From c30e8ac38187d08a4b29ef5c17015108a073073c Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Thu, 16 Jan 2025 16:37:44 +0000 Subject: [PATCH 1/7] Bump Turing.jl to 0.36 and update all mentions of Gibbs to match --- Project.toml | 2 +- _quarto.yml | 2 +- developers/compiler/design-overview/index.qmd | 3 +-- tutorials/01-gaussian-mixture-model/index.qmd | 4 ++-- tutorials/04-hidden-markov-model/index.qmd | 2 +- tutorials/docs-10-using-turing-autodiff/index.qmd | 4 ++-- tutorials/docs-12-using-turing-guide/index.qmd | 4 ++-- tutorials/docs-15-using-turing-sampler-viz/index.qmd | 2 +- 8 files changed, 11 insertions(+), 12 deletions(-) diff --git a/Project.toml b/Project.toml index 7b850e84b..020fb4766 100644 --- a/Project.toml +++ b/Project.toml @@ -55,4 +55,4 @@ UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] -Turing = "0.35" +Turing = "0.36" diff --git a/_quarto.yml b/_quarto.yml index 613e9b87f..113afc13b 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -32,7 +32,7 @@ website: text: Team right: # Current version - - text: "v0.35" + - text: "v0.36" menu: - text: Changelog href: https://turinglang.org/docs/changelog.html diff --git a/developers/compiler/design-overview/index.qmd b/developers/compiler/design-overview/index.qmd index e389c44d0..6b27454dc 100755 --- a/developers/compiler/design-overview/index.qmd +++ b/developers/compiler/design-overview/index.qmd @@ -291,8 +291,7 @@ not. Let `md` be an instance of `Metadata`: `md.vns`, `md.ranges`, `md.dists`, `md.orders` and `md.flags`. - `md.vns[md.idcs[vn]] == vn`. - `md.dists[md.idcs[vn]]` is the distribution of `vn`. - - `md.gids[md.idcs[vn]]` is the set of algorithms used to sample `vn`. This is used in - the Gibbs sampling process. + - `md.gids[md.idcs[vn]]` is the set of algorithms used to sample `vn`. This was used by the Gibbs sampler. Since Turing v0.36 it is unused and will eventually be deleted. - `md.orders[md.idcs[vn]]` is the number of `observe` statements before `vn` is sampled. - `md.ranges[md.idcs[vn]]` is the index range of `vn` in `md.vals`. - `md.vals[md.ranges[md.idcs[vn]]]` is the linearized vector of values of corresponding to `vn`. diff --git a/tutorials/01-gaussian-mixture-model/index.qmd b/tutorials/01-gaussian-mixture-model/index.qmd index 68bda2b37..df0fa7e10 100755 --- a/tutorials/01-gaussian-mixture-model/index.qmd +++ b/tutorials/01-gaussian-mixture-model/index.qmd @@ -110,7 +110,7 @@ model = gaussian_mixture_model(x); ``` We run a MCMC simulation to obtain an approximation of the posterior distribution of the parameters $\mu$ and $w$ and assignments $k$. -We use a `Gibbs` sampler that combines a [particle Gibbs](https://www.stats.ox.ac.uk/%7Edoucet/andrieu_doucet_holenstein_PMCMC.pdf) sampler for the discrete parameters (assignments $k$) and a Hamiltonion Monte Carlo sampler for the continuous parameters ($\mu$ and $w$). +We use a `Gibbs` sampler that combines a [particle Gibbs](https://www.stats.ox.ac.uk/%7Edoucet/andrieu_doucet_holenstein_PMCMC.pdf) sampler for the discrete parameters (assignments $k$) and a Hamiltonian Monte Carlo sampler for the continuous parameters ($\mu$ and $w$). We generate multiple chains in parallel using multi-threading. ```{julia} @@ -121,7 +121,7 @@ setprogress!(false) ```{julia} #| output: false -sampler = Gibbs(PG(100, :k), HMC(0.05, 10, :μ, :w)) +sampler = Gibbs(:k => PG(100), (:μ, :w) => HMC(0.05, 10)) nsamples = 150 nchains = 4 burn = 10 diff --git a/tutorials/04-hidden-markov-model/index.qmd b/tutorials/04-hidden-markov-model/index.qmd index ae9148273..ee0fed1cf 100755 --- a/tutorials/04-hidden-markov-model/index.qmd +++ b/tutorials/04-hidden-markov-model/index.qmd @@ -135,7 +135,7 @@ setprogress!(false) ``` ```{julia} -g = Gibbs(HMC(0.01, 50, :m, :T), PG(120, :s)) +g = Gibbs((:m, :T) => HMC(0.01, 50), :s => PG(120)) chn = sample(BayesHmm(y, 3), g, 1000); ``` diff --git a/tutorials/docs-10-using-turing-autodiff/index.qmd b/tutorials/docs-10-using-turing-autodiff/index.qmd index b46bb2beb..d1c31df9f 100755 --- a/tutorials/docs-10-using-turing-autodiff/index.qmd +++ b/tutorials/docs-10-using-turing-autodiff/index.qmd @@ -55,8 +55,8 @@ end c = sample( gdemo(1.5, 2), Gibbs( - HMC(0.1, 5, :m; adtype=AutoForwardDiff(; chunksize=0)), - HMC(0.1, 5, :s²; adtype=AutoReverseDiff(false)), + :m => HMC(0.1, 5; adtype=AutoForwardDiff(; chunksize=0)), + :s² => HMC(0.1, 5; adtype=AutoReverseDiff(false)), ), 1000, progress=false, diff --git a/tutorials/docs-12-using-turing-guide/index.qmd b/tutorials/docs-12-using-turing-guide/index.qmd index 2558b6a13..6f047825f 100755 --- a/tutorials/docs-12-using-turing-guide/index.qmd +++ b/tutorials/docs-12-using-turing-guide/index.qmd @@ -61,7 +61,7 @@ We can perform inference by using the `sample` function, the first argument of w c1 = sample(gdemo(1.5, 2), SMC(), 1000) c2 = sample(gdemo(1.5, 2), PG(10), 1000) c3 = sample(gdemo(1.5, 2), HMC(0.1, 5), 1000) -c4 = sample(gdemo(1.5, 2), Gibbs(PG(10, :m), HMC(0.1, 5, :s²)), 1000) +c4 = sample(gdemo(1.5, 2), Gibbs(:m => PG(10), :s² => HMC(0.1, 5)), 1000) c5 = sample(gdemo(1.5, 2), HMCDA(0.15, 0.65), 1000) c6 = sample(gdemo(1.5, 2), NUTS(0.65), 1000) ``` @@ -450,7 +450,7 @@ end simple_choice_f = simple_choice([1.5, 2.0, 0.3]) -chn = sample(simple_choice_f, Gibbs(HMC(0.2, 3, :p), PG(20, :z)), 1000) +chn = sample(simple_choice_f, Gibbs(:p => HMC(0.2, 3), :z => PG(20)), 1000) ``` The `Gibbs` sampler can be used to specify unique automatic differentiation backends for different variable spaces. Please see the [Automatic Differentiation]({{}}) article for more. diff --git a/tutorials/docs-15-using-turing-sampler-viz/index.qmd b/tutorials/docs-15-using-turing-sampler-viz/index.qmd index 9b31eab8b..de0e0fb2f 100755 --- a/tutorials/docs-15-using-turing-sampler-viz/index.qmd +++ b/tutorials/docs-15-using-turing-sampler-viz/index.qmd @@ -115,7 +115,7 @@ setprogress!(false) Gibbs sampling tends to exhibit a "jittery" trajectory. The example below combines `HMC` and `PG` sampling to traverse the posterior. ```{julia} -c = sample(model, Gibbs(HMC(0.01, 5, :s²), PG(20, :m)), 1000) +c = sample(model, Gibbs(:s² => HMC(0.01, 5), :m => PG(20)), 1000) plot_sampler(c) ``` From f2032be4dc509feba88bb3a4ab07d28d7f03c8d2 Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Thu, 16 Jan 2025 16:45:01 +0000 Subject: [PATCH 2/7] Replace Pathfinder example code with a link to Pathfinder docs --- Project.toml | 1 - .../index.qmd | 24 ++----------------- 2 files changed, 2 insertions(+), 23 deletions(-) diff --git a/Project.toml b/Project.toml index 020fb4766..71be25738 100644 --- a/Project.toml +++ b/Project.toml @@ -39,7 +39,6 @@ Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba" OptimizationNLopt = "4e6fcdb7-1186-4e1f-a706-475e75c168bb" OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e" PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" -Pathfinder = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" diff --git a/tutorials/docs-16-using-turing-external-samplers/index.qmd b/tutorials/docs-16-using-turing-external-samplers/index.qmd index a5362bed9..2c2d46b96 100755 --- a/tutorials/docs-16-using-turing-external-samplers/index.qmd +++ b/tutorials/docs-16-using-turing-external-samplers/index.qmd @@ -73,30 +73,10 @@ As previously mentioned, the Turing wrappers can often limit the capabilities of