rename and cleanup

Author: isaacsas

src/ModelingToolkit.jl

@@ -120,7 +120,6 @@ export IntervalDomain, ProductDomain, ⊗, CircleDomain
 export Equation, ConstrainedEquation
 export Operation, Expression, Variable
 export independent_variable, states, parameters, equations 
-export numstates, numparameters, numequations
 
 export calculate_jacobian, generate_jacobian, generate_function
 export calculate_tgrad, generate_tgrad

src/systems/abstractsystem.jl

@@ -203,10 +203,6 @@ function parameters(sys::AbstractSystem,args...)
     rename(x,renamespace(sys.name,newname))()
 end
 
-numstates(sys::AbstractSystem)     = length(states(sys))
-numparameters(sys::AbstractSystem) = length(parameters(sys))
-numequations(sys::AbstractSystem)  = length(equations(sys))
-
 struct AbstractSysToExpr
     sys::AbstractSystem
     states::Vector{Variable}

src/systems/dependency_graphs.jl

@@ -1,19 +1,18 @@
+# variables equations depend on as a vector of vectors of variables
 # each system type should define extract_variables! for a single equation
-function extract_variables(eqs, vars)
+function equation_dependencies(sys::AbstractSystem; variables=states(sys))
+    eqs  = equations(sys)
     deps = Set{Variable}()
     depeqs_to_vars = Vector{Vector{Variable}}(undef,length(eqs))
 
     for (i,eq) in enumerate(eqs)      
-        depeqs_to_vars[i] = collect(extract_variables!(deps, eq, vars))
+        depeqs_to_vars[i] = collect(get_variables!(deps, eq, variables))
         empty!(deps)
     end
 
     depeqs_to_vars
 end
 
-# variables equations depend on as a vector of vectors of variables
-equation_dependencies(sys::AbstractSystem; variables=states(sys)) = extract_variables(equations(sys), variables)
-
 # modeled on LightGraphs SimpleGraph
 mutable struct BipartiteGraph{T <: Integer}
     ne::Int
@@ -41,27 +40,7 @@ end
 # could be made to directly generate graph and save memory
 function asgraph(sys::AbstractSystem; variables=nothing, variablestoids=nothing)
     vs   = isnothing(variables) ? states(sys) : variables    
-    eqdeps = extract_variables(equations(sys), vs)
+    eqdeps = equation_dependencies(sys, variables=vs)
     vtois  = isnothing(variablestoids) ? Dict(convert(Variable, v) => i for (i,v) in enumerate(vs)) : variablestoids
     asgraph(eqdeps, vtois)
 end
-
-# map each variable to the eqs depending on it 
-function variables_to_depeqs(sys::AbstractSystem; equationdeps = nothing, statestoids = nothing)
-    sts   = states(sys)
-    stoi  = isnothing(statestoids) ? Dict(convert(Variable,state) => i for (i,state) in enumerate(sts)) : statestoids
-
-    # map from eqs to states they depend on
-    eqdeps = isnothing(equationdeps) ? equation_dependencies(sys) : equationdeps
-
-    # reverse map and switch to integer indices of states
-    dg = [Vector{Int}() for i = 1:length(sts)]
-    for (k,dep) in enumerate(eqdeps)
-        for state in dep
-            push!(dg[stoi[state]],k)
-        end
-    end
-    foreach(dep -> sort!(dep), dg)
-
-    dg
-end

src/systems/jumps/jumpsystem.jl

@@ -128,12 +128,12 @@ end
 
 
 ### Functions to determine which states a jump depends on
-function extract_variables!(dep, jump::Union{ConstantRateJump,VariableRateJump}, variables)
+function get_variables!(dep, jump::Union{ConstantRateJump,VariableRateJump}, variables)
     foreach(var -> (var in variables) && push!(dep, var), vars(jump.rate))
     dep
 end
 
-function extract_variables!(dep, jump::MassActionJump, variables)
+function get_variables!(dep, jump::MassActionJump, variables)
     jsr = jump.scaled_rates
 
     if jsr isa Variable
@@ -151,6 +151,5 @@ function extract_variables!(dep, jump::MassActionJump, variables)
 end
 
 
-
 ### Functions to determine which states are modified by a given jump