4 years ago · 893f8e1cc8
--- a/Book/buildbook.r
+++ b/Book/buildbook.r
@@ -0,0 +1,5 @@
 
				+# create book
			
 
				+
			
 
				+library (bookdown)
			
 
				+
			
 
				+bookdown::render_book("Index.Rmd", "bookdown::gitbook")
			
--- a/_bookdown.yml
+++ b/_bookdown.yml
@@ -0,0 +1,16 @@
 
				+output_dir: "book-output"
			
 
				+
			
 
				+rmd_files: [
			
 
				+  "index.Rmd",
			
 
				+  "intro/sandbox.md",
			
 
				+   "web-interface/cannot-see-a-repo.md",
			
 
				+"web-interface/dashboard.md",
			
 
				+"web-interface/browsing.md",
			
 
				+"web-interface/downloading.md",
			
 
				+"web-interface/uploading.md",
			
 
				+
			
 
				+
			
 
				+"git-applications/README.md",
			
 
				+"git-applications/git-gui.md",
			
 
				+"git-applications/rstudio.md"
			
 
				+]
			
--- a/book-output/browsing-a-repository.html
+++ b/book-output/browsing-a-repository.html
@@ -0,0 +1,250 @@
 
				+<!DOCTYPE html>
			
 
				+<html lang="" xml:lang="">
			
 
				+<head>
			
 
				+
			
 
				+  <meta charset="utf-8" />
			
 
				+  <meta http-equiv="X-UA-Compatible" content="IE=edge" />
			
 
				+  <title>5 Browsing a repository | dealing with gin</title>
			
 
				+  <meta name="description" content="5 Browsing a repository | dealing with gin" />
			
 
				+  <meta name="generator" content="bookdown 0.17 and GitBook 2.6.7" />
			
 
				+
			
 
				+  <meta property="og:title" content="5 Browsing a repository | dealing with gin" />
			
 
				+  <meta property="og:type" content="book" />
			
 
				+  
			
 
				+  
			
 
				+  
			
 
				+  
			
 
				+
			
 
				+  <meta name="twitter:card" content="summary" />
			
 
				+  <meta name="twitter:title" content="5 Browsing a repository | dealing with gin" />
			
 
				+  
			
 
				+  
			
 
				+  
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+  <meta name="viewport" content="width=device-width, initial-scale=1" />
			
 
				+  <meta name="apple-mobile-web-app-capable" content="yes" />
			
 
				+  <meta name="apple-mobile-web-app-status-bar-style" content="black" />
			
 
				+  
			
 
				+  
			
 
				+<link rel="prev" href="dashboard-how-to-use.html"/>
			
 
				+<link rel="next" href="downloading-files.html"/>
			
 
				+<script src="libs/jquery-2.2.3/jquery.min.js"></script>
			
 
				+<link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
			
 
				+<link href="libs/gitbook-2.6.7/css/plugin-table.css" rel="stylesheet" />
			
 
				+<link href="libs/gitbook-2.6.7/css/plugin-bookdown.css" rel="stylesheet" />
			
 
				+<link href="libs/gitbook-2.6.7/css/plugin-highlight.css" rel="stylesheet" />
			
 
				+<link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" />
			
 
				+<link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" />
			
 
				+<link href="libs/gitbook-2.6.7/css/plugin-clipboard.css" rel="stylesheet" />
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+</head>
			
 
				+
			
 
				+<body>
			
 
				+
			
 
				+
			
 
				+
			
 
				+  <div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
			
 
				+
			
 
				+    <div class="book-summary">
			
 
				+      <nav role="navigation">
			
 
				+
			
 
				+<ul class="summary">
			
 
				+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Dealing with Gin</a></li>
			
 
				+<li class="chapter" data-level="2" data-path="play-with-sandbox.html"><a href="play-with-sandbox.html"><i class="fa fa-check"></i><b>2</b> Play with Sandbox</a></li>
			
 
				+<li class="chapter" data-level="3" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html"><i class="fa fa-check"></i><b>3</b> Cannot see a repository?</a><ul>
			
 
				+<li class="chapter" data-level="3.1" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#sign-in-to-gin"><i class="fa fa-check"></i><b>3.1</b> Sign in to Gin</a></li>
			
 
				+<li class="chapter" data-level="3.2" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#check-that-the-repository-exists"><i class="fa fa-check"></i><b>3.2</b> Check that the repository exists</a></li>
			
 
				+<li class="chapter" data-level="3.3" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#make-sure-you-have-access-to-the-repository"><i class="fa fa-check"></i><b>3.3</b> Make sure you have access to the repository</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="4" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html"><i class="fa fa-check"></i><b>4</b> Dashboard: how to use</a><ul>
			
 
				+<li class="chapter" data-level="4.1" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#activity"><i class="fa fa-check"></i><b>4.1</b> Activity</a></li>
			
 
				+<li class="chapter" data-level="4.2" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#collaborative-repositories"><i class="fa fa-check"></i><b>4.2</b> Collaborative repositories</a></li>
			
 
				+<li class="chapter" data-level="4.3" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#private-repositories"><i class="fa fa-check"></i><b>4.3</b> Private repositories</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="5" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html"><i class="fa fa-check"></i><b>5</b> Browsing a repository</a><ul>
			
 
				+<li class="chapter" data-level="5.1" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#overview-of-the-repository"><i class="fa fa-check"></i><b>5.1</b> Overview of the repository</a></li>
			
 
				+<li class="chapter" data-level="5.2" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#browsing-files"><i class="fa fa-check"></i><b>5.2</b> Browsing files</a><ul>
			
 
				+<li class="chapter" data-level="5.2.1" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#a-small-side-note"><i class="fa fa-check"></i><b>5.2.1</b> A small side note</a></li>
			
 
				+</ul></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="6" data-path="downloading-files.html"><a href="downloading-files.html"><i class="fa fa-check"></i><b>6</b> Downloading files</a><ul>
			
 
				+<li class="chapter" data-level="6.1" data-path="downloading-files.html"><a href="downloading-files.html#download-button"><i class="fa fa-check"></i><b>6.1</b> Download button</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="7" data-path="uploading-files.html"><a href="uploading-files.html"><i class="fa fa-check"></i><b>7</b> Uploading files</a><ul>
			
 
				+<li class="chapter" data-level="7.1" data-path="uploading-files.html"><a href="uploading-files.html#location-of-the-buttons"><i class="fa fa-check"></i><b>7.1</b> Location of the buttons</a></li>
			
 
				+<li class="chapter" data-level="7.2" data-path="uploading-files.html"><a href="uploading-files.html#common-features-for-file-upload"><i class="fa fa-check"></i><b>7.2</b> Common features for file-upload</a><ul>
			
 
				+<li class="chapter" data-level="7.2.1" data-path="uploading-files.html"><a href="uploading-files.html#specifying-the-directory-to-be-uploaded"><i class="fa fa-check"></i><b>7.2.1</b> Specifying the directory to be uploaded</a></li>
			
 
				+<li class="chapter" data-level="7.2.2" data-path="uploading-files.html"><a href="uploading-files.html#committing-new-files"><i class="fa fa-check"></i><b>7.2.2</b> Committing new files</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="7.3" data-path="uploading-files.html"><a href="uploading-files.html#uploading-a-set-of-files"><i class="fa fa-check"></i><b>7.3</b> Uploading a set of files</a></li>
			
 
				+<li class="chapter" data-level="7.4" data-path="uploading-files.html"><a href="uploading-files.html#create-a-new-text-file"><i class="fa fa-check"></i><b>7.4</b> Create a new (text) file</a></li>
			
 
				+<li class="chapter" data-level="7.5" data-path="uploading-files.html"><a href="uploading-files.html#edit-a-text-file"><i class="fa fa-check"></i><b>7.5</b> Edit a (text) file</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="8" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html"><i class="fa fa-check"></i><b>8</b> Using application made for git</a></li>
			
 
				+<li class="chapter" data-level="9" data-path="using-rstudio-with-gin.html"><a href="using-rstudio-with-gin.html"><i class="fa fa-check"></i><b>9</b> Using Rstudio with GIN</a></li>
			
 
				+</ul>
			
 
				+
			
 
				+      </nav>
			
 
				+    </div>
			
 
				+
			
 
				+    <div class="book-body">
			
 
				+      <div class="body-inner">
			
 
				+        <div class="book-header" role="navigation">
			
 
				+          <h1>
			
 
				+            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">dealing with gin</a>
			
 
				+          </h1>
			
 
				+        </div>
			
 
				+
			
 
				+        <div class="page-wrapper" tabindex="-1" role="main">
			
 
				+          <div class="page-inner">
			
 
				+
			
 
				+            <section class="normal" id="section-">
			
 
				+<div id="browsing-a-repository" class="section level1">
			
 
				+<h1><span class="header-section-number">5</span> Browsing a repository</h1>
			
 
				+<p>If you visit the repository page, it looks like below:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/repository-top.png" alt="A typical repository page" />
			
 
				+<p class="caption">A typical repository page</p>
			
 
				+</div>
			
 
				+<p>From here, you can browse what is in the repository including:</p>
			
 
				+<ol style="list-style-type: decimal">
			
 
				+<li><a href="browsing-a-repository.html#overview-of-the-repository">overview of the repository</a></li>
			
 
				+<li><a href="browsing-a-repository.html#browsing-files">file contents</a></li>
			
 
				+</ol>
			
 
				+<div id="overview-of-the-repository" class="section level2">
			
 
				+<h2><span class="header-section-number">5.1</span> Overview of the repository</h2>
			
 
				+<p>On top of the page, you will find the header consisting of <code>&lt;owner name&gt;/&lt;repository name&gt;</code>:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/repository-title.png" alt="Repository name" />
			
 
				+<p class="caption">Repository name</p>
			
 
				+</div>
			
 
				+<p>This represents the <em>identifier</em> of the repository so that
			
 
				+you can specify a single repository inside <code>https://gin.g-node.org</code>.</p>
			
 
				+<p>Down to the bottom, you may find some document:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/readme.png" alt="README file" />
			
 
				+<p class="caption">README file</p>
			
 
				+</div>
			
 
				+<p>This represents the (hopefully) detailed description of the repository about what it is
			
 
				+or what it contains.</p>
			
 
				+<blockquote>
			
 
				+<p>In fact, this description comes from the <code>README.md</code> file in the root directory of the repository.
			
 
				+The name of the file comes from a tradition of programmers community to contain the “read-me-first”
			
 
				+file in the top directory of any code.</p>
			
 
				+<p>You can add or edit it by adding / editing the <code>README.md</code> file.</p>
			
 
				+<p>Even inside the sub-directories of the repositories, the description will automatically show up
			
 
				+if you add and edit a <code>README.md</code> file in it.</p>
			
 
				+</blockquote>
			
 
				+</div>
			
 
				+<div id="browsing-files" class="section level2">
			
 
				+<h2><span class="header-section-number">5.2</span> Browsing files</h2>
			
 
				+<p>In the middle, you can find a list of files and directories in the repository:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/files.png" alt="File list" />
			
 
				+<p class="caption">File list</p>
			
 
				+</div>
			
 
				+<p>By clicking on individual file/directory entry, you can browse its contents.</p>
			
 
				+<p>For example, you can see the contents of a sub-directory by clicking on it:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/directory-view.png" alt="Directory view" />
			
 
				+<p class="caption">Directory view</p>
			
 
				+</div>
			
 
				+<p>Contents of normal files may be visible, as long as your browser supports it.</p>
			
 
				+<ul>
			
 
				+<li><p>For example, you can browse to <a href="images/dashboard.png">web-interface/images/dashboard.png</a>,
			
 
				+and you can have a glimpse of the original image file:
			
 
				+<img src="images/image-view.png" alt="Image-file view" /></p></li>
			
 
				+<li><p>If you write the documents in the <a href="https://www.markdownguide.org/getting-started">Markdown</a> format
			
 
				+(and I recommend to do so whenever possible), you can see the formatted-view of the document:
			
 
				+<img src="images/markdown-view.png" alt="Markdown view" /></p></li>
			
 
				+<li>Other text-based files (CSV, TSV etc.) may be seen in its raw format.</li>
			
 
				+<li><p>Binary files (Excel, Word, Spike2 etc.) will not be visible, so you must <a href="downloading.md">download it</a> to see the contents.</p></li>
			
 
				+</ul>
			
 
				+<div id="a-small-side-note" class="section level3">
			
 
				+<h3><span class="header-section-number">5.2.1</span> A small side note</h3>
			
 
				+<p>On the left columns of the files list, you can see some information like below:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/commit-description.png" alt="Commit description" />
			
 
				+<p class="caption">Commit description</p>
			
 
				+</div>
			
 
				+<p>Sadly <strong>it is <em>not</em> about the description to the file itself</strong> but describes the commit
			
 
				+that updated this file most recently.</p>
			
 
				+<p>In the case of the image above, the directory “web-interface” was updated by the commit
			
 
				+with the commit ID being <code>b42b7633f7</code>, and with the commit message <code>update dashboard.md</code>.</p>
			
 
				+
			
 
				+</div>
			
 
				+</div>
			
 
				+</div>
			
 
				+            </section>
			
 
				+
			
 
				+          </div>
			
 
				+        </div>
			
 
				+      </div>
			
 
				+<a href="dashboard-how-to-use.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
			
 
				+<a href="downloading-files.html" class="navigation navigation-next " aria-label="Next page"><i class="fa fa-angle-right"></i></a>
			
 
				+    </div>
			
 
				+  </div>
			
 
				+<script src="libs/gitbook-2.6.7/js/app.min.js"></script>
			
 
				+<script src="libs/gitbook-2.6.7/js/lunr.js"></script>
			
 
				+<script src="libs/gitbook-2.6.7/js/clipboard.min.js"></script>
			
 
				+<script src="libs/gitbook-2.6.7/js/plugin-search.js"></script>
			
 
				+<script src="libs/gitbook-2.6.7/js/plugin-sharing.js"></script>
			
 
				+<script src="libs/gitbook-2.6.7/js/plugin-fontsettings.js"></script>
			
 
				+<script src="libs/gitbook-2.6.7/js/plugin-bookdown.js"></script>
			
 
				+<script src="libs/gitbook-2.6.7/js/jquery.highlight.js"></script>
			
 
				+<script src="libs/gitbook-2.6.7/js/plugin-clipboard.js"></script>
			
 
				+<script>
			
 
				+gitbook.require(["gitbook"], function(gitbook) {
			
 
				+gitbook.start({
			
 
				+"sharing": {
			
 
				+"github": false,
			
 
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				+"twitter": true,
			
 
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				+"theme": "white",
			
 
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				+},
			
 
				+"edit": {
			
 
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				+"text": null
			
 
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				+"download": null,
			
 
				+"toc": {
			
 
				+"collapse": "subsection"
			
 
				+}
			
 
				+});
			
 
				+});
			
 
				+</script>
			
 
				+
			
 
				+</body>
			
 
				+
			
 
				+</html>
			
--- a/book-output/browsing.html
+++ b/book-output/browsing.html
@@ -0,0 +1,483 @@
 
				+<!DOCTYPE html>
			
 
				+<html lang="" xml:lang="">
			
 
				+<head>
			
 
				+
			
 
				+  <meta charset="utf-8" />
			
 
				+  <meta http-equiv="X-UA-Compatible" content="IE=edge" />
			
 
				+  <title>3 Browsing | dealing with gin</title>
			
 
				+  <meta name="description" content="3 Browsing | dealing with gin" />
			
 
				+  <meta name="generator" content="bookdown 0.17 and GitBook 2.6.7" />
			
 
				+
			
 
				+  <meta property="og:title" content="3 Browsing | dealing with gin" />
			
 
				+  <meta property="og:type" content="book" />
			
 
				+  
			
 
				+  
			
 
				+  
			
 
				+  
			
 
				+
			
 
				+  <meta name="twitter:card" content="summary" />
			
 
				+  <meta name="twitter:title" content="3 Browsing | dealing with gin" />
			
 
				+  
			
 
				+  
			
 
				+  
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+  <meta name="viewport" content="width=device-width, initial-scale=1" />
			
 
				+  <meta name="apple-mobile-web-app-capable" content="yes" />
			
 
				+  <meta name="apple-mobile-web-app-status-bar-style" content="black" />
			
 
				+  
			
 
				+  
			
 
				+<link rel="prev" href="intro.html"/>
			
 
				+<link rel="next" href="using-application-made-for-git.html"/>
			
 
				+<script src="libs/jquery-2.2.3/jquery.min.js"></script>
			
 
				+<link href="libs/gitbook-2.6.7/css/style.css" rel="stylesheet" />
			
 
				+<link href="libs/gitbook-2.6.7/css/plugin-table.css" rel="stylesheet" />
			
 
				+<link href="libs/gitbook-2.6.7/css/plugin-bookdown.css" rel="stylesheet" />
			
 
				+<link href="libs/gitbook-2.6.7/css/plugin-highlight.css" rel="stylesheet" />
			
 
				+<link href="libs/gitbook-2.6.7/css/plugin-search.css" rel="stylesheet" />
			
 
				+<link href="libs/gitbook-2.6.7/css/plugin-fontsettings.css" rel="stylesheet" />
			
 
				+<link href="libs/gitbook-2.6.7/css/plugin-clipboard.css" rel="stylesheet" />
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+
			
 
				+</head>
			
 
				+
			
 
				+<body>
			
 
				+
			
 
				+
			
 
				+
			
 
				+  <div class="book without-animation with-summary font-size-2 font-family-1" data-basepath=".">
			
 
				+
			
 
				+    <div class="book-summary">
			
 
				+      <nav role="navigation">
			
 
				+
			
 
				+<ul class="summary">
			
 
				+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Dealing with Gin</a></li>
			
 
				+<li class="chapter" data-level="2" data-path="intro.html"><a href="intro.html"><i class="fa fa-check"></i><b>2</b> Intro</a><ul>
			
 
				+<li class="chapter" data-level="2.1" data-path="intro.html"><a href="intro.html#play-with-sandbox"><i class="fa fa-check"></i><b>2.1</b> Play with Sandbox</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="3" data-path="browsing.html"><a href="browsing.html"><i class="fa fa-check"></i><b>3</b> Browsing</a><ul>
			
 
				+<li class="chapter" data-level="3.1" data-path="browsing.html"><a href="browsing.html#cannot-see-a-repository"><i class="fa fa-check"></i><b>3.1</b> Cannot see a repository?</a><ul>
			
 
				+<li class="chapter" data-level="3.1.1" data-path="browsing.html"><a href="browsing.html#sign-in-to-gin"><i class="fa fa-check"></i><b>3.1.1</b> Sign in to Gin</a></li>
			
 
				+<li class="chapter" data-level="3.1.2" data-path="browsing.html"><a href="browsing.html#check-that-the-repository-exists"><i class="fa fa-check"></i><b>3.1.2</b> Check that the repository exists</a></li>
			
 
				+<li class="chapter" data-level="3.1.3" data-path="browsing.html"><a href="browsing.html#make-sure-you-have-access-to-the-repository"><i class="fa fa-check"></i><b>3.1.3</b> Make sure you have access to the repository</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="3.2" data-path="browsing.html"><a href="browsing.html#dashboard-how-to-use"><i class="fa fa-check"></i><b>3.2</b> Dashboard: how to use</a><ul>
			
 
				+<li class="chapter" data-level="3.2.1" data-path="browsing.html"><a href="browsing.html#activity"><i class="fa fa-check"></i><b>3.2.1</b> Activity</a></li>
			
 
				+<li class="chapter" data-level="3.2.2" data-path="browsing.html"><a href="browsing.html#collaborative-repositories"><i class="fa fa-check"></i><b>3.2.2</b> Collaborative repositories</a></li>
			
 
				+<li class="chapter" data-level="3.2.3" data-path="browsing.html"><a href="browsing.html#private-repositories"><i class="fa fa-check"></i><b>3.2.3</b> Private repositories</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="3.3" data-path="browsing.html"><a href="browsing.html#browsing-a-repository"><i class="fa fa-check"></i><b>3.3</b> Browsing a repository</a><ul>
			
 
				+<li class="chapter" data-level="3.3.1" data-path="browsing.html"><a href="browsing.html#overview-of-the-repository"><i class="fa fa-check"></i><b>3.3.1</b> Overview of the repository</a></li>
			
 
				+<li class="chapter" data-level="3.3.2" data-path="browsing.html"><a href="browsing.html#browsing-files"><i class="fa fa-check"></i><b>3.3.2</b> Browsing files</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="3.4" data-path="browsing.html"><a href="browsing.html#downloading-files"><i class="fa fa-check"></i><b>3.4</b> Downloading files</a><ul>
			
 
				+<li class="chapter" data-level="3.4.1" data-path="browsing.html"><a href="browsing.html#download-button"><i class="fa fa-check"></i><b>3.4.1</b> Download button</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="3.5" data-path="browsing.html"><a href="browsing.html#uploading-files"><i class="fa fa-check"></i><b>3.5</b> Uploading files</a><ul>
			
 
				+<li class="chapter" data-level="3.5.1" data-path="browsing.html"><a href="browsing.html#location-of-the-buttons"><i class="fa fa-check"></i><b>3.5.1</b> Location of the buttons</a></li>
			
 
				+<li class="chapter" data-level="3.5.2" data-path="browsing.html"><a href="browsing.html#common-features-for-file-upload"><i class="fa fa-check"></i><b>3.5.2</b> Common features for file-upload</a></li>
			
 
				+<li class="chapter" data-level="3.5.3" data-path="browsing.html"><a href="browsing.html#uploading-a-set-of-files"><i class="fa fa-check"></i><b>3.5.3</b> Uploading a set of files</a></li>
			
 
				+<li class="chapter" data-level="3.5.4" data-path="browsing.html"><a href="browsing.html#create-a-new-text-file"><i class="fa fa-check"></i><b>3.5.4</b> Create a new (text) file</a></li>
			
 
				+<li class="chapter" data-level="3.5.5" data-path="browsing.html"><a href="browsing.html#edit-a-text-file"><i class="fa fa-check"></i><b>3.5.5</b> Edit a (text) file</a></li>
			
 
				+</ul></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="4" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html"><i class="fa fa-check"></i><b>4</b> Using application made for git</a><ul>
			
 
				+<li class="chapter" data-level="4.1" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#generalities"><i class="fa fa-check"></i><b>4.1</b> generalities</a></li>
			
 
				+<li class="chapter" data-level="4.2" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#git-gui"><i class="fa fa-check"></i><b>4.2</b> Git GUI</a></li>
			
 
				+<li class="chapter" data-level="4.3" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#using-rstudio-with-gin"><i class="fa fa-check"></i><b>4.3</b> Using Rstudio with GIN</a></li>
			
 
				+</ul></li>
			
 
				+</ul>
			
 
				+
			
 
				+      </nav>
			
 
				+    </div>
			
 
				+
			
 
				+    <div class="book-body">
			
 
				+      <div class="body-inner">
			
 
				+        <div class="book-header" role="navigation">
			
 
				+          <h1>
			
 
				+            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">dealing with gin</a>
			
 
				+          </h1>
			
 
				+        </div>
			
 
				+
			
 
				+        <div class="page-wrapper" tabindex="-1" role="main">
			
 
				+          <div class="page-inner">
			
 
				+
			
 
				+            <section class="normal" id="section-">
			
 
				+<div id="browsing" class="section level1">
			
 
				+<h1><span class="header-section-number">3</span> Browsing</h1>
			
 
				+<div id="cannot-see-a-repository" class="section level2">
			
 
				+<h2><span class="header-section-number">3.1</span> Cannot see a repository?</h2>
			
 
				+<p>So often, you try to visit a repository, and find something like below:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/norepository.png" alt="404 page" />
			
 
				+<p class="caption">404 page</p>
			
 
				+</div>
			
 
				+<p>The solutions are:</p>
			
 
				+<ol style="list-style-type: decimal">
			
 
				+<li>Sign in to Gin</li>
			
 
				+<li>Check that the repository exists</li>
			
 
				+<li>Make sure you have access to the repository</li>
			
 
				+</ol>
			
 
				+<div id="sign-in-to-gin" class="section level3">
			
 
				+<h3><span class="header-section-number">3.1.1</span> Sign in to Gin</h3>
			
 
				+<p>It happens when you are not signed in to Gin.</p>
			
 
				+<p>Click on the “Sign in” button at the top-right corner of the page:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/signin.png" alt="Sign-in button" />
			
 
				+<p class="caption">Sign-in button</p>
			
 
				+</div>
			
 
				+<p>(If you have not yet got registered to Gin, then do it first from the “Register” button on the right.</p>
			
 
				+</div>
			
 
				+<div id="check-that-the-repository-exists" class="section level3">
			
 
				+<h3><span class="header-section-number">3.1.2</span> Check that the repository exists</h3>
			
 
				+<p>If the situation persists, go visit your <a href="Dashboard.md">dashboard</a>,
			
 
				+and find the name of the repository from the list.
			
