Move to new numpy.random.Generator

[Lilly-May]

PR Checklist

• Referenced issue is linked (Fixes Move to new numpy.random.Generator #355)

Description of changes

All occurrences of numpy Legacy Generator (RandomState) were replaced with the new numpy.random.Generator. Whenever an instance of the numpy.random.Generator was created, the recommended constructor default_rng was used.

Technical details

I tested that all legacy warnings have disappeared by including the numpy rules from ruff in the pre-commit checks.

[Lilly-May]

I don't think we need to set a seed here. As far as I can see, there is no random number generator used throughout the test. However, please review whether we can indeed delete this (so far, I've only commented it out).

[Zethson]

I don't see one being used in the implementation as well. I guess we can remove it. However, the test should also be a fixture, right? The "make_test_adatashould be aadata` fixture. Can you please implement it?

[Zethson]

Exactly what we wanted. Thank you very much! See my minor comment. Please merge after you've addressed it.

[Zethson]

I don't see one being used in the implementation as well. I guess we can remove it. However, the test should also be a fixture, right? The "make_test_adatashould be aadata` fixture. Can you please implement it?

[codecov]

Codecov Report

Merging #396 (86427ae) into main (b58f7fc) will not change coverage.
Report is 14 commits behind head on main.
The diff coverage is 0.00%.

Additional details and impacted files

@@          Coverage Diff          @@
##            main    #396   +/-   ##
=====================================
  Coverage   0.00%   0.00%           
=====================================
  Files         40      40           
  Lines       4888    4885    -3     
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+ Misses      4888    4885    -3     

Files	Coverage Δ
pertpy/plot/_mixscape.py	0.00% <ø> (ø)
pertpy/tools/_coda/_tasccoda.py	0.00% <ø> (ø)
pertpy/tools/_scgen/_jax_scgen.py	0.00% <ø> (ø)
pertpy/tools/_coda/_sccoda.py	0.00% <0.00%> (ø)
pertpy/tools/_cinemaot.py	0.00% <0.00%> (ø)
pertpy/tools/_coda/_base_coda.py	0.00% <0.00%> (ø)
pertpy/tools/_distances/_distance_tests.py	0.00% <0.00%> (ø)
pertpy/tools/_scgen/_utils.py	0.00% <0.00%> (ø)

... and 17 files with indirect coverage changes