pyproject.toml

[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<=2.0.0",
    "pandas<=2.2.2",
    "pybids<=0.16.5",
    "pyyaml",
    "scikit-learn<=1.5.0",
    "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"