pyproject.toml

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

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

[project.optional-dependencies]
# Variants with dependencies that will get installed on top of those listed unter
# project.dependencies

# Leave this one here for backward-compat
data = []

# Dependencies for MNE-Python functions that use HDF5 I/O
hdf5 = ["h5io>=0.2.4", "pymatreader"]

# 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 = [
    "mne[hdf5]",
    "qtpy",
    "pyobjc-framework-Cocoa>=5.2.0; platform_system=='Darwin'",
    "sip",
    "scikit-learn",
    "nibabel",
    "openmeeg>=2.5.5",
    "numba",
    "h5py",
    "pandas",
    "pyarrow",  # only needed to avoid a deprecation warning in pandas
    "jupyter",
    "python-picard",
    "joblib",
    "psutil",
    "dipy",
    "vtk",
    "nilearn",
    "xlrd",
    "imageio>=2.6.1",
    "imageio-ffmpeg>=0.4.1",
    "traitlets",
    "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",
    "mffpy>=0.5.7",
    "ipywidgets",
    "ipympl",
    "ipyevents",
    "trame",
    "trame-vtk",
    "trame-vuetify",
    "mne-qt-browser",
    "darkdetect",
    "qdarkstyle!=3.2.2",
    "threadpoolctl",
    # duplicated in test_extra:
    "statsmodels",
    "eeglabio",
    "edfio>=0.2.1",
    "pybv",
    "snirf",
    "defusedxml",
    "neo",
    "antio",
]
full = ["mne[full-no-qt]", "PyQt6!=6.6.0", "PyQt6-Qt6!=6.6.0,!=6.7.0"]
full-pyqt6 = ["mne[full]"]
full-pyside6 = ["mne[full-no-qt]", "PySide6!=6.7.0"]


# Dependencies for running the test infrastructure
test = [
    "pytest>=8.0.0rc2",
    "pytest-cov",
    "pytest-timeout",
    "pytest-qt",
    "ruff",
    "numpydoc",
    "codespell",
    "tomli; python_version<'3.11'",
    "twine",
    "wheel",
    "pre-commit",
    "mypy",
    "vulture",
]

# Dependencies for being able to run additional tests (rare/CIs/advanced devs)
test_extra = [
    "mne[test]",
    "nitime",
    "nbclient",
    "sphinx-gallery",
    "statsmodels",
    "eeglabio",
    "edfio>=0.2.1",
    "pybv",
    "imageio>=2.6.1",
    "imageio-ffmpeg>=0.4.1",
    "snirf",
    "neo",
    "mne-bids",
]

# Dependencies for building the documentation
doc = [
    "sphinx>=6",
    "numpydoc",
    "pydata_sphinx_theme>=0.15.2",
    "sphinx-gallery>=0.16",
    "sphinxcontrib-bibtex>=2.5",
    "sphinxcontrib-towncrier",
    "memory_profiler",
    "neo",
    "seaborn!=0.11.2",
    "sphinx_copybutton",
    "sphinx-design",
    "sphinxcontrib-youtube",
    "mne-bids",
    "pyxdf",
    "mne-connectivity",
    "mne-gui-addons",
    "pygments>=2.13",
    "pytest",
    "graphviz",
    "pyzmq!=24.0.0",
    "ipython!=8.7.0",
    "selenium",
    "intersphinx_registry>=0.2405.27",
    # https://github.com/sphinx-contrib/sphinxcontrib-towncrier/issues/92
    "towncrier<24.7",
]
dev = ["mne[test,doc]", "rcssmin"]

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

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

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

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

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

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

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

[tool.ruff.lint.per-file-ignores]
"tutorials/time-freq/10_spectrum_class.py" = [
    "E501", # line too long
]
"mne/datasets/*/*.py" = [
    "D103", # Missing docstring in public function
]
"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
]
"examples/*/*.py" = [
    "D205", # 1 blank line required between summary line and description
]
"examples/preprocessing/eeg_bridging.py" = [
    "E501", # line too long
]

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

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

[tool.mypy]
ignore_errors = true
scripts_are_modules = true
strict = false
modules = ["mne"]
# 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$'

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

[[tool.mypy.overrides]]
module = ['mne.annotations', 'mne.epochs', 'mne.evoked', 'mne.io']
ignore_errors = false
# 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 = [
    'attr-defined',
    'no-untyped-call',
    'no-untyped-def',
    'misc',
    'assignment',
    'operator',
]

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

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

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