Move make_stitched_labels from experimental.im to experimental.tl - #1254
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Co-locate all four steps of the tiling-QC / stitching workflow (calculate_tiling_qc, assign_stitch_groups, make_stitched_labels, and the pl.tiling_qc viz) so the pipeline is discoverable in one place. Previously make_stitched_labels lived in `im` (it emits a labels raster), splitting the workflow across `tl` and `im`. Pure move: the module uses absolute imports, so no internal import changes are needed. Updates both __init__ exports, docs/api.md, and the test references. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
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selmanozleyen
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Aug 11, 2026
Conflict in src/squidpy/experimental/tl/__init__.py: kept the branch's align/AlignResult exports and folded in upstream's make_stitched_labels, which moved from experimental.im to experimental.tl in scverse#1254.
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What
Moves
make_stitched_labelsfromsquidpy.experimental.imtosquidpy.experimental.tl.Why
The tiling-QC / cut-cell stitching workflow is four steps:
tl.calculate_tiling_qc— score cells for tile-boundary artifactstl.assign_stitch_groups— pair the cut pieces across seamsmake_stitched_labels— materialise the merged labelspl.tiling_qc— visualiseSteps 1–2 already live in
tl, but step 3 sat inim. That split the pipeline across two modules and hurt discoverability. This PR co-locates the whole workflow intlso users find all of it in one namespace.