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MAINT: Format (#533)
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@larsoner
larsoner authored Feb 2, 2024
1 parent ed5faa1 commit 017be27
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Showing 76 changed files with 3,357 additions and 2,562 deletions.
3 changes: 1 addition & 2 deletions .github/workflows/docker_tests.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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]
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4 changes: 1 addition & 3 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,4 @@ repos:
hooks:
- id: ruff
args: ["--fix"]
# - id: ruff-format
ci:
skip: [ruff]
- id: ruff-format
182 changes: 107 additions & 75 deletions doc/conf.py
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Original file line number Diff line number Diff line change
@@ -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.
Expand All @@ -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")

Expand All @@ -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])

Expand All @@ -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"
Expand All @@ -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."]
Expand All @@ -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 = {
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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 ---------------------------------------------
Expand All @@ -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",
),
]


Expand All @@ -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)
]


Expand All @@ -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.
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
}
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