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SciML · Nov 29, 2024 · 2e60836 · 2e60836
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diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json
@@ -1 +1 @@
-{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-22T08:57:43","documenter_version":"1.8.0"}}
+{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-29T08:57:12","documenter_version":"1.8.0"}}
diff --git a/dev/assets/Manifest.toml b/dev/assets/Manifest.toml
@@ -5,9 +5,9 @@ manifest_format = "2.0"
 project_hash = "dcbf316fe93870754598cde9a29b095079191c6d"
 
 [[deps.ADTypes]]
-git-tree-sha1 = "30bb95a372787af850addf28ac937f1be7b79173"
+git-tree-sha1 = "72af59f5b8f09faee36b4ec48e014a79210f2f4f"
 uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
-version = "1.10.0"
+version = "1.11.0"
 weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"]
 
     [deps.ADTypes.extensions]
@@ -344,9 +344,9 @@ version = "6.160.0"
 
 [[deps.DiffEqCallbacks]]
 deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"]
-git-tree-sha1 = "0b99b7d5b938a3f09b1552c304ff70e8d0379efd"
+git-tree-sha1 = "f6bc598f21c7bf2f7885cff9b3c9078e606ab075"
 uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def"
-version = "4.2.1"
+version = "4.2.2"
 
 [[deps.DiffEqNoiseProcess]]
 deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"]
@@ -374,9 +374,9 @@ version = "1.15.1"
 
 [[deps.DifferentiationInterface]]
 deps = ["ADTypes", "LinearAlgebra"]
-git-tree-sha1 = "0c99576d0b93df0aff1bed9d9adddef14e4e658f"
+git-tree-sha1 = "94e3189f15c2d9011144c094a89fe3f31cc394b0"
 uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
-version = "0.6.22"
+version = "0.6.23"
 
     [deps.DifferentiationInterface.extensions]
     DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore"
@@ -477,15 +477,15 @@ version = "1.6.0"
 
 [[deps.DynamicPolynomials]]
 deps = ["Future", "LinearAlgebra", "MultivariatePolynomials", "MutableArithmetics", "Reexport", "Test"]
-git-tree-sha1 = "bbf1ace0781d9744cb697fb856bd2c3f6568dadb"
+git-tree-sha1 = "9a3ae38b460449cc9e7dd0cfb059c76028724627"
 uuid = "7c1d4256-1411-5781-91ec-d7bc3513ac07"
-version = "0.6.0"
+version = "0.6.1"
 
 [[deps.DynamicQuantities]]
 deps = ["DispatchDoctor", "TestItems", "Tricks"]
-git-tree-sha1 = "192f34efd3912f4020b225e01d896f567f5f03e8"
+git-tree-sha1 = "4923007a8e500f13be4c0119554776993c055ece"
 uuid = "06fc5a27-2a28-4c7c-a15d-362465fb6821"
-version = "1.3.0"
+version = "1.4.0"
 
     [deps.DynamicQuantities.extensions]
     DynamicQuantitiesLinearAlgebraExt = "LinearAlgebra"
@@ -597,9 +597,9 @@ version = "1.4.1"
 
 [[deps.FiniteDiff]]
 deps = ["ArrayInterface", "LinearAlgebra", "Setfield"]
-git-tree-sha1 = "cdea3469429a3f20a046557d070e21797278d22b"
+git-tree-sha1 = "84e3a47db33be7248daa6274b287507dd6ff84e8"
 uuid = "6a86dc24-6348-571c-b903-95158fe2bd41"
-version = "2.26.1"
+version = "2.26.2"
 
     [deps.FiniteDiff.extensions]
     FiniteDiffBandedMatricesExt = "BandedMatrices"
@@ -1047,9 +1047,9 @@ version = "1.11.0"
 
 [[deps.ModelingToolkit]]
 deps = ["AbstractTrees", "ArrayInterface", "BlockArrays", "Combinatorics", "CommonSolve", "Compat", "ConstructionBase", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributed", "Distributions", "DocStringExtensions", "DomainSets", "DynamicQuantities", "EnumX", "ExprTools", "Expronicon", "FindFirstFunctions", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "Graphs", "InteractiveUtils", "JuliaFormatter", "JumpProcesses", "Latexify", "Libdl", "LinearAlgebra", "MLStyle", "NaNMath", "NonlinearSolve", "OffsetArrays", "OrderedCollections", "PrecompileTools", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"]
-git-tree-sha1 = "c5c654842aa99b6ce5175eb877654bba9ea5c981"
+git-tree-sha1 = "d4d2c1a26e9450499a98b4c9388823697fd130f8"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
-version = "9.51.0"
+version = "9.52.0"
 
     [deps.ModelingToolkit.extensions]
     MTKBifurcationKitExt = "BifurcationKit"
@@ -1362,9 +1362,9 @@ version = "1.3.4"
 
