debug some images, add publish book stuff

Book/buildbook.r

@@ -2,4 +2,8 @@
 
 library (bookdown)
 
-bookdown::render_book("Index.Rmd", "bookdown::gitbook")
+bookdown::render_book("index.Rmd", "bookdown::gitbook")
+bookdown::publish_book(account = "julien79colomb")
+
+
+"web-interface/collaboration.md",

book-output/index.html

@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>dealing with gin</title>
   <meta name="description" content="dealing with gin" />
-  <meta name="generator" content="bookdown 0.17 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.18.1 and GitBook 2.6.7" />
 
   <meta property="og:title" content="dealing with gin" />
   <meta property="og:type" content="book" />
@@ -21,6 +21,7 @@
   
   
 
+<meta name="author" content="Julien Colomb and Keisuke Sehara" />
 
 
 
@@ -117,6 +118,7 @@
             <section class="normal" id="section-">
 <div id="header">
 <h1 class="title">dealing with gin</h1>
+<p class="author"><em>Julien Colomb and Keisuke Sehara</em></p>
 </div>
 <div id="dealing-with-gin" class="section level1">
 <h1><span class="header-section-number">1</span> Dealing with Gin</h1>

book-output/intro.html

@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>2 Intro | dealing with gin</title>
   <meta name="description" content="2 Intro | dealing with gin" />
-  <meta name="generator" content="bookdown 0.17 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.18.1 and GitBook 2.6.7" />
 
   <meta property="og:title" content="2 Intro | dealing with gin" />
   <meta property="og:type" content="book" />
@@ -21,6 +21,7 @@
   
   
 
+<meta name="author" content="Julien Colomb and Keisuke Sehara" />
 
 
 

book-output/using-application-made-for-git.html

@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <title>4 Using application made for git | dealing with gin</title>
   <meta name="description" content="4 Using application made for git | dealing with gin" />
-  <meta name="generator" content="bookdown 0.17 and GitBook 2.6.7" />
+  <meta name="generator" content="bookdown 0.18.1 and GitBook 2.6.7" />
 
   <meta property="og:title" content="4 Using application made for git | dealing with gin" />
   <meta property="og:type" content="book" />
@@ -21,6 +21,7 @@
   
   
 
+<meta name="author" content="Julien Colomb and Keisuke Sehara" />
 
 
 

book-output/web-interface.html

@@ -6,7 +6,7 @@
   <meta http-equiv="X-UA-Compatible" content="IE=edge" />
   <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 name="generator" content="bookdown 0.18.1 and GitBook 2.6.7" />
 
   <meta property="og:title" content="3 Web interface | dealing with gin" />
   <meta property="og:type" content="book" />
@@ -21,6 +21,7 @@
   
   
 
+<meta name="author" content="Julien Colomb and Keisuke Sehara" />
 
 
 
@@ -159,7 +160,7 @@ it is possible that you don’t have access to the repository at all.</p>
 <p>When you simply sign in to Gin, without selecting any specific repository,
 you fill find a page like below (note that this is just an example):</p>
 <div class="figure">
-<img src="images/dashboard.png" alt="Dashboard overview" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/dashboard.png" alt="Dashboard overview" />
 <p class="caption">Dashboard overview</p>
 </div>
 <p>This is called the “dashboard”, and here you can see most of your activity on Gin.</p>
@@ -358,21 +359,21 @@ with the commit ID being <code>b42b7633f7</code>, and with the commit message <c
 <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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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="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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>
@@ -387,12 +388,12 @@ with the commit ID being <code>b42b7633f7</code>, and with the commit message <c
 <h3><span class="header-section-number">3.5.3</span> Uploading a set of files</h3>
 <p>When you click on the “Upload file” button, the file upload view will appear:</p>
 <div class="figure">
-<img src="images/upload-view.png" alt="File-upload view" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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" />
+<img src="https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/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>

index.Rmd

@@ -1,5 +1,7 @@
 ---
 title: "dealing with gin"
+author: "Julien Colomb and Keisuke Sehara"
+site: bookdown::bookdown_site
 ---
 
 # Dealing with Gin

web-interface/dashboard.md

@@ -3,7 +3,7 @@
 When you simply sign in to Gin, without selecting any specific repository,
 you fill find a page like below (note that this is just an example):
 
-![Dashboard overview](images/dashboard.png)
+![Dashboard overview](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/dashboard.png)
 
 This is called the "dashboard", and here you can see most of your activity on Gin.
 

web-interface/uploading.md

@@ -47,15 +47,15 @@ For instance:
 
 - Enter the name of the subdirectory (within the repository) in this field:
 
-![A subdirectory is specified](images/directory-selector-subdir.png)
+![A subdirectory is specified](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/directory-selector-subdir.png)
 
 -  Gin will automatically create a new directory with the given name (in case it does not exist) as you [commit uploads (see the section below)](#committing-new-files):
 
- ![Created subdirectory](images/created-subdir.png)
+ ![Created subdirectory](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/created-subdir.png)
 
 - Inside the subdirectory, you will find the uploaded file(s):
 
-![The uploaded file in the sub-directory](images/subdir-content.png)
+![The uploaded file in the sub-directory](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/subdir-content.png)
 
 You can also specify the _path_ to the directory of interest, by connecting a hierarchy of directories by a `/` (slash):
 
@@ -75,11 +75,11 @@ TODO
 
 When you click on the "Upload file" button, the file upload view will appear:
 
-![File-upload view](images/upload-view.png)
+![File-upload view](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/upload-view.png)
 
 The dotted region in the middle of the page is the _upload area_:
 
-![The upload area](images/upload-view-upload-area.png)
+![The upload area](https://gin.g-node.org/larkumlab/Dealing_with_Gin/raw/book/web-interface/images/upload-view-upload-area.png)
 
 You can add the files to be uploaded by either: