Julianus Pfeuffer

I think we should revise our release checklist: - Mark 90%+ things for automation and start implementing - Remove things we barely ever do (cpplint?) - Deprecate things (upload to...

New Doxygen theme still not displaying parameters correctly

2

 either the CSS update did not work, or something else is wrong.

Combine same modification for different amino acids in CometAdapter

57

See the related issue (#6200) and its comments.

Nightly pypi repo

17

Promised by Tübingen almost 2 years ago. Would be much cleaner than letting people download from actions artifacts..

Upload wheels in action to new pypi server and update docu

4

https://abi-services.informatik.uni-tuebingen.de/pypi/ document usage on pyopenms-docs document setup of pypi server on internal docu pages

Brew boost links to ICU by default

1

Brew dropped support for ALL options in ALL formulae. -> ICU support is the default for boost -> Linking to static boost means linking to ICU (without having any warning...

Support more metadata from MGF format (e.g. from GNPS)

1

And parse things like IONMODE, SMILES, SPECTRUMID etc for spectra. Ionmode probably has a counterpart in spectra metadata. SMILES would probably be a user parameter. Spectrum ID is important too....

libicu has no rpath (anymore?) on linux

13

-> the different icu libraries will not find themselves if in non-standard locations (e.g. after copying to knime plugin)

Update to Qt6

6

Qt5.15 LTS is only for commercial customers. If we are lucky and Qt stays generous, they will release them open source 1 year after commercial release but I don't want...

SiriusAdapter has weird parameter handling of defaults

1

It uses an empty string and -1 to omit passing parameters to the underlying Sirius executable. Therefore empty and -1 are used in our interface to specify that the default...