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Merge pull request #116 from JuliaGraphs/main
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@pitmonticone
pitmonticone committed Jan 26, 2023
2 parents c65624d + 5d11642 commit f7cf015
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2 changes: 1 addition & 1 deletion .github/workflows/CI.yml
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Expand Up @@ -20,7 +20,7 @@ jobs:
version:
- '1'
- '1.8'
#- 'nightly'
# - 'nightly'
os:
- ubuntu-latest
- macOS-latest
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2 changes: 1 addition & 1 deletion Project.toml
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@@ -1,7 +1,7 @@
name = "MultilayerGraphs"
uuid = "af984530-d72f-4904-8b81-b992bbbeaf3f"
authors = ["Claudio Moroni <43729990+ClaudMor@users.noreply.github.com>", "Pietro Monticone <38562595+pitmonticone@users.noreply.github.com>"]
version = "1.1.1"
version = "1.1.2"

[deps]
Bijections = "e2ed5e7c-b2de-5872-ae92-c73ca462fb04"
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9 changes: 1 addition & 8 deletions docs/make.jl
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Expand Up @@ -5,13 +5,6 @@ using Graphs
using MultilayerGraphs
using Documenter

#= function end_user_filter(f)
if f isa Function
for method in methods
tv, decls, file, line = arg_decl_parts(m)
end =#

DocMeta.setdocmeta!(
MultilayerGraphs, :DocTestSetup, :(using MultilayerGraphs); recursive=true
)
Expand All @@ -26,7 +19,7 @@ makedocs(;
canonical="https://juliagraphs.org/MultilayerGraphs.jl",
assets=String[],
),
pages=["Home" => "index.md", "API" => "API_organized.md"],
pages=["Home" => "index.md", "API" => "API.md"],
clean=false,
)

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288 changes: 173 additions & 115 deletions docs/src/API_organized.md → docs/src/API.md
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@@ -1,6 +1,6 @@
# API

This page provides a list of exported methods organized by topic and audience. Methods that act on vertices, edges, and layers are grouped together. Some methods are intended for developers who want to use the `Graphs.jl` library as part of their code, while others are meant for end-users. hello
This page provides a list of exported methods organized by topic and audience. Methods that act on vertices, edges, and layers are grouped together. Some methods are intended for developers who want to use the `Graphs.jl` library as part of their code, while others are meant for end-users.

