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fix reference
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vyudu committed Jan 9, 2025
1 parent a71f454 commit 145c7a6
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4 changes: 2 additions & 2 deletions docs/src/api.md
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Expand Up @@ -247,8 +247,8 @@ conservationlaws
conservedquantities
conservedequations
conservationlaw_constants
Catalyst.ReactionComplexElement
Catalyst.ReactionComplex
ReactionComplexElement
ReactionComplex
reactioncomplexmap
reactioncomplexes
incidencemat
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89 changes: 89 additions & 0 deletions docs/src/assets/Project.toml
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@@ -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"
2 changes: 1 addition & 1 deletion ext/CatalystGraphMakieExtension/rn_graph_plot.jl
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Expand Up @@ -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:
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