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' + _('Hide Search Matches') + '
') 234 | .appendTo($('#searchbox')); 235 | } 236 | }, 237 | 238 | /** 239 | * init the domain index toggle buttons 240 | */ 241 | initIndexTable : function() { 242 | var togglers = $('img.toggler').click(function() { 243 | var src = $(this).attr('src'); 244 | var idnum = $(this).attr('id').substr(7); 245 | $('tr.cg-' + idnum).toggle(); 246 | if (src.substr(-9) === 'minus.png') 247 | $(this).attr('src', src.substr(0, src.length-9) + 'plus.png'); 248 | else 249 | $(this).attr('src', src.substr(0, src.length-8) + 'minus.png'); 250 | }).css('display', ''); 251 | if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) { 252 | togglers.click(); 253 | } 254 | }, 255 | 256 | /** 257 | * helper function to hide the search marks again 258 | */ 259 | hideSearchWords : function() { 260 | $('#searchbox .highlight-link').fadeOut(300); 261 | $('span.highlighted').removeClass('highlighted'); 262 | }, 263 | 264 | /** 265 | * make the url absolute 266 | */ 267 | makeURL : function(relativeURL) { 268 | return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL; 269 | }, 270 | 271 | /** 272 | * get the current relative url 273 | */ 274 | getCurrentURL : function() { 275 | var path = document.location.pathname; 276 | var parts = path.split(/\//); 277 | $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() { 278 | if (this === '..') 279 | parts.pop(); 280 | }); 281 | var url = parts.join('/'); 282 | return path.substring(url.lastIndexOf('/') + 1, path.length - 1); 283 | }, 284 | 285 | initOnKeyListeners: function() { 286 | $(document).keydown(function(event) { 287 | var activeElementType = document.activeElement.tagName; 288 | // don't navigate when in search box or textarea 289 | if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT' 290 | && !event.altKey && !event.ctrlKey && !event.metaKey && !event.shiftKey) { 291 | switch (event.keyCode) { 292 | case 37: // left 293 | var prevHref = $('link[rel="prev"]').prop('href'); 294 | if (prevHref) { 295 | window.location.href = prevHref; 296 | return false; 297 | } 298 | case 39: // right 299 | var nextHref = $('link[rel="next"]').prop('href'); 300 | if (nextHref) { 301 | window.location.href = nextHref; 302 | return false; 303 | } 304 | } 305 | } 306 | }); 307 | } 308 | }; 309 | 310 | // quick alias for translations 311 | _ = Documentation.gettext; 312 | 313 | $(document).ready(function() { 314 | Documentation.init(); 315 | }); 316 | -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python3 2 | # -*- coding: utf-8 -*- 3 | # 4 | # SimpleSBML documentation build configuration file, created by 5 | # sphinx-quickstart on Wed Apr 1 19:33:27 2015. 6 | # 7 | # This file is execfile()d with the current directory set to its 8 | # containing dir. 9 | # 10 | # Note that not all possible configuration values are present in this 11 | # autogenerated file. 12 | # 13 | # All configuration values have a default; values that are commented out 14 | # serve to show the default. 15 | 16 | import sys 17 | import os 18 | import shlex 19 | 20 | import os 21 | import sys 22 | sys.path.insert(0, os.path.abspath('../../simplesbml')) 23 | 24 | import sphinx_rtd_theme 25 | 26 | # If extensions (or modules to document with autodoc) are in another directory, 27 | # add these directories to sys.path here. If the directory is relative to the 28 | # documentation root, use os.path.abspath to make it absolute, like shown here. 29 | #sys.path.insert(0, os.path.abspath('.')) 30 | 31 | # -- General configuration ------------------------------------------------ 32 | 33 | # If your documentation needs a minimal Sphinx version, state it here. 34 | #needs_sphinx = '1.0' 35 | 36 | # Add any Sphinx extension module names here, as strings. They can be 37 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 38 | # ones. 39 | extensions = [ 40 | 'sphinx.ext.viewcode', 41 | 'sphinx.ext.autodoc', 42 | ] 43 | 44 | # Add any paths that contain templates here, relative to this directory. 45 | templates_path = ['_templates'] 46 | 47 | # The suffix(es) of source filenames. 48 | # You can specify multiple suffix as a list of string: 49 | # source_suffix = ['.rst', '.md'] 50 | source_suffix = '.rst' 51 | 52 | # The encoding of source files. 53 | #source_encoding = 'utf-8-sig' 54 | 55 | # The master toctree document. 56 | master_doc = 'index' 57 | 58 | # General information about the project. 59 | project = 'SimpleSBML' 60 | copyright = '2015, 2021, Caroline Cannistra, Kyle Medley, Herbert Sauro' 61 | author = 'Caroline Cannistra, Kyle medley, Herbert Sauro' 62 | 63 | # The version info for the project you're documenting, acts as replacement for 64 | # |version| and |release|, also used in various other places throughout the 65 | # built documents. 66 | # 67 | # The short X.Y version. 68 | version = '2.3.0' 69 | # The full version, including alpha/beta/rc tags. 70 | release = '2.3.0' 71 | 72 | # The language for content autogenerated by Sphinx. Refer to documentation 73 | # for a list of supported languages. 74 | # 75 | # This is also used if you do content translation via gettext catalogs. 76 | # Usually you set "language" from the command line for these cases. 77 | language = None 78 | 79 | # There are two options for replacing |today|: either, you set today to some 80 | # non-false value, then it is used: 81 | #today = '' 82 | # Else, today_fmt is used as the format for a strftime call. 83 | #today_fmt = '%B %d, %Y' 84 | 85 | # List of patterns, relative to source directory, that match files and 86 | # directories to ignore when looking for source files. 87 | exclude_patterns = [] 88 | 89 | # The reST default role (used for this markup: `text`) to use for all 90 | # documents. 91 | #default_role = None 92 | 93 | # If true, '()' will be appended to :func: etc. cross-reference text. 94 | #add_function_parentheses = True 95 | 96 | # If true, the current module name will be prepended to all description 97 | # unit titles (such as .. function::). 98 | #add_module_names = True 99 | 100 | # If true, sectionauthor and moduleauthor directives will be shown in the 101 | # output. They are ignored by default. 102 | #show_authors = False 103 | 104 | # The name of the Pygments (syntax highlighting) style to use. 105 | pygments_style = 'sphinx' 106 | 107 | # A list of ignored prefixes for module index sorting. 108 | #modindex_common_prefix = [] 109 | 110 | # If true, keep warnings as "system message" paragraphs in the built documents. 111 | #keep_warnings = False 112 | 113 | # If true, `todo` and `todoList` produce output, else they produce nothing. 114 | todo_include_todos = False 115 | 116 | 117 | # -- Options for HTML output ---------------------------------------------- 118 | 119 | # The theme to use for HTML and HTML Help pages. See the documentation for 120 | # a list of builtin themes. 121 | html_theme = 'sphinx_rtd_theme' 122 | 123 | # Theme options are theme-specific and customize the look and feel of a theme 124 | # further. For a list of options available for each theme, see the 125 | # documentation. 126 | #html_theme_options = {} 127 | 128 | # Add any paths that contain custom themes here, relative to this directory. 129 | html_theme_path = [sphinx_rtd_theme.get_html_theme_path()] 130 | 131 | # The name for this set of Sphinx documents. If None, it defaults to 132 | # "
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