## End-User

Expand Down Expand Up @@ -171,122 +171,70 @@ graph(subgraph::AbstractSubGraph)
### [Multilayer-Specific Methods](@id msm_eu)

```@docs
MultilayerGraph{T,U}
MultilayerDiGraph{T,U}
MultilayerGraph(T::Type{<:Number}, U::Type{<:Number})
MultilayerDiGraph(T::Type{<:Number}, U::Type{<:Number})
MultilayerGraph(
layers::Vector{<:Layer{T,U}},
specified_interlayers::Vector{<:Interlayer{T,U}};
default_interlayers_null_graph::H = SimpleGraph{T}(),
default_interlayers_structure::String="multiplex",
) where {T,U, H <: AbstractGraph{T}}
MultilayerDiGraph(
layers::Vector{<:Layer{T,U}},
specified_interlayers::Vector{<:Interlayer{T,U}};
default_interlayers_null_graph::H = SimpleGraph{T}(),
default_interlayers_structure::String="multiplex",
) where {T,U, H <: AbstractGraph{T}}
MultilayerGraph(
empty_layers::Vector{<:Layer{T,U}},
empty_interlayers::Vector{<:Interlayer{T,U}},
degree_distribution::UnivariateDistribution;
allow_self_loops::Bool = false,
default_interlayers_null_graph::H = SimpleGraph{T}(),
) where {T <: Integer, U <: Real, H <: AbstractGraph{T}}
MultilayerDiGraph(
empty_layers::Vector{<:Layer{T,U}},
empty_interlayers::Vector{<:Interlayer{T,U}},
indegree_distribution::UnivariateDistribution,
outdegree_distribution::UnivariateDistribution;
allow_self_loops::Bool = false,
default_interlayers_null_graph::H = SimpleGraph{T}(),
) where {T <: Integer, U <: Real, H <: AbstractGraph{T}}
MultilayerGraph(
empty_multilayergraph::MultilayerGraph{T,U},
degree_sequence::Vector{<:Integer};
allow_self_loops::Bool = false,
perform_checks::Bool = true
) where {T,U}
MultilayerDiGraph(
empty_multilayerdigraph::MultilayerDiGraph{T,U},
indegree_sequence::Vector{<:Integer},
outdegree_sequence::Vector{<:Integer};
allow_self_loops::Bool = false,
perform_checks::Bool = false
) where {T,U}
SynchronizedEdgeColoredGraph{T,U}
SynchronizedEdgeColoredGraph(
layers::Vector{<:Layer{T,U}},
) where {T,U}
SynchronizedEdgeColoredDiGraph{T,U}
AbstractMultilayerGraph{T <: Integer, U <: Real}
has_node(mg::AbstractMultilayerGraph, n::Node)
nodes(mg::AbstractMultilayerGraph)
nn(mg::AbstractMultilayerGraph)
<!-- add_node!(mg::AbstractMultilayerGraph, n::Node; add_vertex_to_layers::Union{Vector{Symbol}, Symbol}) -->
<!-- rem_node!(mg::AbstractMultilayerGraph, n::Node) -->
nn(mg::AbstractMultilayerGraph)
has_vertex(mg::AbstractMultilayerGraph, mv::MultilayerVertex)
nv(mg::M) where {M <: AbstractMultilayerGraph }
mv_vertices(mg::AbstractMultilayerGraph)
get_metadata(mg::AbstractMultilayerGraph, mv::MultilayerVertex)
set_metadata!(mg::AbstractMultilayerGraph, mv::MultilayerVertex, metadata::Union{Tuple, NamedTuple})
mv_inneighbors(mg::AbstractMultilayerGraph, mv::MultilayerVertex)
mv_outneighbors(mg::AbstractMultilayerGraph, mv::MultilayerVertex)
mv_neighbors( mg::AbstractMultilayerGraph, mv::MultilayerVertex)
<!-- add_vertex!(mg::AbstractMultilayerGraph, mv::MultilayerVertex; add_node::Bool) -->
<!-- rem_vertex!(mg::AbstractMultilayerUGraph, V::MultilayerVertex) -->
<!-- rem_vertex!(mg::AbstractMultilayerDiGraph, V::MultilayerVertex) -->
has_edge(mg::AbstractMultilayerGraph, edge::MultilayerEdge)
has_edge( subgraph::AbstractMultilayerGraph, s::MultilayerVertex, d::MultilayerVertex)
has_edge(mg::AbstractMultilayerGraph, src::MultilayerVertex, dst::MultilayerVertex)
ne(mg::AbstractMultilayerGraph)
<!-- edges(mg::AbstractMultilayerUGraph) -->
<!-- edges(mg::M) where {T,U,M<:AbstractMultilayerUGraph{T,U}} -->
edges(mg::M) where {T,U,M<:AbstractMultilayerGraph{T,U}; IsDirected{M}}
edges
edges(::Type{IsDirected{M}}, mg::M) where {T, U, M<:AbstractMultilayerGraph{T, U}}
edges(::Type{Not{IsDirected{M}}}, mg::M) where {T, U, M<:AbstractMultilayerGraph{T, U}}
add_edge!(mg::M, src::V, dst::V; weight::Union{Nothing, U} = one(U), metadata::Union{Tuple,NamedTuple} = NamedTuple() ) where {T,U, M <: AbstractMultilayerGraph{T,U}, V <: MultilayerVertex}
add_edge!(mg::M, me::E) where {T,U, M <: AbstractMultilayerGraph{T,U}, E <: MultilayerEdge{ <: Union{U,Nothing}}}
rem_edge!(mg::AbstractMultilayerGraph, me::MultilayerEdge)
rem_edge!(mg::MultilayerGraph, src::MultilayerVertex, dst::MultilayerVertex)
rem_edge!(mg::MultilayerDiGraph, src::MultilayerVertex, dst::MultilayerVertex)
get_metadata(mg::AbstractMultilayerGraph, mv::MultilayerVertex)
get_metadata(mg::AbstractMultilayerGraph, src::MultilayerVertex, dst::MultilayerVertex)
get_weight(mg::AbstractMultilayerGraph, src::MultilayerVertex, dst::MultilayerVertex)
<!-- set_weight!(mg::M, src::MultilayerVertex, dst::MultilayerVertex, weight::U) where { T,U, M <: AbstractMultilayerUGraph{T,U}}
set_weight!(mg::M, src::MultilayerVertex, dst::MultilayerVertex, weight::U) where {T,U,M<:AbstractMultilayerGraph{T,U}; IsDirected{M}} -->
set_weight!
<!-- is_directed(mg::AbstractMultilayerUGraph) -->
<!-- is_directed(m::M) where { M <: Type{ <: AbstractMultilayerUGraph}} -->
<!-- is_directed(mg::AbstractMultilayerDiGraph)
is_directed(m::M) where { M <: Type{ <: AbstractMultilayerDiGraph}} -->
has_node(mg::AbstractMultilayerGraph, n::Node)
<!-- 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}) -->
set_metadata!
set_weight!(::Type{SimpleTraits.Not{Graphs.IsDirected{M}}}, mg::M, src::MultilayerVertex, dst::MultilayerVertex, weight::U) where {T, U, M<:AbstractMultilayerGraph{T, U}}
set_weight!(::Type{Graphs.IsDirected{M}}, mg::M, src::MultilayerVertex, dst::MultilayerVertex, weight::U) where {T, U, M<:AbstractMultilayerGraph{T, U}}
set_metadata!(::Type{SimpleTraits.Not{Graphs.IsDirected{M}}}, mg::M, src::MultilayerVertex, dst::MultilayerVertex, metadata::Union{Tuple, NamedTuple}) where {M<:AbstractMultilayerGraph}
set_metadata!(::Type{Graphs.IsDirected{M}}, mg::M, src::MultilayerVertex, dst::MultilayerVertex, metadata::Union{Tuple, NamedTuple}) where {M<:AbstractMultilayerGraph}
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!
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},
L<:Layer{T,U,G},
H<:AbstractGraph{T},
M<:MultilayerGraph{T,U}
}
add_layer!(
mg::M,
new_layer::L;
default_interlayers_null_graph::H=SimpleDiGraph{T}(),
default_interlayers_structure::String="multiplex",
) where {
T,
U,
G<:AbstractGraph{T},
L<:Layer{T,U,G},
H<:AbstractGraph{T},
M<:MultilayerDiGraph{T,U}
}
specify_interlayer!(::Type{SimpleTraits.Not{Graphs.IsDirected{M}}}, mg::M, new_interlayer::In) where {T, U, G<:Graphs.AbstractGraph{T}, In<:Interlayer{T, U, G}, M<:MultilayerGraph{T, U}}
specify_interlayer!(::Type{Graphs.IsDirected{M}}, mg::M, new_interlayer::In) where {T, U, G<:Graphs.AbstractGraph{T}, In<:Interlayer{T, U, G}, M<:MultilayerDiGraph{T, U}}
get_interlayer(
mg::AbstractMultilayerGraph, layer_1_name::Symbol, layer_2_name::Symbol
Expand All @@ -299,7 +247,9 @@ indegree(mg::AbstractMultilayerGraph, vs::AbstractVector{<:MultilayerVertex}=ver
outdegree(mg::AbstractMultilayerGraph, mv::MultilayerVertex)
outdegree(mg::AbstractMultilayerGraph, vs::AbstractVector{<:MultilayerVertex}=vertices(mg))
degree(mg::AbstractMultilayerGraph, vs::AbstractVector{<:MultilayerVertex}=vertices(mg))
degree(mg::AbstractMultilayerGraph, vs::AbstractVector{<:MultilayerVertex})
degree(::Type{Graphs.IsDirected{M}}, mg::M, mv::V) where {M<:AbstractMultilayerGraph, V<:MultilayerVertex}
degree(::Type{SimpleTraits.Not{Graphs.IsDirected{M}}}, mg::M, v::V) where {M<:AbstractMultilayerGraph, V<:MultilayerVertex}
mean_degree(mg::AbstractMultilayerGraph)
Expand Down Expand Up @@ -327,9 +277,125 @@ modularity(
) where {T,U,M<:AbstractMultilayerGraph{T,U}}
<!-- von_neumann_entropy(mg::M) where {T,U,M<:AbstractMultilayerUGraph{T,U}} -->
von_neumann_entropy(::Type{SimpleTraits.Not{Graphs.IsDirected{M}}}, mg::M) where {T, U, M<:AbstractMultilayerGraph{T, U}}
```

