add code to assert all outputs are produced #40
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| name: Integration Tests | ||
| on: | ||
| push: | ||
| branches: [ master ] | ||
| pull_request: | ||
| branches: [ master ] | ||
| env: | ||
| MODELS: "ambitious-sloth, placid-llama, chatty-frog, hiding-tiger, laid-back-lobster" | ||
| JSON_FPATH: outputs.json | ||
| jobs: | ||
| integration-tests: | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| include: | ||
| - name: ubuntu | ||
| os: ubuntu-latest | ||
| url_file_name: fiji-linux64.zip | ||
| fiji_executable: ImageJ-linux64 | ||
| - name: windows | ||
| os: windows-latest | ||
| url_file_name: fiji-win64.zip | ||
| fiji_executable: ImageJ-win64.exe | ||
| - name: macos-arm64 | ||
| os: macos-14 | ||
| url_file_name: fiji-macosx.zip | ||
| fiji_executable: Contents/MacOS/ImageJ-macosx | ||
| - name: macos-x86_64 | ||
| os: macos-13 | ||
| url_file_name: fiji-macosx.zip | ||
| fiji_executable: Contents/MacOS/ImageJ-macosx | ||
| runs-on: ${{ matrix.os }} | ||
| steps: | ||
| - name: Checkout code | ||
| uses: actions/checkout@v4 | ||
| - name: Set up JDK 8 | ||
| uses: actions/setup-java@v4 | ||
| with: | ||
| java-version: '8' | ||
| distribution: 'zulu' | ||
| - name: Set up Fiji | ||
| shell: bash | ||
| run: | | ||
| mkdir -p fiji | ||
| curl -L -o fiji.zip https://downloads.imagej.net/fiji/latest/${{ matrix.url_file_name }} | ||
| unzip fiji.zip -d fiji | ||
| - name: Build Plugin | ||
| run: mvn clean package | ||
| - name: Get plugin name and version | ||
| shell: bash | ||
| run: | | ||
| MVN_VERSION=$(mvn -q \ | ||
| -Dexec.executable=echo \ | ||
| -Dexec.args='${project.version}' \ | ||
| --non-recursive \ | ||
| exec:exec) | ||
| MVN_NAME=$(mvn -q \ | ||
| -Dexec.executable=echo \ | ||
| -Dexec.args='${project.name}' \ | ||
| --non-recursive \ | ||
| exec:exec) | ||
| echo "version=${MVN_VERSION}" >> $GITHUB_OUTPUT | ||
| echo "name=${MVN_NAME}" >> $GITHUB_OUTPUT | ||
| id: mvn_info | ||
| - name: Copy Plugin to Fiji | ||
| shell: bash | ||
| run: cp target/${{steps.mvn_info.outputs.name}}-${{steps.mvn_info.outputs.version}}.jar fiji/Fiji.app/plugins/ | ||
| - name: Download dependencies | ||
| shell: bash | ||
| run: | | ||
| curl -L --output-dir fiji/Fiji.app/jars/ -O "https://maven.scijava.org/content/groups/public/io/bioimage/dl-modelrunner/0.5.10-SNAPSHOT/dl-modelrunner-0.5.10-20241112.235152-66.jar" | ||
| curl -L --output-dir fiji/Fiji.app/jars/ -O "https://repo1.maven.org/maven2/net/java/dev/jna/jna-platform/5.13.0/jna-platform-5.13.0.jar" | ||
| - name: Set up engine using Jython script and Fiji headless | ||
| shell: bash | ||
| run: | | ||
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console scripts/download_engines.py -engines_path fiji/Fiji.app/engines | ||
| - name: Set up the wanted models to test and create macro | ||
| shell: bash | ||
| run: | | ||
|
Check failure on line 91 in .github/workflows/integration_test.yaml
|
||
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console .github/create_macro.py -model_nicknames "${{ env.MODELS }}" -models_dir fiji/Fiji.app/models -macro_path macro.ijm -json_fpath ${{ JSON_FPATH }} | ||
| - name: Run macros | ||
| shell: bash | ||
| run: | | ||
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console macro.ijm | ||
| - name: Check that the expected result has been produced | ||
| shell: bash | ||
| run: | | ||
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console .github/check_outputs.py -json_fpath ${{ JSON_FPATH }} | ||
