xref/honee/conf.py

#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# HONEE documentation build configuration file
#
# 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
from pathlib import Path
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.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 = 'HONEE'
copyright = '2024, University of Colorado, LLNS, and other authors'
with open(Path('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(Path('ratel.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 = [
    '.gitlab',
    'VENV*',
    'tests/junit-xml/*',
    'tests/README.md',
    'tests/createPyTorchModel/README.md',
    'RELEASING.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 = ['doc/references.bib']

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

myst_heading_anchors = 2
# Note: The config value `myst_url_schemes' defaults to type `list'
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 = 'furo'

# Project logo
# html_logo = 'doc/img/logo.png'

# Project favicon
# html_favicon = 'doc/img/logo.ico'

# 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 = ['doc/css']

# 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}}
\def \sign {\operatorname{sign}}
\def \Pe {\mathrm{Pe}}
\def \CFL {\mathrm{CFL}}
\def \gbar #1{\overline{g}_{#1}}
\def \mean {\braket}
\def \dt {\Delta t}
"""

# 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 = 'HONEEdoc'


# -- 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}
\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 = 'doc/img/logo.jpg'

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, 'honee.tex', 'HONEE 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, 'honee', 'HONEE 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, 'honee', 'HONEE User Manual', latexauthorslist, 'HONEE', 'High-Order Navier-stokes Equation Evaluator'),
]

# -- 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 = {'HONEE': 'xml'}
breathe_default_project = 'HONEE'
breathe_build_directory = 'doc/build/breathe'
breathe_domain_by_extension = {'c': 'c', 'h': 'c', 'cpp': 'cpp', 'hpp': 'cpp'}
breathe_show_define_initializer = True