v0.9.0

16.06.2024 - Version 0.9.0

Maintenance

• Adding more extensive code documentation
• Optimizing imports
• Applying consistent file naming
• Updating dependencies. Note that jupyter was removed as a direct optional dependency.
  You can always add it via poetry add jupyter.
• Adding simple differentiation between t5 and esm tokenizer and models in embedders module

Features

• Adding new residues_to_value protocol.
  Similar to the residues_to_class protocol,
  this protocol predicts a value for each sequence, using per-residue embeddings. It might, in some situations, outperform
  the sequence_to_value protocol.

Bug fixes

• For huggingface_transformer_embedder.py, all special tokens are now always deleted from the final embedding
  (e.g. first/last for esm1b, last for t5)