sphinx/source/conf.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# libCEED documentation build configuration file, created by
# sphinx-quickstart on Tue Jan  7 18:59:28 2020.
#
# 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
# sys.path.insert(0, os.path.abspath('.'))
import glob
import shutil
import sys
import breathe
import os
import subprocess
from sphinxcontrib import katex

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

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    "sphinxext_altair.altairplot",
    "breathe",
    "hoverxref.extension",
    "sphinx_design",
    "myst_parser",
    "sphinx_rtd_theme",
    "sphinx.ext.autodoc",
    "sphinx.ext.coverage",
    "sphinx.ext.doctest",
    "sphinx.ext.ifconfig",
    "sphinx.ext.intersphinx",
    "sphinx.ext.githubpages",
    "sphinxcontrib.katex",
    "sphinxcontrib.mermaid",  # still in beta; fails with latexpdf builder
    "sphinx.ext.todo",
    "sphinx.ext.viewcode",
    "sphinxcontrib.bibtex",
    "sphinxcontrib.rsvgconverter",
]

# The following, if true, allows figures, tables and code-blocks to be
# automatically numbered if they have a caption.
numfig = True

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

# The master toctree document.
master_doc = "index"

# General information about the project.
project = "libCEED"
copyright = "2020, LLNL, University of Colorado, University of Illinois, University of Tennesee, and the authors"
with open("../../../AUTHORS") as f:
    authorlist = f.readlines()
author = ", ".join(authorlist)

# 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.
with open("../../../ceed.pc.template") as f:
    pkgconf_version = "unknown"
    for line in f:
        if line.startswith("Version:"):
            pkgconf_version = line.partition(": ")[2]
            break
version = pkgconf_version
# The full version, including alpha/beta/rc tags.
release = pkgconf_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"

# 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 = [
    "examples/README.md",
    "examples/ceed/README.md",
    "examples/fluids/README.md",
    "examples/nek/README.md",
    "examples/petsc/README.md",
    "examples/solid/README.md",
    "examples/deal.II/README.md",
]

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

# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True

# sphinxcontrib-bibtex 2.0 requires listing all bibtex files here
bibtex_bibfiles = [
    "references.bib",
]

myst_enable_extensions = [
    "deflist",
    "dollarmath",
    "html_image",
    "linkify",
    "colon_fence",
]

myst_heading_anchors = 2
myst_url_schemes = ("http", "https", "mailto")

# -- 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_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 = {}

# 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 = ["css"]

# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# This is required for the alabaster theme
# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
html_sidebars = {
    "**": [
        "relations.html",  # needs 'show_related': True theme option to display
        "searchbox.html",
    ]
}

# hoverxref options
hoverxref_auto_ref = True
hoverxref_mathjax = True
hoverxref_role_types = {
    "ref": "modal",
}

latex_macros = r"""
\def \diff {\operatorname{d}\!}
\def \tcolon {\!:\!}
\def \trace {\operatorname{trace}}
"""

# Translate LaTeX macros to KaTeX and add to options for HTML builder
katex_macros = katex.latex_defs_to_katex_macros(latex_macros)
katex_options = "macros: {" + katex_macros + "}"

# -- Options for HTMLHelp output ------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = "libCEEDdoc"


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

latex_engine = "lualatex"

latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').
    #
    # 'papersize': 'letterpaper',
    # The font size ('10pt', '11pt' or '12pt').
    #
    # 'pointsize': '10pt',
    # Additional stuff for the LaTeX preamble.
    #
    "preamble": r"""
\usepackage{amscd}
\usepackage{cancel}
\newcommand\bm[1]{\symbf{#1}}
"""
    + latex_macros,
    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
    "fontpkg": r"""
\usepackage[math-style=ISO,bold-style=ISO]{unicode-math}
\setmainfont{TeX Gyre Pagella}
\setmathfont{TeX Gyre Pagella Math}
\setsansfont{DejaVu Sans}
\setmonofont{DejaVu Sans Mono}
""",
}

latex_logo = "../../img/ceed-full-name-logo.PNG"

latexauthorslist = r" \and ".join(authorlist)

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, "libCEED.tex", "libCEED User Manual", latexauthorslist, "howto"),
]


# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [(master_doc, "libceed", "libCEED User Manual", [author], 1)]


# -- Options for Texinfo output -------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (
        master_doc,
        "libCEED",
        "libCEED User Manual",
        latexauthorslist,
        "libCEED",
        "Efficient implementations of finite element operators.",
        "Miscellaneous",
    ),
]


# -- Options for Epub output ----------------------------------------------

# Bibliographic Dublin Core info.
epub_title = project
epub_author = author
epub_publisher = author
epub_copyright = copyright

# The unique identifier of the text. This can be a ISBN number
# or the project homepage.
#
# epub_identifier = ''

# A unique identification for the text.
#
# epub_uid = ''

# A list of files that should not be packed into the epub file.
epub_exclude_files = ["search.html"]


# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {
    "python": ("https://docs.python.org/3", None),
    "numpy": ("https://numpy.org/devdocs", None),
}


# -- Options for breathe --------------------------------------------------
breathe_projects = {"libCEED": "../../../xml"}
breathe_default_project = "libCEED"
breathe_build_directory = "../build/breathe"
breathe_domain_by_extension = {"c": "c", "h": "c", "cpp": "cpp", "hpp": "cpp"}

# Run Doxygen if building on Read The Docs
rootdir = os.path.join(
    os.path.dirname(__file__),
    os.pardir,
    os.pardir,
    os.pardir)
if os.environ.get("READTHEDOCS"):
    subprocess.check_call(["doxygen", "Doxyfile"], cwd=rootdir)


def mkdir_p(path):
    try:
        os.makedirs(path)
    except FileExistsError:
        pass


# Copy example documentation from source tree
try:
    shutil.rmtree("examples")
except FileNotFoundError:
    pass
for filename in glob.glob(os.path.join(
        rootdir, "examples/**/*.md"), recursive=True):
    destdir = os.path.dirname(os.path.relpath(filename, rootdir))
    mkdir_p(destdir)
    shutil.copy2(filename, destdir)
shutil.copy2(os.path.join(rootdir, "README.md"), ".")

for filename in glob.glob(os.path.join(
        rootdir, "examples/**/*.csv"), recursive=True):
    destdir = os.path.dirname(os.path.relpath(filename, rootdir))
    mkdir_p(destdir)
    shutil.copy2(filename, destdir)