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Change niche flavor to cellcharter_simple and default distance = 3 #978

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Description

  • Change flavor option in calculate_niche to cellcharter_simple` for CellCharter
  • Default distance = 3 for cellcharter_simple.

How has this been tested?

pytest runs successfully.
However, I see there are no unit tests for calculate_niche with cellcharter (now cellcharter_simple).

Closes

Closes #977

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codecov-commenter commented Mar 24, 2025

Codecov Report

Attention: Patch coverage is 25.00000% with 6 lines in your changes missing coverage. Please review.

Project coverage is 66.56%. Comparing base (4a632d6) to head (69d7d1b).
Report is 187 commits behind head on main.

Files with missing lines Patch % Lines
src/squidpy/gr/_niche.py 14.28% 2 Missing and 4 partials ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #978      +/-   ##
==========================================
- Coverage   69.99%   66.56%   -3.43%     
==========================================
  Files          39       40       +1     
  Lines        5532     6048     +516     
  Branches     1037     1012      -25     
==========================================
+ Hits         3872     4026     +154     
- Misses       1367     1663     +296     
- Partials      293      359      +66     
Files with missing lines Coverage Δ
src/squidpy/_constants/_constants.py 100.00% <100.00%> (ø)
src/squidpy/gr/_niche.py 34.86% <14.28%> (ø)

... and 12 files with indirect coverage changes

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Change CellCharter name and default values
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