Add Hugging Face Spaces Zero GPU support

Co-authored-by: raylim <3074310+raylim@users.noreply.github.com>

.gitignore

@@ -15,3 +15,5 @@ data/
 .pytest_cache/
 .coverage
 htmlcov/
+flagged/
+gradio_cached_examples/

README.md

@@ -1,3 +1,15 @@
+---
+title: Mosaic
+emoji: 🧬
+colorFrom: blue
+colorTo: purple
+sdk: gradio
+sdk_version: 5.49.0
+app_file: app.py
+pinned: false
+license: apache-2.0
+---
+
 # Mosaic: H&E Whole Slide Image Cancer Subtype and Biomarker Inference
 
 Mosaic is a deep learning model designed for predicting cancer subtypes and biomarkers from Hematoxylin and Eosin (H&E) stained whole slide images (WSIs). This repository provides the code, pre-trained models, and instructions to use Mosaic for your own datasets.

app.py

@@ -0,0 +1,20 @@
+"""Entry point for Hugging Face Spaces deployment.
+
+This module serves as the main entry point when deploying Mosaic to
+Hugging Face Spaces. It initializes the models and launches the Gradio interface.
+"""
+
+from mosaic.gradio_app import download_and_process_models, main
+from mosaic.ui import launch_gradio
+
+if __name__ == "__main__":
+    # Download models and initialize cancer subtype mappings
+    download_and_process_models()
+    
+    # Launch the Gradio interface
+    # Use default settings suitable for Hugging Face Spaces
+    launch_gradio(
+        server_name="0.0.0.0",
+        server_port=7860,
+        share=False,
+    )

pyproject.toml

@@ -14,6 +14,7 @@ dependencies = [
   "memory-profiler>=0.61.0",
   "mussel[torch-gpu]",
   "paladin",
+  "spaces>=0.30.0",
 ]
 
 [project.scripts]

requirements.txt

@@ -0,0 +1,16 @@
+gradio>=5.49.0
+loguru>=0.7.3
+memory-profiler>=0.61.0
+spaces>=0.30.0
+torch>=2.0.0
+torchvision>=0.15.0
+pandas>=2.0.0
+numpy>=1.24.0
+pillow>=10.0.0
+opencv-python-headless>=4.8.0
+scikit-learn>=1.3.0
+requests>=2.31.0
+huggingface-hub>=0.20.0
+openslide-python>=1.3.0
+git+https://github.com/pathology-data-mining/Mussel.git@ray-dev
+git+https://github.com/pathology-data-mining/paladin.git@dev

src/mosaic/analysis.py

@@ -15,9 +15,21 @@ from mussel.utils.segment import draw_slide_mask
 from mussel.cli.tessellate import BiopsySegConfig, ResectionSegConfig, TcgaSegConfig
 from loguru import logger
 
+try:
+    import spaces
+    HAS_SPACES = True
+except ImportError:
+    HAS_SPACES = False
+    # Create a no-op decorator if spaces is not available
+    class spaces:
+        @staticmethod
+        def GPU(fn):
+            return fn
+
 from mosaic.inference import run_aeon, run_paladin
 
 
+@spaces.GPU
 def analyze_slide(
     slide_path,
     seg_config,