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Rerender site
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@wlandau
wlandau committed Mar 20, 2024
1 parent bcf0e8d commit efef3e6
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Showing 44 changed files with 20,687 additions and 5,416 deletions.
250 changes: 153 additions & 97 deletions docs/contributing.html
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107 changes: 87 additions & 20 deletions docs/index.html
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
Expand All @@ -50,16 +49,17 @@
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ }
{ color: #00769e; background-color: #f1f3f5; }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span { color: #00769e; } /* Normal */
code span.al { color: #ad0000; } /* Alert */
code span.an { color: #5e5e5e; } /* Annotation */
code span.at { color: #20794d; } /* Attribute */
code span.at { color: #657422; } /* Attribute */
code span.bn { color: #ad0000; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #007ba5; } /* ControlFlow */
code span.cf { color: #00769e; } /* ControlFlow */
code span.ch { color: #20794d; } /* Char */
code span.cn { color: #8f5902; } /* Constant */
code span.co { color: #5e5e5e; } /* Comment */
Expand All @@ -73,18 +73,19 @@
code span.fu { color: #4758ab; } /* Function */
code span.im { } /* Import */
code span.in { color: #5e5e5e; } /* Information */
code span.kw { color: #007ba5; } /* Keyword */
code span.kw { color: #00769e; } /* Keyword */
code span.op { color: #5e5e5e; } /* Operator */
code span.ot { color: #007ba5; } /* Other */
code span.ot { color: #00769e; } /* Other */
code span.pp { color: #ad0000; } /* Preprocessor */
code span.sc { color: #20794d; } /* SpecialChar */
code span.sc { color: #5e5e5e; } /* SpecialChar */
code span.ss { color: #20794d; } /* SpecialString */
code span.st { color: #20794d; } /* String */
code span.va { color: #111111; } /* Variable */
code span.vs { color: #20794d; } /* VerbatimString */
code span.wa { color: #5e5e5e; font-style: italic; } /* Warning */
</style>


<!--radix_placeholder_meta_tags-->
<title>R Targetopia: The R Targetopia</title>

Expand Down Expand Up @@ -456,8 +457,8 @@
</style>

<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<link href="site_libs/font-awesome-5.1.0/css/all.css" rel="stylesheet"/>
<link href="site_libs/font-awesome-5.1.0/css/v4-shims.css" rel="stylesheet"/>
<link href="site_libs/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"/>
<link href="site_libs/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"/>
<script src="site_libs/headroom-0.9.4/headroom.min.js"></script>
<script src="site_libs/autocomplete-0.37.1/autocomplete.min.js"></script>
<script src="site_libs/fuse-6.4.1/fuse.min.js"></script>
Expand Down Expand Up @@ -786,6 +787,7 @@ <h3>${suggestion.title}</h3>
d-article table.gt_table td,
d-article table.gt_table th {
border-bottom: none;
font-size: 100%;
}

.html-widget {
Expand Down Expand Up @@ -826,9 +828,21 @@ <h3>${suggestion.title}</h3>
display: none !important;
}

hr.section-separator {
border: none;
border-top: 1px solid rgba(0, 0, 0, 0.1);
margin: 0px;
}


d-byline {
border-top: none;
}

d-article {
padding-top: 2.5rem;
padding-bottom: 30px;
border-top: none;
}

d-appendix {
Expand Down Expand Up @@ -925,6 +939,11 @@ <h3>${suggestion.title}</h3>
font-size: 14px;
}

/* tweak for Pandoc numbered line within distill */
d-article pre.numberSource code > span {
left: -2em;
}

d-article pre {
font-size: 14px;
}
Expand Down Expand Up @@ -1029,10 +1048,6 @@ <h3>${suggestion.title}</h3>
margin-top: 1.5em;
}

.figure img {
width: 100%;
}

.figure .caption {
color: rgba(0, 0, 0, 0.6);
font-size: 12px;
Expand Down Expand Up @@ -1688,6 +1703,12 @@ <h3>${suggestion.title}</h3>
// create d-title
$('.d-title').changeElementType('d-title');

// separator
var separator = '<hr class="section-separator" style="clear: both"/>';
// prepend separator above appendix
$('.d-byline').before(separator);
$('.d-article').before(separator);

// create d-byline
var byline = $('<d-byline></d-byline>');
$('.d-byline').replaceWith(byline);
Expand Down Expand Up @@ -1765,8 +1786,9 @@ <h3>${suggestion.title}</h3>
$('.distill-force-highlighting-css').parent().remove();

// remove empty line numbers inserted by pandoc when using a
// custom syntax highlighting theme
$('code.sourceCode a:empty').remove();
// custom syntax highlighting theme, except when numbering line
// in code chunk
$('pre:not(.numberLines) code.sourceCode a:empty').remove();

// load distill framework
load_distill_framework();
Expand All @@ -1792,12 +1814,13 @@ <h3>${suggestion.title}</h3>
// add orcid ids
$('.authors-affiliations').find('.author').each(function(i, el) {
var orcid_id = front_matter.authors[i].orcidID;
var author_name = front_matter.authors[i].author
if (orcid_id) {
var a = $('<a></a>');
a.attr('href', 'https://orcid.org/' + orcid_id);
var img = $('<img></img>');
img.addClass('orcid-id');
img.attr('alt', 'ORCID ID');
img.attr('alt', author_name ? 'ORCID ID for ' + author_name : 'ORCID ID');
img.attr('src','data:image/png;base64,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');
a.append(img);
$(this).append(a);
Expand Down Expand Up @@ -1862,7 +1885,22 @@ <h3>${suggestion.title}</h3>

