Merge pull request #4279 from galaxyproject/prefs

User Preferences
galaxyproject · Sep 28, 2023 · c93ee50 · c93ee50
2 parents 4ee4761 + 1e8c2a1
commit c93ee50
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diff --git a/_includes/analytics.html b/_includes/analytics.html
@@ -1,24 +1,59 @@
+<!--
 <script async defer data-domain="training.galaxyproject.org" src="https://plausible.galaxyproject.eu/js/plausible.js"></script>
+-->
+<!-- We let users opt-out, so if they've opted in, we need to append the plausible script to the body -->
+
+<script>
+var scriptElement = document.createElement("script");
+scriptElement.async = true;
+scriptElement.defer = true;
+scriptElement.setAttribute("data-domain", "training.galaxyproject.org");
+scriptElement.src = "https://plausible.galaxyproject.eu/js/plausible.js";
+
+// Appending the script element to the body
+if(localStorage.getItem('plausible-opt-out') !== 'opt-out' && navigator.doNotTrack !== "1") {
+	console.log("Plausible: opt-in");
+	// Wait for the document to be available
+	document.addEventListener("DOMContentLoaded", function(event) {
+		document.body.appendChild(scriptElement);
+	});
+}
+</script>
 
 <!-- JavaScript Error Monitoring, and performance tracking. -->
+<!--
 <script
   src="https://browser.sentry-cdn.com/7.52.1/bundle.tracing.min.js"
   integrity="sha384-muuFXKS3752PNA4rPm9Uq6BLvOfV4CXyr9MHDBPvozOJJUWLKkogEFWOIRoVps43"
   crossorigin="anonymous"
 ></script>
+-->
 <script type="text/javascript">
-Sentry.init({
-  dsn: "https://[email protected]/10",
-  release: "galaxy-training-network@{{ site.git_revision }}",
-  integrations: [new Sentry.BrowserTracing(), new Sentry.Replay()],
-  sampleRate: 0.1,
-  tracesSampleRate: 0.1,
-  // Capture Replay for no sessions by default
-  replaysSessionSampleRate: 0.01,
-  // plus for 1% of sessions with an error
-  replaysOnErrorSampleRate: 0.01,
-  // PII OFF
-  sendDefaultPii: false, // Off by default but just in case.
-  environment: "{{ jekyll.environment }}",
-});
+var scriptElement = document.createElement("script");
+scriptElement.src = "https://browser.sentry-cdn.com/7.52.1/bundle.tracing.min.js";
+scriptElement.integrity = "sha384-muuFXKS3752PNA4rPm9Uq6BLvOfV4CXyr9MHDBPvozOJJUWLKkogEFWOIRoVps43";
+scriptElement.crossOrigin = "anonymous";
+
+if(localStorage.getItem('sentry-opt-out') !== 'opt-out' && navigator.doNotTrack !== "1") {
+	console.log("Sentry: opt-in");
+	// Appending the script element to the body
+	document.addEventListener("DOMContentLoaded", function(event) {
+		document.body.appendChild(scriptElement);
+	});
+
+	Sentry.init({
+	  dsn: "https://[email protected]/10",
+	  release: "galaxy-training-network@{{ site.git_revision }}",
+	  integrations: [new Sentry.BrowserTracing(), new Sentry.Replay()],
+	  sampleRate: 0.1,
+	  tracesSampleRate: 0.1,
+	  // Capture Replay for no sessions by default
+	  replaysSessionSampleRate: 0.01,
+	  // plus for 1% of sessions with an error
+	  replaysOnErrorSampleRate: 0.01,
+	  // PII OFF
+	  sendDefaultPii: false, // Off by default but just in case.
+	  environment: "{{ jekyll.environment }}",
+	});
+}
 </script>
diff --git a/_includes/extras.html b/_includes/extras.html
@@ -45,23 +45,9 @@
             </a>
         {% endif %}
 
-        <div class="dropdown-item">
-            <div>
-                {% icon gtn-theme %} Theme
-            </div>
-
-            <div id="theme-selector" data-toggle="buttons">
-                    <button class="btn" data-theme="default">Default</button>
-                    <button class="btn" data-theme="night">Night</button>
-                    <button class="btn" data-theme="midnight">Midnight</button>
-                    <button class="btn" data-theme="rainbow">Rainbow</button>
-                    <button class="btn" data-theme="blm">✊🏿</button>
-                    <button class="btn" data-theme="progress" >🏳️‍🌈</button>
-                    <button class="btn" data-theme="halloween">🎃</button>
-                    <button class="btn" data-theme="straya">🇦🇺</button>
-            </div>
-
-        </div>
+		<a href="{% link preferences.md %}" class="dropdown-item">
+			{% icon gtn-theme %} Themes have moved <span class="badge badge-secondary">New</span>
+		</a>
 
         <div class="dropdown-item">
             <div>

diff --git a/_includes/help.html b/_includes/help.html
@@ -11,7 +11,7 @@
         </form>
         -->
 
