{2023.06}[foss/2023a] R-bundle-bioconductor v3.18 #129
Workflow file for this run
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| # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions | |
| name: Tests for scripts | |
| on: | |
| push: | |
| paths: | |
| - build_container.sh | |
| - create_directory_tarballs.sh | |
| - create_lmodsitepackage.py | |
| - EESSI-install-software.sh | |
| - install_software_layer.sh | |
| - load_easybuild_module.sh | |
| - run_in_compat_layer_env.sh | |
| - scripts/utils.sh | |
| - update_lmod_cache.sh | |
| pull_request: | |
| paths: | |
| - build_container.sh | |
| - create_directory_tarballs.sh | |
| - create_lmodsitepackage.py | |
| - EESSI-install-software.sh | |
| - install_software_layer.sh | |
| - load_easybuild_module.sh | |
| - run_in_compat_layer_env.sh | |
| - scripts/utils.sh | |
| - update_lmod_cache.sh | |
| permissions: | |
| contents: read # to fetch code (actions/checkout) | |
| jobs: | |
| build: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: checkout | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4.1.1 | |
| - name: install Apptainer | |
| run: | | |
| ./install_apptainer_ubuntu.sh | |
| - name: prepare repos info for NESSI | |
| run: | | |
| curl -Ls https://github.com/NorESSI/filesystem-layer/tarball/v0.4.1 | tar xzf - --strip-components=1 --no-wildcards-match-slash --wildcards '*/repos/' | |
| - name: list available repos | |
| run: | | |
| export EESSI_REPOS_CFG_DIR_OVERRIDE=${PWD}/repos | |
| ./eessi_container.sh --list-repos | |
| - name: test load_easybuild_module.sh script | |
| run: | | |
| # bind current directory into container as /software-layer | |
| export SINGULARITY_BIND="${PWD}:/software-layer" | |
| # can't test with EasyBuild versions older than v4.5.2 when using EESSI 2023.06, | |
| # since Python in compat layer is Python 3.11.x; | |
| # testing with a single EasyBuild version takes a while in GitHub Actions, so stick to a single sensible version | |
| for EB_VERSION in '4.6.0'; do | |
| # Create script that uses load_easybuild_module.sh which we can run in compat layer environment | |
| # note: Be careful with single vs double quotes below! | |
| # ${EB_VERSION} should be expanded, so use double quotes; | |
| # For statements using variables that are only defined in the script, like ${EASYBUILD_INSTALLPATH}, | |
| # use single quotes to avoid expansion while creating the script. | |
| test_script="${PWD}/eb-${EB_VERSION}.sh" | |
| echo '#!/bin/bash' > ${test_script} | |
| # both $EB and $TMPDIR environment must be set, required by load_easybuild_module.sh script | |
| echo 'export EB="eb"' >> ${test_script} | |
| echo 'export TMPDIR=$(mktemp -d)' >> ${test_script} | |
| # set up environment to have utility functions in place that load_easybuild_module.sh script relies on, | |
| # along with $EESSI_* environment variables, and Lmod | |
| echo 'ls -l /software-layer/' >> ${test_script} | |
| echo 'source /software-layer/scripts/utils.sh' >> ${test_script} | |
| echo 'source /software-layer/init/eessi_environment_variables' >> ${test_script} | |
| echo 'source ${EPREFIX}/usr/share/Lmod/init/bash' >> ${test_script} | |
| # minimal configuration for EasyBuild so we can test installation aspect of load_easybuild_module.sh script | |
| echo "export EASYBUILD_INSTALLPATH=/tmp/eb-${EB_VERSION}" >> ${test_script} | |
| echo 'module use ${EASYBUILD_INSTALLPATH}/modules/all' >> ${test_script} | |
| echo '' >> ${test_script} | |
| echo "source /software-layer/load_easybuild_module.sh ${EB_VERSION}" >> ${test_script} | |
| echo 'module list' >> ${test_script} | |
| echo 'eb --version' >> ${test_script} | |
| chmod u+x ${test_script} | |
| # run wrapper script + capture & check output | |
| out="${PWD}/eb-${EB_VERSION}.out" | |
| export EESSI_REPOS_CFG_DIR_OVERRIDE=${PWD}/repos | |
| # skip installation of CUDA SDKs, since this is too heavy for CI | |
| sed -i "s@./EESSI-install-software.sh@./EESSI-install-software.sh --skip-cuda-install@g" install_software_layer.sh | |
| ./eessi_container.sh --access rw --mode run --verbose --repository nessi.no-2023.06-software /software-layer/run_in_compat_layer_env.sh /software-layer/eb-${EB_VERSION}.sh 2>&1 | tee ${out} | |
| pattern="^This is EasyBuild ${EB_VERSION} " | |
| grep "${pattern}" ${out} || (echo "Pattern '${pattern}' not found in output!" && exit 1) | |
| done | |
| - name: test install_software_layer.sh script | |
| run: | | |
| # bind current directory into container as /software-layer | |
| export SINGULARITY_BIND="${PWD}:/software-layer" | |
| # force using x86_64/generic, to avoid triggering an installation from scratch | |
| sed -i "s@./EESSI-install-software.sh@\"export EESSI_SOFTWARE_SUBDIR_OVERRIDE='x86_64/generic'; ./EESSI-install-software.sh\"@g" install_software_layer.sh | |
| export EESSI_REPOS_CFG_DIR_OVERRIDE=${PWD}/repos | |
| ./eessi_container.sh --mode run --verbose --repository nessi.no-2023.06-software /software-layer/install_software_layer.sh | |
| - name: test create_directory_tarballs.sh script | |
| run: | | |
| # bind current directory into container as /software-layer | |
| export SINGULARITY_BIND="${PWD}:/software-layer" | |
| # scripts need to be copied to /tmp, | |
| # since create_directory_tarballs.sh must be accessible from within build container | |
| export EESSI_REPOS_CFG_DIR_OVERRIDE=${PWD}/repos | |
| ./eessi_container.sh --mode run --verbose --repository nessi.no-2023.06-software /software-layer/create_directory_tarballs.sh 2023.06 | |
| # check if tarballs have been produced | |
| ls -l *.tar.gz | |
| - name: test create_lmodsitepackage.py script | |
| run: | | |
| # bind current directory into container as /software-layer | |
| export SINGULARITY_BIND="${PWD}:/software-layer" | |
| # Creates .lmod/SitePackage.lua in current dir, which then gets bind-mounted into /software-layer | |
| python3 create_lmodsitepackage.py . | |
| # run some commands to make sure that generated Lmod SitePackage file works | |
| test_script="${PWD}/test_lmod_sitepackage.sh" | |
| echo '#!/bin/bash' > ${test_script} | |
| echo 'export LMOD_PACKAGE_PATH="/software-layer/.lmod"' > ${test_script} | |
| echo 'ml --config' >> ${test_script} | |
| chmod u+x ${test_script} | |
| out="${PWD}/test_create_lmodsitepackage.out" | |
| ./eessi_container.sh --mode run --verbose /software-layer/run_in_compat_layer_env.sh /software-layer/test_lmod_sitepackage.sh 2>&1 | tee ${out} | |
| for pattern in "^Site Pkg location.*/software-layer/.lmod/SitePackage.lua" "LMOD_SITEPACKAGE_LOCATION.*/software-layer/.lmod/SitePackage.lua"; do | |
| grep "${pattern}" ${out} || (echo "Pattern '${pattern}' not found in output!" && exit 1) | |
| done |