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Draft core 1 #2

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merged 4 commits into from
Sep 28, 2023
Merged

Draft core 1 #2

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3ad9e84
add installation of downlit and xml2 to gh action
3mmaRand Sep 24, 2023
f2b04f5
complete draft
3mmaRand Sep 28, 2023
fc710bd
the end of the complete draft I forgot to ssave before committing!
3mmaRand Sep 28, 2023
8e70e61
fixes
3mmaRand Sep 28, 2023
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7 changes: 6 additions & 1 deletion .github/workflows/quarto-gh-pages-html.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,12 @@ jobs:

# Install any computing dependency you may need, usually either python and Jupyter or R
# More specific examples will be shared on quarto-dev/quarto-actions project


- name: Install R package
run: |
R -e "install.packages('xml2')"
R -e "install.packages('downlit')"

- name: Render book to all format
# Add any command line argument needed
run: |
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131 changes: 12 additions & 119 deletions _site/about.html
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Original file line number Diff line number Diff line change
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-1.3.361">
<meta name="generator" content="quarto-1.2.269">

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

Expand All @@ -18,7 +18,7 @@
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
margin: 0 0.8em 0.2em -1.6em;
vertical-align: middle;
}
</style>
Expand Down Expand Up @@ -56,12 +56,12 @@
"search-more-matches-text": "more matches in this document",
"search-clear-button-title": "Clear",
"search-detached-cancel-button-title": "Cancel",
"search-submit-button-title": "Submit",
"search-label": "Search"
"search-submit-button-title": "Submit"
}
}</script>


