From 18c0279dcdd5c800ed54b209bee0cf6c524e9d1e Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 14:14:10 -0400
Subject: [PATCH 01/21] Add GHA file updates

---
 .github/workflows/check-url.yml      | 107 +++++++++++++
 .github/workflows/delete-preview.yml |   2 +
 .github/workflows/docker-build.yml   |  79 ++++++++++
 .github/workflows/docker-test.yml    |  91 +++++++++++
 .github/workflows/pull_request.yml   | 107 ++++++++++---
 .github/workflows/render-all.yml     | 221 +++++++++++++++++++++------
 6 files changed, 537 insertions(+), 70 deletions(-)
 create mode 100644 .github/workflows/check-url.yml
 create mode 100644 .github/workflows/docker-build.yml
 create mode 100644 .github/workflows/docker-test.yml

diff --git a/.github/workflows/check-url.yml b/.github/workflows/check-url.yml
new file mode 100644
index 0000000..a437049
--- /dev/null
+++ b/.github/workflows/check-url.yml
@@ -0,0 +1,107 @@
+name: Periodic URL Check
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '0 0 1 * *'
+
+jobs:
+  set-up:
+    name: Load user automation choices
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+        # Use the yaml-env-action action.
+      - name: Load environment from YAML
+        uses: doughepi/yaml-env-action@v1.0.0
+        with:
+            files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
+    outputs:
+      toggle_url_check_periodically: "${{ env.URL_CHECK_PERIODICALLY }}"
+
+  url-check:
+    name: Check URLs
+    needs: set-up
+    if: ${{needs.set-up.outputs.toggle_url_check_periodically == 'yes'}}
+    runs-on: ubuntu-latest
+    container:
+      image: jhudsl/base_ottr:main
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+
+    # Delete the branch if this has been run before
+    - name: Delete branch locally and remotely
+      run: git push origin --delete preview-spell-error || echo "No branch to delete"
+
+    # Make the branch fresh
+    - name: Make the branch fresh
+      run: |
+        git config --global --add safe.directory $GITHUB_WORKSPACE
+        git config --global user.name 'github-actions[bot]'
+        git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+        echo branch doesnt exist
+        git checkout -b preview-spell-error || echo branch exists
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+      shell: bash
+
+    - name: Run the check
+      uses: jhudsl/ottr-reports@main
+      id: check_results
+      continue-on-error: true
+      with:
+        check_type: urls
+        error_min: 1
+
+    - name: Declare file path and time
+      id: check-report
+      run: |
+        error_num=$(cat check_reports/url_checks.tsv | wc -l)
+        error_num="$((error_num-1))"
+        echo "error_num=$error_num" >> $GITHUB_OUTPUT
+        echo "error_url=https://github.com/${GITHUB_REPOSITORY}/blob/preview-spell-error/check_reports/url_checks.tsv" >> $GITHUB_OUTPUT
+      shell: bash
+
+    - name: Stop if failure
+      if: steps.check_results.outcome == 'failure'
+      run: exit 1
+
+    - name: Print out error variables
+      run: |
+        echo ${{ steps.check-report.outputs.error_url }}
+        echo ${{ steps.check-report.outputs.error_num }}
+
+    - name: Find issues
+      id: find-issue
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
+      run: |
+        echo "$GITHUB_REPOSITORY"
+        curl -o find_issue.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/find_issue.R
+        issue_exists=$(Rscript --vanilla find_issue.R --repo $GITHUB_REPOSITORY --git_pat $GH_PAT)
+        echo URL issue exists: $issue_exists
+        echo "issue_existence=$issue_exists" >> $GITHUB_OUTPUT
+
+    - name: If too many URL errors, then make an issue
+      if: ${{ steps.check-report.outputs.error_num >= 1 && steps.find-issue.outputs.issue_existence == 0}}
+      uses: JasonEtco/create-an-issue@v2
+      with:
+        filename: .github/ISSUE_TEMPLATE/url-error.md
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        FILE_URL: ${{ steps.check-report.outputs.error_url }}
+        ERROR_NUM: ${{ steps.check-report.outputs.error_num }}
+
+    - name: If no URL errors than delete the branch we made
+      if: ${{ steps.check-report.outputs.error_num < 1 }}
+      run: |
+        git config --system --add safe.directory "$GITHUB_WORKSPACE"
+        git push origin --delete preview-spell-error || echo "No branch to delete"
diff --git a/.github/workflows/delete-preview.yml b/.github/workflows/delete-preview.yml
index 7d8cf01..faa83cc 100644
--- a/.github/workflows/delete-preview.yml
+++ b/.github/workflows/delete-preview.yml
@@ -1,3 +1,5 @@
+# Candace Savonen Apr 2021
+
 name: Delete Preview
 
