Merge branch 'main' into dev

.github/workflows/ci.yml

@@ -80,7 +80,7 @@ jobs:
         run: |
           bundle exec ruby bin/check-indent.rb
 
-      - name: Ensure no unexpected jekyll in output
+      - name: Ensure no unexpected jekyll in output. If this fails, generally it means you should add a page.description to the front matter.
         run: |
           ! fgrep -R 'site.pages' _site
 

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

@@ -54,6 +54,6 @@ jobs:
         uses: peter-evans/create-pull-request@v3
         with:
           title: Update Cached Commit Data
-          branch-suffix: commitcache
+          branch-suffix: timestamp
           commit-message: Update Cached Commit Data
           add-paths: metadata/

.github/workflows/update-libraries.yaml

@@ -49,4 +49,4 @@ jobs:
           title: Add missing data-library.yaml files
           branch-suffix: timestamp
           commit-message: Adds data-library.yaml for tutorials
-
+          add-paths: **/data-library.yaml

404.md

@@ -9,3 +9,5 @@ title: "404 Page Not Found"
 Perhaps you are here due to a mis-typed URL
 
 [Return to the homepage]({{ site.baseurl }}){:.btn.btn-primary}, or [Search]({% link search.md %}){:.btn.btn-secondary} for your page.
+
+<script>document.addEventListener('DOMContentLoaded', function () { plausible('404', { props: { path: document.location.pathname } }); });</script>

CONTRIBUTORS.yaml

@@ -195,6 +195,11 @@ astrovsky01:
     orcid: 0000-0002-7901-7109
     joined: 2019-06
 
+adamtaranto:
+    name: Adam Taranto
+    email: [email protected]
+    joined: 2023-01
+
 aurelienmoumbock:
     name: Aurélien F. A. Moumbock
     email: [email protected]
@@ -362,7 +367,9 @@ burkemlou:
     name: Melissa Burke
     email: [email protected]
     joined: 2023-12
-
+    affiliations: 
+        - AustralianBioCommons
+
 B0r1sD:
     name: Boris Depoortere
     joined: 2024-04
@@ -1364,6 +1371,13 @@ mccalluc:
     name: Chuck McCallum
     joined: 2018-06
 
+mcharleston:
+    name: Michael Charleston
+    email: [email protected]
+    joined: 2023-01
+    affiliations: 
+        - UTas
+
 mcmaniou:
     name: Maria Christina Maniou
     joined: 2021-09
@@ -1635,6 +1649,12 @@ RareSeas:
     name: Adelaide Rhodes
     joined: 2021-05
 
+PatCapon39:
+    name: Patrick Capon
+    joined: 2024-02
+    affiliations: 
+        - AustralianBioCommons
+
 patrick-austin:
     name: Patrick Austin
     email: [email protected]
@@ -1844,6 +1864,11 @@ sbenateau:
     affiliations:
       - elixir-europe
 
+
+sebastian-schaaf:
+    name: Sebastian Schaaf
+    joined: 2024-05
+
 sonalhenson:
     name: Sonal Henson
     joined: 2023-09

Gemfile.lock

@@ -30,6 +30,7 @@ GEM
     fastimage (2.2.7)
     ffi (1.16.2)
     forwardable-extended (2.6.0)
+    google-protobuf (3.24.3-x86_64-darwin)
     google-protobuf (3.24.3-x86_64-linux)
     highline (2.0.3)
     html-proofer (4.4.3)
@@ -80,24 +81,30 @@ GEM
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.4.0)
     namae (1.1.1)
-    nokogiri (1.16.2-x86_64-linux)
+    nokogiri (1.16.5-x86_64-darwin)
+      racc (~> 1.4)
+    nokogiri (1.16.5-x86_64-linux)
       racc (~> 1.4)
     parallel (1.20.1)
     pathutil (0.16.2)
       forwardable-extended (~> 2.6)
     pkg-config (1.5.5)
     public_suffix (5.0.3)
-    racc (1.7.3)
+    racc (1.8.0)
     rainbow (3.1.1)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
-    rexml (3.2.6)
+    rexml (3.2.8)
+      strscan (>= 3.0.9)
     rouge (4.1.3)
     rubyzip (2.3.2)
     safe_yaml (1.0.5)
+    sass-embedded (1.69.5-x86_64-darwin)
+      google-protobuf (~> 3.23)
     sass-embedded (1.69.5-x86_64-linux-gnu)
       google-protobuf (~> 3.23)
+    strscan (3.1.0)
     terminal-table (3.0.2)
       unicode-display_width (>= 1.1.1, < 3)
     typhoeus (1.4.0)
@@ -108,6 +115,7 @@ GEM
     zeitwerk (2.6.12)
 
