elixir-toolkit-theme 1.7.0 → 1.8.0

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Files changed (15) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +82 -24
  3. data/_includes/affiliation-tiles-selection.html +2 -2
  4. data/_includes/more-information-tiles.html +24 -8
  5. data/_includes/pageids-overview.html +3 -3
  6. data/_includes/sidebar.html +12 -14
  7. data/_includes/topnav.html +1 -1
  8. data/assets/css/main.scss +9 -5
  9. data/assets/img/{dsw-compact.svg → dsw_compact_logo.svg} +0 -0
  10. data/assets/img/{fairplus.svg → fairplus_compact_logo.svg} +0 -0
  11. data/assets/img/{FAIRsharing-small.svg → fairsharing_compact_logo.svg} +0 -0
  12. data/assets/img/rdmkit_compact_logo.svg +1 -0
  13. data/assets/js/main.js +1 -1
  14. metadata +6 -6
  15. data/assets/img/bio.tools.svg +0 -76
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data/README.md CHANGED
@@ -1,41 +1,62 @@
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- [![Gem Version](https://badge.fury.io/rb/elixir-toolkit-theme.svg)](https://badge.fury.io/rb/elixir-toolkit-theme)
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+ [![Gem Version](https://badge.fury.io/rb/elixir-toolkit-theme.svg)](https://badge.fury.io/rb/elixir-toolkit-theme) [![Jekyll site CI](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/actions/workflows/jekyll.yml/badge.svg)](https://github.com/ELIXIR-Belgium/elixir-toolkit-theme/actions/workflows/jekyll.yml)
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- # ELIXIR toolkit theme
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+ <p align="center">
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+ <img src="assets/img/main_logo.svg" width="100" float="center"/>
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+ <h1 align="center">ELIXIR toolkit theme </h1>
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+ </p>
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- This repository is used to build a flexible Jekyll theme using bootstrap 5 as CSS framework.
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+ 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.
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- ## Used packages:
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+ Its key features:
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+ - Easy deployment using GitHub pages
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+ - Advanced content search
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+ - Create your own look with the many theme variables
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+ - Change style using custom classes
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+ - Support for a central tools table
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+ - Page tagging and listing of those tagged pages
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+ - Linking to ELIXIR resources including Bio.tools, FAIRSHARING, FAIR Cookbook, TeSS and DSW
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+ - Easy side navigation, top navigation and footer management
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+ - Mobile friendly
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+ - Create website sections with each section having its own sidebar
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+ - Out of the box search engine optimizations including schema.org attributes and many other matadata attributes
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+ - Support for Google Analytics and Plausible
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- - [Bootstrap5](https://github.com/twbs/bootstrap)
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- - [DataTables](https://datatables.net/examples/styling/bootstrap5.html)
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- - [AnchorJS](https://www.bryanbraun.com/anchorjs/)
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- - [lunr.js](https://lunrjs.com/)
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- - [jQuery](https://jquery.com/)
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- - [jekyll-table-of-contents](https://github.com/ghiculescu/jekyll-table-of-contents)
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- - [jQuery Navgoco Menus](https://github.com/tefra/navgoco)
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+ ## Installation
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+ ### via GitHub Pages remote theme
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- ## Using Jekyll
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+ The quickiest way to use Just The Docs is to use GitHub pages [remote theme](https://blog.github.com/2017-11-29-use-any-theme-with-github-pages/) feature in your `config.yml` file:
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- The website is build on GitHub using Jekyll, a simple, static site generator based on ruby. When you have a local copy cloned onto your computer, it is possible to generate the website based on this repo. This makes it possible to preview changes live, every time you save a file from within the GitHub jekyll-bootstrap-theme repo. Follow these steps to deploy the website based on your local clone (copy) of the jekyll-bootstrap-theme repo:
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-
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- Make sure you have cloned the jekyll-bootstrap-theme repo:
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+ ```yaml
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+ remote_theme: ELIXIR-Belgium/elixir-toolkit-theme
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+ ```
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+ ### via RubyGems:
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- git clone git@github.com:USERNAME/jekyll-bootstrap-theme.git
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- cd jekyll-bootstrap-theme
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+ Alternatively you can install it as a Ruby Gem (preferred way if you use GitLab).
