Yet Another GHA Test

.github/workflows/delete-preview.yml

@@ -0,0 +1,25 @@
+name: Delete Preview
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  delete-preview:
+    runs-on: ubuntu-latest
+    steps:
+
+      # This is because if a PR is closed before a render finishes it won't find it.
+      - name: Sleep for 5 minutes
+        run: sleep 300s
+        shell: bash
+
+      # Check out current repository
+      - name: checkout
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      # Delete the branch!
+      - name: Delete branch locally and remotely
+        run: git push origin --delete preview-${{ github.event.pull_request.number }} || echo "No branch to delete"

.github/workflows/pull_request.yml

@@ -0,0 +1,169 @@
+name: Pull Request
+
+on:
+  pull_request:
+    branches: [ main, staging ]
+
+jobs:
+  yaml-check:
+    name: Load user automation choices
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        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.
+
+      # 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 --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 $branch_name
+        shell: bash
+
+    outputs:
+      public_repository: "${{ steps.public_repository.outputs.public }}"
+      toggle_spell_check: "${{ env.SPELL_CHECK }}"
+      toggle_url_check: "${{ env.URL_CHECKER }}"
+      toggle_render_preview: "${{ env.RENDER_PREVIEW }}"
+      rendering_docker_image: "${{ env.RENDERING_DOCKER_IMAGE }}"
+
+########################## Make the error reports ##############################
+  spell-check:
+    name: Check spelling
+    needs: yaml-check
+    if: ${{needs.yaml-check.outputs.toggle_spell_check == 'yes'}}
+    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
+    with:
+      check_type: spelling
+      error_min: 3
+      gh_pat: secrets.GH_PAT
+
+  url-check:
+    name: Check URLs
+    needs: yaml-check
+    if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}}
+    uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main
+    with:
+      check_type: urls
+      error_min: 0
+      gh_pat: secrets.GH_PAT
+
+  render-preview:
+    name: Render preview
+    needs: yaml-check
+    runs-on: ubuntu-latest
+    container:
+      image: ${{needs.yaml-check.outputs.rendering_docker_image}}
+    if: ${{needs.yaml-check.outputs.toggle_render_preview == 'yes'}}
+
+    steps:
+      - name: Checkout files
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      # Set up git checkout
+      - name: Set up git checkout
+        run: |
+          git config --global --add safe.directory $GITHUB_WORKSPACE
+          git config --global user.name 'github-actions[bot]'
+          git config --global user.email 'github-actions[bot]@users.noreply.github.com'
+
+          branch_name='preview-${{ 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
+
+       # Now we want to render all the html files from the qmd files
+      - name: Run render html
+        id: site
+        run: quarto render 
+
+      # 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.site.outcome != 'success'
+        run: |
+          echo site status ${{steps.site.outcome}}
+          exit 1
+
+      - name: Website preview for download
+        run: zip website-preview.zip docs/* -r
+
+      # Commit the rendered website files
+      - name: Commit rendered website files to preview branch
+        id: commit
+        run: |
+          branch_name='preview-${{ github.event.pull_request.number }}'
+          git diff origin/main -- '*.html' >/dev/null && changes=true || changes=false
+          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
+        id: fc
+        with:
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: 'github-actions[bot]'
+          body-includes: latest commit
+
+      - name: Build components of the comment
+        id: build-components
+        run: |
+          course_name=$(head -n 1 _website.yml | cut -d'"' -f 2| tr " " "-")
+          website_link=$(echo "https://htmlpreview.github.io/?https://raw.githubusercontent.com/$GITHUB_REPOSITORY/preview-${{ github.event.pull_request.number }}/docs/index.html")
+          docs_link=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/website-preview.zip")
+          echo "docs_link=$docs_link" >> $GITHUB_OUTPUT
+          echo "website_link=$website_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
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body: |
+            :eyes: [Quick Preview of Website](${{ steps.build-components.outputs.website_link }}) - Click for a preview of recent changes.
+            :file_folder: [Download Full Website](${{ steps.build-components.outputs.docs_link }}) - Download complete Zip file of the website. 
+
+            The Quick Preview may not display all HTML features accurately, but it provides a basic overview.
+
+            _Updated at ${{ steps.build-components.outputs.time }} with changes from the latest commit ${{ steps.build-components.outputs.commit_id }}_
+          edit-mode: replace
+
+      - name: No comment if no changes
+        if: steps.commit.outputs.changes == 'false'
+        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

.gitignore

@@ -2,6 +2,6 @@
 .Rhistory
 .RData
 .Ruserdata
-/.quarto/
 .DS_Store
-_course
+/.quarto/
+docs/*

_quarto.yml

@@ -37,12 +37,18 @@ book:
 
   page-footer:
     left: |
-      This book was built with <a href="https://quarto.org/" style="color: #fff;">Quarto</a> by 
-      <a href="https://hutchdatascience.org/" style="color: #fff;">The Fred Hutch Data Science Lab</a>.
+      This book was built with <a href="https://quarto.org/" style="color: #fff;">Quarto</a> using 
+      <a href="https://github.com/fhdsl/ottr" style="color: #fff;">OTTR</a>.
     center: |
       All illustrations <a href="https://creativecommons.org/licenses/by/4.0/" style="color: #fff;">CC-BY. </a>
       <br>
       All other materials <a href= "https://creativecommons.org/licenses/by/4.0/" style="color: #fff;"> CC-BY </a> unless noted otherwise.
+    right: 
+      - icon: github
+        href: https://github.com/
+      - icon: twitter
+        href: https://twitter.com/
+
 
 bibliography: references.bib
 
@@ -66,8 +72,4 @@ format:
     license: "CC BY"
 knitr:
   opts_chunk:
-    fig.path: "resources/images/figure/"
-
-
-
-
+    fig.path: "resources/images/figure/"

config_automation.yml

@@ -0,0 +1,24 @@
+
+##### Checks run at pull request #####
+# Check quiz formatting
+check-quizzes: no
+# Check that urls in the content are not broken
+url-checker: yes
+# Render preview of content with changes (Rmd's and md's are checked)
+render-preview: yes
+# Spell check Rmds and quizzes
+spell-check: yes
+# Style any R code
+style-code: yes
+# Test build the docker image if any docker-relevant files have been changed
+docker-test: no
+
+##### Renderings run upon merge to main branch #####
+# Rendering each platform's content
+render-bookdown: yes
+render-leanpub: yes
+render-coursera: no
+
+# What docker image should be used for rendering?
+# The default is jhudsl/base_ottr:main
+rendering-docker-image: 'jhudsl/ottr_quarto:main'