Merge pull request #11 from fhdsl/cansavvy/adding-material

Polishing!

.github/workflows/pull_request.yml

@@ -1,5 +1,5 @@
 # Candace Savonen 2021
-# Updated Jan 2023
+# Updated May 2024
 
 name: Pull Request
 
@@ -39,11 +39,12 @@ jobs:
           branch_name='preview-${{ github.event.pull_request.number }}'
           echo branch doesnt exist
           git checkout -b $branch_name || echo branch exists
-          git push --set-upstream origin $branch_name || echo echo branch exists remotely
+          git push --set-upstream origin $branch_name || echo branch exists remotely
         shell: bash
 
 
     outputs:
+      toggle_website: "${{ env.RENDER_WEBSITE }}"
       toggle_spell_check: "${{ env.SPELL_CHECK }}"
       toggle_style_code: "${{ env.STYLE_CODE }}"
       toggle_url_check: "${{ env.URL_CHECKER }}"
@@ -101,13 +102,13 @@ jobs:
           fetch-depth: 0
 
       - name: Run styler
-        run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', recursive = TRUE, full.names = TRUE));warnings()"
+        run: Rscript -e "styler::style_file(list.files(pattern = '(R|q)md$', recursive = FALSE, full.names = TRUE));warnings()"
 
       - name: Commit styled files
         run: |
           git config --system --add safe.directory "$GITHUB_WORKSPACE"
-          git add \*.Rmd
-          git commit -m 'Style Rmds' || echo "No changes to commit"
+          git add \*md
+          git commit -m 'Style *mds' || echo "No changes to commit"
           git push origin || echo "No changes to commit"
 
 ############################# Render Preview ###################################
@@ -142,23 +143,32 @@ jobs:
       # Run bookdown rendering
       - name: Run bookdown render
         id: bookdown
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
         run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
 
-      # Run TOC-less version
-      # Rendered content for Leanpub and Coursera is very similar.
-      # This job creates a shared scaffold for both.
-      - name: Run TOC-less version of render
-        id: tocless
-        run: Rscript -e "ottrpal::render_without_toc()"
+      # Run quarto rendering
+      - name: Render quarto version
+        id: quarto
+        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
+        run: Rscript -e "quarto::quarto_render('.')"
 
       # This checks on the steps before it and makes sure that they completed.
       # If the renders didn't complete we don't want to commit the file changes
-      - name: Check on render steps
-        if: steps.bookdown.outcome != 'success' || steps.tocless.outcome != 'success'
+      - name: Check on Rmd render steps
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
         run: |
           echo Bookdown status ${{steps.bookdown.outcome}}
-          echo Toc-less status ${{steps.tocless.outcome}}
-          exit 1
+          if [${{steps.bookdown.outcome}} != 'success']; then
+            exit 1
+          fi
+
+      - name: Check on quarto render steps
+        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
+        run: |
+          echo Quarto status ${{steps.quarto.outcome}}
+          if [${{steps.quarto.outcome}} != 'success']; then
+            exit 1
+          fi
 
       - name: Website preview for download
         run: zip website-preview.zip docs/* -r
@@ -172,7 +182,7 @@ 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
 
@@ -189,12 +199,10 @@ jobs:
         run: |
           course_name=$(head -n 1 _bookdown.yml | cut -d'"' -f 2| tr " " "-")
           bookdown_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
-          tocless_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
           docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/docs/$course_name.docx")
           zip_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
           echo "zip_link=$zip_link" >> $GITHUB_OUTPUT
           echo "bookdown_link=$bookdown_link" >> $GITHUB_OUTPUT
-          echo "tocless_link=$tocless_link" >> $GITHUB_OUTPUT
           echo "docx_link=$docx_link" >> $GITHUB_OUTPUT
           echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
           echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT

.github/workflows/render-all.yml

@@ -1,5 +1,5 @@
-
-# Candace Savonen Apr 2021
+# Candace Savonen 2021
+# Updated May 2024
 
 name: Render all output courses
 
@@ -8,7 +8,7 @@ on:
   push:
     branches: [ main, staging ]
     paths:
-      - '**.Rmd'
+      - '**md$'
       - assets/*
       - quizzes/*
 
@@ -27,20 +27,19 @@ jobs:
         with:
             files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
     outputs:
-      toggle_bookdown: "${{ env.RENDER_BOOKDOWN }}"
+      toggle_website: "${{ env.RENDER_WEBSITE }}"
       toggle_coursera: "${{ env.RENDER_COURSERA }}"
       toggle_leanpub: "${{ env.RENDER_LEANPUB }}"
       make_book_txt: "${{ env.MAKE_BOOK_TXT }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
 
