pyproject.toml

[build-system]
requires = ["setuptools>=61", "setuptools-scm>=8.0"]
build-backend = "setuptools.build_meta"

[project]
name = "hedtools"
dynamic = ["version"]
description = "HED validation, summary, and analysis tools for annotating events and experimental metadata."
readme = "README.md"
authors = [
    { name = "VisLab" },
    { name = "Ian Callanan" },
    { name = "Monique Dennisen"},
    { name = "Jeremy Cockfield" },
    { name = "Alexander Jones" },
    { name = "Owen Winterberg" },
    { name = "Kay Robbins", email = "Kay.Robbins@utsa.edu" },
]
maintainers = [
    { name = "Kay Robbins", email = "Kay.Robbins@utsa.edu" },
]
license = {text = "MIT"}
keywords = ["HED", "hierarchical event descriptors", "validation", "neuroscience", "BIDS", "events", "metadata", "annotation"]
classifiers = [
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Programming Language :: Python :: 3.13",
    "Programming Language :: Python :: 3.14",
    "Operating System :: OS Independent",
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Developers",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering",
    "Topic :: Software Development :: Libraries :: Python Modules",
    "License :: OSI Approved :: MIT License",
]

requires-python = ">=3.10"

dependencies = [
    "click>=8.0.0",
    "click-option-group>=0.5.0",
    "defusedxml>=0.7.1",
    "inflect>=7.5.0",
    "numpy>=2.0.2",
    "openpyxl>=3.1.5",
    "pandas>=2.2.3,<3.0.0",
    "portalocker>=3.1.1",
    "semantic-version>=2.10.0"
]

[project.urls]
"Homepage" = "https://www.hedtags.org/"
"Documentation" = "https://www.hedtags.org/hed-python/"
"Repository" = "https://github.com/hed-standard/hed-python/"
"Bug Tracker" = "https://github.com/hed-standard/hed-python/issues"
"Changelog" = "https://github.com/hed-standard/hed-python/blob/main/CHANGELOG.md"
"HED Resources" = "https://www.hedtags.org/hed-resources/"

[project.optional-dependencies]
dev = [
    "ruff>=0.8.0",
    "typos>=1.29.0",
    "mdformat>=0.7.0",
    "mdformat-myst>=0.1.5",
]
docs = [
    "sphinx>=7.1.0,<10.0",
    "furo>=2024.1.29",
    "sphinx-copybutton>=0.5.2",
    "myst-parser>=3.0.0",
    "sphinx-autodoc-typehints>=1.24.0",
    "linkify-it-py>=2.0.3",
]
test = [
    "coverage>=7.0.0",
]
examples = [
    "jupyter>=1.0.0",
    "notebook>=7.0.0",
    "nbformat>=5.9.0",
    "nbconvert>=7.0.0",
    "ipykernel>=6.25.0",
]

[project.scripts]
# Main unified CLI
hedpy = "hed.cli.cli:main"

# Legacy commands (deprecated - use 'hedpy' instead)
validate_bids = "hed.scripts.validate_bids:main"
validate_hed_string = "hed.scripts.validate_hed_string:main"
validate_hed_sidecar = "hed.scripts.validate_hed_sidecar:main"
validate_hed_tabular = "hed.scripts.validate_hed_tabular:main"
hed_extract_bids_sidecar = "hed.scripts.hed_extract_bids_sidecar:main"
hed_validate_schemas = "hed.scripts.validate_schemas:main"
hed_update_schemas = "hed.scripts.hed_convert_schema:main"
hed_add_ids = "hed.scripts.add_hed_ids:main"
hed_check_schema_loading = "hed.scripts.check_schema_loading:main"

[tool.setuptools_scm]
write_to = "hed/_version.py"
version_scheme = "no-guess-dev"

[tool.setuptools.packages.find]
where = [""]
include = ["hed*"]
namespaces = false

[tool.setuptools.package-data]
hed = ["schema/schema_data/*.xml", "resources/*.png", "validator/data/*"]

[tool.typos.files]
extend-exclude = [
    "*.pdf",
    "*.svg",
    "deprecated/",
    "venv*/",
    "*.tsv",
    "*.yaml",
    "*.yml",
    "*.json",
    "*.rdf",
    "*.jsonld",
    "spec_tests/",
    "tests/",
    "*.xml",
    "*.mediawiki",
    "*.omn",
    "*.toml",
]

[tool.typos.default.extend-words]
# Domain-specific terms and abbreviations that are not typos
te = "te"
parms = "parms"
assertIn = "assertIn"
covert = "covert"
hed = "hed"
recuse = "recuse"
disjointness = "disjointness"

[tool.ruff]
# Target Python 3.10+
target-version = "py310"
line-length = 120

# Exclude common directories
exclude = [
    '.git',
    '.venv',
    'venv',
    '__pycache__',
    'build',
    'dist',
    '*.egg-info',
    'hed/_version.py',  # Auto-generated by setuptools-scm
    'spec_tests/hed-examples',
    'spec_tests/hed-schemas',
    'spec_tests/hed-tests',
    '.status',
]

[tool.ruff.lint]
# Enable flake8-style checks plus additional rules
select = [
    "E",     # pycodestyle errors
    "W",     # pycodestyle warnings
    "F",     # pyflakes
    "N",     # pep8-naming
    "B",     # flake8-bugbear
    "C4",    # flake8-comprehensions
]

ignore = [
    "E501",   # Line too long (handled by formatter)
    "N802",   # Function name should be lowercase (many test methods use camelCase)
    "N803",   # Argument name should be lowercase (DataFrame df is common)
    "N806",   # Variable in function should be lowercase (common in scientific code)
    # Style rules that are too opinionated
    "SIM108", # if-else-block-instead-of-if-exp (ternary operator preference)
    "SIM105", # suppressible-exception (use contextlib.suppress)
    "SIM118", # in-dict-keys (x in dict vs x in dict.keys())
    "SIM102", # collapsible-if (nested if statements)
    "SIM103", # needless-bool (return bool vs if/else return True/False)
    "SIM110", # reimplemented-builtin (any/all reimplementation)
    "SIM101", # duplicate-isinstance-call
    # Python 3.10+ features
    "UP007",  # Use X | Y for Union types (requires 3.10+)
    "UP008",  # Use super() without parameters (we're okay with explicit)
    "UP031",  # Use format strings over %-formatting (legacy code compatibility)
    "UP028",  # yield in for loop
    "UP045",  # Use X | None for Optional (requires 3.10+)
]

# Allow unused imports in __init__.py files
[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]

[tool.ruff.lint.mccabe]
# Maximum complexity (matching your flake8 setting)
max-complexity = 10

[tool.ruff.lint.isort]
known-first-party = ["hed"]

[tool.ruff.format]
# Ruff format settings
quote-style = "double"
indent-style = "space"
skip-magic-trailing-comma = false
line-ending = "auto"