However, the native HMC sampler within Turing only allows the user to specify the type of the mass matrix despite the two options being possible within `AdvancedHMC`. Thankfully, we can use Turing's support for external samplers to define an HMC sampler with a custom mass matrix in `AdvancedHMC` and then use it to sample our Turing model. -We will use the library `Pathfinder`[^2] ((`Pathfinder`'s GitHub)[https://github.com/mlcolab/Pathfinder.jl]) to construct our estimate of mass matrix. +We can use the library `Pathfinder`[^2] ([`Pathfinder`'s GitHub](https://github.com/mlcolab/Pathfinder.jl)) to construct our estimate of mass matrix. `Pathfinder` is a variational inference algorithm that first finds the maximum a posteriori (MAP) estimate of a target posterior distribution and then uses the trace of the optimization to construct a sequence of multivariate normal approximations to the target distribution. In this process, `Pathfinder` computes an estimate of the mass matrix the user can access. - -The code below shows this can be done in practice. - -```{julia} -using AdvancedHMC, Pathfinder -# Running pathfinder -draws = 1_000 -result_multi = multipathfinder(model, draws; nruns=8) - -# Estimating the metric -inv_metric = result_multi.pathfinder_results[1].fit_distribution.Σ -metric = DenseEuclideanMetric(Matrix(inv_metric)) - -# Creating an AdvancedHMC NUTS sampler with the custom metric. -n_adapts = 1000 # Number of adaptation steps -tap = 0.9 # Large target acceptance probability to deal with the funnel structure of the posterior -nuts = AdvancedHMC.NUTS(tap; metric=metric) - -# Sample -chain = sample(model, externalsampler(nuts), 10_000; n_adapts=1_000) -``` +You can see an example of how to use `Pathfinder` with Turing in [`Pathfinder`'s docs](https://mlcolab.github.io/Pathfinder.jl/stable/examples/turing/). ## Using new inference methods From 5c7974b28043c63c8cc2c1d7d66fcb12259d9912 Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Thu, 16 Jan 2025 16:47:48 +0000 Subject: [PATCH 3/7] Update Manifest.toml --- Manifest.toml | 322 ++++++++++++++++++++++++++------------------------ 1 file changed, 170 insertions(+), 152 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index a42a0aae7..b5d4a85a1 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.11.2" manifest_format = "2.0" -project_hash = "53e97ef537fe2e98eecbe367cd36c4bc6a201e3e" +project_hash = "0a57e5ad0ccec2c044a937dc03323c83ad5b945d" [[deps.ADTypes]] git-tree-sha1 = "72af59f5b8f09faee36b4ec48e014a79210f2f4f" @@ -50,24 +50,24 @@ uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.5" [[deps.Accessors]] -deps = ["CompositionsBase", "ConstructionBase", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown"] -git-tree-sha1 = "96bed9b1b57cf750cca50c311a197e306816a1cc" +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "MacroTools"] +git-tree-sha1 = "0ba8f4c1f06707985ffb4804fdad1bf97b233897" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.39" +version = "0.1.41" [deps.Accessors.extensions] - AccessorsAxisKeysExt = "AxisKeys" - AccessorsDatesExt = "Dates" - AccessorsIntervalSetsExt = "IntervalSets" - AccessorsStaticArraysExt = "StaticArrays" - AccessorsStructArraysExt = "StructArrays" - AccessorsTestExt = "Test" - AccessorsUnitfulExt = "Unitful" + AxisKeysExt = "AxisKeys" + IntervalSetsExt = "IntervalSets" + LinearAlgebraExt = "LinearAlgebra" + StaticArraysExt = "StaticArrays" + StructArraysExt = "StructArrays" + TestExt = "Test" + UnitfulExt = "Unitful" [deps.Accessors.weakdeps] AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" - Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Requires = "ae029012-a4dd-5104-9daa-d747884805df" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" @@ -141,6 +141,12 @@ git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff" uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8" version = "1.1.3" +[[deps.AlmostBlockDiagonals]] +deps = ["ConcreteStructs"] +git-tree-sha1 = "743abe5e5fe8cff96dad4123f263c0d8eee281c0" +uuid = "a95523ee-d6da-40b5-98cc-27bc505739d5" +version = "0.1.10" + [[deps.ArgCheck]] git-tree-sha1 = "680b3b8759bd4c54052ada14e52355ab69e07876" uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" @@ -284,16 +290,16 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.BenchmarkTools]] -deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "f1dff6729bc61f4d49e140da1af55dcd1ac97b2f" +deps = ["Compat", "JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] +git-tree-sha1 = "e38fbc49a620f5d0b660d7f543db1009fe0f8336" uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.5.0" +version = "1.6.0" [[deps.Bijectors]] deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Distributions", "DocStringExtensions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "326420188d2bf91e89906beaa8438cf7a729ee29" +git-tree-sha1 = "af42d5383609f5cd167a2f9b1b2371c2d6604d02" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.15.2" +version = "0.15.4" weakdeps = ["DistributionsAD", "EnzymeCore", "ForwardDiff", "LazyArrays", "Mooncake", "ReverseDiff", "Tracker", "Zygote"] [deps.Bijectors.extensions] @@ -318,10 +324,10 @@ uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" version = "0.1.6" [[deps.BoundaryValueDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "BoundaryValueDiffEqFIRK", "BoundaryValueDiffEqMIRK", "BoundaryValueDiffEqShooting", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LineSearches", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "98da8bd76b89a4ae1b8dde9fc6dcd75dcd6b5282" +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqAscher", "BoundaryValueDiffEqCore", "BoundaryValueDiffEqFIRK", "BoundaryValueDiffEqMIRK", "BoundaryValueDiffEqMIRKN", "BoundaryValueDiffEqShooting", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolveFirstOrder", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "b1389abc8d064d930419714b852c1b584c8f7dd1" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "5.12.0" +version = "5.13.0" [deps.BoundaryValueDiffEq.extensions] BoundaryValueDiffEqODEInterfaceExt = "ODEInterface" @@ -329,29 +335,51 @@ version = "5.12.0" [deps.BoundaryValueDiffEq.weakdeps] ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c" +[[deps.BoundaryValueDiffEqAscher]] +deps = ["ADTypes", "Adapt", "AlmostBlockDiagonals", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "6f1104ac172140ad5dc8d7541357f47e30946031" +uuid = "7227322d-7511-4e07-9247-ad6ff830280e" +version = "1.2.0" + [[deps.BoundaryValueDiffEqCore]] deps = ["ADTypes", "Adapt", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolveFirstOrder", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "34c7d203f7a5002a7c27e69ae4f70f940cd22890" +git-tree-sha1 = "7ecf44dd453add837fda0e7dfb4740d7638e3c81" uuid = "56b672f2-a5fe-4263-ab2d-da677488eb3a" -version = "1.2.0" +version = "1.3.0" [[deps.BoundaryValueDiffEqFIRK]] deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "6305d58ba2f53faec7bf44dfba5b591b524254b0" +git-tree-sha1 = "feee7d8530e65c0ac38cc81321348c0a92c66f91" uuid = "85d9eb09-370e-4000-bb32-543851f73618" -version = "1.2.0" +version = "1.3.0" [[deps.BoundaryValueDiffEqMIRK]] deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "ed6802d8a97a0847060d25261b7561da83a4f044" +git-tree-sha1 = "b642f3b968efa51abba41aaf29d2ad869631cf0c" uuid = "1a22d4ce-7765-49ea-b6f2-13c8438986a6" -version = "1.2.0" +version = "1.3.0" + +[[deps.BoundaryValueDiffEqMIRKN]] +deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] +git-tree-sha1 = "8cb77e53a8695cef049e5d0556e6936f5a7503d6" +uuid = "9255f1d6-53bf-473e-b6bd-23f1ff009da4" +version = "1.1.0" [[deps.BoundaryValueDiffEqShooting]] deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "e30c7383ae1bf5564c139a95711b910b0f4f1a3d" +git-tree-sha1 = "bffd6c187eb8f55057d444754fda85efc2d6f5a6" uuid = "ed55bfe0-3725-4db6-871e-a1dc9f42a757" -version = "1.2.0" +version = "1.3.0" + +[[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"] @@ -440,9 +468,9 @@ version = "0.1.13" [[deps.Clustering]] deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "Random", "SparseArrays", "Statistics", "StatsBase"] -git-tree-sha1 = "9ebb045901e9bbf58767a9f34ff89831ed711aae" +git-tree-sha1 = "3e22db924e2945282e70c33b75d4dde8bfa44c94" uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5" -version = "0.15.7" +version = "0.15.8" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] @@ -520,21 +548,32 @@ version = "1.1.1+0" [[deps.ComponentArrays]] deps = ["Adapt", "ArrayInterface", "ChainRulesCore", "ConstructionBase", "ForwardDiff", "Functors", "LinearAlgebra", "StaticArrayInterface", "StaticArraysCore"] -git-tree-sha1 = "9921db9efec9f395210f02b56b87b93dbb6cfd2b" +git-tree-sha1 = "b926f8f322026c3a1d9539253ab111735eb540f8" uuid = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" -version = "0.15.20" -weakdeps = ["GPUArrays", "KernelAbstractions", "Optimisers", "RecursiveArrayTools", "ReverseDiff", "SciMLBase", "Tracker", "Zygote"] +version = "0.15.22" [deps.ComponentArrays.extensions] ComponentArraysGPUArraysExt = "GPUArrays" ComponentArraysKernelAbstractionsExt = "KernelAbstractions" ComponentArraysOptimisersExt = "Optimisers" + ComponentArraysReactantExt = "Reactant" ComponentArraysRecursiveArrayToolsExt = "RecursiveArrayTools" ComponentArraysReverseDiffExt = "ReverseDiff" ComponentArraysSciMLBaseExt = "SciMLBase" ComponentArraysTrackerExt = "Tracker" ComponentArraysZygoteExt = "Zygote" + [deps.ComponentArrays.weakdeps] + GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" + KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c" + Optimisers = "3bd65402-5787-11e9-1adc-39752487f4e2" + Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" + RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + [[deps.CompositionsBase]] git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" @@ -732,9 +771,9 @@ version = "7.15.0" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "5df172ce4e9da710603591f48c7af74eef288892" +git-tree-sha1 = "56816564cdb73cab9978dfb31dfb477ede88e3e4" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.6.28" +version = "0.6.29" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -803,9 +842,9 @@ version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "4b138e4643b577ccf355377c2bc70fa975af25de" +git-tree-sha1 = "7901a6117656e29fa2c74a58adb682f380922c47" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.115" +version = "0.25.116" weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [deps.Distributions.extensions] @@ -880,9 +919,9 @@ version = "1.0.4" [[deps.Enzyme]] deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] -git-tree-sha1 = "529a01a0ffdb0f490c24cc5308f0f9b6074a1339" +git-tree-sha1 = "f39747b06eb299ca32c237d8423f092a8391e60f" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.27" +version = "0.13.28" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -954,11 +993,6 @@ git-tree-sha1 = "fc3951d4d398b5515f91d7fe5d45fc31dccb3c9b" uuid = "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636" version = "0.8.5" -[[deps.ExternalDocstrings]] -git-tree-sha1 = "1224740fc4d07c989949e1c1b508ebd49a65a5f6" -uuid = "e189563c-0753-4f5e-ad5c-be4293c83fb4" -version = "0.1.1" - [[deps.FFMPEG]] deps = ["FFMPEG_jll"] git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00" @@ -1128,18 +1162,6 @@ version = "0.14.25" NCCL = "3fe64909-d7a1-4096-9b7d-7a0f12cf0f6b" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" -[[deps.Folds]] -deps = ["Accessors", "BangBang", "Baselet", "DefineSingletons", "Distributed", "ExternalDocstrings", "InitialValues", "MicroCollections", "Referenceables", "Requires", "Test", "ThreadedScans", "Transducers"] -git-tree-sha1 = "7eb4bc88d8295e387a667fd43d67c157ddee76cf" -uuid = "41a02a25-b8f0-4f67-bc48-60067656b558" -version = "0.2.10" - - [deps.Folds.extensions] - FoldsOnlineStatsBaseExt = "OnlineStatsBase" - - [deps.Folds.weakdeps] - OnlineStatsBase = "925886fa-5bf2-5e8e-b522-a9147a512338" - [[deps.Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] git-tree-sha1 = "21fac3c77d7b5a9fc03b0ec503aa1a6392c34d2b" @@ -1227,9 +1249,9 @@ version = "0.1.6" [[deps.GPUCompiler]] deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "PrecompileTools", "Preferences", "Scratch", "Serialization", "TOML", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "72408a76694e87e735f515a499ba1e069d232d39" +git-tree-sha1 = "8e30cd0b1934f03dd925416970061c1014c6686f" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "1.0.1" +version = "1.1.0" [[deps.GR]] deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] @@ -1470,9 +1492,9 @@ version = "0.2.4" [[deps.JumpProcesses]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] -git-tree-sha1 = "c3a2cb6f968404ed3b1d5382bbdd7b7d83966598" +git-tree-sha1 = "ed3b5f80be8fc7d1b0185edb862f2273e02cbec2" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.14.0" +version = "9.14.1" weakdeps = ["FastBroadcast"] [[deps.KLU]] @@ -1564,9 +1586,9 @@ weakdeps = ["Serialization"] [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731" +git-tree-sha1 = "1c602b1127f4751facb671441ca72715cc95938a" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.2+3" +version = "2.10.3+0" [[deps.L_BFGS_B_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1603,9 +1625,9 @@ version = "0.1.17" [[deps.LazyArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "f289bee714e11708df257c57514585863aa02b33" +git-tree-sha1 = "bf3957638b78521f286f3b2ebaa46a475dc74817" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "2.3.1" +version = "2.3.2" [deps.LazyArrays.extensions] LazyArraysBandedMatricesExt = "BandedMatrices" @@ -1703,15 +1725,15 @@ version = "1.51.1+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269" +git-tree-sha1 = "be484f5c92fad0bd8acfef35fe017900b0b73809" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.17.0+1" +version = "1.18.