forgot a bunch of files related to the last commit

bench/pkg/catalyst.jl

@@ -15,6 +15,7 @@ ER.buffer_size = 100
 ER.estim_min_states = 8000
 
 bench1_pkg = @benchmark simulate(ER)
+@btime simulate(ER)
 @show minimum(bench1_pkg), mean(bench1_pkg), maximum(bench1_pkg)
 
 rs = @reaction_network begin
@@ -31,6 +32,7 @@ jprob = JumpProblem(rs, dprob, Direct())
 jsol = solve(jprob, SSAStepper())
 
 bench1_catalyst = @benchmark solve(jprob, SSAStepper())
+@btime solve(jprob, SSAStepper())
 @show minimum(bench1_catalyst), mean(bench1_catalyst), maximum(bench1_catalyst)
 
 str_latex_bench1 = "

core/MarkovProcesses.jl

 module MarkovProcesses
 
+## Imports
 import Base: +, -, *
 import Base: copy, getfield, getindex, getproperty, lastindex
 import Base: setindex!, setproperty!, fill!, copyto!
 
-import Distributed: @everywhere, @distributed
-import Distributions: Distribution, Product, Uniform, Normal
 import Dates
+import Distributed: @everywhere, @distributed
+import Distributions: Product, Uniform, Normal
+import Distributions: Distribution, Univariate, Continuous, UnivariateDistribution, 
+                      MultivariateDistribution, product_distribution
 import StaticArrays: SVector
 
+## Exports
 export Distribution, Product, Uniform, Normal
 
 # Common types and constructors

core/common.jl

 
-import Distributions: Distribution, Univariate, Continuous, UnivariateDistribution, 
-                      MultivariateDistribution, product_distribution
 
 abstract type Model end 
 abstract type ContinuousTimeModel <: Model end
 abstract type AbstractTrajectory end
 
+abstract type LHA end
+abstract type Edge end
+
 const VariableModel = Symbol
 const ParameterModel = Symbol
 const Transition = Union{Symbol,Nothing}
@@ -42,27 +43,21 @@ struct Trajectory <: AbstractTrajectory
     transitions::Vector{Transition}
 end
 
-#=
-struct Edge
-    transitions::Union{Nothing,Vector{Symbol}}
-    check_constraints::Function
-    update_state!::Function
-end
-=#
-abstract type Edge end
-
-struct LHA
-    name::String
-    transitions::Vector{Transition}
-    locations::Vector{Location} 
-    Λ::Dict{Location,Function}
-    locations_init::Vector{Location}
-    locations_final::Vector{Location}
-    map_var_automaton_idx::Dict{VariableAutomaton,Int} # nvar keys : str_var => idx in values
-    flow::Dict{Location,Vector{Float64}} # output of length nvar
-    map_edges::Dict{Location, Dict{Location,Vector{Edge}}}
-    constants::Dict{Symbol,Float64}
-    map_var_model_idx::Dict{VariableModel,Int} # of dim d (of a model)
+function generate_code_lha_type_def(lha_name::Symbol, edge_type::Symbol)
+    return quote
+        struct $(lha_name) <: LHA
+            transitions::Vector{Transition}
+            locations::Vector{Location} 
+            Λ::Dict{Location,Function}
+            locations_init::Vector{Location}
+            locations_final::Vector{Location}
+            map_var_automaton_idx::Dict{VariableAutomaton,Int} # nvar keys : str_var => idx in values
+            flow::Dict{Location,Vector{Float64}} # output of length nvar
+            map_edges::Dict{Location, Dict{Location,Vector{$(edge_type)}}}
+            constants::Dict{Symbol,Float64}
+            map_var_model_idx::Dict{VariableModel,Int} # of dim d (of a model)
+        end
+    end
 end
 
 mutable struct StateLHA
@@ -123,9 +118,9 @@ function generate_code_model_type_constructor(model_name::Symbol)
     end
 end
 
-LHA(A::LHA, map_var::Dict{VariableModel,Int}) = LHA(A.name, A.transitions, A.locations, A.Λ, 
-                                                    A.locations_init, A.locations_final, A.map_var_automaton_idx, A.flow,
-                                                    A.map_edges, A.constants, map_var)
+LHA(A::LHA, map_var::Dict{VariableModel,Int}) = 
+getfield(Main, Symbol(typeof(A)))(A.transitions, A.locations, A.Λ, A.locations_init, A.locations_final, 
+                                  A.map_var_automaton_idx, A.flow, A.map_edges, A.constants, map_var)
 
 Base.:*(m::ContinuousTimeModel, A::LHA) = SynchronizedModel(m, A)
 Base.:*(A::LHA, m::ContinuousTimeModel) = SynchronizedModel(m, A)

core/network_model.jl

@@ -145,7 +145,7 @@ macro network_model(expr_network,expr_name...)
     # Creation of names variables
     model_name = isempty(expr_name) ? "Network" : expr_name[1]
     model_name = Symbol(replace(model_name, ' ' => '_') * "Model")
-    id = Dates.format(Dates.now(), "YmHMs")
+    id = MarkovProcesses.newid()
     nbr_reactions = length(list_expr_reactions)
     basename_func = "$(model_name)_$(id)"
     basename_func = replace(basename_func, '-'=>'_')

core/utils.jl

@@ -27,3 +27,5 @@ load_model(name_model::String) = Base.MainInclude.include("$(get_module_path())/
 load_automaton(automaton::String) = Base.MainInclude.include("$(get_module_path())/automata/$(automaton).jl")
 load_plots() = Base.MainInclude.include(get_module_path() * "/core/plots.jl")
 
+newid() = Dates.format(Dates.now(), "YmHMs")
+