Julianus Pfeuffer

Update build scripts according to issues with QSQL

4

- For Jenkins make sure that we build everything from contrib EXCEPT sqlite - Update dockerfiles - Update docs - Update CMake to make sure that we never have two...

https://github.com/OpenMS/OpenMS/blob/develop/doc/doxygen/parameters/DefaultParamHandlerDocumenter.cpp Just list more classes that derive from ParamHandler and therefore have parameters to be documented.

Add basic conan support

2

## Description Test with: ```bash pip install conan git clone https://github.com/OpenMS/OpenMS --depth 1 mkdir -p OpenMS/build && cd OpenMS/build conan install --pr ../conanprofiles/static --build missing .. ./cmake/bin/cmake .. ./cmake/bin/cmake --build...

The libSVM data structures are clearly an implementation detail. None of them are present in the API functions. I think we could/should create a SimpleSVM implementation class and only store...

## Description Some tries to cleanup our pyopenms interface. ## Checklist - [ ] Make sure that you are listed in the AUTHORS file - [ ] Add relevant changes...

Currently, it is literally **impossible** to do FDR filtering on group level in pyopenms since there is no way to reset or set protein groups after calling IDFilter::updateProteinGroups(id.grps, id) This...

This can be a big problem since there is code that often uses empty identifiers as "match all".

Do not go through all adducts if use_feature_adduct is set in AMS

2

https://github.com/OpenMS/OpenMS/blob/develop/src/openms/source/ANALYSIS/ID/AccurateMassSearchEngine.cpp#L386

Combine PSMFeatureExtractor and Percolator in PercolatorAdapter

1

see also #3071

Export OpenMS components

2

So that we or developers including OpenMS can choose to find only parts of OpenMS and the dependencies coming with it: OpenMS::Core, OpenMS::GUI etc. See https://cmake.org/cmake/help/git-stage/guide/importing-exporting/index.html#adding-components For existing libraries it...