Merge pull request 'Removed redundant files; Added Docs; Adjusted project structure' (#2) from feat/ruben into main

Reviewed-on: #2

Manifest.toml

@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.11.4"
+julia_version = "1.11.5"
 manifest_format = "2.0"
 project_hash = "0d147eaf78630b05e95b5317275a880443440272"
 
@@ -181,6 +181,11 @@ version = "1.9.4"
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 version = "1.11.0"
 
+[[deps.BaseDirs]]
+git-tree-sha1 = "03fea4a4efe25d2069c2d5685155005fc251c0a1"
+uuid = "18cc8868-cbac-4acf-b575-c8ff214dc66f"
+version = "1.3.0"
+
 [[deps.BitTwiddlingConvenienceFunctions]]
 deps = ["Static"]
 git-tree-sha1 = "f21cfd4950cb9f0587d5067e69405ad2acd27b87"
@@ -237,12 +242,13 @@ version = "1.7.0"
 
 [[deps.BracketingNonlinearSolve]]
 deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"]
-git-tree-sha1 = "637ebe439ba587828fd997b7810d8171eed2ea1b"
+git-tree-sha1 = "a9014924595b7a2c1dd14aac516e38fa10ada656"
 uuid = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e"
-version = "1.2.0"
+version = "1.3.0"
-weakdeps = ["ForwardDiff"]
+weakdeps = ["ChainRulesCore", "ForwardDiff"]
 
     [deps.BracketingNonlinearSolve.extensions]
+    BracketingNonlinearSolveChainRulesCoreExt = ["ChainRulesCore", "ForwardDiff"]
     BracketingNonlinearSolveForwardDiffExt = "ForwardDiff"
 
 [[deps.Bzip2_jll]]
@@ -280,9 +286,9 @@ version = "1.0.1+0"
 
 [[deps.Cairo_jll]]
 deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
-git-tree-sha1 = "2ac646d71d0d24b44f3f8c84da8c9f4d70fb67df"
+git-tree-sha1 = "fde3bf89aead2e723284a8ff9cdf5b551ed700e8"
 uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a"
-version = "1.18.4+0"
+version = "1.18.5+0"
 
 [[deps.ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra"]
@@ -334,9 +340,9 @@ weakdeps = ["SpecialFunctions"]
 
 [[deps.Colors]]
 deps = ["ColorTypes", "FixedPointNumbers", "Reexport"]
-git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e"
+git-tree-sha1 = "37ea44092930b1811e666c3bc38065d7d87fcc74"
 uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
-version = "0.13.0"
+version = "0.13.1"
 
 [[deps.CommonSolve]]
 git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c"
@@ -451,9 +457,9 @@ version = "5.53.1"
 
 [[deps.DiffEqBase]]
 deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "TruncatedStacktraces"]
-git-tree-sha1 = "1bcd3a5c585c477e5d0595937ea7b5adcda6c621"
+git-tree-sha1 = "a0e5b5669df9465bc3dd32ea4a8ddeefbc0f7b5c"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.174.0"
+version = "6.175.0"
 
     [deps.DiffEqBase.extensions]
     DiffEqBaseCUDAExt = "CUDA"
@@ -466,6 +472,7 @@ version = "6.174.0"
     DiffEqBaseMPIExt = "MPI"
     DiffEqBaseMeasurementsExt = "Measurements"
     DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements"
+    DiffEqBaseMooncakeExt = "Mooncake"
     DiffEqBaseReverseDiffExt = "ReverseDiff"
     DiffEqBaseSparseArraysExt = "SparseArrays"
     DiffEqBaseTrackerExt = "Tracker"
@@ -482,6 +489,7 @@ version = "6.174.0"
     MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
     Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
     MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca"
+    Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
     ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
     SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
     Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
@@ -627,9 +635,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
 version = "1.0.5"
 
 [[deps.EnzymeCore]]
-git-tree-sha1 = "0cdb7af5c39e92d78a0ee8d0a447d32f7593137e"
+git-tree-sha1 = "1eb59f40a772d0fbd4cb75e00b3fa7f5f79c975a"
 uuid = "f151be2c-9106-41f4-ab19-57ee4f262869"
-version = "0.8.8"
+version = "0.8.9"
 weakdeps = ["Adapt"]
 
