Feature/results in memory #490
Workflow file for this run
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name: Analyze | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
jobs: | |
Analyze: | |
runs-on: ${{ matrix.os }} | |
strategy: | |
matrix: | |
python-version: [3.9] | |
os: [ubuntu-latest] | |
steps: | |
- uses: actions/checkout@v3 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v4 | |
with: | |
python-version: ${{ matrix.python-version }} | |
- name: Install Dependencies | |
run: | | |
python -m pip install --upgrade pip | |
pip install .[all] | |
- name: Pack test recipe | |
run: | | |
pack -r cellpack/tests/recipes/v2/test_spheres.json -c cellpack/tests/packing-configs/test_config.json | |
- name: Modify JSON with PR sub_directory path | |
run: | | |
jq --arg branch_name "${{ 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@v3 | |
- name: Configure AWS credentials | |
uses: aws-actions/configure-aws-credentials@v1-node16 | |
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 |