Spaces:
Sleeping
Sleeping
Commit Β·
ba67644
1
Parent(s): d2c2086
Add a markdown note for HF deployment
Browse files- docs/HUGGINGFACE_DEPLOYMENT.md +309 -0
docs/HUGGINGFACE_DEPLOYMENT.md
ADDED
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| 1 |
+
# Hosting on Hugging Face Spaces
|
| 2 |
+
|
| 3 |
+
This guide covers deploying the Brain Lesion Segmentation web app (VTK.js frontend + FastAPI backend) to Hugging Face Spaces.
|
| 4 |
+
|
| 5 |
+
---
|
| 6 |
+
|
| 7 |
+
## Recommended: Docker Space (Full-Stack)
|
| 8 |
+
|
| 9 |
+
For your VTK.js frontend + FastAPI backend architecture, the best approach is a **Docker Space**. This bundles both your FastAPI backend and static frontend in one deployment.
|
| 10 |
+
|
| 11 |
+
### Why Docker Space?
|
| 12 |
+
|
| 13 |
+
| Approach | Pros | Cons |
|
| 14 |
+
|----------|------|------|
|
| 15 |
+
| **Docker Space** β
| Full control, GPU support, single deployment | Requires Dockerfile |
|
| 16 |
+
| Gradio Space | Simple setup | Not suitable for custom JS frontend |
|
| 17 |
+
| Static Space | Free, fast CDN | No backend/API support |
|
| 18 |
+
|
| 19 |
+
---
|
| 20 |
+
|
| 21 |
+
## Step-by-Step Deployment
|
| 22 |
+
|
| 23 |
+
### 1. Create a Dockerfile
|
| 24 |
+
|
| 25 |
+
Create `Dockerfile` in your project root:
|
| 26 |
+
|
| 27 |
+
```dockerfile
|
| 28 |
+
# Dockerfile
|
| 29 |
+
FROM python:3.10-slim
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| 30 |
+
|
| 31 |
+
# Install system dependencies
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| 32 |
+
RUN apt-get update && apt-get install -y \
|
| 33 |
+
build-essential \
|
| 34 |
+
curl \
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| 35 |
+
git \
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| 36 |
+
&& rm -rf /var/lib/apt/lists/*
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| 37 |
+
|
| 38 |
+
WORKDIR /app
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| 39 |
+
|
| 40 |
+
# Copy requirements and install Python dependencies
|
| 41 |
+
COPY requirements.txt .
|
| 42 |
+
RUN pip install --no-cache-dir -r requirements.txt
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| 43 |
+
|
| 44 |
+
# Copy application code
|
| 45 |
+
COPY . .
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| 46 |
+
|
| 47 |
+
# Hugging Face Spaces expects port 7860
|
| 48 |
+
EXPOSE 7860
|
| 49 |
+
|
| 50 |
+
# Start FastAPI serving both API and static files
|
| 51 |
+
CMD ["uvicorn", "seg_app.backend.api:app", "--host", "0.0.0.0", "--port", "7860"]
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| 52 |
+
```
|
| 53 |
+
|
| 54 |
+
### 2. Update FastAPI to Serve Static Frontend
|
| 55 |
+
|
| 56 |
+
Add the following to `seg_app/backend/api.py` (at the END of the file, after all API routes):
|
| 57 |
+
|
| 58 |
+
```python
|
| 59 |
+
from fastapi.staticfiles import StaticFiles
|
| 60 |
+
from fastapi.responses import FileResponse
|
| 61 |
+
import os
|
| 62 |
+
|
| 63 |
+
# Serve static files for VTK.js slicer UI
|
| 64 |
+
static_dir = os.path.join(os.path.dirname(__file__), "..", "ui_slicer")
|
| 65 |
+
app.mount("/slicer", StaticFiles(directory=static_dir, html=True), name="slicer")
|
| 66 |
+
|
| 67 |
+
# Root redirect to slicer UI
|
| 68 |
+
@app.get("/")
|
| 69 |
+
