Add tests, Docker multi-stage build, CI/CD, and SPA serving

- 20 backend tests (5 categories: health, projects, datasets, analysis, schema validation)
- Multi-stage Dockerfile (Node frontend → Rust/maturin builder → Python runtime)
- docker-compose.yml (prod) and docker-compose.dev.yml (hot-reload)
- GitHub Actions CI pipeline (backend-test, frontend-build, docker-build)
- Fix DatasetRef schema (list[str] → list[DatasetRef])
- SPA serving for production (Vue.js from backend/static/)
- README: test coverage section and CI/CD documentation
- Sample data (cirrhosis train/test datasets + param.yaml)

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: eprifti

.github/workflows/ci.yml

@@ -0,0 +1,93 @@
+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  # -------------------------------------------------------------------------
+  # Backend tests (Python + FastAPI)
+  # -------------------------------------------------------------------------
+  backend-test:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: backend
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install dependencies
+        run: pip install -e ".[dev]" pyyaml
+
+      - name: Run tests
+        run: PYTHONPATH=. pytest tests/ -v --tb=short
+        env:
+          PREDOMICS_DATA_DIR: /tmp/predomics-test
+          PREDOMICS_PROJECT_DIR: /tmp/predomics-test/projects
+          PREDOMICS_UPLOAD_DIR: /tmp/predomics-test/uploads
+
+  # -------------------------------------------------------------------------
+  # Frontend lint + build (Vue.js)
+  # -------------------------------------------------------------------------
+  frontend-build:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: frontend
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Node.js
+        uses: actions/setup-node@v4
+        with:
+          node-version: "20"
+
+      - name: Install dependencies
+        run: npm ci
+
+      - name: Build
+        run: npm run build
+
+  # -------------------------------------------------------------------------
+  # Docker build (full stack)
+  # -------------------------------------------------------------------------
+  docker-build:
+    runs-on: ubuntu-latest
+    needs: [backend-test, frontend-build]
+    if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # Also checkout gpredomicspy for Docker build
+          path: predomicsapp-web
+
+      - name: Checkout gpredomicspy
+        uses: actions/checkout@v4
+        with:
+          repository: predomics/gpredomicspy
+          path: gpredomicspy
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v3
+
+      - name: Build Docker image
+        run: |
+          cd predomicsapp-web
+          docker build -t predomicsapp-web:latest -f Dockerfile ..
+
+      - name: Test Docker image
+        run: |
+          docker run -d --name test-app -p 8000:8000 predomicsapp-web:latest
+          sleep 5
+          curl -f http://localhost:8000/health
+          docker stop test-app

Dockerfile

@@ -1,41 +1,64 @@
+# =============================================================================
 # Stage 1: Build Vue.js frontend
+# =============================================================================
 FROM node:20-alpine AS frontend-builder
 WORKDIR /app/frontend
 COPY frontend/package*.json ./
 RUN npm ci
 COPY frontend/ ./
 RUN npm run build
 
-# Stage 2: Python backend + compiled frontend
-FROM python:3.11-slim AS runtime
+# =============================================================================
+# Stage 2: Build gpredomicspy (Rust → Python native module)
+# =============================================================================
+FROM python:3.11-slim AS rust-builder
 
-# Install Rust toolchain for building gpredomicspy
 RUN apt-get update && apt-get install -y --no-install-recommends \
-    build-essential curl && \
+    build-essential curl git pkg-config libssl-dev && \
     curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y && \
     rm -rf /var/lib/apt/lists/*
 ENV PATH="/root/.cargo/bin:${PATH}"
 
+RUN pip install --no-cache-dir maturin
+
+WORKDIR /build
+COPY gpredomicspy/ ./gpredomicspy/
+RUN cd gpredomicspy && maturin build --release --out /build/wheels
+
+# =============================================================================
+# Stage 3: Runtime — Python backend + frontend + gpredomicspy wheel
+# =============================================================================
+FROM python:3.11-slim AS runtime
+
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libgomp1 && \
+    rm -rf /var/lib/apt/lists/*
+
 WORKDIR /app
 
-# Install Python dependencies
-COPY backend/pyproject.toml backend/
-RUN pip install --no-cache-dir -e backend/
+# Install gpredomicspy wheel (built in stage 2)
+COPY --from=rust-builder /build/wheels/*.whl /tmp/wheels/
+RUN pip install --no-cache-dir /tmp/wheels/*.whl && rm -rf /tmp/wheels
 
-# Install gpredomicspy from source (requires Rust)
-# For now, this is optional — the app works in mock mode without it
-# COPY gpredomicspy/ gpredomicspy/
-# RUN cd gpredomicspy && pip install maturin && maturin develop --release
+# Install Python backend dependencies
+COPY backend/pyproject.toml backend/
+RUN pip install --no-cache-dir backend/
 
