elixir-toolkit-theme 1.21.0 → 1.23.0

checksums.yaml

@@ -1,7 +1,7 @@
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data/README.md

@@ -2,11 +2,11 @@
 
 
 <p align="center">
-<img src="assets/img/main_logo.svg" width="100" float="center"/>
+<img src="assets/img/ett_compact_logo.svg" width="100" float="center"/>
 <h1 align="center">ELIXIR toolkit theme </h1>
 </p>
 
-The ELIXIR toolkit theme is a Jekyll theme designed to support easy deployment of documentation websites but also more complex ones that require a central tool table and linking towards ELXIR resources. 
+The ELIXIR toolkit theme is a Jekyll theme designed to support easy deployment of documentation websites but also more complex ones that require a central tool table and linking towards ELIXIR resources. 
 
 Its key features:
 - Easy deployment using GitHub pages
@@ -15,7 +15,7 @@ Its key features:
 - Change style using custom classes
 - Support for a central tools table
 - Page tagging and listing of those tagged pages
-- Linking to ELIXIR resources including Bio.tools, FAIRSHARING, FAIR Cookbook, TeSS and DSW
+- Linking to ELIXIR resources including Bio.tools, FAIRsharing, FAIR Cookbook, TeSS and DSW
 - Easy side navigation, top navigation and footer management
 - Mobile friendly
 - Create website sections with each section having its own sidebar
@@ -104,7 +104,7 @@ This will start the docker container and serve the website locally. Make sure th
 
 - [RDMkit](https://rdmkit.elixir-europe.org/)
 - [WorkflowHub project](https://about.workflowhub.eu/)
-- [RDMGuide](https://rdm.elixir-belgium.org/)
+- [RDM Guide](https://rdm.elixir-belgium.org/)
 - [Infectious Diseases Toolkit](https://www.infectious-diseases-toolkit.org/)
 - [Applied Bioinformatics and Biostatistics intranet page](https://intranet.psb.ugent.be/abb/)
 - [FAIRDOM](https://fair-dom.org/)

data/_includes/contributor-minitiles-page.html

@@ -5,7 +5,7 @@
     {%- assign page_contributors = page.contributors | sort %}
     {%- for contributor in page_contributors %}
     {%- assign id = contributors[contributor].git | default: 'no_github' %}
-    <div class="dropdown d-inline-block">
+    <div class="dropup-center dropup d-inline-block">
       <button class="btn btn-sm dropdown-toggle contributor-link d-flex hover-primary m-1 position-relative"  type="button" data-bs-toggle="dropdown" aria-expanded="false">
         <div class="d-flex align-items-center">
             <div class="flex-shrink-0">

data/_includes/dev-info.html

@@ -0,0 +1,3 @@
+<div class="p-2 text-center text-break bg-warning">
+    <small>Development build for <a href="{{ site.github.repository_url }}/commit/{{ site.github.build_revision }}" target="_blank"><b>{{ site.github.repository_nwo }}@{{ site.github.build_revision | slice: 0, 7 }}</b></a> (branch: <a href="{{ site.github.repository_url }}/tree/{{ site.github.source.branch }}" target="_blank"><b>{{ site.github.source.branch }}</b></a>)</small>
+</div>