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "84eef7acd508ee5b3e956a2ae51b05024181dee0" +git-tree-sha1 = "89211ea35d9df5831fca5d33552c02bd33878419" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.40.2+2" +version = "2.40.3+0" [[deps.Libtask]] deps = ["FunctionWrappers", "LRUCache", "LinearAlgebra", "Statistics"] @@ -1727,9 +1749,9 @@ version = "4.7.1+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "edbf5309f9ddf1cab25afc344b1e8150b7c832f9" +git-tree-sha1 = "e888ad02ce716b319e6bdb985d2ef300e7089889" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.40.2+2" +version = "2.40.3+0" [[deps.LineSearch]] deps = ["ADTypes", "CommonSolve", "ConcreteStructs", "FastClosures", "LinearAlgebra", "MaybeInplace", "SciMLBase", "SciMLJacobianOperators", "StaticArraysCore"] @@ -1960,9 +1982,9 @@ version = "6.0.7" [[deps.MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "DataStructures", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tables"] -git-tree-sha1 = "770527473d1b929bc4a812831f34970f9c6a6ff6" +git-tree-sha1 = "a586f05dd16a50c490ed95415b2a829b8cf5d57f" uuid = "be115224-59cd-429b-ad48-344e309966f0" -version = "0.3.13" +version = "0.3.14" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] @@ -2045,9 +2067,9 @@ version = "0.4.17" [[deps.MLUtils]] deps = ["ChainRulesCore", "Compat", "DataAPI", "DelimitedFiles", "FLoops", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] -git-tree-sha1 = "b45738c2e3d0d402dffa32b2c1654759a2ac35a4" +git-tree-sha1 = "7940c0af802586b97009f254aa6065000a16fa1d" uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" -version = "0.4.4" +version = "0.4.5" [[deps.MPICH_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] @@ -2068,10 +2090,9 @@ uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" version = "5.5.1+2" [[deps.MacroTools]] -deps = ["Markdown", "Random"] -git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" +git-tree-sha1 = "72aebe0b5051e5143a079a4685a46da330a40472" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.13" +version = "0.5.15" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -2170,10 +2191,10 @@ uuid = "78c3b35d-d492-501b-9361-3d52fe80e533" version = "0.8.1" [[deps.Mooncake]] -deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DiffTests", "ExprTools", "FunctionWrappers", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Setfield", "Test"] -git-tree-sha1 = "bf9634a9db60ff8f40c9fc55f8e899c9858a69a2" +deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DiffTests", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Setfield", "Test"] +git-tree-sha1 = "057bcb5b614aef0452aafca4d444bba7da2f4b3f" uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" -version = "0.4.70" +version = "0.4.78" [deps.Mooncake.extensions] MooncakeAllocCheckExt = "AllocCheck" @@ -2216,9 +2237,9 @@ version = "7.8.3" [[deps.NLopt]] deps = ["CEnum", "NLopt_jll"] -git-tree-sha1 = "81a321298aed95631447a1f3afc2ea83682d44a4" +git-tree-sha1 = "dd79cb2a2d779209e42d76795edfde1c778eb5e0" uuid = "76087f3c-5699-56af-9a33-bf431cd00edd" -version = "1.1.1" +version = "1.1.2" [deps.NLopt.extensions] NLoptMathOptInterfaceExt = ["MathOptInterface"] @@ -2228,9 +2249,9 @@ version = "1.1.1" [[deps.NLopt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "3d1eefa627faeabc59ab9edbf00d17f70123ad69" +git-tree-sha1 = "dd645a206cc1e8bc4ff0dcfe3da08e39b60dd662" uuid = "079eb43e-fd8e-5478-9966-2cf3e3edb778" -version = "2.8.0+0" +version = "2.9.0+0" [[deps.NLsolve]] deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"] @@ -2240,9 +2261,9 @@ version = "4.5.1" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "1177f161cda2083543b9967d7ca2a3e24e721e13" +git-tree-sha1 = "bdc9d30f151590aca0af22690f5ab7dc18a551cb" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.26" +version = "0.9.27" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -2262,9 +2283,9 @@ version = "0.9.26" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" +git-tree-sha1 = "030ea22804ef91648f29b7ad3fc15fa49d0e6e71" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.2" +version = "1.0.3" [[deps.NameResolution]] deps = ["PrettyPrint"] @@ -2294,32 +2315,36 @@ 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 = "d0caebdb5a31e1a11ca9f7f189cdbf341ac89f0e" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "3.15.1" +version = "4.3.0" [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", "LinearAlgebra", "Markdown", "MaybeInplace", "Preferences", "Printf", "RecursiveArrayTools", "SciMLBase", "SciMLJacobianOperators", "SciMLOperators", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] @@ -2343,6 +2368,26 @@ git-tree-sha1 = "a1ea35ab0bcc99753e26d574ba1e339f19d100fa" uuid = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d" version = "1.2.0" +[[deps.NonlinearSolveQuasiNewton]] +deps = ["ArrayInterface", "CommonSolve", "ConcreteStructs", "DiffEqBase", "LinearAlgebra", "LinearSolve", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase", "SciMLOperators", "StaticArraysCore"] +git-tree-sha1 = "8f14b848afcfc0a2941cd3cca1bef04c987465bb" +uuid = "9a2c21bd-3a47-402d-9113-8faf9a0ee114" +version = "1.1.0" +weakdeps = ["ForwardDiff"] + + [deps.NonlinearSolveQuasiNewton.extensions] + NonlinearSolveQuasiNewtonForwardDiffExt = "ForwardDiff" + +[[deps.NonlinearSolveSpectralMethods]] +deps = ["CommonSolve", "ConcreteStructs", "DiffEqBase", "LineSearch", "MaybeInplace", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] +git-tree-sha1 = "f28b1ab17b5f15eb2b174eaf8813cf17f0b3e6c0" +uuid = "26075421-4e9a-44e1-8bd1-420ed7ad02b2" +version = "1.1.0" +weakdeps = ["ForwardDiff"] + + [deps.NonlinearSolveSpectralMethods.extensions] + NonlinearSolveSpectralMethodsForwardDiffExt = "ForwardDiff" + [[deps.ObjectFile]] deps = ["Reexport", "StructIO"] git-tree-sha1 = "dfcc26739b1ffa3ab51fb16f01ba7eb144f7bc50" @@ -2685,12 +2730,6 @@ git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" version = "0.11.31" -[[deps.PSIS]] -deps = ["LinearAlgebra", "LogExpFunctions", "Printf", "RecipesBase", "Statistics"] -git-tree-sha1 = "e5433b4c59636f5e8fcb275edcd8e8017dee3fe2" -uuid = "ce719bf2-d5d0-4fb9-925d-10a81b42ad04" -version = "0.9.7" - [[deps.PackageExtensionCompat]] git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930" @@ -2715,17 +2754,6 @@ git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" version = "2.8.1" -[[deps.Pathfinder]] -deps = ["ADTypes", "Distributions", "Folds", "IrrationalConstants", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "Optim", "Optimization", "OptimizationOptimJL", "PDMats", "PSIS", "ProgressLogging", "Random", "Requires", "SciMLBase", "Statistics", "StatsBase", "Transducers"] -git-tree-sha1 = "3a28e8450b63d3657adf804984ed0dd081a74447" -uuid = "b1d3bc72-d0e7-4279-b92f-7fa5d6d2d454" -version = "0.9.9" -weakdeps = ["Accessors", "DynamicHMC", "DynamicPPL", "MCMCChains", "Turing"] - - [deps.Pathfinder.extensions] - PathfinderDynamicHMCExt = "DynamicHMC" - PathfinderTuringExt = ["Accessors", "DynamicPPL", "MCMCChains", "Turing"] - [[deps.Pipe]] git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" @@ -2863,9 +2891,9 @@ uuid = "92933f4c-e287-5a05-a399-4b506db050ca" version = "1.10.2" [[deps.PtrArrays]] -git-tree-sha1 = "77a42d78b6a92df47ab37e177b2deac405e1c88f" +git-tree-sha1 = "1d36ef11a9aaf1e8b74dacc6a731dd1de8fd493d" uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" -version = "1.2.1" +version = "1.3.0" [[deps.Qt6Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"] @@ -3007,12 +3035,6 @@ git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" version = "1.2.2" -[[deps.Referenceables]] -deps = ["Adapt"] -git-tree-sha1 = "02d31ad62838181c1a3a5fd23a1ce5914a643601" -uuid = "42d2dcc6-99eb-4e98-b66c-637b7d73030e" -version = "0.1.3" - [[deps.RelocatableFolders]] deps = ["SHA", "Scratch"] git-tree-sha1 = "ffdaf70d81cf6ff22c2b6e733c900c3321cab864" @@ -3051,9 +3073,9 @@ version = "0.5.1+0" [[deps.Roots]] deps = ["Accessors", "CommonSolve", "Printf"] -git-tree-sha1 = "7e765d947455fbed09e230ee8b63c8904cbf1df9" +git-tree-sha1 = "f233e0a3de30a6eed170b8e1be0440f732fdf456" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.2.3" +version = "2.2.4" [deps.Roots.extensions] RootsChainRulesCoreExt = "ChainRulesCore" @@ -3098,9 +3120,9 @@ version = "0.1.1" [[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 = "3e5a9c5d6432b77a271646b4ada2573f239ac5c4" +git-tree-sha1 = "a263684f4134d50fe1863184281cc04a787a96a2" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.70.0" +version = "2.71.