-  render-bookdown:
-    name: Render bookdown
+  render-course:
+    name: Render course preview
     needs: yaml-check
     runs-on: ubuntu-latest
     container:
       image: ${{needs.yaml-check.outputs.rendering_docker_image}}
-    if: ${{needs.yaml-check.outputs.toggle_bookdown == 'yes'}}
 
     steps:
       - name: checkout
@@ -57,38 +56,56 @@ jobs:
 
       # We want a fresh run of the renders each time
       - name: Delete old docs/*
-        run: rm -rf docs/*
+        run: |
+          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours
 
-      # Run bookdown rendering
+      # Run Rmd rendering
       - name: Run bookdown render
         id: bookdown
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
         run: |
+          rm -rf docs/*
           Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all');
           file.copy(from = 'assets', to = 'docs/assets', overwrite = TRUE)"
 
+      - name: Render quarto version
+        id: quarto
+        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
+        run: Rscript -e "quarto::quarto_render('.')"
+
       # This checks on the steps before it and makes sure that they completed.
       # If the renders didn't complete we don't want to commit the file changes
-      - name: Check on render step
-        if: steps.bookdown.outcome != 'success'
+      - name: Check on Rmd render steps
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
         run: |
           echo Bookdown status ${{steps.bookdown.outcome}}
-          exit 1
+          if [${{steps.bookdown.outcome}} != 'success']; then
+            exit 1
+          fi
 
-      # Commit the rendered bookdown files
-      - name: Commit rendered bookdown files
+      - name: Check on quarto render steps
+        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
+        run: |
+          echo Quarto status ${{steps.quarto.outcome}}
+          if [${{steps.quarto.outcome}} != 'success']; then
+            exit 1
+          fi
+
+      # Commit the rendered course files
+      - name: Commit rendered course files
         env:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
-          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
-          git fetch origin
           git add --force docs/*
-          git commit -m 'Render bookdown' || echo "No changes to commit"
-          git pull --allow-unrelated-histories --strategy-option=ours
+          git commit -m 'Render course' || echo "No changes to commit"
+          git status docs/*
           git push -u origin main  || echo "No changes to push"
 
   render-tocless:
     name: Render TOC-less version for Leanpub or Coursera
-    needs: [yaml-check]
+    needs: [yaml-check, render-course]
     runs-on: ubuntu-latest
     container:
       image: ${{needs.yaml-check.outputs.rendering_docker_image}}
@@ -106,31 +123,40 @@ jobs:
           git config --global --add safe.directory $GITHUB_WORKSPACE
           git config --global user.name 'github-actions[bot]'
           git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours
 
       # Rendered content for Leanpub and Coursera is very similar.
       # This job creates a shared scaffold for both.
-      - name: Run TOC-less version of render
-        id: tocless
+      - name: Run TOC-less version of render -- Rmd version
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
+        id: tocless_rmd
         run: Rscript -e "ottrpal::render_without_toc()"
 
+      - name: Run TOC-less version of render -- quarto version
+        id: tocless_quarto
+        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
+        run: |
+          Rscript -e "quarto::quarto_render('.', metadata = list(sidebar = F, toc = F),
+          quarto_args = c('--output-dir', 'docs/no_toc/'))"
+
       # Commit the TOC-less version files
       - name: Commit tocless bookdown files
         env:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
-          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
-          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 status docs/no_toc*
           git push -u origin main  || echo "No changes to push"
 
   render-leanpub:
     name: Finish Leanpub prep
     needs: [yaml-check, render-tocless]
     runs-on: ubuntu-latest
     container:
-      image: jhudsl/ottrpal:main
+      image: jhudsl/ottrpal
     if: ${{needs.yaml-check.outputs.toggle_leanpub == 'yes'}}
 
     steps:
@@ -145,6 +171,10 @@ jobs:
           git config --global --add safe.directory $GITHUB_WORKSPACE
           git config --global user.name 'github-actions[bot]'
           git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours
+          ls docs/no_toc
 
       # Create screenshots
       - name: Run the screenshot creation
@@ -165,20 +195,19 @@ jobs:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
           rm -rf manuscript/
-          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
-          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 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'
         run: |
+          echo needs.yaml-check.outputs.toggle_make_book_txt == 'yes'
+          echo needs.yaml-check.outputs.toggle_make_book_txt
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \
             chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
-            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt}}'), \
+            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt == 'yes'}}'), \
             quiz_dir = NULL)"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
@@ -187,7 +216,7 @@ jobs:
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \
             chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
-            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt}}'))"
+            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt == 'yes'}}'))"
 
       # Commit the rendered Leanpub files
       - name: Commit rendered Leanpub files
@@ -199,7 +228,8 @@ jobs:
           git add --force resources/*
           git add --force docs/*
           git commit -m 'Render Leanpub' || echo "No changes to commit"
-          git pull --allow-unrelated-histories --strategy-option=ours
+          git status docs/*
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours --autostash
           git push --force --set-upstream origin main || echo "No changes to push"
 
   render-coursera:
@@ -222,27 +252,28 @@ jobs:
           git config --global --add safe.directory $GITHUB_WORKSPACE
           git config --global user.name 'github-actions[bot]'
           git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours
 