 
				+If you click on it, the repository page should show up.</p>
			
 
				+</div>
			
 
				+<div id="make-sure-you-have-access-to-the-repository" class="section level3">
			
 
				+<h3><span class="header-section-number">3.1.3</span> Make sure you have access to the repository</h3>
			
 
				+<p>If you don’t find the repository in your dashboard, then
			
 
				+it is possible that you don’t have access to the repository at all.</p>
			
 
				+<p>Ask somebody who has access rights to the repository <a href="collaboration.md">for adding you as a Collaborator</a>.</p>
			
 
				+
			
 
				+</div>
			
 
				+</div>
			
 
				+<div id="dashboard-how-to-use" class="section level2">
			
 
				+<h2><span class="header-section-number">3.2</span> Dashboard: how to use</h2>
			
 
				+<p>When you simply sign in to Gin, without selecting any specific repository,
			
 
				+you fill find a page like below (note that this is just an example):</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/dashboard.png" alt="Dashboard overview" />
			
 
				+<p class="caption">Dashboard overview</p>
			
 
				+</div>
			
 
				+<p>This is called the “dashboard”, and here you can see most of your activity on Gin.</p>
			
 
				+<p>The dashboard may be divided into several areas:</p>
			
 
				+<ol style="list-style-type: decimal">
			
 
				+<li><a href="browsing.html#activity"><strong>Activity</strong></a> area: shows what you did with your repositories</li>
			
 
				+<li><a href="browsing.html#collaborative-repositories"><strong>Collaborative repository</strong></a> area: lists up the shared repositories you have access to</li>
			
 
				+<li><a href="browsing.html#private-repositories"><strong>Private repository</strong></a> area: lists up your <em>own</em> repositories</li>
			
 
				+</ol>
			
 
				+<div id="activity" class="section level3">
			
 
				+<h3><span class="header-section-number">3.2.1</span> Activity</h3>
			
 
				+<div class="figure">
			
 
				+<img src="images/activity-area.png" alt="Activity area" />
			
 
				+<p class="caption">Activity area</p>
			
 
				+</div>
			
 
				+<p>This shows your recent activity on Gin, e.g.</p>
			
 
				+<ul>
			
 
				+<li>your recent commits to your repositories</li>
			
 
				+<li>issues and comments reported to your repositories</li>
			
 
				+</ul>
			
 
				+</div>
			
 
				+<div id="collaborative-repositories" class="section level3">
			
 
				+<h3><span class="header-section-number">3.2.2</span> Collaborative repositories</h3>
			
 
				+<div class="figure">
			
 
				+<img src="images/collaboration-area.png" alt="Collaborative repository area" />
			
 
				+<p class="caption">Collaborative repository area</p>
			
 
				+</div>
			
 
				+<p>This area lists up the repositories <strong>owned by others</strong> and those you have access to.</p>
			
 
				+<p>Normally, most of your repositories will show up here, as they are owned and managed by <span class="citation">@larkumlab</span>.</p>
			
 
				+</div>
			
 
				+<div id="private-repositories" class="section level3">
			
 
				+<h3><span class="header-section-number">3.2.3</span> Private repositories</h3>
			
 
				+<div class="figure">
			
 
				+<img src="images/private-repositories.png" alt="Private repository area" />
			
 
				+<p class="caption">Private repository area</p>
			
 
				+</div>
			
 
				+<p>This area lists up the repositories owned by yourself.</p>
			
 
				+<p>In many cases, these are visible only to you unless you add a <a href="collaboration.md">Collaborator</a> to one of them.</p>
			
 
				+
			
 
				+</div>
			
 
				+</div>
			
 
				+<div id="browsing-a-repository" class="section level2">
			
 
				+<h2><span class="header-section-number">3.3</span> Browsing a repository</h2>
			
 
				+<p>If you visit the repository page, it looks like below:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/repository-top.png" alt="A typical repository page" />
			
 
				+<p class="caption">A typical repository page</p>
			
 
				+</div>
			
 
				+<p>From here, you can browse what is in the repository including:</p>
			
 
				+<ol style="list-style-type: decimal">
			
 
				+<li><a href="browsing.html#overview-of-the-repository">overview of the repository</a></li>
			
 
				+<li><a href="browsing.html#browsing-files">file contents</a></li>
			
 
				+</ol>
			
 
				+<div id="overview-of-the-repository" class="section level3">
			
 
				+<h3><span class="header-section-number">3.3.1</span> Overview of the repository</h3>
			
 
				+<p>On top of the page, you will find the header consisting of <code>&lt;owner name&gt;/&lt;repository name&gt;</code>:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/repository-title.png" alt="Repository name" />
			
 
				+<p class="caption">Repository name</p>
			
 
				+</div>
			
 
				+<p>This represents the <em>identifier</em> of the repository so that
			
 
				+you can specify a single repository inside <code>https://gin.g-node.org</code>.</p>
			
 
				+<p>Down to the bottom, you may find some document:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/readme.png" alt="README file" />
			
 
				+<p class="caption">README file</p>
			
 
				+</div>
			
 
				+<p>This represents the (hopefully) detailed description of the repository about what it is
			
 
				+or what it contains.</p>
			
 
				+<blockquote>
			
 
				+<p>In fact, this description comes from the <code>README.md</code> file in the root directory of the repository.
			
 
				+The name of the file comes from a tradition of programmers community to contain the “read-me-first”
			
 
				+file in the top directory of any code.</p>
			
 
				+<p>You can add or edit it by adding / editing the <code>README.md</code> file.</p>
			
 
				+<p>Even inside the sub-directories of the repositories, the description will automatically show up
			
 
				+if you add and edit a <code>README.md</code> file in it.</p>
			
 
				+</blockquote>
			
 
				+</div>
			
 
				+<div id="browsing-files" class="section level3">
			
 
				+<h3><span class="header-section-number">3.3.2</span> Browsing files</h3>
			
 
				+<p>In the middle, you can find a list of files and directories in the repository:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/files.png" alt="File list" />
			
 
				+<p class="caption">File list</p>
			
 
				+</div>
			
 
				+<p>By clicking on individual file/directory entry, you can browse its contents.</p>
			
 
				+<p>For example, you can see the contents of a sub-directory by clicking on it:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/directory-view.png" alt="Directory view" />
			
 
				+<p class="caption">Directory view</p>
			
 
				+</div>
			
 
				+<p>Contents of normal files may be visible, as long as your browser supports it.</p>
			
 
				+<ul>
			
 
				+<li><p>For example, you can browse to <a href="images/dashboard.png">web-interface/images/dashboard.png</a>,
			
 
				+and you can have a glimpse of the original image file:
			
 
				+<img src="images/image-view.png" alt="Image-file view" /></p></li>
			
 
				+<li><p>If you write the documents in the <a href="https://www.markdownguide.org/getting-started">Markdown</a> format
			
 
				+(and I recommend to do so whenever possible), you can see the formatted-view of the document:
			
 
				+<img src="images/markdown-view.png" alt="Markdown view" /></p></li>
			
 
				+<li>Other text-based files (CSV, TSV etc.) may be seen in its raw format.</li>
			
 
				+<li><p>Binary files (Excel, Word, Spike2 etc.) will not be visible, so you must <a href="downloading.md">download it</a> to see the contents.</p></li>
			
 
				+</ul>
			
 
				+<div id="a-small-side-note" class="section level4">
			
 
				+<h4><span class="header-section-number">3.3.2.1</span> A small side note</h4>
			
 
				+<p>On the left columns of the files list, you can see some information like below:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/commit-description.png" alt="Commit description" />
			
 
				+<p class="caption">Commit description</p>
			
 
				+</div>
			
 
				+<p>Sadly <strong>it is <em>not</em> about the description to the file itself</strong> but describes the commit
			
 
				+that updated this file most recently.</p>
			
 
				+<p>In the case of the image above, the directory “web-interface” was updated by the commit
			
 
				+with the commit ID being <code>b42b7633f7</code>, and with the commit message <code>update dashboard.md</code>.</p>
			
 
				+
			
 
				+</div>
			
 
				+</div>
			
 
				+</div>
			
 
				+<div id="downloading-files" class="section level2">
			
 
				+<h2><span class="header-section-number">3.4</span> Downloading files</h2>
			
 
				+<p>Although the files may be browsable on the web interface, you might want to interact with them on your desktop, using one of your favorite programs.</p>
			
 
				+<p>It is possible to download files individually from the web interface.</p>
			
 
				+<blockquote>
			
 
				+<p>Note that this “individual download” feature differs from what Git-people call “cloning of the repository”. Git-clone involves downloading of the whole repository, whereas this individual download concerns only with the current single file.</p>
			
 
				+</blockquote>
			
 
				+<div id="download-button" class="section level3">
			
 
				+<h3><span class="header-section-number">3.4.1</span> Download button</h3>
			
 
				+<p>When you open a single file, you will see buttons on the top-right of the file:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/file-actions.png" alt="Location of buttons" />
			
 
				+<p class="caption">Location of buttons</p>
			
 
				+</div>
			
 
				+<p>These buttons represent the actions that you can execute on this specific file, including:</p>
			
 
				+<ul>
			
 
				+<li>Obtaining the link to this specific version of the file (<strong>Permalink</strong>)</li>
			
 
				+<li>Browsing different versions of this file (<strong>History</strong>)</li>
			
 
				+<li>Downloading the file (<strong>Download</strong>)</li>
			
 
				+<li>Editing the file (<strong>the pencil symbol</strong>; it may not be available in the case of read-only repositories, or Gin does not have a way to edit the file e.g. PDF)</li>
			
 
				+<li>Deleting the file from the repository (<strong>the trash-can simbol</strong>; may not be available)</li>
			
 
				+</ul>
			
 
				+<p>For downloading the file, click on the “download” button:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/download-button.png" alt="Download button" />
			
 
				+<p class="caption">Download button</p>
			
 
				+</div>
			
 
				+<p>Then your browser will start downloading the file.</p>
			
 
				+
			
 
				+</div>
			
 
				+</div>
			
 
				+<div id="uploading-files" class="section level2">
			
 
				+<h2><span class="header-section-number">3.5</span> Uploading files</h2>
			
 
				+<p>The Gin web-interface allows you to:</p>
			
 
				+<ul>
			
 
				+<li><a href="browsing.html#create-a-new-text-file">create</a> a new text-based file,</li>
			
 
				+<li><a href="browsing.html#edit-a-text-file">edit</a> a text-based file, or</li>
			
 
				+<li><a href="browsing.html#uploading-a-set-of-files">upload</a> a new set of files.</li>
			
 
				+</ul>
			
 
				+<p>All of the above procedures share some features in common:</p>
			
 
				+<ul>
			
 
				+<li>You can start both of the procedures easily by <a href="browsing.html#location-of-the-buttons">a click of a button</a>.</li>
			
 
				+<li>You can <a href="browsing.html#specifying-the-directory-to-be-uploaded">specify the sub-directory in the repository</a> for the file(s) to be uploaded.</li>
			
 
				+<li>You can <a href="browsing.html#committing-new-files">specify the commit options</a>.</li>
			
 
				+</ul>
			
 
				+<div id="location-of-the-buttons" class="section level3">
			
 
				+<h3><span class="header-section-number">3.5.1</span> Location of the buttons</h3>
			
 
				+<p>When the web interface shows a list of files in a repository, you can see blue buttons in the middle, above the file list.</p>
			
 
				+<blockquote>
			
 
				+<p>Note that, if you don’t have the “write” permission to the repository, these buttons will not appear. If you still want to create or upload files, contact the person responsible for the repository to <a href="collaboration.md">add you as a Collaborator</a>.</p>
			
 
				+</blockquote>
			
 
				+<div class="figure">
			
 
				+<img src="images/upload-actions.png" alt="Where you can find the buttons for file-creation / upload" />
			
 
				+<p class="caption">Where you can find the buttons for file-creation / upload</p>
			
 
				+</div>
			
 
				+<p>There, you have two types of buttons:</p>
			
 
				+<ul>
			
 
				+<li><strong><a href="browsing.html#uploading-a-set-of-files">“Upload file” button</a></strong>: used to upload a set of files.</li>
			
 
				+<li><strong><a href="#create-new-files">“New file” button</a></strong>: used to create a new file in the repository.</li>
			
 
				+</ul>
			
 
				+<div class="figure">
			
 
				+<img src="images/upload-actions-buttons.png" alt="Two buttons for new files" />
			
 
				+<p class="caption">Two buttons for new files</p>
			
 
				+</div>
			
 
				+</div>
			
 
				+<div id="common-features-for-file-upload" class="section level3">
			
 
				+<h3><span class="header-section-number">3.5.2</span> Common features for file-upload</h3>
			
 
				+<p>No matter which button you use, there are some features shared in common.</p>
			
 
				+<div id="specifying-the-directory-to-be-uploaded" class="section level4">
			
 
				+<h4><span class="header-section-number">3.5.2.1</span> Specifying the directory to be uploaded</h4>
			
 
				+<p>On top of the view, an empty text field will show up:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/directory-selector-empty.png" alt="Directory selector" />
			
 
				+<p class="caption">Directory selector</p>
			
 
				+</div>
			
 
				+<p>This is for specifying the directory to upload the file(s).</p>
			
 
				+<p>For instance:</p>
			
 
				+<ul>
			
 
				+<li>Enter the name of the subdirectory (within the repository) in this field:</li>
			
 
				+</ul>
			
 
				+<div class="figure">
			
 
				+<img src="images/directory-selector-subdir.png" alt="A subdirectory is specified" />
			
 
				+<p class="caption">A subdirectory is specified</p>
			
 
				+</div>
			
 
				+<ul>
			
 
				+<li>Gin will automatically create a new directory with the given name (in case it does not exist) as you <a href="browsing.html#committing-new-files">commit uploads (see the section below)</a>:</li>
			
 
				+</ul>
			
 
				+<div class="figure">
			
 
				+<img src="images/created-subdir.png" alt="Created subdirectory" />
			
 
				+<p class="caption">Created subdirectory</p>
			
 
				+</div>
			
 
				+<ul>
			
 
				+<li>Inside the subdirectory, you will find the uploaded file(s):</li>
			
 
				+</ul>
			
 
				+<div class="figure">
			
 
				+<img src="images/subdir-content.png" alt="The uploaded file in the sub-directory" />
			
 
				+<p class="caption">The uploaded file in the sub-directory</p>
			
 
				+</div>
			
 
				+<p>You can also specify the <em>path</em> to the directory of interest, by connecting a hierarchy of directories by a <code>/</code> (slash):</p>
			
 
				+<p>TODO</p>
			
 
				+</div>
			
 
				+<div id="committing-new-files" class="section level4">
			
 
				+<h4><span class="header-section-number">3.5.2.2</span> Committing new files</h4>
			
 
				+<p>TODO</p>
			
 
				+</div>
			
 
				+</div>
			
 
				+<div id="uploading-a-set-of-files" class="section level3">
			
 
				+<h3><span class="header-section-number">3.5.3</span> Uploading a set of files</h3>
			
 
				+<p>When you click on the “Upload file” button, the file upload view will appear:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/upload-view.png" alt="File-upload view" />
			
 
				+<p class="caption">File-upload view</p>
			
 
				+</div>
			
 
				+<p>The dotted region in the middle of the page is the <em>upload area</em>:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/upload-view-upload-area.png" alt="The upload area" />
			
 
				+<p class="caption">The upload area</p>
			
 
				+</div>
			
 
				+<p>You can add the files to be uploaded by either:</p>
			
 
				+<ul>
			
 
				+<li><strong>Clicking on the area</strong>: the file chooser dialog will appear so that you can select files from it.</li>
			
 
				+<li><strong>Drag and drop</strong> individual files or a directory containing a set of files. In the latter case, you can upload the whole directory structure easily.</li>
			
 
				+</ul>
			
 
				+<p>In either case, the upload process will start immediately, and you will see the progress on the area:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/upload-progress.png" alt="Progress of upload" />
			
 
				+<p class="caption">Progress of upload</p>
			
 
				+</div>
			
 
				+<p>You can specify the directory to be uploaded from the <a href="browsing.html#specifying-the-directory-to-be-uploaded">directory selector (see the section above)</a>.</p>
			
 
				+<p>After completion of the upload processes for all files, you can proceed to finish the <a href="browsing.html#committing-new-files">commit process (see the section above)</a>.</p>
			
 
				+<blockquote>
			
 
				+<p>Note, by using this upload view, you can only upload 100 files at once, with each file being less than 10 GB in size. If you want to upload more files at once, or upload larger files, you will have to use the command-line interface or WinGIN.</p>
			
 
				+</blockquote>
			
 
				+</div>
			
 
				+<div id="create-a-new-text-file" class="section level3">
			
 
				+<h3><span class="header-section-number">3.5.4</span> Create a new (text) file</h3>
			
 
				+<p>TODO</p>
			
 
				+</div>
			
 
				+<div id="edit-a-text-file" class="section level3">
			
 
				+<h3><span class="header-section-number">3.5.5</span> Edit a (text) file</h3>
			
 
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				+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Dealing with Gin</a></li>
			
 
				+<li class="chapter" data-level="2" data-path="play-with-sandbox.html"><a href="play-with-sandbox.html"><i class="fa fa-check"></i><b>2</b> Play with Sandbox</a></li>
			
 
				+<li class="chapter" data-level="3" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html"><i class="fa fa-check"></i><b>3</b> Cannot see a repository?</a><ul>
			
 
				+<li class="chapter" data-level="3.1" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#sign-in-to-gin"><i class="fa fa-check"></i><b>3.1</b> Sign in to Gin</a></li>
			
 
				+<li class="chapter" data-level="3.2" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#check-that-the-repository-exists"><i class="fa fa-check"></i><b>3.2</b> Check that the repository exists</a></li>
			
 
				+<li class="chapter" data-level="3.3" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#make-sure-you-have-access-to-the-repository"><i class="fa fa-check"></i><b>3.3</b> Make sure you have access to the repository</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="4" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html"><i class="fa fa-check"></i><b>4</b> Dashboard: how to use</a><ul>
			
 
				+<li class="chapter" data-level="4.1" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#activity"><i class="fa fa-check"></i><b>4.1</b> Activity</a></li>
			
 
				+<li class="chapter" data-level="4.2" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#collaborative-repositories"><i class="fa fa-check"></i><b>4.2</b> Collaborative repositories</a></li>
			
 
				+<li class="chapter" data-level="4.3" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#private-repositories"><i class="fa fa-check"></i><b>4.3</b> Private repositories</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="5" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html"><i class="fa fa-check"></i><b>5</b> Browsing a repository</a><ul>
			
