Modification of print of models + renaming macro for creation of models in...

Modification of print of models + renaming macro for creation of models in order to be more inclusive.

core/MarkovProcesses.jl

@@ -41,14 +41,14 @@ export load_model, load_automaton, load_plots
 export automaton_abc, abc_smc
 
 # About biochemical networks
-export @biochemical_network
+export @network_model
 
 include("common.jl")
 include("trajectory.jl")
 include("lha.jl")
 include("model.jl")
 include("utils.jl")
-include("biochemical_network.jl")
+include("network_model.jl")
 include("../algorithms/abc_smc.jl")
 
 end

core/model.jl

@@ -378,6 +378,10 @@ function Base.show(io::IO, m::ContinuousTimeModel)
     for i in eachindex(m.g)
         print(io, "* $(m.g[i]) (idx = $i in observed state space)\n")
     end
+    print(io, "p = $(m.p)\n")
+    print(io, "x0 = $(m.x0) (in full state space)\n")
+    print(io, "t0 = $(m.t0)\n")
+    print(io, "time bound = $(m.time_bound)")
 end
 
 isbounded(m::Model) = get_proba_model(m).time_bound < Inf

core/biochemical_network.jl → core/network_model.jl

@@ -35,7 +35,7 @@ function get_str_propensity(propensity::Symbol, dict_species::Dict, dict_params:
     return str_propensity
 end
 
-macro biochemical_network(expr_network,expr_name...)
+macro network_model(expr_network,expr_name...)
     model_name = isempty(expr_name) ? "Unnamed macro generated" : expr_name[1]
     transitions = String[]
     dict_species = Dict{String,Int}()

tests/run_unit.jl

@@ -26,7 +26,7 @@ using Test
     @test include("unit/load_module.jl")
     @test include("unit/long_sim_er.jl")
     
-    @test include("unit/macro_biochemical_network.jl")
+    @test include("unit/macro_network_model.jl")
     @test include("unit/model_prior.jl")
     @test include("unit/models_exps_er_1d.jl")
     @test include("unit/observe_all.jl")

tests/unit/macro_biochemical_network.jl → tests/unit/macro_network_model.jl

 
 using MarkovProcesses 
 
-model_SIR = @biochemical_network begin
+model_SIR = @network_model begin
     R1: (S+I => 2I, ki*S*I)
     R2: (I => R, kr*I)
 end "SIR"
 set_x0!(model_SIR, [95,5,0])
 set_param!(model_SIR, [0.012, 0.05])
 
-model_unnamed_SIR = @biochemical_network begin
+model_unnamed_SIR = @network_model begin
     R1: (S+I => 2I, ki*S*I)
     R2: (I => R, kr*I)
 end
 set_x0!(model_unnamed_SIR, [95,5,0])
 set_param!(model_unnamed_SIR, [0.012, 0.05])
 
-model_ER = @biochemical_network begin
+model_ER = @network_model begin
     R1: (E+S => ES, k1*E*S)
     R2: (ES => E+S, k2*ES)
     R3: (ES => E+P, k3*ES)
@@ -26,17 +26,17 @@ set_param!(model_ER, [1.0,1.0,1.0])
 return true
 
 #=
-@biochemical_network "test1" begin
+@network_model "test1" begin
     R1: (S+I => 2I+Z,  ki*S*I)
     R2: (I => R, kr*I)
 end
 
-@biochemical_network "test2" begin
+@network_model "test2" begin
     R1: (S+I => 2I,  ki*S*I)
     R2: (I => R, kr*I)
 end
 
-@biochemical_network "test3" begin
+@network_model "test3" begin
     R1: (S+I => I,  ki)
     R2: (2I => R, kr*I*c)
 end