From 1ef11ec02c3a91ebc73a8d2659184e2173be5216 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Sun, 8 Jun 2025 13:37:22 +0100 Subject: [PATCH 1/7] Bump to v0.39 --- Project.toml | 2 +- _quarto.yml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Project.toml b/Project.toml index 6c1f69ec4..b71ab164c 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 = "0.38" +Turing = "0.39" diff --git a/_quarto.yml b/_quarto.yml index 90f198ca8..70ee04bce 100644 --- a/_quarto.yml +++ b/_quarto.yml @@ -32,7 +32,7 @@ website: text: Team right: # Current version - - text: "v0.38" + - text: "v0.39" menu: - text: Changelog href: https://turinglang.org/docs/changelog.html From 8c5f64a80dda3ad0f43ae7fcade05d6ed3df9d68 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Sun, 8 Jun 2025 13:38:39 +0100 Subject: [PATCH 2/7] Update addlogprob exports --- tutorials/gaussian-mixture-models/index.qmd | 8 ++++---- tutorials/hidden-markov-models/index.qmd | 4 ++-- usage/modifying-logprob/index.qmd | 10 +++++----- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/tutorials/gaussian-mixture-models/index.qmd b/tutorials/gaussian-mixture-models/index.qmd index b93bb6f3e..36449824c 100755 --- a/tutorials/gaussian-mixture-models/index.qmd +++ b/tutorials/gaussian-mixture-models/index.qmd @@ -278,7 +278,7 @@ $$ $$ Where we sum the components with `logsumexp` from the [`LogExpFunctions.jl` package](https://juliastats.org/LogExpFunctions.jl/stable/). -The manually incremented likelihood can be added to the log-probability with `Turing.@addlogprob!`, giving us the following model: +The manually incremented likelihood can be added to the log-probability with `@addlogprob!`, giving us the following model: ```{julia} #| output: false @@ -295,7 +295,7 @@ using LogExpFunctions for k in 1:K lvec[k] = (w[k] + logpdf(dists[k], x[:, i])) end - Turing.@addlogprob! logsumexp(lvec) + @addlogprob! logsumexp(lvec) end end ``` @@ -303,10 +303,10 @@ end ::: {.callout-warning collapse="false"} ## Manually Incrementing Probablity -When possible, use of `Turing.@addlogprob!` should be avoided, as it exists outside the +When possible, use of `@addlogprob!` should be avoided, as it exists outside the usual structure of a Turing model. In most cases, a custom distribution should be used instead. -Here, the next section demonstrates the perfered method --- using the `MixtureModel` distribution we have seen already to +Here, the next section demonstrates the preferred method --- using the `MixtureModel` distribution we have seen already to perform the marginalization automatically. ::: diff --git a/tutorials/hidden-markov-models/index.qmd b/tutorials/hidden-markov-models/index.qmd index 7ce698ada..fd4974f15 100755 --- a/tutorials/hidden-markov-models/index.qmd +++ b/tutorials/hidden-markov-models/index.qmd @@ -191,7 +191,7 @@ using LogExpFunctions T ~ filldist(Dirichlet(fill(1/K, K)), K) hmm = HMM(softmax(ones(K)), copy(T'), [Normal(m[i], 0.1) for i in 1:K]) - Turing.@addlogprob! logdensityof(hmm, y) + @addlogprob! logdensityof(hmm, y) end chn2 = sample(BayesHmm2(y, 3), NUTS(), 1000) @@ -221,7 +221,7 @@ We can use the `viterbi()` algorithm, also from the `HiddenMarkovModels` package T ~ filldist(Dirichlet(fill(1/K, K)), K) hmm = HMM(softmax(ones(K)), copy(T'), [Normal(m[i], 0.1) for i in 1:K]) - Turing.@addlogprob! logdensityof(hmm, y) + @addlogprob! logdensityof(hmm, y) # Conditional generation of the hidden states. if IncludeGenerated diff --git a/usage/modifying-logprob/index.qmd b/usage/modifying-logprob/index.qmd index b44776b51..b3de9e7ee 100755 --- a/usage/modifying-logprob/index.qmd +++ b/usage/modifying-logprob/index.qmd @@ -13,7 +13,7 @@ Pkg.instantiate(); ``` Turing accumulates log probabilities internally in an internal data structure that is accessible through the internal variable `__varinfo__` inside of the model definition. -To avoid users having to deal with internal data structures, Turing provides the `Turing.