From 38196d932df5b3be3ae0eccf9b4604c34fe10ffd Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Mon, 16 Oct 2023 14:33:18 +0200
Subject: [PATCH 1/3] add precise image size

---
 _layouts/tutorial_hands_on.html | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/_layouts/tutorial_hands_on.html b/_layouts/tutorial_hands_on.html
index 5c0d9242a5c669..6ace04b2cd062f 100644
--- a/_layouts/tutorial_hands_on.html
+++ b/_layouts/tutorial_hands_on.html
@@ -63,7 +63,7 @@ <h4 class="alert-heading">Under Development!</h4>
     <blockquote class="overview">
         <div id="overview-box" class="box-title">{{ locale['overview'] | default: "Overview"}}</div>
         {% unless page.license %}
-        <img alt="Creative Commons License: CC-BY" class="float-right" style="border-width:0; display: inline-block; margin:0" src="{% link assets/images/cc-by.png %}"/>
+        <img alt="Creative Commons License: CC-BY" class="float-right" style="border-width:0; display: inline-block; margin:0" src="{% link assets/images/cc-by.png %}" width="88" height="31"/>
         {% endunless %}
         <strong>{% icon question aria=false %} {{ locale['questions'] | default: "Questions" }}:</strong>
         <ul>

From 7a2b529abb5f3708e34444f30ff75644c18eecef Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Mon, 16 Oct 2023 15:08:14 +0200
Subject: [PATCH 2/3] Fixes #4414

---
 _layouts/base.html         | 4 ++++
 _plugins/jekyll-mathjax.rb | 3 +++
 2 files changed, 7 insertions(+)
 create mode 100644 _plugins/jekyll-mathjax.rb

diff --git a/_layouts/base.html b/_layouts/base.html
index 3ba7a5408f3cd6..59d41cdc7b3174 100644
--- a/_layouts/base.html
+++ b/_layouts/base.html
@@ -15,7 +15,9 @@
         <link rel="preload" href="{{ site.baseurl }}/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Regular-102a.woff2" as="font" type="font/woff2" crossorigin>
         <link rel="preload" href="{{ site.baseurl }}/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Bold-102a.woff2" as="font" type="font/woff2" crossorigin>
         <link rel="preload" href="{{ site.baseurl }}/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Italic-102a.woff2" as="font" type="font/woff2" crossorigin>
+        {% if page.mathjax %}
         <link rel="preload" href="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML" as="script" crossorigin>
+        {% endif %}
         <link rel="preload" href="{{ site.baseurl }}/assets/css/main.css?v=3" as="style">
         {{ 'load' | bundle_preloads }}
         <link rel="stylesheet" href="{{ site.baseurl }}/assets/css/main.css?v=3">
@@ -64,6 +66,8 @@
         {% include _includes/default-footer.html %}
 
         {{ 'main' | load_bundle }}
+        {% if page.mathjax %}
         <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+        {% endif %}
     </body>
 </html>
diff --git a/_plugins/jekyll-mathjax.rb b/_plugins/jekyll-mathjax.rb
new file mode 100644
index 00000000000000..0510830a614a2b
--- /dev/null
+++ b/_plugins/jekyll-mathjax.rb
@@ -0,0 +1,3 @@
+Jekyll::Hooks.register :pages, :post_init do |page|
+  page.data['mathjax'] = page.content =~ /\$\$/
+end

From caec7efd70ac16558df42d5fd9878d9300332c84 Mon Sep 17 00:00:00 2001
From: Helena Rasche <hexylena@galaxians.org>
Date: Mon, 16 Oct 2023 15:08:23 +0200
Subject: [PATCH 3/3] bring slides up to date on bundles

