Push for Canelle and Ben

Author: bioinformatics-ca

.Rproj.user/9462ED09/pcs/files-pane.pper

@@ -1,12 +1,12 @@
 {
     "sortOrder": [
-        {
-            "columnIndex": 4,
-            "ascending": false
-        },
         {
             "columnIndex": 2,
             "ascending": true
+        },
+        {
+            "columnIndex": 4,
+            "ascending": false
         }
     ],
     "path": "~/Documents/CBWGithub/bookdown-guide"

.Rproj.user/9462ED09/pcs/source-pane.pper

@@ -1,3 +1,3 @@
 {
-    "activeTab": 6
+    "activeTab": 5
 }

.Rproj.user/9462ED09/sources/prop/INDEX

@@ -11,6 +11,7 @@
 ~%2FDocuments%2FCBWGithub%2Fbookdown-guide%2F0033-faculty.Rmd="4240BBAF"
 ~%2FDocuments%2FCBWGithub%2Fbookdown-guide%2F0034-clone.Rmd="4C99AC25"
 ~%2FDocuments%2FCBWGithub%2Fbookdown-guide%2F0034-finishingtouches.Rmd="CCF0636F"
+~%2FDocuments%2FCBWGithub%2Fbookdown-guide%2F0035-finishingtouches.Rmd="8DF09C6D"
 ~%2FDocuments%2FCBWGithub%2Fbookdown-guide%2F0036-whatsnext.Rmd="1E2FAB72"
 ~%2FDocuments%2FCBWGithub%2Fbookdown-guide%2F016-last.Rmd="7DC9A443"
 ~%2FDocuments%2FCBWGithub%2Fbookdown-guide%2F020-reference.Rmd="712294FF"

.Rproj.user/shared/notebooks/paths

@@ -6,6 +6,7 @@
 /Users/nhughes/Documents/CBWGithub/bookdown-guide/0033-faculty.Rmd="25E83ABE"
 /Users/nhughes/Documents/CBWGithub/bookdown-guide/0034-clone.Rmd="47832F6D"
 /Users/nhughes/Documents/CBWGithub/bookdown-guide/0034-finishingtouches.Rmd="9FA243AD"
+/Users/nhughes/Documents/CBWGithub/bookdown-guide/0035-finishingtouches.Rmd="0C0F301B"
 /Users/nhughes/Documents/CBWGithub/bookdown-guide/0036-whatsnext.Rmd="4F28809C"
 /Users/nhughes/Documents/CBWGithub/bookdown-guide/016-last.Rmd="C5070CAB"
 /Users/nhughes/Documents/CBWGithub/bookdown-guide/020-reference.Rmd="0587BF6F"

0010-cheatsheet.Rmd

@@ -60,19 +60,25 @@ This section is a quick reference on setting up GitHub Pages site for workshops.
 Add your pre-work, schedule, and faculty details. When slides and lab materials are ready, include them in their respective modules.
 
 # Editing Your Workshop {#editing-cheatsheet}
-1. [If you don't already have your repo cloned:](#clone)
+1.  [If you don't already have your repo cloned:](#clone)
 
 * On your repo page on GitHub's website, click the green Code button, ensure SSH is selected, and copy the text in the box
 * On your local machine, open your terminal and navigate to the folder where you store your CBW Github repos
 * Run ``git clone [THE TEXT YOU JUST COPIED]``
 
-2. Make any changes you like
+2.  Make any changes you like, but don't forget:
 
-3. [Click Build to create the HTML files that make up the website](#finishing-touches)
+    :::: {.callout type="red" title="Remember to pull first!" style="subtle" icon="fas fa-circle-info"}
+    
+    **Remember to always run `git pull` before making changes**. It doesn't matter if you do this in RStudio or the command line, but it will save you serious headaches down the road.
+    
+    ::::
 
-4. [Commit and push](#finishing-touches)
+3.  [Click Build to create the HTML files that make up the website](#finishing-touches)
 
-5. Your website will be ready in 1-2 minutes
+4.  [Commit and push](#finishing-touches)
+
+5.  Your website will be ready in 1-2 minutes
 
 For more details on this process, see the Reference Materials section below.
 

