switch LightGraphs to Graphs

Author: isaacsas

Project.toml

@@ -16,13 +16,13 @@ Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 DomainSets = "5b8099bc-c8ec-5219-889f-1d9e522a28bf"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
@@ -55,11 +55,11 @@ DiffRules = "0.1, 1.0"
 Distributions = "0.23, 0.24, 0.25"
 DocStringExtensions = "0.7, 0.8"
 DomainSets = "0.5"
+Graphs = "1.4"
 IfElse = "0.1"
 JuliaFormatter = "0.12, 0.13, 0.14, 0.15, 0.16, 0.17, 0.18"
 LabelledArrays = "1.3"
 Latexify = "0.11, 0.12, 0.13, 0.14, 0.15"
-LightGraphs = "1.3"
 MacroTools = "0.5"
 NaNMath = "0.3"
 NonlinearSolve = "0.3.8"

src/ModelingToolkit.jl

@@ -56,7 +56,7 @@ import Symbolics: rename, get_variables!, _solve, hessian_sparsity,
 
 import DiffEqBase: @add_kwonly
 
-import LightGraphs: SimpleDiGraph, add_edge!, incidence_matrix
+import Graphs: SimpleDiGraph, add_edge!, incidence_matrix
 
 using Requires
 

src/bipartite_graph.jl

@@ -8,15 +8,15 @@ export 𝑠vertices, 𝑑vertices, has_𝑠vertex, has_𝑑vertex, 𝑠neighbors
 using DocStringExtensions
 using UnPack
 using SparseArrays
-using LightGraphs
+using Graphs
 using Setfield
 
 ###
 ### Edges & Vertex
 ###
 @enum VertType SRC DST ALL
 
-struct BipartiteEdge{I<:Integer} <: LightGraphs.AbstractEdge{I}
+struct BipartiteEdge{I<:Integer} <: Graphs.AbstractEdge{I}
     src::I
     dst::I
     function BipartiteEdge(src::I, dst::V) where {I,V}
@@ -25,8 +25,8 @@ struct BipartiteEdge{I<:Integer} <: LightGraphs.AbstractEdge{I}
     end
 end
 
-LightGraphs.src(edge::BipartiteEdge) = edge.src
-LightGraphs.dst(edge::BipartiteEdge) = edge.dst
+Graphs.src(edge::BipartiteEdge) = edge.src
+Graphs.dst(edge::BipartiteEdge) = edge.dst
 