-        <a class="dropdown-item" href="{{ site.baseurl }}/faq" title="Check our FAQs">
+	<a class="dropdown-item" href="{% link faqs/index.md %}" title="Check our FAQs">
            {% icon question %} FAQs
         </a>
         {% if topic %}

diff --git a/_layouts/base.html b/_layouts/base.html
@@ -50,7 +50,7 @@
         </script>
         {% endif %}
     </head>
-    <body data-spy="scroll" data-target="#toc">
+    <body data-spy="scroll" data-target="#toc" data-brightness="auto" data-contrast="auto">
         {{ 'theme' | load_bundle }}
         {% include _includes/default-header.html %}
         {% if topic.custom_css %}

diff --git a/_layouts/base_slides.html b/_layouts/base_slides.html
@@ -39,7 +39,7 @@
             {% include _includes/material.jsonld material=page topic=topic site=site %}
         </script>
     </head>
-  <body>
+  <body data-brightness="auto" data-contrast="auto">
 {% if topic.custom_css %}
 <style>
 {{ topic.custom_css }}
@@ -59,7 +59,7 @@
 {% else %}
   {% capture link %}{{ site.github_repository }}/edit/{{ site.github_repository_branch }}/topics/{{ topic.name }}/tutorials/{{ page.tutorial_name }}/slides.html{% endcapture %}
 {% endif %}
-<a class="nav-link" href="{{ link }}"><i class="fa fa-pencil" aria-hidden="true"></i></a>
+<a href="{{ link }}"><i class="fa fa-pencil" aria-hidden="true"></i></a>
 
 </span></div>
 

diff --git a/_layouts/base_slides_ai4life.html b/_layouts/base_slides_ai4life.html
@@ -36,7 +36,7 @@
             {% include _includes/material.jsonld material=page topic=topic site=site %}
         </script>
     </head>
-  <body>
+  <body data-brightness="auto" data-contrast="auto">
 {% if topic.custom_css %}
 <style>
 {{ topic.custom_css }}

diff --git a/_layouts/tutorial_hands_on.html b/_layouts/tutorial_hands_on.html
@@ -169,7 +169,7 @@ <h4 class="alert-heading">Under Development!</h4>
     <div class="container">
         <div class="row">
             <!-- sidebar, which will move to the top on a small screen -->
-            <div class="col-sm-2">
+            <div class="col-sm-2 hide-when-printing">
                 <nav id="toc" data-toggle="toc" class="sticky-top" aria-label="Table of Contents"></nav>
             </div>
             <div class="col-sm-10">

diff --git a/_plugins/jekyll-figurify.rb b/_plugins/jekyll-figurify.rb
@@ -80,12 +80,14 @@ def figurify(page, site)
           image = insert_image(url, alt, style, dimensions, actual_path)
 
           %(
+          <a href="#{url}" rel="noopener noreferrer">
             <figure id="figure-#{num_figure}" style="max-width: 90%; margin:auto;">
               #{image}
               <figcaption>
                 <span class="figcaption-prefix"><strong>#{prefix}#{num_figure}</strong>:</span> #{title}
               </figcaption>
             </figure>
+          </a>
           ).split("\n").map(&:strip).join
         end
       end
@@ -103,7 +105,9 @@ def figurify(page, site)
         end
 
         %(
+        <a href="#{url}" rel="noopener noreferrer">
           <img src="#{url}"  alt="#{alt}" #{style} #{dimensions} loading="lazy">
+        </a>
         ).split("\n").map(&:strip).join
       end
     end

diff --git a/_plugins/notebook-jupyter.rb b/_plugins/notebook-jupyter.rb
@@ -35,7 +35,7 @@ def json_boxify(h, page)
   h
 end
 
-Jekyll::Hooks.register :site, :pre_render do |site|
+def jupyter_pre_render(site)
   puts '[GTN/Notebooks] Rendering'
 
   site.config['__rendered_notebook_cache'] = {}
@@ -117,8 +117,7 @@ def json_boxify(h, page)
   end
 end
 
-# Basically like `PageWithoutAFile`, we just write out the ones we'd created earlier.
-Jekyll::Hooks.register :site, :post_write do |site|
+def jupyter_post_write(site)
   site.config['__rendered_notebook_cache'].each do |_path, info|
     # Create if missing
     FileUtils.mkdir_p(info['dir'])
@@ -127,3 +126,12 @@ def json_boxify(h, page)
     File.write(info['path2'], info['content2'])
   end
 end
+
+Jekyll::Hooks.register :site, :pre_render do |site|
+  jupyter_pre_render(site)
+end
+
+# Basically like `PageWithoutAFile`, we just write out the ones we'd created earlier.
+Jekyll::Hooks.register :site, :post_write do |site|
+  jupyter_post_write(site)
+end
diff --git a/_plugins_dev/notebook.rb b/_plugins_dev/notebook.rb
@@ -1,3 +1,11 @@
+def jupyter_pre_render(site)
+  nil
+end
+
+def jupyter_post_write(site)
+  nil
+end
+
 module Jekyll
   class RmarkdownGenerator < Generator
     def generate(site)