@addlogprob!` macro which increases the accumulated log probability. +To avoid users having to deal with internal data structures, Turing provides the `@addlogprob!` macro which increases the accumulated log probability. For instance, this allows you to [include arbitrary terms in the likelihood](https://github.com/TuringLang/Turing.jl/issues/1332) @@ -24,7 +24,7 @@ myloglikelihood(x, μ) = loglikelihood(Normal(μ, 1), x) @model function demo(x) μ ~ Normal() - Turing.@addlogprob! myloglikelihood(x, μ) + @addlogprob! myloglikelihood(x, μ) end ``` @@ -37,7 +37,7 @@ using LinearAlgebra @model function demo(x) m ~ MvNormal(zero(x), I) if dot(m, x) < 0 - Turing.@addlogprob! -Inf + @addlogprob! -Inf # Exit the model evaluation early return nothing end @@ -49,11 +49,11 @@ end Note that `@addlogprob!` always increases the accumulated log probability, regardless of the provided sampling context. -For instance, if you do not want to apply `Turing.@addlogprob!` when evaluating the prior of your model but only when computing the log likelihood and the log joint probability, then you should [check the type of the internal variable `__context_`](https://github.com/TuringLang/DynamicPPL.jl/issues/154), as in the following example: +For instance, if you do not want to apply `@addlogprob!` when evaluating the prior of your model but only when computing the log likelihood and the log joint probability, then you should [check the type of the internal variable `__context_`](https://github.com/TuringLang/DynamicPPL.jl/issues/154), as in the following example: ```{julia} #| eval: false if DynamicPPL.leafcontext(__context__) !== Turing.PriorContext() - Turing.@addlogprob! myloglikelihood(x, μ) + @addlogprob! myloglikelihood(x, μ) end ``` From ab924091830882813db07f11def516b3404d592e Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Sun, 8 Jun 2025 13:42:27 +0100 Subject: [PATCH 3/7] Fix more imports --- developers/compiler/minituring-contexts/index.qmd | 2 +- developers/compiler/model-manual/index.qmd | 8 ++++---- developers/inference/implementing-samplers/index.qmd | 4 ++-- tutorials/bayesian-time-series-analysis/index.qmd | 4 +++- tutorials/variational-inference/index.qmd | 10 ++++++---- 5 files changed, 16 insertions(+), 12 deletions(-) diff --git a/developers/compiler/minituring-contexts/index.qmd b/developers/compiler/minituring-contexts/index.qmd index 6468483ef..4fcdda02b 100755 --- a/developers/compiler/minituring-contexts/index.qmd +++ b/developers/compiler/minituring-contexts/index.qmd @@ -294,7 +294,7 @@ Of course, using an MCMC algorithm to sample from the prior is unnecessary and s The use of contexts also goes far beyond just evaluating log probabilities and sampling. Some examples from Turing are * `FixedContext`, which fixes some variables to given values and removes them completely from the evaluation of any log probabilities. They power the `Turing.fix` and `Turing.unfix` functions. -* `ConditionContext` conditions the model on fixed values for some parameters. They are used by `Turing.condition` and `Turing.uncondition`, i.e. the `model | (parameter=value,)` syntax. The difference between `fix` and `condition` is whether the log probability for the corresponding variable is included in the overall log density. +* `ConditionContext` conditions the model on fixed values for some parameters. They are used by `Turing.condition` and `Turing.decondition`, i.e. the `model | (parameter=value,)` syntax. The