[Statistics] Updating confusing language in lab #484
Workflow file for this run
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| # Candace Savonen Dec 2021 | |
| 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: "${{ env.CHECK_QUIZZES }}" | |
| toggle_render_preview: "${{ env.RENDER_PREVIEW }}" | |
| toggle_make_labs: "${{ env.MAKE_LABS }}" | |
| rendering_docker_image: "${{ 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: 1 | |
| 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: 1 | |
| gh_pat: secrets.GH_PAT | |
| branch_name: ${GITHUB_HEAD_REF} | |
| ########################## Style 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 | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ secrets.GH_PAT }} | |
| - name: Run styler | |
| run: Rscript -e "styler::style_file(list.files(pattern = 'Rmd$', recursive = TRUE, full.names = TRUE));warnings()" | |
| - name: Commit styled files | |
| run: | | |
| git config --system --add safe.directory "$GITHUB_WORKSPACE" | |
| git config --global user.name 'github-actions[bot]' | |
| git config --global user.email 'github-actions[bot]@users.noreply.github.com' | |
| git add \*.Rmd | |
| git commit -m 'Style Rmds' || echo "No changes to commit" | |
| git push origin || echo "No changes to commit" | |
| ########################## Preview ############################## | |
| render-preview: | |
| name: Render preview | |
| needs: yaml-check | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ${{needs.yaml-check.outputs.rendering_docker_image}} | |
| if: ${{needs.yaml-check.outputs.toggle_render_preview == 'yes'}} | |
| steps: | |
| # Give permission to access the repo | |
| - name: safelist repository | |
| run: | | |
| repo_name='${{ github.event.repository.name }}' | |
| git config --global --add safe.directory /__w/$repo_name/$repo_name | |
| # # Checks-out your repository with the token so your job can access it | |
| - name: checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| # get the full repo | |
| fetch-depth: 0 | |
| # use github PAT | |
| token: ${{ secrets.GH_PAT }} | |
| # Set up git checkout | |
| - name: Set up git checkout | |
| run: | | |
| git config --global user.name 'github-actions[bot]' | |
| git config --global user.email 'github-actions[bot]@users.noreply.github.com' | |
| branch_name='preview-${{ 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 | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v41 | |
| # NOTE: `since_last_remote_commit: true` is implied by default and falls back to the previous local commit. | |
| - name: List all changed files | |
| run: | | |
| for file in ${{ steps.changed-files.outputs.all_changed_files }}; do | |
| echo "$file was changed" | |
| done | |
| # We want a fresh run of the renders each time - so first delete old html files | |
| - name: Delete old *.html | |
| run: Rscript -e "rmarkdown::clean_site(preview = FALSE)" | |
| # Now we want to render all the html files from the Rmd files | |
| - name: Run render html for the main website | |
| id: site | |
| run: Rscript -e "rmarkdown::render_site()" | |
| # Render module details for syllabus | |
| - name: Render module details for syllabus | |
| run: Rscript "scripts/render_module_details_for_syllabus.R" | |
| # Create blank labs - runs quickly, so just does it for all of them | |
| - name: Run lab converter | |
| if: ${{needs.yaml-check.outputs.toggle_make_labs == 'yes'}} | |
| shell: bash | |
| run: bash scripts/blank_labs_from_keys.sh | |
| # Render all module files | |
| - name: Render html of modules where .Rmd has changed | |
| run: | | |
| Rscript --vanilla "scripts/render_modules.R" --files "${{ steps.changed-files.outputs.all_changed_files }}" | |
| # Render the cheatsheets | |
| - name: Render Cheatsheet pdfs | |
| run: | | |
| Rscript --vanilla "scripts/render_cheatsheets.R" --files "${{ steps.changed-files.outputs.all_changed_files }}" | |
| # Render resource pdfs + html | |
| - name: Render Resource pdfs + html | |
| run: | | |
