elixir-toolkit-theme 3.1.0 → 3.2.0

checksums.yaml

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

@@ -149,16 +149,25 @@ This will start the docker container and serve the website locally. Make sure th
 
 ## This theme is known to be used in
 
-- [RDMkit](https://rdmkit.elixir-europe.org/)
-- [WorkflowHub project](https://about.workflowhub.eu/)
-- [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/)
-- [Australian BioCommons How-to-Guides](https://australianbiocommons.github.io/how-to-guides/)
-- [Norwegian Life Science RDM LookUp](https://elixir.no/rdm-lookup)
-- [ERIM Research Toolbox](https://eur-nl.github.io/erim-research-toolbox/)
-
+- [RDMkit](https://rdmkit.elixir-europe.org/) (CONVERGE)
+- [WorkflowHub](https://about.workflowhub.eu/) (EOSC-life project)
+- [RO-crate](https://www.researchobject.org/ro-crate-2024) (EOSC)
+- [Infectious Diseases Toolkit](https://www.infectious-diseases-toolkit.org/) (BY-COVID)
+- [FAIRDOM](https://fair-dom.org/) (FAIRDOM community)
+- [ABB intranet page at PSB](https://intranet.psb.ugent.be/abb/) (VIB department)
+- [How-to-Guides](https://australianbiocommons.github.io/how-to-guides/) (Australian BioCommons)
+- [SPLASH](https://elixir-europe-training.github.io/ELIXIR-Training-SPLASH/) (ELIXIR Training platform)
+- [1+MG Framework](https://framework.onemilliongenomes.eu/) (GDI)
+- [Human 'Omics Data Sharing Field Guide](https://australianbiocommons.github.io/human-omics-data-sharing-field-guide/) (Australian BioCommons)
+- [ERIM RDM Toolbox](https://eur-nl.github.io/erim-research-toolbox/) (ERIM NL)
+- [ABLeS](https://australianbiocommons.github.io/ables) (Australian BioCommons)
+- [TRE-FX](https://trefx.uk/) (DARE UK, HDR UK)
+- [Norwegian Life Science RDM LookUp](https://elixir.no/rdm-lookup/) (ELIXIR Norway)
+- [RSQkit: Research Software Quality kit](https://everse.software/RSQKit/) (EOSC-EVERSE)
+- [dHMp norge](https://dhp-stottepakke.github.io/pages/) (ELIXIR Norway)
+- [Learning-Library](https://patcapon39.github.io/Learning-Library/) (Australian BioCommons)
+- [ELIXIR-IT Training Platform](https://elixir-iib-training.github.io/site/training_courses) (ELIXIR IT)
+- Want your instance here? [Open an issue](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/issues)
 
 ## Dependencies
 

data/_includes/head.html

@@ -74,13 +74,13 @@
                     language: {
                         searchPlaceholder: "Type here..."
                     },
-                    "fnDrawCallback": function ( oSettings ){
-                        var tableId = oSettings.nTable.id;
-                        if(oSettings.fnRecordsTotal() < 10){     
-                            $('#'+tableId+'_length').hide();
-                            $('#'+tableId+'_paginate').hide();
-                            $('#'+tableId+'_filter').hide();
-                            $('#'+tableId+'_info').hide();
+                    "drawCallback": function ( settings ){
+                        var tableId = settings.nTable.id;
+                        if(settings.fnRecordsTotal() < 10){     
+                            $('#'+tableId+'_wrapper .dt-length').hide();
+                            $('#'+tableId+'_wrapper .dt-paging').hide();
+                            $('#'+tableId+'_wrapper .dt-search').hide();
+                            $('#'+tableId+'_wrapper .dt-info').hide();
                         }
                     }
                 });

