mani regen

Author: AoifeHughes

Manifest.toml

@@ -5,9 +5,9 @@ manifest_format = "2.0"
 project_hash = "296b7e06e398e8898b40f44ed92b4d60c484484c"
 
 [[deps.ADTypes]]
-git-tree-sha1 = "7927b9af540ee964cc5d1b73293f1eb0b761a3a1"
+git-tree-sha1 = "60665b326b75db6517939d0e1875850bc4a54368"
 uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
-version = "1.16.0"
+version = "1.17.0"
 weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"]
 
     [deps.ADTypes.extensions]
@@ -86,9 +86,9 @@ weakdeps = ["SparseArrays", "StaticArrays"]
 
 [[deps.AdvancedHMC]]
 deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Setfield", "Statistics", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "9f75990a04e3ee45d80b19778ba9d2bb7ad4d5ee"
+git-tree-sha1 = "22496647c061d00217759e95a18d601c959df0c9"
 uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d"
-version = "0.8.0"
+version = "0.8.1"
 
     [deps.AdvancedHMC.extensions]
     AdvancedHMCADTypesExt = "ADTypes"
@@ -298,9 +298,9 @@ version = "0.1.1"
 
 [[deps.Bijectors]]
 deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics"]
-git-tree-sha1 = "5eb5a58ed34e012d7f8d665cb5198252e128e907"
+git-tree-sha1 = "35ba30573d4f83242f1e788c87ca792c83553c9e"
 uuid = "76274a88-744f-5084-9051-94815aaf08c4"
-version = "0.15.8"
+version = "0.15.9"
 weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff", "Tracker"]
 
     [deps.Bijectors.extensions]
@@ -703,9 +703,9 @@ version = "0.4.0"
 
 [[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 = "6fecfae8b2d9983e939378c8eacff6562e8a2567"
+git-tree-sha1 = "1b1e070e57681d1176d99a5ec455717e24686612"
 uuid = "2b5f629d-d688-5b77-993f-72d75c75574e"
-version = "6.183.0"
+version = "6.183.2"
 
     [deps.DiffEqBase.extensions]
     DiffEqBaseCUDAExt = "CUDA"
@@ -777,9 +777,9 @@ version = "7.16.1"
 
 [[deps.DifferentiationInterface]]
 deps = ["ADTypes", "LinearAlgebra"]
-git-tree-sha1 = "54d7b8c74408048aea9c055ac8573b2b5c5ec11f"
+git-tree-sha1 = "38989b1532a3c6e2341d52b77c5475c42c3318a8"
 uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
-version = "0.7.4"
+version = "0.7.6"
 
     [deps.DifferentiationInterface.extensions]
     DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore"
@@ -929,9 +929,9 @@ version = "1.0.5"
 
 [[deps.Enzyme]]
 deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"]
-git-tree-sha1 = "1a9c9e3401f5d024612a70d24a19517b2dbc1824"
+git-tree-sha1 = "7297613272c67cb7f11969679960419c5e463974"
 uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9"
-version = "0.13.67"
+version = "0.13.68"
 
     [deps.Enzyme.extensions]
     EnzymeBFloat16sExt = "BFloat16s"
@@ -1123,9 +1123,9 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"]
 
 [[deps.FiniteDiff]]
 deps = ["ArrayInterface", "LinearAlgebra", "Setfield"]
-git-tree-sha1 = "f089ab1f834470c525562030c8cfde4025d5e915"
+git-tree-sha1 = "31fd32af86234b6b71add76229d53129aa1b87a9"
 uuid = "6a86dc24-6348-571c-b903-95158fe2bd41"
-version = "2.27.0"
+version = "2.28.1"
 
     [deps.FiniteDiff.extensions]
     FiniteDiffBandedMatricesExt = "BandedMatrices"
@@ -1290,9 +1290,9 @@ version = "1.3.15+0"
 
 [[deps.Graphs]]
 deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
-git-tree-sha1 = "c5abfa0ae0aaee162a3fbb053c13ecda39be545b"
+git-tree-sha1 = "7a98c6502f4632dbe9fb1973a4244eaa3324e84d"
 uuid = "86223c79-3864-5bf0-83f7-82e725a168b6"
-version = "1.13.0"
+version = "1.13.1"
 
 [[deps.Grisu]]
 git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
@@ -1758,9 +1758,9 @@ 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 = "1c597eceb5ead73dae17ffa4dcc1160e3e4da1f3"
+git-tree-sha1 = "43ad373b1a9ea03250aba3b02b2d70622c7dc5d2"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "3.28.0"
+version = "3.31.0"
 
