MAINT: Format

.github/workflows/docker_tests.py

@@ -16,8 +16,7 @@
 print("Validating image")
 want = np.ones(size)
 dists = np.sqrt(
-    np.linspace(-1, 1, size[0])[:, np.newaxis] ** 2
-    + np.linspace(-1, 1, size[1]) ** 2
+    np.linspace(-1, 1, size[0])[:, np.newaxis] ** 2 + np.linspace(-1, 1, size[1]) ** 2
 )
 want = (dists > 0.5).astype(float)
 corr = np.corrcoef(want.ravel(), data.ravel())[0, 1]

.pre-commit-config.yaml

@@ -5,6 +5,4 @@ repos:
     hooks:
       - id: ruff
         args: ["--fix"]
-      # - id: ruff-format
-ci:
-    skip: [ruff]
+      - id: ruff-format

doc/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # project-template documentation build configuration file, created by
 # sphinx-quickstart on Mon Jan 18 14:44:12 2016.
@@ -12,18 +11,18 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-from datetime import datetime, timezone
-import sys
 import os
+import sys
 import warnings
-import sphinx.util.logging
-from sphinx_gallery.sorting import FileNameSortKey
+from datetime import datetime, timezone
 
-sys.path.append("../")
 import mne
+import sphinx.util.logging
 from mne.fixes import _compare_version
-import mne_nirs
 from mne.tests.test_docstring_parameters import error_ignores
+from sphinx_gallery.sorting import FileNameSortKey
+
+import mne_nirs
 
 sphinx_logger = sphinx.util.logging.getLogger("mne")
 
@@ -42,20 +41,22 @@
 
 # We need to triage which date type we use so that incremental builds work
 # (Sphinx looks at variable changes and rewrites all files if some change)
-copyright = (
+copyright = (  # noqa: A001
     f'2012–{td.year}, MNE Developers. Last updated <time datetime="{td.isoformat()}" class="localized">{td.strftime("%Y-%m-%d %H:%M %Z")}</time>\n'  # noqa: E501
     '<script type="text/javascript">$(function () { $("time.localized").each(function () { var el = $(this); el.text(new Date(el.attr("datetime")).toLocaleString([], {dateStyle: "medium", timeStyle: "long"})); }); } )</script>'  # noqa: E501
 )
 if os.getenv("MNE_FULL_DATE", "false").lower() != "true":
-    copyright = f"2012–{td.year}, {project} Developers. Last updated locally."
+    copyright = f"2012–{td.year}, {project} Developers. Last updated locally."  # noqa: A001, E501
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The full version, including alpha/beta/rc tags.
 release = mne_nirs.__version__
-sphinx_logger.info(f"Building documentation for {project} {release} ({mne_nirs.__file__})")
+sphinx_logger.info(
+    f"Building documentation for {project} {release} ({mne_nirs.__file__})"
+)
 # The short X.Y version.
 version = ".".join(release.split(".")[:2])
 
@@ -68,23 +69,23 @@
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.autosummary',
-    'sphinx.ext.doctest',
-    'sphinx.ext.intersphinx',
-    'sphinx.ext.viewcode',
-    'sphinx_copybutton',
-    'sphinx_gallery.gen_gallery',
-    'numpydoc',
-    'sphinxcontrib.bibtex',
+    "sphinx.ext.autodoc",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.doctest",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.viewcode",
+    "sphinx_copybutton",
+    "sphinx_gallery.gen_gallery",
+    "numpydoc",
+    "sphinxcontrib.bibtex",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
 # generate autosummary even if no references.
 autosummary_generate = True
-autodoc_default_options = {'inherited-members': None}
+autodoc_default_options = {"inherited-members": None}
 
 # The suffix of source filenames.
 source_suffix = ".rst"
@@ -101,7 +102,7 @@
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = ['_build', '_templates']
+exclude_patterns = ["_build", "_templates"]
 
 # A list of ignored prefixes for module index sorting.
 modindex_common_prefix = ["mne_nirs."]
@@ -110,27 +111,48 @@
 # default_role = "py:obj"
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = "sphinx"
 
