Merge pull request galaxyproject#3878 from galaxyproject/snippet-incl…

…uding

Fix box titles in included snippets

.github/workflows/monthly-release.yml

@@ -14,18 +14,18 @@ jobs:
       - name: Release Name
         id: release_name
         run: |
-          echo "::set-output name=title::$(LC_ALL=C date '+%Y %B %d')"
-          echo "::set-output name=tag::$(LC_ALL=C date -I)"
+          echo "release_title=$(LC_ALL=C date '+%Y %B %d')" >> $GITHUB_ENV
+          echo "release_tag=$(LC_ALL=C date -I)" >> $GITHUB_ENV
 
       - name: Create Release
         id: create_release
         uses: actions/create-release@v1
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
-          tag_name: ${{ steps.release_name.outputs.tag }}
+          tag_name: ${{ env.release_tag }}
           commitish: main
-          release_name: Release ${{ steps.release_name.outputs.title }}
+          release_name: Release ${{ env.release_title }}
           body: "Monthly release of the GTN materials"
           draft: false
           prerelease: false
@@ -86,12 +86,12 @@ jobs:
           curl --retry 5 https://gallantries.github.io/video-library/api/sessions.json > metadata/session-library.json
           JEKYLL_ENV=production bundle exec jekyll build --strict_front_matter -d _site/training-material
         env:
-          SOURCE_TAG: ${{ steps.release_name.outputs.tag }}
+          SOURCE_TAG: ${{ env.release_tag }}
           GTN_FORK: ${{ github.repository_owner }}
 
       - name: Deploy 🚀
         run: |
           pip install awscli
           ./bin/publish-archive
         env:
-          SOURCE_TAG: ${{ steps.release_name.outputs.tag }}
+          SOURCE_TAG: ${{ env.release_tag }}

.github/workflows/video.yml

@@ -77,7 +77,7 @@ jobs:
       - name: Previous build ID
         id: build_id
         run: |
-          echo "::set-output name=commit::$(curl https://galaxy-training.s3.amazonaws.com/videos/topics/last-commit -f 2>/dev/null || echo none)"
+          echo "commit=$(curl https://galaxy-training.s3.amazonaws.com/videos/topics/last-commit -f 2>/dev/null || echo none)" >> $GITHUB_ENV
 
       # The actual compilation process deposits everything in the ./videos/ folder.
       - name: Build Videos
@@ -90,7 +90,7 @@ jobs:
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_POLLY_ACCESS_KEY_ID }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_POLLY_SECRET_ACCESS_KEY }}
           AWS_DEFAULT_REGION: us-east-1
-          PREVIOUS_COMMIT_ID: ${{ steps.build_id.outputs.commit }}
+          PREVIOUS_COMMIT_ID: ${{ env.commit }}
 
       # Deploy step, scary.
       - uses: jakejarvis/[email protected]

_layouts/faq.html

@@ -53,7 +53,7 @@ <h1>{{page.title}}</h1>
            {{ page.description }}
 
 
-           {{ content | regex_replace: '<hr.*—<\/p>', '' }}
+           {{ content | fix_box_titles:page.lang,page.path | regex_replace: '<hr.*—<\/p>', '' }}
 
         </div>
         <div class="col-md-4">

_plugins/gtn.rb

@@ -90,6 +90,10 @@ def how_many_tutorial_feedbacks(feedback, name)
       feedback.select{|x| x["tutorial"] == name}.length
     end
 
+    def fix_box_titles(content, lang, key)
+      Gtn::Boxify.replace_elements(content, lang, key)
+    end
+
     def filter_authors(contributors, contributions)
       if not contributors.nil?
         return contributors
@@ -98,6 +102,16 @@ def filter_authors(contributors, contributions)
       end
     end
 
+    def regex_replace(str, regex_search, value_replace)
+      regex = /#{regex_search}/m
+      return str.gsub(regex, value_replace)
+    end
+
+    def regex_replace_once(str, regex_search, value_replace)
+      regex = /#{regex_search}/m
+      return str.sub(regex, value_replace)
+    end
+
     def get_default_link(material)
       url = nil
 