### Concrete Multilayer Graphs
#### [(General) Multilayer Graphs](@id General_Multilayer_Graphs_eu)
##### [MultilayerGraph](@id Multilayer_Graph)
```@docs
MultilayerGraph{T,U}
MultilayerGraph(T::Type{<:Number}, U::Type{<:Number})
MultilayerGraph(
layers::Vector{<:Layer{T,U}},
specified_interlayers::Vector{<:Interlayer{T,U}};
default_interlayers_null_graph::H = SimpleGraph{T}(),
default_interlayers_structure::String="multiplex",
) where {T,U, H <: AbstractGraph{T}}
MultilayerGraph(
empty_layers::Vector{<:Layer{T,U}},
empty_interlayers::Vector{<:Interlayer{T,U}},
degree_distribution::UnivariateDistribution;
allow_self_loops::Bool = false,
default_interlayers_null_graph::H = SimpleGraph{T}(),
) where {T <: Integer, U <: Real, H <: AbstractGraph{T}}
MultilayerGraph(
empty_multilayergraph::MultilayerGraph{T,U},
degree_sequence::Vector{<:Integer};
allow_self_loops::Bool = false,
perform_checks::Bool = true
) where {T,U}
add_node!(mg::MultilayerGraph, n::Node; add_vertex_to_layers)
rem_node!(mg::MultilayerGraph, n::Node)
add_vertex!(mg::MultilayerGraph, mv::MultilayerVertex; add_node::Bool=true)
rem_vertex!(mg::MultilayerGraph, V::MultilayerVertex)
add_edge!(mg::M, me::E) where {T, U, M<:MultilayerGraph{T, U}, E<:(MultilayerEdge{<:Union{Nothing, U}})}
rem_edge!(mg::MultilayerGraph, src::MultilayerVertex, dst::MultilayerVertex)
is_directed(mg::M) where {M<:Type{<:MultilayerGraph}}
```
##### [MultilayerDiGraph](@id Multilayer_Di_Graph_eu)
```@docs
MultilayerDiGraph{T,U}
MultilayerDiGraph(T::Type{<:Number}, U::Type{<:Number})
MultilayerDiGraph(
layers::Vector{<:Layer{T,U}},
specified_interlayers::Vector{<:Interlayer{T,U}};
default_interlayers_null_graph::H = SimpleGraph{T}(),
default_interlayers_structure::String="multiplex",
) where {T,U, H <: AbstractGraph{T}}
MultilayerDiGraph(
empty_layers::Vector{<:Layer{T,U}},
empty_interlayers::Vector{<:Interlayer{T,U}},
indegree_distribution::UnivariateDistribution,
outdegree_distribution::UnivariateDistribution;
allow_self_loops::Bool = false,
default_interlayers_null_graph::H = SimpleGraph{T}(),
) where {T <: Integer, U <: Real, H <: AbstractGraph{T}}
MultilayerDiGraph(
empty_multilayerdigraph::MultilayerDiGraph{T,U},
indegree_sequence::Vector{<:Integer},
outdegree_sequence::Vector{<:Integer};
allow_self_loops::Bool = false,
perform_checks::Bool = false
) where {T,U}
add_node!(mg::MultilayerDiGraph, n::Node; add_vertex_to_layers)
rem_node!(mg::MultilayerDiGraph, n::Node)
add_vertex!(mg::MultilayerDiGraph, mv::MultilayerVertex; add_node::Bool=true)
rem_vertex!(mg::MultilayerDiGraph, V::MultilayerVertex)
add_edge!(mg::M, me::E) where {T, U, M<:MultilayerDiGraph{T, U}, E<:(MultilayerEdge{<:Union{Nothing, U}})}
rem_edge!(mg::MultilayerDiGraph, src::MultilayerVertex, dst::MultilayerVertex)
is_directed(mg::M) where {M<:Type{<:MultilayerDiGraph}}
```

