diff --git a/Project.toml b/Project.toml index 7a2c271..70bd502 100644 --- a/Project.toml +++ b/Project.toml @@ -6,7 +6,7 @@ version = "0.2.0" [deps] AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634" +DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4" FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6" HerbConstraints = "1fa96474-3206-4513-b4fa-23913f296dfc" @@ -22,7 +22,7 @@ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [compat] AbstractTrees = "0.4.5" DocStringExtensions = "0.9.3" -DynamicalSystems = "3" +DynamicalSystemsBase = "3.13.2" FileIO = "1" Graphs = "1.12" HerbConstraints = "0.2.4" @@ -32,6 +32,6 @@ HerbSearch = "0.4.1" MLStyle = "0.4.17" MetaGraphsNext = "0.7" Random = "1.10" -SoleLogics = "0.12" +SoleLogics = "0.12.0" Statistics = "1.10" julia = "1.6" diff --git a/src/GraphDynamicalSystems.jl b/src/GraphDynamicalSystems.jl index 5c7d84c..025dc64 100644 --- a/src/GraphDynamicalSystems.jl +++ b/src/GraphDynamicalSystems.jl @@ -1,9 +1,6 @@ module GraphDynamicalSystems using DocStringExtensions -using DynamicalSystems -using MetaGraphsNext -using SoleLogics include("boolean_networks.jl") diff --git a/src/boolean_networks.jl b/src/boolean_networks.jl index 11b48dd..a051a8a 100644 --- a/src/boolean_networks.jl +++ b/src/boolean_networks.jl @@ -6,7 +6,7 @@ module BooleanNetworks using DocStringExtensions using MetaGraphsNext: MetaGraph, add_edge!, SimpleDiGraph, nv, labels -using DynamicalSystems: ArbitrarySteppable +using DynamicalSystemsBase: ArbitrarySteppable using SoleLogics: Formula, Atom, diff --git a/src/qualitative_networks.jl b/src/qualitative_networks.jl index 799a18c..78fefbe 100644 --- a/src/qualitative_networks.jl +++ b/src/qualitative_networks.jl @@ -1,12 +1,13 @@ -import DynamicalSystems: get_state, set_state! +import DynamicalSystemsBase: get_state, set_state! using AbstractTrees: Leaves +using DynamicalSystemsBase: ArbitrarySteppable +using HerbConstraints: addconstraint!, DomainRuleNode, VarNode, Ordered, Forbidden using HerbCore: AbstractGrammar, RuleNode, get_rule using HerbGrammar: add_rule!, rulenode2expr, @csgrammar -using HerbConstraints: addconstraint!, DomainRuleNode, VarNode, Ordered, Forbidden -using HerbSearch +using HerbSearch: rand using MLStyle: @match -using MetaGraphsNext: MetaGraph, SimpleDiGraph, add_edge!, nv +using MetaGraphsNext: MetaGraph, SimpleDiGraph, add_edge!, nv, labels base_qn_grammar = @csgrammar begin Val = Val + Val diff --git a/test/Project.toml b/test/Project.toml index 1d74f2e..26c35ac 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -1,6 +1,6 @@ [deps] Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595" -DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634" +DynamicalSystemsBase = "6e36e845-645a-534a-86f2-f5d4aa5a06b4" Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6" HerbCore = "2b23ba43-8213-43cb-b5ea-38c12b45bd45" JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b" diff --git a/test/test-bn.jl b/test/test-bn.jl index e587db0..e81b43d 100644 --- a/test/test-bn.jl +++ b/test/test-bn.jl @@ -1,5 +1,5 @@ using MetaGraphsNext: nv, MetaGraph -using DynamicalSystems: trajectory +using DynamicalSystemsBase: trajectory using SoleLogics: cnf, AbstractSyntaxStructure, LeftmostLinearForm, ∧ @testset "Boolean Network Sampling" begin diff --git a/test/test-qn.jl b/test/test-qn.jl index 0006f28..0189333 100644 --- a/test/test-qn.jl +++ b/test/test-qn.jl @@ -1,5 +1,4 @@ -using DynamicalSystems -using GraphDynamicalSystems +using DynamicalSystemsBase: step!, get_state, set_state! using Graphs: ne, nv @testset "QN Grammar Creation" begin