 
 # NumPyDoc configuration -----------------------------------------------------
 
 numpydoc_class_members_toctree = False
 numpydoc_attributes_as_param_list = True
 numpydoc_validate = True
-numpydoc_validation_checks = {'all'} | set(error_ignores)
+numpydoc_validation_checks = {"all"} | set(error_ignores)
 numpydoc_validation_exclude = {  # set of regex
     # dict subclasses
-    r'\.clear', r'\.get$', r'\.copy$', r'\.fromkeys', r'\.items', r'\.keys',
-    r'\.pop', r'\.popitem', r'\.setdefault', r'\.update', r'\.values',
+    r"\.clear",
+    r"\.get$",
+    r"\.copy$",
+    r"\.fromkeys",
+    r"\.items",
+    r"\.keys",
+    r"\.pop",
+    r"\.popitem",
+    r"\.setdefault",
+    r"\.update",
+    r"\.values",
     # list subclasses
-    r'\.append', r'\.count', r'\.extend', r'\.index', r'\.insert', r'\.remove',
-    r'\.sort',
+    r"\.append",
+    r"\.count",
+    r"\.extend",
+    r"\.index",
+    r"\.insert",
+    r"\.remove",
+    r"\.sort",
     # we currently don't document these properly (probably okay)
-    r'\.__getitem__', r'\.__contains__', r'\.__hash__', r'\.__mul__',
-    r'\.__sub__', r'\.__add__', r'\.__iter__', r'\.__div__', r'\.__neg__',
+    r"\.__getitem__",
+    r"\.__contains__",
+    r"\.__hash__",
+    r"\.__mul__",
+    r"\.__sub__",
+    r"\.__add__",
+    r"\.__iter__",
+    r"\.__div__",
+    r"\.__neg__",
     # copied from sklearn
-    r'mne\.utils\.deprecated',
+    r"mne\.utils\.deprecated",
 }
 numpydoc_xref_param_type = True
 numpydoc_xref_aliases = {
@@ -202,9 +224,9 @@
 }
 
 # sphinxcontrib-bibtex
-bibtex_bibfiles = ['./references.bib', './references-nirs.bib']
-bibtex_style = 'unsrt'
-bibtex_footbibliography_header = ''
+bibtex_bibfiles = ["./references.bib", "./references-nirs.bib"]
+bibtex_style = "unsrt"
+bibtex_footbibliography_header = ""
 
 nitpick_ignore_regex = [
     # Type hints for undocumented types
@@ -216,13 +238,13 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-html_theme = 'pydata_sphinx_theme'
+html_theme = "pydata_sphinx_theme"
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
 # documentation.
 # html_theme_options = {}
-switcher_version_match = 'dev' if release.endswith('dev0') else version
+switcher_version_match = "dev" if release.endswith("dev0") else version
 html_context = {
     "default_mode": "auto",
     # next 3 are for the "edit this page" button
@@ -248,11 +270,11 @@
     "footer_start": ["copyright"],
     "analytics": dict(google_analytics_id="UA-188272121-1"),
     "switcher": {
-        "json_url": 'https://mne.tools/mne-nirs/dev/_static/versions.json',
+        "json_url": "https://mne.tools/mne-nirs/dev/_static/versions.json",
         "version_match": switcher_version_match,
     },
-    'pygment_light_style': 'default',
-    'pygment_dark_style': 'github-dark',
+    "pygment_light_style": "default",
+    "pygment_dark_style": "github-dark",
 }
 
 # The name of an image file (relative to this directory) to place at the top
@@ -268,7 +290,7 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
 
 # If true, links to the reST sources are added to the pages.
 html_show_sourcelink = False
@@ -277,7 +299,7 @@
 html_show_sphinx = False
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'mnenirsdoc'
+htmlhelp_basename = "mnenirsdoc"
 
 
 # -- Options for LaTeX output ---------------------------------------------
@@ -291,8 +313,13 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    ('index', 'project-template.tex', u'project-template Documentation',
-     u'Robert Luke', 'manual'),
+    (
+        "index",
+        "project-template.tex",
+        "project-template Documentation",
+        "Robert Luke",
+        "manual",
+    ),
 ]
 
 
@@ -301,8 +328,7 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [
-    ('index', 'project-template', u'project-template Documentation',
-     [u'Robert Luke'], 1)
+    ("index", "project-template", "project-template Documentation", ["Robert Luke"], 1)
 ]
 
 
@@ -312,9 +338,15 @@
 # (source start file, target name, title, author,
 #  dir menu entry, description, category)
 texinfo_documents = [
-    ('index', 'project-template', u'project-template Documentation',
-     u'Robert Luke', 'project-template', 'One line description of project.',
-     'Miscellaneous'),
+    (
+        "index",
+        "project-template",
+        "project-template Documentation",
+        "Robert Luke",
+        "project-template",
+        "One line description of project.",
+        "Miscellaneous",
+    ),
 ]
 
