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chore: Updated compiled documentation [skip ci]
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biosimulatorsdaemon committed Feb 16, 2024
1 parent 9be6621 commit 6cf2cce
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Showing 63 changed files with 5,247 additions and 3,516 deletions.
4 changes: 4 additions & 0 deletions docs/_static/basic.css
Original file line number Diff line number Diff line change
Expand Up @@ -237,6 +237,10 @@ a.headerlink {
visibility: hidden;
}

a:visited {
color: #551A8B;
}

h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
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5 changes: 2 additions & 3 deletions docs/_static/documentation_options.js
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@@ -1,6 +1,5 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '0.1.186',
const DOCUMENTATION_OPTIONS = {
VERSION: '0.1.187',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
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2 changes: 1 addition & 1 deletion docs/_static/scripts/bootstrap.js

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4 changes: 2 additions & 2 deletions docs/_static/scripts/bootstrap.js.LICENSE.txt
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@@ -1,5 +1,5 @@
/*!
* Bootstrap v5.2.3 (https://getbootstrap.com/)
* Copyright 2011-2022 The Bootstrap Authors (https://github.com/twbs/bootstrap/graphs/contributors)
* Bootstrap v5.3.2 (https://getbootstrap.com/)
* Copyright 2011-2023 The Bootstrap Authors (https://github.com/twbs/bootstrap/graphs/contributors)
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
*/
2 changes: 1 addition & 1 deletion docs/_static/scripts/bootstrap.js.map

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2 changes: 1 addition & 1 deletion docs/_static/scripts/pydata-sphinx-theme.js

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2 changes: 1 addition & 1 deletion docs/_static/scripts/pydata-sphinx-theme.js.map

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26 changes: 17 additions & 9 deletions docs/_static/searchtools.js
Original file line number Diff line number Diff line change
Expand Up @@ -57,12 +57,12 @@ const _removeChildren = (element) => {
const _escapeRegExp = (string) =>
string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string

const _displayItem = (item, searchTerms) => {
const _displayItem = (item, searchTerms, highlightTerms) => {
const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
const contentRoot = document.documentElement.dataset.content_root;

const [docName, title, anchor, descr, score, _filename] = item;

Expand All @@ -75,20 +75,24 @@ const _displayItem = (item, searchTerms) => {
if (dirname.match(/\/index\/$/))
dirname = dirname.substring(0, dirname.length - 6);
else if (dirname === "index/") dirname = "";
requestUrl = docUrlRoot + dirname;
requestUrl = contentRoot + dirname;
linkUrl = requestUrl;
} else {
// normal html builders
requestUrl = docUrlRoot + docName + docFileSuffix;
requestUrl = contentRoot + docName + docFileSuffix;
linkUrl = docName + docLinkSuffix;
}
let linkEl = listItem.appendChild(document.createElement("a"));
linkEl.href = linkUrl + anchor;
linkEl.dataset.score = score;
linkEl.innerHTML = title;
if (descr)
if (descr) {
listItem.appendChild(document.createElement("span")).innerHTML =
" (" + descr + ")";
// highlight search terms in the description
if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js
highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
}
else if (showSearchSummary)
fetch(requestUrl)
.then((responseData) => responseData.text())
Expand All @@ -97,6 +101,9 @@ const _displayItem = (item, searchTerms) => {
listItem.appendChild(
Search.makeSearchSummary(data, searchTerms)
);
// highlight search terms in the summary
if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js
highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
});
Search.output.appendChild(listItem);
};
Expand All @@ -115,14 +122,15 @@ const _finishSearch = (resultCount) => {
const _displayNextItem = (
results,
resultCount,
searchTerms
searchTerms,
highlightTerms,
) => {
// results left, load the summary and display it
// this is intended to be dynamic (don't sub resultsCount)
if (results.length) {
_displayItem(results.pop(), searchTerms);
_displayItem(results.pop(), searchTerms, highlightTerms);
setTimeout(
() => _displayNextItem(results, resultCount, searchTerms),
() => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
5
);
}
Expand Down Expand Up @@ -360,7 +368,7 @@ const Search = {
// console.info("search results:", Search.lastresults);

// print the results
_displayNextItem(results, results.length, searchTerms);
_displayNextItem(results, results.length, searchTerms, highlightTerms);
},

/**
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16 changes: 13 additions & 3 deletions docs/_static/sphinx_highlight.js
Original file line number Diff line number Diff line change
Expand Up @@ -29,14 +29,19 @@ const _highlight = (node, addItems, text, className) => {
}

span.appendChild(document.createTextNode(val.substr(pos, text.length)));
const rest = document.createTextNode(val.substr(pos + text.length));
parent.insertBefore(
span,
parent.insertBefore(
document.createTextNode(val.substr(pos + text.length)),
rest,
node.nextSibling
)
);
node.nodeValue = val.substr(0, pos);
/* There may be more occurrences of search term in this node. So call this
* function recursively on the remaining fragment.
*/
_highlight(rest, addItems, text, className);

if (isInSVG) {
const rect = document.createElementNS(
Expand Down Expand Up @@ -140,5 +145,10 @@ const SphinxHighlight = {
},
};

_ready(SphinxHighlight.highlightSearchWords);
_ready(SphinxHighlight.initEscapeListener);
_ready(() => {
/* Do not call highlightSearchWords() when we are on the search page.
* It will highlight words from the *previous* search query.
*/
if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
SphinxHighlight.initEscapeListener();
});
8 changes: 4 additions & 4 deletions docs/_static/styles/bootstrap.css

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1 change: 1 addition & 0 deletions docs/_static/styles/bootstrap.css.map

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3 changes: 2 additions & 1 deletion docs/_static/styles/pydata-sphinx-theme.css

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1 change: 1 addition & 0 deletions docs/_static/styles/pydata-sphinx-theme.css.map

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