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run-tests.yml
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name: "Unit tests"
on: [push, pull_request]
jobs:
build:
runs-on: ubuntu-latest
continue-on-error: ${{ matrix.experimental }} # Experimental builds may fail
defaults:
run:
shell: bash -l -e -o pipefail {0}
env:
SINGULARITY_VERSION: "3.11.1"
PERL_CACHE: ~/perl5 # Perlbrew and CPAN modules installed here, cached
NPG_LIB: ~/perl5npg # NPG modules installed here, not cached
WTSI_NPG_BUILD_BRANCH: ${{ github.base_ref || github.ref }}
strategy:
matrix:
include:
- perl: "5.22.4"
irods: "4.2.7"
client_image: "ghcr.io/wtsi-npg/ub-16.04-irods-clients-4.2.7:latest"
server_image: "ghcr.io/wtsi-npg/ub-16.04-irods-4.2.7:latest"
experimental: false
- perl: "5.22.4"
irods: "4.2.11"
client_image: "ghcr.io/wtsi-npg/ub-18.04-irods-clients-4.2.11:latest"
server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.2.11:latest"
experimental: false
- perl: "5.34.1"
irods: "4.2.11"
client_image: "ghcr.io/wtsi-npg/ub-18.04-irods-clients-4.2.11:latest"
server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.2.11:latest"
experimental: false
- perl: "5.22.4"
irods: "4.2.12"
client_image: "ghcr.io/wtsi-npg/ub-18.04-irods-clients-4.2.12:latest"
server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.2.12:latest"
experimental: false
- perl: "5.22.4"
irods: "4.3.1"
client_image: "ghcr.io/wtsi-npg/ub-22.04-irods-clients-4.3.1:latest"
server_image: "ghcr.io/wtsi-npg/ub-22.04-irods-4.3.1:latest"
experimental: true
- perl: "5.22.4"
irods: "4.3.2"
client_image: "ghcr.io/wtsi-npg/ub-22.04-irods-clients-4.3.2:latest"
server_image: "ghcr.io/wtsi-npg/ub-22.04-irods-4.3.2:latest"
experimental: true
services:
irods-server:
image: ${{ matrix.server_image }}
ports:
- "1247:1247"
- "20000-20199:20000-20199"
options: >-
--health-cmd "nc -z -v localhost 1247"
--health-start-period 30s
--health-interval 10s
--health-timeout 20s
--health-retries 6
steps:
- name: "Set environmental variables based on other environmental variables"
run: |
echo "SINGULARITY_CACHEDIR=$HOME/.singularity-cache" >> $GITHUB_ENV
# '~' in SINGULARITY_CACHEDIR value (from say a env: section in this YAML) is not expanded by
# singularity so that paths used are misleading/unclear
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.10'
architecture: 'x64'
- name: "Install OS dependencies"
run: |
sudo apt-get update
# https://github.com/actions/runner-images/issues/2139
sudo apt-get remove -y nginx libgd3
sudo apt-get install -qq uuid-dev # For Perl UUID module
sudo apt-get install -qq libgd-dev libgd-text-perl # For npg_tracking
sudo apt-get install -qq liblzma-dev # For npg_qc
sudo apt-get install -qq pigz # for BioNano run publication in npg_irods
sudo apt-get install -qq libdevel-patchperl-perl # For perlbrew
- name: "Install Singularity"
run: |
pkg="singularity-ce_${SINGULARITY_VERSION}-$(lsb_release -sc)_amd64.deb"
curl -sSL -O "https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/$pkg"
curl -sSL -O "https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/sha256sums"
grep "$os_release" sha256sums | sha256sum
sudo apt-get install -q -y "./$pkg"
# Avoid the runner's loop devices being exhausted
# sudo singularity config global --set "shared loop devices" yes
sudo singularity config global --set "max loop devices" 128
