Alex Lubbock

This is mostly covered by the `Simulator` class. This ticket could be closed when/if those legacy functions are removed in the future. On that note, is there a plan to...

Thanks for the report. It's possible to manually strip out compartments from a model, see the example code below, which you could use like this: `new_model = remove_compartments(model)`. Not sure...

In principle this could be implemented, but we'd have to implement functions to check referential integrity (i.e. check for initials, rules etc. using the monomer, and delete those too).

Not sure if this would work with ipython's autoreload - probably not. Fixing this would probably need some rethinking of the SelfExporter.

@JamesPino There are a few remaining comments on the code review. Please could you either address those or leave a response? Also, it'd be helpful if could you merge against...

I'm proposing to remove `odesolve` and `run_ssa`. While I can see the value in a couple of "quick" simulation functions, `run_ssa`, `odesolve`, and the `Simulator` class have different arguments and...

Hi Rodrigo, glad you found a workaround. One difference between the two simulations is that BNG's SSA is network-based, whereas Kappa is not. Therefore, BioNetGen's output includes all species plus...

Is removing pysb.generator still a goal? This would be fairly straightforward to do.

I think the semantics of using `1` or `ANY` are different here. `R(lr=1, rf=1)` indicates an internal bond between the `lr` and `rf` sites. `R(lr=ANY, rf=ANY)` means that `lr` and...

Shouldn't each test block just start with `Model()` where a new model is defined? Not sure if I'm completely following. Is this still a current issue?