conf.py
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conf.py
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	# -- coding: utf-8 --
	#
	# Configuration file for the Sphinx documentation builder.
	#
	# This file does only contain a selection of the most common options. For a
	# full list see the documentation:
	# http://www.sphinx-doc.org/en/master/config
	__copyright__ = (
	"Copyright (©) 2020-2023 EPFL (Ecole Polytechnique Fédérale de Lausanne)"
	"Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)"
	)
	__license__ = "LGPLv3"


	# -- 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.
	#
	import os
	import re
	import glob
	import shutil
	import subprocess
	import sys
	import jinja2


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

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

	# Number figures
	numfig = True

	# 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.coverage",
	"sphinx.ext.ifconfig",
	"sphinx.ext.intersphinx",
	"sphinx.ext.mathjax",
	"sphinx.ext.viewcode",
	"sphinx_rtd_theme",
	"sphinxcontrib.bibtex",
	"breathe",
	"myst_parser",
	# "sphinx_gallery.gen_gallery",
	"sphinx_copybutton",
	"sphinx_toolbox.collapse",
	]

	read_the_docs_build = os.environ.get("READTHEDOCS", None) == "True"
	cmake_configure = os.environ.get("RUNNING_IN_CMAKE", None) == "True"
	if read_the_docs_build:
	akantu_path = "."
	akantu_source_path = "../../"
	elif cmake_configure:
	akantu_path = "@CMAKE_CURRENT_BINARY_DIR@"
	akantu_source_path = "@CMAKE_SOURCE_DIR@"
	else: # most probably running by hand
	akantu_path = "build-doc"
	akantu_source_path = "../../"
	try:
	os.mkdir(akantu_path)
	except FileExistsError:
	pass


	if (
	akantu_path == "@" + "CMAKE_CURRENT_BINARY_DIR" + "@"
	): # Concatenation is to avoid cmake to replace it
	raise Exception("Something went really wrong")

	sys.path.insert(0, akantu_source_path)

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

	# The suffix(es) of source filenames.
	# You can specify multiple suffix as a list of string:
	#
	source_suffix = [".rst", ".md"]
	# source_suffix = ".rst"

	# The master toctree document.
	master_doc = "index"

	# 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"


	def callback(dir, files):
	keep_re = re.compile(r".*\.(svg\|gif\|png\|md\|rst\|cc\|dat\|py)")
	ignores = []
	for file in files:
	if (not keep_re.match(file) and
	not os.path.isdir(os.path.join(dir, file))):
	ignores.append(file)
	return ignores


	shutil.copytree(
	os.path.join(akantu_source_path, "examples"),
	os.path.join(akantu_source_path, "doc", "dev-doc", "examples"),
	ignore=callback,
	dirs_exist_ok=True,
	)

	# 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 = [
	"CMakeLists.txt",
	"manual/appendix/elements.rst",
	"manual/appendix/material-parameters.rst",
	"manual/constitutive-laws.rst",
	"manual/new-constitutive-laws.rst",
	]

	exclude_patterns.extend(
	glob.glob(
	"examples/*/.rst",
	root_dir=os.path.join(akantu_source_path, "doc", "dev-doc"),
	recursive=True,
	)
	)

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

	primary_domain = "cpp"
	highlight_language = "cpp"

	bibtex_bibfiles = ["manual/manual-bibliography.bib"]

	# -- Project information -----------------------------------------------------

	project = "Akantu"
	copyright = __copyright__
	author = "Nicolas Richart"

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

	# The theme to use for HTML and HTML Help pages. See the documentation for
	# a list of builtin themes.
	#
	# if read_the_docs_build:
	# html_theme = "default"
	# else:
	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 = ["_static"]
	html_logo = "_static/logo_only_akantu.svg"
	# Custom sidebar templates, must be a dictionary that maps document names
	# to template names.
	#
	# The default sidebars (for documents that don't match any pattern) are
	# defined by theme itself. Builtin themes are using these templates by
	# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
	# 'searchbox.html']``.
	#
	# html_sidebars = {}
	html_sidebars = {
	"**": [
	"relations.html", # needs 'show_related': True theme option to display
	"searchbox.html",
	]
	}

	math_eqref_format = "Eq. {number}"

	# MathJax configuration
	mathjax3_config = {
	"tex": {
	"macros": {
	"st": ["\\mathrm{#1}", 1],
	"mat": ["\\mathbf{#1}", 1],
	"half": "\\frac{1}{2}",
	},
	"packages": {"[+]": ["ams"]},
	},
	"loader": {
	"load": ["[tex]/ams"],
	},
	}

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


	# -- Options for LaTeX output ------------------------------------------------
	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{amsmath}""",
	# Latex figure (float) alignment
	#
	# 'figure_align': 'htbp',
	}

	# 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, "Akantu.tex", "Akantu Documentation",
	"Nicolas Richart", "manual"),
	]


	# -- 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, "akantu",
	"Akantu Documentation", [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,
	"Akantu",
	"Akantu Documentation",
	author,
	"Akantu",
	"One line description of project.",
	"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"]


	# -- Extension configuration -------------------------------------------------
	j2_args = {}
	j2_template_path = "."

	if read_the_docs_build or not cmake_configure:
	j2_template_path = "."
	elif cmake_configure:
	j2_template_path = "@CMAKE_CURRENT_SOURCE_DIR@"
	os.makedirs(os.path.join(akantu_path, "_static"), exist_ok=True)
	shutil.copyfile(
	os.path.join("@CMAKE_CURRENT_SOURCE_DIR@", html_logo),
	os.path.join(akantu_path, html_logo),
	)

	j2_args = {
	"akantu_source_path": akantu_source_path,
	}

	print(akantu_path)
	j2_env = jinja2.Environment(
	loader=jinja2.FileSystemLoader(j2_template_path),
	undefined=jinja2.DebugUndefined
	)

	j2_template = j2_env.get_template("akantu.dox.j2")

	with open(os.path.join(akantu_path, "akantu.dox"), "w") as fh:
	fh.write(j2_template.render(j2_args))

	subprocess.run(["doxygen", "akantu.dox"], cwd=akantu_path)

	# print("akantu_path = '{}'".format(akantu_path))
	breathe_projects = {"Akantu": os.path.join(akantu_path, "xml")}
	breathe_default_project = "Akantu"
	breathe_default_members = ("members", "undoc-members")
	breathe_implementation_filename_extensions = [".c", ".cc", ".cpp", ".hh"]
	breathe_show_enumvalue_initializer = True
	breathe_debug_trace_directives = False
	breathe_short_warning = True

	# -- Gallery ------------------------------------------------------------------
	# sphinx_gallery_conf = {
	# 'examples_dirs': os.path.join(akantu_source_path, 'examples'),
	# 'gallery_dirs': os.path.join(akantu_source_path, 'doc',
	# 'dev-doc', 'auto_examples'),
	# 'download_all_examples': False,
	# 'plot_gallery': 'False',
	# 'only_warn_on_example_error': True,
	# 'log_level': {'backreference_missing': 'debug'},
	# }


	# -- Options for intersphinx extension ----------------------------------------
	intersphinx_mapping = {
	"numpy": ("https://docs.scipy.org/doc/numpy/", None),
	"scipy": ("https://docs.scipy.org/doc/scipy/reference", None),
	}

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