-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathgit-part1.html
700 lines (600 loc) · 21.7 KB
/
git-part1.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
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<title>Week 2. More Git</title>
<script src="site_libs/header-attrs-2.11/header-attrs.js"></script>
<script src="site_libs/jquery-3.6.0/jquery-3.6.0.min.js"></script>
<meta name="viewport" content="width=device-width, initial-scale=1" />
<link href="site_libs/bootstrap-3.3.5/css/readable.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>
<link href="site_libs/highlightjs-9.12.0/textmate.css" rel="stylesheet" />
<script src="site_libs/highlightjs-9.12.0/highlight.js"></script>
<script src="site_libs/kePrint-0.0.1/kePrint.js"></script>
<link href="site_libs/lightable-0.0.1/lightable.css" rel="stylesheet" />
<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 rel="shortcut icon" href="favicon.ico" type="image/x-icon">
<style type="text/css">
code{white-space: pre-wrap;}
span.smallcaps{font-variant: small-caps;}
span.underline{text-decoration: underline;}
div.column{display: inline-block; vertical-align: top; width: 50%;}
div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
ul.task-list{list-style: none;}
</style>
<style type="text/css">code{white-space: pre;}</style>
<script type="text/javascript">
if (window.hljs) {
hljs.configure({languages: []});
hljs.initHighlightingOnLoad();
if (document.readyState && document.readyState === "complete") {
window.setTimeout(function() { hljs.initHighlighting(); }, 0);
}
}
</script>
<link rel="stylesheet" href="styles.css" type="text/css" />
<style type = "text/css">
.main-container {
max-width: 940px;
margin-left: auto;
margin-right: auto;
}
img {
max-width:100%;
}
.tabbed-pane {
padding-top: 12px;
}
.html-widget {
margin-bottom: 20px;
}
button.code-folding-btn:focus {
outline: none;
}
summary {
display: list-item;
}
pre code {
padding: 0;
}
</style>
<style type="text/css">
.dropdown-submenu {
position: relative;
}
.dropdown-submenu>.dropdown-menu {
top: 0;
left: 100%;
margin-top: -6px;
margin-left: -1px;
border-radius: 0 6px 6px 6px;
}
.dropdown-submenu:hover>.dropdown-menu {
display: block;
}
.dropdown-submenu>a:after {
display: block;
content: " ";
float: right;
width: 0;
height: 0;
border-color: transparent;
border-style: solid;
border-width: 5px 0 5px 5px;
border-left-color: #cccccc;
margin-top: 5px;
margin-right: -10px;
}
.dropdown-submenu:hover>a:after {
border-left-color: #adb5bd;
}
.dropdown-submenu.pull-left {
float: none;
}
.dropdown-submenu.pull-left>.dropdown-menu {
left: -100%;
margin-left: 10px;
border-radius: 6px 0 6px 6px;
}
</style>
<script type="text/javascript">
// manage active state of menu based on current page
$(document).ready(function () {
// active menu anchor
href = window.location.pathname
href = href.substr(href.lastIndexOf('/') + 1)
if (href === "")
href = "index.html";
var menuAnchor = $('a[href="' + href + '"]');
// mark it 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>
<!-- tabsets -->
<style type="text/css">
.tabset-dropdown > .nav-tabs {
display: inline-table;
max-height: 500px;
min-height: 44px;
overflow-y: auto;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
<style type="text/css">
#TOC {
margin: 25px 0px 20px 0px;
}
@media (max-width: 768px) {
#TOC {
position: relative;
width: 100%;
}
}
@media print {
.toc-content {
/* see https://github.com/w3c/csswg-drafts/issues/4434 */
float: right;
}
}
.toc-content {
padding-left: 30px;
padding-right: 40px;
}
div.main-container {
max-width: 1200px;
}
div.tocify {
width: 20%;
max-width: 260px;
max-height: 85%;
}
@media (min-width: 768px) and (max-width: 991px) {
div.tocify {
width: 25%;
}
}
@media (max-width: 767px) {
div.tocify {
width: 100%;
max-width: none;
}
}
.tocify ul, .tocify li {
line-height: 20px;
}
.tocify-subheader .tocify-item {
font-size: 0.90em;
}
.tocify .list-group-item {
border-radius: 0px;
}
.tocify-subheader {
display: inline;
}
.tocify-subheader .tocify-item {
font-size: 0.95em;
}
</style>
</head>
<body>
<div class="container-fluid main-container">
<!-- setup 3col/9col grid for toc_float and main content -->
<div class="row">
<div class="col-xs-12 col-sm-4 col-md-3">
<div id="TOC" class="tocify">
</div>
</div>
<div class="toc-content col-xs-12 col-sm-8 col-md-9">
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
<div class="navbar-header">
<button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar">
<span class="icon-bar"></span>
<span class="icon-bar"></span>
<span class="icon-bar"></span>
</button>
