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conf.py
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conf.py
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# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# https://www.sphinx-doc.org/en/master/usage/configuration.html
# -- Path setup --------------------------------------------------------------
# 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.
from pkg_resources import get_distribution
# -- Project information -----------------------------------------------------
project = 'NeuroR'
version = get_distribution('neuror').version
release = version
# -- General configuration ---------------------------------------------------
# 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_click.ext',
'sphinx_autorun',
'sphinx.ext.autodoc',
'sphinx.ext.autosummary',
'sphinx.ext.intersphinx',
'sphinx.ext.todo',
'sphinx.ext.viewcode',
'sphinx.ext.napoleon',
]
# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True
suppress_warnings = ["ref.python"]
autosummary_generate = True
autosummary_imported_members = False
autodoc_default_options = {
'members': True,
'show-inheritance': True,
'private-members': (
'_downstream_pathlength,' # from axon
'_similar_section,' # from axon
'_tree_distance,' # from axon
'_get_sholl_proba,' # from main
'_sanitize_one,' # from sanitize
'_fix_downstream,' # from zero_diameter_fixer
'_fix_in_between,' # from zero_diameter_fixer
'_fix_upstream,' # from zero_diameter_fixer
'_get_cut_leaves,' # from cut_plane.cut_leaves
)
}
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
# 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 = []
# -- Options for HTML output -------------------------------------------------
# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.
#
html_theme = 'sphinx-bluebrain-theme'
html_title = 'NeuroR'
html_show_sourcelink = False
html_theme_options = {
"repo_url": "https://github.com/BlueBrain/NeuroR/",
"repo_name": "BlueBrain/NeuroR"
}
intersphinx_mapping = {
"morphio": ("https://morphio.readthedocs.io/en/latest", None),
"neurom": ("https://neurom.readthedocs.io/en/stable", None),
"numpy": ("https://numpy.org/doc/stable/", None),
"pandas": ("https://pandas.pydata.org/docs", None),
"python": ("https://docs.python.org/3", 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 true, do not generate a @detailmenu in the "Top" node's menu.
#texinfo_no_detailmenu = False
from sphinx.ext.autosummary import Autosummary
class AutosummaryOverride(Autosummary):
"""Extends Autosummary to ensure the nosignatures option is set."""
def run(self):
"""Wrap the autodoc output in a div with autodoc class."""
self.options["nosignatures"] = self.options.get("nosignatures", True)
result = super(AutosummaryOverride, self).run()
return result
def add_autosummary_override(app):
"""Override the autosummary definition to ensure no signatures."""
if "sphinx.ext.autosummary" in app.extensions:
app.add_directive("autosummary", AutosummaryOverride, override=True)
def allow_only_neuror(app, what, name, obj, skip, options):
"""Check that the member is part of neuror, exlude otherwise."""
if what in {"module", "class", "exception", "function"} and "neuror" not in getattr(obj, "__module__", ""):
return True
return skip
def setup(app):
app.connect('builder-inited', add_autosummary_override)
app.connect('autodoc-skip-member', allow_only_neuror)