conf.py

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# SourceXtractor++ documentation build configuration file, created by
# sphinx-quickstart on Thu Jan 31 13:34:56 2019.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
 
# 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 sys
sys.path.insert(0, os.path.abspath('../../SEImplementation/python/sourcextractor'))
 
import sphinx_rtd_theme
 
 
# -- General configuration ------------------------------------------------
 
# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'
 
# 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.intersphinx',
#   'sphinx.ext.todo',
    'sphinx.ext.mathjax',
#    'sphinx.ext.ifconfig',
    'sphinx.ext.autodoc',
    'sphinx.ext.napoleon',
    'sphinx.ext.autosummary',
    'sphinx.ext.doctest',
    'sphinx.ext.inheritance_diagram',
    'sphinxcontrib.bibtex',
    'sphinx.ext.githubpages'
]
 
# 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 encoding of source files.
#
# source_encoding = 'utf-8-sig'
 
# The master toctree document.
master_doc = 'index'
 
# General information about the project.
project = 'SourceXtractor++'
filename = 'sourcextractor'
copyright = '2019,2020,2021,2022 GenevaU/LMU/CNRS/SorbonneU'
author = 'SourceXtractor++ team'
 
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
# built documents.
#
# The short X.Y version.
version = '1.0.0'
# The full version, including alpha/beta/rc tags.
release = '1.0.0'
 
# 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
 
# There are two options for replacing |today|: either, you set today to some
# non-false value, then it is used:
#
#today = 'Wed July 31 2019'
#
# Else, today_fmt is used as the format for a strftime call.
#
today_fmt = '%B %d, %Y'
 
# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This patterns also effect to html_static_path and html_extra_path
exclude_patterns = ['global.rst','keys.rst','roles.rst']
 
# The reST default role (used for this markup: `text`) to use for all
# documents.
#
# default_role = None
 
# If true, '()' will be appended to :func: etc. cross-reference text.
#
# add_function_parentheses = True
 
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
#
# add_module_names = True
 
# If true, sectionauthor and moduleauthor directives will be shown in the
# output. They are ignored by default.
#
# show_authors = False
 
# The name of the Pygments (syntax highlighting) style to use.
pygments_style = 'sphinx'
 
# A list of ignored prefixes for module index sorting.
# modindex_common_prefix = []
 
# If true, keep warnings as "system message" paragraphs in the built documents.
# keep_warnings = False
 
# If true, `todo` and `todoList` produce output, else they produce nothing.
todo_include_todos = True
 
numfig = True
 
# -- Autodoc options ------------------------------------------------------
# If true, the current module name will be prepended to all description
# unit titles (such as .. function::).
add_module_names = False
 
autodoc_mock_imports = ['.measurement_images', '_SourceXtractorPy']
 
# -- Options for HTML output ----------------------------------------------
 
# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
#
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 themes here, relative to this directory.
html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
# The name for this set of Sphinx documents.
# "<project> v<release> documentation" by default.
#
# html_title = 'SourceXtractor++ v1.0.0'
 
# A shorter title for the navigation bar.  Default is the same as html_title.
#
# html_short_title = None
 
# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
#
# html_logo = None
 
# The name of an image file (relative to this directory) to use as a favicon of
# the docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
# pixels large.
#
# html_favicon = None
 
# 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 = ['../theme']
 
# Trick for having ReadTheDocs read custom theme changes
def setup(app):
    app.add_css_file("css/custom.css")
 
# Add any extra paths that contain custom files (such as robots.txt or
# .htaccess) here, relative to this directory. These files are copied
# directly to the root of the documentation.
#
# html_extra_path = []
 
# Custom sidebar templates, must be a dictionary that maps document names
# to template names.
#
# This is required for the alabaster theme
# refs: http://alabaster.readthedocs.io/en/latest/installation.html#sidebars
html_sidebars = {
    '**': [
        'relations.html',  # needs 'show_related': True theme option to display
        'searchbox.html',
    ]
}
 
