Create the CIs for Icy and deepImageJ using JDLL #1
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| name: check compatibility deepimagej | ||
| concurrency: deepimagej | ||
| on: | ||
| push: | ||
| branches: | ||
| - main | ||
| paths: | ||
| - .github/workflows/check_compatibility_deepimagej.yaml | ||
| - scripts/check_compatibility_deepimagej.py | ||
| workflow_dispatch: | ||
| schedule: | ||
| - cron: 0 1 * * * # update compatibility once a day | ||
| jobs: | ||
| run: | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| include: | ||
| - name: ubuntu | ||
| os: ubuntu-latest | ||
| url_file_name: fiji-linux64.zip | ||
| fiji_executable: ImageJ-linux64 | ||
| runs-on: ${{ matrix.os }} | ||
| environment: 'production' | ||
| steps: | ||
| - uses: actions/checkout@v5 | ||
| - uses: actions/setup-python@v5 | ||
| with: | ||
| python-version: "3.10" | ||
| cache: "pip" # caching pip dependencies | ||
| - name: Installing Numpy for output comparison | ||
| run: pip install numpy | ||
| - run: wget https://${{vars.S3_HOST}}/${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}}/all_versions_draft.json | ||
| - run: wget https://${{vars.S3_HOST}}/${{vars.S3_BUCKET}}/${{vars.S3_FOLDER}}/all_versions.json | ||
| - name: Set up Fiji | ||
| shell: bash | ||
| run: | | ||
| mkdir -p fiji | ||
| curl -L -o fiji.zip https://downloads.imagej.net/fiji/latest/${{ matrix.url_file_name }} | ||
| unzip fiji.zip -d fiji | ||
| - name: Install deepimageJ | ||
| run: | | ||
| fiji/Fiji.app/${{ matrix.fiji_executable }} --update add-update-site "deepimagej" "https://sites.imagej.net/DeepImageJ/" | ||
| - name: Install engines | ||
| shell: bash | ||
| run: fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console scripts/deepimagej_jython_scripts/download_engines.py -engines_path fiji/Fiji.app/engines | ||
| - name: Run deepImageJ tests for drafts | ||
| run: python scripts/check_compatibility_deepimagej.py \ | ||
| all_versions_draft.json \ | ||
| generated-reports \ | ||
| "fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console" \ | ||
| fiji | ||
| - rname: Run deepImageJ tests for pusblished versions | ||
| run: python scripts/check_compatibility_deepimagej.py \ | ||
| all_versions_draft.json \ | ||
| generated-reports \ | ||
| "fiji/Fiji.app/${{ matrix.fiji_executable }} --headless --console" \ | ||
| fiji | ||
| - name: Upload reports | ||
| run: python scripts/upload_reports.py generated-reports | ||
| env: | ||
| S3_HOST: ${{vars.S3_HOST}} | ||
| S3_BUCKET: ${{vars.S3_BUCKET}} | ||
| S3_FOLDER: ${{vars.S3_FOLDER}} | ||
| S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}} | ||
| S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}} | ||
| RUN_URL: ${{github.server_url}}/${{github.repository}}/actions/runs/${{github.run_id}} | ||
| JSON_OUTS_FNAME: "dij_ouputs_file.json" | ||
| MACRO_NAME: "dij_macro_ci.ijm" | ||