 on:
diff --git a/.github/workflows/docker-build.yml b/.github/workflows/docker-build.yml
new file mode 100644
index 0000000..51a8302
--- /dev/null
+++ b/.github/workflows/docker-build.yml
@@ -0,0 +1,79 @@
+# Candace Savonen Apr 2021
+
+name: Build Docker
+
+on:
+  workflow_dispatch:
+    inputs:
+      dockerhubpush:
+        description: 'Push to Dockerhub?'
+        required: true
+        default: 'false'
+      tag:
+        description: 'What tag to use?'
+        required: true
+        default: 'none'
+jobs:
+  build-docker:
+    name: Build Docker image
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v4
+
+      - name: Login as github actions bot
+        run: |
+          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'
+
+      - name: Don't re-test if this is a sync branch
+        run: |
+          echo This was tested on OTTR_Template no need to re-run
+
+      # Set up Docker build
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      # Setup layer cache
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      # Set up Docker build
+      - name: Set up Docker Build
+        if: ${{ github.head_ref != 'repo-sync/OTTR_Template/default' }}
+        uses: docker/setup-buildx-action@v1
+
+      - name: Get token
+        run: echo ${{ secrets.GH_PAT }} > docker/git_token.txt
+
+      # Build docker image
+      - name: Build Docker image
+        uses: docker/build-push-action@v2
+        with:
+          push: false
+          load: true
+          context: docker
+          file: docker/Dockerfile
+          tags: jhudsl/base_ottr
+
+      # Login to Dockerhub
+      - name: Login to DockerHub
+        if: ${{ github.event.inputs.dockerhubpush != 'false' }}
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      # Push the Docker image if set to true from a manual trigger
+      - name: Push Docker image if manual trigger set to true
+        if: ${{ github.event.inputs.dockerhubpush != 'false' }}
+        run: |
+          docker tag jhudsl/base_ottr:latest jhudsl/base_ottr:$github.event.inputs.tag
+          docker push jhudsl/base_ottr:$github.event.inputs.tag
diff --git a/.github/workflows/docker-test.yml b/.github/workflows/docker-test.yml
new file mode 100644
index 0000000..5775f41
--- /dev/null
+++ b/.github/workflows/docker-test.yml
@@ -0,0 +1,91 @@
+
+# Candace Savonen Apr 2022
+
+name: Build Docker Image
+
+on:
+  workflow_dispatch:
+    inputs:
+      directory:
+        required: true
+        type: string
+      tag:
+        required: true
+        type: string
+      dockerhubpush:
+        description: 'Push to Dockerhub?'
+        required: false
+        default: 'false'
+        type: string
+    secrets:
+      GH_PAT:
+        required: true
+      DOCKERHUB_USERNAME:
+        required: false
+      DOCKERHUB_TOKEN:
+        required: false
+
+jobs:
+
+  build-docker:
+    name: Build Docker image
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: checkout repo
+        uses: actions/checkout@v4
+
+      - name: Verify Dockerfiles changed?
+        uses: tj-actions/verify-changed-files@v17
+        id: verify-changed-files
+        with:
+          files: |
+             ${{ inputs.directory }}/Dockerfile
+             ${{ inputs.directory }}/github_package_list.tsv
+
+      - name: Login as github actions bot
+        run: |
+          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'
+
+      # Set up Docker build
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v1
+
+      # Setup layer cache
+      - name: Cache Docker layers
+        uses: actions/cache@v2
+        with:
+          path: /tmp/.buildx-cache
+          key: ${{ runner.os }}-buildx-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-buildx-
+
+      - name: Set up Docker Build
+        uses: docker/setup-buildx-action@v1
+
+      - name: Get token
+        run: echo ${{ secrets.GH_PAT }} > ${{ inputs.directory }}/git_token.txt
+
+      - name: Build Docker image
+        uses: docker/build-push-action@v2
+        with:
+          push: false
+          load: true
+          context: ${{ inputs.directory }}
+          file: ${{ inputs.directory }}/Dockerfile
+          tags: ${{ inputs.tag }}
+
+      # Login to Dockerhub
+      - name: Login to DockerHub
+        if: ${{ inputs.dockerhubpush != 'false' }}
+        uses: docker/login-action@v1
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      # Push the Docker image if set to true from a manual trigger
+      - name: Push Docker image if manual trigger set to true
+        if: ${{ inputs.dockerhubpush != 'false' }}
+        run: docker push ${{ inputs.tag }}
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 5b9ee7b..02f5993 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -1,3 +1,6 @@
+# Candace Savonen 2021
+# Updated Jan 2023
+
 name: Pull Request
 
 on:
@@ -5,6 +8,7 @@ on:
     branches: [ main, staging ]
 
 jobs:
+
   yaml-check:
     name: Load user automation choices
     runs-on: ubuntu-latest
@@ -13,6 +17,7 @@ jobs:
         uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          token: ${{ secrets.GH_PAT }}
 
