Merge branch 'main' of https://github.com/jhudsl/Adv_Reproducibility_…

…in_Cancer_Informatics into main

.github/workflows/pull_request.yml

@@ -172,7 +172,7 @@ jobs:
           echo "changes=$changes" >> $GITHUB_OUTPUT
           git add . --force
           git commit -m 'Render preview' || echo "No changes to commit"
-          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
+          git pull --rebase --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
           git push --force || echo "No changes to commit"
         shell: bash
 

.github/workflows/render-all.yml

@@ -88,7 +88,7 @@ jobs:
 
   render-tocless:
     name: Render TOC-less version for Leanpub or Coursera
-    needs: [yaml-check]
+    needs: [yaml-check, render-bookdown]
     runs-on: ubuntu-latest
     container:
       image: ${{needs.yaml-check.outputs.rendering_docker_image}}
@@ -122,7 +122,7 @@ jobs:
           git fetch origin
           git add --force docs/no_toc*
           git commit -m 'Render toc-less' || echo "No changes to commit"
-          git pull --allow-unrelated-histories --strategy-option=ours
+          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
           git push -u origin main  || echo "No changes to push"
 
   render-leanpub:
@@ -169,11 +169,11 @@ jobs:
           git fetch origin
           git add .
           git commit -m 'Delete manuscript folder' || echo "No changes to commit"
-          git pull --allow-unrelated-histories --strategy-option=ours
+          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
           git push -u origin main || echo "No changes to push"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
-        if: needs.yaml-check.outputs.toggle_quiz_check == 'no'
+        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'no'}}
         run: |
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \
@@ -182,7 +182,7 @@ jobs:
             quiz_dir = NULL)"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
-        if: needs.yaml-check.outputs.toggle_quiz_check == 'yes'
+        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'yes'}}
         run: |
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \
@@ -244,5 +244,5 @@ jobs:
           git add --force resources/*
           git add --force docs/*
           git commit -m 'Render Coursera quizzes' || echo "No changes to commit"
-          git pull --allow-unrelated-histories --strategy-option=ours
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours
           git push -u origin main  || echo "No changes to push"

docs/no_toc/About.md

@@ -46,7 +46,7 @@ These credits are based on our [course contributors table guidelines](https://gi
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2024-03-25                  
+##  date     2024-06-28                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version    date       lib source                            

docs/no_toc/about-the-authors.html

@@ -388,7 +388,7 @@ <h1>About the Authors</h1>
 ##  collate  en_US.UTF-8                 
 ##  ctype    en_US.UTF-8                 
 ##  tz       Etc/UTC                     
-##  date     2024-03-25                  
+##  date     2024-06-28                  
 ## 
 ## ─ Packages ───────────────────────────────────────────────────────────────────
 ##  package     * version    date       lib source                            

docs/no_toc/index.html

@@ -264,7 +264,7 @@ <h1>
 </div>
 <div id="header">
 <h1 class="title">Advanced Reproducibility in Cancer Informatics</h1>
-<p class="date"><em>March, 2024</em></p>
+<p class="date"><em>June, 2024</em></p>
 </div>
 <div id="about-this-course" class="section level1 unnumbered">
 <h1>About this Course</h1>

docs/no_toc/index.md

@@ -1,6 +1,6 @@
 ---
 title: "Advanced Reproducibility in Cancer Informatics"
-date: "March, 2024"
+date: "June, 2024"
 site: bookdown::bookdown_site
 documentclass: book
 bibliography: [book.bib, packages.bib]

style-sets/data-trail/_output.yml

@@ -10,7 +10,8 @@ bookdown::gitbook:
       before: |
        <a href="https://www.datatrail.org/"><img src="assets/DataTrail_logo.jpg" style="padding-left: 0px; padding-top: 8px;"</a>
       after: |
-       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
+       <p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
        <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
        <a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
        <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>

style-sets/fhdasl/_output.yml

@@ -11,7 +11,8 @@ bookdown::gitbook:
       before: |
        <a href="https://hutchdatascience.org/" target="_blank"><img src="assets/big-dasl-stacked.png" style="width: 80%; padding-left: 34px; padding-top: 8px;"</a>
       after: |
-       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
+       <p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
        <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
        <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>
        <p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span>  <a href="https://forms.gle/W6Mg4rzuMK6Yk3Am8"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>

style-sets/itcr/_output.yml

@@ -10,7 +10,8 @@ bookdown::gitbook:
       before: |
        <a href="https://www.itcrtraining.org/"><img src="assets/ITN_logo.png" style="padding-left: 15px; padding-top: 8px;"</a>
       after: |
-       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
+       <p style="text-align:center;"> <a href="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
        <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
        <a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
        <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>