chore: Clean up doc builds, environment, style checks

.git-blame-ignore-revs

@@ -1,8 +1,10 @@
+# 2024-07-19 - [email protected] - chore(ruff): ruff check --fix && ruff format [git-blame-ignore-rev]
+6333f4735f341e556113325c7bc9d0f2e284e418
 # 2024-03-07 - [email protected] - STY: ruff format smriprep [git-blame-ignore-rev]
 83a50d465145c6e8176c3f13d4673ed4e0bdb26f
 # 2023-11-21 - [email protected] - STY: ruff --fix smriprep [git-blame-ignore-rev]
-3a586cf46cb1bb963b93d9546f20273194d15de5
+5d4743142c43d415b761230d83a471cd5aae0314
 # 2023-11-20 - [email protected] - STY: ruff --fix smriprep [git-blame-ignore-rev]
-c5e8b6b8ddb69284a4cba58e2512b299f1e29464
+946f030e4409bd2fcc044e4a0716ba8af91df247
 # 2023-11-20 - [email protected] - STY: ruff format smriprep [git-blame-ignore-rev]
-8d62c0f3f3c6a911b1dfe2e9a2016b8de7da051a
+d14bcb0d65defd18affb6164867ab665c780637e

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: trailing-whitespace
         exclude: '.gitignore|.*\.gii$'
@@ -11,7 +11,10 @@ repos:
       - id: check-toml
       - id: check-json
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.1
+    rev: v0.5.3
     hooks:
       - id: ruff
+        args: [ --fix ]
       - id: ruff-format
+      - id: ruff
+        args: [ --select, ISC001, --fix ]

docs/.gitignore

@@ -0,0 +1 @@
+api/

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
@@ -41,30 +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",
-    "numpy",
-    "pandas",
-    "seaborn",
-    "skimage",
-    "svgutils",
-    "transforms3d",
+    'matplotlib',
+    'nilearn',
+    'nitime',
+    'pandas',
+    'seaborn',
+    'skimage',
+    'svgutils',
+    'transforms3d',
 ]
 
 # Accept custom section names to be parsed for numpy-style docstrings
@@ -73,41 +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.
@@ -119,7 +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
@@ -130,7 +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.
@@ -146,7 +150,7 @@
 # -- Options for HTMLHelp output ---------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = "smriprepdoc"
+htmlhelp_basename = 'smriprepdoc'
 
 
 # -- Options for LaTeX output ------------------------------------------------
@@ -172,10 +176,10 @@
 latex_documents = [
     (
         master_doc,
-        "smriprep.tex",
-        "sMRIPrep Documentation",
-        "The NiPreps Developers",
-        "manual",
+        'smriprep.tex',
+        'sMRIPrep Documentation',
+        'The NiPreps Developers',
+        'manual',
     ),
 ]
 
@@ -184,7 +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 ----------------------------------------------
@@ -195,12 +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',
     ),
 ]
 
@@ -220,42 +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 ----------------------------------------

env.yml

@@ -10,14 +10,16 @@ dependencies:
   # Intel Math Kernel Library for numpy
   - mkl=2023.2
   - mkl-service=2.4
+  # ANTs is linked against libitk 5.3 but does not pin the version
+  - libitk=5.3
   # Base scientific python stack; required by FSL, so pinned here
   - numpy=1.26
-  - scipy=1.11
+  - scipy=1.13
   - matplotlib=3.8
   - pandas=2.2
-  - h5py=3.10
+  - h5py=3.11
   # Dependencies compiled against numpy, best to stick with conda
-  - scikit-image=0.22
+  - scikit-image=0.23
   - scikit-learn=1.4
   # Utilities
   - graphviz=9.0
@@ -32,3 +34,5 @@ dependencies:
   - pip
   - pip:
     - -r requirements.txt
+variables:
+  FSLOUTPUTTYPE: NIFTI_GZ

pyproject.toml

@@ -141,6 +141,10 @@ source = [
 
 [tool.ruff]
 line-length = 99
+extend-exclude = [
+  "wrapper/*.py",
+  "docs/sphinxext/*",
+]
 
 [tool.ruff.lint]
 extend-select = [
@@ -177,6 +181,7 @@ inline-quotes = "single"
 
 [tool.ruff.lint.extend-per-file-ignores]
 "*/test_*.py" = ["S101"]
+"docs/conf.py" = ["A001"]
 
 [tool.ruff.format]
 quote-style = "single"