depthcharge v0.3.0

[v0.3.0] - 2023-06-06

Added

• Providing a proper tokenization class (also resolves #24 and #18)
• First-class support for ProForma peptide annotations, thanks to spectrum_utils and pyteomics.
• Adding primitive dataclasses for peptides, peptide ions, mass spectra ... and even small molecules 🚀
• Adding type hints to everything and stricter linting with Ruff.
• Adding a ton of tests.
• Tight integration with spectrum_utils 💪

Changed

• Moving preprocessing onto parsing instead of data loading (similar to @bittremieux's proposal in #31)
• Combining the SpectrumIndex and SpectrumDataset classes into one.
• Changing peak encodings. Instead of encoding the intensity using a linear projection and summing with the sinusoidal m/z encodings, now the intensity is also sinusoidally encoded and is combined with the sinusoidal m/z encodings using a linear layer.