Commit 752aaa3b authored by Davis McCarthy's avatar Davis McCarthy
Browse files

Updating workflowr website

parent 104919f1
Pipeline #7142 passed with stage
in 9 seconds
......@@ -13,20 +13,27 @@
<title>SAHMRI Single-cell RNA-seq Analysis Workshop</title>
<script src="site_libs/header-attrs-2.5/header-attrs.js"></script>
<script src="site_libs/header-attrs-2.9/header-attrs.js"></script>
<script src="site_libs/jquery-1.11.3/jquery.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/journal.min.css" rel="stylesheet" />
<script src="site_libs/bootstrap-3.3.5/js/bootstrap.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/html5shiv.min.js"></script>
<script src="site_libs/bootstrap-3.3.5/shim/respond.min.js"></script>
<style>h1 {font-size: 34px;}
h1.title {font-size: 38px;}
h2 {font-size: 30px;}
h3 {font-size: 24px;}
h4 {font-size: 18px;}
h5 {font-size: 16px;}
h6 {font-size: 12px;}
code {color: inherit; background-color: rgba(0, 0, 0, 0.04);}
pre:not([class]) { background-color: white }</style>
<script src="site_libs/jqueryui-1.11.4/jquery-ui.min.js"></script>
<link href="site_libs/tocify-1.9.1/jquery.tocify.css" rel="stylesheet" />
<script src="site_libs/tocify-1.9.1/jquery.tocify.js"></script>
<script src="site_libs/navigation-1.1/tabsets.js"></script>
<script src="site_libs/navigation-1.1/codefolding.js"></script>
<link href="site_libs/anchor-sections-1.0/anchor-sections.css" rel="stylesheet" />
<script src="site_libs/anchor-sections-1.0/anchor-sections.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" />
......@@ -50,7 +57,14 @@ div.section {
</style>
<style type="text/css">code{white-space: pre;}</style>
<style type="text/css">
code {
white-space: pre;
}
.sourceCode {
overflow: visible;
}
</style>
<style type="text/css" data-origin="pandoc">
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
......@@ -147,39 +161,9 @@ code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warni
}
})();
</script>
<style type="text/css">
pre:not([class]) {
background-color: white;
}
</style>
<style type="text/css">
h1 {
font-size: 34px;
}
h1.title {
font-size: 38px;
}
h2 {
font-size: 30px;
}
h3 {
font-size: 24px;
}
h4 {
font-size: 18px;
}
h5 {
font-size: 16px;
}
h6 {
font-size: 12px;
}
.table th:not([align]) {
text-align: left;
}
</style>
......@@ -190,10 +174,6 @@ h6 {
margin-left: auto;
margin-right: auto;
}
code {
color: inherit;
background-color: rgba(0, 0, 0, 0.04);
}
img {
max-width:100%;
}
......@@ -209,40 +189,13 @@ button.code-folding-btn:focus {
summary {
display: list-item;
}
pre code {
padding: 0;
}
</style>
<style type="text/css">
/* padding for bootstrap navbar */
body {
padding-top: 51px;
padding-bottom: 40px;
}
/* offset scroll position for anchor links (for fixed navbar) */
.section h1 {
padding-top: 56px;
margin-top: -56px;
}
.section h2 {
padding-top: 56px;
margin-top: -56px;
}
.section h3 {
padding-top: 56px;
margin-top: -56px;
}
.section h4 {
padding-top: 56px;
margin-top: -56px;
}
.section h5 {
padding-top: 56px;
margin-top: -56px;
}
.section h6 {
padding-top: 56px;
margin-top: -56px;
}
.dropdown-submenu {
position: relative;
}
......@@ -270,7 +223,7 @@ body {
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #ffffff;
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
......@@ -282,7 +235,7 @@ body {
}
</style>
<script>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
......@@ -293,10 +246,23 @@ $(document).ready(function () {
var menuAnchor = $('a[href="' + href + '"]');
// mark it active
menuAnchor.parent().addClass('active');
menuAnchor.tab('show');
// if it's got a parent navbar menu mark it active as well
menuAnchor.closest('li.dropdown').addClass('active');
// Navbar adjustments
var navHeight = $(".navbar").first().height() + 15;
