Replace spmatrix with _CSMatrix as appropriate

[flying-sheep]

• Closes #
• Tests included or not required because:

• Release notes not necessary because: The only user-facing change is some subtly typing fixes

Preparation for sparray support: make sure spmatrix is only used where it makes sense.

I checked every single instance of spmatrix and either tested that coo_matrix also works or replaced it with _CSMatrix = csr_matrix | csc_matrix.

TODO after this PR:

1. replace spmatrix with _SpBase = sparray | spmatrix and _CSMatrix with _CSBase = cs{cr}_matrix | cs{cr}_array and test
2. figure out bsr_array

[codecov]

Codecov Report

Attention: Patch coverage is 95.32710% with 5 lines in your changes missing coverage. Please review.

Project coverage is 75.43%. Comparing base (fa38823) to head (15bdc02).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/scanpy/metrics/_common.py	85.71%	2 Missing ⚠️
src/scanpy/preprocessing/_utils.py	71.42%	2 Missing ⚠️
src/scanpy/tools/_utils.py	94.11%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3431      +/-   ##
==========================================
+ Coverage   75.36%   75.43%   +0.06%     
==========================================
  Files         112      112              
  Lines       13219    13235      +16     
==========================================
+ Hits         9963     9984      +21     
+ Misses       3256     3251       -5     

Files with missing lines	Coverage Δ
src/scanpy/_utils/__init__.py	74.71% <100.00%> (+0.24%)	⬆️
src/scanpy/_utils/compute/is_constant.py	77.50% <100.00%> (-0.55%)	⬇️
src/scanpy/external/tl/_harmony_timeseries.py	33.33% <ø> (ø)
src/scanpy/external/tl/_palantir.py	32.43% <ø> (ø)
src/scanpy/get/_aggregated.py	92.15% <100.00%> (+0.05%)	⬆️
src/scanpy/get/get.py	91.46% <100.00%> (ø)
src/scanpy/metrics/_gearys_c.py	59.25% <100.00%> (+2.46%)	⬆️
src/scanpy/metrics/_morans_i.py	66.17% <100.00%> (+2.94%)	⬆️
src/scanpy/neighbors/_types.py	100.00% <100.00%> (ø)
...preprocessing/_deprecated/highly_variable_genes.py	93.47% <ø> (ø)
... and 18 more

... and 1 file with indirect coverage changes

[ilan-gold]

Looks good, about the plan:

replace spmatrix with _SpBase = sparray | spmatrix and _CSMatrix with _CSBase = cs{cr}_matrix | cs{cr}_array and test

I am not sure this will go so smoothly because of differing APIs and version compatibility. It was something of a nightmare in AnnData...