Refactor affine transformations and add deprecation utils

[waltsims]

This pull request introduces several changes to the kwave utilities, focusing on handling deprecation warnings, improving affine transformations, and updating rotation matrix calculations. The most important changes include adding a deprecation utility, replacing get_affine_matrix with make_affine, and using scipy.spatial.transform.Rotation for rotation matrices.

Deprecation Handling:

• Added a deprecated decorator in kwave/utils/deprecation.py to mark functions as deprecated and provide warnings.

Affine Transformations:

• Replaced get_affine_matrix with make_affine in kwave/utils/kwave_array.py and kwave/utils/math.py to create affine transformation matrices. [1] [2]
• Deprecated get_affine_matrix in favor of make_affine.

Rotation Matrices:

• Updated rotation matrix calculations to use scipy.spatial.transform.Rotation in kwave/utils/mapgen.py and kwave/utils/math.py. [1] [2] [3]

Code Refactor:

• Removed unused imports and reorganized imports in kwave/utils/kwave_array.py and kwave/utils/mapgen.py. [1] [2]

[codecov]

Codecov Report

Attention: Patch coverage is 96.87500% with 3 lines in your changes missing coverage. Please review.

Project coverage is 73.28%. Comparing base (8ca3f30) to head (98d6a15).

Files with missing lines	Patch %	Lines
kwave/utils/math.py	96.15%	2 Missing and 1 partial ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #550      +/-   ##
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+ Coverage   73.16%   73.28%   +0.12%     
==========================================
  Files          46       47       +1     
  Lines        6830     6857      +27     
  Branches     1308     1308              
==========================================
+ Hits         4997     5025      +28     
  Misses       1284     1284              
+ Partials      549      548       -1     

Flag	Coverage Δ
3.10	73.28% <96.87%> (+0.12%)	⬆️
3.11	73.28% <96.87%> (+0.12%)	⬆️
3.12	73.28% <96.87%> (+0.12%)	⬆️
3.13	73.28% <96.87%> (+0.12%)	⬆️
macos-latest	73.25% <96.87%> (+0.12%)	⬆️
ubuntu-latest	73.25% <96.87%> (+0.12%)	⬆️
windows-latest	73.26% <96.87%> (+0.12%)	⬆️

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[waltsims]

i'll fix these

[faridyagubbayli]

Looks great! Left a single minor comment.

[faridyagubbayli]

Usually these type of calls happen once per application lifecycle. If we display warning every time the function is called, it could be annoying. Perhaps move the warning outside of the wrapper but keep it still inside of the decorator? Since each function gets decorated only once (not sure how this will if the file is imported multiple times), a single log should be printed.