var style = document.createElement('style');
var pt = "padding-top: " + navHeight + "px; ";
var mt = "margin-top: -" + navHeight + "px; ";
var css = "";
// offset scroll position for anchor links (for fixed navbar)
for (var i = 1; i <= 6; i++) {
css += ".section h" + i + "{ " + pt + mt + "}\n";
}
style.innerHTML = "body {" + pt + "padding-bottom: 40px; }\n" + css;
document.head.appendChild(style);
});
</script>
......@@ -308,7 +274,6 @@ $(document).ready(function () {
max-height: 500px;
min-height: 44px;
overflow-y: auto;
background: white;
border: 1px solid #ddd;
border-radius: 4px;
}
......@@ -437,7 +402,7 @@ div.tocify {
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row-fluid">
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
......@@ -482,11 +447,11 @@ div.tocify {
</div><!--/.container -->
</div><!--/.navbar -->
<div class="fluid-row" id="header">
<div id="header">
<div class="btn-group pull-right">
<button type="button" class="btn btn-default btn-xs dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
<ul class="dropdown-menu" style="min-width: 50px;">
<div class="btn-group pull-right float-right">
<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"><span>Code</span> <span class="caret"></span></button>
<ul class="dropdown-menu dropdown-menu-right" style="min-width: 50px;">
<li><a id="rmd-show-all-code" href="#">Show All Code</a></li>
<li><a id="rmd-hide-all-code" href="#">Hide All Code</a></li>
</ul>
......@@ -519,7 +484,7 @@ div.tocify {
<div class="tab-content">
<div id="summary" class="tab-pane fade in active">
<p>
<strong>Last updated:</strong> 2021-06-30
<strong>Last updated:</strong> 2021-07-05
</p>
<p>
<strong>Checks:</strong> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> 7 <span class="glyphicon glyphicon-exclamation-sign text-danger" aria-hidden="true"></span> 0
......@@ -610,22 +575,23 @@ This reproducible <a href="http://rmarkdown.rstudio.com">R Markdown</a> analysis
<div class="panel panel-default">
<div class="panel-heading">
<p class="panel-title">
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytree4bcd6066e4fd3abded90bff112ebec5495654f7atargetblank4bcd606a"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/tree/4bcd6066e4fd3abded90bff112ebec5495654f7a" target="_blank">4bcd606</a> </a>
<a data-toggle="collapse" data-parent="#workflowr-checks" href="#strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytree104919f1b95420ee20db94780607ba9b82fe77a2targetblank104919fa"> <span class="glyphicon glyphicon-ok text-success" aria-hidden="true"></span> <strong>Repository version:</strong> <a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/tree/104919f1b95420ee20db94780607ba9b82fe77a2" target="_blank">104919f</a> </a>
</p>
</div>
<div id="strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytree4bcd6066e4fd3abded90bff112ebec5495654f7atargetblank4bcd606a" class="panel-collapse collapse">
<div id="strongRepositoryversionstrongahrefhttpsgitlabsvieduaubiocellgenpublicsvisahmriscrnaseqworkshop2021julytree104919f1b95420ee20db94780607ba9b82fe77a2targetblank104919fa" class="panel-collapse collapse">
<div class="panel-body">
<p>
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
</p>
<p>
The results in this page were generated with repository version <a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/tree/4bcd6066e4fd3abded90bff112ebec5495654f7a" target="_blank">4bcd606</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
The results in this page were generated with repository version <a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/tree/104919f1b95420ee20db94780607ba9b82fe77a2" target="_blank">104919f</a>. See the <em>Past versions</em> tab to see a history of the changes made to the R Markdown and HTML files.
