Add function to modify path-like environment variable in a context #1908
Workflow file for this run
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| # documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions | |
| name: Tests for Apptainer container support | |
| on: [push, pull_request] | |
| permissions: | |
| contents: read # to fetch code (actions/checkout) | |
| concurrency: | |
| group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| python: [3.7] | |
| apptainer: [1.0.0, 1.1.7] | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: set up Python | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{matrix.python}} | |
| architecture: x64 | |
| - name: install OS & Python packages | |
| run: | | |
| # for building CentOS 7 container images | |
| APT_PKGS="rpm dnf" | |
| # for modules tool | |
| APT_PKGS+=" lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev" | |
| # Avoid apt-get update, as we don't really need it, | |
| # and it does more harm than good (it's fairly expensive, and it results in flaky test runs) | |
| if ! sudo apt-get install $APT_PKGS; then | |
| # Try to update cache, then try again to resolve 404s of old packages | |
| sudo apt-get update -yqq || true | |
| sudo apt-get install $APT_PKGS | |
| fi | |
| # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082 | |
| # needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists | |
| if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then | |
| sudo ln -s /usr/lib/x86_64-linux-gnu/lua/5.2/posix_c.so /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so | |
| fi | |
| - name: install Lmod | |
| run: | | |
| # avoid downloading modules tool sources into easybuild-framework dir | |
| cd $HOME | |
| export INSTALL_DEP=$GITHUB_WORKSPACE/easybuild/scripts/install_eb_dep.sh | |
| # install Lmod | |
| source $INSTALL_DEP Lmod-8.4.27 $HOME | |
| # changes in environment are not passed to other steps, so need to create files... | |
| echo $MOD_INIT > mod_init | |
| echo $PATH > path | |
| if [ ! -z $MODULESHOME ]; then echo $MODULESHOME > moduleshome; fi | |
| - name: install Apptainer | |
| run: | | |
| curl -OL https://github.com/apptainer/apptainer/releases/download/v${{matrix.apptainer}}/apptainer_${{matrix.apptainer}}_amd64.deb | |
| sudo apt install ./apptainer*.deb | |
| # Apptainer provides both apptainer and singularity commands | |
| apptainer --version | |
| singularity --version | |
| - name: install sources | |
| run: | | |
| # install from source distribution tarball, to test release as published on PyPI | |
| python setup.py sdist | |
| ls dist | |
| export PREFIX=/tmp/$USER/$GITHUB_SHA | |
| pip install --prefix $PREFIX dist/easybuild[-_]framework*tar.gz | |
| pip install --prefix $PREFIX https://github.com/easybuilders/easybuild-easyblocks/archive/5.0.x.tar.gz | |
| - name: run test | |
| run: | | |
| # run tests *outside* of checked out easybuild-framework directory, | |
| # to ensure we're testing installed version (see previous step) | |
| cd $HOME | |
| # initialize environment for modules tool | |
| if [ -f $HOME/moduleshome ]; then export MODULESHOME=$(cat $HOME/moduleshome); fi | |
| source $(cat $HOME/mod_init); type module | |
| # make sure 'eb' is available via $PATH, and that $PYTHONPATH is set (some tests expect that); | |
| # also pick up changes to $PATH set by sourcing $MOD_INIT | |
| export PREFIX=/tmp/$USER/$GITHUB_SHA | |
| export PATH=$PREFIX/bin:$(cat $HOME/path) | |
| export PYTHONPATH=$PREFIX/lib/python${{matrix.python}}/site-packages:$PYTHONPATH | |
| eb --version | |
| # create $HOME/.rpmmacros, see also https://github.com/apptainer/singularity/issues/241 | |
| echo '%_var /var' > $HOME/.rpmmacros | |
| echo '%_dbpath %{_var}/lib/rpm' >> $HOME/.rpmmacros | |
| # build CentOS 7 container image for bzip2 1.0.8 using EasyBuild; | |
| # see https://docs.easybuild.io/en/latest/Containers.html | |
| curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/5.0.x/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb | |
| export EASYBUILD_CONTAINERPATH=$PWD | |
| export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/centos-7.9-python3-amd64' | |
| export EASYBUILD_CONTAINER_TYPE='apptainer' | |
| eb bzip2-1.0.8.eb --containerize --experimental --container-build-image | |
| apptainer exec bzip2-1.0.8.sif command -v bzip2 | grep '/app/software/bzip2/1.0.8/bin/bzip2' || (echo "Path to bzip2 '$which_bzip2' is not correct" && exit 1) | |
| apptainer exec bzip2-1.0.8.sif bzip2 --help |