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pyproject.toml
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pyproject.toml
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[build-system]
requires = ["hatchling", "hatch-vcs"]
build-backend = "hatchling.build"
[project]
name = "cubids"
description = "Curation of BIDS (CuBIDS): A sanity-preserving software package for processing BIDS datasets."
authors = [{name = "Neuroinformatics Team of PennLINC"}]
classifiers = [
"Development Status :: 4 - Beta",
"Intended Audience :: Developers",
"Intended Audience :: Science/Research",
"Natural Language :: English",
"Topic :: Scientific/Engineering :: Image Recognition",
"License :: OSI Approved :: MIT License",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
]
license = {file = "LICENSE"}
requires-python = ">=3.8"
dependencies = [
"datalad>=0.13.5,!=0.17.3,!=0.17.0,!=0.16.1",
"numpy<=2.1.0",
"pandas<=2.2.2",
"pybids<=0.17.0",
"pyyaml",
"scikit-learn<=1.5.1",
"tqdm",
]
dynamic = ["version"]
[project.urls]
Homepage = "https://github.com/PennLINC/cubids"
Documentation = "https://www.cubids.readthedocs.io"
Paper = "https://doi.org/10.1016/j.neuroimage.2022.119609"
"Docker Images" = "https://hub.docker.com/r/pennlinc/cubids/tags/"
[project.optional-dependencies]
doc = [
"nbsphinx",
"packaging",
"recommonmark",
"sphinx >= 2.2",
"sphinx-argparse",
"sphinx-copybutton",
"sphinx_gallery",
"sphinx-hoverxref",
"sphinx_markdown_tables",
"sphinx_rtd_theme",
"sphinxcontrib-bibtex",
]
tests = [
"codespell",
"coverage",
"flake8",
"flake8-absolute-import",
"flake8-black",
"flake8-docstrings",
"flake8-isort",
"flake8-pyproject",
"flake8-unused-arguments",
"flake8-use-fstring",
"flake8-warnings",
"pep8-naming",
"pytest",
"pytest-cov",
"tomli",
]
maint = [
"fuzzywuzzy",
"python-Levenshtein",
]
# Aliases
all = ["cubids[doc,maint,tests]"]
[project.scripts]
cubids = "cubids.cli:_main"
cubids-group = "cubids.cli:_enter_group"
cubids-apply = "cubids.cli:_enter_apply"
cubids-purge = "cubids.cli:_enter_purge"
cubids-add-nifti-info = "cubids.cli:_enter_add_nifti_info"
cubids-copy-exemplars = "cubids.cli:_enter_copy_exemplars"
cubids-undo = "cubids.cli:_enter_undo"
bids-sidecar-merge = "cubids.cli:_enter_bids_sidecar_merge"
cubids-validate = "cubids.cli:_enter_validate"
cubids-datalad-save = "cubids.cli:_enter_datalad_save"
cubids-print-metadata-fields = "cubids.cli:_enter_print_metadata_fields"
cubids-remove-metadata-fields = "cubids.cli:_enter_remove_metadata_fields"
#
# Hatch configurations
#
[tool.hatch.metadata]
allow-direct-references = true
[tool.hatch.build.targets.sdist]
exclude = [".git_archival.txt"] # No longer needed in sdist
[tool.hatch.build.targets.wheel]
packages = ["cubids"]
exclude = [
"cubids/tests/data", # Large test data directory
]
## The following two sections configure setuptools_scm in the hatch way
[tool.hatch.version]
source = "vcs"
[tool.hatch.build.hooks.vcs]
version-file = "cubids/_version.py"
#
# Developer tool configurations
#
[tool.black]
line-length = 99
target-version = ['py38']
include = '\.pyi?$'
exclude = '''
(
/(
\.eggs # exclude a few common directories in the
| \.git # root of the project
| \.github
| \.hg
| \.pytest_cache
| _build
| build
| dist
)/
| versioneer.py
| cubids/_version.py
)
'''
[tool.isort]
profile = "black"
multi_line_output = 3
src_paths = ["isort", "test"]
known_local_folder = ["cubids"]
[tool.flake8]
max-line-length = "99"
doctests = "False"
exclude = [
"*build/",
"cubids/_version.py",
"cubids/_warnings.py",
"cubids/config.py",
"cubids/data/",
"cubids/tests/",
"cubids/utils/sentry.py",
]
ignore = ["D107", "E203", "E402", "E722", "W503", "N803", "N806", "N815"]
per-file-ignores = [
"**/__init__.py : F401",
"docs/conf.py : E265",
]
[tool.coverage.run]
parallel = true
omit = [
"*/tests/*",
"*/__init__.py",
"*/conftest.py",
"cubids/_version.py"
]
[tool.coverage.report]
# Regexes for lines to exclude from consideration
exclude_lines = [
'raise NotImplementedError',
'warnings\.warn',
]
[tool.codespell]
skip = "CuBIDS_Toy_Dataset_Curation,notebooks,BIDS_Dataset,_version.py,*.pem,*.json,*.js,*.html,*.css,*.svg"