     [deps.EnzymeCore.extensions]
@@ -822,9 +830,9 @@ version = "1.3.7"
 
 [[deps.ForwardDiff]]
 deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"]
-git-tree-sha1 = "a2df1b776752e3f344e5116c06d75a10436ab853"
+git-tree-sha1 = "910febccb28d493032495b7009dce7d7f7aee554"
 uuid = "f6369f11-7733-5829-9624-2563aa707210"
-version = "0.10.38"
+version = "1.0.1"
 weakdeps = ["StaticArrays"]
 
     [deps.ForwardDiff.extensions]
@@ -843,10 +851,10 @@ uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7"
 version = "2.13.4+0"
 
 [[deps.FreeTypeAbstraction]]
-deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"]
+deps = ["BaseDirs", "ColorVectorSpace", "Colors", "FreeType", "GeometryBasics", "Mmap"]
-git-tree-sha1 = "d52e255138ac21be31fa633200b65e4e71d26802"
+git-tree-sha1 = "eaca92bac73aa42f68c57d1b8df1b746eeb2bdaa"
 uuid = "663a7486-cb36-511b-a19d-713bb74d65c9"
-version = "0.10.6"
+version = "0.10.7"
 
 [[deps.FriBidi_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -890,9 +898,9 @@ version = "3.4.0+2"
 
 [[deps.GLMakie]]
 deps = ["ColorTypes", "Colors", "FileIO", "FixedPointNumbers", "FreeTypeAbstraction", "GLFW", "GeometryBasics", "LinearAlgebra", "Makie", "Markdown", "MeshIO", "ModernGL", "Observables", "PrecompileTools", "Printf", "ShaderAbstractions", "StaticArrays"]
-git-tree-sha1 = "42b458880923d8d2e526ad937ac59bed87e96fc6"
+git-tree-sha1 = "0650df73822ce8808dc473e3e1c7581bdb367083"
 uuid = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
-version = "0.11.7"
+version = "0.11.8"
 
 [[deps.GPUArraysCore]]
 deps = ["Adapt"]
@@ -937,9 +945,9 @@ version = "5.2.3+0"
 
 [[deps.Glib_jll]]
 deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
-git-tree-sha1 = "b0036b392358c80d2d2124746c2bf3d48d457938"
+git-tree-sha1 = "fee60557e4f19d0fe5cd169211fdda80e494f4e8"
 uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
-version = "2.82.4+0"
+version = "2.84.0+0"
 
 [[deps.Graphite2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -966,9 +974,9 @@ version = "1.0.2"
 
 [[deps.HarfBuzz_jll]]
 deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"]
-git-tree-sha1 = "55c53be97790242c29031e5cd45e8ac296dadda3"
+git-tree-sha1 = "f923f9a774fcf3f5cb761bfa43aeadd689714813"
 uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566"
-version = "8.5.0+0"
+version = "8.5.1+0"
 
 [[deps.HypergeometricFunctions]]
 deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
@@ -1136,10 +1144,10 @@ uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8"
 version = "3.1.1+0"
 
 [[deps.JumpProcesses]]
-deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"]
+deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"]
-git-tree-sha1 = "f2bdec5b4580414aee3178c8caa6e46c344c0bbc"
+git-tree-sha1 = "216c196df09c8b80a40a2befcb95760eb979bcfd"
 uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
-version = "9.14.3"
+version = "9.15.0"
 weakdeps = ["FastBroadcast"]
 
 [[deps.KernelDensity]]
@@ -1253,10 +1261,10 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 version = "1.11.0"
 
 [[deps.Libffi_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "27ecae93dd25ee0909666e6835051dd684cc035e"
+git-tree-sha1 = "c8da7e6a91781c41a863611c7e966098d783c57a"
 uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490"
-version = "3.2.2+2"
+version = "3.4.7+0"
 
 [[deps.Libglvnd_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll", "Xorg_libXext_jll"]
@@ -1311,9 +1319,9 @@ version = "1.11.0"
 
 [[deps.LinearSolve]]
 deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"]
-git-tree-sha1 = "c2685cb9d01923f0e63155149c390504e72a8fcc"
+git-tree-sha1 = "c618a6a774d5712c6bf02dbcceb51b6dc6b9bb89"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "3.14.0"
+version = "3.16.0"
 
