Installation

UniVI supports Python 3.10 and newer on Linux, macOS, and Windows.

With pip

python -m pip install univi

To run the tutorial notebooks locally, include the tutorials extra (Jupyter and scikit-misc, which Scanpy’s Seurat-v3 highly-variable-gene selection needs):

python -m pip install "univi[tutorials]"

PyTorch and GPUs

UniVI depends on PyTorch. pip install univi pulls the default PyTorch wheel for your platform, which on Linux includes CUDA support. For a specific CUDA version, or a CPU-only build, install PyTorch first with the selector at pytorch.org, then install UniVI.

Pass device="cuda", "mps" (Apple silicon), or "cpu" to TrainingConfig and the encoding functions. The tutorials pick automatically:

import torch
device = "cuda" if torch.cuda.is_available() else ("mps" if torch.backends.mps.is_available() else "cpu")

Training runs on a CPU, just more slowly. If an operation is not supported on MPS, fall back to CPU.

With conda

conda install -c conda-forge univi

conda-forge releases follow PyPI releases, usually within a few days.

Google Colab

Every tutorial has an Open in Colab badge and a first cell that installs UniVI when it detects Colab. Choose Runtime → Change runtime type → GPU for faster training.

From source

git clone https://github.com/Ashford-A/UniVI.git
cd UniVI
python -m pip install -e ".[tutorials,test]"
python -m pytest -q

Check the installation

import univi
print(univi.__version__)

import univi.datasets as uds
print(uds.list_datasets())

Datasets are cached in ~/.cache/univi by default; set the UNIVI_DATA_DIR environment variable to use another location (for example a scratch disk on a cluster).

Which version to use

Goal	Install
New analyses, tutorials	latest release: pip install univi
Rerun the archived Genome Research notebooks exactly	pip install univi==0.4.7 (the release the article was prepared against)

The tutorials on this site use APIs added after 0.4.7 (fitted preprocessors, reference bundles, refinement, dataset downloads). The reproduction section explains how the archived notebooks relate to them.