cycler>=0.12.1
et-xmlfile>=2.0.0
fonttools>=4.56.0
Jinja2>=3.1.6
joblib>=1.4.2
kiwisolver>=1.4.7
logomaker>=0.8.6
matplotlib>=3.5.3
numpy>=1.24.4
openpyxl>=3.1.5
packaging>=26.1
pandas>=2.2.3
patsy>=1.0.1
Pillow>=12.3.0
pyparsing>=3.2.1
python-dateutil>=2.9.0
pytz>=2024.2
scikit-learn>=1.6.1
scipy>=1.13.1
seaborn>=0.13.2
six>=1.17.0
threadpoolctl>=3.5.0

[bench]
pytest-benchmark>=4.0

[dev]
aaanalysis[docs]
black>=26.3.1
deap>=1.4
hypothesis>=6.124.7
ipykernel==6.29.5
ipython>=8.18.1
pandoc==2.4
poetry>=2.0.1
pytest>=9.0.3
pytest-cov>=7.1.0
pytest-xdist>=3.6.0
pytest-mpl==0.19.0
mutmut>=3.0
pyright>=1.1.400

[docs]
aaanalysis[pro]
docutils==0.21.2
nbconvert>=7.17.0
nbformat==5.10.4
nbsphinx==0.9.6
numpydoc==1.8.0
sphinx==8.1.3
sphinx-autodoc-typehints==1.15.0
sphinx-copybutton==0.5.2
sphinx_design==0.6.1
sphinx_rtd_theme==3.0.2
sphinxext-opengraph==0.9.1
urllib3>=2.7.0
ipywidgets>=8.0.0

[embed]
torch>=2.13.0
transformers>=4.40
sentencepiece>=0.2
huggingface_hub>=0.23

[pro]
biopython>=1.87
shap>=0.46.0
UpSetPlot>=0.9.0
requests>=2.0
afragmenter>=0.0.6
py3Dmol>=2.0
ipywidgets>=8.0.0
