Upgrading to ETT v6.0.0

Gemfile

@@ -1,10 +1,11 @@
 source 'https://rubygems.org'
 
-gem 'elixir-toolkit-theme-plugins', '~> 0.1.10'
-gem 'webrick', '~> 1.9.1'
-gem 'jekyll', '~> 4.4.1'
-gem 'jemoji', '~> 0.13.0'
-gem 'kramdown-parser-gfm', '~> 1.1'
+gem 'elixir-toolkit-theme-plugins', '~> 1.1.0'
+gem "webrick", "~> 1.9.1"
+gem "jekyll", "~> 4.4.1"
+gem "jemoji", "~> 0.13.0"
+gem "kramdown-parser-gfm", "~> 1.1"
+gem 'jekyll-octicons'
 gem "csv"
 
 group :jekyll_plugins do

_config.yml

@@ -4,7 +4,7 @@ title: RDMkit
 description: "Best practices and guidelines you can use for FAIR management of your research data."
 # Metadata description of the website
 
-remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@5.0.0
+remote_theme: ELIXIR-Belgium/elixir-toolkit-theme@6.0.0
 
 sass:
   style: compressed
@@ -101,7 +101,7 @@ defaults:
     scope:
       path: "pages/data_life_cycle/"
     values:
-      type: data_life_cycle
+      type: Data_life_cycle
       type_img: /assets/img/section-icons/reuse-sustain.svg
   -
     scope:

_sass/_bootstrap_variables.scss

@@ -14,17 +14,12 @@ $navbar-dark-hover-color: $primary;
 $navbar-dark-toggler-border-color: transparent;
 $border-radius: 0.45rem;
 $btn-border-radius-sm: $border-radius;
-$card-border-width: 0;
 $link-color: $blue;
 $info: $blue;
-$link-decoration: none;
 $body-bg: $white;
 $body-color: $dark;
 $font-family-sans-serif: "Open Sans", sans-serif;
-$alert-border-width: 0;
 $input-group-addon-bg: $light-x;
-$input-bg: $light;
-$input-border-width: 0;
 $h1-font-size: 1rem * 3.5;
 $h2-font-size: 1rem * 2.2;
 $h3-font-size: 1rem * 1.5;

_sass/_custom_classes.scss

@@ -1,6 +1,6 @@
 /*-----General styling-----*/
 
-@media (min-width: 992px) {
+@include media-breakpoint-up(lg) {
     main h1:not(.has-subtitle):not(.blurb-title),
     main .h1:not(.has-subtitle) {
         margin-top: -1rem;
@@ -12,7 +12,7 @@
 }
 
 // Light gray background on the left
-@media (min-width: 992px) {
+@include media-breakpoint-up(lg) {
     body:not(:has(.landingpage)) {
         .anchorjs-link {
             font-size: 0.7em !important;
@@ -34,17 +34,17 @@
             padding-left: 2.1rem;
             background-color: $white;
         }
-        background-image: url("../img/background.svg"); /* The image used */
-        background-position: center; /* Center the image */
-        background-repeat: no-repeat; /* Do not repeat the image */
-        background-size: cover; /* Resize the background image to cover the entire container */
+        background: linear-gradient(to right, $light 0 50%, $body-bg 50% 100%);    
     }
 }
 
-@media (max-width: 992px) {
+@include media-breakpoint-down(lg) {
     .sidebar-collapse {
         background-color: $light;
     }
+    #sidebar>nav .sidebar-title-wrapper {
+        background: $white;
+}
 }
 
 #main {
@@ -75,19 +75,12 @@
     margin-right: auto;
 }
 
-@media (max-width: 992px) {
+@include media-breakpoint-down(lg) {
     .sidebar_rdm {
         width: 200px;
     }
 }
 
-#side-nav .btn.sidebar-title {
-    border: 0;
-    border-bottom: 0.2rem solid $primary !important;
-    font-weight: bold;
-    padding-bottom: $input-btn-padding-y - 0.2rem;
-}
-
 #side-nav > ul {
     margin-top: $spacer * 0.5;
 }
@@ -171,9 +164,6 @@ section#search-section {
     }
 }
 
-#search-label-tiles {
-    background-color: $light;
-}
 
 
 /*-----Top navigation-----*/
@@ -227,9 +217,7 @@ i.fa-solid.fa-code-branch {
 }
 
 // Search
-nav #search-label,
-.landingpage #search-label,
-nav #search-input {
+.landingpage #search-label {
     background-color: $white;
 }
 i.fa-solid.fa-magnifying-glass {

_sass/_custom_variables.scss

@@ -13,8 +13,10 @@ $info-card-bg-hover: $primary;
 $info-card-color-hover: $white;
 
 /*-----Sidebar-----*/
-$sidebar-bg: transparent;
-$sidebar-lvl2-bg: transparent;
+$sidebar-title-bg: $light;
+
+/*-----Page metadata-----*/
+$page-metadata-bg: rgba($blue, 0.1);
 
 /*-----Section navigation tiles-----*/
 $nav-card-bg: $light;

pages/about/contributors.md

@@ -7,4 +7,4 @@ toc: false
 
 This project would not be possible without the many amazing community contributors. RDMkit is an open community project, and you are welcome to [join us](how_to_contribute)!
 
-{% include contributor-tiles-all.html col=6 %}
+{% include contributor-tiles-all.html col=5 %}

pages/about/editorial_board.md

@@ -4,7 +4,7 @@ title: Editorial board
 
 ## Meet the editorial board members
 
-{% include contributor-carousel-selection.html custom="Bert Droesbeke, Carole Goble, Flora D'Anna, Frederik Coppens, Munazah Andrabi, Ulrike Wittig, Korbinian Bösl, Federico Bianchini, Nazeefa Fatima, Ishwar Chandramouliswaran, Diana Pilvar, Marina Popleteeva, Gil Poiares-Oliveira" %}
+{% include contributor-tiles-all.html custom="Bert Droesbeke, Carole Goble, Flora D'Anna, Frederik Coppens, Munazah Andrabi, Ulrike Wittig, Korbinian Bösl, Federico Bianchini, Nazeefa Fatima, Ishwar Chandramouliswaran, Diana Pilvar, Marina Popleteeva, Gil Poiares-Oliveira" %}
 
 ## Join as an editorial board member
 

pages/contribute/editorial_board_guide.md

@@ -12,7 +12,7 @@ As an editor, try to work as much as possible on a different branch than the mas
 ### The google doc way of contributing
 This process is sketched below.
 
-{% include image.html file="googledoc_way_flow.svg" alt="Process of contributing via Google docs" click=true %}
+{% include image.html file="googledoc_way_flow.svg" alt="Process of contributing via Google docs" click=true col=4 %}
 
 ### Overview of the file structure in GitHub
 

pages/contribute/editors_checklist.md

@@ -10,11 +10,12 @@ summary: Checklist for editors before approving and merging a pull request (PR).
 4. All relevant metadata fields in a specific page are correctly filled in (see the [page metadata](page_metadata) and the [Editorial board guide](editorial_board_guide)). Some critical ones are listed below.
    * unique `page_id` ([List of page IDs](website_overview))
    * `contributors`
+   * `editors`
    * `related_pages` ([Related pages](editorial_board_guide.html#related-pages))
    * `training`
    * `search_exclude` must be deleted
    * `description`
-   * `affiliations`
+   * `affiliations` (only used for Tool assembly pages)
    * `coordinators`(only used in national pages + they must be listed as `contributors` as well)
    * `resources`
 5. Make sure that listed tools or resources are tagged in the text with the [correct snippet](tool_resource_update) + that its metadata is described in the [tool_and_resource_list.yml](https://github.com/elixir-europe/rdmkit/blob/master/_data/tool_and_resource_list.yml) file. 

pages/contribute/page_metadata.md

@@ -20,6 +20,10 @@ title: Title of the page
 
 * `contributors`: list here all the contributors that helped in establishing the page. This will be the full name of the person. Make sure that the person name that is listed can be found in the CONTRIBUTORS.yaml file in the _data directory if you want to link the github id and other contact information.
 
+* `coordinators`: List here all the coordinators of the page. Use the full name of the person. Make sure that the person name that is listed can be found in the *_data/CONTRIBUTORS.yaml* file in the _data directory if you want to link the github id and other contact information.
+
+* `editors`: List here all the editors of the page. Use the full name of the person. Make sure that the person name that is listed can be found in the *_data/CONTRIBUTORS.yaml* file in the _data directory if you want to link the github id and other contact information.
+
 * `search_exclude`: by setting this field true, the page will not end up in the search results of the searchbar. By default this is false.
 
 * `sitemap`: let the page appear in the sitemap.xml. Default: true

pages/national_resources/TEMPLATE_resources.md

@@ -5,6 +5,7 @@ search_exclude: true
 country_code: <!---REPLACE THIS with the ISO 3166-1-alpha-2 country code, capital letters--->
 contributors: [<!---REPLACE THIS with comma separated list of contributors--->]
 coordinators: [<!---REPLACE THIS with the name of data management coordinators of your ELIXIR node--->]
+editors: [<!---REPLACE THIS with comma separated list of editors (to be filled in by an editor)--->]
 
 # Link to other pages in the tool assembly section on the RDMkit by listing the page_id.
 # More information on which page_id you can use can be found at https://rdmkit.elixir-europe.org/website_overview 
@@ -66,3 +67,12 @@ national_resources:
 
