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[build-system]

requires = ["hatchling"]

build-backend = "hatchling.build"

[project]

name = "autobidsify"

version = "0.9.9.1"

description = "Automated BIDS standardization tool powered by LLM-first architecture"

readme = "README.md"

license = {text = "MIT"}

requires-python = ">=3.8"

authors = [

{name = "Yiyi Liu", email = "yiyi.liu3@northeastern.edu"}

]

maintainers = [

{name = "Yiyi Liu", email = "yiyi.liu3@northeastern.edu"}

]

keywords = [

"bids",

"neuroimaging",

"mri",

"fnirs",

"dicom",

"nifti",

"data-standardization",

"brain-imaging",

"medical-imaging",

]

classifiers = [

"Development Status :: 4 - Beta",

"Intended Audience :: Science/Research",

"Intended Audience :: Healthcare Industry",

"License :: OSI Approved :: MIT License",

"Operating System :: OS Independent",

"Programming Language :: Python :: 3",

"Programming Language :: Python :: 3.10",

"Programming Language :: Python :: 3.11",

"Programming Language :: Python :: 3.12",

"Programming Language :: Python :: 3.13",

"Topic :: Scientific/Engineering :: Medical Science Apps.",

"Topic :: Scientific/Engineering :: Bio-Informatics",

"Topic :: Scientific/Engineering :: Image Processing",

]

dependencies = [

"openai>=1.0.0",

"pyyaml>=6.0",

"pdfplumber>=0.8.0",

"PyPDF2>=3.0.0",

"python-docx>=1.0.0",

"pydicom>=2.4.0",

"nibabel>=2.0.0",

"h5py>=3.8.0",

"numpy>=1.21.0",

"pandas>=1.3.0",

"scipy>=1.7.0",

"openpyxl>=3.1.0",

"requests>=2.28.0",

"dcm2niix>=1.0.20220720",

"bids-validator>=1.14.0",

"ollama>=0.6.0",

"snirf",

]

[project.optional-dependencies]

dev = [

"pytest>=7.0",

"pytest-cov>=4.0",

"black>=23.0",

"ruff>=0.1.0",

"mypy>=1.0",

"pre-commit>=1.12",

]

docs = [

"sphinx>=6.0",

"sphinx-rtd-theme>=1.0",

"myst-parser>=2.0",

]

dotenv = [

"python-dotenv>=1.0.0",

]

qwen = [

"ollama>=0.6.0",

"dashscope>=1.0.0",

]

jnifti = [

"bjdata>=0.4.0",

]

all = [

"autobidsify[dev,docs,dotenv,qwen,jnifti]",

]

[project.urls]

Homepage = "https://github.com/cotilab/autobidsify"

Documentation = "https://autobidsify.readthedocs.io"

Repository = "https://github.com/cotilab/autobidsify"

Issues = "https://github.com/cotilab/autobidsify/issues"

Changelog = "https://github.com/cotilab/autobidsify/blob/main/CHANGELOG.md"

[project.scripts]

autobidsify = "autobidsify.__main__:main"

bidsify = "autobidsify.__main__:main"

# ============================================================================

# Build Configuration (FLAT LAYOUT)

# ============================================================================

[tool.hatch.build.targets.wheel]

packages = ["autobidsify"]

[tool.hatch.build.targets.sdist]

include = [

"/autobidsify",

"/tests",

"/README.md",

"/LICENSE",

"/CHANGELOG.md",

]

# ============================================================================

# Tool Configuration

# ============================================================================

[tool.pytest.ini_options]

testpaths = ["tests"]

addopts = "-v --tb=short"

filterwarnings = [

"ignore::DeprecationWarning",

]

[tool.black]

line-length = 100

target-version = ["py310", "py311", "py312"]

[tool.ruff]

line-length = 100

target-version = "py310"

select = ["E", "F", "W", "I", "N", "UP", "B", "C4", "PIE", "SIM", "RUF"]

ignore = ["E501", "B008", "C901", "PLR0913"]

[tool.ruff.per-file-ignores]

"__init__.py" = ["F401"]

"tests/*" = ["ARG001", "S101"]

[tool.ruff.isort]

known-first-party = ["autobidsify"]

[tool.mypy]

python_version = "3.10"

ignore_missing_imports = true

[tool.coverage.run]

source = ["autobidsify"]

branch = true