niftyone/pyproject.toml at main · childmindresearch/niftyone · GitHub

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[build-system]
requires = ["setuptools", "setuptools_scm[toml]>=8.0.4"]
build-backend = "setuptools.build_meta"

[project]
name = "niftyone"
description = "Large-scale neuroimaging visualization using FiftyOne"
authors = [
  { name = "Connor Lane", email = "connor.lane858@gmail.com" },
  { name = "Jason Kai", email = "jason.kai@childmind.org" },
]
readme = "README.md"
requires-python = ">=3.10"
license = { text = "MIT License" }
classifiers = [
  "Development Status :: 3 - Alpha",
  "Intended Audience :: Developers",
  "Topic :: Scientific/Engineering",
  "License :: OSI Approved :: MIT License",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
]
dependencies = [
  "av==14.2.0",
  "bids2table==0.1.0",
  "elbow==0.1.1",
  "fiftyone==1.3.0",
  "matplotlib==3.10.1",
  "nibabel==5.3.2",
  "nifti @ git+https://github.com/childmindresearch/nifti",
  "numpy==2.2.3",
  "pandas==2.2.3",
  "Pillow==11.1.0",
  "scikit-learn==1.6.1",
  "scipy==1.15.2",
  # Last known working elbow dependencies
  "typing_extensions==4.12.2",
  "pyarrow==19.0.1",
  "tqdm==4.67.1",
]
dynamic = ["version"]

[project.optional-dependencies]
test = ["pytest>=8.0.2", "pytest-cov>=4.1.0"]
doc = ["lazydocs>=0.4.8"]
dev = [
  "mypy>=1.12.0",
  "pre-commit>=4.0.1",
  "ruff>=0.7.0",
  "setuptools-scm>=8.0.4",
]

[project.urls]
"Homepage" = "https://github.com/childmindresearch/niftyone"

[project.scripts]
niftyone = "niftyone.__main__:main"

[tool.setuptools_scm]
write_to = "src/niftyone/_version.py"

[tool.pytest.ini_options]
pythonpath = ["src"]
testpaths = ["tests"]
markers = [
  "b2t: mark tests requiring bids2table (deselect with '-m \"not b2t\"')",
]
log_cli = true
log_cli_level = "DEBUG"

[tool.coverage.report]
exclude_also = ["assert", "__enter__", "__exit__", "pass"]

[tool.coverage.run]
omit = [
  "src/**/__init__.py",
  "src/**/typing.py",
  "src/niftyone/__main__.py",
  "src/niftyone/_version.py",
  "src/niftyone/metadata/tags.py",
  "src/niftyone/analysis_levels/*.py",
  "src/niftyone/metrics.py",
  "src/niftyone/figures/*.py",
]

[tool.mypy]
ignore_missing_imports = true
allow_redefinition = true
disable_error_code = ["no-redef"]

[tool.ruff]
line-length = 88
indent-width = 4
src = ["src"]
target-version = "py310"
exclude = ["doc"]

[tool.ruff.lint]
select = ["ANN", "D", "E", "F", "I"]
ignore = [
  "ANN002", # args should not be annotated.
  "ANN003", # kwargs should not be annotated.
  "ANN101", # self should not be annotated.
  "ANN102", # cls should not be annotated.
  "D105",   # undocumented-magic-method (e.g. __str__)
  "D107",   # undocumented-public-init (e.g. __init__)
]
fixable = ["ALL"]
unfixable = []
dummy-variable-rgx = "^(_+|(_+[a-zA-Z0-9_]*[a-zA-Z0-9]+?))$"

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]
"runner.py" = ["D102"]
"tests/**/*.py" = [
  "D",      # ignore missing docstrings
  "ANN201", # ignore missing return type
]
"src/niftyone/figures/*.py" = [
  "D101", # ignore missing class docstrings
  "D102", # ignore missing method docstrings
]

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