diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index 9692bcd..e36ddd2 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-18T19:02:54","documenter_version":"1.8.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.11.2","generation_timestamp":"2024-12-10T17:54:10","documenter_version":"1.8.0"}} \ No newline at end of file diff --git a/dev/api/index.html b/dev/api/index.html index 04e26f0..48b8989 100644 --- a/dev/api/index.html +++ b/dev/api/index.html @@ -1,2 +1,2 @@ -API documentation · SBMLToolkit.jl
GitHub

API documentation

SBML.readSBML — Method
readSBML(sbmlfile::String, ::DefaultImporter)

Create a SBML.Model from an SBML file, using the default import settings for use as Catalyst and ModelingToolkit types.

See also Model and DefaultImporter.

source
+API documentation · SBMLToolkit.jl
GitHub

API documentation

SBML.readSBML — Method
readSBML(sbmlfile::String, ::DefaultImporter)

Create a SBML.Model from an SBML file, using the default import settings for use as Catalyst and ModelingToolkit types.

See also Model and DefaultImporter.

source
diff --git a/dev/assets/Manifest.toml b/dev/assets/Manifest.toml index 7b5e55b..62ef954 100644 --- a/dev/assets/Manifest.toml +++ b/dev/assets/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.11.1" +julia_version = "1.11.2" manifest_format = "2.0" project_hash = "aa8d6397ebfd3ae949b6b3a9e7ca9ff2f6537da5" [[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] @@ -27,9 +27,9 @@ version = "0.4.5" [[deps.Accessors]] deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"] -git-tree-sha1 = "b392ede862e506d451fc1616e79aa6f4c673dab8" +git-tree-sha1 = "96bed9b1b57cf750cca50c311a197e306816a1cc" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.38" +version = "0.1.39" [deps.Accessors.extensions] AccessorsAxisKeysExt = "AxisKeys" @@ -110,9 +110,9 @@ version = "7.17.1" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "492681bc44fac86804706ddb37da10880a2bd528" +git-tree-sha1 = "2bf6e01f453284cb61c312836b4680331ddfc44b" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.10.4" +version = "1.11.0" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -139,9 +139,9 @@ version = "0.1.6" [[deps.BlockArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra"] -git-tree-sha1 = "d434647f798823bcae510aee0bc0401927f64391" +git-tree-sha1 = "b406207917260364a2e0287b42e4c6772cb9db88" uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" -version = "1.1.1" +version = "1.3.0" [deps.BlockArrays.extensions] BlockArraysBandedMatricesExt = "BandedMatrices" @@ -358,15 +358,15 @@ 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"] -git-tree-sha1 = "ab1e6515ce15f01316a9825b02729fefa51726bd" +git-tree-sha1 = "880d1fcf95e6492a4e7d65c2866dbdbf6580d4f8" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.23.0" +version = "5.24.0" [deps.DiffEqNoiseProcess.extensions] DiffEqNoiseProcessReverseDiffExt = "ReverseDiff" @@ -388,21 +388,21 @@ version = "1.15.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "0c99576d0b93df0aff1bed9d9adddef14e4e658f" +git-tree-sha1 = "7ffe68edc2a4ad0ff2eeb5a32cc99ab45746fe3d" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.6.22" +version = "0.6.27" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" DifferentiationInterfaceDiffractorExt = "Diffractor" - DifferentiationInterfaceEnzymeExt = "Enzyme" + DifferentiationInterfaceEnzymeExt = ["EnzymeCore", "Enzyme"] DifferentiationInterfaceFastDifferentiationExt = "FastDifferentiation" DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" - DifferentiationInterfaceForwardDiffExt = "ForwardDiff" + DifferentiationInterfaceForwardDiffExt = ["ForwardDiff", "DiffResults"] DifferentiationInterfaceMooncakeExt = "Mooncake" DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" - DifferentiationInterfaceReverseDiffExt = "ReverseDiff" + DifferentiationInterfaceReverseDiffExt = ["ReverseDiff", "DiffResults"] DifferentiationInterfaceSparseArraysExt = "SparseArrays" DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" DifferentiationInterfaceStaticArraysExt = "StaticArrays" @@ -412,8 +412,10 @@ version = "0.6.22" [deps.DifferentiationInterface.weakdeps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DiffResults = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" Diffractor = "9f5e2b26-1114-432f-b630-d3fe2085c51c" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FastDifferentiation = "eb9bf01b-bf85-4b60-bf87-ee5de06c00be" FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" @@ -491,15 +493,15 @@ 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" @@ -519,9 +521,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.EnzymeCore]] -git-tree-sha1 = "e333ffd38ecffcf5c6c2dafd10788404ac46fb9f" +git-tree-sha1 = "0cdb7af5c39e92d78a0ee8d0a447d32f7593137e" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.8.6" +version = "0.8.8" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -529,9 +531,9 @@ weakdeps = ["Adapt"] [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "cc5231d52eb1771251fbd37171dbc408bcc8a1b6" +git-tree-sha1 = "e51db81749b0777b2147fbe7b783ee79045b8e99" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.6.4+0" +version = "2.6.4+1" [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" @@ -605,9 +607,9 @@ 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" @@ -655,9 +657,9 @@ version = "0.1.3" [[deps.Functors]] deps = ["Compat", "ConstructionBase", "LinearAlgebra", "Random"] -git-tree-sha1 = "15e5397dd1cea034c7c772d9748cdee461fb5496" +git-tree-sha1 = "60a0339f28a233601cb74468032b5c302d5067de" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.5.1" +version = "0.5.2" [[deps.Future]] deps = ["Random"] @@ -666,9 +668,9 @@ version = "1.11.0" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950" +git-tree-sha1 = "83cf05ab16a73219e5f6bd1bdfa9848fa24ac627" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.6" +version = "0.2.0" [[deps.Git]] deps = ["Git_jll"] @@ -678,9 +680,9 @@ 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 = "ea372033d09e4552a04fd38361cd019f9003f4f4" +git-tree-sha1 = "399f4a308c804b446ae4c91eeafadb2fe2c54ff9" uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb" -version = "2.46.2+0" +version = "2.47.1+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -839,9 +841,9 @@ version = "1.3.0" [[deps.LazyArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "376bc148ae72e68a08f0d5d8a69e287025a37687" +git-tree-sha1 = "f289bee714e11708df257c57514585863aa02b33" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "2.2.2" +version = "2.3.1" [deps.LazyArrays.extensions] LazyArraysBandedMatricesExt = "BandedMatrices" @@ -918,9 +920,9 @@ version = "1.11.0" [[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 = "6b79df6e803fb62b79a364b86c790e7e21bd38ce" +git-tree-sha1 = "9d5872d134bd33dd3e120767004f760770958863" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.37.0" +version = "2.38.0" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" @@ -1042,16 +1044,17 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" 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" +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", "SCCNonlinearSolve", "SciMLBase", "SciMLStructures", "Serialization", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SpecialFunctions", "StaticArrays", "SymbolicIndexingInterface", "SymbolicUtils", "Symbolics", "URIs", "UnPack", "Unitful"] +git-tree-sha1 = "afb3f4346dda57caf44cdf3ff8faf9e1afc7f1fd" uuid = "961ee093-0014-501f-94e3-6117800e7a78" -version = "9.51.0" +version = "9.57.0" [deps.ModelingToolkit.extensions] MTKBifurcationKitExt = "BifurcationKit" MTKChainRulesCoreExt = "ChainRulesCore" MTKDeepDiffsExt = "DeepDiffs" MTKHomotopyContinuationExt = "HomotopyContinuation" + MTKInfiniteOptExt = "InfiniteOpt" MTKLabelledArraysExt = "LabelledArrays" [deps.ModelingToolkit.weakdeps] @@ -1059,6 +1062,7 @@ version = "9.51.0" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6" HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327" + InfiniteOpt = "20393b10-9daf-11e9-18c9-8db751c92c57" LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800" [[deps.MozillaCACerts_jll]] @@ -1173,9 +1177,9 @@ uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2" version = "1.0.0" [[deps.OffsetArrays]] -git-tree-sha1 = "1a27764e945a152f7ca7efa04de513d473e9542e" +git-tree-sha1 = "39d000d9c33706b8364817d8894fae1548f40295" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.14.1" +version = "1.14.2" weakdeps = ["Adapt"] [deps.OffsetArrays.extensions] @@ -1216,9 +1220,9 @@ version = "1.10.0" MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" [[deps.OrderedCollections]] -git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" +git-tree-sha1 = "12f1439c4f986bb868acda6ea33ebc78e19b95ad" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.3" +version = "1.7.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1358,9 +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" @@ -1369,6 +1373,7 @@ version = "3.27.3" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] + RecursiveArrayToolsStructArraysExt = "StructArrays" RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" @@ -1379,6 +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" @@ -1447,6 +1453,12 @@ git-tree-sha1 = "7567084bd3defc697c168b8b0ab3d28a9bc47648" uuid = "bb12108a-f4ef-5f88-8ef3-0b33ff7017f1" version = "5.20.1+0" +[[deps.SCCNonlinearSolve]] +deps = ["CommonSolve", "PrecompileTools", "Reexport", "SciMLBase", "SymbolicIndexingInterface"] +git-tree-sha1 = "0caf35e2204c9045ca203b147b5dac4fa8e1cf20" +uuid = "9dfe8606-65a1-4bb3-9748-cb89d1561431" +version = "1.0.0" + [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" @@ -1464,9 +1476,9 @@ 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 = "87e054302a94a2d087f918ad50b0290977db67e6" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.62.0" +version = "2.67.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -1506,9 +1518,9 @@ 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" @@ -1679,9 +1691,9 @@ version = "7.7.0+0" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "6c6761e08bf5a270905cdd065be633abfa1b155b" +git-tree-sha1 = "8db233b54917e474165d582bef2244fa040e0a56" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.35" +version = "0.3.36" [[deps.SymbolicLimits]] deps = ["SymbolicUtils"] @@ -1705,9 +1717,9 @@ 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" @@ -1770,9 +1782,9 @@ version = "0.5.2" [[deps.TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "3a6f063d690135f5c1ba351412c82bae4d1402bf" +git-tree-sha1 = "d7298ebdfa1654583468a487e8e83fae9d72dac3" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.25" +version = "0.5.26" [[deps.Tokenize]] git-tree-sha1 = "468b4685af4abe0e9fd4d7bf495a6554a6276e75" @@ -1822,9 +1834,9 @@ version = "1.11.0" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" +git-tree-sha1 = "01915bfcd62be15329c9a07235447a89d588327c" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.21.0" +version = "1.21.1" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] diff --git a/dev/index.html b/dev/index.html index e3a07d6..b04f4f8 100644 --- a/dev/index.html +++ b/dev/index.html @@ -16,8 +16,8 @@ rs = readSBML(sbmlfile, ReactionSystemImporter()) odesys = readSBML(sbmlfile, ODESystemImporter())

