feat(api): FastAPI REST backend for React frontend

## Summary
- Add FastAPI REST API endpoints for stroke segmentation
- Endpoints: GET /api/cases, POST /api/segment, GET /files/{path}
- CORS configured for HF Spaces frontend
- Sync endpoint handlers for proper threadpool execution
- Update Dockerfile for FastAPI deployment
- 8 backend tests, 58 frontend tests passing

## Changes
- Add src/stroke_deepisles_demo/api/ module (main.py, routes.py, schemas.py)
- Add tests/api/test_endpoints.py
- Update pyproject.toml with [api] extra dependencies
- Update Dockerfile CMD for uvicorn
- Update CI to install api extras

Addresses CodeRabbit feedback:
- Fixed flaky waitFor test
- Changed async def to def for sync handlers
- Fixed exception handling
- Updated spec documentation

.github/workflows/ci.yml

@@ -26,7 +26,7 @@ jobs:
         run: uv python install 3.12
 
       - name: Install dependencies
-        run: uv sync
+        run: uv sync --extra api --extra gradio
 
       - name: Lint with ruff
         run: uv run ruff check .
@@ -46,7 +46,7 @@ jobs:
         run: uv python install 3.12
 
       - name: Install dependencies
-        run: uv sync
+        run: uv sync --extra api --extra gradio
 
       - name: Type check with mypy
         run: uv run mypy src/
@@ -63,7 +63,7 @@ jobs:
         run: uv python install 3.12
 
       - name: Install dependencies
-        run: uv sync
+        run: uv sync --extra api --extra gradio
 
       - name: Run tests
         run: uv run pytest --cov --cov-report=xml
@@ -100,7 +100,7 @@ jobs:
         run: uv python install 3.12
 
       - name: Install dependencies
-        run: uv sync
+        run: uv sync --extra api --extra gradio
 
       - name: Run integration tests
         run: uv run pytest -m integration --timeout=600

Dockerfile

@@ -1,6 +1,6 @@
-# Dockerfile for Hugging Face Spaces deployment
+# Dockerfile for Hugging Face Spaces deployment (FastAPI backend)
 # Base: DeepISLES image with nnU-Net, SEALS, and all ML dependencies
-# See: docs/specs/07-hf-spaces-deployment.md
+# See: docs/specs/frontend/36-frontend-without-gradio-hf-spaces.md
 #
 # IMPORTANT: During Docker build, GPU is NOT available.
 # All GPU operations happen at runtime only.
@@ -31,12 +31,8 @@ WORKDIR /home/user/demo
 # Copy requirements first for better layer caching
 COPY --chown=1000:1000 requirements.txt /home/user/demo/requirements.txt
 
-# Copy local packages (Custom Components) BEFORE pip install
-# This is required because requirements.txt refers to ./packages/niivueviewer
-COPY --chown=1000:1000 packages/ /home/user/demo/packages/
-
 # Install Python dependencies into SYSTEM Python (NOT conda env)
-# DeepISLES conda env is Python 3.8, but Gradio 6 needs Python 3.10+
+# DeepISLES conda env is Python 3.8, but FastAPI needs Python 3.10+
 # We'll shell out to conda env for inference only
 RUN pip install --no-cache-dir -r requirements.txt
 
@@ -44,7 +40,6 @@ RUN pip install --no-cache-dir -r requirements.txt
 COPY --chown=1000:1000 pyproject.toml /home/user/demo/pyproject.toml
 COPY --chown=1000:1000 README.md /home/user/demo/README.md
 COPY --chown=1000:1000 src/ /home/user/demo/src/
-COPY --chown=1000:1000 app.py /home/user/demo/app.py
 
 # Copy adapter script for subprocess invocation of DeepISLES
 # This script runs in the conda env (Py3.8) and is called via subprocess
@@ -67,18 +62,18 @@ ENV DEEPISLES_PATH=/app
 ENV HF_HOME=/home/user/demo/cache
 
 # Create directories for data with proper permissions
-RUN mkdir -p /home/user/demo/data /home/user/demo/results /home/user/demo/cache && \
-    chown -R 1000:1000 /home/user/demo
+# CRITICAL: /tmp/stroke-results is required for FastAPI StaticFiles mount
+RUN mkdir -p /home/user/demo/data /home/user/demo/results /home/user/demo/cache /tmp/stroke-results && \
+    chown -R 1000:1000 /home/user/demo /tmp/stroke-results
 
 # Switch to non-root user (required by HF Spaces)
 USER user
 
-# Expose the Gradio port
+# Expose the API port (HF Spaces expects 7860)
 EXPOSE 7860
 
 # Reset ENTRYPOINT from base image
 ENTRYPOINT []
 
-# Run Gradio app with SYSTEM Python (Py3.10+)
-# DeepISLES inference is invoked via subprocess into conda env
-CMD ["python", "-m", "stroke_deepisles_demo.ui.app"]
+# Run FastAPI with uvicorn (module path: stroke_deepisles_demo.api.main:app)
+CMD ["uvicorn", "stroke_deepisles_demo.api.main:app", "--host", "0.0.0.0", "--port", "7860"]

docs/specs/frontend/36-frontend-without-gradio-hf-spaces.md

@@ -71,7 +71,7 @@ You **need both** because:
 │  Endpoints:                         │
 │  - GET  /api/cases                  │
 │  - POST /api/segment                │
-│  - GET  /api/files/{path}           │
+│  - GET  /files/{run_id}/{case}/...  │
 │                                     │
 │  Sleeps after 48h inactivity        │
 └─────────────────────────────────────┘
@@ -81,9 +81,13 @@ You **need both** because:
 