_plugins/gtn/boxify.rb

@@ -118,6 +118,7 @@ def self.get_id(box_type, title, path)
     end
 
     def self.format_box_title(title, box_type, lang="en")
+      if lang == "" or lang.nil? then lang = "en" end
       title_fmted = ((!title.nil?) && title.length > 0 ? ": #{title}" : "")
       "#{@@BOX_TITLES[lang][box_type]}#{title_fmted}"
     end
@@ -178,7 +179,20 @@ def self.generate_box(box_type, title, lang="en", key)
       ).split(/\n/).map{|x| x.lstrip.rstrip}.join("").lstrip.rstrip
     end
 
-
+    def self.replace_elements(text, lang="en", key)
+      # We want to replace any `<x-title>(.*)</x-title>` bits
+      # And replace them one by one with "proper" boxes, based on generate_title.
+      #
+      # We're going to rely on never having two on one line
+      text.split("\n").map{|line|
+        line.gsub(/<(?<type>[a-z-]*)-title>(?<title>.*?)<\/[a-z-]*-title>/){|m|
+          title = Regexp.last_match[:title]
+          type = Regexp.last_match[:type]
+          _, box = self.generate_title(type, title, lang=lang, key)
+          box
+        }
+      }.join("\n")
+    end
   end
 end
 

_plugins/snippet.rb

@@ -88,6 +88,7 @@ def render(context)
              z = z.gsub(/\R/,"\n> ")
              #puts box_start+y+box_end
           end
+
           #if z =~ /contribute/
             #puts "=== step 3   ===\n#{z}\n\n"
             #puts "=== MARKDOWN ===\n#{box_start+z+box_end}\n\n"
@@ -135,20 +136,12 @@ def add_include_to_dependency(inclusion, context)
       end
     end
   end
+end
 
-  module RegexReplace
-    def regex_replace(str, regex_search, value_replace)
-      regex = /#{regex_search}/m
-      return str.gsub(regex, value_replace)
-    end
+Liquid::Template.register_tag("snippet", Jekyll::Tags::SnippetIncludeTag)
 
-    def regex_replace_once(str, regex_search, value_replace)
-      regex = /#{regex_search}/m
-      return str.sub(regex, value_replace)
-    end
+Jekyll::Hooks.register :pages, :post_render do |page|
+  if page.output =~ /-title>/
+    page.output = Gtn::Boxify.replace_elements(page.output, page.data.fetch('lang', 'en'), page.path)
   end
-
 end
-
-Liquid::Template.register_tag("snippet", Jekyll::Tags::SnippetIncludeTag)
-Liquid::Template.register_filter(Jekyll::RegexReplace)

assets/css/main.scss

@@ -58,6 +58,10 @@ $tutorial-box-spacing: 1rem;
 	--navbar-item-background: transparent;
 	--navbar-item-hover: transparent;
 
+	// Basically only for the breadcrumbs.
+	--secondary-color: #e9ecef;
+	--secondary-color-text: #000;
+
 	// A11y
 	--outline-color: red;
 
@@ -805,6 +809,7 @@ a {
 }
 .gitter-open-chat-button {
     background-color: var(--brand-color) !important;
+    color: var(--brand-color-contrast) !important;
 }
 
 
@@ -1153,7 +1158,7 @@ $btn-pink:$keypoints-color;
 
 .btn-purple{
  background-color: $btn-purple;
- color: white;
+ color: black;
 }
 
 .btn-pink{
@@ -1286,7 +1291,14 @@ ul.text-list, ol.text-list {
 }
 .dropdown-item:focus-visible {
 }
-.dropdown-item:focus, .dropdown-item:hover
+
+ol.breadcrumb {
+	background: var(--secondary-color);
+
+	.breadcrumb-item.active {
+		color: var(--secondary-color-text);
+	}
+}
 
 
 

assets/css/themes.scss

@@ -6,6 +6,9 @@ body.theme-night {
 	--hyperlink-hover: #fff;
 	--brand-color: #424a66;
 	--slide-heading-color: var(--text-color);
+
+	--secondary-color: #222;
+	--secondary-color-text: #fff;
 }
 
 body.theme-midnight {
@@ -18,6 +21,9 @@ body.theme-midnight {
 	--text-color: #eee;
 	--slide-heading-color: #eee;
 	--slide-heading-color: var(--text-color);
+
+	--secondary-color: #222;
+	--secondary-color-text: var(--text-color);
 }
 