 
				+<li class="chapter" data-level="5.1" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#overview-of-the-repository"><i class="fa fa-check"></i><b>5.1</b> Overview of the repository</a></li>
			
 
				+<li class="chapter" data-level="5.2" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#browsing-files"><i class="fa fa-check"></i><b>5.2</b> Browsing files</a><ul>
			
 
				+<li class="chapter" data-level="5.2.1" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#a-small-side-note"><i class="fa fa-check"></i><b>5.2.1</b> A small side note</a></li>
			
 
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				+<li class="chapter" data-level="6" data-path="downloading-files.html"><a href="downloading-files.html"><i class="fa fa-check"></i><b>6</b> Downloading files</a><ul>
			
 
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				+<li class="chapter" data-level="7" data-path="uploading-files.html"><a href="uploading-files.html"><i class="fa fa-check"></i><b>7</b> Uploading files</a><ul>
			
 
				+<li class="chapter" data-level="7.1" data-path="uploading-files.html"><a href="uploading-files.html#location-of-the-buttons"><i class="fa fa-check"></i><b>7.1</b> Location of the buttons</a></li>
			
 
				+<li class="chapter" data-level="7.2" data-path="uploading-files.html"><a href="uploading-files.html#common-features-for-file-upload"><i class="fa fa-check"></i><b>7.2</b> Common features for file-upload</a><ul>
			
 
				+<li class="chapter" data-level="7.2.1" data-path="uploading-files.html"><a href="uploading-files.html#specifying-the-directory-to-be-uploaded"><i class="fa fa-check"></i><b>7.2.1</b> Specifying the directory to be uploaded</a></li>
			
 
				+<li class="chapter" data-level="7.2.2" data-path="uploading-files.html"><a href="uploading-files.html#committing-new-files"><i class="fa fa-check"></i><b>7.2.2</b> Committing new files</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="7.3" data-path="uploading-files.html"><a href="uploading-files.html#uploading-a-set-of-files"><i class="fa fa-check"></i><b>7.3</b> Uploading a set of files</a></li>
			
 
				+<li class="chapter" data-level="7.4" data-path="uploading-files.html"><a href="uploading-files.html#create-a-new-text-file"><i class="fa fa-check"></i><b>7.4</b> Create a new (text) file</a></li>
			
 
				+<li class="chapter" data-level="7.5" data-path="uploading-files.html"><a href="uploading-files.html#edit-a-text-file"><i class="fa fa-check"></i><b>7.5</b> Edit a (text) file</a></li>
			
 
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				+<li class="chapter" data-level="8" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html"><i class="fa fa-check"></i><b>8</b> Using application made for git</a></li>
			
 
				+<li class="chapter" data-level="9" data-path="using-rstudio-with-gin.html"><a href="using-rstudio-with-gin.html"><i class="fa fa-check"></i><b>9</b> Using Rstudio with GIN</a></li>
			
 
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				+<h1><span class="header-section-number">3</span> Cannot see a repository?</h1>
			
 
				+<p>So often, you try to visit a repository, and find something like below:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/norepository.png" alt="404 page" />
			
 
				+<p class="caption">404 page</p>
			
 
				+</div>
			
 
				+<p>The solutions are:</p>
			
 
				+<ol style="list-style-type: decimal">
			
 
				+<li>Sign in to Gin</li>
			
 
				+<li>Check that the repository exists</li>
			
 
				+<li>Make sure you have access to the repository</li>
			
 
				+</ol>
			
 
				+<div id="sign-in-to-gin" class="section level2">
			
 
				+<h2><span class="header-section-number">3.1</span> Sign in to Gin</h2>
			
 
				+<p>It happens when you are not signed in to Gin.</p>
			
 
				+<p>Click on the “Sign in” button at the top-right corner of the page:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/signin.png" alt="Sign-in button" />
			
 
				+<p class="caption">Sign-in button</p>
			
 
				+</div>
			
 
				+<p>(If you have not yet got registered to Gin, then do it first from the “Register” button on the right.</p>
			
 
				+</div>
			
 
				+<div id="check-that-the-repository-exists" class="section level2">
			
 
				+<h2><span class="header-section-number">3.2</span> Check that the repository exists</h2>
			
 
				+<p>If the situation persists, go visit your <a href="Dashboard.md">dashboard</a>,
			
 
				+and find the name of the repository from the list.
			
 
				+If you click on it, the repository page should show up.</p>
			
 
				+</div>
			
 
				+<div id="make-sure-you-have-access-to-the-repository" class="section level2">
			
 
				+<h2><span class="header-section-number">3.3</span> Make sure you have access to the repository</h2>
			
 
				+<p>If you don’t find the repository in your dashboard, then
			
 
				+it is possible that you don’t have access to the repository at all.</p>
			
 
				+<p>Ask somebody who has access rights to the repository <a href="collaboration.md">for adding you as a Collaborator</a>.</p>
			
 
				+
			
 
				+</div>
			
 
				+</div>
			
 
				+            </section>
			
 
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				+<ul class="summary">
			
 
				+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Dealing with Gin</a></li>
			
 
				+<li class="chapter" data-level="2" data-path="play-with-sandbox.html"><a href="play-with-sandbox.html"><i class="fa fa-check"></i><b>2</b> Play with Sandbox</a></li>
			
 
				+<li class="chapter" data-level="3" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html"><i class="fa fa-check"></i><b>3</b> Cannot see a repository?</a><ul>
			
 
				+<li class="chapter" data-level="3.1" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#sign-in-to-gin"><i class="fa fa-check"></i><b>3.1</b> Sign in to Gin</a></li>
			
 
				+<li class="chapter" data-level="3.2" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#check-that-the-repository-exists"><i class="fa fa-check"></i><b>3.2</b> Check that the repository exists</a></li>
			
 
				+<li class="chapter" data-level="3.3" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#make-sure-you-have-access-to-the-repository"><i class="fa fa-check"></i><b>3.3</b> Make sure you have access to the repository</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="4" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html"><i class="fa fa-check"></i><b>4</b> Dashboard: how to use</a><ul>
			
 
				+<li class="chapter" data-level="4.1" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#activity"><i class="fa fa-check"></i><b>4.1</b> Activity</a></li>
			
 
				+<li class="chapter" data-level="4.2" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#collaborative-repositories"><i class="fa fa-check"></i><b>4.2</b> Collaborative repositories</a></li>
			
 
				+<li class="chapter" data-level="4.3" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#private-repositories"><i class="fa fa-check"></i><b>4.3</b> Private repositories</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="5" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html"><i class="fa fa-check"></i><b>5</b> Browsing a repository</a><ul>
			
 
				+<li class="chapter" data-level="5.1" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#overview-of-the-repository"><i class="fa fa-check"></i><b>5.1</b> Overview of the repository</a></li>
			
 
				+<li class="chapter" data-level="5.2" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#browsing-files"><i class="fa fa-check"></i><b>5.2</b> Browsing files</a><ul>
			
 
				+<li class="chapter" data-level="5.2.1" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#a-small-side-note"><i class="fa fa-check"></i><b>5.2.1</b> A small side note</a></li>
			
 
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				+<li class="chapter" data-level="6.1" data-path="downloading-files.html"><a href="downloading-files.html#download-button"><i class="fa fa-check"></i><b>6.1</b> Download button</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="7" data-path="uploading-files.html"><a href="uploading-files.html"><i class="fa fa-check"></i><b>7</b> Uploading files</a><ul>
			
 
				+<li class="chapter" data-level="7.1" data-path="uploading-files.html"><a href="uploading-files.html#location-of-the-buttons"><i class="fa fa-check"></i><b>7.1</b> Location of the buttons</a></li>
			
 
				+<li class="chapter" data-level="7.2" data-path="uploading-files.html"><a href="uploading-files.html#common-features-for-file-upload"><i class="fa fa-check"></i><b>7.2</b> Common features for file-upload</a><ul>
			
 
				+<li class="chapter" data-level="7.2.1" data-path="uploading-files.html"><a href="uploading-files.html#specifying-the-directory-to-be-uploaded"><i class="fa fa-check"></i><b>7.2.1</b> Specifying the directory to be uploaded</a></li>
			
 
				+<li class="chapter" data-level="7.2.2" data-path="uploading-files.html"><a href="uploading-files.html#committing-new-files"><i class="fa fa-check"></i><b>7.2.2</b> Committing new files</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="7.3" data-path="uploading-files.html"><a href="uploading-files.html#uploading-a-set-of-files"><i class="fa fa-check"></i><b>7.3</b> Uploading a set of files</a></li>
			
 
				+<li class="chapter" data-level="7.4" data-path="uploading-files.html"><a href="uploading-files.html#create-a-new-text-file"><i class="fa fa-check"></i><b>7.4</b> Create a new (text) file</a></li>
			
 
				+<li class="chapter" data-level="7.5" data-path="uploading-files.html"><a href="uploading-files.html#edit-a-text-file"><i class="fa fa-check"></i><b>7.5</b> Edit a (text) file</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="8" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html"><i class="fa fa-check"></i><b>8</b> Using application made for git</a></li>
			
 
				+<li class="chapter" data-level="9" data-path="using-rstudio-with-gin.html"><a href="using-rstudio-with-gin.html"><i class="fa fa-check"></i><b>9</b> Using Rstudio with GIN</a></li>
			
 
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				+            <section class="normal" id="section-">
			
 
				+<div id="dashboard-how-to-use" class="section level1">
			
 
				+<h1><span class="header-section-number">4</span> Dashboard: how to use</h1>
			
 
				+<p>When you simply sign in to Gin, without selecting any specific repository,
			
 
				+you fill find a page like below (note that this is just an example):</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/dashboard.png" alt="Dashboard overview" />
			
 
				+<p class="caption">Dashboard overview</p>
			
 
				+</div>
			
 
				+<p>This is called the “dashboard”, and here you can see most of your activity on Gin.</p>
			
 
				+<p>The dashboard may be divided into several areas:</p>
			
 
				+<ol style="list-style-type: decimal">
			
 
				+<li><a href="dashboard-how-to-use.html#activity"><strong>Activity</strong></a> area: shows what you did with your repositories</li>
			
 
				+<li><a href="dashboard-how-to-use.html#collaborative-repositories"><strong>Collaborative repository</strong></a> area: lists up the shared repositories you have access to</li>
			
 
				+<li><a href="dashboard-how-to-use.html#private-repositories"><strong>Private repository</strong></a> area: lists up your <em>own</em> repositories</li>
			
 
				+</ol>
			
 
				+<div id="activity" class="section level2">
			
 
				+<h2><span class="header-section-number">4.1</span> Activity</h2>
			
 
				+<div class="figure">
			
 
				+<img src="images/activity-area.png" alt="Activity area" />
			
 
				+<p class="caption">Activity area</p>
			
 
				+</div>
			
 
				+<p>This shows your recent activity on Gin, e.g.</p>
			
 
				+<ul>
			
 
				+<li>your recent commits to your repositories</li>
			
 
				+<li>issues and comments reported to your repositories</li>
			
 
				+</ul>
			
 
				+</div>
			
 
				+<div id="collaborative-repositories" class="section level2">
			
 
				+<h2><span class="header-section-number">4.2</span> Collaborative repositories</h2>
			
 
				+<div class="figure">
			
 
				+<img src="images/collaboration-area.png" alt="Collaborative repository area" />
			
 
				+<p class="caption">Collaborative repository area</p>
			
 
				+</div>
			
 
				+<p>This area lists up the repositories <strong>owned by others</strong> and those you have access to.</p>
			
 
				+<p>Normally, most of your repositories will show up here, as they are owned and managed by <span class="citation">@larkumlab</span>.</p>
			
 
				+</div>
			
 
				+<div id="private-repositories" class="section level2">
			
 
				+<h2><span class="header-section-number">4.3</span> Private repositories</h2>
			
 
				+<div class="figure">
			
 
				+<img src="images/private-repositories.png" alt="Private repository area" />
			
 
				+<p class="caption">Private repository area</p>
			
 
				+</div>
			
 
				+<p>This area lists up the repositories owned by yourself.</p>
			
 
				+<p>In many cases, these are visible only to you unless you add a <a href="collaboration.md">Collaborator</a> to one of them.</p>
			
 
				+
			
 
				+</div>
			
 
				+</div>
			
 
				+            </section>
			
 
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				+      <nav role="navigation">
			
 
				+
			
 
				+<ul class="summary">
			
 
				+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Dealing with Gin</a></li>
			
 
				+<li class="chapter" data-level="2" data-path="play-with-sandbox.html"><a href="play-with-sandbox.html"><i class="fa fa-check"></i><b>2</b> Play with Sandbox</a></li>
			
 
				+<li class="chapter" data-level="3" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html"><i class="fa fa-check"></i><b>3</b> Cannot see a repository?</a><ul>
			
 
				+<li class="chapter" data-level="3.1" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#sign-in-to-gin"><i class="fa fa-check"></i><b>3.1</b> Sign in to Gin</a></li>
			
 
				+<li class="chapter" data-level="3.2" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#check-that-the-repository-exists"><i class="fa fa-check"></i><b>3.2</b> Check that the repository exists</a></li>
			
 
				+<li class="chapter" data-level="3.3" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#make-sure-you-have-access-to-the-repository"><i class="fa fa-check"></i><b>3.3</b> Make sure you have access to the repository</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="4" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html"><i class="fa fa-check"></i><b>4</b> Dashboard: how to use</a><ul>
			
 
				+<li class="chapter" data-level="4.1" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#activity"><i class="fa fa-check"></i><b>4.1</b> Activity</a></li>
			
 
				+<li class="chapter" data-level="4.2" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#collaborative-repositories"><i class="fa fa-check"></i><b>4.2</b> Collaborative repositories</a></li>
			
 
				+<li class="chapter" data-level="4.3" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#private-repositories"><i class="fa fa-check"></i><b>4.3</b> Private repositories</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="5" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html"><i class="fa fa-check"></i><b>5</b> Browsing a repository</a><ul>
			
 
				+<li class="chapter" data-level="5.1" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#overview-of-the-repository"><i class="fa fa-check"></i><b>5.1</b> Overview of the repository</a></li>
			
 
				+<li class="chapter" data-level="5.2" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#browsing-files"><i class="fa fa-check"></i><b>5.2</b> Browsing files</a><ul>
			
 
				+<li class="chapter" data-level="5.2.1" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#a-small-side-note"><i class="fa fa-check"></i><b>5.2.1</b> A small side note</a></li>
			
 
				+</ul></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="6" data-path="downloading-files.html"><a href="downloading-files.html"><i class="fa fa-check"></i><b>6</b> Downloading files</a><ul>
			
 
				+<li class="chapter" data-level="6.1" data-path="downloading-files.html"><a href="downloading-files.html#download-button"><i class="fa fa-check"></i><b>6.1</b> Download button</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="7" data-path="uploading-files.html"><a href="uploading-files.html"><i class="fa fa-check"></i><b>7</b> Uploading files</a><ul>
			
 
				+<li class="chapter" data-level="7.1" data-path="uploading-files.html"><a href="uploading-files.html#location-of-the-buttons"><i class="fa fa-check"></i><b>7.1</b> Location of the buttons</a></li>
			
 
				+<li class="chapter" data-level="7.2" data-path="uploading-files.html"><a href="uploading-files.html#common-features-for-file-upload"><i class="fa fa-check"></i><b>7.2</b> Common features for file-upload</a><ul>
			
 
				+<li class="chapter" data-level="7.2.1" data-path="uploading-files.html"><a href="uploading-files.html#specifying-the-directory-to-be-uploaded"><i class="fa fa-check"></i><b>7.2.1</b> Specifying the directory to be uploaded</a></li>
			
 
				+<li class="chapter" data-level="7.2.2" data-path="uploading-files.html"><a href="uploading-files.html#committing-new-files"><i class="fa fa-check"></i><b>7.2.2</b> Committing new files</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="7.3" data-path="uploading-files.html"><a href="uploading-files.html#uploading-a-set-of-files"><i class="fa fa-check"></i><b>7.3</b> Uploading a set of files</a></li>
			
 
				+<li class="chapter" data-level="7.4" data-path="uploading-files.html"><a href="uploading-files.html#create-a-new-text-file"><i class="fa fa-check"></i><b>7.4</b> Create a new (text) file</a></li>
			
 
				+<li class="chapter" data-level="7.5" data-path="uploading-files.html"><a href="uploading-files.html#edit-a-text-file"><i class="fa fa-check"></i><b>7.5</b> Edit a (text) file</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="8" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html"><i class="fa fa-check"></i><b>8</b> Using application made for git</a></li>
			
 
				+<li class="chapter" data-level="9" data-path="using-rstudio-with-gin.html"><a href="using-rstudio-with-gin.html"><i class="fa fa-check"></i><b>9</b> Using Rstudio with GIN</a></li>
			
 
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				+            <section class="normal" id="section-">
			
 
				+<div id="downloading-files" class="section level1">
			
 
				+<h1><span class="header-section-number">6</span> Downloading files</h1>
			
 
				+<p>Although the files may be browsable on the web interface, you might want to interact with them on your desktop, using one of your favorite programs.</p>
			
 
				+<p>It is possible to download files individually from the web interface.</p>
			
 
				+<blockquote>
			
 
				+<p>Note that this “individual download” feature differs from what Git-people call “cloning of the repository”. Git-clone involves downloading of the whole repository, whereas this individual download concerns only with the current single file.</p>
			
 
				+</blockquote>
			
 
				+<div id="download-button" class="section level2">
			
 
				+<h2><span class="header-section-number">6.1</span> Download button</h2>
			
 
				+<p>When you open a single file, you will see buttons on the top-right of the file:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/file-actions.png" alt="Location of buttons" />
			
 
				+<p class="caption">Location of buttons</p>
			
 
				+</div>
			
 
				+<p>These buttons represent the actions that you can execute on this specific file, including:</p>
			
 
				+<ul>
			
 
				+<li>Obtaining the link to this specific version of the file (<strong>Permalink</strong>)</li>
			
 
				+<li>Browsing different versions of this file (<strong>History</strong>)</li>
			
 
				+<li>Downloading the file (<strong>Download</strong>)</li>
			
 
				+<li>Editing the file (<strong>the pencil symbol</strong>; it may not be available in the case of read-only repositories, or Gin does not have a way to edit the file e.g. PDF)</li>
			
 
				+<li>Deleting the file from the repository (<strong>the trash-can simbol</strong>; may not be available)</li>
			
 
				+</ul>
			
 
				+<p>For downloading the file, click on the “download” button:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/download-button.png" alt="Download button" />
			
 
				+<p class="caption">Download button</p>
			
 
				+</div>
			
 
				+<p>Then your browser will start downloading the file.</p>
			
 
				+
			
 
				+</div>
			
 
				+</div>
			
 
				+            </section>
			
 
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				+<ul class="summary">
			
 
				+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Dealing with Gin</a></li>
			
 
				+<li class="chapter" data-level="2" data-path="intro.html"><a href="intro.html"><i class="fa fa-check"></i><b>2</b> Intro</a><ul>
			
 
				+<li class="chapter" data-level="2.1" data-path="intro.html"><a href="intro.html#play-with-sandbox"><i class="fa fa-check"></i><b>2.1</b> Play with Sandbox</a></li>
			
 
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				+<li class="chapter" data-level="3.1.1" data-path="browsing.html"><a href="browsing.html#sign-in-to-gin"><i class="fa fa-check"></i><b>3.1.1</b> Sign in to Gin</a></li>
			
 
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				+<li class="chapter" data-level="3.5.2" data-path="browsing.html"><a href="browsing.html#common-features-for-file-upload"><i class="fa fa-check"></i><b>3.5.2</b> Common features for file-upload</a></li>
			
 
				+<li class="chapter" data-level="3.5.3" data-path="browsing.html"><a href="browsing.html#uploading-a-set-of-files"><i class="fa fa-check"></i><b>3.5.3</b> Uploading a set of files</a></li>
			
 
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				+</ul></li>
			
 
				+<li class="chapter" data-level="4" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html"><i class="fa fa-check"></i><b>4</b> Using application made for git</a><ul>
			
 
				+<li class="chapter" data-level="4.1" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#generalities"><i class="fa fa-check"></i><b>4.1</b> generalities</a></li>
			
 
				+<li class="chapter" data-level="4.2" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#git-gui"><i class="fa fa-check"></i><b>4.2</b> Git GUI</a></li>
			
 
				+<li class="chapter" data-level="4.3" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#using-rstudio-with-gin"><i class="fa fa-check"></i><b>4.3</b> Using Rstudio with GIN</a></li>
			
 
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				+<div id="dealing-with-gin" class="section level1">
			
 
				+<h1><span class="header-section-number">1</span> Dealing with Gin</h1>
			
 
				+<p>Introduction to how to deal with gin (web interface, command-line, and probably WinGIN GUI).</p>
			
 
				+<p>This book covers multiple topics, see the table of content to navigate it.</p>
			
 
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				+<li class="chapter" data-level="2" data-path="intro.html"><a href="intro.html"><i class="fa fa-check"></i><b>2</b> Intro</a><ul>
			
 
				+<li class="chapter" data-level="2.1" data-path="intro.html"><a href="intro.html#play-with-sandbox"><i class="fa fa-check"></i><b>2.1</b> Play with Sandbox</a></li>
			
 
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				+<li class="chapter" data-level="3" data-path="browsing.html"><a href="browsing.html"><i class="fa fa-check"></i><b>3</b> Browsing</a><ul>
			
 
				+<li class="chapter" data-level="3.1" data-path="browsing.html"><a href="browsing.html#cannot-see-a-repository"><i class="fa fa-check"></i><b>3.1</b> Cannot see a repository?</a><ul>
			
