Merge branch 'main' of https://github.com/JuliaGraphs/MultilayerGraphs.jl

Author: InterdisciplinaryPhysicsTeam

docs/src/API.md

@@ -136,7 +136,10 @@ get_symmetric_interlayer(
 ### Multilayer-specific methods
 
 ```@docs
-nodes(mg::MultilayerGraph)
+nodes(mg::AbstractMultilayerGraph)
+nn(mg::AbstractMultilayerGraph) 
+add_node!(mg::AbstractMultilayerGraph, n::Node)
+rem_node!(mg::AbstractMultilayerGraph, n::Node)
 has_vertex(mg::AbstractMultilayerGraph, mv::MultilayerVertex)
 nv(mg::M) where {M <: AbstractMultilayerGraph }
 mv_vertices(mg::AbstractMultilayerGraph)
@@ -165,8 +168,51 @@ is_directed(m::M) where { M <: Type{ <: AbstractMultilayerDiGraph}}
 has_node(mg::AbstractMultilayerGraph, n::Node)
 rem_vertex!(mg::AbstractMultilayerUGraph, V::MultilayerVertex)
 rem_vertex!(mg::AbstractMultilayerDiGraph, V::MultilayerVertex)
+set_metadata!(mg::AbstractMultilayerGraph, mv::MultilayerVertex, metadata::Union{Tuple, NamedTuple}) 
+set_metadata!(mg::AbstractMultilayerDiGraph, src::MultilayerVertex, dst::MultilayerVertex, metadata::Union{Tuple, NamedTuple})
+set_metadata!(mg::AbstractMultilayerUGraph, src::MultilayerVertex, dst::MultilayerVertex, metadata::Union{Tuple, NamedTuple})
+nl(mg::AbstractMultilayerGraph)
+nIn(mg::AbstractMultilayerGraph)
+has_layer(mg::AbstractMultilayerGraph, layer_name::Symbol)
+
+add_layer!(mg::M, new_layer::L; default_interlayers_null_graph::H = SimpleGraph{T}(), default_interlayers_structure::String ="multiplex"
+) where {T,U,G<:AbstractGraph{T},M<:AbstractMultilayerUGraph{T,U},L<:Layer{T,U,G}, H <: AbstractGraph{T}}
+
+add_layer!(
+    mg::M, new_layer::L; default_interlayers_null_graph::H = SimpleGraph{T}(), default_interlayers_structure::String ="multiplex"
+) where {T,U,G<:AbstractGraph{T},M<:AbstractMultilayerDiGraph{T,U},L<:Layer{T,U,G}, H <: AbstractGraph{T}}
+
+specify_interlayer!(
+    mg::M,
+    new_interlayer::In
+) where {T,U,G<:AbstractGraph{T},M<:AbstractMultilayerDiGraph{T,U},In<:Interlayer{T,U,G}}
+
+specify_interlayer!(
+    mg::M,
+    new_interlayer::In
+) where {T,U,G<:AbstractGraph{T},M<:AbstractMultilayerUGraph{T,U},In<:Interlayer{T,U,G}}
 ```
 
+### Representations
+```@docs
+array(atr::AbstractTensorRepresentation)
+WeightTensor{U}
+MetadataTensor{U}
+array(amr::AbstractMatrixRepresentation)
+SupraWeightMatrix{T,U}
+```
+
+### Traits
+```@docs
+is_weighted(g::G) where { G <: AbstractGraph}
+is_weighted(g::G) where {G<:Type{<:AbstractGraph}}
+
+is_meta(g::G) where {G <: AbstractGraph}
+is_meta(g::G) where {G<:Type{<:AbstractGraph}}
+```
+
+
+
 ----------------------------------------------------
 ####################################################
 ----------------------------------------------------
@@ -221,13 +267,11 @@ rem_vertex!(layer::L, v::T) where {T, L <: Layer{T}}
 AbstractInterlayer
 ```
 
-### Traits
-```@docs
-```
 
 ### Multilayer-Specific Methods
 
 ```@docs
+AbstractMultilayerGraph{T <: Integer, U <: Real}
 has_vertex(mg::M, v::T) where {T, M <: AbstractMultilayerGraph{T}}
 vertices(mg::AbstractMultilayerGraph)
 inneighbors(mg::AbstractMultilayerUGraph, v::T) where {T <: Integer, M <: AbstractMultilayerUGraph{T}}
@@ -246,11 +290,14 @@ rem_edge!(mg::M, src::T, dst::T) where {T, M <: AbstractMultilayerGraph{T}
 ### Representations
 ```@docs
 AbstractTensorRepresentation{U}
-array(atr::AbstractTensorRepresentation)
-array(amr::AbstractMatrixRepresentation)
+AbstractMatrixRepresentation{T,U}
 ```
 