     [deps.LinearSolve.extensions]
     LinearSolveBandedMatricesExt = "BandedMatrices"
@@ -1384,9 +1392,9 @@ version = "0.5.16"
 
 [[deps.Makie]]
 deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageBase", "ImageIO", "InteractiveUtils", "Interpolations", "IntervalSets", "InverseFunctions", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "PNGFiles", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"]
-git-tree-sha1 = "f79e47c8341376c283d3ff3b6eaeee2f73ce69a1"
+git-tree-sha1 = "968f03dc65c8144a728f988051a88c78fe625e26"
 uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
-version = "0.22.6"
+version = "0.22.7"
 
 [[deps.MakieCore]]
 deps = ["ColorTypes", "GeometryBasics", "IntervalSets", "Observables"]
@@ -1411,9 +1419,9 @@ version = "1.11.0"
 
 [[deps.MathTeXEngine]]
 deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "UnicodeFun"]
-git-tree-sha1 = "f5a6805fb46c0285991009b526ec6fae43c6dec2"
+git-tree-sha1 = "31a99cb7537f812e1d6be893a71804c35979f1be"
 uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53"
-version = "0.6.3"
+version = "0.6.4"
 
 [[deps.MatrixFactorizations]]
 deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"]
@@ -1513,9 +1521,9 @@ version = "1.2.0"
 
 [[deps.NonlinearSolve]]
 deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface"]
-git-tree-sha1 = "7fd96e0e6585063a7193007349799155ba5a069f"
+git-tree-sha1 = "aeb6fb02e63b4d4f90337ed90ce54ceb4c0efe77"
 uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
-version = "4.8.0"
+version = "4.9.0"
 
     [deps.NonlinearSolve.extensions]
     NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt"
@@ -1545,9 +1553,9 @@ version = "4.8.0"
 
 [[deps.NonlinearSolveBase]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"]
-git-tree-sha1 = "df412bac2b517411eabb42c78ff234b01eb3e95b"
+git-tree-sha1 = "404d71dd057759f4d590191a643113485c4a482a"
 uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0"
-version = "1.9.0"
+version = "1.12.0"
 weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"]
 
     [deps.NonlinearSolveBase.extensions]
@@ -1567,9 +1575,9 @@ version = "1.5.0"
 
 [[deps.NonlinearSolveQuasiNewton]]
 deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"]
-git-tree-sha1 = "b69a68ef3a7bba7ab1d5ef6321ed6d9a613142b0"
+git-tree-sha1 = "e3888bdbab6e0bfadbc3164ef4595e40e7b7e954"
 uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114"
-version = "1.5.0"
+version = "1.6.0"
 weakdeps = ["ForwardDiff"]
 
     [deps.NonlinearSolveQuasiNewton.extensions]
@@ -1631,7 +1639,7 @@ version = "3.2.4+0"
 [[deps.OpenLibm_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
-version = "0.8.1+4"
+version = "0.8.5+0"
 
 [[deps.OpenSSL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1664,15 +1672,15 @@ uuid = "91d4177d-7536-5919-b921-800302f37372"
 version = "1.3.3+0"
 
 [[deps.OrderedCollections]]
-git-tree-sha1 = "cc4054e898b852042d7b503313f7ad03de99c3dd"
+git-tree-sha1 = "05868e21324cede2207c6f0f466b4bfef6d5e7ee"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.8.0"
+version = "1.8.1"
 
 [[deps.OrdinaryDiffEq]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FillArrays", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "InteractiveUtils", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "MacroTools", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqAdamsBashforthMoulton", "OrdinaryDiffEqBDF", "OrdinaryDiffEqCore", "OrdinaryDiffEqDefault", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqExplicitRK", "OrdinaryDiffEqExponentialRK", "OrdinaryDiffEqExtrapolation", "OrdinaryDiffEqFIRK", "OrdinaryDiffEqFeagin", "OrdinaryDiffEqFunctionMap", "OrdinaryDiffEqHighOrderRK", "OrdinaryDiffEqIMEXMultistep", "OrdinaryDiffEqLinear", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqLowStorageRK", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqNordsieck", "OrdinaryDiffEqPDIRK", "OrdinaryDiffEqPRK", "OrdinaryDiffEqQPRK", "OrdinaryDiffEqRKN", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqSDIRK", "OrdinaryDiffEqSSPRK", "OrdinaryDiffEqStabilizedIRK", "OrdinaryDiffEqStabilizedRK", "OrdinaryDiffEqSymplecticRK", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Polyester", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "SimpleUnPack", "SparseArrays", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "56d5500e9970f0112a4e1ab6474d6fedde61ef64"
+git-tree-sha1 = "1c2b2df870944e0dc01454fd87479847c55fa26c"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.97.0"
+version = "6.98.0"
 
