numpy<3,>=1.24
pandas<3,>=2.0
matplotlib<4,>=3.7
seaborn<1,>=0.12
scipy<2,>=1.10
scikit-learn<2,>=1.3
tqdm<5,>=4.65
biopython<2,>=1.81
networkx<4,>=3.0
plotly<7,>=5.0

[api]
fastapi>=0.100
uvicorn>=0.23
python-jose[cryptography]>=3.3
slowapi>=0.1.9

[bio]
goatools>=1.3
gseapy>=1.0
cutadapt>=4.0
scanpy>=1.9
anndata>=0.9
scikit-bio>=0.5
biotite>=0.37
ete3>=3.1
cobra>=0.26
shap>=0.42
umap-learn>=0.5
statsmodels>=0.14

[cloning]

[dev]
pytest>=7.0
pytest-asyncio>=0.23
pytest-cov>=4.0
pytest-xdist>=3.0
httpx>=0.24
ruff>=0.4

[full]
biosuite-ultra[bio]
biosuite-ultra[gui]
biosuite-ultra[api]
biosuite-ultra[notebook]
biosuite-ultra[parallel]
pysam>=0.21

[gui]
customtkinter<6,>=5.2

[notebook]
ipython>=8.0
ipywidgets>=8.0

[parallel]
