OMERO #71
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name: OMERO | |
on: | |
push: | |
pull_request: | |
schedule: | |
- cron: '0 0 * * 0' | |
jobs: | |
test: | |
name: Run integration tests against OMERO | |
runs-on: ubuntu-latest | |
env: | |
STAGE: cli | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Launch OMERO test database | |
run: sudo chmod +x .omero/* && .omero/compose up -d | |
env: | |
ROOTPASS: omero | |
POSTGRES_IMAGE: postgres | |
POSTGRES_VERSION: 10 | |
POSTGRES_PASSWORD: postgres | |
OMERO_SERVER_IMAGE: openmicroscopy/omero-server | |
OMERO_SERVER_VERSION: 5 | |
OMERO_SERVER_TCP: "4063:" | |
OMERO_SERVER_SSL: "4064:" | |
OMERO_WEB_IMAGE: openmicroscopy/omero-web-standalone | |
OMERO_WEB_VERSION: 5 | |
OMERO_WEB_PORT: "4080:" | |
BUILD_IMAGE: adoptopenjdk:11-jdk-hotspot-bionic | |
- name: Set up Python | |
uses: actions/setup-python@v4 | |
with: | |
python-version: "3.8" | |
- name: Build omero_arc | |
run: | | |
$CONDA/bin/conda install -c anaconda python=3.8 | |
$CONDA/bin/conda install -c conda-forge zeroc-ice=3.6.5 | |
$CONDA/bin/python -m pip install "omero-cli-transfer @ git+https://github.com/ome/omero-cli-transfer@main" | |
$CONDA/bin/python -m pip install .[dev] | |
- name: Install omero_arc dependencies | |
run: | | |
wget --quiet https://github.com/nfdi4plants/arcCommander/releases/download/v0.5.0-linux.x64/arc | |
mkdir $HOME/bin | |
mv arc $HOME/bin/ | |
chmod a+x $HOME/bin/arc | |
export PATH="$HOME/bin:$PATH" | |
arc --version | |
- name: Run tests | |
run: | | |
$CONDA/bin/conda install pytest | |
export PATH="$CONDA/bin:$PATH" | |
export PATH="$HOME/bin:$PATH" | |
$CONDA/bin/pytest -v | |
env: | |
OMERODIR: . | |
ICE_CONFIG: test/ice.config | |
- name: Stop OMERO test database | |
run: "sudo .omero/compose down" |