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Feature/results in memory #490

Feature/results in memory

Feature/results in memory #490

Workflow file for this run

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