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Add intersphinx_registry and toml-sort (#1314)
* use intersphinx_registry * add 'intersphinx_registry' dependency * add toml-sort to pre-commit * apply sort to pyproject.toml * fix * add config and let pre-commit push the sort * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Update pyproject.toml * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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‎.pre-commit-config.yaml‎

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- id: check-added-large-files
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- id: check-case-conflict
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- id: check-docstring-first
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- repo: https://github.com/pappasam/toml-sort
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rev: v0.23.1
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hooks:
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- id: toml-sort-fix
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files: pyproject.toml

‎doc/conf.py‎

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import sys
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from datetime import date
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from intersphinx_registry import get_intersphinx_mapping
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from sphinx.config import is_serializable
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import mne_bids
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html_sidebars = {}
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# Example configuration for intersphinx: refer to the Python standard library.
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intersphinx_mapping = {
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"python": ("https://docs.python.org/3", None),
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"mne": ("https://mne.tools/dev", None),
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"mne-gui-addons": ("https://mne.tools/mne-gui-addons", None),
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"numpy": ("https://numpy.org/devdocs", None),
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"scipy": ("https://scipy.github.io/devdocs", None),
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"matplotlib": ("https://matplotlib.org/stable", None),
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"nilearn": ("http://nilearn.github.io/stable", None),
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"pandas": ("https://pandas.pydata.org/pandas-docs/dev", None),
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"nibabel": ("https://nipy.org/nibabel", None),
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}
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intersphinx_mapping = get_intersphinx_mapping(
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packages={
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"matplotlib",
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"mne",
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"nibabel",
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"nilearn",
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"numpy",
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"pandas",
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"python",
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"scipy",
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}
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)
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intersphinx_mapping["mne-gui-addons"] = ("https://mne.tools/mne-gui-addons", None)
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intersphinx_timeout = 5
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sphinx_gallery_conf = {

