Aurelian: Agentic Universal Research Engine for Literature, Integration, Annotation, and Navigation

Getting Started

Prerequisites

Ensure you have the following installed:

Poetry (for managing dependencies)
Python 3.11 or later

Installation

Clone the repository:

git clone https://github.com/monarch-initiative/aurelian.git
cd aurelian

Install dependencies:
```
poetry install --extras=gradio
```
Verify installation:
```
poetry run aurelian --help
```

Setting up up Logfire

Aurelian uses Logfire for logging (an observability platform that provides logging, tracing, and metrics), which requires authentication. If you encounter the following error:

No Logfire project credentials found.
You are not authenticated. Please run `logfire auth` to authenticate.

Follow these steps:

Authenticate with Logfire:
```
poetry run logfire auth
```
(Optional) Set a production token: If running in a production environment, set the LOGFIRE_TOKEN environment variable:
```
export LOGFIRE_TOKEN=your_token_here
```

Getting an OpenAI key

In order to use OpenAI models, you'll need an API key. Follow the instructions here. After you have an OpenAI key, set the environment variable OPENAI_API_KEY to this key, for example like this:

export OPENAI_API_KEY="your_api_key_here"

Running Aurelian

Once authenticated, you can use Aurelian's CLI:

Run the mapper tool:

poetry run aurelian mapper

For more details, refer to the project documentation.