Merge branch 'main' into main

CONTRIBUTORS.yaml

@@ -51,6 +51,7 @@ awspolly:
 
 # our real contributors <3 (please add yourself in alphabetical order)
 
+
 a-asai:
     name: Atsushi Asai
     email: [email protected]
@@ -86,6 +87,24 @@ abueg:
     orcid: 0000-0002-6879-3954
     joined: 2022-01
 
+adya29:
+    name: Adya Shreya
+    email: [email protected]
+    joined: 2024-12
+    linkedin: adya-shreya
+    location:
+      country: SG
+
+adairama:
+    name: Adaikalavan Ramasamy
+    email: [email protected]
+    orcid: 0000-0002-7598-2892
+    linkedin: adairama
+    joined: 2024-12
+    location:
+      country: SG
+
+
 ahmedhamidawan:
     name: Ahmed Hamid Awan
     email: [email protected]
@@ -612,6 +631,10 @@ davebx:
     name: Dave B.
     joined: 2021-06
 
+davelopez:
+    name: David López
+    joined: 2021-10
+
 dbrites:
     name: Daniela Brites
     joined: 2022-03
@@ -917,6 +940,15 @@ gmauro:
       - uni-freiburg
       - elixir-europe
 
+GokceOGUZ:
+    name: Gokce Oguz
+    joined: 2024-12
+    email: [email protected]
+    orcid: 0000-0003-1044-7204
+    linkedin: gokce-oguz
+    location: 
+      country: SG
+
 guerler:
     name: Aysam Guerler
     joined: 2017-09
@@ -1518,6 +1550,14 @@ marziacremona:
     email: [email protected]
     joined: 2018-02
 
+matuskalas:
+    name: Matúš Kalaš
+    joined: 2024-06
+
+mkuzak:
+    name: Mateusz Kuzak
+    joined: 2019-10
+
 mateeullah905:
     name: Matee Ullah
     email: [email protected]
@@ -1624,7 +1664,7 @@ miaomiaozhou88:
     joined: 2020-12
     orcid: 0000-0003-4426-1758
 
-michelemaroni89:
+michelemaroni:
     name: Michele Maroni
     joined: 2019-07
 
@@ -1773,6 +1813,10 @@ NickSto:
     twitter: NickStoler
     joined: 2018-07
 
+njall:
+    name: Niall Beard
+    joined: 2019-02
+
 nomadscientist:
     name: Wendi Bacon
     email: [email protected]
@@ -1867,6 +1911,10 @@ otatadeabigail:
     name: Otatade Abigail
     joined: 2021-10
 
+OlegZharkov:
+    name: Oleg Zharkov
+    joined: 2021-06
+
 pajanne:
     name: Anne Pajon
     joined: 2017-09
@@ -2356,6 +2404,10 @@ sunyi000:
     email: [email protected]
     joined: 2021-03
 
+Swathi266:
+    name: Swathi Nataraj
+    joined: 2024-12
+
 sylviamahara:
     name: Sylvia Mahara
     github: false
@@ -2512,6 +2564,10 @@ twishigulati:
     github: false
     joined: 2021-11
 
+tuncK:
+    name:  Tunc Kayikcioglu
+    joined: 2023-10
+
 valentinmarcon:
     name: Valentin Marcon
     joined: 2017-09
@@ -2714,3 +2770,11 @@ tbrown91:
 tStehling:
     name: Thorben Stehling
     joined: 2024-11
+
+rmassei:
+    name: Riccardo Massei
+    email: [email protected]
+    orcid: 0000-0003-2104-9519
+    joined: 2024-11
+    affiliations:
+      - nfdi4bioimage

ORGANISATIONS.yaml

@@ -362,3 +362,10 @@ vib:
     avatar: "/training-material/shared/images/logo-vib.png"
     github: false
     ror: "03xrhmk39"
+
+nfdi4bioimage:
+    short_name: NFDI4BIOIMAGE
+    name: NFDI4BIOIMAGE
+    joined: 2024-11
+    url:  https://nfdi4bioimage.de
+    avatar: "/training-material/shared/images/nfdi4bioimage.jpeg"

_config.yml

@@ -242,6 +242,7 @@ icon-tag:
   trophy: fas fa-trophy
   tutorial: fas fa-laptop
   twitter: fab fa-twitter
+  upgrade_workflow: fas fa-recycle
   warning: fas fa-exclamation-triangle
   wf-input: fas fa-chevron-circle-right
   workflow-runtime-toggle: far fa-caret-square-up

