# Core dependencies
numpy>=2.0.0,<3.0.0
pandas>=2.0.0,<3.0.0
scipy>=1.11.0,<2.0.0
scikit-learn>=1.3.0,<2.0.0
pyyaml>=6.0.0,<7.0.0
tqdm>=4.67.0,<5.0.0

# BioPython and sequence analysis
biopython>=1.85,<2.0.0
pysam>=0.23.0,<1.0.0

# Machine learning and embeddings
torch>=2.0.0,<3.0.0
fair-esm>=2.0.0,<3.0.0

# Visualization
matplotlib>=3.10.0,<4.0.0
seaborn>=0.13.0,<1.0.0
plotly>=6.2.0,<7.0.0

# Web interface
gradio>=5.49.0,<6.0.0
umap-learn>=0.5.9,<1.0.0

# Statistical analysis
statsmodels>=0.14.0,<1.0.0

# Thread pool control
threadpoolctl>=3.6.0,<4.0.0

# Optional dependencies (not required for core functionality)
# bokeh  # Optional visualization
# gunicorn  # Optional for production deployment
# flask  # Optional for custom web interfaces
# docker  # Optional for containerization