fix bugs #19
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| name: Model inference test Fiji stable | |
| on: | |
| push: | |
| branches: [ main ] | |
| paths-ignore: | |
| - .github/workflows/model_inference_test_fiji_latest.yaml | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| integration-tests: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - name: ubuntu | |
| os: ubuntu-latest | |
| url_file_name: fiji-stable-linux64-jdk.zip | |
| fiji_executable: ImageJ-linux64 | |
| - name: windows | |
| os: windows-latest | |
| url_file_name: fiji-stable-win64-jdk.zip | |
| fiji_executable: ImageJ-win64.exe | |
| - name: macos-arm64-14 | |
| os: macos-14 | |
| url_file_name: fiji-stable-macosx-jdk.zip | |
| fiji_executable: Contents/MacOS/ImageJ-macosx | |
| - name: macos-arm64-15 | |
| os: macos-15 | |
| url_file_name: fiji-stable-macosx-jdk.zip | |
| fiji_executable: Contents/MacOS/ImageJ-macosx | |
| - name: macos-x86_64 | |
| os: macos-13 | |
| url_file_name: fiji-stable-macosx-jdk.zip | |
| fiji_executable: Contents/MacOS/ImageJ-macosx | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Set up JDK 8 | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: '8' | |
| distribution: 'zulu' | |
| - name: Set up Fiji | |
| shell: bash | |
| run: | | |
| mkdir -p fiji | |
| curl -L -o fiji.zip https://downloads.imagej.net/fiji/stable/${{ matrix.url_file_name }} | |
| unzip fiji.zip -d fiji | |
| - name: Install SAMJ | |
| shell: bash | |
| run: | | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --update add-update-site "SAMJ" "https://sites.imagej.net/SAMJ/" | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --update update | |
| - name: rm SAMJ-IJ file | |
| shell: bash | |
| run: | | |
| rm -f /fiji/Fiji.app/plugins/SAMJ-IJ-*.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}}-${{steps.mvn_info.outputs.version}}.jar fiji/Fiji.app/plugins/ | |
| - name: Print information about the OS | |
| shell: bash | |
| run: | | |
| python -c "import platform; print(platform.platform())" | |
| - name: Install SAM model | |
| shell: bash | |
| run: | | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console .github/scripts/install_model.py | |
| - name: Get chip | |
| shell: bash | |
| run: | | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console .github/scripts/get_chip.py | |
| - name: Check if mps is available (only macos) | |
| if: runner.os == 'macOS' | |
| shell: bash | |
| run: | | |
| python -c "import os; print(os.listdir());" | |
| fiji/Fiji.app/appose_*/envs/sam2/bin/python -c "import torch; print(torch.backends.mps.is_built()); print(torch.backends.mps.is_available());" | |
| - name: Run Macro for annotation | |
| shell: bash | |
| run: | | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console .github/scripts/run_model.py |