Merge pull request #437 from isaacsas/drop_lightgraphs

switch LightGraphs to Graphs

Project.toml

@@ -8,8 +8,8 @@ DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DiffEqJump = "c894b116-72e5-5b58-be3c-e6d8d4ac2b12"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
@@ -24,8 +24,8 @@ DataStructures = "0.18"
 DiffEqBase = "6.54.0"
 DiffEqJump = "7.0"
 DocStringExtensions = "0.8"
+Graphs = "1.4"
 Latexify = "0.14, 0.15"
-LightGraphs = "1.3"
 MacroTools = "0.5.5"
 ModelingToolkit = "6.3"
 Parameters = "0.12"

src/Catalyst.jl

@@ -20,10 +20,9 @@ import ModelingToolkit: get_variables, namespace_expr, namespace_equation, get_v
 import ModelingToolkit: check_variables, check_parameters, _iszero, _merge, check_units, get_unit
 
 import Base: (==), hash, size, getindex, setindex, isless, Sort.defalg, length, show
-import MacroTools, LightGraphs, AbstractAlgebra
+import MacroTools, Graphs, AbstractAlgebra
 
 # globals for the modulate
-const LG = LightGraphs
 const AA = AbstractAlgebra
 const DEFAULT_IV = (@parameters t)[1]
 

src/networkapi.jl

@@ -580,32 +580,32 @@ incidencegraph   = incidencematgraph(incidencemat)
 function incidencematgraph(incidencemat::Matrix{Int})
     @assert all(∈([-1,0,1]) ,incidencemat)
     n = size(incidencemat,1)  # no. of nodes/complexes
-    graph = LG.DiGraph(n)
+    graph = Graphs.DiGraph(n)
     for col in eachcol(incidencemat)
         src = 0; dst = 0;
         for i in eachindex(col)
                 (col[i] == -1) && (src = i)
                 (col[i] == 1) && (dst = i)
                 (src != 0) && (dst != 0) && break
         end
-        LG.add_edge!(graph, src, dst)
+        Graphs.add_edge!(graph, src, dst)
     end
     return graph
 end
 function incidencematgraph(incidencemat::SparseMatrixCSC{Int,Int})
     @assert all(∈([-1,0,1]) ,incidencemat)
     m,n = size(incidencemat)  
-    graph = LG.DiGraph(m)
+    graph = Graphs.DiGraph(m)
     rows = rowvals(incidencemat)
     vals = nonzeros(incidencemat)
     for j = 1:n
         inds=nzrange(incidencemat, j)
         row = rows[inds];
         val = vals[inds];
         if val[1] == -1
-            LG.add_edge!(graph, row[1], row[2])
+            Graphs.add_edge!(graph, row[1], row[2])
         else
-            LG.add_edge!(graph, row[2], row[1])
+            Graphs.add_edge!(graph, row[2], row[1])
         end
     end
     return graph
@@ -628,7 +628,7 @@ julia> linkageclasses(incidencegraph)
 ```
 """
 function linkageclasses(incidencegraph)
-    LG.connected_components(incidencegraph)
+    Graphs.connected_components(incidencegraph)
 end
 
 
@@ -658,7 +658,7 @@ netstoich_mat    = netstoichmat(sir)
 ```
 """
 function deficiency(ns, ig, lc)
-    LG.nv(ig) - length(lc) - AA.rank(AA.matrix(AA.ZZ,ns))
+    Graphs.nv(ig) - length(lc) - AA.rank(AA.matrix(AA.ZZ,ns))
 end
 
 function subnetworkmapping(linkageclass, allrxs, complextorxmap, p)
@@ -737,8 +737,8 @@ For example, continuing the example from [`linkagedeficiencies`](@ref)
 isreversible(incidence_graph)
 ```
 """
-function isreversible(ig::LG.SimpleDiGraph)
-    LG.reverse(ig) == ig
+function isreversible(ig::Graphs.SimpleDiGraph)
+    Graphs.reverse(ig) == ig
 end
 
 """
@@ -753,7 +753,7 @@ isweaklyreversible(subnets)
 """
 function isweaklyreversible(subnets::Vector{ReactionSystem})
     igs = [incidencematgraph(reactioncomplexes(subrs)[2]) for subrs in subnets]
-    all([LG.is_strongly_connected(ig) for ig in igs])
+    all([Graphs.is_strongly_connected(ig) for ig in igs])
 end