Migrate from LightGraphs to Graphs.jl (#41)

simonschoelly · web-flow · commit 065eebdcc186 · 2021-10-20T18:43:56.000+02:00
* Migrate from LightGraphs to Graphs.jl
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -61,7 +61,7 @@ jobs:
           julia --project=docs -e '
             using Documenter: DocMeta, doctest
             using SimpleValueGraphs
-            DocMeta.setdocmeta!(SimpleValueGraphs, :DocTestSetup, :(using SimpleValueGraphs, LightGraphs, Random); recursive=true)
+            DocMeta.setdocmeta!(SimpleValueGraphs, :DocTestSetup, :(using SimpleValueGraphs, Graphs, Random); recursive=true)
             doctest(SimpleValueGraphs)' # change MYPACKAGE to the name of your package
       - run: julia --project=docs docs/make.jl
         env:
diff --git a/Project.toml b/Project.toml
@@ -1,11 +1,11 @@
 name = "SimpleValueGraphs"
 uuid = "b43c691f-cac2-5415-8122-396fe16a49fc"
 authors = ["Simon Schoelly <sischoel@gmail.com>"]
-version = "0.3.2"
+version = "0.4.0"
 
 [deps]
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SimpleTraits = "699a6c99-e7fa-54fc-8d76-47d257e15c1d"
@@ -15,8 +15,8 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
 DataStructures = "0.18.9"
-LightGraphs = "1.3"
+Graphs = "1.4.1"
 Requires = "1.0"
 SimpleTraits = "0.9.3"
-SimpleWeightedGraphs = "1.1.1"
+SimpleWeightedGraphs = "1.2"
 julia = "1.5"
diff --git a/README.md b/README.md
@@ -8,7 +8,7 @@
 [![codecov](https://codecov.io/gh/simonschoelly/SimpleValueGraphs.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/simonschoelly/SimpleValueGraphs.jl)
 [![](https://img.shields.io/badge/chat-Zulip%23graphs-yellow)](https://julialang.zulipchat.com/#narrow/stream/228745-graphs)
 
-SimpleValueGraphs is as [LightGraphs.jl](https://github.com/JuliaGraphs/LightGraphs.jl) compatible package for graphs with multiple, homogeneous vertex, edge and graph metadata. In particular it provides:
+SimpleValueGraphs is a [Graphs.jl](https://github.com/JuliaGraphs/Graphs.jl) compatible package for graphs with multiple, homogeneous vertex, edge and graph metadata. In particular it provides:
 - an abstract interface for graphs with metadata
 - concrete implementations of mutable graphs with metadata
 