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+ Add this line to your Jekyll site's Gemfile:
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- To run the website locally, you can either use [Docker](https://www.docker.com/) or use Jekyll directly after installing various dependencies.
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+ ```ruby
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+ gem "elixir-toolkit-theme"
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+ ```
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- ### Run using Docker
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+ And add this line to your Jekyll site's `_config.yml`:
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- If not already installed on your machine, install Docker. From the root of the ``jekyll-bootstrap-theme`` directory, run:
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+ ```yaml
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+ theme: elixir-toolkit-theme
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  ```
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- docker run -it --rm -p 4000:4000 -v $PWD:/srv/jekyll jekyll/jekyll:latest /bin/bash -c "chmod a+w /srv/jekyll/Gemfile.lock && chmod 777 /srv/jekyll && jekyll serve -w"
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- ```
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- This will start the docker container and serve the website locally.
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- ### Run using Jekyll directly
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+ ## Usage
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+
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+ [View the documentation](https://elixir-belgium.github.io/elixir-toolkit-theme/) for usage information.
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+
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+ ## Deployment
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+
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+ ### Using GitHub pages
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+
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+ This theme can be used to deploy the website using GitHub pages. Visit the [GitHub documentation](https://docs.github.com/en/pages/setting-up-a-github-pages-site-with-jekyll/) to find out more about how to setup GitHub pages.
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+
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+ ### Locally using Jekyll
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  1. If not already present on your machine, install ruby. Note that incompatibility issues may arise with ruby 3.0.0 (released 25.12.20) or newer versions.
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@@ -64,3 +85,40 @@ If you have never installed or run a Jekyll site locally on your computer, follo
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  Additional information can be found at the following link: [https://docs.github.com/en/free-pro-team@latest/github/working-with-github-pages/testing-your-github-pages-site-locally-with-jekyll](https://docs.github.com/en/free-pro-team@latest/github/working-with-github-pages/testing-your-github-pages-site-locally-with-jekyll)
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+
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+ ### Using Docker
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+
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+ If not already installed on your machine, install Docker. From the root of the `elixir-toolkit-theme` directory, run:
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+
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+ ```
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+ docker run -it --rm -p [::1]:4000:4000 -v $PWD:/srv/jekyll jekyll/jekyll:latest /bin/bash -c "chmod a+w /srv/jekyll/Gemfile.lock && chmod 777 /srv/jekyll && bundle install && bundle exec jekyll serve --host 0.0.0.0"
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+ ```
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+
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+ This will start the docker container and serve the website locally. Make sure the `.\_site` is not yet created to avoid permission errors.
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+
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+ ## This theme is known to be used in:
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+
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+ - [RDMkit](https://rdmkit.elixir-europe.org/)
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+ - [RDMGuide](https://rdm.elixir-belgium.org/)
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+ - [Infectious Diseases Toolkit](https://www.infectious-diseases-toolkit.org/)
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+ - [Applied Bioinformatics and Biostatistics intranet page](https://intranet.psb.ugent.be/abb/)
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+
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+
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+ ## Used packages
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+
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+ This theme would not be possible without following open source projects:
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+
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+ - [Bootstrap5](https://github.com/twbs/bootstrap) - As main CSS framework
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+ - [DataTables](https://github.com/DataTables/DataTablesSrc) - To generate tables that are sortable, searchable and contain pagination
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+ - [AnchorJS](https://github.com/bryanbraun/anchorjs) - Adds deep anchor links to the headings
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+ - [lunr.js](https://github.com/olivernn/lunr.js) - Main tool behind the search bar enabling content search
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+ - [jQuery](https://github.com/jquery/jquery) - A fast, small, and feature-rich JavaScript library for easy scripting
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+ - [jekyll-table-of-contents](https://github.com/ghiculescu/jekyll-table-of-contents) - Lightweight JS script to render the table of contents
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+ - [jQuery Navgoco Menus](https://github.com/tefra/navgoco) - Multi-level slide navigation with accordion effect
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+ - [Font-Awesome](https://github.com/FortAwesome/Font-Awesome) - The famous icon library
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+ - [flag-icons](https://github.com/lipis/flag-icons) - A curated collection of all country flags in SVG + css integration
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+
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+ ## License
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+
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+ The theme is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
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+
data/_includes/affiliation-tiles-selection.html CHANGED
@@ -1,12 +1,12 @@
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  {%- assign alllogos = site.data.affiliations %}
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- <div class="row row-cols-2 row-cols-sm-3 row-cols-md-4 g-5 my-3">
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+ <div class="affiliation-tiles row row-cols-2 row-cols-sm-3 row-cols-md-4 g-5 my-3">
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  {%- assign filtered_logos = alllogos | where: "type", include.type %}
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  {%- for affiliation in filtered_logos %}
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  {%- if affiliation.image_url and affiliation.expose == true %}
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  <div class="col">
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  <div class="card h-100 border-0">
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  <div class="my-auto">
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- {% if affiliation.url %}<a href="{{ affiliation.url }}">{% endif %}<img class="card-img-top" src="{{ affiliation.image_url | relative_url }}" alt="{{ affiliation.name }}">{%- if affiliation.url %}</a>{% endif %}
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+ {% if affiliation.url %}<a href="{{ affiliation.url }}">{% endif %}<img class="rounded" src="{{ affiliation.image_url | relative_url }}" alt="{{ affiliation.name }}">{%- if affiliation.url %}</a>{% endif %}
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  </div>
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  </div>
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  </div>
data/_includes/more-information-tiles.html CHANGED
@@ -1,4 +1,4 @@
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- {%- if page.faircookbook or page.fairsharing or page.training or page.dsw %}
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+ {%- if page.faircookbook or page.fairsharing or page.training or page.dsw or page.rdmkit %}
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  <!-- More information -->
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  <h2>More information</h2>
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@@ -16,7 +16,7 @@
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  <div class="row g-1">
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  <div class="col-2 d-flex align-items-center justify-content-center">
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  {%- if training.registry == "TeSS" %}
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- <img alt="TeSS logo" class="img-fluid h-40px" src="assets/img/tess_logo.svg">
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+ <img alt="TeSS logo" class="img-fluid" src="assets/img/tess_logo.svg">
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  {%- else %}
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  <i class="fas fa-external-link-alt text-primary fs-5"></i>
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  {%- endif %}
@@ -33,7 +33,7 @@
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  </div>
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  </div>
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  {%- endif %}
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- {%- if page.faircookbook or page.fairsharing or page.dsw %}
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+ {%- if page.faircookbook or page.fairsharing or page.dsw or page.RDMkit%}
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  <!-- FAIR Cookbook and FAIRsharing -->
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  <div class="col">
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  <div class="card h-100 info-card">
@@ -46,7 +46,7 @@
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  <a class="btn bg-white hover-primary text-start" data-bs-toggle="tooltip" data-bs-placement="right" title="FAIRCookbook" href="{{ recipe.url }}">
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  <div class="row g-1">
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  <div class="col-2 d-flex align-items-center justify-content-center">
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- <img alt="FAIRCookbook logo" class="img-fluid h-40px" src="assets/img/fairplus.svg">
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+ <img alt="FAIRCookbook logo" class="img-fluid" src="assets/img/fairplus_compact_logo.svg">
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  </div>
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  <div class="col-10 d-flex align-items-center">
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  <span class="text-start">Step-by-step process for: {{recipe.name}}</span>
@@ -62,7 +62,7 @@
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  <a class="btn bg-white hover-primary text-start" data-bs-toggle="tooltip" data-bs-placement="right" title="DSW" href="{{ site.dsw_deep_link_prefix | append: question.uuid }}">
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  <div class="row g-1">
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  <div class="col-2 d-flex align-items-center justify-content-center">
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- <img alt="DSW logo" class="img-fluid h-40px" src="assets/img/dsw-compact.svg">
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+ <img alt="DSW logo" class="img-fluid" src="assets/img/dsw_compact_logo.svg">
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  </div>
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  <div class="col-10 d-flex align-items-center">
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  <span class="text-start">Support for DMP on: {{question.name}}</span>
@@ -75,13 +75,29 @@
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  {%- if page.fairsharing %}
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  {%- for standard in page.fairsharing %}
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  <li class="d-grid">
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- <a class="btn bg-white hover-primary text-start" data-bs-toggle="tooltip" data-bs-placement="right" title="FAIRsharing" href="{{ standard.fairsharing }}">
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+ <a class="btn bg-white hover-primary text-start" data-bs-toggle="tooltip" data-bs-placement="right" title="FAIRsharing" href="{{ standard.url }}">
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  <div class="row g-1">
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  <div class="col-2 d-flex align-items-center justify-content-center">
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- <img alt="fairsharing logo" class="img-fluid h-40px" src="assets/img/FAIRsharing-small.svg">
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+ <img alt="FAIRsharing logo" class="img-fluid" src="assets/img/fairsharing_compact_logo.svg">
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  </div>
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  <div class="col-10 d-flex align-items-center">
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- <span class="text-start">FAIRsharing collection about: {{standard.title}}</span>
