add CEDAR and ARCHS4 and overhaul and simplify code base #71
Workflow file for this run
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 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 |