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chore: fix spatialdata access in squidpy via a helper function#1134

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selmanozleyen wants to merge 18 commits intoscverse:mainfrom
selmanozleyen:chore/sdata-access
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chore: fix spatialdata access in squidpy via a helper function#1134
selmanozleyen wants to merge 18 commits intoscverse:mainfrom
selmanozleyen:chore/sdata-access

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@selmanozleyen selmanozleyen commented Mar 2, 2026

Fixes #1133 and implements the table extraction in a decorator so we won't need to ctrl+f our way to fix a similar bug when it happens

update: decided not to use a decorator as it uses metaprogramming with little to no benefit over using a function. Only plus was not adding table_key to the signature which isn't a plus imo. Explicitly typing a signature of a function is not something I consider as duplicate code

@selmanozleyen selmanozleyen marked this pull request as draft March 2, 2026 15:01
@selmanozleyen selmanozleyen marked this pull request as ready for review March 11, 2026 12:59
@selmanozleyen selmanozleyen requested a review from timtreis March 11, 2026 13:00
@selmanozleyen selmanozleyen changed the title chore: fix spatialdata access in squidpy via a decorator chore: fix spatialdata access in squidpy via a helper function Mar 11, 2026
@selmanozleyen selmanozleyen removed the request for review from timtreis March 11, 2026 13:16
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codecov bot commented Mar 11, 2026

Codecov Report

❌ Patch coverage is 82.60870% with 12 lines in your changes missing coverage. Please review.
✅ Project coverage is 74.45%. Comparing base (b04a951) to head (466124d).

Files with missing lines Patch % Lines
src/squidpy/gr/_build.py 79.41% 4 Missing and 3 partials ⚠️
src/squidpy/gr/_niche.py 37.50% 4 Missing and 1 partial ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1134      +/-   ##
==========================================
+ Coverage   74.05%   74.45%   +0.40%     
==========================================
  Files          39       39              
  Lines        6495     6495              
  Branches     1122     1112      -10     
==========================================
+ Hits         4810     4836      +26     
+ Misses       1230     1213      -17     
+ Partials      455      446       -9     
Files with missing lines Coverage Δ
src/squidpy/_constants/_pkg_constants.py 94.20% <100.00%> (+0.30%) ⬆️
src/squidpy/gr/_ligrec.py 78.18% <100.00%> (+0.59%) ⬆️
src/squidpy/gr/_nhood.py 81.48% <100.00%> (+3.29%) ⬆️
src/squidpy/gr/_ppatterns.py 80.43% <100.00%> (+1.55%) ⬆️
src/squidpy/gr/_ripley.py 96.49% <100.00%> (+1.70%) ⬆️
src/squidpy/gr/_sepal.py 56.20% <100.00%> (+1.13%) ⬆️
src/squidpy/gr/_utils.py 68.62% <100.00%> (+2.31%) ⬆️
src/squidpy/tl/_sliding_window.py 77.90% <100.00%> (+2.04%) ⬆️
src/squidpy/gr/_niche.py 37.53% <37.50%> (+0.99%) ⬆️
src/squidpy/gr/_build.py 88.61% <79.41%> (+0.09%) ⬆️
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@selmanozleyen selmanozleyen requested a review from timtreis March 11, 2026 14:24
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