USe CairoMakie

SciML · Jul 12, 2024 · cc7042b · cc7042b
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diff --git a/HISTORY.md b/HISTORY.md
@@ -6,7 +6,7 @@ The expansion of `ReactionSystem` models to spatial lattices have been enabled.
 simple example where a Brusselator model is expanded to a 20x20 grid of compartments, with diffusion
 for species X, and then simulated using ODEs. Finally, an animation of the simulation is created.
 ```julia
-using Catalyst, GLMakie, OrdinaryDiffEq
+using Catalyst, CairoMakie, OrdinaryDiffEq
 
 # Create `LatticeReactionSystem` model.
 brusselator = @reaction_network begin

diff --git a/Project.toml b/Project.toml
@@ -28,12 +28,12 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 [weakdeps]
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
-GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
 
 [extensions]
 CatalystBifurcationKitExtension = "BifurcationKit"
-CatalystGLMakieExtension = "GLMakie"
+CatalystCairoMakieExtension = "CairoMakie"
 CatalystHomotopyContinuationExtension = "HomotopyContinuation"
 CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability"
 
@@ -70,7 +70,7 @@ Graphviz_jll = "3c863552-8265-54e4-a6dc-903eb78fde85"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
-GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
@@ -88,4 +88,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [targets]
-test = ["BifurcationKit", "DiffEqCallbacks", "DomainSets", "Graphviz_jll", "HomotopyContinuation", "Logging", "GLMakie", "NonlinearSolve", "OrdinaryDiffEq", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "StructuralIdentifiability", "Test", "Unitful"]
+test = ["BifurcationKit", "DiffEqCallbacks", "DomainSets", "Graphviz_jll", "HomotopyContinuation", "Logging", "CairoMakie", "NonlinearSolve", "OrdinaryDiffEq", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "StructuralIdentifiability", "Test", "Unitful"]
diff --git a/docs/src/spatial_modelling/lattice_simulation_plotting.md b/docs/src/spatial_modelling/lattice_simulation_plotting.md
@@ -32,9 +32,9 @@ oprob = ODEProblem(lrs, u0, tspan, ps)
 sol = solve(oprob, FBDF())
 nothing # hide
 ```
-Next, we can animate it using the `lattice_animation` function, which requires the [GLMakie.jl](https://github.com/JuliaPlots/GLMakie.jl) package:
+Next, we can animate it using the `lattice_animation` function, which requires the [CairoMakie.jl](https://github.com/JuliaPlots/CairoMakie.jl) package:
 ```@example lattice_plotting
-using GLMakie
+using CairoMakie
 lattice_animation(sol, :X, "brusselator.mp4", lrs)
 nothing # hide
 ```

diff --git a/ext/CatalystCairoMakieExtension.jl b/ext/CatalystCairoMakieExtension.jl
@@ -0,0 +1,9 @@
+module CatalystCairoMakieExtension
+
+# Fetch packages.
+using Catalyst, CairoMakie
+
+# Creates and exports hc_steady_states function.
+include("CatalystCairoMakieExtension/cairo_makie_extension_spatial_modelling.jl")
+
+end
diff --git a/...on/glmakie_extension_spatial_modelling.jl → ...airo_makie_extension_spatial_modelling.jl b/...on/glmakie_extension_spatial_modelling.jl → ...airo_makie_extension_spatial_modelling.jl
diff --git a/ext/CatalystGLMakieExtension.jl b/ext/CatalystGLMakieExtension.jl
diff --git a/src/spatial_reaction_systems/lattice_sim_struct_interfacing.jl b/src/spatial_reaction_systems/lattice_sim_struct_interfacing.jl
@@ -521,6 +521,8 @@ end
 # Functions which in each sample point reshape the vector of values to the correct form (depending
 # on the type of lattice used).
 function reshape_vals(vals, lattice::CartesianGridRej{N, T}) where {N, T}
+    println(vals)
+    lattice.dims
     return reshape(vals, lattice.dims...)
 end
 function reshape_vals(vals, lattice::AbstractSparseArray{Bool, Int64, 1})

diff --git a/test/spatial_modelling/lattice_simulation_plotting.jl b/test/spatial_modelling/lattice_simulation_plotting.jl
@@ -1,7 +1,7 @@
 ### Preparations ###
 
 # Fetch packages.
-using Catalyst, GLMakie, OrdinaryDiffEq, Test
+using Catalyst, CairoMakie, OrdinaryDiffEq, Test
 
 # Sets stable rng number.
 using StableRNGs