From b6112f4f3a3787324eb6b91a076552024409d2f1 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Wed, 21 May 2025 15:30:02 +0100 Subject: [PATCH 1/5] Add troubleshooting page --- _quarto.yml | 23 ++++---- usage/performance-tips/index.qmd | 2 +- usage/troubleshooting/index.qmd | 98 ++++++++++++++++++++++++++++++++ 3 files changed, 112 insertions(+), 11 deletions(-) create mode 100755 usage/troubleshooting/index.qmd diff --git a/_quarto.yml b/_quarto.yml index 81cd0613d..791b30c20 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -66,6 +66,7 @@ website: - usage/sampler-visualisation/index.qmd - usage/dynamichmc/index.qmd - usage/external-samplers/index.qmd + - usage/troubleshooting/index.qmd - section: "Tutorials" contents: @@ -181,17 +182,19 @@ probabilistic-pca: tutorials/11-probabilistic-pca gplvm: tutorials/12-gplvm seasonal-time-series: tutorials/13-seasonal-time-series using-turing-advanced: tutorials/docs-09-using-turing-advanced -using-turing-autodiff: tutorials/docs-10-using-turing-autodiff -using-turing-dynamichmc: tutorials/docs-11-using-turing-dynamichmc using-turing: tutorials/docs-12-using-turing-guide -using-turing-performance-tips: tutorials/docs-13-using-turing-performance-tips -using-turing-sampler-viz: tutorials/docs-15-using-turing-sampler-viz -using-turing-external-samplers: tutorials/docs-16-using-turing-external-samplers -using-turing-mode-estimation: tutorials/docs-17-mode-estimation -usage-probability-interface: tutorials/usage-probability-interface -usage-custom-distribution: tutorials/usage-custom-distribution -usage-tracking-extra-quantities: tutorials/tracking-extra-quantities -usage-modifying-logprob: tutorials/usage-modifying-logprob + +usage-automatic-differentiation: usage/automatic-differentiation +usage-custom-distribution: usage/custom-distribution +usage-dynamichmc: usage/dynamichmc +usage-external-samplers: usage/external-samplers +usage-mode-estimation: usage/mode-estimation +usage-modifying-logprob: usage/modifying-logprob +usage-performance-tips: usage/performance-tips +usage-probability-interface: usage/probability-interface +usage-sampler-visualisation: usage/sampler-visualisation +usage-tracking-extra-quantities: usage/tracking-extra-quantities +usage-troubleshooting: usage/troubleshooting contributing-guide: developers/contributing dev-model-manual: developers/compiler/model-manual diff --git a/usage/performance-tips/index.qmd b/usage/performance-tips/index.qmd index d5a26a029..4bbab345a 100755 --- a/usage/performance-tips/index.qmd +++ b/usage/performance-tips/index.qmd @@ -52,7 +52,7 @@ supports several AD backends, including [ForwardDiff](https://github.com/JuliaDi For many common types of models, the default ForwardDiff backend performs great, and there is no need to worry about changing it. However, if you need more speed, you can try different backends via the standard [ADTypes](https://github.com/SciML/ADTypes.jl) interface by passing an `AbstractADType` to the sampler with the optional `adtype` argument, e.g. -`NUTS(adtype = AutoZygote())`. See [Automatic Differentiation]({{}}) for details. Generally, `adtype = AutoForwardDiff()` is likely to be the fastest and most reliable for models with +`NUTS(adtype = AutoZygote())`. See [Automatic Differentiation]({{}}) for details. Generally, `adtype = AutoForwardDiff()` is likely to be the fastest and most reliable for models with few parameters (say, less than 20 or so), while reverse-mode backends such as `AutoZygote()` or `AutoReverseDiff()` will perform better for models with many parameters or linear algebra operations. If in doubt, it's easy to try a few different backends to see how they compare. diff --git a/usage/troubleshooting/index.qmd b/usage/troubleshooting/index.qmd new file mode 100755 index 000000000..8e62c6583 --- /dev/null +++ b/usage/troubleshooting/index.qmd @@ -0,0 +1,98 @@ +--- +title: Troubleshooting +engine: julia +--- + +```{julia} +#| echo: false +#| output: false +using Pkg; +Pkg.instantiate(); +``` + +This page collects a number of common error messages observed when using