check.yml

name: check

on:
  workflow_call:
    inputs:
      R-version:
        required: true
        type: string
      make-grouping:
        required: true
        type: string

env:
  R_LIBS_USER: /usr/local/lib/R/site-library
  LC_ALL: en_US.UTF-8
  NCPUS: 2
  PGHOST: postgres
  CI: true

jobs:
  check:
    runs-on: ubuntu-latest

    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${{ 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

    # Forbid spaces in names. Yes, *we* know it's not 1980 anymore, but Make doesn't.
    - name: check for filenames that would confuse Make
      run: |
        SPACENAMES=`find . -name '* *'`
        if [ -n "$SPACENAMES" ]; then
          echo "::error file=${SPACENAMES}::Spaces in filename(s): ${SPACENAMES}. Please rename these files by converting spaces to underscores."
          exit 1
        fi

    # 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
    # The package names of base, modules, and models are passed as matrix variables to avoid repeatability of code
    - name: check
      run: make -j1 ${{ inputs.make-grouping }}
      env:
        REBUILD_DOCS: "FALSE"
        RUN_TESTS: "FALSE"

    - name: check for out-of-date files
      uses: infotroph/tree-is-clean@v1