chore(ruff): ruff check --fix && ruff format [git-blame-ignore-rev]

Author: effigies

docs/conf.py

@@ -12,26 +12,31 @@
 #
 import os
 import sys
+
 from packaging.version import Version
 
+from smriprep import (
+    __copyright__ as _copyright,
+)
 from smriprep import (
     __package__ as _package,
+)
+from smriprep import (
     __version__ as _version,
-    __copyright__ as _copyright,
 )
 
-sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "sphinxext")))
+sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), 'sphinxext')))
 
 from github_link import make_linkcode_resolve  # noqa: E402
 
 os.environ['NO_ET'] = '1'
 
-sys.path.insert(0, os.path.abspath("../wrapper"))
+sys.path.insert(0, os.path.abspath('../wrapper'))
 
 # -- Project information -----------------------------------------------------
 project = _package
-copyright = _copyright
-author = "The sMRIPrep Developers"
+copyright = _copyright  # noqa: A001
+author = 'The sMRIPrep Developers'
 
 # The short X.Y version
 version = Version(_version).public
@@ -41,29 +46,29 @@
 
 # -- General configuration ---------------------------------------------------
 extensions = [
-    "sphinx.ext.autodoc",
-    "sphinx.ext.doctest",
-    "sphinx.ext.intersphinx",
-    "sphinx.ext.coverage",
-    "sphinx.ext.mathjax",
-    "sphinx.ext.ifconfig",
-    "sphinx.ext.viewcode",
-    "sphinx.ext.githubpages",
-    "sphinxarg.ext",  # argparse extension
-    "sphinxcontrib.apidoc",
-    "nipype.sphinxext.plot_workflow",
-    "nipype.sphinxext.apidoc",
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.githubpages',
+    'sphinxarg.ext',  # argparse extension
+    'sphinxcontrib.apidoc',
+    'nipype.sphinxext.plot_workflow',
+    'nipype.sphinxext.apidoc',
 ]
 
 autodoc_mock_imports = [
-    "matplotlib",
-    "nilearn",
-    "nitime",
-    "pandas",
-    "seaborn",
-    "skimage",
-    "svgutils",
-    "transforms3d",
+    'matplotlib',
+    'nilearn',
+    'nitime',
+    'pandas',
+    'seaborn',
+    'skimage',
+    'svgutils',
+    'transforms3d',
 ]
 
 # Accept custom section names to be parsed for numpy-style docstrings
@@ -72,41 +77,41 @@
 # https://github.com/sphinx-contrib/napoleon/pull/10 is merged.
 napoleon_use_param = False
 napoleon_custom_sections = [
-    ("Inputs", "Parameters"),
-    ("Outputs", "Parameters"),
-    ("Attributes", "Parameters"),
-    ("Mandatory Inputs", "Parameters"),
-    ("Optional Inputs", "Parameters"),
+    ('Inputs', 'Parameters'),
+    ('Outputs', 'Parameters'),
+    ('Attributes', 'Parameters'),
+    ('Mandatory Inputs', 'Parameters'),
+    ('Optional Inputs', 'Parameters'),
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ["_templates"]
+templates_path = ['_templates']
 
 # The suffix(es) of source filenames.
 # You can specify multiple suffix as a list of string:
 #
 # source_suffix = ['.rst', '.md']
-source_suffix = ".rst"
+source_suffix = '.rst'
 
 # The master toctree document.
-master_doc = "index"
+master_doc = 'index'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = "en"
+language = 'en'
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This pattern also affects html_static_path and html_extra_path.
 exclude_patterns = [
-    "_build",
-    "Thumbs.db",
-    ".DS_Store",
-    "api/modules.rst",
-    "api/smriprep.rst",
+    '_build',
+    'Thumbs.db',
+    '.DS_Store',
+    'api/modules.rst',
+    'api/smriprep.rst',
 ]
 
 # The name of the Pygments (syntax highlighting) style to use.
@@ -118,7 +123,7 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = "sphinx_rtd_theme"
+html_theme = 'sphinx_rtd_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
@@ -129,7 +134,7 @@
 # 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']
 
 # Custom sidebar templates, must be a dictionary that maps document names
 # to template names.
@@ -145,7 +150,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "smriprepdoc"
+htmlhelp_basename = 'smriprepdoc'
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -171,10 +176,10 @@
 latex_documents = [
     (
         master_doc,
-        "smriprep.tex",
-        "sMRIPrep Documentation",
-        "The NiPreps Developers",
-        "manual",
+        'smriprep.tex',
+        'sMRIPrep Documentation',
+        'The NiPreps Developers',
+        'manual',
     ),
 ]
 