Turing, along with suggestions on how to fix them. + +If the suggestions here do not resolve your problem, please do feel free to [open an issue](https://github.com/TuringLang/Turing.jl/issues). + +```{julia} +using Turing +``` + +## T0001 + +> failed to find valid initial parameters in {N} tries. This may indicate an error with the model or AD backend... + +This error is seen when a Hamiltonian Monte Carlo sampler is unable to determine a valid set of initial parameters for the sampling. +Here, 'valid' means that the log probability density of the model, as well as its gradient with respect to each parameter, is finite and not `NaN`. + +### `NaN` gradient + +One of the most common causes of this error is having a `NaN` gradient. +To find out whether this is happening, you can evaluate the gradient manually. +Here is an example with a model that is known to be problematic: + +```{julia} +using Turing +using DynamicPPL.TestUtils.AD: run_ad + +@model function t0001_bad() + a ~ Normal() + x ~ truncated(Normal(a), 0, Inf) +end + +model = t0001_bad() +adtype = AutoForwardDiff() +result = run_ad(model, adtype; test=false, benchmark=false) +result.grad_actual +``` + +(See [the DynamicPPL docs](https://turinglang.org/DynamicPPL.jl/stable/api/#AD-testing-and-benchmarking-utilities) for more details on the `run_ad` function and its return type.) + +In this case, the `NaN` gradient is caused by the `Inf` argument to `truncated`. +(See, e.g., [this issue on Distributions.jl](https://github.com/JuliaStats/Distributions.jl/issues/1910).) +Here, the upper bound of `Inf` is not needed, so it can be removed: + +```{julia} +@model function t0001_good() + a ~ Normal() + x ~ truncated(Normal(a); lower=0) +end + +model = t0001_good() +adtype = AutoForwardDiff() +run_ad(model, adtype; test=false, benchmark=false).grad_actual +``` + +More generally, you could try using a different AD backend; if you don't know why a model is returning `NaN` gradients, feel free to open an issue. + +### `-Inf` log density + +Another cause of this error is having models with very extreme parameters. +This example is taken from [this Turing.jl issue](https://github.com/TuringLang/Turing.jl/issues/2476): + +```{julia} +@model function t0001_bad2() + x ~ Exponential(100) + y ~ Uniform(0, x) +end +model = t0001_bad2() | (y = 50.0,) +``` + +The problem here is that HMC attempts to find initial values for parameters inside the region of `[-2, 2]`, _after_ the parameters have been transformed to unconstrained space. +For a distribution of `Exponential(100)`, the appropriate transformation is `log(x)` (see the [variable transformation docs]({{< meta dev-transforms-distributions >}}) for more info). + +Thus, HMC attempts to find initial values of `log(x)` in the region of `[-2, 2]`, which corresponds to `x` in the region of `[exp(-2), exp(2)]` = `[0.135, 7.39]`. +However, all of these values of `x` will give rise to a zero probability density for `y` because the value of `y = 50.0` is outside the support of `Uniform(0, x)`. +Thus, the log density of the model is `-Inf`, as can be seen with `logjoint`: + +```{julia} +logjoint(model, (x = exp(-2),)) +``` + +```{julia} +logjoint(model, (x = exp(2),)) +``` + +The most direct way of fixing this is to manually provide a set of initial parameters that are valid. +For example, you can obtain a set of initial parameters with `rand(Dict, model)`, and then pass this as the `initial_params` keyword argument to `sample`. +Otherwise, though, you may want to consider reparameterising the model to avoid such issues. From 0d901a65fa8c1d7e462f375f693baad22f013b70 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Thu, 29 May 2025 15:12:05 +0100 Subject: [PATCH 2/5] Remove codes --- usage/troubleshooting/index.qmd | 31 ++++++++++++++++++++++--------- 1 file changed, 22 insertions(+), 9 deletions(-) diff --git a/usage/troubleshooting/index.qmd b/usage/troubleshooting/index.qmd index 8e62c6583..63c60bbda 100755 --- a/usage/troubleshooting/index.qmd +++ b/usage/troubleshooting/index.qmd @@ -18,7 +18,7 @@ If the suggestions