🔄 Synced file(s) with jhudsl/AnVIL_Template

.github/workflows/check-url.yml

@@ -0,0 +1,117 @@
+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/[email protected]
+        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 }}
+
+      # Commit file
+    - name: Commit tocless bookdown files
+      if: ${{ steps.check-report.outputs.error_num >= 1 }}
+      env:
+        GH_PAT: ${{ secrets.GH_PAT }}
+      run: |
+        git add --force check_reports/url_checks.tsv
+        git commit -m 'Add spell check file' || echo "No changes to commit"
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+
+    - 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"

.github/workflows/delete-preview.yml

@@ -18,7 +18,7 @@ jobs:
 
       # Check out current repository
       - name: checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/pull_request.yml

@@ -1,5 +1,5 @@
 # Candace Savonen 2021
-# Updated Jan 2023
+# Updated May 2024
 
 name: Pull Request
 
@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -31,23 +31,29 @@ jobs:
       # Make the branch fresh
       - name: Make the branch fresh
         run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "jhudsl-robot"
+          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'
 
           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 branch exists remotely
         shell: bash
 
+
     outputs:
+      toggle_website: "${{ env.RENDER_WEBSITE }}"
       toggle_spell_check: "${{ env.SPELL_CHECK }}"
       toggle_style_code: "${{ env.STYLE_CODE }}"
       toggle_url_check: "${{ env.URL_CHECKER }}"
       toggle_quiz_check: "${{ env.CHECK_QUIZZES }}"
+      toggle_feedback_link: "${{ env.FEEDBACK_LINK }}"
+      toggle_md_linter: "${{ env.MARKDOWN_LINTER }}"
+      toggle_readability: "${{ env.READABILITY_REPORT }}"
       toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
+      toggle_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
-      render_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}"
 
 ########################## Make the error reports ##############################
   spell-check:
@@ -58,7 +64,9 @@ jobs:
     with:
       check_type: spelling
       error_min: 3
-      gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
+    secrets:
+      gh_pat: ${{ secrets.GH_PAT }}
 
   url-check:
     name: Check URLs
@@ -68,7 +76,9 @@ jobs:
     with:
       check_type: urls
       error_min: 0
-      gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
+    secrets:
+      gh_pat: ${{ secrets.GH_PAT }}
 
   quiz-check:
     name: Check quiz formatting
@@ -78,7 +88,9 @@ jobs:
     with:
       check_type: quiz_format
       error_min: 0
-      gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
+    secrets:
+      gh_pat: ${{ secrets.GH_PAT }}
 
 ############################# Style the code ###################################
   style-code:
@@ -91,20 +103,40 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       - name: Run styler
-        run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', recursive = TRUE, full.names = TRUE));warnings()"
+        run: Rscript -e "styler::style_file(list.files(pattern = '(R|q)md$', recursive = FALSE, full.names = TRUE));warnings()"
 
       - name: Commit styled files
         run: |
           git config --system --add safe.directory "$GITHUB_WORKSPACE"
-          git add \*.Rmd
-          git commit -m 'Style Rmds' || echo "No changes to commit"
+          git add \*md
+          git commit -m 'Style *mds' || echo "No changes to commit"
           git push origin || echo "No changes to commit"
 
+############################# Readability Report ###################################
+
+  readability-report:
+    name: Readability report
+    needs: yaml-check
+    runs-on: ubuntu-latest
+    if: ${{needs.yaml-check.outputs.toggle_readability == 'yes'}}
+
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Readability report
+        uses: Rebilly/lexi@v2
+        with:
+          github-token: ${{ secrets.GH_PAT }}
+          glob: '**/*.md'
+
 ############################# Render Preview ###################################
 
   render-preview:
@@ -117,33 +149,49 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       # Set up git checkout
       - name: Set up git checkout
         run: |
-          git config --system --add safe.directory "$GITHUB_WORKSPACE"
-          git config --local user.email "[email protected]"
-          git config --local user.name "jhudsl-robot"
+          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'
 
           branch_name='preview-${{ github.event.pull_request.number }}'
           git fetch --all
           git checkout $branch_name
           git merge -s recursive --strategy-option=theirs origin/${{ github.head_ref }} --allow-unrelated-histories
         shell: bash
 
+      # Make sure the link for AnVIL feedback is prepopulated for the specific course
+      - name: Set up feedback link
+        id: feedback
+        if: ${{needs.yaml-check.outputs.toggle_feedback_link == 'yes'}}
+        run: |
+          bash scripts/AnVIL_Feedback_Script.sh
+          git add _output.yml
+          git commit -m 'Set up feedback link' || echo "No changes to commit"
+
       # 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('.')"
+
       # Render a student guide if specified. This is a bit clunky because
       # Bookdown does not work well if the files aren't named as such in the
       # root directory
       - name: Run student guide render
-        if: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
+        if: ${{needs.yaml-check.outputs.toggle_student_guide == 'yes'}}
         id: student_guide
         run: |
           mkdir tmp1
@@ -153,22 +201,29 @@ jobs:
           mv _bookdown.yml _output.yml student-guide
           mv tmp1/_bookdown.yml tmp1/_output.yml .
           rm -r tmp1
-
-      # 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()"
+          git add student-guide/*
+          git commit -m 'Create student guide' || echo "No changes to commit"
 
       # This checks on the steps before it and makes sure that they completed.
       # If the renders didn't complete we don't want to commit the file changes
-      - name: Check on render steps
-        if: steps.bookdown.outcome != 'success' || steps.tocless.outcome != 'success'
+      - name: Check on Rmd render steps
+        if: ${{needs.yaml-check.outputs.toggle_website == 'rmd' }}
         run: |
           echo Bookdown status ${{steps.bookdown.outcome}}
-          echo Toc-less status ${{steps.tocless.outcome}}
-          exit 1
+          if [${{steps.bookdown.outcome}} != 'success']; then
+            exit 1
+          fi
+
+      - name: Check on quarto render steps
+        if: ${{needs.yaml-check.outputs.toggle_website == 'quarto' }}
+        run: |
+          echo Quarto status ${{steps.quarto.outcome}}
+          if [${{steps.quarto.outcome}} != 'success']; then
+            exit 1
+          fi
+
+      - name: Website preview for download
+        run: zip website-preview.zip docs/* -r
 
       # Commit the rendered bookdown files
       - name: Commit rendered bookdown files to preview branch
@@ -179,7 +234,7 @@ 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
 
@@ -196,11 +251,11 @@ jobs:
         run: |
           course_name=$(head -n 1 student-guide/_bookdown.yml | cut -d'"' -f 2| tr " " "-")
           bookdown_link=$(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-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
-          student_docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/$course_name.docx")
+          student_guide=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/Student_Guide.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" >> $GITHUB_OUTPUT
-          echo "student_docx_link=$student_docx_link" >> $GITHUB_OUTPUT
+          echo "student_guide=$student_guide" >> $GITHUB_OUTPUT
           echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
           echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
           echo ${{steps.commit.outputs.changes}}
@@ -213,11 +268,13 @@ jobs:
           issue-number: ${{ github.event.pull_request.number }}
           body: |
             Re-rendered previews from the latest commit:
-            - See [preview of Bookdown here](${{ steps.build-components.outputs.bookdown_link }})
-            - See [preview of Coursera/Leanpub version here](${{ steps.build-components.outputs.tocless_link }})
-            - Download the [preview of the Student Guide .docx file](${{ steps.build-components.outputs.student_docx_link }})
+            - :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 Student Guide [.docx file](${{ steps.build-components.outputs.student_guide }})
 
-            _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
+            \* 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: Comment if no changes