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@btupper
btupper committed Sep 25, 2024
1 parent 612cab1 commit d4096ef
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Showing 60 changed files with 784 additions and 889 deletions.
4 changes: 4 additions & 0 deletions _quarto.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,10 @@ project:
type: website
output-dir: docs
execute-dir: project
render:
- "*.qmd"
- "!manuscript/"
- "!*.Rmd"
execute:
cache: true
website:
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257 changes: 228 additions & 29 deletions docs/about.html
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Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,12 @@
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.3.450">
<meta name="generator" content="quarto-1.5.57">

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


<title>Jellyscape - About</title>
<title>About – Jellyscape</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
Expand Down Expand Up @@ -46,7 +46,13 @@
"collapse-after": 3,
"panel-placement": "start",
"type": "textbox",
"limit": 20,
"limit": 50,
"keyboard-shortcut": [
"f",
"/",
"s"
],
"show-item-context": false,
"language": {
"search-no-results-text": "No results",
"search-matching-documents-text": "matching documents",
Expand All @@ -55,6 +61,7 @@
"search-more-match-text": "more match in this document",
"search-more-matches-text": "more matches in this document",
"search-clear-button-title": "Clear",
"search-text-placeholder": "",
"search-detached-cancel-button-title": "Cancel",
"search-submit-button-title": "Submit",
"search-label": "Search"
Expand All @@ -71,13 +78,13 @@
<header id="quarto-header" class="headroom fixed-top">
<nav class="quarto-secondary-nav">
<div class="container-fluid d-flex">
<button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<button type="button" class="quarto-btn-toggle btn" data-bs-toggle="collapse" role="button" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<i class="bi bi-layout-text-sidebar-reverse"></i>
</button>
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./about.html">About</a></li></ol></nav>
<a class="flex-grow-1" role="button" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
</a>
<button type="button" class="btn quarto-search-button" aria-label="" onclick="window.quartoOpenSearch();">
<nav class="quarto-page-breadcrumbs" aria-label="breadcrumb"><ol class="breadcrumb"><li class="breadcrumb-item"><a href="./about.html">About</a></li></ol></nav>
<a class="flex-grow-1" role="navigation" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item" aria-controls="quarto-sidebar" aria-expanded="false" aria-label="Toggle sidebar navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
</a>
<button type="button" class="btn quarto-search-button" aria-label="Search" onclick="window.quartoOpenSearch();">
<i class="bi bi-search"></i>
</button>
</div>
Expand All @@ -86,7 +93,7 @@
<!-- content -->
<div id="quarto-content" class="quarto-container page-columns page-rows-contents page-layout-article">
<!-- sidebar -->
<nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal sidebar-navigation docked overflow-auto">
<nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation docked overflow-auto">
<div class="pt-lg-2 mt-2 text-left sidebar-header">
<div class="sidebar-title mb-0 py-0">
<a href="./">Jellyscape</a>
Expand Down Expand Up @@ -120,9 +127,9 @@
</ul>
</div>
</nav>
<div id="quarto-sidebar-glass" data-bs-toggle="collapse" data-bs-target="#quarto-sidebar,#quarto-sidebar-glass"></div>
<div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
<!-- margin-sidebar -->
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
<div id="quarto-margin-sidebar" class="sidebar margin-sidebar zindex-bottom">

</div>
<!-- main -->
Expand All @@ -143,8 +150,10 @@ <h1 class="title">About</h1>
</div>



</header>


<p>The <a href="https://github.com/BigelowLab/jellyscape">jellyscape</a> project was developed at <a href="https://www.bigelow.org/services/ocean-forecasting/">Bigelow Laboratory’s Tandy Center for Ocean Forecasting</a> to aid in the development of modeling studies requiring either observation/abundance point data or to modeled rasterized layers for subsequent use in modeling studies. Use the <a href="https://github.com/BigelowLab/jellyscape/issues">github issues tracker</a> to post questions or report issues.</p>