 function Base.show(io::IO, edge::BipartiteEdge)
     @unpack src, dst = edge
@@ -65,7 +65,7 @@ badjlist = [[1,2,5,6],[3,4,6]]
 bg = BipartiteGraph(7, fadjlist, badjlist)
 ```
 """
-mutable struct BipartiteGraph{I<:Integer,F<:Vector{Vector{I}},B<:Union{Vector{Vector{I}},I},M} <: LightGraphs.AbstractGraph{I}
+mutable struct BipartiteGraph{I<:Integer,F<:Vector{Vector{I}},B<:Union{Vector{Vector{I}},I},M} <: Graphs.AbstractGraph{I}
     ne::Int
     fadjlist::F # `fadjlist[src] => dsts`
     badjlist::B # `badjlist[dst] => srcs` or `ndsts`
@@ -112,11 +112,11 @@ Base.length(::BipartiteGraph) = error("length is not well defined! Use `ne` or `
 
 @noinline throw_no_back_edges() = throw(ArgumentError("The graph has no back edges."))
 
-if isdefined(LightGraphs, :has_contiguous_vertices)
-    LightGraphs.has_contiguous_vertices(::Type{<:BipartiteGraph}) = false
+if isdefined(Graphs, :has_contiguous_vertices)
+    Graphs.has_contiguous_vertices(::Type{<:BipartiteGraph}) = false
 end
-LightGraphs.is_directed(::Type{<:BipartiteGraph}) = false
-LightGraphs.vertices(g::BipartiteGraph) = (𝑠vertices(g), 𝑑vertices(g))
+Graphs.is_directed(::Type{<:BipartiteGraph}) = false
+Graphs.vertices(g::BipartiteGraph) = (𝑠vertices(g), 𝑑vertices(g))
 𝑠vertices(g::BipartiteGraph) = axes(g.fadjlist, 1)
 𝑑vertices(g::BipartiteGraph) = g.badjlist isa AbstractVector ? axes(g.badjlist, 1) : Base.OneTo(g.badjlist)
 has_𝑠vertex(g::BipartiteGraph, v::Integer) = v in 𝑠vertices(g)
@@ -126,14 +126,14 @@ function 𝑑neighbors(g::BipartiteGraph, j::Integer, with_metadata::Val{M}=Val(
     g.badjlist isa AbstractVector || throw_no_back_edges()
     M ? zip(g.badjlist[j], (g.metadata[i][j] for i in g.badjlist[j])) : g.badjlist[j]
 end
-LightGraphs.ne(g::BipartiteGraph) = g.ne
-LightGraphs.nv(g::BipartiteGraph) = sum(length, vertices(g))
-LightGraphs.edgetype(g::BipartiteGraph{I}) where I = BipartiteEdge{I}
+Graphs.ne(g::BipartiteGraph) = g.ne
+Graphs.nv(g::BipartiteGraph) = sum(length, vertices(g))
+Graphs.edgetype(g::BipartiteGraph{I}) where I = BipartiteEdge{I}
 
 nsrcs(g::BipartiteGraph) = length(𝑠vertices(g))
 ndsts(g::BipartiteGraph) = length(𝑑vertices(g))
 
-function LightGraphs.has_edge(g::BipartiteGraph, edge::BipartiteEdge)
+function Graphs.has_edge(g::BipartiteGraph, edge::BipartiteEdge)
     @unpack src, dst = edge
     (src in 𝑠vertices(g) && dst in 𝑑vertices(g)) || return false  # edge out of bounds
     insorted(𝑠neighbors(src), dst)
@@ -146,8 +146,8 @@ struct NoMetadata
 end
 const NO_METADATA = NoMetadata()
 
-LightGraphs.add_edge!(g::BipartiteGraph, i::Integer, j::Integer, md=NO_METADATA) = add_edge!(g, BipartiteEdge(i, j), md)
-function LightGraphs.add_edge!(g::BipartiteGraph, edge::BipartiteEdge, md=NO_METADATA)
+Graphs.add_edge!(g::BipartiteGraph, i::Integer, j::Integer, md=NO_METADATA) = add_edge!(g, BipartiteEdge(i, j), md)
+function Graphs.add_edge!(g::BipartiteGraph, edge::BipartiteEdge, md=NO_METADATA)
     @unpack fadjlist, badjlist = g
     s, d = src(edge), dst(edge)
     (has_𝑠vertex(g, s) && has_𝑑vertex(g, d)) || error("edge ($edge) out of range.")
@@ -168,7 +168,7 @@ function LightGraphs.add_edge!(g::BipartiteGraph, edge::BipartiteEdge, md=NO_MET
     return true  # edge successfully added
 end
 
-function LightGraphs.add_vertex!(g::BipartiteGraph{T}, type::VertType) where T
+function Graphs.add_vertex!(g::BipartiteGraph{T}, type::VertType) where T
     if type === DST
         if g.badjlist isa AbstractVector
             push!(g.badjlist, T[])
@@ -186,11 +186,11 @@ end
 ###
 ### Edges iteration
 ###
-LightGraphs.edges(g::BipartiteGraph) = BipartiteEdgeIter(g, Val(ALL))
+Graphs.edges(g::BipartiteGraph) = BipartiteEdgeIter(g, Val(ALL))
 𝑠edges(g::BipartiteGraph) = BipartiteEdgeIter(g, Val(SRC))
 𝑑edges(g::BipartiteGraph) = BipartiteEdgeIter(g, Val(DST))
 
-struct BipartiteEdgeIter{T,G} <: LightGraphs.AbstractEdgeIter
+struct BipartiteEdgeIter{T,G} <: Graphs.AbstractEdgeIter
     g::G
     type::Val{T}
 end
@@ -259,7 +259,7 @@ end
 ###
 ### Utils
 ###
-function LightGraphs.incidence_matrix(g::BipartiteGraph, val=true)
+function Graphs.incidence_matrix(g::BipartiteGraph, val=true)
     I = Int[]
     J = Int[]
     for i in 𝑠vertices(g), n in 𝑠neighbors(g, i)

src/structural_transformation/StructuralTransformations.jl

@@ -24,7 +24,7 @@ using ModelingToolkit: ODESystem, AbstractSystem,var_from_nested_derivative, Dif
                        get_postprocess_fbody
 
 using ModelingToolkit.BipartiteGraphs
-using LightGraphs
+using Graphs
 using ModelingToolkit.SystemStructures
 
 using ModelingToolkit.DiffEqBase

src/structural_transformation/codegen.jl

@@ -51,7 +51,7 @@ function torn_system_jacobian_sparsity(sys)
             for var in 𝑠neighbors(graph, teq)
                 # Skip the tearing variables in the current partition, because
                 # we are computing them from all the other states.
-                LightGraphs.insorted(var, v_residual) && continue
+                Graphs.insorted(var, v_residual) && continue
                 deps = get(avars2dvars, var, nothing)
                 if deps === nothing # differential variable
                     @assert !isalgvar(s, var)

src/systems/systemstructure.jl

@@ -9,7 +9,7 @@ import ..ModelingToolkit: isdiffeq, var_from_nested_derivative, vars!, flatten,
     value, InvalidSystemException, isdifferential, _iszero, isparameter,
     independent_variables, isinput
 using ..BipartiteGraphs
-using LightGraphs
+using Graphs
 using UnPack
 using Setfield
 using SparseArrays

test/dep_graphs.jl

@@ -1,5 +1,5 @@
 using Test
-using ModelingToolkit, LightGraphs, DiffEqJump
+using ModelingToolkit, Graphs, DiffEqJump
 
 import ModelingToolkit: value
 

test/structural_transformation/index_reduction.jl

@@ -1,5 +1,5 @@
 using ModelingToolkit
-using LightGraphs
+using Graphs
 using DiffEqBase
 using Test
 using UnPack

test/structural_transformation/utils.jl

@@ -1,6 +1,6 @@
 using Test
 using ModelingToolkit
-using LightGraphs
+using Graphs
 using SparseArrays
 using UnPack