aqua CI and related fixes

[isaacsas]

Adds Aqua test, seems to indicate that #384 is fixed.

@Vilin97 the Aqua test is giving a bunch of method ambiguities coming from the spatial mass action jump constructors. I think the issue is that you have overlapping definitions because of the union type you are using (i.e. multiple constructors cover the case that an input is typeNothing).

method_ambiguity = (kwcall(::NamedTuple, ::Type{SpatialMassActionJump}, srates::B, rs, ns, pmapper) where B<:Union{Nothing, AbstractMatrix} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:61, kwcall(::NamedTuple, ::Type{SpatialMassActionJump}, urates::A, rs, ns, pmapper) where A<:Union{Nothing, AbstractVector} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:73)
method_ambiguity = (SpatialMassActionJump(urates::A, srates::B, rs, ns; scale_rates, useiszero, nocopy) where {A<:Union{Nothing, AbstractVector}, B<:Union{Nothing, AbstractMatrix}} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:53, SpatialMassActionJump(srates::B, rs, ns, pmapper; scale_rates, useiszero, nocopy) where B<:Union{Nothing, AbstractMatrix} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:61)
method_ambiguity = (SpatialMassActionJump(srates::B, rs, ns; scale_rates, useiszero, nocopy) where B<:Union{Nothing, AbstractMatrix} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:67, SpatialMassActionJump(urates::A, rs, ns; scale_rates, useiszero, nocopy) where A<:Union{Nothing, AbstractVector} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:79)
method_ambiguity = (SpatialMassActionJump(srates::B, rs, ns, pmapper; scale_rates, useiszero, nocopy) where B<:Union{Nothing, AbstractMatrix} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:61, SpatialMassActionJump(urates::A, rs, ns, pmapper; scale_rates, useiszero, nocopy) where A<:Union{Nothing, AbstractVector} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:73)
method_ambiguity = (kwcall(::NamedTuple, ::Type{SpatialMassActionJump}, urates::A, srates::B, rs, ns) where {A<:Union{Nothing, AbstractVector}, B<:Union{Nothing, AbstractMatrix}} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:53, kwcall(::NamedTuple, ::Type{SpatialMassActionJump}, srates::B, rs, ns, pmapper) where B<:Union{Nothing, AbstractMatrix} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:61)
method_ambiguity = (kwcall(::NamedTuple, ::Type{SpatialMassActionJump}, srates::B, rs, ns) where B<:Union{Nothing, AbstractMatrix} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:67, kwcall(::NamedTuple, ::Type{SpatialMassActionJump}, urates::A, rs, ns) where A<:Union{Nothing, AbstractVector} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:79)
method_ambiguity = (JumpSet(vj, cj, rj, maj::MassActionJump{S, T, U, V}) where {S<:Number, T, U, V} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/jumps.jl:497, JumpSet(jumps::JumpProcesses.AbstractJump...) @ JumpProcesses ~/.julia/dev/JumpProcesses/src/jumps.jl:512)
method_ambiguity = (rate_at_site(rx, site, smaj::SpatialMassActionJump{Nothing, B, S, U, V}) where {B, S, U, V} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:112, rate_at_site(rx, site, smaj::SpatialMassActionJump{A, Nothing, S, U, V}) where {A, S, U, V} @ JumpProcesses ~/.julia/dev/JumpProcesses/src/spatial/spatial_massaction_jump.jl:116)

We can fix those in a separate PR, for now I just capped the method ambiguities at 8.

[isaacsas]

@ChrisRackauckas do you have any idea why when testing locally on my Mac I only get 8 ambiguities but CI gets 35? Is this platform dependent?

[isaacsas]

I fixed the ambiguities outside of the spatial solver with the exception of the ODE_DEFAULT_NORM one. I don't really understand why we are getting some of these ambiguities since they seem to often be arising from a version of the function defined on abstract types elsewhere, when we are specifying at least one concrete type in our method. I guess I don't quite understand dispatch rules in that case.

[Vilin97]

I fixed the ambiguities coming from spatial stuff in #392. Once this PR is merged, #392 can be reviewed and merged as well.