Installation

Conda installation

One can install the packages necessary through conda (mamba) using the following commands:

conda install -c conda-forge mamba # mamba is much faster than conda
mamba env create --quiet --name rindti --file workflow/envs/main.yaml

Then one can run optionally run pip install . in the root directory of the repository to install rindti as a package.

Manual installation

In order to use this module, you must first install the following packages (preferably in the order listed here):

• pytorch

• torch_geometric

• pytorch_lightning

• snakemake

• rdkit

• seaborn

• plotly

Then one can run optionally pip install . in the root directory of the repository to install rindti as a package.

Testing

In order to asses whether the installation of the packages was succesfull, please run pytest in the root directory. If the packages were not installed into path using pip, please use python -m pytest instead. Furthermore, if your device has no GPU support, please use pytest -m "not gpu"