‎pyproject.toml‎

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[build-system]
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requires = ["hatchling", "hatch-vcs"]
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build-backend = "hatchling.build"
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requires = ["hatch-vcs", "hatchling"]
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[project]
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name = "mne-bids"
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authors = [{name = "The MNE-BIDS developers"}]
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classifiers = [
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"Intended Audience :: Developers",
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"Intended Audience :: Science/Research",
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"License :: OSI Approved",
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"Operating System :: MacOS",
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"Operating System :: Microsoft :: Windows",
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"Operating System :: POSIX :: Linux",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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"Programming Language :: Python",
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"Topic :: Scientific/Engineering",
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"Topic :: Scientific/Engineering",
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"Topic :: Software Development",
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]
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dependencies = ["mne>=1.6", "numpy>=1.21.2", "scipy>=1.7.1"]
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description = "MNE-BIDS: Organizing MEG, EEG, and iEEG data according to the BIDS specification and facilitating their analysis with MNE-Python"
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dynamic = ["version"]
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authors = [{ name = "The MNE-BIDS developers" }]
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maintainers = [
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{ name = "Stefan Appelhoff", email = "[email protected]" },
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]
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license = { text = "BSD-3-Clause" }
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readme = { file = "README.md", content-type = "text/markdown" }
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requires-python = ">=3.10"
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keywords = [
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"meg",
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"eeg",
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"ieeg",
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"bids",
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"brain imaging data structure",
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"neuroscience",
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"neuroimaging",
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"bids",
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"brain imaging data structure",
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"eeg",
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"ieeg",
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"meg",
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"neuroimaging",
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"neuroscience",
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]
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classifiers = [
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"Topic :: Scientific/Engineering",
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"Intended Audience :: Science/Research",
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"Intended Audience :: Developers",
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"License :: OSI Approved",
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"Topic :: Software Development",
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"Topic :: Scientific/Engineering",
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"Operating System :: Microsoft :: Windows",
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"Operating System :: POSIX :: Linux",
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"Operating System :: MacOS",
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"Programming Language :: Python",
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"Programming Language :: Python :: 3.10",
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"Programming Language :: Python :: 3.11",
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"Programming Language :: Python :: 3.12",
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license = {text = "BSD-3-Clause"}
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maintainers = [
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{email = "[email protected]", name = "Stefan Appelhoff"},
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]
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scripts = { mne_bids = "mne_bids.commands.run:main" }
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dependencies = ["mne>=1.6", "numpy>=1.21.2", "scipy>=1.7.1"]
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name = "mne-bids"
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readme = {content-type = "text/markdown", file = "README.md"}
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requires-python = ">=3.10"
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scripts = {mne_bids = "mne_bids.commands.run:main"}
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[project.optional-dependencies]
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# Variants with dependencies that will get installed on top of those listed unter
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# project.dependencies
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# Dependencies for developer installations
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dev = ["mne_bids[test,doc,full]", "pre-commit"]
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# Dependencies for building the documentation
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doc = [
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"intersphinx_registry",
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"matplotlib",
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"mne-nirs",
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"nilearn",
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"numpydoc",
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"openneuro-py",
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"pandas",
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"pillow",
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"pydata-sphinx-theme",
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"seaborn",
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"sphinx-copybutton",
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"sphinx>=7.4.7",
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"sphinx_gallery",
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]
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# Dependencies for using all mne_bids features
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full = [
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"nibabel >= 3.2.1",
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"pybv >= 0.7.5",
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"eeglabio >= 0.0.2",
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"pymatreader >= 0.0.30",
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"matplotlib >= 3.5.0",
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"pandas >= 1.3.2",
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"EDFlib-Python >= 1.0.6", # XXX: drop once mne <1.7 is no longer supported
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"edfio >= 0.2.1",
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"defusedxml", # For reading EGI MFF data and BrainVision montages
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"defusedxml", # For reading EGI MFF data and BrainVision montages
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"edfio >= 0.2.1",
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"EDFlib-Python >= 1.0.6", # XXX: drop once mne <1.7 is no longer supported
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"eeglabio >= 0.0.2",
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"matplotlib >= 3.5.0",
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"nibabel >= 3.2.1",
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"pandas >= 1.3.2",
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"pybv >= 0.7.5",
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"pymatreader >= 0.0.30",
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]
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# Dependencies for running the test infrastructure
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test = ["mne_bids[full]", "pytest >= 8", "pytest-cov", "pytest-sugar", "ruff"]
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# Dependencies for building the documentation
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doc = [
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"nilearn",
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"sphinx>=7.4.7",
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"sphinx_gallery",
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"sphinx-copybutton",
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"pydata-sphinx-theme",
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"numpydoc",
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"matplotlib",
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"pillow",
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"pandas",
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"mne-nirs",
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"seaborn",
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"openneuro-py",
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]
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# Dependencies for developer installations
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dev = ["mne_bids[test,doc,full]", "pre-commit"]
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[project.urls]
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"Homepage" = "https://mne.tools/mne-bids"
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"Download" = "https://pypi.org/project/mne-bids/#files"
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"Bug Tracker" = "https://github.com/mne-tools/mne-bids/issues/"
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"Documentation" = "https://mne.tools/mne-bids"
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"Download" = "https://pypi.org/project/mne-bids/#files"
