Filter MNI-registered brains out of longitudinal template discovery (… #140
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| name: Full Testing Suite | |
| on: | |
| push: | |
| paths: | |
| - src/** | |
| - scripts/** | |
| - tests/** | |
| - pyproject.toml | |
| - uv.lock | |
| - .github/workflows/test_full.yaml | |
| workflow_dispatch: | |
| inputs: | |
| no_cleanup: | |
| description: Keep intermediate files after running tests | |
| default: false | |
| type: boolean | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: arcana | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - uses: astral-sh/setup-uv@v8.0.0 | |
| with: | |
| version: "0.11.3" | |
| enable-cache: true # not automatic on self-hosted runners | |
| - run: uv sync | |
| - name: Run all tests | |
| shell: bash | |
| run: | | |
| # Clean up stale tmpfs dirs from previous crashed runs | |
| find /dev/shm -maxdepth 1 -name 'rbc_test_*' -mmin +120 -exec rm -rf {} + 2>/dev/null || true | |
| export JOB_TMP="/dev/shm/rbc_test_$(date +%s%N)" | |
| mkdir -p $JOB_TMP | |
| echo "JOB_TMP=$JOB_TMP" >> $GITHUB_ENV | |
| echo "Job temp directory: $JOB_TMP" | |
| export PYTEST_CACHE_DIR="$JOB_TMP/.pytest_cache" | |
| export PYTHONPYCACHEPREFIX="$JOB_TMP/__pycache__" | |
| export COVERAGE_FILE="$JOB_TMP/.coverage" | |
| uv run pytest \ | |
| -n 8 \ | |
| --runner=podman \ | |
| --basetemp=$JOB_TMP/pytest-tmp \ | |
| --cov-report= \ | |
| --cov=src \ | |
| --durations=0 \ | |
| --log-level=DEBUG \ | |
| --verbose tests | |
| - name: Generate pipeline report | |
| if: always() | |
| continue-on-error: true | |
| shell: bash | |
| run: | | |
| uv run scripts/visualize_pipeline.py --output $JOB_TMP/pipeline_report.png | |
| if [ -f "$JOB_TMP/pipeline_report.png" ]; then | |
| echo "## Pipeline Report" >> $GITHUB_STEP_SUMMARY | |
| echo "Download the **pipeline-report** artifact for the full visualization." >> $GITHUB_STEP_SUMMARY | |
| fi | |
| - name: Upload pipeline report | |
| if: always() | |
| uses: actions/upload-artifact@v7 | |
| with: | |
| name: pipeline-report | |
| path: ${{ env.JOB_TMP }}/pipeline_report.png | |
| - name: Coverage summary | |
| if: always() | |
| env: | |
| COVERAGE_FAIL: 75 | |
| shell: bash | |
| run: | | |
| uv run coverage report \ | |
| --data-file=$JOB_TMP/.coverage \ | |
| --fail-under=$COVERAGE_FAIL \ | |
| --show-missing \ | |
| --format=markdown >> $GITHUB_STEP_SUMMARY | |
| - name: Cleanup | |
| if: ${{ always() && github.event.inputs.no_cleanup != true }} | |
| shell: bash | |
| run: | | |
| echo "Cleaning up job temp directory: $JOB_TMP" | |
| echo "Temp directory size: $(du -sh $JOB_TMP 2>/dev/null | cut -f1)" | |
| rm -rf $JOB_TMP |