removed flat layout for hf

Dockerfile

@@ -2,14 +2,11 @@ FROM python:3.12-slim
 
 WORKDIR /code
 
-# Copy only the necessary files
-COPY ./app.py /code/
-COPY ./extractor.py /code/
 COPY ./pyproject.toml /code/
+COPY ./README.md /code/
+COPY ./src /code/src
 COPY ./openapi.yaml /code/
 
-# Install dependencies
 RUN pip install --no-cache-dir .[all]
 
-# Run the application
-CMD ["uvicorn", "app:app", "--host", "0.0.0.0", "--port", "7860"]
+CMD ["python", "-m", "everycure.app"]

README.md

@@ -20,47 +20,3 @@ curl -v -X POST -F "file=@pdfs/MECFS systematic review.pdf" http://localhost:800
 ```
 
 Or use the automatic Swagger documentation at `http://localhost:8000/docs`
-
-## Deploying to HuggingFace Spaces
-
-```dockerfile
-FROM python:3.9-slim
-
-WORKDIR /code
-
-# Copy only the necessary files
-COPY ./app.py /code/
-COPY ./extractor.py /code/
-COPY ./pyproject.toml /code/
-COPY ./openapi.yaml /code/
-
-# Install dependencies
-RUN pip install --no-cache-dir "fastapi[all]" python-multipart pydantic
-
-# Run the application
-CMD ["uvicorn", "app:app", "--host", "0.0.0.0", "--port", "7860"]
-```
-
-3. Push to HuggingFace:
-
-```bash
-# Initialize git repository if not already done
-git init
-git add .
-git commit -m "Initial commit"
-
-# Add HuggingFace remote
-git remote add hf https://huggingface.co/spaces/YOUR_USERNAME/YOUR_SPACE_NAME
-
-# Push to HuggingFace
-git push hf main
-```
-
-Note: Replace `YOUR_USERNAME` and `YOUR_SPACE_NAME` with your HuggingFace username and the name you chose for your Space.
-
-### Important Notes
-
-- HuggingFace Spaces uses port 7860 by default
-- The API will be available at `https://huggingface.co/spaces/YOUR_USERNAME/YOUR_SPACE_NAME`
-- Make sure your model files are included in the repository if needed
-- The free tier of HuggingFace Spaces has limitations on CPU/RAM usage

pyproject.toml

@@ -13,3 +13,11 @@ dependencies = [
     "python-multipart>=0.0.6",  # Required for handling file uploads
     "pydantic>=2.5.3"   
 ]
+
+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+packages = ["everycure"]

src/everycure/__init__.py

@@ -0,0 +1,3 @@
+"""Everycure package for medical entity extraction."""
+
+__version__ = "0.1.0"