# Enable DBus for this user, so that rootless cgroups works and we can create
# Singularity service instances. See https://github.com/containers/podman/issues/5443
systemctl --user enable --now dbus.socket
echo DBUS_SESSION_BUS_ADDRESS="unix:path=/run/user/$(id -u)/bus" >> $GITHUB_ENV
- name: "Cache Singularity images"
uses: actions/cache@v4
with:
path: ${{ env.SINGULARITY_CACHEDIR }}
key: ${{ runner.os }}-singularity
- name: "Install iRODS client wrappers"
env:
DOCKER_IMAGE: ${{ matrix.client_image }}
run: |
# Use -s option for the wrappers to enable re-usable service instances
# Install is to HOME rather than workspace to avoid clashes with repo e.g. in bin/
singularity exec docker://$DOCKER_IMAGE singularity-wrapper -s -p $HOME/.local install
echo $HOME/.local/bin >> $GITHUB_PATH
- name: "Configure iRODS clients"
env:
DOCKER_IMAGE: ${{ matrix.client_image }}
run: |
mkdir -p "$HOME/.irods"
cat <<'EOF' > "$HOME/.irods/irods_environment.json"
{
"irods_host": "localhost",
"irods_port": 1247,
"irods_user_name": "irods",
"irods_zone_name": "testZone",
"irods_home": "/testZone/home/irods",
"irods_default_resource": "replResc",
"irods_default_hash_scheme": "MD5"
}
EOF
echo "irods" | script -q -c "iinit" /dev/null
ienv
ils
ilsresc
baton-do --version
- name: "Cache Perl"
id: cache-perl
uses: actions/cache@v4
with:
path: ${{ env.PERL_CACHE }}
key: ${{ runner.os }}-${{ matrix.perl }}-perl
- name: "Install Perlbrew"
if: steps.cache-perl.outputs.cache-hit != 'true'
run: |
curl -sSL https://install.perlbrew.pl -o perlbrew.sh
sha256sum -c .github/workflows/perlbrew.sha256
export PERLBREW_ROOT=${{ env.PERL_CACHE }}
sh perlbrew.sh
source ${{ env.PERL_CACHE }}/etc/bashrc
perlbrew available
perlbrew install --notest perl-${{ matrix.perl }}
perlbrew use perl-${{ matrix.perl }}
perlbrew install-cpanm
- name: "Initialize Perlbrew"
run: |
echo "source ${{ env.PERL_CACHE }}/etc/bashrc" >> "$HOME/.bash_profile"
- name: "Install Perl dependencies"
run: |
cpanm --local-lib=${{ env.PERL_CACHE }} local::lib
eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
# Required for npg_qc
cpanm --quiet --notest https://github.com/chapmanb/vcftools-cpan/archive/v0.953.tar.gz
# Work around the circular dependency between npg_irods and
# npg_ml_warehouse. The latter dependency requires the former (which
# is this repository itself).
export PERL5LIB="$GITHUB_WORKSPACE/lib:$PERL5LIB"
./scripts/install_wsi_dependencies.sh "$NPG_LIB" \
perl-dnap-utilities \
perl-irods-wrap \
ml_warehouse \
npg_ml_warehouse \
npg_tracking \
npg_seq_common \
npg_qc
cpanm --installdeps --notest .
- name: "Install Python dependencies"
run: |
python3 -m pip install git+https://github.com/wtsi-npg/npg_id_generation@$WTSI_NPG_BUILD_BRANCH ||
python3 -m pip install git+https://github.com/wtsi-npg/npg_id_generation@devel
- name: "Log install failure"
if: ${{ failure() }}
run: |
find ~/.cpanm/work -cmin -1 -name '*.log' -exec tail -n20 {} \;
- name: "Run tests"
run: |
eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib)
eval $(perl -I ${{ env.PERL_CACHE }}/lib/perl5/ -Mlocal::lib="$NPG_LIB")
export PERL5LIB="$PWD:$PERL5LIB"
perl Build.PL
export WTSI_NPG_iRODS_Test_IRODS_ENVIRONMENT_FILE="$HOME/.irods/irods_environment.json"
./Build test --verbose