Fresh QN design

Project.toml

@@ -1,13 +1,12 @@
 name = "GraphDynamicalSystems"
 uuid = "13529e2e-ed53-56b1-bd6f-420b01fca819"
 authors = ["Reuben Gardos Reid <[email protected]>"]
-version = "0.0.2"
+version = "0.0.3"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4"
-FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 HerbConstraints = "1fa96474-3206-4513-b4fa-23913f296dfc"
 HerbCore = "2b23ba43-8213-43cb-b5ea-38c12b45bd45"
@@ -17,15 +16,12 @@ MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
 MetaGraphsNext = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-SoleLogics = "b002da8f-3cb3-4d91-bbe3-2953433912b5"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
-Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
 [compat]
 AbstractTrees = "0.4.5"
 DocStringExtensions = "0.9.3"
 DynamicalSystemsBase = "3.13.2"
-FileIO = "1"
 Graphs = "1.12"
 HerbConstraints = "0.4"
 HerbCore = "0.3.4"
@@ -35,7 +31,5 @@ MLStyle = "0.4.17"
 MetaGraphsNext = "0.7"
 Random = "1.10"
 SciMLBase = "2.74.1"
-SoleLogics = "0.13"
 StaticArrays = "1.9.12"
-Statistics = "1.10"
-julia = "1.6"
+julia = "1.10"

src/GraphDynamicalSystems.jl

@@ -2,20 +2,19 @@ module GraphDynamicalSystems
 
 using DocStringExtensions
 
-
-include("boolean_networks.jl")
-export BooleanNetworks
+include("gds_interface.jl")
+export ScheduleStyle, Asynchronous, Synchronous, get_schedule, get_state, get_graph
 
 include("qualitative_networks.jl")
 export QualitativeNetwork,
     QN,
     build_qn_grammar,
-    update_functions_to_network,
+    update_functions_to_interaction_graph,
     sample_qualitative_network,
-    max_level,
-    components,
+    entities,
+    get_domain,
     target_functions,
     interpret,
-    aqn
+    create_qn_system
 
 end

src/gds_interface.jl

@@ -0,0 +1,54 @@
+import DynamicalSystemsBase.get_state
+using MetaGraphsNext: labels
+
+abstract type ScheduleStyle end
+struct Asynchronous <: ScheduleStyle end
+struct Synchronous <: ScheduleStyle end
+
+abstract type GraphDynamicalSystem{N,S} end
+const GDS = GraphDynamicalSystem
+
+"""
+    $(TYPEDSIGNATURES)
+
+Get the number of entities `N` in the GDS.
+"""
+function get_n_entities(::GDS{N,S}) where {N,S}
+    return N
+end
+
+"""
+    $(TYPEDSIGNATURES)
+
+Get the schedule for the GDS.
+"""
+function get_schedule(::GDS{N,S}) where {N,S}
+    return S
+end
+
+"""
+    $(TYPEDSIGNATURES)
+
+Get the underlying graph of the GDS.
+"""
+function get_graph(gds::GDS)
+    return gds.graph
+end
+
+"""
+    $(TYPEDSIGNATURES)
+
+List all entities in `gds`.
+"""
+function entities(gds::GDS)
+    return collect(labels(get_graph(gds)))
+end
+
+"""
+    $(TYPEDSIGNATURES)
+
+Get the state of the GDS.
+"""
+function get_state(gds::GDS)
+    return gds.state
+end