Merge branch 'main' into elixir-lesson-template

Gemfile

@@ -2,4 +2,5 @@ source "https://rubygems.org"
 
 group :jekyll_plugins do
     gem "github-pages"
-  end
+    gem "jekyll-glossary_tooltip", "~> 1.5"
+end

_config.yml

@@ -68,4 +68,5 @@ plugins:
   - jemoji
   - jekyll-sitemap
   - jekyll-github-metadata
+  - jekyll-glossary_tooltip
   - webrick

_data/glossary.yml

@@ -0,0 +1,11 @@
+- term: SPLASH
+  definition: Backronym for SPLASH (to be defined)
+  url: https://elixir-europe-training.github.io/ELIXIR-Training-SPLASH/about
+- term: TODO
+  definition: Work to be done
+- term: PR
+  definition: Pull Request
+  url: https://docs.github.com/en/pull-requests/collaborating-with-pull-requests/proposing-changes-to-your-work-with-pull-requests/about-pull-requests
+- term: URL
+  definition: Uniform Resource Locator
+  url: https://en.wikipedia.org/wiki/URL

_data/sidebars/resources.yml

@@ -1,10 +1,8 @@
 title: Resources
 title_url: /resources
 subitems:
-  - title: TEMPLATE
-    url: /TEMPLATE_resource_page
   - title: TeSS
-    url: /tess
+    url: /TeSS
   - title: Tango
     url: /tango
   - title: Train-the-Trainer
@@ -15,3 +13,5 @@ subitems:
     url: /learning-paths
   - title: ELIXIR lesson template
     url: /elixir-lesson-template
+  - title: E-learning
+    url: /elearning

_includes/index/roles-and-resources.html

@@ -1,32 +1,17 @@
-<div class="col-12">
-    <h2>Resources</h2>
-</div>
-<div class="container py-3 mb-5 bg-red rounded text-white">
-    <div class="row">
-        <div class="col">
-            <a href="tess" style="color: white;">
-                <div><img src="assets/img/path323.svg" width="20px" style="margin-right: 10px;">TeSS</div>
-            </a> 
-        </div>
-        <div class="col">
-            <a href="train-the-trainer" style="color: white;">
-                <div><img src="assets/img/path323.svg" width="20px" style="margin-right: 10px;">Train-the-Trainer</div>
-            </a>
-        </div>
-        <div class="col">
-            <a href="tango" style="color: white;">
-                <div><img src="assets/img/path323.svg" width="20px" style="margin-right: 10px;">Tango</div>
-            </a>
-        </div>
-        <div class="col">
-            <a href="fair-training-handbook" style="color: white;">
-                <div><img src="assets/img/path323.svg" width="20px" style="margin-right: 10px;">FAIR Training Handbook</div>
-            </a>
-        </div>
-        <div class="col">
-            <a href="learning-paths" style="color: white;">
-                <div><img src="assets/img/path323.svg" width="20px" style="margin-right: 10px;">Learning Paths</div>
-            </a>
-        </div>
-    </div>
+<div class="row text-white mt-5">
+    <a class="col mx-1 py-3 mb-5 rounded text-center btn btn-primary" href="tess">
+        <div>TeSS</div>
+    </a> 
+    <a class="col mx-1 py-3 mb-5 rounded text-center btn btn-primary" href="train-the-trainer" style="color: white;">
+        <div>Train-the-Trainer</div>
+    </a>
+    <a class="col mx-1 py-3 mb-5 rounded text-center btn btn-primary" href="tango" style="color: white;">
+        <div>Tango</div>
+    </a>
+    <a class="col mx-1 py-3 mb-5 rounded text-center btn btn-primary" href="fair-training-handbook" style="color: white;">
+        <div>FAIR Training Handbook</div>
+    </a>
+    <a class="col mx-1 py-3 mb-5 rounded text-center btn btn-primary" href="learning-paths" style="color: white;">
+        <div>Learning Paths</div>
+    </a>
 </div>

_layouts/resource_page.html

@@ -48,11 +48,15 @@ <h2>Description</h2>
         <h2>What can you do with {{ page.title }}</h2>
         {{ page.objective | markdownify }}
 
-        <h2>Our mission</h2>
-        {{ page.mission | markdownify }}
+        {%- unless page.mission == nil or page.mission == false %}
+            <h2>Our mission</h2>
+            {{ page.mission | markdownify }}
+        {% endunless %}
 
-        <h2>Benefit</h2>
-        {{ page.benefit | markdownify }}
+        {%- unless page.benefit == nil or page.benefit == false %}
+            <h2>Benefit</h2>
+            {{ page.benefit | markdownify }}
+        {% endunless %}
 
