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docs: fix outdated statements in the SpatialData class docstring - #1273

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jan-glx wants to merge 3 commits into
scverse:mainfrom
jan-glx:docs/spatialdata-class-docstring

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@jan-glx

@jan-glx jan-glx commented Oct 15, 2026 •

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Fixes several outdated statements in the SpatialData class docstring (src/spatialdata/_core/spatialdata.py), one commit each:

  1. table → tables: the parameter was renamed to tables (a dict of AnnData) but the docstring still documented table. Also documents the previously undocumented attrs parameter.
  2. Tables can annotate points: the docstring said points "can't be annotated by a table", but tables can annotate points just like labels and shapes (see docs/design_doc.md and the join/query code).
  3. datatree.DataTree → xarray.DataTree: matches the type actually used (spatialdata._types.Raster_T).

Still open: the line saying tables store "the spatial coordinates ... in the obsm slot". this is covered in a separate PR #1274 that might need some discussion.

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codecov Bot commented Oct 15, 2026

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 91.42%. Comparing base (560caf9) to head (913faf0).

Additional details and impacted files
@@           Coverage Diff           @@
##             main    #1273   +/-   ##
=======================================
  Coverage   91.42%   91.42%           
=======================================
  Files          53       53           
  Lines        8381     8381           
=======================================
  Hits         7662     7662           
  Misses        719      719           
Files with missing lines Coverage Δ
src/spatialdata/_core/spatialdata.py 93.46% <ø> (ø)
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  • ❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

@jan-glx
jan-glx marked this pull request as ready for review October 15, 2026 09:03
@jan-glx
jan-glx requested a review from LucaMarconato October 15, 2026 09:03
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