chore(deps): bump rustyms from 0.8.3 to 0.11.0

[dependabot]

Bumps rustyms from 0.8.3 to 0.11.0.

Release notes

Sourced from rustyms's releases.

v0.11.0

This release adds the following major points:

• Added standard proteases (thanks to @​aukeheerdink)
• Refactored and updated identified peptidoform files
  • Added support for opening specific versions and reporting which version was detected
  • Moved all metadata functions to a new trait MetaData
  • Added support for CSV files with a byte order mark (BOM)
• Added and updated many specific identified peptidoform file formats
  • Added support for more FragPipe and MSFragger output files and versions and parsed more of the data
  • Added support for Peaks 13 DIA data
  • Added support for proteoscape
  • Added support for pUniFind
  • Added support for AdaNovo (thanks to @​aukeheerdink)
  • Added support for InstaNovo v1.1.4 (thanks to @​aukeheerdink)
  • Added support for π-HelixNovo (thanks to @​aukeheerdink)
  • Added support for π-PrimeNovo (thanks to @​aukeheerdink)
  • Added support for Casanovo v5 specific flavoured mzTab files
  • Fully parse the de novo sequences from MaxNovo
  • Expanded support for mzTab files, modifications, ambiguous modifications, and proteins
• Added AsRef implementations for Peptidoform to allow more flexibility in the mixing of different complexity levels
• Added a HasPeptidoform trait and used this in the alignments allowing for flexibility in the exact data structures used during the alignment
• Extended neutral losses to allow for multiples, for example two times a water loss can now be expressed as -2H2O instead of -H4O2
• Refactored ppm calculation for higher performance
• Refactored mass based alignment for higher performance (~2x faster!) (thanks to @​gritukan)
• Bumped msrv to 1.88
• Added ambiguous nucleotides to the codon translation code
• Factored out the error handling code into a separate crate, this does change the API slightly but also makes the errors much more correct
• Lots of refactoring and reorganising

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.

... (truncated)

Commits

• b1a6d91 Update dependencies (and rename of custom_error to context_error)
• f6006e8 Updated update databases script to download unimod xml file
• db9d198 Fixed update databases script
• bafdef5 Update databases
• cd3de42 Do not fail fast in github actions
• e7cfc0e Merge pull request #91 from gritukan/main
• 962f589 Optimize alignment dynamic programming by small code restructuring
• 70e84d8 Update alignments test to create the new file to easily accept new behaviour
• b2515cc Merge pull request #88 from gritukan:gritukan/optimize_alignment_dp
• 5a6177f Merge branch 'gritukan/optimize_alignment_dp' of https://github.com/gritukan/...
• Additional commits viewable in compare view

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