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align with hs2p#116

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clemsgrs merged 5 commits intomainfrom
codex/atlaspatch-hs2p-3-3-0
Apr 18, 2026
Merged

align with hs2p#116
clemsgrs merged 5 commits intomainfrom
codex/atlaspatch-hs2p-3-3-0

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@clemsgrs clemsgrs commented Apr 17, 2026

Summary

  • align slide2vec with hs2p 3.3.0 and 4.0.0
  • keep the bundled preprocessing schema in sync with hs2p's AtlasPatch-capable sam2 segmentation path
  • update slide2vec for hs2p's unified tiling/sampling contract, including the explicit preview toggles and annotation process-list column

Why

hs2p 3.3.0 introduced the segmentation.method / sam2_* schema, and hs2p 4.0.0 unified tiling and sampling around a stricter process-list contract plus explicit preview toggles. Without this update, slide2vec would keep shipping config/docs/tests that no longer match the upstream dependency.

What changed

  • bumped the hs2p dependency floor to 3.3.0 and included the sam2 extra in the packaged install
  • updated slide2vec/configs/default.yaml to use the new preview booleans and tissue contour styling fields expected by hs2p 4.0.0
  • preserved hs2p's new annotation column when slide2vec reloads and rewrites process lists
  • refreshed the Python API and CLI docs to describe sam2, AtlasPatch-backed segmentation, and the explicit preview toggles
  • updated regression coverage and the stored metadata fixtures to match the new hs2p schema

@clemsgrs clemsgrs marked this pull request as ready for review April 17, 2026 12:44
@clemsgrs clemsgrs changed the title [codex] align hs2p 3.3.0 align hs2p 3.3.0 Apr 17, 2026
@clemsgrs clemsgrs changed the title align hs2p 3.3.0 align with hs2p Apr 18, 2026
@clemsgrs clemsgrs merged commit 46d4a1f into main Apr 18, 2026
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@clemsgrs clemsgrs deleted the codex/atlaspatch-hs2p-3-3-0 branch April 18, 2026 18:55
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