Installation#
Requirements#
Peach requires Python 3.10 or later and is compatible with the scverse ecosystem.
Core Dependencies#
anndata >=0.8.0 - Single-cell data structures
scanpy >=1.9.0 - Single-cell analysis toolkit
torch >=2.0.0 - Deep learning framework
scikit-learn >=1.0.0 - Machine learning utilities
pandas >=2.0.0 - Data manipulation
numpy >=1.24.0 - Numerical computing
plotly >=5.0.0 - Interactive visualization
scipy >=1.10.0 - Scientific computing
statsmodels >=0.14.0 - Statistical analysis
Installation Options#
Option 1: PyPI (Recommended)#
pip install peach
See included environment.yaml file to create a working conda env for this package
Option 2: Development Installation#
For the latest features and development:
git clone https://github.com/xhonkala/PEACH.git
cd peach
pip install -e ".[dev]"
Option 3: Conda Environment (Recommended)#
Use the provided environment file:
git clone https://github.com/xhonkala/PEACH.git
cd PEACH
conda env create -f environment.yaml
conda activate peach
pip install -e .
Verify Installation#
Test your installation:
import peach as pc
print(pc.__version__)
# Quick test with synthetic data
adata = pc.pp.generate_synthetic(n_points=100, n_dimensions=50, n_archetypes=3)
results = pc.tl.train_archetypal(adata, n_archetypes=3, n_epochs=5)
print(f"Test R²: {results['history']['archetype_r2'][-1]:.3f}")
GPU Support (Optional)#
For GPU acceleration with large datasets:
NB: this is not yet fully supported but will be included in the next release.
# Install PyTorch with CUDA support
pip install torch torchvision torchaudio --index-url https://download.pytorch.org/whl/cu121
# Verify GPU availability
python -c "import torch; print(f'CUDA available: {torch.cuda.is_available()}')"
Troubleshooting#
Common Issues#
Import errors: Ensure all dependencies are installed with correct versions
CUDA errors: Make sure PyTorch CUDA version matches your system
Memory errors: Consider using CPU for large datasets or reducing batch size
Getting Help#
GitHub Issues: Report bugs
Discussions: Ask questions
scverse Discord: Join the broader community
System Requirements#
Memory: Minimum 4GB RAM, 16GB+ recommended for large datasets
Storage: ~1GB for installation plus data storage
CPU: Multi-core recommended for optimal performance
GPU: Optional but recommended for datasets >10k cells