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pyproject.toml
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pyproject.toml
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# https://peps.python.org/pep-0517/
[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
[project]
name = "nd2"
description = "Yet another nd2 (Nikon NIS Elements) file reader"
readme = "README.md"
requires-python = ">=3.8"
license = { text = "BSD 3-Clause License" }
authors = [{ email = "talley.lambert@gmail.com", name = "Talley Lambert" }]
classifiers = [
"Development Status :: 4 - Beta",
"License :: OSI Approved :: BSD License",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
]
dynamic = ["version"]
dependencies = [
"numpy",
"ome-types >=0.5.1",
"resource-backed-dask-array",
"typing-extensions",
]
[project.optional-dependencies]
legacy = ["imagecodecs"]
tiff = ["tifffile"]
test = [
"nd2[legacy]",
"nd2[tiff]",
"aicsimageio",
"dask[array]",
"lxml; python_version >= '3.9'",
"numpy",
"psutil",
"pytest-codspeed",
"pytest-cov",
"pytest-pretty",
"pytest>=6.0",
"tifffile",
"xarray",
]
dev = [
"nd2[test]",
"ipython",
"mypy",
"pre-commit",
"rich",
"ruff",
"types-lxml",
]
docs = ["mkdocs", "mkdocs-material", "mkdocstrings-python"]
[project.urls]
homepage = "https://github.com/tlambert03/nd2"
repository = "https://github.com/tlambert03/nd2"
changelog = "https://github.com/tlambert03/nd2/blob/main/CHANGELOG.md"
documentation = "https://tlambert03.github.io/nd2/"
# https://hatch.pypa.io/latest/config/metadata/
[tool.hatch.version]
source = "vcs"
[tool.hatch.build.targets.wheel]
only-include = ["src"]
sources = ["src"]
# https://docs.astral.sh/ruff/rules
[tool.ruff]
line-length = 88
target-version = "py38"
src = ["src/nd2", "tests"]
[tool.ruff.lint]
pydocstyle = { convention = "numpy" }
select = [
"E", # style errors
"W", # style warnings
"F", # flakes
"D", # pydocstyle
"D417", # Missing argument descriptions in Docstrings
"I", # isort
"UP", # pyupgrade
"S", # bandit
"C4", # flake8-comprehensions
"B", # flake8-bugbear
"A001", # flake8-builtins
"RUF", # ruff-specific rules
"SIM105", # contextlib.suppress
"TID", # tidy imports
"TCH", # flake8-type-checking
]
ignore = [
"D401", # First line should be in imperative mood
"D100", # Missing docstring in public module
]
[tool.ruff.lint.per-file-ignores]
"src/nd2/structures.py" = ["D101", "D105"] # Fix someday
"tests/*.py" = ["D", "S"]
"scripts/*.py" = ["D", "S"]
# https://docs.astral.sh/ruff/formatter/
[tool.ruff.format]
docstring-code-format = true
# https://docs.pytest.org/en/6.2.x/customize.html
[tool.pytest.ini_options]
minversion = "6.0"
addopts = '--color=yes --cov-config=pyproject.toml'
testpaths = ["tests"]
filterwarnings = [
"error",
"ignore:The distutils package is deprecated::",
"ignore:The distutils.sysconfig module is deprecated::",
"ignore:distutils Version classes are deprecated:",
"ignore:::xarray",
]
# https://mypy.readthedocs.io/en/stable/config_file.html
[tool.mypy]
files = "src"
strict = true
disallow_any_generics = false
show_column_numbers = true
show_error_codes = true
pretty = true
plugins = ["pydantic.mypy"]
[tool.pydantic-mypy]
init_typed = false
[[tool.mypy.overrides]]
module = ["imagecodecs", "resource_backed_dask_array"]
ignore_missing_imports = true
# https://coverage.readthedocs.io/en/6.4/config.html
[tool.coverage.report]
show_missing = true
exclude_lines = [
"pragma: no cover",
"if TYPE_CHECKING:",
"@overload",
"\\.\\.\\.",
"except ImportError",
"except NotImplementedError",
"if __name__ == .__main__.:",
" in flags:", # all the OME modality flags... don't need to test
"return None", # just there for mypy
]
[tool.coverage.run]
source = ["src"]
# https://github.com/mgedmin/check-manifest#configuration
[tool.check-manifest]
ignore = [
".github_changelog_generator",
".pre-commit-config.yaml",
"tests/**/*",
"src/nd2/_version.py",
]
[tool.typos.default]
extend-ignore-identifiers-re = ["(?i)nd2?.*", "(?i)ome"]
[tool.typos.files]
extend-exclude = ["*.json", "**/_sdk_types.py"]