difference between `fix` and `condition` is whether the log probability for the corresponding variable is included in the overall log density. * `PriorExtractorContext` collects information about what the prior distribution of each variable is. * `PrefixContext` adds prefixes to variable names, allowing models to be used within other models without variable name collisions. diff --git a/developers/compiler/model-manual/index.qmd b/developers/compiler/model-manual/index.qmd index cdf3fa829..4571254c8 100755 --- a/developers/compiler/model-manual/index.qmd +++ b/developers/compiler/model-manual/index.qmd @@ -36,18 +36,18 @@ using DynamicPPL function gdemo2(model, varinfo, context, x) # Assume s² has an InverseGamma distribution. s², varinfo = DynamicPPL.tilde_assume!!( - context, InverseGamma(2, 3), Turing.@varname(s²), varinfo + context, InverseGamma(2, 3), @varname(s²), varinfo ) # Assume m has a Normal distribution. m, varinfo = DynamicPPL.tilde_assume!!( - context, Normal(0, sqrt(s²)), Turing.@varname(m), varinfo + context, Normal(0, sqrt(s²)), @varname(m), varinfo ) # Observe each value of x[i] according to a Normal distribution. for i in eachindex(x) _retval, varinfo = DynamicPPL.tilde_observe!!( - context, Normal(m, sqrt(s²)), x[i], Turing.@varname(x[i]), varinfo + context, Normal(m, sqrt(s²)), x[i], @varname(x[i]), varinfo ) end @@ -55,7 +55,7 @@ function gdemo2(model, varinfo, context, x) # value and the updated varinfo. return nothing, varinfo end -gdemo2(x) = Turing.Model(gdemo2, (; x)) +gdemo2(x) = DynamicPPL.Model(gdemo2, (; x)) # Instantiate a Model object with our data variables. model2 = gdemo2([1.5, 2.0]) diff --git a/developers/inference/implementing-samplers/index.qmd b/developers/inference/implementing-samplers/index.qmd index 9d69fbb80..1d8aa3d6c 100644 --- a/developers/inference/implementing-samplers/index.qmd +++ b/developers/inference/implementing-samplers/index.qmd @@ -403,11 +403,11 @@ As we promised, all of this hassle of implementing our `MALA` sampler in a way t It also enables use with Turing.jl through the `externalsampler`, but we need to do one final thing first: we need to tell Turing.jl how to extract a vector of parameters from the "sample" returned in our implementation of `AbstractMCMC.step`. In our case, the "sample" is a `MALASample`, so we just need the following line: ```{julia} -# Load Turing.jl. using Turing +using DynamicPPL # Overload the `getparams` method for our "sample" type, which is just a vector. -Turing.Inference.getparams(::Turing.Model, sample::MALASample) = sample.x +Turing.Inference.getparams(::DynamicPPL.Model, sample::MALASample) = sample.x ``` And with that, we're good to go! diff --git a/tutorials/bayesian-time-series-analysis/index.qmd b/tutorials/bayesian-time-series-analysis/index.qmd index 33dcb9962..0cdf201d6 100755 --- a/tutorials/bayesian-time-series-analysis/index.qmd +++ b/tutorials/bayesian-time-series-analysis/index.qmd @@ -165,6 +165,8 @@ scatter!(t, yf; color=2, label="Data") With the model specified and with a reasonable prior we can now let Turing decompose the time series for us! ```{julia} +using MCMCChains: get_sections + function mean_ribbon(samples) qs = quantile(samples) low = qs[:, Symbol("2.5%")] @@ -174,7 +176,7 @@ function mean_ribbon(samples) end function get_decomposition(model, x, cyclic_features, chain, op) - chain_params = Turing.MCMCChains.get_sections(chain, :parameters) + chain_params = get_sections(chain, :parameters) return returned(model(x, cyclic_features, op), chain_params) end diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd index f25808534..0f0cc51a5 100755 --- a/tutorials/variational-inference/index.qmd +++ b/tutorials/variational-inference/index.qmd @@ -18,7 +18,7 @@ Here we will focus on how to use VI in Turing and not much on the theory underly If you are interested in understanding the mathematics you can checkout [our write-up]({{}}) or any other resource online (there a lot of great ones). Using VI in Turing.jl is very straight forward. -If `model` denotes a definition of a `Turing.Model`, performing VI is as simple as +If `model` denotes a definition of a `DynamicPPL.Model`, performing VI is as simple as ```{julia} #| eval: false @@ -54,7 +54,7 @@ x_i &\overset{\text{i.i.d.