     [deps.LinearSolve.extensions]
     LinearSolveAMDGPUExt = "AMDGPU"
@@ -1770,6 +1770,7 @@ version = "3.28.0"
     LinearSolveCUDAExt = "CUDA"
     LinearSolveCUDSSExt = "CUDSS"
     LinearSolveCUSOLVERRFExt = ["CUSOLVERRF", "SparseArrays"]
+    LinearSolveCliqueTreesExt = ["CliqueTrees", "SparseArrays"]
     LinearSolveEnzymeExt = "EnzymeCore"
     LinearSolveFastAlmostBandedMatricesExt = "FastAlmostBandedMatrices"
     LinearSolveFastLapackInterfaceExt = "FastLapackInterface"
@@ -1791,6 +1792,7 @@ version = "3.28.0"
     CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
     CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e"
     CUSOLVERRF = "a8cc9031-bad2-4722-94f5-40deabb4245c"
+    CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8"
     EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869"
     FastAlmostBandedMatrices = "9d29842c-ecb8-4973-b1e9-a27b1157504e"
     FastLapackInterface = "29a986be-02c6-4525-aec4-84b980013641"
@@ -1865,9 +1867,9 @@ version = "1.1.0"
 
 [[deps.Lux]]
 deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "DiffResults", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "Preferences", "Random", "Reexport", "SIMDTypes", "Setfield", "Static", "StaticArraysCore", "Statistics", "WeightInitializers"]
-git-tree-sha1 = "c05e5c3dca1810e728429771763b485057322ad2"
+git-tree-sha1 = "c01b012bbf84e6d5aab7b75782a73f453d34be87"
 uuid = "b2108857-7c20-44ae-9111-449ecde12c47"
-version = "1.16.0"
+version = "1.17.0"
 
     [deps.Lux.extensions]
     LuxComponentArraysExt = "ComponentArrays"
@@ -1932,9 +1934,9 @@ version = "1.3.0"
 
 [[deps.LuxLib]]
 deps = ["ArrayInterface", "CPUSummary", "ChainRulesCore", "Compat", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "KernelAbstractions", "LinearAlgebra", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Polyester", "Preferences", "Random", "Reexport", "Static", "StaticArraysCore", "Statistics"]
-git-tree-sha1 = "bf64921ca8182e3ee34a56b05b9f1ed568141a13"
+git-tree-sha1 = "5d1d796c8b2878b5cad2849970c52897ff8c0271"
 uuid = "82251201-b29d-42c6-8e01-566dec8acb11"
-version = "1.10.1"
+version = "1.10.2"
 
     [deps.LuxLib.extensions]
     LuxLibAppleAccelerateExt = "AppleAccelerate"
@@ -1943,7 +1945,6 @@ version = "1.10.1"
     LuxLibEnzymeExt = "Enzyme"
     LuxLibLoopVectorizationExt = "LoopVectorization"
     LuxLibMKLExt = "MKL"
-    LuxLibMooncakeExt = "Mooncake"
     LuxLibOctavianExt = ["Octavian", "LoopVectorization"]
     LuxLibReactantExt = "Reactant"
     LuxLibReverseDiffExt = "ReverseDiff"
@@ -1960,7 +1961,6 @@ version = "1.10.1"
     Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
     LoopVectorization = "bdcacae8-1622-11e9-2a5c-532679323890"
     MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
-    Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
     Octavian = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4"
     Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
     ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
@@ -2194,17 +2194,17 @@ version = "0.8.1"
 
 [[deps.Mooncake]]
 deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DispatchDoctor", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Test"]
-git-tree-sha1 = "88bb6e5054ba4a341c8fb7047af859720669628d"
+git-tree-sha1 = "955bad945bc815c4b48fb4d17ce39cf3ba6abcf3"
 uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
-version = "0.4.142"
+version = "0.4.150"
 
     [deps.Mooncake.extensions]
     MooncakeAllocCheckExt = "AllocCheck"
     MooncakeCUDAExt = "CUDA"
     MooncakeDynamicExpressionsExt = "DynamicExpressions"
     MooncakeFluxExt = "Flux"
     MooncakeJETExt = "JET"
-    MooncakeLuxLibExt = "LuxLib"
+    MooncakeLuxLibExt = ["LuxLib", "MLDataDevices", "Static"]
     MooncakeLuxLibSLEEFPiratesExtension = ["LuxLib", "SLEEFPirates"]
     MooncakeNNlibExt = "NNlib"
     MooncakeSpecialFunctionsExt = "SpecialFunctions"
@@ -2216,9 +2216,11 @@ version = "0.4.142"
     Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
     JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
     LuxLib = "82251201-b29d-42c6-8e01-566dec8acb11"
+    MLDataDevices = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40"
     NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
     SLEEFPirates = "476501e8-09a2-5ece-8869-fb82de89a1fa"
     SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+    Static = "aedffcd0-7271-4cad-89d0-dc628f76c6d3"
 
