fix(visium): build the circles from the spot coordinates again - #416
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`visium()` used `coords` for two things: the raw `tissue_positions` table merged into `adata.obs`, and, after a rebinding, the `(n, 2)` array of spot coordinates that `ShapesModel.parse()` consumes. In #411 the rebinding was inlined into the `adata.obsm["spatial"]` assignment (`coords` changing type is what mypy rejects), so the raw table reached `ShapesModel.parse()` and the reader raised `TypeError: ShapesModel.parse() does not support the type <class 'pandas.core.frame.DataFrame'>`. Use a separate name for the coordinates, which keeps mypy happy without changing the runtime behaviour, and add a regression test on a minimal synthetic dataset (the plain Visium reader had no test coverage). Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
LucaMarconato
enabled auto-merge (squash)
September 9, 2026 10:59
Codecov Report❌ Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #416 +/- ##
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- Coverage 63.15% 63.13% -0.02%
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Files 26 26
Lines 3257 3258 +1
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Hits 2057 2057
- Misses 1200 1201 +1
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Fixes a bug introduced by #411
below: AI generated–manually reviewed
visium()usedcoordsfor two things: the rawtissue_positionstable merged intoadata.obs, and, after a rebinding, the(n, 2)array of spot coordinates thatShapesModel.parse()consumes.In #411 the rebinding was inlined into the
adata.obsm["spatial"]assignment (coordschanging type is what mypy rejects), so the raw table reachedShapesModel.parse()and the reader raisedTypeError: ShapesModel.parse() does not support the type <class 'pandas.core.frame.DataFrame'>.Use a separate name for the coordinates, which keeps mypy happy without changing the runtime behaviour, and add a regression test on a minimal synthetic dataset (the plain Visium reader had no test coverage).