Merge pull request #87 from jhudsl/repo-sync/OTTR_Template/default

🔄 Synced file(s) with jhudsl/OTTR_Template
jhudsl · Mar 25, 2024 · 7c88706 · 7c88706
2 parents ff94364 + ebbd250
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diff --git a/.github/ISSUE_TEMPLATE/url-error.md b/.github/ISSUE_TEMPLATE/url-error.md
@@ -0,0 +1,8 @@
+---
+title: Broken URLs found in the course!
+labels: url-error
+---
+URL's in this course were just checked and some broken URLs were found.
+
+**Number of errors:** {{ env.ERROR_NUM }}  
+**File where errors are:** [url checks file here]({{ env.FILE_URL }})
diff --git a/.github/workflows/check-url.yml 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/[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 $GITHUB_WORKSPACE
+        git config --global user.email "[email protected]"
+        git config --global user.name "jhudsl-robot"
+
+        echo branch doesnt exist
+        git checkout -b preview-spell-error || echo branch exists
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+      shell: bash
+
+    - name: Run the check
+      uses: jhudsl/ottr-reports@main
+      id: check_results
+      continue-on-error: true
+      with:
+        check_type: urls
+        error_min: 1
+
+    - name: Declare file path and time
+      id: check-report
+      run: |
+        error_num=$(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
@@ -18,7 +18,7 @@ jobs:
 
       # Check out current repository
       - name: checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -1,4 +1,5 @@
-# Candace Savonen Aug 2022
+# Candace Savonen 2021
+# Updated Jan 2023
 
 name: Pull Request
 
@@ -13,49 +14,42 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          token: ${{ secrets.GH_PAT }}
 
         # 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.
 
-      - name: Verify Dockerfiles changed?
-        uses: tj-actions/[email protected]
-        id: verify-changed-files
-        with:
-          files: |
-             docker/Dockerfile
-             docker/github_package_list.tsv
-
       # Delete the branch if this has been run before
       - name: Delete branch locally and remotely
         run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"
 
       # 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.email "[email protected]"
+          git config --global user.name "jhudsl-robot"
 
           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:
       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: "${{ env.RENDER_PREVIEW }}"
-      toggle_docker_build: "${{ env.DOCKER_BUILD }}"
       rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
-      dockerfiles_changed: steps.verify-changed-files.outputs.files_changed
 
 ########################## Make the error reports ##############################
   spell-check:
@@ -67,6 +61,7 @@ jobs:
       check_type: spelling
       error_min: 3
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
   url-check:
     name: Check URLs
@@ -77,6 +72,7 @@ jobs:
       check_type: urls
       error_min: 0
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
   quiz-check:
     name: Check quiz formatting
@@ -87,6 +83,7 @@ jobs:
       check_type: quiz_format
       error_min: 0
       gh_pat: secrets.GH_PAT
+      branch_name: ${GITHUB_HEAD_REF}
 
 ############################# Style the code ###################################
   style-code:
@@ -99,7 +96,7 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -108,6 +105,7 @@ 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 push origin || echo "No changes to commit"
@@ -124,15 +122,16 @@ jobs:
 
     steps:
       - name: Checkout files
-        uses: actions/checkout@v2
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
       # Set up git checkout
       - name: Set up git checkout
         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.email "[email protected]"
+          git config --global user.name "jhudsl-robot"
 
           branch_name='preview-${{ github.event.pull_request.number }}'
           git fetch --all
@@ -167,15 +166,15 @@ jobs:
         run: |
           branch_name='preview-${{ github.event.pull_request.number }}'
           git diff origin/main -- docs >/dev/null && changes=true || changes=false
-          echo ::set-output name=changes::$changes
+          echo "changes=$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 push --force || echo "No changes to commit"
         shell: bash
 
       - name: Find Comment
-        uses: peter-evans/find-comment@v1
+        uses: peter-evans/find-comment@v2
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}
@@ -189,16 +188,16 @@ jobs:
           bookdown_link=$(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/$course_name.docx")
-          echo ::set-output name=bookdown_link::$bookdown_link
-          echo ::set-output name=tocless_link::$tocless_link
-          echo ::set-output name=docx_link::$docx_link
-          echo ::set-output name=time::$(date +'%Y-%m-%d')
-          echo ::set-output name=commit_id::$GITHUB_SHA
+          echo "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
           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 }}
@@ -213,7 +212,7 @@ jobs:
 
       - 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 }}
@@ -222,56 +221,3 @@ jobs:
 
             _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_
           edit-mode: replace
-
-############################## Build Docker ####################################
-
-  build-docker:
-    name: Build Docker image
-    needs: yaml-check
-    runs-on: ubuntu-latest
-    if: ${{needs.yaml-check.outputs.toggle_docker_build == 'yes' && needs.yaml-check.outputs.dockerfiles_changed == 'true' && github.head_ref != 'repo-sync/OTTR_Template/default'}}
-
-    steps:
-      - name: checkout repo
-        uses: actions/checkout@v2
-
-      - name: Verify Dockerfiles changed?
-        uses: tj-actions/[email protected]
-        id: verify-changed-files
-        with:
-          files: |
-             docker/Dockerfile
-             docker/github_package_list.tsv
-
-      - name: Login as jhudsl-robot
-        run: |
-          git config --local user.email "[email protected]"
-          git config --local user.name "jhudsl-robot"
-
-      # 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 }} > docker/git_token.txt
-
-      - name: Build Docker image
-        uses: docker/build-push-action@v2
-        with:
-          push: false
-          load: true
-          context: docker
-          file: docker/Dockerfile
-          tags: jhudsl/base_ottr