         <!-- BLOCK 2 -->
         {%- unless page.licenses == nil or page.licenses == false %}

pages/contribute/editorial_board_guide.md

@@ -23,27 +23,27 @@ These markdown files are divided over subdirectories (your_role, your_tools, you
 
 ### GitHub checks
 
-With each PR or merge to the master, some checks are done using GitHub actions. One of them checks wether the website builds correctly. The other checks for changes in the tool/resource Excel table. When each of them fails, the PR will not be able to be merged. Click on the red dot/failed check to understand better what caused the fail. 
+With each {% glossary PR %} or merge to the master, some checks are done using GitHub actions. One of them checks wether the website builds correctly. The other checks for changes in the tool/resource Excel table. When each of them fails, the {% glossary PR %} will not be able to be merged. Click on the red dot/failed check to understand better what caused the fail. 
 
 ## Label, discuss and assign issues
 
   * Check open issues regularly or enable notifications by clicking the "WATCH" icon in the top-right side of the [GitHub repository](https://github.com/elixir-europe-training/ELIXIR-Training-SPLASH/issues).
   * Assign labels to issues.
   * Discuss who is going to be responsible for each issue with other editors and reviewers (via issue comments or other communication channels).
   * Assign at least one editor/reviewer to the issue, who will discuss the possible content with the contributor.
-  * When a Pull Request (PR) or a draft PR related to an issue is created, link the PR to the issue.
+  * When a Pull Request ({% glossary PR %}) or a draft {% glossary PR %} related to an issue is created, link the {% glossary PR %} to the issue.
 
 More information about these topics can be found in the GitHub documentation:
-- [commenting on PRs](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/commenting-on-a-pull-request)
+- [commenting on {% glossary PR %}s](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/commenting-on-a-pull-request)
 - [start a review](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/reviewing-proposed-changes-in-a-pull-request)
 
 ## Review pull requests
 
-If contributors make a pull request to make changes, by default the editors that are responsible for files that will be changed by the PR will be assigned and notified. All PR should be assigned to one of the editors. Before merging a PR, pages' tags, and tools and resources' tags should be checked and assigned according to the established tagging system. The editor who provides the last approval to a PR should also merge it.
+If contributors make a pull request to make changes, by default the editors that are responsible for files that will be changed by the {% glossary PR %} will be assigned and notified. All {% glossary PR %} should be assigned to one of the editors. Before merging a {% glossary PR %}, pages' tags, and tools and resources' tags should be checked and assigned according to the established tagging system. The editor who provides the last approval to a {% glossary PR %} should also merge it.
 
 ## Link a pull request to an issue
 
-When you make a pull request resolving an issue, it is possible to link this pull request to that specific issue. This can be easily done by writing in the conversation of the PR: `closes #number_of_issue`, or `fixes #number_of_issue` or even `resolves #number_of_issue`. This is definitely applicable when authors first open an issue announcing a change or requesting a new page, followed up by the pull request. 
+When you make a pull request resolving an issue, it is possible to link this pull request to that specific issue. This can be easily done by writing in the conversation of the {% glossary PR %}: `closes #number_of_issue`, or `fixes #number_of_issue` or even `resolves #number_of_issue`. This is definitely applicable when authors first open an issue announcing a change or requesting a new page, followed up by the pull request. 
 For more information about this topic please visit the [GitHub documentation page](https://docs.github.com/en/free-pro-team@latest/github/managing-your-work-on-github/linking-a-pull-request-to-an-issue).
 
 ## Create a new page
@@ -93,12 +93,12 @@ By default your page will not be linked in the sidebar on the website, or on the
 
 Make sure all pages are accessible from the navigation sidebar. Please, avoid generating sub-pages that are not directly accessible from the navigation sidebar.
 
-This website supports multiple sidebars, the one in the main sections of the website is for example different from the one in the contribute section. Both of them are defined by `.yaml` files in the *_data/sidebars* directory. Changing these yaml file will immediately impact the sidebars and the frontpage of the website. The sidebar supports multiple levels and each level in the hierarchy can contain a URL to a page within this website or an external URL.
+This website supports multiple sidebars, the one in the main sections of the website is for example different from the one in the contribute section. Both of them are defined by `.yaml` files in the *_data/sidebars* directory. Changing these yaml file will immediately impact the sidebars and the frontpage of the website. The sidebar supports multiple levels and each level in the hierarchy can contain a {% glossary URL %} to a page within this website or an external {% glossary URL %}.
 
