Merge branch 'galaxyproject:main' into ampvis2_tutorialfirst_upload

.github/workflows/ci-main.yml

@@ -15,6 +15,11 @@ on:
       - 'learning-pathways/*'
       - 'faqs/**'
       - 'news/**'
+      - 'events/**'
+      - CONTRIBUTORS.yaml
+      - FUNDERS.yaml
+      - ORGANISATIONS.yaml
+
 
 jobs:
   lint:

.github/workflows/cron-commit-cache.yml

@@ -49,11 +49,16 @@ jobs:
 
           bundle exec ruby bin/commit-cache-update.rb
 
+      - name: Update geocoding of events
+        id: generate
+        run: |
+          bundle exec ruby bin/geocode.rb
+
       - name: Create Pull Request
         # If it's not a Pull Request then commit any changes as a new PR.
         uses: peter-evans/create-pull-request@v3
         with:
           title: Update Cached Commit Data
           branch-suffix: timestamp
           commit-message: Update Cached Commit Data
-          add-paths: metadata/
+          add-paths: metadata/,events/

CONTRIBUTORS.yaml

@@ -12,7 +12,7 @@
 #   email: [email protected]                      # your email address
 #   fediverse: https://mstdn.science/@myname   # your fediverse username
 #   fediverse_flavor: mastodon                 # your fediverse flavor
-#   bluesky: username.bsky.social              # your bluesky username 
+#   bluesky: username.bsky.social              # your bluesky username
 #   linkedin: username                         # your linkedin username
 #   matrix: 'user:matrix.org'                  # where can we find you on matrix?
 #   orcid: 0000-0003-3803-468X                 # your ORCID ID
@@ -120,6 +120,13 @@ almahmoud:
     name: Alex Mahmoud
     joined: 2019-06
 
+andreacabibbe:
+    name: Andrea Cabibbe
+    affiliations:
+    - irccs
+    github: false
+    joined: 2024-06
+
 andreasrichter:
     name: Andreas Richter
     github: false
@@ -178,6 +185,13 @@ anuprulez:
       - eurosciencegateway
       - elixir-europe
 
+arashghodousi:
+    name: Arash Ghodousi
+    affiliations:
+    - irccs
+    - san-raffaele-uni
+    joined: 2024-06
+
 asmasonomics:
     name: Andrew Mason
     joined: 2024-02
@@ -367,9 +381,9 @@ burkemlou:
     name: Melissa Burke
     email: [email protected]
     joined: 2023-12
-    affiliations: 
+    affiliations:
         - AustralianBioCommons
-    
+
 B0r1sD:
     name: Boris Depoortere
     joined: 2024-04
@@ -717,6 +731,12 @@ fboyer:
     name: Frédéric Boyer
     joined: 2022-02
 
+federicodimarco:
+    name: Federico DiMarco
+    affiliations:
+    - irccs
+    joined: 2024-06
+
 fmareuil:
     name: Fabien Mareuil
     joined: 2017-09
@@ -1056,7 +1076,7 @@ jxtx:
 katherinecox:
     name: Katherine Cox
     joined: 2023-06
-    
+
 katherine-d21:
     name: Katherine Do
     joined: 2023-08
@@ -1174,7 +1194,7 @@ leandro-liborio:
     name: Leandro Liborio
     email: [email protected]
     joined: 2022-11
-    
+
 Laura190:
     name: Laura Cooper
     email: [email protected]
@@ -1375,7 +1395,7 @@ mcharleston:
     name: Michael Charleston
     email: [email protected]
     joined: 2023-01
-    affiliations: 
+    affiliations:
         - UTas
 
 mcmaniou:
@@ -1652,7 +1672,7 @@ RareSeas:
 PatCapon39:
     name: Patrick Capon
     joined: 2024-02
-    affiliations: 
+    affiliations:
         - AustralianBioCommons
 
 patrick-austin:
@@ -1710,7 +1730,7 @@ plushz:
     orcid: 0000-0002-0507-4602
     joined: 2022-03
     affiliations:
-      - uni-freiburg    
+      - uni-freiburg
 
 polkhe:
     name: Ekaterina Polkh
@@ -2007,7 +2027,7 @@ supernord:
     name: Johan Gustafsson
     joined: 2024-02
     orcid: 0000-0002-2977-5032
-    elixir_node: au 
+    elixir_node: au
     affiliations:
       - elixir-europe
 