 body.theme-blm {
@@ -36,6 +42,9 @@ body.theme-blm {
 	--text-color: #eee;
 	--slide-heading-color: #eee;
 	--slide-heading-color: var(--text-color);
+
+	--secondary-color: #222;
+	--secondary-color-text: var(--text-color);
 }
 
 body.theme-halloween {
@@ -51,6 +60,9 @@ body.theme-halloween {
 	--h1-theme-after: " 🎃 ";
 	--h2-theme-before: " 👻 ";
 	--h2-theme-after: " 👻 ";
+
+	--secondary-color: #402900;
+	--secondary-color-text: var(--text-color);
 }
 
 body.theme-progress, body.theme-rainbow {

faqs/galaxy/interactive_tools_jupyter_launch.md

@@ -6,10 +6,10 @@ layout: faq
 contributors: [annefou,shiltemann,nomadscientist]
 ---
 
-> ### {% icon tip %} Tip: Launch JupyterLab in Galaxy
+> <tip-title>Launch JupyterLab in Galaxy</tip-title>
 > Currently JupyterLab in Galaxy is available on [Live.useGalaxy.eu](https://live.usegalaxy.eu), [usegalaxy.org](https://usegalaxy.org) and [usegalaxy.eu](https://usegalaxy.eu).
 >
-> > ### {% icon hands_on %} Hands-on: Run JupyterLab
+> > <hands-on-title>Run JupyterLab</hands-on-title>
 > >
 > > 1. {% tool [Interactive Jupyter Notebook](interactive_tool_jupyter_notebook) %}:
 > > 2. Click Run Tool
@@ -20,10 +20,8 @@ contributors: [annefou,shiltemann,nomadscientist]
 > {: .hands_on}
 {: .tip}
 
-> ### {% icon tip %} Tip: Launch Try JupyterLab if not available on Galaxy
+> <tip-title>Launch Try JupyterLab if not available on Galaxy</tip-title>
 >
 > If JupyterLab is not available on the Galaxy instance:
 > 1. Start [Try JupyterLab](https://mybinder.org/v2/gh/jupyterlab/jupyterlab-demo/try.jupyter.org?urlpath=lab)
 {: .tip}
-
-<!-- GTN:IGNORE:010 -->

topics/genome-annotation/tutorials/annotation-with-maker/content.md

@@ -5,7 +5,6 @@
 {% endif %}
 
 # Introduction
-{:.no_toc}
 
 Genome annotation of eukaryotes is a little more complicated than for prokaryotes: eukaryotic genomes are usually larger than prokaryotes, with more genes. The sequences determining the beginning and the end of a gene are generally less conserved than the prokaryotic ones. Many genes also contain introns, and the limits of these introns (acceptor and donor sites) are not highly conserved.
 
@@ -19,7 +18,7 @@ Maker uses ab-initio predictors (like [Augustus](http://bioinf.uni-greifswald.de
 
 In this tutorial you will learn how to perform a genome annotation, and how to evaluate its quality. {% unless include.short %}You will see how training ab-initio predictors is an important step to produce good results. {% endunless %}Finally, you will learn how to use the [JBrowse](http://jbrowse.org/) genome browser to visualise the results.
 
-More information about Maker can be found [here](http://www.yandell-lab.org/software/maker.html).
+More information about Maker can be found [on their website](http://www.yandell-lab.org/software/maker.html).
 
 This tutorial was inspired by the MAKER Tutorial for [WGS Assembly and Annotation Winter School 2018](http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018), don't hesitate to consult it for more information on Maker, and on how to run it with command line.
 
@@ -685,7 +684,6 @@ You will now see new tracks displaying all the evidences used by Maker to genera
 {% endunless %}
 
 # Conclusion
-{:.no_toc}
 
 Congratulations, you finished this tutorial! You learned how to annotate an eukaryotic genome using Maker, how to evaluate the quality of the annotation, and how to visualize it using the JBrowse genome browser.
 

topics/genome-annotation/tutorials/annotation-with-maker/tutorial.md

@@ -24,4 +24,4 @@ subtopic: eukaryote
 priority: 4
 ---
 
-{% include {{ page.dir }}content.md short=false %}
+{% include topics/genome-annotation/tutorials/annotation-with-maker/content.md short=false %}

topics/genome-annotation/tutorials/functional/tutorial.md

@@ -64,7 +64,7 @@ We will annotate a small set of **protein sequences**. These sequences were pred
 >
 {: .hands_on}
 
