Update API and add support for small molecules

[wfondrie]

This PR makes some pretty large API changes, but provide a lot more flexibility than before.

Changed

• PeptideTransformer* is now AnalyteTransformer* to reflect support for small molecules as well.
• Similarly, PeptideDataset was renamed AnalyteDataset.
• All the forward() methods for the Transformer modules have been updated to with additional keyword arguments. This enables BERT-style masking for training and such.
• All transformer modules now have a global_token_hook() method. This can be overwritten in a subclass to customize how a global token (the first element of the sequence) is created using the *args and **kwargs provided in the forward methods.

Added

• A new tokenizer for small molecules, MoleculeTokenizer.
• The PeptideIonTokenizer.calculate_precursor_ions() method is fully PyTorch, so it should be efficient for use during model training and inference. (see Optimize beam search Noble-Lab/casanovo#269)

Next PR will be docs!

[codecov]

Codecov Report

Attention: Patch coverage is 94.65241% with 10 lines in your changes are missing coverage. Please review.

Project coverage is 96.13%. Comparing base (bd2861f) to head (38287c9).

Files	Patch %	Lines
depthcharge/tokenizers/peptides.py	87.09%	4 Missing ⚠️
depthcharge/tokenizers/tokenizer.py	81.25%	3 Missing ⚠️
depthcharge/transformers/analytes.py	95.65%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #43      +/-   ##
==========================================
+ Coverage   92.48%   96.13%   +3.65%     
==========================================
  Files          22       24       +2     
  Lines         971      957      -14     
==========================================
+ Hits          898      920      +22     
+ Misses         73       37      -36     

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[bittremieux]

Massive effort! In general I think it looks pretty good. I have some small suggestions and a few questions.

[wfondrie]

Thanks a lot @bittremieux! It turns out a missed a lot of documentation and you caught at least two potential bugs 🎉

Sorry the update has so many new changes - Ruff updated and apparently added another rule to the autoformatting.

[wfondrie]

I'm going to go ahead and merge so I can build atop this. @bittremieux, if there's anything else please let me know and I'll address it in a fresh PR!