 
				+<li class="chapter" data-level="3.1.1" data-path="browsing.html"><a href="browsing.html#sign-in-to-gin"><i class="fa fa-check"></i><b>3.1.1</b> Sign in to Gin</a></li>
			
 
				+<li class="chapter" data-level="3.1.2" data-path="browsing.html"><a href="browsing.html#check-that-the-repository-exists"><i class="fa fa-check"></i><b>3.1.2</b> Check that the repository exists</a></li>
			
 
				+<li class="chapter" data-level="3.1.3" data-path="browsing.html"><a href="browsing.html#make-sure-you-have-access-to-the-repository"><i class="fa fa-check"></i><b>3.1.3</b> Make sure you have access to the repository</a></li>
			
 
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				+<li class="chapter" data-level="3.2" data-path="browsing.html"><a href="browsing.html#dashboard-how-to-use"><i class="fa fa-check"></i><b>3.2</b> Dashboard: how to use</a><ul>
			
 
				+<li class="chapter" data-level="3.2.1" data-path="browsing.html"><a href="browsing.html#activity"><i class="fa fa-check"></i><b>3.2.1</b> Activity</a></li>
			
 
				+<li class="chapter" data-level="3.2.2" data-path="browsing.html"><a href="browsing.html#collaborative-repositories"><i class="fa fa-check"></i><b>3.2.2</b> Collaborative repositories</a></li>
			
 
				+<li class="chapter" data-level="3.2.3" data-path="browsing.html"><a href="browsing.html#private-repositories"><i class="fa fa-check"></i><b>3.2.3</b> Private repositories</a></li>
			
 
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				+<li class="chapter" data-level="3.3" data-path="browsing.html"><a href="browsing.html#browsing-a-repository"><i class="fa fa-check"></i><b>3.3</b> Browsing a repository</a><ul>
			
 
				+<li class="chapter" data-level="3.3.1" data-path="browsing.html"><a href="browsing.html#overview-of-the-repository"><i class="fa fa-check"></i><b>3.3.1</b> Overview of the repository</a></li>
			
 
				+<li class="chapter" data-level="3.3.2" data-path="browsing.html"><a href="browsing.html#browsing-files"><i class="fa fa-check"></i><b>3.3.2</b> Browsing files</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="3.4" data-path="browsing.html"><a href="browsing.html#downloading-files"><i class="fa fa-check"></i><b>3.4</b> Downloading files</a><ul>
			
 
				+<li class="chapter" data-level="3.4.1" data-path="browsing.html"><a href="browsing.html#download-button"><i class="fa fa-check"></i><b>3.4.1</b> Download button</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="3.5" data-path="browsing.html"><a href="browsing.html#uploading-files"><i class="fa fa-check"></i><b>3.5</b> Uploading files</a><ul>
			
 
				+<li class="chapter" data-level="3.5.1" data-path="browsing.html"><a href="browsing.html#location-of-the-buttons"><i class="fa fa-check"></i><b>3.5.1</b> Location of the buttons</a></li>
			
 
				+<li class="chapter" data-level="3.5.2" data-path="browsing.html"><a href="browsing.html#common-features-for-file-upload"><i class="fa fa-check"></i><b>3.5.2</b> Common features for file-upload</a></li>
			
 
				+<li class="chapter" data-level="3.5.3" data-path="browsing.html"><a href="browsing.html#uploading-a-set-of-files"><i class="fa fa-check"></i><b>3.5.3</b> Uploading a set of files</a></li>
			
 
				+<li class="chapter" data-level="3.5.4" data-path="browsing.html"><a href="browsing.html#create-a-new-text-file"><i class="fa fa-check"></i><b>3.5.4</b> Create a new (text) file</a></li>
			
 
				+<li class="chapter" data-level="3.5.5" data-path="browsing.html"><a href="browsing.html#edit-a-text-file"><i class="fa fa-check"></i><b>3.5.5</b> Edit a (text) file</a></li>
			
 
				+</ul></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="4" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html"><i class="fa fa-check"></i><b>4</b> Using application made for git</a><ul>
			
 
				+<li class="chapter" data-level="4.1" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#generalities"><i class="fa fa-check"></i><b>4.1</b> generalities</a></li>
			
 
				+<li class="chapter" data-level="4.2" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#git-gui"><i class="fa fa-check"></i><b>4.2</b> Git GUI</a></li>
			
 
				+<li class="chapter" data-level="4.3" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#using-rstudio-with-gin"><i class="fa fa-check"></i><b>4.3</b> Using Rstudio with GIN</a></li>
			
 
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				+<h1><span class="header-section-number">2</span> Intro</h1>
			
 
				+<div id="play-with-sandbox" class="section level2">
			
 
				+<h2><span class="header-section-number">2.1</span> Play with Sandbox</h2>
			
 
				+<p>To avoid accidentally deleting your precious data, it is better
			
 
				+that we have a repository that you can mess up.</p>
			
 
				+<p>And here it is:</p>
			
 
				+<p><a href="https://gin.g-node.org/larkumlab/GinSandbox">larkumlab/GinSandbox</a></p>
			
 
				+<p>You can add, edit, and move any documents, make commits, clone or fork, make issues etc.</p>
			
 
				+<p>Have fun!</p>
			
 
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				+},
			
 
				+"download": null,
			
 
				+"toc": {
			
 
				+"collapse": "subsection"
			
 
				+}
			
 
				+});
			
 
				+});
			
 
				+</script>
			
 
				+
			
 
				+</body>
			
 
				+
			
 
				+</html>
			
--- a/book-output/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf
+++ b/book-output/libs/gitbook-2.6.7/css/fontawesome/fontawesome-webfont.ttf
--- a/book-output/libs/gitbook-2.6.7/css/plugin-bookdown.css
+++ b/book-output/libs/gitbook-2.6.7/css/plugin-bookdown.css
@@ -0,0 +1,99 @@
 
				+.book .book-header h1 {
			
 
				+  padding-left: 20px;
			
 
				+  padding-right: 20px;
			
 
				+}
			
 
				+.book .book-header.fixed {
			
 
				+  position: fixed;
			
 
				+  right: 0;
			
 
				+  top: 0;
			
 
				+  left: 0;
			
 
				+  border-bottom: 1px solid rgba(0,0,0,.07);
			
 
				+}
			
 
				+span.search-highlight {
			
 
				+  background-color: #ffff88;
			
 
				+}
			
 
				+@media (min-width: 600px) {
			
 
				+  .book.with-summary .book-header.fixed {
			
 
				+    left: 300px;
			
 
				+  }
			
 
				+}
			
 
				+@media (max-width: 1240px) {
			
 
				+  .book .book-body.fixed {
			
 
				+    top: 50px;
			
 
				+  }
			
 
				+  .book .book-body.fixed .body-inner {
			
 
				+    top: auto;
			
 
				+  }
			
 
				+}
			
 
				+@media (max-width: 600px) {
			
 
				+  .book.with-summary .book-header.fixed {
			
 
				+    left: calc(100% - 60px);
			
 
				+    min-width: 300px;
			
 
				+  }
			
 
				+  .book.with-summary .book-body {
			
 
				+    transform: none;
			
 
				+    left: calc(100% - 60px);
			
 
				+    min-width: 300px;
			
 
				+  }
			
 
				+  .book .book-body.fixed {
			
 
				+    top: 0;
			
 
				+  }
			
 
				+}
			
 
				+
			
 
				+.book .book-body.fixed .body-inner {
			
 
				+  top: 50px;
			
 
				+}
			
 
				+.book .book-body .page-wrapper .page-inner section.normal sub, .book .book-body .page-wrapper .page-inner section.normal sup {
			
 
				+  font-size: 85%;
			
 
				+}
			
 
				+
			
 
				+@media print {
			
 
				+  .book .book-summary, .book .book-body .book-header, .fa {
			
 
				+    display: none !important;
			
 
				+  }
			
 
				+  .book .book-body.fixed {
			
 
				+    left: 0px;
			
 
				+  }
			
 
				+  .book .book-body,.book .book-body .body-inner, .book.with-summary {
			
 
				+    overflow: visible !important;
			
 
				+  }
			
 
				+}
			
 
				+.kable_wrapper {
			
 
				+  border-spacing: 20px 0;
			
 
				+  border-collapse: separate;
			
 
				+  border: none;
			
 
				+  margin: auto;
			
 
				+}
			
 
				+.kable_wrapper > tbody > tr > td {
			
 
				+  vertical-align: top;
			
 
				+}
			
 
				+.book .book-body .page-wrapper .page-inner section.normal table tr.header {
			
 
				+  border-top-width: 2px;
			
 
				+}
			
 
				+.book .book-body .page-wrapper .page-inner section.normal table tr:last-child td {
			
 
				+  border-bottom-width: 2px;
			
 
				+}
			
 
				+.book .book-body .page-wrapper .page-inner section.normal table td, .book .book-body .page-wrapper .page-inner section.normal table th {
			
 
				+  border-left: none;
			
 
				+  border-right: none;
			
 
				+}
			
 
				+.book .book-body .page-wrapper .page-inner section.normal table.kable_wrapper > tbody > tr, .book .book-body .page-wrapper .page-inner section.normal table.kable_wrapper > tbody > tr > td {
			
 
				+  border-top: none;
			
 
				+}
			
 
				+.book .book-body .page-wrapper .page-inner section.normal table.kable_wrapper > tbody > tr:last-child > td {
			
 
				+    border-bottom: none;
			
 
				+}
			
 
				+
			
 
				+div.theorem, div.lemma, div.corollary, div.proposition, div.conjecture {
			
 
				+  font-style: italic;
			
 
				+}
			
 
				+span.theorem, span.lemma, span.corollary, span.proposition, span.conjecture {
			
 
				+  font-style: normal;
			
 
				+}
			
 
				+div.proof:after {
			
 
				+  content: "\25a2";
			
 
				+  float: right;
			
 
				+}
			
 
				+.header-section-number {
			
 
				+  padding-right: .5em;
			
 
				+}
			
--- a/book-output/libs/gitbook-2.6.7/css/plugin-clipboard.css
+++ b/book-output/libs/gitbook-2.6.7/css/plugin-clipboard.css
@@ -0,0 +1,18 @@
 
				+div.sourceCode {
			
 
				+  position: relative;
			
 
				+}
			
 
				+
			
 
				+.copy-to-clipboard-button {
			
 
				+  position: absolute;
			
 
				+  right: 0;
			
 
				+  top: 0;
			
 
				+  visibility: hidden;
			
 
				+}
			
 
				+
			
 
				+.copy-to-clipboard-button:focus {
			
 
				+  outline: 0;
			
 
				+}
			
 
				+
			
 
				+div.sourceCode:hover > .copy-to-clipboard-button {
			
 
				+  visibility: visible;
			
 
				+}
			
--- a/book-output/libs/gitbook-2.6.7/css/plugin-fontsettings.css
+++ b/book-output/libs/gitbook-2.6.7/css/plugin-fontsettings.css
@@ -0,0 +1,292 @@
 
				+/*
			
 
				+ * Theme 1
			
 
				+ */
			
 
				+.color-theme-1 .dropdown-menu {
			
 
				+  background-color: #111111;
			
 
				+  border-color: #7e888b;
			
 
				+}
			
 
				+.color-theme-1 .dropdown-menu .dropdown-caret .caret-inner {
			
 
				+  border-bottom: 9px solid #111111;
			
 
				+}
			
 
				+.color-theme-1 .dropdown-menu .buttons {
			
 
				+  border-color: #7e888b;
			
 
				+}
			
 
				+.color-theme-1 .dropdown-menu .button {
			
 
				+  color: #afa790;
			
 
				+}
			
 
				+.color-theme-1 .dropdown-menu .button:hover {
			
 
				+  color: #73553c;
			
 
				+}
			
 
				+/*
			
 
				+ * Theme 2
			
 
				+ */
			
 
				+.color-theme-2 .dropdown-menu {
			
 
				+  background-color: #2d3143;
			
 
				+  border-color: #272a3a;
			
 
				+}
			
 
				+.color-theme-2 .dropdown-menu .dropdown-caret .caret-inner {
			
 
				+  border-bottom: 9px solid #2d3143;
			
 
				+}
			
 
				+.color-theme-2 .dropdown-menu .buttons {
			
 
				+  border-color: #272a3a;
			
 
				+}
			
 
				+.color-theme-2 .dropdown-menu .button {
			
 
				+  color: #62677f;
			
 
				+}
			
 
				+.color-theme-2 .dropdown-menu .button:hover {
			
 
				+  color: #f4f4f5;
			
 
				+}
			
 
				+.book .book-header .font-settings .font-enlarge {
			
 
				+  line-height: 30px;
			
 
				+  font-size: 1.4em;
			
 
				+}
			
 
				+.book .book-header .font-settings .font-reduce {
			
 
				+  line-height: 30px;
			
 
				+  font-size: 1em;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body {
			
 
				+  color: #704214;
			
 
				+  background: #f3eacb;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section {
			
 
				+  background: #f3eacb;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body {
			
 
				+  color: #bdcadb;
			
 
				+  background: #1c1f2b;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section {
			
 
				+  background: #1c1f2b;
			
 
				+}
			
 
				+.book.font-size-0 .book-body .page-inner section {
			
 
				+  font-size: 1.2rem;
			
 
				+}
			
 
				+.book.font-size-1 .book-body .page-inner section {
			
 
				+  font-size: 1.4rem;
			
 
				+}
			
 
				+.book.font-size-2 .book-body .page-inner section {
			
 
				+  font-size: 1.6rem;
			
 
				+}
			
 
				+.book.font-size-3 .book-body .page-inner section {
			
 
				+  font-size: 2.2rem;
			
 
				+}
			
 
				+.book.font-size-4 .book-body .page-inner section {
			
 
				+  font-size: 4rem;
			
 
				+}
			
 
				+.book.font-family-0 {
			
 
				+  font-family: Georgia, serif;
			
 
				+}
			
 
				+.book.font-family-1 {
			
 
				+  font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal {
			
 
				+  color: #704214;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal a {
			
 
				+  color: inherit;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h1,
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h2,
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h3,
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h4,
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h5,
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h6 {
			
 
				+  color: inherit;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h1,
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h2 {
			
 
				+  border-color: inherit;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal h6 {
			
 
				+  color: inherit;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal hr {
			
 
				+  background-color: inherit;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal blockquote {
			
 
				+  border-color: #c4b29f;
			
 
				+  opacity: 0.9;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal pre,
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal code {
			
 
				+  background: #fdf6e3;
			
 
				+  color: #657b83;
			
 
				+  border-color: #f8df9c;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal .highlight {
			
 
				+  background-color: inherit;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal table th,
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal table td {
			
 
				+  border-color: #f5d06c;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal table tr {
			
 
				+  color: inherit;
			
 
				+  background-color: #fdf6e3;
			
 
				+  border-color: #444444;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .page-wrapper .page-inner section.normal table tr:nth-child(2n) {
			
 
				+  background-color: #fbeecb;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal {
			
 
				+  color: #bdcadb;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal a {
			
 
				+  color: #3eb1d0;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h1,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h2,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h3,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h4,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h5,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h6 {
			
 
				+  color: #fffffa;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h1,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h2 {
			
 
				+  border-color: #373b4e;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal h6 {
			
 
				+  color: #373b4e;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal hr {
			
 
				+  background-color: #373b4e;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal blockquote {
			
 
				+  border-color: #373b4e;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code {
			
 
				+  color: #9dbed8;
			
 
				+  background: #2d3143;
			
 
				+  border-color: #2d3143;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal .highlight {
			
 
				+  background-color: #282a39;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal table th,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal table td {
			
 
				+  border-color: #3b3f54;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal table tr {
			
 
				+  color: #b6c2d2;
			
 
				+  background-color: #2d3143;
			
 
				+  border-color: #3b3f54;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal table tr:nth-child(2n) {
			
 
				+  background-color: #35394b;
			
 
				+}
			
 
				+.book.color-theme-1 .book-header {
			
 
				+  color: #afa790;
			
 
				+  background: transparent;
			
 
				+}
			
 
				+.book.color-theme-1 .book-header .btn {
			
 
				+  color: #afa790;
			
 
				+}
			
 
				+.book.color-theme-1 .book-header .btn:hover {
			
 
				+  color: #73553c;
			
 
				+  background: none;
			
 
				+}
			
 
				+.book.color-theme-1 .book-header h1 {
			
 
				+  color: #704214;
			
 
				+}
			
 
				+.book.color-theme-2 .book-header {
			
 
				+  color: #7e888b;
			
 
				+  background: transparent;
			
 
				+}
			
 
				+.book.color-theme-2 .book-header .btn {
			
 
				+  color: #3b3f54;
			
 
				+}
			
 
				+.book.color-theme-2 .book-header .btn:hover {
			
 
				+  color: #fffff5;
			
 
				+  background: none;
			
 
				+}
			
 
				+.book.color-theme-2 .book-header h1 {
			
 
				+  color: #bdcadb;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .navigation {
			
 
				+  color: #afa790;
			
 
				+}
			
 
				+.book.color-theme-1 .book-body .navigation:hover {
			
 
				+  color: #73553c;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .navigation {
			
 
				+  color: #383f52;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .navigation:hover {
			
 
				+  color: #fffff5;
			
 
				+}
			
 
				+/*
			
 
				+ * Theme 1
			
 
				+ */
			
 
				+.book.color-theme-1 .book-summary {
			
 
				+  color: #afa790;
			
 
				+  background: #111111;
			
 
				+  border-right: 1px solid rgba(0, 0, 0, 0.07);
			
 
				+}
			
 
				+.book.color-theme-1 .book-summary .book-search {
			
 
				+  background: transparent;
			
 
				+}
			
 
				+.book.color-theme-1 .book-summary .book-search input,
			
 
				+.book.color-theme-1 .book-summary .book-search input:focus {
			
 
				+  border: 1px solid transparent;
			
 
				+}
			
 
				+.book.color-theme-1 .book-summary ul.summary li.divider {
			
 
				+  background: #7e888b;
			
 
				+  box-shadow: none;
			
 
				+}
			
 
				+.book.color-theme-1 .book-summary ul.summary li i.fa-check {
			
 
				+  color: #33cc33;
			
 
				+}
			
 
				+.book.color-theme-1 .book-summary ul.summary li.done > a {
			
 
				+  color: #877f6a;
			
 
				+}
			
 
				+.book.color-theme-1 .book-summary ul.summary li a,
			
 
				+.book.color-theme-1 .book-summary ul.summary li span {
			
 
				+  color: #877f6a;
			
 
				+  background: transparent;
			
 
				+  font-weight: normal;
			
 
				+}
			
 
				+.book.color-theme-1 .book-summary ul.summary li.active > a,
			
 
				+.book.color-theme-1 .book-summary ul.summary li a:hover {
			
 
				+  color: #704214;
			
 
				+  background: transparent;
			
 
				+  font-weight: normal;
			
 
				+}
			
 
				+/*
			
 
				+ * Theme 2
			
 
				+ */
			
 
				+.book.color-theme-2 .book-summary {
			
 
				+  color: #bcc1d2;
			
 
				+  background: #2d3143;
			
 
				+  border-right: none;
			
 
				+}
			
 
				+.book.color-theme-2 .book-summary .book-search {
			
 
				+  background: transparent;
			
 
				+}
			
 
				+.book.color-theme-2 .book-summary .book-search input,
			
 
				+.book.color-theme-2 .book-summary .book-search input:focus {
			
 
				+  border: 1px solid transparent;
			
 
				+}
			
 
				+.book.color-theme-2 .book-summary ul.summary li.divider {
			
 
				+  background: #272a3a;
			
 
				+  box-shadow: none;
			
 
				+}
			
 
				+.book.color-theme-2 .book-summary ul.summary li i.fa-check {
			
 
				+  color: #33cc33;
			
 
				+}
			
 
				+.book.color-theme-2 .book-summary ul.summary li.done > a {
			
 
				+  color: #62687f;
			
 
				+}
			
 
				+.book.color-theme-2 .book-summary ul.summary li a,
			
 
				+.book.color-theme-2 .book-summary ul.summary li span {
			
 
				+  color: #c1c6d7;
			
 
				+  background: transparent;
			
 
				+  font-weight: 600;
			
 
				+}
			
 
				+.book.color-theme-2 .book-summary ul.summary li.active > a,
			
 
				+.book.color-theme-2 .book-summary ul.summary li a:hover {
			
 
				+  color: #f4f4f5;
			
 
				+  background: #252737;
			
 
				+  font-weight: 600;
			
 
				+}
			
--- a/book-output/libs/gitbook-2.6.7/css/plugin-highlight.css
+++ b/book-output/libs/gitbook-2.6.7/css/plugin-highlight.css
@@ -0,0 +1,426 @@
 
				+.book .book-body .page-wrapper .page-inner section.normal pre,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code {
			
 
				+  /* http://jmblog.github.com/color-themes-for-google-code-highlightjs */
			
 
				+  /* Tomorrow Comment */
			
 
				+  /* Tomorrow Red */
			
 
				+  /* Tomorrow Orange */
			
 
				+  /* Tomorrow Yellow */
			
 
				+  /* Tomorrow Green */
			
 
				+  /* Tomorrow Aqua */
			
 
				+  /* Tomorrow Blue */
			
 
				+  /* Tomorrow Purple */
			
 
				+}
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-comment,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-comment,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-title,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-title {
			
 
				+  color: #8e908c;
			
 
				+}
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-variable,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-variable,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-attribute,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-attribute,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-tag,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-tag,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-regexp,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-regexp,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .ruby .hljs-constant,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .ruby .hljs-constant,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .xml .hljs-tag .hljs-title,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .xml .hljs-tag .hljs-title,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .xml .hljs-pi,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .xml .hljs-pi,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .xml .hljs-doctype,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .xml .hljs-doctype,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .html .hljs-doctype,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .html .hljs-doctype,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .css .hljs-id,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .css .hljs-id,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .css .hljs-class,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .css .hljs-class,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .css .hljs-pseudo,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .css .hljs-pseudo {
			
