container_tests.yml

# documentation: https://help.github.com/en/articles/workflow-syntax-for-github-actions
name: Tests for Singularity 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]
      fail-fast: false
    steps:
    - uses: actions/checkout@v3

    - name: set up Python
      uses: actions/setup-python@v4
      with:
        python-version: ${{matrix.python}}
        architecture: x64

    - name: install OS & Python packages
      run: |
        # for modules tool
        APT_PKGS="lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev"
        # for building Singularity images
        APT_PKGS+=" rpm dnf"

        # 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

    - 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-8.7.6 $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

    # see https://github.com/apptainer/singularity/issues/5390#issuecomment-899111181
    - name: install Singularity
      run: |
        sudo apt-get update
        # install alien, which can be used to convert RPMs to Debian packages
        sudo apt-get install alien
        alien --version
        # determine latest version of Singularity available in EPEL, and download RPM
        singularity_rpm=$(curl -sL https://dl.fedoraproject.org/pub/archive/epel/8.5/Everything/x86_64/Packages/s/ | grep singularity | sed 's/.*singularity/singularity/g' | sed 's/rpm.*/rpm/g')
        curl -OL https://dl.fedoraproject.org/pub/archive/epel/8.5/Everything/x86_64/Packages/s/${singularity_rpm}
        # convert Singularity RPM to Debian package, and install it
        sudo alien -d ${singularity_rpm}
        sudo apt-get install ./singularity*.deb
        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'
          eb bzip2-1.0.8.eb --containerize --experimental --container-build-image
          singularity 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)
          singularity exec bzip2-1.0.8.sif bzip2 --help