bumps

Author: ChrisRackauckas

benchmarks/Bio/BCR.jmd

@@ -295,8 +295,7 @@ wp = WorkPrecisionSet([oprob,oprob_sparse,sparsejacprob],abstols,reltols,setups;
 names = ["CVODE_BDF (GMRES, iLU)" "QNDF (GMRES, iLU)" "FBDF (GMRES, iLU)" "QNDF (KLU, sparse jac)" "FBDF (KLU, sparse jac)" "KenCarp4 (KLU, sparse jac)"]
 colors = [:green :deepskyblue1 :dodgerblue2 :royalblue2 :slateblue3 :lightskyblue]
 markershapes = [:octagon :hexagon :rtriangle :pentagon :ltriangle :star5]
-xlimit = xlimit .* [0.95,1/0.95]; ylimit = ylimit .* [0.95,1/0.95];
-plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xlimit=xlimit,ylimit=ylimit,xticks=[1e-3,1e-2,1e-1,1e0,1e1,1e2,1e3],yticks=[1e0,1e1,1e2,1e3],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000))
+plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xticks=[1e-3,1e-2,1e-1,1e0,1e1,1e2,1e3],yticks=[1e0,1e1,1e2,1e3],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000))
 ```
 
 ```julia, echo = false

benchmarks/Bio/Manifest.toml

@@ -152,6 +152,16 @@ version = "1.1.1"
     [deps.BlockArrays.weakdeps]
     BandedMatrices = "aae01518-5342-5314-be14-df237901396f"
 
+[[deps.BracketingNonlinearSolve]]
+deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"]
+git-tree-sha1 = "95cb19c37ea427617e9795655667712f03058d98"
+uuid = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e"
+version = "1.1.0"
+weakdeps = ["ForwardDiff"]
+
+    [deps.BracketingNonlinearSolve.extensions]
+    BracketingNonlinearSolveForwardDiffExt = "ForwardDiff"
+
 [[deps.Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1"
@@ -181,6 +191,11 @@ git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642"
 uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a"
 version = "1.18.2+1"
 
+[[deps.Cassette]]
+git-tree-sha1 = "f8764df8d9d2aec2812f009a1ac39e46c33354b8"
+uuid = "7057c7e9-c182-5462-911a-8362d720325c"
+version = "0.3.14"
+
 [[deps.Catalyst]]
 deps = ["Combinatorics", "DataStructures", "DiffEqBase", "DocStringExtensions", "DynamicPolynomials", "DynamicQuantities", "Graphs", "JumpProcesses", "LaTeXStrings", "Latexify", "LinearAlgebra", "MacroTools", "ModelingToolkit", "Parameters", "Reexport", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "Setfield", "SparseArrays", "SymbolicUtils", "Symbolics", "Unitful"]
 git-tree-sha1 = "dafd059c1d80ba02006978cd05ea7264ff1f362e"
@@ -574,9 +589,9 @@ version = "0.6.0"
 
 [[deps.DynamicQuantities]]
 deps = ["DispatchDoctor", "TestItems", "Tricks"]
-git-tree-sha1 = "9f826f051e3d2c76f924d39c9aa4fcfd18cc9256"
+git-tree-sha1 = "192f34efd3912f4020b225e01d896f567f5f03e8"
 uuid = "06fc5a27-2a28-4c7c-a15d-362465fb6821"
-version = "1.2.0"
+version = "1.3.0"
 
     [deps.DynamicQuantities.extensions]
     DynamicQuantitiesLinearAlgebraExt = "LinearAlgebra"
@@ -772,6 +787,12 @@ git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2"
 uuid = "559328eb-81f9-559d-9380-de523a88c83c"
 version = "1.0.14+0"
 
+[[deps.FunctionProperties]]
+deps = ["Cassette", "DiffRules"]
+git-tree-sha1 = "bf7c740307eb0ee80e05d8aafbd0c5a901578398"
+uuid = "f62d2435-5019-4c03-9749-2d4c77af0cbc"
+version = "0.1.2"
+
 [[deps.FunctionWrappers]]
 git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e"
 uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
@@ -901,9 +922,9 @@ version = "0.1.17"
 
