requests>=2.32.0
numpy>=2.2.0
sympy>=1.12.0
graphql-core>=3.2.0
fastapi>=0.116.0
uvicorn>=0.36.0
pydantic>=2.11.0
epam.indigo>=1.34.0
networkx>=3.4.0
openai>=1.107.0
pyyaml>=6.0.0
google-genai>=1.36.0
google-generativeai>=0.7.2
mcp[cli]>=1.9.3
fastmcp<4.0.0,>=2.12.3
xmltodict>=1.0.0
lxml>=6.0.0
huggingface_hub>=0.34.0
jsonpath-ng>=1.6.0
rcsb-api>=1.4.0
fitz>=0.0.1.dev2
pandas>=2.2.3
setuptools<81.0.0,>=70.0.0
pdfplumber>=0.11.0
playwright>=1.55.0
faiss-cpu==1.12.0
flask>=2.0.0
aiohttp
beautifulsoup4>=4.12.0
python-dotenv>=1.0.0
markitdown[all]>=0.1.0
psutil>=5.9.0
ddgs>=9.0.0
pip>=25.3
jsonschema>=4.23.0

[all]
tooluniverse[bioinformatics,dev,docs,embedding,graph,ml,space,visualization]

[bioinformatics]
biopython>=1.80

[build]
pyinstaller>=6.0.0

[client]
requests>=2.32.0
pydantic>=2.11.0

[dev]
pytest>=7.0
pytest-cov>=4.0
pytest-timeout>=2.3.1
pytest-mock>=3.14.0
pytest-asyncio>=0.21.0
pre-commit>=2.0
pytest-xdist>=3.0
pytest-html>=3.0
requests-mock>=1.12.1
ruff>=0.14.5

[docs]
sphinx>=4.0
furo>=2024.8.6
pydata-sphinx-theme>=0.15.0
sphinx-rtd-theme>=1.0
shibuya>=0.10.0
myst-parser>=0.18
linkify-it-py>=2.0.0
sphinx-autobuild>=2021.3.14
sphinx-copybutton>=0.5.0
sphinx-tabs>=3.2.0
sphinx-design>=0.3.0
sphinx-notfound-page>=0.8
sphinx-autodoc-typehints>=1.12.0

[embedding]
sentence-transformers>=5.1.0
faiss-cpu==1.12.0
huggingface_hub>=0.34.0

[graph]
flask>=2.0.0
matplotlib>=3.5.0
plotly>=5.0.0
scipy>=1.7.0
pydot>=1.4.0
pygraphviz>=1.7
jinja2>=3.0.0
werkzeug>=2.0.0

[ml]
admet-ai>=1.2.0
sentence-transformers>=5.1.0
faiss-cpu==1.12.0
huggingface_hub>=0.34.0

[singlecell]
cellxgene-census>=1.10.0
tiledbsoma>=1.15.3

[smolagents]
smolagents>=1.22.0
gradio>=4.0.0

[space]
huggingface_hub>=0.34.0
pyyaml>=6.0.0
requests>=2.32.0

[visualization]
py3Dmol>=2.0.0
rdkit>=2023.9.1
plotly>=5.18.0
kaleido>=0.2.1
scipy>=1.7.0
matplotlib>=3.5.0
networkx>=3.4.0
