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"

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>