@@ -26,12 +26,12 @@ Compared to [MetaGraphs.jl](https://github.com/JuliaGraphs/MetaGraphs.jl) it has
 ```julia
 using SimpleValueGraphs
 
-using LightGraphs: smallgraph
+using Graphs: smallgraph
 using Plots
 using GraphRecipes: graphplot
 using Colors: RGB, Color
 
-# Load a LightGraphs.SimpleGraph
+# Load a Graphs.SimpleGraph
 gs = smallgraph(:house)
 
 # Convert to a ValGraph with vertex and edge values
@@ -58,25 +58,25 @@ graphplot(gv;
 
 ## Benchmarks
 
-This is a comparison of running `LightGraphs.dijkstra_shortest_paths` on the [egonets-Facebook](https://snap.stanford.edu/data/egonets-Facebook.html) graph for multiple graph types.
+This is a comparison of running `Graphs.dijkstra_shortest_paths` on the [egonets-Facebook](https://snap.stanford.edu/data/egonets-Facebook.html) graph for multiple graph types.
 
 | graph type                                        | time (ms) |
 | ------------------------------------------------- | --------- |
-| LightGraphs.SimpleGraph + Matrix weights          | 6.5       |
-| LightGraphs.SimpleGraph + SparseMatrixCSC weights | 11.4      |
+| Graphs.SimpleGraph + Matrix weights               | 6.5       |
+| Graphs.SimpleGraph + SparseMatrixCSC weights      | 11.4      |
 | SimpleWeightedGraphs.SimpleWeightedGraph          | 11.7      |
 | MetaGraphs.MetaGraph                              | 141.9     |
 | SimpleValueGraphs.ValGraph                        | 12.4      |
 
-Currently a lot of LightGraphs algorithm do not optimally work with graphs that store edge metadata
+Currently a lot of Graphs.jl algorithms do not optimally work with graphs that store edge metadata
 internally. The next benchmark is an optimized version of the same algorithm that can be found
 in `SimpleValueGraphs.Experimental.dijkstra_shortests_pasts`. Clearly, this is a huge improvement for
 `ValGraph` and `SimpleWeightedGraph`.
 
 | graph type                                        | time (ms) |
 | ------------------------------------------------- | --------- |
-| LightGraphs.SimpleGraph + Matrix weights          | 6.8       |
-| LightGraphs.SimpleGraph + SparseMatrixCSC weights | 10.8      |
+| Graphs.SimpleGraph + Matrix weights               | 6.8       |
+| Graphs.SimpleGraph + SparseMatrixCSC weights      | 10.8      |
 | SimpleWeightedGraphs.SimpleWeightedGraph          | 2.9       |
 | MetaGraphs.MetaGraph                              | 147.3     |
 | SimpleValueGraphs.ValGraph                        | 3.1       |
diff --git a/benchmarks/Project.toml b/benchmarks/Project.toml
@@ -1,6 +1,6 @@
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 SNAPDatasets = "fc66bc1b-447b-53fc-8f09-bc9cfb0b0c10"
 SimpleValueGraphs = "b43c691f-cac2-5415-8122-396fe16a49fc"
diff --git a/benchmarks/benchmarks.jl b/benchmarks/benchmarks.jl
@@ -1,5 +1,5 @@
 using BenchmarkTools
-using SimpleValueGraphs, LightGraphs
+using SimpleValueGraphs, Graphs
 using SimpleWeightedGraphs, MetaGraphs
 using SNAPDatasets: loadsnap, snap_graphs
 using SparseArrays
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,5 +1,5 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SimpleValueGraphs = "b43c691f-cac2-5415-8122-396fe16a49fc"
diff --git a/docs/make.jl b/docs/make.jl
@@ -1,6 +1,6 @@
 using Documenter, SimpleValueGraphs
 
-DocMeta.setdocmeta!(SimpleValueGraphs, :DocTestSetup, :(using SimpleValueGraphs, LightGraphs, Random); recursive=true)
+DocMeta.setdocmeta!(SimpleValueGraphs, :DocTestSetup, :(using SimpleValueGraphs, Graphs, Random); recursive=true)
 makedocs(
     sitename = "SimpleValueGraphs.jl",
     authors = "Simon Schoelly",
diff --git a/docs/src/custom-valuegraph-types.md b/docs/src/custom-valuegraph-types.md
@@ -3,14 +3,14 @@
 While this package provides some concrete graph types, one is often interested in creating
 their own graph types. This section will explain how one can create a custom graph type that
 will work well with the methods from as package as well as the ones from
-[LightGraphs.jl](https://github.com/JuliaGraphs/LightGraphs.jl)
+[Graphs.jl](https://github.com/JuliaGraphs/Graphs.jl)
 
 ## The AbstractValGraph type
 
 All value graphs should be subtypes of *AbstractValGraph* that has the signature
 
 ```julia
-    AbstractValGraph{V <: Integer, V_VALS, E_VALS, G_VALS} <: LightGraphs.AbstractGraph{V}
+    AbstractValGraph{V <: Integer, V_VALS, E_VALS, G_VALS} <: Graphs.AbstractGraph{V}
 ```
 where the parameters have the following meaning:
 - `V` is the type used for indexing vertices, called the *eltype* of the graph. Should
@@ -29,8 +29,8 @@ MyGraphType{W} <: AbstractValGraph{Int, Tuple{}, Tuple{Int, W}, Tuple{}}
 is a graph  type that has neither vertex nor graph values and two edge values,
 one of them of type `Int` and the other of type `W`.
 
-As a subtype of `LightGraphs.AbstractGraph`, an `AbstractValGraph` should implement the
-[methods required by LightGraphs](https://github.com/JuliaGraphs/LightGraphs.jl) as well as some
+As a subtype of `Graphs.AbstractGraph`, an `AbstractValGraph` should implement the
+[methods required by Graphs.jl](https://github.com/JuliaGraphs/Graphs.jl) as well as some
 other methods. Luckily a lot of the methods required for `AbstractGraph` already have a default
 implementation, so the number of necessary methods is actually much shorter.
 
diff --git a/docs/src/graphtypes.md b/docs/src/graphtypes.md
@@ -8,7 +8,7 @@ and three concrete implementations.
 The abstract type `AbstractValGraph` denotes a graph that can have multiple vertex
 and edge values. It has the signature 
 ```julia
-    AbstractValGraph{V, V_VALS, E_VALS} <: LightGraphs.AbstractGraph{V}
+    AbstractValGraph{V, V_VALS, E_VALS} <: Graphs.AbstractGraph{V}
 ```
 where the parameters have the following meaning:
 - `V` is the type used for indexing vertices, called the *eltype* of the graph. Should
@@ -116,7 +116,7 @@ Graphs without any values an be created with
 ```julia
     ValGraph{V = Int32}(n)
 ```
-where `n` is the number of vertices. One notable difference to LightGraphs is that the
+where `n` is the number of vertices. One notable difference to Graphs.jl is that the
 eltype is not bases on the type of `n` but is always taken from the parameter `V`.
 