 [[deps.HypergeometricFunctions]]
 deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
-git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb"
+git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9"
 uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a"
-version = "0.3.24"
+version = "0.3.25"
 
 [[deps.IJulia]]
 deps = ["Base64", "Conda", "Dates", "InteractiveUtils", "JSON", "Libdl", "Logging", "Markdown", "MbedTLS", "Pkg", "Printf", "REPL", "Random", "SoftGlobalScope", "Test", "UUIDs", "ZMQ"]
@@ -1411,32 +1432,78 @@ uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 version = "1.2.0"
 
 [[deps.NonlinearSolve]]
-deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "Setfield", "SimpleNonlinearSolve", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"]
-git-tree-sha1 = "4d8944f32db2b07a2bdf8477e878bcb9c9ea2308"
+deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "NonlinearSolveBase", "NonlinearSolveFirstOrder", "NonlinearSolveQuasiNewton", "NonlinearSolveSpectralMethods", "PrecompileTools", "Preferences", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseMatrixColorings", "StaticArraysCore", "SymbolicIndexingInterface"]
+git-tree-sha1 = "22f3efdd47bd18d8a26bd559fff254e6b21000fd"
 uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
-version = "3.15.1"
+version = "4.1.0"
 
     [deps.NonlinearSolve.extensions]
-    NonlinearSolveBandedMatricesExt = "BandedMatrices"
     NonlinearSolveFastLevenbergMarquardtExt = "FastLevenbergMarquardt"
     NonlinearSolveFixedPointAccelerationExt = "FixedPointAcceleration"
     NonlinearSolveLeastSquaresOptimExt = "LeastSquaresOptim"
     NonlinearSolveMINPACKExt = "MINPACK"
     NonlinearSolveNLSolversExt = "NLSolvers"
-    NonlinearSolveNLsolveExt = "NLsolve"
+    NonlinearSolveNLsolveExt = ["NLsolve", "LineSearches"]
+    NonlinearSolvePETScExt = ["PETSc", "MPI"]
     NonlinearSolveSIAMFANLEquationsExt = "SIAMFANLEquations"
     NonlinearSolveSpeedMappingExt = "SpeedMapping"
+    NonlinearSolveSundialsExt = "Sundials"
 
     [deps.NonlinearSolve.weakdeps]
-    BandedMatrices = "aae01518-5342-5314-be14-df237901396f"
     FastLevenbergMarquardt = "7a0df574-e128-4d35-8cbd-3d84502bf7ce"
     FixedPointAcceleration = "817d07cb-a79a-5c30-9a31-890123675176"
     LeastSquaresOptim = "0fc2ff8b-aaa3-5acd-a817-1944a5e08891"
+    LineSearches = "d3d80556-e9d4-5f37-9878-2ab0fcc64255"
     MINPACK = "4854310b-de5a-5eb6-a2a5-c1dee2bd17f9"
+    MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
     NLSolvers = "337daf1e-9722-11e9-073e-8b9effe078ba"
     NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
+    PETSc = "ace2c81b-2b5f-4b1e-a30d-d662738edfe0"
     SIAMFANLEquations = "084e46ad-d928-497d-ad5e-07fa361a48c4"
     SpeedMapping = "f1835b91-879b-4a3f-a438-e4baacf14412"
+    Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
+
+[[deps.NonlinearSolveBase]]
+deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "FunctionProperties", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"]
+git-tree-sha1 = "1589ef8aac99a21d132adf1ec5cbe6ef651760ff"
+uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0"
+version = "1.3.1"
+
+    [deps.NonlinearSolveBase.extensions]
+    NonlinearSolveBaseBandedMatricesExt = "BandedMatrices"
+    NonlinearSolveBaseDiffEqBaseExt = "DiffEqBase"
+    NonlinearSolveBaseForwardDiffExt = "ForwardDiff"
+    NonlinearSolveBaseLineSearchExt = "LineSearch"
+    NonlinearSolveBaseLinearSolveExt = "LinearSolve"
+    NonlinearSolveBaseSparseArraysExt = "SparseArrays"
+    NonlinearSolveBaseSparseMatrixColoringsExt = "SparseMatrixColorings"
+
+    [deps.NonlinearSolveBase.weakdeps]
+    BandedMatrices = "aae01518-5342-5314-be14-df237901396f"
+    DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
+    ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+    LineSearch = "87fe0de2-c867-4266-b59a-2f0a94fc965b"
+    LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
+    SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+    SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35"
+
+[[deps.NonlinearSolveFirstOrder]]
+deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLJacobianOperators", "Setfield", "StaticArraysCore"]
+git-tree-sha1 = "dc8535cecb0f9d978019e44b7144b9e84ab85424"
+uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d"
+version = "1.0.0"
+
+[[deps.NonlinearSolveQuasiNewton]]
+deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"]
+git-tree-sha1 = "066d4940938f4bb5fd1ce146e61a373f40b89d31"
+uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114"
+version = "1.0.0"
+
+[[deps.NonlinearSolveSpectralMethods]]
+deps = ["CommonSolve", "ConcreteStructs", "DiffEqBase", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"]
+git-tree-sha1 = "cc97c44e396ab820401c8c404bc1fd18d4c884bd"
+uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2"
+version = "1.0.0"
 
