Changed from LightGraphs to Graphs, fixed docs build

Project.toml

@@ -10,8 +10,8 @@ Discretizers = "6e83dbb3-75ca-525b-8ae2-3751f0dd50b4"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 GraphPlot = "a2cc645c-3eea-5389-862e-a155d0052231"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LightXML = "9c8b4983-aa76-5018-a973-4c85ecc9e179"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
@@ -32,7 +32,7 @@ Distributions = "0.17,0.18,0.19,0.20,0.21,0.22,0.23,0.24, 0.25"
 Documenter = "0.26, 0.27"
 GraphPlot = "0.3,0.3.1,0.4,0.4.1"
 IterTools = "1.3"
-LightGraphs = "1.0"
+Graphs = "1.0"
 LightXML = "0.8,0.9"
 NBInclude = "2.0"
 Parameters = "0.10,0.11,0.12"

docs/make.jl

@@ -1,6 +1,6 @@
 push!(LOAD_PATH, "../src")
 import Pkg
-Pkg.add("BayesNets")
+Pkg.develop(path=".")
 Pkg.add("TikzPictures")
 Pkg.add("TikzGraphs")
 Pkg.add("Documenter")
@@ -25,6 +25,6 @@ makedocs(
 )
 
 deploydocs(
- repo = "github.com/dwijenchawra/BayesNets.jl.git",
+ repo = "github.com/sisl/BayesNets.jl.git",
 )
 return true

src/BayesNets.jl

@@ -20,7 +20,7 @@ import DataStructures: PriorityQueue, peek
 import BayesNets.CPDs.ProbabilisticGraphicalModels: markov_blanket, is_independent, infer
 import StatsBase: sample, Weights
 import GraphPlot: gplot, stressmajorize_layout
-import LightGraphs: DiGraph, add_edge!, rem_edge!,
+import Graphs: DiGraph, add_edge!, rem_edge!,
  add_vertex!, rem_vertex!, has_edge,
  edges, topological_sort_by_dfs, inneighbors,
  outneighbors, neighbors, is_cyclic, nv, ne,

src/Factors/auxiliary.jl

@@ -25,14 +25,14 @@ Custom version of repeate, but only outer repetition, and only duplicates
 the array for the number of times specified in `dims` for dimensions greater
 than `ndims(A)`. If `dims` is empty, returns a copy of `A`.
 
-```jldoctest
-julia> duplicate(collect(1:3), 2)
+```julia
+julia> duplicate(collect(1:3), (2,))
 3×2 Array{Int64,2}:
  1 1
  2 2
  3 3
 
-julia> duplicate([1 3; 2 4], 3)
+julia> duplicate([1 3; 2 4], (3,))
 2×2×3 Array{Int64,3}:
 [:, :, 1] =
  1 3

src/bayes_nets.jl

@@ -109,7 +109,7 @@ end
 """
 Returns all descendants as a list of NodeNames.
 """
-dst(edge::Pair{Int,Int}) = edge[2] # LightGraphs used to return a Pair, now it returns a SimpleEdge
+dst(edge::Pair{Int,Int}) = edge[2] # Graphs used to return a Pair, now it returns a SimpleEdge
 function descendants(bn::BayesNet, target::NodeName)
  retval = Set{Int}()
  for edge in edges(bfs_tree(bn.dag, bn.name_to_index[target]))

test/runtests.jl

@@ -1,7 +1,7 @@
 using BayesNets
 using DataFrames
 using Test
-using LightGraphs
+using Graphs
 using Statistics
 using LinearAlgebra
 using Random