From eb9651a542284c2d4cfe9f2bcff49709139f92a3 Mon Sep 17 00:00:00 2001
From: Adrian Henle <eahenle@gmail.com>
Date: Wed, 27 Oct 2021 14:40:48 -0700
Subject: [PATCH] migrate (#89)

* migrate

* fix extras
---
 Project.toml                      | 13 ++++++-------
 docs/Project.toml                 |  8 ++++----
 examples/correct_missing_Hs.jl    |  8 ++++----
 examples/disorder_and_guests.jl   |  8 ++++----
 examples/make_hypothetical_MOF.jl |  8 ++++----
 examples/missing_linker_defect.jl |  8 ++++----
 examples/replacement_modes.jl     |  8 ++++----
 examples/substructure_search.jl   | 14 +++++++-------
 src/PoreMatMod.jl                 |  2 +-
 src/PoreMatModGO.jl               |  8 ++++----
 src/replace.jl                    |  2 +-
 test/findreplace.jl               |  2 +-
 test/ullmann.jl                   |  2 +-
 13 files changed, 45 insertions(+), 46 deletions(-)

diff --git a/Project.toml b/Project.toml
index 302f7e3..7044b7a 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,14 +1,14 @@
 name = "PoreMatMod"
 uuid = "2de0d7f0-0963-4438-8bc8-7e7ffe3dc69a"
 authors = ["SimonEnsemble <cory.simon@oregonstate.edu>"]
-version = "0.2.3"
+version = "0.2.4"
 
 [deps]
 Bio3DView = "99c8bb3a-9d13-5280-9740-b4880ed9c598"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 FIGlet = "3064a664-84fe-4d92-92c7-ed492f3d8fae"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 PlutoSliderServer = "2fc8631c-6f24-4c5b-bca7-cbb509c42db4"
@@ -22,13 +22,13 @@ Bio3DView = "^0.1.0"
 CSV = "^0.8.0"
 DataFrames = "^0.22.0"
 FIGlet = "^0.2.0"
-LightGraphs = "^1.3.0"
-MetaGraphs = "^0.6.6"
+Graphs = "^1.4.1"
+MetaGraphs = "^0.7.0"
 PlutoSliderServer = "^0.2.4"
 PlutoUI = "^0.7.9"
 Reexport = "^1.1.0"
 StatsBase = "^0.33.0"
-Xtals = "^0.3.6"
+Xtals = "^0.3.8"
 julia = "^1.6"
 
 [extras]
@@ -36,7 +36,6 @@ CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 Markdown = "d6f4376e-aef5-505a-96c1-9c027394607a"
@@ -47,4 +46,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Xtals = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 
 [targets]
-test = ["Test", "Documenter", "CSV", "DataFrames", "LightGraphs", "LinearAlgebra", "Printf", "PyCall", "InteractiveUtils", "Logging", "Markdown", "Pkg"]
+test = ["Test", "Documenter", "CSV", "DataFrames", "LinearAlgebra", "Printf", "PyCall", "InteractiveUtils", "Logging", "Markdown", "Pkg"]
diff --git a/docs/Project.toml b/docs/Project.toml
index 57948e3..4670e3a 100644
--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -4,7 +4,7 @@ CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 FIGlet = "3064a664-84fe-4d92-92c7-ed492f3d8fae"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 PlutoSliderServer = "2fc8631c-6f24-4c5b-bca7-cbb509c42db4"
@@ -19,13 +19,13 @@ CSV = "^0.8.0"
 DataFrames = "^0.22.0"
 Documenter = "^0.27.0"
 FIGlet = "^0.2.0"
-LightGraphs = "^1.3.0"
-MetaGraphs = "^0.6.6"
+Graphs = "^1.4.1"
+MetaGraphs = "^0.7.0"
 PlutoSliderServer = "^0.2.4"
 PlutoUI = "^0.7.9"
 Reexport = "^1.1.0"
 StatsBase = "^0.33.0"
-Xtals = "0.3.0"
+Xtals = "^0.3.8"
 julia = "^1.6"
 
 [extras]
diff --git a/examples/correct_missing_Hs.jl b/examples/correct_missing_Hs.jl
index 2f23cc3..dfef39b 100644
--- a/examples/correct_missing_Hs.jl
+++ b/examples/correct_missing_Hs.jl
@@ -398,7 +398,7 @@ uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
-[[LightGraphs]]
+[[Graphs]]
 deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
 git-tree-sha1 = "432428df5f360964040ed60418dd5601ecd240b6"
 uuid = "093fc24a-ae57-5d10-9952-331d41423f4d"
@@ -432,7 +432,7 @@ deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
 