# If not None, a 'Last updated on:' timestamp is inserted at every page
# bottom, using the given strftime format.
# The empty string is equivalent to '%b %d, %Y'.
#
# html_last_updated_fmt = None
 
# If true, SmartyPants will be used to convert quotes and dashes to
# typographically correct entities.
#
# html_use_smartypants = True
 
# Custom sidebar templates, maps document names to template names.
#
# html_sidebars = {}
 
# Additional templates that should be rendered to pages, maps page names to
# template names.
#
# html_additional_pages = {}
 
# If false, no module index is generated.
#
# html_domain_indices = True
 
# If false, no index is generated.
#
# html_use_index = True
 
# If true, the index is split into individual pages for each letter.
#
# html_split_index = False
 
# If true, links to the reST sources are added to the pages.
#
html_show_sourcelink = False
 
# If true, "Created using Sphinx" is shown in the HTML footer. Default is True.
#
html_show_sphinx = False
 
# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
#
# html_show_copyright = True
 
# If true, an OpenSearch description file will be output, and all pages will
# contain a <link> tag referring to it.  The value of this option must be the
# base URL from which the finished HTML is served.
#
# html_use_opensearch = ''
 
# This is the file name suffix for HTML files (e.g. ".xhtml").
# html_file_suffix = None
 
# Language to be used for generating the HTML full-text search index.
# Sphinx supports the following languages:
#   'da', 'de', 'en', 'es', 'fi', 'fr', 'hu', 'it', 'ja'
#   'nl', 'no', 'pt', 'ro', 'ru', 'sv', 'tr', 'zh'
#
# html_search_language = 'en'
 
# A dictionary with options for the search language support, empty by default.
# 'ja' uses this config value.
# 'zh' user can custom change `jieba` dictionary path.
#
# html_search_options = {'type': 'default'}
 
# The name of a javascript file (relative to the configuration directory) that
# implements a search results scorer. If empty, the default will be used.
#
# html_search_scorer = 'scorer.js'
 
# Output file base name for HTML help builder.
htmlhelp_basename = filename + 'doc'
 
# -- Options for LaTeX output ---------------------------------------------
 
latex_elements = {
     # The paper size ('letterpaper' or 'a4paper').
     #
'papersize': 'a4paper',
 
     # The font size ('10pt', '11pt' or '12pt').
     #
     # 'pointsize': '10pt',
 
     # Additional stuff for the LaTeX preamble.
     #
'preamble': '\\usepackage{amssymb}',
 
     # 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, filename + '.tex', project + ' Documentation',
     author, 'manual'),
]
 
# The name of an image file (relative to this directory) to place at the top of
# the title page.
#
# latex_logo = None
 
# For "manual" documents, if this is true, then toplevel headings are parts,
# not chapters.
#
# latex_use_parts = False
 
# If true, show page references after internal links.
#
# latex_show_pagerefs = False
 
# If true, show URL addresses after external links.
#
# latex_show_urls = 'footnote'
 
# Documents to append as an appendix to all manuals.
#
# latex_appendices = []
 
# It false, will not define \strong, \code,     itleref, \crossref ... but only
# \sphinxstrong, ..., \sphinxtitleref, ... To help avoid clash with user added
# packages.
#
# latex_keep_old_macro_names = True
 
# If false, no module index is generated.
#
# latex_domain_indices = True
 
 
# -- 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, filename, project + ' Documentation',
     author, 1)
]
 
# If true, show URL addresses after external links.
#
# man_show_urls = False
 
 
# -- 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, filename, project + ' Documentation',
     author, project, 'One line description of project.',
     'Miscellaneous'),
]
 