0036-whatsnext.Rmd

@@ -2,6 +2,12 @@
 
 Now that you have your repo set up, you can start filling it out! Some of the details you'll need to include are below.
 
+:::: {.callout type="red" title="Remember to pull first!" style="subtle" icon="fas fa-circle-info"}
+
+**Remember to always run `git pull` before making changes**. It doesn't matter if you do this in RStudio or the command line, but it will save you serious headaches down the road.
+
+::::
+
 ## Homepage
 The index.Rmd file creates your landing page, which has a few different components.
 
@@ -98,6 +104,12 @@ Copy the below code chunk and paste into your slide. Replace `YOUTUBE EMBED LINK
 ### Adding lab material
 RCs and faculty can add lab material directly into your bookdown website. Use the details in the Formatting section below to include features like code chunks, callouts, and images.
 
+## Bioschemas
+The `_bioschemas.html` file contains the Bioschemas metadata. It is mostly complete, but you'll need to update:  
+
+* *inLanguage* if the language is not English  
+* *keywords* with 3-5 keywords  
+
 ## What if I need to add a new file or change the existing file structure?
 Bookdown renders the Rmd files in the main repo in alphabetical order, hence the numbers at the beginning of each file. To create a new file, simply name it starting with the numbers that place it where you want it in your output website.
 

016-last.Rmd

@@ -1,6 +1,6 @@
 # (PART) Formatting {-}
-<!--    ![Image showing how to ](img/template/.png)\
-    <br>-->
+
+# Markdown {#markdown}
 
 
 # Callouts {#callouts}
@@ -70,22 +70,22 @@ You can override any of these defaults by specifying a different icon class, for
 
 Here are some practical examples you can copy and adapt.
 
-### Example 1: Static Informational Note
+### Example 1: Informational Note
 
-A standard blue callout for providing information.
+A subtle blue callout for providing information.
 
 ```markdown
-:::: {.callout type="blue" title="Information"}
+:::: {.callout type="blue" title="Information" style="subtle"}
 
-This is a standard blue informational callout.
+This is a blue informational callout using the Subtle styling.
 The default icon for 'blue' will be used.
 
 ::::
 ```
 
-:::: {.callout type="blue" title="Information"}
+:::: {.callout type="blue" title="Information" style="subtle"}
 
-This is a standard blue informational callout.
+This is a blue informational callout using the Subtle styling.
 The default icon for 'blue' will be used.
 
 ::::
@@ -227,3 +227,10 @@ You can nest callouts inside other elements, such as lists, by indenting the ent
     ::::
 
 3.  This is the third item in the list, appearing after the callout.
+
+
+
+# Code {#code}
+
+
+

020-reference.Rmd

@@ -1,5 +1,7 @@
 # (PART) Reference Material {-}
 
+# Command line crash course {#command-line}
+
 # Bookdown crash course {#bookdown-crash-course}
 
 Here is a general summary of how Bookdown creates html websites from .Rmd files when you hit Build.
@@ -269,3 +271,4 @@ Now, we're done! We should see the updates on GitHub now. Also note, if we ever
 
 Git pushing will automatically update the website, you can see the updates and progress in the actions window we saw previously. (Check out your website on the web once it's done deploying!)
 
+# Danger zones {#danger-zones}

_output.yml

@@ -14,8 +14,7 @@ bookdown::gitbook:
         <a href="https://bioinformaticsdotca.github.io/">
          <img src="img/bioinformatics_logo.png" width="90%" alt="bioinformatics.ca logo" style="display:block; margin-left:auto; margin-right:auto; margin-top:15px;">
          </a>
-        <li><center><strong><a href="./"><br>CBW Bookdown Guide<br><br></a></strong></center></li>
-        <br>
+        <li><center><strong><a href="./"><br>CBW Bookdown Guide</a></strong></center></li>
 
       after: |
         <h1 id="sponsors">Sponsors</h1>