#### [Node Aligned Edge Colored Graphs](@id Node_Aligned_Edge_Colored_Graphs_eu)
```@docs
AbstractNodeAlignedEdgeColoredGraph
add_node!(mg::AbstractNodeAlignedEdgeColoredGraph, n::Node)
rem_node!(mg::AbstractNodeAlignedEdgeColoredGraph, n::Node)
add_edge!(mg::M, me::E) where {T, U, M<:AbstractNodeAlignedEdgeColoredGraph{T, U}, E<:(MultilayerEdge{<:Union{Nothing, U}})}
rem_edge!(mg::AbstractNodeAlignedEdgeColoredGraph, src::MultilayerVertex, dst::MultilayerVertex)
add_layer!(mg::M, new_layer::L) where {T, U, G<:Graphs.AbstractGraph{T}, L<:Layer{T, U, G}, M<:AbstractNodeAlignedEdgeColoredGraph{T, U}}
```
##### [NodeAlignedEdgeColoredGraph](@id Node_Aligned_Edge_Colored_Graph_eu)
```@docs
NodeAlignedEdgeColoredGraph{T,U}
NodeAlignedEdgeColoredGraph(layers::Vector{<:Layer{T,U}}) where {T,U}
is_directed(mg::M) where {M<:Type{<:NodeAlignedEdgeColoredGraph}}
```

