numpy>=1.26
pandas>=2.2
pyarrow>=16
scipy>=1.13
scikit-learn>=1.5
lightgbm>=4.5
pydantic>=2.8
pyyaml>=6.0
click>=8.1
requests>=2.32
tqdm>=4.66

[bio]
biopython>=1.84
pysam>=0.22
pyBigWig>=0.3
pybedtools>=0.10
ViennaRNA>=2.6

[bridge]
bridgernadesigner>=0.1.1
ViennaRNA>=2.6
pysam>=0.22

[dev]
pytest>=8
ruff>=0.5
pytest-cov>=5

[docs]
mkdocs>=1.6
mkdocs-material>=9.5

[models]
xgboost>=2.1
torch>=2.3
statsmodels>=0.14

[orchestrate]
paramiko>=3.4
scp>=0.15
rich>=13.7
python-dotenv>=1.0

[server]
fastapi>=0.111
uvicorn>=0.30

[services]
litellm>=1.44
paper-qa>=5.10
streamlit>=1.37
fastmcp>=2.3
beautifulsoup4>=4.12
