conf.py

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#
#   See COPYING file distributed along with the NiBabel package for the
#   copyright and license terms.
#
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#
# nipype documentation build configuration file, created by
# sphinx-quickstart on Mon Jul 20 12:30:18 2009.
#
# This file is exec()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.

import os
from pathlib import Path
from runpy import run_path

try:
    import tomllib
except ImportError:
    import tomli as tomllib

# Check for external Sphinx extensions we depend on
try:
    import numpy as np
except ImportError:
    raise RuntimeError('Need to install "numpy" package for doc build')
try:
    import numpydoc
except ImportError:
    raise RuntimeError('Need to install "numpydoc" package for doc build')
try:
    import texext
except ImportError:
    raise RuntimeError('Need to install "texext" package for doc build')

# Need nibabel installed as well
try:
    import nibabel
except ImportError:
    raise RuntimeError(
        'Need nibabel on Python PATH; consider "make htmldoc" from nibabel root directory'
    )

from packaging.version import Version

if Version(np.__version__) >= Version('1.22'):
    np.set_printoptions(legacy='1.21')

# -- General configuration ----------------------------------------------------

# We load the nibabel release info into a dict by explicit execution
rel = run_path(os.path.join('..', '..', 'nibabel', 'info.py'))

# Write long description from info
with open('_long_description.inc', 'wt') as fobj:
    fobj.write(rel['long_description'])

# Load metadata from setup.cfg
with open(Path('../../pyproject.toml'), 'rb') as fobj:
    pyproject = tomllib.load(fobj)
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',
]

# Autosummary always wants to use a `generated/` directory.
# We generate with `make api-stamp`
# This could change in the future
autosummary_generate = False

# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']

# The suffix of source filenames.
source_suffix = '.rst'

# The encoding of source files.
# source_encoding = 'utf-8'

# The master toctree document.
master_doc = 'index'

# General information about the project.
project = 'NiBabel'
copyright = f"2006, {authors['name']} <{authors['email']}>"

# 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 = nibabel.__version__
# The full version, including alpha/beta/rc tags.
release = version

# The language for content autogenerated by Sphinx. Refer to documentation
# for a list of supported languages.
# language = None

# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
# today = ''
# Else, today_fmt is used as the format for a strftime call.
today_fmt = '%B %d, %Y, %H:%M PDT'

# List of documents that shouldn't be included in the build.
unused_docs = ['api/generated/gen']

# what to put into API doc (just class doc, just init, or both
autoclass_content = 'both'

# List of directories, relative to source directory, that shouldn't be searched
# for source files.
exclude_trees = ['_build']

# The reST default role (used for this markup: `text`) to use for all documents
# default_role = None

# If true, '()' will be appended to :func: etc. cross-reference text.
# 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

# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
# 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 = []

# -- 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'
)

# Flag to show todo items in rendered output
todo_include_todos = True

# -- Options for HTML output --------------------------------------------------

# The theme to use for HTML and HTML Help pages.  Major themes that come with
# Sphinx are currently 'default' and 'sphinxdoc'.
html_theme = 'sphinxdoc'

# The style sheet to use for HTML and HTML Help pages. A file of that name
# must exist either in Sphinx' static/ path, or in one of the custom paths
# given in html_static_path.
html_style = 'nibabel.css'

# 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 = {}

# Add any paths that contain custom themes here, relative to this directory.
# html_theme_path = []

# The name for this set of Sphinx documents.  If None, it defaults to
# "<project> v<release> documentation".
# html_title = ''

# A shorter title for the navigation bar.  Default is the same as html_title.
# 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

# 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

# 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']

# 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'

# 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

# Custom sidebar templates, maps document names to template names.
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'}

# If false, no module index is generated.
# html_use_modindex = True

# If false, no index is generated.
# html_use_index = True

# If true, the index is split into individual pages for each letter.
# 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 = ''

# If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
# html_file_suffix = ''

# Output file base name for HTML help builder.
htmlhelp_basename = 'nibabeldoc'

mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'

# -- Options for LaTeX output -------------------------------------------------

# The paper size ('letter' or 'a4').
# latex_paper_size = 'letter'

# The font size ('10pt', '11pt' or '12pt').
# 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', '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

# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
# latex_use_parts = False

# Additional stuff for the LaTeX preamble.
# latex_preamble = ''

# Documents to append as an appendix to all manuals.
# latex_appendices = []

# If false, no module index is generated.
# latex_use_modindex = True


# 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),
}

# Config of plot_directive
plot_include_source = True
plot_html_show_source_link = False

# Numpy extensions
# ----------------
# Worked out by Steven Silvester in
# https://github.com/scikit-image/scikit-image/pull/1356
numpydoc_show_class_members = False
numpydoc_class_members_toctree = False