-
+### Traits
+```@docs
+IsWeighted{X}
+IsMeta{X}
+```
 
 
 ```@docs

src/abstractmultilayerdigraph.jl

@@ -149,11 +149,11 @@ function set_weight!(mg::M, src::MultilayerVertex, dst::MultilayerVertex, weight
 end
 
 """
-    set_metadata!(mg::M, src::MultilayerVertex{L1}, dst::MultilayerVertex{L2}, metadata::U) where {L1 <: Symbol, L2 <: Symbol, T,U, M <: AbstractMultilayerGraph{T,U}}
+    set_metadata!(mg::AbstractMultilayerDiGraph, src::MultilayerVertex, dst::MultilayerVertex, metadata::Union{Tuple, NamedTuple})
 
 Set the metadata of the edge between `src` and `dst` to `metadata`. Return true if succeeds (i.e. if the edge exists and the underlying graph chosen for the Layer/Interlayer where the edge lies supports metadata at the edge level  under the `IsMeta` trait).
 """
-function set_metadata!(mg::M, src::MultilayerVertex, dst::MultilayerVertex, metadata::Union{Tuple, NamedTuple}) where M <: AbstractMultilayerDiGraph
+function set_metadata!(mg::AbstractMultilayerDiGraph, src::MultilayerVertex, dst::MultilayerVertex, metadata::Union{Tuple, NamedTuple})
     # Get the subgraph descriptor that corresponds to the layer of src and dst
     descriptor = get_subgraph_descriptor(mg, layer(src), layer(dst))
     # If the subgraph descriptor's null graph is true, then the edge does not exist
@@ -198,8 +198,14 @@ end
 
 # Layers and Interlayers
 """
-    add_layer!(mg::M,layer::L; interlayers_type = "multiplex") where { T, U, G<: AbstractGraph{T}, M <: AbstractMultilayerDiGraph{T, U}, L <: Layer{T,U,G}}
-    Add layer `layer` to `mg`.
+    add_layer!(
+        mg::M, 
+        new_layer::L; 
+        default_interlayers_null_graph::H = SimpleGraph{T}(), 
+        default_interlayers_structure::String ="multiplex"
+    ) where {T,U,G<:AbstractGraph{T},M<:AbstractMultilayerDiGraph{T,U},L<:Layer{T,U,G}, H <: AbstractGraph{T}}
+    
+Add layer `layer` to `mg`.
 
 # ARGUMENTS
     
@@ -222,7 +228,10 @@ function add_layer!(
 end
 
 """
-    specify_interlayer!(mg::M, new_interlayer::In; symmetric_interlayer_name::String) where { T, U, G<: AbstractGraph{T}, M <: AbstractMultilayerDiGraph{T, U}, In <: Interlayer{T,U,G}}
+    specify_interlayer!(
+        mg::M,
+        new_interlayer::In
+    ) where {T,U,G<:AbstractGraph{T},M<:AbstractMultilayerDiGraph{T,U},In<:Interlayer{T,U,G}}
 
 Specify the interlayer `new_interlayer` as part of `mg`.
 """

src/abstractmultilayergraph.jl

@@ -44,7 +44,7 @@ nodes(mg::AbstractMultilayerGraph) = [couple[2] for couple in sort(collect(mg.id
 
 Return the number of nodes in `mg`.
 """
-nn(mg::M) where {M<:AbstractMultilayerGraph} = length(nodes(mg))
+nn(mg::AbstractMultilayerGraph) = length(nodes(mg))
 
 """
     has_node(mg::AbstractMultilayerGraph, n::Node)
@@ -54,11 +54,11 @@ Return true if `n` is a node of `mg`.
 has_node(mg::AbstractMultilayerGraph, n::Node) = n in image(mg.idx_N_associations)
 
 """
-    add_node!(mg::M, n::Node)  where {T,U, M <: AbstractMultilayerGraph{T,U}}
+    add_node!(mg::AbstractMultilayerGraph, n::Node)
 
 Add node `n` to `mg`. Return true if succeeds.
 """
-function add_node!(mg::M, n::Node)  where {T,U, M <: AbstractMultilayerGraph{T,U}}
+function add_node!(mg::AbstractMultilayerGraph, n::Node)
     !has_node(mg, n) || return false
 
     maximum_idx = isempty(domain(mg.idx_N_associations)) ?  0 : maximum(domain(mg.idx_N_associations))
@@ -70,11 +70,11 @@ function add_node!(mg::M, n::Node)  where {T,U, M <: AbstractMultilayerGraph{T,U
 end
 
 """
-    rem_node!(mg::M, n::Node)  where {T,U, M <: AbstractMultilayerGraph{T,U}}
+    rem_node!(mg::AbstractMultilayerGraph, n::Node)
 
 Remove node `n` to `mg`. Return true if succeeds.
 """
-function rem_node!(mg::M, n::Node)  where {T,U, M <: AbstractMultilayerGraph{T,U}}
+function rem_node!(mg::AbstractMultilayerGraph, n::Node)
     has_node(mg, n) || return false
 
