Update docstrings

Co-Authored-By: Claudio Moroni <[email protected]>
Co-Authored-By: Pietro Monticone <[email protected]>

Author: 3 people

src/abstractmultilayerdigraph.jl

@@ -6,7 +6,6 @@ Abstract type representing an undirected multilayer graph.
 abstract type AbstractMultilayerDiGraph{T,U} <: AbstractMultilayerGraph{T,U} end
 
 # Nodes
-
 # Vertices
 """
     add_vertex!(mg::M, V::MultilayerVertex) where {T, U, M <: AbstractMultilayerDiGraph{T,U}}
@@ -171,7 +170,7 @@ function set_metadata!(mg::AbstractMultilayerDiGraph, src::MultilayerVertex, dst
     return true
 end
 
-# Overloads that make AbstractMultilayerDiGraph an extension of Graphs.jl. These are all well-inferred .
+# Overloads that make AbstractMultilayerDiGraph an extension of Graphs.jl. These are all well-inferred.
 """
     edges(mg::M) where {T,U,M<:AbstractMultilayerDiGraph{T,U}}
 
@@ -378,17 +377,16 @@ Graphs.is_directed(mg::M) where {M<:Type{<:AbstractMultilayerDiGraph}} = true
 
 Return the list of inneighbors of `v` within `mg`.
 """
-function Graphs.inneighbors(
-    mg::M, v::T
-) where {M<:AbstractMultilayerGraph{T,<:Real}} where {T}
+function Graphs.inneighbors(mg::M, v::T
+    ) where {M<:AbstractMultilayerGraph{T,<:Real}} where {T}
 
-_inneighbors = T[]
+    _inneighbors = T[]
 
-for helfedge in mg.badjlist[v]
-    push!(_inneighbors, get_v(mg, vertex(helfedge)))
-end
+    for helfedge in mg.badjlist[v]
+        push!(_inneighbors, get_v(mg, vertex(helfedge)))
+    end
 
-return _inneighbors
+    return _inneighbors
 end
 
 """

src/abstractmultilayergraph.jl

@@ -107,7 +107,7 @@ Base.eltype(::M) where {T,M<:AbstractMultilayerGraph{T}} = T
 
 Return true if `v` is in mg, else false.
 """
-Graphs.has_vertex(mg::M, v::T ) where {T, M <: AbstractMultilayerGraph{T}} = v in domain(mg.v_V_associations) # && !(mg.v_V_associations[v] isa MissingVertex)
+Graphs.has_vertex(mg::M, v::T ) where {T, M <: AbstractMultilayerGraph{T}} = v in domain(mg.v_V_associations) 
 
 """
     has_vertex(mg::AbstractMultilayerGraph, mv::MultilayerVertex) 
@@ -151,7 +151,7 @@ Set the metadata of vertex `mv` to `metadata`. Return true if succeeds
 """
 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))
+    descriptor = mg.layers[get_layer_idx(mg, layer(mv))]
     is_meta(descriptor.null_graph) || return false
     has_vertex(mg, mv) || return false
     mg.v_metadata_dict[get_v(mg, mv)] = metadata
@@ -160,7 +160,6 @@ function set_metadata!(mg::AbstractMultilayerGraph, mv::MultilayerVertex, metada
 
