FullCopilot/pyproject.toml at main · lulaiao/FullCopilot · GitHub

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[build-system]
requires = ["setuptools>=61.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "FullCopilot"
version = "0.1.0"
description = "FullCopilot - trustworthy biomedical tool planning and execution verification"
readme = "README.md"
license = {text = "Apache-2.0"}
authors = [
    {name = "FullCopilot Contributors"}
]
requires-python = ">=3.11"
dependencies = [
    # LLM stack
    "langchain-core>=0.3",
    "langchain-openai>=0.2",
    "langchain-anthropic>=0.2",
    "langgraph>=0.2",
    # Web backend
    "fastapi>=0.110",
    "uvicorn[standard]>=0.27",
    "python-multipart>=0.0.9",  # FastAPI file uploads
    "pydantic>=2.0",
    # Utilities
    "python-dotenv>=1.0",
    "requests>=2.31",
    "rich>=13.0",
    "prompt_toolkit>=3.0",
    # Jupyter kernel for code execution (real process isolation + true timeout)
    "jupyter_client>=8.0",
    "ipykernel>=6.0",
    "cloudpickle>=3.0",
    # PDF export
    "markdown>=3.5",
    "weasyprint>=60.0",
]

[project.urls]
Homepage = "https://github.com/<your-org>/FullCopilot"
Repository = "https://github.com/<your-org>/FullCopilot"

[project.optional-dependencies]
# Legacy Gradio UI (superseded by the built-in Web UI)
gradio = ["gradio>=5.0,<6.0"]
# Chemistry toolkit extras
chemistry = [
    "rdkit",
    "pyyaml",
]
# Development / testing
dev = [
    "pytest>=7.0",
    "pytest-asyncio>=0.21",
    "ruff>=0.5",
]

[project.scripts]
cai = "CAi.main:main"
fullcopilot = "CAi.main:main"

[tool.setuptools]
include-package-data = true

[tool.setuptools.packages.find]
include = ["CAi*"]
exclude = ["tests*", "tutorials*", "example*", "docs*"]

[tool.setuptools.package-data]
"CAi.web_ui.frontend" = ["*.html", "*.css", "*.js"]

# ---------------------------------------------------------------------------
# Ruff linting
# ---------------------------------------------------------------------------
[tool.ruff]
line-length = 120
target-version = "py311"
exclude = [
    ".git",
    ".venv",
    "CAi/toolkit/server/tools/*/Lib-INVENT",  # vendored library
    "CAi/toolkit/server/tools/*/REINVENT*",   # vendored library
    "build",
    "dist",
]

[tool.ruff.format]
docstring-code-format = true

[tool.ruff.lint]
select = [
    "F",      # Pyflakes
    "E",      # Pycodestyle errors
    "W",      # Pycodestyle warnings
    "I",      # isort
    "B",      # flake8-bugbear
    "TID",    # flake8-tidy-imports
    "C4",     # flake8-comprehensions
    "BLE",    # flake8-blind-except
    "UP",     # pyupgrade
    "RUF100", # Unused noqa
    "TCH",    # Typing imports
]
ignore = [
    "E501",   # line too long
    "E731",   # lambda assignment
    "E741",   # ambiguous variable names (I, O, l)
    "D104", "D100", "D107", "D105", "D400", "D401", "D203", "D213",
    "B008",   # function call in default argument
    "N813",   # camelcase imported as lowercase
    "E402",   # module import not at top of file
    "PLR0913", "PLR0912", "PLR2004", "PLR0915",
    "PLC0206", "PLC0415",
    "BLE001", # blind exception
    "B005",
]

# ---------------------------------------------------------------------------
# Pytest
# ---------------------------------------------------------------------------
[tool.pytest.ini_options]
testpaths = ["tests"]
asyncio_mode = "auto"
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
markers = [
    "slow: marks tests as slow (requires kernel operations or real LLM)",
]
filterwarnings = [
    "ignore::DeprecationWarning",
]