diff --git a/assets/css/fonts.css b/assets/css/fonts.css
@@ -1,32 +1,7 @@
-/* cyrillic */
 @font-face {
   font-family: 'Yanone Kaffeesatz';
   font-style: normal;
-  font-weight: 400;
-  src: url(/training-material/assets/fonts/yanonekaffeesatz/v24/3y9I6aknfjLm_3lMKjiMgmUUYBs04aUXNxt9gW2LIfto9tWZc2GKOnU.woff2) format('woff2');
-  unicode-range: U+0301, U+0400-045F, U+0490-0491, U+04B0-04B1, U+2116;
-}
-/* vietnamese */
-@font-face {
-  font-family: 'Yanone Kaffeesatz';
-  font-style: normal;
-  font-weight: 400;
-  src: url(/training-material/assets/fonts/yanonekaffeesatz/v24/3y9I6aknfjLm_3lMKjiMgmUUYBs04aUXNxt9gW2LIfto9tWZeGGKOnU.woff2) format('woff2');
-  unicode-range: U+0102-0103, U+0110-0111, U+0128-0129, U+0168-0169, U+01A0-01A1, U+01AF-01B0, U+0300-0301, U+0303-0304, U+0308-0309, U+0323, U+0329, U+1EA0-1EF9, U+20AB;
-}
-/* latin-ext */
-@font-face {
-  font-family: 'Yanone Kaffeesatz';
-  font-style: normal;
-  font-weight: 400;
-  src: url(/training-material/assets/fonts/yanonekaffeesatz/v24/3y9I6aknfjLm_3lMKjiMgmUUYBs04aUXNxt9gW2LIfto9tWZeWGKOnU.woff2) format('woff2');
-  unicode-range: U+0100-02AF, U+0304, U+0308, U+0329, U+1E00-1E9F, U+1EF2-1EFF, U+2020, U+20A0-20AB, U+20AD-20CF, U+2113, U+2C60-2C7F, U+A720-A7FF;
-}
-/* latin */
-@font-face {
-  font-family: 'Yanone Kaffeesatz';
-  font-style: normal;
-  font-weight: 400;
-  src: url(/training-material/assets/fonts/yanonekaffeesatz/v24/3y9I6aknfjLm_3lMKjiMgmUUYBs04aUXNxt9gW2LIfto9tWZd2GK.woff2) format('woff2');
-  unicode-range: U+0000-00FF, U+0131, U+0152-0153, U+02BB-02BC, U+02C6, U+02DA, U+02DC, U+0304, U+0308, U+0329, U+2000-206F, U+2074, U+20AC, U+2122, U+2191, U+2193, U+2212, U+2215, U+FEFF, U+FFFD;
+  font-weight: 100 900;
+  font-style: normal oblique;
+  src: url(/training-material/assets/fonts/yanonekaffeesatz/YanoneKaffeesatz-VariableFont_wght.woff2);
 }
diff --git a/assets/css/fontsmain.scss b/assets/css/fontsmain.scss
@@ -0,0 +1,66 @@
+@font-face {
+  font-family: "Atkinson Hyperlegible";
+  src: url(/training-material/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Regular-102a.woff2);
+  font-display: swap;
+}
+
+@font-face {
+  font-family: "Atkinson Hyperlegible";
+  src: url(/training-material/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-BoldItalic-102a.woff2);
+  font-weight: bold;
+  font-style: oblique;
+  font-display: swap;
+}
+
+@font-face {
+  font-family: "Atkinson Hyperlegible";
+  src: url(/training-material/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Italic-102a.woff2);
+  font-style: oblique;
+  font-display: swap;
+}
+
+@font-face {
+  font-family: "Atkinson Hyperlegible";
+  src: url(/training-material/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Bold-102a.woff2);
+  font-weight: bold;
+  font-display: swap;
+}
+
+
+@font-face {
+	font-family: "OpenDyslexic";
+	src: url(/training-material/assets/fonts/OpenDyslexic/OpenDyslexic-Bold-Italic.woff2);
+	font-weight: bold;
+	font-style: oblique;
+	font-display: swap;
+}
+@font-face {
+	font-family: "OpenDyslexic";
+	src: url(/training-material/assets/fonts/OpenDyslexic/OpenDyslexic-Bold.woff2);
+	font-weight: bold;
+	font-display: swap;
+}
+@font-face {
+	font-family: "OpenDyslexic";
+	src: url(/training-material/assets/fonts/OpenDyslexic/OpenDyslexic-Italic.woff2);
+	font-style: oblique;
+	font-display: swap;
+}
+@font-face {
+	font-family: "OpenDyslexic";
+	src: url(/training-material/assets/fonts/OpenDyslexic/OpenDyslexic-Regular.woff2);
+	font-display: swap;
+}
+
+
+@font-face {
+	font-family: "Comic Mono";
+	src: url(/training-material/assets/fonts/ComicMono/ComicMono-Bold.ttf);
+	font-weight: bold;
+	font-display: swap;
+}
+@font-face {
+	font-family: "Comic Mono";
+	src: url(/training-material/assets/fonts/ComicMono/ComicMono.ttf);
+	font-display: swap;
+}