Julianus Pfeuffer

Hm yes. However, shipping an own dll should actually prevent problems in this case. We usually only had problems with pyarrow clashing with their dll. I would suggest trying some...

Aaah right, missing instruction sets also can cause this issue! Thanks for reporting back.

https://cython.readthedocs.io/en/latest/src/userguide/external_C_code.html#acquiring-and-releasing-the-gil

There is nothing to be done in this repository specifically and it needs to be evaluated first. Also, this issue is not for beginners.

Yes, ideally you would set the [build-system] entry in the project.toml to something like https://tttapa.github.io/py-build-cmake/reference/config.html Then, also specify build dependencies in the toml. No requirements.txt dev/bld anymore. You can have...

Yeah. Right direction. But unless you add the py-build-cmake (link in previous comment but there are probably other alternatives) as a build-backend and make it call our CMake, you still...

I think it needs manual intervention or a new PR. We don't want ANY python script anymore. No get_requires.py, no check_py_requirements.py, ideally even no env.py and setup.py. It should be...

In my opinion, checking dependencies after installing them in the same environment with a fully controlled configuration file just makes no sense. All this trash should be thrown out.

This is however a breaking change and needs update in docs and pyopenms scripts. I was hoping for some more opinions.

The problem is, that this is not about "building" but "installing". So you need to do `pip install pyopenms[full]` now to get what you want.