data/_includes/footer.html

@@ -38,9 +38,35 @@
         </div>
         {%- endunless %}
     </div>
-    {%- unless site.data.footer.copyright == nil %}
-    <div class="copyright text-center p-4">
-        {{ site.data.footer.copyright | markdownify }}
+    <div class="copyright p-4">
+        <div class="container d-flex justify-content-between flex-column flex-lg-row">
+            {%- unless site.data.footer.copyright == nil %}
+            <div class="d-flex align-items-center mb-3 mb-lg-0 mx-auto mx-lg-0 text-center">{{ site.data.footer.copyright | markdownify }}</div>
+            {%- endunless %}
+            <div class="d-flex align-items-center mx-auto ms-lg-4 me-lg-0">
+                <a id="ett-logo" class="text-nowrap" href="https://elixir-belgium.github.io/elixir-toolkit-theme">Built with
+                    <svg data-name="ETT logo" xmlns="http://www.w3.org/2000/svg" width="30" height="30" viewBox="0 0 77.2 77.12">
+                        <defs>
+                            <style>
+                                .cls-2,
+                                .cls-3 {
+                                    fill: #fff;
+                                    pointer-events: none;
+                                }
+
+                                .cls-2 {
+                                    opacity: 0.18;
+                                }
+                            </style>
+                        </defs>
+                        <g>
+                            <circle class="cls-1" cx="38.56" cy="38.56" r="38.56" />
+                            <path class="cls-2" d="M9,48.08a44.19,44.19,0,0,0,4.68,19.84A38.56,38.56,0,1,0,55.16,3.72c-.59,0-1.19-.05-1.79-.05A44.4,44.4,0,0,0,9,48.08Z" />
+                            <path class="cls-3" d="M54,20.52H13.64a.85.85,0,0,0-.84.85v34a.84.84,0,0,0,.84.84H30a.84.84,0,0,0,.85-.84V51.16a.85.85,0,0,0-.85-.85H20.07a.85.85,0,0,1-.85-.85V42a.85.85,0,0,1,.85-.84h8.66a.85.85,0,0,0,.85-.85V36.06a.85.85,0,0,0-.85-.85H20.07a.85.85,0,0,1-.85-.84V27.29a.85.85,0,0,1,.85-.85H38.26a.85.85,0,0,1,.85.85V55.38a.84.84,0,0,0,.85.84h4.73a.84.84,0,0,0,.85-.84V27.29a.85.85,0,0,1,.84-.85H61.27a.85.85,0,0,1,.84.85V55.38a.84.84,0,0,0,.85.84h4.73a.84.84,0,0,0,.85-.84V27.29a.85.85,0,0,1,.85-.85h6.77a.84.84,0,0,0,.84-.85V21.37a.84.84,0,0,0-.84-.85Z" />
+                        </g>
+                    </svg>
+                </a>
+            </div>
+        </div>
     </div>
-    {%- endunless %}
 </footer>

data/_includes/section-navigation-tiles-simple.html

@@ -1,10 +1,13 @@
 {%- assign allcountries = site.data.countries %}
+{%- assign except = include.except | split: ", " %}
 <div class="row row-cols-1 row-cols-md-2 g-3 mb-5 navigation-tiles">
     {%- for current_page in site.pages | sorted %}
     {%- if current_page.title and current_page.search_exclude != true and current_page.type == include.type %}
+    {%- unless except contains current_page.name %}
     <div class="col d-grid">
         <a role="button" class="btn bg-light py-4 fs-3 hover-primary" href="{{ current_page.url | relative_url }}">{{current_page.title}}<span class="flag-icon ms-3 flag-icon-{{current_page.country_code | downcase }}"></span></a>
     </div>
+    {% endunless %}
     {%- endif %}
     {%- endfor %}
 </div>

data/_includes/section-navigation-tiles.html

@@ -1,4 +1,4 @@
-{%- unless include.affiliations == nil and include.search == nil and include.related_pages == nil %}
+{%- unless include.affiliations == nil and include.search == nil %}
 {%- assign allcountries = site.data.countries %}
 {%- for current_page in site.pages | sorted %}
 {%- if current_page.affiliations and current_page.search_exclude != true and current_page.type == include.type %}
@@ -147,7 +147,7 @@
                     {%- if country_link %}
                     <a role="button" href="{{country_link.url | relative_url}}" data-bs-toggle="tooltip" title="{{allcountries[country]}}" class="btn btn-sm bg-white hover-primary">
                         {%- else %}
-                        <a role="button" data-bs-toggle="tooltip" title="{{allcountries[country]}}" class="btn btn-sm bg-white hover-primary disabled" aria-disabled="true">
+                        <a role="button" data-bs-toggle="tooltip" title="{{allcountries[country]}}" class="btn btn-sm bg-white hover-primary disabled border-white" aria-disabled="true">
                             {%- endif %}
                             <div class="d-block h-24px">
                                 <span class="flag-icon flag-icon-{{affiliation | downcase}} align-items-center"></span>

