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Work with pre-computed objects for imputed values and k-NN graphs#21

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Marius1311 merged 20 commits intomainfrom
feat/input_imputed
May 4, 2025
Merged

Work with pre-computed objects for imputed values and k-NN graphs#21
Marius1311 merged 20 commits intomainfrom
feat/input_imputed

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First, this PR makes CellMapper more versatile as an evaluation tool for expression imputation computed externally. Second, it allows importing externally computed k-NN graphs (we test for scanpy and squidpy) via a new self-mapping mode. This can be useful e.g. for spatial smoothing, like in UTAG.

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codecov bot commented May 4, 2025

Codecov Report

❌ Patch coverage is 87.16578% with 24 lines in your changes missing coverage. Please review.
✅ Project coverage is 85.17%. Comparing base (f0fb6eb) to head (5fb88f1).
⚠️ Report is 201 commits behind head on main.

Files with missing lines Patch % Lines
src/cellmapper/utils.py 85.50% 10 Missing ⚠️
src/cellmapper/cellmapper.py 82.69% 9 Missing ⚠️
src/cellmapper/knn.py 92.98% 4 Missing ⚠️
src/cellmapper/evaluate.py 88.88% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main      #21      +/-   ##
==========================================
+ Coverage   84.48%   85.17%   +0.68%     
==========================================
  Files           6        7       +1     
  Lines         477      607     +130     
==========================================
+ Hits          403      517     +114     
- Misses         74       90      +16     
Files with missing lines Coverage Δ
src/cellmapper/check.py 100.00% <ø> (ø)
src/cellmapper/evaluate.py 84.45% <88.88%> (-0.21%) ⬇️
src/cellmapper/knn.py 79.41% <92.98%> (+4.02%) ⬆️
src/cellmapper/cellmapper.py 87.71% <82.69%> (-0.12%) ⬇️
src/cellmapper/utils.py 85.50% <85.50%> (ø)
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@Marius1311 Marius1311 merged commit b95cae7 into main May 4, 2025
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@Marius1311 Marius1311 deleted the feat/input_imputed branch May 4, 2025 15:42
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