rbc/pyproject.toml at 7d5d2cc52e97981c811c8f82dbd03d8c71713248 · childmindresearch/rbc · GitHub

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[project]
name = "rbc"
version = "0.1.0"
description = "Standalone implementations of the RBC protocol for anatomical and functional pre-processing."
authors = [{name = "CMI DAIR", email = "dair@childmind.org"}]
license = "LGPL-3.0-or-later"
readme = "README.md"
requires-python = ">=3.12"
dependencies = [
  "bids2table>=2.1.2",
  "nibabel>=5.3.3",
  "niwrap>=0.9.3",
  "numpy>=2.4.2",
  "polars>=1.38.1",
  "scipy>=1.17.0",
  "styxcache>=0.2.0,<0.3",
  "styxpodman>=0.1.1",
  "tqdm>=4.67.3"
]

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

[dependency-groups]
dev = [
  "pytest>=9.0.2",
  "mypy>=2.0.0",
  "pre-commit>=4.0.1",
  "pytest-cov>=7.0.0",
  "ruff>=0.8.1",
  "deptry>=0.23.0",
  "pytest-xdist[psutil]>=3.8.0"
]
docs = ["pdoc>=15.0.0"]

[tool.pytest.ini_options]
pythonpath = ["src"]
testpaths = ["tests"]
norecursedirs = ["tests/data"]
markers = [
  "unit: Fast (<1s) unit tests (e.g. utilities, BIDS parsing, file operations)",
  "integration: Integration tests with real data",
  "slow: Long-running tests (manual marker on individual tests)",
  "full_pipeline: End-to-end workflow tests"
]

[tool.coverage.report]
omit = ["src/rbc_resources/"]

[tool.mypy]
ignore_missing_imports = true
exclude = ["src/rbc/bids/_schema\\.py$", "tests/unit/bids/test_bids\\.py$", "tests/data/"]

[tool.ruff]
line-length = 88
indent-width = 4
src = ["src"]
target-version = "py312"
extend-exclude = [
  "src/rbc/bids/_schema.py",
  "tests/unit/bids/test_bids.py",
  "scripts/visualize_pipeline.py",
  "scripts/build_robust_template.py"
]

[tool.ruff.lint]
select = [
  "ANN",  # flake8-annotations
  "ARG",  # flake8-unused-arguments
  "B",  # flake8-bugbear
  "C4",  # flake8-comprehensions
  "C90",  # mccabe
  "D",  # pydocstyle
  "E",  # pycodestyle errors
  "ERA",  # eradicate
  "F",  # Pyflakes
  "FA",  # flake8-future-annotations
  "FBT",  # flake8-boolean-trap
  "FURB",  # refurb
  "I",  # isort
  "N",  # pep8-naming
  "NPY",  # NumPy-specific rules
  "PD",  # pandas-vet
  "PERF",  # Perflint
  "PIE",  # flake8-pie
  "PT",  # flake8-pytest-style
  "PTH",  # flake8-use-pathlib
  "Q",  # flake8-quotes
  "RET",  # flake8-return
  "RUF",  # Ruff-specific rules
  "S",  # flake8-bandit
  "SIM",  # flake8-simplify
  "T20",  # flake8-print
  "TID",  # flake8-tidy-imports
  "TC",  # flake8-type-checking
  "UP"  # pyupgrade
]
ignore = []
fixable = ["ALL"]
unfixable = []

[tool.ruff.lint.flake8-tidy-imports.banned-api]
"bids2table.format_bids_path".msg = "Prefer rbc.bids.bids_path / rbc.bids.bids_name"
"bids2table.parse_bids_entities".msg = "Prefer rbc.bids.parse_bids_name"
"types.SimpleNamespace".msg = "Prefer NamedTuple"

[tool.ruff.lint.pydocstyle]
convention = "google"

[tool.ruff.lint.per-file-ignores]
"tests/**/*.py" = ["S101"]
"src/rbc/core/qc/xcp.py" = [
  "N815"
]  # camelCase field names required by XCP-D TSV spec

[tool.uv.build-backend]
module-name = ["rbc", "rbc_resources"]

[build-system]
requires = ["uv_build>=0.9.3,<0.12.0"]
build-backend = "uv_build"