data/_includes/more-information-tiles.html

@@ -38,15 +38,25 @@
 {%- endif %}
 {%- endfor %}
 {%- endif %}
-{%- if page.page_id %}
+{%- if page.page_id and site.theme_variables.headings.resource-table-all-collapse%}
 {%- assign tools = site.data.tool_and_resource_list | where:"related_pages", page.page_id %}
-{%- unless tools.size == 0 or tools == nil %}
-{%- if site.theme_variables.headings.resource-table-all-collapse %}
+{%- unless tools.size == 0 %}
 {%- assign actual_tools = 1 %}
-{%- endif %}
+{%- endunless %}
+{%- assign country_pages = site.pages | where_exp: "item", "item.search_exclude != true" | where_exp:"item","item.national_resources != nil" %}
+{%- unless country_pages.size == 0 %}
+{%- assign tool_matches_total = 0 %}
+{%- assign query = "related_pages." | append: page.type %}
+{%- for country_page in country_pages %}
+{%- assign tool_matches = country_page.national_resources | where_exp:"resource","resource.related_pages != nil" | where: query, page.page_id %}
+{%- assign tool_matches_total = tool_matches_total | plus: tool_matches.size %}
+{%- endfor %}
+{%- endunless %}
+{%- unless tool_matches_total == 0 %}
+{%- assign actual_nat_tools = 1 %}
 {%- endunless %}
 {%- endif %}
-{%- if actual_fairsharing or actual_faircookbook or actual_dsw or actual_rdmkit or actual_dsw or actual_training or actual_tools %}
+{%- if actual_fairsharing or actual_faircookbook or actual_dsw or actual_rdmkit or actual_dsw or actual_training or actual_tools or actual_nat_tools %}
 <h2 class="mb-4">{{site.theme_variables.headings.more-information-tiles | default: 'More information' }}</h2>
 {%- endif %}
 

data/_includes/pageids-overview.html

@@ -1,7 +1,7 @@
 {%- assign sidebar = site.data.sidebars[include.sidebar]['subitems'] -%}
 {%- for sections in sidebar %}
 {%- assign section = sections.title | downcase | replace: " ", "_" %}
-{%- assign section_pages = site.pages | where:"type", section %}
+{%- assign section_pages = site.pages | where:"type", section | where_exp: "item", "item.search_exclude != true" | where_exp: "item", "item.page_id != nil"   %}
 {%- unless section_pages.size == 0 %}
 <h2>{{sections.title}}</h2>
 <div class="table-responsive">
@@ -16,14 +16,12 @@
         </thead>
         <tbody>
             {%- for section_page in section_pages %}
-            {%- if section_page.page_id and section_page.search_exclude != true %}
             <tr>
                 <td><a href="{{ section_page.url | relative_url }}">{{section_page.title}}</a></td>
                 <td>{{section_page.page_id}}</td>
                 <td>{{section_page.description | default: "no description"}}</td>
                 <td>{{section_page.url}}</td>
             </tr>
-            {%- endif %}
             {%- endfor %}
         </tbody>
     </table>

data/_includes/resource-table-all.html

@@ -18,8 +18,8 @@
 {%- endif %}
 {%- endfor %}
 {%- endunless %}
-{%- unless tools.size == 0  and tool_matches_total.size == 0 %}
-{%- if include.tag %}
+{%- unless tools.size == 0  and tool_matches_total == 0 %}
+{%- if include.tag and tools.size != 0 %}
 <a class="visually-hidden-focusable" href='#skip-tool-table'>Skip tool table</a>
 {%- if site.theme_variables.headings.resource-table-all-collapse %}
 <a data-bs-toggle="collapse" href="#tools_collapse" role="button" aria-expanded="false" aria-controls="tools_collapse" class="d-flex align-items-baseline pb-3 border-top info-collapse">
@@ -30,6 +30,8 @@
 </a>
 <div class="collapse info-card" id="tools_collapse">
 {%- endif %}
+{%- elsif tools.size == 0 and site.theme_variables.headings.resource-table-all-collapse == false or site.theme_variables.headings.resource-table-all-collapse == nil %}
+<h2 class="h2-like fs-2">{{site.theme_variables.headings.resource-table-all | default: 'Tools and resources on this page' }}</h2>
 {%- endif %}
 {%- unless tools.size == 0 %}
 <div class="table-responsive mt-4">

