test.yml

name: test

on:
  workflow_call:
    inputs:
      R-version:
        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:
  test:
    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: 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    - name: check for out-of-date dependencies files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    - name: check for out-of-date files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