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+ <span class="text-start">FAIRsharing collection about: {{standard.name}}</span>
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+ </div>
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+ </div>
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+ </a>
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+ </li>
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+ {%- endfor %}
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+ {%- endif %}
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+ {%- if page.rdmkit %}
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+ {%- for rdmdoc in page.rdmkit %}
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+ <li class="d-grid">
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+ <a class="btn bg-white hover-primary text-start" data-bs-toggle="tooltip" data-bs-placement="right" title="RDMkit" href="{{ rdmdoc.url }}">
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+ <div class="row g-1">
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+ <div class="col-2 d-flex align-items-center justify-content-center">
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+ <img alt="RDMkit logo" class="img-fluid" src="assets/img/rdmkit_compact_logo.svg">
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+ </div>
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+ <div class="col-10 d-flex align-items-center">
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+ <span class="text-start">Data management guidelines on: {{rdmdoc.name}}</span>
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  </div>
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  </div>
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  </a>
data/_includes/pageids-overview.html CHANGED
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  <th>title</th>
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  <th>page_id</th>
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  <th>description</th>
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+ <th>url</th>
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  </tr>
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  </thead>
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  <tbody>
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  <tr>
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  <td><a href="{{ section_page.url | relative_url }}">{{section_page.title}}</a></td>
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  <td>{{section_page.page_id}}</td>
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- {%- if section_page.description %}
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- <td>{{section_page.description}}</td>
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- {%- endif %}
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+ <td>{{section_page.description | default: "no description"}}</td>
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+ <td>{{section_page.url}}</td>
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  </tr>
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  {%- endif %}
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  {%- endfor %}
data/_includes/sidebar.html CHANGED
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  {{ page.sidebar | capitalize | replace: "_", " " }} menu <i title="navbar-toggler" class="fa fa-bars ms-2"></i>
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  </button>
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  <nav class="collapse" id="side-nav" aria-label="Side navigation">
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- <ul id="menu" class="list-unstyled mb-4 mb-lg-0">
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- {%- if sidebar.title or sidebar.version %}
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- {%- if sidebar.title_url and page.url == sidebar.title_url %}
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- <li class="sidebar-title active">
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- {%- else %}
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- <li class="sidebar-title">
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- {%- endif %}
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- {%- if sidebar.title_url %}
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- <a class="btn active hover-primary text-start d-block mb-1" href="{{ sidebar.title_url | relative_url }}">{{sidebar.title}} {{sidebar.version}}</a>
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- {%- else %}
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- <a class="btn active hover-primary text-start d-block mb-1 disabled" aria-disabled="true">{{sidebar.title}} {{sidebar.version}}</a>
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- {%- endif %}
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- </li>
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- {%- endif %}
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+ {%- if sidebar.title or sidebar.version %}
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+ {%- if sidebar.title_url %}
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+ {%- if page.url == sidebar.title_url %}
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+ <a class="btn hover-primary text-start d-block mb-1 sidebar-title active" href="{{ sidebar.title_url | relative_url }}">{{sidebar.title}} {{sidebar.version}}</a>
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+ {%- else %}
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+ <a class="btn hover-primary text-start d-block mb-1 sidebar-title" href="{{ sidebar.title_url | relative_url }}">{{sidebar.title}} {{sidebar.version}}</a>
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+ {%- endif %}
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+ {%- else %}
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+ <a class="btn text-start d-block mb-1 sidebar-title disabled" aria-disabled="true">{{sidebar.title}} {{sidebar.version}}</a>
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+ {%- endif %}
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+ {%- endif %}
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+ <ul class="list-unstyled mb-4 mb-lg-0">
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  {%- for folder in sidebar.subitems %}
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  {%- if page.url == folder.url %}
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  <li class="active{%- if folder.hr %} mt-3{% endif %}">
data/_includes/topnav.html CHANGED
@@ -4,7 +4,7 @@
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  <a class="visually-hidden-focusable" href='#footer'>Skip to footer</a>
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  <nav class="navbar navbar-expand-lg mb-3 mb-lg-5">
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  <div class="container">
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- <a class="navbar-brand" href="{{ 'index.html' | relative_url }}"><img class="me-3 img-fluid" alt="{{site.title}} logo" src="{{ 'assets/img/main_logo.svg' | relative_url }}">{% if site.topnav_title %}<span>{{site.topnav_title}}</span>{% endif %}</a>
