Expand test cases to cover readCoordinates() and read()
#3
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| name: "Build" | |
| on: | |
| push: | |
| pull_request: | |
| schedule: | |
| - cron: '0 0 * * *' | |
| jobs: | |
| build: | |
| strategy: | |
| matrix: | |
| build_bf: [false] | |
| build_zarr: [false] | |
| build_snapshot: [false] | |
| python-version: | |
| - '3.10' | |
| - '3.11' | |
| - '3.12' | |
| name: Build OMERO from source | |
| runs-on: ubuntu-22.04 | |
| env: | |
| ICE_HOME: /opt/ice-3.6.5 | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Ice and Ice python binding | |
| if: matrix.build_snapshot | |
| uses: jburel/action-ice@v3 | |
| - name: Set up Gradle 6.8.3 | |
| if: matrix.build_snapshot | |
| uses: gradle/gradle-build-action@v2 | |
| with: | |
| gradle-version: 6.8.3 | |
| arguments: build -x test | |
| build-root-directory: components/tools/OmeroJava # required by the action to have a *.gradle file" | |
| - name: Install and run flake8 | |
| run: | | |
| pip install flake8 'setuptools<69' | |
| flake8 . | |
| - name: install dependencies | |
| run: | | |
| sudo apt-get install -y git | |
| - name: Build Bio-Formats | |
| id: bf | |
| if: matrix.build_bf | |
| run: | | |
| git clone https://github.com/ome/bioformats /tmp/bioformats --depth 1 | |
| cd /tmp/bioformats | |
| mvn install -DskipTests -q | |
| echo "bf_version=$(mvn help:evaluate -Dexpression=project.version -q -DforceStdout)" >> $GITHUB_OUTPUT | |
| echo "ome_common_version=$(mvn help:evaluate -Dexpression=ome-common.version -q -DforceStdout)" >> $GITHUB_OUTPUT | |
| - name: Build ZarrReader | |
| id: zarr_reader | |
| if: matrix.build_zarr | |
| run: | | |
| git clone https://github.com/ome/ZarrReader /tmp/ZarrReader --depth 1 | |
| cd /tmp/ZarrReader | |
| mvn install -DskipTests -q | |
| echo "zarr_reader_version=$(mvn help:evaluate -Dexpression=project.version -q -DforceStdout)" >> $GITHUB_OUTPUT | |
| - name: Set ZarrReader version | |
| if: matrix.build_zarr | |
| run: | | |
| sed -i 's/versions.OMEZarrReader=.*/versions.OMEZarrReader=${{ steps.zarr_reader.outputs.zarr_reader_version }}/' etc/omero.properties | |
| - name: Set Bio-Formats version | |
| if: matrix.build_bf | |
| run: | | |
| DEPENDENCY="<dependency org=\"org.openmicroscopy\" name=\"ome-common\" rev=\"${{ steps.bf.outputs.ome_common_version }}\">\n<artifact name=\"ome-common\" type=\"jar\" ext=\"jar\"\/>\n<\/dependency>" | |
| sed -i 's/versions.bioformats=.*/versions.bioformats=${{ steps.bf.outputs.bf_version }}/' etc/omero.properties | |
| sed -i "s/<dependencies>/<dependencies>\n $DEPENDENCY/" components/tools/OmeroJava/ivy.xml | |
| - name: Build snapshot | |
| if: matrix.build_snapshot | |
| id: snapshot | |
| run: | | |
| # to use own repo | |
| # git clone -b your_branch https://github.com/your_repo/omero-gateway-java /tmp/omero-gateway-java | |
| git clone https://github.com/ome/omero-gateway-java /tmp/omero-gateway-java --depth 1 | |
| cd /tmp/omero-gateway-java | |
| gradle publishToMavenLocal -x test | |
| echo "gateway_version=$(gradle properties -q | grep "version:" | awk '{print $2}')" >> $GITHUB_OUTPUT | |
| - name: Set snapshot version | |
| if: matrix.build_snapshot | |
| run: | | |
| sed -i 's/versions.omero-gateway=.*/versions.omero-gateway=${{ steps.snapshot.outputs.gateway_version }}/' etc/omero.properties | |
| - name: Build | |
| run: ./build.py | |
| - name: Rebuild | |
| run: ./build.py clean && ./build.py |