 [[MetaGraphs]]
-deps = ["JLD2", "LightGraphs", "Random"]
+deps = ["JLD2", "Graphs", "Random"]
 git-tree-sha1 = "81c0488104fb0dc977f38b4acaff81e6e79efc4d"
 uuid = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 version = "0.6.8"
@@ -521,7 +521,7 @@ uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 version = "1.3.0"
 
 [[PoreMatMod]]
-deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "LightGraphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
+deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "Graphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
 git-tree-sha1 = "e159b06034ebf5912c900540e7c6763d4d862bbb"
 uuid = "2de0d7f0-0963-4438-8bc8-7e7ffe3dc69a"
 version = "0.2.0"
@@ -700,7 +700,7 @@ uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62"
 version = "0.6.4"
 
 [[Xtals]]
-deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "LightGraphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
+deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "Graphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
 git-tree-sha1 = "345604daffc6812d79a1c4e252ab2015c9ac3fd0"
 uuid = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 version = "0.3.5"
diff --git a/examples/disorder_and_guests.jl b/examples/disorder_and_guests.jl
index a75b570..02f29a9 100644
--- a/examples/disorder_and_guests.jl
+++ b/examples/disorder_and_guests.jl
@@ -429,7 +429,7 @@ uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
-[[LightGraphs]]
+[[Graphs]]
 deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
 git-tree-sha1 = "432428df5f360964040ed60418dd5601ecd240b6"
 uuid = "093fc24a-ae57-5d10-9952-331d41423f4d"
@@ -463,7 +463,7 @@ deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
 
 [[MetaGraphs]]
-deps = ["JLD2", "LightGraphs", "Random"]
+deps = ["JLD2", "Graphs", "Random"]
 git-tree-sha1 = "81c0488104fb0dc977f38b4acaff81e6e79efc4d"
 uuid = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 version = "0.6.8"
@@ -552,7 +552,7 @@ uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 version = "1.3.0"
 
 [[PoreMatMod]]
-deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "LightGraphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
+deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "Graphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
 git-tree-sha1 = "e159b06034ebf5912c900540e7c6763d4d862bbb"
 uuid = "2de0d7f0-0963-4438-8bc8-7e7ffe3dc69a"
 version = "0.2.0"
@@ -731,7 +731,7 @@ uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62"
 version = "0.6.4"
 
 [[Xtals]]
-deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "LightGraphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
+deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "Graphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
 git-tree-sha1 = "345604daffc6812d79a1c4e252ab2015c9ac3fd0"
 uuid = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 version = "0.3.5"
diff --git a/examples/make_hypothetical_MOF.jl b/examples/make_hypothetical_MOF.jl
index acfff61..c42e7c8 100644
--- a/examples/make_hypothetical_MOF.jl
+++ b/examples/make_hypothetical_MOF.jl
@@ -403,7 +403,7 @@ uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
-[[LightGraphs]]
+[[Graphs]]
 deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
 git-tree-sha1 = "432428df5f360964040ed60418dd5601ecd240b6"
 uuid = "093fc24a-ae57-5d10-9952-331d41423f4d"
@@ -437,7 +437,7 @@ deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
 
 [[MetaGraphs]]
-deps = ["JLD2", "LightGraphs", "Random"]
+deps = ["JLD2", "Graphs", "Random"]
 git-tree-sha1 = "81c0488104fb0dc977f38b4acaff81e6e79efc4d"
 uuid = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 version = "0.6.8"
@@ -526,7 +526,7 @@ uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 version = "1.3.0"
 
 [[PoreMatMod]]
-deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "LightGraphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
+deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "Graphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
 git-tree-sha1 = "e159b06034ebf5912c900540e7c6763d4d862bbb"
 uuid = "2de0d7f0-0963-4438-8bc8-7e7ffe3dc69a"
 version = "0.2.0"
@@ -705,7 +705,7 @@ uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62"
 version = "0.6.4"
 
 [[Xtals]]
-deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "LightGraphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
+deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "Graphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
 git-tree-sha1 = "345604daffc6812d79a1c4e252ab2015c9ac3fd0"
 uuid = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 version = "0.3.5"
diff --git a/examples/missing_linker_defect.jl b/examples/missing_linker_defect.jl
index 522b2fc..58df7d2 100644
--- a/examples/missing_linker_defect.jl
+++ b/examples/missing_linker_defect.jl
@@ -407,7 +407,7 @@ uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
-[[LightGraphs]]
+[[Graphs]]
 deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
 git-tree-sha1 = "432428df5f360964040ed60418dd5601ecd240b6"
 uuid = "093fc24a-ae57-5d10-9952-331d41423f4d"
@@ -441,7 +441,7 @@ deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
 