---
 _layouts/base_slides.html         | 18 +++++---------
 _layouts/base_slides_ai4life.html | 40 +++++++++++++++----------------
 2 files changed, 25 insertions(+), 33 deletions(-)

diff --git a/_layouts/base_slides.html b/_layouts/base_slides.html
index bb8dd2197d37ce..80f9995771a9e5 100644
--- a/_layouts/base_slides.html
+++ b/_layouts/base_slides.html
@@ -17,6 +17,7 @@
         <link rel="preload" href="{{ site.baseurl}}/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Regular-102a.woff2" as="font" type="font/woff2" crossorigin>
         <link rel="preload" href="{{ site.baseurl}}/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Bold-102a.woff2" as="font" type="font/woff2" crossorigin>
         <link rel="preload" href="{{ site.baseurl}}/assets/fonts/AtkinsonHyperlegible/Atkinson-Hyperlegible-Italic-102a.woff2" as="font" type="font/woff2" crossorigin>
+        {{ 'load' | bundle_preloads }}
         <link rel="stylesheet" href="{{ "/assets/css/main.css?v=3" | prepend: site.baseurl }}">
         <script src="https://kit.fontawesome.com/67b3f98409.js" crossorigin="anonymous"></script>
 
@@ -46,7 +47,7 @@
 </style>
 {% endif %}
 
-    <script type="text/javascript" src="{{ "/assets/js/theme.js" | prepend: site.baseurl }}"></script>
+    {{ 'theme' | load_bundle }}
     <textarea id="source">
 name: inverse
 layout: true
@@ -177,7 +178,6 @@
 {% endif %}
     </textarea>
 	<script src="{{ "/assets/js/remark-latest.min.js" | prepend: site.baseurl }}"></script>
-    <script src="{{ "/assets/js/theme.js" | prepend: site.baseurl }}"></script>
     <script src="{{ "/assets/js/clipboard.min.js" | prepend: site.baseurl }}"></script>
     <script>
       var slideshow = remark.create({navigation: {scroll: false}, ratio: '16:9'});
@@ -203,15 +203,9 @@
 
         }
     </script>
-        <script type="text/javascript" src="{{ "/assets/js/jquery.slim.min.js" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="{{ "/assets/js/popper.min.js" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="{{ "/assets/js/bootstrap.min.js?v=3" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="{{ "/assets/js/details-element-polyfill.js" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-        <script type="text/javascript" src="{{ "/assets/js/bootstrap-toc.min.js" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="{{ "/assets/js/main.js" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="{{ "/assets/js/theme.js" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="{{ "/assets/js/clipboard.min.js" | prepend: site.baseurl }}"></script>
-
+        {{ 'main' | load_bundle }}
+        {% if page.mathjax %}
+        <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+        {% endif %}
     </body>
 </html>
diff --git a/_layouts/base_slides_ai4life.html b/_layouts/base_slides_ai4life.html
index 7d2fb7fc84756e..f4cba1cd32d73e 100644
--- a/_layouts/base_slides_ai4life.html
+++ b/_layouts/base_slides_ai4life.html
@@ -6,16 +6,17 @@
         <meta charset="utf-8">
         <meta http-equiv="x-ua-compatible" content="ie=edge">
         <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
-        <title>{{ page.title | default: site.title }}</title>
+        <title>{{ page.title | default: site.title | strip_html }}</title>
         {% if jekyll.environment == 'production' %}
             {% include _includes/analytics.html %}
         {% endif %}
+        <link rel="shortcut icon" href="{{ "/favicon.ico" | prepend: site.baseurl }}" type="image/x-icon">
+        <link rel="alternate" type="application/atom+xml" href="{{ "/feed.xml" | prepend: site.baseurl }}">
+        <link rel="canonical" href="{{ site.url }}{{ site.baseurl }}{{ page.url }}">
+        <link rel="license" href="https://spdx.org/licenses/{% if page.license %}{{ page.license }}{% else %}CC-BY-4.0{% endif %}">
+        {{ 'load' | bundle_preloads }}
         <link rel="stylesheet" href="{{ "/assets/css/main.css?v=3" | prepend: site.baseurl }}">
         <script src="https://kit.fontawesome.com/67b3f98409.js" crossorigin="anonymous"></script>
-        <link rel="shortcut icon" href="{{ "/favicon.ico" | prepend: site.baseurl }}" type="image/x-icon" />
-        <link rel="alternate" type="application/atom+xml" href="{{ "/feed.xml" | prepend: site.baseurl }}" />
-        <link rel="canonical" href="{{ site.url }}{{ site.baseurl }}{{ page.url }}" />
-        <link rel="license" href="https://creativecommons.org/licenses/by/4.0/" />
 
