Fix anndata warnings

[flying-sheep]

• Closes #
• Tests included or not required because:

• Release notes not necessary because:

[codecov]

Codecov Report

Merging #2779 (dcd85f3) into master (737da3a) will increase coverage by 0.05%.
The diff coverage is 90.90%.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #2779      +/-   ##
==========================================
+ Coverage   72.47%   72.53%   +0.05%     
==========================================
  Files         111      111              
  Lines       12422    12185     -237     
==========================================
- Hits         9003     8838     -165     
+ Misses       3419     3347      -72     

Files	Coverage Δ
scanpy/datasets/_ebi_expression_atlas.py	90.36% <100.00%> (ø)
scanpy/external/pp/_bbknn.py	50.00% <ø> (+3.84%)	⬆️
scanpy/external/pp/_hashsolo.py	89.56% <ø> (+0.67%)	⬆️
scanpy/preprocessing/_simple.py	82.81% <ø> (+0.54%)	⬆️
scanpy/testing/_helpers/data.py	89.47% <100.00%> (+2.98%)	⬆️
scanpy/tools/_rank_genes_groups.py	94.30% <100.00%> (+0.78%)	⬆️
scanpy/readwrite.py	67.95% <0.00%> (-0.08%)	⬇️
scanpy/testing/_pytest/fixtures/__init__.py	96.66% <92.85%> (+1.92%)	⬆️

... and 70 files with indirect coverage changes