 ## Domain-specific infrastructures or resources 
 <!--- e.g. human data, covid-19. Please, only add domain-specific resources that you think don't fit in the table at the bottom--->
+
+<!--- IF APPLICABLE
+## Bibliography 
+
+{% bibliography --cited %}
+
+
+More info on how to use a bibliography can be found in our style guide: https://rdmkit.elixir-europe.org/style_guide#bibliography
+--->

pages/tool_assembly/TEMPLATE_tool_assembly.md

@@ -1,7 +1,8 @@
 ---
 title: Assembly page title
 search_exclude: true
-contributors: [<!---REPLACE THIS with comma separated list of contributors--->] 
+contributors: [<!---REPLACE THIS with comma separated list of contributors--->]
+editors: [<!---REPLACE THIS with comma separated list of editors (to be filled in by an editor)--->]
 description: <!---REPLACE THIS with a very short summary (one sentence) this should include if there are limitiations for the audience--->
 affiliations: [<!---REPLACE THIS with comma separated list of affiliations. Countries use the ISO 3166-1-alpha-2 notation, other affiliations must be present in the affiliations.yaml in the _data directory in order to work--->]
 page_id: <!---REPLACE THIS with a shortened page name. The shortened page name should be in lowercase and separated by underscore(s) if needed. For example, page_id of structural bioinformatics will be struct_bioinfo
@@ -37,3 +38,11 @@ In the event that you describe a domain specific tool assembly and no adequate D
 <!--- Add more sections as needed. --->
 ...
 
+<!--- IF APPLICABLE
+## Bibliography 
+
+{% bibliography --cited %}
+
+
+More info on how to use a bibliography can be found in our style guide: https://rdmkit.elixir-europe.org/style_guide#bibliography
+--->

pages/your_domain/TEMPLATE_your_domain.md

@@ -3,6 +3,7 @@ title: Domain page title
 search_exclude: true
 description: <!---REPLACE THIS with a one sentence description of the page--->
 contributors: [<!---REPLACE THIS with comma separated list of contributors--->]
+editors: [<!---REPLACE THIS with comma separated list of editors (to be filled in by an editor)--->]
 page_id: <!---REPLACE THIS with a shortened page name. The shortened page name should be in lowercase and separated by underscore(s) if needed. For example, page_id of structural bioinformatics will be struct_bioinfo
 related_pages: 
   Your_tasks: [<!---REPLACE THIS with the page ID of the your_tasks pages that you want to list here as related pages--->]
@@ -43,3 +44,12 @@ For detailing the domain-specific challenges of a problem that is generic, pleas
 <!--- Add more sections as needed, with the same subsections as above. --->
 ...
 
+<!--- IF APPLICABLE
+## Bibliography 
+
+{% bibliography --cited %}
+
+
+More info on how to use a bibliography can be found in our style guide: https://rdmkit.elixir-europe.org/style_guide#bibliography
+--->
+

pages/your_domain/virology.md

@@ -2,6 +2,7 @@
 title: Virology
 description: Data management solutions for virology data.
 contributors: [Niels Geudens, Flora D'Anna, Romain David, Philippe Lieutaud]
+editors: [Gil Poiares-Oliveira, Federico Bianchini, Flora D'Anna, Bert Droesbeke]
 page_id: virology
 related_pages: 
   Your_tasks: [data_brokering, gdpr_compliance, ethics, compliance, sensitive, data_security, data_discoverability, identifiers]

pages/your_role/TEMPLATE_your_role.md

@@ -3,6 +3,7 @@ title: <Your persona>
 search_exclude: true
 description: <!---REPLACE THIS with a one sentence description of the page--->
 contributors: [<!---REPLACE THIS with comma separated list of contributors--->]
+editors: [<!---REPLACE THIS with comma separated list of editors (to be filled in by an editor)--->]
 page_id: <!---REPLACE THIS with a shortened page name. The shortened page name should be in lowercase and separated by underscore(s) if needed. For example, page_id of structural bioinformatics will be struct_bioinfo
 related_pages: 
   Your_tasks: [<!---REPLACE THIS with the page ID of the your_tasks pages that you want to list here as related pages--->]

pages/your_tasks/TEMPLATE_your_tasks.md

@@ -3,6 +3,7 @@ title: Global problem title (e.g. metadata management)
 search_exclude: true
 description: <!---REPLACE THIS with a one sentence description of the page--->
 contributors: [<!---REPLACE THIS with comma separated list of contributors--->]
+editors: [<!---REPLACE THIS with comma separated list of editors (to be filled in by an editor)--->]
 page_id: <!---REPLACE THIS with a shortened page name. The shortened page name should be in lowercase and separated by underscore(s) if needed. For example, page_id of structural bioinformatics will be struct_bioinfo --->
 related_pages: 
   Tool_assembly: [<!---REPLACE THIS with the page ID of the tool_assembly pages that you want to list here as related pages--->]
@@ -47,3 +48,11 @@ Same as above
 ### Solutions <!-- do not delete this heading and write your text below it -->
 Same as above
 
+<!--- IF APPLICABLE
+## Bibliography 
+
+{% bibliography --cited %}
+
+
+More info on how to use a bibliography can be found in our style guide: https://rdmkit.elixir-europe.org/style_guide#bibliography
+--->