here do not resolve your problem, please do feel free to [ope using Turing ``` -## T0001 +## Initial parameters > failed to find valid initial parameters in {N} tries. This may indicate an error with the model or AD backend... @@ -35,12 +35,12 @@ Here is an example with a model that is known to be problematic: using Turing using DynamicPPL.TestUtils.AD: run_ad -@model function t0001_bad() +@model function initial_bad() a ~ Normal() x ~ truncated(Normal(a), 0, Inf) end -model = t0001_bad() +model = initial_bad() adtype = AutoForwardDiff() result = run_ad(model, adtype; test=false, benchmark=false) result.grad_actual @@ -53,12 +53,12 @@ In this case, the `NaN` gradient is caused by the `Inf` argument to `truncated`. Here, the upper bound of `Inf` is not needed, so it can be removed: ```{julia} -@model function t0001_good() +@model function initial_good() a ~ Normal() x ~ truncated(Normal(a); lower=0) end -model = t0001_good() +model = initial_good() adtype = AutoForwardDiff() run_ad(model, adtype; test=false, benchmark=false).grad_actual ``` @@ -71,11 +71,19 @@ Another cause of this error is having models with very extreme parameters. This example is taken from [this Turing.jl issue](https://github.com/TuringLang/Turing.jl/issues/2476): ```{julia} -@model function t0001_bad2() +@model function initial_bad2() x ~ Exponential(100) y ~ Uniform(0, x) end -model = t0001_bad2() | (y = 50.0,) +model = initial_bad2() | (y = 50.0,) + +@model function initial_bad3() + x_trf ~ Uniform(0, 1) + x := -log(x_trf) / 100 + @show x + y ~ Uniform(0, x) +end +model3 = initial_bad3() | (y = 50.0,) ``` The problem here is that HMC attempts to find initial values for parameters inside the region of `[-2, 2]`, _after_ the parameters have been transformed to unconstrained space. @@ -94,5 +102,10 @@ logjoint(model, (x = exp(2),)) ``` The most direct way of fixing this is to manually provide a set of initial parameters that are valid. -For example, you can obtain a set of initial parameters with `rand(Dict, model)`, and then pass this as the `initial_params` keyword argument to `sample`. -Otherwise, though, you may want to consider reparameterising the model to avoid such issues. +For example, you can obtain a set of initial parameters with `rand(Vector, model)`, and then pass this as the `initial_params` keyword argument to `sample`: + +```{julia} +sample(model, NUTS(), 1000; initial_params=rand(Vector, model)) +``` + +More generally, you may also consider reparameterising the model to avoid such issues. From 319f89d5b4b209352288ddec8dba84f692ec8863 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Mon, 2 Jun 2025 10:34:18 +0100 Subject: [PATCH 3/5] Disable progress --- usage/troubleshooting/index.qmd | 1 + 1 file changed, 1 insertion(+) diff --git a/usage/troubleshooting/index.qmd b/usage/troubleshooting/index.qmd index 63c60bbda..a21108a23 100755 --- a/usage/troubleshooting/index.qmd +++ b/usage/troubleshooting/index.qmd @@ -16,6 +16,7 @@ If the suggestions here do not resolve your problem, please do feel free to [ope ```{julia} using Turing +Turing.setprogress!(false) ``` ## Initial parameters From 5bb81b64803987f8a483d6c23971ec5c38f6e843 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Mon, 2 Jun 2025 11:35:03 +0100 Subject: [PATCH 4/5] Fix code --- usage/troubleshooting/index.qmd | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/usage/troubleshooting/index.qmd b/usage/troubleshooting/index.qmd index a21108a23..26a8257c9 100755 --- a/usage/troubleshooting/index.qmd +++ b/usage/troubleshooting/index.qmd @@ -73,18 +73,10 @@ This example is taken from [this Turing.jl issue](https://github.com/TuringLang/ ```{julia} @model function initial_bad2() - x ~ Exponential(100) - y ~ Uniform(0, x) + x ~ Exponential(100) + y ~ Uniform(0, x) end model = initial_bad2() | (y = 50.0,) - -@model function initial_bad3() - x_trf ~ Uniform(0, 1) - x := -log(x_trf) / 100 - @show x - y ~ Uniform(0, x) -end -model3 = initial_bad3() | (y = 50.0,) ``` The problem here is that HMC attempts to find initial values for parameters inside