 The attributes that define the structure are:
 - `title`: This is the text that will show up in the sidebar.
-- `url`: The URL to the internal page you want to link to. This is mostly in the form of: */markdown_file_name.html*.
-- `external_url`: Use this instead of URL if you want to link to an external page.
+- `url`: The {% glossary URL %} to the internal page you want to link to. This is mostly in the form of: */markdown_file_name.html*.
+- `external_url`: Use this instead of {% glossary URL %} if you want to link to an external page.
 - `subitems`: to define a sublevel.
 
 ```yaml
@@ -164,7 +164,7 @@ The logos can be added to the [/images/institutions](https://github.com/elixir-e
 {% include callout.html type="important" content="Upload vector images (.svg filetype) of the institute logo for better quality, scaleability and file size, if possible." %}
 
 
-TODO:
+{% glossary TODO %}:
 
 ## Related pages
 

pages/contribute/editors_checklist.md

@@ -1,12 +1,12 @@
 ---
 title: Editors checklist
-summary: Checklist for editors before approving and merging a pull request (PR).
+summary: Checklist for editors before approving and merging a pull request ({% glossary PR %}).
 ---
 
-## Before approving and merging a pull request (PR), the editors must check that
+## Before approving and merging a pull request ({% glossary PR %}), the editors must check that
 1. The page layout in preview looks correct.
-2. The new page is linked in the appropriate [sidebar](https://github.com/elixir-europe-training/ELIXIR-Training-SPLASH/tree/master/_data/sidebars) menu, in the same branch of the PR.
-3. The contributors' names are listed in the [CONTRIBUTORS file](https://github.com/elixir-europe-training/ELIXIR-Training-SPLASH/blob/master/_data/CONTRIBUTORS.yaml), in the same branch of the PR. Advice to have at least one  contributor per page having its contact information in this  [CONTRIBUTORS file](https://github.com/elixir-europe-training/ELIXIR-Training-SPLASH/blob/master/_data/CONTRIBUTORS.yaml).
+2. The new page is linked in the appropriate [sidebar](https://github.com/elixir-europe-training/ELIXIR-Training-SPLASH/tree/master/_data/sidebars) menu, in the same branch of the {% glossary PR %}.
+3. The contributors' names are listed in the [CONTRIBUTORS file](https://github.com/elixir-europe-training/ELIXIR-Training-SPLASH/blob/master/_data/CONTRIBUTORS.yaml), in the same branch of the {% glossary PR %}. Advice to have at least one  contributor per page having its contact information in this  [CONTRIBUTORS file](https://github.com/elixir-europe-training/ELIXIR-Training-SPLASH/blob/master/_data/CONTRIBUTORS.yaml).
 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`
@@ -21,4 +21,4 @@ summary: Checklist for editors before approving and merging a pull request (PR).
 6. There are no [copyright](copyright) issues related to the content of the page.
 7. The contributors implemented the requested changes.
 8. The contributors are thanked for their effort and informed about the publication of their content.
-9. The PR is linked to related issues and can be merged in main branch with no conflicts.
+9. The {% glossary PR %} is linked to related issues and can be merged in main branch with no conflicts.

pages/contribute/github_way.md

@@ -28,7 +28,7 @@ This guide tells you how you can easily request and edit a page on this website.
 1. When you are happy with your first draft of the content, go to the “Propose changes” section at the end of the page and write a title and a brief explanation of your changes.
 1. Click on “Propose changes”.
    {% include image.html file="propose_changes_github.png" inline=true alt="Propose changes on GitHub" %}
-1. You are now redirected to the Pull Request (PR) page. A "pull request" is a request to "pull" your changes into the website. Click on the "Create Pull Request" green button. Here you can choose to:
+1. You are now redirected to the Pull Request ({% glossary PR %}) page. A "pull request" is a request to "pull" your changes into the website. Click on the "Create Pull Request" green button. Here you can choose to:
      * "Create draft pull request": choose this if you have not finished writing. Later on you can always click on "Ready for review" to switch to a normal pull request. You can find more information about draft pull requests in the [GitHub documentation](https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/about-pull-requests#draft-pull-requests).
      * "Create pull request": choose this if you have finished your text. Editors will then review your request.
        {% include image.html file="draft_pullrequest_github.png" inline=true alt="PrDraft pull request on GitHub" %}

pages/contribute/preview_changes.md

@@ -51,9 +51,9 @@ This step is important. Make sure to commit to a new feature branch which you na
 {% include image.html file="deploy_using_gh_actions.png" alt="Got to the settings tab in your repo to enable GitHub pages" %}
 
 
-## Open a Pull Request (PR) with you changes
+## Open a Pull Request ({% glossary PR %}) with you changes
 
-Got to your newly created branch and click 'Contribute'. This will create a PR to the main repository.
+Got to your newly created branch and click 'Contribute'. This will create a {% glossary PR %} to the main repository.
 
 {% include image.html file="create_pr_from_fork.png" alt="Create new PR from fork." %}