-
Notifications
You must be signed in to change notification settings - Fork 10
/
README.html
343 lines (325 loc) · 17.9 KB
/
README.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.2.269">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<title>readme</title>
<style>
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
div.columns{display: flex; gap: min(4vw, 1.5em);}
div.column{flex: auto; overflow-x: auto;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
ul.task-list li input[type="checkbox"] {
width: 0.8em;
margin: 0 0.8em 0.2em -1.6em;
vertical-align: middle;
}
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; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
{ counter-reset: source-line 0; }
pre.numberSource code > span
{ position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
{ content: counter(source-line);
position: relative; left: -1em; text-align: right; vertical-align: baseline;
border: none; display: inline-block;
-webkit-touch-callout: none; -webkit-user-select: none;
-khtml-user-select: none; -moz-user-select: none;
-ms-user-select: none; user-select: none;
padding: 0 4px; width: 4em;
color: #aaaaaa;
}
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa; padding-left: 4px; }
div.sourceCode
{ }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { color: #008000; } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { color: #008000; font-weight: bold; } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */
</style>
<script src="README_files/libs/clipboard/clipboard.min.js"></script>
<script src="README_files/libs/quarto-html/quarto.js"></script>
<script src="README_files/libs/quarto-html/popper.min.js"></script>
<script src="README_files/libs/quarto-html/tippy.umd.min.js"></script>
<script src="README_files/libs/quarto-html/anchor.min.js"></script>
<link href="README_files/libs/quarto-html/tippy.css" rel="stylesheet">
<link href="README_files/libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
<script src="README_files/libs/bootstrap/bootstrap.min.js"></script>
<link href="README_files/libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
<link href="README_files/libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
</head>
<body class="fullcontent">
<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
<main class="content" id="quarto-document-content">
<section id="pharmaverse-blog" class="level1">
<h1>pharmaverse blog <img src="media/pharmaverseblog.png" align="right" width="200" style="margin-left:50px;"></h1>
<section id="purpose" class="level2">
<h2 class="anchored" data-anchor-id="purpose">Purpose</h2>
<p>The communications working group (CWG) seeks to promote and showcase how R can be used in the Clinical Reporting pipeline through short and informative blog posts. These posts will be hosted on this <a href="https://pharmaverse.github.io/blog/">pharmaverse blog</a> and promoted on the pharmaverse slack channels as well as on LinkedIn.</p>
<p>As the CWG is a small team, we hope to make the blog development process easy enough that pharmaverse community members will be able to easily write blog posts with guidance from the CWG team.</p>
</section>
<section id="spirit-of-a-blog-post" class="level2">
<h2 class="anchored" data-anchor-id="spirit-of-a-blog-post">Spirit of a Blog Post</h2>
<p>The CWG believes that the following 4 points will help guide the creation of Blog Posts.</p>
<ul>
<li><strong>Short</strong></li>
<li><strong>Personalized</strong></li>
<li><strong>Reproducible</strong></li>
<li><strong>Readable</strong></li>
</ul>
<p><strong>Short:</strong> Posts should aim to be under a 10 minute read. We encourage longer posts to be broken up into multiple posts.</p>
<p><strong>Personalized:</strong> Posts should have a personality! For example, a person wishing to post on a function in a package needs to differentiate the post from the documentation for function, i.e. we don’t want to just recycle the documentation. How can you add your voice and experience? A bit of cheeky language is also encouraged.</p>
<p><strong>Reproducible:</strong> Posts should work with minimal dependencies with data, packages and outside sources. Every dependency introduced in a post adds some risk to the post longevity. As package dependencies change, posts should be built in a way that they can be updated to stay relevant.</p>
<p><strong>Readable:</strong> The CWG sees this site as more of introductory site rather advanced user site. Therefore, the CWG feels that code should be introduced in a way that promotes readability over complexity.</p>
</section>
<section id="what-types-of-posts-are-allowed-on-this-site" class="level2">
<h2 class="anchored" data-anchor-id="what-types-of-posts-are-allowed-on-this-site">What types of posts are allowed on this site?</h2>
<p>Overall, we want to stay focus on the Clinical Reporting Pipeline, which we see as the following topics:</p>