     idx_tbr = mg.idx_N_associations(n)
@@ -145,11 +145,12 @@ Return the metadata associated to `MultilayerVertex` mv (regardless of metadata
 get_metadata(mg::AbstractMultilayerGraph, mv::MultilayerVertex) = mg.v_metadata_dict[get_v(mg, mv)]
 
 """
-    set_metadata!(mg::M, mv::MultilayerVertex, metadata::Union{Tuple, NamedTuple}) where M <: AbstractMultilayerGraph
+    set_metadata!(mg::AbstractMultilayerGraph, mv::MultilayerVertex, metadata::Union{Tuple, NamedTuple}) 
 
 Set the metadata of vertex `mv` to `metadata`. Return true if succeeds
 """
-function set_metadata!(mg::M, mv::MultilayerVertex, metadata::Union{Tuple, NamedTuple}) where M <: AbstractMultilayerGraph
+function set_metadata!(mg::AbstractMultilayerGraph, mv::MultilayerVertex, metadata::Union{Tuple, NamedTuple}) 
+
     descriptor = mg.layers[get_layer_idx(mg, layer(mv))]#get_subgraph_descriptor(mg, layer(mv))
     is_meta(descriptor.null_graph) || return false
     has_vertex(mg, mv) || return false
@@ -248,18 +249,18 @@ SimpleWeightedGraphs.get_weight(mg::AbstractMultilayerGraph, src::MultilayerVert
 # Layers and Interlayers
 
 """
-    nl(mg::M) where {M <: AbstractMultilayerGraph }
+    nl(mg::AbstractMultilayerGraph)
 
 Return the number of layers in `mg`.
 """
-nl(mg::M) where {M<:AbstractMultilayerGraph} = length(mg.layers)
+nl(mg::AbstractMultilayerGraph) = length(mg.layers)
 
 """
-    nIn(mg::M) where {M <: AbstractMultilayerGraph }
+    nIn(mg::AbstractMultilayerGraph)
 
 Return the number of interlayers in `mg`.
 """
-nIn(mg::M) where {M<:AbstractMultilayerGraph} = length(mg.interlayers)
+nIn(mg::AbstractMultilayerGraph) = length(mg.interlayers)
 
 """
     has_layer(mg::AbstractMultilayerGraph, layer_name::Symbol)

src/abstractmultilayerugraph.jl

@@ -136,11 +136,11 @@ end
 
 
 """
-    set_metadata!(mg::M, src::MultilayerVertex{L1}, dst::MultilayerVertex{L2}, metadata::U) where {L1 <: Symbol, L2 <: Symbol, T,U, M <: AbstractMultilayerGraph{T,U}}
+    set_metadata!(mg::AbstractMultilayerUGraph, src::MultilayerVertex, dst::MultilayerVertex, metadata::Union{Tuple, NamedTuple})
 
 Set the metadata of the edge between `src` and `dst` to `metadata`. Return true if succeeds (i.e. if the edge exists and the underlying graph chosen for the Layer/Interlayer where the edge lies supports metadata at the edge level  under the `IsMeta` trait).
 """
-function set_metadata!(mg::M, src::MultilayerVertex, dst::MultilayerVertex, metadata::Union{Tuple, NamedTuple}) where M <: AbstractMultilayerUGraph
+function set_metadata!(mg::AbstractMultilayerUGraph, src::MultilayerVertex, dst::MultilayerVertex, metadata::Union{Tuple, NamedTuple})
     descriptor = get_subgraph_descriptor(mg, layer(src), layer(dst))
     is_meta(descriptor.null_graph) || return false
     has_edge(mg, src, dst) ||  return false
@@ -188,7 +188,11 @@ end
 
 # Layers and Interlayers
 """
-    add_layer!(mg::M,layer::L; interlayers_type = "multiplex") where { T, U, G<: AbstractGraph{T}, M <: AbstractMultilayerUGraph{T, U}, L <: Layer{T,U,G}}
+    add_layer!( mg::M,
+        new_layer::L; 
+        default_interlayers_null_graph::H = SimpleGraph{T}(), 
+        default_interlayers_structure::String ="multiplex"
+    ) where {T,U,G<:AbstractGraph{T},M<:AbstractMultilayerUGraph{T,U},L<:Layer{T,U,G}, H <: AbstractGraph{T}}
 
 Add layer `layer` to `mg`.
 
@@ -213,7 +217,10 @@ function add_layer!(
 end
 
 """
-    specify_interlayer!(mg::M, new_interlayer::In; symmetric_interlayer_name::String) where { T, U, G<: AbstractGraph{T}, M <: AbstractMultilayerUGraph{T, U}, In <: Interlayer{T,U,G}}
+    specify_interlayer!(
+        mg::M,
+        new_interlayer::In
+    ) where {T,U,G<:AbstractGraph{T},M<:AbstractMultilayerUGraph{T,U},In<:Interlayer{T,U,G}}
 
 Specify the interlayer `new_interlayer` as part of `mg`.
 """