pyproject.toml

[build-system]
build-backend = "hatchling.build"
requires = ["hatch-vcs", "hatchling"]

[project]
authors = [
  {email = "alexandre.gramfort@inria.fr", name = "Alexandre Gramfort"},
]
classifiers = [
  "Intended Audience :: Developers",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved",
  "Operating System :: MacOS",
  "Operating System :: Microsoft :: Windows",
  "Operating System :: POSIX",
  "Operating System :: Unix",
  "Programming Language :: Python :: 3",
  "Programming Language :: Python",
  "Topic :: Scientific/Engineering",
  "Topic :: Software Development",
]
dependencies = [
  "decorator",
  "jinja2",
  "lazy_loader>=0.3",
  "matplotlib>=3.6",
  "numpy>=1.23,<3",
  "packaging",
  "pooch>=1.5",
  "scipy>=1.9",
  "tqdm",
]
description = "MNE-Python project for MEG and EEG data analysis."
dynamic = ["version"]
keywords = [
  "brain",
  "ECoG",
  "EEG",
  "fNIRS",
  "MEG",
  "neuroimaging",
  "neuroscience",
]
license = {text = "BSD-3-Clause"}
maintainers = [{email = "dan@mccloy.info", name = "Dan McCloy"}]
name = "mne"
readme = {content-type = "text/x-rst", file = "README.rst"}
requires-python = ">=3.10"
scripts = {mne = "mne.commands.utils:main"}

[project.optional-dependencies]
# Leave this one here for backward-compat
data = []
dev = ["mne[test,doc]", "rcssmin"]
# Dependencies for building the documentation
doc = [
  "graphviz",
  "intersphinx_registry>=0.2405.27",
  "ipython!=8.7.0",
  "memory_profiler",
  "mne-bids",
  "mne-connectivity",
  "mne-gui-addons",
  "neo",
  "numpydoc",
  "psutil",
  "pydata_sphinx_theme>=0.15.2",
  "pygments>=2.13",
  "pytest",
  "pyxdf",
  "pyzmq!=24.0.0",
  "seaborn!=0.11.2",
  "selenium",
  "sphinx-design",
  "sphinx-gallery>=0.16",
  "sphinx>=6",
  "sphinx_copybutton",
  "sphinxcontrib-bibtex>=2.5",
  "sphinxcontrib-towncrier",
  "sphinxcontrib-youtube",
  # https://github.com/sphinx-contrib/sphinxcontrib-towncrier/issues/92
  "towncrier<24.7",
]
full = ["mne[full-no-qt]", "PyQt6!=6.6.0", "PyQt6-Qt6!=6.6.0,!=6.7.0"]
# Dependencies for full MNE-Python functionality (other than raw/epochs export)
# We first define a variant without any Qt bindings. The "complete" variant, mne[full],
# makes an opinionated choice and installs PyQt6.
# We also offter two more variants: mne[full-qt6] (which is equivalent to mne[full]),
# and mne[full-pyside6], which will install PySide6 instead of PyQt6.
full-no-qt = [
  "antio>=0.4.0",
  "darkdetect",
  "defusedxml",
  "dipy",
  "edfio>=0.2.1",
  "eeglabio",
  "h5py",
  "imageio-ffmpeg>=0.4.1",
  "imageio>=2.6.1",
  "ipyevents",
  "ipympl",
  "ipywidgets",
  "joblib",
  "jupyter",
  "mffpy>=0.5.7",
  "mne-qt-browser",
  "mne[hdf5]",
  "neo",
  "nibabel",
  "nilearn",
  "numba",
  "openmeeg>=2.5.5",
  "pandas",
  "pyarrow", # only needed to avoid a deprecation warning in pandas
  "pybv",
  "pyobjc-framework-Cocoa>=5.2.0; platform_system=='Darwin'",
  "python-picard",
  "pyvista>=0.32,!=0.35.2,!=0.38.0,!=0.38.1,!=0.38.2,!=0.38.3,!=0.38.4,!=0.38.5,!=0.38.6,!=0.42.0",
  "pyvistaqt>=0.4",
  "qdarkstyle!=3.2.2",
  "qtpy",
  "scikit-learn",
  "sip",
  "snirf",
  # duplicated in test_extra:
  "statsmodels",
  "threadpoolctl",
  "traitlets",
  "trame",
  "trame-vtk",
  "trame-vuetify",
  "vtk",
  "xlrd",
]
full-pyqt6 = ["mne[full]"]
full-pyside6 = ["mne[full-no-qt]", "PySide6!=6.7.0"]
# Dependencies for MNE-Python functions that use HDF5 I/O
hdf5 = ["h5io>=0.2.4", "pymatreader"]
# Dependencies for running the test infrastructure
test = [
  "codespell",
  "mypy",
  "numpydoc",
  "pre-commit",
  "pytest-cov",
  "pytest-qt",
  "pytest-timeout",
  "pytest>=8.0.0rc2",
  "ruff",
  "toml-sort",
  "tomli; python_version<'3.11'",
  "twine",
  "vulture",
  "wheel",
]
# Dependencies for being able to run additional tests (rare/CIs/advanced devs)
test_extra = [
  "edfio>=0.2.1",
  "eeglabio",
  "imageio-ffmpeg>=0.4.1",
  "imageio>=2.6.1",
  "mne-bids",
  "mne[test]",
  "nbclient",
  "neo",
  "nitime",
  "pybv",
  "snirf",
  "sphinx-gallery",
  "statsmodels",
]

[project.urls]
"Bug Tracker" = "https://github.com/mne-tools/mne-python/issues/"
Documentation = "https://mne.tools/"
Download = "https://pypi.org/project/mne/#files"
Forum = "https://mne.discourse.group/"
Homepage = "https://mne.tools/"
"Source Code" = "https://github.com/mne-tools/mne-python/"