data/_includes/scroll-top.html

@@ -0,0 +1,5 @@
+{%- if site.theme_variables.back_to_top or site.theme_variables.back_to_top == nil %}
+<button id="back-to-top" class="btn btn-primary btn-sm rounded-pill" type="button" aria-hidden="true" onclick="topFunction()">
+    <i class="fa-solid fa-arrow-up"></i>
+</button>
+{%- endif %}

data/_includes/section-navigation-tiles.html

@@ -99,7 +99,7 @@
                 {%- if current_page.affiliations %}
                 {%- assign alllogos = site.data.affiliations %}
                 {%- assign allcountries = site.data.countries %}
-                <div class="d-flex align-items-center gap-2">
+                <div class="d-flex align-items-center flex-wrap gap-2">
                     <span><b><small>Affiliations:</small></b></span>
                     {%- for affiliation in current_page.affiliations %}
                     {%- assign filter_affiliation = alllogos | where: "name", affiliation | first %}

data/_includes/toc.html

@@ -1,6 +1,36 @@
 <script>
   $(document).ready(function () {
-    $('#toc-contents').toc({ minimumHeaders: {{site.theme_variables.toc.min_headings | default: 2 }}, listType: 'ul', classes: { list: 'list-unstyled' }, noBackToTopLinks: true, showSpeed: 0, headers: '{{site.theme_variables.toc.headings | default: 'main h2' }}' , title: '<strong class="my-2">On this page</strong><hr class="my-2">' });
+    // Ensure that the TOC is generated after the document is fully loaded
+    $('#toc-contents').toc({
+      minimumHeaders: {{ site.theme_variables.toc.min_headings | default: 1 }},
+      listType: 'ul',
+      classes: { list: 'list-unstyled' },
+      showSpeed: 0,
+      headers: '{{site.theme_variables.toc.headings | default: "main h2" }}',
+      title: '<strong class="my-2">On this page</strong><hr class="my-2">' 
+    });
+    // After generating the TOC, check the hash in the URL and scroll to the anchor if present
+    if (window.location.hash) {
+      var target = $(window.location.hash);
+      if (target.length) {
+        $('html, body').animate({
+          scrollTop: target.offset().top
+        }, 0);
+      }
+    }
+    // Allow the browser to handle the scrolling to the anchor
+    $('#toc-contents a').on('click', function (e) {
+      e.preventDefault(); // Prevent the default link click behavior
+
+      var target = this.hash; // Get the hash (e.g., #heading-id)
+      var $target = $(target); // Find the element with the corresponding ID
+
+      if ($target.length) {
+        // Change the URL hash
+        window.location.hash = target;
+      }
+    });
+
   });
 </script>
 <button id="btn-toc-hide" class="btn bg-light d-xl-none hover-primary mb-3" type="button" data-bs-toggle="collapse" data-bs-target="#toc-contents" aria-expanded="true" aria-controls="toc-contents">

data/_layouts/default.html

@@ -3,7 +3,7 @@
 {% include head.html %}
 <body class="d-flex flex-column min-vh-100"{% unless page.toc == false %} data-bs-spy="scroll" data-bs-target="#toc-contents" data-bs-smooth-scroll="true" tabindex="0"{% endunless %}>
     {% if site.topnav_banner %}{% include banner.html %}{% endif %}
-    {% if jekyll.environment == "development" %}{% include dev-info.html %}{% endif %}
+    {% if jekyll.environment == "development" and site.theme_variables.dev-info-banner == true %}{% include dev-info.html %}{% endif %}
     {% include topnav.html %}
     <!-- Page Content -->
     <div class="container flex-grow-1">
@@ -19,11 +19,7 @@
             {{content}}
         </div>
     </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 btn-sm rounded-pill" type="button" aria-hidden="true" onclick="topFunction()">
-        <i class="fa-solid fa-arrow-up"></i>
-    </button>
-    {%- endif %}
+    {% include scroll-top.html %}
     {% include footer.html %}
     {% include cookie-popup.html %}
 </body>