@@ -183,7 +188,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "smriprep", "sMRIPrep Documentation", [author], 1)]
+man_pages = [(master_doc, 'smriprep', 'sMRIPrep Documentation', [author], 1)]
 
 
 # -- Options for Texinfo output ----------------------------------------------
@@ -194,12 +199,12 @@
 texinfo_documents = [
     (
         master_doc,
-        "smriprep",
-        "sMRIPrep Documentation",
+        'smriprep',
+        'sMRIPrep Documentation',
         author,
-        "sMRIPrep",
-        "One line description of project.",
-        "Miscellaneous",
+        'sMRIPrep',
+        'One line description of project.',
+        'Miscellaneous',
     ),
 ]
 
@@ -219,42 +224,42 @@
 # epub_uid = ''
 
 # A list of files that should not be packed into the epub file.
-epub_exclude_files = ["search.html"]
+epub_exclude_files = ['search.html']
 
 
 # -- Extension configuration -------------------------------------------------
 
-apidoc_module_dir = "../smriprep"
-apidoc_output_dir = "api"
+apidoc_module_dir = '../smriprep'
+apidoc_output_dir = 'api'
 apidoc_excluded_paths = [
-    "conftest.py",
-    "*/conftest.py",
-    "*/tests/*",
-    "tests/*",
-    "data/*",
-    "conf/*",
+    'conftest.py',
+    '*/conftest.py',
+    '*/tests/*',
+    'tests/*',
+    'data/*',
+    'conf/*',
 ]
 apidoc_separate_modules = True
-apidoc_extra_args = ["--module-first", "-d 1", "-T"]
+apidoc_extra_args = ['--module-first', '-d 1', '-T']
 
 # Options for github links
 # The following is used by sphinx.ext.linkcode to provide links to github
 linkcode_resolve = make_linkcode_resolve(
-    "smriprep",
-    "https://github.com/nipreps/smriprep/blob/{revision}/{package}/{path}#L{lineno}",
+    'smriprep',
+    'https://github.com/nipreps/smriprep/blob/{revision}/{package}/{path}#L{lineno}',
 )
 
 # -- Options for intersphinx extension ---------------------------------------
 intersphinx_mapping = {
-    "python": ("https://docs.python.org/3/", None),
-    "numpy": ("https://numpy.org/doc/stable/", None),
-    "scipy": ("https://docs.scipy.org/doc/scipy/", None),
-    "matplotlib": ("https://matplotlib.org/", None),
-    "bids": ("https://bids-standard.github.io/pybids/", None),
-    "nibabel": ("https://nipy.org/nibabel/", None),
-    "nipype": ("https://nipype.readthedocs.io/en/latest/", None),
-    "niworkflows": ("https://www.nipreps.org/niworkflows/", None),
-    "templateflow": ("https://www.templateflow.org/python-client", None),
+    'python': ('https://docs.python.org/3/', None),
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'scipy': ('https://docs.scipy.org/doc/scipy/', None),
+    'matplotlib': ('https://matplotlib.org/', None),
+    'bids': ('https://bids-standard.github.io/pybids/', None),
+    'nibabel': ('https://nipy.org/nibabel/', None),
+    'nipype': ('https://nipype.readthedocs.io/en/latest/', None),
+    'niworkflows': ('https://www.nipreps.org/niworkflows/', None),
+    'templateflow': ('https://www.templateflow.org/python-client', None),
 }
 
 # -- Options for versioning extension ----------------------------------------

scripts/fetch_templates.py

@@ -23,13 +23,13 @@ def fetch_MNI2009():
     tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz
     tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-brain_probseg.nii.gz
     """
-    template = "MNI152NLin2009cAsym"
+    template = 'MNI152NLin2009cAsym'
 
-    tf.get(template, resolution=(1, 2), desc=None, suffix="T1w")
-    tf.get(template, resolution=(1, 2), desc="brain", suffix="mask")
-    tf.get(template, resolution=1, atlas=None, desc="carpet", suffix="dseg")
-    tf.get(template, resolution=2, desc="fMRIPrep", suffix="boldref")
-    tf.get(template, resolution=1, label="brain", suffix="probseg")
+    tf.get(template, resolution=(1, 2), desc=None, suffix='T1w')
+    tf.get(template, resolution=(1, 2), desc='brain', suffix='mask')
+    tf.get(template, resolution=1, atlas=None, desc='carpet', suffix='dseg')
+    tf.get(template, resolution=2, desc='fMRIPrep', suffix='boldref')
+    tf.get(template, resolution=1, label='brain', suffix='probseg')
 
 
 def fetch_MNI6():
@@ -42,12 +42,12 @@ def fetch_MNI6():
     tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_desc-brain_mask.nii.gz
     tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_atlas-HCP_dseg.nii.gz
     """
-    template = "MNI152NLin6Asym"
+    template = 'MNI152NLin6Asym'
 
