Installation

Requirements

• Python 3.8 or higher
• PyTorch 1.9+
• AnnData 0.8+

Install from PyPI

pip install gge-eval

This installs GGE with all dependencies including geomloss for optimal transport metrics. GPU acceleration is automatic when available, and falls back to CPU otherwise.

Verify Installation

import gge
print(gge.__version__)

# Test basic import
from gge import evaluate
print("GGE installed successfully!")

Troubleshooting

Common Issues

ImportError: anndata/scanpy not found

pip install anndata scanpy

CUDA/GPU issues with geomloss

If you don't have a GPU, geomloss will automatically fall back to CPU computation. No action needed.

PyKeOps compilation errors

Ensure you have: - CUDA toolkit installed - Compatible C++ compiler - Correct CUDA_HOME environment variable