data/_includes/topnav.html

@@ -58,7 +58,15 @@
                     {%- endif %}
                     {%- if site.theme_variables.topnav.github or site.theme_variables.topnav.github == nil %}
                     <li class="nav-item ms-0 ms-lg-3 mt-2 mt-lg-0">
-                        <a class="nav-link ps-2 d-flex align-items-center" href="{{site.github.repository_url}}"><i class="fa-brands fa-github me-2"></i>{{site.theme_variables.git_host | default: 'GitHub' }}</a>
+                        <a class="nav-link ps-2 d-flex align-items-center" href="{{site.github.repository_url}}">
+                            {%- assign git_host = site.theme_variables.git_host | downcase %}
+                            {%- if git_host == 'gitlab' %}
+                            <i class="fa-brands fa-gitlab me-2"></i>
+                            {%- else %}
+                            <i class="fa-brands fa-github me-2"></i>
+                            {%- endif %}
+                            {{site.theme_variables.git_host | default: 'GitHub' }}
+                        </a>
                     </li>
                     {%- endif %}
                     {%- unless include.search == false %}

data/_includes/training-table-all.html

@@ -15,13 +15,23 @@
         <tbody>
             {%- for page in site.pages %}
             {%- unless page.search_exclude == true %}
-            {%- for training in page.training%}
+            {%- if page.training %}
+            {%- assign actual_training = nil %}
+            {%- for training in page.training %}
+            {%- if training.name %}
+            {%- assign actual_training = 1 %}
+            {%- endif %}
+            {%- endfor %}
+            {%- endif %}
+            {%- if actual_training %}
+            {%- for training in page.training %}
             <tr>
                 <td><a href="{{training.url | relative_url }}">{{training.name}}{%- if training.name == 'Training in TeSS'%} about {{page.title}}{%- endif %}</a></td>
                 <td><a href="{{page.url | relative_url }}"><span class="badge default-badge">{{page.title}}</span></a></td>
                 <td>{%- if training.registry %}<span class="badge bg-dark text-white hover-primary">{{training.registry}}</span>{%- endif %}</td>
             </tr>
             {%- endfor %}
+            {%- endif %}
             {%- endunless %}
             {%- endfor %}
         </tbody>

data/_layouts/default.html

@@ -2,6 +2,7 @@
 <html lang="en">
 {% include head.html %}
 <body>
+    {% if jekyll.environment == "development" %}{% include dev-info.html %}{% endif %}
     {% include topnav.html %}
     <!-- Page Content -->
     <div class="container min-vh-100">
@@ -21,7 +22,7 @@
     </div>
     {%- if site.theme_variables.back_to_top or site.theme_variables.back_to_top == nil %}
     <button id="back-to-top" class="btn btn-primary" type="button" aria-hidden="true" onclick="topFunction()">
-        <i class="fa-solid fa-arrow-up"></i><span class="ms-2 d-none d-sm-inline">Back to top</span>
+        <i class="fa-solid fa-arrow-up"></i>
     </button>
     {%- endif %}
     {% include footer.html %}

data/_sass/_variables.scss

@@ -68,3 +68,4 @@ $footer-color: $dark;
 $footer-link-color: $dark;
 $footer-link-color-hover: $primary;
 $footer-copyright-bg: $gray-200;
+$footer-ett: $dark;

