chore(deps): bump rustyms from 0.8.3 to 0.10.0

[dependabot]

Bumps rustyms from 0.8.3 to 0.10.0.

Release notes

Sourced from rustyms's releases.

v0.10.0

This release adds the following major points:

• Added glycan rendering
• Added some missing information in glycans and fixed some bugs
• Added trait IsAminoAcid (note that this renamed some of the methods on AminoAcid)
• Split Model in FragmentationModel and MatchingParameters
• Added much more complexity in FragmentationModel
  • More complex satellite ions
  • More neutral loss types, based on the amino acid/monosaccharide and side chain losses
  • Added options for glycan fragmentation on peptide fragments
• Added pKA and isoelectric point estimations for peptides (thanks to @​aukeheerdink)
• Updated built in fragmentation models to use the added complexity and added ones for EAD, EACID, and UVPD
• Added basic CSV format
• Added the options to keep all CSV lines when parsing an identified peptides file
• Added mzPAF exporting for fragments
• Restructured some parts of the API surface
• Updated all databases
• Fixed many bugs and performance issues

Many of these introduce breaking changes so any code written for earlier version will needs some (minor to medium) revisions. If there is anything unclear please reach out.

For a full run down of the changed API use 'cargo-public-api' (this changelog is too big for inclusion here).

Version 0.10.0 (Python version)

See 0.10.0.

v0.9.0

This release adds the following major points:

• Integration with mzdata for raw file handling
• Full ProForma 2.0 compliance by adding support for cross-links, note that many functions and types are renamed
• More control over fragmentation model
• Many more identified peptide file formats
• Updated and somewhat expanded Python bindings
• More reliability thanks to fuzzing efforts
• Updated complexity API, any Peptidoform (formerly LinearPeptide), SequenceElement, and CheckedAminoAcid now has its maximal complexity tracked. This changes many functions on these elements, but should be straightforward to change.
• Added a simple function to open any identified peptides file (see open_identified_peptides_file)
• Updated Unimod, GNOme, and IMGT to the newest versions
• Updated the documentation
• Many many bug fixes
• Optimised memory usage, mostly for identified peptides file (should expect ~20% of the original memory usage)

Many of these introduce breaking changes so any code written for earlier version will needs some (minor to medium) revisions. If there is anything unclear please reach out.

For a full run down of the changed API use 'cargo-public-api' (this changelog is too big for inclusion here).

v0.9.0-alpha.3

Third alpha release for v0.9.0. This release adds the following major points:

• Safer API for peptides, peptidoforms, and compound peptidoforms

... (truncated)

Commits

• a46afae Updated dependecies and changed code to work for bincode 2.0
• 9d2df43 Version bump
• d43df75 Digest bug fix
• f2a3ee8 Update databases, fixed mzpaf export issues, and fixed clippy and docs lints
• eec5fac Fixed glycan peptide fragmentation for HCD
• 4a10b0b Annotated use of scan number versus scan index
• 6bcd9fb Allow more fasta file extensions
• 2bf79a2 Fixed two small bugs
• 5f2031e Extended CSV parsing for a basic CSV format and possibly keeping the full ine...
• 85cf3b6 Merge branch 'model-extension'
• Additional commits viewable in compare view

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[dependabot]

Superseded by #40.