Merge branch 'main' into main

CONTRIBUTORS.yaml

@@ -612,6 +612,10 @@ davebx:
     name: Dave B.
     joined: 2021-06
 
+davelopez:
+    name: David López
+    joined: 2021-10
+
 dbrites:
     name: Daniela Brites
     joined: 2022-03
@@ -1518,6 +1522,14 @@ 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 +1636,7 @@ miaomiaozhou88:
     joined: 2020-12
     orcid: 0000-0003-4426-1758
 
-michelemaroni89:
+michelemaroni:
     name: Michele Maroni
     joined: 2019-07
 
@@ -1773,6 +1785,10 @@ NickSto:
     twitter: NickStoler
     joined: 2018-07
 
+njall:
+    name: Niall Beard
+    joined: 2019-02
+
 nomadscientist:
     name: Wendi Bacon
     email: [email protected]
@@ -1867,6 +1883,10 @@ otatadeabigail:
     name: Otatade Abigail
     joined: 2021-10
 
+OlegZharkov:
+    name: Oleg Zharkov
+    joined: 2021-06
+
 pajanne:
     name: Anne Pajon
     joined: 2017-09
@@ -2356,6 +2376,10 @@ sunyi000:
     email: [email protected]
     joined: 2021-03
 
+Swathi266:
+    name: Swathi Nataraj
+    joined: 2024-12
+
 sylviamahara:
     name: Sylvia Mahara
     github: false
@@ -2512,6 +2536,10 @@ twishigulati:
     github: false
     joined: 2021-11
 
+tuncK:
+    name:  Tunc Kayikcioglu
+    joined: 2023-10
+
 valentinmarcon:
     name: Valentin Marcon
     joined: 2017-09

_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/tutorial_hands_on.html

@@ -404,7 +404,7 @@ <h1>{{locale['citing-tutorial'] | default: "Citing this Tutorial"}}</h1>
 	title = "{{ page.title }} (Galaxy Training Materials)",
 	year = "{{ page.last_modified_at | date: "%Y"}}",
 	month = "{{ page.last_modified_at | date: "%m"}}",
-	day = "{{ page.last_modified_at | date: "%d" }}"
+	day = "{{ page.last_modified_at | date: "%d" }}",
 	url = "{% raw %}\url{{% endraw %}{{ site.url }}{{ site.baseurl }}{{page.url}}{% raw %}}{% endraw %}",
 	note = "[Online; accessed TODAY]"
 }
@@ -420,7 +420,7 @@ <h1>{{locale['citing-tutorial'] | default: "Citing this Tutorial"}}</h1>
 	author = {Saskia Hiltemann and Helena Rasche and Simon Gladman and Hans-Rudolf Hotz and Delphine Larivi{\`{e}}re and Daniel Blankenberg and Pratik D. Jagtap and Thomas Wollmann and Anthony Bretaudeau and Nadia Gou{\'{e}} and Timothy J. Griffin and Coline Royaux and Yvan Le Bras and Subina Mehta and Anna Syme and Frederik Coppens and Bert Droesbeke and Nicola Soranzo and Wendi Bacon and Fotis Psomopoulos and Crist{\'{o}}bal Gallardo-Alba and John Davis and Melanie Christine Föll and Matthias Fahrner and Maria A. Doyle and Beatriz Serrano-Solano and Anne Claire Fouilloux and Peter van Heusden and Wolfgang Maier and Dave Clements and Florian Heyl and Björn Grüning and B{\'{e}}r{\'{e}}nice Batut and},
 	editor = {Francis Ouellette},
 	title = {Galaxy Training: A powerful framework for teaching!},
-	journal = {PLoS Comput Biol} Computational Biology}
+	journal = {PLoS Comput Biol}
 }
 </code>
                    </pre></div></div>