 end
 
-
 # Edges
 """
     edgetype(::M) where {T,U,M<:AbstractMultilayerGraph{T,U}}
@@ -379,40 +378,38 @@ end
 Internal function. It is called by the `specify_interlayer!` API functions.
 """
 function _specify_interlayer!(
- mg::M, new_interlayer::In
-) where {T,U,G<:AbstractGraph{T},M<:AbstractMultilayerGraph{T,U},In<:Interlayer{T,U,G}}
-
- all(in.([new_interlayer.layer_1, new_interlayer.layer_2], Ref(mg.layers_names))) ||
-#  throw(
-#      ErrorException(
-         throw(ErrorException("The new interlayer connects two layers that are not (one or both) part of the multilayer graph. Make sure you spelled the `layer_1` and `layer_2` arguments of the `Interlayer` correctly. Available layers are $(mg.layers_names), found $(new_interlayer.layer_1) and $(new_interlayer.layer_2)."))
-#      ),
-#  )
-
- # Check that it has the correct number of nodes on both layers
- (isempty(setdiff(Set(new_interlayer.layer_1_nodes), Set(nodes(Base.getproperty(mg, new_interlayer.layer_1)))) ) &&  isempty(setdiff(Set(new_interlayer.layer_2_nodes), Set(nodes(Base.getproperty(mg, new_interlayer.layer_2)))) )) || throw(ErrorException("The nodes in the interlayer $(new_interlayer.name) do not correspond to the nodes in the respective layers $(new_interlayer.layer_1) and $(new_interlayer.layer_2). Found $( setdiff(Set(new_interlayer.layer_1_nodes), Set(nodes(Base.getproperty(mg, new_interlayer.layer_1)))) ) and $(setdiff(Set(new_interlayer.layer_2_nodes), Set(nodes(Base.getproperty(mg, new_interlayer.layer_2)))))"))
-
-# A rem_interlayer! function may not exist since there always must be all interlayers. We then proceed to effectively remove the interlayer here
-key = Set([new_interlayer.layer_1, new_interlayer.layer_2])
-if haskey(mg.interlayers, key)
-    existing_interlayer = getproperty(mg, mg.interlayers[key].name)
-
-    for edge in edges(existing_interlayer)
-        rem_edge!(mg, edge)
-    end
-end
+    mg::M, new_interlayer::In
+    ) where {T,U,G<:AbstractGraph{T},M<:AbstractMultilayerGraph{T,U},In<:Interlayer{T,U,G}}
 
-mg.interlayers[Set([new_interlayer.layer_1, new_interlayer.layer_2])] = new_interlayer.descriptor
+    all(in.([new_interlayer.layer_1, new_interlayer.layer_2], Ref(mg.layers_names))) ||
+    #  throw(
+    #      ErrorException(
+            throw(ErrorException("The new interlayer connects two layers that are not (one or both) part of the multilayer graph. Make sure you spelled the `layer_1` and `layer_2` arguments of the `Interlayer` correctly. Available layers are $(mg.layers_names), found $(new_interlayer.layer_1) and $(new_interlayer.layer_2)."))
+    #      ),
+    #  )
 
-for edge in edges(new_interlayer)
-    success = add_edge!(mg, edge)
-    @assert success
-end
+    # Check that it has the correct number of nodes on both layers
+    (isempty(setdiff(Set(new_interlayer.layer_1_nodes), Set(nodes(Base.getproperty(mg, new_interlayer.layer_1)))) ) &&  isempty(setdiff(Set(new_interlayer.layer_2_nodes), Set(nodes(Base.getproperty(mg, new_interlayer.layer_2)))) )) || throw(ErrorException("The nodes in the interlayer $(new_interlayer.name) do not correspond to the nodes in the respective layers $(new_interlayer.layer_1) and $(new_interlayer.layer_2). Found $( setdiff(Set(new_interlayer.layer_1_nodes), Set(nodes(Base.getproperty(mg, new_interlayer.layer_1)))) ) and $(setdiff(Set(new_interlayer.layer_2_nodes), Set(nodes(Base.getproperty(mg, new_interlayer.layer_2)))))"))
 
- return true
-end
+    # A rem_interlayer! function may not exist since there always must be all interlayers. We then proceed to effectively remove the interlayer here
+    key = Set([new_interlayer.layer_1, new_interlayer.layer_2])
+    if haskey(mg.interlayers, key)
+        existing_interlayer = getproperty(mg, mg.interlayers[key].name)
+
+        for edge in edges(existing_interlayer)
+            rem_edge!(mg, edge)
+        end
+    end
 
