Merge pull request #4536 from galaxyproject/greyhound-cobra

Import "friends don't let friends" slide deck

.github/workflows/video-dry.yml

@@ -67,4 +67,4 @@ jobs:
 
           echo "Software Versions"
           $FFMPEG_PATH/ffmpeg -version
-          $(npm bin)/editly --version
+          ./node_modules/.bin/editly --version

CONTRIBUTORS.yaml

@@ -393,6 +393,10 @@ cutsort:
     name: Frederick Tan
     joined: 2023-06
 
+cxli233:
+    name: Chenxin Li
+    joined: 2023-11
+
 d-salgado:
     name: David Salgado
     joined: 2022-10

Makefile

@@ -217,17 +217,17 @@ _site/%/tutorial.pdf: _site/%/tutorial.html
 
 _site/%/slides.pdf: _site/%/slides.html
 	$(ACTIVATE_ENV) && \
-	$(shell npm bin)/http-server _site -p 9876 & \
+	./node_modules/.bin/http-server _site -p 9876 & \
 	docker run --rm --network host -v $(shell pwd):/slides astefanutti/decktape  automatic -s 1920x1080 http://127.0.0.1:9876/$(<:_site/%=%) /slides/$@
 
 _site/%/slides_ES.pdf: _site/%/slides_ES.html
 	$(ACTIVATE_ENV) && \
-	$(shell npm bin)/http-server _site -p 9876 & \
+	./node_modules/.bin/http-server _site -p 9876 & \
 	docker run --rm --network host -v $(shell pwd):/slides astefanutti/decktape  automatic -s 1920x1080 http://127.0.0.1:9876/$(<:_site/%=%) /slides/$@
 
 _site/%/slides_CAT_ES.pdf: _site/%/slides_CAT_ES.html
 	$(ACTIVATE_ENV) && \
-	$(shell npm bin)/http-server _site -p 9876 & \
+	./node_modules/.bin/http-server _site -p 9876 & \
 	docker run --rm --network host -v $(shell pwd):/slides astefanutti/decktape  automatic -s 1920x1080 http://127.0.0.1:9876/$(<:_site/%=%) /slides/$@
 
 video: ## Build all videos

_layouts/base_slides.html

@@ -104,7 +104,7 @@
 <!-- modified date -->
 <div class="footnote" style="bottom: 8em;">
   {% icon last_modification %} {{locale['last-modification'] | default: "Updated"}}: {{ page.last_modified_at | date: "%b %-d, %Y"}} &nbsp;
-  {% icon purl %}<abbr title="Persistent URL">PURL</abbr>: <a href="https://gxy.io/GTN:{{ page.short_id }}">gxy.io/GTN:{{ page.short_id }}</a>
+  {% if page.short_id %}{% icon purl %}<abbr title="Persistent URL">PURL</abbr>: <a href="https://gxy.io/GTN:{{ page.short_id }}">gxy.io/GTN:{{ page.short_id }}</a>{% endif %}
 </div>
 
 
@@ -177,8 +177,8 @@
 {% endif %}
 </div>
 
-<a rel="license" href="https://creativecommons.org/licenses/by/4.0/">
-{{ locale['license-tutorial'] | default: "This material is licensed under the Creative Commons Attribution 4.0 International License" }}</a>.
+{{ locale['license-framework'] | default: "Tutorial Content is licensed under" }} {% if page.license%} <a rel="license" href="https://spdx.org/licenses/{{ page.license }}">{{ page.license }}</a>.{% else %}<a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.{% endif %}<br/>
+{% if page.copyright %}{{ page.copyright }}{% endif %}
 
 {% if page.layout == "base_slides" %}
 .footnote[Found a typo? Something is wrong in this tutorial? <br/>Edit it on [GitHub]({{ site.github_repository }}/tree/main{{ page.url }})]

_layouts/base_slides_ai4life.html

@@ -171,8 +171,8 @@
 {% endif %}
 </div>
 
-<a rel="license" href="https://creativecommons.org/licenses/by/4.0/">
-{{ locale['license-tutorial'] | default: "This material is licensed under the Creative Commons Attribution 4.0 International License" }}</a>.
+{{ locale['license-framework'] | default: "Tutorial Content is licensed under" }} {% if page.license %} <a rel="license" href="https://spdx.org/licenses/{{ page.license }}">{{ page.license }}</a>.
+{% else %}<a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.{% endif %}
 
 {% if page.layout == "base_slides" %}
 .footnote[Found a typo? Something is wrong in this tutorial? <br/>Edit it on [GitHub]({{ site.github_repository }}/tree/main{{ page.url }})]

_layouts/slides-plain.html

@@ -78,7 +78,12 @@ <h2>Thank you!</h2>
 {% endif %}
 {% endif %}
 
-This material is licensed under the <a rel="license" href="https://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
+{{ locale['license-framework'] | default: "Tutorial Content is licensed under" }}
+{% if page.license %}
+  <a rel="license" href="https://spdx.org/licenses/{{ page.license }}">{{ page.license }}</a>.
+{% else %}
+  <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
+{% endif %}
 </section>
 