@@ -2151,6 +2171,19 @@ vivekbhr:
     name: Vivek Bhardwaj
     joined: 2017-09
 
+vladvisan:
+    name: Vlad Visan
+    email: [email protected]
+    matrix: 'vlad.visan:matrix.org'
+    orcid: 0009-0007-0529-1002
+    joined: 2023-02
+    affiliations:
+      - uga
+    location:
+      country: FR
+      lat: 45.19
+      lon: 5.76
+
 vloux:
     name: Valentin Loux
     joined: 2019-04

ORGANISATIONS.yaml

@@ -49,12 +49,24 @@ embl-ebi:
     avatar: https://raw.githubusercontent.com/nomadscientist/scrnaseq_training/d0fccaa9dc8dc8615eb7146d6c5e96bd36f11f3a/EMBL_EBI_Logo_black.svg
     github: false
 
+irccs:
+    name: IRCCS Ospedale San Raffaele
+    url: "https://www.hsr.it/"
+    avatar: "/training-material/shared/images/irccs.jpg"
+
+
 MPIIE:
     name: Max Planck Institute of Immunology and Epigenetics
     url: https://www.ie-freiburg.mpg.de
     avatar: https://raw.githubusercontent.com/bgruening/presentations/master/shared/resources/img/14_MPI_IE_logo_mit_180.gif
     github: false
 
+uga:
+    name: Université Grenoble-Alpes
+    url: https://www.univ-grenoble-alpes.fr/
+    avatar: /training-material/shared/images/logo-uga.svg
+    github: false
+
 uni-freiburg:
     name: University of Freiburg
     url: https://www.uni-freiburg.de/
@@ -90,6 +102,11 @@ pndb:
     avatar: "/training-material/shared/images/PNDB_sub.png"
     github: false
 
+san-raffaele-uni:
+  name: Università Vita-Salute San Raffaele
+  url: "https://www.unisr.it/"
+  avatar: "/training-material/shared/images/uni_san_raffaele.svg"
+
 vib:
     name: Vlaams Instituut voor Biotechnologie
     url: https://vib.be/
@@ -106,3 +123,9 @@ jetstream2:
     url: https://jetstream-cloud.org/
     avatar: https://jetstream-cloud.org/images/home/jetstream-2.png
     github: false
+
+egi:
+    name: EGI
+    url: https://www.egi.eu/
+    avatar: https://cdn.egi.eu/app/uploads/2021/11/egi-logo.svg
+    github: false

