big #66
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Macos Tests | |
| 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 | |
| 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 | |
| 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}}-${{steps.mvn_info.outputs.version}}.jar fiji/Fiji.app/plugins/ | |
| - name: Copy Plugin to Fiji | |
| shell: bash | |
| run: cp dl-modelrunner-0.5.11-SNAPSHOT.jar fiji/Fiji.app/plugins/ | |
| - name: Download dependencies | |
| shell: bash | |
| run: | | |
| curl -L --output-dir fiji/Fiji.app/jars/ -O "https://repo1.maven.org/maven2/net/java/dev/jna/jna-platform/5.13.0/jna-platform-5.13.0.jar" | |
| curl -L --output-dir fiji/Fiji.app/jars/ -O "https://maven.scijava.org/content/groups/public/net/imglib2/imglib2/7.1.4/imglib2-7.1.4.jar" | |
| - name: Set up engine using Jython script and Fiji headless | |
| shell: bash | |
| run: | | |
| fiji/Fiji.app/${{ 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 | |
| run: mkdir -p outputs | |
| - name: Create a New Directory 2 | |
| 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 | |
| - name: Upload artifact | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: my-artifact-${{ matrix.name }} # Name of the artifact | |
| path: outputs |