_includes/contributor-badge.html

@@ -3,6 +3,11 @@
 {%- else -%}
   {%- assign contributor_badge_entity = site | fetch_contributor: include.id -%}
   {%- assign name = contributor_badge_entity.short_name | default: contributor_badge_entity.name | default: include.id -%}
+  {% if include.small %}
+  <a href="{{ site.baseurl }}/hall-of-fame/{{ include.id }}/" class="contributor-badge contributor-{{ include.id }}">
+    {{ contributor_badge_entity | fetch_entity_avatar:include.id, 36 }}
+  </a>
+  {% else %}
   <a href="{{ site.baseurl }}/hall-of-fame/{{ include.id }}/" class="contributor-badge contributor-{{ include.id }}">
     {%- if contributor_badge_entity.orcid -%}<img src="{% link assets/images/orcid.png %}" alt="orcid logo" width="36" height="36"/>{%- endif -%}
     {{ contributor_badge_entity | fetch_entity_avatar:include.id, 36 }}
@@ -11,4 +16,5 @@
   {%- include _includes/contributor-human-icons.html activity=include.activity -%}
   {%- endif -%}
   </a>
+  {% endif %}
 {%- endif -%}

_includes/contributor-human-icons.html

@@ -8,6 +8,8 @@
 	<abbr title="This person managed and provided infrastructure to the GTN or for training purposes">🖥</abbr>
 {% elsif include.activity == "testing" %}
 	<abbr title="This person tested the tutorial to ensure it works correctly for students, or reported issues with the tutorial.">⚙️</abbr>
+{% elsif include.activity == "reviewing" %}
+	<abbr title="This person reviewed this material for accuracy and correctness">🧐</abbr>
 {% elsif include.activity == "ux" %}
 	<abbr title="This person contributed UX or Design improvements to this tutorial or the GTN as a whole">✨</abbr>
 {% elsif include.activity == "funding" %}

_includes/contributor-list2.html

@@ -80,6 +80,15 @@
 	</tr>
 	{% endif %}
 
+	{% if include.contributors.reviewing %}
+	<tr class="reviewers">
+		<td><abbr title="These people reviewed this material for accuracy and correctness">Reviewers</abbr></td>
+		<td>
+			{% for id in include.contributors.reviewing %}{{ include.sep }}{% if include.badge %}{% include _includes/contributor-badge.html id=id small=true %}{% else %}{{ contributors[id].name | default: id }}{% endif %}{%- endfor -%}
+		</td>
+	</tr>
+	{% endif %}
+
 	{% if include.contributors.ux %}
 	<tr>
 		<td><abbr title="These people contributed UX or Design improvements to this tutorial or the GTN as a whole">UX/Designer(s)</abbr></td>

_includes/contributors-line.html

@@ -1,7 +1,7 @@
 <div markdown="0">
 {% if include.page.contributors %}
 	<div class="contributors-line">
-		{% unless include.authorsonly %}{{ locale['authors'] | default: "Authors" }}: {% endunless %}{% include _includes/contributor-list.html contributors=include.page.contributors badge=true newcontributors=include.newcontributors %}
+		{% include _includes/contributor-list.html contributors=include.page.contributors badge=true newcontributors=include.newcontributors %}
 	</div>
 {% elsif include.page.contributions %}
 	<div class="contributors-line">

_layouts/topic.html

@@ -45,6 +45,20 @@ <h3 style="margin: unset;">Not sure where to start?</h3>
     {% endif %}
 
     <h2 id="material">Material</h2>
+
+    {% if topic.toc %}
+      <p>
+      <blockquote class="agenda">
+      <div class="box-title agenda-title" id="agenda">Jump to a section!</div>
+      <ul class="markdown-toc">
+      {% for subtopic in topic_material %}
+        <li><a href="#st-{{ subtopic[0] | slugify }}">{{subtopic[1].subtopic.title}}</a></li>
+      {% endfor %}
+      </ul>
+      </blockquote>
+      </p>
+    {% endif %}
+
     <i>You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides ({% icon slides %}) and tutorial ({% icon tutorial %}) buttons below. </i>
 
     {% if topic.draft %}

_layouts/workflow-list.html

@@ -4,71 +4,44 @@
 
 {% assign material = site | fetch_tutorial_material:page.topic_name,page.tutorial_name%}
 
