Refactoring and releasing second coembedding algorithm under new name proteingps

• Rename auto coembedding name and proteinGPS. --algorithm auto option is depreacted and --algorithm proteingps
  should be used. The coembedding implementation was moved to ProteinGPSCoEmbeddingGenerator class and
  AutoCoEmbeddingGenerator is deprecated and calls proteingps. The package name was renamed from autoembed_sc
  to proteingps.

• Added mean_losses mean loses flag and argument in ProteinGPSCoEmbeddingGenerator. If set, uses mean of losses
  otherwise sum of losses.

• Constants updated in ProteinGPSCoEmbeddingGenerator (triplet_margin=0.2) and in proteingps's fit_predict
  (triplet_margin=0.2, lambda_reconstruction=5.0, lambda_triplet=5.0)

• Bug fix: add missing a .to(device) call to ensure tensors are correctly moved to the appropriate device.

• Update version bounds of required packages

Add readme generation

• Added README generation.

• Refactor code.

Bug fix for error when no overlapping embeddings

• Bug fix: raise more informative error when no embeddings overlap.

Added provenance flag

• Added --provenance flag to pass a path to json file with provenance information. This removes the
  necessity of input directory to be an RO-Crate.

Added new coembedding algorithm

• Added a new coembedding algorithm accessible via flag --algorithm auto. This algorithm utilizes neural networks
  to generate latent embeddings, optimizing both reconstruction and triplet losses to improve embedding accuracy
  by learning intra- and inter-modality relationships.

First release

• First release