GDS <: DiscreteDynamicalSystem

.github/workflows/Lint.yml

@@ -27,7 +27,7 @@ jobs:
             - name: Use Julia cache
               uses: julia-actions/cache@v2
             - name: Install JuliaFormatter.jl
-              run: julia -e 'using Pkg; pkg"add JuliaFormatter@1"'
+              run: julia -e 'using Pkg; pkg"add JuliaFormatter@2"'
             - name: Setup Python
               uses: actions/setup-python@v6
               with:

Project.toml

@@ -1,43 +1,31 @@
 name = "GraphDynamicalSystems"
 uuid = "13529e2e-ed53-56b1-bd6f-420b01fca819"
+version = "0.0.7"
 authors = ["Reuben Gardos Reid <5456207+ReubenJ@users.noreply.github.com>"]
-version = "0.0.6"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
-AutoHashEquals = "15f4f7f2-30c1-5605-9d31-71845cf9641f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
-HerbConstraints = "1fa96474-3206-4513-b4fa-23913f296dfc"
-HerbCore = "2b23ba43-8213-43cb-b5ea-38c12b45bd45"
-HerbGrammar = "4ef9e186-2fe5-4b24-8de7-9f7291f24af7"
-HerbSearch = "3008d8e8-f9aa-438a-92ed-26e9c7b4829f"
-JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 MetaGraphsNext = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
-StructUtils = "ec057cc2-7a8d-4b58-b3b3-92acb9f63b42"
+TermInterface = "8ea1fca8-c5ef-4a55-8b96-4e9afe9c9a3c"
 
 [compat]
 AbstractTrees = "0.4.5"
-AutoHashEquals = "2.2.0"
 DocStringExtensions = "0.9.3"
 DynamicalSystemsBase = "3.10"
 Graphs = "1.12"
-HerbConstraints = "0.4"
-HerbCore = "0.3.4"
-HerbGrammar = "0.6"
-HerbSearch = "0.4.1"
-JSON = "1"
 MLStyle = "0.4.17"
 MacroTools = "0.5.16"
 MetaGraphsNext = "0.7"
 Random = "1.10"
 SciMLBase = "2.74.1"
 StaticArrays = "1.9.12"
-StructUtils = "2.5.1"
+TermInterface = "2.0.0"
 julia = "1.10"

src/GraphDynamicalSystems.jl

@@ -3,32 +3,9 @@ module GraphDynamicalSystems
 using DocStringExtensions
 
 include("gds_interface.jl")
-export GraphDynamicalSystem,
-    GDS,
-    ScheduleStyle,
-    Asynchronous,
-    Synchronous,
-    get_n_entities,
-    entities,
-    get_schedule,
-    get_state,
-    get_graph
 
 include("qualitative_networks.jl")
-export QualitativeNetwork,
-    QN,
-    Entity,
-    build_qn_grammar,
-    update_functions_to_interaction_graph,
-    sample_qualitative_network,
-    get_domain,
-    target_functions,
-    interpret,
-    create_qn_system,
-    default_target_function,
-    set_state!,
-    current_parameters
 
-include("io/bma.jl")
+# include("io/bma.jl")
 
 end

src/gds_interface.jl

@@ -1,11 +1,27 @@
-import DynamicalSystemsBase.get_state
+import DynamicalSystemsBase as DSB
 using MetaGraphsNext: labels
 
+public ScheduleStyle,
+    Asynchronous,
+    Synchronous,
+    GraphDynamicalSystem,
+    GDS,
+    get_n_entities,
+    get_schedule,
+    get_graph,
+    get_domain,
+    get_fn
+
 abstract type ScheduleStyle end
 struct Asynchronous <: ScheduleStyle end
 struct Synchronous <: ScheduleStyle end
 
-abstract type GraphDynamicalSystem{N,S} end
+# A GDS is a DiscreteTimeDynamicalSystem where the model is a MetaGraph with
+# functions at each of the vertices in the graph. The parameters of the system
+# include the ranges of each of the entities. The state of the system is just
+# the current value of each of the entities
+
+abstract type GraphDynamicalSystem{N,S} <: DSB.DiscreteTimeDynamicalSystem end
 const GDS = GraphDynamicalSystem
 
 """
@@ -44,11 +60,34 @@ function entities(gds::GDS)
     return collect(labels(get_graph(gds)))
 end
 
+abstract type AbstractEntity end
+
+function get_fn end
+
 """
     $(TYPEDSIGNATURES)
 
 Get the state of the GDS.
 """
-function get_state(gds::GDS)
-    return gds.state
+function DSB.current_state(gds::GDS)
+    g = get_graph(gds)
+    l = labels(g)
+    return DSB.current_state.(getindex.((g,), l))
+end
+
+function DSB.current_state(gds::GDS, entity)
+    g = get_graph(gds)
+    return DSB.current_state(g[entity])
+end
+
+function get_fn(gds::GDS)
+    g = get_graph(gds)
+    l = labels(g)
+    return get_fn.(getindex.((g,), l))
+end
+
+function get_domain(gds::GDS)
+    g = get_graph(gds)
+    l = labels(g)
+    return get_domain.(getindex.((g,), l))
 end