pyproject.toml

[build-system]
build-backend = "setuptools.build_meta"
requires = ["setuptools>=64", "setuptools_scm[toml]>=8", "wheel"]

[project]
classifiers = [
  'Intended Audience :: Developers',
  'Intended Audience :: Science/Research',
  'License :: OSI Approved :: BSD License',
  'Natural Language :: English',
  'Operating System :: MacOS',
  'Operating System :: Microsoft :: Windows',
  'Operating System :: Unix',
  'Programming Language :: Python :: 3 :: Only',
  'Programming Language :: Python :: 3.10',
  'Programming Language :: Python :: 3.11',
  'Programming Language :: Python :: 3.12',
  'Topic :: Scientific/Engineering',
  'Topic :: Software Development',
]
dependencies = [
  'mne >= 1.6',
  'netCDF4 >= 1.6.5',
  'numpy >= 1.21',
  'pandas >= 1.3.2',
  'scikit-learn >= 1.2',
  'scipy >= 1.4.0',
  'tqdm',
  'xarray >= 2023.11.0',
]
description = 'mne-connectivity: A module for connectivity data analysis with MNE.'
dynamic = ["version"]
keywords = [
  'connectivity',
  'eeg',
  'ieeg',
  'meg',
  'neuroscience',
]
license = {file = 'LICENSE'}
maintainers = [
  {email = 'adam.li@columbia.edu', name = 'Adam Li'},
]
name = 'mne-connectivity'
readme = {content-type = "text/x-rst", file = 'README.rst'}
requires-python = '>=3.10'

[project.optional-dependencies]
all = [
  'mne-connectivity[build]',
  'mne-connectivity[doc]',
  'mne-connectivity[gui]',
  'mne-connectivity[style]',
  'mne-connectivity[test]',
  'PyQt6',
]
build = [
  'build',
  'twine',
]
doc = [
  'memory-profiler',
  'mne-bids',
  'mne-connectivity[gui]',
  'nibabel',
  'nilearn',
  'numpydoc',
  'pooch',
  'pydata-sphinx-theme==0.14.1',
  'PyQt6',
  'sphinx',
  'sphinx-copybutton',
  'sphinx-design',
  'sphinx-gallery>=0.17.0',
  'sphinx-issues',
  'sphinx_autodoc_typehints',
  'sphinxcontrib-bibtex',
]
full = [
  'mne-connectivity[all]',
]
gui = [
  'h5netcdf',
  'matplotlib',
  'mne-qt-browser>=0.6.0',
  'pyvista',
  'pyvistaqt',
  'qtpy',
  'sip',
  'vtk',
]
style = [
  "pre-commit",
  'codespell',
  'isort',
  'pydocstyle',
  'pydocstyle[toml]',
  'rstcheck',
  'ruff',
  'toml-sort',
  'yamllint',
]
test = [
  "pytest-timeout",
  'joblib',
  'mne-bids',
  'mne-connectivity[gui]',
  'pandas',
  'pymatreader',
  'pytest',
  'pytest-cov',
  'statsmodels',
]

[project.urls]
documentation = 'https://mne.tools/mne-connectivity'
source = 'https://github.com/mne-tools/mne-connectivity'
tracker = 'https://github.com/mne-tools/mne-connectivity/issues'

[tool.codespell]
builtin = "clear,rare,informal,names,usage"
ignore-words = ".codespellignore"
skip = "doc/references.bib"

[tool.coverage.report]
exclude_lines = [
  'if __name__ == .__main__.:',
  'if TYPE_CHECKING:',
  'pragma: no cover',
]
precision = 2

[tool.coverage.run]
branch = true
cover_pylib = false
omit = [
  '**/__init__.py',
  '**/mne_connectivity/conftest.py',
  '**/tests/**',
]

[tool.isort]
extend_skip_glob = [
  'doc/*',
  'examples/*',
  'setup.py',
]
line_length = 88
multi_line_output = 3
py_version = 39

[tool.mypy]
ignore_missing_imports = true
no_site_packages = true

[tool.pydocstyle]
add_ignore = 'D100,D104,D107'
convention = 'numpy'
ignore-decorators = '(copy_doc|property|.*setter|.*getter|pyqtSlot|Slot)'
match = '^(?!setup|__init__|test_).*\.py'
match-dir = '^mne_connectivity.*'

[tool.pytest.ini_options]
addopts = '--durations 20 --junit-xml=junit-results.xml -v -rfEXs --tb=short --color=yes'
junit_family = 'xunit2'
minversion = '6.0'

[tool.rstcheck]
ignore_directives = [
  "autoclass",
  "autofunction",
  "automodule",
  "autosummary",
  "bibliography",
  "cssclass",
  "currentmodule",
  "dropdown",
  "footbibliography",
  "glossary",
  "graphviz",
  "grid",
  "highlight",
  "minigallery",
  "rst-class",
  "tab-set",
  "tabularcolumns",
  "toctree",
]
ignore_messages = "^.*(Unknown target name|Undefined substitution referenced)[^`]*$"
ignore_roles = [
  "attr",
  "class",
  "doc",
  "eq",
  "exc",
  "file",
  "footcite",
  "footcite:t",
  "func",
  "gh",
  "kbd",
  "meth",
  "mod",
  "newcontrib",
  "pr",
  "py:mod",
  "ref",
  "samp",
  "term",
]
report_level = "WARNING"

[tool.ruff]
extend-exclude = [
  'benchmarks',
  'doc',
  'setup.py',
]
line-length = 88

[tool.ruff.lint]
ignore = [
  "D100", # Missing docstring in public module
  "D104", # Missing docstring in public package
  "D413", # Missing blank line after last section
  "UP008", # TODO: Use `super()`
  "UP031", # TODO: Use format specifiers
]
select = ["A", "B006", "D", "E", "F", "I", "UP", "W"]

[tool.ruff.lint.per-file-ignores]
'__init__.py' = ['F401']
'examples/*.py' = ["D205"]
'mne_connectivity/base.py' = ["D101", "D102", "D105"]

[tool.ruff.lint.pydocstyle]
convention = "numpy"
ignore-decorators = [
  "mne.utils.copy_doc",
  "mne.utils.copy_function_doc_to_method_doc",
  "mne.utils.deprecated",
  "property",
  "setter",
]

[tool.setuptools]
include-package-data = true

[tool.setuptools.packages.find]
exclude = ['mne_connectivity*tests']
include = ['mne_connectivity*']

[tool.setuptools_scm]
version_scheme = "release-branch-semver"

[tool.tomlsort]
all = true
ignore_case = true
trailing_comma_inline_array = true