 PLATFORMS
+  x86_64-darwin-19
   x86_64-linux
 
 DEPENDENCIES

Makefile

@@ -83,9 +83,13 @@ serve-quick: api/swagger.json ## run a local server (faster, some plugins disabl
 .PHONY: serve-quick
 
 serve-gitpod: bundle-install  ## run a server on a gitpod.io environment
-	bundle exec jekyll serve --config _config.yml --incremental
+	bundle exec jekyll serve --config _config.yml --incremental --livereload
 .PHONY: serve-gitpod
 
+serve-gitpod-quick: bundle-install  ## run a server on a gitpod.io environment
+	bundle exec jekyll serve --config _config.yml,_config-dev.yml --incremental --livereload
+.PHONY: serve-gitpod-quick
+
 build-gitpod: bundle-install  ## run a build on a gitpod.io environment
 	bundle exec jekyll build --config _config.yml
 .PHONY: build-gitpod

ORGANISATIONS.yaml

@@ -73,6 +73,17 @@ ifb:
     avatar: "/training-material/shared/images/ifb.png"
     github: false
 
+AustralianBioCommons:
+    name: Australian BioCommons
+    url: https://www.biocommons.org.au/
+    avatar: "/training-material/shared/images/Australian-Biocommons-Favicon-RGB.png"
+
+UTas:
+    name: University of Tasmania
+    url: https://www.utas.edu.au/
+    avatar: "/training-material/shared/images/UTas_logo.png"
+    github: false
+
 pndb:
     name: Pôle National de Données de Biodiversité
     url: https://www.pndb.fr/
@@ -84,8 +95,14 @@ vib:
     url: https://vib.be/
     avatar: "/training-material/shared/images/logo-vib.png"
     github: false
-    
+
 qiime2:
     name: QIIME2
     url: https://qiime2.org/
     avatar: https://avatars.githubusercontent.com/u/18176583?s=200&v=4
+
+jetstream2:
+    name: JetStream
+    url: https://jetstream-cloud.org/
+    avatar: https://jetstream-cloud.org/images/home/jetstream-2.png
+    github: false

_config.yml

@@ -58,6 +58,7 @@ javascript_bundles:
       - assets/js/bootstrap.min.js     # Everywhere
       - assets/js/bootstrap-toc.min.js # Only tutorials, faqs
       - assets/js/clipboard.min.js     # Used on anything with a pre
+      - assets/js/anchor.min.js        # Used on every page.
       - assets/js/main.js
       # - assets/js/list.min.js # Potentially unused?
 
@@ -87,6 +88,13 @@ abbreviate:
     - tutorial_slides
     - base_slides
 
+# for event pages, invite link expires after 400 uses :s
+slack:
+  invite: https://join.slack.com/t/gtnsmrgsbord/shared_invite/zt-1vuywk2t2-5FFAfFU1JImaulNGz4DMcw
+  general_channel: https://gtnsmrgsbord.slack.com/archives/C01MNM98X9V
+  social_channel: https://gtnsmrgsbord.slack.com/archives/C01EDBVMHBQ
+
+
 # Icon tag config
 icon-tag:
   announcement: fas fa-bullhorn
@@ -105,10 +113,17 @@ icon-tag:
   external-link: fas fa-external-link-alt
   switch-histories: fas fa-exchange-alt
   event: far fa-calendar
+  event-date: far fa-calendar
+  event-location: fas fa-location-dot
+  event-cost: fas fa-tag
   feedback: far fa-comments
   galaxy-advanced-search: fas fa-angle-double-down
   galaxy-show-active: fa fa-map-marker
-  galaxy-barchart: fas fa-chart-bar
+  galaxy-barchart: fas fa-chart-column
+  galaxy-visualise: fas fa-chart-column
+  galaxy-visualize: fas fa-chart-column
+  galaxy-vis-config: fas fa-angle-double-left
+  galaxy-viz-config: fas fa-angle-double-left
   galaxy-bug: fas fa-bug
   galaxy-chart-select-data: fas fa-database
   galaxy-clear: fas fa-times-circle
@@ -123,6 +138,8 @@ icon-tag:
   galaxy-gear: fas fa-cog
   galaxy-history: fas fa-columns
   galaxy-history-archive: fas fa-archive
+  galaxy-history-input: fas fa-sign-in-alt
+  galaxy-history-answer: fas fa-sign-out-alt
   galaxy-home: fas fa-home
   galaxy-info: fas fa-info-circle
   galaxy-lab: fa fa-tv

