Unpin rdkit, handle a few other installation issues.

[andrewtarzia]

1. Unpin numpy and rdkit
2. Move installation of mdanalysis and openmm from conda (in just or github actions) into pyproject.toml
3. Adding a logo also.
4. Force sphinx-rtd-theme to >= 0.5.1 to allow for this theme in sphinx>9
5. Found that we cannot use uv until openff moves to pypi
6. Introduced Reintroduce openbabel dependency and tests when it is available in python >= 3.13 #208
7. Handling Handle espaloma_charge dependancy issues #200
8. Handling Make plane parameters accessible #205
9. Cleaned up geometry comparison tests to use saved jsons. Which will need updating if rdkit versions change geometries again.