         # Use the yaml-env-action action.
       - name: Load environment from YAML
@@ -34,13 +39,16 @@ 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
+          git push --set-upstream origin $branch_name || echo echo branch exists remotely
         shell: bash
 
+
     outputs:
-      public_repository: "${{ steps.public_repository.outputs.public }}"
+      toggle_website: "${{ env.RENDER_WEBSITE }}"
       toggle_spell_check: "${{ env.SPELL_CHECK }}"
+      toggle_style_code: "${{ env.STYLE_CODE }}"
       toggle_url_check: "${{ env.URL_CHECKER }}"
+      toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
 
@@ -54,6 +62,7 @@ jobs:
       check_type: spelling
       error_min: 3
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
   url-check:
     name: Check URLs
@@ -64,6 +73,45 @@ jobs:
       check_type: urls
       error_min: 0
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
+
+  quiz-check:
+    name: Check quiz formatting
+    if: ${{needs.yaml-check.outputs.toggle_quiz_check == 'yes'}}
+    needs: yaml-check
+    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
+    with:
+      check_type: quiz_format
+      error_min: 0
+      gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
+
+############################# Style the code ###################################
+  style-code:
+    name: Style code
+    needs: yaml-check
+    runs-on: ubuntu-latest
+    if: ${{needs.yaml-check.outputs.toggle_style_code == 'yes'}}
+    container:
+      image: jhudsl/base_ottr:main
+
+    steps:
+      - name: Checkout files
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Run styler
+        run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', recursive = TRUE, 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 push origin || echo "No changes to commit"
+
+############################# Render Preview ###################################
 
   render-preview:
     name: Render preview
@@ -92,28 +140,35 @@ jobs:
           git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
         shell: bash
 
-       # Now we want to render all the html files from the qmd files
-      - name: Run render html
-        id: site
-        run: quarto render 
+      # 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 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.site.outcome != 'success'
+        if: steps.bookdown.outcome != 'success' && steps.quarto.outcome != 'success'
         run: |
-          echo site status ${{steps.site.outcome}}
+          echo Bookdown status ${{steps.bookdown.outcome}}
           exit 1
 
       - name: Website preview for download
         run: zip website-preview.zip docs/* -r
 
-      # Commit the rendered website files
-      - name: Commit rendered website files to preview branch
+      # Commit the rendered bookdown files
+      - name: Commit rendered bookdown files to preview branch
         id: commit
         run: |
           branch_name='preview-${{ github.event.pull_request.number }}'
-          git diff origin/main -- '*.html' >/dev/null && changes=true || changes=false
+          git diff origin/main -- docs >/dev/null && changes=true || changes=false
           echo "changes=$changes" >> $GITHUB_OUTPUT
           git add . --force
           git commit -m 'Render preview' || echo "No changes to commit"
@@ -122,7 +177,7 @@ jobs:
         shell: bash
 
       - name: Find Comment
-        uses: peter-evans/find-comment@v1
+        uses: peter-evans/find-comment@v2
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}
@@ -132,33 +187,37 @@ jobs:
       - name: Build components of the comment
         id: build-components
         run: |
-          course_name=$(head -n 1 _website.yml | cut -d'"' -f 2| tr " " "-")
-          website_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
-          docs_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
-          echo "docs_link=$docs_link" >> $GITHUB_OUTPUT
-          echo "website_link=$website_link" >> $GITHUB_OUTPUT
+          course_name=$(head -n 1 _bookdown.yml | cut -d'"' -f 2| tr " " "-")
+          bookdown_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
+          docx_link=$(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" >> $GITHUB_OUTPUT
+          echo "docx_link=$docx_link" >> $GITHUB_OUTPUT
           echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
           echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
           echo ${{steps.commit.outputs.changes}}
 
       - name: Create or update comment
         if: steps.commit.outputs.changes == 'true'
-        uses: peter-evans/create-or-update-comment@v1
+        uses: peter-evans/create-or-update-comment@v2
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}
           body: |
-            :eyes: [Quick Preview of Website](${{ steps.build-components.outputs.website_link }}) - Click for a preview of recent changes.
-            :file_folder: [Download Full Website](${{ steps.build-components.outputs.docs_link }}) - Download complete Zip file of the website. 
-            
-            The Quick Preview may not display all HTML features accurately, but it provides a basic overview.
+            Re-rendered previews from the latest commit:
+            - :eyes: Quick [preview of course website here](${{ steps.build-components.outputs.bookdown_link }}) \*
+            - :microscope: Comprehensive [download of the course website here](${{ steps.build-components.outputs.zip_link }})
+            - Download the [.docx file](${{ steps.build-components.outputs.docx_link }})
+
+            \* note not all html features will be properly displayed in the "quick preview" but it will give you a rough idea.
 
