This PR updates the matchms dependencies.

python = ">=3.9,<3.13" -> python = ">=3.10,<3.13"
numpy = ">1.22, <1.27" -> numpy = "^2.0"
scipy = ">=1.11" -> scipy = "^1.14.1"
pandas = ">=2.0.3" -> pandas = "^2.2.3"
networkx = ">=3.0" -> networkx = "^3.4.2"
numba = ">=0.57.1,<0.60" -> numba = "^0.60.0"
sparsestack = ">=0.4.1" -> sparsestack = "^0.6.0"

Especially updating the deps of numpy, scipy, numba and pandas will make a big difference.

This closes #639

This will also help with https://github.com/iomega/spec2vec