 # Example configuration for intersphinx: refer to the Python standard library.
@@ -332,14 +364,14 @@
     "statsmodels": ("https://www.statsmodels.org/stable", None),
 }
 
-scrapers = ('matplotlib',)
+scrapers = ("matplotlib",)
 try:
     mne.viz.set_3d_backend(mne.viz.get_3d_backend())
 except Exception:
     report_scraper = None
 else:
     backend = mne.viz.get_3d_backend()
-    if backend in ('notebook', 'pyvistaqt'):
+    if backend in ("notebook", "pyvistaqt"):
         with warnings.catch_warnings():
             warnings.filterwarnings("ignore", category=DeprecationWarning)
             import pyvista
@@ -348,15 +380,16 @@
         scrapers += (
             mne.gui._GUIScraper(),
             mne.viz._brain._BrainScraper(),
-            'pyvista',
+            "pyvista",
         )
     report_scraper = mne.report._ReportScraper()
     scrapers += (report_scraper,)
     del backend
 try:
     import mne_qt_browser
-    _min_ver = _compare_version(mne_qt_browser.__version__, '>=', '0.2')
-    if mne.viz.get_browser_backend() == 'qt' and _min_ver:
+
+    _min_ver = _compare_version(mne_qt_browser.__version__, ">=", "0.2")
+    if mne.viz.get_browser_backend() == "qt" and _min_ver:
         scrapers += (mne.viz._scraper._MNEQtBrowserScraper(),)
 except ImportError:
     pass
@@ -367,33 +400,32 @@
 # instead of in the root."
 # we will store dev docs in a `dev` subdirectory and all other docs in a
 # directory "v" + version_str. E.g., "v0.3"
-if 'dev' in version:
-    filepath_prefix = 'dev'
+if "dev" in version:
+    filepath_prefix = "dev"
 else:
-    filepath_prefix = 'stable'
+    filepath_prefix = "stable"
 
 # sphinx-gallery configuration
 sphinx_gallery_conf = {
-    'doc_module': 'mne_nirs',
-    'backreferences_dir': os.path.join('generated'),
-    'image_scrapers': scrapers,
-    'reference_url': {
-        'mne_nirs': None},
-    'download_all_examples': False,
-    'show_memory': sys.platform.startswith("linux"),
-    'within_subsection_order': FileNameSortKey,
-    'junit': os.path.join('..', 'test-results', 'sphinx-gallery', 'junit.xml'),
-    'binder': {
-    # Required keys
-    'org': 'mne-tools',
-    'repo': 'mne-nirs',
-    'branch': 'gh-pages',  # noqa: E501 Can be any branch, tag, or commit hash. Use a branch that hosts your docs.
-    'binderhub_url': 'https://mybinder.org',  # noqa: E501 Any URL of a binderhub deployment. Must be full URL (e.g. https://mybinder.org).
-        'filepath_prefix': filepath_prefix,  # noqa: E501 A prefix to prepend to any filepaths in Binder links.
-        'dependencies': [
-            '../requirements.txt',
-            '../requirements_doc.txt',
+    "doc_module": "mne_nirs",
+    "backreferences_dir": os.path.join("generated"),
+    "image_scrapers": scrapers,
+    "reference_url": {"mne_nirs": None},
+    "download_all_examples": False,
+    "show_memory": sys.platform.startswith("linux"),
+    "within_subsection_order": FileNameSortKey,
+    "junit": os.path.join("..", "test-results", "sphinx-gallery", "junit.xml"),
+    "binder": {
+        # Required keys
+        "org": "mne-tools",
+        "repo": "mne-nirs",
+        "branch": "gh-pages",  # noqa: E501 Can be any branch, tag, or commit hash. Use a branch that hosts your docs.
+        "binderhub_url": "https://mybinder.org",  # noqa: E501 Any URL of a binderhub deployment. Must be full URL (e.g. https://mybinder.org).
+        "filepath_prefix": filepath_prefix,  # noqa: E501 A prefix to prepend to any filepaths in Binder links.
+        "dependencies": [
+            "../requirements.txt",
+            "../requirements_doc.txt",
         ],
     },
-    'plot_gallery': 'True',  # Avoid annoying str/bool default warning
+    "plot_gallery": "True",  # Avoid annoying str/bool default warning
 }