data/_layouts/page.html

@@ -1,7 +1,7 @@
 ---
 layout: default
 ---
-<main id="main" class="order-1">
+<main id="main" class="order-1{% unless page.toc == false %} add-grid{% endunless %}">
     <div id="intro">
         {%- if page.title %}
         {%- if page.type %}

data/_sass/bootstrap/_accordion.scss

@@ -20,7 +20,6 @@
   --#{$prefix}accordion-btn-icon-transform: #{$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};
@@ -74,7 +73,6 @@
 
   &:focus {
     z-index: 3;
-    border-color: var(--#{$prefix}accordion-btn-focus-border-color);
     outline: 0;
     box-shadow: var(--#{$prefix}accordion-btn-focus-box-shadow);
   }
@@ -92,7 +90,7 @@
   &:first-of-type {
     @include border-top-radius(var(--#{$prefix}accordion-border-radius));
 
-    .accordion-button {
+    > .accordion-header .accordion-button {
       @include border-top-radius(var(--#{$prefix}accordion-inner-border-radius));
     }
   }
@@ -105,13 +103,13 @@
   &:last-of-type {
     @include border-bottom-radius(var(--#{$prefix}accordion-border-radius));
 
-    .accordion-button {
+    > .accordion-header .accordion-button {
       &.collapsed {
         @include border-bottom-radius(var(--#{$prefix}accordion-inner-border-radius));
       }
     }
 
-    .accordion-collapse {
+    > .accordion-collapse {
       @include border-bottom-radius(var(--#{$prefix}accordion-border-radius));
     }
   }
@@ -127,11 +125,7 @@
 // Remove borders and border-radius to keep accordion items edge-to-edge.
 
 .accordion-flush {
-  .accordion-collapse {
-    border-width: 0;
-  }
-
-  .accordion-item {
+  > .accordion-item {
     border-right: 0;
     border-left: 0;
     @include border-radius(0);
@@ -139,12 +133,18 @@
     &:first-child { border-top: 0; }
     &:last-child { border-bottom: 0; }
 
-    .accordion-button {
+    // stylelint-disable selector-max-class
+    > .accordion-header .accordion-button {
       &,
       &.collapsed {
         @include border-radius(0);
       }
     }
+    // stylelint-enable selector-max-class
+
+    > .accordion-collapse {
+      @include border-radius(0);
+    }
   }
 }
 

data/_sass/bootstrap/_buttons.scss

@@ -100,6 +100,15 @@
     }
   }
 
+  .btn-check:checked:focus-visible + & {
+    // Avoid using mixin so we can pass custom focus shadow properly
+    @if $enable-shadows {
+      box-shadow: var(--#{$prefix}btn-active-shadow), var(--#{$prefix}btn-focus-box-shadow);
+    } @else {
+      box-shadow: var(--#{$prefix}btn-focus-box-shadow);
+    }
+  }
+
   &:disabled,
   &.disabled,
   fieldset:disabled & {

data/_sass/bootstrap/_carousel.scss

@@ -132,19 +132,11 @@
   background-size: 100% 100%;
 }
 
-/* rtl:options: {
-  "autoRename": true,
-  "stringMap":[ {
-    "name"    : "prev-next",
-    "search"  : "prev",
-    "replace" : "next"
-  } ]
-} */
 .carousel-control-prev-icon {
-  background-image: escape-svg($carousel-control-prev-icon-bg);
+  background-image: escape-svg($carousel-control-prev-icon-bg) #{"/*rtl:" + escape-svg($carousel-control-next-icon-bg) + "*/"};
 }
 .carousel-control-next-icon {
-  background-image: escape-svg($carousel-control-next-icon-bg);
+  background-image: escape-svg($carousel-control-next-icon-bg) #{"/*rtl:" + escape-svg($carousel-control-prev-icon-bg) + "*/"};
 }
 