 {% if page.cited %}

_layouts/tutorial_hands_on.html

@@ -154,11 +154,13 @@ <h4 class="alert-heading">Under Development!</h4>
 		{% if page.copyright %}
 		{{ page.copyright }}.
 		{% endif %}
+            {{ locale['license-framework'] | default: "Tutorial Content is licensed under" }}
             {% if page.license %}
-	    Tutorial Content is licensed under <a rel="license" href="https://spdx.org/licenses/{{ page.license }}">{{ page.license }}</a>.
+              <a rel="license" href="https://spdx.org/licenses/{{ page.license }}">{{ page.license }}</a>.
             {% else %}
-            <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">{{ locale['license-framework'] | default: "Tutorial Content is licensed under Creative Commons Attribution 4.0 International License" }}</a>.
-            {% endif %} The GTN Framework is licensed under <a rel="license" href="{{ site.github_repository }}/blob/main/LICENSE.md">MIT</a>
+              <a rel="license" href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution 4.0 International License</a>.
+            {% endif %}
+            The GTN Framework is licensed under <a rel="license" href="{{ site.github_repository }}/blob/main/LICENSE.md">MIT</a>
         </div>
         {% if page.short_id %}
         <div><strong>{% icon purl %} <abbr title="Persistent URL">PURL</abbr>:</strong> <a href="https://gxy.io/GTN:{{ page.short_id }}">https://gxy.io/GTN:{{ page.short_id }}</a> </div>

_plugins/gtn/contributors.rb

@@ -61,7 +61,7 @@ def self.get_non_authors(material)
     # from disk ourselves.
     def self._load_file(site, category)
       if site.nil?
-        Jekyll.logger.warning "[GTN/Contributor] Loading #{category} from disk, this access could be improved"
+        Jekyll.logger.warn "[GTN/Contributor] Loading #{category} from disk, this access could be improved"
         File.open("_data/#{category}.yml", 'r') { |f| YAML.safe_load(f) }
       else
         site.data[category]
@@ -84,10 +84,10 @@ def self.fetch(site, c)
       elsif _load_file(site, 'funders').key?(c)
         return ['funder', site.data['funders'][c]]
       else
-        Jekyll.logger.error "Contributor #{c} not found"
+        Jekyll.logger.warn "Contributor #{c} not found"
       end
 
-      [nil, nil]
+      ['contributor', { 'name' => c }]
     end
 
     ##

bin/ari-make.sh

@@ -15,7 +15,7 @@ else
 	changed_slides="$(echo "$videos" | xargs ./bin/filter-resource-metadata video)"
 fi
 
-$(npm bin)/http-server -p 9876 _site &
+./node_modules/.bin/http-server -p 9876 _site &
 
 for slides in $changed_slides; do
 	echo "====== $slides ======"

bin/ari.sh

@@ -82,9 +82,9 @@ ruby bin/ari-prep-script.rb "${build_dir}" "${engine}"
 echo "  Extracting slides"
 convert "${slides}" -resize 1920x1080 "${build_dir}/slides.%03d.png"
 
-echo "  Building Video | $(npm bin)/editly --json ${build_dir}/editly.json5"
+echo "  Building Video | ./node_modules/.bin/editly --json ${build_dir}/editly.json5"
 $FFMPEG_PATH/ffmpeg -version
-$(npm bin)/editly --json "${build_dir}/editly.json5"
+./node_modules/.bin/editly --json "${build_dir}/editly.json5"
 
 # Mux it together
 echo "  Muxing"

bin/schema-slides.yaml

@@ -372,6 +372,16 @@ mapping:
                       type: str
                       description: |
                         URL of the external resource
+    copyright:
+        type: str
+        description: |
+          A copyright attribution string, as required by some licenses.
+        examples:
+            - © Copyright 2021-2023 University of Technology Sydney, The University of Manchester UK and RO-Crate contributors
+    license:
+        type: str
+        description: |
+            An [SPDX](https://spdx.org/) identifier for the alternative license that is used for that particular material. This is **only** relevant for materials which have been imported from an external source and were originally licensed under another license. For new materials we strongly encourage contributors to not use this key as materials are CC-BY, by default.
     draft:
         type: bool
         description: |

metadata/lang/es.yml

@@ -49,7 +49,7 @@ recommended-followup: "Continúa tu aprendizaje completando uno de nuestros entr
 
 
 license: "Licencia" # "License"
-license-tutorial: "El contenido de este tutorial tiene la licencia Creative Commons Attribution 4.0 International License." # "Tutorial Content is licensed under Creative Commons Attribution 4.0 International License."
+license-tutorial: "El contenido de este tutorial tiene la licencia" # "Tutorial Content is licensed under Creative Commons Attribution 4.0 International License."
 license-framework: "GTN Framework tiene licencia del MIT" # "The GTN Framework is licensed under MIT"
 
 

metadata/lang/fr.yml

@@ -49,7 +49,7 @@ recommended-followup: "Poursuivez votre apprentissage en suivant l'une de nos fo
 
 
 license: "Licence" # "License"
-license-tutorial: "Le contenu de ce didacticiel est sous licence Creative Commons Attribution 4.0 International License." # "Tutorial Content is licensed under Creative Commons Attribution 4.0 International License."
+license-tutorial: "Le contenu de ce didacticiel est sous licence" # "Tutorial Content is licensed under Creative Commons Attribution 4.0 International License."
 license-framework: "Le Framework GTN est sous licence MIT" # "The GTN Framework is licensed under MIT
 
 

topics/visualisation/metadata.yaml

@@ -5,10 +5,6 @@ title: "Visualisation"
 summary: "Training material for data visualisation in Galaxy"
 edam_ontology: ["topic_0337"]
 
-requirements:
-  - type: "internal"
-    topic_name: introduction
-
 editorial_board:
   - shiltemann
   - hexylena