Installation

Installation using Conda

git clone https://github.com/StatBiomed/FineST.git
conda create --name FineST python=3.8
conda activate FineST
cd FineST
pip install -r requirements.txt

Verify the installation using the following command:

python
>>> import torch
>>> print(torch.__version__)
2.1.2+cu121 (or your installed version)
>>> print(torch.cuda.is_available())
True

Installation using PyPI

FineST package is available through PyPI.

pip install -U FineST

Alternatively, install from GitHub for latest version:

pip install -U git+https://github.com/StatBiomed/FineST

Setup Jupyter Notebook Kernel

The FineST conda environment can be used for Jupyter notebooks:

python -m pip install ipykernel
python -m ipykernel install --user --name=FineST

Tutorial notebooks:

NPC_Train_Impute_demo.ipynb (using Virchow2; requires Hugging Face token, approval may take days)
NPC_Train_Impute_demo_HIPT.ipynb (using HIPT; recommended for quick start)