// hoverable references
$('span.citation[data-cites]').each(function() {
var refHtml = $('#ref-' + $(this).attr('data-cites')).html();
const citeChild = $(this).children()[0]
// Do not process if @xyz has been used without escaping and without bibliography activated
// https://github.com/rstudio/distill/issues/466
if (citeChild === undefined) return true

if (citeChild.nodeName == "D-FOOTNOTE") {
var fn = citeChild
$(this).html(fn.shadowRoot.querySelector("sup"))
$(this).id = fn.id
fn.remove()
}
var refs = $(this).attr('data-cites').split(" ");
var refHtml = refs.map(function(ref) {
// Could use CSS.escape too here, we insure backward compatibility in navigator
return "<p>" + $('div[id="ref-' + ref + '"]').html() + "</p>";
}).join("\n");
window.tippy(this, {
allowHTML: true,
content: refHtml,
Expand All @@ -1874,6 +1912,31 @@ <h3>${suggestion.title}</h3>
});
});

// fix footnotes in tables (#411)
// replacing broken distill.pub feature
$('table d-footnote').each(function() {
// we replace internal showAtNode methode which is triggered when hovering a footnote
this.hoverBox.showAtNode = function(node) {
// ported from https://github.com/distillpub/template/pull/105/files
calcOffset = function(elem) {
let x = elem.offsetLeft;
let y = elem.offsetTop;
// Traverse upwards until an `absolute` element is found or `elem`
// becomes null.
while (elem = elem.offsetParent && elem.style.position != 'absolute') {
x += elem.offsetLeft;
y += elem.offsetTop;
}

return { left: x, top: y };
}
// https://developer.mozilla.org/en-US/docs/Web/API/HTMLElement/offsetTop
const bbox = node.getBoundingClientRect();
const offset = calcOffset(node);
this.show([offset.left + bbox.width, offset.top + bbox.height]);
}
})

// clear polling timer
clearInterval(tid);

Expand Down Expand Up @@ -1972,6 +2035,8 @@ <h3>${suggestion.title}</h3>
// mark non-body figures created by knitr chunks as 100% width
$('.layout-chunk').each(function(i, val) {
var figures = $(this).find('img, .html-widget');
// ignore leaflet img layers (#106)
figures = figures.filter(':not(img[class*="leaflet"])')
if ($(this).attr('data-layout') !== "l-body") {
figures.css('width', '100%');
} else {
Expand All @@ -1994,7 +2059,7 @@ <h3>${suggestion.title}</h3>
// get rid of index.html references in header
if (window.location.protocol !== "file:") {
$('.distill-site-header a[href]').each(function(i,val) {
$(this).attr('href', $(this).attr('href').replace("index.html", "./"));
$(this).attr('href', $(this).attr('href').replace(/^index[.]html/, "./"));
});
}

Expand Down Expand Up @@ -2033,7 +2098,7 @@ <h3>${suggestion.title}</h3>
</script>

<!--/radix_placeholder_distill-->
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.25/header-attrs.js"></script>
<script src="site_libs/popper-2.6.0/popper.min.js"></script>
<link href="site_libs/tippy-6.2.7/tippy.css" rel="stylesheet" />
<link href="site_libs/tippy-6.2.7/tippy-light-border.css" rel="stylesheet" />
Expand Down Expand Up @@ -2085,6 +2150,7 @@ <h3>${suggestion.title}</h3>

<div class="d-title">
<h1>The R Targetopia</h1>

<!--radix_placeholder_categories-->
<!--/radix_placeholder_categories-->
<p>An R package ecosystem for democratized reproducible pipelines at scale</p>
Expand All @@ -2098,7 +2164,8 @@ <h1>The R Targetopia</h1>
<a href="https://raw.githubusercontent.com/wlandau/targetopia/main/images/targetopia.png"><img src="images/targetopia/logo.png" height="200px"></a>
</th>
<th style="font-weight:normal;">
The R Targetopia makes it easy to create powerful <a href="https://www.gnu.org/software/make/">Make</a>-like reproducible analysis pipelines in R, accelerating development and reducing frustration for research papers, simulation studies, and other projects with copious workloads and demanding runtimes. R Targetopia packages are specialized workflow frameworks tailored to individual fields of Statistics and data science, and they use domain knowledge to abstract away most of the tricky planning and engineering typically required to write pipelines. They leverage the full power of <a href="https://github.com/ropensci/targets"><code>targets</code></a> while requiring minimal expertise with <a href="https://github.com/ropensci/targets"><code>targets</code></a> itself. <br><br>
The R Targetopia makes it easy to create powerful <a href="https://www.gnu.org/software/make/">Make</a>-like reproducible analysis pipelines in R, accelerating development and reducing frustration for research papers, simulation studies, and other projects with copious workloads and demanding runtimes. R Targetopia packages are specialized workflow frameworks tailored to individual fields of Statistics and data science, and they use domain knowledge to abstract away most of the tricky planning and engineering typically required to write pipelines. They leverage the full power of <a href="https://github.com/ropensci/targets"><code>targets</code></a> while requiring minimal expertise with <a href="https://github.com/ropensci/targets"><code>targets</code></a> itself.
<br><br>
</th>
</tr>
</table>
Expand Down

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