async def root():
|
| 70 |
+
return FileResponse(os.path.join(static_dir, "index.html"))
|
| 71 |
+
```
|
| 72 |
+
|
| 73 |
+
### 3. Update Frontend API URL
|
| 74 |
+
|
| 75 |
+
In `seg_app/ui_slicer/api-client.js`, update the base URL to work in both local and production:
|
| 76 |
+
|
| 77 |
+
```javascript
|
| 78 |
+
class ApiClient {
|
| 79 |
+
constructor() {
|
| 80 |
+
// Use same origin in production, localhost for development
|
| 81 |
+
this.baseUrl = window.location.hostname === 'localhost'
|
| 82 |
+
? 'http://localhost:8000'
|
| 83 |
+
: window.location.origin;
|
| 84 |
+
}
|
| 85 |
+
// ... rest of the class
|
| 86 |
+
}
|
| 87 |
+
```
|
| 88 |
+
|
| 89 |
+
### 4. Update README.md with HF Spaces Metadata
|
| 90 |
+
|
| 91 |
+
Add YAML frontmatter to the top of your `README.md`:
|
| 92 |
+
|
| 93 |
+
```yaml
|
| 94 |
+
---
|
| 95 |
+
title: Brain Lesion Segmentation
|
| 96 |
+
emoji: π§
|
| 97 |
+
colorFrom: blue
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| 98 |
+
colorTo: purple
|
| 99 |
+
sdk: docker
|
| 100 |
+
app_port: 7860
|
| 101 |
+
pinned: false
|
| 102 |
+
license: mit
|
| 103 |
+
---
|
| 104 |
+
|
| 105 |
+
# Brain Lesion Segmentation Tool
|
| 106 |
+
... (rest of your README)
|
| 107 |
+
```
|
| 108 |
+
|
| 109 |
+
### 5. Create .dockerignore
|
| 110 |
+
|
| 111 |
+
Create `.dockerignore` to exclude unnecessary files:
|
| 112 |
+
|
| 113 |
+
```
|
| 114 |
+
__pycache__/
|
| 115 |
+
*.pyc
|
| 116 |
+
*.pyo
|
| 117 |
+
.git/
|
| 118 |
+
.gitignore
|
| 119 |
+
*.md
|
| 120 |
+
!README.md
|
| 121 |
+
.env
|
| 122 |
+
.vscode/
|
| 123 |
+
*.ipynb
|
| 124 |
+
test_*.py
|
| 125 |
+
```
|
| 126 |
+
|
| 127 |
+
### 6. Deploy to Hugging Face
|
| 128 |
+
|
| 129 |
+
#### Option A: Using HF CLI
|
| 130 |
+
|
| 131 |
+
```bash
|
| 132 |
+
# Install Hugging Face CLI
|
| 133 |
+
pip install huggingface_hub
|
| 134 |
+
|
| 135 |
+
# Login to Hugging Face
|
| 136 |
+
huggingface-cli login
|
| 137 |
+
|
| 138 |
+
# Create a new Space
|
| 139 |
+
huggingface-cli repo create YOUR_USERNAME/brain-lesion-seg --type space --space_sdk docker
|
| 140 |
+
|
| 141 |
+
# Add HF as remote and push
|
| 142 |
+
git remote add hf https://huggingface.co/spaces/YOUR_USERNAME/brain-lesion-seg
|
| 143 |
+
git push hf main
|
| 144 |
+
```
|
| 145 |
+
|
| 146 |
+
#### Option B: Using Web Interface
|
| 147 |
+
|
| 148 |
+
1. Go to [huggingface.co/new-space](https://huggingface.co/new-space)
|
| 149 |
+
2. Select **Docker** as the SDK
|
| 150 |
+
3. Choose a hardware tier (see recommendations below)
|
| 151 |
+
4. Upload files or connect your GitHub repo
|
| 152 |
+
|
| 153 |
+
---
|
| 154 |
+
|
| 155 |
+
## Hardware Recommendations
|
| 156 |
+
|
| 157 |
+
| Tier | Cost | RAM | Best For |
|
| 158 |
+
|------|------|-----|----------|
|
| 159 |
+
| **CPU Basic** (free) | $0 | 16GB | Testing, demos |
|
| 160 |
+
| **CPU Upgrade** | ~$0.03/hr | 32GB | Small volumes |
|
| 161 |
+
| **T4 Small** β
| ~$0.60/hr | 16GB + GPU | SAM-Med3D, nnUNet |
|
| 162 |
+
| **T4 Medium** | ~$0.90/hr | 32GB + GPU | Large volumes |
|
| 163 |
+
| **A10G Small** | ~$1.50/hr | 24GB VRAM | Fast inference |
|
| 164 |
+
|
| 165 |
+
**Recommendation**: Start with **CPU Basic** for testing, upgrade to **T4 Small** for GPU inference with deep learning models.
