Add methods, tests for QN properties

Author: ReubenJ

Project.toml

@@ -5,19 +5,24 @@ version = "0.1.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
+DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
 FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 HerbCore = "2b23ba43-8213-43cb-b5ea-38c12b45bd45"
 HerbGrammar = "4ef9e186-2fe5-4b24-8de7-9f7291f24af7"
 HerbSearch = "3008d8e8-f9aa-438a-92ed-26e9c7b4829f"
+MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
 MetaGraphsNext = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SoleLogics = "b002da8f-3cb3-4d91-bbe3-2953433912b5"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
+DocStringExtensions = "0.9.3"
 DynamicalSystems = "3"
 FileIO = "1"
+HerbGrammar = "0.4.0"
+MLStyle = "0.4.17"
 MetaGraphsNext = "0.7"
 SoleLogics = "0.9, 0.10"
 Statistics = "1.11.1"

src/GraphDynamicalSystems.jl

@@ -1,14 +1,29 @@
 module GraphDynamicalSystems
 
-using SoleLogics
-using MetaGraphsNext
+using DocStringExtensions
 using DynamicalSystems
+using MetaGraphsNext
+using SoleLogics
+
 
 include("boolean_networks.jl")
 export BooleanNetworks
 
 include("qualitative_networks.jl")
-export QualitativeNetworks
+export QualitativeNetwork,
+    build_qn_grammar,
+    update_functions_to_network,
+    sample_qualitative_network,
+    max_level,
+    components,
+    C,
+    get_state,
+    S,
+    target_functions,
+    T,
+    set_state!,
+    interpret,
+    aqn
 
 # """
 #     gds(bn::MetaGraph)

src/qualitative_networks.jl

@@ -1,10 +1,9 @@
-module QualitativeNetworks
-
 using AbstractTrees: Leaves
 using HerbCore: AbstractGrammar, AbstractRuleNode, RuleNode, get_rule
 using HerbGrammar: @csgrammar, add_rule!
 using HerbSearch
 using MetaGraphsNext: MetaGraph, SimpleDiGraph, add_edge!
+using MLStyle: @match
 
 const base_qn_grammar = @csgrammar begin
     ManyVals = Pos() | Neg()
@@ -77,20 +76,70 @@ function sample_qualitative_network(size::Int, max_eq_depth::Int)
     sample_qualitative_network(entities, max_eq_depth)
 end
 
-mutable struct QualitativeNetwork
+struct QualitativeNetwork
     graph::MetaGraph
     state::AbstractVector{Int}
+    N::Int
+
+    function QualitativeNetwork(g, s, N)
+        if any(s .> N)
+            error("All values in state must be <= N (N=$N)")
+        else
+            return new(g, s, N)
+        end
+    end
 end
 
 const QN = QualitativeNetwork
 
-function qn_step!(model::QN) end
+function max_level(qn::QN)
+    return qn.N
+end
+
+function _get_component_index(qn::QN, component::Symbol)
+    return findfirst(isequal(component), components(qn))
+end
+
+function components(qn::QN)
+    return labels(qn.graph)
+end
+
+C(qn::QN) = components(qn)
+
+function target_functions(qn::QN)
+    return qn.graph.vertex_properties
+end
+
+T(qn::QN) = target_functions(qn)
+
+get_state(qn::QN) = qn.state
+
+function get_state(qn::QN, component::Symbol)
+    i = _get_component_index(qn, component)
+    return qn.state[i]
+end
+
+S(qn::QN) = qn.state
+S(qn::QN, component::Symbol) = get_state(qn, component)
+
+function _set_state!(qn::QN, component::Symbol, value::Integer)
+    i = _get_component_index(qn::QN, component::Symbol)
+    qn.state[i] = value
+end
+
+function set_state!(qn::QN, component::Symbol, value::Integer)
+    if value > max_level(qn)
+        error(
+            "Value ($value) cannot be larger than the QN's maximum level (N=$(max_level(qn)))",
+        )
+    end
+
+    _set_state!(qn, component, value)
+end
 
 extract_state(model::QN) = model.state
 extract_parameters(model::QN) = model.graph
 
 function reset_model!(model::QN, u, _)
     model.state .= u
 end
-
-end

test/test-qn.jl

@@ -1,14 +1,16 @@
 using Graphs: ne, nv
+using GraphDynamicalSystems
+using HerbCore
 
 @testset "QN Grammar Creation" begin
     entities = [:a, :b, :c]
     constants = [i for i = 1:10]
-    g = QualitativeNetworks.build_qn_grammar(entities, constants)
+    g = build_qn_grammar(entities, constants)
 
     @test issubset(Set(entities), Set(g.rules))
     @test issubset(Set(constants), Set(g.rules))
 
-    g2 = QualitativeNetworks.build_qn_grammar(Symbol[], Integer[])
+    g2 = build_qn_grammar(Symbol[], Integer[])
 
     @test isempty(intersect(Set(g2.rules), Set(entities)))
     @test isempty(intersect(Set(g2.rules), Set(constants)))
@@ -17,7 +19,27 @@ end
 @testset "QN Sampling" begin
     size = 3
     max_eq_depth = 3
-    qn = QualitativeNetworks.sample_qualitative_network(size, max_eq_depth)
+    qn = sample_qualitative_network(size, max_eq_depth)
     @test nv(qn.graph) == size
     @test ne(qn.graph) > 0
 end
+
+@testset "QN properties, fields" begin
+    size = 3
+    max_eq_depth = 3
+    N = 5
+    network = sample_qualitative_network(size, max_eq_depth)
+    initial_state = ones(size)
+    qn = QualitativeNetwork(network, initial_state, N)
+
+    @test length(components(qn)) == size
+    @test length(C(qn)) == size
+
+    @test length(target_functions(qn)) == size
+    @test length(T(qn)) == size
+    @test all(depth(T(qn)) .<= max_eq_depth)
+
+    @test all(get_state(qn) .<= max_level(qn))
+
+    @test_throws r"max" set_state!(qn, Symbol(1), 6)
+end