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-  <title>5 Browsing a repository | dealing with gin</title>
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-  <meta name="generator" content="bookdown 0.17 and GitBook 2.6.7" />
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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>
-</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>
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-  <meta name="description" content="3 Cannot see a repository? | dealing with gin" />
-  <meta name="generator" content="bookdown 0.17 and GitBook 2.6.7" />
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-<link rel="prev" href="play-with-sandbox.html"/>
-<link rel="next" href="dashboard-how-to-use.html"/>
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-  <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="cannot-see-a-repository" class="section level1">
-<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>
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-<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>
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-<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>
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-<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="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>
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-</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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-            <i class="fa fa-circle-o-notch fa-spin"></i><a href="./">dealing with gin</a>
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-<h2><span class="header-section-number">4.3</span> Private repositories</h2>
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-
-</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="play-with-sandbox.html"><a href="play-with-sandbox.html"><i class="fa fa-check"></i><b>2</b> Play with Sandbox</a></li>
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-<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="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>
-
-          </div>
-        </div>
-      </div>
-<a href="browsing-a-repository.html" class="navigation navigation-prev " aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
-<a href="uploading-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>
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+ 20 - 20
book-output/index.html

@@ -67,30 +67,30 @@
 <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>
+<li class="chapter" data-level="3" data-path="web-interface.html"><a href="web-interface.html"><i class="fa fa-check"></i><b>3</b> Web interface</a><ul>
+<li class="chapter" data-level="3.1" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.2" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.3" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.4" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.5" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>

+ 22 - 22
book-output/intro.html

@@ -30,7 +30,7 @@
   
   
 <link rel="prev" href="index.html"/>
-<link rel="next" href="browsing.html"/>
+<link rel="next" href="web-interface.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" />
@@ -67,30 +67,30 @@
 <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>
+<li class="chapter" data-level="3" data-path="web-interface.html"><a href="web-interface.html"><i class="fa fa-check"></i><b>3</b> Web interface</a><ul>
+<li class="chapter" data-level="3.1" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.2" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.3" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.4" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.5" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.html#create-a-new-text-file"><i class="fa fa-check"></i><b>3.5.4</b> Create a new (text) file</a></li>
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@@ -134,7 +134,7 @@ that we have a repository that you can mess up.</p>
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-<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>
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-<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>
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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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-</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>
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-<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>
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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>
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@@ -29,7 +29,7 @@
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@@ -67,30 +67,30 @@
 <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>
+<li class="chapter" data-level="3" data-path="web-interface.html"><a href="web-interface.html"><i class="fa fa-check"></i><b>3</b> Web interface</a><ul>
+<li class="chapter" data-level="3.1" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
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+<li class="chapter" data-level="3.2" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
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+<li class="chapter" data-level="3.3" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.html#browsing-files"><i class="fa fa-check"></i><b>3.3.2</b> Browsing files</a></li>
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-<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>
+<li class="chapter" data-level="3.4" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.5" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
@@ -155,7 +155,7 @@ git config --global user.email &quot;MY_NAME@example.com&quot;</code></pre>
           </div>
         </div>
       </div>
-<a href="browsing.html" class="navigation navigation-prev navigation-unique" aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
+<a href="web-interface.html" class="navigation navigation-prev navigation-unique" aria-label="Previous page"><i class="fa fa-angle-left"></i></a>
 
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+ 0 - 185
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-<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>
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-        </div>
-
-        <div class="page-wrapper" tabindex="-1" role="main">
-          <div class="page-inner">
-
-            <section class="normal" id="section-">
-<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>
-
-          </div>
-        </div>
-      </div>
-<a href="using-application-made-for-git.html" class="navigation navigation-prev navigation-unique" aria-label="Previous page"><i class="fa fa-angle-left"></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>
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-<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) {
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-"twitter": true,
-"linkedin": false,
-"weibo": false,
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-"vk": false,
-"all": ["facebook", "twitter", "linkedin", "weibo", "instapaper"]
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+ 61 - 61
book-output/browsing.html

@@ -4,11 +4,11 @@
 
   <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" />
+  <title>3 Web interface | dealing with gin</title>
+  <meta name="description" content="3 Web interface | 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:title" content="3 Web interface | dealing with gin" />
   <meta property="og:type" content="book" />
   
   
@@ -16,7 +16,7 @@
   
 
   <meta name="twitter:card" content="summary" />
-  <meta name="twitter:title" content="3 Browsing | dealing with gin" />
+  <meta name="twitter:title" content="3 Web interface | dealing with gin" />
   
