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| 1 | +# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions |
| 2 | +name: Tests for Apptainer container support |
| 3 | +on: [push, pull_request] |
| 4 | + |
| 5 | +permissions: |
| 6 | + contents: read # to fetch code (actions/checkout) |
| 7 | + |
| 8 | +concurrency: |
| 9 | + group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}} |
| 10 | + cancel-in-progress: true |
| 11 | + |
| 12 | +jobs: |
| 13 | + build: |
| 14 | + runs-on: ubuntu-22.04 |
| 15 | + strategy: |
| 16 | + matrix: |
| 17 | + python: [2.7, 3.7] |
| 18 | + apptainer: [1.0.0, 1.1.7] |
| 19 | + fail-fast: false |
| 20 | + steps: |
| 21 | + - uses: actions/checkout@v2 |
| 22 | + |
| 23 | + - name: set up Python |
| 24 | + uses: actions/setup-python@v2 |
| 25 | + with: |
| 26 | + python-version: ${{matrix.python}} |
| 27 | + architecture: x64 |
| 28 | + |
| 29 | + - name: install OS & Python packages |
| 30 | + run: | |
| 31 | + # for building CentOS 7 container images |
| 32 | + sudo apt-get install rpm |
| 33 | + sudo apt-get install dnf |
| 34 | + # for modules tool |
| 35 | + sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev |
| 36 | + # fix for lua-posix packaging issue, see https://bugs.launchpad.net/ubuntu/+source/lua-posix/+bug/1752082 |
| 37 | + # needed for Ubuntu 18.04, but not for Ubuntu 20.04, so skipping symlinking if posix.so already exists |
| 38 | + if [ ! -e /usr/lib/x86_64-linux-gnu/lua/5.2/posix.so ] ; then |
| 39 | + 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 |
| 40 | + fi |
| 41 | +
|
| 42 | + - name: install Lmod |
| 43 | + run: | |
| 44 | + # avoid downloading modules tool sources into easybuild-framework dir |
| 45 | + cd $HOME |
| 46 | + export INSTALL_DEP=$GITHUB_WORKSPACE/easybuild/scripts/install_eb_dep.sh |
| 47 | + # install Lmod |
| 48 | + source $INSTALL_DEP Lmod-8.4.27 $HOME |
| 49 | + # changes in environment are not passed to other steps, so need to create files... |
| 50 | + echo $MOD_INIT > mod_init |
| 51 | + echo $PATH > path |
| 52 | + if [ ! -z $MODULESHOME ]; then echo $MODULESHOME > moduleshome; fi |
| 53 | +
|
| 54 | + - name: install Apptainer |
| 55 | + run: | |
| 56 | + curl -OL https://github.com/apptainer/apptainer/releases/download/v${{matrix.apptainer}}/apptainer_${{matrix.apptainer}}_amd64.deb |
| 57 | + sudo apt install ./apptainer*.deb |
| 58 | + # Apptainer provides both apptainer and singularity commands |
| 59 | + apptainer --version |
| 60 | + singularity --version |
| 61 | +
|
| 62 | + - name: install sources |
| 63 | + run: | |
| 64 | + # install from source distribution tarball, to test release as published on PyPI |
| 65 | + python setup.py sdist |
| 66 | + ls dist |
| 67 | + export PREFIX=/tmp/$USER/$GITHUB_SHA |
| 68 | + pip install --prefix $PREFIX dist/easybuild-framework*tar.gz |
| 69 | + pip install --prefix $PREFIX https://github.com/easybuilders/easybuild-easyblocks/archive/develop.tar.gz |
| 70 | +
|
| 71 | + - name: run test |
| 72 | + run: | |
| 73 | + # run tests *outside* of checked out easybuild-framework directory, |
| 74 | + # to ensure we're testing installed version (see previous step) |
| 75 | + cd $HOME |
| 76 | + # initialize environment for modules tool |
| 77 | + if [ -f $HOME/moduleshome ]; then export MODULESHOME=$(cat $HOME/moduleshome); fi |
| 78 | + source $(cat $HOME/mod_init); type module |
| 79 | + # make sure 'eb' is available via $PATH, and that $PYTHONPATH is set (some tests expect that); |
| 80 | + # also pick up changes to $PATH set by sourcing $MOD_INIT |
| 81 | + export PREFIX=/tmp/$USER/$GITHUB_SHA |
| 82 | + export PATH=$PREFIX/bin:$(cat $HOME/path) |
| 83 | + export PYTHONPATH=$PREFIX/lib/python${{matrix.python}}/site-packages:$PYTHONPATH |
| 84 | + eb --version |
| 85 | + # create $HOME/.rpmmacros, see also https://github.com/apptainer/singularity/issues/241 |
| 86 | + echo '%_var /var' > $HOME/.rpmmacros |
| 87 | + echo '%_dbpath %{_var}/lib/rpm' >> $HOME/.rpmmacros |
| 88 | + # build CentOS 7 container image for bzip2 1.0.8 using EasyBuild; |
| 89 | + # see https://docs.easybuild.io/en/latest/Containers.html |
| 90 | + curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/develop/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb |
| 91 | + export EASYBUILD_CONTAINERPATH=$PWD |
| 92 | + export EASYBUILD_CONTAINER_CONFIG='bootstrap=docker,from=ghcr.io/easybuilders/centos-7.9-python3-amd64' |
| 93 | + export EASYBUILD_CONTAINER_TYPE='apptainer' |
| 94 | + eb bzip2-1.0.8.eb --containerize --experimental --container-build-image |
| 95 | + 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) |
| 96 | + apptainer exec bzip2-1.0.8.sif bzip2 --help |
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