 ```julia
@@ -185,9 +185,9 @@ julia> g2 = ValDiGraph{Int8}(4;
     edge value types: ()
 ```
 
-#### Graph from LightGraphs SimpleGraphs
+#### Graph from Graphs.jl SimpleGraphs
 
-One can also initialize a graph from a LightGraphs `SimpleGraph` or `SimpleDiGraph`. If
+One can also initialize a graph from a Graphs.jl `SimpleGraph` or `SimpleDiGraph`. If
 edge values are specified (with the `edgeval_types` keyword) we also need an initializer for
 edge values. We do that by using the `edgeval_init` keyword argument which can be
 either `undef` or a function `(s, d) -> values` that takes a source and target vertex and
@@ -199,7 +199,7 @@ Furthermore, if the eltype is not specified as a parameter, it is taken from the
 graph.
 
 ```julia
-julia> using LightGraphs: smallgraph, PathDiGraph
+julia> using Graphs.jl: smallgraph, PathDiGraph
 
 julia> g_simple = smallgraph(:house)
 {5, 6} undirected simple Int64 graph
diff --git a/docs/src/matrices.md b/docs/src/matrices.md
@@ -6,12 +6,12 @@ that contain the topology of the graph.
 ## Adjacency matrices
 
 The `adjacency_matrix` function creates an adjacency matrix from a value graph . In contrast
-to LightGraphs, this is just a immutable *matrix view* of the graph, i.e if the graph
+to Graphs.jl, this is just a immutable *matrix view* of the graph, i.e if the graph
 changes, then so does this matrix. Therefore to get a mutable adjacency matrix one has to convert
 it before to some other matrix type.
 
 It is also possible to use the constructor `AdjacencyMatrix` to create a view of any
-`LightGraphs.AbstractGraph`.
+`Graphs.AbstractGraph`.
 
 ```julia
 julia> g1 = SimpleValueGraphs.swissmetro_graph();
@@ -65,8 +65,8 @@ julia> ValMatrix(g, :b, nothing)
  "xyz"    nothing  nothing
 ```
  
-One can also use the `LightGraphs.weights` function to obtain this matrix. If the graph
-does not have any edge values, this returns a `LightGraphs.DefaultDistance` instead.
+One can also use the `Graphs.weights` function to obtain this matrix. If the graph
+does not have any edge values, this returns a `Graphs.DefaultDistance` instead.
  
