refactor: pandas3 support

[ori-kron-wis]

need to wait for anndata, mudata, scanpy updates

[chatgpt-codex-connector]

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 88.46%. Comparing base (04787b9) to head (7c0ea11).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3638      +/-   ##
==========================================
+ Coverage   86.62%   88.46%   +1.83%     
==========================================
  Files         226      226              
  Lines       21859    21859              
==========================================
+ Hits        18936    19338     +402     
+ Misses       2923     2521     -402     

see 11 files with indirect coverage changes

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[ori-kron-wis]

also mlflow is not yet supported with pandas3

[ori-kron-wis]

We will have to remove all pip install git+https://github.com/scverse/anndata appears in the yaml of test once anndata is released as well as the changes in pyproject (will not need to pin anything)