License

The package is released under the MIT license.

Development team

This package was developed by Paul F. Lang at the University of Oxford, UK and Anand Jain at the University of Chicago, USA.

Questions and comments

Please use GitHub issues, the #sciml-sysbio channel in the Julia Slack workspace or email Paul F. Lang or Anand Jain with any questions or comments.

Reproducibility

The documentation of this SciML package was built using these direct dependencies,
Status `~/work/SBMLToolkit.jl/SBMLToolkit.jl/docs/Project.toml`
   [e30172f5] Documenter v1.8.0
-  [86080e66] SBMLToolkit v0.1.29 `~/work/SBMLToolkit.jl/SBMLToolkit.jl`
and using this machine and Julia version.
Julia Version 1.11.1
-Commit 8f5b7ca12ad (2024-10-16 10:53 UTC)
+  [86080e66] SBMLToolkit v0.1.29 `~/work/SBMLToolkit.jl/SBMLToolkit.jl`
and using this machine and Julia version.
Julia Version 1.11.2
+Commit 5e9a32e7af2 (2024-12-01 20:02 UTC)
 Build Info:
   Official https://julialang.org/ release
 Platform Info:
@@ -26,18 +26,18 @@
   WORD_SIZE: 64
   LLVM: libLLVM-16.0.6 (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/SBMLToolkit.jl/SBMLToolkit.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
+  [7d9f7c33] Accessors v0.1.39
   [79e6a3ab] Adapt v4.1.1
   [66dad0bd] AliasTables v1.1.3
   [ec485272] ArnoldiMethod v0.4.0
   [4fba245c] ArrayInterface v7.17.1
-  [4c555306] ArrayLayouts v1.10.4
+  [4c555306] ArrayLayouts v1.11.0
   [e2ed5e7c] Bijections v0.1.9
   [62783981] BitTwiddlingConvenienceFunctions v0.1.6
-  [8e7c35d0] BlockArrays v1.1.1
+  [8e7c35d0] BlockArrays v1.3.0
   [70df07ce] BracketingNonlinearSolve v1.1.0
   [2a0fbf3d] CPUSummary v0.2.6
   [00ebfdb7] CSTParser v3.4.3
@@ -62,20 +62,20 @@
   [864edb3b] DataStructures v0.18.20
   [e2d170a0] DataValueInterfaces v1.0.0
   [2b5f629d] DiffEqBase v6.160.0
-  [459566f4] DiffEqCallbacks v4.2.1
-  [77a26b50] DiffEqNoiseProcess v5.23.0
+  [459566f4] DiffEqCallbacks v4.2.2
+  [77a26b50] DiffEqNoiseProcess v5.24.0
   [163ba53b] DiffResults v1.1.0
   [b552c78f] DiffRules v1.15.1
-  [a0c0ee7d] DifferentiationInterface v0.6.22
+  [a0c0ee7d] DifferentiationInterface v0.6.27
   [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
+  [f151be2c] EnzymeCore v0.8.8
   [e2ba6199] ExprTools v0.1.10
 ⌅ [6b7a57c9] Expronicon v0.8.5
   [7034ab61] FastBroadcast v0.3.5
@@ -84,14 +84,14 @@
   [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
   [069b7b12] FunctionWrappers v1.1.3
   [77dc65aa] FunctionWrappersWrappers v0.1.3
-  [d9f16b24] Functors v0.5.1
-⌅ [46192b85] GPUArraysCore v0.1.6
+  [d9f16b24] Functors v0.5.2
+  [46192b85] GPUArraysCore v0.2.0
   [d7ba0133] Git v1.3.1
   [c27321d9] Glob v1.3.1
   [86223c79] Graphs v1.12.0
@@ -115,10 +115,10 @@
   [23fbe1c1] Latexify v0.16.5
   [10f19ff3] LayoutPointers v0.1.17