 
				+  color: #c82829;
			
 
				+}
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-number,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-number,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-preprocessor,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-preprocessor,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-pragma,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-pragma,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-built_in,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-built_in,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-literal,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-literal,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-params,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-params,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .hljs-constant,
			
 
				+.book .book-body .page-wrapper .page-inner section.normal code .hljs-constant {
			
 
				+  color: #f5871f;
			
 
				+}
			
 
				+.book .book-body .page-wrapper .page-inner section.normal pre .ruby .hljs-class .hljs-title,
			
 
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				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .hljs-built_in,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .hljs-literal,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .hljs-literal,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .hljs-params,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .hljs-params,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .hljs-constant,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .hljs-constant {
			
 
				+  color: #e78c45;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .ruby .hljs-class .hljs-title,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .ruby .hljs-class .hljs-title,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .css .hljs-rules .hljs-attribute,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .css .hljs-rules .hljs-attribute {
			
 
				+  color: #e7c547;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .hljs-string,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .hljs-string,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .hljs-value,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .hljs-value,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .hljs-inheritance,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .hljs-inheritance,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .hljs-header,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .hljs-header,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .ruby .hljs-symbol,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .ruby .hljs-symbol,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .xml .hljs-cdata,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .xml .hljs-cdata {
			
 
				+  color: #b9ca4a;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .css .hljs-hexcolor,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .css .hljs-hexcolor {
			
 
				+  color: #70c0b1;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .hljs-function,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .hljs-function,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .python .hljs-decorator,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .python .hljs-decorator,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .python .hljs-title,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .python .hljs-title,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .ruby .hljs-function .hljs-title,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .ruby .hljs-function .hljs-title,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .ruby .hljs-title .hljs-keyword,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .ruby .hljs-title .hljs-keyword,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .perl .hljs-sub,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .perl .hljs-sub,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .javascript .hljs-title,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .javascript .hljs-title,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .coffeescript .hljs-title,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .coffeescript .hljs-title {
			
 
				+  color: #7aa6da;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .hljs-keyword,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .hljs-keyword,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .javascript .hljs-function,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .javascript .hljs-function {
			
 
				+  color: #c397d8;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .hljs,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .hljs {
			
 
				+  display: block;
			
 
				+  background: black;
			
 
				+  color: #eaeaea;
			
 
				+  padding: 0.5em;
			
 
				+}
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .coffeescript .javascript,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .coffeescript .javascript,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .javascript .xml,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .javascript .xml,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .tex .hljs-formula,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .tex .hljs-formula,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .xml .javascript,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .xml .javascript,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .xml .vbscript,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .xml .vbscript,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .xml .css,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .xml .css,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal pre .xml .hljs-cdata,
			
 
				+.book.color-theme-2 .book-body .page-wrapper .page-inner section.normal code .xml .hljs-cdata {
			
 
				+  opacity: 0.5;
			
 
				+}
			
--- a/book-output/libs/gitbook-2.6.7/css/plugin-search.css
+++ b/book-output/libs/gitbook-2.6.7/css/plugin-search.css
@@ -0,0 +1,31 @@
 
				+.book .book-summary .book-search {
			
 
				+  padding: 6px;
			
 
				+  background: transparent;
			
 
				+  position: absolute;
			
 
				+  top: -50px;
			
 
				+  left: 0px;
			
 
				+  right: 0px;
			
 
				+  transition: top 0.5s ease;
			
 
				+}
			
 
				+.book .book-summary .book-search input,
			
 
				+.book .book-summary .book-search input:focus,
			
 
				+.book .book-summary .book-search input:hover {
			
 
				+  width: 100%;
			
 
				+  background: transparent;
			
 
				+  border: 1px solid #ccc;
			
 
				+  box-shadow: none;
			
 
				+  outline: none;
			
 
				+  line-height: 22px;
			
 
				+  padding: 7px 4px;
			
 
				+  color: inherit;
			
 
				+  box-sizing: border-box;
			
 
				+}
			
 
				+.book.with-search .book-summary .book-search {
			
 
				+  top: 0px;
			
 
				+}
			
 
				+.book.with-search .book-summary ul.summary {
			
 
				+  top: 50px;
			
 
				+}
			
 
				+.with-search .summary li[data-level] a[href*=".html#"] {
			
 
				+  display: none;
			
 
				+}
			
--- a/book-output/libs/gitbook-2.6.7/css/plugin-table.css
+++ b/book-output/libs/gitbook-2.6.7/css/plugin-table.css
@@ -0,0 +1 @@
 
				+.book .book-body .page-wrapper .page-inner section.normal table{display:table;width:100%;border-collapse:collapse;border-spacing:0;overflow:auto}.book .book-body .page-wrapper .page-inner section.normal table td,.book .book-body .page-wrapper .page-inner section.normal table th{padding:6px 13px;border:1px solid #ddd}.book .book-body .page-wrapper .page-inner section.normal table tr{background-color:#fff;border-top:1px solid #ccc}.book .book-body .page-wrapper .page-inner section.normal table tr:nth-child(2n){background-color:#f8f8f8}.book .book-body .page-wrapper .page-inner section.normal table th{font-weight:700}
			
--- a/book-output/libs/gitbook-2.6.7/css/style.css
+++ b/book-output/libs/gitbook-2.6.7/css/style.css
--- a/book-output/libs/gitbook-2.6.7/js/app.min.js
+++ b/book-output/libs/gitbook-2.6.7/js/app.min.js
--- a/book-output/libs/gitbook-2.6.7/js/clipboard.min.js
+++ b/book-output/libs/gitbook-2.6.7/js/clipboard.min.js
--- a/book-output/libs/gitbook-2.6.7/js/jquery.highlight.js
+++ b/book-output/libs/gitbook-2.6.7/js/jquery.highlight.js
@@ -0,0 +1,86 @@
 
				+gitbook.require(["jQuery"], function(jQuery) {
			
 
				+
			
 
				+/*
			
 
				+ * jQuery Highlight plugin
			
 
				+ *
			
 
				+ * Based on highlight v3 by Johann Burkard
			
 
				+ * http://johannburkard.de/blog/programming/javascript/highlight-javascript-text-higlighting-jquery-plugin.html
			
 
				+ *
			
 
				+ * Code a little bit refactored and cleaned (in my humble opinion).
			
 
				+ * Most important changes:
			
 
				+ *  - has an option to highlight only entire words (wordsOnly - false by default),
			
 
				+ *  - has an option to be case sensitive (caseSensitive - false by default)
			
 
				+ *  - highlight element tag and class names can be specified in options
			
 
				+ *
			
 
				+ * Copyright (c) 2009 Bartek Szopka
			
 
				+ *
			
 
				+ * Licensed under MIT license.
			
 
				+ *
			
 
				+ */
			
 
				+
			
 
				+jQuery.extend({
			
 
				+    highlight: function (node, re, nodeName, className) {
			
 
				+        if (node.nodeType === 3) {
			
 
				+            var match = node.data.match(re);
			
 
				+            if (match) {
			
 
				+                var highlight = document.createElement(nodeName || 'span');
			
 
				+                highlight.className = className || 'highlight';
			
 
				+                var wordNode = node.splitText(match.index);
			
 
				+                wordNode.splitText(match[0].length);
			
 
				+                var wordClone = wordNode.cloneNode(true);
			
 
				+                highlight.appendChild(wordClone);
			
 
				+                wordNode.parentNode.replaceChild(highlight, wordNode);
			
 
				+                return 1; //skip added node in parent
			
 
				+            }
			
 
				+        } else if ((node.nodeType === 1 && node.childNodes) && // only element nodes that have children
			
 
				+                !/(script|style)/i.test(node.tagName) && // ignore script and style nodes
			
 
				+                !(node.tagName === nodeName.toUpperCase() && node.className === className)) { // skip if already highlighted
			
 
				+            for (var i = 0; i < node.childNodes.length; i++) {
			
 
				+                i += jQuery.highlight(node.childNodes[i], re, nodeName, className);
			
 
				+            }
			
 
				+        }
			
 
				+        return 0;
			
 
				+    }
			
 
				+});
			
 
				+
			
 
				+jQuery.fn.unhighlight = function (options) {
			
 
				+    var settings = { className: 'highlight', element: 'span' };
			
 
				+    jQuery.extend(settings, options);
			
 
				+
			
 
				+    return this.find(settings.element + "." + settings.className).each(function () {
			
 
				+        var parent = this.parentNode;
			
 
				+        parent.replaceChild(this.firstChild, this);
			
 
				+        parent.normalize();
			
 
				+    }).end();
			
 
				+};
			
 
				+
			
 
				+jQuery.fn.highlight = function (words, options) {
			
 
				+    var settings = { className: 'highlight', element: 'span', caseSensitive: false, wordsOnly: false };
			
 
				+    jQuery.extend(settings, options);
			
 
				+
			
 
				+    if (words.constructor === String) {
			
 
				+        words = [words];
			
 
				+        // also match 'foo-bar' if search for 'foo bar'
			
 
				+        if (/\s/.test(words[0])) words.push(words[0].replace(/\s+/, '-'));
			
 
				+    }
			
 
				+    words = jQuery.grep(words, function(word, i){
			
 
				+      return word !== '';
			
 
				+    });
			
 
				+    words = jQuery.map(words, function(word, i) {
			
 
				+      return word.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, "\\$&");
			
 
				+    });
			
 
				+    if (words.length === 0) { return this; }
			
 
				+
			
 
				+    var flag = settings.caseSensitive ? "" : "i";
			
 
				+    var pattern = "(" + words.join("|") + ")";
			
 
				+    if (settings.wordsOnly) {
			
 
				+        pattern = "\\b" + pattern + "\\b";
			
 
				+    }
			
 
				+    var re = new RegExp(pattern, flag);
			
 
				+
			
 
				+    return this.each(function () {
			
 
				+        jQuery.highlight(this, re, settings.element, settings.className);
			
 
				+    });
			
 
				+};
			
 
				+
			
 
				+});
			
--- a/book-output/libs/gitbook-2.6.7/js/lunr.js
+++ b/book-output/libs/gitbook-2.6.7/js/lunr.js
--- a/book-output/libs/gitbook-2.6.7/js/plugin-bookdown.js
+++ b/book-output/libs/gitbook-2.6.7/js/plugin-bookdown.js
@@ -0,0 +1,259 @@
 
				+gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
			
 
				+
			
 
				+  var gs = gitbook.storage;
			
 
				+
			
 
				+  gitbook.events.bind("start", function(e, config) {
			
 
				+
			
 
				+    // add the Edit button (edit on Github)
			
 
				+    var edit = config.edit;
			
 
				+    if (edit && edit.link) gitbook.toolbar.createButton({
			
 
				+      icon: 'fa fa-edit',
			
 
				+      label: edit.text || 'Edit',
			
 
				+      position: 'left',
			
 
				+      onClick: function(e) {
			
 
				+        e.preventDefault();
			
 
				+        window.open(edit.link);
			
 
				+      }
			
 
				+    });
			
 
				+
			
 
				+    // add the History button (file history on Github)
			
 
				+    var history = config.history;
			
 
				+    if (history && history.link) gitbook.toolbar.createButton({
			
 
				+      icon: 'fa fa-history',
			
 
				+      label: history.text || 'History',
			
 
				+      position: 'left',
			
 
				+      onClick: function(e) {
			
 
				+        e.preventDefault();
			
 
				+        window.open(history.link);
			
 
				+      }
			
 
				+    });
			
 
				+
			
 
				+    // add the View button (file view on Github)
			
 
				+    var view = config.view;
			
 
				+    if (view && view.link) gitbook.toolbar.createButton({
			
 
				+      icon: 'fa fa-eye',
			
 
				+      label: view.text || 'View Source',
			
 
				+      position: 'left',
			
 
				+      onClick: function(e) {
			
 
				+        e.preventDefault();
			
 
				+        window.open(view.link);
			
 
				+      }
			
 
				+    });
			
 
				+
			
 
				+    // add the Download button
			
 
				+    var down = config.download;
			
 
				+    var normalizeDownload = function() {
			
 
				+      if (!down || !(down instanceof Array) || down.length === 0) return;
			
 
				+      if (down[0] instanceof Array) return down;
			
 
				+      return $.map(down, function(file, i) {
			
 
				+        return [[file, file.replace(/.*[.]/g, '').toUpperCase()]];
			
 
				+      });
			
 
				+    };
			
 
				+    down = normalizeDownload(down);
			
 
				+    if (down) if (down.length === 1 && /[.]pdf$/.test(down[0][0])) {
			
 
				+      gitbook.toolbar.createButton({
			
 
				+        icon: 'fa fa-file-pdf-o',
			
 
				+        label: down[0][1],
			
 
				+        position: 'left',
			
 
				+        onClick: function(e) {
			
 
				+          e.preventDefault();
			
 
				+          window.open(down[0][0]);
			
 
				+        }
			
 
				+      });
			
 
				+    } else {
			
 
				+      gitbook.toolbar.createButton({
			
 
				+        icon: 'fa fa-download',
			
 
				+        label: 'Download',
			
 
				+        position: 'left',
			
 
				+        dropdown: $.map(down, function(item, i) {
			
 
				+          return {
			
 
				+            text: item[1],
			
 
				+            onClick: function(e) {
			
 
				+              e.preventDefault();
			
 
				+              window.open(item[0]);
			
 
				+            }
			
 
				+          };
			
 
				+        })
			
 
				+      });
			
 
				+    }
			
 
				+
			
 
				+    // add the Information button
			
 
				+    var info = ['Keyboard shortcuts (<> indicates arrow keys):',
			
 
				+      '<left>/<right>: navigate to previous/next page',
			
 
				+      's: Toggle sidebar'];
			
 
				+    if (config.search !== false) info.push('f: Toggle search input ' +
			
 
				+      '(use <up>/<down>/Enter in the search input to navigate through search matches; ' +
			
 
				+      'press Esc to cancel search)');
			
 
				+    if (config.info !== false) gitbook.toolbar.createButton({
			
 
				+      icon: 'fa fa-info',
			
 
				+      label: 'Information about the toolbar',
			
 
				+      position: 'left',
			
 
				+      onClick: function(e) {
			
 
				+        e.preventDefault();
			
 
				+        window.alert(info.join('\n\n'));
			
 
				+      }
			
 
				+    });
			
 
				+
			
 
				+    // highlight the current section in TOC
			
 
				+    var href = window.location.pathname;
			
 
				+    href = href.substr(href.lastIndexOf('/') + 1);
			
 
				+    // accentuated characters need to be decoded (#819)
			
 
				+    href = decodeURIComponent(href);
			
 
				+    if (href === '') href = 'index.html';
			
 
				+    var li = $('a[href^="' + href + location.hash + '"]').parent('li.chapter').first();
			
 
				+    var summary = $('ul.summary'), chaps = summary.find('li.chapter');
			
 
				+    if (li.length === 0) li = chaps.first();
			
 
				+    li.addClass('active');
			
 
				+    chaps.on('click', function(e) {
			
 
				+      chaps.removeClass('active');
			
 
				+      $(this).addClass('active');
			
 
				+      gs.set('tocScrollTop', summary.scrollTop());
			
 
				+    });
			
 
				+
			
 
				+    var toc = config.toc;
			
 
				+    // collapse TOC items that are not for the current chapter
			
 
				+    if (toc && toc.collapse) (function() {
			
 
				+      var type = toc.collapse;
			
 
				+      if (type === 'none') return;
			
 
				+      if (type !== 'section' && type !== 'subsection') return;
			
 
				+      // sections under chapters
			
 
				+      var toc_sub = summary.children('li[data-level]').children('ul');
			
 
				+      if (type === 'section') {
			
 
				+        toc_sub.hide()
			
 
				+          .parent().has(li).children('ul').show();
			
 
				+      } else {
			
 
				+        toc_sub.children('li').children('ul').hide()
			
 
				+          .parent().has(li).children('ul').show();
			
 
				+      }
			
 
				+      li.children('ul').show();
			
 
				+      var toc_sub2 = toc_sub.children('li');
			
 
				+      if (type === 'section') toc_sub2.children('ul').hide();
			
 
				+      summary.children('li[data-level]').find('a')
			
 
				+        .on('click.bookdown', function(e) {
			
 
				+          if (href === $(this).attr('href').replace(/#.*/, ''))
			
 
				+            $(this).parent('li').children('ul').toggle();
			
 
				+        });
			
 
				+    })();
			
 
				+
			
 
				+    // add tooltips to the <a>'s that are truncated
			
 
				+    $('a').each(function(i, el) {
			
 
				+      if (el.offsetWidth >= el.scrollWidth) return;
			
 
				+      if (typeof el.title === 'undefined') return;
			
 
				+      el.title = el.text;
			
 
				+    });
			
 
				+
			
 
				+    // restore TOC scroll position
			
 
				+    var pos = gs.get('tocScrollTop');
			
 
				+    if (typeof pos !== 'undefined') summary.scrollTop(pos);
			
 
				+
			
 
				+    // highlight the TOC item that has same text as the heading in view as scrolling
			
 
				+    if (toc && toc.scroll_highlight !== false) (function() {
			
 
				+      // scroll the current TOC item into viewport
			
 
				+      var ht = $(window).height(), rect = li[0].getBoundingClientRect();
			
 
				+      if (rect.top >= ht || rect.top <= 0 || rect.bottom <= 0) {
			
 
				+        summary.scrollTop(li[0].offsetTop);
			
 
				+      }
			
 
				+      // current chapter TOC items
			
 
				+      var items = $('a[href^="' + href + '"]').parent('li.chapter'),
			
 
				+          m = items.length;
			
 
				+      if (m === 0) {
			
 
				+        items = summary.find('li.chapter');
			
 
				+        m = items.length;
			
 
				+      }
			
 
				+      if (m === 0) return;
			
 
				+      // all section titles on current page
			
 
				+      var hs = bookInner.find('.page-inner').find('h1,h2,h3'), n = hs.length,
			
 
				+          ts = hs.map(function(i, el) { return $(el).text(); });
			
 
				+      if (n === 0) return;
			
 
				+      var scrollHandler = function(e) {
			
 
				+        var ht = $(window).height();
			
 
				+        clearTimeout($.data(this, 'scrollTimer'));
			
 
				+        $.data(this, 'scrollTimer', setTimeout(function() {
			
 
				+          // find the first visible title in the viewport
			
 
				+          for (var i = 0; i < n; i++) {
			
 
				+            var rect = hs[i].getBoundingClientRect();
			
 
				+            if (rect.top >= 0 && rect.bottom <= ht) break;
			
 
				+          }
			
 
				+          if (i === n) return;
			
 
				+          items.removeClass('active');
			
 
				+          for (var j = 0; j < m; j++) {
			
 
				+            if (items.eq(j).children('a').first().text() === ts[i]) break;
			
 
				+          }
			
 
				+          if (j === m) j = 0;  // highlight the chapter title
			
 
				+          // search bottom-up for a visible TOC item to highlight; if an item is
			
 
				+          // hidden, we check if its parent is visible, and so on
			
 
				+          while (j > 0 && items.eq(j).is(':hidden')) j--;
			
 
				+          items.eq(j).addClass('active');
			
 
				+        }, 250));
			
 
				+      };
			
 
				+      bookInner.on('scroll.bookdown', scrollHandler);
			
 
				+      bookBody.on('scroll.bookdown', scrollHandler);
			
 
				+    })();
			
 
				+
			
 
				+    // do not refresh the page if the TOC item points to the current page
			
 
				+    $('a[href="' + href + '"]').parent('li.chapter').children('a')
			
 
				+      .on('click', function(e) {
			
 
				+        bookInner.scrollTop(0);
			
 
				+        bookBody.scrollTop(0);
			
 
				+        return false;
			
 
				+      });
			
 
				+
			
 
				+    var toolbar = config.toolbar;
			
 
				+    if (!toolbar || toolbar.position !== 'static') {
			
 
				+      var bookHeader = $('.book-header');
			
 
				+      bookBody.addClass('fixed');
			
 
				+      bookHeader.addClass('fixed')
			
 
				+      .css('background-color', bookBody.css('background-color'))
			
 
				+      .on('click.bookdown', function(e) {
			
 
				+        // the theme may have changed after user clicks the theme button
			
 
				+        bookHeader.css('background-color', bookBody.css('background-color'));
			
 
				+      });
			
 
				+    }
			
 
				+
			
 
				+  });
			
 
				+
			
 
				+  gitbook.events.bind("page.change", function(e) {
			
 
				+    // store TOC scroll position
			
 
				+    var summary = $('ul.summary');
			
 
				+    gs.set('tocScrollTop', summary.scrollTop());
			
 
				+  });
			
 
				+
			
 
				+  var bookBody = $('.book-body'), bookInner = bookBody.find('.body-inner');
			
 
				+  var chapterTitle = function() {
			
 
				+    return bookInner.find('.page-inner').find('h1,h2').first().text();
			
 
				+  };
			
 
				+  var saveScrollPos = function(e) {
			
 
				+    // save scroll position before page is reloaded
			
 
				+    gs.set('bodyScrollTop', {
			
 
				+      body: bookBody.scrollTop(),
			
 
				+      inner: bookInner.scrollTop(),
			
 
				+      focused: document.hasFocus(),
			
 
				+      title: chapterTitle()
			
 
				+    });
			
 
				+  };
			
 
				+  $(document).on('servr:reload', saveScrollPos);
			
 
				+
			
 
				+  // check if the page is loaded in an iframe (e.g. the RStudio preview window)
			
