LightGraphs => Graphs, some other minor changes to type names

Vincent Landau · Vincent Landau · commit 559fe35dfc55 · 2021-10-19T17:19:49.000Z
diff --git a/Project.toml b/Project.toml
@@ -5,10 +5,12 @@ version = "0.0.1"
 
 [deps]
 GeoData = "9b6fcbb8-86d6-11e9-1ce7-23a6bb139a78"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 SimpleWeightedGraphs = "47aef6b3-ad0c-573a-a1e2-d07658019622"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
+GeoData = "0.5"
+Graphs = "1.4"
 julia = "1.6"
diff --git a/README.md b/README.md
@@ -5,8 +5,8 @@
 [![docs](https://img.shields.io/badge/docs-latest-blue.svg)](https://docs.circuitscape.org/SpatialGraphs.jl/latest) | [![Build Status](https://github.com/Circuitscape/SpatialGraphs.jl/workflows/CI/badge.svg)](https://github.com/Circuitscape/SpatialGraphs.jl/actions?query=workflow%3ACI) [![codecov](https://codecov.io/gh/Circuitscape/SpatialGraphs.jl/branch/main/graph/badge.svg?token=67OX4UPWOL)](https://codecov.io/gh/Circuitscape/SpatialGraphs.jl)
 
 SpatialGraphs.jl introduces the `AbstractSpatialGraph`. `AbstractSpatialGraphs` 
-are a subtype of `LightGraphs.AbstractGraph`, and can be weighted or directed. 
-AbstractSpatialGraphs are AbstractGraphs, so methods from LightGraphs.jl work right
+are a subtype of `Graphs.AbstractGraph`, and can be weighted or directed. 
+AbstractSpatialGraphs are AbstractGraphs, so methods from Graphs.jl work right
 out of the box.
 
 `AbstractSpatialGraph`s themselves contain an `AbstractGraph` in addition to 
diff --git a/docs/src/graphtypes.md b/docs/src/graphtypes.md
@@ -12,7 +12,7 @@ an `AbstractGraph`.
 AbstractSpatialGraph
 ```
 
-The `AbstractRasterGraph` type is as subtype of `AbstractSpatialGraph`. All
+The `AbstractRasterGraph` type is a subtype of `AbstractSpatialGraph`. All
 `AbstractRasterGraph` subtypes contain a field called `vertex_raster`, which is 
 a `GeoData.GeoArray` that describes the spatial locations for the vertices in 
 the graph. If your graph has 10 vertices, then the corresponding `vertex_raster` 
@@ -30,8 +30,8 @@ SpatialGraphs.jl has raster graph types for undirected, directed, unweighted,
 and weighted graphs, each detailed below.
 
