fixed sidebar and updated theme version

Author: cmirzayi

_pkgdown.yml

@@ -6,8 +6,12 @@ title: BugSigDB Stats and Analysis
 url: http://waldronlab.io/BugSigDBStats
 
 template:
+  bootstrap: 5
+  bootswatch: flatly
   params:
-    bootswatch: flatly
+    toc: true
+  includes:
+    after: pkgdown/extra.css
 
 navbar:
   title: ~

pkgdown/extra.css

@@ -0,0 +1,17 @@
+/* Reduce navbar height */
+.navbar {
+  min-height: 50px !important; /* Adjust as needed */
+  padding-top: 5px;
+  padding-bottom: 5px;
+}
+
+/* Adjust menu items */
+.navbar-nav > li > a {
+  padding-top: 10px;
+  padding-bottom: 10px;
+}
+
+/* Prevent content from being cut off */
+body {
+  padding-top: 20px; /* Adjust to match navbar height */
+}

vignettes/BugSigDBStats.Rmd

@@ -8,6 +8,7 @@ output:
   html_document:
     mathjax: null  
     toc: true
+    toc_depth: 2
     toc_float: true
 ---