From 145c7a6ea6eeb6aefdb6e75f7ac5c0431be33035 Mon Sep 17 00:00:00 2001
From: vyudu <vincent.duyuan@gmail.com>
Date: Thu, 9 Jan 2025 10:13:25 -0500
Subject: [PATCH] fix reference

---
 docs/src/api.md                               |  4 +-
 docs/src/assets/Project.toml                  | 89 +++++++++++++++++++
 .../rn_graph_plot.jl                          |  2 +-
 3 files changed, 92 insertions(+), 3 deletions(-)
 create mode 100644 docs/src/assets/Project.toml

diff --git a/docs/src/api.md b/docs/src/api.md
index b12cff3b6b..f78a5f70e4 100644
--- a/docs/src/api.md
+++ b/docs/src/api.md
@@ -247,8 +247,8 @@ conservationlaws
 conservedquantities
 conservedequations
 conservationlaw_constants
-Catalyst.ReactionComplexElement
-Catalyst.ReactionComplex
+ReactionComplexElement
+ReactionComplex
 reactioncomplexmap
 reactioncomplexes
 incidencemat
diff --git a/docs/src/assets/Project.toml b/docs/src/assets/Project.toml
new file mode 100644
index 0000000000..10e6eeda3f
--- /dev/null
+++ b/docs/src/assets/Project.toml
@@ -0,0 +1,89 @@
+[deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
+GlobalSensitivity = "af5da776-676b-467e-8baf-acd8249e4f0f"
+GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
+IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895"
+JumpProcesses = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
+Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
+LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
+ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+NetworkLayout = "46757867-2c16-5918-afeb-47bfcb05e46a"
+NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
+Optim = "429524aa-4258-5aef-a3af-852621145aeb"
+Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
+OptimizationBBO = "3e6eede4-6085-4f62-9a71-46d9bc1eb92b"
+OptimizationEvolutionary = "cb963754-43f6-435e-8d4b-99009ff27753"
+OptimizationNLopt = "4e6fcdb7-1186-4e1f-a706-475e75c168bb"
+OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
+OptimizationOptimisers = "42dfb2eb-d2b4-4451-abcd-913932933ac1"
+OrdinaryDiffEqBDF = "6ad6398a-0878-4a85-9266-38940aa047c8"
+OrdinaryDiffEqDefault = "50262376-6c5a-4cf5-baba-aaf4f84d72d7"
+OrdinaryDiffEqRosenbrock = "43230ef6-c299-4910-a778-202eb28ce4ce"
+OrdinaryDiffEqSDIRK = "2d112036-d095-4a1e-ab9a-08536f3ecdbf"
+OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
+OrdinaryDiffEqVerner = "79d7bb75-1356-48c1-b8c0-6832512096c2"
+PEtab = "48d54b35-e43e-4a66-a5a1-dde6b987cf69"
+Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+QuasiMonteCarlo = "8a4e6c94-4038-4cdc-81c3-7e6ffdb2a71b"
+SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
+SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1"
+SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
+StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
+Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
+
+[compat]
+BenchmarkTools = "1.5"
+BifurcationKit = "0.4.4"
+CairoMakie = "0.12"
+Catalyst = "14.4"
+DataFrames = "1.6"
+DiffEqBase = "6.159.0"
+Distributions = "0.25"
+Documenter = "1.4.1"
+DynamicalSystems = "3.3"
+GlobalSensitivity = "2.6"
+GraphMakie = "0.5"
+Graphs = "1.11.1"
+HomotopyContinuation = "2.9"
+IncompleteLU = "0.2"
+JumpProcesses = "9.13.2"
+Latexify = "0.16.5"
+LinearSolve = "2.30"
+ModelingToolkit = "< 9.60"
+NonlinearSolve = "3.12, 4"
+Optim = "1.9"
+Optimization = "4"
+OptimizationBBO = "0.4"
+OptimizationEvolutionary = "0.4"
+OptimizationNLopt = "0.3"
+OptimizationOptimJL = "0.4"
+OptimizationOptimisers = "0.3"
+OrdinaryDiffEqBDF = "1"
+OrdinaryDiffEqDefault = "1"
+OrdinaryDiffEqRosenbrock = "1"
+OrdinaryDiffEqSDIRK = "1"
+OrdinaryDiffEqTsit5 = "1"
+OrdinaryDiffEqVerner = "1"
+PEtab = "3.5"
+Plots = "1.40"
+QuasiMonteCarlo = "0.3"
+SciMLBase = "2.46"
+SciMLSensitivity = "7.60"
+SpecialFunctions = "2.4"
+StaticArrays = "1.9"
+SteadyStateDiffEq = "2.2"
+StochasticDiffEq = "6.65"
+Symbolics = "6.22"
diff --git a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
index 452041f4b9..26271e2b38 100644
--- a/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
+++ b/ext/CatalystGraphMakieExtension/rn_graph_plot.jl
@@ -216,7 +216,7 @@ end
 """
     plot_complexes(rn::ReactionSystem; show_rate_labels = false, kwargs...)
 
-Creates a GraphMakie plot of the [`ReactionComplex`](@ref)s in `rn`. Reactions
+Creates a GraphMakie plot of the [`Catalyst.ReactionComplex`](@ref)s in `rn`. Reactions
 correspond to arrows and reaction complexes to blue circles.
 
 Notes: