Backport PR #4208 on branch 1.12.x (fix: PCA centering in ingest)

[flying-sheep]

Backport PR #4208 on branch 1.12.x

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.69%. Comparing base (8e45222) to head (22a0b19).
✅ All tests successful. No failed tests found.

Additional details and impacted files

@@            Coverage Diff             @@
##           1.12.x    #4235      +/-   ##
==========================================
+ Coverage   78.64%   78.69%   +0.04%     
==========================================
  Files         121      121              
  Lines       12730    12735       +5     
==========================================
+ Hits        10012    10022      +10     
+ Misses       2718     2713       -5     

Flag	Coverage Δ
hatch-test.low-vers	77.76% <100.00%> (+0.04%)	⬆️
hatch-test.pre	78.58% <100.00%> (+0.04%)	⬆️

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Files with missing lines	Coverage Δ
src/scanpy/tools/_ingest.py	78.50% <100.00%> (+2.72%)	⬆️