Add simpleabm

[cliffckerr]

Update: SimpleABM now lives at http://github.com/starsimhub/simpleabm. This PR instead provides a fix to StaticNet, so it works with no input arguments.

Implements a SimpleABM module, which is an as-simple-as-reasonable SIR (for now) ABM, including a spatial network.

Definitely not the PR I thought I'd be making now, but I ended up doing this for debugging Starsim's SIR model, and I feel like it might be useful for (a) debugging to know what the "simple" answer should be (eg do my SIR parameters make sense?), (b) rapid prototyping (eg a new network structure), (c) teaching (eg a rough approximation of what Starsim itself is doing).

Closes #124

[daniel-klein]

I don’t think we want to include simpleabm within Starsim. Or the comparison for that matter. Consider as a separate repo?

[cliffckerr]

I've gone back and forth on this, as illustrated by me opening, then closing, then reopening the original issue! But I've long thought something like this could be useful for testing and debugging (as it has been for SIR already, and maybe e.g. different networks down the track). If it would eventually be incorporated in CI tests, then it would be nice to have it in the same repo. But keen for everyone's input!

[kaa2102]

I've found simpleabm to be useful for the purpose of comparison and debugging. Also, the implementation of the SIR calculations are different from the Starsim SIR calculations/methods I observed in tests/test_simple.py + test_sir_epi(). I agree with incorporating this into CI tests.

[daniel-klein]

Including simpleabm as a separate module in the Starsim framework has potential to create significant confusion. It is not compatible with Starsim and gives different answers. I think it belongs as part of our training materials considering it lacks capabilities and performance as required for actual (re)use.

[cliffckerr]

I think that's a good question -- does it give different answers? My feeling is that it should be possible for Starsim (specifically, ss.Sim(diseases='sir', networks='static')) to reproduce the results of SimpleABM, stochastic effects notwithstanding. If it can't, I think that's a bug!

I also have a different feeling about the second part -- a lot (perhaps too much) of "actual" work in epidemiology is done with simple SIR-derived models. I could see SimpleABM having genuine use as a starting point for a simpler and less black-box model. I say this because I was surprised how much participants at the Makerere training liked it (and used it as a starting point for their policy-relevant modeling questions), and I think we have an opportunity to embrace this impulse rather than try to redirect it towards a tool that might be overly complex for their needs.

The question remains whether this belongs in a separate repo, though. I could definitely see an argument that it does, since it's an almost entirely separate codebase (although I do think it would be cool if we could make network objects compatible with either). But I think Starsim and SimpleABM do have an opportunity to strengthen each other if paired -- e.g., for someone who is inclined to use SimpleABM, it lowers the barrier for entry to switch to Starsim.

I also think there's an opportunity to make SimpleABM a little less simple and more flexible/performant -- but that is probably not on the critical path here, unless we want to more formally support this for use in the upcoming training for less technically focused participants.

[daniel-klein]

Agree it's useful, it just doesn't belong within the Starsim framework repo.

[RomeshA]

If it was in this repo, then putting it somewhere like the tests folder would make more sense, it is quite confusing for it to sit at the top alongside starsim. But I think a separate repo under starsimhub would be my preference too

[menriquez-IDM]

Maybe having a starsim-sandbox or starsim-samples will be a good place to share implementations like this. I see a lot of value on keeping them around in a visible spot.