_includes/display_extra_training.md

@@ -1,37 +1,42 @@
 {% for training in include.extra_trainings %}
-    <li>
     {% if training.type == "internal" %}
         {% assign extra_topic_metadata = site.data[training.topic_name] %}
         {% assign extra_topic = site | topic_filter:training.topic_name %}
-        <a href="{{ site.baseurl }}/topics/{{ training.topic_name }}">{{ extra_topic_metadata.title }}</a>
-        {% if training.tutorials %}
-            <ul>
-                {% for extra_tuto in training.tutorials %}
-                    {% for topic_tuto in extra_topic %}
-                        {% if extra_tuto == topic_tuto.tutorial_name %}
-                            {% assign sep = "" %}
-                            <li> {{ topic_tuto.title }}:
-                            {% if topic_tuto.slides %}
-                                <a href="{{ site.baseurl }}/topics/{{ training.topic_name }}/tutorials/{{ topic_tuto.tutorial_name }}/slides.html">{% icon slides %} slides</a>
-                                {% assign sep = "-" %}
-                            {% endif %}
-                            {% if topic_tuto.hands_on %}
-                                {% if topic_tuto.hands_on_url %}
-                                    {{ sep }} <a href="{{ topic_tuto.hands_on_url }}">{% icon tutorial %} hands-on</a>
-                                {% else %}
-                                    {{ sep }} <a href="{{ site.baseurl }}/topics/{{ training.topic_name }}/tutorials/{{ topic_tuto.tutorial_name }}/tutorial.html">{% icon tutorial %} hands-on</a>
-                                {% endif %}
-                            {% endif %}
+        {% unless training.tutorials %}
+        <li>
+          <a href="{{ site.baseurl }}/topics/{{ training.topic_name }}">{{ extra_topic_metadata.title }}</a>
+        </li>
+        {% else training.tutorials %}
+            {% for extra_tuto in training.tutorials %}
+                {% for topic_tuto in extra_topic %}
+                    {% if extra_tuto == topic_tuto.tutorial_name %}
+                        {% if topic_tuto.slides %}
+                            <li>
+                              <a href="{{ site.baseurl }}/topics/{{ training.topic_name }}/tutorials/{{ topic_tuto.tutorial_name }}/slides.html">{% icon slides %} Slides: {{ topic_tuto.title }}</a>
                             </li>
                         {% endif %}
-                    {% endfor %}
+                        {% if topic_tuto.hands_on %}
+                            {% if topic_tuto.hands_on_url %}
+                                <li>
+                                  <a href="{{ topic_tuto.hands_on_url }}">{% icon tutorial %} Hands-on: {{ topic_tuto.title }}</a>
+                                </li>
+                            {% else %}
+                                <li>
+                                  <a href="{{ site.baseurl }}/topics/{{ training.topic_name }}/tutorials/{{ topic_tuto.tutorial_name }}/tutorial.html">{% icon tutorial %} Hands-on: {{ topic_tuto.title }}</a>
+                                </li>
+                            {% endif %}
+                        {% endif %}
+                    {% endif %}
                 {% endfor %}
-            </ul>
-        {% endif %}
+            {% endfor %}
+        {% endunless %}
     {% elsif training.type == "none" %}
+      <li>
         {{ training.title }}
+      </li>
     {% else %}
+      <li>
         <a href="{{ training.link }}">{{ training.title }}</a>
+      </li>
     {% endif %}
-    </li>
-{% endfor %}
+{% endfor %}

_includes/event-table.html

@@ -14,7 +14,7 @@
   <td class="eventtable-date"> {{event | collapse_date_pretty }} </td>
   <td>
 
-   <a class="eventtable-title" href="{% if event.external %}{{event.external}}{% else %}{{site.baseurl}}{{event.url}}{% endif %}">{{event.title}}{% if event.draft %} (draft, will be hidden) {% endif %}</a>
+	  <a class="eventtable-title" href="{% if event.external %}{{event.external}}{% else %}{{site.baseurl}}{{event.url}}{% endif %}{% if include.campaign %}?utm_source=gtn&utm_medium=event-table&utm_campaign={{ include.campaign }}{% endif %}">{{event.title}}{% if event.draft %} (draft, will be hidden) {% endif %}</a>
    <div class="eventtable-description"> {{event.description}} </div>
   </td>
   <td> {{event.location | format_location_short }} </td>

_includes/funding-statement.md

@@ -1,10 +1,6 @@
-{% if include.contributions.funding %}
-<div markdown="1">
-<h2 id="funding">{{locale['references']| default: "Funding" }}</h2>
-<p>These individuals or organisations provided funding support for the development of this resource</p>
-
+{% if include.funders %}
 <div class="d-flex flex-wrap">
-{% for id in include.contributions.funding %}
+{% for id in include.funders %}
 	{% assign name = site.data.contributors[id].name | default: id -%}
 	<a href="{{ site.baseurl }}/hall-of-fame/{{ id }}/" class="funder-badge">
 		{% assign pfo = site.data.funders[id] | default: site.data.organisations[id] | default: site.data.contributors[id] | default: nil %}
@@ -27,5 +23,4 @@
 	</a>
 {% endfor %}
 </div>
-</div>
 {% endif %}

_includes/help.html

@@ -3,14 +3,6 @@
         {% icon help %} Help
     </a>
     <div class="dropdown-menu dropdown-menu-right">
-        <!-- disable Tess for now
-        <form method="get" action="https://tess.elixir-europe.org/materials">
-            <input type="text" id="search" name="q" value="" style="margin-left: 0.5em;/*! border-radius: 0px; */">
-            <input type="hidden" value="Galaxy Training" name="content_provider">
-            <input type="submit" value="Search on TeSS" style="width: 92%;border-radius: 0px;margin: 0.5em;background: #f47d20;border: 0px;padding: 0.25em;" class="">
-        </form>
-        -->
-
 	<a class="dropdown-item" href="{% link faqs/index.md %}" title="Check our FAQs">
            {% icon question %} FAQs
         </a>

