add CEDAR and ARCHS4 and overhaul and simplify code base #66
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@v2 | |
| 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. | |
| - name: Make branch if it doesn't exist | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "jhudsl-robot" | |
| branch_name='preview-${{ github.event.pull_request.number }}' | |
| exists=$(git ls-remote https://${{ secrets.GH_PAT }}@github.com/$GITHUB_REPOSITORY $branch_name | wc -l | xargs) | |
| if [[ $exists == 0 ]];then | |
| echo branch doesnt exist | |
| git checkout -b $branch_name || echo branch exists | |
| git push --set-upstream origin $branch_name | |
| else | |
| echo branch does exist | |
| fi | |
| shell: bash | |
| - name: Check if this is a private repository | |
| id: public_repository | |
| run: | | |
| public=$(curl -Is https://github.com/${GITHUB_REPOSITORY} | head -1 | tr -dc '0-9') | |
| if [ $public -eq 2200 ];then | |
| public='true' | |
| echo 'public repository' | |
| else | |
| public='false' | |
| echo 'private repository' | |
| fi | |
| echo ::set-output name=public::$public | |
| 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 }}" | |
| spell-check: | |
| name: Check spelling | |
| needs: yaml-check | |
| runs-on: ubuntu-latest | |
| if: ${{needs.yaml-check.outputs.toggle_spell_check == 'yes'}} | |
| container: | |
| image: jhudsl/course_template:main | |
| steps: | |
| - name: Checkout files | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| - name: Configure git | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "jhudsl-robot" | |
| branch_name='preview-${{ 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 | |
| - name: Run spell check | |
| id: spell_check_run | |
| run: | | |
| results=$(Rscript "scripts/spell-check.R") | |
| echo "::set-output name=sp_chk_results::$results" | |
| - name: Archive spelling errors | |
| if: ${{ steps.spell_check_run.outputs.sp_chk_results > 0 }} | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: spell-check-results | |
| path: check_reports/spell_check_results.tsv | |
| - name: Commit spell check errors | |
| run: | | |
| branch_name='preview-${{ github.event.pull_request.number }}' | |
| git add --force check_reports/spell_check_results.tsv || echo "No changes to commit" | |
| git commit -m 'Add spell check file' || echo "No changes to commit" | |
| git pull --set-upstream origin $branch_name --allow-unrelated-histories --strategy-option=ours | |
| git push --force origin $branch_name || echo "No changes to commit" | |
| - name: Build components of the spell check comment | |
| id: build-components | |
| env: | |
| GH_PAT: ${{ secrets.GH_PAT }} | |
| run: | | |
| branch_name='preview-${{ github.event.pull_request.number }}' | |
| if ${{ needs.yaml-check.outputs.public_repository }} == 'true' | |
| then | |
| sp_error_url=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/$branch_name/check_reports/spell_check_results.tsv | |
| else | |
| sp_error_url=https://github.com/${GITHUB_REPOSITORY}/blob/$branch_name/check_reports/spell_check_results.tsv | |
| fi | |
| echo ::set-output name=time::$(date +'%Y-%m-%d') | |
| echo ::set-output name=commit_id::$GITHUB_SHA | |
| echo ::set-output name=sp_error_url::$sp_error_url | |
| # Handle the commenting | |
| - 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: spelling errors | |
| - name: Spelling errors! | |
| if: ${{ steps.spell_check_run.outputs.sp_chk_results >= 3 }} | |
| uses: peter-evans/create-or-update-comment@v1 | |
| with: | |
| comment-id: ${{ steps.fc.outputs.comment-id }} | |
| issue-number: ${{ github.event.pull_request.number }} | |
| body: | | |
| :warning: There are spelling errors that need to be addressed. [Read this guide for more info](https://github.com/jhudsl/OTTR_Template/wiki/Spell-check). | |
| [Download the errors here.](${{ steps.build-components.outputs.sp_error_url }}) | |
| _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_ | |
| edit-mode: replace | |
| - name: Check spell check results - fail if too many errors | |
| if: ${{ steps.spell_check_run.outputs.sp_chk_results >= 3 }} | |
| run: exit 1 | |
| - name: No spelling errors | |
| if: ${{ steps.spell_check_run.outputs.sp_chk_results < 3 }} | |
| uses: peter-evans/create-or-update-comment@v1 | |
| with: | |
| comment-id: ${{ steps.fc.outputs.comment-id }} | |
| issue-number: ${{ github.event.pull_request.number }} | |
| body: | | |
| No spelling errors! :tada: | |
| _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_ | |
| edit-mode: replace | |
| url-check: | |
| name: Check URLs | |
| needs: yaml-check | |
| runs-on: ubuntu-latest | |
| if: ${{needs.yaml-check.outputs.toggle_url_check == 'yes'}} | |
| container: | |
| image: jhudsl/course_template:main | |
| steps: | |
| - name: checkout repo | |
| uses: actions/checkout@v2 | |
| - name: Configure git | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "jhudsl-robot" | |
| branch_name='preview-${{ 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 | |
| - name: URLs checker | |
