bootstracts/pyproject.toml at main · rdneuro/bootstracts · GitHub

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[build-system]
requires = ["setuptools>=68.0"]
build-backend = "setuptools.build_meta"

[project]
name = "bootstracts"
version = "0.2.0"
description = "Probabilistic structural connectomics via tractogram bootstrap"
readme = "README.md"
license = "MIT"
requires-python = ">=3.9"
authors = [
    { name = "Velho Mago", email = "rdneuro@users.noreply.github.com" },
]
keywords = [
    "neuroscience",
    "connectomics",
    "tractography",
    "bootstrap",
    "uncertainty-quantification",
    "diffusion-mri",
    "structural-connectivity",
    "brain-networks",
    "neuroimaging",
]
classifiers = [
    "Development Status :: 3 - Alpha",
    "Intended Audience :: Science/Research",
    "Operating System :: OS Independent",
    "Programming Language :: Python :: 3",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
    "Topic :: Scientific/Engineering :: Medical Science Apps.",
    "Topic :: Scientific/Engineering :: Bio-Informatics",
    "Typing :: Typed",
]

dependencies = [
    "numpy>=1.22",
    "scipy>=1.9",
    "matplotlib>=3.5",
    "h5py>=3.7",
]

[project.optional-dependencies]
gpu = [
    "cupy>=12.0",
]
jax = [
    "jax>=0.4",
    "jaxlib>=0.4",
]
all = [
    "cupy>=12.0",
    "jax>=0.4",
    "jaxlib>=0.4",
    "nilearn>=0.10",
    "dipy>=1.7",
]
dev = [
    "pytest>=7.0",
    "pytest-cov>=4.0",
    "hypothesis>=6.0",
    "ruff>=0.1",
    "mypy>=1.0",
    "pre-commit>=3.0",
]
docs = [
    "sphinx>=6.0",
    "sphinx-rtd-theme>=1.0",
    "numpydoc>=1.5",
    "myst-parser>=2.0",
]

[project.urls]
Homepage = "https://github.com/rdneuro/bootstracts"
Documentation = "https://bootstracts.readthedocs.io"
Repository = "https://github.com/rdneuro/bootstracts"
Issues = "https://github.com/rdneuro/bootstracts/issues"
Changelog = "https://github.com/rdneuro/bootstracts/blob/main/CHANGELOG.md"

[tool.setuptools.packages.find]
where = ["src"]

[tool.setuptools.package-data]
bootstracts = ["py.typed"]

# ── ruff ──────────────────────────────────────────────────────────────
[tool.ruff]
target-version = "py39"
line-length = 88

[tool.ruff.lint]
select = [
    "E",    # pycodestyle errors
    "W",    # pycodestyle warnings
    "F",    # pyflakes
    "I",    # isort
    "N",    # pep8-naming
    "UP",   # pyupgrade
    "B",    # flake8-bugbear
    "SIM",  # flake8-simplify
    "NPY",  # numpy-specific
]
ignore = [
    "E501",  # line too long (handled by formatter)
    "N802",  # function name lowercase (numpy convention)
    "N803",  # argument name lowercase
    "N806",  # variable lowercase
    "B023",  # loop variable not used
    "SIM108",  # ternary operator
]

[tool.ruff.lint.isort]
known-first-party = ["bootstracts"]

# ── mypy ──────────────────────────────────────────────────────────────
[tool.mypy]
python_version = "3.9"
warn_return_any = true
warn_unused_configs = true
ignore_missing_imports = true

# ── pytest ────────────────────────────────────────────────────────────
[tool.pytest.ini_options]
testpaths = ["tests"]
addopts = "-v --tb=short"
markers = [
    "slow: marks tests as slow (run with --runslow)",
    "gpu: marks tests requiring GPU",
]