pyproject.toml

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

[project]
name = "fmriprep"
description = "A robust and easy-to-use pipeline for preprocessing of diverse fMRI data"
readme = "long_description.rst"
authors = [{name = "The NiPreps Developers", email = "nipreps@gmail.com"}]
classifiers = [
    "Development Status :: 5 - Production/Stable",
    "Intended Audience :: Science/Research",
    "Topic :: Scientific/Engineering :: Image Recognition",
    "License :: OSI Approved :: Apache Software License",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
]
license = {file = "LICENSE"}
requires-python = ">=3.10"
dependencies = [
    "acres >= 0.2.0",
    "looseversion >= 1.3",
    "nibabel >= 4.0.1",
    "nipype >= 1.8.5",
    "nireports >= 24.0.3",
    "nitime >= 0.9",
    "nitransforms >= 24.1.0",
    "niworkflows >= 1.12.1",
    "numpy >= 1.24",
    "packaging >= 24",
    "pandas >= 1.2",
    "psutil >= 5.4",
    "pybids >= 0.16",
    "requests >= 2.27",
    "sdcflows >= 2.10.0",
    "smriprep @ git+https://github.com/nipreps/smriprep.git",
    "tedana >= 23.0.2",
    "templateflow >= 24.2.2",
    "transforms3d >= 0.4",
    "toml >= 0.10",
    "codecarbon >= 2",
    "APScheduler >= 3.10",
]
dynamic = ["version"]

[project.urls]
Homepage = "https://github.com/nipreps/fmriprep"
Documentation = "https://fmriprep.org"
Paper = "https://doi.org/10.1038/s41592-018-0235-4"
"Docker Images" = "https://hub.docker.com/r/nipreps/fmriprep/tags/"
NiPreps = "https://www.nipreps.org/"

[project.optional-dependencies]
doc = [
    "pydot >= 1.2.3",
    "sphinx >= 5",
    "sphinx-argparse !=0.5.0",
    "sphinx_rtd_theme>=0.5.2",
]
dev = [
    "ruff",
    "pre-commit",
]
duecredit = ["duecredit"]
resmon = []
container = [
    "fmriprep[telemetry]",
    # templateflow extras
    "datalad",
    "datalad-osf",
]
telemetry = [
    "migas >= 0.4.0",
    "sentry-sdk >= 1.3",
]
test = [
    "coverage[toml] >= 5.2.1",
    "pytest >= 8.1",
    "pytest-cov >= 2.11",
    "pytest-env",
    "pytest-xdist >= 2.5",
]
maint = [
    "fuzzywuzzy",
    "python-Levenshtein",
]
# Aliases
docs = ["fmriprep[doc]"]
tests = ["fmriprep[test]"]
all = ["fmriprep[doc,maint,telemetry,test]"]

[project.scripts]
fmriprep = "fmriprep.cli.run: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 = ["fmriprep"]
exclude = [
    "fmriprep/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 = "nipreps-calver" }

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

#
# Developer tool configurations
#

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

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

[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]
"*/test_*.py" = ["S101"]
"fmriprep/utils/debug.py" = ["A002", "T100"]
"docs/conf.py" = ["A001"]
"docs/sphinxext/github_link.py" = ["BLE001"]

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

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

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