Add some JS scripts to improve the styling of the documentation

docs/_static/js/apitoc.js

+$(document).ready(function() {
+  (function ($) {
+    if (window.location.href.match("/api/*") !== null) {
+      $(".nav-list")
+        .children()
+        .filter("li")
+        .append("<ul id='apitoc' class='nav nav-list'></ul>");
+      $( "dt" )
+        .has( ".sig-name" )
+        .slice(1)
+        .each(function( index ) {
+          var html = (
+            "<li><a href='#"
+            + $( this ).attr("id")
+            + "'><code>"
+            + $( this ).find(".sig-name").text()
+            + "</code></a></li>"
+          );
+          $("#apitoc").append(html);
+        });
+    } else if (window.location.href.match("/api/errors.html") !== null) {
+      $(".nav-list")
+        .children()
+        .filter("li")
+        .append("<ul id='apitoc' class='nav nav-list scrollable-menu'></ul>");
+      $( "dt" )
+        .each(function( index ) {
+          var html = (
+            "<li><a href='#"
+            + $( this ).attr("id")
+            + "'><code>"
+            + $( this ).find(".sig-name").text()
+            + "</code></a></li>"
+          );
+          $("#apitoc").append(html);
+        });
+    }
+  })(window.$jqTheme || window.jQuery);
+})

docs/_static/js/example-admonition.js

+$(document).ready(function() {
+  (function ($) {
+    $(".admonition-example")
+      .removeClass("panel-info")
+      .addClass("panel-success").end()
+  })(window.$jqTheme || window.jQuery);
+})

docs/conf.py

@@ -36,8 +36,8 @@ sys.modules['peptides.tables'] = types.ModuleType('peptides.tables')
 def setup(app):
     # Add custom stylesheet
     app.add_css_file(os.path.join("_static/css/main.css"))
-    # app.add_js_file("js/apitoc.js")
-    # app.add_js_file("js/example-admonition.js")
+    app.add_js_file("js/apitoc.js")
+    app.add_js_file("js/example-admonition.js")
 
 
 # -- Project information -----------------------------------------------------
@@ -181,8 +181,8 @@ htmlhelp_basename = peptides.__name__
 # -- Options for extlinks extension ------------------------------------------
 
 extlinks = {
-    'doi': ('https://doi.org/%s', 'doi:%s'),
-    'pmid': ('https://pubmed.ncbi.nlm.nih.gov/%s', 'PMID:%s'),
+    'doi': ('https://doi.org/%s', 'doi:'),
+    'pmid': ('https://pubmed.ncbi.nlm.nih.gov/%s', 'PMID:'),
 }