# Documents to append as an appendix to all manuals.
#
# texinfo_appendices = []
 
# If false, no module index is generated.
#
# texinfo_domain_indices = True
 
# How to display URL addresses: 'footnote', 'no', or 'inline'.
#
# texinfo_show_urls = 'footnote'
 
# If true, do not generate a @detailmenu in the "Top" node's menu.
#
# texinfo_no_detailmenu = False
 
 
# -- Options for Epub output ----------------------------------------------
 
# Bibliographic Dublin Core info.
epub_title = project
epub_author = author
epub_publisher = author
epub_copyright = copyright
 
# The basename for the epub file. It defaults to the project name.
# epub_basename = project
 
# The HTML theme for the epub output. Since the default themes are not
# optimized for small screen space, using the same theme for HTML and epub
# output is usually not wise. This defaults to 'epub', a theme designed to save
# visual space.
#
# epub_theme = 'epub'
 
# The language of the text. It defaults to the language option
# or 'en' if the language is not set.
#
# epub_language = ''
 
# The scheme of the identifier. Typical schemes are ISBN or URL.
# epub_scheme = ''
 
# 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 tuple containing the cover image and cover page html template filenames.
#
# epub_cover = ()
 
# A sequence of (type, uri, title) tuples for the guide element of content.opf.
#
# epub_guide = ()
 
# HTML files that should be inserted before the pages created by sphinx.
# The format is a list of tuples containing the path and title.
#
# epub_pre_files = []
 
# HTML files that should be inserted after the pages created by sphinx.
# The format is a list of tuples containing the path and title.
#
# epub_post_files = []
 
# A list of files that should not be packed into the epub file.
epub_exclude_files = ['search.html']
 
# The depth of the table of contents in toc.ncx.
#
# epub_tocdepth = 3
 
# Allow duplicate toc entries.
#
# epub_tocdup = True
 
# Choose between 'default' and 'includehidden'.
#
# epub_tocscope = 'default'
 
# Fix unsupported image types using the Pillow.
#
# epub_fix_images = False
 
# Scale large images.
#
# epub_max_image_width = 0
 
# How to display URL addresses: 'footnote', 'no', or 'inline'.
#
# epub_show_urls = 'inline'
 
# If false, no index is generated.
#
# epub_use_index = True
 
 
# Example configuration for intersphinx: refer to the Python standard library.
intersphinx_mapping = {'https://docs.python.org/': None}
 
# -- Options for pybtex ----------------------------------------------
bibtex_bibfiles = ["references.bib"]
    
from packaging import version as vers
from pybtex import __version__ as pybtex_version
from pybtex.style.formatting.unsrt import Style as UnsrtStyle, date, pages, toplevel
from pybtex.style.template import * # ... and anything else needed
from pybtex.plugin import register_plugin
import inspect
 
new_version = vers.parse(pybtex_version) >= vers.parse("0.22")
 
if new_version:
    def _format_data(node, data):
        try:
            f = node.format_data
        except AttributeError:
            return node
        else:
            return f(data)
 
 
    def _format_list(list_, data):
        return (_format_data(part, data) for part in list_)
 
    @node
    def href2(children, data):
        parts = _format_list(children, data)
        if "http" in list(parts)[0]:
            parts = _format_list(children, data)
            return richtext.HRef(*parts)
        else:
            return richtext.Tag('strong', *parts)
 
class ADSArxivStyle(UnsrtStyle):
 
    if new_version:
        def format_names(self, role, as_sentence=True):
            formatted_names = names(role, sep=', ', sep2 = ' and ', last_sep=', and ')
            if as_sentence:
                return sentence[ formatted_names ]
            else:
               return formatted_names
 
