Reusable action workflows #1
Workflow file for this run
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| 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 | ||