 
				+  var inIFrame = function() {
			
 
				+    var inIframe = true;
			
 
				+    try { inIframe = window.self !== window.top; } catch (e) {}
			
 
				+    return inIframe;
			
 
				+  };
			
 
				+  if (inIFrame()) {
			
 
				+    $(window).on('blur unload', saveScrollPos);
			
 
				+  }
			
 
				+
			
 
				+  $(function(e) {
			
 
				+    var pos = gs.get('bodyScrollTop');
			
 
				+    if (pos) {
			
 
				+      if (pos.title === chapterTitle()) {
			
 
				+        if (pos.body !== 0) bookBody.scrollTop(pos.body);
			
 
				+        if (pos.inner !== 0) bookInner.scrollTop(pos.inner);
			
 
				+      }
			
 
				+    }
			
 
				+    if ((pos && pos.focused) || !inIFrame()) bookInner.find('.page-wrapper').focus();
			
 
				+    // clear book body scroll position
			
 
				+    gs.remove('bodyScrollTop');
			
 
				+  });
			
 
				+
			
 
				+});
			
--- a/book-output/libs/gitbook-2.6.7/js/plugin-clipboard.js
+++ b/book-output/libs/gitbook-2.6.7/js/plugin-clipboard.js
@@ -0,0 +1,29 @@
 
				+gitbook.require(["gitbook", "jQuery"], function(gitbook, $) {
			
 
				+
			
 
				+  var copyButton = '<button type="button" class="copy-to-clipboard-button" title="Copy to clipboard" aria-label="Copy to clipboard"><i class="fa fa-copy"></i></button>';
			
 
				+  var clipboard;
			
 
				+
			
 
				+  gitbook.events.bind("page.change", function() {
			
 
				+
			
 
				+    if (!ClipboardJS.isSupported()) return;
			
 
				+
			
 
				+    // the page.change event is thrown twice: before and after the page changes
			
 
				+    if (clipboard) {
			
 
				+      // clipboard is already defined
			
 
				+      // we can deduct that we are before page changes
			
 
				+      clipboard.destroy(); // destroy the previous events listeners
			
 
				+      clipboard = undefined; // reset the clipboard object
			
 
				+      return;
			
 
				+    }
			
 
				+
			
 
				+    $(copyButton).prependTo("div.sourceCode");
			
 
				+
			
 
				+    clipboard = new ClipboardJS(".copy-to-clipboard-button", {
			
 
				+      text: function(trigger) {
			
 
				+        return trigger.parentNode.textContent;
			
 
				+      }
			
 
				+    });
			
 
				+
			
 
				+  });
			
 
				+
			
 
				+});
			
--- a/book-output/libs/gitbook-2.6.7/js/plugin-fontsettings.js
+++ b/book-output/libs/gitbook-2.6.7/js/plugin-fontsettings.js
@@ -0,0 +1,152 @@
 
				+gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
			
 
				+    var fontState;
			
 
				+
			
 
				+    var THEMES = {
			
 
				+        "white": 0,
			
 
				+        "sepia": 1,
			
 
				+        "night": 2
			
 
				+    };
			
 
				+
			
 
				+    var FAMILY = {
			
 
				+        "serif": 0,
			
 
				+        "sans": 1
			
 
				+    };
			
 
				+
			
 
				+    // Save current font settings
			
 
				+    function saveFontSettings() {
			
 
				+        gitbook.storage.set("fontState", fontState);
			
 
				+        update();
			
 
				+    }
			
 
				+
			
 
				+    // Increase font size
			
 
				+    function enlargeFontSize(e) {
			
 
				+        e.preventDefault();
			
 
				+        if (fontState.size >= 4) return;
			
 
				+
			
 
				+        fontState.size++;
			
 
				+        saveFontSettings();
			
 
				+    };
			
 
				+
			
 
				+    // Decrease font size
			
 
				+    function reduceFontSize(e) {
			
 
				+        e.preventDefault();
			
 
				+        if (fontState.size <= 0) return;
			
 
				+
			
 
				+        fontState.size--;
			
 
				+        saveFontSettings();
			
 
				+    };
			
 
				+
			
 
				+    // Change font family
			
 
				+    function changeFontFamily(index, e) {
			
 
				+        e.preventDefault();
			
 
				+
			
 
				+        fontState.family = index;
			
 
				+        saveFontSettings();
			
 
				+    };
			
 
				+
			
 
				+    // Change type of color
			
 
				+    function changeColorTheme(index, e) {
			
 
				+        e.preventDefault();
			
 
				+
			
 
				+        var $book = $(".book");
			
 
				+
			
 
				+        if (fontState.theme !== 0)
			
 
				+            $book.removeClass("color-theme-"+fontState.theme);
			
 
				+
			
 
				+        fontState.theme = index;
			
 
				+        if (fontState.theme !== 0)
			
 
				+            $book.addClass("color-theme-"+fontState.theme);
			
 
				+
			
 
				+        saveFontSettings();
			
 
				+    };
			
 
				+
			
 
				+    function update() {
			
 
				+        var $book = gitbook.state.$book;
			
 
				+
			
 
				+        $(".font-settings .font-family-list li").removeClass("active");
			
 
				+        $(".font-settings .font-family-list li:nth-child("+(fontState.family+1)+")").addClass("active");
			
 
				+
			
 
				+        $book[0].className = $book[0].className.replace(/\bfont-\S+/g, '');
			
 
				+        $book.addClass("font-size-"+fontState.size);
			
 
				+        $book.addClass("font-family-"+fontState.family);
			
 
				+
			
 
				+        if(fontState.theme !== 0) {
			
 
				+            $book[0].className = $book[0].className.replace(/\bcolor-theme-\S+/g, '');
			
 
				+            $book.addClass("color-theme-"+fontState.theme);
			
 
				+        }
			
 
				+    };
			
 
				+
			
 
				+    function init(config) {
			
 
				+        var $bookBody, $book;
			
 
				+
			
 
				+        //Find DOM elements.
			
 
				+        $book = gitbook.state.$book;
			
 
				+        $bookBody = $book.find(".book-body");
			
 
				+
			
 
				+        // Instantiate font state object
			
 
				+        fontState = gitbook.storage.get("fontState", {
			
 
				+            size: config.size || 2,
			
 
				+            family: FAMILY[config.family || "sans"],
			
 
				+            theme: THEMES[config.theme || "white"]
			
 
				+        });
			
 
				+
			
 
				+        update();
			
 
				+    };
			
 
				+
			
 
				+
			
 
				+    gitbook.events.bind("start", function(e, config) {
			
 
				+        var opts = config.fontsettings;
			
 
				+        if (!opts) return;
			
 
				+        
			
 
				+        // Create buttons in toolbar
			
 
				+        gitbook.toolbar.createButton({
			
 
				+            icon: 'fa fa-font',
			
 
				+            label: 'Font Settings',
			
 
				+            className: 'font-settings',
			
 
				+            dropdown: [
			
 
				+                [
			
 
				+                    {
			
 
				+                        text: 'A',
			
 
				+                        className: 'font-reduce',
			
 
				+                        onClick: reduceFontSize
			
 
				+                    },
			
 
				+                    {
			
 
				+                        text: 'A',
			
 
				+                        className: 'font-enlarge',
			
 
				+                        onClick: enlargeFontSize
			
 
				+                    }
			
 
				+                ],
			
 
				+                [
			
 
				+                    {
			
 
				+                        text: 'Serif',
			
 
				+                        onClick: _.partial(changeFontFamily, 0)
			
 
				+                    },
			
 
				+                    {
			
 
				+                        text: 'Sans',
			
 
				+                        onClick: _.partial(changeFontFamily, 1)
			
 
				+                    }
			
 
				+                ],
			
 
				+                [
			
 
				+                    {
			
 
				+                        text: 'White',
			
 
				+                        onClick: _.partial(changeColorTheme, 0)
			
 
				+                    },
			
 
				+                    {
			
 
				+                        text: 'Sepia',
			
 
				+                        onClick: _.partial(changeColorTheme, 1)
			
 
				+                    },
			
 
				+                    {
			
 
				+                        text: 'Night',
			
 
				+                        onClick: _.partial(changeColorTheme, 2)
			
 
				+                    }
			
 
				+                ]
			
 
				+            ]
			
 
				+        });
			
 
				+
			
 
				+
			
 
				+        // Init current settings
			
 
				+        init(opts);
			
 
				+    });
			
 
				+});
			
 
				+
			
 
				+
			
--- a/book-output/libs/gitbook-2.6.7/js/plugin-search.js
+++ b/book-output/libs/gitbook-2.6.7/js/plugin-search.js
@@ -0,0 +1,223 @@
 
				+gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
			
 
				+    var index = null;
			
 
				+    var $searchInput, $searchLabel, $searchForm;
			
 
				+    var $highlighted = [], hi, hiOpts = { className: 'search-highlight' };
			
 
				+    var collapse = false, toc_visible = [];
			
 
				+
			
 
				+    // Use a specific index
			
 
				+    function loadIndex(data) {
			
 
				+        // [Yihui] In bookdown, I use a character matrix to store the chapter
			
 
				+        // content, and the index is dynamically built on the client side.
			
 
				+        // Gitbook prebuilds the index data instead: https://github.com/GitbookIO/plugin-search
			
 
				+        // We can certainly do that via R packages V8 and jsonlite, but let's
			
 
				+        // see how slow it really is before improving it. On the other hand,
			
 
				+        // lunr cannot handle non-English text very well, e.g. the default
			
 
				+        // tokenizer cannot deal with Chinese text, so we may want to replace
			
 
				+        // lunr with a dumb simple text matching approach.
			
 
				+        index = lunr(function () {
			
 
				+          this.ref('url');
			
 
				+          this.field('title', { boost: 10 });
			
 
				+          this.field('body');
			
 
				+        });
			
 
				+        data.map(function(item) {
			
 
				+          index.add({
			
 
				+            url: item[0],
			
 
				+            title: item[1],
			
 
				+            body: item[2]
			
 
				+          });
			
 
				+        });
			
 
				+    }
			
 
				+
			
 
				+    // Fetch the search index
			
 
				+    function fetchIndex() {
			
 
				+        return $.getJSON(gitbook.state.basePath+"/search_index.json")
			
 
				+                .then(loadIndex);  // [Yihui] we need to use this object later
			
 
				+    }
			
 
				+
			
 
				+    // Search for a term and return results
			
 
				+    function search(q) {
			
 
				+        if (!index) return;
			
 
				+
			
 
				+        var results = _.chain(index.search(q))
			
 
				+        .map(function(result) {
			
 
				+            var parts = result.ref.split("#");
			
 
				+            return {
			
 
				+                path: parts[0],
			
 
				+                hash: parts[1]
			
 
				+            };
			
 
				+        })
			
 
				+        .value();
			
 
				+
			
 
				+        // [Yihui] Highlight the search keyword on current page
			
 
				+        $highlighted = results.length === 0 ? [] : $('.page-inner')
			
 
				+          .unhighlight(hiOpts).highlight(q, hiOpts).find('span.search-highlight');
			
 
				+        scrollToHighlighted(0);
			
 
				+
			
 
				+        return results;
			
 
				+    }
			
 
				+
			
 
				+    // [Yihui] Scroll the chapter body to the i-th highlighted string
			
 
				+    function scrollToHighlighted(d) {
			
 
				+      var n = $highlighted.length;
			
 
				+      hi = hi === undefined ? 0 : hi + d;
			
 
				+      // navignate to the previous/next page in the search results if reached the top/bottom
			
 
				+      var b = hi < 0;
			
 
				+      if (d !== 0 && (b || hi >= n)) {
			
 
				+        var path = currentPath(), n2 = toc_visible.length;
			
 
				+        if (n2 === 0) return;
			
 
				+        for (var i = b ? 0 : n2; (b && i < n2) || (!b && i >= 0); i += b ? 1 : -1) {
			
 
				+          if (toc_visible.eq(i).data('path') === path) break;
			
 
				+        }
			
 
				+        i += b ? -1 : 1;
			
 
				+        if (i < 0) i = n2 - 1;
			
 
				+        if (i >= n2) i = 0;
			
 
				+        var lnk = toc_visible.eq(i).find('a[href$=".html"]');
			
 
				+        if (lnk.length) lnk[0].click();
			
 
				+        return;
			
 
				+      }
			
 
				+      if (n === 0) return;
			
 
				+      var $p = $highlighted.eq(hi);
			
 
				+      $p[0].scrollIntoView();
			
 
				+      $highlighted.css('background-color', '');
			
 
				+      // an orange background color on the current item and removed later
			
 
				+      $p.css('background-color', 'orange');
			
 
				+      setTimeout(function() {
			
 
				+        $p.css('background-color', '');
			
 
				+      }, 2000);
			
 
				+    }
			
 
				+
			
 
				+    function currentPath() {
			
 
				+      var href = window.location.pathname;
			
 
				+      href = href.substr(href.lastIndexOf('/') + 1);
			
 
				+      return href === '' ? 'index.html' : href;
			
 
				+    }
			
 
				+
			
 
				+    // Create search form
			
 
				+    function createForm(value) {
			
 
				+        if ($searchForm) $searchForm.remove();
			
 
				+        if ($searchLabel) $searchLabel.remove();
			
 
				+        if ($searchInput) $searchInput.remove();
			
 
				+
			
 
				+        $searchForm = $('<div>', {
			
 
				+            'class': 'book-search',
			
 
				+            'role': 'search'
			
 
				+        });
			
 
				+
			
 
				+        $searchLabel = $('<label>', {
			
 
				+            'for': 'search-box',
			
 
				+            'aria-hidden': 'false',
			
 
				+            'hidden': ''
			
 
				+        });
			
 
				+
			
 
				+        $searchInput = $('<input>', {
			
 
				+            'id': 'search-box',
			
 
				+            'type': 'search',
			
 
				+            'class': 'form-control',
			
 
				+            'val': value,
			
 
				+            'placeholder': 'Type to search (Enter for navigation)',
			
 
				+            'title': 'Use Enter or the <Down> key to navigate to the next match, or the <Up> key to the previous match'
			
 
				+        });
			
 
				+
			
 
				+        $searchLabel.append("Type to search");
			
 
				+        $searchLabel.appendTo($searchForm);
			
 
				+        $searchInput.appendTo($searchForm);
			
 
				+        $searchForm.prependTo(gitbook.state.$book.find('.book-summary'));
			
 
				+    }
			
 
				+
			
 
				+    // Return true if search is open
			
 
				+    function isSearchOpen() {
			
 
				+        return gitbook.state.$book.hasClass("with-search");
			
 
				+    }
			
 
				+
			
 
				+    // Toggle the search
			
 
				+    function toggleSearch(_state) {
			
 
				+        if (isSearchOpen() === _state) return;
			
 
				+        if (!$searchInput) return;
			
 
				+
			
 
				+        gitbook.state.$book.toggleClass("with-search", _state);
			
 
				+
			
 
				+        // If search bar is open: focus input
			
 
				+        if (isSearchOpen()) {
			
 
				+            gitbook.sidebar.toggle(true);
			
 
				+            $searchInput.focus();
			
 
				+        } else {
			
 
				+            $searchInput.blur();
			
 
				+            $searchInput.val("");
			
 
				+            gitbook.storage.remove("keyword");
			
 
				+            gitbook.sidebar.filter(null);
			
 
				+            $('.page-inner').unhighlight(hiOpts);
			
 
				+        }
			
 
				+    }
			
 
				+
			
 
				+    function sidebarFilter(results) {
			
 
				+        gitbook.sidebar.filter(_.pluck(results, "path"));
			
 
				+        toc_visible = $('ul.summary').find('li:visible');
			
 
				+    }
			
 
				+
			
 
				+    // Recover current search when page changed
			
 
				+    function recoverSearch() {
			
 
				+        var keyword = gitbook.storage.get("keyword", "");
			
 
				+
			
 
				+        createForm(keyword);
			
 
				+
			
 
				+        if (keyword.length > 0) {
			
 
				+            if(!isSearchOpen()) {
			
 
				+                toggleSearch(true); // [Yihui] open the search box
			
 
				+            }
			
 
				+            sidebarFilter(search(keyword));
			
 
				+        }
			
 
				+    }
			
 
				+
			
 
				+
			
 
				+    gitbook.events.bind("start", function(e, config) {
			
 
				+        // [Yihui] disable search
			
 
				+        if (config.search === false) return;
			
 
				+        collapse = !config.toc || config.toc.collapse === 'section' ||
			
 
				+          config.toc.collapse === 'subsection';
			
 
				+
			
 
				+        // Pre-fetch search index and create the form
			
 
				+        fetchIndex()
			
 
				+        // [Yihui] recover search after the page is loaded
			
 
				+        .then(recoverSearch);
			
 
				+
			
 
				+
			
 
				+        // Type in search bar
			
 
				+        $(document).on("keyup", ".book-search input", function(e) {
			
 
				+            var key = (e.keyCode ? e.keyCode : e.which);
			
 
				+            // [Yihui] Escape -> close search box; Up/Down/Enter: previous/next highlighted
			
 
				+            if (key == 27) {
			
 
				+                e.preventDefault();
			
 
				+                toggleSearch(false);
			
 
				+            } else if (key == 38) {
			
 
				+              scrollToHighlighted(-1);
			
 
				+            } else if (key == 40 || key == 13) {
			
 
				+              scrollToHighlighted(1);
			
 
				+            }
			
 
				+        }).on("input", ".book-search input", function(e) {
			
 
				+            var q = $(this).val().trim();
			
 
				+            if (q.length === 0) {
			
 
				+                gitbook.sidebar.filter(null);
			
 
				+                gitbook.storage.remove("keyword");
			
 
				+                $('.page-inner').unhighlight(hiOpts);
			
 
				+            } else {
			
 
				+                var results = search(q);
			
 
				+                sidebarFilter(results);
			
 
				+                gitbook.storage.set("keyword", q);
			
 
				+            }
			
 
				+        });
			
 
				+
			
 
				+        // Create the toggle search button
			
 
				+        gitbook.toolbar.createButton({
			
 
				+            icon: 'fa fa-search',
			
 
				+            label: 'Search',
			
 
				+            position: 'left',
			
 
				+            onClick: toggleSearch
			
 
				+        });
			
 
				+
			
 
				+        // Bind keyboard to toggle search
			
 
				+        gitbook.keyboard.bind(['f'], toggleSearch);
			
 
				+    });
			
 
				+
			
 
				+    // [Yihui] do not try to recover search; always start fresh
			
 
				+    // gitbook.events.bind("page.change", recoverSearch);
			
 
				+});
			
--- a/book-output/libs/gitbook-2.6.7/js/plugin-sharing.js
+++ b/book-output/libs/gitbook-2.6.7/js/plugin-sharing.js
@@ -0,0 +1,105 @@
 
				+gitbook.require(["gitbook", "lodash", "jQuery"], function(gitbook, _, $) {
			
 
				+    var SITES = {
			
 
				+        'github': {
			
 
				+            'label': 'Github',
			
 
				+            'icon': 'fa fa-github',
			
 
				+            'onClick': function(e) {
			
 
				+                e.preventDefault();
			
 
				+                var repo = $('meta[name="github-repo"]').attr('content');
			
 
				+                if (typeof repo === 'undefined') throw("Github repo not defined");
			
 
				+                window.open("https://github.com/"+repo);
			
 
				+            }
			
 
				+        },
			
 
				+        'facebook': {
			
 
				+            'label': 'Facebook',
			
 
				+            'icon': 'fa fa-facebook',
			
 
				+            'onClick': function(e) {
			
 
				+                e.preventDefault();
			
 
				+                window.open("http://www.facebook.com/sharer/sharer.php?u="+encodeURIComponent(location.href));
			
 
				+            }
			
 
				+        },
			
 
				+        'twitter': {
			
 
				+            'label': 'Twitter',
			
 
				+            'icon': 'fa fa-twitter',
			
 
				+            'onClick': function(e) {
			
 
				+                e.preventDefault();
			
 
				+                window.open("http://twitter.com/intent/tweet?text="+document.title+"&url="+encodeURIComponent(location.href)+"&hashtags=rmarkdown,bookdown");
			
 
				+            }
			
 
				+        },
			
 
				+        'linkedin': {
			
 
				+            'label': 'LinkedIn',
			
 
				+            'icon': 'fa fa-linkedin',
			
 
				+            'onClick': function(e) {
			
 
				+                e.preventDefault();
			
 
				+                window.open("https://www.linkedin.com/shareArticle?mini=true&url="+encodeURIComponent(location.href)+"&title="+encodeURIComponent(document.title));
			
 
				+            }
			
 
				+        },
			
 
				+        'weibo': {
			
 
				+            'label': 'Weibo',
			
 
				+            'icon': 'fa fa-weibo',
			
 
				+            'onClick': function(e) {
			
 
				+                e.preventDefault();
			
 
				+                window.open("http://service.weibo.com/share/share.php?content=utf-8&url="+encodeURIComponent(location.href)+"&title="+encodeURIComponent(document.title));
			
 
				+            }
			
 
				+        },
			
 
				+        'instapaper': {
			
 
				+            'label': 'Instapaper',
			
 
				+            'icon': 'fa fa-italic',
			
 
				+            'onClick': function(e) {
			
 
				+                e.preventDefault();
			
 
				+                window.open("http://www.instapaper.com/text?u="+encodeURIComponent(location.href));
			
 
				+            }
			
 
				+        },
			
 
				+        'vk': {
			
 
				+            'label': 'VK',
			
 
				+            'icon': 'fa fa-vk',
			
 
				+            'onClick': function(e) {
			
 
				+                e.preventDefault();
			
 
				+                window.open("http://vkontakte.ru/share.php?url="+encodeURIComponent(location.href));
			
 
				+            }
			
 
				+        }
			
 
				+    };
			