 [[deps.RecursiveArrayTools]]
 deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
-git-tree-sha1 = "6f4dca5fd8e97087a76b7ab8384d1c3086ace0b7"
+git-tree-sha1 = "32f824db4e5bab64e25a12b22483a30a6b813d08"
 uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
-version = "3.27.3"
+version = "3.27.4"
 
     [deps.RecursiveArrayTools.extensions]
     RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
@@ -1373,6 +1373,7 @@ version = "3.27.3"
     RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements"
     RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"]
     RecursiveArrayToolsSparseArraysExt = ["SparseArrays"]
+    RecursiveArrayToolsStructArraysExt = "StructArrays"
     RecursiveArrayToolsTrackerExt = "Tracker"
     RecursiveArrayToolsZygoteExt = "Zygote"
 
@@ -1383,6 +1384,7 @@ version = "3.27.3"
     MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca"
     ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
     SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+    StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
     Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
     Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
@@ -1450,9 +1452,9 @@ version = "0.6.43"
 
 [[deps.SciMLBase]]
 deps = ["ADTypes", "Accessors", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "Expronicon", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
-git-tree-sha1 = "57db8ea2a39fc25c11f44d46c52b7a8d110f5324"
+git-tree-sha1 = "6a5fac56e8084323fec06daf2877c6b4781e593a"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.62.0"
+version = "2.63.1"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -1492,9 +1494,9 @@ weakdeps = ["SparseArrays", "StaticArraysCore"]
 
 [[deps.SciMLStructures]]
 deps = ["ArrayInterface"]
-git-tree-sha1 = "25514a6f200219cd1073e4ff23a6324e4a7efe64"
+git-tree-sha1 = "0444a37a25fab98adbd90baa806ee492a3af133a"
 uuid = "53ae85a6-f571-4167-b2af-e1d143709226"
-version = "1.5.0"
+version = "1.6.1"
 
 [[deps.Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
@@ -1691,9 +1693,9 @@ version = "3.7.2"
 
 [[deps.Symbolics]]
 deps = ["ADTypes", "ArrayInterface", "Bijections", "CommonWorldInvalidations", "ConstructionBase", "DataStructures", "DiffRules", "Distributions", "DocStringExtensions", "DomainSets", "DynamicPolynomials", "IfElse", "LaTeXStrings", "Latexify", "Libdl", "LinearAlgebra", "LogExpFunctions", "MacroTools", "Markdown", "NaNMath", "PrecompileTools", "Primes", "RecipesBase", "Reexport", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SpecialFunctions", "StaticArraysCore", "SymbolicIndexingInterface", "SymbolicLimits", "SymbolicUtils", "TermInterface"]
-git-tree-sha1 = "d5c0ea92aa7b14b0ffca575e07af48ecb9e83f7b"
+git-tree-sha1 = "ce9c95fc859007747a4faf10166201e0b10d4313"
 uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7"
-version = "6.21.0"
+version = "6.22.0"
 
     [deps.Symbolics.extensions]
     SymbolicsForwardDiffExt = "ForwardDiff"

