content: [project]
  name = "ontogpt"
  version = "1.0.18"
  description = "OntoGPT is a Python package for extracting structured information from text with large language models (LLMs), instruction prompts, and ontology-based grounding."
  readme = "README.md"
  authors = [
      {name = "Chris Mungall", email = "cjmungall@lbl.gov"},
      {name = "J. Harry Caufield", email = "jhc@lbl.gov"},
  ]
  license = {text = "BSD-3"}
  requires-python = ">=3.9,!=3.9.7,<3.14"
  dependencies = [
      "ruamel-yaml>=0.17.31",
      "aiohttp>=3.8.4",
      "beautifulsoup4>=4.11.1",
      "bioc>=2.0",
      "cachier>=2.1.0",
      "click>=8.1.3",
      "inflect>=6.0.2",
      "inflection>=0.5.1",
      "linkml>=1.9.3-rc1",
      "linkml-owl<1.0.0,>=0.3.0",
      "oaklib>=0.5.28",
      "pydantic>=2.4.0",
      "requests<3.0.0,>=2.31.0",
      "requests-cache>=1.2.0",
      "tiktoken>=0.7.0",
      "wikipedia>=1.4.0",
      "wikipedia-api>=0.5.8",
      "dpath<3.0.0,>=2.1.6",
      "toml>=0.10.2",
      "frontend>=0.0.3",
      "litellm[caching]>=1.44.28",
      "diskcache<6.0.0,>=5.6.3",
      "pymupdf<2.0.0,>=1.24.9",
      "scipy<2.0.0,>=1.13.0; python_version < \"3.13\"",
      "scipy<2.0.0,>=1.14.1; python_version >= \"3.13\"",
      "numpy<2.1,>=1.23; python_version < \"3.13\"",
      "numpy>=2.0.0; python_version >= \"3.13\"",
  ]
  
  [build-system]
  requires = ["setuptools>=61.0"]
  build-backend = "setuptools.build_meta"
  
  [dependency-groups]
  dev = [
      "pytest>=7.1.2",
      "setuptools>=65.5.0",
      "tox>=3.25.1",
      "mkdocs-mermaid2-plugin>=0.6.0",
      "jupyter<2.0.0,>=1.0.0",
      "seaborn<1.0.0,>=0.12.2",
      "papermill<3.0.0,>=2.4.0",
  ]
  web = [
      "Jinja2>=3.1.2",
      "fastapi>=0.115.0",
      "python-multipart>=0.0.7",
      "uvicorn>=0.20.0",
  ]
  docs = [
      "myst-parser>=0.18.1",
      "sphinx>=5.3.0",
      "sphinx-autodoc-typehints>=1.19.4",
      "sphinx-click>=4.3.0",
      "sphinx-rtd-theme>=1.0.0",
  ]
  recipes = [
      "recipe-scrapers>=14.35.0",
  ]
  gilda = [
      "gilda>=1.0.0",
  ]
  
  [project.scripts]
  ontogpt = "ontogpt.cli:main"
  web-ontogpt = "ontogpt.webapp.main:start"
  
  [tool.uv]
  default-groups = []
  package = true
  
  [tool.setuptools]
  include-package-data = true
  
  [tool.setuptools.package-data]
  ontogpt = ["*.yaml"]
  
  [tool.black]
  line-length = 100
  target-version = ["py39", "py310", "py313"]
  
  [tool.isort]
  profile = "black"
  multi_line_output = 3
  line_length = 100
  include_trailing_comma = true
  reverse_relative = true
  
  [tool.codespell]
  skip = '.git,*.pdf,*.svg,output,*.tsv,./tests/input,old'
  # some specific phrases, variables and mixed case (CamelCase etc)
  ignore-regex = '\b(Torsades de pointes|[A-Z][a-zA-Z]*|[a-z]+[A-Z][a-zA-Z]*|de pointes)\b|\bcommments:'
  ignore-words-list = 'langual,sting,infarction,holliday,cyclin,convertor,ser,collapsin,infarctions,euclidian,dependant,vrsatile,anc,disjointness'
  