refactor: move jumpsystem functions to generalized locations

Author: AayushSabharwal

src/problems/jumpproblem.jl

@@ -151,6 +151,18 @@ function (ratemap::JumpSysMajParamMapper{U, V, W})(maj::MassActionJump, newparam
     nothing
 end
 
+# create the initial parameter vector for use in a MassActionJump
+function (ratemap::JumpSysMajParamMapper{
+        U,
+        V,
+        W
+})(params) where {U <: AbstractArray,
+        V <: AbstractArray, W}
+    updateparams!(ratemap, params)
+    [convert(W, value(substitute(paramexpr, ratemap.subdict)))
+     for paramexpr in ratemap.paramexprs]
+end
+
 ##### MTK dispatches for Symbolic jumps #####
 eqtype_supports_collect_vars(j::MassActionJump) = true
 function collect_vars!(unknowns, parameters, j::MassActionJump, iv; depth = 0,

src/systems/codegen.jl

@@ -545,6 +545,31 @@ function assemble_maj(majv::Vector{U}, unknowntoid, pmapper) where {U <: MassAct
     MassActionJump(rs, ns; param_mapper = pmapper, nocopy = true)
 end
 
+function numericrstoich(mtrs::Vector{Pair{V, W}}, unknowntoid) where {V, W}
+    rs = Vector{Pair{Int, W}}()
+    for (wspec, stoich) in mtrs
+        spec = value(wspec)
+        if !iscall(spec) && _iszero(spec)
+            push!(rs, 0 => stoich)
+        else
+            push!(rs, unknowntoid[spec] => stoich)
+        end
+    end
+    sort!(rs)
+    rs
+end
+
+function numericnstoich(mtrs::Vector{Pair{V, W}}, unknowntoid) where {V, W}
+    ns = Vector{Pair{Int, W}}()
+    for (wspec, stoich) in mtrs
+        spec = value(wspec)
+        !iscall(spec) && _iszero(spec) &&
+            error("Net stoichiometry can not have a species labelled 0.")
+        push!(ns, unknowntoid[spec] => stoich)
+    end
+    sort!(ns)
+end
+
 """
     build_explicit_observed_function(sys, ts; kwargs...) -> Function(s)