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

v2.11.0

What's Changed

• Replace internal functions by Spectra equivalents by @Adafede in #168
• Update JamesIves/github-pages-deploy-action action to v4.6.3 by @renovate in #169
• Update actions/checkout action to v4 by @renovate in #170
• Update oxsecurity/megalinter action to v8 by @renovate in #171
• Update JamesIves/github-pages-deploy-action action to v4.6.4 by @renovate in #172
• Update JamesIves/github-pages-deploy-action action to v4.6.6 by @renovate in #174
• Update JamesIves/github-pages-deploy-action action to v4.6.7 by @renovate in #175
• Update JamesIves/github-pages-deploy-action action to v4.6.8 by @renovate in #176
• Adding convenience function to change params (fixes #177) by @Adafede in #178
• fix warnings by @Adafede in #179
• Update JamesIves/github-pages-deploy-action action to v4.6.9 by @renovate in #180
• Update JamesIves/github-pages-deploy-action action to v4.7.1 by @renovate in #183
• Update JamesIves/github-pages-deploy-action action to v4.7.2 by @renovate in #184

Full Changelog: 2.10.0...2.11.0

v2.10.0

What's Changed

• Exposing more parameters by @Adafede in #160
• [ImgBot] Optimize images by @imgbot in #161
• [ImgBot] Optimize images by @imgbot in #162
• Various issue fixes by @Adafede in #163
• WIP #140 by @Adafede in #164

Full Changelog: 2.9.6...2.9.10

v2.9.6

What's Changed

• Update docker/build-push-action action to v6 by @renovate in #136
• Update isbang/compose-action action to v2.0.1 by @renovate in #137
• Fixing super old incorrect adducts difference annotation by @Adafede in #143
• Ion species refactoring by @Adafede in #145
• Fix some TODOs by @Adafede in #150
• Neutral loss fix by @Adafede in #151
• Refactor MS1 annotation by @Adafede in #152
• Come back to old working setwd version by @Adafede in #153
• Dev by @Adafede in #154
• Update JamesIves/github-pages-deploy-action action to v4.6.3 by @renovate in #155
• small additions by @Adafede in #156
• Adding translations for cliqueMS (#141) by @Adafede in #157

Full Changelog: 2.9.5...2.9.6

v2.9.5

Full Changelog: 2.9.4...2.9.5

v2.9.4

What's Changed

• Update JamesIves/github-pages-deploy-action action to v4.6.0 by @renovate in #126
• 2.9.4 by @Adafede in #129
• Update JamesIves/github-pages-deploy-action action to v4.6.1 by @renovate in #130

Full Changelog: 2.9.3...2.9.4

v2.9.3

Full Changelog: 2.9.2...2.9.3

v2.9.2

What's Changed

• Update actions/cache action to v4 by @renovate in #117
• [ImgBot] Optimize images by @imgbot in #104
• Update peter-evans/create-pull-request action to v6 by @renovate in #119

Full Changelog: 2.9.1...2.9.2

v2.9.1

What's Changed

• Refactoring parameters by @Adafede in #109

Full Changelog: 2.9.0...2.9.1

v2.9.0

What's Changed

• Refactoring RT matching (#76) by @Adafede in #83
• adding example retention time library (addition to #76, #83) by @Adafede in #84
• Refactor for all default paths to be params (#81) by @Adafede in #85

Full Changelog: 2.8.2...2.9.0