ci-weekly.yml

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'

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    - name: check for out-of-date dependencies files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    - name: check for out-of-date files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