        def get_article_template(self, e):
            volume_and_pages = first_of[
            # volume and pages, with optional issue number
                optional[
                    join[
                        field('volume'),
                        optional[ '(', field('number'),')' ],
                        ':', pages
                    ],
                ],
                # pages only
                words[ 'pages', pages ],
            ]
            myurl = first_of[
                    optional_field('adsurl'),
                    optional[ join[ 'http://arxiv.org/abs/', field('eprint') ]],
                    optional_field('url'),
                    optional[ join ['http://dx.doi.org/', field('doi') ]]
            ]
            template = toplevel[
                sentence[ self.format_names('author', as_sentence=False), field('year') ],
                href2[ myurl, self.format_title(e, 'title') ],
                sentence(capfirst=False) [
                    tag('emph')[ field('journal') ],
                    optional[ volume_and_pages ]],
                sentence(capfirst=False) [ optional_field('note') ],
            ]
            return template
 
        def get_inproceedings_template(self, e):
            myurl = first_of[
                optional_field('adsurl'),
                optional[ join ['http://arxiv.org/abs/', field('eprint') ]],
                optional_field('url'),
                optional[ join ['http://dx.doi.org/', field('doi') ]]
            ]
            template = toplevel[
                sentence[ self.format_names('author', as_sentence=False), field('year') ],
                href2[ myurl, self.format_title(e, 'title') ],
                words[
                    'In',
                    sentence(capfirst=False)[
                        optional[ self.format_editor(e, as_sentence=False) ],
                        self.format_btitle(e, 'booktitle', as_sentence=False),
                        self.format_volume_and_series(e, as_sentence=False),
                        optional[ pages ],
                    ],
                    self.format_address_organization_publisher_date(e),
                ],
                sentence(capfirst=False)[ optional_field('note') ],
            ]
            return template
 
        def get_misc_template(self, e):
            myurl = first_of[
                    optional_field('adsurl'),
                    optional[ join ['http://arxiv.org/abs/', field('eprint') ]],
                    optional_field('url'),
                    optional[ join ['http://dx.doi.org/', field('doi') ]]
            ]
            template = toplevel[
                optional[ sentence[ self.format_names('author', as_sentence=False), optional [ field('year') ]]],
                optional[ href2[ myurl, self.format_title(e, 'title') ]],
                sentence[ optional[ field('howpublished') ]],
                sentence[ optional_field('note') ],
            ]
            return template
    else:
 
        def format_article(self, e):
            volume_and_pages = first_of [
            # volume and pages, with optional issue number
                optional [
                    join [
                        field('volume'),
                        optional['(', field('number'),')'],
                        ':', pages
                    ],
                ],
                # pages only
                words ['pages', pages],
            ]
            myurl = first_of [
                    optional_field('adsurl'),
                    optional [join ['http://arxiv.org/abs/'], field('eprint')],
                    optional_field('url'),
                    optional [join ['http://dx.doi.org/', field('doi')]]
            ]
            template = toplevel [
                self.format_names('author'),
                href [myurl, self.format_title(e, 'title')],
                sentence(capfirst=False) [
                    tag('emph') [field('journal')],
                    optional[ volume_and_pages ],
                    field('year')],
                sentence(capfirst=False) [ optional_field('note') ],
            ]
            return template.format_data(e)
 
        def format_inproceedings(self, e):
            myurl = first_of [
                optional_field('adsurl'),
                optional [join ['http://arxiv.org/abs/', field('eprint')]],
                optional_field('url'),
                optional [join ['http://dx.doi.org/', field('doi')]]
            ]
            template = toplevel [
                sentence [self.format_names('author')],
                href [myurl, self.format_title(e, 'title')] \
                    if len(myurl.format_data(e)) > 0 \
                    else tag('strong') [self.format_title(e, 'title')],
                words [
                    'In',
                    sentence(capfirst=False) [
                        optional[ self.format_editor(e, as_sentence=False) ],
                        self.format_btitle(e, 'booktitle', as_sentence=False),
                        self.format_volume_and_series(e, as_sentence=False),
                        optional[ pages ],
                    ],
                    self.format_address_organization_publisher_date(e),
                ],
                sentence(capfirst=False) [ optional_field('note') ],
            ]
            return template.format_data(e)
 
register_plugin('pybtex.style.formatting', 'adsarxiv', ADSArxivStyle)