Merge branch 'develop' into qt6

AUTHORS

@@ -75,6 +75,7 @@ the authors tag in the respective file header.
  - Martin Langwisch
  - Mateusz Łącki
  - Mathias Walzer
+ - Matteo Pilz
  - Matthew The
  - Matthias Bernt
  - Michael R. Crusoe
@@ -87,6 +88,7 @@ the authors tag in the respective file header.
  - Patricia Scheil
  - Peter Kunszt
  - Petra Gutenbrunner
+ - Radu Suciu
  - Ralf Gabriels
  - Rene Hussong
  - Ruben Grünberg
@@ -114,4 +116,4 @@ the authors tag in the respective file header.
  - Volker Mosthaf
  - Witold Wolski
  - Xiao Liang
- - Radu Suciu
+ - Yasset Perez-Riverol

CHANGELOG

@@ -13,11 +13,13 @@ PR - Pull Request (on GitHub), i.e. integration of a new feature or bugfix
 #<number>, e.g. #4957 - a reference to an issue or pull request on GitHub, visit e.g. https://github.com/OpenMS/OpenMS/pull/XXXX (replace XXXX with number of interest) for details
 
 ------------------------------------------------------------------------------------------
-----                                OpenMS 3.2     (in development)                   ----
+----                                OpenMS 3.2.0     (under development)              ----
 ------------------------------------------------------------------------------------------
 
 What's new:
-- Breaking change: Rename of parameters for FeatureFinderCentroided (debug->advanced), and PeakPickerWavelet/TOFCalibration (optimization -> optimization:type) (#7154)
+- Changes breaking backwards compatibility: 
+   - Rename of parameters for TOPP tool FeatureFinderCentroided (debug -> advanced), and PeakPickerWavelet/TOFCalibration (optimization -> optimization:type) (#7154)
+   - Rename of parameters for TOPP tool IDFilter (score:pep -> score:psm; score:prot -> score:protein; score:protgroup -> score:proteingroup) with 'nan' as new default (#7541)
 
 Library:
 - Extend FileHandler to support load and store operations for our major datastructures (spectra, features, identifications, etc.). Replaced file type specific code with the more generic FileHandler calls to decouple the IO code from other parts of the library.
@@ -30,11 +32,14 @@ Library:
 
 New Tools:
 - IonMobilityBinning - Merges spectra with similar IM values and creates @p N output mzML's by discretizing the IM range (#7459)
+- AssayGeneratorMetaboSirius -- Assay library generation from a SIRIUS project directory (Metabolomics)
+- SiriusExport -- Metabolite identification using single and tandem mass spectrometry
 
 Fixes:
 - FileConverter: more robust (#7176)
 - MSFragger: allow relative path to database (#7155)
 - MSGFPlusAdapter: allow concurrent creation of indexed database (#7272)
+- CometAdapter: work around bug in Comet 2024.01 rev. 0 to avoid empty results (#7540)
 - ParamEditor: fixed error for the subsection parameter (ParamNode) to go through store function (#7180)
 - TOPPView: fix crash when viewing certain Chromatograms (#7220)
 - TOPPView: in 2D view, show correct adjacent layers in context menu, if user clicked to the right of the last MS1 scan (now shows the 4 rightmost MS1 scans, used to show the 4 leftmost scans) (#7423)
@@ -49,6 +54,8 @@ Misc:
 - Add export for Common Workflow Language (CWL) (#6156)
 - Add tool description lib (TDL) dependency (#6156)
 
+Changed/new parameters: see CHANGELOG_PARAMS for details
+
 Note: The goal of our library is to provide useful, reusable code in a way that’s easy to understand and use.
 To make OpenMS simpler, more focused and more accessible we gradually remove potentially outdated tools and algorithms.
 If you, as a user, are negatively affected by this step please contact us. We listen to our users and will try to find 
@@ -57,14 +64,20 @@ an alternative solution or reverse a particular decision for removal.
 Cleanup/Removal:
 
 - removed tools:
-  - Removed SpectraFilterMarkerMower TOPP tool (#7183)
-  - FeatureFinderIsotopeWavelet
-  - PeakPickerWavelet
-  - PrecursorMassCorrector
-  - TOFCalibration
-  - ERPairFinder
-  - RNPxlSearch
-  - SpectraFilterParentPeakMower
+  - SpectraFilterMarkerMower -- Applies thresholdfilter to peak spectra (#7183)
+  - FeatureFinderIsotopeWavelet -- Detects two-dimensional features in LC-MS data
+  - PeakPickerWavelet -- Finds mass spectrometric peaks in profile mass spectra
+  - PrecursorMassCorrector -- Corrects the precursor entries of MS/MS spectra, by using MS1 information
+  - TOFCalibration -- Applies time of flight calibration
+  - ERPairFinder -- Util which can be used to evaluate pair ratios on enhanced resolution (zoom) scans
+  - RNPxlSearch -- Annotate RNA/DNA-peptide cross-links in MS/MS spectra
+  - SpectraFilterSqrtMower -- Applies thresholdfilter to peak spectra
+  - FeatureFinderMRM -- Detects two-dimensional features in LC-MS data
+  - MapAlignerSpectrum -- Corrects retention time distortions between maps by spectrum alignment
+  - ProteinResolver -- protein inference
+  - SiriusAdapter -- Tool for metabolite identification using single and tandem mass spectrometry
+  - SpectraFilterBernNorm -- Applies thresholdfilter to peak spectra
+  - SpectraFilterScaler -- Applies thresholdfilter to peak spectra
 
 - removed library code:
   - HiddenMarkovModel
@@ -89,6 +102,7 @@ Cleanup/Removal:
 
 - Deprecated (and likely removed in the next release)
   - XTandemAdapter
+
 ------------------------------------------------------------------------------------------
 ----                                OpenMS 3.1     (released 10/2023)                 ----
 ------------------------------------------------------------------------------------------