 // Optional indicator pips/controls

data/_sass/bootstrap/_modal.scss

@@ -126,7 +126,6 @@
   display: flex;
   flex-shrink: 0;
   align-items: center;
-  justify-content: space-between; // Put modal header elements (title and dismiss) on opposite ends
   padding: var(--#{$prefix}modal-header-padding);
   border-bottom: var(--#{$prefix}modal-header-border-width) solid var(--#{$prefix}modal-header-border-color);
   @include border-top-radius(var(--#{$prefix}modal-inner-border-radius));

data/_sass/bootstrap/_offcanvas.scss

@@ -123,14 +123,11 @@
 .offcanvas-header {
   display: flex;
   align-items: center;
-  justify-content: space-between;
   padding: var(--#{$prefix}offcanvas-padding-y) var(--#{$prefix}offcanvas-padding-x);
 
   .btn-close {
     padding: calc(var(--#{$prefix}offcanvas-padding-y) * .5) calc(var(--#{$prefix}offcanvas-padding-x) * .5);
-    margin-top: calc(-.5 * var(--#{$prefix}offcanvas-padding-y));
-    margin-right: calc(-.5 * var(--#{$prefix}offcanvas-padding-x));
-    margin-bottom: calc(-.5 * var(--#{$prefix}offcanvas-padding-y));
+    margin: calc(-.5 * var(--#{$prefix}offcanvas-padding-y)) calc(-.5 * var(--#{$prefix}offcanvas-padding-x)) calc(-.5 * var(--#{$prefix}offcanvas-padding-y)) auto;
   }
 }
 

data/_sass/bootstrap/_tables.scss

@@ -79,7 +79,7 @@
 //
 // When borders are added on all sides of the cells, the corners can render odd when
 // these borders do not have the same color or if they are semi-transparent.
-// Therefor we add top and border bottoms to the `tr`s and left and right borders
+// Therefore we add top and border bottoms to the `tr`s and left and right borders
 // to the `td`s or `th`s
 
 .table-bordered {

data/_sass/bootstrap/_variables.scss

@@ -1383,7 +1383,9 @@ $accordion-transition:                    $btn-transition, border-radius .15s ea
 $accordion-button-active-bg:              var(--#{$prefix}primary-bg-subtle) !default;
 $accordion-button-active-color:           var(--#{$prefix}primary-text-emphasis) !default;
 
-$accordion-button-focus-border-color:     $input-focus-border-color !default;
+// fusv-disable
+$accordion-button-focus-border-color:     $input-focus-border-color !default; // Deprecated in v5.3.3
+// fusv-enable
 $accordion-button-focus-box-shadow:       $btn-focus-box-shadow !default;
 
 $accordion-icon-width:                    1.25rem !default;
@@ -1392,8 +1394,8 @@ $accordion-icon-active-color:             $primary-text-emphasis !default;
 $accordion-icon-transition:               transform .2s ease-in-out !default;
 $accordion-icon-transform:                rotate(-180deg) !default;
 
-$accordion-button-icon:         url("data:image/svg+xml,<svg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='#{$accordion-icon-color}'><path fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/></svg>") !default;
-$accordion-button-active-icon:  url("data:image/svg+xml,<svg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='#{$accordion-icon-active-color}'><path fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/></svg>") !default;
+$accordion-button-icon:         url("data:image/svg+xml,<svg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='none' stroke='#{$accordion-icon-color}' stroke-linecap='round' stroke-linejoin='round'><path d='M2 5L8 11L14 5'/></svg>") !default;
+$accordion-button-active-icon:  url("data:image/svg+xml,<svg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='none' stroke='#{$accordion-icon-active-color}' stroke-linecap='round' stroke-linejoin='round'><path d='M2 5L8 11L14 5'/></svg>") !default;
 // scss-docs-end accordion-variables
 