 ## Project Structure
 
+This is an **existing monorepo** (`stroke-deepisles-demo`), NOT a new project. The frontend is
+added alongside the existing Python package. The "backend" is the existing `src/stroke_deepisles_demo/`
+package with a new `api/` submodule.
+
 ```
-stroke-viewer/
-├── frontend/                    # Static Space
+stroke-deepisles-demo/           # EXISTING monorepo
+├── frontend/                    # NEW: React + NiiVue (Static Space)
 │   ├── src/
 │   │   ├── components/
 │   │   │   ├── NiiVueViewer.tsx
@@ -99,26 +103,43 @@ stroke-viewer/
 │   │   ├── App.tsx
 │   │   ├── main.tsx
 │   │   └── index.css
+│   ├── e2e/                     # Playwright E2E tests
 │   ├── public/
 │   ├── index.html
 │   ├── vite.config.ts
+│   ├── vitest.config.ts
+│   ├── playwright.config.ts
 │   ├── tsconfig.json
 │   ├── package.json
 │   └── README.md                # HF Spaces YAML config
 │
-├── backend/                     # Docker Space
-│   ├── api/
+├── src/stroke_deepisles_demo/   # EXISTING Python package (Docker Space)
+│   ├── api/                     # NEW: FastAPI REST API submodule
 │   │   ├── __init__.py
 │   │   ├── main.py              # FastAPI app
 │   │   ├── routes.py            # API endpoints
 │   │   └── schemas.py           # Pydantic models
-│   ├── Dockerfile
-│   ├── requirements.txt
-│   └── README.md                # HF Spaces YAML config
+│   ├── core/                    # Config, logging (existing)
+│   ├── data/                    # Data adapters (existing)
+│   ├── inference/               # DeepISLES integration (existing)
+│   ├── ui/                      # Gradio UI (being replaced)
+│   ├── pipeline.py              # ML pipeline (existing)
+│   └── metrics.py               # Metrics computation (existing)
+│
+├── tests/
+│   ├── api/                     # NEW: API endpoint tests
+│   │   ├── __init__.py
+│   │   └── test_endpoints.py
+│   └── ...                      # Existing tests
 │
-└── README.md                    # Project overview
+├── Dockerfile                   # Docker for HF Spaces (existing)
+├── pyproject.toml               # Python package config (existing)
+└── README.md
 ```
 
+**Key difference from a greenfield project:** We're adding `frontend/` and `src/stroke_deepisles_demo/api/`
+to an existing codebase, NOT creating separate `frontend/` and `backend/` directories.
+
 ---
 
 ## Frontend Implementation
@@ -706,37 +727,44 @@ Built with React, TypeScript, Tailwind CSS, and Vite.
 
 ## Backend Implementation
 
-### requirements.txt
+The backend is the **existing** `src/stroke_deepisles_demo/` Python package. We add a new
+`api/` submodule for FastAPI endpoints. This keeps all Python code in one package with
+proper imports (e.g., `from stroke_deepisles_demo.api.routes import router`).
 
-```
-fastapi==0.124.2
-uvicorn[standard]==0.34.0
-pydantic==2.10.4
-python-multipart>=0.0.18
+### pyproject.toml (additions)
 
-# Existing project dependencies
-stroke-deepisles-demo @ file:.
+Add these dependencies to the existing `pyproject.toml`:
+
+```toml
+[project.optional-dependencies]
+api = [
+    "fastapi>=0.115.0",
+    "uvicorn[standard]>=0.32.0",
+]
 ```
 
-**Why these exact versions (Dec 2025):**
-- `fastapi` **0.124.2**: Latest stable (Dec 10, 2025)
-- `uvicorn[standard]` **0.34.0**: Latest stable
-- `pydantic` **2.10.4**: Latest stable
-- `python-multipart` **>=0.0.18**: Required by FastAPI 0.124.x
+### src/stroke_deepisles_demo/api/__init__.py
+
+```python
+"""FastAPI REST API for stroke segmentation."""
+
+from stroke_deepisles_demo.api.main import app
 
-### backend/api/main.py
+__all__ = ["app"]
+```
+
+### src/stroke_deepisles_demo/api/main.py
 
 ```python
-"""FastAPI backend for stroke segmentation."""
+"""FastAPI application for stroke segmentation API."""
 
 import os
-import re
 
 from fastapi import FastAPI
 from fastapi.middleware.cors import CORSMiddleware
 from fastapi.staticfiles import StaticFiles
 
-from api.routes import router
+from stroke_deepisles_demo.api.routes import router
 
 app = FastAPI(
     title="Stroke Segmentation API",
@@ -744,11 +772,10 @@ app = FastAPI(
     version="1.0.0",
 )
 
-# CORS for frontend - HF Spaces use dashed hostnames: {org}--{space}.hf.space
-# Also supports PR previews: pr-{n}--{org}--{space}.hf.space
+# CORS configuration
 FRONTEND_ORIGIN = os.environ.get("FRONTEND_ORIGIN", "")
 CORS_ORIGINS = [
-    "http://localhost:5173",  # Local Vite dev server
+    "http://localhost:5173",  # Vite dev server
     "http://localhost:3000",  # Alternative local port
 ]
 if FRONTEND_ORIGIN:
@@ -757,12 +784,7 @@ if FRONTEND_ORIGIN:
 app.add_middleware(
     CORSMiddleware,
     allow_origins=CORS_ORIGINS,
-    # Regex matches HuggingFace Spaces origins:
-    # - Production: https://{org}--stroke-viewer-frontend.hf.space
-    # - PR preview: https://{org}--stroke-viewer-frontend--pr-{N}.hf.space
-    # - Branch:     https://{org}--stroke-viewer-frontend--{branch}.hf.space
-    # Pattern: anything--stroke-viewer-frontend, optionally followed by --anything
-    allow_origin_regex=r"https://.*--stroke-viewer-frontend(--.*)?\.hf\.space",
+    allow_origin_regex=r"https://.*--stroke-viewer-frontend(--.*)?\\.hf\\.space",
     allow_credentials=True,
     allow_methods=["*"],
     allow_headers=["*"],
@@ -771,17 +793,19 @@ app.add_middleware(
 # API routes
 app.include_router(router, prefix="/api")
 
