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Avoid errors when calling .get_conn_flattened with jax array

Vicentini Filippo requested to merge pv/numba into master

Created by: PhilipVinc

Right now if we call .get_conn_flattened with a jax array we have a crash due to a numba bug https://github.com/numba/numba/issues/6980

In this PR we convert everything to numpy before calling numba.

This is useful as when we will remove legacy all states will mostly be jax and not numpy...

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