# Repo Guidelines

This repository contains the LLM-based Cancer Risk Assessment Assistant.

## Core Technologies
- **FastAPI** for the web framework
- **LangChain** for LLM orchestration
- **uv** for environment and dependency management
- **hydra:** for configuration management

## Coding Philosophy
- Prioritize clarity and reusability.
- Favor simple replication over heavy abstraction.
- Keep comments short and only where the code isn't self-explanatory.
- Avoid verbose docstrings for simple functions.

## Testing
- Write meaningful tests that verify core functionality and prevent regressions.
- Run tests with `uv run pytest`.

## Development Setup
- Create the virtual environment (at '.venv') with `uv sync`.

## Running commands
- As the repository uses uv, the uv should be used to run all commands, e.g., "uv run python ..." NOT "python ...".

These guidelines apply to the entire repository. A multi-page Streamlit
interface for expert feedback can be launched with `uv run streamlit run
apps/streamlit_ui/main.py`.
The first page, **User Profile**, allows experts to load or create a profile
stored in `st.session_state.user_profile`.
The second page, **Configuration**, lets experts choose the model and knowledge base modules while previewing the generated prompt.
The third page, **Assessment**, runs the AI analysis, displays a results dashboard, and provides export and chat options.

## Important Note for Developers

When making changes to the project, ensure that the following files are updated to reflect the changes:

- `README.md`
- `AGENTS.md`
- `GEMINI.md`

## Risk Model Availability

Risk calculators exposed to Gemini-based agents include:
- **Gail** - Breast cancer risk
- **Claus** - Breast cancer risk based on family history
- **Tyrer-Cuzick** - Breast cancer risk (IBIS model)
- **BOADICEA** - Breast and ovarian cancer risk (via CanRisk API)
- **PLCOm2012** - Lung cancer risk
- **LLPi** - Liverpool Lung Project improved model for lung cancer risk (8.7-year prediction)
- **CRC-PRO** - Colorectal cancer risk
- **PCPT** - Prostate cancer risk
- **Extended PBCG** - Prostate cancer risk (extended model)
- **Prostate Mortality** - Prostate cancer-specific mortality prediction
- **MRAT** - Melanoma risk (5-year prediction)
- **aMAP** - Hepatocellular carcinoma (liver cancer) risk
- **QCancer** - Multi-site cancer differential

Register additional models in `src/sentinel/risk_models/__init__.py` so they are available system-wide.