MNT: Add and apply pre-commit configuration

.git-blame-ignore-revs

@@ -1,3 +1,5 @@
+# Sun Jan 1 12:38:02 2023 -0500 - [email protected] - STY: Run pre-commit config on all files
+d14c1cf282a9c3b19189f490f10c35f5739e24d1
 # Thu Dec 29 22:53:17 2022 -0500 - [email protected] - STY: Reduce array().astype() and similar constructs
 bf298113da99079c9c7b5e1690e41879828cd472
 # Thu Dec 29 22:32:46 2022 -0500 - [email protected] - STY: pyupgrade --py37-plus
@@ -9,4 +11,4 @@ bf298113da99079c9c7b5e1690e41879828cd472
 # Thu Dec 29 21:32:00 2022 -0500 - [email protected] - STY: isort
 0ab2856cac4d4baae7ab3e2f6d58421db55d807f
 # Thu Dec 29 21:30:29 2022 -0500 - [email protected] - STY: blue
-1a8dd302ff85b1136c81d492509b80e7748339f0
+1a8dd302ff85b1136c81d492509b80e7748339f0

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+exclude: '.*/data/.*'
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+    -   id: trailing-whitespace
+    -   id: end-of-file-fixer
+    -   id: check-yaml
+    -   id: check-json
+    -   id: check-toml
+    -   id: check-added-large-files
+    -   id: check-case-conflict
+    -   id: check-merge-conflict
+    -   id: check-vcs-permalinks
+  - repo: https://github.com/grantjenks/blue
+    rev: v0.9.1
+    hooks:
+      - id: blue
+  - repo: https://github.com/pycqa/isort
+    rev: 5.11.2
+    hooks:
+      - id: isort

Makefile

@@ -38,7 +38,7 @@ RELEASE_VERSION ?= $(SETUPPY_VERSION)
 
 all: build
 
-build: 
+build:
 	$(PYTHON) setup.py config --noisy
 	$(PYTHON) setup.py build
 
@@ -81,6 +81,7 @@ $(WWW_DIR):
 .git-blame-ignore-revs:
 	git log --grep "\[git-blame-ignore-rev\]" --pretty=format:"# %ad - %ae - %s%n%H" \
 		> .git-blame-ignore-revs
+	echo >> .git-blame-ignore-revs
 
 #
 # Tests

Makefile.win

@@ -1,6 +1,6 @@
 # Makefile NiBabel under Windows using a standard Python distribution
 
-installer: 
+installer:
 	# now the installer
 	python setup.py bdist_wininst
 

bin/nib-ls

@@ -13,6 +13,5 @@ Output a summary table for neuroimaging files (resolution, dimensionality, etc.)
 
 from nibabel.cmdline.ls import main
 
-
 if __name__ == '__main__':
     main()

bin/nib-nifti-dx

@@ -7,7 +7,7 @@
 #   copyright and license terms.
 #
 ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
-""" Print nifti diagnostics for header files """
+"""Print nifti diagnostics for header files"""
 
 from nibabel.cmdline.nifti_dx import main
 

bin/parrec2nii

@@ -4,6 +4,5 @@
 
 from nibabel.cmdline.parrec2nii import main
 
-
 if __name__ == '__main__':
     main()

doc/source/README.txt

@@ -16,7 +16,7 @@ Discover available make targets::
   make help
 
 Clean up previous build::
-  
+
   make clean
 
 Build html documentation::

doc/source/_templates/indexsidebar.html

@@ -19,4 +19,3 @@ <h3>Search mailing list archive</h3>
 <input name="userquery" size="18" type="text" /> <input type="submit" value="Go" />
 <input name="q" type="hidden" />
 </form>
-

doc/source/conf.py

@@ -42,8 +42,9 @@
 try:
     import nibabel
 except ImportError:
-    raise RuntimeError('Need nibabel on Python PATH; consider "make htmldoc" '
-                       'from nibabel root directory')
+    raise RuntimeError(
+        'Need nibabel on Python PATH; consider "make htmldoc" from nibabel root directory'
+    )
 
 # -- General configuration ----------------------------------------------------
 
@@ -55,23 +56,24 @@
     fobj.write(rel['long_description'])
 
 # Load metadata from setup.cfg
-with open(Path("../../pyproject.toml"), 'rb') as fobj:
+with open(Path('../../pyproject.toml'), 'rb') as fobj:
     pyproject = tomllib.load(fobj)
-authors = pyproject["project"]["authors"][0]
+authors = pyproject['project']['authors'][0]
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc',
-              'sphinx.ext.doctest',
-              'sphinx.ext.intersphinx',
-              'sphinx.ext.todo',
-              'sphinx.ext.mathjax',
-              'sphinx.ext.inheritance_diagram',
-              'sphinx.ext.autosummary',
-              'texext.math_dollar',  # has to go before numpydoc
-              'numpydoc',
-              'matplotlib.sphinxext.plot_directive',
-              ]
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.todo',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.inheritance_diagram',
+    'sphinx.ext.autosummary',
+    'texext.math_dollar',  # has to go before numpydoc
+    'numpydoc',
+    'matplotlib.sphinxext.plot_directive',
+]
 
 # Autosummary always wants to use a `generated/` directory.
 # We generate with `make api-stamp`
@@ -85,13 +87,13 @@
 source_suffix = '.rst'
 