 ```@docs
-SimpleRasterGraph
-SimpleRasterDiGraph
+RasterGraph
+RasterDiGraph
 WeightedRasterGraph
 WeightedRasterDiGraph
 ```
diff --git a/docs/src/index.md b/docs/src/index.md
@@ -1,10 +1,10 @@
 # SpatialGraphs.jl
 
 SpatialGraphs.jl introduces the `AbstractSpatialGraph`. `AbstractSpatialGraphs` 
-are a subtype of `LightGraphs.AbstractGraph`, and can be weighted or directed.
+are a subtype of `Graphs.AbstractGraph`, and can be weighted or directed.
 SpatialGraphs.jl is useful for turning spatial data into graphs. This can be
 useful for landscape connectivity analysis, hydrology, and other spatial
 network processes. AbstractSpatialGraphs are AbstractGraphs, so methods from 
-LightGraphs.jl work right out of the box. Go to [Graph Types](@ref graph_types) 
+Graphs.jl work right out of the box. Go to [Graph Types](@ref graph_types) 
 for more details on the graph types implemented in this package.
 
diff --git a/docs/src/userguide.md b/docs/src/userguide.md
@@ -7,7 +7,7 @@ data.
 
 ### Simple Graphs
 ```@docs
-simplerastergraph
+rastergraph
 make_simple_raster_graph
 ```
 
diff --git a/src/SpatialGraphs.jl b/src/SpatialGraphs.jl
@@ -1,6 +1,6 @@
 module SpatialGraphs
 
-using LightGraphs, SimpleWeightedGraphs, SparseArrays, GeoData
+using Graphs, SimpleWeightedGraphs, SparseArrays, GeoData
 
 include("structs.jl")
 include("graph_interface.jl")
@@ -9,12 +9,12 @@ include("utils.jl")
 include("show.jl")
 
 ## Types and Structs
-export AbstractSpatialGraph, AbstractRasterGraph, SimpleRasterGraph,
-       SimpleRasterDiGraph, WeightedRasterGraph, WeightedRasterDiGraph
+export AbstractSpatialGraph, AbstractRasterGraph, RasterGraph,
+       RasterDiGraph, WeightedRasterGraph, WeightedRasterDiGraph
 
 ## Raster graph
 export make_weighted_raster_graph, weightedrastergraph,
-    make_simple_raster_graph, simplerastergraph
+    make_simple_raster_graph, rastergraph
 
 
 end # module
diff --git a/src/graph_interface.jl b/src/graph_interface.jl
@@ -1,6 +1,6 @@
-## Methods for the LightGraphs ad SimpleWeightedGraphs interfaces
-## With these methods defined, functions from LightGraphs should "just work"
-import LightGraphs: 
+## Methods for the Graphs ad SimpleWeightedGraphs interfaces
+## With these methods defined, functions from Graphs should "just work"
+import Graphs: 
     nv, ne, vertices, edges, eltype, edgetype, has_edge, has_vertex,
     inneighbors, outneighbors, is_directed, add_edge!
 
@@ -9,7 +9,7 @@ import SimpleWeightedGraphs:
 
 import Base: zero
 
-### LightGraphs interface
+### Graphs interface
 nv(g::AbstractSpatialGraph) = nv(g.graph)
 ne(g::AbstractSpatialGraph) = ne(g.graph)
 vertices(g::AbstractSpatialGraph) = vertices(g.graph)
@@ -22,13 +22,13 @@ inneighbors(g::AbstractSpatialGraph, v) = inneighbors(g.graph, v)
 outneighbors(g::AbstractSpatialGraph, v) = outneighbors(g.graph, v)
 is_directed(g::AbstractSpatialGraph) = is_directed(g.graph)
 function Base.zero(g::AbstractRasterGraph)
-    if g.graph isa SimpleGraph
-        SimpleRasterGraph(
+    if g.graph isa Graph
+        RasterGraph(
             zero(typeof(g.graph)),
             g.vertex_raster
         )
-    elseif g.graph isa SimpleDiGraph
-        SimpleRasterDiGraph(
+    elseif g.graph isa DiGraph
+        RasterDiGraph(
             zero(typeof(g.graph)),
             g.vertex_raster
         )
diff --git a/src/rastergraphs.jl b/src/rastergraphs.jl
@@ -119,14 +119,14 @@ function weightedrastergraph(
 end
 
 """
-    simplerastergraph(
+    RasterGraph(
         raster::GeoArray;
         directed::Bool = true,
         condition::Function = is_data,
         cardinal_neighbors_only::Bool = false
     )
 
-Construct a `SimpleRasterGraph` or `SimpleRasterDiGraph` (if 
+Construct a `RasterGraph` or `RasterDiGraph` (if 
 `directed = true`) from a raster dataset.
 
 ## Parameters
@@ -161,7 +161,7 @@ connected. Note that when determining weights between diagonal neighbors, the
 increased distance between them (as compared to the distance between cardinal
 neighbors) is accounted for.
 """
-function simplerastergraph(
+function rastergraph(
         raster::GeoArray;
         condition::Function = is_data,
         directed::Bool = true,
@@ -177,9 +177,9 @@ function simplerastergraph(
     )
 
     if directed
-        sg = SimpleRasterDiGraph(g, v)
+        sg = RasterDiGraph(g, v)
     else
-        sg = SimpleRasterGraph(g, v)
+        sg = RasterGraph(g, v)
     end
 
     return sg
@@ -587,7 +587,7 @@ function make_raster_graph(
             )
         else
             n_nodes = max(maximum(sources), maximum(destinations))
-            g = SimpleDiGraph(
+            g = DiGraph(
                 sparse(sources, destinations, 1, n_nodes, n_nodes, combine)
             )
         end
