From 88ca7a9d2ee40aa51cd537d26f54603329085e5d Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Fri, 4 Oct 2024 08:56:01 +0000 Subject: [PATCH] build based on ff0d0b3 --- dev/.documenter-siteinfo.json | 2 +- dev/assets/Manifest.toml | 77 +++++++++++++++++------------------ dev/index.html | 31 +++++++------- dev/tutorial/index.html | 2 +- 4 files changed, 54 insertions(+), 58 deletions(-) diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index fed8981..cb528fa 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-09-27T08:55:41","documenter_version":"1.7.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.5","generation_timestamp":"2024-10-04T08:55:57","documenter_version":"1.7.0"}} \ No newline at end of file diff --git a/dev/assets/Manifest.toml b/dev/assets/Manifest.toml index 7c61959..33c87c8 100644 --- a/dev/assets/Manifest.toml +++ b/dev/assets/Manifest.toml @@ -5,9 +5,9 @@ manifest_format = "2.0" project_hash = "22ff5a0bf52029bad32356c8a808b24e6af8d6af" [[deps.ADTypes]] -git-tree-sha1 = "5a5eafb8344b81b8c2237f8a6f6b3602b3f6180e" +git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.8.1" +version = "1.9.0" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.ADTypes.extensions] @@ -277,9 +277,9 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" [[deps.DiffEqBase]] deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "Tricks", "TruncatedStacktraces"] -git-tree-sha1 = "fa7d580038451a8df4434ef5b079ac9b2d486194" +git-tree-sha1 = "6b1af0db32958b200b7b1745796432e75821bf48" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.155.1" +version = "6.155.2" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -345,10 +345,10 @@ uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" version = "1.15.1" [[deps.DifferentiationInterface]] -deps = ["ADTypes", "Compat", "DocStringExtensions", "FillArrays", "LinearAlgebra", "PackageExtensionCompat", "SparseArrays", "SparseMatrixColorings"] -git-tree-sha1 = "9b23f9a816790b8ab9914c3c86321a546e92cbe7" +deps = ["ADTypes", "Compat", "LinearAlgebra", "PackageExtensionCompat"] +git-tree-sha1 = "50a19de1b366cbdcf2849dc5335bbd66e1db0dae" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.5.17" +version = "0.6.1" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -358,10 +358,12 @@ version = "0.5.17" DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" DifferentiationInterfaceForwardDiffExt = "ForwardDiff" + DifferentiationInterfaceMooncakeExt = "Mooncake" DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" DifferentiationInterfaceReverseDiffExt = "ReverseDiff" + DifferentiationInterfaceSparseArraysExt = "SparseArrays" + DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" DifferentiationInterfaceSymbolicsExt = "Symbolics" - DifferentiationInterfaceTapirExt = "Tapir" DifferentiationInterfaceTrackerExt = "Tracker" DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] @@ -373,10 +375,12 @@ version = "0.5.17" FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" - Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -386,9 +390,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "e6c693a0e4394f8fda0e51a5bdf5aef26f8235e9" +git-tree-sha1 = "d7477ecdafb813ddee2ae727afa94e9dcb5f3fb0" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.111" +version = "0.25.112" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -459,9 +463,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.EnzymeCore]] -git-tree-sha1 = "8f205a601760f4798a10f138c3940f0451d95188" +git-tree-sha1 = "ee11500b17d87b22bc638e9ed8c71a7478c53d61" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.7.8" +version = "0.8.3" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -593,9 +597,9 @@ version = "1.3.1" [[deps.Git_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "d18fb8a1f3609361ebda9bf029b60fd0f120c809" +git-tree-sha1 = "ea372033d09e4552a04fd38361cd019f9003f4f4" uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb" -version = "2.44.0+2" +version = "2.46.2+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -658,9 +662,9 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] IntervalSetsStatisticsExt = "Statistics" [[deps.InverseFunctions]] -git-tree-sha1 = "2787db24f4e03daf859c6509ff87764e4182f7d1" +git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.16" +version = "0.1.17" weakdeps = ["Dates", "Test"] [deps.InverseFunctions.extensions] @@ -824,17 +828,17 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearSolve]] deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "6c5e4555ac2bc449a28604e184f759d18fc08420" +git-tree-sha1 = "8941ad4bdd83768359801982e143008349b1a827" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.34.0" +version = "2.35.0" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" LinearSolveBlockDiagonalsExt = "BlockDiagonals" LinearSolveCUDAExt = "CUDA" LinearSolveCUDSSExt = "CUDSS" - LinearSolveEnzymeExt = ["Enzyme", "EnzymeCore"] - LinearSolveFastAlmostBandedMatricesExt = ["FastAlmostBandedMatrices"] + LinearSolveEnzymeExt = "EnzymeCore" + LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices" LinearSolveHYPREExt = "HYPRE" LinearSolveIterativeSolversExt = "IterativeSolvers" LinearSolveKernelAbstractionsExt = "KernelAbstractions" @@ -848,7 +852,6 @@ version = "2.34.0" BlockDiagonals = "0a1fb500-61f7-11e9-3c65-f5ef3456f9f0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" - Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e" HYPRE = "b5ffcf37-a2bd-41ab-a3da-4bd9bc8ad771" @@ -988,9 +991,9 @@ version = "0.5.6" [[deps.MutableArithmetics]] deps = ["LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "d0a6b1096b584a2b88efb70a92f8cb8c881eb38a" +git-tree-sha1 = "3eba928678787843e504c153a9b8e80d7d73ab17" uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0" -version = "1.4.6" +version = "1.5.0" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1061,9 +1064,9 @@ version = "0.8.1+2" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1b35263570443fdd9e76c76b7062116e2f374ab8" +git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.15+0" +version = "3.0.15+1" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1307,9 +1310,9 @@ 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", "Tables"] -git-tree-sha1 = "c96f81c3e98d5e2f0848fb42aba4383d772c3bb7" +git-tree-sha1 = "71857d6bab17e7ac6802d86ffcc75423b8c1d812" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.53.1" +version = "2.54.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -1362,9 +1365,9 @@ uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" [[deps.SimpleNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "536c0ee0b4b766ddee24220c6bb60932df4e2c39" +git-tree-sha1 = "44021f3efc023be3871195d8ad98b865001a2fa1" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.12.1" +version = "1.12.3" [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" @@ -1400,9 +1403,9 @@ version = "1.10.0" [[deps.SparseDiffTools]] deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "c9e5d7ee75cf6a1ca3a22c9a6a4ef451792cf62b" +git-tree-sha1 = "7db12cef226aaa8ca730040c9c35e32b86a69b83" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.20.0" +version = "2.22.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -1418,12 +1421,6 @@ version = "2.20.0" Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" -[[deps.SparseMatrixColorings]] -deps = ["ADTypes", "Compat", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "996dff77d814c45c3f2342fa0113e4ad31e712e8" -uuid = "0a514795-09f3-496d-8182-132a7b665d35" -version = "0.4.0" - [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] git-tree-sha1 = "342cf4b449c299d8d1ceaf00b7a49f4fbc7940e7" @@ -1518,9 +1515,9 @@ version = "7.2.1+1" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "988e04b34a4c3b824fb656f542473df99a4f610d" +git-tree-sha1 = "0225f7c62f5f78db35aae6abb2e5cabe38ce578f" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.30" +version = "0.3.31" [[deps.SymbolicLimits]] deps = ["SymbolicUtils"] diff --git a/dev/index.html b/dev/index.html index db009af..d1e0872 100644 --- a/dev/index.html +++ b/dev/index.html @@ -22,7 +22,7 @@ LIBM: libopenlibm LLVM: libLLVM-15.0.7 (ORCJIT, znver3) Threads: 1 default, 0 interactive, 1 GC (on 4 virtual cores)
A more complete overview of all dependencies and their versions is also provided.
Status `~/work/CellMLToolkit.jl/CellMLToolkit.jl/docs/Manifest.toml`
-  [47edcb42] ADTypes v1.8.1
+  [47edcb42] ADTypes v1.9.0
   [a4c015fc] ANSIColoredPrinters v0.0.1