-# Serve NIfTI files from results directory
-# Files are stored as /tmp/stroke-results/{run_id}/{case_id}/{filename}
-app.mount("/files", StaticFiles(directory="/tmp/stroke-results"), name="files")
+# Static files for NIfTI results (only mount if directory exists)
+RESULTS_DIR = "/tmp/stroke-results"
+if os.path.exists(RESULTS_DIR):
+    app.mount("/files", StaticFiles(directory=RESULTS_DIR), name="files")
 
 
 @app.get("/")
 async def root():
+    """Health check endpoint."""
     return {"status": "healthy", "service": "stroke-segmentation-api"}
 ```
 
-### backend/api/routes.py
+### src/stroke_deepisles_demo/api/routes.py
 
 ```python
 """API route handlers."""
@@ -791,15 +815,15 @@ import uuid
 from pathlib import Path
 
 from fastapi import APIRouter, HTTPException, Request
-from api.schemas import SegmentRequest, SegmentResponse, CasesResponse
 
+from stroke_deepisles_demo.api.schemas import CasesResponse, SegmentRequest, SegmentResponse
 from stroke_deepisles_demo.data import list_case_ids
 from stroke_deepisles_demo.pipeline import run_pipeline_on_case
 from stroke_deepisles_demo.metrics import compute_volume_ml
 
 router = APIRouter()
 
-# Base directory for results (must match StaticFiles mount in main.py)
+# Base directory for results
 RESULTS_BASE = Path("/tmp/stroke-results")
 
 
@@ -813,7 +837,6 @@ def get_backend_base_url(request: Request) -> str:
     env_url = os.environ.get("BACKEND_PUBLIC_URL", "").rstrip("/")
     if env_url:
         return env_url
-    # Fall back to request origin (works for local dev)
     return str(request.base_url).rstrip("/")
 
 
@@ -831,7 +854,7 @@ async def get_cases():
 async def run_segmentation(request: Request, body: SegmentRequest):
     """Run DeepISLES segmentation on a case."""
     try:
-        # Generate unique run ID to avoid conflicts between concurrent requests
+        # Generate unique run ID to avoid conflicts
         run_id = str(uuid.uuid4())[:8]
         output_dir = RESULTS_BASE / run_id
 
@@ -850,14 +873,11 @@ async def run_segmentation(request: Request, body: SegmentRequest):
         except Exception:
             pass
 
-        # Build ABSOLUTE file URLs for cross-origin NiiVue loading
-        # Files are at: /tmp/stroke-results/{run_id}/{case_id}/{filename}
-        # Served at: /files/{run_id}/{case_id}/{filename}
+        # Build absolute file URLs
         backend_url = get_backend_base_url(request)
         dwi_filename = result.input_files["dwi"].name
         pred_filename = result.prediction_mask.name
 
-        # URL path: /files/{run_id}/{case_id}/{filename}
         file_path_prefix = f"/files/{run_id}/{result.case_id}"
 
         return SegmentResponse(
@@ -868,29 +888,34 @@ async def run_segmentation(request: Request, body: SegmentRequest):
             dwiUrl=f"{backend_url}{file_path_prefix}/{dwi_filename}",
             predictionUrl=f"{backend_url}{file_path_prefix}/{pred_filename}",
         )
-
     except Exception as e:
         raise HTTPException(status_code=500, detail=str(e))
 ```
 
-### backend/api/schemas.py
+### src/stroke_deepisles_demo/api/schemas.py
 
 ```python
-"""Pydantic schemas for API."""
+"""Pydantic schemas for API requests and responses."""
 
 from pydantic import BaseModel
 
 
 class CasesResponse(BaseModel):
+    """Response for GET /api/cases."""
+
     cases: list[str]
 
 
 class SegmentRequest(BaseModel):
+    """Request body for POST /api/segment."""
+
     case_id: str
     fast_mode: bool = True
 
 
 class SegmentResponse(BaseModel):
+    """Response for POST /api/segment."""
+
     caseId: str
     diceScore: float | None
     volumeMl: float | None
@@ -899,7 +924,9 @@ class SegmentResponse(BaseModel):
     predictionUrl: str
 ```
 
-### backend/Dockerfile
+### Dockerfile (update existing)
+
+The existing `Dockerfile` at project root needs to be updated for the API:
 
 ```dockerfile
 # CRITICAL: Must use isleschallenge/deepisles base image
@@ -907,26 +934,17 @@ class SegmentResponse(BaseModel):
 # - PyTorch with CUDA support
 # - Pre-installed DeepISLES model weights (~18GB)
 # - All medical imaging dependencies (nibabel, nnunet, etc.)
-#
-# Using python:3.11-slim would require manually downloading weights
-# and reinstalling all CUDA/PyTorch dependencies - not feasible.
 FROM isleschallenge/deepisles:latest
 
 WORKDIR /app
 
-# Copy the ENTIRE project (stroke-deepisles-demo package)
-# This is required because requirements.txt references "stroke-deepisles-demo @ file:."
+# Copy the project
 COPY pyproject.toml .
 COPY src/ src/
 COPY README.md .
 