 [[deps.Moshi]]
 deps = ["ExproniconLite", "Jieko"]
@@ -2567,9 +2569,9 @@ version = "1.5.0"
 
 [[deps.OrdinaryDiffEqBDF]]
 deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TruncatedStacktraces"]
-git-tree-sha1 = "8fdcc6e46e55eb7c6332e4040df82c3f69fe5b9c"
+git-tree-sha1 = "ce8db53fd1e4e41c020fd53961e7314f75e4c21c"
 uuid = "6ad6398a-0878-4a85-9266-38940aa047c8"
-version = "1.10.0"
+version = "1.10.1"
 
 [[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"]
@@ -2590,9 +2592,9 @@ version = "1.8.0"
 
 [[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 = "c7c01ae1a6eb15ac73f3d3da2161df9af2117085"
+git-tree-sha1 = "4c270747152db513dd80bfd5f2f9df48befff28a"
 uuid = "4302a76b-040a-498a-8c04-15b101fed76b"
-version = "1.13.0"
+version = "1.14.0"
 
 [[deps.OrdinaryDiffEqExplicitRK]]
 deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"]
@@ -2662,9 +2664,9 @@ version = "1.6.0"
 
 [[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 = "36171d94ed6406ba9264eef88326ebc65646fbf5"
+git-tree-sha1 = "b05226afc8fa6b8fc6f2258a89987b4f5bd0db4e"
 uuid = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8"
-version = "1.14.0"
+version = "1.14.1"
 
 [[deps.OrdinaryDiffEqNordsieck]]
 deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"]
@@ -2698,9 +2700,9 @@ version = "1.5.0"
 
 [[deps.OrdinaryDiffEqRosenbrock]]
 deps = ["ADTypes", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Static"]
-git-tree-sha1 = "bd17c40752ff4c54edad67ddf3f32ec6699668b9"
+git-tree-sha1 = "a06c1263d71ea42a1881b4d49c8a087035d4a3ff"
 uuid = "43230ef6-c299-4910-a778-202eb28ce4ce"
-version = "1.16.0"
+version = "1.16.1"
 
 [[deps.OrdinaryDiffEqSDIRK]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"]
@@ -2858,9 +2860,9 @@ version = "0.2.4"
 
 [[deps.PreallocationTools]]
 deps = ["Adapt", "ArrayInterface", "PrecompileTools"]
-git-tree-sha1 = "a0d5f963cfee70bee26dfa137a732e759e24436a"
+git-tree-sha1 = "520070df581845686c8c488b6dadce6b2c316856"
 uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46"
-version = "0.4.31"
+version = "0.4.32"
 weakdeps = ["ForwardDiff", "ReverseDiff", "SparseConnectivityTracer"]
 
     [deps.PreallocationTools.extensions]
@@ -3016,9 +3018,9 @@ version = "0.6.12"
 
 [[deps.RecursiveArrayTools]]
 deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
-git-tree-sha1 = "7c7ac305885b1e0292585d087ecd60331a705965"
+git-tree-sha1 = "96bef5b9ac123fff1b379acf0303cf914aaabdfd"
 uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
-version = "3.37.0"
+version = "3.37.1"
 
     [deps.RecursiveArrayTools.extensions]
     RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
@@ -3129,10 +3131,10 @@ uuid = "26aad666-b158-4e64-9d35-0e672562fa48"
 version = "0.5.1"
 
 [[deps.SciMLBase]]
-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 = "c056c723b68700fec386dfde8c577089df720c8e"
+deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PreallocationTools", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
+git-tree-sha1 = "4398bda451c3c7aaca91a8077bcba227fe236d72"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.108.0"
+version = "2.111.1"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -3516,10 +3518,14 @@ uuid = "fb77eaff-e24c-56d4-86b1-d163f2edb164"
 version = "5.2.3+0"
 
 [[deps.SymbolicIndexingInterface]]
-deps = ["Accessors", "ArrayInterface", "PrettyTables", "RuntimeGeneratedFunctions", "StaticArraysCore"]
-git-tree-sha1 = "59ca6eddaaa9849e7de9fd1153b6faf0b1db7b80"
+deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"]
+git-tree-sha1 = "93104ca226670c0cb92ba8bc6998852ad55a2d4c"
 uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
-version = "0.3.42"
+version = "0.3.43"
+weakdeps = ["PrettyTables"]
+
+    [deps.SymbolicIndexingInterface.extensions]
+    SymbolicIndexingInterfacePrettyTablesExt = "PrettyTables"
 
 [[deps.TOML]]
 deps = ["Dates"]