🔄 Synced file(s) with jhudsl/AnVIL_Template

.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/[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 }}
+
+    - 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

@@ -139,11 +139,31 @@ jobs:
           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
+        run: bash scripts/AnVIL_Feedback_Script.sh
+
       # Run bookdown rendering
       - name: Run bookdown render
         id: bookdown
         run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
 
+      # 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: ${{needs.yaml-check.outputs.render_student_guide == 'yes'}}
+        id: student_guide
+        run: |
+          mkdir tmp1
+          mv _bookdown.yml _output.yml tmp1
+          mv student-guide/_bookdown.yml student-guide/_output.yml .
+          Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')"
+          mv _bookdown.yml _output.yml student-guide
+          mv tmp1/_bookdown.yml tmp1/_output.yml .
+          rm -r tmp1
+
       # Run TOC-less version
       # Rendered content for Leanpub and Coursera is very similar.
       # This job creates a shared scaffold for both.
@@ -187,15 +207,14 @@ jobs:
       - name: Build components of the comment
         id: build-components
         run: |
-          course_name=$(head -n 1 _bookdown.yml | cut -d'"' -f 2| tr " " "-")
+          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-${{ github.event.pull_request.number }}/docs/no_toc/index.html")
-          docx_link=$(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")
+          student_docx_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/$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" >> $GITHUB_OUTPUT
+          echo "student_docx_link=$student_docx_link" >> $GITHUB_OUTPUT
           echo "time=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
           echo "commit_id=$GITHUB_SHA" >> $GITHUB_OUTPUT
           echo ${{steps.commit.outputs.changes}}

.github/workflows/render-all.yml

@@ -10,6 +10,7 @@ on:
     paths:
       - '**.Rmd'
       - assets/*
+      - quizzes/*
 
 jobs:
 
@@ -57,7 +58,7 @@ jobs:
       # We want a fresh run of the renders each time
       - name: Delete old docs/*
         run: rm -rf docs/*
-      
+
       # Make sure the link for AnVIL feedback is prepopulated for the specific course
       - name: Set up feedback link
         id: feedback
@@ -102,7 +103,7 @@ jobs:
           git fetch origin
           git add --force docs/*
           git commit -m 'Render bookdown' || echo "No changes to commit"
-          git pull --rebase --allow-unrelated-histories --strategy-option=ours
+          git pull --allow-unrelated-histories --strategy-option=ours
           git push -u origin main  || echo "No changes to push"
 
   render-tocless:
@@ -141,7 +142,7 @@ jobs:
           git fetch origin
           git add --force docs/no_toc*
           git commit -m 'Render toc-less' || echo "No changes to commit"
-          git pull --rebase --allow-unrelated-histories --strategy-option=ours
+          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
           git push -u origin main  || echo "No changes to push"
 
   render-leanpub:
@@ -188,7 +189,7 @@ jobs:
           git fetch origin
           git add .
           git commit -m 'Delete manuscript folder' || echo "No changes to commit"
-          git pull --rebase --allow-unrelated-histories --strategy-option=ours
+          git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
           git push -u origin main || echo "No changes to push"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
@@ -218,7 +219,7 @@ jobs:
           git add --force resources/*
           git add --force docs/*
           git commit -m 'Render Leanpub' || echo "No changes to commit"
-          git pull --rebase --allow-unrelated-histories --strategy-option=ours
+          git pull --allow-unrelated-histories --strategy-option=ours
           git push --force --set-upstream origin main || echo "No changes to push"
 
   render-coursera: