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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),
			}

rAKA/doc/dev-doc/conf.py08360b35de3bfeatures/mesh-periodic…

conf.pyView Options

rAKA/doc/dev-doc/conf.py
08360b35de3bfeatures/mesh-periodic…

conf.py
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