Update python-app.yml #16
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: OMERO | |
| on: | |
| push: | |
| pull_request: | |
| jobs: | |
| test: | |
| name: Run integration tests against OMERO | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout omero-test-infra | |
| uses: actions/checkout@main | |
| with: | |
| repository: ome/omero-test-infra | |
| path: .omero | |
| - name: Launch OMERO test database | |
| run: .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: checkout arc_omero | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: "3.9" | |
| cache: 'pip' # caching pip dependencies | |
| - name: Build arc_omero | |
| run: | | |
| wget https://downloads.openmicroscopy.org/bio-formats/7.2.0/artifacts/bftools.zip | |
| unzip bftools.zip | |
| pip install --upgrade pip | |
| pip install "omero-cli-transfer @ git+https://github.com/MicheleBortol/omero-cli-transfer.git@omero_arc_importer" | |
| pip install ".[dev]" | |
| - name: Import datasets | |
| run: | | |
| export PATH=$(pwd)/bftools:$PATH | |
| omero login --user root --password omero localhost | |
| omero transfer prepare --plugin arc_omero test/data/arcs/Resolve/assays/ResolveMolecularCartography/dataset | |
| omero transfer unpack --folder test/data/arcs/Resolve/assays/ResolveMolecularCartography/dataset | |
| - name: Run tests | |
| run: | | |
| pip install pytest | |
| - name: Checkout omero-test-infra | |
| uses: actions/checkout@main | |
| with: | |
| repository: ome/omero-test-infra | |
| path: .omero | |
| - name: Stop OMERO test database | |
| run: .omero/compose down |