Expand Down Expand Up @@ -185,18 +194,7 @@ <h1 class="title">About</h1>
}
return false;
}
const clipboard = new window.ClipboardJS('.code-copy-button', {
text: function(trigger) {
const codeEl = trigger.previousElementSibling.cloneNode(true);
for (const childEl of codeEl.children) {
if (isCodeAnnotation(childEl)) {
childEl.remove();
}
}
return codeEl.innerText;
}
});
clipboard.on('success', function(e) {
const onCopySuccess = function(e) {
// button target
const button = e.trigger;
// don't keep focus
Expand Down Expand Up @@ -228,11 +226,50 @@ <h1 class="title">About</h1>
}, 1000);
// clear code selection
e.clearSelection();
}
const getTextToCopy = function(trigger) {
const codeEl = trigger.previousElementSibling.cloneNode(true);
for (const childEl of codeEl.children) {
if (isCodeAnnotation(childEl)) {
childEl.remove();
}
}
return codeEl.innerText;
}
const clipboard = new window.ClipboardJS('.code-copy-button:not([data-in-quarto-modal])', {
text: getTextToCopy
});
function tippyHover(el, contentFn) {
clipboard.on('success', onCopySuccess);
if (window.document.getElementById('quarto-embedded-source-code-modal')) {
// For code content inside modals, clipBoardJS needs to be initialized with a container option
// TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
text: getTextToCopy,
container: window.document.getElementById('quarto-embedded-source-code-modal')
});
clipboardModal.on('success', onCopySuccess);
}
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):not(.about-link)');
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,
content: contentFn,
maxWidth: 500,
delay: 100,
arrow: false,
Expand All @@ -242,8 +279,17 @@ <h1 class="title">About</h1>
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start'
placement: 'bottom-start',
};
if (contentFn) {
config.content = contentFn;
}
if (onTriggerFn) {
config.onTrigger = onTriggerFn;
}
if (onUntriggerFn) {
config.onUntrigger = onUntriggerFn;
}
window.tippy(el, config);
}
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
Expand All @@ -255,7 +301,130 @@ <h1 class="title">About</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');
const processXRef = (id, note) => {
// Strip column container classes
const stripColumnClz = (el) => {
el.classList.remove("page-full", "page-columns");
if (el.children) {
for (const child of el.children) {
stripColumnClz(child);
}
}
}
stripColumnClz(note)
if (id === null || id.startsWith('sec-')) {
// Special case sections, only their first couple elements
const container = document.createElement("div");
if (note.children && note.children.length > 2) {
container.appendChild(note.children[0].cloneNode(true));
for (let i = 1; i < note.children.length; i++) {
const child = note.children[i];
if (child.tagName === "P" && child.innerText === "") {
continue;
} else {
container.appendChild(child.cloneNode(true));
break;
}
}
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(container);
}
return container.innerHTML
} else {
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(note);
}
return note.innerHTML;
}
} else {
// Remove any anchor links if they are present
const anchorLink = note.querySelector('a.anchorjs-link');
if (anchorLink) {
anchorLink.remove();
}
if (window.Quarto?.typesetMath) {
window.Quarto.typesetMath(note);
}
// TODO in 1.5, we should make sure this works without a callout special case
if (note.classList.contains("callout")) {
return note.outerHTML;
} else {
return note.innerHTML;
}
}
}
for (var i=0; i<xrefs.length; i++) {
const xref = xrefs[i];
tippyHover(xref, undefined, function(instance) {
instance.disable();
let url = xref.getAttribute('href');
let hash = undefined;
if (url.startsWith('#')) {
hash = url;
} else {
try { hash = new URL(url).hash; } catch {}
}
if (hash) {
const id = hash.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
if (note !== null) {
try {
const html = processXRef(id, note.cloneNode(true));
instance.setContent(html);
} finally {
instance.enable();
instance.show();
}
} else {
// See if we can fetch this
fetch(url.split('#')[0])
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.getElementById(id);
if (note !== null) {
const html = processXRef(id, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
} else {
// See if we can fetch a full url (with no hash to target)
// This is a special case and we should probably do some content thinning / targeting
fetch(url)
.then(res => res.text())
.then(html => {
const parser = new DOMParser();
const htmlDoc = parser.parseFromString(html, "text/html");
const note = htmlDoc.querySelector('main.content');
if (note !== null) {
// This should only happen for chapter cross references
// (since there is no id in the URL)
// remove the first header
if (note.children.length > 0 && note.children[0].tagName === "HEADER") {
note.children[0].remove();
}
const html = processXRef(null, note);
instance.setContent(html);
}
}).finally(() => {
instance.enable();
instance.show();
});
}
}, function(instance) {
});
}
let selectedAnnoteEl;
Expand Down Expand Up @@ -299,6 +468,7 @@ <h1 class="title">About</h1>
}
div.style.top = top - 2 + "px";
div.style.height = height + 4 + "px";
div.style.left = 0;
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
if (gutterDiv === null) {
gutterDiv = window.document.createElement("div");
Expand All @@ -324,6 +494,32 @@ <h1 class="title">About</h1>
});
selectedAnnoteEl = undefined;
};
// Handle positioning of the toggle
window.addEventListener(
"resize",
throttle(() => {
elRect = undefined;
if (selectedAnnoteEl) {
selectCodeLines(selectedAnnoteEl);
}
}, 10)
);
function throttle(fn, ms) {
let throttle = false;
let timer;
return (...args) => {
if(!throttle) { // first call gets through
fn.apply(this, args);
throttle = true;
} else { // all the others get throttled
if(timer) clearTimeout(timer); // cancel #2
timer = setTimeout(() => {
fn.apply(this, args);
timer = throttle = false;
}, ms);
}
};
}
// Attach click handler to the DT
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
for (const annoteDlNode of annoteDls) {
Expand Down Expand Up @@ -385,7 +581,7 @@ <h1 class="title">About</h1>
</script>
<nav class="page-navigation">
<div class="nav-page nav-page-previous">
<a href="./salps.html" class="pagination-link">
<a href="./salps.html" class="pagination-link" aria-label="Salpsae">
<i class="bi bi-arrow-left-short"></i> <span class="nav-page-text">Salpsae</span>
</a>
</div>
Expand All @@ -398,7 +594,9 @@ <h1 class="title">About</h1>
<div class="nav-footer-left">
&nbsp;
</div>
<div class="nav-footer-center">Copyright 2024, Bigelow Laboratory for Ocean Science</div>
<div class="nav-footer-center">
<p>Copyright 2024, Bigelow Laboratory for Ocean Science</p>
</div>
<div class="nav-footer-right">
&nbsp;
</div>
Expand All @@ -407,4 +605,5 @@ <h1 class="title">About</h1>




</body></html>
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