##### [NodeAlignedEdgeColoredDiGraph](@id Node_Aligned_Edge_Colored_Di_Graph_eu)
```@docs
NodeAlignedEdgeColoredDiGraph{T,U}
NodeAlignedEdgeColoredDiGraph(layers::Vector{<:Layer{T,U}}) where {T,U}
is_directed(mg::M) where {M<:Type{<:NodeAlignedEdgeColoredDiGraph}}
```


### [Representations](@id representations_eu)
```@docs
array(atr::AbstractTensorRepresentation)
Expand Down Expand Up @@ -415,25 +481,18 @@ AbstractInterlayer
### [Multilayer-Specific Methods](@id msm_dev)

```@docs
AbstractMultilayerGraph{T <: Integer, U <: Real}
fadjlist
has_vertex(mg::M, v::T) where {T, M <: AbstractMultilayerGraph{T}}
vertices(mg::AbstractMultilayerGraph)
<!-- inneighbors(mg::M, v::T) where {T,M<:AbstractMultilayerUGraph{T,<:Real}} -->
inneighbors(mg::M, v::T) where {T, M<:AbstractMultilayerGraph{T,<:Real}}
inneighbors(::Type{SimpleTraits.Not{Graphs.IsDirected{M}}}, mg::M, v::T) where {T, M<:AbstractMultilayerGraph}
inneighbors(::Type{Graphs.IsDirected{M}}, mg::M, v::T) where {T, M<:AbstractMultilayerGraph}
inneighbors(mg::AbstractMultilayerGraph, mv::MultilayerVertex)
outneighbors(mg::M, v::T) where {T, M<:AbstractMultilayerGraph{T}}
neighbors(mg::AbstractMultilayerGraph, mv::MultilayerVertex)
edgetype(::M) where {T,U,M<:AbstractMultilayerGraph{T,U}}
<!-- has_edge(mg::M, src::T, dst::T) where { T, M <: AbstractMultilayerUGraph{T}}
has_edge(mg::M, src::T, dst::T) where {T,M<:AbstractMultilayerGraph{T}; IsDirected{M}} -->
has_edge
add_edge!(mg::M,src::T,dst::T;weight::Union{Nothing,U}=one(U),metadata::Union{Tuple,NamedTuple}=NamedTuple(),) where {T,U,M<:AbstractMultilayerGraph{T,U}}
rem_edge!(mg::M, src::T, dst::T) where {T, M <: AbstractMultilayerGraph{T}
<!-- AbstractMultilayerUGraph{T,U} -->
<!-- AbstractMultilayerDiGraph{T,U} -->
AbstractMultiplexUGraph
AbstractMultiplexDiGraph
has_edge(::Type{Not{IsDirected{M}}}, mg::M, src::T, dst::T) where {T, M<:(AbstractMultilayerGraph{T})}
has_edge(::Type{IsDirected{M}}, mg::M, src::T, dst::T) where {T, M<:(AbstractMultilayerGraph{T})}
add_edge!(mg::M, src::T, dst::T; weight, metadata) where {T, U, M<:AbstractMultilayerGraph{T, U}}
rem_edge!(mg::M, src::T, dst::T) where {T, M<:(AbstractMultilayerGraph{T})}
```

### [Representations](@id representations_dev)
Expand All @@ -446,5 +505,4 @@ AbstractMatrixRepresentation{T,U}
```@docs
IsWeighted{X}
IsMeta{X}
IsMultiplex{X}
```
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