switch to Graphs.jl from LightGraphs.jl (#147)

* switch to Graphs.jl

* add Graphs.jl

* add Graphs.jl

Author: jbrightuniverse

lectures/Manifest.toml

@@ -177,9 +177,9 @@ version = "0.8.5"
 
 [[Cairo_jll]]
 deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
-git-tree-sha1 = "f2202b55d816427cd385a9a4f3ffb226bee80f99"
+git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2"
 uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a"
-version = "1.16.1+0"
+version = "1.16.1+1"
 
 [[Calculus]]
 deps = ["LinearAlgebra"]
@@ -600,9 +600,9 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
 [[GLFW_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"]
-git-tree-sha1 = "dba1e8614e98949abfa60480b13653813d8f0157"
+git-tree-sha1 = "0c603255764a1fa0b61752d2bec14cfbd18f7fe8"
 uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89"
-version = "3.3.5+0"
+version = "3.3.5+1"
 
 [[GLM]]
 deps = ["Distributions", "LinearAlgebra", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "StatsModels"]
@@ -646,16 +646,22 @@ version = "5.7.0"
 
 [[Glib_jll]]
 deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"]
-git-tree-sha1 = "7bf67e9a481712b3dbe9cb3dac852dc4b1162e02"
+git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06"
 uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
-version = "2.68.3+0"
+version = "2.68.3+2"
 
 [[Graphite2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011"
 uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472"
 version = "1.3.14+0"
 
+[[Graphs]]
+deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
+git-tree-sha1 = "92243c07e786ea3458532e199eb3feee0e7e08eb"
+uuid = "86223c79-3864-5bf0-83f7-82e725a168b6"
+version = "1.4.1"
+
 [[Grisu]]
 git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
 uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe"
@@ -675,9 +681,9 @@ version = "0.9.14"
 
 [[HarfBuzz_jll]]
 deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"]
-git-tree-sha1 = "8a954fed8ac097d5be04921d595f741115c1b2ad"
+git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3"
 uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566"
-version = "2.8.1+0"
+version = "2.8.1+1"
 
 [[HostCPUFeatures]]
 deps = ["IfElse", "Libdl", "Static"]
@@ -911,9 +917,9 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
 [[Libffi_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "761a393aeccd6aa92ec3515e428c26bf99575b3b"
+git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290"
 uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490"
-version = "3.2.2+0"
+version = "3.2.2+1"
 
 [[Libgcrypt_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"]

lectures/Project.toml

@@ -19,14 +19,14 @@ FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838"
 FixedEffectModels = "9d5cd8c9-2029-5cab-9928-427838db53e3"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 Ipopt = "b6b21f68-93f8-5de0-b562-5493be1d77c9"
 IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
 JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
 KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
 LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 LinearMaps = "7a12625a-238d-50fd-b39a-03d52299707e"
 NLopt = "76087f3c-5699-56af-9a33-bf431cd00edd"

lectures/tools_and_techniques/numerical_linear_algebra.md

@@ -764,7 +764,7 @@ As with the discrete-time Markov chains, a key question is whether CTMCs are red
 is isomorphic to determining whether the directed graph of the Markov chain is [strongly connected](https://en.wikipedia.org/wiki/Strongly_connected_component).
 
 ```{code-cell} julia
-using LightGraphs
+using Graphs
 α = 0.1
 N = 6
 Q = Tridiagonal(fill(α, N-1), [-α; fill(-2α, N-2); -α], fill(α, N-1))