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ChrisRackauckasChrisRackauckas
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should fix the polyesterthreads issue
1 parent b2bd2f1 commit e1a5758

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‎benchmarks/Bio/Manifest.toml‎

Lines changed: 49 additions & 48 deletions
Original file line numberDiff line numberDiff line change
@@ -5,13 +5,14 @@ manifest_format = "2.0"
55
project_hash = "9369fd634569cdb6d6ee43acaa4c552a88a1af3f"
66

77
[[deps.ADTypes]]
8-
git-tree-sha1 = "eea5d80188827b35333801ef97a40c2ed653b081"
8+
git-tree-sha1 = "30bb95a372787af850addf28ac937f1be7b79173"
99
uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
10-
version = "1.9.0"
11-
weakdeps = ["ChainRulesCore", "EnzymeCore"]
10+
version = "1.10.0"
11+
weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"]
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1313
[deps.ADTypes.extensions]
1414
ADTypesChainRulesCoreExt = "ChainRulesCore"
15+
ADTypesConstructionBaseExt = "ConstructionBase"
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ADTypesEnzymeCoreExt = "EnzymeCore"
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[[deps.AbstractTrees]]
@@ -405,10 +406,10 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
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version = "1.9.1"
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[[deps.DiffEqBase]]
408-
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", "TruncatedStacktraces"]
409-
git-tree-sha1 = "f8eefbb7e910f59087c4bb09ce670f235758ee4a"
409+
deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PreallocationTools", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"]
410+
git-tree-sha1 = "b7dbeaa770bad0980ddddf606de814cff2acb3bc"
410411
uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
411-
version = "6.158.3"
412+
version = "6.160.0"
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[deps.DiffEqBase.extensions]
414415
DiffEqBaseCUDAExt = "CUDA"
@@ -440,9 +441,9 @@ version = "6.158.3"
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[[deps.DiffEqCallbacks]]
442443
deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"]
443-
git-tree-sha1 = "b1f970a2873a2cf76ce35fb0ed2b755a11b31052"
444+
git-tree-sha1 = "5458b607a6639b0e9c587d5afffc5d41a8f9cfb7"
444445
uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def"
445-
version = "4.1.0"
446+
version = "4.2.0"
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[[deps.DiffEqDevTools]]
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deps = ["DiffEqBase", "DiffEqNoiseProcess", "Distributed", "LinearAlgebra", "Logging", "NLsolve", "RecipesBase", "RecursiveArrayTools", "RootedTrees", "SciMLBase", "Statistics", "StructArrays"]
@@ -611,9 +612,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56"
611612
version = "1.0.4"
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[[deps.EnzymeCore]]
614-
git-tree-sha1 = "04c777af6ef65530a96ab68f0a81a4608113aa1d"
615+
git-tree-sha1 = "e333ffd38ecffcf5c6c2dafd10788404ac46fb9f"
615616
uuid = "f151be2c-9106-41f4-ab19-57ee4f262869"
616-
version = "0.8.5"
617+
version = "0.8.6"
617618
weakdeps = ["Adapt"]
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[deps.EnzymeCore.extensions]
@@ -633,9 +634,9 @@ version = "0.1.10"
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[[deps.Expat_jll]]
635636
deps = ["Artifacts", "JLLWrappers", "Libdl"]
636-
git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7"
637+
git-tree-sha1 = "cc5231d52eb1771251fbd37171dbc408bcc8a1b6"
637638
uuid = "2e619515-83b5-522b-bb60-26c02a35a201"
638-
version = "2.6.2+0"
639+
version = "2.6.4+0"
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[[deps.ExponentialUtilities]]