 # The encoding of source files.
-#source_encoding = 'utf-8'
+# source_encoding = 'utf-8'
 
 # The master toctree document.
 master_doc = 'index'
 
 # General information about the project.
-project = u'NiBabel'
+project = 'NiBabel'
 copyright = f"2006-2022, {authors['name']} <{authors['email']}>"
 
 # The version info for the project you're documenting, acts as replacement for
@@ -105,11 +107,11 @@
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
 today_fmt = '%B %d, %Y, %H:%M PDT'
 
@@ -124,32 +126,32 @@
 exclude_trees = ['_build']
 
 # The reST default role (used for this markup: `text`) to use for all documents
-#default_role = None
+# default_role = None
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'sphinx'
 
 # A list of ignored prefixes for module index sorting.
-#modindex_common_prefix = []
+# modindex_common_prefix = []
 
 # -- Sphinxext configuration --------------------------------------------------
 
 # Set attributes for layout of inheritance diagrams
-inheritance_graph_attrs = dict(rankdir="LR", size='"6.0, 8.0"', fontsize=14,
-                               ratio='compress')
-inheritance_node_attrs = dict(shape='ellipse', fontsize=14, height=0.75,
-                              color='dodgerblue1', style='filled')
+inheritance_graph_attrs = dict(rankdir='LR', size='"6.0, 8.0"', fontsize=14, ratio='compress')
+inheritance_node_attrs = dict(
+    shape='ellipse', fontsize=14, height=0.75, color='dodgerblue1', style='filled'
+)
 
 # Flag to show todo items in rendered output
 todo_include_todos = True
@@ -168,26 +170,26 @@
 # 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 = {}
+# html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-#html_theme_path = []
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = ''
+# html_title = ''
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+# html_logo = None
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
 # pixels large.
-#html_favicon = None
+# html_favicon = None
 
 # 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,
@@ -196,42 +198,50 @@
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # Content template for the index page.
 html_index = 'index.html'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-html_sidebars = {'index': ['localtoc.html', 'relations.html', 'sourcelink.html',
-                           'indexsidebar.html', 'searchbox.html', 'reggie.html']}
+html_sidebars = {
+    'index': [
+        'localtoc.html',
+        'relations.html',
+        'sourcelink.html',
+        'indexsidebar.html',
+        'searchbox.html',
+        'reggie.html',
+    ]
+}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {'index': 'index.html'}
+# html_additional_pages = {'index': 'index.html'}
 
 # If false, no module index is generated.
-#html_use_modindex = True
+# html_use_modindex = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
 html_show_sourcelink = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = ''
+# html_file_suffix = ''
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'nibabeldoc'
@@ -241,34 +251,32 @@
 # -- Options for LaTeX output -------------------------------------------------
 
 # The paper size ('letter' or 'a4').
-#latex_paper_size = 'letter'
+# latex_paper_size = 'letter'
 
 # The font size ('10pt', '11pt' or '12pt').
-#latex_font_size = '10pt'
+# latex_font_size = '10pt'
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author,
 #  documentclass [howto/manual]).
-latex_documents = [
-    ('index', 'nibabel.tex', u'NiBabel Documentation', u'NiBabel Authors',
-     'manual')]
+latex_documents = [('index', 'nibabel.tex', 'NiBabel Documentation', 'NiBabel Authors', 'manual')]
 
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
-#latex_logo = None
+# latex_logo = None
 
 # For "manual" documents, if this is true, then toplevel headings are parts,
 # not chapters.
-#latex_use_parts = False
+# latex_use_parts = False
 
 # Additional stuff for the LaTeX preamble.
-#latex_preamble = ''
+# latex_preamble = ''
 
 # Documents to append as an appendix to all manuals.
-#latex_appendices = []
+# latex_appendices = []
 
 # If false, no module index is generated.
-#latex_use_modindex = True
+# latex_use_modindex = True
 
 
 # Example configuration for intersphinx: refer to the Python standard library.

doc/source/devel/biaps/biap_0001.rst

@@ -297,4 +297,3 @@ How about the names in the proposal?  ``is_proxy``; ``unproxy=True``?
 
 
 .. vim: ft=rst
-

doc/source/devel/biaps/biap_0003.rst

@@ -41,7 +41,7 @@ From `adding nifti extensions`_:
 * 4 = NIFTI_ECODE_AFNI = AFNI header attributes: The format of the AFNI
   extension in the NIfTI-1.1 format is described at
   http://nifti.nimh.nih.gov/nifti-1/AFNIextension1/
-* 6 = NIFTI_ECODE_COMMENT = comment: arbitrary non-NUL ASCII text, with no  
+* 6 = NIFTI_ECODE_COMMENT = comment: arbitrary non-NUL ASCII text, with no
   additional structure implied
 * 8 = NIFTI_ECODE_XCEDE = XCEDE metadata:
   http://www.nbirn.net/Resources/Users/Applications/xcede/index.htm
@@ -369,7 +369,7 @@ apply to the Cartesian product of the image axis values.  For example, if the
 values of ``applies_to`` == ``['slice', 'time']``, and the slice and time axes
 in the array are lengths (6, 10) respectively, then the values apply to all
 combinations of the 6 possible values for slice indices and the 10 possible
-values for the time indices (ie apply to all 6x10=60 values).  The axis metadata 
+values for the time indices (ie apply to all 6x10=60 values).  The axis metadata
 values in this case can be:
 
 * a scalar. The value applies to every combination of (slice, time)