genome-atlas<0.8.0,>=0.7.2
mech-class<0.6.0,>=0.5.4
pen-score<0.2.0,>=0.1.3
pen-assemble<0.6.0,>=0.5.2
numpy>=1.24
pandas>=2.0
scipy>=1.10
scikit-learn>=1.3
pyyaml>=6.0
pyarrow>=14.0
click>=8.0
tqdm>=4.66
joblib>=1.3
pydantic>=2.5

[all-papers]
pen-compare[literature,rag,webserver]

[dev]
pytest>=7.4
pytest-cov>=4.1
pytest-asyncio>=0.23
ruff>=0.4
mypy>=1.8
pre-commit>=3.5

[docs]
sphinx>=7.2
sphinx-rtd-theme>=2.0
myst-parser>=2.0
sphinx-copybutton>=0.5

[everything]
pen-compare[dev,docs,literature,rag,webserver]

[literature]
biopython>=1.83

[rag]
ollama>=0.1.7
sentence-transformers>=2.5
chromadb>=0.4.20
requests>=2.31

[webserver]
streamlit>=1.32
plotly>=5.18
matplotlib>=3.8
