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

	# -- 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 shutil
	import jinja2
	import git
	import re
	import subprocess

	# -- 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.intersphinx',
	'sphinx.ext.coverage',
	'sphinx.ext.mathjax',
	'sphinx.ext.ifconfig',
	'sphinx.ext.viewcode',
	'sphinxcontrib.bibtex',
	'breathe',
	]

	read_the_docs_build = os.environ.get('READTHEDOCS', None) == 'True'
	if read_the_docs_build:
	akantu_path = "."
	akantu_source_path = "../../"
	else:
	akantu_path = "@CMAKE_CURRENT_BINARY_DIR@"
	akantu_source_path = "@CMAKE_SOURCE_DIR@"

	# 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 = None

	# 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']

	# 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 = '2021 EPFL (Ecole Polytechnique Fédérale de Lausanne)' + \
	' Laboratory (LSMS - Laboratoire de Simulation en Mécanique des Solides)'
	author = 'Nicolas Richart'

	with open(os.path.join(akantu_source_path, 'VERSION'), 'r') as fh:
	version_file = fh.readlines()
	file_release = version_file[0].strip()

	try:
	tag_prefix = 'v'
	git_repo = git.Repo(akantu_source_path)

	git_describe = git_repo.git.describe('--tags', '--dirty', '--always',
	'--long',
	'--match', '{}*'.format(tag_prefix))

	print("GIT Describe: {}".format(git_describe))

	# git describe to PEP404 version
	describe_matches = re.search(
	(r'^{}(?P<version>.+?)' +
	r'(?:-(?P<distance>\d+)-g(?P<sha>[0-9a-f]+)' +
	r'(?:-(?P<dirty>dirty))?)?$').format(tag_prefix),
	git_describe)

	if describe_matches:
	describe_matches = describe_matches.groupdict()

	release = describe_matches['version']
	if describe_matches['distance']:
	release += '.' if '+' in release else '+'
	release += '{distance}.{sha}'.format(**describe_matches)
	if describe_matches['dirty']:
	release += '.dirty'
	else:
	count = git_repo.git.rev_list('HEAD', '--count')
	describe_matches = re.search(
	(r'^(?P<sha>[0-9a-f]+)' +
	r'(?:-(?P<dirty>dirty))?$').format(tag_prefix),
	git_describe).groupdict()
	release = '{}.{}+{}'.format(file_release, count,
	describe_matches['sha'])

	except git.InvalidGitRepositoryError:
	release = file_release

	version = re.sub(r'^([0-9]+)\.([0-9+]).*',
	r'\1.\2',
	release)

	print('Release: {} - Version: {}'.format(release, version))

	# -- 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
	if not read_the_docs_build:
	mathjax_config = {
	'extensions': [
	"tex2jax.js",
	"siunitx.js"
	],
	'TeX': {
	'Macros': {
	'st': [r'\mathrm{#1}', 1],
	'mat': [r'\mathbf{#1}', 1],
	'half': [r'\frac{1}{2}', 0],
	},
	'extensions': ["AMSmath.js", "AMSsymbols.js", "sinuitx.js"],
	},
	}
	else:
	mathjax3_config = {
	'tex': {
	'macros': {
	'st': [r'\mathrm{#1}', 1],
	'mat': [r'\mathbf{#1}', 1],
	'half': [r'\frac{1}{2}', 0],
	},
	'packages': ['base', '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 = {}

	if read_the_docs_build:
	j2_template_path = '.'
	else:
	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,
	'akantu_version': version.replace('v', ''),
	}

	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']
	breathe_show_enumvalue_initializer = True
	breathe_debug_trace_directives = True

	# -- 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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