diff --git a/dev/index.html b/dev/index.html
@@ -21,7 +21,7 @@
   WORD_SIZE: 64
   LLVM: libLLVM-16.0.6 (ORCJIT, znver3)
 Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)</code></pre></details><details><summary>A more complete overview of all dependencies and their versions is also provided.</summary><pre class="documenter-example-output"><code class="nohighlight hljs ansi">Status `~/work/CellMLToolkit.jl/CellMLToolkit.jl/docs/Manifest.toml`
-  [47edcb42] ADTypes v1.10.0
+  [47edcb42] ADTypes v1.11.0
   [a4c015fc] ANSIColoredPrinters v0.0.1
   [1520ce14] AbstractTrees v0.4.5
   [7d9f7c33] Accessors v0.1.38
@@ -57,18 +57,18 @@
   [864edb3b] DataStructures v0.18.20
   [e2d170a0] DataValueInterfaces v1.0.0
   [2b5f629d] DiffEqBase v6.160.0
-  [459566f4] DiffEqCallbacks v4.2.1
+  [459566f4] DiffEqCallbacks v4.2.2
   [77a26b50] DiffEqNoiseProcess v5.23.0
   [163ba53b] DiffResults v1.1.0
   [b552c78f] DiffRules v1.15.1
-  [a0c0ee7d] DifferentiationInterface v0.6.22
+  [a0c0ee7d] DifferentiationInterface v0.6.23
   [8d63f2c5] DispatchDoctor v0.4.17
   [31c24e10] Distributions v0.25.113
   [ffbed154] DocStringExtensions v0.9.3
   [e30172f5] Documenter v1.8.0
   [5b8099bc] DomainSets v0.7.14
-  [7c1d4256] DynamicPolynomials v0.6.0
-  [06fc5a27] DynamicQuantities v1.3.0
+  [7c1d4256] DynamicPolynomials v0.6.1
+  [06fc5a27] DynamicQuantities v1.4.0
   [4e289a0a] EnumX v1.0.4
   [f151be2c] EnzymeCore v0.8.6
   [e2ba6199] ExprTools v0.1.10
@@ -80,7 +80,7 @@
   [a4df4552] FastPower v1.1.1
   [1a297f60] FillArrays v1.13.0
   [64ca27bc] FindFirstFunctions v1.4.1
-  [6a86dc24] FiniteDiff v2.26.1
+  [6a86dc24] FiniteDiff v2.26.2
   [1fa38f19] Format v1.3.7
   [f6369f11] ForwardDiff v0.10.38
   [f62d2435] FunctionProperties v0.1.2
@@ -125,7 +125,7 @@
   [bb5d69b7] MaybeInplace v0.1.4
   [c03570c3] Memoize v0.4.4
   [e1d29d7a] Missings v1.2.0
-  [961ee093] ModelingToolkit v9.51.0
+  [961ee093] ModelingToolkit v9.52.0
   [46d2c3a1] MuladdMacro v0.2.4
   [102ac46a] MultivariatePolynomials v0.5.7
   [d8a4904e] MutableArithmetics v1.6.0
@@ -155,7 +155,7 @@
   [74087812] Random123 v1.7.0
   [e6cf234a] RandomNumbers v1.6.0
   [3cdcf5f2] RecipesBase v1.3.4
-  [731186ca] RecursiveArrayTools v3.27.3
+  [731186ca] RecursiveArrayTools v3.27.4
   [f2c3362d] RecursiveFactorization v0.2.23
   [189a3867] Reexport v1.2.2
   [2792f1a3] RegistryInstances v0.1.0
@@ -165,10 +165,10 @@
   [7e49a35a] RuntimeGeneratedFunctions v0.5.13
   [94e857df] SIMDTypes v0.1.0
   [476501e8] SLEEFPirates v0.6.43
-  [0bca4576] SciMLBase v2.62.0
+  [0bca4576] SciMLBase v2.63.1
   [19f34311] SciMLJacobianOperators v0.1.1
   [c0aeaf25] SciMLOperators v0.3.12
-  [53ae85a6] SciMLStructures v1.5.0
+  [53ae85a6] SciMLStructures v1.6.1
   [efcf1570] Setfield v1.1.1
   [727e6d20] SimpleNonlinearSolve v2.0.0
   [699a6c99] SimpleTraits v0.9.4
@@ -188,7 +188,7 @@
   [2efcf032] SymbolicIndexingInterface v0.3.35
   [19f23fe9] SymbolicLimits v0.2.2
   [d1185830] SymbolicUtils v3.7.2
-  [0c5d862f] Symbolics v6.21.0
+  [0c5d862f] Symbolics v6.22.0
   [3783bdb8] TableTraits v1.0.1
   [bd369af6] Tables v1.12.0
   [8ea1fca8] TermInterface v2.0.0
@@ -263,4 +263,4 @@
   [8e850b90] libblastrampoline_jll v5.11.0+0
   [8e850ede] nghttp2_jll v1.59.0+0
   [3f19e933] p7zip_jll v17.4.0+2
-Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`</code></pre></details><p>You can also download the <a href="https://github.com/SciML/CellMLToolkit.jl/tree/gh-pages/v2.13.0/assets/Manifest.toml">manifest</a> file and the <a href="https://github.com/SciML/CellMLToolkit.jl/tree/gh-pages/v2.13.0/assets/Project.toml">project</a> file.</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="tutorial/">Tutorial »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Friday 22 November 2024 08:57">Friday 22 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`</code></pre></details><p>You can also download the <a href="https://github.com/SciML/CellMLToolkit.jl/tree/gh-pages/v2.13.0/assets/Manifest.toml">manifest</a> file and the <a href="https://github.com/SciML/CellMLToolkit.jl/tree/gh-pages/v2.13.0/assets/Project.toml">project</a> file.</p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="tutorial/">Tutorial »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Friday 29 November 2024 08:57">Friday 29 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
diff --git a/dev/tutorial/index.html b/dev/tutorial/index.html
@@ -36,4 +36,4 @@
 prob = ODEProblem(ml, tspan; p = p)
 sol = solve(prob, TRBDF2(), dtmax = 1.0)
 V = map(x -&gt; x[1], sol.u)
-plot(sol.t, V)</code></pre><p><img src="../assets/ten_400.png" alt/></p><p><code>ODEProblem</code> also accepts a <code>u0</code> parameter to change the initial conditions (remember <code>u0 = list_initial_conditions(ml)</code>).</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Friday 22 November 2024 08:57">Friday 22 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+plot(sol.t, V)</code></pre><p><img src="../assets/ten_400.png" alt/></p><p><code>ODEProblem</code> also accepts a <code>u0</code> parameter to change the initial conditions (remember <code>u0 = list_initial_conditions(ml)</code>).</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.8.0 on <span class="colophon-date" title="Friday 29 November 2024 08:57">Friday 29 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-22T08:57:43","documenter_version":"1.8.0"}}
		{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-29T08:57:12","documenter_version":"1.8.0"}}