tests failing due to issues with shapely and python 3.12

[jlahovnik]

If python 3.12 is used, during the python 3.12 test run several tests are failing due to an error in the shapely library, see for example this failed run: test run

There are 2 possible solutions:

• downgrade numpy to 2.0.1 to ensure compatibility with the current shapely version
• wait for shapely 2.0.6 (containing this PR which should fix the issue) to be released and upgrade to this version

Environment:

• Python version: 3.12

Additional context
Add any other context about the bug here.

[EwoutH]

Shapely 2.0.6 is now released, which resolved the issue with NumPy 2.1.0.

[jlahovnik]

pull request created to enforce the use of shapely 2.0.6