🔄 Synced file(s) with jhudsl/DaSL_Course_Template_Bookdown

.github/ISSUE_TEMPLATE/course-content-add.md

@@ -3,15 +3,15 @@ name: New content idea
 about: Suggest an idea for the course
 title: ''
 labels: ''
-assignees: cansavvy
+assignees:
 
 ---
 
-**Describe the your scope of your content idea**
-What will this cover and how does it relate to the current course material?
+## Describe the your scope of your content idea
+<!-- What will this cover and how does it relate to the current course material? -->
 
-**Describe the learning objectives for your content idea**
-What will users learn from this new content? 
+## Describe the learning objectives for your content idea
+<!-- What will users learn from this new content? -->
 
-**Additional context or resources**
-Add any other context or related resources we should know about? 
+## Additional context or resources
+<!-- Add any other context or related resources we should know about? -->

.github/ISSUE_TEMPLATE/course-problem-report.md

@@ -1,27 +1,28 @@
 ---
 name: Course Problem Report
 about: Create a report to help improve the course
-title: problem
+title: [Problem]
 labels: bug
-assignees: cansavvy
+assignees:
 
 ---
 
-**Describe what is not working with the course**
-A clear and concise description of what the bug is.
+## Describe what is not working with the course
+<!-- A clear and concise description of what the bug is. -->
 
-**To Reproduce**
-Steps to reproduce the behavior:
+## Steps to Reproduce
+<!-- Steps to reproduce the behavior:
 1. Go to '...'
 2. Click on '....'
 3. Scroll down to '....'
 4. See error
+-->
 
-**Expected behavior**
-A clear and concise description of what you expected to happen.
+## Expected behavior
+<!-- A clear and concise description of what you expected to happen. -->
 
-**Screenshots**
-If applicable, add screenshots to help explain your problem.
+## Screenshots
+<!-- If applicable, add screenshots to help explain your problem. -->
 
-**Additional context**
-Add any other context about the problem here.
+## Additional context
+<!-- Add any other context about the problem here. -->

.github/workflows/render-bookdown.yml

@@ -15,7 +15,7 @@ on:
     branches: [ main ]
     paths:
       - '**.Rmd'
-      - docker/Dockerfile
+      - docker/*
       - assets/*
 jobs:
   # This workflow contains a single job called "build-all"
@@ -67,17 +67,23 @@ jobs:
 
 ###### END OF DOCKER UPDATE CHUNK ##############################################
 
+      # We want a fresh run of the renders each time
+      - name: Delete old docs/*
+        run: rm -r docs/*
+
       # Run bookdown rendering
       - name: Run bookdown render
+        id: bookdown
         run: |
           docker run \
           --mount type=bind,target=/home/rstudio,source=$PWD \
           jhudsl/course_template \
-          Rscript -e "bookdown::render_book('index.Rmd')"
+          Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
 
 ##### If you do not wish to host your course on Coursera, you can delete this section #####
       # Run Coursera version
       - name: Run Coursera version of render
+        id: coursera
         run: |
           docker run \
           --mount type=bind,target=/home/rstudio,source=$PWD \
@@ -86,6 +92,15 @@ jobs:
 
 ##### End of Coursera rendering section ########################################
 
+      # 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.coursera.outcome != 'success'
+        run: |
+          echo Bookdown status ${{steps.bookdown.outcome}}
+          echo Coursera status ${{steps.coursera.outcome}}
+          exit 1
+
       # Commit the rendered bookdown files
       - name: Commit rendered bookdown files
         run: |

.github/workflows/render-preview.yml

@@ -7,6 +7,8 @@ on:
   pull_request:
     branches: [ main ]
 
+permissions: write-all
+
 jobs:
   # This workflow contains a single job called "build-all"
   build-all:
@@ -20,20 +22,24 @@ jobs:
         with:
           # get the full repo
           fetch-depth: 0
-          # use github PAT
-          token: ${{ secrets.GH_PAT }}
+
+      # We want a fresh run of the renders each time
+      - name: Delete old docs/*
+        run: rm -r docs/*
 
       # Run bookdown rendering
       - name: Run bookdown render
+        id: bookdown
         run: |
           docker run \
           --mount type=bind,target=/home/rstudio,source=$PWD \
           jhudsl/course_template \
-          Rscript -e "bookdown::render_book('index.Rmd')"
+          Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
 
 ##### If you do not wish to host your course on Coursera, you can delete this section #####
       # Run Coursera version
       - name: Run Coursera version of render
+        id: coursera
         run: |
           docker run \
           --mount type=bind,target=/home/rstudio,source=$PWD \
@@ -42,35 +48,57 @@ jobs:
 
 ##### End of Coursera rendering section ########################################
 
+      # 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.coursera.outcome != 'success'
+        run: |
+          echo Bookdown status ${{steps.bookdown.outcome}}
+          echo Coursera status ${{steps.coursera.outcome}}
+          exit 1
+
       # Commit the rendered bookdown files
       - name: Commit rendered bookdown files to development branch
+        id: commit
         run: |
           git checkout -b "preview-${{ github.event.pull_request.number }}"
           git config --local user.email "[email protected]"
           git config --local user.name "GitHub Actions"
+          changes=$(git diff --name-only origin/main -- docs)
           git add -A
           git commit -m 'Render bookdown preview' || echo "No changes to commit"
           git push --force origin "preview-${{ github.event.pull_request.number }}" || echo "No changes to push"
 