</p>
<p>
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use <code>wflow_publish</code> or <code>wflow_git_commit</code>). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
</p>
<pre><code>
Ignored files:
Ignored: .Rhistory
Ignored: .Rproj.user/
Untracked files:
......@@ -633,9 +599,6 @@ Untracked files:
Untracked: svi-sahmri_scrna-seq-workshop_2021-july.Rproj
Untracked: untar_path/
Unstaged changes:
Modified: analysis/sahmri_analysis-workflow.Rmd
</code></pre>
<p>
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
......@@ -675,6 +638,23 @@ Message
<tbody>
<tr>
<td>
html
</td>
<td>
<a href="https://gitlab.svi.edu.au/biocellgen-public/svi-sahmri_scrna-seq-workshop_2021-july/blob/15804b7544afe2b71ca744905eee77e930f21e8e/public/index.html" target="_blank">15804b7</a>
</td>
<td>
Davis McCarthy
</td>
<td>
2021-07-01
</td>
<td>
Checking in edits
</td>
</tr>
<tr>
<td>
Rmd
</td>
<td>
......@@ -806,56 +786,62 @@ Updating materials for workshop in July 2021
collate en_AU.UTF-8
ctype en_AU.UTF-8
tz Australia/Melbourne
date 2021-06-30
date 2021-07-05
─ Packages ───────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.2)
cli 2.4.0 2021-04-05 [1] CRAN (R 4.0.2)
bslib 0.2.5.1 2021-05-18 [1] CRAN (R 4.0.2)
cachem 1.0.5 2021-05-15 [1] CRAN (R 4.0.2)
callr 3.7.0 2021-04-20 [1] CRAN (R 4.0.2)
cli 3.0.0 2021-06-30 [1] CRAN (R 4.0.3)
crayon 1.4.1 2021-02-08 [1] CRAN (R 4.0.2)
desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2)
devtools 2.3.2 2020-09-18 [1] CRAN (R 4.0.2)
desc 1.3.0 2021-03-05 [1] CRAN (R 4.0.2)
devtools 2.4.2 2021-06-07 [1] CRAN (R 4.0.2)
digest 0.6.27 2020-10-24 [1] CRAN (R 4.0.2)
ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.0.2)
evaluate 0.14 2019-05-28 [1] CRAN (R 4.0.1)
fansi 0.4.2 2021-01-15 [1] CRAN (R 4.0.2)
fansi 0.5.0 2021-05-25 [1] CRAN (R 4.0.2)
fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.0.2)
fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2)
git2r 0.27.1 2020-05-03 [1] CRAN (R 4.0.2)
git2r 0.28.0 2021-01-10 [1] CRAN (R 4.0.2)
glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
htmltools 0.5.0 2020-06-16 [1] CRAN (R 4.0.2)
httpuv 1.5.4 2020-06-06 [1] CRAN (R 4.0.2)
knitr 1.30 2020-09-22 [1] CRAN (R 4.0.2)
later 1.1.0.1 2020-06-05 [1] CRAN (R 4.0.2)
htmltools 0.5.1.1 2021-01-22 [1] CRAN (R 4.0.2)
httpuv 1.6.1 2021-05-07 [1] CRAN (R 4.0.2)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.0.2)
jsonlite 1.7.2 2020-12-09 [1] CRAN (R 4.0.2)
knitr 1.33 2021-04-24 [1] CRAN (R 4.0.2)
later 1.2.0 2021-04-23 [1] CRAN (R 4.0.2)
lifecycle 1.0.0 2021-02-15 [1] CRAN (R 4.0.2)
magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.2)
memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2)
pillar 1.6.0 2021-04-13 [1] CRAN (R 4.0.2)
pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2)
memoise 2.0.0 2021-01-26 [1] CRAN (R 4.0.2)
pillar 1.6.1 2021-05-16 [1] CRAN (R 4.0.2)
pkgbuild 1.2.0 2020-12-15 [1] CRAN (R 4.0.2)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2)
pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2)
pkgload 1.2.1 2021-04-06 [1] CRAN (R 4.0.2)
prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2)
processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2)
promises 1.1.1 2020-06-09 [1] CRAN (R 4.0.2)
ps 1.4.0 2020-10-07 [1] CRAN (R 4.0.2)
processx 3.5.2 2021-04-30 [1] CRAN (R 4.0.2)
promises 1.2.0.1 2021-02-11 [1] CRAN (R 4.0.2)
ps 1.6.0 2021-02-28 [1] CRAN (R 4.0.2)
purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2)
Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2)
remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2)
rlang 0.4.10 2020-12-30 [1] CRAN (R 4.0.2)
rmarkdown 2.5 2020-10-21 [1] CRAN (R 4.0.2)
Rcpp 1.0.6 2021-01-15 [1] CRAN (R 4.0.2)
remotes 2.4.0 2021-06-02 [1] CRAN (R 4.0.2)
rlang 0.4.11 2021-04-30 [1] CRAN (R 4.0.2)
rmarkdown 2.9 2021-06-15 [1] CRAN (R 4.0.2)
rprojroot 2.0.2 2020-11-15 [1] CRAN (R 4.0.2)