-# Copy API code
-COPY backend/api/ api/
-COPY backend/requirements.txt .
-
-# Install API dependencies (FastAPI, uvicorn) + local package
-# Note: Base image already has torch, nibabel, etc.
-RUN pip install --no-cache-dir -r requirements.txt
+# Install the package with API dependencies
+RUN pip install --no-cache-dir -e ".[api]"
 
 # Create results directory (used by StaticFiles mount)
 RUN mkdir -p /tmp/stroke-results
@@ -938,8 +956,8 @@ ENV DEEPISLES_DIRECT_INVOCATION=1
 # Expose port (HF Spaces expects 7860)
 EXPOSE 7860
 
-# Run FastAPI
-CMD ["uvicorn", "api.main:app", "--host", "0.0.0.0", "--port", "7860"]
+# Run FastAPI (note: module path is stroke_deepisles_demo.api.main:app)
+CMD ["uvicorn", "stroke_deepisles_demo.api.main:app", "--host", "0.0.0.0", "--port", "7860"]
 ```
 
 **CRITICAL: GPU Required**
@@ -992,48 +1010,48 @@ FastAPI backend running DeepISLES stroke lesion segmentation.
 ### Frontend (Local Development)
 
 ```bash
-# Create project
-npm create vite@latest stroke-viewer-frontend -- --template react-ts
-cd stroke-viewer-frontend
-
-# Install dependencies
-npm install @niivue/niivue
-npm install -D tailwindcss @tailwindcss/vite
+cd frontend
 
-# Copy the files from this spec into src/
+# Install dependencies (already configured in package.json)
+npm install
 
 # Run dev server
 npm run dev
 # Opens http://localhost:5173
+
+# Run tests
+npm test                  # Unit tests with Vitest
+npm run test:e2e          # E2E tests with Playwright
+npm run test:coverage     # Coverage report
 ```
 
 ### Backend (Local Development)
 
 ```bash
-cd backend
-
-# Create virtual environment
-python -m venv venv
-source venv/bin/activate
+# From project root (stroke-deepisles-demo/)
 
-# Install dependencies
-pip install -r requirements.txt
+# Install with API dependencies
+pip install -e ".[api]"
 
 # Run server
-uvicorn api.main:app --reload --port 7860
+uvicorn stroke_deepisles_demo.api.main:app --reload --port 7860
 # Opens http://localhost:7860
+
+# Run API tests
+pytest tests/api/ -v
 ```
 
 ### Deploy to HuggingFace
 
 ```bash
-# Frontend (Static Space)
+# Frontend (Static Space) - deploy from frontend/ directory
 cd frontend
+npm run build
 huggingface-cli repo create stroke-viewer-frontend --type space --space-sdk static
 huggingface-cli upload stroke-viewer-frontend ./dist . --repo-type space
 
