pvraw/pyproject.toml at main · CoBrALab/pvraw · GitHub

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[build-system]
build-backend = "hatchling.build"
# >=1.27 for PEP 639 license metadata (SPDX expression + license-files)
requires = ["hatchling>=1.27"]

[project]
classifiers = [
    'Development Status :: 5 - Production/Stable',
    'Intended Audience :: Science/Research',
    'Topic :: Scientific/Engineering :: Medical Science Apps.',
    'Natural Language :: English',
    'Operating System :: OS Independent',
    'Programming Language :: Python :: 3',
    'Programming Language :: Python :: 3.11',
    'Programming Language :: Python :: 3.12',
    'Programming Language :: Python :: 3.13',
    'Programming Language :: Python :: 3.14',
]
dependencies = [
    # >=0.4.6 for the identity properties read through the Dataset: 2dseq
    # subj_id from VisuSubjectId (isi-nmr/brukerapi-python#219) and
    # study_id/study_nr as identifier/number (#220).
    'brukerapi>=0.4.6',
    'pyyaml>=6.0.1',
    'numpy>=1.23.2',
    'nibabel>=3.2.1',
    'pandas>=1.5.0',
    # >=1.2 for `schema.bids_version` and the `rules.sidecars` layout the BIDS
    # conformance work reads; 0.7 predates both.
    'bidsschematools>=1.2',
    # Sidecar values are checked against the schema's own `objects/metadata`
    # definitions, which are valid JSON Schema (lib/bids.py::value_problem).
    'jsonschema>=4.0',
]
description = "Read raw Bruker ParaVision MRI data and convert it to NIfTI or BIDS"
license = "GPL-3.0-or-later"
license-files = ["LICENSE"]
dynamic = ["version"]
authors = [
    {name = "SungHo Lee", email = 'shlee@unc.edu'},
    {name = "Woomi Ban", email = 'banwoomi@unc.edu'},
    {name = "Jaiden Dumas"},
    {name = "Gabriel A. Devenyi", email = 'gdevenyi@gmail.com'},
    {name = "Yen-Yu Ian Shih", email = 'shihy@neurology.unc.edu'},
]
maintainers = [
    {name = "Gabriel A. Devenyi", email = 'gdevenyi@gmail.com'}
]
name = "pvraw"
readme = "README.md"
requires-python = ">=3.11"
keywords = [
    'bruker',
    'paravision',
    'mri',
    'preclinical',
    'nifti',
    'bids',
    'converter',
    'neuroimaging',
]

[project.urls]
Homepage = "https://github.com/CoBrALab/pvraw"
Repository = "https://github.com/CoBrALab/pvraw"
Issues = "https://github.com/CoBrALab/pvraw/issues"

[project.optional-dependencies]
dev = [
    "ruff>=0.16.0",
    "pytest",
    "types-PyYAML",
    "bids-validator-deno",
]

[tool.hatch.version]
path = "pvraw/__init__.py"
style = "pep440"

[tool.hatch.build.targets.wheel]
packages = ["pvraw"]

# The sdist is an allowlist so local tooling (.claude/, .serena/, agent
# instructions, planning notes) can never leak into a published artifact.
# README, LICENSE and pyproject.toml are always included by hatchling.
[tool.hatch.build.targets.sdist]
only-include = [
    "pvraw",
    "tests",
    "tools",
    "docs",
    "FILE_FORMAT.md",
    "DATASETS.md",
]

[project.scripts]
pvraw = "pvraw.scripts.pvraw:main"

[tool.pytest.ini_options]
log_cli = true
log_cli_level = "DEBUG"
testpaths = ["tests"]
markers = [
    "data: needs sample data fetched from the network",
]

[tool.ruff]
target-version = "py311"

[tool.ruff.format]
# The codebase quotes with '...'; this is what ruff's autofixes generate with.
quote-style = "single"

[tool.ruff.lint]
# Ruff's default rule set is the baseline. Listed below are the rules this
# project deliberately does not follow -- everything else is expected to pass,
# so a new violation is a real finding rather than noise.
ignore = [
    # Converting a study must not abort because one scan of it fails. The
    # per-scan conversion loops, the optional-parameter fallbacks and the
    # sweep harnesses under tools/ all catch broadly on purpose; each one
    # warns, falls back to a documented default, or re-raises a typed error.
    "BLE001",
]

[tool.ruff.lint.per-file-ignores]
# Test modules are named for the layer they cover (02_api_analyzer,
# 04_api_data, ...) so the suite reads in dependency order; the leading digits
# are the documented convention, not an invalid module name.
# S112 flags the scan-and-skip loops that hunt for a convertible scan, which
# is what those tests are for.
"tests/*" = ["N999", "S112"]