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Quarto GHA Workflow Runner committed Mar 28, 2024
1 parent 256f07e commit deaad06
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2 changes: 1 addition & 1 deletion .nojekyll
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897321c9
d2fcc496
28 changes: 25 additions & 3 deletions chapters/appendices.html
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Expand Up @@ -2,7 +2,7 @@
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.549">
<meta name="generator" content="quarto-1.4.552">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -574,6 +574,24 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
Expand Down Expand Up @@ -608,7 +626,11 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
Expand Down Expand Up @@ -884,7 +906,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
</script>
<nav class="page-navigation">
<div class="nav-page nav-page-previous">
<a href="../chapters/chapter_02.html" class="pagination-link aria-label=" &lt;span="" 2:="" transcriptomic="" analyses="" of="" heterosis="" in="" rice="" root="" traits&lt;="" span&gt;"="">
<a href="../chapters/chapter_02.html" class="pagination-link" aria-label="Benchmark 2: transcriptomic analyses of heterosis in rice root traits">
<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Benchmark 2: transcriptomic analyses of heterosis in rice root traits</span></span>
</a>
</div>
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30 changes: 26 additions & 4 deletions chapters/chapter_01.html
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Expand Up @@ -2,7 +2,7 @@
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.549">
<meta name="generator" content="quarto-1.4.552">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -1071,6 +1071,24 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
Expand Down Expand Up @@ -1105,7 +1123,11 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
Expand Down Expand Up @@ -1381,12 +1403,12 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
</script>
<nav class="page-navigation">
<div class="nav-page nav-page-previous">
<a href="../index.html" class="pagination-link aria-label=" preface"="">
<a href="../index.html" class="pagination-link" aria-label="Preface">
<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Preface</span>
</a>
</div>
<div class="nav-page nav-page-next">
<a href="../chapters/chapter_02.html" class="pagination-link" aria-label="<span class='chapter-number'>2</span>&nbsp; <span class='chapter-title'>Benchmark 2: transcriptomic analyses of heterosis in rice root traits</span>">
<a href="../chapters/chapter_02.html" class="pagination-link" aria-label="Benchmark 2: transcriptomic analyses of heterosis in rice root traits">
<span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Benchmark 2: transcriptomic analyses of heterosis in rice root traits</span></span> <i class="bi bi-arrow-right-short"></i>
</a>
</div>
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28 changes: 25 additions & 3 deletions chapters/chapter_02.html
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Expand Up @@ -2,7 +2,7 @@
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.549">
<meta name="generator" content="quarto-1.4.552">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -822,6 +822,24 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
Expand Down Expand Up @@ -856,7 +874,11 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
Expand Down Expand Up @@ -1132,7 +1154,7 @@ <h2 class="unnumbered anchored" data-anchor-id="references">References</h2>
</script>
<nav class="page-navigation">
<div class="nav-page nav-page-previous">
<a href="../chapters/chapter_01.html" class="pagination-link aria-label=" &lt;span="" 1:="" allopolyploid="" and="" diploid="" cotton="" species="" under="" salt="" stress&lt;="" span&gt;"="">
<a href="../chapters/chapter_01.html" class="pagination-link" aria-label="Benchmark 1: allopolyploid and diploid cotton species under salt stress">
<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Benchmark 1: allopolyploid and diploid cotton species under salt stress</span></span>
</a>
</div>
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28 changes: 25 additions & 3 deletions index.html
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Expand Up @@ -2,7 +2,7 @@
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.549">
<meta name="generator" content="quarto-1.4.552">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -265,6 +265,24 @@ <h1 class="unnumbered">Preface</h1>
// clear code selection
e.clearSelection();
});
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp('/' + window.location.host + '/');
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
// Inspect non-navigation links and adorn them if external
var links = window.document.querySelectorAll('a[href]:not(.nav-link):not(.navbar-brand):not(.toc-action):not(.sidebar-link):not(.sidebar-item-toggle):not(.pagination-link):not(.no-external):not([aria-hidden]):not(.dropdown-item):not(.quarto-navigation-tool)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
// undo the damage that might have been done by quarto-nav.js in the case of
// links that we want to consider external
if (link.dataset.originalHref !== undefined) {
link.href = link.dataset.originalHref;
}
}
}
function tippyHover(el, contentFn, onTriggerFn, onUntriggerFn) {
const config = {
allowHTML: true,
Expand Down Expand Up @@ -299,7 +317,11 @@ <h1 class="unnumbered">Preface</h1>
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
if (note) {
return note.innerHTML;
} else {
return "";
}
});
}
const xrefs = window.document.querySelectorAll('a.quarto-xref');
Expand Down Expand Up @@ -577,7 +599,7 @@ <h1 class="unnumbered">Preface</h1>
<div class="nav-page nav-page-previous">
</div>
<div class="nav-page nav-page-next">
<a href="./chapters/chapter_01.html" class="pagination-link" aria-label="<span class='chapter-number'>1</span>&nbsp; <span class='chapter-title'>Benchmark 1: allopolyploid and diploid cotton species under salt stress</span>">
<a href="./chapters/chapter_01.html" class="pagination-link" aria-label="Benchmark 1: allopolyploid and diploid cotton species under salt stress">
<span class="nav-page-text"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Benchmark 1: allopolyploid and diploid cotton species under salt stress</span></span> <i class="bi bi-arrow-right-short"></i>
</a>
</div>
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2 changes: 1 addition & 1 deletion site_libs/bootstrap/bootstrap.min.css
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Large diffs are not rendered by default.

