Installation

OnionNet requires graph-tool to be installed. Because graph-tool is built around C++ for efficiency, unfortunately there is no straightforward pip installation. Nonetheless, there are a number of ways to install graph-tool besides pip, see here for more details. The easiest way for most users is probably to create a new env via conda:

conda create --name gt -c conda-forge graph-tool ipython jupyter
conda activate gt

Then you can install OnionNet within the conda env with:

pip install git+https://github.com/saezlab/onionnet.git