v2.12.0

What's Changed

• Added automatic retention time conversion (in minutes)
• Added a minimal output
• Added a parameter to limit the numbers of neighbors used for chemical consistency calculation (#193)
• Added MERLIN spectral libraries (#190)
• Added optional compound name from RT libraries
• Added RDKit-based structures processing through reticulate (#19)
• Breaking Change: .RDS spectra are now stored more efficiently. To avoid errors, delete any .RDS files created before version 2.12.0
• Externalized spectral libraries preparation to SpectRalLibRaRies
• Fix memory crashes in case of large number of ties, limiting to 7 with note (#216)
• Introduced similarity method argument (entropy and GNPS for now)
• Implemented GNPS similarity method in C
• Improved high confidence filtering
• Improved logs using logger (#189)
• Keep (only) the best molecular formula and canopus annotations from SIRIUS
• New ISDB version with 1 million compounds (see https://doi.org/10.5281/zenodo.14887271)
• Reduced dependencies and moved some to Suggests
• Refactored adducts parsing to read adducts like [M+H]+/[M]+
• Refactored MS1 annotation step to work per sample (#194)
• Refactored tests
• Renamed some functions/utils for consistency
• Replaced logger with lgr for covr compatibility
• Switched documentation from pkgdown to altdoc
• tima_full() has been deprecated in favor of run_tima()
• Updated to Massbank version 2025.05.1
• Updated minimal R version to 4.4.0 (and related Bioconductor dependencies)

Full Changelog: 2.11.0...2.12.0