| uses: urlstechie/urlchecker-action@master | |
| with: | |
| # Specify a branch | |
| branch: preview-${{ github.event.pull_request.number }} | |
| # Cleanup | |
| cleanup: false | |
| # A comma-separated list of file types to cover in the URL checks | |
| file_types: .Rmd,.md | |
| # Choose whether to include file with no URLs in the prints. | |
| print_all: false | |
| exclude_files: .github/PULL_REQUEST_TEMPLATE.md | |
| # A comma separated links to exclude during URL checks | |
| exclude_urls: https://jhudatascience.org/{Course_Name}} | |
| force_pass: true | |
| # A path to a csv file to save results to | |
| save: check_reports/url_checks.csv | |
| - name: Count URL errors | |
| id: url_errors | |
| run: | | |
| results=$(Rscript "scripts/url-check.R") | |
| echo "::set-output name=url_results::$results" | |
| - name: Commit URL check | |
| run: | | |
| branch_name='preview-${{ github.event.pull_request.number }}' | |
| git add --force check_reports/url_checks.csv || echo "No changes to commit" | |
| git commit -m 'Add URL check file' || echo "No changes to commit" | |
| git fetch | |
| git merge -s recursive --strategy-option=ours origin/${{ github.head_ref }} --allow-unrelated-histories | |
| git push --force origin $branch_name || echo "No changes to commit" | |
| - name: Build components of the spell check comment | |
| id: build-components | |
| env: | |
| GH_PAT: ${{ secrets.GH_PAT }} | |
| run: | | |
| branch_name='preview-${{ github.event.pull_request.number }}' | |
| if ${{ needs.yaml-check.outputs.public_repository }} == 'true' | |
| then | |
| url_errors=https://raw.githubusercontent.com/${GITHUB_REPOSITORY}/$branch_name/check_reports/url_checks.csv | |
| else | |
| url_errors=https://github.com/${GITHUB_REPOSITORY}/blob/$branch_name/check_reports/url_checks.csv | |
| fi | |
| echo ::set-output name=time::$(date +'%Y-%m-%d') | |
| echo ::set-output name=commit_id::$GITHUB_SHA | |
| echo ::set-output name=url_errors::$url_errors | |
| # Handle the commenting | |
| - 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: broken URLs | |
| - name: URL errors! | |
| if: ${{ steps.url_errors.outputs.url_results > 0 }} | |
| uses: peter-evans/create-or-update-comment@v1 | |
| with: | |
| comment-id: ${{ steps.fc.outputs.comment-id }} | |
| issue-number: ${{ github.event.pull_request.number }} | |
| body: | | |
| :warning: There are broken URLs that need to be addressed. [Read this guide for more info](https://github.com/jhudsl/OTTR_Template/wiki/How-to-set-up-and-customize-GitHub-actions-robots#check-for-broken-urls). | |
| [Download the errors here.](${{ steps.build-components.outputs.url_errors }}) | |
| _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_ | |
| edit-mode: replace | |
| - name: Check URL results - fail if too many errors | |
| if: ${{ steps.url_errors.outputs.url_results > 0 }} | |
| run: exit 1 | |
| - name: No URL errors | |
| if: ${{ steps.url_errors.outputs.url_results == 0 }} | |
| uses: peter-evans/create-or-update-comment@v1 | |
| with: | |
| comment-id: ${{ steps.fc.outputs.comment-id }} | |
| issue-number: ${{ github.event.pull_request.number }} | |
| body: | | |
| No broken URLs detected! :tada: | |
| _Comment updated at ${{ steps.build-components.outputs.time }} with changes from ${{ steps.build-components.outputs.commit_id }}_ | |
| edit-mode: replace | |
| render-preview: | |
| name: Render preview | |
| needs: yaml-check | |
| runs-on: ubuntu-latest | |
| container: | |
| image: jhudsl/course_template:main | |
| if: ${{needs.yaml-check.outputs.toggle_render_preview == 'yes'}} | |
| steps: | |
| - name: Checkout files | |
| uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: 0 | |
| # Set up git checkout | |
| - name: Set up git checkout | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "jhudsl-robot" | |
| branch_name='preview-${{ 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 | |
| # 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 | |
| id: site | |
| run: Rscript -e "rmarkdown::render_site()" | |
| # We may have html files that we want to render to add as links on the pages -these will be stored in a dir called subdir_html | |
| - name: Render subdir_html | |
| id: subdir_html | |
| run: Rscript -e "for (i in list.files(path = './subdir_html', pattern = 'Rmd$', recursive = TRUE, full.names = TRUE)){rmarkdown::render(i)}" | |
| # 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 ::set-output name=changes::$changes | |
| 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-${{ github.event.pull_request.number }}/index.html") | |
| echo ::set-output name=website_link::$website_link | |
| echo ::set-output name=time::$(date +'%Y-%m-%d') | |
| echo ::set-output name=commit_id::$GITHUB_SHA | |
| 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: ${{ github.event.pull_request.number }} | |
| body: | | |
| Re-rendered previews from the latest commit: See [preview of website here](${{ 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/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 |