 [[deps.OrdinaryDiffEqAdamsBashforthMoulton]]
 deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"]
@@ -1682,9 +1690,9 @@ version = "1.2.0"
 
 [[deps.OrdinaryDiffEqBDF]]
 deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "a72bf554d5fd1f33a8d2aead3562eddd28ba4c76"
+git-tree-sha1 = "42755bd13fe56e9d9ce1bc005f8b206a6b56b731"
 uuid = "6ad6398a-0878-4a85-9266-38940aa047c8"
-version = "1.5.0"
+version = "1.5.1"
 
 [[deps.OrdinaryDiffEqCore]]
 deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "EnumX", "FastBroadcast", "FastClosures", "FastPower", "FillArrays", "FunctionWrappersWrappers", "InteractiveUtils", "LinearAlgebra", "Logging", "MacroTools", "MuladdMacro", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleUnPack", "Static", "StaticArrayInterface", "StaticArraysCore", "SymbolicIndexingInterface", "TruncatedStacktraces"]
@@ -1704,9 +1712,9 @@ version = "1.4.0"
 
 [[deps.OrdinaryDiffEqDifferentiation]]
 deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseMatrixColorings", "StaticArrayInterface", "StaticArrays"]
-git-tree-sha1 = "315d25dd06614e199973cc13d22e533073bd7458"
+git-tree-sha1 = "c78060115fa4ea9d70ac47fa49496acbc630aefa"
 uuid = "4302a76b-040a-498a-8c04-15b101fed76b"
-version = "1.9.0"
+version = "1.9.1"
 
 [[deps.OrdinaryDiffEqExplicitRK]]
 deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "TruncatedStacktraces"]
@@ -1776,9 +1784,9 @@ version = "1.3.0"
 
 [[deps.OrdinaryDiffEqNonlinearSolve]]
 deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MuladdMacro", "NonlinearSolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "PreallocationTools", "RecursiveArrayTools", "SciMLBase", "SciMLOperators", "SciMLStructures", "SimpleNonlinearSolve", "StaticArrays"]
-git-tree-sha1 = "2f956f14c97ff507e855703ac760d513f7c3e372"
+git-tree-sha1 = "ffdb0f5207b0e30f8b1edf99b3b9546d9c48ccaf"
 uuid = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8"
-version = "1.9.0"
+version = "1.10.0"
 
 [[deps.OrdinaryDiffEqNordsieck]]
 deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "Static"]
@@ -1788,9 +1796,9 @@ version = "1.1.0"
 
 [[deps.OrdinaryDiffEqPDIRK]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polyester", "Reexport", "StaticArrays"]
-git-tree-sha1 = "f74b27b8b811a83d77a9cad6293e793ab0804cdc"
+git-tree-sha1 = "ab9897e4bc8e3cf8e15f1cf61dbdd15d6a2341d7"
 uuid = "5dd0a6cf-3d4b-4314-aa06-06d4e299bc89"
-version = "1.3.0"
+version = "1.3.1"
 
 [[deps.OrdinaryDiffEqPRK]]
 deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "Reexport"]
@@ -1812,9 +1820,9 @@ version = "1.1.0"
 
 [[deps.OrdinaryDiffEqRosenbrock]]
 deps = ["ADTypes", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static"]
-git-tree-sha1 = "a9b9aff8e740bfc09a2ea669f7fc02e867f95ab7"
+git-tree-sha1 = "063e5ff1447b3869856ed264b6dcbb21e6e8bdb0"
 uuid = "43230ef6-c299-4910-a778-202eb28ce4ce"
-version = "1.10.0"
+version = "1.10.1"
 