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3208,17 +3230,17 @@ 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 = "a3868a6add9f5989d1f4bd21de0333ef89fb9d9f" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.12.3" -weakdeps = ["ChainRulesCore", "ReverseDiff", "Tracker", "Zygote"] +version = "2.1.0" +weakdeps = ["ChainRulesCore", "DiffEqBase", "ReverseDiff", "Tracker"] [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" + SimpleNonlinearSolveDiffEqBaseExt = "DiffEqBase" SimpleNonlinearSolveReverseDiffExt = "ReverseDiff" SimpleNonlinearSolveTrackerExt = "Tracker" - SimpleNonlinearSolveZygoteExt = "Zygote" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -3501,9 +3523,9 @@ version = "5.2.3+0" [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "8db233b54917e474165d582bef2244fa040e0a56" +git-tree-sha1 = "fd2d4f0499f6bb4a0d9f5030f5c7d61eed385e03" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.36" +version = "0.3.37" [[deps.TOML]] deps = ["Dates"] @@ -3562,12 +3584,6 @@ deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" version = "1.11.0" -[[deps.ThreadedScans]] -deps = ["ArgCheck"] -git-tree-sha1 = "ca1ba3000289eacba571aaa4efcefb642e7a1de6" -uuid = "24d252fe-5d94-4a69-83ea-56a14333d47a" -version = "0.1.0" - [[deps.ThreadingUtilities]] deps = ["ManualMemory"] git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27" @@ -3652,9 +3668,9 @@ 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", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d1b261f1a37d5daed651ef6f332d09b9cf22823d" +git-tree-sha1 = "0f842be484159f158958355088f6cf3d674e2ded" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.35.5" +version = "0.36.0" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] @@ -3767,9 +3783,9 @@ version = "1.4.2" [[deps.WeightInitializers]] deps = ["ArgCheck", "ConcreteStructs", "GPUArraysCore", "LinearAlgebra", "Random", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "0b935265795ccccf12bc89e693b6380934451780" +git-tree-sha1 = "47b97ba36fcbbf9cc6707ed6ab60cf24fe50b981" uuid = "d49dbf32-c5c2-4618-8acc-27bb2598ef2d" -version = "1.0.4" +version = "1.1.1" [deps.WeightInitializers.extensions] WeightInitializersAMDGPUExt = ["AMDGPU", "GPUArrays"] @@ -3777,6 +3793,7 @@ version = "1.0.4" WeightInitializersChainRulesCoreExt = "ChainRulesCore" WeightInitializersGPUArraysExt = "GPUArrays" WeightInitializersMetalExt = ["Metal", "GPUArrays"] + WeightInitializersReactantExt = "Reactant" WeightInitializersoneAPIExt = ["oneAPI", "GPUArrays"] [deps.WeightInitializers.weakdeps] @@ -3785,6 +3802,7 @@ version = "1.0.4" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b" [[deps.Widgets]] @@ -3842,9 +3860,9 @@ version = "1.8.6+3" [[deps.Xorg_libXau_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "2b0e27d52ec9d8d483e2ca0b72b3cb1a8df5c27a" +git-tree-sha1 = "e9216fdcd8514b7072b43653874fd688e4c6c003" uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.11+3" +version = "1.0.12+0" [[deps.Xorg_libXcursor_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] @@ -3854,9 +3872,9 @@ version = "1.2.3+0" [[deps.Xorg_libXdmcp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "02054ee01980c90297412e4c809c8694d7323af3" +git-tree-sha1 = "89799ae67c17caa5b3b5a19b8469eeee474377db" uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.4+3" +version = "1.1.5+0" [[deps.Xorg_libXext_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] @@ -3896,9 +3914,9 @@ version = "0.9.11+1" [[deps.Xorg_libpthread_stubs_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "fee57a273563e273f0f53275101cd41a8153517a" +git-tree-sha1 = "c57201109a9e4c0585b208bb408bc41d205ac4e9" uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.1+3" +version = "0.1.2+0" [[deps.Xorg_libxcb_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] @@ -3962,9 +3980,9 @@ version = "2.39.0+0" [[deps.Xorg_xtrans_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "b9ead2d2bdb27330545eb14234a2e300da61232e" +git-tree-sha1 = "6dba04dbfb72ae3ebe5418ba33d087ba8aa8cb00" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.5.0+3" +version = "1.5.1+0" [[deps.Zlib_jll]] deps = ["Libdl"] @@ -4015,9 +4033,9 @@ version = "3.1.1+1" [[deps.libaec_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "46bf7be2917b59b761247be3f317ddf75e50e997" +git-tree-sha1 = "f5733a5a9047722470b95a81e1b172383971105c" uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0" -version = "1.1.2+2" +version = "1.1.3+0" [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -4062,9 +4080,9 @@ version = "1.18.0+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "b7bfd3ab9d2c58c3829684142f5804e4c6499abc" +git-tree-sha1 = "d7b5bbf1efbafb5eca466700949625e07533aff2" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.45+0" +version = "1.6.45+1" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] From c15ba5e3434842db6fd7d234c055604f99a1f55b Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Thu, 23 Jan 2025 14:35:49 +0000 Subject: [PATCH 4/7] Bump Turing compat to 0.36.2 --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 71be25738..e8381eb34 100644 --- a/Project.toml +++ b/Project.toml @@ -54,4 +54,4 @@ UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] -Turing = "0.36" +Turing = "0.36.2" From b27faf86abb9a47dc6bc6aa2aa229650ee982f38 Mon Sep 17 00:00:00 2001 From: Markus Hauru Date: Fri, 24 Jan 2025 14:41:18 +0000 Subject: [PATCH 5/7] Regenerate Manifest.toml with TuringBenchmarking.jl v0.5.8 --- Manifest.toml | 150 +++++++++++++++++++++++++------------------------- 1 file changed, 75 insertions(+), 75 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index b5d4a85a1..d3fc4da73 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,12 +2,12 @@ julia_version = "1.11.2" manifest_format = "2.0" -project_hash = "0a57e5ad0ccec2c044a937dc03323c83ad5b945d" +project_hash = "16b1d007f281b947709b24063dec56b6638fa9b1" [[deps.ADTypes]] -git-tree-sha1 = "72af59f5b8f09faee36b4ec48e014a79210f2f4f" +git-tree-sha1 = "e1ce448a0d7f88168ffe2eeac4549c32d45a42d1" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.11.0" +version = "1.12.1" weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] [deps.ADTypes.extensions] @@ -39,10 +39,10 @@ uuid = "80f14c24-f653-4e6a-9b94-39d6b0f70001" version = "5.6.0" [[deps.AbstractPPL]] -deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random"] -git-tree-sha1 = "bdb19638644450ee1b0fd63740381835069d34b9" +deps = ["AbstractMCMC", "Accessors", "DensityInterface", "JSON", "Random", "StatsBase"] +git-tree-sha1 = "b155685b5daa9d9d19dfe42684a53fa8cbbb83b8" uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" -version = "0.9.0" +version = "0.10.1" [[deps.AbstractTrees]] git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177" @@ -114,9 +114,9 @@ weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"] [[deps.AdvancedPS]] deps = ["AbstractMCMC", "Distributions", "Random", "Random123", "Requires", "SSMProblems", "StatsFuns"] -git-tree-sha1 = "5dcd3de7e7346f48739256e71a86d0f96690b8c8" +git-tree-sha1 = "c017e6cded5495294ff82d5c8a176492f752b22e" uuid = "576499cb-2369-40b2-a588-c64705576edc" -version = "0.6.0" +version = "0.6.1" weakdeps = ["Libtask"] [deps.AdvancedPS.extensions] @@ -324,10 +324,10 @@ uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" version = "0.1.6" [[deps.BoundaryValueDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqAscher", "BoundaryValueDiffEqCore", "BoundaryValueDiffEqFIRK", "BoundaryValueDiffEqMIRK", "BoundaryValueDiffEqMIRKN", "BoundaryValueDiffEqShooting", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolveFirstOrder", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "b1389abc8d064d930419714b852c1b584c8f7dd1" +deps = ["ADTypes", "ArrayInterface", "BoundaryValueDiffEqAscher", "BoundaryValueDiffEqCore", "BoundaryValueDiffEqFIRK", "BoundaryValueDiffEqMIRK", "BoundaryValueDiffEqMIRKN", "BoundaryValueDiffEqShooting", "DiffEqBase", "FastClosures", "ForwardDiff", "LinearAlgebra", "Reexport", "SciMLBase"] +git-tree-sha1 = "c6f965b14b4073171b5404e005d0abda3888f8b6" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "5.13.0" +version = "5.14.0" [deps.BoundaryValueDiffEq.extensions] BoundaryValueDiffEqODEInterfaceExt = "ODEInterface" @@ -337,39 +337,39 @@ version = "5.13.0" [[deps.BoundaryValueDiffEqAscher]] deps = ["ADTypes", "Adapt", "AlmostBlockDiagonals", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "6f1104ac172140ad5dc8d7541357f47e30946031" +git-tree-sha1 = "ab8999d481e102421361f8ca514aa75fcc4feb3f" uuid = "7227322d-7511-4e07-9247-ad6ff830280e" -version = "1.2.0" +version = "1.3.0" [[deps.BoundaryValueDiffEqCore]] deps = ["ADTypes", "Adapt", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "Logging", "NonlinearSolveFirstOrder", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "7ecf44dd453add837fda0e7dfb4740d7638e3c81" +git-tree-sha1 = "54eef71b725661a87089b11c629b1a410fd65c90" uuid = "56b672f2-a5fe-4263-ab2d-da677488eb3a" -version = "1.3.0" +version = "1.6.0" [[deps.BoundaryValueDiffEqFIRK]] deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "feee7d8530e65c0ac38cc81321348c0a92c66f91" +git-tree-sha1 = "314c6e0ea597f6d733f78c0d553fdfacc7abb6c1" uuid = "85d9eb09-370e-4000-bb32-543851f73618" -version = "1.3.0" +version = "1.4.0" [[deps.BoundaryValueDiffEqMIRK]] deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "b642f3b968efa51abba41aaf29d2ad869631cf0c" +git-tree-sha1 = "4be1e7bbe1681a713427ab8384774c7edaf20f73" uuid = "1a22d4ce-7765-49ea-b6f2-13c8438986a6" -version = "1.3.0" +version = "1.4.0" [[deps.BoundaryValueDiffEqMIRKN]] deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LineSearch", "LinearAlgebra", "LinearSolve", "Logging", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "8cb77e53a8695cef049e5d0556e6936f5a7503d6" +git-tree-sha1 = "62bdd5cb9b8dbcb5a6a728d12efa5d20b538370a" uuid = "9255f1d6-53bf-473e-b6bd-23f1ff009da4" -version = "1.1.0" +version = "1.3.0" [[deps.BoundaryValueDiffEqShooting]] deps = ["ADTypes", "Adapt", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "OrdinaryDiffEq", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseDiffTools"] -git-tree-sha1 = "bffd6c187eb8f55057d444754fda85efc2d6f5a6" +git-tree-sha1 = "4d4ced45c733f6691bdcda11ae62ec0de02ddf06" uuid = "ed55bfe0-3725-4db6-871e-a1dc9f42a757" -version = "1.3.0" +version = "1.4.0" [[deps.BracketingNonlinearSolve]] deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] @@ -480,9 +480,9 @@ version = "0.7.6" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "c785dfb1b3bfddd1da557e861b919819b82bbe5b" +git-tree-sha1 = "26ec26c98ae1453c692efded2b17e15125a5bea1" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.27.1" +version = "3.28.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -737,9 +737,9 @@ version = "4.1.0" [[deps.DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "880d1fcf95e6492a4e7d65c2866dbdbf6580d4f8" +git-tree-sha1 = "516d553f5deee7c55b2945b5edf05b6542837887" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.24.0" +version = "5.24.1" weakdeps = ["ReverseDiff"] [deps.DiffEqNoiseProcess.extensions] @@ -771,9 +771,9 @@ version = "7.15.0" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "56816564cdb73cab9978dfb31dfb477ede88e3e4" +git-tree-sha1 = "d86f29074367f1bb92957e8d0b77badd187a97bc" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.6.29" +version = "0.6.32" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -842,9 +842,9 @@ version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "7901a6117656e29fa2c74a58adb682f380922c47" +git-tree-sha1 = "03aa5d44647eaec98e1920635cdfed5d5560a8b9" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.116" +version = "0.25.117" weakdeps = ["ChainRulesCore", "DensityInterface", "Test"] [deps.Distributions.extensions] @@ -877,16 +877,16 @@ uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" [[deps.DynamicHMC]] -deps = ["ArgCheck", "DocStringExtensions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "LogExpFunctions", "ProgressMeter", "Random", "SimpleUnPack", "Statistics", "TensorCast"] -git-tree-sha1 = "9285af003a31272b4105c8e80d90b99eaf4b8c05" +deps = ["ArgCheck", "DocStringExtensions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "LogExpFunctions", "ProgressMeter", "Random", "Statistics", "TensorCast"] +git-tree-sha1 = "ba30c83b20dce95e7353b1d7f7f3a6d151722b55" uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb" -version = "3.4.7" +version = "3.5.0" [[deps.DynamicPPL]] -deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "InteractiveUtils", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"] -git-tree-sha1 = "5c2bc37cbc946902e1af5ae8486f24bb585d20cb" +deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "InteractiveUtils", "KernelAbstractions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"] +git-tree-sha1 = "1e033aa6126051f5fed765c22671561a2808be91" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.32.2" +version = "0.34.1" [deps.DynamicPPL.extensions] DynamicPPLChainRulesCoreExt = ["ChainRulesCore"] @@ -1007,9 +1007,9 @@ version = "4.4.4+1" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "4820348781ae578893311153d69049a93d05f39d" +git-tree-sha1 = "7de7c78d681078f027389e067864a8d53bd7c3c9" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.8.0" +version = "1.8.1" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1255,15 +1255,15 @@ version = "1.1.0" [[deps.GR]] deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] -git-tree-sha1 = "424c8f76017e39fdfcdbb5935a8e6742244959e8" +git-tree-sha1 = "9bf00ba4c45867c86251a7fd4cb646dcbeb41bf0" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.10" +version = "0.73.12" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "b90934c8cb33920a8dc66736471dc3961b42ec9f" +git-tree-sha1 = "36d5430819123553bf31dfdceb3653ca7d9e62d7" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.10+0" +version = "0.73.12+0" [[deps.GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -1354,9 +1354,9 @@ version = "2.11.2+3" [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9" +git-tree-sha1 = "2bd56245074fab4015b9174f24ceba8293209053" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.25" +version = "0.3.27" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools"] @@ -1400,9 +1400,9 @@ version = "0.3.0" [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"] -git-tree-sha1 = "10bd689145d2c3b2a9844005d01087cc1194e79e" +git-tree-sha1 = "0f14a5456bdc6b9731a5682f439a672750a09e48" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2024.2.1+0" +version = "2025.0.4+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -1529,9 +1529,9 @@ version = "0.10.64" [[deps.Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "4f20a2df85a9e5d55c9e84634bbf808ed038cabd" +git-tree-sha1 = "d1c697c53d3041a371c1da21305d0dc9259dbc8a" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.9.8" +version = "0.9.9" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1553,9 +1553,9 @@ version = "4.0.1+0" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"] -git-tree-sha1 = "d422dfd9707bec6617335dc2ea3c5172a87d5908" +git-tree-sha1 = "5fcfea6df2ff3e4da708a40c969c3812162346df" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "9.1.3" +version = "9.2.0" [deps.LLVM.extensions] BFloat16sExt = "BFloat16s" @@ -1565,9 +1565,9 @@ version = "9.1.3" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "05a8bd5a42309a9ec82f700876903abce1017dd3" +git-tree-sha1 = "4b5ad6a4ffa91a00050a964492bc4f86bb48cea0" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.34+0" +version = "0.0.35+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1988,9 +1988,9 @@ version = "0.3.14" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] -git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f" +git-tree-sha1 = "5de60bc6cb3899cd318d80d627560fae2e2d99ae" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2024.2.0+0" +version = "2025.0.1+1" [[deps.MLDataDevices]] deps = ["Adapt", "Compat", "Functors", "Preferences", "Random"] @@ -2283,9 +2283,9 @@ version = "0.9.27" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "030ea22804ef91648f29b7ad3fc15fa49d0e6e71" +git-tree-sha1 = "fe891aea7ccd23897520db7f16931212454e277e" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.3" +version = "1.1.1" [[deps.NameResolution]] deps = ["PrettyPrint"] @@ -2456,9 +2456,9 @@ version = "0.5.6+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "ab7edad78cdef22099f43c54ef77ac63c2c9cc64" +git-tree-sha1 = "c1f51f704f689f87f28b33836fd460ecf9b34583" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.10.0" +version = "1.11.0" [deps.Optim.extensions] OptimMOIExt = "MathOptInterface" @@ -2474,9 +2474,9 @@ version = "0.3.4" [[deps.Optimization]] deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] -git-tree-sha1 = "4b59eef21418fbdf28afbe2d7e945d8efbe5057d" +git-tree-sha1 = "e246ed7381acdc9d39042ba4c263b19f29232de9" uuid = "7f7a1694-90dd-40f0-9382-eb1efda571ba" -version = "4.0.5" +version = "4.1.0" [[deps.OptimizationBase]] deps = ["ADTypes", "ArrayInterface", "DifferentiationInterface", "DocStringExtensions", "FastClosures", "LinearAlgebra", "PDMats", "Reexport", "Requires", "SciMLBase", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] @@ -2549,9 +2549,9 @@ version = "1.2.0" [[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"] -git-tree-sha1 = "72c77ae685fddb6291fff22dba13f4f32602475c" +git-tree-sha1 = "f5f5af4cd0776eb17bb0a90cf82c6d2be17b59b2" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.14.1" +version = "1.15.0" weakdeps = ["EnzymeCore"] [deps.OrdinaryDiffEqCore.extensions] @@ -2726,9 +2726,9 @@ version = "10.42.0+1" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" +git-tree-sha1 = "966b85253e959ea89c53a9abebbf2e964fbf593b" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.31" +version = "0.11.32" [[deps.PackageExtensionCompat]] git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518" @@ -3120,9 +3120,9 @@ version = "0.1.1" [[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 = "a263684f4134d50fe1863184281cc04a787a96a2" +git-tree-sha1 = "80396dc3496a1718fc356797fa54034b6c533a18" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.71.0" +version = "2.72.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3316,9 +3316,9 @@ version = "0.1.2" [[deps.SparseMatrixColorings]] deps = ["ADTypes", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "76b44c879661552d64f382acf66faa29ab56b3d9" +git-tree-sha1 = "45b5ef11e75839e174d5728fd1e73597e7593634" uuid = "0a514795-09f3-496d-8182-132a7b665d35" -version = "0.4.10" +version = "0.4.12" weakdeps = ["Colors"] [deps.SparseMatrixColorings.extensions] @@ -3668,9 +3668,9 @@ 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", "LogDensityProblemsAD", "MCMCChains", "NamedArrays", "Optimization", "OptimizationOptimJL", "OrderedCollections", "Printf", "Random", "Reexport", "SciMLBase", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "0f842be484159f158958355088f6cf3d674e2ded" +git-tree-sha1 = "5218eb833eaaffa0021de7a550564ff6bd53b96c" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.36.0" +version = "0.36.2" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] @@ -3679,9 +3679,9 @@ weakdeps = ["DynamicHMC", "Optim"] [[deps.TuringBenchmarking]] deps = ["ADTypes", "AbstractMCMC", "BenchmarkTools", "DynamicPPL", "ForwardDiff", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "PrettyTables", "Requires", "ReverseDiff", "Zygote"] -git-tree-sha1 = "1489ccf0fff5b2b1d612003a95772c1fda6f0e62" +git-tree-sha1 = "bac1a0af7e13099ff24a7315f1b4728b503abca2" uuid = "0db1332d-5c25-4deb-809f-459bc696f94f" -version = "0.5.7" +version = "0.5.8" [deps.TuringBenchmarking.extensions] TuringBenchmarkingBridgeStanExt = "BridgeStan" @@ -4009,9 +4009,9 @@ weakdeps = ["Colors", "Distances", "Tracker"] [[deps.ZygoteRules]] deps = ["ChainRulesCore", "MacroTools"] -git-tree-sha1 = "27798139afc0a2afa7b1824c206d5e87ea587a00" +git-tree-sha1 = "434b3de333c75fc446aa0d19fc394edafd07ab08" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.5" +version = "0.2.7" [[deps.eudev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] From ad35b9e9784ce8907ccacd6f13a5938444b94c58 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Tue, 28 Jan 2025 12:06:21 +0000 Subject: [PATCH 6/7] Update dependencies --- Manifest.toml | 52 +++++++++++++++++++++++++++------------------------ 1 file changed, 28 insertions(+), 24 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index d3fc4da73..66fcf1623 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,6 +1,6 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.11.2" +julia_version = "1.11.3" manifest_format = "2.0" project_hash = "16b1d007f281b947709b24063dec56b6638fa9b1" @@ -222,18 +222,20 @@ version = "1.11.0" [[deps.Atomix]] deps = ["UnsafeAtomics"] -git-tree-sha1 = "c3b238aa28c1bebd4b5ea4988bebf27e9a01b72b" +git-tree-sha1 = "93da6c8228993b0052e358ad592ee7c1eccaa639" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" -version = "1.0.1" +version = "1.1.0" [deps.Atomix.extensions] AtomixCUDAExt = "CUDA" AtomixMetalExt = "Metal" + AtomixOpenCLExt = "OpenCL" AtomixoneAPIExt = "oneAPI" [deps.Atomix.weakdeps] CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + OpenCL = "08131aa3-fb12-5dee-8b74-c09406e224a2" oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b" [[deps.AxisAlgorithms]] @@ -771,9 +773,9 @@ version = "7.15.0" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "d86f29074367f1bb92957e8d0b77badd187a97bc" +git-tree-sha1 = "b44d8cedd863c1c7a9f3ec82555539ec9935d07f" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.6.32" +version = "0.6.33" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -783,6 +785,7 @@ version = "0.6.32" DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" DifferentiationInterfaceForwardDiffExt = ["ForwardDiff", "DiffResults"] + DifferentiationInterfaceGTPSAExt = "GTPSA" DifferentiationInterfaceMooncakeExt = "Mooncake" DifferentiationInterfacePolyesterForwardDiffExt = "PolyesterForwardDiff" DifferentiationInterfaceReverseDiffExt = ["ReverseDiff", "DiffResults"] @@ -803,6 +806,7 @@ version = "0.6.32" FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + GTPSA = "b27dd330-f138-47c5-815b-40db9dd9b6e8" Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" @@ -884,9 +888,9 @@ version = "3.5.0" [[deps.DynamicPPL]] deps = ["ADTypes", "AbstractMCMC", "AbstractPPL", "Accessors", "BangBang", "Bijectors", "Compat", "ConstructionBase", "Distributions", "DocStringExtensions", "InteractiveUtils", "KernelAbstractions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "MacroTools", "OrderedCollections", "Random", "Requires", "Test"] -git-tree-sha1 = "1e033aa6126051f5fed765c22671561a2808be91" +git-tree-sha1 = "18fcc77ba683967339473b731143fa269ea671f5" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.34.1" +version = "0.34.2" [deps.DynamicPPL.extensions] DynamicPPLChainRulesCoreExt = ["ChainRulesCore"] @@ -1625,9 +1629,9 @@ version = "0.1.17" [[deps.LazyArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "bf3957638b78521f286f3b2ebaa46a475dc74817" +git-tree-sha1 = "795ae125c98c58ceb1de562633703e0b120a1b17" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "2.3.2" +version = "2.4.0" [deps.LazyArrays.extensions] LazyArraysBandedMatricesExt = "BandedMatrices" @@ -2549,9 +2553,9 @@ version = "1.2.0" [[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"] -git-tree-sha1 = "f5f5af4cd0776eb17bb0a90cf82c6d2be17b59b2" +git-tree-sha1 = "6a58da59c5f7640fd09636231bd73dfb4744ce53" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.15.0" +version = "1.15.1" weakdeps = ["EnzymeCore"] [deps.OrdinaryDiffEqCore.extensions] @@ -2998,9 +3002,9 @@ version = "0.6.12" [[deps.RecursiveArrayTools]] deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "32f824db4e5bab64e25a12b22483a30a6b813d08" +git-tree-sha1 = "ea6ad53c168c7c1c2e8f870aefda269692a8a91f" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.27.4" +version = "3.28.0" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -3120,9 +3124,9 @@ version = "0.1.1" [[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 = "80396dc3496a1718fc356797fa54034b6c533a18" +git-tree-sha1 = "fcb73c66a5071d4d026aa84f9950a4d1f0dadf33" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.72.0" +version = "2.72.1" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3270,9 +3274,9 @@ version = "1.11.0" [[deps.SparseConnectivityTracer]] deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "010b3c44301805d1ede9159f449a351d61172aa6" +git-tree-sha1 = "f6d636dcf886cf498b3bc484f48c37741d8aac6e" uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" -version = "0.6.9" +version = "0.6.10" [deps.SparseConnectivityTracer.extensions] SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" @@ -3371,9 +3375,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "47091a0340a675c738b1304b58161f3b0839d454" +git-tree-sha1 = "02c8bd479d26dbeff8a7eb1d77edfc10dacabc01" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.10" +version = "1.9.11" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -3443,10 +3447,10 @@ uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f" version = "2.4.1" [[deps.StochasticDiffEq]] -deps = ["ADTypes", "Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FastPower", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "OrdinaryDiffEqCore", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "b0a5dce397b3bc5478ee1de3127878daa061db28" +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 = "1f1161aca132f7f776acfb3785abf449aa99a1e9" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.72.1" +version = "6.73.0" [[deps.StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static", "StaticArrayInterface", "ThreadingUtilities"] @@ -3836,9 +3840,9 @@ version = "1.1.42+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "beef98d5aad604d9e7d60b2ece5181f7888e2fd6" +git-tree-sha1 = "56c6604ec8b2d82cc4cfe01aa03b00426aac7e1f" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.6.4+0" +version = "5.6.4+1" [[deps.Xorg_libICE_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] From 167f899de3483e6eb51b1e8f88a95e21f97c778a Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Tue, 28 Jan 2025 14:04:53 +0000 Subject: [PATCH 7/7] Host golf.dat file ourselves --- Manifest.toml | 8 +------- Project.toml | 1 - .../gaussian-processes-introduction/golf.dat | 20 +++++++++++++++++++ .../gaussian-processes-introduction/index.qmd | 17 +++------------- 4 files changed, 24 insertions(+), 22 deletions(-) create mode 100644 tutorials/gaussian-processes-introduction/golf.dat diff --git a/Manifest.toml b/Manifest.toml index 66fcf1623..92b7fafc8 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.11.3" manifest_format = "2.0" -project_hash = "16b1d007f281b947709b24063dec56b6638fa9b1" +project_hash = "547d92b7c2cee83d66812c3662de0a43b46d819f" [[deps.ADTypes]] git-tree-sha1 = "e1ce448a0d7f88168ffe2eeac4549c32d45a42d1" @@ -640,12 +640,6 @@ git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" version = "1.16.0" -[[deps.DataDeps]] -deps = ["HTTP", "Libdl", "Reexport", "SHA", "Scratch", "p7zip_jll"] -git-tree-sha1 = "8ae085b71c462c2cb1cfedcb10c3c877ec6cf03f" -uuid = "124859b0-ceae-595e-8997-d05f6a7a8dfe" -version = "0.7.13" - [[deps.DataFrames]] deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6" diff --git a/Project.toml b/Project.toml index e8381eb34..13df0a8fc 100644 --- a/Project.toml +++ b/Project.toml @@ -7,7 +7,6 @@ AdvancedMH = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" Bijectors = "76274a88-744f-5084-9051-94815aaf08c4" CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" -DataDeps = "124859b0-ceae-595e-8997-d05f6a7a8dfe" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" diff --git a/tutorials/gaussian-processes-introduction/golf.dat b/tutorials/gaussian-processes-introduction/golf.dat new file mode 100644 index 000000000..9ec86ff0a --- /dev/null +++ b/tutorials/gaussian-processes-introduction/golf.dat @@ -0,0 +1,20 @@ +distance n y +2 1443 1346 +3 694 577 +4 455 337 +5 353 208 +6 272 149 +7 256 136 +8 240 111 +9 217 69 +10 200 67 +11 237 75 +12 202 52 +13 192 46 +14 174 54 +15 167 28 +16 201 27 +17 195 31 +18 191 33 +19 147 20 +20 152 24 diff --git a/tutorials/gaussian-processes-introduction/index.qmd b/tutorials/gaussian-processes-introduction/index.qmd index 33389b556..5f7378157 100755 --- a/tutorials/gaussian-processes-introduction/index.qmd +++ b/tutorials/gaussian-processes-introduction/index.qmd @@ -30,20 +30,9 @@ given distance. ### Let's download the data and take a look at it: ```{julia} -using CSV, DataDeps, DataFrames - -ENV["DATADEPS_ALWAYS_ACCEPT"] = true -register( - DataDep( - "putting", - "Putting data from BDA", - "http://www.stat.columbia.edu/~gelman/book/data/golf.dat", - "fc28d83896af7094d765789714524d5a389532279b64902866574079c1a977cc", - ), -) - -fname = joinpath(datadep"putting", "golf.dat") -df = CSV.read(fname, DataFrame; delim=' ', ignorerepeated=true) +using CSV, DataFrames + +df = CSV.read("golf.dat", DataFrame; delim=' ', ignorerepeated=true) df[1:5, :] ```