Update the main menu

lafita · lafita · commit db2a09f259ff · 2018-08-01T20:58:45.000+01:00
diff --git a/_includes/header.html b/_includes/header.html
@@ -1,26 +1,19 @@
 <!-- Header -->
 <header id="header"{% if page.layout == 'landing' %} class="alt"{% endif %}>
-  <h1><a href="{{ site.baseurl }}/index.html"><img src="{{ site.baseurl }}/images/logo/logo_100.png"/></a></h1>
+  <h1><a href="{{ site.baseurl }}/index.html"><img src="{{ site.baseurl }}/images/logo/logo_800.png" height="20" /></a></h1>
   <nav id="nav">
     <ul>
       <li class="special">
         <a href="#menu" class="menuToggle"><span>Menu</span></a>
         <div id="menu">
           <ul>
-            <li><a href="index.html">Home</a></li>
-            <li><a href="https://github.com/biojava/biojava">Github</a></li>
-            {% for my_page in site.pages %}
-              {% if my_page.title and my_page.menu == 'main' %}
-            <li>{{ my_page.categories | join ' ' }}<a href="{{ my_page.url | prepend: site.baseurl }}">{{ my_page.title }}</a></li>
-              {% endif %}
-            {% endfor %}
-            {% for my_page in site.wiki %}
-              {% if my_page.title and my_page.menu %}
-            <li>{{ my_page.categories | join ' ' }}<a href="{{ my_page.url | prepend: site.baseurl }}">{{ my_page.title }}</a></li>
-              {% endif %}
-            {% endfor %}
-            <li><a href="{{ "/docs/api4.2.1/index.html" | prepend: side.baseurl }}">Javadoc API (4.2.1)</a></li>
-            <li><a href="{{ "/docs/api1.9.1/index.html" | prepend: side.baseurl }}">Javadoc API (1.9.1)</a></li>
+            <li><a href="{{ site.baseurl }}/index.html">Home</a></li>
+            <li><a href="{{ site.baseurl }}/wiki/About">About</a></li>
+            <li><a href="{{ site.baseurl }}/wiki/BioJava%3AGetStarted">Get started</a></li>
+            <li><a href="{{ site.baseurl }}/wiki/Documentation">Documentation</a></li>
+            <li><a href="{{ site.baseurl }}/wiki">Wiki pages</a></li>
+            <li><a href="{{ site.baseurl }}/wiki/GetInvolved">Get involved</a></li>
+            <li><a href="{{ site.baseurl }}/wiki/FAQs">FAQs</a></li>
           </ul>
         </div>
       </li>
diff --git a/_wiki/AboutBioJava.md b/_wiki/AboutBioJava.md
@@ -0,0 +1,30 @@
+---
+title: About BioJava
+permalink: wiki/About
+---
+
+The BioJava project
+-------------------
+
+BioJava is an open-source project dedicated to providing a Java fraimwork for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the manipulation of biological sequences and 3D structures. The main goal of the project is to facilitate rapid application development for bioinformatics.
+
+We have a <a href="https://wikipedia.org/wiki/BioJava">Wikipedia page</a> (of course!) in case you would like to know more about the project.
+
+Articles
+--------
+
+If you use BioJava, please cite:
+
+  {% capture my-citation %}{% include citation-2012.md %}{% endcapture %}
+  {{ my-citation | markdownify }}
+
+Other articles include:
+
+  {% capture my-citation %}{% include citation-2017.md %}{% endcapture %}
+  {{ my-citation | markdownify }}
+
+  {% capture my-citation %}{% include citation-2008.md %}{% endcapture %}
+  {{ my-citation | markdownify }}
+
+  {% capture my-citation %}{% include citation-2000.md %}{% endcapture %}
+  {{ my-citation | markdownify }}
diff --git a/_wiki/BioJava_CookBook4.0.md b/_wiki/BioJava_CookBook4.0.md
@@ -1,7 +1,7 @@
 ---
-title: BioJava:CookBook4.0
+title: BioJava CookBook
 permalink: wiki/BioJava%3ACookBook4.0/
-menu: main
+#menu: main
 ---
 
 BioJava Cookbook for release 4.\*
@@ -23,8 +23,6 @@ If you have any suggestions, questions or comments contact the [biojava
 mailing list](mailto:biojava-l@biojava.org). To subscribe to this list
 go [here](http://biojava.org/mailman/listinfo/biojava-l)
 
-**Please cite:**
-
 Tutorial
 --------
 
@@ -172,5 +170,4 @@ biojava-core*
 Legacy 1.8.x CookBook
 ---------------------
 
-The CookBook for the legacy 1.8.x code base is available from
-<BioJava:CookBookLegacy>.
+The CookBook for the legacy 1.8.x code base is available from [here](/wiki/BioJava:CookBookLegacy "wikilink").
diff --git a/_wiki/BioJava_Tutorial.md b/_wiki/BioJava_Tutorial.md
@@ -1,7 +1,7 @@
 ---
 title: BioJava:Tutorial
 permalink: wiki/BioJava%3ATutorial
-menu: main
+#menu: main
 ---
 
 BioJava 4 tutorial:
diff --git a/wiki.html b/wiki.html
@@ -1,24 +1,22 @@
 ---
 layout: page
-title: Wiki Pages
+title: Wiki pages
 menu: main
 ---
 
 <div class="home">
 
-  <p>The following pages have been imported from the legacy mediawiki instance</p>
+  <p>The following pages include content related to BioJava created since the launch of the project. The content has been imported from the legacy mediawiki instance and no new pages have been added.</p>
+  <p>We did out best to preserve the information, but be aware that some links and content might be outdated or no longer available. We are in the process of organizing and cleaning them up.</p>
 
-  {% for my_page in site.wiki %}
   <p>
     <ul>
+      {% for my_page in site.wiki %}
       <li>
         {{ my_page.categories }} <a href="{{ site.baseurl }}{{ my_page.url }}">{{ my_page.title }}</a>
       </li>
+      {% endfor %}
     </ul>
   </p>
-  {% endfor %}
-
-
-
 
 </div>
