Merge remote-tracking branch 'upstream/main' into resampler

.pre-commit-config.yaml

@@ -1,19 +1,21 @@
 exclude: ".*/data/.*"
 repos:
--   repo: https://github.com/pre-commit/pre-commit-hooks
+  - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.4.0
     hooks:
-    -   id: trailing-whitespace
-    -   id: end-of-file-fixer
-    -   id: check-yaml
-    -   id: check-added-large-files
--   repo: https://github.com/psf/black
-    rev: 23.1.0
+      - id: trailing-whitespace
+        exclude: '.*\.svg'
+      - id: end-of-file-fixer
+        exclude: '.*\.svg'
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-added-large-files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.3
     hooks:
-    -   id: black
-        files: ^src/fmripost_aroma/
--   repo: https://github.com/pycqa/isort
-    rev: 5.12.0
-    hooks:
-    -   id: isort
-        files: ^src/fmripost_aroma/
+      - id: ruff
+        args: [ --fix ]
+      - id: ruff-format
+      - id: ruff
+        args: [ --select, ISC001, --fix ]

docs/conf.py

@@ -21,89 +21,89 @@
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
-sys.path.append(os.path.abspath("sphinxext"))
-sys.path.insert(0, os.path.abspath("../wrapper"))
+sys.path.append(os.path.abspath('sphinxext'))
+sys.path.insert(0, os.path.abspath('../wrapper'))
 
 from github_link import make_linkcode_resolve  # noqa: E402
 
 # -- General configuration ------------------------------------------------
 
 # If your documentation needs a minimal Sphinx version, state it here.
-needs_sphinx = "1.5.3"
+needs_sphinx = '1.5.3'
 
 # 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.coverage",
-    "sphinx.ext.mathjax",
-    "sphinx.ext.linkcode",
-    "sphinx.ext.napoleon",
-    "sphinxarg.ext",  # argparse extension
-    "nipype.sphinxext.plot_workflow",
+    'sphinx.ext.autodoc',
+    'sphinx.ext.doctest',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.linkcode',
+    'sphinx.ext.napoleon',
+    'sphinxarg.ext',  # argparse extension
+    'nipype.sphinxext.plot_workflow',
 ]
 
 # Mock modules in autodoc:
 autodoc_mock_imports = [
-    "numpy",
-    "nitime",
-    "matplotlib",
+    'numpy',
+    'nitime',
+    'matplotlib',
 ]
 
-if pver.parse(sphinxversion) >= pver.parse("1.7.0"):
+if pver.parse(sphinxversion) >= pver.parse('1.7.0'):
     autodoc_mock_imports += [
-        "pandas",
-        "nilearn",
-        "seaborn",
+        'pandas',
+        'nilearn',
+        'seaborn',
     ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ["_templates"]
+templates_path = ['_templates']
 
 # Accept custom section names to be parsed for numpy-style docstrings
 # of parameters.
 # Requires pinning sphinxcontrib-napoleon to a specific commit while
 # https://github.com/sphinx-contrib/napoleon/pull/10 is merged.
 napoleon_use_param = False
 napoleon_custom_sections = [
-    ("Inputs", "Parameters"),
-    ("Outputs", "Parameters"),
+    ('Inputs', 'Parameters'),
+    ('Outputs', 'Parameters'),
 ]
 
 # 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 encoding of source files.
 # source_encoding = "utf-8-sig"
 
 # The master toctree document.
-master_doc = "index"
+master_doc = 'index'
 
 # General information about the project.
-project = "fMRIPost-AROMA"
-author = "The fMRIPost-AROMA developers"
-copyright = f"2016-, {author}"
+project = 'fMRIPost-AROMA'
+author = 'The fMRIPost-AROMA developers'
+copyright = f'2016-, {author}'
 
 # 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 short X.Y version.
-version = "version"
+version = 'version'
 # The full version, including alpha/beta/rc tags.
-release = "version"
+release = 'version'
 
 # 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'
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -114,7 +114,7 @@
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
 # This patterns also effect to html_static_path and html_extra_path
-exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 
 # The reST default role (used for this markup: `text`) to use for all
 # documents.
@@ -132,7 +132,7 @@
 # show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = "sphinx"
+pygments_style = 'sphinx'
 
 # A list of ignored prefixes for module index sorting.
 # modindex_common_prefix = []
@@ -148,7 +148,7 @@
 
 # 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
@@ -177,7 +177,7 @@
 # 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']
 
 # Add any extra paths that contain custom files (such as robots.txt or
 # .htaccess) here, relative to this directory. These files are copied
@@ -242,7 +242,7 @@
 # html_search_scorer = 'scorer.js'
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "fmripost_aroma_doc"
+htmlhelp_basename = 'fmripost_aroma_doc'
 
 # -- Options for LaTeX output ---------------------------------------------
 
@@ -261,7 +261,7 @@
 # (source start file, target name, title,
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
-    (master_doc, "fmripost_aroma.tex", "fMRIPost-AROMA Documentation", author, "manual"),
+    (master_doc, 'fmripost_aroma.tex', 'fMRIPost-AROMA Documentation', author, 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -289,7 +289,7 @@
 
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
-man_pages = [(master_doc, "fmripost-aroma", "fMRIPost-AROMA Documentation", [author], 1)]
+man_pages = [(master_doc, 'fmripost-aroma', 'fMRIPost-AROMA Documentation', [author], 1)]
 