             _Updated at ${{ steps.build-components.outputs.time }} with changes from the latest commit ${{ steps.build-components.outputs.commit_id }}_
           edit-mode: replace
 
-      - name: No comment if no changes
+      - name: Comment if no changes
         if: steps.commit.outputs.changes == 'false'
-        uses: peter-evans/create-or-update-comment@v1
+        uses: peter-evans/create-or-update-comment@v2
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
           issue-number: ${{ github.event.pull_request.number }}
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 137040e..8dd7dc4 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -1,15 +1,22 @@
-name: Render All Output
+
+# Candace Savonen Apr 2021
+
+name: Render all output courses
 
 on:
   workflow_dispatch:
   push:
-    branches: [ main ]
+    branches: [ main, staging ]
     paths:
-      - '**/*.qmd'
+      - '**md$'
+      - assets/*
+      - quizzes/*
+      - !docs/*
 
 jobs:
+
   yaml-check:
-    name: Load User Automation Choices
+    name: Load user automation choices
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
@@ -21,35 +28,17 @@ jobs:
         with:
             files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence.
     outputs:
+      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 }}"
 
-  clean-docs:
-    name: Clean docs folder
+  render-bookdown:
+    name: Render bookdown
     needs: yaml-check
     runs-on: ubuntu-latest
-    steps:
-      - name: Checkout Repository
-        uses: actions/checkout@v4
-
-      - name: Delete all files inside docs
-        run: |
-          rm -rf docs/*
-          mkdir -p docs
-
-      - name: Commit changes
-        run: |
-          git config --global user.name 'github-actions[bot]'
-          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
-          git add docs/
-          git commit -m "Clean docs directory" || echo "No changes to commit"
-          git push
-
-  render-quarto-book:
-    name: Render Quarto Book
-    needs: [yaml-check, clean-docs]
-    runs-on: ubuntu-latest
     container:
       image: ${{needs.yaml-check.outputs.rendering_docker_image}}
 
@@ -65,37 +54,47 @@ 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'
-          echo ${{needs.yaml-check.outputs.rendering_docker_image}}
 
-      # Run quarto::quarto_render()
-      - name: Run quarto render
-        id: quarto-render
+      # We want a fresh run of the renders each time
+      - name: Delete old docs/*
+        run: rm -rf docs/*
+
+      # Run bookdown rendering
+      - name: Run bookdown render
+        id: bookdown
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
         run: |
-          Rscript -e "quarto::quarto_render()"
+          Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all');
+          file.copy(from = 'assets', to = 'docs/assets', overwrite = TRUE)"
+
+      - name: Render quarto version
+        id: tocless_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.quarto-render.outcome != 'success'
+        if: steps.bookdown.outcome != 'success'
         run: |
-          echo Quarto Render status ${{steps.quarto-render.outcome}}
+          echo Bookdown status ${{steps.bookdown.outcome}}
           exit 1
 
-      # Commit the rendered files inside docs/
-      - name: Commit rendered files
+      # Commit the rendered bookdown files
+      - name: Commit rendered 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/*
-          git commit -m 'Render Quarto Book' || echo "No changes to commit"
+          git commit -m 'Render bookdown' || echo "No changes to commit"
           git pull --allow-unrelated-histories --strategy-option=ours
           git push -u origin main  || echo "No changes to push"
 
   render-tocless:
-    name: Render TOC-less Quarto Book
-    needs: [yaml-check, clean-docs, render-quarto-book]
+    name: Render TOC-less version for Leanpub or Coursera
+    needs: [yaml-check]
     runs-on: ubuntu-latest
     container:
       image: ${{needs.yaml-check.outputs.rendering_docker_image}}
@@ -114,20 +113,150 @@ jobs:
           git config --global user.name 'github-actions[bot]'
           git config --global user.email 'github-actions[bot]@users.noreply.github.com'
 