-# Backend (Docker Space)
-cd backend
+# Backend (Docker Space) - deploy from project root
+# The Dockerfile at project root builds the full package including API
 huggingface-cli repo create stroke-viewer-api --type space --space-sdk docker
 huggingface-cli upload stroke-viewer-api . . --repo-type space
 ```
@@ -1068,35 +1086,35 @@ No additional env vars needed - uses existing stroke-deepisles-demo configuratio
 
 ## Next Steps
 
-1. Create `frontend/` directory with files from this spec
-2. Create `backend/` directory with files from this spec
-3. Test locally: `npm run dev` + `uvicorn api.main:app`
-4. Create HuggingFace Spaces (one Static, one Docker)
-5. Deploy and test
+1. ✅ Create `frontend/` directory with React + NiiVue (DONE - PR #32 merged)
+2. ✅ Create `src/stroke_deepisles_demo/api/` submodule with FastAPI (DONE)
+3. ✅ Create `tests/api/` with endpoint tests (DONE - 8 tests passing)
+4. Test locally: `npm run dev` + `uvicorn stroke_deepisles_demo.api.main:app`
+5. Create HuggingFace Spaces (one Static, one Docker)
+6. Deploy and test
 
 ---
 
 ## Dependencies Summary (Verified Dec 11, 2025)
 
-**Frontend (npm) - PINNED VERSIONS:**
+**Frontend (npm) - ACTUAL VERSIONS (from package.json):**
 | Package | Version | Notes |
 |---------|---------|-------|
-| react | 18.3.1 | NOT React 19 (CVE-2025-55182) |
-| react-dom | 18.3.1 | Must match react version |
-| @niivue/niivue | 0.65.0 | Latest stable |
-| typescript | 5.6.3 | Latest 5.6.x |
-| vite | 6.0.5 | Stable v6 (not v7/v8 beta) |
-| tailwindcss | 4.1.7 | Latest v4 |
-| @tailwindcss/vite | 4.1.7 | Must match tailwindcss |
-| @vitejs/plugin-react | 4.3.4 | Latest stable |
-
-**Backend (pip) - PINNED VERSIONS:**
+| react | ^19.2.0 | React 19 client-only (safe from CVE-2025-55182) |
+| react-dom | ^19.2.0 | Must match react version |
+| @niivue/niivue | ^0.65.0 | Latest stable |
+| typescript | ~5.9.3 | Latest 5.9.x |
+| vite | ^7.2.4 | Latest v7 |
+| tailwindcss | ^4.1.17 | Latest v4 |
+| @tailwindcss/vite | ^4.1.17 | Must match tailwindcss |
+| @vitejs/plugin-react | ^5.1.1 | Latest stable |
+
+**Backend (pip) - VERSIONS (from pyproject.toml):**
 | Package | Version | Notes |
 |---------|---------|-------|
-| fastapi | 0.124.2 | Latest (Dec 10, 2025) |
-| uvicorn[standard] | 0.34.0 | Latest stable |
-| pydantic | 2.10.4 | Latest stable |
-| python-multipart | >=0.0.18 | Required by FastAPI |
+| fastapi | >=0.115.0 | Latest compatible |
+| uvicorn[standard] | >=0.32.0 | Latest stable |
+| pydantic | (bundled) | Included with FastAPI |
 
-**Node.js:** >= 20.0.0 (required for Vite 6)
+**Node.js:** >= 20.0.0 (required for Vite 7)
 **Python:** >= 3.11 (recommended for FastAPI)

frontend/README.md

@@ -1,73 +1,65 @@
-# React + TypeScript + Vite
+---
+title: Stroke Lesion Viewer
+emoji: 🧠
+colorFrom: blue
+colorTo: purple
+sdk: static
+app_file: dist/index.html
+app_build_command: npm run build
+# CRITICAL: Vite 6 requires Node.js >= 20. HF Spaces defaults to Node 18.
+# Without this, the build will fail or produce warnings.
+nodejs_version: "20"
+pinned: false
+---
 
-This template provides a minimal setup to get React working in Vite with HMR and some ESLint rules.
+# Stroke Lesion Segmentation Viewer
 
-Currently, two official plugins are available:
+Interactive 3D viewer for stroke lesion segmentation results using NiiVue.
 
-- [@vitejs/plugin-react](https://github.com/vitejs/vite-plugin-react/blob/main/packages/plugin-react) uses [Babel](https://babeljs.io/) (or [oxc](https://oxc.rs) when used in [rolldown-vite](https://vite.dev/guide/rolldown)) for Fast Refresh
-- [@vitejs/plugin-react-swc](https://github.com/vitejs/vite-plugin-react/blob/main/packages/plugin-react-swc) uses [SWC](https://swc.rs/) for Fast Refresh
+Built with React, TypeScript, Tailwind CSS, and Vite.
 
-## React Compiler
+## Features
 
-The React Compiler is not enabled on this template because of its impact on dev & build performances. To add it, see [this documentation](https://react.dev/learn/react-compiler/installation).
+- **NiiVue WebGL2 Viewer**: Pan, zoom, and navigate through NIfTI volumes
+- **Real-time Segmentation**: Run DeepISLES inference on ISLES24 dataset cases
+- **Metrics Display**: Dice score, volume (mL), processing time
 
-## Expanding the ESLint configuration
+## Architecture
 
-If you are developing a production application, we recommend updating the configuration to enable type-aware lint rules:
+This is the **frontend Static Space** of a two-Space deployment:
 
-```js
-export default defineConfig([
-  globalIgnores(['dist']),
-  {
-    files: ['**/*.{ts,tsx}'],
-    extends: [
-      // Other configs...
+```
+┌─────────────────────────────────────┐
+│  HuggingFace Static Space           │  ← You are here
+│  stroke-viewer-frontend             │
+│                                     │
+│  React 19 + TypeScript + Tailwind   │
+│  @niivue/niivue for 3D viewing      │
+└──────────────┬──────────────────────┘
+               │ HTTPS API calls
+               ▼
+┌─────────────────────────────────────┐
+│  HuggingFace Docker Space           │
+│  stroke-viewer-api                  │
+│                                     │
+│  FastAPI + DeepISLES + PyTorch      │
+└─────────────────────────────────────┘
+```
 
-      // Remove tseslint.configs.recommended and replace with this
-      tseslint.configs.recommendedTypeChecked,
-      // Alternatively, use this for stricter rules
-      tseslint.configs.strictTypeChecked,
-      // Optionally, add this for stylistic rules
-      tseslint.configs.stylisticTypeChecked,
+## Local Development
 
-      // Other configs...
-    ],
-    languageOptions: {
-      parserOptions: {
-        project: ['./tsconfig.node.json', './tsconfig.app.json'],
-        tsconfigRootDir: import.meta.dirname,
-      },
-      // other options...
-    },
-  },
-])
+```bash
+npm install
+npm run dev          # Start dev server at http://localhost:5173
+npm test             # Run unit tests
+npm run test:e2e     # Run E2E tests
+npm run build        # Production build
 ```
 
-You can also install [eslint-plugin-react-x](https://github.com/Rel1cx/eslint-react/tree/main/packages/plugins/eslint-plugin-react-x) and [eslint-plugin-react-dom](https://github.com/Rel1cx/eslint-react/tree/main/packages/plugins/eslint-plugin-react-dom) for React-specific lint rules:
+## Environment Variables
 
-```js
-// eslint.config.js
-import reactX from 'eslint-plugin-react-x'
-import reactDom from 'eslint-plugin-react-dom'
+Set `VITE_API_URL` to point to your backend:
 
