Sam Isaacson

Per Slack discussion with @ChrisRackauckas, opening an issue about the need to have an interface for users to get at the `W` operator components. In my case I have a...

System transformations sometimes dropping fields

2

This is something that came up as I was looking at adding events into other system types. Maybe this isn't an easy fix, or desired, but right now when new...

Seems like it would be useful to add support for scalar mappings in `varmap_to_vars`: https://discourse.julialang.org/t/error-with-user-defined-rates-in-catalyst-jl/79229/3

correctly handling random variables

7

I'd like to resurrect https://github.com/SciML/ModelingToolkit.jl/pull/942 by @kaandocal, but there are a few issues with general handling of random variables that seemed worth discussing. The idea is that users could write...

substituter error

1

It seems something has changed in `substitute`, breaking `ex2` below ```julia using ModelingToolkit @parameters k @variables t Y(t) ex1 = Symbolics.unwrap(Y^2) ex2 = Symbolics.unwrap(k*Y^2) subber = Symbolics.substituter(Dict(Symbolics.unwrap(Y) => Symbolics.operation(Symbolics.unwrap(Y)))) subber(ex1)...

using StaticArrays increases allocations by a factor of 4

3

This gives about 40MB of allocations, with the allocations scaling linearly in the number of trajectories. @ChrisRackauckas said on Slack this is likely due to allocations in random number generation...

format for short begin end block

4

In Catalyst.jl with SciMLStyle we are seeing that ```julia rn = @reaction_network begin k/$V, A + B --> C end k ``` gets formatted as ```julia rn = @reaction_network begin...

Would be good to add some non-spatial jump tutorials too showing off how to use the newer MassActionJumps and the general lower-level interface. Event handling is something that gets asked...

disallow repeated substrates or products in reactions

2

From https://discourse.julialang.org/t/read-in-network-does-not-match-hard-coded-network/81997/5 ```julia rx = @reaction k, A+A --> B @parameters k @variables t A(t) B(t) rx2 = Reaction(k, [A,A], [B], [1,1], [1]) rx != rx2 # true ``` We...

Sometimes a user might know a conservation law and have a specific notation they want to use for the constant (along with knowing which species they'd want to eliminate). We...