TSNE layout does not work anymore

[ObT1337]

Problem:

In the embed_tsne_2D function within cartoGRAPHs.py, there's an unexpected error occurring. Specifically, it's triggered by an unexpected keyword argument square_distances in the TSNE initialization.

Error Traceback:

  File ".../lib/python3.9/site-packages/cartoGRAPHs/func_embed_plot.py", line 77, in embed_tsne_3D
    tsne3d = TSNE(n_components=3, random_state=0, perplexity=prplxty, square_distances=True)
TypeError: __init__() got an unexpected keyword argument 'square_distances'

Reference:
The unexpected keyword argument square_distances is detailed in the TSNE documentation as deprecated since version 1.1 of scikit-learn:

square_distances=True, default='deprecated'
This parameter has no effect since distance values are always squared since 1.1.

Deprecated since version 1.1: square_distances has no effect from 1.1 and will be removed in 1.3. scikit-learn==1.3.2

Suggested Fix:

To resolve this issue, I suggest adjusting the package requirements to ensure compatibility with scikit-learn versions where the square_distances argument is still supported, although without any effect.

Proposed Solution:

1. Set requirements to scikit-learn==1.2 or lower, where the argument square_distances is still supported but has no impact on functionality.
2. Update to the newest version and remove the suqare_distance argument as it as not effect anymore and is no more supported.

This adjustment should resolve the unexpected keyword argument issue and ensure compatibility across different scikit-learn versions.