Fix numpy 2.0 support; add numba to deps

[LucaMarconato]

Closes #602
Also adds numba to the dependencies as asked by @ilan-gold.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 91.89%. Comparing base (851a267) to head (da99a8c).
Report is 60 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #734   +/-   ##
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  Coverage   91.89%   91.89%           
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  Files          45       45           
  Lines        6919     6919           
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  Hits         6358     6358           
  Misses        561      561           

Files with missing lines	Coverage Δ
src/spatialdata/datasets.py	100.00% <100.00%> (ø)