 [[deps.OrdinaryDiffEqSDIRK]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"]
@@ -1875,12 +1883,6 @@ git-tree-sha1 = "cf181f0b1e6a18dfeb0ee8acc4a9d1672499626c"
 uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883"
 version = "0.4.4"
 
-[[deps.PackageExtensionCompat]]
-git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518"
-uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930"
-version = "1.0.2"
-weakdeps = ["Requires", "TOML"]
-
 [[deps.Packing]]
 deps = ["GeometryBasics"]
 git-tree-sha1 = "bc5bf2ea3d5351edf285a06b0016788a121ce92c"
@@ -1895,9 +1897,9 @@ version = "0.5.12"
 
 [[deps.Pango_jll]]
 deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "3b31172c032a1def20c98dae3f2cdc9d10e3b561"
+git-tree-sha1 = "275a9a6d85dc86c24d03d1837a0010226a96f540"
 uuid = "36c8627f-9965-5494-a995-c6b170f724f3"
-version = "1.56.1+0"
+version = "1.56.3+0"
 
 [[deps.Parameters]]
 deps = ["OrderedCollections", "UnPack"]
@@ -1946,9 +1948,9 @@ version = "0.4.4"
 
 [[deps.Polyester]]
 deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"]
-git-tree-sha1 = "2082cc4be5e765bd982ed04ea06c068f4f702410"
+git-tree-sha1 = "6f7cd22a802094d239824c57d94c8e2d0f7cfc7d"
 uuid = "f517fe37-dbe3-4b94-8317-1923a5111588"
-version = "0.7.17"
+version = "0.7.18"
 
 [[deps.PolyesterWeave]]
 deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"]
@@ -2146,9 +2148,9 @@ version = "0.2.1"
 
 [[deps.RuntimeGeneratedFunctions]]
 deps = ["ExprTools", "SHA", "Serialization"]
-git-tree-sha1 = "7cb9d10026d630ce2dd2a1fc6006a3d5041b34c0"
+git-tree-sha1 = "86a8a8b783481e1ea6b9c91dd949cb32191f8ab4"
 uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"
-version = "0.5.14"
+version = "0.5.15"
 
 [[deps.SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
@@ -2166,10 +2168,10 @@ uuid = "94e857df-77ce-4151-89e5-788b33177be4"
 version = "0.1.0"
 
 [[deps.SciMLBase]]
-deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
+deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
-git-tree-sha1 = "846e89af4ec4ba471d3050a70405978cbdf70681"
+git-tree-sha1 = "ce947672206f6a3a2bee1017c690cfd5fd82d897"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.91.1"
+version = "2.96.0"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -2194,15 +2196,15 @@ version = "2.91.1"
 
 [[deps.SciMLJacobianOperators]]
 deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"]
-git-tree-sha1 = "d563758f3ce5153810adebc534d88e24d34eeb95"
+git-tree-sha1 = "7da1216346ad79499d08d7e2a3dbf297dc80c829"
 uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e"
-version = "0.1.5"
+version = "0.1.6"
 
 [[deps.SciMLOperators]]
 deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"]
-git-tree-sha1 = "d82853c515a8d9d42c1ab493a2687a37f1e26c91"
+git-tree-sha1 = "85608e4aaf758547ffc4030c908318b432114ec9"
 uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
-version = "0.4.0"
+version = "1.3.0"
 weakdeps = ["SparseArrays", "StaticArraysCore"]
 
     [deps.SciMLOperators.extensions]
@@ -2324,31 +2326,11 @@ version = "0.6.18"
     NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
     SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 
-[[deps.SparseDiffTools]]
-deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "UnPack", "VertexSafeGraphs"]
-git-tree-sha1 = "ccbf06a08573200853b1bd06203d8ccce8449578"
-uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804"
-version = "2.26.0"
-
-    [deps.SparseDiffTools.extensions]
-    SparseDiffToolsEnzymeExt = "Enzyme"
-    SparseDiffToolsPolyesterExt = "Polyester"
-    SparseDiffToolsPolyesterForwardDiffExt = "PolyesterForwardDiff"
-    SparseDiffToolsSymbolicsExt = "Symbolics"
-    SparseDiffToolsZygoteExt = "Zygote"
-
-    [deps.SparseDiffTools.weakdeps]
-    Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
-    Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588"
-    PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b"
-    Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
-    Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
-
 [[deps.SparseMatrixColorings]]
-deps = ["ADTypes", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"]
+deps = ["ADTypes", "DocStringExtensions", "LinearAlgebra", "PrecompileTools", "Random", "SparseArrays"]
-git-tree-sha1 = "76e9564f0de0d1d7a46095e758ae13ceba680cfb"
+git-tree-sha1 = "ab958b4fec46d1f1d057bb8e2a99bfdb90744646"
 uuid = "0a514795-09f3-496d-8182-132a7b665d35"
-version = "0.4.19"
+version = "0.4.20"
 
