Noise scaling update

[TorkelE]

Updates the noise scaling feature with:

• Ensures that species/variables/parameters introduced by the noise scaling metadata is always properly added to the new system.
• Add additional tests.

[isaacsas]

unwrapping should be handled in the Reaction constructor. We shouldn't be storing things that aren't unwrapped as we don't want to have to think about this internally later on (at least every internal Catalyst function I've written assumes its input is unwrapped as this is the MTK convention).

[TorkelE]

Right now we just use the same convention for Reaction metadata as MTK/Symbolics does for symbolic variables (i.e. metadata is stored as they are provided by the user, if the user sets a metadata as Num it remain as a Num).

If you want we can add a specific routine in the Reaction constructor that checks if there is any noise_scaling metadata, and if it is Num unwraps it at that stage.

[isaacsas]

Does union! not work?

[isaacsas]

Also, can't you use generators to avoid allocating vectors to store the ps and such?

[TorkelE]

I never really knew about union! until I discovered that you use it in a few cases, so not that familiar with it. That said I should start using it, will implement it here.

[TorkelE]

Yeah, I can probably use generators, I think at this stage it was late and I was getting increasingly annoyed at all the effort doing this extra step. Will update to use generators though.

[TorkelE]

actually, I am a little bit uncertain exactly how you suggest we use union! and generators in these cases

[isaacsas]

Suggested change

	ns_syms = [Symbolics.unwrap(sym) for sym in get_variables(ns_expr)]
	ns_ps = filter(ModelingToolkit.isparameter, ns_syms)
	ns_sps = filter(Catalyst.isspecies, ns_syms)
	ns_vs = filter(sym -> !Catalyst.isspecies(sym) && !ModelingToolkit.isparameter(sym), ns_syms)
	# Adds parameters, species, and variables to the `ReactionSystem`.
	if any(!any(isequal(p1, p2) for p2 in get_ps(rs)) for p1 in ns_ps)
	@set! rs.ps = unique([get_ps(rs); ns_ps])
	end
	if any(!any(isequal(sp1, sp2) for sp2 in get_species(rs)) for sp1 in ns_sps)
	sps_new = unique([get_species(rs); ns_sps])
	vs_old = get_unknowns(rs)[length(get_species(rs))+1 : end]
	@set! rs.species = sps_new
	@set! rs.unknowns = [sps_new; vs_old]
	end
	if any(!any(isequal(v1, v2) for v2 in get_unknowns(rs)) for v1 in ns_vs)
	us_new = unique([get_unknowns(rs); ns_vs])
	@set! rs.unknowns = us_new
	end
	end
	ns_syms = [Symbolics.unwrap(sym) for sym in get_variables(ns_expr)]
	ns_ps = Iterators.filter(ModelingToolkit.isparameter, ns_syms)
	ns_sps = Iterators.filter(Catalyst.isspecies, ns_syms)
	ns_vs = Iterators.filter(sym -> !Catalyst.isspecies(sym) && !ModelingToolkit.isparameter(sym), ns_syms)
	# Adds parameters, species, and variables to the `ReactionSystem`.
	@set! rs.ps = union(get_ps(rs), ns_ps])
	sps_new = union(get_species(rs), ns_sps)
	@set! rs.species = sps_new
	vs_old = @view get_unknowns(rs)[length(get_species(rs))+1 : end]
	@set! rs.unknowns = union(sps_new, vs_old, ns_vs)
	end
	end

If this is acceptable and works / tests pass I'm fine with merging after switching to this.