test-container-dl-calc.yaml

name: Test Coverage for Download and Calculate via Apptainer

on:
  push:
    branches: [main, master, dev]
  pull_request:
    branches: [main, master, dev]

jobs:
  build:
    runs-on: ubuntu-latest

    steps:
      - name: Checkout code
        uses: actions/checkout@v2

      - name: Create run_dl_calc_tests.R dynamically
        run: |
          mkdir -p tests/testthat  # Ensure the directory exists
          echo 'testthat::test_file("tests/testthat/test_download.R")' > tests/testthat/run_dl_calc_tests.R
          echo 'testthat::test_file("tests/testthat/test_calculate.R")' >> tests/testthat/run_dl_calc_tests.R

      - name: Install Apptainer dependencies
        run: |
          sudo apt-get update && sudo apt-get install -y \
          libseccomp-dev \
          squashfs-tools \
          cryptsetup \
          wget

      - name: Install Apptainer
        run: |
          wget https://github.com/apptainer/apptainer/releases/download/v1.1.0/apptainer-1.1.0.tar.gz
          tar -xvf apptainer-1.1.0.tar.gz
          cd apptainer-1.1.0
          ./mconfig && make -C builddir && sudo make -C builddir install

      - name: Restore .sif file from cache
        id: cache-sif
        uses: actions/cache@v3
        with:
          path: beethoven_dl_calc.sif
          key: sif-cache-${{ runner.os }}-${{ hashFiles('container/beethoven_dl_calc.def') }}
          restore-keys: |
            sif-cache-${{ runner.os }}-

      - name: Build the Apptainer container (if cache miss)
        if: steps.cache-sif.outputs.cache-hit != 'true'
        run: |
          apptainer build --force --fakeroot beethoven_dl_calc.sif container/beethoven_dl_calc.def

      - name: Cache the .sif file
        if: steps.cache-sif.outputs.cache-hit != 'true'
        uses: actions/cache@v3
        with:
          path: beethoven_dl_calc.sif
          key: sif-cache-${{ runner.os }}-${{ hashFiles('container/beethoven_dl_calc.def') }}

      - name: Check if .sif file exists
        run: |
          if [ ! -f beethoven_dl_calc.sif ]; then
            echo "Error: .sif file not found!"
            exit 1
          fi

      - name: Run R tests
        run: |
          apptainer exec \
            --bind $PWD/inst:/pipeline \
            --bind $PWD/input:/input \
            --bind $PWD:/mnt \
            beethoven_dl_calc.sif \
            Rscript /mnt/tests/testthat/run_dl_calc_tests.R