     [deps.SparseMatrixColorings.extensions]
     SparseMatrixColoringsCliqueTreesExt = "CliqueTrees"
@@ -2376,9 +2358,9 @@ version = "1.0.3"
 
 [[deps.StackViews]]
 deps = ["OffsetArrays"]
-git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c"
+git-tree-sha1 = "be1cf4eb0ac528d96f5115b4ed80c26a8d8ae621"
 uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15"
-version = "0.1.1"
+version = "0.1.2"
 
 [[deps.Static]]
 deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"]
@@ -2425,9 +2407,9 @@ weakdeps = ["SparseArrays"]
 
 [[deps.StatsAPI]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed"
+git-tree-sha1 = "9d72a13a3f4dd3795a195ac5a44d7d6ff5f552ff"
 uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
-version = "1.7.0"
+version = "1.7.1"
 
 [[deps.StatsBase]]
 deps = ["AliasTables", "DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
@@ -2453,10 +2435,10 @@ uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 version = "2.5.0"
 
 [[deps.StochasticDiffEq]]
-deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
+deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "StaticArrays", "UnPack"]
-git-tree-sha1 = "b1e151feffd589382530930da1467474fe8c37e4"
+git-tree-sha1 = "2992af2739fdcf5862b12dcf53a5f6e3e4acd358"
 uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
-version = "6.79.0"
+version = "6.80.0"
 
 [[deps.StrideArraysCore]]
 deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"]
@@ -2557,9 +2539,9 @@ version = "1.11.0"
 
 [[deps.ThreadingUtilities]]
 deps = ["ManualMemory"]
-git-tree-sha1 = "18ad3613e129312fe67789a71720c3747e598a61"
+git-tree-sha1 = "2d529b6b22791f3e22e7ec5c60b9016e78f5f6bf"
 uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5"
-version = "0.5.3"
+version = "0.5.4"
 
 [[deps.TiffImages]]
 deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "SIMD", "UUIDs"]
@@ -2569,9 +2551,9 @@ version = "0.11.3"
 
 [[deps.TimerOutputs]]
 deps = ["ExprTools", "Printf"]
-git-tree-sha1 = "f57facfd1be61c42321765d3551b3df50f7e09f6"
+git-tree-sha1 = "3748bd928e68c7c346b52125cf41fff0de6937d0"
 uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
-version = "0.5.28"
+version = "0.5.29"
 
     [deps.TimerOutputs.extensions]
     FlameGraphsExt = "FlameGraphs"
@@ -2626,17 +2608,11 @@ weakdeps = ["ConstructionBase", "InverseFunctions"]
     ConstructionBaseUnitfulExt = "ConstructionBase"
     InverseFunctionsUnitfulExt = "InverseFunctions"
 
-[[deps.VertexSafeGraphs]]
-deps = ["Graphs"]
-git-tree-sha1 = "8351f8d73d7e880bfc042a8b6922684ebeafb35c"
-uuid = "19fa3120-7c27-5ec5-8db8-b0b0aa330d6f"
-version = "0.2.0"
-
 [[deps.Wayland_jll]]
-deps = ["Artifacts", "EpollShim_jll", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"]
+deps = ["Artifacts", "EpollShim_jll", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "XML2_jll"]
-git-tree-sha1 = "85c7811eddec9e7f22615371c3cc81a504c508ee"
+git-tree-sha1 = "49be0be57db8f863a902d59c0083d73281ecae8e"
 uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89"
-version = "1.21.0+2"
+version = "1.23.1+0"
 
