From df47bf26bc31871091b79a162def8fbbfff46951 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 18 Apr 2024 15:42:28 -0400
Subject: [PATCH 01/10] Update render-all.yml

---
 .github/workflows/render-all.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 12643d87..37f396d4 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -8,9 +8,10 @@ on:
   push:
     branches: [ main, staging ]
     paths:
-      - '**.Rmd'
+      - '**md$'
       - assets/*
       - quizzes/*
+      - !docs/*
 
 jobs:
 

From f16ef32abadd82fb21d7c19b639599e774b12ace Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 18 Apr 2024 15:50:01 -0400
Subject: [PATCH 02/10] add if statement

---
 .github/workflows/render-all.yml | 13 +++++++++----
 1 file changed, 9 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 37f396d4..f8e1de64 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -28,7 +28,7 @@ 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 }}"
@@ -41,7 +41,6 @@ jobs:
     runs-on: ubuntu-latest
     container:
       image: ${{needs.yaml-check.outputs.rendering_docker_image}}
-    if: ${{needs.yaml-check.outputs.toggle_bookdown == 'yes'}}
 
     steps:
       - name: checkout
@@ -110,10 +109,16 @@ jobs:
 
       # 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))"
+      
       # Commit the TOC-less version files
       - name: Commit tocless bookdown files
         env:

From ce7a8fe741b664d8c74463e7e0fc5984698800c1 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Thu, 18 Apr 2024 15:50:52 -0400
Subject: [PATCH 03/10] Update config_automation.yml

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

diff --git a/config_automation.yml b/config_automation.yml
index 1a1a5776..9258b069 100644
--- a/config_automation.yml
+++ b/config_automation.yml
@@ -17,7 +17,7 @@ url-check-periodically: yes
 
 ##### Renderings run upon merge to main branch #####
 # Rendering each platform's content
-render-bookdown: yes
+render-website: rmd
 render-leanpub: yes
 render-coursera: no
 

From 5cd8c8e534cde44369f818288e671334da273ed6 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 15 May 2024 13:48:24 -0400
Subject: [PATCH 04/10] Add quarto rendering

---
 .github/workflows/render-all.yml | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index f8e1de64..8dd7dc44 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -62,10 +62,16 @@ 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');
           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
@@ -110,15 +116,17 @@ jobs:
       # Rendered content for Leanpub and Coursera is very similar.
       # This job creates a shared scaffold for both.
       - name: Run TOC-less version of render -- Rmd version
-        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }} 
+        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))"
-      
+        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:

From 2ed2b72c0cfb7abc5c9257eff8c6eb14a4e2eaee Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 15 May 2024 13:58:30 -0400
Subject: [PATCH 05/10] Update pull request.yml

---
 .github/workflows/pull_request.yml | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index d81d7802..02f59937 100644
--- a/.github/workflows/pull_request.yml
+++ b/.github/workflows/pull_request.yml
@@ -44,6 +44,7 @@ jobs:
 
 
     outputs:
+      toggle_website: "${{ env.RENDER_WEBSITE }}"
       toggle_spell_check: "${{ env.SPELL_CHECK }}"
       toggle_style_code: "${{ env.STYLE_CODE }}"
       toggle_url_check: "${{ env.URL_CHECKER }}"
@@ -142,22 +143,21 @@ 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'
+        if: steps.bookdown.outcome != 'success' && steps.quarto.outcome != 'success'
         run: |
           echo Bookdown status ${{steps.bookdown.outcome}}
-          echo Toc-less status ${{steps.tocless.outcome}}
           exit 1
 
       - name: Website preview for download
@@ -189,12 +189,10 @@ 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

From 50cde80fd9dc360e69e4854858ccf57f72b46643 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 14:16:06 -0400
Subject: [PATCH 06/10] Add fhdsl/ottr to sync.yml

---
 .github/sync.yml | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/.github/sync.yml b/.github/sync.yml
index af867704..f0e528c0 100755
--- a/.github/sync.yml
+++ b/.github/sync.yml
@@ -67,7 +67,8 @@ group:
       fhdsl/WDL_Workflows_Guide
       fhdsl/S2-Collaborative-Git-GitHub
       fhdsl/GitHub_Automation_for_Scientists
-      williamtmillsiv/introduction_to_bioinformatics 
+      williamtmillsiv/introduction_to_bioinformatics
+      fhdsl/ottr
 ###ADD NEW REPO HERE following the format above#
 
 ### These are custom groups for syncing -- not all files needs to be synced
@@ -144,7 +145,7 @@ group:
       deleteOrphaned: true
     repos: |
       C-MOOR/C-MOOR_Template
-      
+
   - files:
     - source: config_automation.yml
       dest: config_automation.yml

From e84527ca38348681f0d2474305529809eb81c1b0 Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Wed, 15 May 2024 15:51:00 -0400
Subject: [PATCH 07/10] Update with the changes on fhdsl/ottr

---
 .github/workflows/pull_request.yml | 26 ++++++++++++++++++--------
 .github/workflows/render-all.yml   | 30 ++++++++++++++++++++----------
 2 files changed, 38 insertions(+), 18 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 02f59937..8b589602 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
 
