From 4162776bdfec66c952d6ce508449600eea827825 Mon Sep 17 00:00:00 2001
From: Mahmoud Bentriou <mahmoud.bentriou@centralesupelec.fr>
Date: Sun, 6 Dec 2020 14:40:26 +0100
Subject: [PATCH] Modification of print of models + renaming macro for creation
of models in order to be more inclusive.
---
core/MarkovProcesses.jl | 4 ++--
core/model.jl | 4 ++++
core/{biochemical_network.jl => network_model.jl} | 2 +-
tests/run_unit.jl | 2 +-
...biochemical_network.jl => macro_network_model.jl} | 12 ++++++------
5 files changed, 14 insertions(+), 10 deletions(-)
rename core/{biochemical_network.jl => network_model.jl} (99%)
rename tests/unit/{macro_biochemical_network.jl => macro_network_model.jl} (73%)
diff --git a/core/MarkovProcesses.jl b/core/MarkovProcesses.jl
index f344999..623d1fd 100644
--- a/core/MarkovProcesses.jl
+++ b/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
diff --git a/core/model.jl b/core/model.jl
index be93b4d..edae92b 100644
--- a/core/model.jl
+++ b/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
diff --git a/core/biochemical_network.jl b/core/network_model.jl
similarity index 99%
rename from core/biochemical_network.jl
rename to core/network_model.jl
index 3ae5b5f..2c578ef 100644
--- a/core/biochemical_network.jl
+++ b/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}()
diff --git a/tests/run_unit.jl b/tests/run_unit.jl
index f12a930..c37422c 100644
--- a/tests/run_unit.jl
+++ b/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")
diff --git a/tests/unit/macro_biochemical_network.jl b/tests/unit/macro_network_model.jl
similarity index 73%
rename from tests/unit/macro_biochemical_network.jl
rename to tests/unit/macro_network_model.jl
index 1329597..9644a0e 100644
--- a/tests/unit/macro_biochemical_network.jl
+++ b/tests/unit/macro_network_model.jl
@@ -1,21 +1,21 @@
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
--
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