Merge pull request #46 from Neves-P/samtools #115
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| # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions | |
| name: Tests for eessi_container.sh script | |
| on: [push, pull_request, workflow_dispatch] | |
| permissions: | |
| contents: read # to fetch code (actions/checkout) | |
| jobs: | |
| eessi_container_script: | |
| runs-on: ubuntu-20.04 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| SCRIPT_TEST: | |
| - help | |
| - listrepos_default | |
| - listrepos_custom | |
| - run | |
| - shell | |
| - container | |
| - resume | |
| # FIXME disabled because '--access rw' is not working in CI environment | |
| #- readwrite | |
| #- save | |
| steps: | |
| - name: Check out software-layer repository | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1 | |
| - name: install Apptainer | |
| run: | | |
| ./install_apptainer_ubuntu.sh | |
| - name: Collect info on test environment | |
| run: | | |
| mount | |
| df -h | |
| - name: Test eessi_container.sh script | |
| run: | | |
| test_cmd="cat /etc/os-release" | |
| out_pattern="Debian GNU/Linux 11" | |
| if [[ ${{matrix.SCRIPT_TEST}} == 'help' ]]; then | |
| ./eessi_container.sh --help | |
| # test use of --list-repos without custom repos.cfg | |
| elif [[ ${{matrix.SCRIPT_TEST}} == 'listrepos_default' ]]; then | |
| outfile=out_listrepos.txt | |
| ./eessi_container.sh --verbose --list-repos | tee ${outfile} | |
| grep "EESSI" ${outfile} | |
| # test use of --list-repos with custom repos.cfg | |
| elif [[ ${{matrix.SCRIPT_TEST}} == 'listrepos_custom' ]]; then | |
| outfile=out_listrepos.txt | |
| outfile2=out_listrepos_2.txt | |
| mkdir -p ${PWD}/cfg | |
| echo "[EESSI/20AB.CD]" > cfg/repos.cfg | |
| echo "repo_version = 20AB.CD" >> cfg/repos.cfg | |
| echo "[EESSI/20HT.TP]" >> cfg/repos.cfg | |
| echo "repo_version = 20HT.TP" >> cfg/repos.cfg | |
| ./eessi_container.sh --verbose --list-repos | tee ${outfile} | |
| grep "EESSI" ${outfile} | |
| export EESSI_REPOS_CFG_DIR_OVERRIDE=${PWD}/cfg | |
| ./eessi_container.sh --verbose --list-repos | tee ${outfile2} | |
| grep "[EESSI/2023.02]" ${outfile2} | |
| # test use of --mode run | |
| elif [[ ${{matrix.SCRIPT_TEST}} == 'run' ]]; then | |
| outfile=out_run.txt | |
| echo "${test_cmd}" > test_script.sh | |
| chmod u+x test_script.sh | |
| export SINGULARITY_BIND="$PWD:/test" | |
| ./eessi_container.sh --verbose --mode run /test/test_script.sh | tee ${outfile} | |
| grep "${out_pattern}" ${outfile} | |
| # test use of --mode shell | |
| elif [[ ${{matrix.SCRIPT_TEST}} == 'shell' ]]; then | |
| outfile=out_shell.txt | |
| ./eessi_container.sh --verbose --mode shell <<< "${test_cmd}" 2>&1 | tee ${outfile} | |
| grep "${out_pattern}" ${outfile} | |
| # test use of --container option, using a totally different container; | |
| # cfr. https://github.com/easybuilders/easybuild-containers | |
| elif [[ ${{matrix.SCRIPT_TEST}} == 'container' ]]; then | |
| outfile=out_container.txt | |
| container="docker://ghcr.io/eessi/build-node:debian10" | |
| ./eessi_container.sh --verbose --container ${container} --mode shell <<< "${test_cmd}" 2>&1 | tee ${outfile} | |
| grep "Debian GNU/Linux 10" ${outfile} | |
| # test use of '--access rw' to get write access in container | |
| elif [[ ${{matrix.SCRIPT_TEST}} == 'readwrite' ]]; then | |
| outfile=out_readwrite.txt | |
| fn="test_${RANDOM}.txt" | |
| echo "touch /cvmfs/software.eessi.io/${fn}" > test_script.sh | |
| chmod u+x test_script.sh | |
| export SINGULARITY_BIND="$PWD:/test" | |
| ./eessi_container.sh --verbose --access rw --mode run /test/test_script.sh > ${outfile} | |
| tmpdir=$(grep "\-\-resume" ${outfile} | sed "s/.*--resume \([^']*\).*/\1/g") | |
| # note: must use '--access rw' again here, since touched file is in overlay upper dir | |
| ./eessi_container.sh --verbose --resume ${tmpdir} --access rw --mode shell <<< "ls -l /cvmfs/software.eessi.io/${fn}" > ${outfile} | |
| grep "/cvmfs/software.eessi.io/${fn}$" $outfile | |
| # test use of --resume | |
| elif [[ ${{matrix.SCRIPT_TEST}} == 'resume' ]]; then | |
| outfile=out_resume.txt | |
| ./eessi_container.sh --verbose --mode shell <<< "${test_cmd}" > ${outfile} | |
| tmpdir=$(grep "\-\-resume" ${outfile} | sed "s/.*--resume \([^']*\).*/\1/g") | |
| rm -f ${outfile} | |
| # make sure that container image exists | |
| test -f ${tmpdir}/ghcr.io_eessi_build_node_debian11.sif || (echo "Container image not found in ${tmpdir}" >&2 && ls ${tmpdir} && exit 1) | |
| ./eessi_container.sh --verbose --resume ${tmpdir} --mode shell <<< "${test_cmd}" > ${outfile} | |
| cat ${outfile} | |
| grep "Resuming from previous run using temporary storage at ${tmpdir}" ${outfile} | |
| grep "${out_pattern}" ${outfile} | |
| # test use of --save (+ --resume) | |
| elif [[ ${{matrix.SCRIPT_TEST}} == 'save' ]]; then | |
| outfile=out_save.txt | |
| fn="test_${RANDOM}.txt" | |
| test_cmd="touch /cvmfs/software.eessi.io/${fn}" | |
| ./eessi_container.sh --verbose --mode shell --access rw --save test-save.tar <<< "${test_cmd}" 2>&1 | tee ${outfile} | |
| rm -f ${outfile} | |
| ./eessi_container.sh --verbose --mode shell --access rw --resume test-save.tar <<< "ls -l /cvmfs/software.eessi.io/${fn}" > ${outfile} | |
| grep "/cvmfs/software.eessi.io/${fn}$" $outfile | |
| tar tfv test-save.tar | grep "overlay-upper/${fn}" | |
| else | |
| echo "Unknown test case: ${{matrix.SCRIPT_TEST}}" >&2 | |
| exit 1 | |
| fi |