Merge pull request #442 from isaacsas/var_to_name

Add var_to_name field

HISTORY.md

@@ -1,6 +1,7 @@
 # Breaking updates and feature summaries across releases
 
 ## Catalyst unreleased (master branch) 
+- **BREAKING:** Added support for `@unpack observable_variable = rn` and `rn.observable_variable`. This requires a new inner constructor definition.
 
 ## Catalyst 10.0
 - `ReactionSystem(rxs::Vector{Reaction}, t)` should now work and will infer the

src/networkapi.jl

@@ -1083,8 +1083,12 @@ function validate(rs::ReactionSystem, info::String="")
         end
     end
     timeunits = get_unit(get_iv(rs))
-    rateunits = specunits / timeunits
 
+    # no units for species, time or parameters then assume validated
+    (specunits in (MT.unitless,nothing)) && (timeunits in (MT.unitless,nothing)) && 
+        MT.all_dimensionless(get_ps(rs)) && return true
+
+    rateunits = specunits / timeunits
     for rx in get_eqs(rs)
         rxunits = get_unit(rx.rate)
         for (i,sub) in enumerate(rx.substrates)

src/reactionsystem.jl

@@ -188,6 +188,8 @@ struct ReactionSystem{U <: Union{Nothing,MT.AbstractSystem}} <: MT.AbstractTimeD
     states::Vector
     """Parameter variables. Must not contain the independent variable."""
     ps::Vector
+    """Maps Symbol to corresponding variable."""
+    var_to_name::Dict{Symbol,Any}
     """Equations for observed variables."""
     observed::Vector{Equation}
     """The name of the system"""
@@ -204,24 +206,19 @@ struct ReactionSystem{U <: Union{Nothing,MT.AbstractSystem}} <: MT.AbstractTimeD
     """Non-`Reaction` equations that further constrain the system"""
     constraints::U
 
-    function ReactionSystem(eqs, iv, states, ps, observed, name, systems, defaults, connection_type, csys; 
+    function ReactionSystem(eqs, iv, states, ps, var_to_name, observed, name, systems, defaults, connection_type, csys; 
                             checks::Bool=true, skipvalue=false)
-        iv′     = value(iv)        
-        states′ = skipvalue ? states : value.(MT.scalarize(states))
-        ps′     = skipvalue ? ps : value.(MT.scalarize(ps))
-
         if checks
-            check_variables(states′, iv′)
-            check_parameters(ps′, iv′)
-            # check_units(eqs)    # disable as check the newly generated system below
+            check_variables(states, iv)
+            check_parameters(ps, iv)
         end
-        rs = new{typeof(csys)}(collect(eqs), iv′, states′, ps′, observed, name, systems, defaults, connection_type, csys)
+        rs = new{typeof(csys)}(eqs, iv, states, ps, var_to_name, observed, name, systems, defaults, connection_type, csys)
         checks && validate(rs)
         rs
     end
 end
 
-function ReactionSystem(eqs, iv, species, ps;
+function ReactionSystem(eqs, iv, states, ps;
                         observed = [],
                         systems = [],
                         name = nothing,
@@ -232,10 +229,31 @@ function ReactionSystem(eqs, iv, species, ps;
                         checks = true, 
                         constraints = nothing,
                         skipvalue = false)
+
     name === nothing && throw(ArgumentError("The `name` keyword must be provided. Please consider using the `@named` macro"))
+    sysnames = nameof.(systems)
+    (length(unique(sysnames)) == length(sysnames)) ||
+        throw(ArgumentError("System names must be unique."))
 
-    ReactionSystem(eqs, iv, species, ps, observed, name, systems, defaults, connection_type, 
-                   constraints; checks = checks, skipvalue = skipvalue)
+    if !(isempty(default_u0) && isempty(default_p))
+        Base.depwarn("`default_u0` and `default_p` are deprecated. Use `defaults` instead.", :ReactionSystem, force=true)
+    end
+    defaults = MT.todict(defaults)
+    defaults = Dict{Any,Any}(value(k) => value(v) for (k, v) in pairs(defaults))
+
+    iv′     = value(iv)        
+    states′ = skipvalue ? states : value.(MT.scalarize(states))
+    ps′     = skipvalue ? ps : value.(MT.scalarize(ps))
+    eqs′    = (eqs isa Vector) ? eqs : collect(eqs)
+
+    var_to_name = Dict()
+    MT.process_variables!(var_to_name, defaults, states′)
+    MT.process_variables!(var_to_name, defaults, ps′)
+    MT.collect_var_to_name!(var_to_name, (eq.lhs for eq in observed))
+
+    ReactionSystem(eqs′, iv′, states′, ps′, var_to_name, observed, name, systems, 
+                   defaults, connection_type, constraints; 
+                   checks = checks, skipvalue = skipvalue)
 end
 
 function ReactionSystem(rxs::Vector{<:Reaction}, iv; kwargs...)  

test/reactionsystem.jl

@@ -282,4 +282,11 @@ js = convert(JumpSystem,rs; combinatoric_ratelaws=false)
 rxs = [Reaction(x*t*A*B+y, [A], nothing)]
 @named rs1 = ReactionSystem(rxs, t, [A,B], [x,y])
 @named rs2 = ReactionSystem(rxs, t)
-@test Catalyst.isequal_ignore_names(rs1,rs2)
+@test Catalyst.isequal_ignore_names(rs1,rs2)
+
+@variables t, L(t), H(t)
+obs = [Equation(L, 2*x + y)]
+@named rs3 = ReactionSystem(rxs, t; observed=obs)
+L2 = L
+@unpack L = rs3
+@test isequal(L,L2)