 [[deps.ODEInterface]]
 deps = ["Dates", "Libdl", "LinearAlgebra", "Markdown", "ODEInterface_jll", "Unicode"]
@@ -1524,9 +1591,9 @@ version = "1.6.3"
 
 [[deps.OrdinaryDiffEq]]
 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"]
-git-tree-sha1 = "cd892f12371c287dc50d6ad3af075b088b6f2d48"
+git-tree-sha1 = "aa3897f89be34bdfd86472f5345d5f1f6576bcc5"
 uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
-version = "6.89.0"
+version = "6.90.0"
 
 [[deps.OrdinaryDiffEqAdamsBashforthMoulton]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"]
@@ -1558,9 +1625,9 @@ version = "1.1.0"
 
 [[deps.OrdinaryDiffEqDifferentiation]]
 deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEqCore", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrayInterface", "StaticArrays"]
-git-tree-sha1 = "e63ec633b1efa99e3caa2e26a01faaa88ba6cef9"
+git-tree-sha1 = "8977f283a7d89c5d5c06c933467ed4af0a99f2f7"
 uuid = "4302a76b-040a-498a-8c04-15b101fed76b"
-version = "1.1.0"
+version = "1.2.0"
 
 [[deps.OrdinaryDiffEqExplicitRK]]
 deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "TruncatedStacktraces"]
@@ -1630,9 +1697,9 @@ version = "1.2.1"
 
 [[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 = "e4be6539f4aaae8db1f29fcfdf6ef817df1f25cf"
+git-tree-sha1 = "5e1b316555fa95892edc13f6a429ac784d0be4dd"
 uuid = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8"
-version = "1.2.2"
+version = "1.2.4"
 
 [[deps.OrdinaryDiffEqNordsieck]]
 deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "Static"]
@@ -1666,9 +1733,9 @@ version = "1.1.0"
 
 [[deps.OrdinaryDiffEqRosenbrock]]
 deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static"]
-git-tree-sha1 = "96b47cdd12cb4ce8f70d701b49f855271a462bd4"
+git-tree-sha1 = "56cbbdc43bd0e88083fcef3efa296501b5a435da"
 uuid = "43230ef6-c299-4910-a778-202eb28ce4ce"
-version = "1.2.0"
+version = "1.3.0"
 
 [[deps.OrdinaryDiffEqSDIRK]]
 deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"]
@@ -2054,9 +2121,9 @@ 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 = "ad0d4e32b7adf6871f60c3379d76fdc231b434c8"
+git-tree-sha1 = "7527b9adb22904f0f51d8ab85d826f81ebb6f78d"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "2.59.1"
+version = "2.59.2"
 