data/_sass/bootstrap/_accordion.scss

@@ -2,43 +2,70 @@
 // Base styles
 //
 
+.accordion {
+  // scss-docs-start accordion-css-vars
+  --#{$prefix}accordion-color: #{$accordion-color};
+  --#{$prefix}accordion-bg: #{$accordion-bg};
+  --#{$prefix}accordion-transition: #{$accordion-transition};
+  --#{$prefix}accordion-border-color: #{$accordion-border-color};
+  --#{$prefix}accordion-border-width: #{$accordion-border-width};
+  --#{$prefix}accordion-border-radius: #{$accordion-border-radius};
+  --#{$prefix}accordion-inner-border-radius: #{$accordion-inner-border-radius};
+  --#{$prefix}accordion-btn-padding-x: #{$accordion-button-padding-x};
+  --#{$prefix}accordion-btn-padding-y: #{$accordion-button-padding-y};
+  --#{$prefix}accordion-btn-color: #{$accordion-button-color};
+  --#{$prefix}accordion-btn-bg: #{$accordion-button-bg};
+  --#{$prefix}accordion-btn-icon: #{escape-svg($accordion-button-icon)};
+  --#{$prefix}accordion-btn-icon-width: #{$accordion-icon-width};
+  --#{$prefix}accordion-btn-icon-transform: #{$accordion-icon-transform};
+  --#{$prefix}accordion-btn-icon-transition: #{$accordion-icon-transition};
+  --#{$prefix}accordion-btn-active-icon: #{escape-svg($accordion-button-active-icon)};
+  --#{$prefix}accordion-btn-focus-border-color: #{$accordion-button-focus-border-color};
+  --#{$prefix}accordion-btn-focus-box-shadow: #{$accordion-button-focus-box-shadow};
+  --#{$prefix}accordion-body-padding-x: #{$accordion-body-padding-x};
+  --#{$prefix}accordion-body-padding-y: #{$accordion-body-padding-y};
+  --#{$prefix}accordion-active-color: #{$accordion-button-active-color};
+  --#{$prefix}accordion-active-bg: #{$accordion-button-active-bg};
+  // scss-docs-end accordion-css-vars
+}
+
 .accordion-button {
   position: relative;
   display: flex;
   align-items: center;
   width: 100%;
-  padding: $accordion-button-padding-y $accordion-button-padding-x;
+  padding: var(--#{$prefix}accordion-btn-padding-y) var(--#{$prefix}accordion-btn-padding-x);
   @include font-size($font-size-base);
-  color: $accordion-button-color;
+  color: var(--#{$prefix}accordion-btn-color);
   text-align: left; // Reset button style
-  background-color: $accordion-button-bg;
+  background-color: var(--#{$prefix}accordion-btn-bg);
   border: 0;
   @include border-radius(0);
   overflow-anchor: none;
-  @include transition($accordion-transition);
+  @include transition(var(--#{$prefix}accordion-transition));
 
   &:not(.collapsed) {
-    color: $accordion-button-active-color;
-    background-color: $accordion-button-active-bg;
-    box-shadow: inset 0 ($accordion-border-width * -1) 0 $accordion-border-color;
+    color: var(--#{$prefix}accordion-active-color);
+    background-color: var(--#{$prefix}accordion-active-bg);
+    box-shadow: inset 0 calc(-1 * var(--#{$prefix}accordion-border-width)) 0 var(--#{$prefix}accordion-border-color); // stylelint-disable-line function-disallowed-list
 
     &::after {
-      background-image: escape-svg($accordion-button-active-icon);
-      transform: $accordion-icon-transform;
+      background-image: var(--#{$prefix}accordion-btn-active-icon);
+      transform: var(--#{$prefix}accordion-btn-icon-transform);
     }
   }
 
   // Accordion icon
   &::after {
     flex-shrink: 0;
-    width: $accordion-icon-width;
-    height: $accordion-icon-width;
+    width: var(--#{$prefix}accordion-btn-icon-width);
+    height: var(--#{$prefix}accordion-btn-icon-width);
     margin-left: auto;
     content: "";
-    background-image: escape-svg($accordion-button-icon);
+    background-image: var(--#{$prefix}accordion-btn-icon);
     background-repeat: no-repeat;
-    background-size: $accordion-icon-width;
-    @include transition($accordion-icon-transition);
+    background-size: var(--#{$prefix}accordion-btn-icon-width);
+    @include transition(var(--#{$prefix}accordion-btn-icon-transition));
   }
 
   &:hover {
@@ -47,9 +74,9 @@
 
   &:focus {
     z-index: 3;
-    border-color: $accordion-button-focus-border-color;
+    border-color: var(--#{$prefix}accordion-btn-focus-border-color);
     outline: 0;
-    box-shadow: $accordion-button-focus-box-shadow;
+    box-shadow: var(--#{$prefix}accordion-btn-focus-box-shadow);
   }
 }
 
@@ -58,14 +85,15 @@
 }
 
 .accordion-item {
-  background-color: $accordion-bg;
-  border: $accordion-border-width solid $accordion-border-color;
+  color: var(--#{$prefix}accordion-color);
+  background-color: var(--#{$prefix}accordion-bg);
+  border: var(--#{$prefix}accordion-border-width) solid var(--#{$prefix}accordion-border-color);
 
   &:first-of-type {
-    @include border-top-radius($accordion-border-radius);
+    @include border-top-radius(var(--#{$prefix}accordion-border-radius));
 