-      # Rendered content for Leanpub and Coursera is similar.
+      # 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: toc_less_quarto
-        run: Rscript -e "quarto::quarto_render('.', quarto_args = c('--output-dir', 'docs/no_toc'), metadata = list(sidebar = F, toc = F))"
+      - 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 TOC-less Quarto 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 Quarto Book' || echo "No changes to commit"
+          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 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
+    if: ${{needs.yaml-check.outputs.toggle_leanpub == 'yes'}}
+
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.GH_PAT }}
+
+      - name: Login as github actions bot
+        run: |
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+      # Create screenshots
+      - name: Run the screenshot creation
+        run: |
+          # Remove old folder
+          rm -rf resources/chapt_screen_images
+
+          # Make new screenshots
+          curl -o make_screenshots.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/make_screenshots.R
+          chapt_urls=$(Rscript --vanilla make_screenshots.R \
+            --git_pat ${{ secrets.GH_PAT }} \
+            --repo $GITHUB_REPOSITORY \
+            --output_dir resources/chapt_screen_images)
+
+      # We want a fresh run of the renders each time
+      - name: Delete manuscript/
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+        run: |
+          rm -rf manuscript/
+          git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
+          git fetch origin
+          git add .
+          git commit -m 'Delete manuscript folder' || echo "No changes to commit"
+          git pull --allow-unrelated-histories --strategy-option=ours
+          git push -u origin main || echo "No changes to push"
+
+      - name: Run ottrpal::bookdown_to_embed_leanpub
+        if: needs.yaml-check.outputs.toggle_quiz_check == 'no'
+        run: |
+          Rscript -e "ottrpal::bookdown_to_embed_leanpub(
+            render = FALSE, \
+            chapt_img_key = 'resources/chapt_screen_images/chapter_urls.tsv', \
+            make_book_txt = as.logical('${{needs.yaml-check.outputs.make_book_txt}}'), \
+            quiz_dir = NULL)"
+
+      - name: Run ottrpal::bookdown_to_embed_leanpub
+        if: needs.yaml-check.outputs.toggle_quiz_check == 'yes'
+        run: |
+          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}}'))"
+
+      # Commit the rendered Leanpub files
+      - name: Commit rendered Leanpub files
+        env:
+          GH_PAT: ${{ secrets.GH_PAT }}
+        run: |
+          mkdir -p manuscript
+          git add --force manuscript/*
+          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 push --force --set-upstream origin main || echo "No changes to push"
+
+  render-coursera:
+    name: Finish Coursera prep
+    needs: [yaml-check, render-tocless]
+    runs-on: ubuntu-latest
+    container:
+      image: ${{needs.yaml-check.outputs.rendering_docker_image}}
+    if: ${{needs.yaml-check.outputs.toggle_coursera == 'yes'}}
+
+    steps:
+      - name: checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ secrets.GH_PAT }}
+
+      - name: Login as github action
+        run: |
+          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'
+
+      # 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
+      # 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 push -u origin main  || echo "No changes to push"

From 6d37220701665471fe7ec76cd51b14a3aa7090e0 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 14:37:04 -0400
Subject: [PATCH 02/21] Update pull_request.yml for outcome checks

---
 .github/workflows/pull_request.yml | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 02f5993..5490000 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -154,11 +154,21 @@ jobs:
 
       # 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.quarto.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
+
+      - 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

From 6892193ef6d4c8f15b2914208608c171627ee22c Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 14:53:24 -0400
Subject: [PATCH 03/21] Update dictionary

---
 resources/dictionary.txt | 243 +++++++++++++++++++++++++++++++++++++++
 1 file changed, 243 insertions(+)