 [[MetaGraphs]]
-deps = ["JLD2", "LightGraphs", "Random"]
+deps = ["JLD2", "Graphs", "Random"]
 git-tree-sha1 = "81c0488104fb0dc977f38b4acaff81e6e79efc4d"
 uuid = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 version = "0.6.8"
@@ -530,7 +530,7 @@ uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 version = "1.3.0"
 
 [[PoreMatMod]]
-deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "LightGraphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
+deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "Graphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
 git-tree-sha1 = "e159b06034ebf5912c900540e7c6763d4d862bbb"
 uuid = "2de0d7f0-0963-4438-8bc8-7e7ffe3dc69a"
 version = "0.2.0"
@@ -709,7 +709,7 @@ uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62"
 version = "0.6.4"
 
 [[Xtals]]
-deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "LightGraphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
+deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "Graphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
 git-tree-sha1 = "345604daffc6812d79a1c4e252ab2015c9ac3fd0"
 uuid = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 version = "0.3.5"
diff --git a/examples/replacement_modes.jl b/examples/replacement_modes.jl
index f1c4555..8200af8 100644
--- a/examples/replacement_modes.jl
+++ b/examples/replacement_modes.jl
@@ -467,7 +467,7 @@ uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
-[[LightGraphs]]
+[[Graphs]]
 deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
 git-tree-sha1 = "432428df5f360964040ed60418dd5601ecd240b6"
 uuid = "093fc24a-ae57-5d10-9952-331d41423f4d"
@@ -501,7 +501,7 @@ deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
 
 [[MetaGraphs]]
-deps = ["JLD2", "LightGraphs", "Random"]
+deps = ["JLD2", "Graphs", "Random"]
 git-tree-sha1 = "81c0488104fb0dc977f38b4acaff81e6e79efc4d"
 uuid = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 version = "0.6.8"
@@ -590,7 +590,7 @@ uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 version = "1.3.0"
 
 [[PoreMatMod]]
-deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "LightGraphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
+deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "Graphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
 git-tree-sha1 = "e159b06034ebf5912c900540e7c6763d4d862bbb"
 uuid = "2de0d7f0-0963-4438-8bc8-7e7ffe3dc69a"
 version = "0.2.0"
@@ -769,7 +769,7 @@ uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62"
 version = "0.6.4"
 
 [[Xtals]]
-deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "LightGraphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
+deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "Graphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
 git-tree-sha1 = "345604daffc6812d79a1c4e252ab2015c9ac3fd0"
 uuid = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 version = "0.3.5"
diff --git a/examples/substructure_search.jl b/examples/substructure_search.jl
index 4b8343e..78b6798 100644
--- a/examples/substructure_search.jl
+++ b/examples/substructure_search.jl
@@ -6,7 +6,7 @@ using InteractiveUtils
 
 # ╔═╡ 37939a7a-0651-11ec-11c1-6b5ef0a19ec2
 # load required packages (Pluto.jl will automatically install them)
-using PoreMatMod, PlutoUI, Bio3DView, Logging, LightGraphs, MetaGraphs
+using PoreMatMod, PlutoUI, Bio3DView, Logging, Graphs, MetaGraphs
 
 # ╔═╡ 8ca1eb06-df90-4837-87b1-2e76e1670504
 # helper functions for viewing molecules and crystals and gathering input files
@@ -87,7 +87,7 @@ view_structure(hits)
 PLUTO_PROJECT_TOML_CONTENTS = """
 [deps]
 Bio3DView = "99c8bb3a-9d13-5280-9740-b4880ed9c598"
-LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
+Graphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 PlutoUI = "7f904dfe-b85e-4ff6-b463-dae2292396a8"
@@ -95,7 +95,7 @@ PoreMatMod = "2de0d7f0-0963-4438-8bc8-7e7ffe3dc69a"
 
 [compat]
 Bio3DView = "~0.1.3"
-LightGraphs = "~1.3.5"
+Graphs = "~1.3.5"
 MetaGraphs = "~0.6.8"
 PlutoUI = "~0.7.14"
 PoreMatMod = "~0.2.0"
@@ -385,7 +385,7 @@ uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
-[[LightGraphs]]
+[[Graphs]]
 deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
 git-tree-sha1 = "432428df5f360964040ed60418dd5601ecd240b6"
 uuid = "093fc24a-ae57-5d10-9952-331d41423f4d"
@@ -419,7 +419,7 @@ deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
 
 [[MetaGraphs]]
-deps = ["JLD2", "LightGraphs", "Random"]
+deps = ["JLD2", "Graphs", "Random"]
 git-tree-sha1 = "81c0488104fb0dc977f38b4acaff81e6e79efc4d"
 uuid = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 version = "0.6.8"
@@ -508,7 +508,7 @@ uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 version = "1.3.0"
 
