pyproject.toml

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

[project]
name = "sdcflows"
description = "Susceptibility Distortion Correction (SDC) workflows for EPI MR schemes."
readme = "README.rst"
authors = [{name = "The NiPreps Developers", email = "nipreps@gmail.com"}]
classifiers = [
    "Development Status :: 4 - Beta",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Image Recognition",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "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",
    "Programming Language :: Python :: 3.13",
]
license = "Apache-2.0"
requires-python = ">=3.9"
dependencies = [
    "acres >= 0.2.0",
    "attrs >= 20.1.0",
    "nibabel >= 3.0",
    "nipype >= 1.8.5",
    "migas >= 0.4.0",
    "nireports >= 24.1.0",
    "niworkflows >= 1.7.0",
    "nitransforms >= 24.1.0",
    "numpy >= 1.22",
    "pybids >= 0.16.4",
    "scikit-image >= 0.18",
    "scipy >= 1.8.1",
    "templateflow >= 23.1",
    "toml >= 0.10",
]
dynamic = ["version"]

[project.urls]
Documentation = "https://www.nipreps.org/sdcflows"
Home = "https://github.com/nipreps/sdcflows"
NiPreps = "https://www.nipreps.org/"

[project.optional-dependencies]
doc = [
    "attrs >= 20.1.0",
    "furo",
    "importlib_resources",
    "ipykernel",
    "ipython",
    "nbsphinx",
    "pandoc",
    "pydot >= 1.2.3",
    "pydotplus",
    "sphinx >= 7.2.2",
    "sphinx-argparse",
    "sphinxcontrib-apidoc",
]

mem = [
    "psutil"
]

dev = [
    "black",
    "pre-commit",
    "isort",
    "flake8-pyproject",
]

test = [
    "coverage[toml] >=5.2.1",
    "pytest >= 6",
    "pytest-cov >= 2.11",
    "pytest-env",
    "pytest-xdist >= 2.5",
]

# Aliases
docs = ["sdcflows[doc]"]
tests = ["sdcflows[test]"]
all = ["sdcflows[doc,test,mem,dev,test]"]

[project.scripts]
sdcflows = "sdcflows.cli.main:main"

#
# 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 = ["sdcflows"]
# exclude = [
#     "sdcflows/tests/data",  # Large test data directory
# ]

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

[tool.hatch.version]
validate-bump = true
source = "vcs"
raw-options = { version_scheme = "nipreps-calver" }

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

#
# Developer tool configurations
#

[tool.black]
line-length = 99
target-version = ['py39']
skip-string-normalization = true
exclude = '''
# Directories
/(
    \.eggs
  | \.git
  | \.hg
  | \.mypy_cache
  | \.tox
  | \.venv
  | venv
  | _build
  | build
  | dist
)/
'''

[tool.isort]
profile = 'black'
skip_gitignore = true

[tool.flake8]
max-line-length = "99"
doctests = "False"
exclude = "*build/"
ignore = ["W503", "E203"]
per-file-ignores = [
    "**/__init__.py : F401",
    "docs/conf.py : E265",
]

[tool.pytest.ini_options]
minversion = "6"
testpaths = ["sdcflows"]
log_cli_level = "INFO"
xfail_strict = true
norecursedirs = [".git"]
addopts = [
  "-svx",
  "-ra",
  "--strict-config",
  "--strict-markers",
  "--doctest-modules",
  # Config pytest-cov
  "--cov=sdcflows",
  "--cov-report=xml",
  "--cov-config=pyproject.toml",
]
doctest_optionflags = "ALLOW_UNICODE NORMALIZE_WHITESPACE ELLIPSIS"
env = "PYTHONHASHSEED=0"
filterwarnings = ["ignore::DeprecationWarning"]
junit_family = "xunit2"
markers = [
  "slow: marks tests as slow (deselect with '-m \"not slow\"')",
  "veryslow: marks tests as very slow (>5min)",
]


[tool.coverage.run]
branch = true
omit = [
    '*/tests/*',
    '*/__init__.py',
    '*/conftest.py',
    'sdcflows/_version.py'
]

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

[tool.codespell]
# nd - import scipy.ndimage as nd
# mapp, reson -- Mapp. and Reson. abbreviations in citation
ignore-words-list = 'nd,mapp,reson'
skip = """
./.git,*.pdf,*.svg,*.min.js,*.ipynb,ORIGINAL_LICENSE,\
./docs/source/_static/example_anatreport.html"""

[tool.check-wheel-contents]
ignore = [
  "W002",  # Test data contains duplicates
]