Cellmaps-coembedding

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* 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

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* Added README generation.

* Refactor code.

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

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* 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.

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* 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.

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* First release on PyPI.