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+ <a class="navbar-brand" href="{{ 'index.html' | relative_url }}"><img class="me-3 img-fluid" alt="{{site.title}} logo" src="{{ 'assets/img/main_logo.svg' | relative_url }}">{% if site.topnav_title %}<span class="me-3">{{site.topnav_title}}</span>{% endif %}</a>
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  <button class="navbar-toggler text-primary" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation">
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  <i title="navbar-toggler" class="fa fa-bars"></i>
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  </button>
data/assets/css/main.scss CHANGED
@@ -44,6 +44,10 @@ main {
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  a:not(.btn):hover {
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  text-decoration: underline;
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+ overflow-wrap: break-word;
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+ word-wrap: break-word;
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+ -ms-word-break: break-all;
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+ word-break: break-word;
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  }
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  ol li,
@@ -271,7 +275,7 @@ header .navbar {
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  background-color: $sidebar-bg-active;
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  }
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- ul#menu {
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+ #side-nav>ul {
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  > li:not(.sidebar-title) > a {
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  background-color: $sidebar-bg;
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  color: $sidebar-color;
@@ -571,10 +575,6 @@ footer {
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575
 
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  /*-----Size components-----*/
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- .h-40px {
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- height: 40px;
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- }
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-
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  .h-24px {
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  height: 24px;
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  }
@@ -630,6 +630,10 @@ li.past_event,
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  color: $white !important;
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  }
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  }
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+ img {
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+ height: 40px;
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+ max-width: 45px;
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+ }
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  }
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  /*-----Country flags-----*/
data/assets/img/rdmkit_compact_logo.svg ADDED
@@ -0,0 +1 @@
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data/assets/js/main.js CHANGED
@@ -31,7 +31,7 @@ $(document).ready(function external_new_window() {
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  */
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  $(document).ready(function () {
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  // Initialize navgoco with default options
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- $("#menu").navgoco({
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+ $("#side-nav>ul").navgoco({
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  caretHtml: '',
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  accordion: true,
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  openClass: 'active', // open
metadata CHANGED
@@ -1,14 +1,14 @@
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1
  --- !ruby/object:Gem::Specification
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2
  name: elixir-toolkit-theme
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3
  version: !ruby/object:Gem::Version
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- version: 1.7.0
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+ version: 1.8.0
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5
  platform: ruby
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  authors:
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7
  - bedroesb
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8
  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2022-03-08 00:00:00.000000000 Z
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+ date: 2022-03-16 00:00:00.000000000 Z
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12
  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: jekyll
@@ -440,15 +440,14 @@ files:
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  - assets/flags/za.svg
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  - assets/flags/zm.svg
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  - assets/flags/zw.svg
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- - assets/img/FAIRsharing-small.svg
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  - assets/img/Flag_of_Europe.svg
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  - assets/img/android-chrome-192x192.png
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  - assets/img/android-chrome-512x512.png
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  - assets/img/apple-touch-icon.png
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- - assets/img/bio.tools.svg
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- - assets/img/dsw-compact.svg
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+ - assets/img/dsw_compact_logo.svg
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  - assets/img/elixir_logo.svg
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- - assets/img/fairplus.svg
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+ - assets/img/fairplus_compact_logo.svg
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+ - assets/img/fairsharing_compact_logo.svg
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  - assets/img/favicon-16x16.png
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  - assets/img/favicon-32x32.png
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  - assets/img/favicon.ico
@@ -456,6 +455,7 @@ files:
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  - assets/img/jekyll_theme_question_inverted.svg
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  - assets/img/main_logo.svg
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  - assets/img/main_logo_condesed.svg
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+ - assets/img/rdmkit_compact_logo.svg
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  - assets/img/safari-pinned-tab.svg
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  - assets/img/site.webmanifest
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  - assets/img/tess_logo.svg
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