the region of `[-2, 2]`, _after_ the parameters have been transformed to unconstrained space. From 7e654eadd77affab54562710492845ba22228418 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Mon, 2 Jun 2025 11:43:59 +0100 Subject: [PATCH 5/5] Update versions --- Manifest.toml | 203 ++++++++++++++++++++++---------------------------- 1 file changed, 91 insertions(+), 112 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index a8dd9e3df..b40efdad2 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -128,9 +128,9 @@ weakdeps = ["Libtask"] [[deps.AdvancedVI]] deps = ["ADTypes", "Bijectors", "DiffResults", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "e45e57cea1879400952fe34b0cbc971950408af8" +git-tree-sha1 = "e913c2794cf9d2db9d36d28f67abd27595101f49" uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c" -version = "0.2.11" +version = "0.2.12" weakdeps = ["Enzyme", "Flux", "ReverseDiff", "Zygote"] [deps.AdvancedVI.extensions] @@ -301,9 +301,9 @@ 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 = "803e3c6bfd5c2655eb040d252144b7519ce1e70e" +git-tree-sha1 = "8dbfc7cdb433ffbbcaaa7807c53a90c97c431a27" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.15.6" +version = "0.15.7" weakdeps = ["ChainRules", "DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff", "Tracker", "Zygote"] [deps.Bijectors.extensions] @@ -342,9 +342,9 @@ version = "5.17.0" [[deps.BoundaryValueDiffEqAscher]] deps = ["ADTypes", "AlmostBlockDiagonals", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield"] -git-tree-sha1 = "add7560694794f30eec7803b9c4036efb96bf493" +git-tree-sha1 = "2e8239379bdd0f8254407ca2b2cb7b3430da687f" uuid = "7227322d-7511-4e07-9247-ad6ff830280e" -version = "1.6.0" +version = "1.6.1" [[deps.BoundaryValueDiffEqCore]] deps = ["ADTypes", "Adapt", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearAlgebra", "Logging", "NonlinearSolveFirstOrder", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] @@ -366,9 +366,9 @@ version = "1.7.0" [[deps.BoundaryValueDiffEqMIRKN]] deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] -git-tree-sha1 = "dfde7afe34137182a4bb8cd98f01d870772be999" +git-tree-sha1 = "1000b18a380773f049ac2f34bc12abd3d99cf21c" uuid = "9255f1d6-53bf-473e-b6bd-23f1ff009da4" -version = "1.6.0" +version = "1.6.1" [[deps.BoundaryValueDiffEqShooting]] deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] @@ -378,12 +378,13 @@ version = "1.7.0" [[deps.BracketingNonlinearSolve]] deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] -git-tree-sha1 = "637ebe439ba587828fd997b7810d8171eed2ea1b" +git-tree-sha1 = "a9014924595b7a2c1dd14aac516e38fa10ada656" uuid = "70df07ce-3d50-431d-a3e7-ca6ddb60ac1e" -version = "1.2.0" -weakdeps = ["ForwardDiff"] +version = "1.3.0" +weakdeps = ["ChainRulesCore", "ForwardDiff"] [deps.BracketingNonlinearSolve.extensions] + BracketingNonlinearSolveChainRulesCoreExt = ["ChainRulesCore", "ForwardDiff"] BracketingNonlinearSolveForwardDiffExt = "ForwardDiff" [[deps.Bzip2_jll]] @@ -411,9 +412,9 @@ version = "0.10.15" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "2ac646d71d0d24b44f3f8c84da8c9f4d70fb67df" +git-tree-sha1 = "fde3bf89aead2e723284a8ff9cdf5b551ed700e8" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.4+0" +version = "1.18.5+0" [[deps.Cassette]] git-tree-sha1 = "f8764df8d9d2aec2812f009a1ac39e46c33354b8" @@ -440,9 +441,9 @@ version = "0.10.8" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "a975ae558af61a2a48720a6271661bf2621e0f4e" +git-tree-sha1 = "204e9b212da5cc7df632b58af8d49763383f47fa" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.72.3" +version = "1.72.4" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] @@ -706,9 +707,9 @@ 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 = "1bcd3a5c585c477e5d0595937ea7b5adcda6c621" +git-tree-sha1 = "a0e5b5669df9465bc3dd32ea4a8ddeefbc0f7b5c" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.174.0" +version = "6.175.0" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -721,6 +722,7 @@ version = "6.174.0" DiffEqBaseMPIExt = "MPI" DiffEqBaseMeasurementsExt = "Measurements" DiffEqBaseMonteCarloMeasurementsExt = "MonteCarloMeasurements" + DiffEqBaseMooncakeExt = "Mooncake" DiffEqBaseReverseDiffExt = "ReverseDiff" DiffEqBaseSparseArraysExt = "SparseArrays" DiffEqBaseTrackerExt = "Tracker" @@ -737,6 +739,7 @@ version = "6.174.0" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" @@ -902,9 +905,9 @@ version = "3.5.1" [[deps.DynamicPPL]] deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Chairmarks", "Compat", "ConstructionBase", "DifferentiationInterface", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "MacroTools", "OrderedCollections", "Random", "Requires", "Statistics", "Test"] -git-tree-sha1 = "e6b9e984f7a4aa114190c573504d61da41bc7b20" +git-tree-sha1 = "b694a7408cc1083af9f338d83d4a7e11395d6a10" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.36.9" +version = "0.36.10" [deps.DynamicPPL.extensions] DynamicPPLChainRulesCoreExt = ["ChainRulesCore"] @@ -935,10 +938,10 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.5" [[deps.Enzyme]] -deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] -git-tree-sha1 = "d695c5fd956d98b3f38b9b1c12f22700a9c91549" +deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] +git-tree-sha1 = "be2c627bf432a3a17d6d0e9c461d88bd1a28d3cf" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.46" +version = "0.13.48" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -957,9 +960,9 @@ version = "0.13.46" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.EnzymeCore]] -git-tree-sha1 = "1eb59f40a772d0fbd4cb75e00b3fa7f5f79c975a" +git-tree-sha1 = "7d7822a643c33bbff4eab9c87ca8459d7c688db0" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.8.9" +version = "0.8.11" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -967,9 +970,9 @@ weakdeps = ["Adapt"] [[deps.Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "fd483a1d847401a21460090f3f358049b20fbcac" +git-tree-sha1 = "168b7e5924b1fdb14bb246e7263438bb26d040c5" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.180+0" +version = "0.0.181+0" [[deps.EpollShim_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1289,9 +1292,9 @@ version = "0.21.0+0" [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "b0036b392358c80d2d2124746c2bf3d48d457938" +git-tree-sha1 = "fee60557e4f19d0fe5cd169211fdda80e494f4e8" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.82.4+0" +version = "2.84.0+0" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1336,9 +1339,9 @@ version = "1.10.16" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] -git-tree-sha1 = "55c53be97790242c29031e5cd45e8ac296dadda3" +git-tree-sha1 = "f923f9a774fcf3f5cb761bfa43aeadd689714813" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "8.5.0+0" +version = "8.5.1+0" [[deps.HashArrayMappedTries]] git-tree-sha1 = "2eaa69a7cab70a52b9687c8bf950a5a93ec895ae" @@ -1606,19 +1609,21 @@ version = "1.4.0" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "cd10d2cc78d34c0e2a3a36420ab607b611debfbb" +git-tree-sha1 = "4f34eaabe49ecb3fb0d58d6015e32fd31a733199" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.7" +version = "0.16.8" [deps.Latexify.extensions] DataFramesExt = "DataFrames" SparseArraysExt = "SparseArrays" SymEngineExt = "SymEngine" + TectonicExt = "tectonic_jll" [deps.Latexify.weakdeps] DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" + tectonic_jll = "d7dd28d6-a5e6-559c-9131-7eb760cdacc5" [[deps.LayoutPointers]] deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface"] @@ -1709,10 +1714,10 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" version = "1.11.0" [[deps.Libffi_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "27ecae93dd25ee0909666e6835051dd684cc035e" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "c8da7e6a91781c41a863611c7e966098d783c57a" uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" -version = "3.2.2+2" +version = "3.4.7+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll", "Xorg_libXext_jll"] @@ -2301,9 +2306,9 @@ version = "0.1.5" [[deps.NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "58e317b3b956b8aaddfd33ff4c3e33199cd8efce" +git-tree-sha1 = "b0219babbb69e4f0b292a11ad7f33520bdfcea8f" uuid = "86f7a689-2022-50b4-a561-43c23ac3c673" -version = "0.10.3" +version = "0.10.4" [[deps.NaturalSort]] git-tree-sha1 = "eda490d06b9f7c00752ee81cfa451efe55521e21" @@ -2354,9 +2359,9 @@ version = "4.9.0" [[deps.NonlinearSolveBase]] deps = ["ADTypes", "Adapt", "ArrayInterface", "CommonSolve", "Compat", "ConcreteStructs", "DifferentiationInterface", "EnzymeCore", "FastClosures", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "1a6f6b161a644beac3c46a46f9bbb830c24abffb" +git-tree-sha1 = "404d71dd057759f4d590191a643113485c4a482a" uuid = "be0214bd-f91f-a760-ac4e-3421ce2b2da0" -version = "1.8.0" +version = "1.12.0" weakdeps = ["BandedMatrices", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearSolve", "SparseArrays", "SparseMatrixColorings"] [deps.NonlinearSolveBase.extensions] @@ -2376,9 +2381,9 @@ version = "1.5.0" [[deps.NonlinearSolveQuasiNewton]] deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] -git-tree-sha1 = "b69a68ef3a7bba7ab1d5ef6321ed6d9a613142b0" +git-tree-sha1 = "e3888bdbab6e0bfadbc3164ef4595e40e7b7e954" uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" -version = "1.5.0" +version = "1.6.0" weakdeps = ["ForwardDiff"] [deps.NonlinearSolveQuasiNewton.extensions] @@ -2422,9 +2427,9 @@ version = "1.3.5+1" [[deps.OneHotArrays]] deps = ["Adapt", "ChainRulesCore", "Compat", "GPUArraysCore", "LinearAlgebra", "NNlib"] -git-tree-sha1 = "3685584454b04cd52169c787ba4d196da8a04d10" +git-tree-sha1 = "bfe8e84c71972f77e775f75e6d8048ad3fdbe8bc" uuid = "0b1bfda6-eb8a-41d2-88d8-f5af5cad476f" -version = "0.2.9" +version = "0.2.10" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] @@ -2486,9 +2491,9 @@ version = "4.3.0" [[deps.OptimizationBase]] deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "Requires", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] -git-tree-sha1 = "070d2c33da5f0b33d57b61f7f601c4ea6185af15" +git-tree-sha1 = "918d9bf579a355222e62ceac955b5382fea7bd61" uuid = "bca83a33-5cc9-4baa-983d-23429ab6bcbb" -version = "2.5.0" +version = "2.7.0" [deps.OptimizationBase.extensions] OptimizationEnzymeExt = "Enzyme" @@ -2537,9 +2542,9 @@ version = "1.8.1" [[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", "Static", "StaticArrayInterface", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "56d5500e9970f0112a4e1ab6474d6fedde61ef64" +git-tree-sha1 = "1c2b2df870944e0dc01454fd87479847c55fa26c" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.97.0" +version = "6.98.0" [[deps.OrdinaryDiffEqAdamsBashforthMoulton]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqLowOrderRK", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2549,9 +2554,9 @@ version = "1.2.0" [[deps.OrdinaryDiffEqBDF]] deps = ["ADTypes", "ArrayInterface", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "OrdinaryDiffEqSDIRK", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "StaticArrays", "TruncatedStacktraces"] -git-tree-sha1 = "a72bf554d5fd1f33a8d2aead3562eddd28ba4c76" +git-tree-sha1 = "42755bd13fe56e9d9ce1bc005f8b206a6b56b731" uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" -version = "1.5.0" +version = "1.5.1" [[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"] @@ -2571,9 +2576,9 @@ version = "1.4.0" [[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 = "315d25dd06614e199973cc13d22e533073bd7458" +git-tree-sha1 = "c78060115fa4ea9d70ac47fa49496acbc630aefa" uuid = "4302a76b-040a-498a-8c04-15b101fed76b" -version = "1.9.0" +version = "1.9.1" [[deps.OrdinaryDiffEqExplicitRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "TruncatedStacktraces"] @@ -2643,9 +2648,9 @@ version = "1.3.0" [[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 = "2f956f14c97ff507e855703ac760d513f7c3e372" +git-tree-sha1 = "ffdb0f5207b0e30f8b1edf99b3b9546d9c48ccaf" uuid = "127b3ac7-2247-4354-8eb6-78cf4e7c58e8" -version = "1.9.0" +version = "1.10.0" [[deps.OrdinaryDiffEqNordsieck]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqTsit5", "Polyester", "RecursiveArrayTools", "Reexport", "Static"] @@ -2655,9 +2660,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqPDIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Polyester", "Reexport", "StaticArrays"] -git-tree-sha1 = "f74b27b8b811a83d77a9cad6293e793ab0804cdc" +git-tree-sha1 = "ab9897e4bc8e3cf8e15f1cf61dbdd15d6a2341d7" uuid = "5dd0a6cf-3d4b-4314-aa06-06d4e299bc89" -version = "1.3.0" +version = "1.3.1" [[deps.OrdinaryDiffEqPRK]] deps = ["DiffEqBase", "FastBroadcast", "MuladdMacro", "OrdinaryDiffEqCore", "Polyester", "Reexport"] @@ -2679,9 +2684,9 @@ version = "1.1.0" [[deps.OrdinaryDiffEqRosenbrock]] deps = ["ADTypes", "DiffEqBase", "DifferentiationInterface", "FastBroadcast", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "Polyester", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "Static"] -git-tree-sha1 = "a9b9aff8e740bfc09a2ea669f7fc02e867f95ab7" +git-tree-sha1 = "063e5ff1447b3869856ed264b6dcbb21e6e8bdb0" uuid = "43230ef6-c299-4910-a778-202eb28ce4ce" -version = "1.10.0" +version = "1.10.1" [[deps.OrdinaryDiffEqSDIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] @@ -2744,9 +2749,9 @@ weakdeps = ["Requires", "TOML"] [[deps.Pango_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "3b31172c032a1def20c98dae3f2cdc9d10e3b561" +git-tree-sha1 = "275a9a6d85dc86c24d03d1837a0010226a96f540" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.56.1+0" +version = "1.56.3+0" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -2815,9 +2820,9 @@ version = "0.4.4" [[deps.Polyester]] deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "2082cc4be5e765bd982ed04ea06c068f4f702410" +git-tree-sha1 = "6f7cd22a802094d239824c57d94c8e2d0f7cfc7d" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.7.17" +version = "0.7.18" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] @@ -3085,9 +3090,9 @@ version = "2.2.7" [[deps.RuntimeGeneratedFunctions]] deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "7cb9d10026d630ce2dd2a1fc6006a3d5041b34c0" +git-tree-sha1 = "86a8a8b783481e1ea6b9c91dd949cb32191f8ab4" uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.14" +version = "0.5.15" [[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -3105,10 +3110,10 @@ uuid = "26aad666-b158-4e64-9d35-0e672562fa48" version = "0.5.0" [[deps.SciMLBase]] -deps = ["ADTypes", "Accessors", "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 = "2fd047893cb0089b180fcbb7e8434ba15dcc2841" +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 = "ce947672206f6a3a2bee1017c690cfd5fd82d897" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.87.0" +version = "2.96.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3133,15 +3138,15 @@ version = "2.87.0" [[deps.SciMLJacobianOperators]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "ConstructionBase", "DifferentiationInterface", "FastClosures", "LinearAlgebra", "SciMLBase", "SciMLOperators"] -git-tree-sha1 = "d563758f3ce5153810adebc534d88e24d34eeb95" +git-tree-sha1 = "7da1216346ad79499d08d7e2a3dbf297dc80c829" uuid = "19f34311-ddf3-4b8b-af20-060888a46c0e" -version = "0.1.5" +version = "0.1.6" [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] -git-tree-sha1 = "1c4b7f6c3e14e6de0af66e66b86d525cae10ecb4" +git-tree-sha1 = "85608e4aaf758547ffc4030c908318b432114ec9" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.13" +version = "1.3.0" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -3150,9 +3155,9 @@ weakdeps = ["SparseArrays", "StaticArraysCore"] [[deps.SciMLSensitivity]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "Distributions", "Enzyme", "FastBroadcast", "FiniteDiff", "ForwardDiff", "FunctionProperties", "FunctionWrappersWrappers", "Functors", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEqCore", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "SciMLJacobianOperators", "SciMLStructures", "StaticArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tracker", "Zygote"] -git-tree-sha1 = "58e0e458e6a22b8288230531ec2fc51fd4172597" +git-tree-sha1 = "22402dfac0823491e0d3ae3b916940e6761f6e86" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.83.0" +version = "7.84.0" weakdeps = ["Mooncake"] [deps.SciMLSensitivity.extensions] @@ -3282,26 +3287,6 @@ version = "0.6.18" 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 = "d79802152d958607f414f5447cb25e314db979c0" -uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.23.1" - - [deps.SparseDiffTools.extensions] - SparseDiffToolsEnzymeExt = "Enzyme" - SparseDiffToolsPolyesterExt = "Polyester" - SparseDiffToolsPolyesterForwardDiffExt = "PolyesterForwardDiff" - SparseDiffToolsSymbolicsExt = "Symbolics" - SparseDiffToolsZygoteExt = "Zygote" - - [deps.SparseDiffTools.weakdeps] - Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" - Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588" - PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" - Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" - [[deps.SparseInverseSubset]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] git-tree-sha1 = "52962839426b75b3021296f7df242e40ecfc0852" @@ -3395,9 +3380,9 @@ weakdeps = ["SparseArrays"] [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" +git-tree-sha1 = "9d72a13a3f4dd3795a195ac5a44d7d6ff5f552ff" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.7.0" +version = "1.7.1" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -3435,10 +3420,10 @@ uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" version = "2.5.0" [[deps.StochasticDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "b1e151feffd589382530930da1467474fe8c37e4" +deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "StaticArrays", "UnPack"] +git-tree-sha1 = "2992af2739fdcf5862b12dcf53a5f6e3e4acd358" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.79.0" +version = "6.80.0" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] @@ -3675,9 +3660,9 @@ version = "1.6.0" [[deps.Turing]] deps = ["ADTypes", "AbstractMCMC", "Accessors", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "Compat", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "50278624e9f897592db26d498f7a94c856051169" +git-tree-sha1 = "a22c829eaf08b3c40f7e106e81b21233c726052e" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.38.3" +version = "0.38.4" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] @@ -3722,9 +3707,9 @@ weakdeps = ["ConstructionBase", "InverseFunctions"] [[deps.UnitfulLatexify]] deps = ["LaTeXStrings", "Latexify", "Unitful"] -git-tree-sha1 = "975c354fcd5f7e1ddcc1f1a23e6e091d99e99bc8" +git-tree-sha1 = "af305cc62419f9bd61b6644d19170a4d258c7967" uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" -version = "1.6.4" +version = "1.7.0" [[deps.UnsafeAtomics]] git-tree-sha1 = "b13c4edda90890e5b04ba24e20a310fbe6f249ff" @@ -3740,12 +3725,6 @@ git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" version = "0.2.0" -[[deps.VertexSafeGraphs]] -deps = ["Graphs"] -git-tree-sha1 = "8351f8d73d7e880bfc042a8b6922684ebeafb35c" -uuid = "19fa3120-7c27-5ec5-8db8-b0b0aa330d6f" -version = "0.2.0" - [[deps.Vulkan_Loader_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Wayland_jll", "Xorg_libX11_jll", "Xorg_libXrandr_jll", "xkbcommon_jll"] git-tree-sha1 = "2f0486047a07670caad3a81a075d2e518acc5c59" @@ -3753,10 +3732,10 @@ uuid = "a44049a8-05dd-5a78-86c9-5fde0876e88c" version = "1.3.243+0" [[deps.Wayland_jll]] -deps = ["Artifacts", "EpollShim_jll", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "85c7811eddec9e7f22615371c3cc81a504c508ee" +deps = ["Artifacts", "EpollShim_jll", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "XML2_jll"] +git-tree-sha1 = "49be0be57db8f863a902d59c0083d73281ecae8e" uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" -version = "1.21.0+2" +version = "1.23.1+0" [[deps.Wayland_protocols_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -3772,9 +3751,9 @@ version = "1.4.2" [[deps.WeightInitializers]] deps = ["ArgCheck", "ConcreteStructs", "GPUArraysCore", "LinearAlgebra", "Random", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "b7f5993dc0a6f9ac74f53de588db96235cdd79a2" +git-tree-sha1 = "57db7a10930d4ccc9e4ee3d9122748f845e645cf" uuid = "d49dbf32-c5c2-4618-8acc-27bb2598ef2d" -version = "1.1.2" +version = "1.1.3" [deps.WeightInitializers.extensions] WeightInitializersAMDGPUExt = ["AMDGPU", "GPUArrays"]