Installation

PyPI (recommended)

Install the core package from PyPI:

pip install isograph

Supports Python 3.11 through 3.14.

Optional Backends

VAE

IsoGraph installs mpmath, which is required by modern SymPy releases. The vae backend also requires PyTorch, but PyTorch is intentionally not installed by IsoGraph because CPU/GPU/CUDA builds are platform-specific. Install the build that matches your environment before using backend=vae or importing isograph.models.vae:

pip install torch

See the PyTorch installation guide for GPU/CUDA builds.

WGCNA

The wgcna backend requires R with the WGCNA package and Rscript on PATH:

install.packages("WGCNA")

Documentation

To build the Sphinx documentation locally:

pip install isograph[docs]
python -m sphinx -W -b html docs docs/_build/html

Development

To install in editable mode with development dependencies:

git clone https://github.com/heart-gen/IsoGraph
cd IsoGraph
pip install -e .[dev]

Install PyTorch separately when developing or testing the VAE backend.