Move and restructure CPAC comparison notes #270
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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 | |
| styxcache_dir: | |
| description: Override persistent styxcache directory on the self-hosted runner | |
| default: "" | |
| type: string | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| test: | |
| runs-on: arcana | |
| env: | |
| STYXCACHE_DIR_OVERRIDE: ${{ inputs.styxcache_dir }} | |
| STYXCACHE_MAX_GB: "50" | |
| steps: | |
| - uses: actions/checkout@v6 | |
| - uses: astral-sh/setup-uv@v8.1.0 | |
| with: | |
| version: "0.11.3" | |
| enable-cache: true # not automatic on self-hosted runners | |
| - run: uv sync | |
| - name: Cache ds000114 longitudinal fixture | |
| uses: actions/cache@v5 | |
| with: | |
| path: tests/data/ds000114 | |
| key: ds000114-${{ hashFiles('scripts/download_ds000114.py') }} | |
| - name: Prepare styx cache | |
| shell: bash | |
| run: | | |
| # Resolve cache dir: honor explicit override, else use the runner user's | |
| # home cache (persistent across runs, user-owned — no sudo required). | |
| STYXCACHE_DIR="${STYXCACHE_DIR_OVERRIDE:-$HOME/.cache/rbc-styxcache}" | |
| echo "STYXCACHE_DIR=$STYXCACHE_DIR" >> "$GITHUB_ENV" | |
| mkdir -p "$STYXCACHE_DIR" | |
| # Purge stale staging dirs from crashed previous runs (safe: atomic-rename commits) | |
| rm -rf "$STYXCACHE_DIR/.incoming" 2>/dev/null || true | |
| # Drop entries that contain any truncated .gz (styxcache's own | |
| # stdout/stderr streams or cached .nii.gz outputs). Atomic commits | |
| # should prevent these, but crashes before commit have been observed. | |
| corrupt=0 | |
| while IFS= read -r entry; do | |
| bad=0 | |
| for gz in $(find "$entry" -type f -name '*.gz'); do | |
| if ! gzip -t "$gz" 2>/dev/null; then | |
| bad=1 | |
| break | |
| fi | |
| done | |
| if [ "$bad" = "1" ]; then | |
| rm -rf "$entry" | |
| corrupt=$((corrupt + 1)) | |
| fi | |
| done < <(find "$STYXCACHE_DIR" -mindepth 2 -maxdepth 2 -type d 2>/dev/null) | |
| if [ "$corrupt" -gt 0 ]; then | |
| echo "evicted $corrupt entries with corrupt gzip streams" | |
| fi | |
| size_kb=$(du -sk "$STYXCACHE_DIR" 2>/dev/null | awk '{print $1}') | |
| size_kb=${size_kb:-0} | |
| cap_kb=$(( STYXCACHE_MAX_GB * 1024 * 1024 )) | |
| if [ "$size_kb" -gt "$cap_kb" ]; then | |
| echo "Cache size ${size_kb}KB exceeds cap ${cap_kb}KB; evicting oldest shards" | |
| find "$STYXCACHE_DIR" -mindepth 2 -maxdepth 2 -type d -printf '%T@ %p\n' \ | |
| | sort -n \ | |
| | while read -r _ path; do | |
| rm -rf "$path" | |
| cur=$(du -sk "$STYXCACHE_DIR" 2>/dev/null | awk '{print $1}') | |
| [ "${cur:-0}" -le "$cap_kb" ] && break | |
| done | |
| fi | |
| { | |
| echo "## styxcache" | |
| echo "- dir: \`$STYXCACHE_DIR\`" | |
| echo "- size before: $(du -sh "$STYXCACHE_DIR" 2>/dev/null | cut -f1)" | |
| } >> "$GITHUB_STEP_SUMMARY" | |
| - name: Run all tests | |
| shell: bash | |
| run: | | |
| # Clean up stale job tmp dirs from previous crashed runs | |
| find "$RUNNER_TEMP" -maxdepth 1 -name 'rbc_test_*' -mmin +120 -exec rm -rf {} + 2>/dev/null || true | |
| export JOB_TMP="$RUNNER_TEMP/rbc_test_$(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" | |
| export RBC_STYXCACHE_DIR="$STYXCACHE_DIR" | |
| # Pin rbc's scratch + niwrap data_dir under JOB_TMP so the Cleanup step | |
| # reclaims them automatically. Default is a system tmpdir otherwise. | |
| export RBC_WORK_DIR="$JOB_TMP/rbc_work" | |
| 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 >> $GITHUB_STEP_SUMMARY | |
| - name: styxcache summary | |
| if: always() | |
| shell: bash | |
| run: | | |
| size=$(du -sh "$STYXCACHE_DIR" 2>/dev/null | cut -f1) | |
| entries=$(find "$STYXCACHE_DIR" -mindepth 2 -maxdepth 2 -type d 2>/dev/null | wc -l) | |
| { | |
| echo "- size after: ${size:-0}" | |
| echo "- entries: ${entries:-0}" | |
| } >> "$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 |