   [0e77f7df] LazilyInitializedFields v1.3.0
-  [5078a376] LazyArrays v2.2.2
+  [5078a376] LazyArrays v2.3.1
   [87fe0de2] LineSearch v0.1.4
   [d3d80556] LineSearches v7.3.0
-  [7ed4a6bd] LinearSolve v2.37.0
+  [7ed4a6bd] LinearSolve v2.38.0
   [2ab3a3ac] LogExpFunctions v0.3.28
   [bdcacae8] LoopVectorization v0.12.171
   [d8e11817] MLStyle v0.4.17
@@ -127,7 +127,7 @@
   [d0879d2d] MarkdownAST v0.1.2
   [bb5d69b7] MaybeInplace v0.1.4
   [e1d29d7a] Missings v1.2.0
-  [961ee093] ModelingToolkit v9.51.0
+  [961ee093] ModelingToolkit v9.57.0
   [46d2c3a1] MuladdMacro v0.2.4
   [102ac46a] MultivariatePolynomials v0.5.7
   [d8a4904e] MutableArithmetics v1.6.0
@@ -138,9 +138,9 @@
   [5959db7a] NonlinearSolveFirstOrder v1.1.0
   [9a2c21bd] NonlinearSolveQuasiNewton v1.0.0
   [26075421] NonlinearSolveSpectralMethods v1.0.0
-  [6fe1bfb0] OffsetArrays v1.14.1
+  [6fe1bfb0] OffsetArrays v1.14.2
   [429524aa] Optim v1.10.0
-  [bac558e1] OrderedCollections v1.6.3
+  [bac558e1] OrderedCollections v1.7.0
   [90014a1f] PDMats v0.11.31
   [d96e819e] Parameters v0.12.3
   [69de0a69] Parsers v2.8.1
@@ -157,7 +157,7 @@
   [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
@@ -167,12 +167,13 @@
   [7e49a35a] RuntimeGeneratedFunctions v0.5.13
   [e5567a89] SBML v1.5.1
   [86080e66] SBMLToolkit v0.1.29 `~/work/SBMLToolkit.jl/SBMLToolkit.jl`
+  [9dfe8606] SCCNonlinearSolve v1.0.0
   [94e857df] SIMDTypes v0.1.0
   [476501e8] SLEEFPirates v0.6.43
-  [0bca4576] SciMLBase v2.62.0
+  [0bca4576] SciMLBase v2.67.0
   [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
@@ -189,16 +190,16 @@
   [2913bbd2] StatsBase v0.34.3
   [4c63d2b9] StatsFuns v1.3.2
   [7792a7ef] StrideArraysCore v0.5.7
-  [2efcf032] SymbolicIndexingInterface v0.3.35
+  [2efcf032] SymbolicIndexingInterface v0.3.36
   [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
   [1c621080] TestItems v1.0.0
   [8290d209] ThreadingUtilities v0.5.2
-  [a759f4b9] TimerOutputs v0.5.25
+  [a759f4b9] TimerOutputs v0.5.26
   [0796e94c] Tokenize v0.5.29
   [3bb67fe8] TranscodingStreams v0.11.3
   [d5829a12] TriangularSolve v0.2.1
@@ -206,11 +207,11 @@
   [781d530d] TruncatedStacktraces v1.4.0
   [5c2747f8] URIs v1.5.1
   [3a884ed6] UnPack v1.0.2
-  [1986cc42] Unitful v1.21.0
+  [1986cc42] Unitful v1.21.1
   [a7c27f48] Unityper v0.1.6
   [3d5dd08c] VectorizationBase v0.21.71
-  [2e619515] Expat_jll v2.6.4+0
-  [f8c6e375] Git_jll v2.46.2+0
+  [2e619515] Expat_jll v2.6.4+1
+  [f8c6e375] Git_jll v2.47.1+0
   [1d5cc7b8] IntelOpenMP_jll v2024.2.1+0
   [94ce4f54] Libiconv_jll v1.17.0+1
   [856f044c] MKL_jll v2024.2.0+0
@@ -268,4 +269,4 @@
   [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`

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

+Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m`

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