Change niche flavor to cellcharter_simple and default distance = 3

[marcovarrone]

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

[codecov-commenter]

Codecov Report

:x: Patch coverage is 0% with 18 lines in your changes missing coverage. Please review. :white_check_mark: Project coverage is 24.24%. Comparing base (d8b8f91) to head (98a3a78). :warning: Report is 13 commits behind head on main.

Files with missing lines	Patch %	Lines
src/squidpy/gr/_niche.py	0.00%	18 Missing :warning:

:exclamation: There is a different number of reports uploaded between BASE (d8b8f91) and HEAD (98a3a78). Click for more details.

HEAD has 3 uploads less than BASE

Flag	BASE (d8b8f91)	HEAD (98a3a78)
	4	1

Additional details and impacted files

@@             Coverage Diff             @@
##             main     #978       +/-   ##
===========================================
- Coverage   66.63%   24.24%   -42.40%     
===========================================
  Files          40       41        +1     
  Lines        6060     6072       +12     
  Branches     1015     1018        +3     
===========================================
- Hits         4038     1472     -2566     
- Misses       1662     4583     +2921     
+ Partials      360       17      -343     

Files with missing lines	Coverage Δ
src/squidpy/gr/_niche.py	11.76% <0.00%> (-23.10%)	:arrow_down:

... and 31 files with indirect coverage changes

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[timtreis]

Hey @marcovarrone, sorry for having let this gone stale. I'm not the biggest fan of changing the name but very much see your point - I've added the use_rep parameter and a warning in case the user now goes with the PCA approach - would this work for you?

[marcovarrone]

Hi @timtreis, no worries! Looks great to me