pyproject.toml

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

[project]
name = "niworkflows"
dynamic = ["version"]
description = "NeuroImaging Workflows provides processing tools for magnetic resonance images of the brain."
readme = "README.rst"
license = {file = "LICENSE"}
requires-python = ">= 3.9"
authors = [
    { name = "The NiPreps Developers", email = "nipreps@gmail.com" },
]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "License :: OSI Approved :: Apache Software License",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Image Recognition",
]
dependencies = [
    "acres",
    "attrs >=20.1",
    "importlib_resources >= 5.7; python_version < '3.11'",
    "jinja2 >=3",
    "looseversion",
    "matplotlib >= 3.5",
    "nibabel >= 3.0",
    "nilearn >= 0.8",
    "nipype >= 1.8.5",
    "nitransforms >= 22.0.0",
    "numpy >= 1.20",
    "packaging",
    "pandas >= 1.2",
    "pybids >= 0.15.1",
    "PyYAML >= 5.4",
    "scikit-image >= 0.18",
    "scipy >= 1.8",
    "seaborn >= 0.11",
    "svgutils >= 0.3.4",
    "templateflow >= 23.1",
    "transforms3d >= 0.4",
]

[project.optional-dependencies]
doc = [
    "furo",
    "pydot >= 1.2.3",
    "pydotplus",
    "sphinx",
    "sphinxcontrib-apidoc",
    "sphinxcontrib-napoleon",
]
pointclouds = [
    "pyntcloud",
]
style = [
    "flake8 >= 3.7.0",
]
tests = [
    "coverage[toml] >=5.2.1",
    "pytest >= 6",
    "pytest-cov >= 2.11",
    "pytest-env",
    "pytest-xdist >= 2.5",
    "pytest-xvfb >= 2",
]
# Aliases
all = ["niworkflows[doc,pointclouds,style,tests]"]
docs = ["niworkflows[doc]"]

[project.scripts]
niworkflows-boldref = "niworkflows.cli.boldref:main"

[project.urls]
"Bug Tracker" = "https://github.com/nipreps/niworkflows/issues"
Documentation = "https://www.nipreps.org/niworkflows"
GitHub = "https://github.com/nipreps/niworkflows"
Homepage = "https://www.nipreps.org"
"Source Code" = "https://github.com/nipreps/niworkflows"
Zenodo = "https://doi.org/10.5281/zenodo.2650331"

#
# Hatch configurations
#

[tool.hatch.metadata]
allow-direct-references = true

[tool.hatch.build.targets.sdist]
exclude = [".git_archival.txt"]  # No longer needed in sdist

[tool.hatch.build.targets.wheel]
packages = ["niworkflows"]
exclude = [
    "niworkflows/data/tests/work",  # Large test data directory
]

##  The following two sections configure setuptools_scm in the hatch way

[tool.hatch.version]
source = "vcs"
raw-options = {version_scheme = "release-branch-semver" }

[tool.hatch.build.hooks.vcs]
version-file = "niworkflows/_version.py"

# Disable black
[tool.black]
exclude = ".*"

[tool.ruff]
line-length = 99

[tool.ruff.lint]
extend-select = [
  "F",
  "E",
  "W",
  "I",
  "UP",
  "YTT",
  "S",
  "BLE",
  "B",
  "A",
  # "CPY",
  "C4",
  "DTZ",
  "T10",
  # "EM",
  "EXE",
  "FA",
  "ISC",
  "ICN",
  "PT",
  "Q",
]
ignore = [
  "S311",  # We are not using random for cryptographic purposes
  "ISC001",
  "S603",
]

[tool.ruff.lint.flake8-quotes]
inline-quotes = "single"

[tool.ruff.lint.extend-per-file-ignores]
"*/__init__.py" = ["F401"]
"*/test_*.py" = ["S101"]
"docs/conf.py" = ["A001"]
"niworkflows/engine/plugin.py" = [
  "BLE001",  # except Exception is intentional
  "S101",  # Assertions are intentional
]

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

[tool.pytest.ini_options]
minversion = "6"
testpaths = ["niworkflows"]
log_cli_level = "INFO"
xfail_strict = true
norecursedirs = [".git"]
addopts = [
  "-svx",
  "-ra",
  "--strict-config",
  "--strict-markers",
  "--doctest-modules",
  # Config pytest-cov
  "--cov=niworkflows",
  "--cov-report=xml",
  "--cov-config=pyproject.toml",
]
doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
env = "PYTHONHASHSEED=0"
filterwarnings = ["ignore::DeprecationWarning"]
junit_family = "xunit2"

[tool.coverage.run]
branch = true
omit = [
    "*/_version.py",
]

[tool.coverage.report]
# Regexes for lines to exclude from consideration
exclude_lines = [
    "raise NotImplementedError",
    "warnings\\.warn",
]

[tool.coverage.paths]
source = [
  "niworkflows",
  "**/site-packages/niworkflows"
]

[tool.codespell]
skip = "*/data/*,*/docs/_build/*,./examples/viz-report.*"
ignore-words-list = "objekt,nd"