container_tests_apptainer.yml

# 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/develop.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' >> $HOME/.rpmmacros
          # build CentOS 7 container image for bzip2 1.0.8 using EasyBuild;
          # see https://docs.easybuild.io/en/latest/Containers.html
          curl -OL https://raw.githubusercontent.com/easybuilders/easybuild-easyconfigs/develop/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8.eb
          export EASYBUILD_CONTAINERPATH=$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