diff --git a/doc/dev-doc/akantu.dox.j2 b/doc/dev-doc/akantu.dox.j2 index b71a6141b..c55a9d2b4 100644 --- a/doc/dev-doc/akantu.dox.j2 +++ b/doc/dev-doc/akantu.dox.j2 @@ -1,43 +1,47 @@ PROJECT_NAME = Akantu PROJECT_NUMBER = {{ akantu_version }} STRIP_FROM_PATH = {{ akantu_source_path }} STRIP_FROM_INC_PATH = {{ akantu_source_path }} TAB_SIZE = 4 ALIASES = "rst=\verbatim embed:rst" \ "endrst=\endverbatim" QUIET = NO WARN_IF_UNDOCUMENTED = NO WARN_IF_DOC_ERROR = NO WARN_AS_ERROR = NO INPUT = {{ akantu_source_path }}/src FILE_PATTERNS = *.c *.cc *.hh *.py EXCLUDE = {{ akantu_source_path }}/src/common/aka_fwd.hh RECURSIVE = YES EXAMPLE_PATH = {{ akantu_source_path }}/examples EXAMPLE_RECURSIVE = YES SOURCE_BROWSER = NO GENERATE_HTML = NO GENERATE_HTMLHELP = NO USE_MATHJAX = YES GENERATE_LATEX = NO GENERATE_XML = YES XML_OUTPUT = xml ENABLE_PREPROCESSING = YES MACRO_EXPANSION = YES PREDEFINED = DOXYGEN +DOXYGEN_INCLUDE_PATH = {{ akantu_source_path }}/src/common \ + {{ akantu_source_path }}/src/fe_engine \ + {{ akantu_source_path }}/src/mesh \ + {{ akantu_source_path }}/src/model EXPAND_AS_DEFINED = __BEGIN_AKANTU__ \ __END_AKANTU__ \ __BEGIN_AKANTU_DUMPER__ \ __END_AKANTU_DUMPER__ \ AKANTU_SET_MACRO \ AKANTU_GET_MACRO \ AKANTU_GET_MACRO_NOT_CONST \ AKANTU_GET_MACRO_DEREF_PTR \ AKANTU_GET_MACRO_BY_ELEMENT_TYPE \ AKANTU_GET_MACRO_BY_ELEMENT_TYPE_CONST COLLABORATION_GRAPH = NO UML_LOOK = YES TEMPLATE_RELATIONS = YES CALL_GRAPH = YES CALLER_GRAPH = YES LOOKUP_CACHE_SIZE = 0 diff --git a/doc/dev-doc/conf.py b/doc/dev-doc/conf.py index ef9532f98..059a57c66 100644 --- a/doc/dev-doc/conf.py +++ b/doc/dev-doc/conf.py @@ -1,317 +1,333 @@ # -*- 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.+?)' + r'(?:-(?P\d+)-g(?P[0-9a-f]+)' + r'(?:-(?Pdirty))?)?$').format(tag_prefix), git_describe) if describe_matches: describe_matches = describe_matches.groupdict() release = 'v' + describe_matches['version'] if describe_matches['distance']: release += '.' if '+' in release else '+' release += '{distance}.{sha}'.format(**describe_matches) if describe_matches['dirty']: release += '.dirty' else: count = git_repo.git.rev_list('HEAD', '--count') describe_matches = re.search( (r'^(?P[0-9a-f]+)' + r'(?:-(?Pdirty))?$').format(tag_prefix), git_describe).groupdict() release = 'v{}.{}+{}'.format(file_release, count, describe_matches['sha']) + except git.InvalidGitRepositoryError: release = 'v' + file_release version = re.sub(r'^v([0-9]+)\.([0-9+]).*', r'v\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 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"], }, } +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 # -- Options for intersphinx extension --------------------------------------- intersphinx_mapping = { 'numpy': ('https://docs.scipy.org/doc/numpy/', None), 'scipy': ('https://docs.scipy.org/doc/scipy/reference', None), }