 
				+
			
 
				+
			
 
				+
			
 
				+    gitbook.events.bind("start", function(e, config) {
			
 
				+        var opts = config.sharing;
			
 
				+        if (!opts) return;
			
 
				+
			
 
				+        // Create dropdown menu
			
 
				+        var menu = _.chain(opts.all)
			
 
				+            .map(function(id) {
			
 
				+                var site = SITES[id];
			
 
				+                if (!site) return;
			
 
				+                return {
			
 
				+                    text: site.label,
			
 
				+                    onClick: site.onClick
			
 
				+                };
			
 
				+            })
			
 
				+            .compact()
			
 
				+            .value();
			
 
				+
			
 
				+        // Create main button with dropdown
			
 
				+        if (menu.length > 0) {
			
 
				+            gitbook.toolbar.createButton({
			
 
				+                icon: 'fa fa-share-alt',
			
 
				+                label: 'Share',
			
 
				+                position: 'right',
			
 
				+                dropdown: [menu]
			
 
				+            });
			
 
				+        }
			
 
				+
			
 
				+        // Direct actions to share
			
 
				+        _.each(SITES, function(site, sideId) {
			
 
				+            if (!opts[sideId]) return;
			
 
				+
			
 
				+            gitbook.toolbar.createButton({
			
 
				+                icon: site.icon,
			
 
				+                label: site.label,
			
 
				+                title: site.label,
			
 
				+                position: 'right',
			
 
				+                onClick: site.onClick
			
 
				+            });
			
 
				+        });
			
 
				+    });
			
 
				+});
			
--- a/book-output/libs/jquery-2.2.3/jquery.min.js
+++ b/book-output/libs/jquery-2.2.3/jquery.min.js
--- a/book-output/play-with-sandbox.html
+++ b/book-output/play-with-sandbox.html
@@ -0,0 +1,184 @@
 
				+<!DOCTYPE html>
			
 
				+<html lang="" xml:lang="">
			
 
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				+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Dealing with Gin</a></li>
			
 
				+<li class="chapter" data-level="2" data-path="play-with-sandbox.html"><a href="play-with-sandbox.html"><i class="fa fa-check"></i><b>2</b> Play with Sandbox</a></li>
			
 
				+<li class="chapter" data-level="3" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html"><i class="fa fa-check"></i><b>3</b> Cannot see a repository?</a><ul>
			
 
				+<li class="chapter" data-level="3.1" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#sign-in-to-gin"><i class="fa fa-check"></i><b>3.1</b> Sign in to Gin</a></li>
			
 
				+<li class="chapter" data-level="3.2" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#check-that-the-repository-exists"><i class="fa fa-check"></i><b>3.2</b> Check that the repository exists</a></li>
			
 
				+<li class="chapter" data-level="3.3" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#make-sure-you-have-access-to-the-repository"><i class="fa fa-check"></i><b>3.3</b> Make sure you have access to the repository</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="4" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html"><i class="fa fa-check"></i><b>4</b> Dashboard: how to use</a><ul>
			
 
				+<li class="chapter" data-level="4.1" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#activity"><i class="fa fa-check"></i><b>4.1</b> Activity</a></li>
			
 
				+<li class="chapter" data-level="4.2" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#collaborative-repositories"><i class="fa fa-check"></i><b>4.2</b> Collaborative repositories</a></li>
			
 
				+<li class="chapter" data-level="4.3" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#private-repositories"><i class="fa fa-check"></i><b>4.3</b> Private repositories</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="5" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html"><i class="fa fa-check"></i><b>5</b> Browsing a repository</a><ul>
			
 
				+<li class="chapter" data-level="5.1" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#overview-of-the-repository"><i class="fa fa-check"></i><b>5.1</b> Overview of the repository</a></li>
			
 
				+<li class="chapter" data-level="5.2" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#browsing-files"><i class="fa fa-check"></i><b>5.2</b> Browsing files</a><ul>
			
 
				+<li class="chapter" data-level="5.2.1" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#a-small-side-note"><i class="fa fa-check"></i><b>5.2.1</b> A small side note</a></li>
			
 
				+</ul></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="6" data-path="downloading-files.html"><a href="downloading-files.html"><i class="fa fa-check"></i><b>6</b> Downloading files</a><ul>
			
 
				+<li class="chapter" data-level="6.1" data-path="downloading-files.html"><a href="downloading-files.html#download-button"><i class="fa fa-check"></i><b>6.1</b> Download button</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="7" data-path="uploading-files.html"><a href="uploading-files.html"><i class="fa fa-check"></i><b>7</b> Uploading files</a><ul>
			
 
				+<li class="chapter" data-level="7.1" data-path="uploading-files.html"><a href="uploading-files.html#location-of-the-buttons"><i class="fa fa-check"></i><b>7.1</b> Location of the buttons</a></li>
			
 
				+<li class="chapter" data-level="7.2" data-path="uploading-files.html"><a href="uploading-files.html#common-features-for-file-upload"><i class="fa fa-check"></i><b>7.2</b> Common features for file-upload</a><ul>
			
 
				+<li class="chapter" data-level="7.2.1" data-path="uploading-files.html"><a href="uploading-files.html#specifying-the-directory-to-be-uploaded"><i class="fa fa-check"></i><b>7.2.1</b> Specifying the directory to be uploaded</a></li>
			
 
				+<li class="chapter" data-level="7.2.2" data-path="uploading-files.html"><a href="uploading-files.html#committing-new-files"><i class="fa fa-check"></i><b>7.2.2</b> Committing new files</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="7.3" data-path="uploading-files.html"><a href="uploading-files.html#uploading-a-set-of-files"><i class="fa fa-check"></i><b>7.3</b> Uploading a set of files</a></li>
			
 
				+<li class="chapter" data-level="7.4" data-path="uploading-files.html"><a href="uploading-files.html#create-a-new-text-file"><i class="fa fa-check"></i><b>7.4</b> Create a new (text) file</a></li>
			
 
				+<li class="chapter" data-level="7.5" data-path="uploading-files.html"><a href="uploading-files.html#edit-a-text-file"><i class="fa fa-check"></i><b>7.5</b> Edit a (text) file</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="8" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html"><i class="fa fa-check"></i><b>8</b> Using application made for git</a></li>
			
 
				+<li class="chapter" data-level="9" data-path="using-rstudio-with-gin.html"><a href="using-rstudio-with-gin.html"><i class="fa fa-check"></i><b>9</b> Using Rstudio with GIN</a></li>
			
 
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				+            <section class="normal" id="section-">
			
 
				+<div id="play-with-sandbox" class="section level1">
			
 
				+<h1><span class="header-section-number">2</span> Play with Sandbox</h1>
			
 
				+<p>To avoid accidentally deleting your precious data, it is better
			
 
				+that we have a repository that you can mess up.</p>
			
 
				+<p>And here it is:</p>
			
 
				+<p><a href="https://gin.g-node.org/larkumlab/GinSandbox">larkumlab/GinSandbox</a></p>
			
 
				+<p>You can add, edit, and move any documents, make commits, clone or fork, make issues etc.</p>
			
 
				+<p>Have fun!</p>
			
 
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				+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Dealing with Gin</a></li>
			
 
				+<li class="chapter" data-level="2" data-path="play-with-sandbox.html"><a href="play-with-sandbox.html"><i class="fa fa-check"></i><b>2</b> Play with Sandbox</a></li>
			
 
				+<li class="chapter" data-level="3" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html"><i class="fa fa-check"></i><b>3</b> Cannot see a repository?</a><ul>
			
 
				+<li class="chapter" data-level="3.1" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#sign-in-to-gin"><i class="fa fa-check"></i><b>3.1</b> Sign in to Gin</a></li>
			
 
				+<li class="chapter" data-level="3.2" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#check-that-the-repository-exists"><i class="fa fa-check"></i><b>3.2</b> Check that the repository exists</a></li>
			
 
				+<li class="chapter" data-level="3.3" data-path="cannot-see-a-repository.html"><a href="cannot-see-a-repository.html#make-sure-you-have-access-to-the-repository"><i class="fa fa-check"></i><b>3.3</b> Make sure you have access to the repository</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="4" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html"><i class="fa fa-check"></i><b>4</b> Dashboard: how to use</a><ul>
			
 
				+<li class="chapter" data-level="4.1" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#activity"><i class="fa fa-check"></i><b>4.1</b> Activity</a></li>
			
 
				+<li class="chapter" data-level="4.2" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#collaborative-repositories"><i class="fa fa-check"></i><b>4.2</b> Collaborative repositories</a></li>
			
 
				+<li class="chapter" data-level="4.3" data-path="dashboard-how-to-use.html"><a href="dashboard-how-to-use.html#private-repositories"><i class="fa fa-check"></i><b>4.3</b> Private repositories</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="5" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html"><i class="fa fa-check"></i><b>5</b> Browsing a repository</a><ul>
			
 
				+<li class="chapter" data-level="5.1" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#overview-of-the-repository"><i class="fa fa-check"></i><b>5.1</b> Overview of the repository</a></li>
			
 
				+<li class="chapter" data-level="5.2" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#browsing-files"><i class="fa fa-check"></i><b>5.2</b> Browsing files</a><ul>
			
 
				+<li class="chapter" data-level="5.2.1" data-path="browsing-a-repository.html"><a href="browsing-a-repository.html#a-small-side-note"><i class="fa fa-check"></i><b>5.2.1</b> A small side note</a></li>
			
 
				+</ul></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="6" data-path="downloading-files.html"><a href="downloading-files.html"><i class="fa fa-check"></i><b>6</b> Downloading files</a><ul>
			
 
				+<li class="chapter" data-level="6.1" data-path="downloading-files.html"><a href="downloading-files.html#download-button"><i class="fa fa-check"></i><b>6.1</b> Download button</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="7" data-path="uploading-files.html"><a href="uploading-files.html"><i class="fa fa-check"></i><b>7</b> Uploading files</a><ul>
			
 
				+<li class="chapter" data-level="7.1" data-path="uploading-files.html"><a href="uploading-files.html#location-of-the-buttons"><i class="fa fa-check"></i><b>7.1</b> Location of the buttons</a></li>
			
 
				+<li class="chapter" data-level="7.2" data-path="uploading-files.html"><a href="uploading-files.html#common-features-for-file-upload"><i class="fa fa-check"></i><b>7.2</b> Common features for file-upload</a><ul>
			
 
				+<li class="chapter" data-level="7.2.1" data-path="uploading-files.html"><a href="uploading-files.html#specifying-the-directory-to-be-uploaded"><i class="fa fa-check"></i><b>7.2.1</b> Specifying the directory to be uploaded</a></li>
			
 
				+<li class="chapter" data-level="7.2.2" data-path="uploading-files.html"><a href="uploading-files.html#committing-new-files"><i class="fa fa-check"></i><b>7.2.2</b> Committing new files</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="7.3" data-path="uploading-files.html"><a href="uploading-files.html#uploading-a-set-of-files"><i class="fa fa-check"></i><b>7.3</b> Uploading a set of files</a></li>
			
 
				+<li class="chapter" data-level="7.4" data-path="uploading-files.html"><a href="uploading-files.html#create-a-new-text-file"><i class="fa fa-check"></i><b>7.4</b> Create a new (text) file</a></li>
			
 
				+<li class="chapter" data-level="7.5" data-path="uploading-files.html"><a href="uploading-files.html#edit-a-text-file"><i class="fa fa-check"></i><b>7.5</b> Edit a (text) file</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="8" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html"><i class="fa fa-check"></i><b>8</b> Using application made for git</a></li>
			
 
				+<li class="chapter" data-level="9" data-path="using-rstudio-with-gin.html"><a href="using-rstudio-with-gin.html"><i class="fa fa-check"></i><b>9</b> Using Rstudio with GIN</a></li>
			
 
				+</ul>
			
 
				+
			
 
				+      </nav>
			
 
				+    </div>
			
 
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				+    <div class="book-body">
			
 
				+      <div class="body-inner">
			
 
				+        <div class="book-header" role="navigation">
			
 
				+          <h1>
			
 
				+            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">dealing with gin</a>
			
 
				+          </h1>
			
 
				+        </div>
			
 
				+
			
 
				+        <div class="page-wrapper" tabindex="-1" role="main">
			
 
				+          <div class="page-inner">
			
 
				+
			
 
				+            <section class="normal" id="section-">
			
 
				+<div id="uploading-files" class="section level1">
			
 
				+<h1><span class="header-section-number">7</span> Uploading files</h1>
			
 
				+<p>The Gin web-interface allows you to:</p>
			
 
				+<ul>
			
 
				+<li><a href="uploading-files.html#create-a-new-text-file">create</a> a new text-based file,</li>
			
 
				+<li><a href="uploading-files.html#edit-a-text-file">edit</a> a text-based file, or</li>
			
 
				+<li><a href="uploading-files.html#uploading-a-set-of-files">upload</a> a new set of files.</li>
			
 
				+</ul>
			
 
				+<p>All of the above procedures share some features in common:</p>
			
 
				+<ul>
			
 
				+<li>You can start both of the procedures easily by <a href="uploading-files.html#location-of-the-buttons">a click of a button</a>.</li>
			
 
				+<li>You can <a href="uploading-files.html#specifying-the-directory-to-be-uploaded">specify the sub-directory in the repository</a> for the file(s) to be uploaded.</li>
			
 
				+<li>You can <a href="uploading-files.html#committing-new-files">specify the commit options</a>.</li>
			
 
				+</ul>
			
 
				+<div id="location-of-the-buttons" class="section level2">
			
 
				+<h2><span class="header-section-number">7.1</span> Location of the buttons</h2>
			
 
				+<p>When the web interface shows a list of files in a repository, you can see blue buttons in the middle, above the file list.</p>
			
 
				+<blockquote>
			
 
				+<p>Note that, if you don’t have the “write” permission to the repository, these buttons will not appear. If you still want to create or upload files, contact the person responsible for the repository to <a href="collaboration.md">add you as a Collaborator</a>.</p>
			
 
				+</blockquote>
			
 
				+<div class="figure">
			
 
				+<img src="images/upload-actions.png" alt="Where you can find the buttons for file-creation / upload" />
			
 
				+<p class="caption">Where you can find the buttons for file-creation / upload</p>
			
 
				+</div>
			
 
				+<p>There, you have two types of buttons:</p>
			
 
				+<ul>
			
 
				+<li><strong><a href="uploading-files.html#uploading-a-set-of-files">“Upload file” button</a></strong>: used to upload a set of files.</li>
			
 
				+<li><strong><a href="#create-new-files">“New file” button</a></strong>: used to create a new file in the repository.</li>
			
 
				+</ul>
			
 
				+<div class="figure">
			
 
				+<img src="images/upload-actions-buttons.png" alt="Two buttons for new files" />
			
 
				+<p class="caption">Two buttons for new files</p>
			
 
				+</div>
			
 
				+</div>
			
 
				+<div id="common-features-for-file-upload" class="section level2">
			
 
				+<h2><span class="header-section-number">7.2</span> Common features for file-upload</h2>
			
 
				+<p>No matter which button you use, there are some features shared in common.</p>
			
 
				+<div id="specifying-the-directory-to-be-uploaded" class="section level3">
			
 
				+<h3><span class="header-section-number">7.2.1</span> Specifying the directory to be uploaded</h3>
			
 
				+<p>On top of the view, an empty text field will show up:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/directory-selector-empty.png" alt="Directory selector" />
			
 
				+<p class="caption">Directory selector</p>
			
 
				+</div>
			
 
				+<p>This is for specifying the directory to upload the file(s).</p>
			
 
				+<p>For instance:</p>
			
 
				+<ul>
			
 
				+<li>Enter the name of the subdirectory (within the repository) in this field:</li>
			
 
				+</ul>
			
 
				+<div class="figure">
			
 
				+<img src="images/directory-selector-subdir.png" alt="A subdirectory is specified" />
			
 
				+<p class="caption">A subdirectory is specified</p>
			
 
				+</div>
			
 
				+<ul>
			
 
				+<li>Gin will automatically create a new directory with the given name (in case it does not exist) as you <a href="uploading-files.html#committing-new-files">commit uploads (see the section below)</a>:</li>
			
 
				+</ul>
			
 
				+<div class="figure">
			
 
				+<img src="images/created-subdir.png" alt="Created subdirectory" />
			
 
				+<p class="caption">Created subdirectory</p>
			
 
				+</div>
			
 
				+<ul>
			
 
				+<li>Inside the subdirectory, you will find the uploaded file(s):</li>
			
 
				+</ul>
			
 
				+<div class="figure">
			
 
				+<img src="images/subdir-content.png" alt="The uploaded file in the sub-directory" />
			
 
				+<p class="caption">The uploaded file in the sub-directory</p>
			
 
				+</div>
			
 
				+<p>You can also specify the <em>path</em> to the directory of interest, by connecting a hierarchy of directories by a <code>/</code> (slash):</p>
			
 
				+<p>TODO</p>
			
 
				+</div>
			
 
				+<div id="committing-new-files" class="section level3">
			
 
				+<h3><span class="header-section-number">7.2.2</span> Committing new files</h3>
			
 
				+<p>TODO</p>
			
 
				+</div>
			
 
				+</div>
			
 
				+<div id="uploading-a-set-of-files" class="section level2">
			
 
				+<h2><span class="header-section-number">7.3</span> Uploading a set of files</h2>
			
 
				+<p>When you click on the “Upload file” button, the file upload view will appear:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/upload-view.png" alt="File-upload view" />
			
 
				+<p class="caption">File-upload view</p>
			
 
				+</div>
			
 
				+<p>The dotted region in the middle of the page is the <em>upload area</em>:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/upload-view-upload-area.png" alt="The upload area" />
			
 
				+<p class="caption">The upload area</p>
			
 
				+</div>
			
 
				+<p>You can add the files to be uploaded by either:</p>
			
 
				+<ul>
			
 
				+<li><strong>Clicking on the area</strong>: the file chooser dialog will appear so that you can select files from it.</li>
			
 
				+<li><strong>Drag and drop</strong> individual files or a directory containing a set of files. In the latter case, you can upload the whole directory structure easily.</li>
			
 
				+</ul>
			
 
				+<p>In either case, the upload process will start immediately, and you will see the progress on the area:</p>
			
 
				+<div class="figure">
			
 
				+<img src="images/upload-progress.png" alt="Progress of upload" />
			
 
				+<p class="caption">Progress of upload</p>
			
 
				+</div>
			
 
				+<p>You can specify the directory to be uploaded from the <a href="uploading-files.html#specifying-the-directory-to-be-uploaded">directory selector (see the section above)</a>.</p>
			
 
				+<p>After completion of the upload processes for all files, you can proceed to finish the <a href="uploading-files.html#committing-new-files">commit process (see the section above)</a>.</p>
			
 
				+<blockquote>
			
 
				+<p>Note, by using this upload view, you can only upload 100 files at once, with each file being less than 10 GB in size. If you want to upload more files at once, or upload larger files, you will have to use the command-line interface or WinGIN.</p>
			
 
				+</blockquote>
			
 
				+</div>
			
 
				+<div id="create-a-new-text-file" class="section level2">
			
 
				+<h2><span class="header-section-number">7.4</span> Create a new (text) file</h2>
			
 
				+<p>TODO</p>
			
 
				+</div>
			
 
				+<div id="edit-a-text-file" class="section level2">
			
 
				+<h2><span class="header-section-number">7.5</span> Edit a (text) file</h2>
			
 
				+<p>TODO</p>
			
 
				+
			
 
				+</div>
			
 
				+</div>
			
 
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				+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Dealing with Gin</a></li>
			
 
				+<li class="chapter" data-level="2" data-path="intro.html"><a href="intro.html"><i class="fa fa-check"></i><b>2</b> Intro</a><ul>
			
 
				+<li class="chapter" data-level="2.1" data-path="intro.html"><a href="intro.html#play-with-sandbox"><i class="fa fa-check"></i><b>2.1</b> Play with Sandbox</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="3" data-path="browsing.html"><a href="browsing.html"><i class="fa fa-check"></i><b>3</b> Browsing</a><ul>
			
 
				+<li class="chapter" data-level="3.1" data-path="browsing.html"><a href="browsing.html#cannot-see-a-repository"><i class="fa fa-check"></i><b>3.1</b> Cannot see a repository?</a><ul>
			
 
				+<li class="chapter" data-level="3.1.1" data-path="browsing.html"><a href="browsing.html#sign-in-to-gin"><i class="fa fa-check"></i><b>3.1.1</b> Sign in to Gin</a></li>
			
 
				+<li class="chapter" data-level="3.1.2" data-path="browsing.html"><a href="browsing.html#check-that-the-repository-exists"><i class="fa fa-check"></i><b>3.1.2</b> Check that the repository exists</a></li>
			
 
				+<li class="chapter" data-level="3.1.3" data-path="browsing.html"><a href="browsing.html#make-sure-you-have-access-to-the-repository"><i class="fa fa-check"></i><b>3.1.3</b> Make sure you have access to the repository</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="3.2" data-path="browsing.html"><a href="browsing.html#dashboard-how-to-use"><i class="fa fa-check"></i><b>3.2</b> Dashboard: how to use</a><ul>
			
 
				+<li class="chapter" data-level="3.2.1" data-path="browsing.html"><a href="browsing.html#activity"><i class="fa fa-check"></i><b>3.2.1</b> Activity</a></li>
			
 
				+<li class="chapter" data-level="3.2.2" data-path="browsing.html"><a href="browsing.html#collaborative-repositories"><i class="fa fa-check"></i><b>3.2.2</b> Collaborative repositories</a></li>
			
 
				+<li class="chapter" data-level="3.2.3" data-path="browsing.html"><a href="browsing.html#private-repositories"><i class="fa fa-check"></i><b>3.2.3</b> Private repositories</a></li>
			