   [1520ce14] AbstractTrees v0.4.5
   [7d9f7c33] Accessors v0.1.38
@@ -54,20 +54,20 @@
   [9a962f9c] DataAPI v1.16.0
   [864edb3b] DataStructures v0.18.20
   [e2d170a0] DataValueInterfaces v1.0.0
-  [2b5f629d] DiffEqBase v6.155.1
+  [2b5f629d] DiffEqBase v6.155.2
   [459566f4] DiffEqCallbacks v3.9.1
   [77a26b50] DiffEqNoiseProcess v5.23.0
   [163ba53b] DiffResults v1.1.0
   [b552c78f] DiffRules v1.15.1
-  [a0c0ee7d] DifferentiationInterface v0.5.17
-  [31c24e10] Distributions v0.25.111
+  [a0c0ee7d] DifferentiationInterface v0.6.1
+  [31c24e10] Distributions v0.25.112
   [ffbed154] DocStringExtensions v0.9.3
   [e30172f5] Documenter v1.7.0
   [5b8099bc] DomainSets v0.7.14
 ⌅ [7c1d4256] DynamicPolynomials v0.5.7
 ⌅ [06fc5a27] DynamicQuantities v0.13.2
   [4e289a0a] EnumX v1.0.4
-⌅ [f151be2c] EnzymeCore v0.7.8
+  [f151be2c] EnzymeCore v0.8.3
   [e2ba6199] ExprTools v0.1.10
 ⌅ [6b7a57c9] Expronicon v0.8.5
   [8f5d6c58] EzXML v1.2.0
@@ -92,7 +92,7 @@
   [615f187c] IfElse v0.1.1
   [d25df0c9] Inflate v0.1.5
   [8197267c] IntervalSets v0.7.10
-  [3587e190] InverseFunctions v0.1.16
+  [3587e190] InverseFunctions v0.1.17
   [92d709cd] IrrationalConstants v0.2.2
   [82899510] IteratorInterfaceExtensions v1.0.0
   [692b3bcd] JLLWrappers v1.6.0
@@ -109,7 +109,7 @@
   [0e77f7df] LazilyInitializedFields v1.2.2
   [5078a376] LazyArrays v2.2.1
   [d3d80556] LineSearches v7.3.0
-  [7ed4a6bd] LinearSolve v2.34.0
+  [7ed4a6bd] LinearSolve v2.35.0
   [2ab3a3ac] LogExpFunctions v0.3.28
   [bdcacae8] LoopVectorization v0.12.171
   [d8e11817] MLStyle v0.4.17
@@ -123,7 +123,7 @@
 ⌃ [961ee093] ModelingToolkit v9.32.0
   [46d2c3a1] MuladdMacro v0.2.4
   [102ac46a] MultivariatePolynomials v0.5.6
-  [d8a4904e] MutableArithmetics v1.4.6
+  [d8a4904e] MutableArithmetics v1.5.0
   [d41bc354] NLSolversBase v7.8.3
   [77ba4419] NaNMath v1.0.2
   [8913a72c] NonlinearSolve v3.14.0
@@ -156,15 +156,14 @@
   [7e49a35a] RuntimeGeneratedFunctions v0.5.13
   [94e857df] SIMDTypes v0.1.0
   [476501e8] SLEEFPirates v0.6.43
-  [0bca4576] SciMLBase v2.53.1
+  [0bca4576] SciMLBase v2.54.0
   [c0aeaf25] SciMLOperators v0.3.10
   [53ae85a6] SciMLStructures v1.5.0
   [efcf1570] Setfield v1.1.1
-  [727e6d20] SimpleNonlinearSolve v1.12.1
+  [727e6d20] SimpleNonlinearSolve v1.12.3
   [699a6c99] SimpleTraits v0.9.4
   [a2af1166] SortingAlgorithms v1.2.1
-  [47a9eef4] SparseDiffTools v2.20.0
-  [0a514795] SparseMatrixColorings v0.4.0
+  [47a9eef4] SparseDiffTools v2.22.0
   [e56a9233] Sparspak v0.3.9
   [276daf66] SpecialFunctions v2.4.0
   [aedffcd0] Static v1.1.1
@@ -175,7 +174,7 @@
   [2913bbd2] StatsBase v0.34.3
   [4c63d2b9] StatsFuns v1.3.2
   [7792a7ef] StrideArraysCore v0.5.7
-  [2efcf032] SymbolicIndexingInterface v0.3.30
+  [2efcf032] SymbolicIndexingInterface v0.3.31
 ⌃ [19f23fe9] SymbolicLimits v0.2.1
 ⌅ [d1185830] SymbolicUtils v2.1.3
 ⌅ [0c5d862f] Symbolics v5.36.0
@@ -196,11 +195,11 @@
   [3d5dd08c] VectorizationBase v0.21.70
   [19fa3120] VertexSafeGraphs v0.2.0
   [2e619515] Expat_jll v2.6.2+0
-  [f8c6e375] Git_jll v2.44.0+2
+  [f8c6e375] Git_jll v2.46.2+0
   [1d5cc7b8] IntelOpenMP_jll v2024.2.1+0
   [94ce4f54] Libiconv_jll v1.17.0+0
   [856f044c] MKL_jll v2024.2.0+0
-  [458c3c95] OpenSSL_jll v3.0.15+0
+  [458c3c95] OpenSSL_jll v3.0.15+1
   [efe28fd5] OpenSpecFun_jll v0.5.5+0
   [f50d1b31] Rmath_jll v0.5.1+0
   [02c8fc9c] XML2_jll v2.13.3+0
@@ -253,4 +252,4 @@
   [8e850b90] libblastrampoline_jll v5.11.0+0
   [8e850ede] nghttp2_jll v1.52.0+1
   [3f19e933] p7zip_jll v17.4.0+2
-Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`

You can also download the manifest file and the project file.

+Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m`

You can also download the manifest file and the project file.

diff --git a/dev/tutorial/index.html b/dev/tutorial/index.html index a4669fb..1de55b3 100644 --- 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 -> x[1], sol.u) -plot(sol.t, V)

ODEProblem also accepts a u0 parameter to change the initial conditions (remember u0 = list_initial_conditions(ml)).

+plot(sol.t, V)

ODEProblem also accepts a u0 parameter to change the initial conditions (remember u0 = list_initial_conditions(ml)).