 # Copy backend code
 COPY backend/ backend/
 
-# Copy built frontend
+# Copy built frontend into static directory
 COPY --from=frontend-builder /app/frontend/dist backend/static/
 
 # Copy sample data
 COPY data/sample/ data/sample/
 
+# Create directories for runtime data
+RUN mkdir -p data/uploads data/projects
+
 EXPOSE 8000
 
+HEALTHCHECK --interval=30s --timeout=5s --start-period=10s \
+    CMD python -c "import urllib.request; urllib.request.urlopen('http://localhost:8000/health')" || exit 1
+
 CMD ["uvicorn", "backend.app.main:app", "--host", "0.0.0.0", "--port", "8000"]

README.md

@@ -72,6 +72,56 @@ predomicsapp-web/
 └── docker-compose.yml
 ```
 
+## Tests
+
+### Running Tests
+
+```bash
+cd backend
+pip install -e ".[dev]"
+pytest -v
+```
+
+### Coverage Summary
+
+The backend test suite contains **20 tests** organized in 5 categories, covering all API endpoints and input validation:
+
+| Test Class | Tests | What's Covered |
+|------------|-------|----------------|
+| **TestHealth** | 2 | `/health` endpoint returns correct fields (`status`, `engine_available`, `version`); status is always `"ok"` |
+| **TestProjects** | 7 | Full CRUD lifecycle — create, list, get, delete; 404 on missing project; unique IDs; ISO timestamps |
+| **TestDatasets** | 4 | TSV and CSV file upload via multipart; 404 on missing project; project metadata updated after upload |
+| **TestAnalysis** | 3 | `/run` returns `job_id` with `pending` status; 404 on missing project; empty job list for new projects |
+| **TestSchemaValidation** | 4 | Rejects invalid `algo` values (422); rejects invalid `fit` values (422); accepts valid non-default params; defaults are applied correctly |
+
+**Total: 20 tests — all passing.**
+
+### What's Tested
+
+- All 9 REST API endpoints (see table above)
+- Request validation via Pydantic schemas (invalid enum values return 422)
+- File upload with correct content-type handling
+- Project isolation (operations on non-existent projects return 404)
+- Default parameter injection for analysis configuration
+- Async request handling (tests use `httpx.AsyncClient` with `ASGITransport`)
+
+### Not Yet Covered
+
+- End-to-end analysis execution (requires gpredomicspy + sample data)
+- WebSocket/SSE progress streaming (not yet implemented)
+- Frontend component tests (planned for Phase 3)
+- Docker build integration tests
+
+## CI/CD
+
+GitHub Actions runs on every push and PR:
+
+- **backend-test**: Installs dependencies and runs `pytest`
+- **frontend-build**: Installs npm packages and runs `npm run build`
+- **docker-build**: Builds the multi-stage Docker image
+
+See [.github/workflows/ci.yml](.github/workflows/ci.yml).
+
 ## License
 
 GPL-3.0

backend/app/main.py

@@ -2,6 +2,7 @@
 
 import logging
 from contextlib import asynccontextmanager
+from pathlib import Path
 
 from fastapi import FastAPI
 from fastapi.middleware.cors import CORSMiddleware
@@ -47,3 +48,18 @@ async def lifespan(app: FastAPI):
 app.include_router(health.router)
 app.include_router(projects.router, prefix="/api")
 app.include_router(analysis.router, prefix="/api")
+
+# Serve Vue.js frontend (production: built into backend/static/)
+_static_dir = Path(__file__).parent / "static"
+if _static_dir.is_dir():
+    from fastapi.responses import FileResponse
+
+    app.mount("/assets", StaticFiles(directory=_static_dir / "assets"), name="assets")
+
+    @app.get("/{full_path:path}")
+    async def serve_spa(full_path: str):
+        """Serve Vue.js SPA — all non-API routes return index.html."""
+        file_path = _static_dir / full_path
+        if file_path.is_file():
+            return FileResponse(file_path)
+        return FileResponse(_static_dir / "index.html")

backend/app/models/schemas.py

@@ -150,11 +150,17 @@ class DatasetInfo(BaseModel):
     features_in_rows: bool = True
 
 
+class DatasetRef(BaseModel):
+    id: str
+    filename: str
+    path: str = ""
+
+
 class ProjectInfo(BaseModel):
     project_id: str
     name: str
     created_at: str
-    datasets: list[str] = []
+    datasets: list[DatasetRef] = []
     jobs: list[str] = []
 
 

backend/pyproject.toml

@@ -24,3 +24,6 @@ dev = [
 [build-system]
 requires = ["setuptools>=68"]
 build-backend = "setuptools.build_meta"
+
+[tool.pytest.ini_options]
+asyncio_mode = "auto"