Feature/pass recipe to docker #743
Workflow file for this run
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| name: Analyze | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| jobs: | |
| Analyze: | |
| if: ${{ !contains(github.event.head_commit.message, 'Bump version') }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python-version: [3.9] | |
| os: [ubuntu-latest] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| cache: "pip" | |
| cache-dependency-path: setup.py | |
| - name: Install Dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install .[all] | |
| - name: Pack test recipe | |
| run: | | |
| pack -r cellpack/tests/recipes/v2/test_spheres.json -c cellpack/tests/packing-configs/test_config.json | |
| - name: Modify JSON with PR sub_directory path | |
| run: | | |
| jq --arg branch_name "${{ github.ref_name }}" '.create_report.output_image_location |= "https://cellpack-results.s3.us-west-2.amazonaws.com/\($branch_name)/spheresSST/figures"' cellpack/tests/analysis-configs/PR_analysis_config.json > cellpack/tests/analysis-configs/PR_analysis_config_temp.json | |
| mv cellpack/tests/analysis-configs/PR_analysis_config_temp.json cellpack/tests/analysis-configs/PR_analysis_config.json | |
| - name: Run analysis code | |
| run: analyze -r cellpack/tests/recipes/v2/test_spheres.json -a cellpack/tests/analysis-configs/PR_analysis_config.json -p cellpack/tests/outputs/test_spheres/spheresSST | |
| - name: Upload results | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: results | |
| path: cellpack/tests/outputs/test_spheres/ | |
| Comment: | |
| runs-on: ubuntu-latest | |
| needs: [Analyze] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Configure AWS credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| aws-region: us-west-2 | |
| - uses: actions/download-artifact@v3 | |
| - name: Copy files to results bucket | |
| run: aws s3 cp ./results s3://cellpack-results/${{ github.ref_name }}/ --recursive --acl public-read | |
| - uses: iterative/setup-cml@v1 | |
| - name: Update comment | |
| env: | |
| REPO_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| cml comment update --watermark-title="{workflow} report" ./results/analysis_report.md --target=pr | |
| cat ./results/analysis_report.md |