@@ -601,7 +601,7 @@ function make_raster_graph(
             )
         else
             n_nodes = max(maximum(sources), maximum(destinations))
-            g = SimpleGraph(
+            g = Graph(
                 sparse(
                     vcat(sources, destinations),
                     vcat(destinations, sources),
diff --git a/src/structs.jl b/src/structs.jl
@@ -42,21 +42,21 @@ mutable struct WeightedRasterDiGraph{T<:Integer, U<:Real} <: AbstractRasterGraph
 end
 
 """
-    SimpleRasterGraph{T}
+    RasterGraph{T}
 
 A composite type for a spatially referenced graph. Vertices are spatially referenced based on a raster.
 """
-mutable struct SimpleRasterGraph{T<:Integer} <: AbstractRasterGraph{T}
-    graph::SimpleGraph{T} # A SimpleGraph
+mutable struct RasterGraph{T<:Integer} <: AbstractRasterGraph{T}
+    graph::Graph{T} # A Graph
     vertex_raster::GeoArray # A GeoArray raster, where a pixel's value denotes its vertex ID in the graph
 end
 
 """
-    SimpleRasterDiGraph{T}
+    RasterDiGraph{T}
 
 A composite type for a spatially referenced directed graph. Vertices are spatially referenced based on a raster.
 """
-mutable struct SimpleRasterDiGraph{T<:Integer} <: AbstractRasterGraph{T}
-    graph::SimpleDiGraph{T} # A SimpleDiGraph
+mutable struct RasterDiGraph{T<:Integer} <: AbstractRasterGraph{T}
+    graph::DiGraph{T} # A DiGraph
     vertex_raster::GeoArray # A GeoArray raster, where a pixel's value denotes its vertex ID in the graph
 end
diff --git a/test/lg_interface.jl b/test/lg_interface.jl
@@ -1,4 +1,4 @@
-using SpatialGraphs, Test, GeoData, LightGraphs, SimpleWeightedGraphs
+using SpatialGraphs, Test, GeoData, Graphs, SimpleWeightedGraphs
 ## This script tests methods for the LightGraph interface that aren't already 
 ## used in other tests
 
diff --git a/test/rasterdigraphs.jl b/test/rasterdigraphs.jl
@@ -1,4 +1,4 @@
-using GeoData, LightGraphs, SimpleWeightedGraphs, SpatialGraphs, Test
+using GeoData, Graphs, SimpleWeightedGraphs, SpatialGraphs, Test
 
 condition_array = Array{Float64}(undef, (3, 4, 1))
 condition_array[:,:,:] = [1, 0.5, 5, 2, 4, 8, 5, -9999, 2, 3, 6, 7]
@@ -10,7 +10,7 @@ band = Band(1:1)
 condition_raster = GeoArray(condition_array, (y, x, band), missingval = -9999)
 
 compare = <
-rasgraph = simplerastergraph(
+rasgraph = rastergraph(
     condition_raster,
     directed = true,
     condition = compare
diff --git a/test/rastergraphs.jl b/test/rastergraphs.jl
@@ -1,4 +1,4 @@
-using GeoData, LightGraphs, SimpleWeightedGraphs, SpatialGraphs, Test
+using GeoData, Graphs, SimpleWeightedGraphs, SpatialGraphs, Test
 
 array = Array{Int}(undef, (3, 4, 1))
 array[:,:,:] = [1, 1, 1, 1, 2, 2, 2, -9999, 2, 3, 3, 3]
@@ -10,7 +10,7 @@ band = Band(1:1)
 raster = GeoArray(array, (y, x, band), missingval = -9999)
 
 compare = ==
-rasgraph = simplerastergraph(
+rasgraph = rastergraph(
     raster,
     directed = false,
     condition = compare
diff --git a/test/runtests.jl b/test/runtests.jl
@@ -1,22 +1,22 @@
-using GeoData, LightGraphs, SimpleWeightedGraphs, SpatialGraphs, Test
+using GeoData, Graphs, SimpleWeightedGraphs, SpatialGraphs, Test
 
 @testset "Simple Raster Graph Construction" begin
-    include("simplerastergraphs.jl")
+    include("rastergraphs.jl")
 end
 
 @testset "Weighted Raster Graph Construction" begin
     include("weightedrastergraphs.jl")
 end
 
 @testset "Simple Raster DiGraph Construction" begin
-    include("simplerasterdigraphs.jl")
+    include("rasterdigraphs.jl")
 end
 
 @testset "Weighted Raster DiGraph Construction" begin
     include("weightedrasterdigraphs.jl")
 end
 
-@testset "LightGraphs Interface" begin
+@testset "Graphs Interface" begin
     include("lg_interface.jl")
 end
 
diff --git a/test/weightedrasterdigraphs.jl b/test/weightedrasterdigraphs.jl
@@ -1,4 +1,4 @@
-using GeoData, LightGraphs, SimpleWeightedGraphs, SpatialGraphs, Test
+using GeoData, Graphs, SimpleWeightedGraphs, SpatialGraphs, Test
 A_array = Array{Float64}(undef, (3, 4, 1))
 A_array[:,:,:] = [1, 3, 2, 0.5, 10, 8, 5, -9999, 3, 1, 2, 6]
 
diff --git a/test/weightedrastergraphs.jl b/test/weightedrastergraphs.jl
@@ -1,4 +1,4 @@
-using GeoData, LightGraphs, SimpleWeightedGraphs, SpatialGraphs, Test
+using GeoData, Graphs, SimpleWeightedGraphs, SpatialGraphs, Test
 A_array = Array{Float64}(undef, (3, 4, 1))
 A_array[:,:,:] = [1, 3, 2, 0.5, 10, 8, 5, -9999, 3, 1, 2, 6]
 

Original file line number	Diff line number	Diff line change
`@@ -1,4 +1,4 @@`
`1`		`-using SpatialGraphs, Test, GeoData, LightGraphs, SimpleWeightedGraphs`
	`1`	`+using SpatialGraphs, Test, GeoData, Graphs, SimpleWeightedGraphs`
`2`	`2`	`## This script tests methods for the LightGraph interface that aren't already`
`3`	`3`	`## used in other tests`
`4`	`4`