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"Forum" = "https://mne.discourse.group/"
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"Homepage" = "https://mne.tools/mne-bids"
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"Source Code" = "https://github.com/mne-tools/mne-bids"
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[tool.hatch.metadata]
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allow-direct-references = true # allow specifying URLs in our dependencies
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[tool.coverage.report]
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# Regexes for lines to exclude from consideration
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exclude_lines = ["if 0:", "if __name__ == .__main__.:", "pragma: no cover"]
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[tool.coverage.run]
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omit = ["*tests*"]
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[tool.hatch.build]
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exclude = [
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"/.*",
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"**/tests",
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"/paper",
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"/examples",
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"/doc",
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"/Makefile",
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"/CITATION.cff",
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"/CONTRIBUTING.md",
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"**/tests",
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"/.*",
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"/CITATION.cff",
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"/CONTRIBUTING.md",
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"/doc",
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"/examples",
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"/Makefile",
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"/paper",
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]
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[tool.hatch.metadata]
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allow-direct-references = true # allow specifying URLs in our dependencies
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[tool.hatch.version]
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raw-options = {version_scheme = "release-branch-semver"}
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source = "vcs"
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raw-options = { version_scheme = "release-branch-semver" }
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[tool.pytest.ini_options]
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addopts = """--durations=20 -ra --junit-xml=junit-results.xml --tb=short
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--ignore=doc --ignore=examples --ignore=mne_bids/tests/data"""
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filterwarnings = [
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"error",
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# Python 3.10+ and NumPy 1.22 (and maybe also newer NumPy versions?)
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"ignore:.*distutils\\.sysconfig module is deprecated.*:DeprecationWarning",
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# NumPy 2.1 bug (probably)
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"ignore:__array__ implementation doesn.*:DeprecationWarning",
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# numba with NumPy dev
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"ignore:`np.MachAr` is deprecated.*:DeprecationWarning",
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"ignore:`product` is deprecated as of NumPy.*:DeprecationWarning",
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"ignore:Converting data files to BrainVision format:RuntimeWarning",
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"ignore:Converting to BV for anonymization:RuntimeWarning",
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"ignore:Converting to FIF for anonymization:RuntimeWarning",
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"ignore:datetime\\.datetime\\.utcfromtimestamp.* is deprecated and scheduled for removal in a future version.*:DeprecationWarning",
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"ignore:Did not find any coordsystem.json.*:RuntimeWarning",
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"ignore:Did not find any electrodes.tsv.*:RuntimeWarning",
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"ignore:Did not find any events.tsv.*:RuntimeWarning",
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"ignore:Estimation of line frequency only supports.*:RuntimeWarning",
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# matplotlib
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"ignore:Figure.*is non-interactive.*cannot be shown:UserWarning",
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"ignore:MEG ref channel RMSP did not.*:RuntimeWarning",
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"ignore:No events found or provided.*:RuntimeWarning",
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"ignore:numpy.ufunc size changed.*:RuntimeWarning",
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"ignore:Participants file not found for.*:RuntimeWarning",
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# old MNE _fake_click
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"ignore:The .*_event function was deprecated in Matplotlib.*:",
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"ignore:There are channels without locations (n/a)*:RuntimeWarning",
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"ignore:tostring\\(\\) is deprecated.*:DeprecationWarning",
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"ignore:Writing of electrodes.tsv is not supported for datatype.*:RuntimeWarning",
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]
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[tool.ruff.lint]
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select = ["A", "D", "E", "F", "I", "UP", "W"]
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ignore = ["A002"]
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exclude = ["__init__.py"]
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ignore = ["A002"]
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select = ["A", "D", "E", "F", "I", "UP", "W"]
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[tool.ruff.lint.pydocstyle]
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convention = "numpy"
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[tool.coverage.run]
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omit = ["*tests*"]
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[tool.coverage.report]
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# Regexes for lines to exclude from consideration
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exclude_lines = ["pragma: no cover", "if 0:", "if __name__ == .__main__.:"]
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[tool.pytest.ini_options]
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addopts = """--durations=20 -ra --junit-xml=junit-results.xml --tb=short
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--ignore=doc --ignore=examples --ignore=mne_bids/tests/data"""
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filterwarnings = [
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"error",
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"ignore:Estimation of line frequency only supports.*:RuntimeWarning",
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"ignore:There are channels without locations (n/a)*:RuntimeWarning",
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"ignore:Did not find any electrodes.tsv.*:RuntimeWarning",
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"ignore:Did not find any coordsystem.json.*:RuntimeWarning",
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"ignore:Did not find any events.tsv.*:RuntimeWarning",
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"ignore:No events found or provided.*:RuntimeWarning",
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"ignore:Participants file not found for.*:RuntimeWarning",
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"ignore:Converting to FIF for anonymization:RuntimeWarning",
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"ignore:Converting to BV for anonymization:RuntimeWarning",
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"ignore:Converting data files to BrainVision format:RuntimeWarning",
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"ignore:Writing of electrodes.tsv is not supported for datatype.*:RuntimeWarning",
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"ignore:numpy.ufunc size changed.*:RuntimeWarning",
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"ignore:tostring\\(\\) is deprecated.*:DeprecationWarning",
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"ignore:MEG ref channel RMSP did not.*:RuntimeWarning",
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"ignore:`product` is deprecated as of NumPy.*:DeprecationWarning",
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# Python 3.10+ and NumPy 1.22 (and maybe also newer NumPy versions?)
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"ignore:.*distutils\\.sysconfig module is deprecated.*:DeprecationWarning",
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# numba with NumPy dev
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"ignore:`np.MachAr` is deprecated.*:DeprecationWarning",
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# old MNE _fake_click
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"ignore:The .*_event function was deprecated in Matplotlib.*:",
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"ignore:datetime\\.datetime\\.utcfromtimestamp.* is deprecated and scheduled for removal in a future version.*:DeprecationWarning",
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# matplotlib
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"ignore:Figure.*is non-interactive.*cannot be shown:UserWarning",
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# NumPy 2.1 bug (probably)
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"ignore:__array__ implementation doesn.*:DeprecationWarning",
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]
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[tool.tomlsort]
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all = true
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ignore_case = true
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spaces_before_inline_comment = 2
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trailing_comma_inline_array = true

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