-{% include {{ page.dir }}content.md short=true %}
+{% include topics/genome-annotation/tutorials/functional/content.md short=true %}
 
 # Conclusion
 

topics/introduction/tutorials/galaxy-intro-short/tutorial_ES.md

@@ -32,7 +32,7 @@ contributors:
 ---
 
 # Descripción General
-{:.no_toc}
+
 * Esta es una breve introducción a la interfaz de usuario de Galaxy -  La página web con la que vas a interactuar.
 * En este tutorial vamos a cubrir tareas clave en Galaxy: cargar archivos, uso de herramientas y visualización de historiales.
 
@@ -306,6 +306,5 @@ Tu ventana principal de Galaxy mostrará el historia actual como "Nuevo-Analisis
 Puedes regresar a la página "View all histories" en cualquier momento para cambiar de historial.
 
 # Conclusión
-{:.no_toc}
 
 {% icon trophy %} ¡Bien hecho! Has completado el tutorial de Breve introducción a Galaxy, donde aprendiste a nombrar un historial, cargar un archivo, utilizar una herramienta y visualizar los resultados. Hay tutoriales adicionales disponibles para una introducción más detallada a las funciones de Galaxy.

topics/metagenomics/tutorials/metatranscriptomics/content.md

@@ -27,7 +27,6 @@ In this tutorial we will perform a metatranscriptomics analysis based on the ASA
 {: .comment}
 
 # Introduction
-{:.no_toc}
 
 Microbiomes play a critical role in host health, disease, and the environment. The study of microbiota and microbial communities has been facilitated by the evolution of technologies, specifically the sequencing techniques. We can now study the microbiome dynamics by investigating the DNA content (metagenomics), RNA expression (metatranscriptomics), protein expression (metaproteomics) or small molecules (metabolomics):
 
@@ -1141,7 +1140,6 @@ Hungateiclostridium	94.67418	Hungateiclostridium_thermocellum	94.67418	UniRef90_
 We could now apply the same tool to the pathways and run similar analysis.
 
 # Conclusion
-{:.no_toc}
 
 In this tutorial, we analyzed one metatranscriptomics sample from raw sequences to community structure, functional profiling. To do that, we:
 

topics/metagenomics/tutorials/metatranscriptomics/tutorial.md

@@ -34,7 +34,4 @@ contributors:
 
 ---
 
-
-
-
-{% include {{ page.dir }}content.md short=false %}
+{% include topics/metagenomics/tutorials/metatranscriptomics/content.md short=false %}

topics/metagenomics/tutorials/mothur-miseq-sop/content.md

@@ -1661,7 +1661,7 @@ taxonomy files. In the following exercise, we will create a Krona plot with per-
 > >
 > > <br> The final result should look something like this (switch between samples via the list on the left): <br><br>
 > >
-> > <iframe id="krona" src="krona_multisample.html" frameBorder="0" width="100%" height="900px"> ![Krona](../../images/krona_multisample.png) </iframe>
+> > <iframe id="krona" src="krona_multisample.html" frameBorder="0" width="100%" height="900px"></iframe>
 > >
 > {: .solution }
 {: .question}

topics/metagenomics/tutorials/mothur-miseq-sop/tutorial.md

@@ -21,4 +21,4 @@ contributors:
   - tnabtaf
 ---
 
-{% include {{ page.dir }}content.md short=false %}
+{% include topics/metagenomics/tutorials/mothur-miseq-sop/content.md short=false %}

topics/teaching/tutorials/hybrid-training/tutorial.bib

@@ -0,0 +1,14 @@
+@article{Hall_2021,
+	doi = {10.1371/journal.pcbi.1008715},
+	url = {https://doi.org/10.1371%2Fjournal.pcbi.1008715},
+	year = 2021,
+	month = {mar},
+	publisher = {Public Library of Science ({PLoS})},
+	volume = {17},
+	number = {3},
+	pages = {e1008715},
+	author = {Christina R. Hall and Philippa C. Griffin and Andrew J. Lonie and Jeffrey H. Christiansen},
+	editor = {Patricia M. Palagi},
+	title = {Application of a bioinformatics training delivery method for reaching dispersed and distant trainees},
+	journal = {PLoS Comput Biol}
+}