| Rscript --vanilla "scripts/render_resources.R" --files "${{ steps.changed-files.outputs.all_changed_files }}" | |
| # Generate list of files that need pdfs | |
| - name: Generate list of lectures that need pdfs generated | |
| run: | | |
| Rscript --vanilla "scripts/render_html_list.R" | |
| echo the following need pdfs: | |
| echo "$(cat files.txt)" | |
| - name: Store list of lectures that need pdfs generated // Delete intermediate files | |
| id: getfiles | |
| run: | | |
| echo "files=$(cat files.txt)" >> $GITHUB_OUTPUT | |
| rm files.txt | |
| rm cheatsheet_files.csv | |
| rm lab_files.csv | |
| rm lecture_files.csv | |
| # 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 ${{steps.site.outcome}} | |
| exit 1 | |
| # Commit the rendered website files | |
| - name: Commit rendered website files to preview branch | |
| id: commit | |
| run: | | |
| branch_name='preview-${{ 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 --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/[email protected] | |
| 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-${{ github.event.pull_request.number }}/index.html") | |
| echo "website_link=$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/[email protected] | |
| with: | |
| comment-id: ${{ steps.fc.outputs.comment-id }} | |
| issue-number: ${{ github.event.pull_request.number }} | |
| body: | | |
| Re-rendered previews from the latest commit: See [preview of website here](${{ steps.build-components.outputs.website_link }}) | |
| _Updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_ | |
| edit-mode: replace | |
| - name: No comment if no changes | |
| if: steps.commit.outputs.changes == 'false' | |
| uses: peter-evans/[email protected] | |
| 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 ${{ steps.build-components.outputs.commit_id }}_ | |
| edit-mode: replace | |
| # Save files for conversion to pdf | |
| outputs: | |
| pdffiles: "${{ steps.getfiles.outputs.files }}" | |
| ########################## PDFs ############################## | |
| render-pdf-lectures: | |
| name: Render pdf lecture slides | |
| needs: render-preview | |
| runs-on: ubuntu-latest | |
| container: | |
| image: ${{needs.yaml-check.outputs.rendering_docker_image}} | |
| if: ${{needs.yaml-check.outputs.toggle_render_preview == 'yes'}} | |
| strategy: | |
| matrix: | |
| modulenames: ${{fromJson(needs.render-preview.outputs.pdffiles)}} | |
| steps: | |
| # Give permission to access the repo | |
| - name: safelist repository | |
| run: | | |
| repo_name='${{ github.event.repository.name }}' | |
| git config --global --add safe.directory /__w/$repo_name/$repo_name | |
| - name: Checkout files | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 | |
| token: ${{ secrets.GH_PAT }} | |
| # Set up git checkout | |
| - name: Set up git checkout | |
| run: | | |
| git config --global user.name 'github-actions[bot]' | |
| git config --global user.email 'github-actions[bot]@users.noreply.github.com' | |
| branch_name='preview-${{ 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 | |
| # Render pdfs of slides | |
| - name: Convert HTML to PDF | |
| uses: fifsky/html-to-pdf-action@master | |
| with: | |
| htmlFile: ./modules/${{ matrix.modulenames }}/${{ matrix.modulenames }}.html | |
| outputFile: ./modules/${{ matrix.modulenames }}/${{ matrix.modulenames }}.pdf | |
| # Commit the rendered website files | |
| - name: Commit rendered website pdf files to preview branch | |
| id: commit_pdfs | |
| run: | | |
| branch_name='preview-${{ github.event.pull_request.number }}' | |
| git diff origin/main -- '*.pdf' >/dev/null && changes=true || changes=false | |
| echo "changes=$changes" >> $GITHUB_OUTPUT | |
| git status | |
| git add *.pdf --force | |
| git commit -m 'Render preview' || echo "No changes to commit" | |
| git status | |
| git pull --rebase --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours | |
| git push --force || echo "No changes to commit" | |
| shell: bash | |