# Core dependencies
numpy>=1.21.0
scipy>=1.7.0
pandas>=1.3.0

# Scientific computing
scikit-learn>=1.0.0
matplotlib>=3.5.0
seaborn>=0.11.0

# Molecular modeling and chemistry
rdkit>=2022.03.1
biopython>=1.79
openmm>=7.7.0

# Machine learning (optional but recommended)
torch>=1.9.0
torch-geometric>=2.0.0
transformers>=4.0.0
xgboost>=1.5.0

# Optimization and numerical methods
cvxpy>=1.1.0
pyomo>=6.0.0

# File I/O and data formats
h5py>=3.1.0
netcdf4>=1.5.0
tables>=3.6.0

# Visualization
plotly>=5.0.0
bokeh>=2.4.0
py3dmol>=1.8.0

# Parallel computing
joblib>=1.1.0
dask>=2021.8.0
mpi4py>=3.1.0

# GPU acceleration (optional)
cupy-cuda11x>=9.0.0; platform_system != "Darwin"

# Web and API
flask>=2.0.0
fastapi>=0.70.0
uvicorn>=0.15.0
requests>=2.25.0

# Configuration and utilities
pyyaml>=5.4.0
toml>=0.10.0
click>=8.0.0
tqdm>=4.62.0
psutil>=5.8.0

# Testing and development
pytest>=6.0.0
pytest-cov>=3.0.0
black>=22.0.0
flake8>=4.0.0
mypy>=0.910
sphinx>=4.0.0
sphinx-rtd-theme>=1.0.0

# Optional molecular visualization (install manually if needed)
# pymol-open-source>=2.5.0  # Comment out - causes CI issues, install via conda if needed
nglview>=3.0.0

# Optional enhanced features (install separately if needed)
# openeye-toolkits>=2021.10.0
# schrodinger-suite>=2021.4