-    tf.get(template, resolution=(1, 2), desc=None, suffix="T1w")
-    tf.get(template, resolution=(1, 2), desc="brain", suffix="mask")
+    tf.get(template, resolution=(1, 2), desc=None, suffix='T1w')
+    tf.get(template, resolution=(1, 2), desc='brain', suffix='mask')
     # CIFTI
-    tf.get(template, resolution=2, atlas="HCP", suffix="dseg")
+    tf.get(template, resolution=2, atlas='HCP', suffix='dseg')
 
 
 def fetch_OASIS():
@@ -61,14 +61,14 @@ def fetch_OASIS():
     tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-brain_mask.nii.gz
     tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz
     """
-    template = "OASIS30ANTs"
+    template = 'OASIS30ANTs'
 
-    tf.get(template, resolution=1, desc=None, label=None, suffix="T1w")
-    tf.get(template, resolution=1, label="WM", suffix="probseg")
-    tf.get(template, resolution=1, label="BS", suffix="probseg")
-    tf.get(template, resolution=1, label="brain", suffix="probseg")
-    tf.get(template, resolution=1, label="brain", suffix="mask")
-    tf.get(template, resolution=1, desc="BrainCerebellumExtraction", suffix="mask")
+    tf.get(template, resolution=1, desc=None, label=None, suffix='T1w')
+    tf.get(template, resolution=1, label='WM', suffix='probseg')
+    tf.get(template, resolution=1, label='BS', suffix='probseg')
+    tf.get(template, resolution=1, label='brain', suffix='probseg')
+    tf.get(template, resolution=1, label='brain', suffix='mask')
+    tf.get(template, resolution=1, desc='BrainCerebellumExtraction', suffix='mask')
 
 
 def fetch_fsaverage():
@@ -82,9 +82,9 @@ def fetch_fsaverage():
     tpl-fsaverage/tpl-fsaverage_hemi-L_den-164k_sulc.shape.gii
     tpl-fsaverage/tpl-fsaverage_hemi-R_den-164k_sulc.shape.gii
     """
-    template = "fsaverage"
+    template = 'fsaverage'
 
-    tf.get(template, density="164k", suffix="dseg", extension=".tsv")
+    tf.get(template, density='164k', suffix='dseg', extension='.tsv')
     tf.get(template, density='164k', desc='std', suffix='sphere', extension='.surf.gii')
     tf.get(template, density='164k', suffix='sulc', extension='.shape.gii')
 
@@ -102,7 +102,7 @@ def fetch_fsLR():
     tpl-fsLR/tpl-fsLR_space-fsaverage_hemi-L_den-32k_sphere.surf.gii
     tpl-fsLR/tpl-fsLR_space-fsaverage_hemi-R_den-32k_sphere.surf.gii
     """
-    tf.get("fsLR", density="32k")
+    tf.get('fsLR', density='32k')
 
 
 def fetch_all():
@@ -113,21 +113,21 @@ def fetch_all():
     fetch_fsLR()
 
 
-if __name__ == "__main__":
+if __name__ == '__main__':
     parser = argparse.ArgumentParser(
-        description="Helper script for pre-caching required templates to run fMRIPrep",
+        description='Helper script for pre-caching required templates to run fMRIPrep',
     )
     parser.add_argument(
-        "--tf-dir",
+        '--tf-dir',
         type=os.path.abspath,
-        help="Directory to save templates in. If not provided, templates will be saved to"
-        " `${HOME}/.cache/templateflow`.",
+        help='Directory to save templates in. If not provided, templates will be saved to'
+        ' `${HOME}/.cache/templateflow`.',
     )
     opts = parser.parse_args()
 
     # set envvar (if necessary) prior to templateflow import
     if opts.tf_dir is not None:
-        os.environ["TEMPLATEFLOW_HOME"] = opts.tf_dir
+        os.environ['TEMPLATEFLOW_HOME'] = opts.tf_dir
 
     import templateflow.api as tf