[tool.bandit.assert_used]
skips = ["*/test_*.py"] # assert statements are good practice with pytest

[tool.changelog-bot]

[tool.changelog-bot.towncrier_changelog]
changelog_skip_label = "no-changelog-entry-needed"
enabled = true
verify_pr_number = true

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

[tool.hatch.build]
exclude = [
  "/*.toml",
  "/*.txt",
  "/*.yaml",
  "/*.yml",
  "/.*",
  "/CITATION.cff",
  "/codemeta.json",
  "/CONTRIBUTING.md",
  "/doc",
  "/examples",
  "/ignore_words.txt",
  "/logo",
  "/Makefile",
  "/mne/**/tests",
  "/tools",
  "/tutorials",
] # tracked by git, but we don't want to ship those files

[tool.hatch.version]
raw-options = {version_scheme = "release-branch-semver"}
source = "vcs"

[tool.mypy]
# Avoid the conflict between mne/__init__.py and mne/__init__.pyi by ignoring the former
exclude = '^mne/(beamformer|channels|commands|datasets|decoding|export|forward|gui|html_templates|inverse_sparse|io|minimum_norm|preprocessing|report|simulation|source_space|stats|time_frequency|utils|viz)?/?__init__\.py$'
ignore_errors = true
modules = ["mne"]
scripts_are_modules = true
strict = false

[[tool.mypy.overrides]]
ignore_missing_imports = true
module = ['scipy.*']

[[tool.mypy.overrides]]
# Ignore "attr-defined" until we fix stuff like:
# - BunchConstNamed: '"BunchConstNamed" has no attribute "FIFFB_EVOKED"'
# - Missing __all__: 'Module "mne.io.snirf" does not explicitly export attribute "read_raw_snirf"'
# Ignore "no-untyped-call" until we fix stuff like:
# - 'Call to untyped function "end_block" in typed context'
# Ignore "no-untyped-def" until we fix stuff like:
# - 'Function is missing a type annotation'
# Ignore "misc" until we fix stuff like:
# - 'Cannot determine type of "_projector" in base class "ProjMixin"'
# Ignore "assignment" until we fix stuff like:
# - 'Incompatible types in assignment (expression has type "tuple[str, ...]", variable has type "str")'
# Ignore "operator" until we fix stuff like:
# - Unsupported operand types for - ("None" and "int")
disable_error_code = [
  'assignment',
  'attr-defined',
  'misc',
  'no-untyped-call',
  'no-untyped-def',
  'operator',
]
ignore_errors = false
module = ['mne.annotations', 'mne.epochs', 'mne.evoked', 'mne.io']

[tool.pytest.ini_options]
# -r f (failed), E (error), s (skipped), x (xfail), X (xpassed), w (warnings)
# don't put in xfail for pytest 8.0+ because then it prints the tracebacks,
# which look like real errors
addopts = """--durations=20 --doctest-modules -rfEXs --cov-report= --tb=short \
    --cov-branch --doctest-ignore-import-errors --junit-xml=junit-results.xml \
    --ignore=doc --ignore=logo --ignore=examples --ignore=tutorials \
    --ignore=mne/gui/_*.py --ignore=mne/icons --ignore=tools \
    --ignore=mne/report/js_and_css \
    --color=yes --capture=sys"""
junit_family = "xunit2"

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

[tool.ruff]
exclude = ["__init__.py", "constants.py", "resources.py"]

[tool.ruff.lint]
ignore = [
  "D100", # Missing docstring in public module
  "D104", # Missing docstring in public package
  "D413", # Missing blank line after last section
]
select = ["A", "B006", "D", "E", "F", "I", "UP", "UP031", "W"]

[tool.ruff.lint.per-file-ignores]
"examples/*/*.py" = [
  "D205", # 1 blank line required between summary line and description
  "D400", # First line should end with a period
]
"examples/preprocessing/eeg_bridging.py" = [
  "E501", # line too long
]
"mne/datasets/*/*.py" = [
  "D103", # Missing docstring in public function
]
"mne/decoding/tests/test_*.py" = [
  "E402", # Module level import not at top of file
]
"mne/utils/tests/test_docs.py" = [
  "D101", # Missing docstring in public class
  "D410", # Missing blank line after section
  "D411", # Missing blank line before section
  "D414", # Section has no content
]
"tutorials/*/*.py" = [
  "D400", # First line should end with a period
]
"tutorials/time-freq/10_spectrum_class.py" = [
  "E501", # line too long
]

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

[tool.towncrier]
directory = "doc/changes/devel/"
filename = "doc/changes/devel.rst"
issue_format = "`#{issue} <https://github.com/mne-tools/mne-python/pull/{issue}>`__"
package = "mne"
title_format = "{version} ({project_date})"

[[tool.towncrier.type]]
directory = "notable"
name = "Notable changes"
showcontent = true

[[tool.towncrier.type]]
directory = "dependency"
name = "Dependencies"
showcontent = true

[[tool.towncrier.type]]
directory = "bugfix"
name = "Bugfixes"
showcontent = true

[[tool.towncrier.type]]
directory = "apichange"
name = "API changes by deprecation"
showcontent = true

[[tool.towncrier.type]]
directory = "newfeature"
name = "New features"
showcontent = true

[[tool.towncrier.type]]
directory = "other"
name = "Other changes"
showcontent = true

[tool.vulture]
exclude = [
  'conftest.py',
  'constants.py',
  'mne/viz/backends/_abstract.py',
  'mne/viz/backends/_notebook.py',
  'mne/viz/backends/_qt.py',
]
ignore_decorators = ['@observe']
min_confidence = 60
paths = ['mne', 'tools/vulture_allowlist.py']
verbose = false