bugfix in _calculate_neighborhood_profile in gr/_niche.py

[shashkat]

Description

I am currently working on refactoring the niche code and API to make more modular similar to how it was done for graph construction strategies in #1147 and discussed in #1192. However, before that, in a separate, smaller PR, I wanted to make aware of a bug in the niche code, and fix it. This is that PR.

The bug was in the function _calculate_neighborhood_profile() in gr/_niche.py. This is called when calculate_niche() is called with flavor = 'neighborhood', inside _get_nhood_profile_niches(). The goal of _calculate_neighborhood_profile() is to get a dataframe of shape num_cells x num_categories (categories could be something like celltype), where each entry stores the number of neighbors of a cell of a particular category. However, it wasn't working correctly when different cells had different number of neighbors. I believe it was written to be meant for grid-based data only.
Now, it handles correctly the case when cells have different number of neighbors.

How has this been tested?

I created a new dummy adata object (dummy_adata2 in tests/conftest.py) with explicitly defined locations of the cells, not necessarily organized in a grid. Then, I determined how the neighborhood profile for this object would look like and wrote a test function accordingly in tests/graph/test_niche.py called test_calculate_neighborhood_profile(). It failed with the original version of _calculate_neighborhood_profile() due to incorrect values and passed with the new version.

Other points

• The purpose of this PR is to just make aware of this bug and fix it first. But it is not gonna be the final version of this function as there would be many changes with the niche-refactor PR.
• I also believe that dummy_adata2 object can be useful for writing other tests cases too in the future for niche code and possibly graph building code too.

[codecov]

Codecov Report

❌ Patch coverage is 91.30435% with 2 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.23%. Comparing base (ac08971) to head (5a010bc).
⚠️ Report is 3 commits behind head on main.

Files with missing lines	Patch %	Lines
src/squidpy/gr/_niche.py	91.30%	0 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1229      +/-   ##
==========================================
+ Coverage   77.08%   77.23%   +0.15%     
==========================================
  Files          63       63              
  Lines        9368     9384      +16     
  Branches     1576     1583       +7     
==========================================
+ Hits         7221     7248      +27     
+ Misses       1545     1532      -13     
- Partials      602      604       +2     

Files with missing lines	Coverage Δ
src/squidpy/gr/_niche.py	38.01% <91.30%> (+0.48%)	⬆️

... and 1 file with indirect coverage changes

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[selmanozleyen]

closing this since it's included in #1245