@@ -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
 
 
@@ -102,13 +102,13 @@ jobs:
           fetch-depth: 0
 
       - name: Run styler
-        run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', recursive = TRUE, full.names = TRUE));warnings()"
+        run: Rscript -e "styler::style_file(list.files(pattern = 'md$', 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 ###################################
@@ -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
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 8dd7dc44..873357d5 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
 
@@ -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:
@@ -74,14 +74,24 @@ 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 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 +253,7 @@ 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 fc8ccb29aa309b7f2e5e79fcf5ec3e8487d749ec Mon Sep 17 00:00:00 2001
From: cansavvy <cansav09@gmail.com>
Date: Thu, 16 May 2024 08:14:59 -0400
Subject: [PATCH 08/10] 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 8b589602..9867bc2d 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 f547e95bb655fbf15ebc8421b1e5a533fbf7b894 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Wed, 26 Jun 2024 11:07:18 -0400
Subject: [PATCH 09/10] Updates to git handling

---
 .github/workflows/release-notes.yml |  2 +-
 .github/workflows/render-all.yml    | 45 ++++++++++++++++-------------
 2 files changed, 26 insertions(+), 21 deletions(-)

diff --git a/.github/workflows/release-notes.yml b/.github/workflows/release-notes.yml
index d76e0e2f..30a6ab7d 100644
--- a/.github/workflows/release-notes.yml
+++ b/.github/workflows/release-notes.yml
@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
 
-      - uses: mshick/add-pr-comment@v1
+      - uses: mshick/add-pr-comment@v2
         if: ${{ github.head_ref == 'repo-sync/OTTR_Template/default' }}
         with:
           message: |
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 873357d5..89772639 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -11,7 +11,6 @@ on:
       - '**md$'
       - assets/*
       - quizzes/*
-      - !docs/*
 
 jobs:
 
@@ -57,9 +56,13 @@ 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
+          rm -rf docs/*
 
-      # Run bookdown rendering
+      # Run Rmd rendering
       - name: Run bookdown render
         id: bookdown
         if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
@@ -68,7 +71,7 @@ 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('.')"
 
@@ -95,16 +98,14 @@ jobs:
         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
           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}}
@@ -122,6 +123,9 @@ 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.
@@ -142,11 +146,9 @@ jobs:
         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
           git push -u origin main  || echo "No changes to push"
 
   render-leanpub:
@@ -154,7 +156,7 @@ 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:
@@ -169,6 +171,9 @@ 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
 
       # Create screenshots
       - name: Run the screenshot creation
@@ -189,11 +194,9 @@ 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 status
           git push -u origin main || echo "No changes to push"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
@@ -223,7 +226,8 @@ 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
+          git pull --rebase --allow-unrelated-histories --strategy-option=ours --autostash
           git push --force --set-upstream origin main || echo "No changes to push"
 
   render-coursera:
@@ -246,6 +250,9 @@ 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
@@ -259,8 +266,6 @@ jobs:
         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
@@ -268,5 +273,5 @@ 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 status
           git push -u origin main  || echo "No changes to push"

From ce1dc462f9468bc0c4f7ce54d4a61131193752c2 Mon Sep 17 00:00:00 2001
From: Candace Savonen <cansav09@gmail.com>
Date: Fri, 28 Jun 2024 16:11:00 -0400
Subject: [PATCH 10/10] Some rebases and some rearrangements of git stuffs

---
 .github/workflows/pull_request.yml |  2 +-
 .github/workflows/render-all.yml   | 16 +++++++++-------
 2 files changed, 10 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
index 9867bc2d..5cd835ee 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
 
diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
index 89772639..0d0a4356 100644
--- a/.github/workflows/render-all.yml
+++ b/.github/workflows/render-all.yml
@@ -60,13 +60,13 @@ jobs:
           git remote set-url origin https://${GH_PAT}@github.com/${GITHUB_REPOSITORY}
           git fetch origin
           git pull --rebase --allow-unrelated-histories --strategy-option=ours
-          rm -rf docs/*
 
       # 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)"
 
@@ -100,7 +100,7 @@ jobs:
         run: |
           git add --force docs/*
           git commit -m 'Render course' || echo "No changes to commit"
-          git status
+          git status docs/*
           git push -u origin main  || echo "No changes to push"
 
   render-tocless:
@@ -148,7 +148,7 @@ jobs:
         run: |
           git add --force docs/no_toc*
           git commit -m 'Render toc-less' || echo "No changes to commit"
-          git status
+          git status docs/no_toc*
           git push -u origin main  || echo "No changes to push"
 
   render-leanpub:
@@ -174,6 +174,7 @@ jobs:
           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
@@ -196,16 +197,17 @@ jobs:
           rm -rf manuscript/
           git add .
           git commit -m 'Delete manuscript folder' || echo "No changes to commit"
-          git status
           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
@@ -214,7 +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
@@ -226,7 +228,7 @@ jobs:
           git add --force resources/*
           git add --force docs/*
           git commit -m 'Render Leanpub' || echo "No changes to commit"
-          git status
+          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"