response_model=AskResponse)
@@ -66,12 +67,12 @@ async def ask_question(request: AskRequest):
         answer=f"Query '{request.query}' received. Full implementation coming in Phase 2.",
         sources=[],
         query_type="unknown",
-        cypher_query=None
+        cypher_query=None,
     )
 
 
 @router.post("/ingest")
-async def ingest_document(path: str, doc_type: Optional[str] = None):
+async def ingest_document(path: str, doc_type: str | None = None):
     """
     Manually ingest a document into the knowledge graph.
 
@@ -86,8 +87,4 @@ async def ingest_document(path: str, doc_type: Optional[str] = None):
 
     # TODO: Implement in Phase 1 (System Graph)
 
-    return {
-        "status": "queued",
-        "path": path,
-        "message": "Document queued for ingestion"
-    }
+    return {"status": "queued", "path": path, "message": "Document queued for ingestion"}

app/api/health.py

@@ -2,18 +2,20 @@
 Health check endpoint.
 """
 
+from datetime import datetime
+
 from fastapi import APIRouter
 from pydantic import BaseModel
-from datetime import datetime
 
-from app.utils.neo4j_client import get_neo4j_client
 from app.utils.config import get_settings
+from app.utils.neo4j_client import get_neo4j_client
 
 router = APIRouter()
 
 
 class HealthResponse(BaseModel):
     """Health check response model."""
+
     status: str
     timestamp: datetime
     neo4j_connected: bool
@@ -44,5 +46,5 @@ async def health_check():
         status="healthy" if neo4j_connected else "degraded",
         timestamp=datetime.now(),
         neo4j_connected=neo4j_connected,
-        version=settings.api_version
+        version=settings.api_version,
     )