<a class="navbar-brand" href="index.html">PSAW-2022</a>
</div>
<div id="navbar" class="navbar-collapse collapse">
<ul class="nav navbar-nav">
<li>
<a href="set-up.html">
<span class="fa fa-clone"></span>
Set-up
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<span class="fa fa-calendar"></span>
Workshop Notes
<span class="caret"></span>
</a>
<ul class="dropdown-menu" role="menu">
<li>
<a href="git-part1.html">
<span class="fa fa-cogs"></span>
Git Basics
</a>
</li>
<li>
<a href="git-part2.html">
<span class="fab fa-github-alt"></span>
GitHub Basics
</a>
</li>
<li>
<a href="git-part3.html">
<span class="fab fa-github"></span>
More Git Skills
</a>
</li>
<li>
<a href="rstudiocloud-part1.html">
<span class="fa fa-cloud"></span>
RStudio Cloud 1
</a>
</li>
<li>
<a href="rstudiocloud-part2.html">
<span class="fa fa-graduation-cap"></span>
RStudio Cloud 2
</a>
</li>
</ul>
</li>
<li>
<a href="https://rverse-tutorials.github.io/">
<span class="fa fa-folder"></span>
More Resources
</a>
</li>
<li>
<a href="aboutme.html">
<span class="fa fa-info"></span>
About Me
</a>
</li>
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/RVerse-Tutorials/PSAW-2022">
<span class="fab fa-github"></span>
Repo
</a>
</li>
</ul>
</div><!--/.nav-collapse -->
</div><!--/.container -->
</div><!--/.navbar -->
<div id="header">
<h1 class="title toc-ignore">Week 2. More Git</h1>
</div>
<table class="table" style="margin-left: auto; margin-right: auto;">
<tbody>
<tr>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Compartmentalized
</td>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Documented
</td>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Extendible
</td>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Reproducible
</td>
<td style="text-align:left;color: white !important;background-color: blue !important;width: 20%; ">
Robust
</td>
</tr>
</tbody>
</table>
<div id="what-is-git-and-github" class="section level1">
<h1>What is Git and GitHub?</h1>
<p><strong>Git</strong> A program to track your file changes and create a history of those changes. Creates a ‘container’ for a set of files called a repository.</p>
<p><strong>GitHub</strong> A website to host these repositories and allow you to sync local copies (on your computer) to the website. <em>Lots</em> of functionality built on top of this.</p>
<div id="some-basic-git-jargon" class="section level2">
<h2>Some basic Git jargon</h2>
<ul>
<li>Repo: Repository. It is your code and the record of your changes. In a hidden folder called <code>.git</code> (so if you wanted to get rid of the history and other Git info, you could delete that folder). You have a local repo and a remote repo (on GitHub/GitLab).</li>
<li>Actions: Commit, Push, Pull</li>
<li>Git: The program that keeps track of the changes on local and remote(“origin”) repo.</li>
<li>Git GUIs: A graphical interface for Git (which is command line). There are <a href="https://git-scm.com/downloads/guis">many</a>. I am teaching an easy-entry one, <a href="https://desktop.github.com/">GitHub Desktop</a>.</li>
</ul>
</div>
</div>
<div id="overview" class="section level1">
<h1>Overview</h1>
<p>Today I will cover the basic Git/GitHub skills (and info) that are all most people need for 95% of their work. I am using <a href="https://desktop.github.com/">GitHub Desktop</a>. <a href="#fn1" class="footnote-ref" id="fnref1"><sup>1</sup></a> If you want to use Git from RStudio, <a href="set-up.html">go to set-up</a> and scroll to the section on RStudio and Git.</p>
<p>Simple Workflow:</p>
<ul>
<li>Make local (on your computer) changes to code.</li>
<li>Record what those changes were about and commit to the code change record (history).</li>
<li>Push those changes to your remote repository (aka origin)</li>
</ul>
<p>We’ll do this</p>
<p><img src="images/git-linear-flow-2.png" /></p>
<p>Not this, i.e. what you would see if you Google “Git”.</p>
<p><img src="images/git-online.png" width="400" /></p>
</div>
<div id="the-key-skills" class="section level1">
<h1>The Key Skills</h1>
<p><a href="https://youtu.be/nNl8KqA57A0?t=1152">Jump to this part of the video</a></p>
<p>Repository skills (using GitHub Desktop)</p>
<ul>
<li><p>Skill 1: Create a blank repo on GitHub</p></li>
<li><p>Skill 2: Clone one of your <strong>GitHub</strong> repos onto your computer</p></li>
<li><p>Skill 0: Open your repository in your editing platform. I am going to use RStudio, but you use whatever you edit in.</p></li>
<li><p>Skill 3: Commit local changes</p></li>
<li><p>Skill 4: Push local changes GitHub</p></li>
