Getting started

Installation

Novae can be installed on every OS and for any Python version >=3.11.

Advice (optional)

We advise creating a new environment via a package manager.

For instance, you can create a new conda environment:

conda create --name novae python=3.12
conda activate novae

Choose one of the following installation mode, depending on your needs.

From PyPIuv (editable mode)Using condapip (editable mode)

pip install novae

If you want to use Novae in multimodal mode, you can also install the following extras: multimodal, conch, and llm. You can install them as follows:

pip install 'novae[multimodal,conch,llm]'

Contributing

If you want to contribute to Novae, using uv is recommended. You'll also need create a fork, see the CONTRIBUTING guidelines.

git clone https://github.com/prism-oncology/novae.git # or your own fork of Novae
cd novae

uv sync --all-extras --dev # all extras and the dev dependencies

conda install bioconda::novae

Warning

You won't be able to install the extra dependencies of Novae with conda.

git clone https://github.com/prism-oncology/novae.git
cd novae

pip install -e . # no extra
pip install -e '.[multimodal,conch,llm]' # all extras

Next steps

• We recommend to start with our first tutorial.
• You can also read the API.
• If you have questions, please check our FAQ or open an issue on the GitHub repository.
• If you want to contribute, check our contributing guide.