Add new PRO assays and data types #182
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
| name: schematic-ci | |
| on: | |
| pull_request: # default types: opened, synchronize, reopened | |
| branches: [main] | |
| paths: | |
| - 'modules/**' | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| persist-credentials: false # otherwise, the token used is the GITHUB_TOKEN, instead of your personal access token. | |
| fetch-depth: 0 # otherwise, there would be errors pushing refs to the destination repository | |
| - name: Setup custom build tools and make jsonld | |
| shell: bash | |
| run: | | |
| bash < <(curl -s https://raw.githubusercontent.com/babashka/babashka/master/install) | |
| git clone --depth 1 https://github.com/anngvu/retold.git | |
| make | |
| - name: Commit files | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "nf-osi[bot]" | |
| git add "NF.jsonld" | |
| git commit -m "Build jsonld" | |
| - name: Push changes | |
| uses: ad-m/github-push-action@master | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| branch: ${{ github.event.pull_request.head.ref }} | |
| # Additionally test PRs | |
| test: | |
| name: Test with schematic | |
| if: "!contains( github.event.pull_request.labels.*.name, 'skip tests')" | |
| needs: [build] | |
| runs-on: ubuntu-22.04 | |
| env: | |
| SCHEMATIC_SERVICE_ACCT_CREDS: ${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }} | |
| permissions: | |
| pull-requests: write | |
| strategy: | |
| matrix: | |
| schematic-version: [23.9.1] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| fetch-depth: 1 | |
| - name: Setup schematic | |
| id: setup-schematic | |
| run: pip3 install schematicpy==${{ matrix.schematic-version }} | |
| - name: Test generate | |
| working-directory: tests/generate | |
| continue-on-error: true | |
| run: ./basic_templates.sh | |
| - name: Test validate | |
| working-directory: tests/validate | |
| continue-on-error: true | |
| run: ./run_config.sh | |
| # TODO Step for test submission of data | |
| - name: Create test suite report | |
| working-directory: tests | |
| continue-on-error: true | |
| run: docker run -v $(pwd):/tests rocker/tidyverse R -e "rmarkdown::render('tests/test-suite-report.Rmd')" | |
| - name: Report on test suite as PR comment | |
| uses: mshick/add-pr-comment@v2 | |
| with: | |
| message-id: test-suite-report | |
| message-path: | | |
| tests/test-suite-report.md | |
| - name: Upload test artifacts | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: test-logs-${{ matrix.schematic-version }} | |
| path: tests/**/logs | |