pyproject.toml

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

[project]
name = "mne-bids"
description = "MNE-BIDS: Organizing MEG, EEG, and iEEG data according to the BIDS specification and facilitating their analysis with MNE-Python"
dynamic = ["version"]
authors = [{ name = "MNE-BIDS Developers" }]
maintainers = [
    { name = "Stefan Appelhoff", email = "stefan.appelhoff@mailbox.org" },
]
license = { text = "BSD-3-Clause" }
readme = { file = "README.md", content-type = "text/markdown" }
requires-python = ">=3.9"
keywords = [
    "meg",
    "eeg",
    "ieeg",
    "bids",
    "brain imaging data structure",
    "neuroscience",
    "neuroimaging",
]
classifiers = [
    "Topic :: Scientific/Engineering",
    "Intended Audience :: Science/Research",
    "Intended Audience :: Developers",
    "License :: OSI Approved",
    "Topic :: Software Development",
    "Topic :: Scientific/Engineering",
    "Operating System :: Microsoft :: Windows",
    "Operating System :: POSIX :: Linux",
    "Operating System :: MacOS",
    "Programming Language :: Python",
    "Programming Language :: Python :: 3.9",
    "Programming Language :: Python :: 3.10",
    "Programming Language :: Python :: 3.11",
    "Programming Language :: Python :: 3.12",
]
scripts = { mne_bids = "mne_bids.commands.run:main" }
dependencies = ["mne>=1.5", "numpy>=1.21.2", "scipy>=1.7.1"]

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

# Dependencies for using all mne_bids features
full = [
    "nibabel >= 3.2.1",
    "pybv >= 0.7.5",
    "eeglabio >= 0.0.2",
    "pymatreader >= 0.0.30",
    "matplotlib >= 3.5.0",
    "pandas >= 1.3.2",
    "EDFlib-Python >= 1.0.6", # drop once mne <1.7 is no longer supported
    "edfio >= 0.2.1",
    "defusedxml",             # For reading EGI MFF data abd BrainVision monatges
]

# Dependencies for running the test infrastructure
test = ["mne_bids[full]", "pytest < 8", "pytest-cov", "pytest-sugar", "ruff"]

# Dependencies for building the documentation
doc = [
    "nilearn",
    "sphinx",
    "sphinx_gallery",
    "sphinx-copybutton",
    "pydata-sphinx-theme",
    "numpydoc",
    "matplotlib",
    "pillow",
    "pandas",
    "mne-nirs @ https://github.com/mne-tools/mne-nirs/archive/refs/heads/main.zip",
    "seaborn",
    "openneuro-py",
]

# Dependencies for developer installations
dev = ["mne_bids[test,doc,full]", "pre-commit"]

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

[tool.hatch.metadata]
allow-direct-references = true # allow specifying URLs in our dependencies

[tool.hatch.build]
exclude = [
    "/.*",
    "**/tests",
    "/paper",
    "/examples",
    "/doc",
    "/Makefile",
    "/CITATION.cff",
    "/CONTRIBUTING.md",
]

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

[tool.ruff.lint]
select = ["E", "F", "W", "D", "I"]
exclude = ["__init__.py"]

[tool.ruff.lint.pydocstyle]
convention = "numpy"

[tool.coverage.run]
omit = ["*tests*"]

[tool.coverage.report]
# Regexes for lines to exclude from consideration
exclude_lines = ["pragma: no cover", "if 0:", "if __name__ == .__main__.:"]

[tool.pytest.ini_options]
addopts = """--durations=20 -ra --junit-xml=junit-results.xml --tb=short
    --ignore=doc --ignore=examples --ignore=mne_bids/tests/data"""
filterwarnings = [
    "error",
    "ignore:Estimation of line frequency only supports.*:RuntimeWarning",
    "ignore:There are channels without locations (n/a)*:RuntimeWarning",
    "ignore:Did not find any electrodes.tsv.*:RuntimeWarning",
    "ignore:Did not find any coordsystem.json.*:RuntimeWarning",
    "ignore:Did not find any events.tsv.*:RuntimeWarning",
    "ignore:No events found or provided.*:RuntimeWarning",
    "ignore:Participants file not found for.*:RuntimeWarning",
    "ignore:Converting to FIF for anonymization:RuntimeWarning",
    "ignore:Converting to BV for anonymization:RuntimeWarning",
    "ignore:Converting data files to BrainVision format:RuntimeWarning",
    "ignore:Writing of electrodes.tsv is not supported for datatype.*:RuntimeWarning",
    "ignore:numpy.ufunc size changed.*:RuntimeWarning",
    "ignore:tostring\\(\\) is deprecated.*:DeprecationWarning",
    "ignore:MEG ref channel RMSP did not.*:RuntimeWarning",
    "ignore:`product` is deprecated as of NumPy.*:DeprecationWarning",
    # Python 3.10+ and NumPy 1.22 (and maybe also newer NumPy versions?)
    "ignore:.*distutils\\.sysconfig module is deprecated.*:DeprecationWarning",
    # numba with NumPy dev
    "ignore:`np.MachAr` is deprecated.*:DeprecationWarning",
    # old MNE _fake_click
    "ignore:The .*_event function was deprecated in Matplotlib.*:",
    "ignore:datetime\\.datetime\\.utcfromtimestamp.* is deprecated and scheduled for removal in a future version.*:DeprecationWarning",
]