   
   
@@ -67,30 +67,30 @@
 <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>
+<li class="chapter" data-level="3" data-path="web-interface.html"><a href="web-interface.html"><i class="fa fa-check"></i><b>3</b> Web interface</a><ul>
+<li class="chapter" data-level="3.1" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.2" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.3" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.4" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
+<li class="chapter" data-level="3.5" data-path="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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="web-interface.html"><a href="web-interface.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>
@@ -115,13 +115,13 @@
           <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="web-interface" class="section level1">
+<h1><span class="header-section-number">3</span> Web interface</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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/norepository.png" alt="404 page" />
 <p class="caption">404 page</p>
 </div>
 <p>The solutions are:</p>
@@ -135,14 +135,14 @@
 <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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>,
+<p>If the situation persists, go visit your <a href="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>
@@ -165,14 +165,14 @@ you fill find a page like below (note that this is just an example):</p>
 <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>
+<li><a href="web-interface.html#activity"><strong>Activity</strong></a> area: shows what you did with your repositories</li>
+<li><a href="web-interface.html#collaborative-repositories"><strong>Collaborative repository</strong></a> area: lists up the shared repositories you have access to</li>
+<li><a href="web-interface.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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>
@@ -184,7 +184,7 @@ you fill find a page like below (note that this is just an example):</p>
 <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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>
@@ -193,7 +193,7 @@ you fill find a page like below (note that this is just an example):</p>
 <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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>
@@ -205,26 +205,26 @@ you fill find a page like below (note that this is just an example):</p>
 <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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>
+<li><a href="web-interface.html#overview-of-the-repository">overview of the repository</a></li>
+<li><a href="web-interface.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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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
@@ -242,23 +242,23 @@ if you add and edit a <code>README.md</code> file in it.</p>
 <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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>
@@ -266,7 +266,7 @@ and you can have a glimpse of the original image file:
 <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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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
@@ -288,7 +288,7 @@ with the commit ID being <code>b42b7633f7</code>, and with the commit message <c
 <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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>
@@ -301,7 +301,7 @@ with the commit ID being <code>b42b7633f7</code>, and with the commit message <c
 </ul>
 <p>For downloading the file, click on the “download” button:</p>
 <div class="figure">
-<img src="images/download-button.png" alt="Download button" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/download-button.png" alt="Download button" />
 <p class="caption">Download button</p>
 </div>
 <p>Then your browser will start downloading the file.</p>
@@ -312,15 +312,15 @@ with the commit ID being <code>b42b7633f7</code>, and with the commit message <c
 <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>
+<li><a href="web-interface.html#create-a-new-text-file">create</a> a new text-based file,</li>
+<li><a href="web-interface.html#edit-a-text-file">edit</a> a text-based file, or</li>
+<li><a href="web-interface.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>
+<li>You can start both of the procedures easily by <a href="web-interface.html#location-of-the-buttons">a click of a button</a>.</li>
+<li>You can <a href="web-interface.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="web-interface.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>
@@ -329,16 +329,16 @@ with the commit ID being <code>b42b7633f7</code>, and with the commit message <c
 <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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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="web-interface.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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/upload-actions-buttons.png" alt="Two buttons for new files" />
 <p class="caption">Two buttons for new files</p>
 </div>
 </div>
@@ -349,7 +349,7 @@ with the commit ID being <code>b42b7633f7</code>, and with the commit message <c
 <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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>
@@ -362,7 +362,7 @@ with the commit ID being <code>b42b7633f7</code>, and with the commit message <c
 <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>
+<li>Gin will automatically create a new directory with the given name (in case it does not exist) as you <a href="web-interface.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" />
@@ -402,11 +402,11 @@ with the commit ID being <code>b42b7633f7</code>, and with the commit message <c
 </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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>
+<p>You can specify the directory to be uploaded from the <a href="web-interface.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="web-interface.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>

+ 8 - 8
web-interface/browsing.md

@@ -2,7 +2,7 @@
 
 If you visit the repository page, it looks like below:
 
-![A typical repository page](images/repository-top.png)
+![A typical repository page](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/repository-top.png)
 
 From here, you can browse what is in the repository including:
 
@@ -13,14 +13,14 @@ From here, you can browse what is in the repository including:
 
 On top of the page, you will find the header consisting of `<owner name>/<repository name>`:
 
-![Repository name](images/repository-title.png)
+![Repository name](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/repository-title.png)
 
 This represents the _identifier_ of the repository so that 
 you can specify a single repository inside `https://gin.g-node.org`.
 