       # Run Coursera version
       - name: Convert Leanpub quizzes to Coursera
         if: needs.yaml-check.outputs.toggle_leanpub == 'yes' && needs.yaml-check.outputs.toggle_quiz_check == 'yes'
         id: coursera
         run: Rscript -e "ottrpal::convert_coursera_quizzes()"
 
-      # Commit the rendered bookdown files
+      # Commit the rendered files
       # Only commit coursera quizzes if the directory is present
       - name: Commit rendered Coursera files
         env:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
-          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
-          git fetch origin
           if [ -d 'coursera_quizzes' ]; then
             git add --force coursera_quizzes/*
           fi
           git add --force manuscript/*
           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 status
           git push -u origin main  || echo "No changes to push"

03-why-nih-dms.Rmd

@@ -1,5 +1,3 @@
-# Why NIH DMS Policy?
-
 # Why this new DMS policy?
 
 First we will discuss the motivations behind the new data management and sharing policy that will go into effect for (most) grant proposals submitted to the NIH after January 25, 2023.
@@ -43,7 +41,7 @@ A plan describing an approach to data management, preservation, and sharing of s
 
 # How will this policy affect me?
 
-> You can refer to the [NIH overview](https://sharing.nih.gov/data-management-and-sharing-policy/about-data-management-and-sharing-policy/research-covered-under-the-data-management-sharing-policy#after){target="_blank"} of which research will be covered by this new policy.  
+> You can refer to the [NIH overview](https://sharing.nih.gov/node/112){target="_blank"} of which research will be covered by this new policy.  
 
 ```{r, echo=FALSE, fig.alt='We are on the second step of the pathway - personal considerations of the policy.', out.width = '80%', fig.align = 'center'}
 ottrpal::include_slide("https://docs.google.com/presentation/d/1luFoDzF6aDJEebbL6iWoJ_s8s9nQnaWLL5jghbmWdak/edit#slide=id.g16b04bd80e5_4_12")

05-data-privacy.Rmd

@@ -149,7 +149,7 @@ ottrpal::include_slide("https://docs.google.com/presentation/d/1SRokLaGAc2hiwJSN
 
 <!-- GINA is critical to the well-being of research participants, however this does not nullify the benefits and necessity of data sharing. Indeed both things are true: genetic data is sensitive and its protection is imperative *but* for research to benefit society and reach cures data sharing is also critical. -->
 
-<!-- So what does GINA mean in terms of data sharing? The principle of [least privilege](https://jhudatascience.org/Ethical_Data_Handling_for_Cancer_Research/data-security.html#the-principal-of-least-privilege) discussed in the previous security chapter still applies. -->
+<!-- So what does GINA mean in terms of data sharing? The principle of [least privilege](https://hutchdatascience.org/Ethical_Data_Handling_for_Cancer_Research/data-security.html#the-principal-of-least-privilege) discussed in the previous security chapter still applies. -->
 
 <!-- For many genetic data types a controlled access database is the appropriate solution to balance data sharing while maintaining the security of these data. One such database is dbGaP. dbGaP holds genetic dataset information but for individuals to gain access, they must apply and explain how their project and access will be of benefit. More details about how these applications for access are [described here](https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetPdf.cgi?document_name=GeneralAAInstructions.pdf). -->
 

08-creating-guides.Rmd

@@ -159,8 +159,9 @@ Here's some options for automated URL-checking:
 
 ### Set aside time to do maintenance
 
-TODO: Write this!
+In an academic setting it can be hard to find time for things that don't have urgent deadlines. But long term we know maintenance is best done little by little. In order to best maintain your work long term its best to set aside time on your calendar to actually do the maintenance. Otherwise it may never happen.
 
+We encourage funding institutions to recognize that maintenance is the most frugal strategy. Whether it be for software or course or other products, maintenance should be prioritized for the long term benefit of the research community. More funding opportunities should be set aside for maintenance of current products as opposed to always creating new products that will also decay if not maintained.
 
 ## Exercise 1: Add a reminder for documentation updates to your task manager
 
@@ -172,7 +173,7 @@ TODO: Write this!
 
 - If you use GitHub for your documentation, add a url checking GitHub action to your repository.
 We used a url-checker GitHub action for developing this course!
-You can see [ours here for an example](https://github.com/jhudsl/Documentation_and_Usability/blob/main/.github/workflows/url-checker.yml).  
+You can see [ours here for an example](https://github.com/jhudsl/ottr-reports).  
 - If you use something else for version control, look into URL checkers that you can easily implement into your development process.