Merge pull request #4275 from branfosj/ft #361
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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 | |
sudo apt-get install rpm | |
sudo apt-get install dnf | |
# for modules tool | |
sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev | |
# 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 |