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Merge branch 'develop' into 5.0.x #227

Merge branch 'develop' into 5.0.x

Merge branch 'develop' into 5.0.x #227

# 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/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'
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