def files, bash scipts for containers, testing yaml #5
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| 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: 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-${{ hashFiles('containers/beethoven_dl_calc.def') }} | |
| restore-keys: sif-cache- | |
| - name: Build the Apptainer container (if cache miss) | |
| if: steps.cache-sif.outputs.cache-hit != 'true' | |
| run: | | |
| apptainer build container/beethoven_dl_calc.sif beethoven_dl_calc.def | |
| - name: Cache the .sif file | |
| if: steps.cache-sif.outputs.cache-hit != 'true' | |
| uses: actions/cache@v3 | |
| with: | |
| path: beethoven_dl_calc.sif | |
| key: sif-cache-${{ hashFiles('containers/beethoven_dl_calc.def') }} | |
| - name: Create run_dl_calc_tests.R dynamically | |
| run: | | |
| echo 'testthat::test_file("/mnt/tests/testthat/test_download.R")' > tests/testthat/run_dl_calc_tests.R | |
| echo 'testthat::test_file("/mnt/tests/testthat/test_calculate.R")' >> tests/testthat/run_dl_calc_tests.R | |
| - name: Run tests inside the container | |
| run: | | |
| apptainer exec \ | |
| --bind $PWD/inst:/pipeline \ | |
| --bind $PWD/input:/input \ | |
| --bind $PWD/_targets:/opt/_targets \ | |
| --bind $PWD:/mnt \ | |
| Rscript mnt/tests/testhat/run_dl_calc_tests.R |