MsReport v0.0.29 - Optional R dependencies and Ion ID support

Released: 2025-04-30

This release makes the R interface optional, allowing MsReport to be used without requiring an R installation. To enable statistical analysis with LIMMA, install MsReport with the optional dependency group [R] and follow the installation instructions in the README.

A new "Ion ID" column has been added to ion and ion evidence tables. This column serves as a unique identifier for each ion entry and is intended to be used as the id_column when creating a Qtable instance.

Changelog

Added

• Added reader.FragPipeReader.import_psm_evidence() to concatenate all PSM tables from a FragPipe result folder into a single table.
• Added a unique "Ion ID" column to ion and ion evidence tables from all supported tools (FragPipe, MaxQuant, Spectronaut), which is generated by concatenating "Modified sequence", "Charge", and optionally "Compensation voltage".
  • The "Ion ID" column is meant to be used as id_column when creating a Qtable instance.

Dependencies

• Made the R interface optional by moving rpy2 to optional dependencies
  • Install with pip install msreport[R] to enable statistical analysis with LIMMA
• Added optional test dependencies for running tests with GitHub actions
• Dropped Python 3.9 support, now requires Python 3.10+

Internal

• Added automated testing via GitHub Actions
• Improved README structure, documentation of features, and installation instructions
• Added release dates to CHANGELOG entries