     [deps.SciMLBase.extensions]
     SciMLBaseChainRulesCoreExt = "ChainRulesCore"
@@ -2137,22 +2204,22 @@ uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7"
 version = "1.2.0"
 
 [[deps.SimpleNonlinearSolve]]
-deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"]
-git-tree-sha1 = "44021f3efc023be3871195d8ad98b865001a2fa1"
+deps = ["ADTypes", "ArrayInterface", "BracketingNonlinearSolve", "CommonSolve", "ConcreteStructs", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LineSearch", "LinearAlgebra", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"]
+git-tree-sha1 = "f7e2042e0b68c6bb19a0a1594839792737f51d84"
 uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7"
-version = "1.12.3"
+version = "2.0.0"
 
     [deps.SimpleNonlinearSolve.extensions]
     SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore"
+    SimpleNonlinearSolveDiffEqBaseExt = "DiffEqBase"
     SimpleNonlinearSolveReverseDiffExt = "ReverseDiff"
     SimpleNonlinearSolveTrackerExt = "Tracker"
-    SimpleNonlinearSolveZygoteExt = "Zygote"
 
     [deps.SimpleNonlinearSolve.weakdeps]
     ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
+    DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
     ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
     Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
-    Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [[deps.SimpleTraits]]
 deps = ["InteractiveUtils", "MacroTools"]
@@ -2185,26 +2252,6 @@ deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"]
 uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 version = "1.10.0"
 
-[[deps.SparseConnectivityTracer]]
-deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "6914df6005bab9940e2a96879a97a43e1fb1ce78"
-uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
-version = "0.6.8"
-
-    [deps.SparseConnectivityTracer.extensions]
-    SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations"
-    SparseConnectivityTracerLogExpFunctionsExt = "LogExpFunctions"
-    SparseConnectivityTracerNNlibExt = "NNlib"
-    SparseConnectivityTracerNaNMathExt = "NaNMath"
-    SparseConnectivityTracerSpecialFunctionsExt = "SpecialFunctions"
-
-    [deps.SparseConnectivityTracer.weakdeps]
-    DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
-    LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-    NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
-    NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
-    SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
-
 [[deps.SparseDiffTools]]
 deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "UnPack", "VertexSafeGraphs"]
 git-tree-sha1 = "b906758c107b049b6b71599b9f928d9b14e5554a"

benchmarks/Bio/egfr_net.jmd

@@ -261,8 +261,7 @@ wp = WorkPrecisionSet([oprob,sparsejacprob],abstols,reltols,setups;error_estimat
 names = ["lsoda" "CVODE_BDF (GMRES)" "QNDF (GMRES)" "QNDF (KLU)" "BS5" "Vern6" "ROCK4"]
 colors = [:seagreen1 :darkgreen :deepskyblue1 :deepskyblue4 :thistle2 :lightslateblue :purple4]
 markershapes = [:star4 :rect :hexagon :octagon :star8 :rtriangle :square]
-xlimit = xlimit .* [0.95,1/0.95]; ylimit = ylimit .* [0.95,1/0.95];
-plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xlimit=xlimit,ylimit=ylimit,xticks=[1e-9,1e-8,1e-7,1e-6,1e-5,1e-4,1e-3,1e-2],yticks=[1e-2,1e-1],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000))
+plot(wp;label=names,left_margin=10Plots.mm,right_margin=10Plots.mm,xticks=[1e-9,1e-8,1e-7,1e-6,1e-5,1e-4,1e-3,1e-2],yticks=[1e-2,1e-1],color=colors,markershape=markershapes,legendfontsize=15,tickfontsize=15,guidefontsize=15, legend=:topright, lw=20, la=0.8, markersize=20,markerstrokealpha=1.0, markerstrokewidth=1.5, gridalpha=0.3, gridlinewidth=7.5,size=(1100,1000))
 ```