Fix dependency conflict

[CunliangGeng]

Dependency issue when running install-nplinker-deps:

ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.

types-networkx 3.2.1.20240918 requires numpy<2.1.0,>=1.20, but you have numpy 2.1.2 which is incompatible.

• [ ] take into account nplinker, bigscape, networkx, etc requirements on numpy