Errors when resuming simulations from storage with recent numba 0.57

[ijpulidos]

Many changes were made in the latest numba release 0.57. Some of them are API breaking changes, specifically we cannot use MakedArrays with numba, they appear to never been supported but now trying to use them is raising an exception with the changes upstream in numba/numba#8597

We are getting these exceptions in our CI in https://github.com/choderalab/perses/actions/runs/5116171967/jobs/9198059420#step:9:858

Note that openmmtools CI is not affected by this, so my guess is that this is something that perses is doing when passing the arguments to openmmtools.multistate.MultiStateSampler especially in the replica mixing as pointed in the previous error.

[ijpulidos]

Now, this makes me realize if this is somewhat related to what @IAlibay is hitting in #696 (comment) since I guess it could be possible that numba is not being used to do the mixing at some point.

[ijpulidos]

So, the problem seems to be present only when resuming the simulations from a checkpoint (from storage), it is indeed an openmmtools issue, but we are just not exhaustively testing all the possibilities of resuming form storage there, I guess.

I'm going to transfer the issue to openmmtools.

[ijpulidos]

Closed via #701