 [[PoreMatMod]]
-deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "LightGraphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
+deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "Graphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
 git-tree-sha1 = "e159b06034ebf5912c900540e7c6763d4d862bbb"
 uuid = "2de0d7f0-0963-4438-8bc8-7e7ffe3dc69a"
 version = "0.2.0"
@@ -687,7 +687,7 @@ uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62"
 version = "0.6.4"
 
 [[Xtals]]
-deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "LightGraphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
+deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "Graphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
 git-tree-sha1 = "a40db3ec7ac5c1d4a08d97e8d577a18672008b73"
 uuid = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 version = "0.3.6"
diff --git a/src/PoreMatMod.jl b/src/PoreMatMod.jl
index aa810a1..46615ec 100644
--- a/src/PoreMatMod.jl
+++ b/src/PoreMatMod.jl
@@ -1,6 +1,6 @@
 module PoreMatMod
 
-using StatsBase, LightGraphs, MetaGraphs, LinearAlgebra, DataFrames, Reexport
+using StatsBase, Graphs, MetaGraphs, LinearAlgebra, DataFrames, Reexport
 @reexport using Xtals
 
 import Base.(∈), Base.show, Base.replace
diff --git a/src/PoreMatModGO.jl b/src/PoreMatModGO.jl
index e3befc0..840b352 100644
--- a/src/PoreMatModGO.jl
+++ b/src/PoreMatModGO.jl
@@ -481,7 +481,7 @@ uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
 [[Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 
-[[LightGraphs]]
+[[Graphs]]
 deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
 git-tree-sha1 = "432428df5f360964040ed60418dd5601ecd240b6"
 uuid = "093fc24a-ae57-5d10-9952-331d41423f4d"
@@ -515,7 +515,7 @@ deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
 
 [[MetaGraphs]]
-deps = ["JLD2", "LightGraphs", "Random"]
+deps = ["JLD2", "Graphs", "Random"]
 git-tree-sha1 = "81c0488104fb0dc977f38b4acaff81e6e79efc4d"
 uuid = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
 version = "0.6.8"
@@ -604,7 +604,7 @@ uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 version = "1.3.0"
 
 [[PoreMatMod]]
-deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "LightGraphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
+deps = ["Bio3DView", "Blink", "CSV", "DataFrames", "FIGlet", "Graphs", "LinearAlgebra", "MetaGraphs", "PlutoSliderServer", "PlutoUI", "Reexport", "StatsBase", "Xtals"]
 git-tree-sha1 = "e159b06034ebf5912c900540e7c6763d4d862bbb"
 uuid = "2de0d7f0-0963-4438-8bc8-7e7ffe3dc69a"
 version = "0.2.0"
@@ -783,7 +783,7 @@ uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62"
 version = "0.6.4"
 
 [[Xtals]]
-deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "LightGraphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
+deps = ["Bio3DView", "CSV", "DataFrames", "JLD2", "Graphs", "LinearAlgebra", "Logging", "MetaGraphs", "Printf", "PyCall", "UUIDs"]
 git-tree-sha1 = "345604daffc6812d79a1c4e252ab2015c9ac3fd0"
 uuid = "ede5f01d-793e-4c47-9885-c447d1f18d6d"
 version = "0.3.5"
diff --git a/src/replace.jl b/src/replace.jl
index 3678529..28c9838 100644
--- a/src/replace.jl
+++ b/src/replace.jl
@@ -63,7 +63,7 @@ function accumulate_bonds!(bonds::Array{Tuple{Int,Int}}, q2p_isom::Array{Int},
             break
         end
         # find neighbors of parent_subset atoms
-        n = LightGraphs.neighbors(parent.bonds, p)
+        n = Graphs.neighbors(parent.bonds, p)
         # loop over neighbors
         for nᵢ in n
             # if neighbor not in q2p_isom, must bond it to replacement replacement
diff --git a/test/findreplace.jl b/test/findreplace.jl
index d529d77..7b59a0a 100644
--- a/test/findreplace.jl
+++ b/test/findreplace.jl
@@ -1,6 +1,6 @@
 module PoreMatMod_Test
 
-using Test, LightGraphs, PoreMatMod
+using Test, Graphs, PoreMatMod
 
 @testset "substructure_search" begin
 irmof1 = Crystal("IRMOF-1.cif")
diff --git a/test/ullmann.jl b/test/ullmann.jl
index 8ba1d8a..71f6c44 100644
--- a/test/ullmann.jl
+++ b/test/ullmann.jl
@@ -1,6 +1,6 @@
 module Ullmann_Test
 
-using Test, LightGraphs, MetaGraphs, PoreMatMod
+using Test, Graphs, MetaGraphs, PoreMatMod
 
 
 # add a list of edges to a graph