BioImage.IO Model Testing #20
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| name: BioImage.IO Model Testing | |
| on: | |
| schedule: | |
| # Run daily at 2:00 AM UTC | |
| - cron: '0 2 * * *' | |
| pull_request: | |
| # Run on pull requests to test changes | |
| types: [opened, synchronize, reopened] | |
| workflow_dispatch: | |
| inputs: | |
| skip_exists: | |
| description: 'Skip models that already have test results' | |
| required: false | |
| default: 'true' | |
| type: choice | |
| options: | |
| - 'true' | |
| - 'false' | |
| model_ids: | |
| description: 'Specific model IDs to test (comma-separated, leave empty for all)' | |
| required: false | |
| type: string | |
| dry_run: | |
| description: "Run in dry-run mode (don't update artifacts)" | |
| required: false | |
| default: false | |
| type: boolean | |
| jobs: | |
| test-bioimageio-models: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: ${{ github.event_name == 'pull_request' && 60 || 480 }} # 1 hour for PRs, 8 hours for scheduled runs | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: '3.11' | |
| - name: Cache pip dependencies | |
| uses: actions/cache@v3 | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt', 'requirements-dev.txt') }} | |
| restore-keys: | | |
| ${{ runner.os }}-pip- | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install hypha-rpc numpy httpx pydantic | |
| - name: Create test results directory | |
| run: mkdir -p bioimageio_test_reports | |
| - name: Run BioImage.IO model tests | |
| env: | |
| HYPHA_TOKEN: ${{ secrets.HYPHA_TOKEN }} | |
| run: | | |
| cd scripts | |
| # Build command arguments | |
| ARGS="" | |
| # Handle skip_exists argument | |
| if [ "${{ github.event.inputs.skip_exists }}" = "false" ]; then | |
| ARGS="$ARGS --no-skip-exists" | |
| else | |
| ARGS="$ARGS --skip-exists" | |
| fi | |
| # Handle model_ids argument | |
| if [ -n "${{ github.event.inputs.model_ids }}" ]; then | |
| # Convert comma-separated list to space-separated for the script | |
| MODEL_IDS=$(echo "${{ github.event.inputs.model_ids }}" | tr ',' ' ') | |
| ARGS="$ARGS --model-ids $MODEL_IDS" | |
| fi | |
| # Handle dry_run argument | |
| if [ "${{ github.event.inputs.dry_run }}" = "true" ]; then | |
| ARGS="$ARGS --dry-run" | |
| fi | |
| # For pull requests, always run in dry-run mode to avoid updating artifacts | |
| if [ "${{ github.event_name }}" = "pull_request" ]; then | |
| ARGS="$ARGS --dry-run --skip-exists" | |
| echo "Running in dry-run mode for pull request" | |
| # For PR testing, limit to a small subset of models for faster feedback | |
| # This can be overridden by manually specifying model_ids in workflow_dispatch | |
| if [ -z "${{ github.event.inputs.model_ids }}" ]; then | |
| echo "Using limited model set for pull request testing" | |
| # You can modify this list to include specific models for PR testing | |
| ARGS="$ARGS --model-ids affable-shark chatty-frog zealous-oxen" | |
| fi | |
| fi | |
| # For scheduled runs, always use skip-exists to avoid re-testing | |
| if [ "${{ github.event_name }}" = "schedule" ]; then | |
| ARGS="--skip-exists" | |
| fi | |
| echo "Running: python bioimageio_test_reports.py $ARGS" | |
| python bioimageio_test_reports.py $ARGS | |
| - name: Upload test results as artifact | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: bioimageio-test-results-${{ github.run_number }} | |