     .accordion-button {
-      @include border-top-radius($accordion-inner-border-radius);
+      @include border-top-radius(var(--#{$prefix}accordion-inner-border-radius));
     }
   }
 
@@ -75,22 +103,22 @@
 
   // Only set a border-radius on the last item if the accordion is collapsed
   &:last-of-type {
-    @include border-bottom-radius($accordion-border-radius);
+    @include border-bottom-radius(var(--#{$prefix}accordion-border-radius));
 
     .accordion-button {
       &.collapsed {
-        @include border-bottom-radius($accordion-inner-border-radius);
+        @include border-bottom-radius(var(--#{$prefix}accordion-inner-border-radius));
       }
     }
 
     .accordion-collapse {
-      @include border-bottom-radius($accordion-border-radius);
+      @include border-bottom-radius(var(--#{$prefix}accordion-border-radius));
     }
   }
 }
 
 .accordion-body {
-  padding: $accordion-body-padding-y $accordion-body-padding-x;
+  padding: var(--#{$prefix}accordion-body-padding-y) var(--#{$prefix}accordion-body-padding-x);
 }
 
 
@@ -112,7 +140,10 @@
     &:last-child { border-bottom: 0; }
 
     .accordion-button {
-      @include border-radius(0);
+      &,
+      &.collapsed {
+        @include border-radius(0);
+      }
     }
   }
 }

data/_sass/bootstrap/_alert.scss

@@ -3,11 +3,24 @@
 //
 
 .alert {
+  // scss-docs-start alert-css-vars
+  --#{$prefix}alert-bg: transparent;
+  --#{$prefix}alert-padding-x: #{$alert-padding-x};
+  --#{$prefix}alert-padding-y: #{$alert-padding-y};
+  --#{$prefix}alert-margin-bottom: #{$alert-margin-bottom};
+  --#{$prefix}alert-color: inherit;
+  --#{$prefix}alert-border-color: transparent;
+  --#{$prefix}alert-border: #{$alert-border-width} solid var(--#{$prefix}alert-border-color);
+  --#{$prefix}alert-border-radius: #{$alert-border-radius};
+  // scss-docs-end alert-css-vars
+
   position: relative;
-  padding: $alert-padding-y $alert-padding-x;
-  margin-bottom: $alert-margin-bottom;
-  border: $alert-border-width solid transparent;
-  @include border-radius($alert-border-radius);
+  padding: var(--#{$prefix}alert-padding-y) var(--#{$prefix}alert-padding-x);
+  margin-bottom: var(--#{$prefix}alert-margin-bottom);
+  color: var(--#{$prefix}alert-color);
+  background-color: var(--#{$prefix}alert-bg);
+  border: var(--#{$prefix}alert-border);
+  @include border-radius(var(--#{$prefix}alert-border-radius));
 }
 
 // Headings for larger alerts
@@ -47,6 +60,7 @@
   $alert-background: shift-color($value, $alert-bg-scale);
   $alert-border: shift-color($value, $alert-border-scale);
   $alert-color: shift-color($value, $alert-color-scale);
+
   @if (contrast-ratio($alert-background, $alert-color) < $min-contrast-ratio) {
     $alert-color: mix($value, color-contrast($alert-background), abs($alert-color-scale));
   }

data/_sass/bootstrap/_badge.scss

@@ -4,16 +4,25 @@
 // `background-color`.
 
 .badge {
+  // scss-docs-start badge-css-vars
+  --#{$prefix}badge-padding-x: #{$badge-padding-x};
+  --#{$prefix}badge-padding-y: #{$badge-padding-y};
+  @include rfs($badge-font-size, --#{$prefix}badge-font-size);
+  --#{$prefix}badge-font-weight: #{$badge-font-weight};
+  --#{$prefix}badge-color: #{$badge-color};
+  --#{$prefix}badge-border-radius: #{$badge-border-radius};
+  // scss-docs-end badge-css-vars
+
   display: inline-block;
-  padding: $badge-padding-y $badge-padding-x;
-  @include font-size($badge-font-size);
-  font-weight: $badge-font-weight;
+  padding: var(--#{$prefix}badge-padding-y) var(--#{$prefix}badge-padding-x);
+  @include font-size(var(--#{$prefix}badge-font-size));
+  font-weight: var(--#{$prefix}badge-font-weight);
   line-height: 1;
-  color: $badge-color;
+  color: var(--#{$prefix}badge-color);
   text-align: center;
   white-space: nowrap;
   vertical-align: baseline;
-  @include border-radius($badge-border-radius);
+  @include border-radius(var(--#{$prefix}badge-border-radius));
   @include gradient-bg();
 
