def files, bash scipts for containers, testing yaml #8
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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-${{ runner.os }}-${{ hashFiles('container/beethoven_dl_calc.def') }} | |
| restore-keys: | | |
| sif-cache-${{ runner.os }}- | |
| - name: Build the Apptainer container (if cache miss) | |
| if: steps.cache-sif.outputs.cache-hit != 'true' | |
| run: | | |
| apptainer build --fakeroot beethoven_dl_calc.sif container/beethoven_dl_calc.def | |
| - name: Cache the .sif file | |
| if: steps.cache-sif.outputs.cache-hit != 'true' | |
| uses: actions/cache@v3 | |
| with: | |
| path: beethoven_dl_calc.sif | |
| key: sif-cache-${{ hashFiles('container/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 container/beethoven_dl_calc.sif Rscript tests/testhat/run_dl_calc_tests.R |