Bump setuptools from 75.3.0 to 75.4.0 #735
Workflow file for this run
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name: "Unit tests" | |
on: [push, pull_request] | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
continue-on-error: ${{ matrix.irods.experimental }} # Experimental builds may fail | |
defaults: | |
run: | |
shell: bash -l -e -o pipefail {0} | |
env: | |
SINGULARITY_VERSION: "3.11.1" | |
strategy: | |
matrix: | |
python-version: ["3.10", "3.11", "3.12", "3.13"] | |
irods: [ | |
{version: "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}, | |
{version: "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}, | |
{version: "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}, | |
{version: "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}, | |
{version: "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: false}, | |
{version: "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: false} | |
] | |
services: | |
irods-server: | |
image: ${{ matrix.irods.server_image }} | |
ports: | |
- "1247:1247" | |
- "20000-20199:20000-20199" | |
volumes: | |
- /dev/shm:/dev/shm | |
options: >- | |
--health-cmd "nc -z -v localhost 1247" | |
--health-start-period 60s | |
--health-interval 10s | |
--health-timeout 20s | |
--health-retries 6 | |
steps: | |
- name: "Set environmental variables based on other environmental variables" | |
run: | | |
echo "SINGULARITY_CACHEDIR=$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: ${{ matrix.irods.client_image }} | |
run: | | |
# Use -s option for the wrappers to enable re-usable service instances | |
# Install is to HOME rather than workspace to avoid clashes with repo e.g. in bin/ | |
singularity exec docker://$DOCKER_IMAGE singularity-wrapper -s -p $HOME/.local install | |
echo "$HOME/.local/bin" >> $GITHUB_PATH | |
- name: "Configure iRODS clients" | |
env: | |
DOCKER_IMAGE: ${{ matrix.irods.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: ${{ matrix.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 | |
- name: "Run tests" | |
env: | |
IRODS_VERSION: ${{ matrix.irods.version }} | |
SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity-cache | |
run: | | |
pip install . | |
pytest --it | |
- name: "Log on failure" | |
if: ${{ failure() }} | |
run: journalctl --no-pager |