<link rel="stylesheet" href="styles.css">
</head>

<body class="nav-fixed fullcontent">
Expand All @@ -75,29 +75,25 @@
<span class="navbar-title">Data Analysis for Group Project</span>
</a>
</div>
<div id="quarto-search" class="" title="Search"></div>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarCollapse">
<ul class="navbar-nav navbar-nav-scroll me-auto">
<li class="nav-item">
<a class="nav-link" href="./index.html" rel="" target="">
<a class="nav-link" href="./index.html">
<span class="menu-text">Welcome!</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="./core/core.html" rel="" target="">
<a class="nav-link" href="./core/core.html">
<span class="menu-text">Core</span></a>
</li>
<li class="nav-item">
<a class="nav-link" href="./omics/omics.html" rel="" target="">
<a class="nav-link" href="./omics/omics.html">
<span class="menu-text">Omics</span></a>
</li>
</ul>
<div class="quarto-navbar-tools ms-auto">
<a href="https://twitter.com/er_13" title="Emma's Twitter" class="quarto-navigation-tool px-1" aria-label="Emma's Twitter"><i class="bi bi-twitter"></i></a>
<a href="https://github.com/3mmaRand/BIO00088H-data" title="BIO00088H-data GitHub" class="quarto-navigation-tool px-1" aria-label="BIO00088H-data GitHub"><i class="bi bi-github"></i></a>
</div>
<div id="quarto-search" class="" title="Search"></div>
</div> <!-- /navcollapse -->
</div> <!-- /container-fluid -->
</nav>
Expand Down Expand Up @@ -159,23 +155,9 @@ <h1 class="title">About</h1>
icon: icon
};
anchorJS.add('.anchored');
const isCodeAnnotation = (el) => {
for (const clz of el.classList) {
if (clz.startsWith('code-annotation-')) {
return true;
}
}
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;
target: function(trigger) {
return trigger.previousElementSibling;
}
});
clipboard.on('success', function(e) {
Expand Down Expand Up @@ -240,92 +222,6 @@ <h1 class="title">About</h1>
return note.innerHTML;
});
}
let selectedAnnoteEl;
const selectorForAnnotation = ( cell, annotation) => {
let cellAttr = 'data-code-cell="' + cell + '"';
let lineAttr = 'data-code-annotation="' + annotation + '"';
const selector = 'span[' + cellAttr + '][' + lineAttr + ']';
return selector;
}
const selectCodeLines = (annoteEl) => {
const doc = window.document;
const targetCell = annoteEl.getAttribute("data-target-cell");
const targetAnnotation = annoteEl.getAttribute("data-target-annotation");
const annoteSpan = window.document.querySelector(selectorForAnnotation(targetCell, targetAnnotation));
const lines = annoteSpan.getAttribute("data-code-lines").split(",");
const lineIds = lines.map((line) => {
return targetCell + "-" + line;
})
let top = null;
let height = null;
let parent = null;
if (lineIds.length > 0) {
//compute the position of the single el (top and bottom and make a div)
const el = window.document.getElementById(lineIds[0]);
top = el.offsetTop;
height = el.offsetHeight;
parent = el.parentElement.parentElement;
if (lineIds.length > 1) {
const lastEl = window.document.getElementById(lineIds[lineIds.length - 1]);
const bottom = lastEl.offsetTop + lastEl.offsetHeight;
height = bottom - top;
}
if (top !== null && height !== null && parent !== null) {
// cook up a div (if necessary) and position it
let div = window.document.getElementById("code-annotation-line-highlight");
if (div === null) {
div = window.document.createElement("div");
div.setAttribute("id", "code-annotation-line-highlight");
div.style.position = 'absolute';
parent.appendChild(div);
}
div.style.top = top - 2 + "px";
div.style.height = height + 4 + "px";
let gutterDiv = window.document.getElementById("code-annotation-line-highlight-gutter");
if (gutterDiv === null) {
gutterDiv = window.document.createElement("div");
gutterDiv.setAttribute("id", "code-annotation-line-highlight-gutter");
gutterDiv.style.position = 'absolute';
const codeCell = window.document.getElementById(targetCell);
const gutter = codeCell.querySelector('.code-annotation-gutter');
gutter.appendChild(gutterDiv);
}
gutterDiv.style.top = top - 2 + "px";
gutterDiv.style.height = height + 4 + "px";
}
selectedAnnoteEl = annoteEl;
}
};
const unselectCodeLines = () => {
const elementsIds = ["code-annotation-line-highlight", "code-annotation-line-highlight-gutter"];
elementsIds.forEach((elId) => {
const div = window.document.getElementById(elId);
if (div) {
div.remove();
}
});
selectedAnnoteEl = undefined;
};
// Attach click handler to the DT
const annoteDls = window.document.querySelectorAll('dt[data-target-cell]');
for (const annoteDlNode of annoteDls) {
annoteDlNode.addEventListener('click', (event) => {
const clickedEl = event.target;
if (clickedEl !== selectedAnnoteEl) {
unselectCodeLines();
const activeEl = window.document.querySelector('dt[data-target-cell].code-annotation-active');
if (activeEl) {
activeEl.classList.remove('code-annotation-active');
}
selectCodeLines(clickedEl);
clickedEl.classList.add('code-annotation-active');
} else {
// Unselect the line
unselectCodeLines();
clickedEl.classList.remove('code-annotation-active');
}
});
}
const findCites = (el) => {
const parentEl = el.parentElement;
if (parentEl) {
Expand Down Expand Up @@ -364,12 +260,12 @@ <h1 class="title">About</h1>
}
}
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var filterRegex = new RegExp("^(?:http:|https:)\/\/3mmarand\.github\.io\/BIO00088H-data");
var filterRegex = new RegExp(/^(?:http:|https:)\/\/3mmarand\.github\.io\/BIO00088H-data/);
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.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)');
var links = window.document.querySelectorAll('a: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)');
for (var i=0; i<links.length; i++) {
const link = links[i];
if (!isInternal(link.href)) {
Expand All @@ -383,9 +279,6 @@ <h1 class="title">About</h1>
<footer class="footer">
<div class="nav-footer">
<div class="nav-footer-left"><code>r cffr::cff_to_bibtex("CITATION.cff")</code></div>
<div class="nav-footer-center">
&nbsp;
</div>
<div class="nav-footer-right">
<ul class="footer-items list-unstyled">
<li class="nav-item compact">
Expand Down
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