Merge pull request #2879 from galaxyproject/update-r-notebooks

Easier link to notebook, better tagging
galaxyproject · Oct 19, 2021 · ba184c3 · ba184c3
2 parents 738506e + 2419020
commit ba184c3
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Showing 14 changed files with 53 additions and 28 deletions.
diff --git a/_layouts/tutorial_hands_on.html b/_layouts/tutorial_hands_on.html
@@ -181,6 +181,12 @@ <h3>{% icon comment aria=false %} {{locale['best-in-jupyter'] | default: "Best v
                             <li>Select the notebook that appears in the list of files on the left.</li>
                         </ol>
                     </p>
+                    <p><b>Downloading the notebook</b>
+                        <ol>
+                            <li>Right click this link: <a href="{{ site.url }}{{ site.baseurl }}/{{ page.path }}.ipynb">tutorial.ipynb</a></li>
+                            <li>Save Link As..</li>
+                        </ol>
+                    </p>
                 </blockquote>
                 {% endif %}
 

diff --git a/_plugins/notebook-page.rb b/_plugins/notebook-page.rb
@@ -239,7 +239,7 @@ def renderMarkdownCells(site, notebook, metadata, page)
 
     def generate(site)
       if find_executable('notedown').nil?
-        puts "We could not find the notedown executable, so, notebooks will not be rendered."
+        puts "[GTN/Notebooks] We could not find the notedown executable, so, notebooks will not be rendered."
         return
       end
 
@@ -267,6 +267,8 @@ def generate(site)
           notebook = fixRNotebook(notebook)
         end
 
+        puts "[GTN/Notebooks] Rendering #{notebook_language} #{fn}"
+
         # Here we loop over the markdown cells and render them to HTML. This
         # allows us to get rid of classes like {: .tip} that would be left in
         # the output by Jupyter's markdown renderer, and additionally do any

diff --git a/_plugins/sitemap.rb b/_plugins/sitemap.rb
@@ -5,7 +5,7 @@ class SitemapGenerator < Generator
     safe true
 
     def generate(site)
-      puts "Generating Sitemap"
+      puts "[GTN/Sitemap] Generating"
       result = '<?xml version="1.0" encoding="UTF-8"?>'
       result += '<urlset xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.sitemaps.org/schemas/sitemap/0.9 http://www.sitemaps.org/schemas/sitemap/0.9/sitemap.xsd" xmlns="http://www.sitemaps.org/schemas/sitemap/0.9">'
 

diff --git a/_plugins_dev/notebook-fake.rb b/_plugins_dev/notebook-fake.rb
@@ -0,0 +1,10 @@
+module Jekyll
+  class JupyterNotebookGenerator < Generator
+    safe true
+
+    def generate(site)
+      puts "[GTN/Notebooks] Disabled"
+    end
+  end
+end
+
diff --git a/topics/data-science/tutorials/cli-advanced/tutorial.md b/topics/data-science/tutorials/cli-advanced/tutorial.md
@@ -67,6 +67,9 @@ contributors:
   - carpentries
   - hexylena
   - bazante1
+tags:
+- jupyter-notebook
+- bash
 ---
 
 This tutorial will walk you through the basics of how to use the Unix command line.

diff --git a/topics/data-science/tutorials/cli-bashcrawl/tutorial.md b/topics/data-science/tutorials/cli-bashcrawl/tutorial.md
@@ -31,6 +31,8 @@ contributors:
 - hexylena
 tags:
 - game
+- jupyter-notebook
+- bash
 ---
 
 This is not a tutorial like most GTN content but a fun exercise for you to play around and learn a bit about the command line, and hopefully re-inforce the skills you covered in Basic and Advanced CLI skills.

diff --git a/topics/data-science/tutorials/cli-basics/tutorial.md b/topics/data-science/tutorials/cli-basics/tutorial.md
@@ -67,6 +67,9 @@ contributors:
   - carpentries
   - hexylena
   - bazante1
+tags:
+- jupyter-notebook
+- bash
 ---
 
 This tutorial will walk you through the basics of how to use the Unix command line.

diff --git a/topics/data-science/tutorials/r-advanced/tutorial.md b/topics/data-science/tutorials/r-advanced/tutorial.md
@@ -39,11 +39,14 @@ key_points:
 - Use the `dplyr` package to manipulate data frames.
 - Pipes can be used to combine simple operations into complex procedures.
 subtopic: r
+priority: 2
 contributors:
   - carpentries
   - bebatut
   - fpsom
   - tobyhodges
+tags:
+- R
 ---
 