 ```julia
  julia> weights(g1, :a)
diff --git a/examples/Project.toml b/examples/Project.toml
@@ -1,6 +1,6 @@
 [deps]
 GraphRecipes = "bd48cda9-67a9-57be-86fa-5b3c104eda73"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781"
 SimpleValueGraphs = "b43c691f-cac2-5415-8122-396fe16a49fc"
diff --git a/examples/custom-graph-type.jl b/examples/custom-graph-type.jl
@@ -16,8 +16,8 @@ begin
 	using SparseArrays
 
 	# We are going to test our new packages with some functions
-	# from LightGraphs and GraphsRecipes
-	using LightGraphs
+	# from Graphs.jl and GraphsRecipes
+	using Graphs
 	using GraphRecipes, Plots
 	pyplot() # gr backend has issues showing edge labels so we use pyplot instead
 end
@@ -46,7 +46,7 @@ where
 * `E_VALS` are the types of the edge values
 * `G_VALS` are the types of the edge values
 
-As this type of `LightGraphs.AbstractGraph`, it can also be used with LightGraphs functions as long as we correctly implement the `AbstractGraph` interface.
+As this type of `Graphs.AbstractGraph`, it can also be used with Graphs functions as long as we correctly implement the `AbstractGraph` interface.
 
 In our case the vertex type will be `Int` as this type is also used for indexing rows and columns in a matrix.
 
@@ -73,7 +73,7 @@ md"""
 
 ## Implementing the AbstractValGraph interface
 
-To be able to do anything meaningful with that graph, we have to implement the interface for `LightGraphs.AbstractGraph` as well as the interface for `SimpleGraphs.AbstractValGraph`. Luckily, SimpleValueGraphs provides already some sensible defaults (that can be overriden for performance or other reasons) for a lot of LightGraphs functions so that what we will have to implement is less than is usually required by LightGraphs. Nevertheless we need to implement the following functions:
+To be able to do anything meaningful with that graph, we have to implement the interface for `Graphs.AbstractGraph` as well as the interface for `SimpleGraphs.AbstractValGraph`. Luckily, SimpleValueGraphs provides already some sensible defaults (that can be overriden for performance or other reasons) for a lot of Graphs.jl functions so that what we will have to implement is less than is usually required by Graphs.jl. Nevertheless we need to implement the following functions:
 
 * `nv(::GraphView)`
 * `is_directed(::Type{<:GraphView})`
@@ -134,7 +134,7 @@ SimpleValueGraphs.get_edgeval(g::GraphView, u, v, key::Integer) = weight=g.matri
 # ╔═╡ ed96451c-5596-11eb-1c39-8b28c0e661af
 md"""
 ##### zero
-This function is a bit of an anomaly and should in my opinion not be part of the LightGraphs interface. It is also rarely used in LightGraphs, so it might not be a very big issue to omit it. Nevertheless we implement it here for the sake of completeness.
+This function is a bit of an anomaly and should in my opinion not be part of the Graphs.jl interface. It is also rarely used in Graphs.jl, so it might not be a very big issue to omit it. Nevertheless we implement it here for the sake of completeness.
 
 `zero(G)` should create a graph with zero vertices, given a graph type. We do this here by trying to create a matrix of size (0, 0) and the correct matrix type, and then wrap a `GraphView` around it:
 """
@@ -235,7 +235,7 @@ md"""
 ### Shortest paths
 
 
-Let's use some functions from LightGraphs to find the shortest path from vertex `2` to `5`:
+Let's use some functions from Graphs.jl to find the shortest path from vertex `2` to `5`:
 """
 
 # ╔═╡ 1147357a-2095-11eb-224e-61ad831db786
diff --git a/src/Experimental.jl b/src/Experimental.jl
@@ -6,7 +6,7 @@ This module contains experimental stuff that does not respect SemVer
 """
 module Experimental
 
-using LightGraphs: AbstractGraph, weights, nv, vertices, outneighbors, DijkstraState, DefaultDistance
+using Graphs: AbstractGraph, weights, nv, vertices, outneighbors, DijkstraState, DefaultDistance
 using DataStructures: PriorityQueue, dequeue!
 using SimpleValueGraphs: ValGraph, edgevals_type, outedgevals
 using SimpleWeightedGraphs: SimpleWeightedGraph, weighttype
diff --git a/src/SimpleValueGraphs.jl b/src/SimpleValueGraphs.jl
@@ -1,17 +1,16 @@
 module SimpleValueGraphs
 
-using LightGraphs: AbstractGraph, AbstractEdgeIter, AbstractEdge, num_self_loops
+using Graphs: AbstractGraph, AbstractEdgeIter, AbstractEdge, num_self_loops
 