sass 0.4.0 2021-05-12 [1] CRAN (R 4.0.2)
sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
stringi 1.5.3 2020-09-09 [1] CRAN (R 4.0.2)
stringi 1.6.2 2021-05-17 [1] CRAN (R 4.0.2)
stringr 1.4.0 2019-02-10 [1] CRAN (R 4.0.2)
testthat 3.0.0 2020-10-31 [1] CRAN (R 4.0.2)
tibble 3.1.1 2021-04-18 [1] CRAN (R 4.0.2)
usethis 1.6.3 2020-09-17 [1] CRAN (R 4.0.2)
testthat 3.0.3 2021-06-16 [1] CRAN (R 4.0.2)
tibble 3.1.2 2021-05-16 [1] CRAN (R 4.0.2)
usethis 2.0.1 2021-02-10 [1] CRAN (R 4.0.2)
utf8 1.2.1 2021-03-12 [1] CRAN (R 4.0.2)
vctrs 0.3.7 2021-03-29 [1] CRAN (R 4.0.2)
vctrs 0.3.8 2021-04-29 [1] CRAN (R 4.0.2)
whisker 0.4 2019-08-28 [1] CRAN (R 4.0.2)
withr 2.4.2 2021-04-18 [1] CRAN (R 4.0.2)
workflowr 1.6.2 2020-04-30 [1] CRAN (R 4.0.2)
xfun 0.19 2020-10-30 [1] CRAN (R 4.0.2)
xfun 0.24 2021-06-15 [1] CRAN (R 4.0.2)
yaml 2.2.1 2020-02-01 [1] CRAN (R 4.0.2)
[1] /Users/dmccarthy/Library/R/4.0/library
......@@ -906,7 +892,7 @@ $(document).ready(function () {
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open')
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
......@@ -921,6 +907,9 @@ $(document).ready(function () {
<script>
$(document).ready(function () {
// temporarily add toc-ignore selector to headers for the consistency with Pandoc
$('.unlisted.unnumbered').addClass('toc-ignore')
// move toc-ignore selectors from section div to header
$('div.section.toc-ignore')
.removeClass('toc-ignore')
......
This diff is collapsed.
// Pandoc 2.9 adds attributes on both header and div. We remove the former (to
// be compatible with the behavior of Pandoc < 2.8).
document.addEventListener('DOMContentLoaded', function(e) {
var hs = document.querySelectorAll("div.section[class*='level'] > :first-child");
var i, h, a;
for (i = 0; i < hs.length; i++) {
h = hs[i];
if (!/^h[1-6]$/i.test(h.tagName)) continue; // it should be a header h1-h6
a = h.attributes;
while (a.length > 0) h.removeAttribute(a[0].name);
}
});
......@@ -23,7 +23,6 @@ window.initializeCodeFolding = function(show) {
// create a collapsable div to wrap the code in
var div = $('<div class="collapse r-code-collapse"></div>');
var showThis = (show || $(this).hasClass('fold-show')) && !$(this).hasClass('fold-hide');
if (showThis) div.addClass('in');
var id = 'rcode-643E0F36' + currentIndex++;
div.attr('id', id);
$(this).before(div);
......@@ -31,7 +30,7 @@ window.initializeCodeFolding = function(show) {
// add a show code button right above
var showCodeText = $('<span>' + (showThis ? 'Hide' : 'Code') + '</span>');
var showCodeButton = $('<button type="button" class="btn btn-default btn-xs code-folding-btn pull-right"></button>');
var showCodeButton = $('<button type="button" class="btn btn-default btn-xs btn-secondary btn-sm code-folding-btn pull-right float-right"></button>');
showCodeButton.append(showCodeText);
showCodeButton
.attr('data-toggle', 'collapse')
......@@ -47,13 +46,27 @@ window.initializeCodeFolding = function(show) {
div.before(buttonRow);
// show the div if necessary
if (showThis) div.collapse('show');
// update state of button on show/hide
div.on('hidden.bs.collapse', function () {
// * Change text
// * add a class for intermediate states styling
div.on('hide.bs.collapse', function () {
showCodeText.text('Code');
showCodeButton.addClass('btn-collapsing');
});
div.on('hidden.bs.collapse', function () {
showCodeButton.removeClass('btn-collapsing');
});
div.on('show.bs.collapse', function () {
showCodeText.text('Hide');
showCodeButton.addClass('btn-expanding');
});
div.on('shown.bs.collapse', function () {
showCodeButton.removeClass('btn-expanding');
});
});
}
......@@ -176,7 +176,7 @@
self._setEventHandlers();
// Binding to the Window load event to make sure the correct scrollTop is calculated
$(window).load(function() {
$(window).on("load", function() {
// Sets the active TOC item
self._setActiveElement(true);
......
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