update docs

cnyuanh · Dec 11, 2016 · c77b529 · c77b529
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diff --git a/README.md b/README.md
@@ -2,9 +2,9 @@
 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
 ===========================================================================================================================
 
-[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.5-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.4-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-18149/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.5-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.4-green.svg?style=flat)](https://github.com/GuangchuangYu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![total](https://img.shields.io/badge/downloads-18329/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />
 
-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--12--09-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2016--12--12-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)
 
 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)
 
@@ -51,7 +51,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
 
 ### Download stats
 
-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-18149/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-18329/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
 
          +----------------------+----------------------+----------------------+----------------------+-+
          |                                                                                        *    |

diff --git a/docs/css/base.css b/docs/css/base.css
@@ -2,11 +2,42 @@ body {
     padding-top: 70px;
 }
 
-h1[id]:before, h2[id]:before, h3[id]:before, h4[id]:before, h5[id]:before, h6[id]:before {
+/*
+ * The code below adds some padding to the top of the current anchor target so
+ * that, when navigating to it, the header isn't hidden by the navbar at the
+ * top. This is especially complicated because we want to *remove* the padding
+ * after navigation so that hovering over the header shows the permalink icon
+ * correctly. Thus, we create a CSS animation to remove the extra padding after
+ * a second. We have two animations so that navigating to an anchor within the
+ * page always restarts the animation.
+ *
+ * See <https://github.com/mkdocs/mkdocs/issues/843> for more details.
+ */
+:target::before {
     content: "";
     display: block;
     margin-top: -75px;
     height: 75px;
+    pointer-events: none;
+    animation: 0s 1s forwards collapse-anchor-padding-1;
+}
+
+body.clicky :target::before {
+    animation-name: collapse-anchor-padding-2;
+}
+
+@keyframes collapse-anchor-padding-1 {
+    to {
+        margin-top: 0;
+        height: 0;
+    }
+}
+
+@keyframes collapse-anchor-padding-2 {
+    to {
+        margin-top: 0;
+        height: 0;
+    }
 }
 
 ul.nav li.main {
@@ -26,7 +57,27 @@ div.source-links {
 }
 
 div.col-md-9 img {
-  max-width: 100%;
+    max-width: 100%;
+}
+
+code {
+    padding: 1px 3px;
+    background: #f5f5f5;
+    border: solid 1px #ccc;
+    color: #333;
+}
+
+pre code {
+    background: transparent;
+    border: none;
+}
+
+a > code {
+    color: #008cba;
+}
+
+a > code:hover, a > code:focus {
+    color: #00526e;
 }
 
 /*
@@ -116,6 +167,15 @@ div.col-md-9 img {
     }
 }
 
+.headerlink {
+    display: none;
+    padding-left: .5em;
+}
+
+h1:hover .headerlink, h2:hover .headerlink, h3:hover .headerlink, h4:hover .headerlink, h5:hover .headerlink, h6:hover .headerlink{
+    display:inline-block;
+}
+
 /* display submenu relative to parent*/
 .dropdown-submenu {
     position: relative;

diff --git a/docs/featuredArticles/index.html b/docs/featuredArticles/index.html
@@ -223,11 +223,11 @@
   }  
   </style>
 
-<div id = 'chart47cdaaf4ab' class = 'rChart morris'></div>
+<div id = 'chart4492ca05dfe' class = 'rChart morris'></div>
 
 <script type='text/javascript'>
     var chartParams = {
- "element": "chart47cdaaf4ab",
+ "element": "chart4492ca05dfe",
 "width":            800,
 "height":            400,
 "xkey": "year",
@@ -241,7 +241,7 @@
 "pubid": "HtEfBTGE9r8C" 
 } 
 ],
-"id": "chart47cdaaf4ab",
+"id": "chart4492ca05dfe",
 "labels": "cites" 
 },
       chartType = "Bar"

diff --git a/docs/index.html b/docs/index.html
@@ -237,7 +237,7 @@
 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>
 <p><a href="https://bioconductor.org/packages/ggtree"><img alt="releaseVersion" src="https://img.shields.io/badge/release%20version-1.6.5-blue.svg?style=flat" /></a>
 <a href="https://github.com/GuangchuangYu/ggtree"><img alt="develVersion" src="https://img.shields.io/badge/devel%20version-1.7.4-blue.svg?style=flat" /></a>
-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-18149/total-blue.svg?style=flat" /></a>
+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="total" src="https://img.shields.io/badge/downloads-18329/total-blue.svg?style=flat" /></a>
 <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="month" src="https://img.shields.io/badge/downloads-1852/month-blue.svg?style=flat" /></a></p>
 <p>The <code>ggtree</code> package extending the <code>ggplot2</code> package. It based on grammar of graphics and takes all the good parts of <code>ggplot2</code>.  <code>ggtree</code> is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.
 <code>ggtree</code> is released within the <a href="https://bioconductor.org/packages/ggtree/">Bioconductor</a> project and the source code is hosted on <a href="https://github.com/GuangchuangYu/ggtree"><i class="fa fa-github fa-lg"></i> GitHub</a>.</p>

diff --git a/docs/js/base.js b/docs/js/base.js
@@ -38,6 +38,11 @@ $('body').scrollspy({
     target: '.bs-sidebar',
 });
 
+/* Toggle the `clicky` class on the body when clicking links to let us
+   retrigger CSS animations. See ../css/base.css for more details. */
+$('a').click(function(e) {
+    $('body').toggleClass('clicky');
+});
 
 /* Prevent disabled links from causing a page reload */
 $("li.disabled a").click(function() {