pyproject.toml

[build-system]
requires = ["setuptools", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "tooluniverse"
version = "1.3.0"
description = "A comprehensive collection of scientific tools for Agentic AI, offering integration with the ToolUniverse SDK and MCP Server to support advanced scientific workflows."
authors = [
    { name = "Shanghua Gao", email = "shanghuagao@gmail.com" }
]
dependencies = [
    "requests>=2.32.0",
    "numpy>=2.2.0",
    "sympy>=1.12.0", # Symbolic mathematics for Python executor
    "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",
    "mcp[cli]>=1.9.3",
    "fastmcp>=2.12.3,<4.0.0",
    "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>=70.0.0", # Fix pkg_resources deprecation warnings
    "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",
]
requires-python = ">=3.10"
readme = "README.md"

[project.optional-dependencies]
client = [
    "requests>=2.32.0",
    "pydantic>=2.11.0",
]
smolagents = [
    "smolagents>=1.22.0",
    "gradio>=4.0.0",  # Required for GradioUI web interface
]
# Single-cell and spatial transcriptomics tools
singlecell = [
    "cellxgene-census>=1.10.0",  # CELLxGENE Census API
    "tiledbsoma>=1.15.3",  # Required for spatial data
]
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>=3.5.0",
    "sphinx-design>=0.3.0",
    "sphinx-notfound-page>=0.8",
    "sphinx-autodoc-typehints>=1.12.0",
    "sphinx-reredirects>=0.1.5",
]
embedding = [
    "sentence-transformers>=5.1.0",
    "faiss-cpu==1.12.0",
    "huggingface_hub>=0.34.0",
]
ml = [
    "admet-ai>=1.2.0",
    "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",
]
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",
]
space = [
    "huggingface_hub>=0.34.0",
    "pyyaml>=6.0.0",
    "requests>=2.32.0",
]
bioinformatics = [
    "biopython>=1.80",
    "freesasa>=2.2.0",
]
# circuit: install manually with `pip install git+https://github.com/tooluniverse/circuit.git`
all = [
    "tooluniverse[dev,docs,graph,visualization,space,embedding,ml,bioinformatics]",
]
build = [
    "pyinstaller>=6.0.0",
]

[project.urls]
Homepage = "https://github.com/mims-harvard/ToolUniverse"

[project.scripts]
tu = "tooluniverse.cli:main"
tooluniverse = "tooluniverse.smcp_server:run_default_stdio_server"
tooluniverse-mcp = "tooluniverse.smcp_server:run_http_server"
tooluniverse-smcp = "tooluniverse.smcp_server:run_smcp_server"
tooluniverse-smcp-server = "tooluniverse.smcp_server:run_http_server"
tooluniverse-smcp-stdio = "tooluniverse.smcp_server:run_stdio_server"
# HTTP API Server for ToolUniverse class methods
tooluniverse-http-api = "tooluniverse.http_api_server_cli:run_http_api_server"
generate-mcp-tools = "tooluniverse.generate_mcp_tools:run_generate"
# Human Expert Feedback System
tooluniverse-expert-feedback = "tooluniverse.remote.expert_feedback.human_expert_mcp_tools:main"
tooluniverse-expert-feedback-web = "tooluniverse.remote.expert_feedback.start_web_interface:main"
tu-datastore = "tooluniverse.database_setup.cli:main"
# Literature Search Web UIs (Under testing)
# tooluniverse-regular-search = "tooluniverse.web_tools.literature_search_ui.regular_search_app:main"
# tooluniverse-agent-search = "tooluniverse.web_tools.literature_search_ui.agent_search_app:main"
# tooluniverse-wide-research = "tooluniverse.web_tools.literature_search_ui.simple_app:main"
# Health Check Tool
tooluniverse-doctor = "tooluniverse.doctor:main"

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-data]
tooluniverse = ["data/*", "data/packages/*"]

[dependency-groups]
dev = [
    "tooluniverse[dev,embedding]",
]

[tool.uv.sources]
tooluniverse = { workspace = true }

[tool.ruff]
line-length = 88
exclude = [
    ".venv",
    "docs",
    "examples",
    "skills",
    "temp_docs_and_tests",
]
unsafe-fixes = true

[tool.ruff.lint]
ignore = ["E203", "E402", "E501", "F401", "F541"]