 Down to the bottom, you may find some document:
 
-![README file](images/readme.png)
+![README file](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/readme.png)
 
 This represents the (hopefully) detailed description of the repository about what it is
 or what it contains.
@@ -38,23 +38,23 @@ or what it contains.
 
 In the middle, you can find a list of files and directories in the repository:
 
-![File list](images/files.png)
+![File list](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/files.png)
 
 By clicking on individual file/directory entry, you can browse its contents.
 
 For example, you can see the contents of a sub-directory by clicking on it:
 
-![Directory view](images/directory-view.png)
+![Directory view](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/directory-view.png)
 
 Contents of normal files may be visible, as long as your browser supports it.
 
 - For example, you can browse to [web-interface/images/dashboard.png](images/dashboard.png),
 and you can have a glimpse of the original image file:
-  ![Image-file view](images/image-view.png)
+  ![Image-file view](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/image-view.png)
 
 - If you write the documents in the [Markdown](https://www.markdownguide.org/getting-started) format
   (and I recommend to do so whenever possible), you can see the formatted-view of the document:
-  ![Markdown view](images/markdown-view.png)
+  ![Markdown view](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/markdown-view.png)
 
 - 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.
@@ -63,7 +63,7 @@ and you can have a glimpse of the original image file:
 
 On the left columns of the files list, you can see some information like below:
 
-![Commit description](images/commit-description.png)
+![Commit description](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/commit-description.png)
 
 Sadly **it is _not_ about the description to the file itself** but describes the commit
 that updated this file most recently.

+ 3 - 3
web-interface/dashboard.md

@@ -17,7 +17,7 @@ The dashboard may be divided into several areas:
 
 ### Activity
 
-![Activity area](images/activity-area.png)
+![Activity area](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/activity-area.png)
 
 This shows your recent activity on Gin, e.g.
 
@@ -28,7 +28,7 @@ This shows your recent activity on Gin, e.g.
 
 ### Collaborative repositories
 
-![Collaborative repository area](images/collaboration-area.png)
+![Collaborative repository area](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/collaboration-area.png)
 
 This area lists up the repositories **owned by others** and those you have access to.
 
@@ -38,7 +38,7 @@ Normally, most of your repositories will show up here, as they are owned and man
 
 ### Private repositories
 
-![Private repository area](images/private-repositories.png)
+![Private repository area](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/private-repositories.png)
 
 This area lists up the repositories owned by yourself.
 

+ 2 - 2
web-interface/downloading.md

@@ -10,7 +10,7 @@ It is possible to download files individually from the web interface.
 
 When you open a single file, you will see buttons on the top-right of the file:
 
-![Location of buttons](images/file-actions.png)
+![Location of buttons](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/file-actions.png)
 
 These buttons represent the actions that you can execute on this specific file, including:
 
@@ -24,6 +24,6 @@ These buttons represent the actions that you can execute on this specific file,
 
 For downloading the file, click on the "download" button:
 
-![Download button](images/download-button.png)
+![Download button](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/download-button.png)
 
 Then your browser will start downloading the file.

+ 4 - 4
web-interface/uploading.md

@@ -20,7 +20,7 @@ When the web interface shows a list of files in a repository, you can see blue b
 
 > 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 [add you as a Collaborator](collaboration.md).
 
-![Where you can find the buttons for file-creation / upload](images/upload-actions.png)
+![Where you can find the buttons for file-creation / upload](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/upload-actions.png)
 
 There, you have two types of buttons:
 
@@ -29,7 +29,7 @@ There, you have two types of buttons:
 
 
 
-![Two buttons for new files](images/upload-actions-buttons.png)
+![Two buttons for new files](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/upload-actions-buttons.png)
 
 ### Common features for file-upload
 
@@ -39,7 +39,7 @@ No matter which button you use, there are some features shared in common.
 
 On top of the view, an empty text field will show up:
 
-![Directory selector](images/directory-selector-empty.png)
+![Directory selector](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/directory-selector-empty.png)
 
 This is for specifying the directory to upload the file(s).
 
@@ -88,7 +88,7 @@ You can add the files to be uploaded by either:
 
 In either case, the upload process will start immediately, and you will see the progress on the area:
 
-![Progress of upload](images/upload-progress.png)
+![Progress of upload](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/upload-progress.png)
 
 You can specify the directory to be uploaded from the [directory selector (see the section above)](#specifying-the-directory-to-be-uploaded).