641642
deps = ["Adapt", "ArrayInterface", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "PrecompileTools", "Printf", "SparseArrays", "libblastrampoline_jll"]
@@ -706,9 +707,9 @@ version = "1.1.1"
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[[deps.FileIO]]
708709
deps = ["Pkg", "Requires", "UUIDs"]
709-
git-tree-sha1 = "62ca0547a14c57e98154423419d8a342dca75ca9"
710+
git-tree-sha1 = "91e0e5c68d02bcdaae76d3c8ceb4361e8f28d2e9"
710711
uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
711-
version = "1.16.4"
712+
version = "1.16.5"
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[[deps.FileWatching]]
714715
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
@@ -805,10 +806,10 @@ uuid = "77dc65aa-8811-40c2-897b-53d922fa7daf"
805806
version = "0.1.3"
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[[deps.Functors]]
808-
deps = ["LinearAlgebra"]
809-
git-tree-sha1 = "64d8e93700c7a3f28f717d265382d52fac9fa1c1"
809+
deps = ["Compat", "ConstructionBase", "LinearAlgebra", "Random"]
810+
git-tree-sha1 = "15e5397dd1cea034c7c772d9748cdee461fb5496"
810811
uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196"
811-
version = "0.4.12"
812+
version = "0.5.1"
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[[deps.Future]]
814815
deps = ["Random"]
@@ -1114,9 +1115,9 @@ version = "0.1.17"
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[[deps.LazyArrays]]
11161117
deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"]
1117-
git-tree-sha1 = "360f6039babd6e4d6364eff0d4fc9120834a2d9a"
1118+
git-tree-sha1 = "376bc148ae72e68a08f0d5d8a69e287025a37687"
11181119
uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02"
1119-
version = "2.2.1"
1120+
version = "2.2.2"
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11211122
[deps.LazyArrays.extensions]
11221123
LazyArraysBandedMatricesExt = "BandedMatrices"
@@ -1231,9 +1232,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
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[[deps.LinearSolve]]
12331234
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"]
1234-
git-tree-sha1 = "591de175461afd8323aa24b7686062574527aa3a"
1235+
git-tree-sha1 = "6b79df6e803fb62b79a364b86c790e7e21bd38ce"
12351236
uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
1236-
version = "2.36.2"
1237+
version = "2.37.0"
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[deps.LinearSolve.extensions]
12391240
LinearSolveBandedMatricesExt = "BandedMatrices"
@@ -1465,9 +1466,9 @@ version = "4.1.0"
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[[deps.NonlinearSolveBase]]
14671468
deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "FunctionProperties", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"]
1468-
git-tree-sha1 = "1589ef8aac99a21d132adf1ec5cbe6ef651760ff"
1469+
git-tree-sha1 = "46772fc296d9f16c3ab78a8ef00008ab075de677"
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uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0"
1470-
version = "1.3.1"
1471+
version = "1.3.3"
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[deps.NonlinearSolveBase.extensions]
14731474
NonlinearSolveBaseBandedMatricesExt = "BandedMatrices"
@@ -1568,9 +1569,9 @@ version = "0.5.5+0"
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[[deps.Optim]]
15701571
deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"]
1571-
git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89"
1572+
git-tree-sha1 = "ab7edad78cdef22099f43c54ef77ac63c2c9cc64"
15721573
uuid = "429524aa-4258-5aef-a3af-852621145aeb"
1573-
version = "1.9.4"
1574+
version = "1.10.0"
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[deps.Optim.extensions]
15761577
OptimMOIExt = "MathOptInterface"
@@ -1591,9 +1592,9 @@ version = "1.6.3"
15911592