 [[deps.Wayland_protocols_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]

model_fhn.jl

@@ -1,14 +0,0 @@
-function fhn!(du, u, p::FHNParams, t)
-    N, dx = p.N, p.dx
-
-    u_mat = reshape(u[1:N^2], N, N)
-    v_mat = reshape(u[N^2+1:end], N, N)
-
-    Δu = laplacian(u_mat) / dx^2
-    Δv = laplacian(v_mat) / dx^2
-
-    fu = p.Du * Δu .+ u_mat .- u_mat .^ 3 ./ 3 .- v_mat
-    fv = p.Dv * Δv .+ p.ε * (u_mat .+ p.a .- p.b .* v_mat)
-
-    du .= vcat(vec(fu), vec(fv))
-end

scripts/run_simulation.jl

@@ -5,9 +5,9 @@ include("../src/visualization.jl")
 using .Visualization
 
 N = 100
-tspan = (0.0, 100.0)
+tspan = (0.0, 1000.0)
 
-sol = run_simulation(N, tspan)
+sol = AnimalFurFHN.run_simulation(tspan, N)
 
 
 Visualization.step_through_solution(sol, N)

src/AnimalFurFHN.jl

@@ -2,9 +2,7 @@
 module AnimalFurFHN
 
 include("constants.jl")
-include("initial_conditions.jl")
 include("laplacian.jl")
-include("model_fhn.jl")
 include("solver.jl")
 
 export run_simulation   # Make sure this is here!

src/constants.jl

@@ -1,9 +1,20 @@
+module Constants
+
 struct FHNParams
     N::Int
-    dx::Float64
+    dx::Float64 # grid spacing
     Du::Float64
     Dv::Float64
-    ε::Float64
+    ϵ::Float64
     a::Float64
     b::Float64
+
+    # Inner constructor that takes keyword arguments
+    # The semicolon ';' separates positional arguments from keyword arguments
+    FHNParams(; N::Int, dx::Float64, Du::Float64, Dv::Float64, ϵ::Float64, a::Float64, b::Float64) =
+        new(N, dx, Du, Dv, ϵ, a, b)
 end
+
+export FHNParams
+
+end # module Constants

src/initial_conditions.jl

@@ -1,8 +0,0 @@
-import Random
-
-function initial_conditions(N)
-    Random.seed!(1234)
-    u = 0.1 .+ 0.01 .* rand(N, N)
-    v = 0.1 .+ 0.01 .* rand(N, N)
-    return vec(u), vec(v)
-end

src/laplacian.jl

@@ -1,4 +1,19 @@
+"""
+    laplacian(U::Matrix{Float64}, N::Int, h::Float64)
+
+    Computes the discrete 2D Laplacian of a matrix `U` using a 5-point stencil
+    and circular boundary conditions.
+
+    # Arguments
+    - `U::Matrix{Float64}`: The input 2D matrix representing the field or image.
+    - `N::Int`: Integer
+    - `h::Float64`: The spatial step size or grid spacing between points in the discretization.
+
+    # Returns
+    - `Vector{Float64}`: A flattened (vectorized) representation of the approximated Laplacian values for each element in `U`. The boundary conditions are handled circularly.
+"""
 function laplacian(U::Matrix{Float64}, N::Int, h::Float64)
+    # shifts matrices and sums them up
     padded = circshift(U, (-1, 0)) .+ circshift(U, (1, 0)) .+
              circshift(U, (0, -1)) .+ circshift(U, (0, 1)) .- 4 .* U
     return vec(padded) ./ h^2

src/model_fhn.jl

@@ -1,14 +0,0 @@
-function fhn!(du, u, p::FHNParams, t)
-    N, dx = p.N, p.dx
-
-    u_mat = reshape(u[1:N^2], N, N)
-    v_mat = reshape(u[N^2+1:end], N, N)
-
-    Δu = laplacian(u_mat) / dx^2
-    Δv = laplacian(v_mat) / dx^2
-
-    fu = p.Du * Δu .+ u_mat .- u_mat .^ 3 ./ 3 .- v_mat
-    fv = p.Dv * Δv .+ p.ε * (u_mat .+ p.a .- p.b .* v_mat)
-
-    du .= vcat(vec(fu), vec(fv))
-end

src/solver.jl

@@ -1,34 +1,60 @@
 using DifferentialEquations
+using Random
+using .Constants
 
+"""
+    fhn(du, u, p:FHNParams, t:)
 
