Add Oxford Nanopore #13
Workflow file for this run
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| name: main-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@v4 | |
| 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: Install tools and regenerate registered jsons for Superdataset, PortalDataset, etc | |
| run: | | |
| pip install linkml | |
| npm install -g json-dereference-cli | |
| make Dataset | |
| make Superdataset | |
| make PortalDataset | |
| make PortalStudy | |
| - name: Commit files | |
| run: | | |
| git config --local user.email "[email protected]" | |
| git config --local user.name "nf-osi[bot]" | |
| git add . | |
| git commit -m "Rebuild NF.jsonld, json" | |
| - 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 | |
| needs: [build] | |
| runs-on: ubuntu-latest | |
| env: | |
| SCHEMATIC_SERVICE_ACCT_CREDS: ${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }} | |
| permissions: | |
| pull-requests: write | |
| strategy: | |
| matrix: | |
| schematic-version: [24.1.1] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| ref: ${{ github.event.pull_request.head.ref }} | |
| fetch-depth: 1 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.10.12' | |
| - name: Setup schematic | |
| id: setup-schematic | |
| run: pip install schematicpy==${{ matrix.schematic-version }} | |
| - name: Sanity-check successful installation and version | |
| run: pip show schematicpy | |
| - 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 | |