_includes/analytics.html

@@ -27,11 +27,12 @@
 </script>
 
 <!-- Page view tracking -->
-<script async defer data-domain="training.galaxyproject.org" src="https://plausible.galaxyproject.eu/js/plausible.js"></script>
+<script defer data-domain="training.galaxyproject.org" src="https://plausible.galaxyproject.eu/js/plausible.js"></script>
 <script>
 if(localStorage.getItem('plausible-opt-out') !== 'opt-out' && navigator.doNotTrack !== "1") {
 	localStorage.removeItem("plausible_ignore")
 	console.log("Plausible: opt-in");
+	window.plausible = window.plausible || function() { (window.plausible.q = window.plausible.q || []).push(arguments) }
 } else {
 	// if they're opting-out, or DNT
 	// we might get one page by accident but we won't get future ones.

_includes/calendar-buttons.html

@@ -0,0 +1,11 @@
+{% assign startdate = include.start | default: page.date_start %}
+{% assign enddate = include.end | default: page.date_end | default: page.date_start %}
+{% assign eventurl = include.url | default: page.url | prepend: site.baseurl | prepend: site.url %}
+{% assign eventname = include.name | default: page.title | default: ""%}
+{% assign location = include.location | default: page.location | format_location_simple  %}
+
+<a href="https://calendar.google.com/calendar/render?action=TEMPLATE&dates={{startdate | date: '%Y%m%d'}}%2F{{enddate | date: '%Y%m%d'}}&details=Event%20Information%20{{eventurl}}&location={{location}}&text={{eventname}}" class="btn btn-info btn-sm" alt="Add to Google Calendar">Google</a>
+
+<a href="https://outlook.live.com/calendar/0/deeplink/compose?body=Event%20Information%20{{eventurl}}&enddt={{enddate | date: '%Y-%m-%d'}}&location={{location}}&path=%2Fcalendar%2Faction%2Fcompose&rru=addevent&startdt={{startdate | date: '%Y-%m-%d'}}&subject={{eventname}}" class="btn btn-info btn-sm">Outlook</a>
+
+<a href="https://outlook.office.com/calendar/0/deeplink/compose/?body=Event%20Information%20{{eventurl}}&enddt={{enddate | date: '%Y-%m-%d'}}&allday=true&location={{location}}&path=%2fcalendar%2faction%2fcompose&rru=addevent&startdt={{startdate | date: '%Y-%m-%d'}}&subject={{eventname}}" class="btn btn-info btn-sm">Office 365</a>

