fix .A removal

[flying-sheep]

• Closes Pre-release jobs fail because scipy removed .A from csr/csc matrices #3083
• Tests included or not required because:

• Release notes not necessary because:

Two different fixes:

1. The np.asarray cases are when we e.g. had spmat.sum(axis=1).A (i.e. a dense matrix). I could also leave these as .A.
2. the .toarray() cases are when we converted a sparse matrix to dense directly.

[codecov]

Codecov Report

Attention: Patch coverage is 62.50000% with 3 lines in your changes missing coverage. Please review.

Project coverage is 75.85%. Comparing base (5dc489d) to head (6ba3676).
Report is 46 commits behind head on main.

Files with missing lines	Patch %	Lines
scanpy/external/exporting.py	0.00%	2 Missing ⚠️
scanpy/preprocessing/_combat.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #3084   +/-   ##
=======================================
  Coverage   75.85%   75.85%           
=======================================
  Files         110      110           
  Lines       12531    12531           
=======================================
  Hits         9506     9506           
  Misses       3025     3025           

Files with missing lines	Coverage Δ
scanpy/plotting/_qc.py	86.84% <100.00%> (ø)
scanpy/plotting/_tools/paga.py	66.98% <100.00%> (ø)
scanpy/preprocessing/_pca.py	92.93% <100.00%> (ø)
scanpy/preprocessing/_scrublet/core.py	92.90% <ø> (ø)
scanpy/preprocessing/_scrublet/sparse_utils.py	89.28% <100.00%> (ø)
scanpy/tools/_score_genes.py	85.54% <100.00%> (ø)
scanpy/preprocessing/_combat.py	90.83% <0.00%> (ø)
scanpy/external/exporting.py	13.44% <0.00%> (ø)

[flying-sheep]

ignoring flaky tests:

• Broken Scrublet Test #3068
• https://scverse.zulipchat.com/#narrow/stream/393966-scanpy-anndata-dev/topic/Dask.20minimum.20version.20issue