|
| 166 |
+
|
| 167 |
+
---
|
| 168 |
+
|
| 169 |
+
## Environment Variables & Secrets
|
| 170 |
+
|
| 171 |
+
For sensitive configuration (model paths, API keys), use HF Spaces Secrets:
|
| 172 |
+
|
| 173 |
+
1. Go to Space Settings β Repository secrets
|
| 174 |
+
2. Add secrets like:
|
| 175 |
+
- `HF_TOKEN` (if loading private models)
|
| 176 |
+
- `MODEL_PATH` (custom model locations)
|
| 177 |
+
|
| 178 |
+
Access in Python:
|
| 179 |
+
```python
|
| 180 |
+
import os
|
| 181 |
+
hf_token = os.environ.get("HF_TOKEN")
|
| 182 |
+
```
|
| 183 |
+
|
| 184 |
+
---
|
| 185 |
+
|
| 186 |
+
## GPU Support for Deep Learning Models
|
| 187 |
+
|
| 188 |
+
If using SAM-Med3D or nnUNet, ensure GPU support:
|
| 189 |
+
|
| 190 |
+
### Update Dockerfile for GPU:
|
| 191 |
+
|
| 192 |
+
```dockerfile
|
| 193 |
+
FROM pytorch/pytorch:2.0.1-cuda11.7-cudnn8-runtime
|
| 194 |
+
|
| 195 |
+
# ... rest of Dockerfile
|
| 196 |
+
```
|
| 197 |
+
|
| 198 |
+
### Update requirements.txt:
|
| 199 |
+
|
| 200 |
+
```
|
| 201 |
+
torch>=2.0.0
|
| 202 |
+
monai>=1.3.0
|
| 203 |
+
nnunetv2>=2.2
|
| 204 |
+
# ... other dependencies
|
| 205 |
+
```
|
| 206 |
+
|
| 207 |
+
---
|
| 208 |
+
|
| 209 |
+
## Troubleshooting
|
| 210 |
+
|
| 211 |
+
### Build Fails
|
| 212 |
+
|
| 213 |
+
Check the build logs in your Space's "Logs" tab. Common issues:
|
| 214 |
+
- Missing system dependencies β Add to `apt-get install`
|
| 215 |
+
- Python package conflicts β Pin versions in requirements.txt
|
| 216 |
+
|
| 217 |
+
### App Not Loading
|
| 218 |
+
|
| 219 |
+
- Ensure port 7860 is exposed and used
|
| 220 |
+
- Check that static files are correctly mounted
|
| 221 |
+
- Verify API routes don't conflict with static file routes
|
| 222 |
+
|
| 223 |
+
### Slow Inference
|
| 224 |
+
|
| 225 |
+
- Upgrade to GPU hardware tier
|
| 226 |
+
- Enable model caching (load once, reuse)
|
| 227 |
+
- Consider model quantization for faster inference
|
| 228 |
+
|
| 229 |
+
### CORS Issues
|
| 230 |
+
|
| 231 |
+
If frontend/backend are on different origins, add CORS middleware:
|
| 232 |
+
|
| 233 |
+
```python
|
| 234 |
+
from fastapi.middleware.cors import CORSMiddleware
|
| 235 |
+
|
| 236 |
+
app.add_middleware(
|
| 237 |
+
CORSMiddleware,
|
| 238 |
+
allow_origins=["*"], # Or specify your frontend URL
|
| 239 |
+
allow_credentials=True,
|
| 240 |
+
allow_methods=["*"],
|
| 241 |
+
allow_headers=["*"],
|
| 242 |
+
)
|
| 243 |
+
```
|
| 244 |
+
|
| 245 |
+
---
|
| 246 |
+
|
| 247 |
+
## Local Testing with Docker
|
| 248 |
+
|
| 249 |
+
Before deploying, test locally:
|
| 250 |
+
|
| 251 |
+
```bash
|
| 252 |
+
# Build the image
|
| 253 |
+
docker build -t brain-seg-app .