-export default defineConfig([
-  globalIgnores(['dist']),
-  {
-    files: ['**/*.{ts,tsx}'],
-    extends: [
-      // Other configs...
-      // Enable lint rules for React
-      reactX.configs['recommended-typescript'],
-      // Enable lint rules for React DOM
-      reactDom.configs.recommended,
-    ],
-    languageOptions: {
-      parserOptions: {
-        project: ['./tsconfig.node.json', './tsconfig.app.json'],
-        tsconfigRootDir: import.meta.dirname,
-      },
-      // other options...
-    },
-  },
-])
+```bash
+VITE_API_URL=http://localhost:7860 npm run dev
 ```

frontend/src/components/__tests__/NiiVueViewer.test.tsx

@@ -1,5 +1,5 @@
 import { describe, it, expect, vi, beforeEach } from 'vitest'
-import { render, screen } from '@testing-library/react'
+import { render, screen, waitFor } from '@testing-library/react'
 import { NiiVueViewer } from '../NiiVueViewer'
 
 // Store mock function references so tests can verify calls
@@ -119,8 +119,8 @@ describe('NiiVueViewer', () => {
 
     render(<NiiVueViewer {...defaultProps} onError={onError} />)
 
-    // Wait for error callback to be invoked
-    await vi.waitFor(() => {
+    // Wait for error callback to be invoked (use RTL's waitFor, not vi.waitFor)
+    await waitFor(() => {
       expect(onError).toHaveBeenCalledWith(errorMessage)
     })
   })
@@ -152,9 +152,9 @@ describe('NiiVueViewer', () => {
     // Now reject the second load (stale)
     rejectSecondLoad!(new Error('Stale load error'))
 
-    // Wait a tick and verify onError was NOT called with stale error
-    await vi.waitFor(() => {
-      expect(onError).not.toHaveBeenCalledWith('Stale load error')
-    })
+    // Flush async work (let rejection be processed) before asserting
+    // Using waitFor with negative assertions is flaky - it passes immediately
+    await new Promise(resolve => setTimeout(resolve, 0))
+    expect(onError).not.toHaveBeenCalledWith('Stale load error')
   })
 })

pyproject.toml

@@ -31,15 +31,22 @@ dependencies = [
     "pydantic>=2.5.0",
     "pydantic-settings>=2.1.0",
 
-    # UI (Gradio 6.x - Dec 2025 stable)
+    # Networking
+    "requests>=2.0.0",
+]
+
+[project.optional-dependencies]
+# API server (FastAPI backend for HF Spaces Docker deployment)
+api = [
+    "fastapi>=0.115.0",
+    "uvicorn[standard]>=0.32.0",
+]
+
+# Legacy Gradio UI (being replaced by React frontend)
+gradio = [
     "gradio>=6.0.0,<7.0.0",
     "matplotlib>=3.8.0",
-
-    # Custom component for NiiVue WebGL viewer (local package)
     "gradio_niivueviewer",
-
-    # Networking
-    "requests>=2.0.0",
 ]
 
 [project.scripts]
@@ -124,6 +131,11 @@ module = [
     "numpy.*",
     "pyarrow.*",
     "pytest.*",
+    # FastAPI route decorators cause "untyped decorator" errors in strict mode
+    # See: https://github.com/tiangolo/fastapi/discussions/7463
+    "fastapi.*",
+    "starlette.*",
+    "uvicorn.*",
     # DeepISLES modules (only available in DeepISLES Docker image)
     "src.isles22_ensemble",
 ]

requirements.txt

@@ -17,12 +17,9 @@ numpy>=1.26.0,<2.0.0
 pydantic>=2.5.0
 pydantic-settings>=2.1.0
 
-# UI - Gradio 6.x (latest stable as of Dec 2025)
-gradio>=6.0.0,<7.0.0
-matplotlib>=3.8.0
-
 # Networking
 requests>=2.0.0
 
-# Custom Components
-./packages/niivueviewer
+# API server (FastAPI backend)
+fastapi>=0.115.0
+uvicorn[standard]>=0.32.0

src/stroke_deepisles_demo/api/__init__.py

@@ -0,0 +1,5 @@
+"""FastAPI REST API for stroke segmentation."""
+
+from stroke_deepisles_demo.api.main import app
+
+__all__ = ["app"]

src/stroke_deepisles_demo/api/main.py

@@ -0,0 +1,50 @@
+"""FastAPI application for stroke segmentation API."""
+
+import os
+from pathlib import Path
+from typing import Any
+
+from fastapi import FastAPI
+from fastapi.middleware.cors import CORSMiddleware
+from fastapi.staticfiles import StaticFiles
+
+from stroke_deepisles_demo.api.routes import router
+
+app = FastAPI(
+    title="Stroke Segmentation API",
+    description="DeepISLES stroke lesion segmentation",
+    version="1.0.0",
+)
+
+# CORS configuration
+FRONTEND_ORIGIN = os.environ.get("FRONTEND_ORIGIN", "")
+CORS_ORIGINS = [
+    "http://localhost:5173",  # Vite dev server
+    "http://localhost:3000",  # Alternative local port
+]
+if FRONTEND_ORIGIN:
+    CORS_ORIGINS.append(FRONTEND_ORIGIN)
+
+app.add_middleware(
+    CORSMiddleware,
+    allow_origins=CORS_ORIGINS,
+    allow_origin_regex=r"https://.*--stroke-viewer-frontend(--.*)?\.hf\.space",
+    allow_credentials=True,
+    allow_methods=["*"],
+    allow_headers=["*"],
+)
+
+# API routes
+app.include_router(router, prefix="/api")
+
+# Static files for NIfTI results
+# Create directory if it doesn't exist (ensures mount works on first run)
+RESULTS_DIR = Path("/tmp/stroke-results")
+RESULTS_DIR.mkdir(parents=True, exist_ok=True)
+app.mount("/files", StaticFiles(directory=str(RESULTS_DIR)), name="files")
+
+
+@app.get("/")
+async def root() -> dict[str, Any]:
+    """Health check endpoint."""
+    return {"status": "healthy", "service": "stroke-segmentation-api"}

src/stroke_deepisles_demo/api/routes.py

@@ -0,0 +1,94 @@
+"""API route handlers."""
+
+import contextlib
+import os
+import uuid
+from pathlib import Path
+
+from fastapi import APIRouter, HTTPException, Request
+
+from stroke_deepisles_demo.api.schemas import CasesResponse, SegmentRequest, SegmentResponse
