NEWS.md

v0.3.16 by jan.lisec@bam.de (2026-04-14)

• plot_spec() can modify size of depicted chemical structures
• plot_spec() better handles xlim and ylim when user zoomes
• UI elements in output section are better structured
• test data results are shown upon startup (precalculated)

v0.3.10 by jan.lisec@bam.de (2026-03-30)

• plot_spec() function is now exported (it allows to overlay chemical structures on a spectrum plot)
• minor fix correcting the position of SMILES subplots (had been shifted to the right plot border on Server)

v0.3.9 by jan.lisec@bam.de (2026-01-29)

• minor modifications to trigger update on server shn01

v0.3.8 by jan.lisec@bam.de (2026-01-28)

• spectra intensities can be scaled to a user selected maximum value
• invalid formula/adduct combinations are removed upon import
• stereo isomer intensities are combined and only the highest isomer formula is kept/depicted
• spectra table shows formula and adduct additionally

v0.3.7 by jan.lisec@bam.de (2026-01-22)

• several improvements regarding the shiny app
• plot output for spectra improved a lot, i.e. isomeric peaks are combined now, neutral losses are computed between fragments in addition to the precursor, annotation can be omitted for minor peaks, all sum formulas are depicted using subscript for numbers to improve readability, font size was increased
• Help page received some input (very basic, for first time users)

v0.3.6 by jan.lisec@bam.de

• read_fiora() now exported function
• result can be converted to object of class Spectra (see Spectra package)
• result can be written to a file path only (no console output)
• parallel conda environments for different FIORA versions are now supported by using the conda_name parameter in install_fiora()

v0.3.5 by jan.lisec@bam.de

• CRAN badge
• modified module of selectInputWithButtons to be better tested

v0.3.4 by jan.lisec@bam.de

• App GUI improved (better selection of individual results)
• default python environment switched to conda

v0.3.3 by jan.lisec@bam.de

• run_script gains an argument fmt which allows to export results in a data frame
• additional test_that tests implemented to prepare for CRAN release

v0.3.2 by jan.lisec@bam.de

• included test_data object in the package
• modified the run_script() function to accept a data frame with multiple lines as input

v0.3.1 by jan.lisec@bam.de

• updated to fiora model 1.0.1
• increased resolution of spectra plots in app
• allowed to use different fiora models (from different python environments) in function run_script()

v0.2.5 by jan.lisec@bam.de

• neutral losses shown in spectra plots
• sum formulas corrected for H number using the adduct annotation of fiora
• sum formulas scaled to comparable size in spectra plots

v0.2.4 by jan.lisec@bam.de

• predict() renamed to run_script()
• detection of python and script path platform specific
• script evaluation platform specific

v0.2.3 by jan.lisec@bam.de

• script path hardcoded; reticulate not used

v0.2.2 by jan.lisec@bam.de

• moved reticulate to Suggest in Description if python installation and script is found

v0.2.1 by jan.lisec@bam.de

• modified fiora installation using a conda environment

v0.1.1 by jan.lisec@bam.de

• Shiny App working on shinyapps.io
• local function predict is working
• spectrum plot is showing formulas and molecular structures
• several testthat tests implemented
• ReadMe and News.md set up

v0.0.0.9000 by jan.lisec@bam.de

• initial GitHub submission