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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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