+from stroke_deepisles_demo.data import list_case_ids
+from stroke_deepisles_demo.metrics import compute_volume_ml
+from stroke_deepisles_demo.pipeline import run_pipeline_on_case
+
+router = APIRouter()
+
+# Base directory for results
+RESULTS_BASE = Path("/tmp/stroke-results")
+
+
+def get_backend_base_url(request: Request) -> str:
+    """Get the backend's public URL for building absolute file URLs.
+
+    Priority:
+    1. BACKEND_PUBLIC_URL env var (for production HF Spaces)
+    2. Request's base URL (for local development)
+    """
+    env_url = os.environ.get("BACKEND_PUBLIC_URL", "").rstrip("/")
+    if env_url:
+        return env_url
+    return str(request.base_url).rstrip("/")
+
+
+@router.get("/cases", response_model=CasesResponse)
+def get_cases() -> CasesResponse:
+    """List available cases from dataset.
+
+    Note: This is a sync def (not async) because list_case_ids() is synchronous.
+    FastAPI automatically runs sync endpoints in a threadpool to avoid blocking.
+    """
+    try:
+        cases = list_case_ids()
+        return CasesResponse(cases=cases)
+    except HTTPException:
+        raise
+    except Exception as e:
+        raise HTTPException(status_code=500, detail=str(e)) from None
+
+
+@router.post("/segment", response_model=SegmentResponse)
+def run_segmentation(request: Request, body: SegmentRequest) -> SegmentResponse:
+    """Run DeepISLES segmentation on a case.
+
+    Note: This is a sync def (not async) because run_pipeline_on_case() is synchronous
+    and CPU/GPU-bound. FastAPI automatically runs sync endpoints in a threadpool,
+    which prevents blocking the event loop during inference.
+    """
+    try:
+        # Generate unique run ID to avoid conflicts
+        run_id = str(uuid.uuid4())[:8]
+        output_dir = RESULTS_BASE / run_id
+
+        result = run_pipeline_on_case(
+            body.case_id,
+            output_dir=output_dir,
+            fast=body.fast_mode,
+            compute_dice=True,
+            cleanup_staging=True,
+        )
+
+        # Compute volume (may fail for edge cases)
+        volume_ml = None
+        with contextlib.suppress(Exception):
+            volume_ml = round(compute_volume_ml(result.prediction_mask, threshold=0.5), 2)
+
+        # Build absolute file URLs
+        backend_url = get_backend_base_url(request)
+        dwi_filename = result.input_files["dwi"].name
+        pred_filename = result.prediction_mask.name
+
+        file_path_prefix = f"/files/{run_id}/{result.case_id}"
+
+        return SegmentResponse(
+            caseId=result.case_id,
+            diceScore=result.dice_score,
+            volumeMl=volume_ml,
+            elapsedSeconds=round(result.elapsed_seconds, 2),
+            dwiUrl=f"{backend_url}{file_path_prefix}/{dwi_filename}",
+            predictionUrl=f"{backend_url}{file_path_prefix}/{pred_filename}",
+        )
+    except HTTPException:
+        raise
+    except Exception as e:
+        raise HTTPException(status_code=500, detail=str(e)) from None

src/stroke_deepisles_demo/api/schemas.py

@@ -0,0 +1,27 @@
+"""Pydantic schemas for API requests and responses."""
+
+from pydantic import BaseModel
+
+
+class CasesResponse(BaseModel):
+    """Response for GET /api/cases."""
+
+    cases: list[str]
+
+
+class SegmentRequest(BaseModel):
+    """Request body for POST /api/segment."""
+
+    case_id: str
+    fast_mode: bool = True
+
+
+class SegmentResponse(BaseModel):
+    """Response for POST /api/segment."""
+
+    caseId: str
+    diceScore: float | None
+    volumeMl: float | None
+    elapsedSeconds: float
+    dwiUrl: str
+    predictionUrl: str

tests/api/__init__.py

@@ -0,0 +1 @@
+"""Tests for REST API endpoints."""

tests/api/test_endpoints.py

@@ -0,0 +1,145 @@
+"""TDD tests for API endpoints.
+
+RED-GREEN-REFACTOR: Tests written FIRST, before implementation.
+"""
+
+from unittest.mock import MagicMock, patch
+
+import pytest
+from fastapi.testclient import TestClient
+
+from stroke_deepisles_demo.api import app
+
+
+@pytest.fixture
+def client() -> TestClient:
+    """Create test client for FastAPI app."""
+    return TestClient(app)
+
+
+class TestHealthCheck:
+    """Tests for root health check endpoint."""
+
+    def test_root_returns_healthy_status(self, client: TestClient) -> None:
+        """GET / returns healthy status."""
+        response = client.get("/")
+
+        assert response.status_code == 200
+        data = response.json()
+        assert data["status"] == "healthy"
+        assert "service" in data
+
+
+class TestGetCases:
+    """Tests for GET /api/cases endpoint."""
+
+    def test_returns_list_of_case_ids(self, client: TestClient) -> None:
+        """GET /api/cases returns a list of case IDs."""
+        with patch("stroke_deepisles_demo.api.routes.list_case_ids") as mock_list:
+            mock_list.return_value = ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
+
+            response = client.get("/api/cases")
+
+            assert response.status_code == 200
+            data = response.json()
+            assert "cases" in data
+            assert data["cases"] == ["sub-stroke0001", "sub-stroke0002", "sub-stroke0003"]
+
+    def test_returns_empty_list_when_no_cases(self, client: TestClient) -> None:
+        """GET /api/cases returns empty list when no cases available."""
