Heterogeneous lags for networks with delay (#104)

* refactor submodules * remove unused code * set up a simple test * remove internal exports * first attempts * adding type information everywhere * minor * Static Edge promotion is not used anymore * remove history from NetworkDE * tuple syntax not necessary anymore * fixing the tests * simplify tests (minor) * new example with delay * wrap `h`, change function signature * adjustments to new conventions * bump version * test on 1.8 * update docs with DDE * update dde test * Literate compatible example * rename * remove compat * fix arguments * Update tests.yml * Update src/NetworkDiffEq.jl Co-authored-by: Hans Würfel <[email protected]> * Update NetworkDiffEq.jl * Improve docstrings * fix test * Apply suggestions from code review Co-authored-by: Hans Würfel <[email protected]> * hopefully lower docs build time Co-authored-by: Hans Würfel <[email protected]> Closes #39.
JuliaDynamics · Jun 22, 2022 · 9978f01 · 9978f01 · lindnemi · Jun 22, 2022
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diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "NetworkDynamics"
 uuid = "22e9dc34-2a0d-11e9-0de0-8588d035468b"
 authors = ["Frank Hellmann <[email protected]>, Michael Lindner <[email protected]>"]
-version = "0.7.1"
+version = "0.8"
 
 [deps]
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,13 +1,12 @@
 [deps]
 DelayDiffEq = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
 NetworkDynamics = "22e9dc34-2a0d-11e9-0de0-8588d035468b"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SimpleWeightedGraphs = "47aef6b3-ad0c-573a-a1e2-d07658019622"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
-
-[compat]
-Documenter = "0.26"
diff --git a/docs/localmake.jl b/docs/localmake.jl
@@ -3,7 +3,6 @@ julia localmake.jl
 python3 -m http.server --bind localhost
 =#
 
-
 using Pkg
 Pkg.activate(@__DIR__)
 Pkg.develop(PackageSpec(; path=dirname(@__DIR__))) # adds the package this script is called from
@@ -22,6 +21,7 @@ makedocs(; sitename="NetworkDynamics",
                 "accessing_edge_variables.md",
                 "Tutorials" => ["Getting started" => "getting_started_with_network_dynamics.md",
                                 "Directed and weighted graphs" => "directed_and_weighted_graphs.md",
-                                "Delay differential equations" => "getting_started_with_DDEs.md",
+                                "Delay differential equations" => "kura_delay.md",
                                 "Heterogeneous systems" => "heterogeneous_system.md",
-                                "Stochastic differential equations" => "SDEVertex.md"]])
+                                "Stochastic differential equations" => "SDEVertex.md"
+                                ]])
diff --git a/docs/make.jl b/docs/make.jl
@@ -16,7 +16,7 @@ makedocs(; sitename  = "NetworkDynamics",
          "Directed and weighted graphs" => "directed_and_weighted_graphs.md",
          "Heterogeneous systems" => "heterogeneous_system.md",
          "Stochastic differential equations" => "SDEVertex.md",
-         "Delay differential equations" => "getting_started_with_DDEs.md"]])
+         "Delay differential equations" => "kuramoto_delay.md"]])
 
 deploydocs(; repo="github.com/PIK-ICoNe/NetworkDynamics.jl.git",
            devbranch="main")
diff --git a/docs/src/BasicConstructors.md b/docs/src/BasicConstructors.md
@@ -80,7 +80,7 @@ The function then defaults to using the identity as mass matrix and `[:v for i i
 
 ### [`DDEVertex`](@ref)
 
-If a vertex has local dynamics described by a delay differential equation (DDE) the local dynamics need to have the signature `vertexfunction!(dv, v, edges, h_v, p, t)`, where `h_v` are the history values of `v`. Then the `VertexFunction` is constructed as
+If a vertex has local dynamics described by a delay differential equation (DDE) the local dynamics need to have the signature `vertexfunction!(dv, v, edges, h_v, p, t)`, where `h_v` is an automatically generated wrapper of the global history function, providing history values for`v`. Then the `VertexFunction` is constructed as
 
 ```julia
 DDEVertex(vertexfunction!, dim, mass_matrix, sym)
@@ -150,12 +150,12 @@ In this case the function defaults to using the identity matrix as mass matrix a
 
 ### [`StaticDelayEdge`](@ref)
 
-This constructor is used when edge variables depend on past values of the vertex variables. In this case the `edgefunction!` has to accept two additional arguments `h_v_s` and `h_v_d` that hold the history of `v_s` and `v_d`. *Static* means that the edge depends only on the dynamics of the vertices the edge is connected to and not on an internal derivative of the edge variables itself.
+This constructor is used when edge variables depend on past values of the vertex variables. In this case the `edgefunction!` has to accept two additional arguments `h_v_s` and `h_v_d` that hold the (automatically generated) localised history functions of `v_s` and `v_d`. *Static* means that the edge depends only on the dynamics of the vertices the edge is connected to and not on an internal derivative of the edge variables itself.
 
 As an example for such system, we show a diffusive coupling with delay:
 
 ```julia
-edgefunction! = (e, v_s, v_d, h_v_s, h_v_d, p, t) -> e .= 0.1 * (h_v_s .- v_d)
+edgefunction! = (e, v_s, v_d, h_v_s, h_v_d, p, t) -> e .= 0.1 * (h_v_s(t - p) .- v_d)
 ```
 
 The `EdgeFunction` object is constructed as

diff --git a/docs/src/getting_started_with_DDEs.md b/docs/src/getting_started_with_DDEs.md