 
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				+<li class="chapter" data-level="3.3" data-path="browsing.html"><a href="browsing.html#browsing-a-repository"><i class="fa fa-check"></i><b>3.3</b> Browsing a repository</a><ul>
			
 
				+<li class="chapter" data-level="3.3.1" data-path="browsing.html"><a href="browsing.html#overview-of-the-repository"><i class="fa fa-check"></i><b>3.3.1</b> Overview of the repository</a></li>
			
 
				+<li class="chapter" data-level="3.3.2" data-path="browsing.html"><a href="browsing.html#browsing-files"><i class="fa fa-check"></i><b>3.3.2</b> Browsing files</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="3.4" data-path="browsing.html"><a href="browsing.html#downloading-files"><i class="fa fa-check"></i><b>3.4</b> Downloading files</a><ul>
			
 
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				+<li class="chapter" data-level="4" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html"><i class="fa fa-check"></i><b>4</b> Using application made for git</a><ul>
			
 
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				+<li class="chapter" data-level="4.2" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#git-gui"><i class="fa fa-check"></i><b>4.2</b> Git GUI</a></li>
			
 
				+<li class="chapter" data-level="4.3" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html#using-rstudio-with-gin"><i class="fa fa-check"></i><b>4.3</b> Using Rstudio with GIN</a></li>
			
 
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				+<h1><span class="header-section-number">4</span> Using application made for git</h1>
			
 
				+<div id="generalities" class="section level2">
			
 
				+<h2><span class="header-section-number">4.1</span> generalities</h2>
			
 
				+<p>Several application are meant to deal with git commands without having to use the terminal. They usually do not deal with git annex commands, so only small files (&lt; 50MB) can be pushed via their interface. If most of your files are below that limit, one can use these application for routine work, and use either the command line (with <code>gin update .</code>) or the browser interface from time to time to upload big files.</p>
			
 
				+<p>Most of them have a way to push to external servers like GitHub, gitlab, or bitbucket. They are usually to ways to make this connection: via https or via ssh. The ssh version is more secure, but you need to set up keys for each computer you are using, and add these keys to the server. Gin can be used as a git server and usual git commands will work normally, but GIN has no https connection: one needs to use ssh. One finds easily walkthrough to set up ssh connections for different application. Some examples will be given in the next chapters.</p>
			
 
				+<p>In addition, you need to set some configuration for git to push to a git server. This is often best done via the command lines:</p>
			
 
				+<pre><code>git config --global user.name &quot;FIRST_NAME LAST_NAME&quot;
			
 
				+git config --global user.email &quot;MY_NAME@example.com&quot;</code></pre>
			
 
				+
			
 
				+</div>
			
 
				+<div id="git-gui" class="section level2">
			
 
				+<h2><span class="header-section-number">4.2</span> Git GUI</h2>
			
 
				+<p>The <code>git gui</code> command comes with the normal Git bundle. Git GUI can be used to visualize:</p>
			
 
				+<ul>
			
 
				+<li>modifications in the repository</li>
			
 
				+<li>files in the staging area</li>
			
 
				+<li>the commit message</li>
			
 
				+</ul>
			
 
				+
			
 
				+</div>
			
 
				+<div id="using-rstudio-with-gin" class="section level2">
			
 
				+<h2><span class="header-section-number">4.3</span> Using Rstudio with GIN</h2>
			
 
				+<p>Rstudio is a very nice application that was created to write and run R code. It now also has the possibilities to run python code and create reproducible reports in Rmarkdown (there are also specific tools to deal with citations in these reports). It also has git functionalities, allowing to <code>commit</code> (save a new version of your repository locally), <code>pull</code>(download changes existant on the server but absent of your local folder) and <code>push</code> (save all new versions present locally to the server version).</p>
			
 
				+<p>You need first to make sure git is installed and found by Rstudio: go the menu <code>tools &gt; global options &gt; git</code> browse to the git.exe if Rstudio did not find it automatically (a git.exe is installed together with the gin-cli, but you can also install another via <a href="https://git-scm.com/downloads" class="uri">https://git-scm.com/downloads</a>. Find a walkthrough on how to set up ssh here: <a href="https://happygitwithr.com/ssh-keys.html" class="uri">https://happygitwithr.com/ssh-keys.html</a>. What you are asked to do on github will be done on GIN (<a href="https://gin.g-node.org/user/settings/ssh" class="uri">https://gin.g-node.org/user/settings/ssh</a>).</p>
			
 
				+<p>You can now download new repositories using <code>file &gt; new project... &gt;&gt;version control &gt;&gt; git</code> insert the ssh link you get on the gin repository page (for this repo <code>git@gin.g-node.org:/larkumlab/Dealing_with_Gin.git</code>) and decide the folder name and where to save it on your machine. I put all my repositories in a special <code>gin</code> folder in my document folder, but this is up to you to organise your files.</p>
			
 
				+<p>You can then make changes, on the right part of the Rstudio window, you can access a <code>git</code> tab, where changed files are listed. You can then use the buttons of the tab to commit changes, pull, or push commits to GIN. Git advices:</p>
			
 
				+<ul>
			
 
				+<li>make small commits</li>
			
 
				+<li>give commits a meaningfull comment which will allow you to spot changes easily in the history tab</li>
			
 
				+<li>if you are working on different machines, do not forget to pull changes when you start working, and push before you go.</li>
			
 
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				+
			
 
				+<ul class="summary">
			
 
				+<li class="chapter" data-level="1" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i><b>1</b> Dealing with Gin</a><ul>
			
 
				+<li class="chapter" data-level="1.1" data-path="index.html"><a href="index.html#play-with-sandbox"><i class="fa fa-check"></i><b>1.1</b> Play with Sandbox</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="2" data-path="browsing.html"><a href="browsing.html"><i class="fa fa-check"></i><b>2</b> Browsing</a><ul>
			
 
				+<li class="chapter" data-level="2.1" data-path="browsing.html"><a href="browsing.html#cannot-see-a-repository"><i class="fa fa-check"></i><b>2.1</b> Cannot see a repository?</a><ul>
			
 
				+<li class="chapter" data-level="2.1.1" data-path="browsing.html"><a href="browsing.html#sign-in-to-gin"><i class="fa fa-check"></i><b>2.1.1</b> Sign in to Gin</a></li>
			
 
				+<li class="chapter" data-level="2.1.2" data-path="browsing.html"><a href="browsing.html#check-that-the-repository-exists"><i class="fa fa-check"></i><b>2.1.2</b> Check that the repository exists</a></li>
			
 
				+<li class="chapter" data-level="2.1.3" data-path="browsing.html"><a href="browsing.html#make-sure-you-have-access-to-the-repository"><i class="fa fa-check"></i><b>2.1.3</b> Make sure you have access to the repository</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="2.2" data-path="browsing.html"><a href="browsing.html#dashboard-how-to-use"><i class="fa fa-check"></i><b>2.2</b> Dashboard: how to use</a><ul>
			
 
				+<li class="chapter" data-level="2.2.1" data-path="browsing.html"><a href="browsing.html#activity"><i class="fa fa-check"></i><b>2.2.1</b> Activity</a></li>
			
 
				+<li class="chapter" data-level="2.2.2" data-path="browsing.html"><a href="browsing.html#collaborative-repositories"><i class="fa fa-check"></i><b>2.2.2</b> Collaborative repositories</a></li>
			
 
				+<li class="chapter" data-level="2.2.3" data-path="browsing.html"><a href="browsing.html#private-repositories"><i class="fa fa-check"></i><b>2.2.3</b> Private repositories</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="2.3" data-path="browsing.html"><a href="browsing.html#browsing-a-repository"><i class="fa fa-check"></i><b>2.3</b> Browsing a repository</a><ul>
			
 
				+<li class="chapter" data-level="2.3.1" data-path="browsing.html"><a href="browsing.html#overview-of-the-repository"><i class="fa fa-check"></i><b>2.3.1</b> Overview of the repository</a></li>
			
 
				+<li class="chapter" data-level="2.3.2" data-path="browsing.html"><a href="browsing.html#browsing-files"><i class="fa fa-check"></i><b>2.3.2</b> Browsing files</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="2.4" data-path="browsing.html"><a href="browsing.html#downloading-files"><i class="fa fa-check"></i><b>2.4</b> Downloading files</a><ul>
			
 
				+<li class="chapter" data-level="2.4.1" data-path="browsing.html"><a href="browsing.html#download-button"><i class="fa fa-check"></i><b>2.4.1</b> Download button</a></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="2.5" data-path="browsing.html"><a href="browsing.html#uploading-files"><i class="fa fa-check"></i><b>2.5</b> Uploading files</a><ul>
			
 
				+<li class="chapter" data-level="2.5.1" data-path="browsing.html"><a href="browsing.html#location-of-the-buttons"><i class="fa fa-check"></i><b>2.5.1</b> Location of the buttons</a></li>
			
 
				+<li class="chapter" data-level="2.5.2" data-path="browsing.html"><a href="browsing.html#common-features-for-file-upload"><i class="fa fa-check"></i><b>2.5.2</b> Common features for file-upload</a></li>
			
 
				+<li class="chapter" data-level="2.5.3" data-path="browsing.html"><a href="browsing.html#uploading-a-set-of-files"><i class="fa fa-check"></i><b>2.5.3</b> Uploading a set of files</a></li>
			
 
				+<li class="chapter" data-level="2.5.4" data-path="browsing.html"><a href="browsing.html#create-a-new-text-file"><i class="fa fa-check"></i><b>2.5.4</b> Create a new (text) file</a></li>
			
 
				+<li class="chapter" data-level="2.5.5" data-path="browsing.html"><a href="browsing.html#edit-a-text-file"><i class="fa fa-check"></i><b>2.5.5</b> Edit a (text) file</a></li>
			
 
				+</ul></li>
			
 
				+</ul></li>
			
 
				+<li class="chapter" data-level="3" data-path="using-application-made-for-git.html"><a href="using-application-made-for-git.html"><i class="fa fa-check"></i><b>3</b> Using application made for git</a></li>
			
 
				+<li class="chapter" data-level="4" data-path="using-rstudio-with-gin.html"><a href="using-rstudio-with-gin.html"><i class="fa fa-check"></i><b>4</b> Using Rstudio with GIN</a></li>
			
 
				+</ul>
			
 
				+
			
 
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				+          <h1>
			
 
				+            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">dealing with gin</a>
			
 
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				+<div id="using-rstudio-with-gin" class="section level1">
			
 
				+<h1><span class="header-section-number">4</span> Using Rstudio with GIN</h1>
			
 
				+<p>Rstudio is a very nice application that was created to write and run R code. It now also has the possibilities to run python code and create reproducible reports in Rmarkdown (there are also specific tools to deal with citations in these reports). It also has git functionalities, allowing to <code>commit</code> (save a new version of your repository locally), <code>pull</code>(download changes existant on the server but absent of your local folder) and <code>push</code> (save all new versions present locally to the server version).</p>
			
 
				+<p>You need first to make sure git is installed and found by Rstudio: go the menu <code>tools &gt; global options &gt; git</code> browse to the git.exe if Rstudio did not find it automatically (a git.exe is installed together with the gin-cli, but you can also install another via <a href="https://git-scm.com/downloads" class="uri">https://git-scm.com/downloads</a>. Find a walkthrough on how to set up ssh here: <a href="https://happygitwithr.com/ssh-keys.html" class="uri">https://happygitwithr.com/ssh-keys.html</a>. What you are asked to do on github will be done on GIN (<a href="https://gin.g-node.org/user/settings/ssh" class="uri">https://gin.g-node.org/user/settings/ssh</a>).</p>
			
 
				+<p>You can now download new repositories using <code>file &gt; new project... &gt;&gt;version control &gt;&gt; git</code> insert the ssh link you get on the gin repository page (for this repo <code>git@gin.g-node.org:/larkumlab/Dealing_with_Gin.git</code>) and decide the folder name and where to save it on your machine. I put all my repositories in a special <code>gin</code> folder in my document folder, but this is up to you to organise your files.</p>
			
 
				+<p>You can then make changes, on the right part of the Rstudio window, you can access a <code>git</code> tab, where changed files are listed. You can then use the buttons of the tab to commit changes, pull, or push commits to GIN. Git advices:</p>
			
 
				+<ul>
			
 
				+<li>make small commits</li>
			
 
				+<li>give commits a meaningfull comment which will allow you to spot changes easily in the history tab</li>
			
 
				+<li>if you are working on different machines, do not forget to pull changes when you start working, and push before you go.</li>
			
 
				+</ul>
			
 
				+
			
 
				+</div>
			
 
				+            </section>
			
 
				+
			
 
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--- a/git-applications/README.md
+++ b/git-applications/README.md
@@ -1,5 +1,7 @@
 
				 # Using application made for git
			
 
				 
			
 
				+## generalities
			
 
				+
			
 
				 Several application are meant to deal with git commands without having to use the terminal. They usually do not deal with git annex commands, so only small files (< 50MB) can be pushed via their interface. If most of your files are below that limit, one can use these application for routine work, and use either the command line (with `gin update .`) or the browser interface from time to time to upload big files.
			
 
				 
			
 
				 
			
--- a/git-applications/git-gui.md
+++ b/git-applications/git-gui.md
@@ -1,4 +1,4 @@
 
				-# Git GUI
			
 
				+## Git GUI
			
 
				 
			
 
				 The `git gui` command comes with the normal Git bundle. Git GUI can be used to visualize:
			
 
				 
			
--- a/git-applications/rstudio.md
+++ b/git-applications/rstudio.md
@@ -1,4 +1,4 @@
 
				-# Using Rstudio with GIN
			
 
				+## Using Rstudio with GIN
			
 
				 
			
 
				 Rstudio is a very nice application that was created to write and run R code. It now also has the possibilities to run python code and create reproducible reports in Rmarkdown (there are also specific tools to deal with citations in these reports). It also has git functionalities, allowing to `commit` (save a new version of your repository locally), `pull`(download changes existant on the server but absent of your local folder) and `push` (save all new versions present locally to the server version).
			
 
				 
			
--- a/index.Rmd
+++ b/index.Rmd
@@ -0,0 +1,9 @@
 
				+---
			
 
				+title: "dealing with gin"
			
 
				+---
			
 
				+
			
 
				+# Dealing with Gin
			
 
				+
			
 
				+Introduction to how to deal with gin (web interface, command-line, and probably WinGIN GUI).
			
 
				+
			
 
				+This book covers multiple topics, see the table of content to navigate it.
			
--- a/intro/sandbox.md
+++ b/intro/sandbox.md
@@ -1,4 +1,6 @@
 
				-# Play with Sandbox
			
 
				+# Intro
			
 
				+
			
 
				+## Play with Sandbox
			
 
				 
			
 
				 To avoid accidentally deleting your precious data, it is better
			
 
				 that we have a repository that you can mess up.
			
--- a/web-interface/browsing.md
+++ b/web-interface/browsing.md
@@ -1,4 +1,4 @@
 
				-# Browsing a repository
			
 
				+## Browsing a repository
			
 
				 
			
 
				 If you visit the repository page, it looks like below:
			
 
				 
			
@@ -9,7 +9,7 @@ From here, you can browse what is in the repository including:
 
				 1. [overview of the repository](#overview-of-the-repository)
			
 
				 2. [file contents](#browsing-files)
			
 
				 
			
 
				-## Overview of the repository
			
 
				+### Overview of the repository
			
 
				 
			
 
				 On top of the page, you will find the header consisting of `<owner name>/<repository name>`:
			
 
				 
			
@@ -34,7 +34,7 @@ or what it contains.
 
				 > Even inside the sub-directories of the repositories, the description will automatically show up
			
 
				 > if you add and edit a `README.md` file in it.
			
 
				 
			
 
				-## Browsing files
			
 
				+### Browsing files
			
 
				 
			
 
				 In the middle, you can find a list of files and directories in the repository:
			
 
				 
			
@@ -59,7 +59,7 @@ and you can have a glimpse of the original image file:
 
				 - Other text-based files (CSV, TSV etc.) may be seen in its raw format.
			
 
				 - Binary files (Excel, Word, Spike2 etc.) will not be visible, so you must [download it](downloading.md) to see the contents.
			
 
				 
			
 
				-### A small side note
			
 
				+#### A small side note
			
 
				 
			
 
				 On the left columns of the files list, you can see some information like below:
			
 
				 
			
--- a/web-interface/cannot-see-a-repo.md
+++ b/web-interface/cannot-see-a-repo.md
@@ -1,4 +1,5 @@
 
				-# Cannot see a repository?
			
 
				+# Browsing
			
 
				+## Cannot see a repository?
			
 
				 
			
 
				 So often, you try to visit a repository, and find something like below:
			
 
				 
			
@@ -11,7 +12,7 @@ The solutions are:
 
				 3. Make sure you have access to the repository
			
 
				 
			
 
				 
			
 
				-## Sign in to Gin
			
 
				+### Sign in to Gin
			
 
				 
			
 
				 It happens when you are not signed in to Gin.
			
 
				 
			
@@ -21,13 +22,13 @@ Click on the "Sign in" button at the top-right corner of the page:
 
				 
			
 
				 (If you have not yet got registered to Gin, then do it first from the "Register" button on the right.
			
 
				 
			
 
				-## Check that the repository exists
			
 
				+### Check that the repository exists
			
 
				 
			
 
				 If the situation persists, go visit your [dashboard](Dashboard.md), 
			
 
				 and find the name of the repository from the list.
			
 
				 If you click on it, the repository page should show up.
			
 
				 
			
 
				-## Make sure you have access to the repository
			
 
				+### Make sure you have access to the repository
			
 
				 
			
 
				 If you don't find the repository in your dashboard, then
			
 
				 it is possible that you don't have access to the repository at all.
			
--- a/web-interface/dashboard.md
+++ b/web-interface/dashboard.md
@@ -1,4 +1,4 @@
 
				-# Dashboard: how to use
			
 
				+## Dashboard: how to use
			
 
				 
			
 
				 When you simply sign in to Gin, without selecting any specific repository,
			
 
				 you fill find a page like below (note that this is just an example):
			
@@ -15,7 +15,7 @@ The dashboard may be divided into several areas:
 
				 
			
 
				 
			
 
				 
			
 
				-## Activity
			
 
				+### Activity
			
 
				 
			
 
				 ![Activity area](images/activity-area.png)
			
 
				 
			
@@ -26,7 +26,7 @@ This shows your recent activity on Gin, e.g.
 
				 
			
 
				 
			
 
				 
			
 
				-## Collaborative repositories
			
 
				+### Collaborative repositories
			
 
				 
			
 
				 ![Collaborative repository area](images/collaboration-area.png)
			
 
				 
			
@@ -36,7 +36,7 @@ Normally, most of your repositories will show up here, as they are owned and man
 
				 
			
 
				 
			
 
				 
			
 
				-## Private repositories
			
 
				+### Private repositories
			
 
				 
			
 
				 ![Private repository area](images/private-repositories.png)
			
 
				 
			
--- a/web-interface/downloading.md
+++ b/web-interface/downloading.md
@@ -1,4 +1,4 @@
 
				-# Downloading files
			
 
				+## Downloading files
			
 
				 
			
 
				 Although the files may be browsable on the web interface, you might want to interact with them on your desktop, using one of your favorite programs.
			
 
				 
			
@@ -6,7 +6,7 @@ It is possible to download files individually from the web interface.
 
				 
			
 
				 > Note that this "individual download" feature differs from what Git-people call "cloning of the repository". Git-clone involves downloading of the whole repository, whereas this individual download concerns only with the current single file.
			
 
				 
			
 
				-## Download button
			
 
				+### Download button
			
 
				 
			
 
				 When you open a single file, you will see buttons on the top-right of the file:
			
 
				 
			
--- a/web-interface/uploading.md
+++ b/web-interface/uploading.md
@@ -1,4 +1,4 @@
 
				-# Uploading files
			
 
				+## Uploading files
			
 
				 
			
 
				 The Gin web-interface allows you to:
			
 
				 
			
@@ -14,7 +14,7 @@ All of the above procedures share some features in common:
 
				 
			
 
				 
			
 
				 
			
 
				-## Location of the buttons
			
 
				+### Location of the buttons
			
 
				 
			
 
				 When the web interface shows a list of files in a repository, you can see blue buttons in the middle, above the file list.
			
 
				 
			
@@ -31,11 +31,11 @@ There, you have two types of buttons:
 
				 
			
 
				 ![Two buttons for new files](images/upload-actions-buttons.png)
			
 
				 
			
 
				-## Common features for file-upload
			
 
				+### Common features for file-upload
			
 
				 
			
 
				 No matter which button you use, there are some features shared in common.
			
 
				 
			
 
				-### Specifying the directory to be uploaded
			
 
				+#### Specifying the directory to be uploaded
			
 
				 
			
 
				 On top of the view, an empty text field will show up:
			
 
				 
			
@@ -65,13 +65,13 @@ TODO
 
				 
			
 
				 
			
 
				 
			
 
				-### Committing new files
			
 
				+#### Committing new files
			
 
				 
			
 
				 TODO
			
 
				 
			
 
				 
			
 
				 
			
 
				-## Uploading a set of files
			
 
				+### Uploading a set of files
			
 
				 
			
 
				 When you click on the "Upload file" button, the file upload view will appear:
			
 
				 
			
@@ -98,12 +98,12 @@ After completion of the upload processes for all files, you can proceed to finis
 
				 
			
 
				 
			
 
				 
			
 
				-## Create a new (text) file
			
 
				+### Create a new (text) file
			
 
				 
			
 
				 TODO
			
 
				 
			
 
				 
			
 
				 
			
 
				-## Edit a (text) file
			
 
				+### Edit a (text) file
			
 
				 
			
 
				 TODO