| path: bioimageio_test_reports/ | |
| retention-days: 30 | |
| - name: Generate summary report | |
| if: always() | |
| run: | | |
| echo "# BioImage.IO Test Results Summary" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| # Add dry-run notice for pull requests | |
| if [ "${{ github.event_name }}" = "pull_request" ]; then | |
| echo "🧪 **Pull Request Test Mode**" >> $GITHUB_STEP_SUMMARY | |
| echo "- Running in DRY-RUN mode (no artifacts updated)" >> $GITHUB_STEP_SUMMARY | |
| echo "- Testing limited model subset for faster feedback" >> $GITHUB_STEP_SUMMARY | |
| echo "- Using existing test results where available" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| fi | |
| # Use the analysis function to get statistics | |
| cd scripts | |
| ANALYSIS_OUTPUT=$(python3 bioimageio_test_reports.py --analyze-results) | |
| echo "$ANALYSIS_OUTPUT" | |
| # Parse the analysis output | |
| eval "$ANALYSIS_OUTPUT" | |
| if [ "$TOTAL_MODELS" -gt 0 ]; then | |
| echo "**Total models tested:** $TOTAL_MODELS" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| # Main results table | |
| echo "| Test Type | Passed | Total | Rate |" >> $GITHUB_STEP_SUMMARY | |
| echo "|-----------|--------|-------|------|" >> $GITHUB_STEP_SUMMARY | |
| echo "| RDF Validation | $PASSED_RDF | $TOTAL_MODELS | ${RDF_RATE}% |" >> $GITHUB_STEP_SUMMARY | |
| echo "| Model Test Run | $PASSED_MODEL | $TOTAL_MODELS | ${MODEL_RATE}% |" >> $GITHUB_STEP_SUMMARY | |
| echo "| Reproduce Outputs | $PASSED_REPRODUCE | $TOTAL_MODELS | ${REPRODUCE_RATE}% |" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| # Score and performance metrics | |
| echo "## Performance Metrics" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "| Metric | Value |" >> $GITHUB_STEP_SUMMARY | |
| echo "|--------|-------|" >> $GITHUB_STEP_SUMMARY | |
| echo "| **Total Score** | $TOTAL_SCORE |" >> $GITHUB_STEP_SUMMARY | |
| echo "| **Average Score per Model** | ${AVERAGE_SCORE} |" >> $GITHUB_STEP_SUMMARY | |
| # Add execution time info if available | |
| if [ -n "$TOTAL_EXECUTION_TIME" ] && [ "$TOTAL_EXECUTION_TIME" != "0.00" ]; then | |
| echo "| **Total Execution Time** | ${TOTAL_EXECUTION_TIME}s |" >> $GITHUB_STEP_SUMMARY | |
| echo "| **Average Execution Time** | ${AVERAGE_EXECUTION_TIME}s |" >> $GITHUB_STEP_SUMMARY | |
| fi | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "**Test completed at:** $(date -u '+%Y-%m-%d %H:%M:%S UTC')" >> $GITHUB_STEP_SUMMARY | |
| # Add score explanation | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "### Scoring System" >> $GITHUB_STEP_SUMMARY | |
| echo "- Each model gets 1 point for each test that passes (max 3 points per model)" >> $GITHUB_STEP_SUMMARY | |
| echo "- Collection score: 3 points per model that passes all tests" >> $GITHUB_STEP_SUMMARY | |
| echo "- Perfect score would be: $(($TOTAL_MODELS * 3)) points" >> $GITHUB_STEP_SUMMARY | |
| else | |
| echo "No test results found." >> $GITHUB_STEP_SUMMARY | |
| fi | |
| - name: Comment on failure | |
| if: failure() | |
| run: | | |
| echo "# ❌ BioImage.IO Tests Failed" >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "The daily BioImage.IO model testing workflow has failed." >> $GITHUB_STEP_SUMMARY | |
| echo "Please check the logs for more details." >> $GITHUB_STEP_SUMMARY | |
| echo "" >> $GITHUB_STEP_SUMMARY | |
| echo "**Failed at:** $(date -u '+%Y-%m-%d %H:%M:%S UTC')" >> $GITHUB_STEP_SUMMARY |