_includes/slides-youtube-selector.html

@@ -1,19 +1,19 @@
 <blockquote class="agenda">
 	<div class="box-title hands-on-title" id="slides-{{ include.slides }}">{{ include.title }}</div>
 	<p class="text-muted">This content is available in multiple, equivalent formats. Choose your preferred format below.</p>
-<ul class="nav nav-pills mb-3" id="pills-tab" role="tablist">
+<ul class="nav nav-tabs" id="{{include.id}}-pills-tab" role="tablist">
   <li class="nav-item" role="presentation">
-    <button class="nav-link active" id="pills-home-tab" data-toggle="pill" data-target="#pills-home" type="button" role="tab" aria-controls="pills-home" aria-selected="true">Teacher Recording</button>
+    <button class="nav-link active" id="{{include.id}}-pills-home-tab" data-toggle="pill" data-target="#{{include.id}}-pills-home" type="button" role="tab" aria-controls="{{include.id}}-pills-home" aria-selected="true">Teacher Recording</button>
   </li>
   <li class="nav-item" role="presentation">
-    <button class="nav-link" id="pills-profile-tab" data-toggle="pill" data-target="#pills-profile" type="button" role="tab" aria-controls="pills-profile" aria-selected="false">Slides</button>
+    <button class="nav-link" id="{{include.id}}-pills-profile-tab" data-toggle="pill" data-target="#{{include.id}}-pills-profile" type="button" role="tab" aria-controls="{{include.id}}-pills-profile" aria-selected="false">Slides</button>
   </li>
   <li class="nav-item" role="presentation">
-    <button class="nav-link" id="pills-contact-tab" data-toggle="pill" data-target="#pills-contact" type="button" role="tab" aria-controls="pills-contact" aria-selected="false">Plain Text</button>
+    <button class="nav-link" id="{{include.id}}-pills-contact-tab" data-toggle="pill" data-target="#{{include.id}}-pills-contact" type="button" role="tab" aria-controls="{{include.id}}-pills-contact" aria-selected="false">Plain Text</button>
   </li>
 </ul>
-<div class="tab-content" id="pills-tabContent">
-  <div class="tab-pane show active" id="pills-home" role="tabpanel" aria-labelledby="pills-home-tab">
+<div class="tab-content" id="{{include.id}}-pills-tabContent">
+  <div class="tab-pane show active" id="{{include.id}}-pills-home" role="tabpanel" aria-labelledby="{{include.id}}-pills-home-tab">
     <div class="embed-responsive embed-responsive-16by9">
     <iframe class="embed-responsive-item"
       credentialless
@@ -28,7 +28,7 @@
       loading="lazy"></iframe>
     </div>
   </div>
-  <div class="tab-pane" id="pills-profile" role="tabpanel" aria-labelledby="pills-profile-tab">
+  <div class="tab-pane" id="{{include.id}}-pills-profile" role="tabpanel" aria-labelledby="{{include.id}}-pills-profile-tab">
     <a href="{{ site.baseurl }}/{{ include.slides }}/slides.html">Open in new tab</a><br/>
     <div class="embed-responsive embed-responsive-16by9">
     <iframe class="embed-responsive-item"
@@ -38,7 +38,7 @@
       loading="lazy"></iframe>
     </div>
   </div>
-  <div class="tab-pane" id="pills-contact" role="tabpanel" aria-labelledby="pills-contact-tab">
+  <div class="tab-pane" id="{{include.id}}-pills-contact" role="tabpanel" aria-labelledby="{{include.id}}-pills-contact-tab">
     <a href="{{ site.baseurl }}/{{ include.slides }}/slides-plain.html">Open in new tab</a><br/>
     <div class="embed-responsive embed-responsive-16by9">
     <iframe class="embed-responsive-item"