-using LightGraphs.SimpleGraphs: AbstractSimpleGraph, AbstractSimpleEdge,
+using Graphs.SimpleGraphs: AbstractSimpleGraph, AbstractSimpleEdge,
     SimpleGraph, SimpleDiGraph, SimpleEdge, IsDirected
 
 using Base: OneTo
 
 
-import LightGraphs
-const LG = LightGraphs
+import Graphs
 
-import LightGraphs:
+import Graphs:
     nv, ne, is_directed,
     eltype, vertices, add_vertex!, rem_vertex!, has_vertex,
     edgetype, edges, src, dst, reverse,
@@ -67,7 +66,7 @@ export
     AdjacencyMatrix,
     ValMatrix,
 
-    # overridden methods from LightGraphs
+    # overridden methods from Graphs.jl
     nv,
     ne,
     is_directed,
diff --git a/src/abstractvaluegraph.jl b/src/abstractvaluegraph.jl
@@ -39,11 +39,11 @@ ZeroGraphValGraph{V, V_VALS, E_VALS} = AbstractValGraph{V, V_VALS, E_VALS, <: Ab
 #  eltype
 #  ------------------------------------------------------
 
-LG.eltype(::Type{<:AbstractValGraph{V}}) where {V} = V
+Graphs.eltype(::Type{<:AbstractValGraph{V}}) where {V} = V
 
 # This should not be necessary, as Base implements `eltype(x) = eltype(typeof(x))`
-# but unfortunately LightGraphs redefines `eltype(::AbstractGraph)` as not defined
-LG.eltype(g::AbstractValGraph) = eltype(typeof(g))
+# but unfortunately Graphs.jl redefines `eltype(::AbstractGraph)` as not defined
+Graphs.eltype(g::AbstractValGraph) = eltype(typeof(g))
 
 
 #  ------------------------------------------------------
@@ -214,30 +214,30 @@ end
 
 
 # ======================================================
-# Partial default implementation of LightGraphs interface
+# Partial default implementation of Graphs.jl interface
 # ======================================================
 
-LG.vertices(g::AbstractValGraph) = OneTo{eltype(g)}(nv(g))
+Graphs.vertices(g::AbstractValGraph) = OneTo{eltype(g)}(nv(g))
 
-LG.has_vertex(g::AbstractValGraph, v) = v ∈ vertices(g)
+Graphs.has_vertex(g::AbstractValGraph, v) = v ∈ vertices(g)
 
 """
     edges(g::AbstractValGraph[, key])
 
 Return the edges of `g`. By default add no edge values
 but when `key=:` then add edge values.
 """
-LG.edges(g::AbstractValGraph, key=nothing) = ValEdgeIter(g, key)
+Graphs.edges(g::AbstractValGraph, key=nothing) = ValEdgeIter(g, key)
 
-LG.edgetype(g::AbstractValGraph) = eltype(edges(g))
+Graphs.edgetype(g::AbstractValGraph) = eltype(edges(g))
 
-LG.ne(g::AbstractValGraph) = length(edges(g))
+Graphs.ne(g::AbstractValGraph) = length(edges(g))
 
 # TODO a Base.Generator would be better here, but it causes problems with sort. Maybe
 # add a custom iterator
-LG.outneighbors(g::AbstractValGraph, u) = [v for v ∈ vertices(g) if has_edge(g, u, v)]
+Graphs.outneighbors(g::AbstractValGraph, u) = [v for v ∈ vertices(g) if has_edge(g, u, v)]
 
-LG.inneighbors(g::AbstractValGraph, v) = is_directed(g) ? [u for u ∈ vertices(g) if has_edge(g, u, v)] : outneighbors(g, v)
+Graphs.inneighbors(g::AbstractValGraph, v) = is_directed(g) ? [u for u ∈ vertices(g) if has_edge(g, u, v)] : outneighbors(g, v)
 
 
 # ======================================================
@@ -264,9 +264,9 @@ If the edge already exists, return `false` but still change the edge values.
 """
 function add_edge! end
 
-LG.add_edge!(g::ZeroEdgeValGraph, s, d) = add_edge!(g, s, d, ())
+Graphs.add_edge!(g::ZeroEdgeValGraph, s, d) = add_edge!(g, s, d, ())
 
-LG.add_edge!(g::OneEdgeValGraph, s, d; val) = add_edge!(g, s, d, tuple(val))
+Graphs.add_edge!(g::OneEdgeValGraph, s, d; val) = add_edge!(g, s, d, tuple(val))
 
 
 #  -----------------------------------------------------
@@ -288,9 +288,9 @@ Return `true` if the vertex was added successfully, otherwise return `false`.
 """
 function add_vertex! end
 
-LG.add_vertex!(g::ZeroVertexValGraph) = add_vertex!(g, ())
+Graphs.add_vertex!(g::ZeroVertexValGraph) = add_vertex!(g, ())
 
-LG.add_vertex!(g::OneVertexValGraph; val) = add_vertex!(g, tuple(val))
+Graphs.add_vertex!(g::OneVertexValGraph; val) = add_vertex!(g, tuple(val))
 
 
 # ======================================================
diff --git a/src/integrations/SimpleGraphs.jl b/src/integrations/SimpleGraphs.jl
diff --git a/src/matrices.jl b/src/matrices.jl
diff --git a/src/valueedge.jl b/src/valueedge.jl
diff --git a/src/valuegraph.jl b/src/valuegraph.jl
diff --git a/test/matrices.jl b/test/matrices.jl
diff --git a/test/runtests.jl b/test/runtests.jl
