pull_request.yml

name: Build and test conda env
on: pull_request
jobs:
  generate_matrix:
    uses: ./.github/workflows/get_changed_env.yml
  
  setup:
    runs-on: ubuntu-latest
    needs: generate_matrix
    if: ${{ needs.generate_matrix.outputs.matrix != '{"include":[]}' }}
    container:
      image: quay.io/singularity/singularity:v3.11.4
      options: --privileged
    steps:
      - name: Checkout repository
        ### Latest at time of writing
        uses: actions/checkout@v4
      - name: Check if container definition has changed
        id: changed-container-def
        uses: tj-actions/changed-files@v41
        with:
          files_yaml: |
            containerdef:
              - container/container.def
      - name: Build container if definition has changed
        if: steps.changed-container-def.outputs.containerdef_any_changed == 'true'
        run: |
            echo ${{ needs.generate_matrix.outputs.matrix }}
            sudo -E singularity build container/base.sif container/container.def
      - name: Sync repository to Gadi
        ### Latest at time of writing
        uses: up9cloud/action-rsync@v1.3
        env:
          HOST: gadi.nci.org.au
          TARGET: ${{secrets.GADI_REPO_PATH}}
          KEY: ${{secrets.DEPLOY_KEY}}
          USER: ${{secrets.GADI_USER}}
      - name: Create Admin dirs on Gadi
        uses: appleboy/ssh-action@v0.1.7
        with:
          host: gadi.nci.org.au
          username: ${{secrets.GADI_USER}}
          key: ${{secrets.DEPLOY_KEY}}
          script: |
            source ${{secrets.GADI_REPO_PATH}}/scripts/install_config.sh
            source ${{secrets.GADI_REPO_PATH}}/scripts/functions.sh
            mkdir -p $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR
            set_admin_perms $ADMIN_DIR $JOB_LOG_DIR $BUILD_STAGE_DIR

  build:
    needs: [ generate_matrix, setup ]
    uses: ./.github/workflows/build.yml
    with:
      environment: ${{ matrix.environment }}
    secrets: inherit
    if: ${{ needs.generate_matrix.outputs.matrix != '{"include":[]}' }}
    strategy:
      matrix: ${{fromJson(needs.generate_matrix.outputs.matrix)}}
      max-parallel: 1
      fail-fast: false
  test:
    needs: [ generate_matrix, build ]
    uses: ./.github/workflows/test.yml
    with:
      environment: ${{ matrix.environment }}
    secrets: inherit
    if: ${{ needs.generate_matrix.outputs.matrix != '{"include":[]}' }}
    strategy:
      matrix: ${{fromJson(needs.generate_matrix.outputs.matrix)}}
      max-parallel: 1
      fail-fast: false