+    mg.interlayers[Set([new_interlayer.layer_1, new_interlayer.layer_2])] = new_interlayer.descriptor
 
+    for edge in edges(new_interlayer)
+        success = add_edge!(mg, edge)
+        @assert success
+    end
+
+    return true
+end
 
 """
     get_interlayer(
@@ -425,7 +422,6 @@ Return the `Interlayer` between `layer_1` and `layer_2`.
 function get_interlayer(
     mg::AbstractMultilayerGraph, layer_1_name::Symbol, layer_2_name::Symbol
 )
-
     layer_1_name ∈ mg.layers_names || throw(ErrorException("$layer_1_name doesn't belong to the multilayer graph. Available layers are $(mg.layers_names)."))
     layer_2_name ∈ mg.layers_names || throw(ErrorException("$layer_2_name doesn't belong to the multilayer graph. Available layers are $(mg.layers_names)."))
     layer_1_name != layer_2_name || throw(ErrorException("`layer_1` argument is the same as `layer_2`. There is no interlayer between a layer and itself."))
@@ -447,14 +443,12 @@ end
 Return the index of the `Layer` whose name is `layer_name` within `mg.layers`.
 """
 function get_layer_idx(mg::M, layer_name::Symbol) where {T,U,M<:AbstractMultilayerGraph{T,U}}
-
     idx = findfirst(descriptor -> descriptor.name == layer_name, mg.layers)
     if !isnothing(idx)
         return idx
     else
         return nothing
     end 
-
 end
 
 """
@@ -463,15 +457,13 @@ end
 Return the descriptor associated to the interlayer connecting `layer_1` to `layer_2` (or to the Layer named `layer_1` if `layer_1` == `layer_2`)
 """
 function get_subgraph_descriptor(mg::M, layer_1_name::Symbol, layer_2_name::Symbol) where {T,U,M<:AbstractMultilayerGraph{T,U}}
-
     if layer_1_name == layer_2_name
         idx = get_layer_idx(mg, layer_1_name)
         if !isnothing(idx)
             return mg.layers[idx] 
         else
             throw(ErrorException("The multilayer graph does not contain any Layer named $(layer_1_name). Available layers are $(mg.layers_names)."))
         end
-
     else
         layer_1_name ∈ mg.layers_names || throw(ErrorException("$layer_1_name does nto belong to the multilayer graph. Available layers are $(mg.layers_names)."))
         layer_2_name ∈ mg.layers_names ||throw(ErrorException("$layer_2_name does nto belong to the multilayer graph. Available layers are $(mg.layers_names)."))

src/abstractmultilayerugraph.jl

@@ -1,7 +1,3 @@
-# ne
-# has_edge
-# edges
-
 """
     AbstractMultilayerUGraph{T,U} <: AbstractMultilayerGraph{T,U} 
 
@@ -201,7 +197,7 @@ Add layer `layer` to `mg`.
 - `mg::M`: the `MultilayerGraph` which the new layer will be added to;
 - `new_layer::L`: the new `Layer` to add to `mg`;
 - `default_interlayers_null_graph::H = SimpleGraph{T}()`: upon addition of a new `Layer`, all the `Interlayer`s between the new and the existing `Layer`s are immediately created. This keyword argument specifies their `null_graph` See the `Layer` constructor for more information. Defaults to `SimpleGraph{T}()`;
-- `default_interlayers_structure::String = "multiplex"`: The structure of the `Interlayer`s created by deafault. May either be "multiplex" to have diagonally-coupled only interlayers, or "empty" for empty interlayers. Defaults to "multiplex".
+- `default_interlayers_structure::String = "multiplex"`: The structure of the `Interlayer`s created by default. May either be "multiplex" to have diagonally-coupled only interlayers, or "empty" for empty interlayers. Defaults to "multiplex".
 """
 function add_layer!(
     mg::M, new_layer::L; default_interlayers_null_graph::H = SimpleGraph{T}(), default_interlayers_structure::String ="multiplex"