pyproject.toml

[build-system]
requires = ["hatchling>=1.27", "hatch-vcs"]
build-backend = "hatchling.build"

[project]
name = "nibabel"
description = "Access a multitude of neuroimaging data formats"
authors = [{ name = "NiBabel developers", email = "neuroimaging@python.org" }]
maintainers = [{ name = "Christopher Markiewicz" }]
readme = "README.rst"
license = "MIT"
requires-python = ">=3.10"
dependencies = [
  "numpy >=1.25",
  "packaging >=20",
  "importlib_resources >=5.12; python_version < '3.12'",
  "typing_extensions >=4.6; python_version < '3.13'",
]
classifiers = [
  "Development Status :: 5 - Production/Stable",
  "Environment :: Console",
  "Intended Audience :: Science/Research",
  "Operating System :: OS Independent",
  "Programming Language :: Python",
  "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",
  "Topic :: Scientific/Engineering",
]
# Version from hatch-vcs
dynamic = ["version"]

[project.urls]
homepage = "https://nipy.org/nibabel"
source = "https://github.com/nipy/nibabel"

[project.scripts]
nib-conform = "nibabel.cmdline.conform:main"
nib-convert = "nibabel.cmdline.convert:main"
nib-ls = "nibabel.cmdline.ls:main"
nib-dicomfs = "nibabel.cmdline.dicomfs:main"
nib-diff = "nibabel.cmdline.diff:main"
nib-stats = "nibabel.cmdline.stats:main"
nib-nifti-dx = "nibabel.cmdline.nifti_dx:main"
nib-tck2trk = "nibabel.cmdline.tck2trk:main"
nib-trk2tck = "nibabel.cmdline.trk2tck:main"
nib-roi = "nibabel.cmdline.roi:main"
parrec2nii = "nibabel.cmdline.parrec2nii:main"

[project.optional-dependencies]
all = ["nibabel[dicomfs,indexed_gzip,minc2,spm,zstd]"]
# Features
indexed_gzip = ["indexed_gzip >=1.6"]
dicom = ["pydicom >=2.3"]
dicomfs = ["nibabel[dicom]", "pillow >=8.4"]
minc2 = ["h5py >=3.8"]
spm = ["scipy >=1.11"]
viewers = ["matplotlib >=3.7"]
zstd = ["backports.zstd >=1.1; python_version<'3.14'"]
# Test dependencies, to allow testing an installed package
test = [
  "pytest >=8",
  "pytest-doctestplus >=1.4",
  "pytest-cov >=6",
  "pytest-httpserver >=1.0.7",
  "pytest-xdist >=3.5",
  "pytest-run-parallel >=0.8.2",
  "coverage[toml]>=7.2",
]
# Development dependencies; transferred to dependency-groups, here to avoid
# breaking existing users of these extras.
doc = []
dev = []
doctest = []
style = []
typing = []

[dependency-groups]
dev = [
  "pre-commit>=4.5.1",
  "pre-commit-uv>=4.2.1",
  "tox>=4.48.1",
  "tox-uv>=1.33.1",
]
doc = [
  "sphinx >=7.4",
  "pydata-sphinx-theme >= 0.17.0",
  "sphinx-design <= 0.7.0",
  "sphinx-copybutton >= 0.5.2",
  "matplotlib>=3.5",
  "numpydoc >=1.9",
  "texext >=0.6.8",
  "tomli >=2.3; python_version < '3.11'",
]
typecheck = [
  "mypy >=1.15",
  "nibabel[all]",
  # Easier than including a bunch of unnecessary deps
  "pytest >=8",
  "types-pillow>=10.2.0.20240822",
]
# Replaced by pre-commit
style = []

[tool.hatch.build.targets.sdist]
exclude = [
  ".git_archival.txt",
  # Submodules with large files; if we don't want them in the repo...
  "nibabel-data/",
]

[tool.hatch.build.targets.wheel]
packages = ["nibabel"]
exclude = [
  # 56MB test file does not need to be installed everywhere
  "nibabel/nicom/tests/data/4d_multiframe_test.dcm",
]

[tool.hatch.version]
source = "vcs"
tag-pattern = '(?P<version>\d+(?:\.\d+){0,2}[^+]*)(?:\+.*)?$'
raw-options = { version_scheme = "release-branch-semver" }

[tool.hatch.build.hooks.vcs]
version-file = "nibabel/_version.py"
# Old default setuptools_scm template; hatch-vcs currently causes
# a noisy warning if template is missing.
template = '''
# file generated by setuptools_scm
# don't change, don't track in version control
__version__ = version = {version!r}
__version_tuple__ = version_tuple = {version_tuple!r}
'''

[tool.ruff]
line-length = 99
exclude = ["doc", "nibabel/externals", "tools", "version.py", "versioneer.py"]

[tool.ruff.lint]
select = [
    "B",
    "C4",
    "F",
    "FLY",
    "FURB",
    "I",
    "ISC",
    "PERF",
    "PGH",
    "PIE",
    "PLE",
    "PT",
    "PYI",
    "Q",
    "RSE",
    "RUF",
    "TCH",
    "UP",
]
ignore = [
    "B006",   # TODO: enable
    "B008",   # TODO: enable
    "B007",
    "B011",
    "B017",   # TODO: enable
    "B018",
    "B020",
    "B023",   # TODO: enable
    "B028",
    "B904",
    "B905",  # Consider: add explicit strict kwarg to zip calls
    "C401",
    "C408",
    "C416",
    "PERF203",
    "PIE790",
    "PT007",
    "PT010",  # Consider: Set expected exception in pytest.raises
    "PT011",
    "PT012",
    "PT017",
    "PT018",
    "PT028",  # Consider: Test function parameter has default argument
    "PT030",  # Consider: pytest.warns(UserWarning) is too broad
    "PT031",  # Consider: pytest.warns(UserWarning) block should contain 1 statement
    "PYI024",
    "RUF005",
    "RUF007", # Consider: itertools.pairwise(x) over zip(x[:-1], x[1:])
    "RUF012", # TODO: enable
    "RUF015",
    "RUF017", # TODO: enable
    "RUF059", # Consider: Unpacked variables never used
    "RUF061", # Consider: Use context-manager form of pytest.raises
    "TC003",  # Consider: Move import into type-checking block
    # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
    "W191",
    "E111",
    "E114",
    "E117",
    "D206",
    "D300",
    "Q000",
    "Q001",
    "Q002",
    "Q003",
    "COM812",
    "COM819",
]

[tool.ruff.lint.per-file-ignores]
"__init__.py" = ["F401"]
"doc/source/conf.py" = ["F401"]

[tool.ruff.format]
quote-style = "single"

[tool.mypy]
python_version = "3.11"
exclude = [
  "/tests",
]
warn_unreachable = true
enable_error_code = ["ignore-without-code", "redundant-expr", "truthy-bool"]

[tool.codespell]
skip = "*/data/*,./nibabel-data"
ignore-words-list = "ans,te,ue,ist,nin,nd,ccompiler,ser"

[tool.uv.pip]
only-binary = ["numpy", "scipy", "h5py"]