Merge pull request #119 from fhdsl/repo-sync/OTTR_Template/default

🔄 Synced file(s) with jhudsl/OTTR_Template
fhdsl · Sep 4, 2024 · c087c92 · c087c92
2 parents bd30d44 + adf677b
commit c087c92
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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 $GITHUB_WORKSPACE
+        git config --global user.name 'github-actions[bot]'
+        git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+        echo branch doesnt exist
+        git checkout -b preview-spell-error || echo branch exists
+        git push --set-upstream origin preview-spell-error || echo echo branch exists remotely
+      shell: bash
+
+    - name: Run the check
+      uses: jhudsl/ottr-reports@main
+      id: check_results
+      continue-on-error: true
+      with:
+        check_type: urls
+        error_min: 1
+
+    - name: Declare file path and time
+      id: check-report
+      run: |
+        error_num=$(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"
diff --git a/.github/workflows/pull_request.yml b/.github/workflows/pull_request.yml
@@ -33,13 +33,13 @@ jobs:
       - 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"
+          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 echo branch exists remotely
         shell: bash
 
 
@@ -130,8 +130,8 @@ jobs:
       - name: Set up git checkout
         run: |
           git config --global --add safe.directory $GITHUB_WORKSPACE
-          git config --global user.email "[email protected]"
-          git config --global user.name "jhudsl-robot"
+          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
@@ -160,6 +160,9 @@ jobs:
           echo Toc-less status ${{steps.tocless.outcome}}
           exit 1
 
+      - 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
         id: commit
@@ -169,7 +172,7 @@ 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
 
@@ -188,6 +191,8 @@ 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")
+          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
@@ -203,11 +208,13 @@ 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](${{ steps.build-components.outputs.tocless_link }})
-            - Download the [preview of .docx file](${{ steps.build-components.outputs.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 [.docx file](${{ steps.build-components.outputs.docx_link }})
 
-            _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

diff --git a/.github/workflows/render-all.yml b/.github/workflows/render-all.yml
@@ -49,11 +49,11 @@ jobs:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
 
-      - name: Login as jhudsl-robot
+      - name: Login as github actions bot
         run: |
           git config --global --add safe.directory $GITHUB_WORKSPACE
-          git config --global user.email "[email protected]"
-          git config --global user.name "jhudsl-robot"
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
 
       # We want a fresh run of the renders each time
       - name: Delete old docs/*
@@ -88,7 +88,7 @@ jobs:
 
   render-tocless:
     name: Render TOC-less version for Leanpub or Coursera
-    needs: [yaml-check]
+    needs: [yaml-check, render-bookdown]
     runs-on: ubuntu-latest
     container:
       image: ${{needs.yaml-check.outputs.rendering_docker_image}}
@@ -101,11 +101,11 @@ jobs:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
 
-      - name: Login as jhudsl-robot
+      - name: Login as github-actions bot
         run: |
           git config --global --add safe.directory $GITHUB_WORKSPACE
-          git config --global user.email "[email protected]"
-          git config --global user.name "jhudsl-robot"
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
 
       # Rendered content for Leanpub and Coursera is very similar.
       # This job creates a shared scaffold for both.
@@ -122,7 +122,7 @@ jobs:
           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 pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours
           git push -u origin main  || echo "No changes to push"
 
   render-leanpub:
@@ -140,11 +140,11 @@ jobs:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
 
-      - name: Login as jhudsl-robot
+      - name: Login as github actions bot
         run: |
           git config --global --add safe.directory $GITHUB_WORKSPACE
-          git config --global user.email "[email protected]"
-          git config --global user.name "jhudsl-robot"
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
 
       # Create screenshots
       - name: Run the screenshot creation
@@ -153,7 +153,8 @@ jobs:
           rm -rf resources/chapt_screen_images
 
           # Make new screenshots
-          chapt_urls=$(Rscript --vanilla scripts/make_screenshots.R \
+          curl -o make_screenshots.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/make_screenshots.R
+          chapt_urls=$(Rscript --vanilla make_screenshots.R \
             --git_pat ${{ secrets.GH_PAT }} \
             --repo $GITHUB_REPOSITORY \
             --output_dir resources/chapt_screen_images)
@@ -168,11 +169,11 @@ jobs:
           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 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
-        if: needs.yaml-check.outputs.toggle_quiz_check == 'no'
+        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'no'}}
         run: |
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \
@@ -181,7 +182,7 @@ jobs:
             quiz_dir = NULL)"
 
       - name: Run ottrpal::bookdown_to_embed_leanpub
-        if: needs.yaml-check.outputs.toggle_quiz_check == 'yes'
+        if: ${{ needs.yaml-check.outputs.toggle_quiz_check == 'yes'}}
         run: |
           Rscript -e "ottrpal::bookdown_to_embed_leanpub(
             render = FALSE, \
@@ -216,11 +217,11 @@ jobs:
           fetch-depth: 0
           token: ${{ secrets.GH_PAT }}
 
