Reusable action workflows #1
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: sipnet | ||
| on: | ||
| workflow_call: | ||
| inputs: | ||
| R-version: | ||
| required: true | ||
| type: string | ||
| secrets: | ||
| GITHUB_TOKEN: | ||
| required: true | ||
| env: | ||
| R_LIBS_USER: /usr/local/lib/R/site-library | ||
| LC_ALL: en_US.UTF-8 | ||
| NCPUS: 2 | ||
| PGHOST: postgres | ||
| CI: true | ||
| jobs: | ||
| sipnet: | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| services: | ||
| postgres: | ||
| image: mdillon/postgis:9.5 | ||
| options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 | ||
| container: | ||
| image: pecan/depends:R${{ inputs.R-version }} | ||
| steps: | ||
| # checkout source code | ||
| - name: work around https://github.com/actions/checkout/issues/766 | ||
| run: git config --global --add safe.directory "$GITHUB_WORKSPACE" | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| set-safe-directory: false | ||
| # install additional tools needed | ||
| - name: install utils | ||
| run: apt-get update && apt-get install -y postgresql-client qpdf | ||
| - name: install new dependencies | ||
| run: Rscript scripts/generate_dependencies.R && Rscript docker/depends/pecan.depends.R | ||
| # initialize database | ||
| - name: db setup | ||
| uses: docker://pecan/db:ci | ||
| - name: add models to db | ||
| run: ./scripts/add.models.sh | ||
| # install sipnet | ||
| - name: Check out SIPNET | ||
| uses: actions/checkout@v4 | ||
| with: | ||
| repository: PecanProject/sipnet | ||
| path: sipnet | ||
| set-safe-directory: false | ||
| - name: install sipnet | ||
| run: | | ||
| cd ${GITHUB_WORKSPACE}/sipnet | ||
| make | ||
| # compile PEcAn code | ||
| - name: build | ||
| run: make -j1 | ||
| # run SIPNET test | ||
| - name: integration test | ||
| run: ./tests/integration.sh ghaction | ||
GitHub Actions