Remove `pygeos` dependency

[LucaMarconato]

As pointed out here https://github.com/ckmah/bento-tools/pull/104#discussion_r1454146578, we should be able to drop the pygeos dependency. We need to try it out.

Also this could be a solution to this behavior: https://github.com/scverse/spatialdata/issues/272.

[leoschwarz]

Hi, thank you for your work on spatialdata. I think it would be great if pygeos could be removed as a dependency in the next release, because currently it prevents the installation with Python 3.12 since it uses some config parse related functionality that was removed from Python.

I haven't tested the full effects of removing it yet.