Update to work with newer Catalyst versions

[kaandocal]

No description provided.

[TorkelE]

Do you have any hunch of when/if this is planned? I am trying to use this in conjecture with MTK/Catalyst, and it would be good to be able to do this on the latest version.

[augustinas1]

HI @TorkelE, hoping to get things updated in the next couple of weeks, sorry for the delay!

[kaandocal]

I've created a fork here - it will print superfluous output for now, but the tests work for Catalyst v14 (except latexify).

[kaandocal]

The relatively new Catalyst API (species indexed by name, not number) will take a bit more work to implement, see the other currently active issue.

[TorkelE]

Sounds great, looking forward to it :)

One though I had, do you ever do anything but

u0 = [...]
u0 = deterministic_IC(u0, moment_eqs)
oprob = ODEProblem(moment_eqs, u0, tspan, ps)

?

I.e. is there a reason that the deterministic_IC call could not be integrated into the ODEProblem call?

[augustinas1]

The function deterministic_IC is supposed to construct deterministic initial conditions so that the molecule numbers at initial time take the specified integer values with probability one. Although this is the most commonly used case, one could consider alternative custom initial conditions, and for this reason I chose to keep the initial condition setup general. It's a good question though, will have a think about integrating deterministic_IC by default but leaving alternative options possible too.

[TorkelE]

Hello, just checking whether updates on if an update is planned? It is a good package, and it would be nice if it remained useful for the wider community. If we can get this to work with latest Catalysts versions and you are OK with it, I was hoping to write a small example of how it could be used and add to the Catalyst docs. I could then link that directly to this package so people could go here for more info. That might also help give MomentClosure.jl more users as well.

[augustinas1]

Hi, sorry, it's been a very busy time, but an update is definitely planned. Hopefully I'll be able to get around to patching it up next week. Thanks for your initiative (and patience) Torkel!

[TorkelE]

No worries! Yeah, things are always busier than one would hope. Looking forward to the update, whenever it drops :)