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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:
PYTHON_VERSION: "3.12"
SINGULARITY_VERSION: "3.11.1"
strategy:
matrix:
include:
- 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
- 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
- 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
- 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: false
- 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
- irods: "4.3.3"
client_image: "ghcr.io/wtsi-npg/ub-22.04-irods-clients-4.3.3:latest"
server_image: "ghcr.io/wtsi-npg/ub-22.04-irods-4.3.3:latest"
experimental: true
services:
mysql:
image: "mysql:8.0"
ports:
- "3306:3306"
options: >-
--health-cmd "mysqladmin ping"
--health-interval 10s
--health-timeout 5s
--health-retries 10
env:
MYSQL_RANDOM_ROOT_PASSWORD: yes
MYSQL_TCP_PORT: 3306
MYSQL_USER: "test"
MYSQL_PASSWORD: "test"
MYSQL_DATABASE: "mlwarehouse"
irods-server:
image: ${{ matrix.server_image }}
ports:
- "1247:1247"
- "20000-20199:20000-20199"
volumes:
- /dev/shm:/dev/shm
options: >-
--health-cmd "nc -z -v localhost 1247"
--health-start-period 60s
--health-interval 10s
--health-timeout 20s
--health-retries 6
steps:
- name: "Set environmental variables based on other environmental variables"
run: |
echo "SINGULARITY_CACHEDIR=$HOME/.singularity-cache" >> $GITHUB_ENV
# '~' in SINGULARITY_CACHEDIR value (from say a env: section in this YAML) is not expanded by
# singularity so that paths used are misleading/unclear
- uses: actions/checkout@v4
- name: "Install Singularity"
run: |
pkg="singularity-ce_${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 "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 }}
PREFIX: ${{ github.workspace }}
run: |
mkdir -p "$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
- uses: actions/setup-python@v5
with:
python-version: ${{ env.PYTHON_VERSION }}
cache: "pip"
- name: "Setup Python dependencies"
run: |
pip install -r requirements.txt
pip install -r test-requirements.txt
- name: "Check code formatting [Black]"
run: |
black --check --diff ./src ./tests ./scripts
- name: "Run tests"
run: |
pip install .
pytest --it
- name: "Log on failure"
if: ${{ failure() }}
run: journalctl --no-pager