 // Tooltips
@@ -1745,3 +1747,5 @@ $kbd-bg:                            var(--#{$prefix}body-color) !default;
 $nested-kbd-font-weight:            null !default; // Deprecated in v5.2.0, removing in v6
 
 $pre-color:                         null !default;
+
+@import "variables-dark"; // TODO: can be removed safely in v6, only here to avoid breaking changes in v5.3

data/_sass/bootstrap/forms/_form-check.scss

@@ -131,7 +131,7 @@
     margin-left: $form-switch-padding-start * -1;
     background-image: var(--#{$prefix}form-switch-bg);
     background-position: left center;
-    @include border-radius($form-switch-border-radius);
+    @include border-radius($form-switch-border-radius, 0);
     @include transition($form-switch-transition);
 
     &:focus {

data/_sass/bootstrap/mixins/_banner.scss

@@ -1,7 +1,7 @@
 @mixin bsBanner($file) {
   /*!
-   * Bootstrap #{$file} v5.3.2 (https://getbootstrap.com/)
-   * Copyright 2011-2023 The Bootstrap Authors
+   * Bootstrap #{$file} v5.3.3 (https://getbootstrap.com/)
+   * Copyright 2011-2024 The Bootstrap Authors
    * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
    */
 }

data/_sass/bootstrap/mixins/_forms.scss

@@ -69,7 +69,12 @@
 
       &:focus {
         border-color: $border-color;
-        box-shadow: $focus-box-shadow;
+        @if $enable-shadows {
+          @include box-shadow($input-box-shadow, $focus-box-shadow);
+        } @else {
+          // Avoid using mixin so we can pass custom focus shadow properly
+          box-shadow: $focus-box-shadow;
+        }
       }
     }
   }
@@ -100,7 +105,12 @@
 
       &:focus {
         border-color: $border-color;
-        box-shadow: $focus-box-shadow;
+        @if $enable-shadows {
+          @include box-shadow($form-select-box-shadow, $focus-box-shadow);
+        } @else {
+          // Avoid using mixin so we can pass custom focus shadow properly
+          box-shadow: $focus-box-shadow;
+        }
       }
     }
   }

data/_sass/bootstrap/mixins/_grid.scss

@@ -138,7 +138,7 @@
           }
         }
 
-        // Start with `1` because `0` is and invalid value.
+        // Start with `1` because `0` is an invalid value.
         // Ends with `$columns - 1` because offsetting by the width of an entire row isn't possible.
         @for $i from 1 through ($columns - 1) {
           .g-start#{$infix}-#{$i} {

data/_sass/bootstrap/tests/mixins/_auto-import-of-variables-dark.test.scss

@@ -0,0 +1,7 @@
+// TODO: this file can be removed safely in v6 when `@import "variables-dark"` will be removed at the end of _variables.scss
+
+@import "../../functions";
+@import "../../variables";
+// Voluntarily not importing _variables-dark.scss
+@import "../../maps";
+@import "../../mixins";

data/_sass/bootstrap/tests/mixins/_utilities.test.scss

@@ -258,7 +258,7 @@ $enable-important-utilities: false;
           .desaturated-color-blue {
             --bs-color-opacity: 1;
             // Sass compilation will put a leading zero so we want to keep that one
-            // stylelint-disable-next-line stylistic/number-leading-zero
+            // stylelint-disable-next-line @stylistic/number-leading-zero
             --bs-color-saturation: 0.25;
             color: hsla(192deg, var(--bs-color-saturation), 0, var(--bs-color-opacity));
           }