diff --git a/resources/dictionary.txt b/resources/dictionary.txt
index aeef22e..9180d42 100644
--- a/resources/dictionary.txt
+++ b/resources/dictionary.txt
@@ -1,3 +1,246 @@
+acm
+ACM
+adipiscing
+aenean
+aenean
+Aenean
+aliqua
+aliqua
+aliquam
+aliquet
+amet
+amet
+Amet
+arcu
+auctor
+augue
+BAUjQigf
+BeQ
+Bibendum
+blandit
+bookdown
+cheatsheet
+cheatsheet
+commodo
+Computable
+congue
+consectetur
+consectetur
+consequat
+Consequat
+Convallis
+coursera
+cras
+Cras
+cursus
+das
+dev
+DfFD
+Dignissim
+dir
+dir
+dir
+dl
+doi
+dolore
+donec
+dui
+Dw
+dWF
+edu
+egestas
+eget
+eiusmod
+eleifend
+Eleifend
+elementum
+elit
+enim
+Entscheidungsproblem
+erat
+Erat
+EShgZhvtb
+et
+Et
+etiam
+eu
+euismod
+euismod
+Facilisi
+facilisis
+fames
+faucibus
+fbee
+felis
+fermentum
+Fermentum
+feugiat
+fhdsl
+fN
+FNbr
+fqpgAfWkr
+fringilla
+fringilla
+Fringilla
+gcc
+gdQ
+gfs
+Ghemawat
+github
+Gobioff
+gravida
+habitant
+hendrerit
+Hendrerit
+https
+https
+HTZrc
+hySN
+hySN
+iaculis
+iDX
+ieee
+ieeexplore
+iframe
+img
+imperdiet
+incididunt
+interdum
+ipsum
+itcr
+jhudsl
+justo
+knitr
+labore
+Lacus
+leanpub
+lectus
+Lectus
+leo
+Leung
+libero
+lobortis
+Lobortis
+lorem
+Lorem
+maecenas
+Maecenas
+magna
+magnis
+magrittr
+malesuada
+massa
+Massa
+mauris
+Mauris
+Metus
+MgR
+MgR
+MgR
+molestie
+Molestie
+mollis
+montes
+morbi
+morbi
+nam
+Natoque
+nec
+neque
+netus
+nibh
+nisi
+nulla
+nulla
+nullam
+nunc
+Nunc
+odio
+odio
+orci
+ottr
+ottr
+OTTR
+ottrproject
+oxfordjournals
+pandoc
+pandocs
+parturient
+pellentesque
+penatibus
+phasellus
+Phasellus
+placerat
+png
+porta
+porttitor
+posuere
+praesent
+pretium
+proin
+pulvinar
+purus
+px
+quam
+quis
+Quis
+quisque
+rBb
+rhoncus
+Rhoncus
+risus
+rmarkdown
+rstudio
+rutrum
+sagittis
+sapien
+Scelerisque
+sed
+sed
+sem
+sem
+semper
+Semper
+senectus
+sollicitudin
+sosp
+src
+src
+src
+suspendisse
+tellus
+tempor
+tempor
+tempus
+tincidunt
+Tincidunt
+tortor
+Tortor
+tristique
+turpis
+ultrices
+ultricies
+urna
+ut
+ut
+varius
+vehicula
+vel
+vestibulum
+virginia
+vivamus
+viverra
+Viverra
+VOCYL
+volutpat
+vulputate
+Vulputate
+wip
+wp
+xh
+yihui
+YmwKdIy
+youtube
 ai
 Ai
 AI

From 702ec88ca6c0bcee4bc69458700006f5b74c803b Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 14:55:23 -0400
Subject: [PATCH 04/21] Updates to comments

---
 .github/workflows/render-all.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 8dd7dc4..4c2c22e 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -35,8 +35,8 @@ jobs:
       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:
@@ -80,8 +80,8 @@ jobs:
           echo Bookdown status ${{steps.bookdown.outcome}}
           exit 1
 
-      # Commit the rendered bookdown files
-      - name: Commit rendered bookdown files
+      # Commit the rendered course files
+      - name: Commit rendered course files
         env:
           GH_PAT: ${{ secrets.GH_PAT }}
         run: |
@@ -243,7 +243,7 @@ jobs:
         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:

From 6ae406a7993e1a948df224df8008bc3b321e1a4a Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 14:56:22 -0400
Subject: [PATCH 05/21] Update github actions comments

---
 .github/workflows/pull_request.yml | 2 +-
 .github/workflows/render-all.yml   | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 5490000..eff0ee0 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -1,5 +1,5 @@
 # Candace Savonen 2021
-# Updated Jan 2023
+# Updated May 2024
 
 name: Pull Request
 
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 4c2c22e..b545e7a 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -1,5 +1,5 @@
-
-# Candace Savonen Apr 2021
+# Candace Savonen 2021
+# Updated May 2024
 
 name: Render all output courses
 

From d4eb0330069d459e708089fa68a827cee2ccd340 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 14:57:15 -0400
Subject: [PATCH 06/21] render-website: quarto

---
 config_automation.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config_automation.yml b/config_automation.yml
index a5fb422..d198f18 100644
--- a/config_automation.yml
+++ b/config_automation.yml
@@ -15,7 +15,7 @@ docker-test: no
 
 ##### Renderings run upon merge to main branch #####
 # Rendering each platform's content
-render-bookdown: yes
+render-website: quarto
 render-leanpub: yes
 render-coursera: no
 

From db8cf0754f2b6e389754b8118953de1a6551ac99 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 15:25:11 -0400
Subject: [PATCH 07/21] -1 echo

---
 .github/workflows/pull_request.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index eff0ee0..153b43d 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -39,7 +39,7 @@ 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
 
 

From 9cb8a2b2608b5ae2b4f3229bce7c737996273cc8 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 15:28:57 -0400
Subject: [PATCH 08/21] Delete some text to test preview

---
 intro.qmd | 2 --
 1 file changed, 2 deletions(-)

diff --git a/intro.qmd b/intro.qmd
index f815c20..82db80e 100644
--- a/intro.qmd
+++ b/intro.qmd
@@ -1,7 +1,5 @@
 # Introduction to the Course
 
-Testing testing
-
 We think understanding AI is essential for executives. It helps today’s leaders make strategic decisions, drive innovation, enhance efficiency, and foster a culture that embraces the transformative power of these technologies. Specifically, AI proficiency can help leaders in the following ways.
 
