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Feat/gene imputation#1161

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MDLDan wants to merge 13 commits intoscverse:mainfrom
MDLDan:feat/gene_imputation
Draft

Feat/gene imputation#1161
MDLDan wants to merge 13 commits intoscverse:mainfrom
MDLDan:feat/gene_imputation

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@MDLDan MDLDan commented Apr 16, 2026

Description

  • Introduced a new tl.impute API for gene imputation in spatial data using scRNA-seq reference data.
  • Added a SpaGE implementation with a dedicated parameter object to support future extension to additional methods.
  • Added method-based dispatch in the main api entry point.
  • Added tests for SpaGE behavior and dispatcher validation
  • Added tl.impute to the API docs autosummary.
  • Added tests for SpaGE behavior and dispatcher validation in tests/tools/test_impute.py

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codecov Bot commented Apr 16, 2026

Codecov Report

❌ Patch coverage is 82.31293% with 26 lines in your changes missing coverage. Please review.
✅ Project coverage is 73.85%. Comparing base (373228d) to head (772ce91).
⚠️ Report is 1 commits behind head on main.

Files with missing lines Patch % Lines
src/squidpy/tl/_spage_impute.py 80.45% 21 Missing and 5 partials ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main    #1161      +/-   ##
==========================================
+ Coverage   73.56%   73.85%   +0.29%     
==========================================
  Files          44       46       +2     
  Lines        6929     7076     +147     
  Branches     1174     1194      +20     
==========================================
+ Hits         5097     5226     +129     
- Misses       1347     1360      +13     
- Partials      485      490       +5     
Files with missing lines Coverage Δ
src/squidpy/tl/_impute.py 100.00% <100.00%> (ø)
src/squidpy/tl/_spage_impute.py 80.45% <80.45%> (ø)

... and 1 file with indirect coverage changes

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@MDLDan MDLDan marked this pull request as draft April 17, 2026 08:43
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