+          if [[ -n $changes ]]; then
+            echo ::set-output name=changes::$(echo 'changes')
+          else
+            echo ::set-output name=changes::$(echo 'no_changes')
+          fi
+
       - name: Find Comment
         uses: peter-evans/find-comment@v1
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}
           comment-author: 'github-actions[bot]'
-          body-includes: Re-rendered
+          body-includes: latest commit
 
       - name: Build components of the comment
         id: build-components
         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")
           coursera_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/coursera/index.html")
+          docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/docs/$course_name.docx")
           echo ::set-output name=bookdown_link::$bookdown_link
           echo ::set-output name=coursera_link::$coursera_link
+          echo ::set-output name=docx_link::$docx_link
           echo ::set-output name=time::$(date +'%Y-%m-%d')
           echo ::set-output name=commit_id::$GITHUB_SHA
+          echo ${{steps.commit.outputs.changes}}
 
       - name: Create or update comment
+        if: steps.commit.outputs.changes == 'changes'
         uses: peter-evans/create-or-update-comment@v1
         with:
           comment-id: ${{ steps.fc.outputs.comment-id }}
@@ -79,6 +107,19 @@ jobs:
             Re-rendered previews from the latest commit:
             - See [preview of Bookdown here](${{ steps.build-components.outputs.bookdown_link }})
             - See [preview of Coursera version here](${{ steps.build-components.outputs.coursera_link }})
+            - Download the [preview of .docx file](${{ steps.build-components.outputs.docx_link }})
+
+            _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+          edit-mode: replace
+
+      - name: No comment if no changes
+        if: steps.commit.outputs.changes == 'no_changes'
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            The latest commit did not produce rendering changes.
 
             _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
           edit-mode: replace

.github/workflows/transfer-rendered-files.yml

@@ -106,6 +106,12 @@ jobs:
             curl --fail -s ${base_url}/${line} > ${line}
           done < "$input"
 
+
+          # Get rid of GA Script spec in output yaml
+          sed 's/GA_Script.Rhtml,//' _output.yml > output.txt
+          cat output.txt > _output.yml
+          rm output.txt
+
       - name: Create PR with rendered docs files
         if: ${{ steps.git_repo_check.outputs.git_results == 'TRUE' }}
         uses: peter-evans/create-pull-request@v3

code_of_conduct.md

@@ -58,7 +58,7 @@ representative at an online or offline event.
 ## Enforcement
 
 Instances of abusive, harassing, or otherwise unacceptable behavior may be
-reported to the Jeff Leek at [email protected].
+reported to Jeff Leek at [email protected].
 All complaints will be reviewed and investigated promptly and fairly.
 
 All community leaders are obligated to respect the privacy and security of the

scripts/spell-check.R

@@ -19,9 +19,10 @@ dictionary <- readLines(file.path(root_dir, 'resources', 'dictionary.txt'))
 # Add mysterious emoji joining character
 dictionary <- c(dictionary, spelling::spell_check_text("⬇️")$word)
 
-# Only declare `.Rmd` files
+# Only declare `.Rmd` files but not the ones in the style-sets directory
 files <- list.files(pattern = 'Rmd$', recursive = TRUE, full.names = TRUE)
 files <- grep("About.Rmd", files, ignore.case = TRUE, invert = TRUE, value = TRUE)
+files <- grep("style-sets", files, ignore.case = TRUE, invert = TRUE, value = TRUE)
 
 # Run spell check
 sp_errors <- spelling::spell_check_files(files, ignore = dictionary) %>%

style-sets/AnVIL/_output.yml

@@ -0,0 +1,16 @@
+bookdown::gitbook:
+  css: assets/style_anvil.css
+  includes:
+    before_body: assets/big-image.html
+    after_body: assets/footer.html
+  highlight: tango
+  config:
+    toc:
+      collapse: section
+      before: |
+       <a href="https://anvilproject.org/"><img src="assets/anvil_logo.png" style="padding-left: 15px; padding-top: 8px;"</a>
+      after: |
+       <p style="text-align:center;"> <a href="https://github.com/jhudsl/DaSL_Course_Template_Bookdown" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown by: </a> </p>
+       <p style="text-align:center;"> <a href="http://jhudatascience.org/"> The Johns Hopkins Data Science Lab </a></p>
+       <a href="http://jhudatascience.org/"><img src="https://jhudatascience.org/images/dasl.png" style=" width: 80%; filter: grayscale(100%); padding-left: 40px; padding-top: 8px; vertical-align: top "</a>
+       <p style="text-align:center; font-size: 12px;"> <a href="https://github.com/rstudio4edu/rstudio4edu-book/"> Style adapted from: rstudio4edu-book </a> <a href ="https://creativecommons.org/licenses/by/2.0/"> (CC-BY 2.0) </a></p>