1 change: 1 addition & 0 deletions site_libs/quarto-nav/quarto-nav.js
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Expand Up @@ -237,6 +237,7 @@ window.document.addEventListener("DOMContentLoaded", function () {
const links = window.document.querySelectorAll("a");
for (let i = 0; i < links.length; i++) {
if (links[i].href) {
links[i].dataset.originalHref = links[i].href;
links[i].href = links[i].href.replace(/\/index\.html/, "/");
}
}
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65 changes: 52 additions & 13 deletions site_libs/quarto-search/quarto-search.js
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Original file line number Diff line number Diff line change
Expand Up @@ -675,6 +675,18 @@ function showCopyLink(query, options) {
// create the index
var fuseIndex = undefined;
var shownWarning = false;

// fuse index options
const kFuseIndexOptions = {
keys: [
{ name: "title", weight: 20 },
{ name: "section", weight: 20 },
{ name: "text", weight: 10 },
],
ignoreLocation: true,
threshold: 0.1,
};

async function readSearchData() {
// Initialize the search index on demand
if (fuseIndex === undefined) {
Expand All @@ -685,17 +697,7 @@ async function readSearchData() {
shownWarning = true;
return;
}
// create fuse index
const options = {
keys: [
{ name: "title", weight: 20 },
{ name: "section", weight: 20 },
{ name: "text", weight: 10 },
],
ignoreLocation: true,
threshold: 0.1,
};
const fuse = new window.Fuse([], options);
const fuse = new window.Fuse([], kFuseIndexOptions);

// fetch the main search.json
const response = await fetch(offsetURL("search.json"));
Expand Down Expand Up @@ -1226,8 +1228,34 @@ function algoliaSearch(query, limit, algoliaOptions) {
});
}

function fuseSearch(query, fuse, fuseOptions) {
return fuse.search(query, fuseOptions).map((result) => {
let subSearchTerm = undefined;
let subSearchFuse = undefined;
const kFuseMaxWait = 125;

async function fuseSearch(query, fuse, fuseOptions) {
let index = fuse;
// Fuse.js using the Bitap algorithm for text matching which runs in
// O(nm) time (no matter the structure of the text). In our case this
// means that long search terms mixed with large index gets very slow
//
// This injects a subIndex that will be used once the terms get long enough
// Usually making this subindex is cheap since there will typically be
// a subset of results matching the existing query
if (subSearchFuse !== undefined && query.startsWith(subSearchTerm)) {
// Use the existing subSearchFuse
index = subSearchFuse;
} else if (subSearchFuse !== undefined) {
// The term changed, discard the existing fuse
subSearchFuse = undefined;
subSearchTerm = undefined;
}

// Search using the active fuse
const then = performance.now();
const resultsRaw = await index.search(query, fuseOptions);
const now = performance.now();

const results = resultsRaw.map((result) => {
const addParam = (url, name, value) => {
const anchorParts = url.split("#");
const baseUrl = anchorParts[0];
Expand All @@ -1244,4 +1272,15 @@ function fuseSearch(query, fuse, fuseOptions) {
crumbs: result.item.crumbs,
};
});

// If we don't have a subfuse and the query is long enough, go ahead
// and create a subfuse to use for subsequent queries
if (now - then > kFuseMaxWait && subSearchFuse === undefined) {
subSearchTerm = query;
subSearchFuse = new window.Fuse([], kFuseIndexOptions);
resultsRaw.forEach((rr) => {
subSearchFuse.add(rr.item);
});
}
return results;
}

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