chore(deps): bump rustyms from 0.8.3 to 0.9.0

[dependabot]

Bumps rustyms from 0.8.3 to 0.9.0.

Release notes

Sourced from rustyms's releases.

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
• Added general open peptides file function
• Added many new identified peptides file formats (MZTab, more peaks versions, deepnovo, powernovo, novob, pgpointnovo, pointnovo, plink, instanovo)
• Many many bug fixes
• Optimised memory usage, mostly for identified peptides file (should expect ~20% of the original memory usage)

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.3p

This is a retry of alpha 3 as the last time the Python release failed.

v0.9.0-alpha.2

This is the second alpha release for v0.9.0. Below are the changes compared to v0.9.0-alpha.1.

• Updated complexity API, any 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
• Fixed some bugs

For all changes since v0.8.3 also see the previous alpha release.

v0.9.0-alpha.1

Alpha release for 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
• More control over fragmentation model
• More identified peptide file formats (now allows Fasta, MaxQuant, MSFragger, Novor, OPair, Peaks, and Sage)
• Updated and somewhat expanded Python bindings

... (truncated)

Commits

• 3ea728b Fixed invalid Python version selection
• 2282b92 fmt
• be8206f Merge issues
• df2f277 Updated version number
• cf3f252 Removed accidentally added file
• 1643e74 Renamed peptidoform types
• 6047b70 Updated IMGT
• 1e06308 Fixed many failing tests
• 0b8d6ff Allow older python versions
• 43ecc27 More control over MUP behaviour
• Additional commits viewable in compare view

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[dependabot]

Dependabot can't resolve your Rust dependency files. Because of this, Dependabot cannot update this pull request.

[dependabot]

Superseded by #22.