swap in hs2p submodule #33
Workflow file for this run
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| name: Test WSI to embedding consistency | |
| on: | |
| pull_request: | |
| types: [opened, synchronize, reopened] | |
| workflow_dispatch: | |
| jobs: | |
| docker-test: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| permissions: | |
| contents: read | |
| actions: write # needed for Buildx GHA cache | |
| # don't run secret-using job on forked PRs | |
| if: ${{ github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository }} | |
| env: | |
| HF_TOKEN: ${{ secrets.HF_TOKEN }} | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Verify required folders exist | |
| run: | | |
| set -euo pipefail | |
| test -d test/input | |
| test -d test/gt | |
| mkdir -p test/output # ensure host-mapped output exists | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Free disk space on runner | |
| run: | | |
| set -euxo pipefail | |
| df -h | |
| sudo rm -rf /usr/local/lib/android || true | |
| sudo rm -rf /usr/share/dotnet || true | |
| sudo rm -rf /opt/ghc || true | |
| sudo rm -rf "${AGENT_TOOLSDIRECTORY:-/opt/hostedtoolcache}" || true | |
| docker system prune -af || true | |
| sudo apt-get clean | |
| df -h | |
| - name: Build image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| file: Dockerfile.ci | |
| push: false | |
| load: true | |
| tags: slide2vec-ci:${{ github.sha }} | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| - name: Guard required secret (if needed) | |
| if: ${{ github.event_name != 'pull_request' }} # or drop the condition if PRs from same repo need it | |
| run: | | |
| set -euo pipefail | |
| test -n "${HF_TOKEN:-}" || { echo "HF_TOKEN is required but not set"; exit 1; } | |
| - name: Generate outputs in container | |
| run: | | |
| set -euo pipefail | |
| docker run --rm \ | |
| -e HF_TOKEN="$HF_TOKEN" \ | |
| -v "$GITHUB_WORKSPACE/test/input:/input" \ | |
| -v "$GITHUB_WORKSPACE/test/output:/output" \ | |
| slide2vec-ci:${{ github.sha }} \ | |
| python slide2vec/main.py \ | |
| --config-file /input/config.yaml \ | |
| --skip-datetime \ | |
| --run-on-cpu | |
| - name: Verify output consistency (inside container) | |
| run: | | |
| set -euo pipefail | |
| docker run --rm \ | |
| -v "$GITHUB_WORKSPACE/test/gt:/gt" \ | |
| -v "$GITHUB_WORKSPACE/test/output:/output" \ | |
| slide2vec-ci:${{ github.sha }} \ | |
| bash -lc "python - <<'PY' | |
| import numpy as np, torch | |
| from numpy.testing import assert_array_equal | |
| # coordinates must match exactly (deterministic tiling) | |
| gt_coordinates = np.load('/gt/test-wsi.npy') | |
| coordinates = np.load('/output/coordinates/test-wsi.npy') | |
| assert_array_equal(coordinates, gt_coordinates), f'Coordinates mismatch: {coordinates} vs {gt_coordinates}' | |
| # embeddings: allow tiny numeric drift | |
| gt = torch.load('/gt/test-wsi.pt', map_location='cpu') | |
| emb = torch.load('/output/features/test-wsi.pt', map_location='cpu') | |
| assert emb.shape == gt.shape, f'Shape mismatch: {emb.shape} vs {gt.shape}' | |
| cos = torch.nn.functional.cosine_similarity(emb, gt, dim=-1) | |
| mean_cos = float(cos.mean()) | |
| atol, rtol = 1e-2, 1e-3 | |
| if not torch.allclose(emb, gt, atol=atol, rtol=rtol): | |
| if mean_cos < 0.99: | |
| raise AssertionError(f'Embedding mismatch: mean cosine similarity={mean_cos:.4f} (atol={atol}, rtol={rtol})') | |
| else: | |
| print(f'WARNING: embeddings not allclose, but mean cosine similarity={mean_cos:.4f} (atol={atol}, rtol={rtol})') | |
| else: | |
| print(f'OK: embeddings within tolerance; mean cosine similarity={mean_cos:.4f}') | |
| PY" |