adapt to model family #144
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| name: Integration Tests | |
| on: | |
| push: | |
| branches: [ master ] | |
| paths-ignore: | |
| - .github/workflows/macos_test.yaml | |
| - dl-modelrunner-0.5.11-SNAPSHOT.jar | |
| pull_request: | |
| branches: [ master ] | |
| env: | |
| MODELS: "ambitious-sloth, placid-llama, chatty-frog, hiding-tiger, laid-back-lobster" | |
| JSON_FPATH: outputs.json | |
| MACRO_FPATH: macro.ijm | |
| 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: Install deepimageJ | |
| shell: bash | |
| run: | | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --update add-update-site "DeepImageJ" "https://sites.imagej.net/DeepImageJ/" | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --update update | |
| - name: rm deepimagej file | |
| shell: bash | |
| run: | | |
| rm -f /fiji/Fiji.app/plugins/deepimagej-*.jar | |
| - name: Build Plugin | |
| shell: bash | |
| 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.artifactId}' \ | |
| --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}}-${{steps.mvn_info.outputs.version}}.jar fiji/Fiji.app/plugins/ | |
| - name: Set up engine using Jython script and Fiji headless | |
| shell: bash | |
| run: | | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console scripts/download_engines.py -engines_path fiji/Fiji.app/engines | |
| - name: Check files in the engines | |
| shell: bash | |
| run: | | |
| DIR_OF_INTEREST="fiji/Fiji.app/engines" | |
| for dir in "$DIR_OF_INTEREST"/*/; do | |
| echo "Directory: $dir" | |
| find "$dir" -type f -exec echo " File: {}" \; | |
| done | |
| - name: Set up the wanted models to test and create macro | |
| shell: bash | |
| run: | | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console .github/create_macro.py \ | |
| -model_nicknames "${{ env.MODELS }}" \ | |
| -models_dir fiji/Fiji.app/models \ | |
| -macro_path ${{ env.MACRO_FPATH }} \ | |
| -json_fpath ${{ env.JSON_FPATH }} | |
| - name: Run macros | |
| shell: bash | |
| run: | | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console -macro ${{ env.MACRO_FPATH }} | |
| - name: Check that the expected result has been produced | |
| shell: bash | |
| run: | | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console .github/check_outputs.py -json_fpath ${{ env.JSON_FPATH }} |