conf.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# NiMARE documentation build configuration file, created by
# sphinx-quickstart
#
# This file is execfile()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.

# 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.
import os
import sys
from datetime import datetime
from distutils.version import LooseVersion

import sphinx
from m2r import MdInclude
from sphinx_gallery.sorting import FileNameSortKey

sys.path.insert(0, os.path.abspath(os.path.pardir))
sys.path.insert(0, os.path.abspath("sphinxext"))

from github_link import make_linkcode_resolve

import nimare

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

# If your documentation needs a minimal Sphinx version, state it here.
needs_sphinx = "3.5"

# generate autosummary even if no references
autosummary_generate = True
add_module_names = False

# 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",  # standard
    "sphinx.ext.autosummary",  # standard
    "sphinx.ext.doctest",  # runs doctests
    "sphinx.ext.intersphinx",  # links code to other packages
    "sphinx.ext.linkcode",  # links to code from api
    "sphinx.ext.napoleon",  # alternative to numpydoc
    "sphinx_copybutton",  # for copying code snippets
    "sphinx_gallery.gen_gallery",  # example gallery
    "sphinxarg.ext",  # argparse
    "sphinxcontrib.bibtex",  # for foot-citations
    "recommonmark",  # markdown parser
]

if LooseVersion(sphinx.__version__) < LooseVersion("1.4"):
    extensions.append("sphinx.ext.pngmath")
else:
    extensions.append("sphinx.ext.imgmath")

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

# source_suffix = ['.rst', '.md']
source_suffix = ".rst"

# The master toctree document.
master_doc = "index"

# General information about the project.
project = "NiMARE"
copyright = "2018-" + datetime.today().strftime("%Y") + ", NiMARE developers"
author = "NiMARE developers"

# 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 = nimare.__version__
# The full version, including alpha/beta/rc tags.
release = nimare.__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 = None

# 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", "utils/*"]

# The reST default role (used for this markup: `text`) to use for all documents.
default_role = "autolink"

# The name of the Pygments (syntax highlighting) style to use.
pygments_style = "default"

# -----------------------------------------------------------------------------
# Napoleon settings
# -----------------------------------------------------------------------------
napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_custom_sections = ["License"]
napoleon_include_init_with_doc = True
napoleon_include_private_with_doc = False
napoleon_include_special_with_doc = False
napoleon_use_admonition_for_examples = True
napoleon_use_admonition_for_notes = True
napoleon_use_admonition_for_references = True
napoleon_use_ivar = True
napoleon_use_param = True
napoleon_use_keyword = True
napoleon_use_rtype = True
napoleon_preprocess_types = False
napoleon_type_aliases = None
napoleon_attr_annotations = True

# -----------------------------------------------------------------------------
# HTML output
# -----------------------------------------------------------------------------
# The theme to use for HTML and HTML Help pages.
# See the documentation for a list of builtin themes.
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 documentation.
html_theme_options = {
    "includehidden": False,  # don't show hidden TOCs in sidebar
}
html_sidebars = {"**": ["globaltoc.html", "relations.html", "searchbox.html", "indexsidebar.html"]}

# 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_favicon = "_static/nimare_favicon.png"
html_logo = "_static/nimare_banner.png"

# -----------------------------------------------------------------------------
# HTMLHelp output
# -----------------------------------------------------------------------------
# Output file base name for HTML help builder.
htmlhelp_basename = "nimaredoc"

# The following is used by sphinx.ext.linkcode to provide links to github
linkcode_resolve = make_linkcode_resolve(
    "nimare",
    "https://github.com/neurostuff/nimare/blob/{revision}/{package}/{path}#L{lineno}",
)

# -----------------------------------------------------------------------------
# intersphinx
# -----------------------------------------------------------------------------
_python_version_str = "{0.major}.{0.minor}".format(sys.version_info)
_python_doc_base = "https://docs.python.org/" + _python_version_str
intersphinx_mapping = {
    "python": (_python_doc_base, None),
    "numpy": ("https://numpy.org/doc/stable/", (None, "./_intersphinx/numpy-objects.inv")),
    "scipy": (
        "https://docs.scipy.org/doc/scipy/reference",
        (None, "./_intersphinx/scipy-objects.inv"),
    ),
    "sklearn": ("https://scikit-learn.org/stable", (None, "./_intersphinx/sklearn-objects.inv")),
    "matplotlib": ("https://matplotlib.org/", (None, "https://matplotlib.org/objects.inv")),
    "pandas": ("https://pandas.pydata.org/pandas-docs/stable/", None),
    "nibabel": ("https://nipy.org/nibabel/", None),
    "nilearn": ("http://nilearn.github.io/stable/", None),
    "pymare": ("https://pymare.readthedocs.io/en/latest/", None),
    "skimage": ("https://scikit-image.org/docs/stable/", None),
}

# -----------------------------------------------------------------------------
# Sphinx gallery
# -----------------------------------------------------------------------------
sphinx_gallery_conf = {
    # path to your examples scripts
    "examples_dirs": "../examples",
    # run examples with a number, then "plot"
    "filename_pattern": "/[0-9]+_plot_",
    # path where to save gallery generated examples
    "gallery_dirs": "auto_examples",
    "backreferences_dir": "generated",
    # Modules for which function level galleries are created.
    # In this case sphinx_gallery and numpy in a tuple of strings.
    "doc_module": ("nimare"),
    "ignore_pattern": r"misc-notebooks/.",
    "reference_url": {
        # The module you locally document uses None
        "nimare": None
    },
    "within_subsection_order": FileNameSortKey,
    "default_thumb_file": "_static/nimare_favicon.png",
    "remove_config_comments": True,
}

# Generate the plots for the gallery
plot_gallery = True

# -----------------------------------------------------------------------------
# sphinxcontrib-bibtex
# -----------------------------------------------------------------------------
bibtex_bibfiles = ["./references.bib"]
bibtex_style = "unsrt"
bibtex_reference_style = "author_year"
bibtex_footbibliography_header = ""


def setup(app):
    """From https://github.com/rtfd/sphinx_rtd_theme/issues/117"""
    app.add_css_file("theme_overrides.css")
    app.add_css_file("nimare.css")
    app.connect("autodoc-process-docstring", generate_example_rst)
    # Fix to https://github.com/sphinx-doc/sphinx/issues/7420
    # from https://github.com/life4/deal/commit/7f33cbc595ed31519cefdfaaf6f415dada5acd94
    # from m2r to make `mdinclude` work
    app.add_config_value("no_underscore_emphasis", False, "env")
    app.add_config_value("m2r_parse_relative_links", False, "env")
    app.add_config_value("m2r_anonymous_references", False, "env")
    app.add_config_value("m2r_disable_inline_math", False, "env")
    app.add_directive("mdinclude", MdInclude)


def generate_example_rst(app, what, name, obj, options, lines):
    # generate empty examples files, so that we don't get
    # inclusion errors if there are no examples for a class / module
    folder = os.path.join(app.srcdir, "generated")
    if not os.path.isdir(folder):
        os.makedirs(folder)
    examples_path = os.path.join(app.srcdir, "generated", "%s.examples" % name)
    if not os.path.exists(examples_path):
        # touch file
        open(examples_path, "w").close()