+        with patch("stroke_deepisles_demo.api.routes.list_case_ids") as mock_list:
+            mock_list.return_value = []
+
+            response = client.get("/api/cases")
+
+            assert response.status_code == 200
+            assert response.json()["cases"] == []
+
+    def test_returns_500_on_data_error(self, client: TestClient) -> None:
+        """GET /api/cases returns 500 when data layer raises exception."""
+        with patch("stroke_deepisles_demo.api.routes.list_case_ids") as mock_list:
+            mock_list.side_effect = RuntimeError("Dataset not found")
+
+            response = client.get("/api/cases")
+
+            assert response.status_code == 500
+            assert "Dataset not found" in response.json()["detail"]
+
+
+class TestPostSegment:
+    """Tests for POST /api/segment endpoint."""
+
+    def test_runs_segmentation_and_returns_result(self, client: TestClient) -> None:
+        """POST /api/segment runs pipeline and returns metrics + URLs."""
+        mock_result = MagicMock()
+        mock_result.case_id = "sub-stroke0001"
+        mock_result.dice_score = 0.847
+        mock_result.elapsed_seconds = 12.5
+        mock_result.prediction_mask.name = "prediction.nii.gz"
+        mock_result.input_files = {"dwi": MagicMock(name="dwi.nii.gz")}
+        mock_result.input_files["dwi"].name = "dwi.nii.gz"
+
+        with (
+            patch("stroke_deepisles_demo.api.routes.run_pipeline_on_case") as mock_pipeline,
+            patch("stroke_deepisles_demo.api.routes.compute_volume_ml") as mock_volume,
+        ):
+            mock_pipeline.return_value = mock_result
+            mock_volume.return_value = 15.32
+
+            response = client.post(
+                "/api/segment",
+                json={"case_id": "sub-stroke0001", "fast_mode": True},
+            )
+
+            assert response.status_code == 200
+            data = response.json()
+            assert data["caseId"] == "sub-stroke0001"
+            assert data["diceScore"] == 0.847
+            assert data["volumeMl"] == 15.32
+            assert data["elapsedSeconds"] == 12.5
+            assert "dwi.nii.gz" in data["dwiUrl"]
+            assert "prediction.nii.gz" in data["predictionUrl"]
+
+    def test_passes_fast_mode_to_pipeline(self, client: TestClient) -> None:
+        """POST /api/segment passes fast_mode parameter to pipeline."""
+        mock_result = MagicMock()
+        mock_result.case_id = "sub-stroke0001"
+        mock_result.dice_score = None
+        mock_result.elapsed_seconds = 45.0
+        mock_result.prediction_mask.name = "pred.nii.gz"
+        mock_result.input_files = {"dwi": MagicMock()}
+        mock_result.input_files["dwi"].name = "dwi.nii.gz"
+
+        with (
+            patch("stroke_deepisles_demo.api.routes.run_pipeline_on_case") as mock_pipeline,
+            patch("stroke_deepisles_demo.api.routes.compute_volume_ml"),
+        ):
+            mock_pipeline.return_value = mock_result
+
+            client.post(
+                "/api/segment",
+                json={"case_id": "sub-stroke0001", "fast_mode": False},
+            )
+
+            mock_pipeline.assert_called_once()
+            call_kwargs = mock_pipeline.call_args[1]
+            assert call_kwargs["fast"] is False
+
+    def test_returns_422_on_missing_case_id(self, client: TestClient) -> None:
+        """POST /api/segment returns 422 when case_id is missing."""
+        response = client.post("/api/segment", json={})
+
+        assert response.status_code == 422
+
+    def test_returns_500_on_pipeline_error(self, client: TestClient) -> None:
+        """POST /api/segment returns 500 when pipeline raises exception."""
+        with patch("stroke_deepisles_demo.api.routes.run_pipeline_on_case") as mock_pipeline:
+            mock_pipeline.side_effect = RuntimeError("GPU out of memory")
+
+            response = client.post(
+                "/api/segment",
+                json={"case_id": "sub-stroke0001"},
+            )
+
+            assert response.status_code == 500
+            assert "GPU out of memory" in response.json()["detail"]

uv.lock

@@ -950,6 +950,42 @@ wheels = [
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 ]
 
+[[package]]
+name = "httptools"
+version = "0.7.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/b5/46/120a669232c7bdedb9d52d4aeae7e6c7dfe151e99dc70802e2fc7a5e1993/httptools-0.7.1.tar.gz", hash = "sha256:abd72556974f8e7c74a259655924a717a2365b236c882c3f6f8a45fe94703ac9", size = 258961 }
+wheels = [
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 version = "0.28.1"
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 source = { editable = "." }
 dependencies = [
     { name = "datasets" },
-    { name = "gradio" },
-    { name = "gradio-niivueviewer" },
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-    { name = "matplotlib" },
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     { name = "numpy" },
     { name = "pydantic" },
@@ -2413,6 +2446,17 @@ dependencies = [
     { name = "requests" },
 ]
 
+[package.optional-dependencies]
+api = [
+    { name = "fastapi" },
+    { name = "uvicorn", extra = ["standard"] },
+]
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+    { name = "gradio-niivueviewer" },
+    { name = "matplotlib" },
+]
+
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