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[[deps.OrdinaryDiffEq]]
15931594
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", "SparseDiffTools", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"]
1594-
git-tree-sha1 = "aa3897f89be34bdfd86472f5345d5f1f6576bcc5"
1595+
git-tree-sha1 = "36ce9bfc14a4b3dcf1490e80b5f1f4d35bfddf39"
15951596
uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
1596-
version = "6.90.0"
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version = "6.90.1"
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[[deps.OrdinaryDiffEqAdamsBashforthMoulton]]
15991600
deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"]
@@ -1609,9 +1610,9 @@ version = "1.1.2"
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[[deps.OrdinaryDiffEqCore]]
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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"]
1612-
git-tree-sha1 = "5e8c500a80674850543394ce3c745b73ad51fea0"
1613+
git-tree-sha1 = "6f86041d5978ce3574f022f4098e0c216e2a3395"
16131614
uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8"
1614-
version = "1.10.0"
1615+
version = "1.10.2"
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weakdeps = ["EnzymeCore"]
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[deps.OrdinaryDiffEqCore.extensions]
@@ -1649,9 +1650,9 @@ version = "1.2.1"
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[[deps.OrdinaryDiffEqFIRK]]
16511652
deps = ["DiffEqBase", "FastBroadcast", "FastPower", "GenericLinearAlgebra", "GenericSchur", "LinearAlgebra", "LinearSolve", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polynomials", "RecursiveArrayTools", "Reexport", "RootedTrees", "SciMLOperators", "Symbolics"]
1652-
git-tree-sha1 = "5735f4c094dff311f5064d1a351da9669e4647e3"
1653+
git-tree-sha1 = "1dcf5bebc5179c1c119a7a30f99bbb93eec02d44"
16531654
uuid = "5960d6e9-dd7a-4743-88e7-cf307b64f125"
1654-
version = "1.2.0"
1655+
version = "1.3.0"
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[[deps.OrdinaryDiffEqFeagin]]
16571658
deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "RecursiveArrayTools", "Reexport", "Static"]
@@ -1733,9 +1734,9 @@ version = "1.1.0"
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[[deps.OrdinaryDiffEqRosenbrock]]
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deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static"]
1736-
git-tree-sha1 = "56cbbdc43bd0e88083fcef3efa296501b5a435da"
1737+
git-tree-sha1 = "760a51a626d0065455847e4a3f788b07e86e5090"
17371738
uuid = "43230ef6-c299-4910-a778-202eb28ce4ce"
1738-
version = "1.3.0"
1739+
version = "1.3.1"
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[[deps.OrdinaryDiffEqSDIRK]]
17411742
deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"]
@@ -1844,9 +1845,9 @@ version = "1.4.3"
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[[deps.Plots]]
18461847
deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"]
1847-
git-tree-sha1 = "45470145863035bb124ca51b320ed35d071cc6c2"
1848+
git-tree-sha1 = "dae01f8c2e069a683d3a6e17bbae5070ab94786f"
18481849
uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
1849-
version = "1.40.8"
1850+
version = "1.40.9"
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[deps.Plots.extensions]
18521853
FileIOExt = "FileIO"
@@ -1881,10 +1882,10 @@ uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad"
18811882
version = "0.2.2"
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[[deps.Polynomials]]
1884-
deps = ["LinearAlgebra", "RecipesBase", "Requires", "Setfield", "SparseArrays"]
1885-
git-tree-sha1 = "1a9cfb2dc2c2f1bd63f1906d72af39a79b49b736"
1885+
deps = ["LinearAlgebra", "OrderedCollections", "RecipesBase", "Requires", "Setfield", "SparseArrays"]
1886+
git-tree-sha1 = "adc25dbd4d13f148f3256b6d4743fe7e63a71c4a"
18861887
uuid = "f27b6e38-b328-58d1-80ce-0feddd5e7a45"
1887-
version = "4.0.11"
1888+
version = "4.0.12"
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[deps.Polynomials.extensions]
18901891
PolynomialsChainRulesCoreExt = "ChainRulesCore"
@@ -2121,9 +2122,9 @@ version = "0.6.43"
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[[deps.SciMLBase]]
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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"]
2124-
git-tree-sha1 = "7527b9adb22904f0f51d8ab85d826f81ebb6f78d"
2125+
git-tree-sha1 = "cacc7bc54bab8749b1fc1032c4911fe80cffb959"
21252126
uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
2126-
version = "2.59.2"
2127+
version = "2.61.0"
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[deps.SciMLBase.extensions]
21292130
SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -2274,9 +2275,9 @@ version = "2.23.0"
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[[deps.SparseMatrixColorings]]
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deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"]
2277-
git-tree-sha1 = "670f2c8109e87d79788baef47880b946e529f1a2"
2278+
git-tree-sha1 = "76b44c879661552d64f382acf66faa29ab56b3d9"
22782279
uuid = "0a514795-09f3-496d-8182-132a7b665d35"
2279-
version = "0.4.9"
2280+
version = "0.4.10"
22802281
weakdeps = ["Colors"]
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[deps.SparseMatrixColorings.extensions]
@@ -2413,9 +2414,9 @@ version = "5.2.2+0"
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[[deps.SymbolicIndexingInterface]]
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deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"]
2416-
git-tree-sha1 = "20cf607cafb31f922bce84d60379203e7a126911"
2417+
git-tree-sha1 = "6c6761e08bf5a270905cdd065be633abfa1b155b"
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uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
2418-
version = "0.3.34"
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version = "0.3.35"
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[[deps.SymbolicLimits]]
24212422
deps = ["SymbolicUtils"]
@@ -2439,9 +2440,9 @@ version = "3.7.2"
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[[deps.Symbolics]]
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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"]
2442-
git-tree-sha1 = "0caef7687abf7094132fa3112bf5514c36a99226"
2443+
git-tree-sha1 = "d5c0ea92aa7b14b0ffca575e07af48ecb9e83f7b"
24432444
uuid = "0c5d862f-8b57-4792-8d23-62f2024744c7"
2444-
version = "6.18.3"
2445+
version = "6.21.0"
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[deps.Symbolics.extensions]
24472448
SymbolicsForwardDiffExt = "ForwardDiff"
@@ -2634,9 +2635,9 @@ version = "0.10.12"
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[[deps.XML2_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
2637-
git-tree-sha1 = "6a451c6f33a176150f315726eba8b92fbfdb9ae7"
2638+
git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6"
26382639
uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
2639-
version = "2.13.4+0"
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version = "2.13.5+0"
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[[deps.XSLT_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"]

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