<li><p>Skill 1b: How to clone someone else’s GitHub repository</p></li>
</ul>
<p><img src="images/git-repo-structure.png" width="200" /> # Let’s see it done!</p>
<div id="github-desktop" class="section level2">
<h2>GitHub Desktop</h2>
</div>
<div id="rstudio-cloud" class="section level2">
<h2>RStudio Cloud</h2>
<p>See <a href="set-up.html">Set-up</a></p>
</div>
<div id="skill-1-create-a-blank-repo-on-github" class="section level2">
<h2>Skill 1: Create a blank repo on GitHub</h2>
<p><a href="https://youtu.be/nNl8KqA57A0?t=1336">Jump to this part of the video</a></p>
<ol style="list-style-type: decimal">
<li>Click the + in the upper left from YOUR GitHub page.</li>
<li>Click new and add the Readme file and .gitignore</li>
</ol>
</div>
<div id="skill-2-clone-your-repo-to-your-computer" class="section level2">
<h2>Skill 2: Clone your repo to your computer</h2>
<p><a href="https://youtu.be/nNl8KqA57A0?t=1627">Jump to this part of the video</a></p>
<ol style="list-style-type: decimal">
<li>Copy the URL of your repo. <code>https://www.github.com/yourname/yourrepo</code></li>
<li>Open GitHub Desktop on your computer. Click File > Clone Repository</li>
<li>Click URL in the box that pops up and paste in the URL above</li>
<li>Double check that you are saving the repo in the right place</li>
</ol>
</div>
<div id="skill-0-make-a-project-in-rstudio" class="section level2">
<h2>Skill 0: Make a project in RStudio</h2>
<p><strong>This is just for RStudio users. Others can ignore this step.</strong></p>
<ol style="list-style-type: decimal">
<li>Open RStudio and click the project tab in the top right and select, <code>New Project</code>.</li>
<li>Select <code>Existing Directory</code> and navigate to the directory where you just saved the repo.</li>
<li>Click ‘Create project’</li>
</ol>
</div>
<div id="skill-3-commit-your-changes" class="section level2">
<h2>Skill 3: Commit your changes</h2>
<p><a href="https://youtu.be/nNl8KqA57A0?t=2497">Jump to this part of the video</a></p>
<ol style="list-style-type: decimal">
<li>Make some changes to a file or add a file. <strong>Make changes however you want. For example you can just open the Readme file in a text editor, or in RStudio, or in Jupyter Notebook.</strong></li>
<li>Open GitHub Desktop, click the little checkboxes next to the changes.</li>
<li>Add a commit comment, commit.</li>
</ol>
</div>
<div id="skill-4-push-changes-to-github" class="section level2">
<h2>Skill 4: Push changes to GitHub</h2>
<ol style="list-style-type: decimal">
<li>In GitHub Desktop, click Push at top to push the changes to GitHub</li>
</ol>
</div>
<div id="skill-1b-copy-a-repo-on-github" class="section level2">
<h2>Skill 1b: Copy a repo on GitHub</h2>
<p><a href="https://youtu.be/nNl8KqA57A0?t=4190">Jump to this part of the video</a></p>
<p>You can clone your own or other people’s repos.</p>
<ol style="list-style-type: decimal">
<li>In a browser, go to the GitHub repository you want to copy.</li>
<li>Copy its url.</li>
<li>Navigate to your GitHub page: click your icon in the upper right and then ‘your repositories’</li>
<li>Click the <code>+</code> in top right and click <code>import repository</code>. Paste in the url and give your repo a name.</li>
<li>Use Skill #1 to clone your new repo to your computer</li>
</ol>
</div>
<div id="skill-1c.-use-an-existing-repository-as-a-template-for-something-new" class="section level2">
<h2>Skill 1c. Use an existing repository as a template for something new</h2>
<p>Let say you want to make a copy of one of your GitHub repositories and use it as a template to make something brand new.</p>
<ol style="list-style-type: decimal">
<li>Clone the repository that you will be building off of to GitHub</li>
<li>Use skill #1 to pull that repository onto your computer</li>
<li>Get rid of any files you don’t want in the new repo and use skill #3 to push those to GitHub.</li>
</ol>
</div>
</div>
<div id="other-skills" class="section level1">
<h1>Other skills</h1>
<div id="pull-changes-made-on-github" class="section level2">
<h2>Pull changes made on GitHub</h2>
<ol style="list-style-type: decimal">
<li>Make some changes directly on GitHub</li>
<li>Click Pull in GitHub Desktop</li>
</ol>
</div>
<div id="make-an-existing-folder-on-your-computer-a-github-repository" class="section level2">
<h2>Make an existing folder on your computer a GitHub repository</h2>
<ol style="list-style-type: decimal">
<li>Use skill #1 to create a blank repo on GitHub and clone onto your computer</li>
<li>Copy the files you want to your new repository folder</li>
<li>Use skill #3 to push those to GitHub</li>