 

From ea00b2c56e9f5755bc59c44d8cf7b561f94fb161 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 15:35:08 -0400
Subject: [PATCH 09/21] Add updates for status checks for quarto or rmd

---
 .github/workflows/render-all.yml | 16 +++++++++++++---
 1 file changed, 13 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index b545e7a..873357d 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -74,11 +74,21 @@ jobs:
 
       # 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
+
+      - 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

From bffdaf394779217d5b3058b3d85c0001ce311c1d Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 15:42:47 -0400
Subject: [PATCH 10/21] Fix spelling and style code

---
 .github/workflows/pull_request.yml | 2 +-
 resources/dictionary.txt           | 2 ++
 2 files changed, 3 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 153b43d..f3d5478 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -102,7 +102,7 @@ jobs:
           fetch-depth: 0
 
       - name: Run styler
-        run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', recursive = TRUE, full.names = TRUE));warnings()"
+        run: Rscript -e "styler::style_file(list.files(pattern = 'md$', recursive = FALSE, full.names = TRUE));warnings()"
 
       - name: Commit styled files
         run: |
diff --git a/resources/dictionary.txt b/resources/dictionary.txt
index 9180d42..e336441 100644
--- a/resources/dictionary.txt
+++ b/resources/dictionary.txt
@@ -131,6 +131,7 @@ magrittr
 malesuada
 massa
 Massa
+mattis
 mauris
 Mauris
 Metus
@@ -203,6 +204,7 @@ semper
 Semper
 senectus
 sollicitudin
+scelerisque	
 sosp
 src
 src

From 5b02ae745500cf426f05a658400c7054f3eb9d27 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 15:46:14 -0400
Subject: [PATCH 11/21] Fix styler step part 2

---
 .github/workflows/pull_request.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index f3d5478..8b58960 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -107,8 +107,8 @@ jobs:
       - 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 ###################################

From 892c846849475f05283f9c4f941d30031f72ddf8 Mon Sep 17 00:00:00 2001
From: Howard Baek <50791792+howardbaek@users.noreply.github.com>
Date: Wed, 15 May 2024 14:06:11 -0700
Subject: [PATCH 12/21] Address bug: `Unexpected tag '!docs/*'`

---
 .github/workflows/render-all.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 873357d..c2ba36c 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -11,7 +11,6 @@ on:
       - '**md$'
       - assets/*
       - quizzes/*
-      - !docs/*
 
 jobs:
 

From 65d3c78d4a6b53147ea2e8bd799b02e7e7639bd5 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 16 May 2024 08:11:12 -0400
Subject: [PATCH 13/21] Fix styler part 3

---
 .github/workflows/pull_request.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 8b58960..9867bc2 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -102,7 +102,7 @@ jobs:
           fetch-depth: 0
 
       - name: Run styler
-        run: Rscript -e "styler::style_file(list.files(pattern = 'md$', recursive = FALSE, full.names = TRUE));warnings()"
+        run: Rscript -e "styler::style_file(list.files(pattern = '(R|q)md$', recursive = FALSE, full.names = TRUE));warnings()"
 
       - name: Commit styled files
         run: |

From 3bfb0e15221edfd99c2618d680fa665d839ef1fa Mon Sep 17 00:00:00 2001
From: Howard Baek <50791792+howardbaek@users.noreply.github.com>
Date: Fri, 14 Jun 2024 11:19:58 -0700
Subject: [PATCH 14/21] Change the docker image

---
 config_automation.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config_automation.yml b/config_automation.yml
index d198f18..2dd2347 100644
--- a/config_automation.yml
+++ b/config_automation.yml
@@ -21,4 +21,4 @@ render-coursera: no
 
 # What docker image should be used for rendering?
 # The default is jhudsl/base_ottr:latest
-rendering-docker-image: 'jhudsl/ottr_quarto:latest'
+rendering-docker-image: 'jhudsl/base_ottr:main'