-function run_simulation(N::Int, tspan::Tuple{Float64,Float64})
+    Implements the spatial dynamics of FitzHugh-Nagumo (fhn). Designed to be 
+    within a larger numerical solver of partial differential equations.
+
+    # Arguments
+    - `du`: output argument which stores the calculated derivatives 
+    - `u`: input vector containing the current state of the system at time t
+    - `p`: holds all the fixed parameters of the FHN model
+    - `t`: current time 
+
+    # Returns
+    - `du`: calculated derivatives put back into the du array
+"""
+function fhn!(du, u, p::FHNParams, t = 0)
+    u_mat = reshape(u[1:p.N^2], p.N, p.N) # activation variable
+    v_mat = reshape(u[p.N^2+1:end], p.N, p.N) # deactivation variable
+
+    Δu = reshape(laplacian(u_mat, p.N, p.dx), p.N, p.N)
+    Δv = reshape(laplacian(v_mat, p.N, p.dx), p.N, p.N)
+
+    fu = p.Du * Δu .+ u_mat .- u_mat .^ 3 ./ 3 .- v_mat
+    fv = p.Dv * Δv .+ p.ϵ * (u_mat .+ p.a .- p.b .* v_mat)
+
+    du .= vcat(vec(fu), vec(fv))
+end
+
+"""
+    run_simulation(tspan::Tuple{Float64,Float64}, N::Int)
+
+    solving the ODE and modelling it after FHN
+
+    # Arguments
+    - `tspan`: tuple of two Float64's representing start and end times for simulation
+    - `N`: size of the N×N grid
+
+    # Returns
+    - `sol`: solved differential equation (ODE)
+"""
+function run_simulation(tspan::Tuple{Float64,Float64}, N::Int)
     # Turing-spot parameters
-    a = 0.1
+    p = FHNParams(N = N, dx = 1.0, Du = 1e-5, Dv = 1e-3, ϵ = 0.01, a = 0.1, b = 0.5)
-    b = 0.5
-    ϵ = 0.01
-    Du = 1e-5
-    Dv = 1e-3
-
-    dx = 1.0  # grid spacing
 
     # Initial conditions (random noise)
-    u0, v0 = initial_conditions(N)
+    Random.seed!(1234)
+    # Create two vectors with length N*N with numbers between 0.1 and 0.11
+    u0 = vec(0.1 .+ 0.01 .* rand(N, N))
+    v0 = vec(0.1 .+ 0.01 .* rand(N, N))
+
     y0 = vcat(u0, v0)
 
-    function f!(du, u, p, t)
+    prob = ODEProblem(fhn!, y0, tspan, p)
-        u_mat = reshape(u[1:N^2], N, N)
-        v_mat = reshape(u[N^2+1:end], N, N)
-
-        Δu = reshape(laplacian(u_mat, N, dx), N, N)
-        Δv = reshape(laplacian(v_mat, N, dx), N, N)
-
-        fu = Du * Δu .+ u_mat .- u_mat .^ 3 ./ 3 .- v_mat
-        fv = Dv * Δv .+ ϵ * (u_mat .+ a .- b .* v_mat)
-
-        du .= vcat(vec(fu), vec(fv))
-    end
-
-    prob = ODEProblem(f!, y0, tspan)
     sol = solve(prob, BS3(), saveat=1.0)  # You can try `Rosenbrock23()` too
 
     return sol

src/visualization.jl

@@ -1,8 +1,19 @@
 module Visualization
 
 using GLMakie
+"""
+    step_through_solution(sol::SolutionType, N::Int)
 
-function step_through_solution(sol, N)
+    Function for visualization for the output of run_simulation
+
+    # Arguments
+    - `sol`: computed differential equation by run_simulation
+    - `N`: size of the N×N grid
+
+    # Returns
+    - ``: Displays created figure
+"""
+function step_through_solution(sol, N::Int)
     fig = Figure(resolution=(600, 600))
     ax = Axis(fig[1, 1])
     slider = Slider(fig[2, 1], range=1:length(sol), startvalue=1)