</ol>
<p>Note there are some easier ways to do this but the above is how to do it with your skills 1-3.</p>
</div>
</div>
<div id="definitions" class="section level1">
<h1>Definitions</h1>
<div id="forking-versus-cloning" class="section level2">
<h2>Forking versus Cloning</h2>
<p>Forking is if you are contributing to someone else’s repository. In that case, you need to make ‘pull requests’. Pull request = ‘here is a suggested change’ request.</p>
<p>Cloning is if you want your own copy of the repository because you want to make your own version of the code or use it as a starting point for your own project. Or you need to clone a blank repository to get started on a project.</p>
</div>
<div id="merge-conflicts" class="section level2">
<h2>Merge conflicts</h2>
<p>Merge conflicts happen when there are changes to a file on your remote repository (GitHub) but also changes to that same file on your local repository. Git doesn’t know how to resolve the conflicting changes and needs your help. GitHub Desktop will warn you and give you some helpful options to resolve these.</p>
</div>
<div id="branches" class="section level2">
<h2>Branches</h2>
<p>A copy of your repository that you can work on without changing the main repository. Once you are done, you incorporate the changes into the main repository. <strong>Most of you should steer clear of branches</strong> because they are incompatible with our common workflows!! I maintain many repositories and use branches on only 2 of them.</p>
</div>
</div>
<div id="review-a-workflow-to-minimize-headaches" class="section level1">
<h1>Review: A workflow to minimize headaches</h1>
<ul>
<li>Open GitHub Desktop</li>
<li>Do a pull from GitHub</li>
<li>Work</li>
<li>Commit changes and push up</li>
</ul>
<div id="starting-out" class="section level3">
<h3>Starting out</h3>
<ul>
<li>Don’t use branches when you are just starting. You might never need them.</li>
<li>Skills 1-3 are most of what anyone needs.</li>
<li>Get in the habit of always doing a Pull/Push before you start work in your project.</li>
</ul>
<p>FAQ</p>
<ul>
<li>Fork or clone? Which should I use?</li>
</ul>
</div>
</div>
<div class="footnotes">
<hr />
<ol>
<li id="fn1"><p><strong>Why GitHub Desktop?</strong> I teach using it because it is made by GitHub and all you have to do is download and login with your GitHub account. No hassles for students. Also it is not specific to RStudio or JupyterLab which my students might not use. I use it in my personal work because my Git and GitHub work is simply much faster using it. I have many GitHub repos so speed and being able to track multiple repos is important to me. Also I use GitHub issues to plan and track my work. Being able to type ‘#’ in my commit message and see what issues are open on GitHub is critical for my workflow. Other people use RStudio’s Git GUI but it doesn’t have the functions I need. I also like GitKrakken. Search around and find something that works for your purposes. In JupyterLab I use the jupyter-git extension.<a href="#fnref1" class="footnote-back">↩︎</a></p></li>
</ol>
</div>
<hr>
<div style="text-align: center">
<i class="fas fa-cubes"></i> NWFSC Math Bio Program <i class="fas fa-cubes"></i>
</div>
</div>
</div>
</div>
<script>
// add bootstrap table styles to pandoc tables
function bootstrapStylePandocTables() {
$('tr.odd').parent('tbody').parent('table').addClass('table table-condensed');
}
$(document).ready(function () {
bootstrapStylePandocTables();
});
</script>
<!-- tabsets -->
<script>
$(document).ready(function () {
window.buildTabsets("TOC");
});
$(document).ready(function () {
$('.tabset-dropdown > .nav-tabs > li').click(function () {
$(this).parent().toggleClass('nav-tabs-open');
});
});
</script>
<!-- code folding -->
<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')
.children('h1,h2,h3,h4,h5').addClass('toc-ignore');
// establish options
var options = {
selectors: "h1,h2",
theme: "bootstrap3",
context: '.toc-content',
hashGenerator: function (text) {
return text.replace(/[.\\/?&!#<>]/g, '').replace(/\s/g, '_');
},
ignoreSelector: ".toc-ignore",
scrollTo: 0
};
options.showAndHide = false;
options.smoothScroll = true;
// tocify
var toc = $("#TOC").tocify(options).data("toc-tocify");
});
</script>
<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
(function () {
var script = document.createElement("script");
script.type = "text/javascript";
script.src = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
document.getElementsByTagName("head")[0].appendChild(script);
})();
</script>
</body>
</html>