[Docker, CI] Allow building pecan/depends from pecan/depends #106
Workflow file for this run
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| name: Weekly Checks | ||
| on: | ||
| # every Monday at 4:30 AM | ||
| # (hopefully after the 1:30 AM `depends` build has completed) | ||
| schedule: | ||
| - cron: '30 4 * * 1' | ||
| workflow_dispatch: | ||
| env: | ||
| R_LIBS_USER: /usr/local/lib/R/site-library | ||
| LC_ALL: en_US.UTF-8 | ||
| NCPUS: 2 | ||
| PGHOST: postgres | ||
| CI: true | ||
| jobs: | ||
| # ---------------------------------------------------------------------- | ||
| # R TEST | ||
| # ---------------------------------------------------------------------- | ||
| test: | ||
| if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| R: | ||
| - "devel" | ||
| services: | ||
| postgres: | ||
| image: mdillon/postgis:9.5 | ||
| options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 | ||
| container: | ||
| image: pecan/depends:R${{ matrix.R }} | ||
| 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: update dependency lists | ||
| run: Rscript scripts/generate_dependencies.R | ||
| - name: check for out-of-date dependencies files | ||
| uses: infotroph/tree-is-clean@v1 | ||
| - name: install newly-added dependencies | ||
| working-directory: docker/depends | ||
| run: Rscript pecan.depends.R | ||
| # initialize database | ||
| - name: db setup | ||
| uses: docker://pecan/db:ci | ||
| - name: add models to db | ||
| run: ./scripts/add.models.sh | ||
| # run PEcAn tests | ||
| - name: test | ||
| run: make -j1 test | ||
| - name: check for out-of-date files | ||
| uses: infotroph/tree-is-clean@v1 | ||
| # ---------------------------------------------------------------------- | ||
| # R CHECK | ||
| # ---------------------------------------------------------------------- | ||
| check: | ||
| if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| R: | ||
| - "devel" | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| _R_CHECK_LENGTH_1_CONDITION_: true | ||
| _R_CHECK_LENGTH_1_LOGIC2_: true | ||
| # Avoid compilation check warnings that come from the system Makevars | ||
| # See https://stat.ethz.ch/pipermail/r-package-devel/2019q2/003898.html | ||
| _R_CHECK_COMPILATION_FLAGS_KNOWN_: -Wformat -Werror=format-security -Wdate-time | ||
| # Keep R checks from trying to consult the very flaky worldclockapi.com | ||
| _R_CHECK_SYSTEM_CLOCK_: 0 | ||
| container: | ||
| image: pecan/depends:R${{ matrix.R }} | ||
| 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 && cd docker/depends && Rscript pecan.depends.R | ||
| # run PEcAn checks | ||
| - name: check | ||
| run: make -j1 check | ||
| env: | ||
| REBUILD_DOCS: "FALSE" | ||
| RUN_TESTS: "FALSE" | ||
| - name: check for out-of-date files | ||
| uses: infotroph/tree-is-clean@v1 | ||
| # ---------------------------------------------------------------------- | ||
| # SIPNET TESTS | ||
| # ---------------------------------------------------------------------- | ||
| sipnet: | ||
| if: github.event_name != 'issue_comment' || startsWith(github.event.comment.body, '/build') | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| R: | ||
| - "devel" | ||
| services: | ||
| postgres: | ||
| image: mdillon/postgis:9.5 | ||
| options: --health-cmd pg_isready --health-interval 10s --health-timeout 5s --health-retries 5 | ||
| container: | ||
| image: pecan/depends:R${{ matrix.R }} | ||
| 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 && cd docker/depends && Rscript 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 | ||