-<section class="tutorial">
-    <h1 data-toc-skip>Workflows</h1>
-    <p>These workflows are associated with <a href="../tutorial.html">{{ material.title }}</a></p>
-    <p>To use these workflows in Galaxy you can either click the links to download the workflows, or you can right-click and copy the link to the workflow which can be used in the Galaxy form to import workflows.</p>
-
-
-    <div class="row">
-    {% for workflow in material.workflows %}
-	<div class="col-md-6">
-		<div class="card">
-		<div class="card-body">
-			<h5 class="card-title">{{ workflow.title }}</h5>
-			<h6 class="card-subtitle mb-2 text-muted">
-				{% for entity in workflow.creators %}
-				{{ entity.name }}{% if forloop.last == false %}, {% endif %}
-				{% endfor %}
-			</h6>
-
-			<p class="card-text">
-				<small class="text-muted">Last updated {{ workflow.path | gtn_mod_date | date: "%b %-d, %Y" }}</small>
-			</p>
-			<p class="card-text">
-			<span tabindex="0" role="button" class="workflow show-when-galaxy-proxy-active" data-workflow="{{ workflow.trs_endpoint }}">Launch in Tutorial Mode</span>
-			<a href="{% link faqs/galaxy/tutorial_mode.md %}" class="hide-when-galaxy-proxy-active">{% icon question %}</a>
-			<br/>
-
-
-			License: 
+<section>
+	<h1 data-toc-skip>Workflows</h1>
+	<p>These workflows are associated with <a href="../tutorial.html">{{ material.title }}</a></p>
+
+<table  class="table table-striped">
+	<thead>
+		<tr>
+			<th>Workflow</th>
+
+			<th>Updated</th>
+			<th>Version</th>
+			<th>License</th>
+
+			<th>Tests</th>
+			<th>Reports</th>
+			<th>Comments</th>
+		</tr>
+	</thead>
+	<tbody>
+	{% for workflow in material.workflows %}
+		<tr>
+			<td><a href="{{ workflow.url_html }}">{{ workflow.title }}</a></td>
+
+			<td>{{ workflow.path | gtn_mod_date | date: "%b %-d, %Y" }}</td>
+			<td>{{ workflow.version }}</td>
+			<td>
 				{% if workflow.license %}
 				<a href="https://spdx.org/licenses/{{ workflow.license }}">{{ workflow.license }}</a>
 				{% else %}
-				None Specified, defaults to
 				<a href="https://spdx.org/licenses/CC-BY-4.0">CC-BY-4.0</a>
 				{% endif %}
-				<br/>
-			Tests: {% if workflow.tests %}✅{% else %}❌{% endif %}
-			Results: {% if workflow.test_results == nil %}Not yet automated{% endif %}
-			</p>
-<div class="dropdown">
-  <button class="btn btn-primary dropdown-toggle" type="button" data-toggle="dropdown" aria-expanded="false">
-    Import or Download
-  </button>
-  <div class="dropdown-menu">
-			<a href="{{ site.url }}{{ site.baseurl }}/{{ workflow.path }}" class="dropdown-item">Download Galaxy Workflow.ga</a>
-			{% assign servers = nil | list_usegalaxy_servers_shuffle %}
-			{% for server in servers %}
-			<a href="{{ server.url }}/workflows/trs_import?run_form=true&trs_url={{ workflow.trs_endpoint }}" class="dropdown-item hide-when-galaxy-proxy-active">{{ server.human }}</a>
-			{% endfor %}
-			<a href="https://my.galaxy.training/?path=/workflows/trs_import%3Frun_form=true%26trs_url={{ workflow.trs_endpoint }}"
-			   class="dropdown-item hide-when-galaxy-proxy-active">Import to another server (≥23.0+ only!)</a>
-  </div>
-</div>
-
-	<pre class="mermaid">{{ workflow.mermaid }}
-	</pre>
-		</div><!-- card-body -->
-	</div><!-- card -->
-</div><!-- col -->
-{% endfor %}
-
-</div>
-
-   <h1 style="margin-top:2em">Importing into Galaxy</h1>
-   Below are the instructions for importing these workflows directly into your Galaxy server of choice to start using them!
-
-   {% snippet faqs/galaxy/workflows_import.md box_type="hands_on" %}
-
+			</td>
+
+			<td>{% if workflow.tests %} ✅ {% else %} ❌ {% endif %}</td>
+			<td>{% if workflow.features.report %} ✅ {% else %} ❌ {% endif %}</td>
+			<td>{% if workflow.features.comments %} ✅ {% else %} ❌ {% endif %}</td>
+		</tr>
+	{% endfor %}
+	</tbody>
+</table>
 </section>

_layouts/workflow.html

@@ -120,7 +120,7 @@ <h1 data-toc-skip>{{ workflow.title }}</h1>
 			{% endif %}
 
 			{% if workflow.workflowhub_id %}
-			<a style="margin-bottom: 0.2rem" href="https://workflowhub.eu/workflows/{{ workflow.workflowhub_id }}" class="btn btn-secondary"><img src="{% link assets/images/workflowhub-icon.svg %}" style="height: 32px" alt="Workflowhub cloud with gears logo"/> View on WorkflowHub</a>
+			<a style="margin-bottom: 0.2rem" href="https://dev.workflowhub.eu/workflows/{{ workflow.workflowhub_id }}" class="btn btn-secondary"><img src="{% link assets/images/workflowhub-icon.svg %}" style="height: 32px" alt="Workflowhub cloud with gears logo"/> View on (Dev) WorkflowHub</a>
 			{% endif %}
 
 		</div>