# Core dependencies - required for basic functionality
numpy>=1.19.0
pandas>=1.3.0
scipy>=1.7.0
scikit-learn>=1.0.0
scikit-bio>=0.5.6
python-igraph
loguru
fastcluster>=1.2.0
kneed>=0.8.0

# Optional dependencies
# =====================
# For dynamic tree cutting algorithms
# dynamicTreeCut>=0.1.0

# For KNN
# faiss-cpu

# For Leiden clustering
# leidenalg
