adding README and updating Makefile

Makefile

@@ -9,4 +9,7 @@ test:
 	PYTHONPATH=. pytest -vv 
 
 format:
-	black app.py chatlib
+	black app.py chatlib
+
+run:
+	python app.py

README.md

@@ -1,6 +1,110 @@
-# clinician-assistant-lg
+# Clinician Assistant LG
 
-curl -fsSL https://ollama.com/install.sh | sh
-ollama pull llama3.1:8b
-ollama serve
-ollama run llama3
+A conversational assistant designed to help clinicians in Kenya access patient data and clinical guidelines efficiently. This project uses LangChain, LangGraph, and OpenAI models to provide context-aware, tool-augmented chat for clinical decision support.
+
+---
+
+## Features
+
+- **RAG (Retrieval-Augmented Generation):** Retrieve relevant HIV clinical guidelines using natural language queries.
+- **SQL Chain:** Query and summarize patient data from a structured database.
+- **IDSR Check:** Analyze clinical cases for possible notifiable diseases and suggest clarifying questions.
+- **PHI Filtering:** Detect and filter personally identifiable information from free text.
+- **Session Management:** Supports persistent chat sessions with unique thread IDs.
+- **Gradio UI:** Simple web interface for clinicians to interact with the assistant.
+
+---
+
+## Project Structure
+
+```
+.
+├── app.py                # Gradio web app entry point
+├── chatlib/              # Core logic, tools, and utilities
+│   ├── assistant_node.py
+│   ├── guidlines_rag_agent_li.py
+│   ├── idsr_check.py
+│   ├── patient_all_data.py
+│   ├── patient_sql_agent.py
+│   ├── phi_filter.py
+│   └── state_types.py
+├── requirements.txt      # Python dependencies
+├── Makefile              # Common dev commands (lint, test, format)
+└── README.md             # Project documentation
+```
+
+---
+
+## Setup
+
+1. **Clone the repository:**
+   ```sh
+   git clone <repo-url>
+   cd clinician-assistant-lg
+   ```
+
+2. **Install dependencies:**
+   ```sh
+   make install
+   ```
+
+3. **Set up environment variables:**
+   - Copy `config.env.example` to `config.env` and fill in your OpenAI and LangSmith API keys.
+
+4. **Run the app:**
+   ```sh
+   python app.py
+   ```
+   Or use the Makefile:
+   ```sh
+   make run
+   ```
+
+---
+
+## Usage
+
+- Open the Gradio web interface (URL will be shown in the terminal).
+- Enter a clinical question and (optionally) a patient identifier.
+- The assistant will use the appropriate tools to answer, referencing guidelines and patient data as needed.
+
+---
+
+## Development
+
+- **Lint code:** `make lint`
+- **Format code:** `make format`
+- **Run tests:** `make test`
+
+---
+
+## Requirements
+
+See `requirements.txt` for the full list. Key dependencies:
+- Python 3.10+
+- gradio
+- langchain_core, langchain_community, langchain_openai
+- langgraph
+- pandas
+- pydantic
+
+---
+
+## Notes
+
+- Patient data and guideline retrieval are tailored for Kenyan clinical workflows.
+- The assistant is not a substitute for clinical judgment.
+- All PHI is filtered to protect patient privacy.
+
+---
+
+## License
+
+MIT License
+
+---
+
+## Acknowledgements
+
+- [LangChain](https://github.com/langchain-ai/langchain)
+- [Gradio](https://github.com/gradio-app/gradio)

config.env.example

@@ -0,0 +1,3 @@
+OPENAI_API_KEY = ""
+LANGCHAIN_API_KEY = ""
+PK_HASH = ""