pyproject.toml

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

[project]
name = "fmripost-phase"
description = 'Run phase postprocessing on fMRIPrep derivatives'
readme = "README.md"
requires-python = ">=3.8"
license = {file = "LICENSE"}
keywords = []
authors = [{name = "The NiPreps Developers", email = "nipreps@gmail.com"}]
classifiers = [
  "Development Status :: 2 - Pre-Alpha",
  "Programming Language :: Python",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
]
dependencies = [
  "fmriprep @ git+https://github.com/nipreps/fmriprep.git@master",
  "nipype >= 1.8.5",
  "nireports @ git+https://github.com/nipreps/nireports.git@main",
  "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
  "pybids >= 0.15.6",
  "sdcflows @ git+https://github.com/nipreps/sdcflows.git@master",
  "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
  "typer",
]
dynamic = ["version"]

[project.optional-dependencies]
doc = [
    "doctest-ignore-unicode",
    "pydot >=1.2.3",
    "pydotplus",
    "recommonmark",
    "sphinx >= 4.2.0",
    "sphinx-argparse",
    "sphinx-markdown-tables",
    "sphinx_rtd_theme",
    "sphinxcontrib-apidoc",
    "sphinxcontrib-bibtex",
    "svgutils",
]
test = [
  "coverage",
  "pytest",
  "pytest-cov",
  "pytest-env",
]

# Aliases
all = ["fmripost_phase[doc,test]"]

[project.urls]
Documentation = "https://github.com/nipreps/fmripost-phase#readme"
Issues = "https://github.com/nipreps/fmripost-phase/issues"
Source = "https://github.com/nipreps/fmripost-phase"

[project.scripts]
fmripost-phase = "fmripost_phase.cli.run:main"

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

[tool.hatch.version]
source = "vcs"

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

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

[tool.hatch.build.targets.wheel]
packages = ["src/fmripost_phase"]

[tool.hatch.envs.default]
dependencies = [
  "pytest",
  "pytest-cov",
]
[tool.hatch.envs.default.scripts]
cov = "pytest --cov-report=term-missing --cov-config=pyproject.toml --cov=src/fmripost_phase --cov=tests {args}"
no-cov = "cov --no-cov {args}"

[tool.hatch.envs.type]
detached = true
dependencies = [
  "mypy",
  "nibabel",
  "typer",
  "pytest",
]

[tool.hatch.envs.type.scripts]
check = "mypy . {args}"

[tool.hatch.envs.style]
detached = true
dependencies = [
  "black",
  "isort",
  "ruff",
]

[tool.hatch.envs.style.scripts]
fix = [
  "black src/",
  "ruff check --fix src/",
  "isort src/",
]
check = [
  "black --check --diff src/",
  "ruff check --diff src/",
  "isort --check --diff src/",
]

[[tool.hatch.envs.test.matrix]]
python = ["38", "39", "310", "311"]

[tool.coverage.run]
branch = true
parallel = true
omit = [
  "src/fmripost_phase/__about__.py",
]

[tool.coverage.report]
exclude_lines = [
  "no cov",
  "if __name__ == .__main__.:",
  "if TYPE_CHECKING:",
]

# 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",
  "PT023",
  "S113",
  "S202",
  "S602",
]

[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.isort]
profile = "black"
multi_line_output = 3
src_paths = ["isort", "test"]
known_local_folder = ["fmripost_phase"]

[tool.pytest.ini_options]
addopts = '-m "not integration"'
markers = [
    "integration: mark test as an integration test",
    "ds005115_deriv_only: ds005115 with full fMRIPrep and derivatives only",
    "ds005115_deriv_and_raw: ds005115 with full fMRIPrep and raw BIDS",
    "ds005115_resampling_and_raw: ds005115 with resampling-level fMRIPrep and raw BIDS",
]
env = [
    "RUNNING_PYTEST = 1",
]