pyproject.toml

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

[project]
authors = [{name = "The MNE-BIDS developers"}]
classifiers = [
  "Intended Audience :: Developers",
  "Intended Audience :: Science/Research",
  "License :: OSI Approved",
  "Operating System :: MacOS",
  "Operating System :: Microsoft :: Windows",
  "Operating System :: POSIX :: Linux",
  "Programming Language :: Python :: 3.10",
  "Programming Language :: Python :: 3.11",
  "Programming Language :: Python :: 3.12",
  "Programming Language :: Python",
  "Topic :: Scientific/Engineering",
  "Topic :: Scientific/Engineering",
  "Topic :: Software Development",
]
dependencies = ["mne>=1.7", "numpy>=1.21.2", "scipy>=1.7.1"]
description = "MNE-BIDS: Organizing MEG, EEG, and iEEG data according to the BIDS specification and facilitating their analysis with MNE-Python"
dynamic = ["version"]
keywords = [
  "bids",
  "brain imaging data structure",
  "eeg",
  "ieeg",
  "meg",
  "neuroimaging",
  "neuroscience",
]
license = {text = "BSD-3-Clause"}
maintainers = [
  {email = "stefan.appelhoff@mailbox.org", name = "Stefan Appelhoff"},
]
name = "mne-bids"
readme = {content-type = "text/markdown", file = "README.md"}
requires-python = ">=3.10"
scripts = {mne_bids = "mne_bids.commands.run:main"}

[project.optional-dependencies]
# Dependencies for developer installations
dev = ["mne_bids[test,doc,full]", "pre-commit"]
# Dependencies for building the documentation
doc = [
  "intersphinx_registry",
  "matplotlib",
  "mne-nirs",
  "nilearn",
  "numpydoc",
  "openneuro-py",
  "pandas",
  "pillow",
  "pydata-sphinx-theme",
  "seaborn",
  "sphinx-copybutton",
  "sphinx>=7.4.7",
  "sphinx_gallery @ https://github.com/sphinx-gallery/sphinx-gallery/archive/refs/heads/master.zip",
]
# Dependencies for using all mne_bids features
full = [
  "defusedxml",  # For reading EGI MFF data and BrainVision montages
  "edfio >= 0.2.1",
  "eeglabio >= 0.0.2",
  "matplotlib >= 3.5.0",
  "nibabel >= 3.2.1",
  "pandas >= 1.3.2",
  "pybv >= 0.7.5",
  "pymatreader",
]
# Dependencies for running the test infrastructure
test = ["mne_bids[full]", "pytest >= 8", "pytest-cov", "pytest-sugar", "ruff"]

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

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

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

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

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

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

[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",
  # Python 3.10+ and NumPy 1.22 (and maybe also newer NumPy versions?)
  "ignore:.*distutils\\.sysconfig module is deprecated.*:DeprecationWarning",
  # NumPy 2.1 bug (probably)
  "ignore:__array__ implementation doesn.*:DeprecationWarning",
  # numba with NumPy dev
  "ignore:`np.MachAr` is deprecated.*:DeprecationWarning",
  "ignore:`product` is deprecated as of NumPy.*:DeprecationWarning",
  "ignore:Converting data files to BrainVision format:RuntimeWarning",
  "ignore:Converting to BV for anonymization:RuntimeWarning",
  "ignore:Converting to FIF for anonymization:RuntimeWarning",
  "ignore:datetime\\.datetime\\.utcfromtimestamp.* is deprecated and scheduled for removal in a future version.*:DeprecationWarning",
  "ignore:Did not find any coordsystem.json.*:RuntimeWarning",
  "ignore:Did not find any electrodes.tsv.*:RuntimeWarning",
  "ignore:Did not find any events.tsv.*:RuntimeWarning",
  "ignore:Estimation of line frequency only supports.*:RuntimeWarning",
  # matplotlib
  "ignore:Figure.*is non-interactive.*cannot be shown:UserWarning",
  "ignore:MEG ref channel RMSP did not.*:RuntimeWarning",
  "ignore:No events found or provided.*:RuntimeWarning",
  "ignore:numpy.ufunc size changed.*:RuntimeWarning",
  "ignore:Participants file not found for.*:RuntimeWarning",
  # old MNE _fake_click
  "ignore:The .*_event function was deprecated in Matplotlib.*:",
  "ignore:There are channels without locations (n/a)*:RuntimeWarning",
  "ignore:tostring\\(\\) is deprecated.*:DeprecationWarning",
  "ignore:Writing of electrodes.tsv is not supported for datatype.*:RuntimeWarning",
]

[tool.ruff.lint]
exclude = ["__init__.py"]
ignore = ["A002"]
select = ["A", "D", "E", "F", "I", "UP", "W"]

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

[tool.tomlsort]
all = true
ignore_case = true
spaces_before_inline_comment = 2
trailing_comma_inline_array = true