requirements.txt

# Core dependencies
biopython>=1.85
biotite>=1.4.0
chembl-webresource-client>=0.10.9
numpy>=2.3.3
pandas>=2.3.2
pyyaml>=6.0
rdkit>=2025.3.6
scikit-learn>=1.7.2
tqdm>=4.67.1

# Visualization
matplotlib>=3.10.2
seaborn>=0.13.2
plotly>=6.3.1

# ML models
xgboost>=2.0.0
lightgbm>=4.0.0
shap>=0.44.0
pydantic>=2.0.0

# Utilities
rich>=14.1.0
openpyxl>=3.1.0
umap-learn>=0.5.0
xmltodict>=1.0.0

# Jupyter/Notebooks
jupyter>=1.1.1
ipywidgets>=8.1.7
nglview>=3.1.4
py3dmol>=2.5.2

# Development tools
black>=25.1.0
ruff>=0.13.2

# Optional ML packages (install with: pip install -e .[ml])
# catboost>=1.2.0
# boruta>=0.3.0
# optuna>=3.5.0

# Optional dev tools (install with: pip install -e .[dev])
# pytest>=7.4.0
# pytest-cov>=4.1.0
# pytest-mock>=3.12.0
# pylint>=3.0.0
# mypy>=1.8.0
# bandit>=1.7.0
# radon>=6.0.0
# safety>=3.0.0