   // Empty badges collapse automatically

data/_sass/bootstrap/_breadcrumb.scss

@@ -1,28 +1,40 @@
 .breadcrumb {
+  // scss-docs-start breadcrumb-css-vars
+  --#{$prefix}breadcrumb-padding-x: #{$breadcrumb-padding-x};
+  --#{$prefix}breadcrumb-padding-y: #{$breadcrumb-padding-y};
+  --#{$prefix}breadcrumb-margin-bottom: #{$breadcrumb-margin-bottom};
+  @include rfs($breadcrumb-font-size, --#{$prefix}breadcrumb-font-size);
+  --#{$prefix}breadcrumb-bg: #{$breadcrumb-bg};
+  --#{$prefix}breadcrumb-border-radius: #{$breadcrumb-border-radius};
+  --#{$prefix}breadcrumb-divider-color: #{$breadcrumb-divider-color};
+  --#{$prefix}breadcrumb-item-padding-x: #{$breadcrumb-item-padding-x};
+  --#{$prefix}breadcrumb-item-active-color: #{$breadcrumb-active-color};
+  // scss-docs-end breadcrumb-css-vars
+
   display: flex;
   flex-wrap: wrap;
-  padding: $breadcrumb-padding-y $breadcrumb-padding-x;
-  margin-bottom: $breadcrumb-margin-bottom;
-  @include font-size($breadcrumb-font-size);
+  padding: var(--#{$prefix}breadcrumb-padding-y) var(--#{$prefix}breadcrumb-padding-x);
+  margin-bottom: var(--#{$prefix}breadcrumb-margin-bottom);
+  @include font-size(var(--#{$prefix}breadcrumb-font-size));
   list-style: none;
-  background-color: $breadcrumb-bg;
-  @include border-radius($breadcrumb-border-radius);
+  background-color: var(--#{$prefix}breadcrumb-bg);
+  @include border-radius(var(--#{$prefix}breadcrumb-border-radius));
 }
 
 .breadcrumb-item {
   // The separator between breadcrumbs (by default, a forward-slash: "/")
   + .breadcrumb-item {
-    padding-left: $breadcrumb-item-padding-x;
+    padding-left: var(--#{$prefix}breadcrumb-item-padding-x);
 
     &::before {
       float: left; // Suppress inline spacings and underlining of the separator
-      padding-right: $breadcrumb-item-padding-x;
-      color: $breadcrumb-divider-color;
-      content: var(--#{$variable-prefix}breadcrumb-divider, escape-svg($breadcrumb-divider)) #{"/* rtl:"} var(--#{$variable-prefix}breadcrumb-divider, escape-svg($breadcrumb-divider-flipped)) #{"*/"};
+      padding-right: var(--#{$prefix}breadcrumb-item-padding-x);
+      color: var(--#{$prefix}breadcrumb-divider-color);
+      content: var(--#{$prefix}breadcrumb-divider, escape-svg($breadcrumb-divider)) #{"/* rtl:"} var(--#{$prefix}breadcrumb-divider, escape-svg($breadcrumb-divider-flipped)) #{"*/"};
     }
   }
 
   &.active {
-    color: $breadcrumb-active-color;
+    color: var(--#{$prefix}breadcrumb-item-active-color);
   }
 }

data/_sass/bootstrap/_button-group.scss

@@ -34,14 +34,17 @@
 }
 
 .btn-group {
+  @include border-radius($btn-border-radius);
+
   // Prevent double borders when buttons are next to each other
-  > .btn:not(:first-child),
+  > :not(.btn-check:first-child) + .btn,
   > .btn-group:not(:first-child) {
     margin-left: -$btn-border-width;
   }
 
   // Reset rounded corners
   > .btn:not(:last-child):not(.dropdown-toggle),
+  > .btn.dropdown-toggle-split:first-child,
   > .btn-group:not(:last-child) > .btn {
     @include border-end-radius(0);
   }