 # Introduction

diff --git a/topics/data-science/tutorials/r-basics/tutorial.md b/topics/data-science/tutorials/r-basics/tutorial.md
@@ -30,7 +30,9 @@ key_points:
 - It is important to understand how data are organised by R in a given object type (e.g. numeric, character, logical, etc.) and how the mode of that type determines how R will operate on that data.
 tags:
   - interactive-tools
+  - R
 subtopic: r
+priority: 1
 contributors:
   - carpentries
   - bebatut

diff --git a/topics/data-science/tutorials/sql-advanced/tutorial.md b/topics/data-science/tutorials/sql-advanced/tutorial.md
@@ -83,6 +83,10 @@ notebook:
 
 abbreviations:
     SQL: "Structured Query Language"
+
+tags:
+- SQL
+- jupyter-notebook
 ---
 
 > ### {% icon comment %} Comment
@@ -334,7 +338,6 @@ this query:
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -362,7 +365,6 @@ this query:
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -410,7 +412,6 @@ this query:
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -431,7 +432,6 @@ this query:
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -591,7 +591,6 @@ SELECT rowid, * FROM Person;
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -616,7 +615,6 @@ SELECT rowid, * FROM Person;
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -631,7 +629,6 @@ SELECT rowid, * FROM Person;
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -675,7 +672,6 @@ SELECT rowid, * FROM Person;
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -769,7 +765,6 @@ the tool shapes the hand that shapes the tool.
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -788,7 +783,6 @@ the tool shapes the hand that shapes the tool.
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -975,7 +969,6 @@ this technique is outside the scope of this chapter.
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -1005,7 +998,6 @@ this technique is outside the scope of this chapter.
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 

diff --git a/topics/data-science/tutorials/sql-basic/tutorial.md b/topics/data-science/tutorials/sql-basic/tutorial.md
@@ -64,6 +64,10 @@ notebook:
 
 abbreviations:
     SQL: "Structured Query Language"
+
+tags:
+- SQL
+- jupyter-notebook
 ---
 
 > ### {% icon comment %} Comment
@@ -260,7 +264,6 @@ the convention that we will use for this lesson.
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -324,7 +327,6 @@ SELECT * FROM Person;
 
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -346,7 +348,6 @@ SELECT * FROM Person;
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -484,7 +485,6 @@ SELECT DISTINCT quant, person FROM Survey ORDER BY quant ASC;
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -510,7 +510,6 @@ SELECT DISTINCT quant, person FROM Survey ORDER BY quant ASC;
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -740,7 +739,6 @@ not to the entire rows as they are being processed.
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -764,7 +762,6 @@ not to the entire rows as they are being processed.
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -789,7 +786,6 @@ not to the entire rows as they are being processed.
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -877,7 +873,6 @@ issues.
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -929,7 +924,6 @@ issues.
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -966,7 +960,6 @@ issues.
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -1114,7 +1107,6 @@ detail in [the next section](#).
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -1149,7 +1141,6 @@ detail in [the next section](#).
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
 
@@ -1167,6 +1158,5 @@ detail in [the next section](#).
 {: .question}
 
 ```sql
-%%sql
 -- Try solutions here!
 ```
diff --git a/topics/data-science/tutorials/sql-game/tutorial.md b/topics/data-science/tutorials/sql-game/tutorial.md
@@ -28,6 +28,8 @@ contributors:
 - NUKnightLab
 tags:
 - game
+- SQL
+- jupyter-notebook
 ---
 
 This is not a tutorial like most GTN content but a fun exercise for you to play around and learn a bit about SQL in a more 'practical', and hopefully re-inforce the skills you covered in Basic and Advanced SQL skills. It makes use of the [NUKnightLab/sql-mysteries](https://github.com/NUKnightLab/sql-mysteries) SQL murder mystery project and released under open licenses:

diff --git a/topics/data-science/tutorials/sql-python/tutorial.md b/topics/data-science/tutorials/sql-python/tutorial.md
@@ -33,6 +33,11 @@ subtopic: sql
 
 notebook:
     language: python
+
+tags:
+- SQL
+- Python
+- jupyter-notebook
 ---
 
 > ### {% icon comment %} Comment

diff --git a/topics/data-science/tutorials/sql-r/tutorial.md b/topics/data-science/tutorials/sql-r/tutorial.md
@@ -38,6 +38,11 @@ subtopic: sql
 
 notebook:
     language: r
+
+tags:
+- SQL
+- R
+- jupyter-notebook
 ---
 
 > ### {% icon comment %} Comment