add microbiome champions to inspired by #34
Workflow file for this run
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| # 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@v4 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ secrets.GH_PAT }} | |
| # Use the yaml-env-action action. | |
| - name: Load environment from YAML | |
| uses: doughepi/[email protected] | |
| with: | |
| files: config_automation.yml # Pass a space-separated list of configuration files. Rightmost files take precedence. | |
| # Delete the branch if this has been run before | |
| - name: Delete branch locally and remotely | |
| run: git push origin --delete preview-${{ 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 $branch_name || echo echo branch exists remotely | |
| shell: bash | |
| outputs: | |
| toggle_spell_check: "${{ env.SPELL_CHECK }}" | |
| toggle_style_code: "${{ env.STYLE_CODE }}" | |
| toggle_url_check: "${{ env.URL_CHECKER }}" | |
| toggle_quiz_check: "${{ env.CHECK_QUIZZES }}" | |
| toggle_feedback_link: "${{ env.FEEDBACK_LINK }}" | |
| toggle_render_preview: "${{ env.RENDER_PREVIEW }}" | |
| toggle_student_guide: "${{ env.RENDER_STUDENT_GUIDE }}" | |
| 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 | |
| branch_name: ${GITHUB_HEAD_REF} | |
| 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 | |
| branch_name: ${GITHUB_HEAD_REF} | |
| 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 | |
| branch_name: ${GITHUB_HEAD_REF} | |
| ############################# Style the code ################################### | |
| style-code: | |
| name: Style code | |
| needs: yaml-check | |
| runs-on: ubuntu-latest | |
| if: ${{needs.yaml-check.outputs.toggle_style_code == 'yes'}} | |
| container: | |
| image: jhudsl/base_ottr:main | |
| steps: | |
| - name: Checkout files | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| - name: Run styler | |
| run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', 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@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 | |
| # Make sure the link for AnVIL feedback is prepopulated for the specific course | |
| - name: Set up feedback link | |
| id: feedback | |
| if: ${{needs.yaml-check.outputs.toggle_feedback_link == 'yes'}} | |
| run: | | |
| bash scripts/AnVIL_Feedback_Script.sh | |
| git add _output.yml | |
| git commit -m 'Set up feedback link' || echo "No changes to commit" | |
| # 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.toggle_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 | |
| git add student-guide/* | |
| git commit -m 'Create student guide' || echo "No changes to commit" | |
| # 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 ${{steps.tocless.outcome}} | |
| exit 1 | |
| - name: Website preview for download | |
| run: zip website-preview.zip docs/* -r | |
| # Commit the rendered bookdown files | |
| - name: Commit rendered bookdown files to preview branch | |
| id: commit | |
| run: | | |
| branch_name='preview-${{ 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 --rebase --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 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") | |
| student_guide=$(echo "https://github.com/$GITHUB_REPOSITORY/raw/preview-${{ github.event.pull_request.number }}/student-guide/Student_Guide.docx") | |
| zip_link=$(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" >> $GITHUB_OUTPUT | |
| echo "student_guide=$student_guide" >> $GITHUB_OUTPUT | |
| echo "time=$(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: ${{ github.event.pull_request.number }} | |
| body: | | |
| Re-rendered previews from the latest commit: | |
| - :eyes: Quick [preview of course website here](${{ steps.build-components.outputs.bookdown_link }}) \* | |
| - :microscope: Comprehensive [download of the course website here](${{ steps.build-components.outputs.zip_link }}) | |
| - Download the Student Guide [.docx file](${{ steps.build-components.outputs.student_guide }}) | |
| \* 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 | |
| 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 |