correct yaml error #73
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| name: Tiling test | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| env: | |
| 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: 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 | |
| - name: windows | |
| os: windows-latest | |
| url_file_name: fiji-win64.zip | |
| fiji_executable: ImageJ-win64.exe | |
| runs-on: ${{ matrix.os }} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - name: Install Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: '3.13' | |
| - name: Set up JDK 8 | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: '8' | |
| distribution: 'zulu' | |
| - name: Set up Fiji | |
| shell: bash | |
| run: | | |
| mkdir -p fiji | |
| curl -L -o fiji.zip https://downloads.imagej.net/fiji/latest/${{ matrix.url_file_name }} | |
| unzip fiji.zip -d fiji | |
| - name: Build Plugin | |
| 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.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}}-${{steps.mvn_info.outputs.version}}.jar fiji/Fiji.app/plugins/ | |
| - name: Checkout JDLL repository | |
| shell: bash | |
| run: | | |
| git clone https://github.com/bioimage-io/JDLL.git JDLL | |
| - name: Build JDLL | |
| shell: bash | |
| run: | | |
| cd JDLL | |
| mvn clean install | |
| MVN_VERSION=$(mvn -q \ | |
| -Dexec.executable=echo \ | |
| -Dexec.args='${project.version}' \ | |
| --non-recursive \ | |
| exec:exec) | |
| MVN_NAME=$(mvn -q \ | |
| -Dexec.executable=echo \ | |
| -Dexec.args='${project.name}' \ | |
| --non-recursive \ | |
| exec:exec) | |
| cp target/${MVN_NAME}-${MVN_VERSION}.jar ../fiji/Fiji.app/jars/ | |
| - name: Download dependencies | |
| shell: bash | |
| run: | | |
| curl -L --output-dir fiji/Fiji.app/jars/ -O "https://repo1.maven.org/maven2/net/java/dev/jna/jna-platform/5.13.0/jna-platform-5.13.0.jar" | |
| - name: Set up engine using Jython script and Fiji headless | |
| shell: bash | |
| run: | | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console scripts/download_engines.py -engines_path fiji/Fiji.app/engines | |
| - name: Unzip model to models folder | |
| shell: bash | |
| run: | | |
| unzip test_samples/brightfield_nuclei_.zip -d fiji/Fiji.app/models | |
| - name: check model is there | |
| shell: bash | |
| run: | | |
| ls fiji/Fiji.app/models/brightfield_nuclei | |
| - name: Create a New Directory | |
| shell: bash | |
| run: mkdir -p outputs | |
| - name: Create a New Directory 2 | |
| shell: bash | |
| run: mkdir -p outputs_npy | |
| - name: Run macros | |
| shell: bash | |
| run: | | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console -macro test_samples/test.ijm | |
| - name: Convert to npy | |
| shell: bash | |
| run: | | |
| ls .github | |
| fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console .github/to_numpy.py | |
| - name: Run final python | |
| shell: bash | |
| run: | | |
| python -m pip install numpy | |
| python .github/check_numpy_vals.py |