|
| 254 |
+
|
| 255 |
+
# Run the container
|
| 256 |
+
docker run -p 7860:7860 brain-seg-app
|
| 257 |
+
|
| 258 |
+
# Open in browser
|
| 259 |
+
# http://localhost:7860
|
| 260 |
+
```
|
| 261 |
+
|
| 262 |
+
---
|
| 263 |
+
|
| 264 |
+
## File Structure for Deployment
|
| 265 |
+
|
| 266 |
+
```
|
| 267 |
+
web_app/
|
| 268 |
+
βββ Dockerfile # Container definition
|
| 269 |
+
βββ .dockerignore # Exclude unnecessary files
|
| 270 |
+
βββ README.md # With HF YAML frontmatter
|
| 271 |
+
βββ requirements.txt # Python dependencies
|
| 272 |
+
βββ seg_app/
|
| 273 |
+
β βββ backend/
|
| 274 |
+
β β βββ api.py # FastAPI + static file serving
|
| 275 |
+
β βββ ui_slicer/
|
| 276 |
+
β β βββ index.html # VTK.js frontend
|
| 277 |
+
β β βββ app.js
|
| 278 |
+
β β βββ api-client.js # Updated for production URLs
|
| 279 |
+
β β βββ ...
|
| 280 |
+
β βββ models/
|
| 281 |
+
β βββ ...
|
| 282 |
+
```
|
| 283 |
+
|
| 284 |
+
---
|
| 285 |
+
|
| 286 |
+
## Alternative: Split Deployment
|
| 287 |
+
|
| 288 |
+
For more flexibility, deploy frontend and backend separately:
|
| 289 |
+
|
| 290 |
+
| Component | Space Type | URL |
|
| 291 |
+
|-----------|------------|-----|
|
| 292 |
+
| Frontend | Static Space (free) | `your-user/brain-seg-frontend` |
|
| 293 |
+
| Backend | Docker Space (GPU) | `your-user/brain-seg-api` |
|
| 294 |
+
|
| 295 |
+
This allows:
|
| 296 |
+
- Free hosting for static files
|
| 297 |
+
- GPU only when needed for inference
|
| 298 |
+
- Independent scaling
|
| 299 |
+
|
| 300 |
+
Configure the frontend to point to the backend API URL.
|
| 301 |
+
|
| 302 |
+
---
|
| 303 |
+
|
| 304 |
+
## Useful Links
|
| 305 |
+
|
| 306 |
+
- [HF Spaces Documentation](https://huggingface.co/docs/hub/spaces)
|
| 307 |
+
- [Docker Spaces Guide](https://huggingface.co/docs/hub/spaces-sdks-docker)
|
| 308 |
+
- [Spaces GPU Guide](https://huggingface.co/docs/hub/spaces-gpus)
|
| 309 |
+
- [Secrets & Environment Variables](https://huggingface.co/docs/hub/spaces-overview#managing-secrets)
|