<ol type="1">
<li>Packages in the Clinical Reporting Pipeline</li>
<li>Functions from packages in the Clinical Reporting Pipeline</li>
<li>Wider experiences of using R in the Clinical Reporting Pipeline</li>
<li>Conference experiences and the Clinical Reporting Pipeline</li>
</ol>
<p>However, it never hurts to ask if you topic might fit into this medium!.</p>
<section id="minimum-post-requirements" class="level3">
<h3 class="anchored" data-anchor-id="minimum-post-requirements">Minimum Post Requirements</h3>
<ul>
<li>A unique image to help showcase the post.</li>
<li>Working Code</li>
<li>Self-contained data or package data.</li>
<li>Documentation of package versions</li>
</ul>
<p>That is it! After that you can go wild, but we do ask that it is kept short!</p>
</section>
</section>
<section id="how-can-i-make-a-blog-post" class="level2">
<h2 class="anchored" data-anchor-id="how-can-i-make-a-blog-post">How can I make a Blog Post</h2>
<p><strong>Step 1:</strong> Reach out to us through <a href="https://pharmaverse.slack.com">pharmaverse/slack</a> or make an issue on our <a href="https://github.com/pharmaverse/blog/issues">GitHub</a>.</p>
<p><strong>Step 2:</strong> Branch off <code>main</code></p>
<p><strong>Step 3:</strong> Create a new Blog Post skeleton using the <code>create_blog_post.R</code> script in the <code>R/</code> folder.</p>
<ul>
<li><p>Open the <code>create_blogpost.R</code> file.</p></li>
<li><p>Source the script <code>help_create_blogpost.R</code> from within the <code>create_blogpost.R</code> file.</p></li>
<li><p>Enter your information into the <code>create_post</code> function. Please note that we do not currently allow users to specify their own categories (or <code>tags</code>), so you must chose (possibly several) from this list: <code>c("metadata", "submission", "qc", "ADaMs", "SDTMs", "community", "conferences", "admiral", "roak", "xportr", "metatools", "metacore")</code>.</p></li>
<li><p>Running that function will create a subfolder with a quarto file (<code>*.qmd</code>) in the <code>posts/</code> folder. Both should be named based on the supplied <code>post_date</code> and <code>post_name</code> information.</p></li>
<li><p>Open the newly created folder and start working within the <code>*.qmd</code> file.</p></li>
</ul>
<p><strong>Step 4:</strong> After you have finished your Blog Post, open the <code>CICD.R</code> file in the <code>R/</code> folder. Run the script line by line to first check the spelling in your post and then to make sure your code is compatible with our code-style.</p>
<p><strong>Step 5:</strong> Push to your branch, create a Pull Request, and review the Spirit of the Blog Post in the Pull Request Template.</p>
<p><strong>Step 6:</strong> Poke us to do a review!</p>
<p>Most importantly:</p>
<p><strong>Step 7:</strong> Have fun :)</p>
</section>
<section id="how-to-use-the-blog-docker-image-for-local-development" class="level2">
<h2 class="anchored" data-anchor-id="how-to-use-the-blog-docker-image-for-local-development">How to Use the <code>blog</code> Docker Image for Local Development</h2>
<p>Contributors can benefit from using the <a href="https://github.com/pharmaverse/blog/pkgs/container/blog"><code>blog</code> Docker image</a> when creating their blog posts. This way, contributors don’t have to install all dependencies from other blog posts and can solely focus on their own blog post and its dependencies.</p>
<p>Here are the steps to use the blog’s Docker image:</p>
<ol type="1">
<li>Ensure you have <a href="https://docs.docker.com/get-docker/">Docker Desktop</a> installed.</li>
<li>Start Docker Desktop on your machine.</li>
<li>Perform a Docker pull from the blog’s GitHub registry by running this code:</li>
</ol>
<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">docker</span> pull ghcr.io/pharmaverse/blog:latest</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<ol start="4" type="1">
<li>Clone this <code>blog</code> repository and take note of the location of the repo in your local machine.</li>
<li>Update the code below specifying the location of your ‘blog’ repository and execute the script:</li>
</ol>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="ex">docker</span> run <span class="at">--rm</span> <span class="at">-ti</span> <span class="at">-e</span> PASSWORD=yourpassword <span class="at">-p</span> 8787:8787 <span class="at">-v</span> <span class="op"><</span>location of your blog repo<span class="op">></span>:/home/rstudio/work ghcr.io/pharmaverse/blog</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>Here’s an example:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="ex">docker</span> run <span class="at">--rm</span> <span class="at">-ti</span> <span class="at">-e</span> PASSWORD=yourpassword <span class="at">-p</span> 8787:8787 <span class="at">-v</span> ~/Documents/blog:/home/rstudio/work ghcr.io/pharmaverse/blog</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>This command will run the <code>blog</code> Docker image and mount your local folder to the image.</p>