From 7e2cdf98e8b6f4bdecc867a21080acf8bb630612 Mon Sep 17 00:00:00 2001
From: Howard Baek <50791792+howardbaek@users.noreply.github.com>
Date: Fri, 21 Jun 2024 11:07:39 -0700
Subject: [PATCH 15/21] Switch Docker image to `ottr_quarto`

---
 config_automation.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/config_automation.yml b/config_automation.yml
index 2dd2347..83fdbd6 100644
--- a/config_automation.yml
+++ b/config_automation.yml
@@ -21,4 +21,4 @@ render-coursera: no
 
 # What docker image should be used for rendering?
 # The default is jhudsl/base_ottr:latest
-rendering-docker-image: 'jhudsl/base_ottr:main'
+rendering-docker-image: 'jhudsl/ottr_quarto:main'

From 0fca99381e02f78e0d8e1218daca785c3eebf2e7 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Mon, 24 Jun 2024 14:25:09 -0400
Subject: [PATCH 16/21] It's not pulling the ottr_quarto docker image

---
 .github/workflows/render-all.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index c2ba36c..4987013 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -153,7 +153,7 @@ jobs:
     needs: [yaml-check, render-tocless]
     runs-on: ubuntu-latest
     container:
-      image: jhudsl/ottrpal:main
+      image: ${{needs.yaml-check.outputs.rendering_docker_image}}
     if: ${{needs.yaml-check.outputs.toggle_leanpub == 'yes'}}
 
     steps:

From 3dc8be6290e2b871ae5d6990abe2c04de28b7378 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Mon, 24 Jun 2024 14:33:05 -0400
Subject: [PATCH 17/21] Update pull_request.yml

---
 .github/workflows/pull_request.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 9867bc2..5cd835e 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -182,7 +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
 

From 4eac593c206461f761d8bb0dba7a672ab43e04b1 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Mon, 24 Jun 2024 14:34:08 -0400
Subject: [PATCH 18/21] Update render-all.yml

---
 .github/workflows/render-all.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 4987013..c2ba36c 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -153,7 +153,7 @@ jobs:
     needs: [yaml-check, render-tocless]
     runs-on: ubuntu-latest
     container:
-      image: ${{needs.yaml-check.outputs.rendering_docker_image}}
+      image: jhudsl/ottrpal:main
     if: ${{needs.yaml-check.outputs.toggle_leanpub == 'yes'}}
 
     steps:

From e8934943ae097b7654ffd5fc94de720bfe95dae2 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 26 Jun 2024 08:58:41 -0400
Subject: [PATCH 19/21] Update render-all.yml

---
 .github/workflows/render-all.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index c2ba36c..34cbb15 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -153,7 +153,7 @@ jobs:
     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:

From 70e8b2f07caa6ab52c3476a2d02cf2b9f597b467 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 26 Jun 2024 10:24:55 -0400
Subject: [PATCH 20/21] Update render-all.yml

---
 .github/workflows/render-all.yml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 34cbb15..b4b3955 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -98,12 +98,12 @@ jobs:
           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 pull --rebase --allow-unrelated-histories --strategy-option=ours
           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}}
@@ -145,7 +145,7 @@ 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 --rebase --allow-unrelated-histories --strategy-option=ours
           git push -u origin main  || echo "No changes to push"
 
   render-leanpub:
@@ -192,7 +192,7 @@ 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 --rebase --allow-unrelated-histories --strategy-option=ours
           git push -u origin main || echo "No changes to push"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
@@ -222,7 +222,7 @@ 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 pull --rebase --allow-unrelated-histories --strategy-option=ours
           git push --force --set-upstream origin main || echo "No changes to push"
 
   render-coursera:
@@ -267,5 +267,5 @@ 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"

From 1a4955629105d7708e5ce381086c5305778a751b Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 26 Jun 2024 10:34:21 -0400
Subject: [PATCH 21/21] Update render-all.yml

---
 .github/workflows/render-all.yml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index b4b3955..c5e2bc5 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -58,7 +58,7 @@ jobs:
       - name: Delete old docs/*
         run: rm -rf docs/*
 
-      # Run bookdown rendering
+      # Run Rmd rendering
       - name: Run bookdown render
         id: bookdown
         if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
@@ -67,7 +67,7 @@ jobs:
           file.copy(from = 'assets', to = 'docs/assets', overwrite = TRUE)"
 
       - name: Render quarto version
-        id: tocless_quarto
+        id: quarto
         if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
         run: Rscript -e "quarto::quarto_render('.')"
 
@@ -97,7 +97,7 @@ jobs:
           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 commit -m 'Render course' || echo "No changes to commit"
           git pull --rebase --allow-unrelated-histories --strategy-option=ours
           git push -u origin main  || echo "No changes to push"