numpy>=1.26
pandas>=2.0
matplotlib>=3.7
seaborn>=0.13
scipy>=1.11
scikit-learn>=1.3
tqdm>=4.66
biopython>=1.83
networkx>=3.0
plotly>=5.18

[api]
fastapi>=0.100
uvicorn[standard]>=0.23
python-jose[cryptography]>=3.3
passlib[bcrypt]>=1.7
slowapi>=0.1.9
python-multipart>=0.0.6

[bio]
goatools>=1.3
gseapy>=1.0
scanpy>=1.9
anndata>=0.9
scikit-bio>=0.5
biotite>=0.37
ete3>=3.1
cobra>=3.0
shap>=0.42
umap-learn>=0.5
statsmodels>=0.14
pysam>=0.21

[dev]
pytest>=7.4
pytest-cov>=4.1
pytest-xdist>=3.0
pytest-benchmark>=4.0
ruff>=0.1
mypy>=1.5
bandit>=1.7
types-requests

[full]
biosuite-ultra[api,bio,gui,notebook]

[gui]
PyQt6>=6.5
qasync>=0.23

[notebook]
ipython>=8.0
ipywidgets>=8.0
