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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["hatchling"]
build-backend = "hatchling.build"
[project]
name = "oai-analysis"
dynamic = ["version"]
description = 'Image analysis for the Osteoarthritis Initiative (OAI) knee magnetic resonance image (MRI) dataset.'
readme = "README.md"
requires-python = ">=3.8"
license = "MIT"
keywords = []
authors = [
{ name = "Marc Niethammer", email = "[email protected]" },
{ name = "Hastings Greer", email = "[email protected]" },
{ name = "Matt McCormick", email = "[email protected]" },
{ name = "Pranjal Sahu", email = "[email protected]" },
]
classifiers = [
"Development Status :: 4 - Beta",
"Programming Language :: Python",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: Implementation :: CPython",
"Programming Language :: Python :: Implementation :: PyPy",
]
dependencies = [
"torch",
"itk==5.3",
"itk-cuberille",
"trimesh",
"vtk",
"icon_registration==1.1.2",
"pooch",
"scikit-image",
"scikit-learn",
]
[project.urls]
Documentation = "https://github.com/uncbiag/OAI_analysis_2#readme"
Issues = "https://github.com/uncbiag/OAI_analysis_2/issues"
Source = "https://github.com/uncbiag/OAI_analysis_2"
[tool.hatch.version]
path = "oai_analysis/__about__.py"
[tool.hatch.envs.default]
dependencies = [
"coverage[toml]>=6.5",
"pytest",
]
[tool.hatch.envs.default.scripts]
test = "pytest {args:tests}"
test-cov = "coverage run -m pytest {args:tests}"
cov-report = [
"- coverage combine",
"coverage report",
]
cov = [
"test-cov",
"cov-report",
]
[[tool.hatch.envs.all.matrix]]
python = ["3.7", "3.8", "3.9", "3.10", "3.11"]
[tool.hatch.envs.lint]
detached = true
dependencies = [
"black>=23.1.0",
"mypy>=1.0.0",
"ruff>=0.0.243",
]
[tool.hatch.envs.lint.scripts]
typing = "mypy --install-types --non-interactive {args:oai_analysis tests}"
style = [
"ruff {args:.}",
"black --check --diff {args:.}",
]
fmt = [
"black {args:.}",
"ruff --fix {args:.}",
"style",
]
all = [
"style",
"typing",
]
[tool.black]
target-version = ["py37"]
line-length = 120
skip-string-normalization = true
[tool.ruff]
target-version = "py37"
line-length = 120
select = [
"A",
"ARG",
"B",
"C",
"DTZ",
"E",
"EM",
"F",
"FBT",
"I",
"ICN",
"ISC",
"N",
"PLC",
"PLE",
"PLR",
"PLW",
"Q",
"RUF",
"S",
"T",
"TID",
"UP",
"W",
"YTT",
]
ignore = [
# Allow non-abstract empty methods in abstract base classes
"B027",
# Allow boolean positional values in function calls, like `dict.get(... True)`
"FBT003",
# Ignore checks for possible passwords
"S105", "S106", "S107",
# Ignore complexity
"C901", "PLR0911", "PLR0912", "PLR0913", "PLR0915",
]
unfixable = [
# Don't touch unused imports
"F401",
]
[tool.ruff.isort]
known-first-party = ["oai_analysis"]
[tool.ruff.flake8-tidy-imports]
ban-relative-imports = "all"
[tool.ruff.per-file-ignores]
# Tests can use magic values, assertions, and relative imports
"tests/**/*" = ["PLR2004", "S101", "TID252"]
[tool.coverage.run]
source_pkgs = ["oai_analysis", "tests"]
branch = true
parallel = true
omit = [
"oai_analysis/__about__.py",
]
[tool.coverage.paths]
oai_analysis = ["oai_analysis", "*/oai-analysis/oai_analysis"]
tests = ["tests", "*/oai-analysis/tests"]
[tool.coverage.report]
exclude_lines = [
"no cov",
"if __name__ == .__main__.:",
"if TYPE_CHECKING:",
]