Merge pull request #215 from jaakkor2/master

LightGraphs to Graphs
SciML · Nov 10, 2021 · f71fd29 · f71fd29
2 parents 16f64bb + 1250c90
commit f71fd29
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Showing 7 changed files with 17 additions and 17 deletions.
diff --git a/Project.toml b/Project.toml
@@ -9,7 +9,7 @@ Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 FunctionWrappers = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 PoissonRandom = "e409e4f3-bfea-5376-8464-e040bb5c01ab"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -26,7 +26,7 @@ Compat = "2.2, 3.0"
 DataStructures = "0.17, 0.18"
 DiffEqBase = "6.45.0"
 FunctionWrappers = "1.0"
-LightGraphs = "1.3.5"
+Graphs = "1.4"
 PoissonRandom = "0.4"
 RandomNumbers = "1.3"
 RecursiveArrayTools = "2"

diff --git a/src/DiffEqJump.jl b/src/DiffEqJump.jl
@@ -6,12 +6,12 @@ using Reexport
 using Compat, RandomNumbers, TreeViews, LinearAlgebra
 using DataStructures, PoissonRandom, Random, ArrayInterface
 using FunctionWrappers, UnPack
-using LightGraphs
+using Graphs
 
 import DiffEqBase: DiscreteCallback, init, solve, solve!, plot_indices, initialize!
 import Base: size, getindex, setindex!, length, similar, show, merge!, merge
 import DataStructures: update!
-import LightGraphs: neighbors, outdegree
+import Graphs: neighbors, outdegree
 
 import RecursiveArrayTools: recursivecopy!
 using StaticArrays, Base.Threads

diff --git a/src/spatial/flatten.jl b/src/spatial/flatten.jl
@@ -1,4 +1,4 @@
-using DiffEqJump, DiffEqBase, LightGraphs
+using DiffEqJump, DiffEqBase, Graphs
 
 """
 prob.u0 must be a Matrix with prob.u0[i,j] being the number of species i at site j

diff --git a/src/spatial/topology.jl b/src/spatial/topology.jl
@@ -2,10 +2,10 @@
 A file with structs and functions for setting up and using the topology of the spatial system (e.g. a graph or a Cartesian grid)
 """
 
-################### LightGraph ########################
-num_sites(graph::AbstractGraph) = LightGraphs.nv(graph)
-# neighbors(graph::AbstractGraph, site) = LightGraphs.neighbors(graph, site)
-# outdegree(graph::AbstractGraph, site) = LightGraphs.outdegree(graph, site)
+################### Graph ########################
+num_sites(graph::AbstractGraph) = Graphs.nv(graph)
+# neighbors(graph::AbstractGraph, site) = Graphs.neighbors(graph, site)
+# outdegree(graph::AbstractGraph, site) = Graphs.outdegree(graph, site)
 rand_nbr(rng, graph::AbstractGraph, site) = rand(rng, neighbors(graph, site))
 nth_nbr(graph::AbstractGraph, site, n) = @inbounds neighbors(graph, site)[n]
 

diff --git a/test/spatial/ABC.jl b/test/spatial/ABC.jl
@@ -1,6 +1,6 @@
 using DiffEqJump, DiffEqBase
 # using BenchmarkTools
-using Test, LightGraphs
+using Test, Graphs
 
 Nsims        = 100
 reltol       = 0.05
@@ -46,7 +46,7 @@ function get_mean_end_state(jump_prob, Nsims)
 end
 
 # testing
-grids = [CartesianGridRej(dims), CartesianGridIter(dims), LightGraphs.grid(dims)]
+grids = [CartesianGridRej(dims), CartesianGridIter(dims), Graphs.grid(dims)]
 jump_problems = JumpProblem[JumpProblem(prob, NSM(), majumps, hopping_constants=hopping_constants, spatial_system = grid, save_positions=(false,false)) for grid in grids]
 push!(jump_problems, JumpProblem(prob, DirectCRDirect(), majumps, hopping_constants=hopping_constants, spatial_system = grids[1], save_positions=(false,false)))
 # setup flattenned jump prob

diff --git a/test/spatial/diffusion.jl b/test/spatial/diffusion.jl
@@ -1,7 +1,7 @@
 using DiffEqJump, DiffEqBase
 using Test
 using LinearAlgebra
-using LightGraphs
+using Graphs
 
 function get_mean_sol(jump_prob, Nsims, saveat)
     sol = solve(jump_prob, SSAStepper(), saveat = saveat).u
@@ -49,7 +49,7 @@ hopping_rate = diffusivity * (linear_size/domain_size)^2
 hopping_constants = [hopping_rate for i in starting_state]
 
 # analytic solution
-lap = discrete_laplacian_from_spatial_system(LightGraphs.grid(dims), hopping_rate)
+lap = discrete_laplacian_from_spatial_system(Graphs.grid(dims), hopping_rate)
 evals, B = eigen(lap) # lap == B*diagm(evals)*B'
 Bt = B'
 analytic_solution(t) = B*diagm(ℯ.^(t*evals))*Bt * reshape(prob.u0, num_nodes, 1)
@@ -60,7 +60,7 @@ rel_tol = 0.01
 times = 0.0:tf/num_time_points:tf
 
 algs = [NSM(), DirectCRDirect()]
-grids = [CartesianGridRej(dims), CartesianGridIter(dims), LightGraphs.grid(dims)]
+grids = [CartesianGridRej(dims), CartesianGridIter(dims), Graphs.grid(dims)]
 jump_problems = JumpProblem[JumpProblem(prob, algs[2], majumps, hopping_constants=hopping_constants, spatial_system = grid, save_positions=(false,false)) for grid in grids]
 sizehint!(jump_problems, 15 + length(jump_problems))
 
@@ -119,7 +119,7 @@ end
 # testing non-uniform hopping rates
 dims = (2,2)
 num_nodes = prod(dims)
-grid = LightGraphs.grid(dims)
+grid = Graphs.grid(dims)
 hopping_constants = Matrix{Vector{Float64}}(undef, 1, num_nodes)
 for ci in CartesianIndices(hopping_constants)
     (species, site) = Tuple(ci)

diff --git a/test/spatial/utils_test.jl b/test/spatial/utils_test.jl
@@ -1,5 +1,5 @@
 # Tests for CartesianGrid
-using DiffEqJump, LightGraphs
+using DiffEqJump, Graphs
 using Test, Random
 
 io = IOBuffer()
@@ -8,7 +8,7 @@ dims = (4,3,2)
 sites = rand(1:prod(dims), 10)
 num_samples = 10^5
 rel_tol = 0.01
-grids = [DiffEqJump.CartesianGridRej(dims), DiffEqJump.CartesianGridIter(dims), LightGraphs.grid(dims)]
+grids = [DiffEqJump.CartesianGridRej(dims), DiffEqJump.CartesianGridIter(dims), Graphs.grid(dims)]
 for grid in grids
     show(io, "text/plain", grid)
     @test String(take!(io)) !== nothing