_includes/contributor-list2.html

@@ -25,6 +25,26 @@
 	{% endif %}
 
 
+	{% if include.contributors.organisers %}
+	<tr>
+		<td><abbr title="These were responsible for organisation of this event">Organisers(s)</abbr></td>
+		<td>
+			{% for id in include.contributors.organisers %}{{ include.sep }}{% if include.badge %}{% include _includes/contributor-badge.html id=id %}{% else %}{% assign name = contributors[id].name | default: id -%}{{ name -}}{% endif %}{%- endfor -%}
+			{%- if include.newcontributors -%}{{ include.sep }}{% if include.badge %}{% include _includes/contributor-badge.html id='newcontributors' %}{% endif %}{% endif %}
+		</td>
+	</tr>
+	{% endif %}
+
+	{% if include.contributors.instructors %}
+	<tr>
+		<td><abbr title="These folks either taught at the event or supported its instruction">Instructor(s)</abbr></td>
+		<td>
+			{% for id in include.contributors.instructors %}{{ include.sep }}{% if include.badge %}{% include _includes/contributor-badge.html id=id %}{% else %}{% assign name = contributors[id].name | default: id -%}{{ name -}}{% endif %}{%- endfor -%}
+			{%- if include.newcontributors -%}{{ include.sep }}{% if include.badge %}{% include _includes/contributor-badge.html id='newcontributors' %}{% endif %}{% endif %}
+		</td>
+	</tr>
+	{% endif %}
+
 	{% if include.contributors.translation %}
 	<tr>
 		<td><abbr title="These people did the translation and localisation of this text.">Translation</abbr></td>
@@ -69,5 +89,6 @@
 		</td>
 	</tr>
 	{% endif %}
+
 </table>
 {% endif %}

_includes/contributors-line.html

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

_includes/default-header.html

@@ -32,9 +32,15 @@
                     </li>
 
                     <li class="nav-item">
+                        {% if page.layout == "event" %}
+                        <a class="nav-link" href="{% link events/index.md %}" title="Events">
+                           {% icon curriculum %} GTN Events
+                        </a>
+                        {% else %}
                         <a class="nav-link" href="{{ site.baseurl }}/learning-pathways" title="Learning Pathways">
                            {% icon curriculum %} Learning Pathways
                         </a>
+                        {% endif %}
                     </li>
 
                     {% include _includes/help.html %}

_includes/event-table.html

@@ -0,0 +1,30 @@
+<table class="eventtable table table-striped">
+ <thead>
+  <tr>
+   <th>Date</th>
+   <th>Event</th>
+   <th>Location</th>
+   <th>Contact</th>
+  </tr>
+ </thead>
+ <tbody>
+ {% for event in include.events %}
+ {% unless event.draft and jekyll.environment == "production" %}
+ <tr>
+  <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>
+   <div class="eventtable-description"> {{event.description}} </div>
+  </td>
+  <td> {{event.location | format_location_short }} </td>
+  <td> {% for org in event.contributions.organisers %}
+			{% include _includes/contributor-badge-inline.html id=org %}
+		{% endfor %}
+  </td>
+ </tr>
+ {% endunless %}
+ {% endfor %}
+ </tbody>
+</table>
+

_includes/funding-statement.md

@@ -3,20 +3,28 @@
 <h2 id="funding">{{locale['references']| default: "Funding" }}</h2>
 <p>These individuals or organisations provided funding support for the development of this resource</p>
 
-<div class="row">
+<div class="d-flex flex-wrap">
 {% for id in include.contributions.funding %}
 	{% assign name = site.data.contributors[id].name | default: id -%}
-	<div class="col-md-3 col-xs-12">
-		{% if site.data.contributors[id].avatar %}
-		<img class="funder-avatar" src="{{ site.data.contributors[id].avatar }}" alt="Logo">
-		{% else %}
-		<img class="funder-avatar" src="https://avatars.githubusercontent.com/{{ id }}" alt="Logo">
-		{% endif %}
-		<a href="{{ site.baseurl }}/hall-of-fame/{{ id }}/" class="btn btn-secondary">See Funder Profile</a>
-	</div>
-	<div class="col-md-9 col-xs-12">
-		{{ site.data.contributors[id].funding_statement | markdownify }}
-	</div>
+	<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 %}
+		<div class="avatar">
+			{% if pfo.avatar %}
+			<img class="funder-avatar" src="{{ pfo.avatar }}" alt="Logo">
+			{% else %}
+				{% unless pfo.github %}
+				<img class="funder-avatar" src="https://avatars.githubusercontent.com/{{ id }}" alt="Logo">
+				{% endunless %}
+			{% endif %}
+		</div>
+
+		<div class="info">
+			<div class="name">{{ pfo.short_name | default: pfo.name | default: id }}</div>
+			<div class="description">
+			{{ site.data.funders[id].funding_statement | markdownify | strip_html }}
+			</div>
+		</div>
+	</a>
 {% endfor %}
 </div>
 </div>