LightGraphs -> Graphs and associated other compats

Signed-off-by: Rachel Kurchin <[email protected]>

Project.toml

@@ -1,7 +1,7 @@
 name = "Nodariety"
 uuid = "ffab58b1-199d-4bd9-83d9-8aaad2b4ff2e"
 authors = ["Rachel Kurchin <[email protected]>"]
-version = "0.1.0"
+version = "0.1.1"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
@@ -13,7 +13,7 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Fontconfig = "186bb1d3-e1f7-5a2c-a377-96d770f13627"
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 LongestPaths = "3a25c17e-307c-411a-a047-890a9a5fbb4d"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 NetworkLayout = "46757867-2c16-5918-afeb-47bfcb05e46a"
@@ -30,9 +30,8 @@ DataFrames = "1"
 Fontconfig = "0.4"
 GLMakie = "0.4"
 GraphMakie = "0.2"
-LightGraphs = "1.3"
-LongestPaths = "0.1"
-MetaGraphs = "0.6"
-NetworkLayout = "0.4"
+LongestPaths = "0.2.4"
+MetaGraphs = "0.7"
+NetworkLayout = "0.4.6"
 StatsBase = "0.33"
 julia = "1.6"

src/Nodariety.jl

@@ -1,7 +1,7 @@
 module Nodariety
 
 using CSV, DataFrames
-using LightGraphs
+using Graphs
 
 include("hyphengraph.jl")
 hg = HyphenGraph()

src/graph_analysis.jl

@@ -23,7 +23,7 @@ function longest_path(graph::HyphenGraph = hg)
     local longest_length = 0
     local longest_start_inds = [1]
     for i = 1:nv(graph)
-        p = find_longest_path(graph, i, log_level = 0)
+        p = find_longest_path(graph.graph, i, log_level = 0)
         len = length(p.longest_path) - 1
         if len > longest_length
             longest_length = len
@@ -33,15 +33,15 @@ function longest_path(graph::HyphenGraph = hg)
         end
     end
     paths = [
-        find_longest_path(graph, i, log_level = 0).longest_path for i in longest_start_inds
+        find_longest_path(graph.graph, i, log_level = 0).longest_path for i in longest_start_inds
     ]
     return paths
 end
 
 """
     most_central(centrality_fcn, g=hg)
 
-Return the most central node in `g` according to the provided centrality measure. `centrality_fcn` can be any of the LightGraphs centrality measures: https://juliagraphs.org/LightGraphs.jl/stable/centrality/ e.g. betweenness_centrality, closeness_centrality, degree_centrality, and many others...
+Return the most central node in `g` according to the provided centrality measure. `centrality_fcn` can be any of the Graphs centrality measures: https://juliagraphs.org/Graphs.jl/stable/algorithms/centrality/ e.g. betweenness_centrality, closeness_centrality, degree_centrality, and many others...
 
 See also: [`all_centrals`](@ref)
 """
@@ -64,7 +64,7 @@ const centrality_fcns = [
 """
     all_centrals(fcns=centrality_fcns, graph=hg)
 
-Iterate through every centrality measure provided (defaults to the LightGraphs list) and find the most central node of it in `graph`. Print results.
+Iterate through every centrality measure provided (defaults to the Graphs.jl list) and find the most central node of it in `graph`. Print results.
 
 See also: [`most_central`](@ref)
 

src/graph_vis.jl

@@ -1,5 +1,5 @@
 using Colors
-using LightGraphs
+using Graphs
 using DataFrames
 using Serialization
 using GLMakie

src/hyphengraph.jl

@@ -1,4 +1,4 @@
-using LightGraphs, MetaGraphs
+using Graphs, MetaGraphs
 using DataFrames
 using Serialization
 
@@ -82,26 +82,20 @@ function Base.show(io::IO, g::HyphenGraph)
     print(io, st)
 end
 
-# implement LightGraphs API...
-const lg = LightGraphs
-# Base.reverse
+# implement Graphs API...
 Base.zero(HyphenGraph) =
     HyphenGraph(MetaDiGraph(zero(SimpleDiGraph)), DataFrame(), DataFrame())
-lg.edges(g::HyphenGraph) = lg.edges(g.graph)
-lg.edgetype(g::HyphenGraph) = lg.edgetype(g.graph)
-lg.has_edge(g::HyphenGraph, i, j) = lg.has_edge(g.graph, i, j)
-lg.has_vertex(g::HyphenGraph, v::Integer) = lg.has_vertex(g.graph, v)
-lg.inneighbors(g::HyphenGraph, node) = lg.inneighbors(g.graph, node)
-lg.ne(g::HyphenGraph) = lg.ne(g.graph)
-lg.nv(g::HyphenGraph) = lg.nv(g.graph)
-lg.outneighbors(g::HyphenGraph, node) = lg.outneighbors(g.graph, node)
-lg.vertices(g::HyphenGraph) = lg.vertices(g.graph)
-lg.eltype(g::HyphenGraph) = lg.eltype(g.graph)
-lg.weights(g::HyphenGraph) = lg.weights(g.graph)
-# I'm  not sure which one of these I need, but even with all of them calling some of the centrality stuff directly on the HyphenGraph doesn't seem to work :/
-lg.is_directed(g::HyphenGraph) = true
-lg.is_directed(::Type{HyphenGraph}) = true
-#lg.is_directed(HyphenGraph) = true
+Graphs.edges(g::HyphenGraph) = Graphs.edges(g.graph)
+Graphs.edgetype(g::HyphenGraph) = Graphs.edgetype(g.graph)
+Graphs.has_edge(g::HyphenGraph, i, j) = Graphs.has_edge(g.graph, i, j)
+Graphs.has_vertex(g::HyphenGraph, v::Integer) = Graphs.has_vertex(g.graph, v)
+Graphs.inneighbors(g::HyphenGraph, node) = Graphs.inneighbors(g.graph, node)
+Graphs.ne(g::HyphenGraph) = Graphs.ne(g.graph)
+Graphs.nv(g::HyphenGraph) = Graphs.nv(g.graph)
+Graphs.outneighbors(g::HyphenGraph, node) = Graphs.outneighbors(g.graph, node)
+Graphs.vertices(g::HyphenGraph) = Graphs.vertices(g.graph)
+Graphs.is_directed(g::HyphenGraph) = true
+Graphs.is_directed(::Type{HyphenGraph}) = true
 
 # helper fcn
 function edge_has_nodes(edge, new_edges, index_map)
@@ -116,7 +110,10 @@ function edge_has_nodes(edge, new_edges, index_map)
     end
 end
 
-function lg.induced_subgraph(
+# NB that this implementation messes up the indices currently
+# which is why in graph_analysis.jl, I have to call induced_subraph on graph.graph
+# instead of just graph
+function Graphs.induced_subgraph(
     g::HyphenGraph{T},
     vlist::AbstractVector{U},
 ) where {U<:Integer,T<:Integer}