Start filling in the pVACview chapter #48
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # Candace Savonen 2021 | |
| # Updated Jan 2023 | |
| 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@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. | |
| # 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 $GITHUB_WORKSPACE | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "jhudsl-robot" | |
| branch_name='preview-${{ github.event.pull_request.number }}' | |
| echo branch doesnt exist | |
| git checkout -b $branch_name || echo branch exists | |
| git push --set-upstream origin $branch_name | |
| shell: bash | |
| outputs: | |
| toggle_spell_check: "${{ 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 }}" | |
| 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 | |
| quiz-check: | |
| name: Check quiz formatting | |
| if: ${{needs.yaml-check.outputs.toggle_quiz_check == 'yes'}} | |
| needs: yaml-check | |
| uses: jhudsl/ottr-reports/.github/workflows/report-maker.yml@main | |
| with: | |
| check_type: quiz_format | |
| error_min: 0 | |
| gh_pat: secrets.GH_PAT | |
| ############################# Style the code ################################### | |
| style-code: | |
| name: Style code | |
| needs: yaml-check | |
| runs-on: ubuntu-latest | |
| if: ${{needs.yaml-check.outputs.toggle_style_code == 'yes'}} | |
| container: | |
| image: jhudsl/base_ottr:main | |
| steps: | |
| - name: Checkout files | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Run styler | |
| run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', recursive = TRUE, 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 push origin || echo "No changes to commit" | |
| ############################# Render Preview ################################### | |
| 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@v3 | |
| with: | |
| fetch-depth: 0 | |
| # Set up git checkout | |
| - name: Set up git checkout | |
| run: | | |
| git config --global --add safe.directory $GITHUB_WORKSPACE | |
| git config --global user.email "[email protected]" | |
| git config --global user.name "jhudsl-robot" | |
| branch_name='preview-${{ 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 | |
| # Run bookdown rendering | |
| - name: Run bookdown render | |
| id: bookdown | |
| run: Rscript -e "bookdown::render_book('index.Rmd', output_format = 'all')" | |
| # 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()" | |
| # 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' | |
| run: | | |
| echo Bookdown status ${{steps.bookdown.outcome}} | |
| echo Toc-less status ${{steps.tocless.outcome}} | |
| exit 1 | |
| # Commit the rendered bookdown files | |
| - name: Commit rendered bookdown files to preview branch | |
| id: commit | |
| run: | | |
| branch_name='preview-${{ github.event.pull_request.number }}' | |
| git diff origin/main -- docs >/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@v2 | |
| 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 _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") | |
| 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@v2 | |
| with: | |
| comment-id: ${{ steps.fc.outputs.comment-id }} | |
| 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 }}) | |
| _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_ | |
| edit-mode: replace | |
| - name: Comment if no changes | |
| if: steps.commit.outputs.changes == 'false' | |
| uses: peter-evans/create-or-update-comment@v2 | |
| 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 |