pyproject.toml

[build-system]
requires = ["setuptools>=65.0", "wheel"]
build-backend = "setuptools.build_meta"

[project]
name = "hedit"
version = "0.7.5a1"
description = "Multi-agent system for HED annotation generation and validation"
readme = "PKG_README.md"
requires-python = ">=3.12"
license = "MIT"
authors = [
    {name = "Annotation Garden Initiative", email = "info@annotation.garden"}
]
keywords = ["hed", "annotation", "neuroscience", "bids", "cli"]
classifiers = [
    "Development Status :: 4 - Beta",
    "Environment :: Console",
    "Intended Audience :: Science/Research",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering",
]

# Core CLI dependencies (lightweight, ~100MB)
# For full standalone mode, install with: pip install hedit[standalone]
dependencies = [
    # CLI framework
    "typer>=0.20.0",
    "rich>=14.0.0",
    "platformdirs>=4.5.0",
    "pyyaml>=6.0.2",
    # HTTP client for API mode
    "httpx>=0.28.0",
    # Data validation
    "pydantic>=2.12.0",
]

[project.scripts]
hedit = "src.cli.main:cli"

[project.urls]
Homepage = "https://annotation.garden/hedit"
Documentation = "https://docs.annotation.garden/hedit"
Repository = "https://github.com/Annotation-Garden/hedit"
Issues = "https://github.com/Annotation-Garden/hedit/issues"

[project.optional-dependencies]
# Standalone mode: run LangGraph workflow locally without backend (~2GB)
# Note: hed-lsp CLI is recommended for semantic tag suggestions
# Install separately: https://github.com/hed-standard/hed-lsp
standalone = [
    "langgraph>=0.2.0",
    "langchain>=0.3.0",
    "langchain-community>=0.3.0",
    "langchain-core>=0.3.0",
    "langchain-openai>=0.3.0",
    "litellm>=1.50.0",  # LLM proxy with native prompt caching support
    "langchain-litellm>=0.2.0",  # LangChain integration for LiteLLM
    "hedtools>=0.5.0",
    "lxml>=5.3.0",
    "beautifulsoup4>=4.12.3",
    "pillow>=11.0.0",
    "nest-asyncio>=1.6.0",
]
# API server: run the HEDit backend server
api = [
    "hedit[standalone]",  # Server needs workflow capabilities
    "fastapi>=0.121.0",
    "uvicorn[standard]>=0.38.0",
    "python-multipart>=0.0.17",
    "aiofiles>=25.1.0",
    "python-dotenv>=1.0.0",
]
# Development dependencies
dev = [
    "hedit[api]",  # Dev needs full installation
    "pytest>=8.3.0",
    "pytest-cov>=5.0.0",
    "pytest-asyncio>=0.24.0",
    "ruff>=0.7.0",
    "black>=24.8.0",
    "mypy>=1.11.0",
]
# All dependencies
all = [
    "hedit[api,dev]",
]

[tool.ruff]
line-length = 100
target-version = "py312"

[tool.ruff.lint]
select = [
    "E",   # pycodestyle errors
    "W",   # pycodestyle warnings
    "F",   # pyflakes
    "I",   # isort
    "B",   # flake8-bugbear
    "C4",  # flake8-comprehensions
    "UP",  # pyupgrade
]
ignore = [
    "E501",  # line too long (handled by formatter)
]

[tool.ruff.format]
quote-style = "double"
indent-style = "space"

[tool.pytest.ini_options]
testpaths = ["tests"]
python_files = ["test_*.py"]
python_classes = ["Test*"]
python_functions = ["test_*"]
addopts = [
    "--cov=src",
    "--cov-report=html",
    "--cov-report=term-missing",
    "--strict-markers",
]
# Note: Coverage threshold is enforced by Codecov (80% project, 70% patch)
# Unit tests alone get ~18%, integration tests combined get 70%+
markers = [
    "integration: marks tests that make real API calls (deselect with '-m \"not integration\"')",
    "standalone: marks tests that run locally without backend (requires OPENROUTER_API_KEY_FOR_TESTING)",
    "timeout: marks tests with a timeout (requires pytest-timeout)",
]
asyncio_mode = "auto"

[tool.coverage.run]
# Enable branch coverage for more accurate metrics
branch = true
# Use data_file for combining multiple test runs
data_file = ".coverage"
# Parallel mode allows combining coverage from multiple processes
parallel = true
omit = [
    "src/utils/hed_rules.py",  # Just a string constant, no logic to test
]

[tool.coverage.report]
exclude_lines = [
    "pragma: no cover",
    "if __name__ == .__main__.:",
    "raise NotImplementedError",
]

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

[tool.mypy]
python_version = "3.12"
warn_return_any = true
warn_unused_configs = true
disallow_untyped_defs = true

[tool.codespell]
# Ref: https://github.com/codespell-project/codespell#using-a-config-file
skip = '.git*,.venv,*.svg,package-lock.json,examples'
check-hidden = true
# ignore-regex = ''
# ignore-words-list = ''