         {{ page | generate_dublin_core: site }}
 
@@ -43,7 +44,7 @@
 </style>
 {% endif %}
 
-    <script type="text/javascript" src="{{ "/assets/js/theme.js" | prepend: site.baseurl }}"></script>
+    {{ 'theme' | load_bundle }}
     <textarea id="source">
 name: inverse
 layout: true
@@ -94,7 +95,10 @@
 {% include _includes/contributors-line.html page=page authorsonly=true %}
 
 <!-- modified date -->
-<div class="footnote" style="bottom: 8em;">{% icon last_modification %} {{locale['last-modification'] | default: "Updated"}}: {{ page.last_modified_at | date: "%b %-d, %Y"}}</div>
+<div class="footnote" style="bottom: 8em;">
+  {% icon last_modification %} {{locale['last-modification'] | default: "Updated"}}: {{ page.last_modified_at | date: "%b %-d, %Y"}} &nbsp;
+  {% icon purl %}<abbr title="Persistent URL">PURL</abbr>: <a href="https://gxy.io/GTN:{{ page.short_id }}">gxy.io/GTN:{{ page.short_id }}</a>
+</div>
 
 
 <!-- other slide formats (video and plain-text) -->
@@ -173,9 +177,9 @@
 .footnote[Found a typo? Something is wrong in this tutorial? <br/>Edit it on [GitHub]({{ site.github_repository }}/tree/main{{ page.url }})]
 {% endif %}
     </textarea>
-	<script src="{{ "/assets/js/remark-latest.min.js" | prepend: site.baseurl }}" type="text/javascript"></script>
-    <script type="text/javascript" src="{{ "/assets/js/clipboard.min.js" | prepend: site.baseurl }}"></script>
-    <script type="text/javascript">
+	<script src="{{ "/assets/js/remark-latest.min.js" | prepend: site.baseurl }}"></script>
+    <script src="{{ "/assets/js/clipboard.min.js" | prepend: site.baseurl }}"></script>
+    <script>
       var slideshow = remark.create({navigation: {scroll: false}, ratio: '16:9'});
       var hljs = remark.highlighter.engine;
       var snippets = document.querySelectorAll('code.remark-code');
@@ -187,7 +191,7 @@
       }});
     </script>
 
-    <script type="text/javascript">
+    <script>
         if(window.location.hostname === "galaxyproject.github.io") {
             // Redirect
             var redirect = "https://training.galaxyproject.org" + window.location.pathname + window.location.search;
@@ -199,15 +203,9 @@
 
         }
     </script>
-        <script type="text/javascript" src="{{ "/assets/js/jquery.slim.min.js" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="{{ "/assets/js/popper.min.js" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="{{ "/assets/js/bootstrap.min.js?v=3" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="{{ "/assets/js/details-element-polyfill.js" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
-        <script type="text/javascript" src="{{ "/assets/js/bootstrap-toc.min.js" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="{{ "/assets/js/main.js" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="{{ "/assets/js/theme.js" | prepend: site.baseurl }}"></script>
-        <script type="text/javascript" src="{{ "/assets/js/clipboard.min.js" | prepend: site.baseurl }}"></script>
-
+        {{ 'main' | load_bundle }}
+        {% if page.mathjax %}
+        <script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.1/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>
+        {% endif %}
     </body>
 </html>