 # If true, show URL addresses after external links.
 # man_show_urls = False
@@ -303,12 +303,12 @@
 texinfo_documents = [
     (
         master_doc,
-        "fMRIPost-AROMA",
-        "fMRIPost-AROMA Documentation",
+        'fMRIPost-AROMA',
+        'fMRIPost-AROMA Documentation',
         author,
-        "fMRIPost-AROMA",
-        "One line description of project.",
-        "Miscellaneous",
+        'fMRIPost-AROMA',
+        'One line description of project.',
+        'Miscellaneous',
     ),
 ]
 
@@ -326,31 +326,31 @@
 
 # The following is used by sphinx.ext.linkcode to provide links to github
 linkcode_resolve = make_linkcode_resolve(
-    "fmripost_aroma",
-    "https://github.com/nipreps/fMRIPost-AROMA/blob/{revision}/{package}/{path}#L{lineno}",
+    'fmripost_aroma',
+    'https://github.com/nipreps/fMRIPost-AROMA/blob/{revision}/{package}/{path}#L{lineno}',
 )
 
 # Example configuration for intersphinx: refer to the Python standard library.
 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/stable/", 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),
-    "fmriprep": ("https://fmriprep.org/en/stable/", None),
-    "sdcflows": ("https://www.nipreps.org/sdcflows/", None),
-    "smriprep": ("https://www.nipreps.org/smriprep/", None),
-    "templateflow": ("https://www.templateflow.org/python-client", None),
-    "tedana": ("https://tedana.readthedocs.io/en/latest/", 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/stable/', 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),
+    'fmriprep': ('https://fmriprep.org/en/stable/', None),
+    'sdcflows': ('https://www.nipreps.org/sdcflows/', None),
+    'smriprep': ('https://www.nipreps.org/smriprep/', None),
+    'templateflow': ('https://www.templateflow.org/python-client', None),
+    'tedana': ('https://tedana.readthedocs.io/en/latest/', None),
 }
 
-suppress_warnings = ["image.nonlocal_uri"]
+suppress_warnings = ['image.nonlocal_uri']
 
 
 def setup(app):
-    app.add_css_file("theme_overrides.css")
+    app.add_css_file('theme_overrides.css')
     # We need this for the boilerplate script
-    app.add_js_file("https://cdn.rawgit.com/chrisfilo/zenodo.js/v0.1/zenodo.js")
+    app.add_js_file('https://cdn.rawgit.com/chrisfilo/zenodo.js/v0.1/zenodo.js')

docs/sphinxext/github_link.py

@@ -10,16 +10,16 @@
 from functools import partial
 from operator import attrgetter
 
-REVISION_CMD = "git rev-parse --short HEAD"
+REVISION_CMD = 'git rev-parse --short HEAD'
 
 
 def _get_git_revision():
     try:
         revision = subprocess.check_output(REVISION_CMD.split()).strip()
     except (subprocess.CalledProcessError, OSError):
-        print("Failed to execute git to get revision")
+        print('Failed to execute git to get revision')
         return None
-    return revision.decode("utf-8")
+    return revision.decode('utf-8')
 
 
 def _linkcode_resolve(domain, info, package, url_fmt, revision):
@@ -39,14 +39,14 @@ def _linkcode_resolve(domain, info, package, url_fmt, revision):
 
     if revision is None:
         return
-    if domain not in ("py", "pyx"):
+    if domain not in ('py', 'pyx'):
         return
-    if not info.get("module") or not info.get("fullname"):
+    if not info.get('module') or not info.get('fullname'):
         return
 
-    class_name = info["fullname"].split(".")[0]
-    module = __import__(info["module"], fromlist=[class_name])
-    obj = attrgetter(info["fullname"])(module)
+    class_name = info['fullname'].split('.')[0]
+    module = __import__(info['module'], fromlist=[class_name])
+    obj = attrgetter(info['fullname'])(module)
 
     # Unwrap the object to get the correct source
     # file in case that is wrapped by a decorator
@@ -68,7 +68,7 @@ def _linkcode_resolve(domain, info, package, url_fmt, revision):
     try:
         lineno = inspect.getsourcelines(obj)[1]
     except Exception:
-        lineno = ""
+        lineno = ''
     return url_fmt.format(revision=revision, package=package, path=fn, lineno=lineno)
 
 

pyproject.toml

@@ -116,12 +116,51 @@ exclude_lines = [
   "if TYPE_CHECKING:",
 ]
 
+# Disable black
 [tool.black]
-line-length = 99
-target-version = ['py39']
-
-[tool.isort]
-profile = 'black'
+exclude = ".*"
 
 [tool.ruff]
 line-length = 99
+
+[tool.ruff.lint]
+extend-select = [
+  "F",
+  "E",
+  "W",
+  "I",
+  "UP",
+  "YTT",
+  "S",
+  "BLE",
+  "B",
+  "A",
+  # "CPY",
+  "C4",
+  "DTZ",
+  "T10",
+  # "EM",
+  "EXE",
+  "FA",
+  "ISC",
+  "ICN",
+  "PT",
+  "Q",
+]
+ignore = [
+  "S311",  # We are not using random for cryptographic purposes
+  "ISC001",
+  "S603",
+]
+
+[tool.ruff.lint.flake8-quotes]
+inline-quotes = "single"
+
+[tool.ruff.lint.extend-per-file-ignores]
+"*/test_*.py" = ["S101"]
+"fmriprep/utils/debug.py" = ["A002", "T100"]
+"docs/conf.py" = ["A001"]
+"docs/sphinxext/github_link.py" = ["BLE001"]
+
+[tool.ruff.format]
+quote-style = "single"