[python] Add support for transforms in the Scene add_new_* methods

[jp-dark]

Add support for setting the transform when a PointCloud or MultiscaleImage is first added to a Scene.

[codecov]

Codecov Report

Attention: Patch coverage is 96.66667% with 1 line in your changes missing coverage. Please review.

Project coverage is 83.86%. Comparing base (89377d0) to head (caa07d8).
Report is 8 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #3206      +/-   ##
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+ Coverage   83.58%   83.86%   +0.27%     
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  Files          51       51              
  Lines        5422     5460      +38     
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+ Hits         4532     4579      +47     
+ Misses        890      881       -9     

Flag	Coverage Δ
python	83.86% <96.66%> (+0.27%)	⬆️

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Components	Coverage Δ
python_api	83.86% <96.66%> (+0.27%)	⬆️
libtiledbsoma	∅ <ø> (∅)

[nguyenv]

Not in this PR, but one thing I'd like to do in the future is make it so that the user can't modify these metadata values directly.

In the C++ API, we throw an error if there is an attempt to modify these reserved metadata keys. BUT there is a way to bypass this by passing the force flag. Internally, we could use coll._handle.add_metadata(f"soma_scene_registry_{key}", transform_to_json(transform), force=True). This way we can still modify the metadata values as needed but the user cannot.