-      - name: Login as jhudsl-robot
+      - name: Login as github action
         run: |
           git config --global --add safe.directory $GITHUB_WORKSPACE
-          git config --global user.email "[email protected]"
-          git config --global user.name "jhudsl-robot"
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
 
       # Run Coursera version
       - name: Convert Leanpub quizzes to Coursera
@@ -243,5 +244,5 @@ 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 pull --rebase --allow-unrelated-histories --strategy-option=ours
           git push -u origin main  || echo "No changes to push"
diff --git a/.github/workflows/transfer-rendered-files.yml b/.github/workflows/transfer-rendered-files.yml
@@ -42,12 +42,12 @@ jobs:
     if: ${{needs.yaml-check.outputs.toggle_coursera == 'yes' || needs.yaml-check.outputs.toggle_leanpub == 'yes'}}
 
     steps:
-      - name: checkout
+      - name: Checkout from Bookdown Repo
         uses: actions/checkout@v4
         with:
           path: bookdown
           token: ${{ secrets.GH_PAT }}
-    
+
       - name: Run git repo check
         id: git_repo_check
         env:
@@ -58,7 +58,8 @@ jobs:
           echo $QUIZ_REPO
 
           # Run repo check script
-          results=$(Rscript --vanilla bookdown/scripts/git_repo_check.R --repo "$GITHUB_REPOSITORY" --git_pat "$GH_PAT")
+          curl -o git_repo_check.R https://raw.githubusercontent.com/jhudsl/ottr-reports/main/scripts/git_repo_check.R
+          results=$(Rscript --vanilla git_repo_check.R --repo "$GITHUB_REPOSITORY" --git_pat "$GH_PAT")
           echo $QUIZ_REPO exists: $results
 
           echo "git_results=$results" >> $GITHUB_OUTPUT
@@ -81,7 +82,7 @@ jobs:
           # Copy over images folder (from bookdown to quizzes repo)
           mkdir -p quizzes/resources/chapt_screen_images
           cp bookdown/resources/chapt_screen_images/* quizzes/resources/chapt_screen_images
-          
+
           # Copy over _bookdown.yml (from bookdown to quizzes repo)
           cp bookdown/_bookdown.yml quizzes/_bookdown.yml
 

diff --git a/assets/footer.html b/assets/footer.html
@@ -1,3 +1,13 @@
+<hr>
+<center>
+<div class="container">
+  <iframe class="responsive-iframe" src="https://c-savonen.shinyapps.io/widget-survey/?course_name=nih_data_sharing" style="width: 400px; height: 220px; overflow: auto;"></iframe>
+</div>
+  </div>
+</center>
+
+
+
 <hr>
 <center>
   <div class="footer">

diff --git a/resources/exclude_files.txt b/resources/exclude_files.txt
@@ -0,0 +1,8 @@
+About.Rmd
+docs/*
+style-sets/*
+manuscript/*
+CONTRIBUTING.md
+LICENSE.md
+code_of_conduct.md
+README.md
diff --git a/style-sets/data-trail/_output.yml b/style-sets/data-trail/_output.yml
@@ -10,7 +10,8 @@ bookdown::gitbook:
       before: |
        <a href="https://www.datatrail.org/"><img src="assets/DataTrail_logo.jpg" style="padding-left: 0px; padding-top: 8px;"</a>
       after: |
-       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" 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="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template 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>

diff --git a/style-sets/fhdasl/_output.yml b/style-sets/fhdasl/_output.yml
@@ -11,7 +11,8 @@ bookdown::gitbook:
       before: |
        <a href="https://hutchdatascience.org/" target="_blank"><img src="assets/big-dasl-stacked.png" style="width: 80%; padding-left: 34px; padding-top: 8px;"</a>
       after: |
-       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" 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="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template by:</a></p>
        <p style="text-align:center;"> <a href="https://hutchdatascience.org/"> The Fred Hutch Data Science Lab </a></p>
        <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>
        <p style="padding-left: 40px;"><div class="trapezoid" style = "padding-left: 40px;"><span>  <a href="https://forms.gle/W6Mg4rzuMK6Yk3Am8"> Click here to provide feedback</a> <img src="assets/itcr_arrow.png" style=" width: 10%" ></span></div></p>
diff --git a/style-sets/itcr/_output.yml b/style-sets/itcr/_output.yml
@@ -10,7 +10,8 @@ bookdown::gitbook:
       before: |
        <a href="https://www.itcrtraining.org/"><img src="assets/ITN_logo.png" style="padding-left: 15px; padding-top: 8px;"</a>
       after: |
-       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template" 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="https://www.ottrproject.org/" target="blank" > This content was published with</a> <a href="https://bookdown.org/" target="blank"> bookdown using</a> </p>
+       <p style="text-align:center;"> <a href="https://github.com/jhudsl/OTTR_Template"> The OTTR Template 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>