# Core dependencies
numpy>=1.20.0
pandas>=1.3.0
scipy>=1.7.0
matplotlib>=3.4.0
seaborn>=0.11.0

# Single-cell analysis
scanpy>=1.8.0
anndata>=0.8.0

# Network analysis
networkx>=2.6.0

# Phylogenetic analysis
ete3>=3.1.2

# Machine learning
scikit-learn>=1.0.0

# Utilities
tqdm>=4.60.0
icecream>=2.1.0

# Random walk functionality
graph-walker>=1.0.6

# Optional dependencies (install separately if needed)
# cassiopeia-lineage>=2.0.0  # For lineage tracing simulation
# py-pcha>=0.1.0            # For archetype analysis  
# igraph>=0.9.0             # For Leiden clustering in simulations