<ol start="6" type="1">
<li>Open http://localhost:8787/ and you should see the RStudio welcome page.</li>
<li>The username will be <code>rstudio</code>, and the password is <code>yourpassword</code>.</li>
<li>Once logged in, go to the work folder, and you should see the contents of the <code>blog</code> repository.</li>
<li>Click the <code>quarto-blog.Rproj</code> file to open the project.</li>
<li>You can test by opening the <code>index.qmd</code> and rendering the document.</li>
<li>Quarto should run, and you should be able to see the rendered blog locally.</li>
<li>Develop your blog post and re-render as needed.</li>
<li>Once complete, you can close the RStudio session, shut down the image, and push your update to the blog repo.</li>
</ol>
<p>Please note that there is no SSH or git capability in the docker image, so you can’t push your update to the repo from the image directly. To push the update, you would have to do it from your local RStudio or terminal.</p>
<p>A Dockerfile is also provided in this repo if you want to build the image locally and add more functionalities.</p>
</section>
</section>
</main>
<!-- /main column -->
<script id="quarto-html-after-body" type="application/javascript">
window.document.addEventListener("DOMContentLoaded", function (event) {
const toggleBodyColorMode = (bsSheetEl) => {
const mode = bsSheetEl.getAttribute("data-mode");
const bodyEl = window.document.querySelector("body");
if (mode === "dark") {
bodyEl.classList.add("quarto-dark");
bodyEl.classList.remove("quarto-light");
} else {
bodyEl.classList.add("quarto-light");
bodyEl.classList.remove("quarto-dark");
}
}
const toggleBodyColorPrimary = () => {
const bsSheetEl = window.document.querySelector("link#quarto-bootstrap");
if (bsSheetEl) {
toggleBodyColorMode(bsSheetEl);
}
}
toggleBodyColorPrimary();
const icon = "";
const anchorJS = new window.AnchorJS();
anchorJS.options = {
placement: 'right',
icon: icon
};
anchorJS.add('.anchored');
const clipboard = new window.ClipboardJS('.code-copy-button', {
target: function(trigger) {
return trigger.previousElementSibling;
}
});
clipboard.on('success', function(e) {
// button target
const button = e.trigger;
// don't keep focus
button.blur();
// flash "checked"
button.classList.add('code-copy-button-checked');
var currentTitle = button.getAttribute("title");
button.setAttribute("title", "Copied!");
let tooltip;
if (window.bootstrap) {
button.setAttribute("data-bs-toggle", "tooltip");
button.setAttribute("data-bs-placement", "left");
button.setAttribute("data-bs-title", "Copied!");
tooltip = new bootstrap.Tooltip(button,
{ trigger: "manual",
customClass: "code-copy-button-tooltip",
offset: [0, -8]});
tooltip.show();
}
setTimeout(function() {
if (tooltip) {
tooltip.hide();
button.removeAttribute("data-bs-title");
button.removeAttribute("data-bs-toggle");
button.removeAttribute("data-bs-placement");
}
button.setAttribute("title", currentTitle);
button.classList.remove('code-copy-button-checked');
}, 1000);
// clear code selection
e.clearSelection();
});
function tippyHover(el, contentFn) {
const config = {
allowHTML: true,
content: contentFn,
maxWidth: 500,
delay: 100,
arrow: false,
appendTo: function(el) {
return el.parentElement;
},
interactive: true,
interactiveBorder: 10,
theme: 'quarto',
placement: 'bottom-start'
};
window.tippy(el, config);
}
const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
for (var i=0; i<noterefs.length; i++) {
const ref = noterefs[i];
tippyHover(ref, function() {
// use id or data attribute instead here
let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
try { href = new URL(href).hash; } catch {}
const id = href.replace(/^#\/?/, "");
const note = window.document.getElementById(id);
return note.innerHTML;
});
}
const findCites = (el) => {
const parentEl = el.parentElement;
if (parentEl) {
const cites = parentEl.dataset.cites;
if (cites) {
return {
el,
cites: cites.split(' ')
};
} else {
return findCites(el.parentElement)
}
} else {
return undefined;
}
};
var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
for (var i=0; i<bibliorefs.length; i++) {
const ref = bibliorefs[i];
const citeInfo = findCites(ref);
if (citeInfo) {
tippyHover(citeInfo.el, function() {
var popup = window.document.createElement('div');
citeInfo.cites.forEach(function(cite) {
var citeDiv = window.document.createElement('div');
citeDiv.classList.add('hanging-indent');
citeDiv.classList.add('csl-entry');
var biblioDiv = window.document.getElementById('ref-' + cite);
if (biblioDiv) {
citeDiv.innerHTML = biblioDiv.innerHTML;
}
popup.appendChild(citeDiv);
});
return popup.innerHTML;
});
}
}
});
</script>
</div> <!-- /content -->
</body></html>