_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>

_plugins/author-page.rb

@@ -1,5 +1,6 @@
 # frozen_string_literal: true
 
+require './_plugins/gtn/mod'
 require './_plugins/gtn'
 
 module Jekyll
@@ -168,3 +169,70 @@ def generate(site)
     end
   end
 end
+
+Jekyll::Hooks.register :site, :post_read do |site|
+  if Jekyll.env == 'production'
+    Jekyll.logger.info "[GTN/Reviewers] Ingesting GitHub reviewer metadata"
+    start_time = Time.now
+    # Maps a lowercase version of their name to the potential mixed-case version
+    contribs_lower = site.data['contributors'].map{|k, v| [k.downcase, k]}.to_h
+
+    # Annotate the from github metadata
+    gh_reviewers_by_path = Hash.new { |hash, key| hash[key] = [] }
+    # Hash of PRs by path
+    site.data['github'].each do |num, pr|
+      # Within a PR we have some reviews, let's get that set organised:
+      reviewers = pr['reviews'].map do |review|
+        # Just "people"
+        contribs_lower.fetch(review['author']['login'].downcase, review['author']['login'])
+      end.uniq.reject{|x| x == 'github-actions'}
+
+      pr['files'].select{|p| p['path'] =~ /.(md|html)$/}.each do |file|
+        real_path = Gtn::PublicationTimes.chase_rename(file['path'])
+        gh_reviewers_by_path[real_path] += reviewers
+        gh_reviewers_by_path[real_path].uniq!
+      end
+    end
+
+    # For all of our pages, if the path is mentioned above, then, tag it.
+    site.pages.select{|t| gh_reviewers_by_path.key?(t.path)}.each do |t|
+      if t['layout'] == 'tutorial_hands_on' or !%w[base_slides introduction_slides tutorial_slides].index(t['layout']).nil?
+        if t.data.key?('contributors')
+          # Automatically 'upgrade' to new structure
+          t.data['contributions'] = {
+            'authorship' => t.data['contributors'],
+            'reviewing' => gh_reviewers_by_path[t.path]
+          }
+          t.data.delete('contributors')
+        elsif t.data.key?('contributions')
+          if t.data['contributions'].key?('reviewing')
+            t.data['contributions']['reviewing'] += gh_reviewers_by_path[t.path]
+          else
+            t.data['contributions']['reviewing'] = gh_reviewers_by_path[t.path]
+          end
+          t.data['contributions']['reviewing'].uniq!
+        end
+      end
+    end
+
+    site.posts.docs.select{|t| gh_reviewers_by_path.key?(t.path)}.each do |t|
+      if t['layout'] == 'news'
+        if t.data.key?('contributors')
+          t.data['contributions'] = {
+            'authorship' => t.data['contributors'],
+            'reviewing' => gh_reviewers_by_path[t.path]
+          }
+          t.data.delete('contributors')
+        elsif t.data.key?('contributions')
+          if t.data['contributions'].key?('reviewing')
+            t.data['contributions']['reviewing'] += gh_reviewers_by_path[t.path]
+          else
+            t.data['contributions']['reviewing'] = gh_reviewers_by_path[t.path]
+          end
+          t.data['contributions']['reviewing'].uniq!
+        end
+      end
+    end
+    Jekyll.logger.info "[GTN/Reviewers] Complete in #{Time.now - start_time} seconds"
+  end
+end

_plugins/gtn/contributors.rb

@@ -6,6 +6,8 @@
 module Gtn
   # Parse the git repo to get some facts
   module Contributors
+    @HAS_WARNED_ON = []
+
     ##
     # Returns contributors, regardless of whether they are 'contributor' or 'contributions' style
     # Params:
@@ -150,7 +152,10 @@ def self.fetch(site, c, warn: false)
         return ['grant', site.data['grants'][c]]
       else
         if ! warn
-          Jekyll.logger.warn "Contributor #{c} not found"
+          if ! @HAS_WARNED_ON.include?(c)
+            Jekyll.logger.warn "Contributor #{c} not found"
+            @HAS_WARNED_ON.push(c)
+          end
         end
       end