This document provides instructions on setting up scLENS-py.
Project Setup and Usage This document provides instructions on how to set up the environment and get started with the project.
For a straightforward setup, we highly recommend installing the Anaconda Distribution. It includes Python, the conda package manager, and other essential scientific computing libraries.
Download Anaconda here: https://www.anaconda.com/download
Please follow these two steps to set up your environment.
First, create the base conda environment using the provided environment.yml file. This will install all necessary packages except for PyTorch.
Bash
conda env create -f environment.yml
After the environment is created, you must activate it:
Bash
conda activate sclens-py
(Note: You can find the correct environment name inside the environment.yml file, specified under the name: key.)
Next, install PyTorch with CUDA 12.8 support using pip. This step is performed separately to ensure the correct GPU-accelerated version is installed.
Bash
pip3 install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu128
For different system configurations (e.g., CPU-only, different CUDA versions, or macOS), please generate the appropriate installation command on the official PyTorch website: https://pytorch.org/get-started/locally/
For detailed examples and a guide on how to use the code, please see the Tutorial.ipynb notebook.