}}{=} \mathcal{N}(m, s), \quad i = 1, \dots, n Recall that *conjugate* refers to the fact that we can obtain a closed-form expression for the posterior. Of course one wouldn't use something like variational inference for a conjugate model, but it's useful as a simple demonstration as we can compare the result to the true posterior. -First we generate some synthetic data, define the `Turing.Model` and instantiate the model on the data: +First we generate some synthetic data, define the `DynamicPPL.Model` and instantiate the model on the data: ```{julia} # generate data @@ -666,11 +666,13 @@ using Bijectors: Scale, Shift ``` ```{julia} +using DistributionsAD + d = length(q) -base_dist = Turing.DistributionsAD.TuringDiagMvNormal(zeros(d), ones(d)) +base_dist = DistributionsAD.TuringDiagMvNormal(zeros(d), ones(d)) ``` -`bijector(model::Turing.Model)` is defined by Turing, and will return a `bijector` which takes you from the space of the latent variables to the real space. In this particular case, this is a mapping `((0, ∞) × ℝ × ℝ¹⁰) → ℝ¹²`. We're interested in using a normal distribution as a base-distribution and transform samples to the latent space, thus we need the inverse mapping from the reals to the latent space: +`bijector(model::DynamicPPL.Model)` is defined in DynamicPPL, and will return a `bijector` which takes you from the space of the latent variables to the real space. In this particular case, this is a mapping `((0, ∞) × ℝ × ℝ¹⁰) → ℝ¹²`. We're interested in using a normal distribution as a base-distribution and transform samples to the latent space, thus we need the inverse mapping from the reals to the latent space: ```{julia} to_constrained = inverse(bijector(m)); From 25f6234b608bdac9f91f8a171176348b04505cc7 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Sun, 8 Jun 2025 13:46:10 +0100 Subject: [PATCH 4/7] Update Manifest --- Manifest.toml | 165 +++++++++++++++++++++++++------------------------- Project.toml | 1 + 2 files changed, 83 insertions(+), 83 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 4ce67feb2..be908332f 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.11.5" manifest_format = "2.0" -project_hash = "93e3f90921e5771e56e7b8d21131b1107faa4765" +project_hash = "5ea45087374f193fc9b541533d3ffc8025f44bcd" [[deps.ADTypes]] git-tree-sha1 = "e2478490447631aedba0823d4d7a80b2cc8cdb32" @@ -86,9 +86,9 @@ weakdeps = ["SparseArrays", "StaticArrays"] [[deps.AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "LogDensityProblemsAD", "ProgressMeter", "Random", "Setfield", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "a340008fc9c43f85f3b3e33c0ea66fdd33ec79a9" +git-tree-sha1 = "9f75990a04e3ee45d80b19778ba9d2bb7ad4d5ee" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.7.1" +version = "0.8.0" [deps.AdvancedHMC.extensions] AdvancedHMCADTypesExt = "ADTypes" @@ -127,17 +127,14 @@ weakdeps = ["Libtask"] AdvancedPSLibtaskExt = "Libtask" [[deps.AdvancedVI]] -deps = ["ADTypes", "Bijectors", "DiffResults", "Distributions", "DistributionsAD", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "StatsBase", "StatsFuns", "Tracker"] -git-tree-sha1 = "e913c2794cf9d2db9d36d28f67abd27595101f49" +deps = ["ADTypes", "Accessors", "DiffResults", "DifferentiationInterface", "Distributions", "DocStringExtensions", "FillArrays", "Functors", "LinearAlgebra", "LogDensityProblems", "Optimisers", "ProgressMeter", "Random", "StatsBase"] +git-tree-sha1 = "59c9723a71ed815eafec430d4cafa592b5889b96" uuid = "b5ca4192-6429-45e5-a2d9-87aec30a685c" -version = "0.2.12" -weakdeps = ["Enzyme", "Flux", "ReverseDiff", "Zygote"] +version = "0.4.1" +weakdeps = ["Bijectors"] [deps.AdvancedVI.extensions] - AdvancedVIEnzymeExt = ["Enzyme"] - AdvancedVIFluxExt = ["Flux"] - AdvancedVIReverseDiffExt = ["ReverseDiff"] - AdvancedVIZygoteExt = ["Zygote"] + AdvancedVIBijectorsExt = "Bijectors" [[deps.AliasTables]] deps = ["PtrArrays", "Random"] @@ -747,9 +744,9 @@ version = "6.175.0" [[deps.DiffEqCallbacks]] deps = ["ConcreteStructs", "DataStructures", "DiffEqBase", "DifferentiationInterface", "Functors", "LinearAlgebra", "Markdown", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "b1f970a2873a2cf76ce35fb0ed2b755a11b31052" +git-tree-sha1 = "76292e889472e810d40a844b714743c0ffb1c53b" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "4.1.0" +version = "4.6.0" [[deps.DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArraysCore", "Statistics"] @@ -773,12 +770,6 @@ git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" version = "1.15.1" -[[deps.DiffTests]] -deps = ["LinearAlgebra", "SparseArrays", "Statistics"] -git-tree-sha1 = "b92beb1933df01bf4915d3a05e54c2a0aad312c7" -uuid = "de460e47-3fe3-5279-bb4a-814414816d5d" -version = "0.1.2" - [[deps.DifferentialEquations]] deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "NonlinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] git-tree-sha1 = "afdc7dfee475828b4f0286d63ffe66b97d7a3fa7" @@ -888,9 +879,9 @@ weakdeps = ["ForwardDiff", "LazyArrays", "ReverseDiff", "Tracker"] DistributionsADTrackerExt = "Tracker" [[deps.DocStringExtensions]] -git-tree-sha1 = "e7b7e6f178525d17c720ab9c081e4ef04429f860" +git-tree-sha1 = "7442a5dfe1ebb773c29cc2962a8980f47221d76c" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.9.4" +version = "0.9.5" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] @@ -939,9 +930,9 @@ version = "1.0.5" [[deps.Enzyme]] deps = ["CEnum", "EnzymeCore", "Enzyme_jll", "GPUCompiler", "InteractiveUtils", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "PrecompileTools", "Preferences", "Printf", "Random", "SparseArrays"] -git-tree-sha1 = "be2c627bf432a3a17d6d0e9c461d88bd1a28d3cf" +git-tree-sha1 = "ef9aa10938d97cd42c524482eda5c523ec4bf0d5" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.13.48" +version = "0.13.49" [deps.Enzyme.extensions] EnzymeBFloat16sExt = "BFloat16s" @@ -1026,9 +1017,9 @@ version = "4.4.4+1" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "7de7c78d681078f027389e067864a8d53bd7c3c9" +git-tree-sha1 = "797762812ed063b9b94f6cc7742bc8883bb5e69e" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.8.1" +version = "1.9.0" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1154,10 +1145,10 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.5" [[deps.Flux]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Functors", "LinearAlgebra", "MLDataDevices", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "Setfield", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] -git-tree-sha1 = "df520a0727f843576801a0294f5be1a94be28e23" +deps = ["Adapt", "ChainRulesCore", "Compat", "EnzymeCore", "Functors", "LinearAlgebra", "MLCore", "MLDataDevices", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "Setfield", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] +git-tree-sha1 = "2c35003ec8dafabdc48549102208b1b15552cb33" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.14.25" +version = "0.16.4" [deps.Flux.extensions] FluxAMDGPUExt = "AMDGPU" @@ -1226,10 +1217,10 @@ uuid = "77dc65aa-8811-40c2-897b-53d922fa7daf" version = "0.1.3" [[deps.Functors]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "64d8e93700c7a3f28f717d265382d52fac9fa1c1" +deps = ["Compat", "ConstructionBase", "LinearAlgebra", "Random"] +git-tree-sha1 = "60a0339f28a233601cb74468032b5c302d5067de" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.4.12" +version = "0.5.2" [[deps.Future]] deps = ["Random"] @@ -1303,10 +1294,10 @@ uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" version = "1.3.15+0" [[deps.Graphs]] -deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "3169fd3440a02f35e549728b0890904cfd4ae58a" +deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] +git-tree-sha1 = "c5abfa0ae0aaee162a3fbb053c13ecda39be545b" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.12.1" +version = "1.13.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -1358,16 +1349,6 @@ weakdeps = ["Distributions"] [deps.HiddenMarkovModels.extensions] HiddenMarkovModelsDistributionsExt = "Distributions" -[[deps.Hwloc]] -deps = ["CEnum", "Hwloc_jll", "Printf"] -git-tree-sha1 = "6a3d80f31ff87bc94ab22a7b8ec2f263f9a6a583" -uuid = "0e44f5e4-bd66-52a0-8798-143a42290a1d" -version = "3.3.0" -weakdeps = ["AbstractTrees"] - - [deps.Hwloc.extensions] - HwlocTrees = "AbstractTrees" - [[deps.Hwloc_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "92f65c4d78ce8cdbb6b68daf88889950b0a99d11" @@ -1513,10 +1494,10 @@ uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" 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 = "f2bdec5b4580414aee3178c8caa6e46c344c0bbc" +deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "SymbolicIndexingInterface", "UnPack"] +git-tree-sha1 = "fb7fd516de38db80f50fe15e57d44da2836365e7" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.14.3" +version = "9.16.0" weakdeps = ["FastBroadcast"] [[deps.KernelAbstractions]] @@ -1788,9 +1769,9 @@ version = "1.11.0" [[deps.LinearSolve]] deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "GPUArraysCore", "InteractiveUtils", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "c618a6a774d5712c6bf02dbcceb51b6dc6b9bb89" +git-tree-sha1 = "c0d1a91a50af6778863d320761f807f641f74935" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "3.16.0" +version = "3.17.0" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" @@ -1885,10 +1866,10 @@ uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" version = "1.1.0" [[deps.Lux]] -deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "Preferences", "Random", "Reexport", "SIMDTypes", "Setfield", "Static", "StaticArraysCore", "Statistics", "WeightInitializers"] -git-tree-sha1 = "39cc335d2601d4b0d74b209f718e7e3641771448" +deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "DiffResults", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "Preferences", "Random", "Reexport", "SIMDTypes", "Setfield", "Static", "StaticArraysCore", "Statistics", "WeightInitializers"] +git-tree-sha1 = "bc06b534ec9a93815ccb86c233950c14619e5cf6" uuid = "b2108857-7c20-44ae-9111-449ecde12c47" -version = "1.2.3" +version = "1.13.3" [deps.Lux.extensions] LuxComponentArraysExt = "ComponentArrays" @@ -1898,7 +1879,7 @@ version = "1.2.3" LuxMLUtilsExt = "MLUtils" LuxMPIExt = "MPI" LuxMPINCCLExt = ["CUDA", "MPI", "NCCL"] - LuxReactantExt = ["Enzyme", "Reactant"] + LuxReactantExt = ["Enzyme", "Reactant", "ReactantCore"] LuxReverseDiffExt = ["FunctionWrappers", "ReverseDiff"] LuxSimpleChainsExt = "SimpleChains" LuxTrackerExt = "Tracker" @@ -1915,6 +1896,7 @@ version = "1.2.3" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" NCCL = "3fe64909-d7a1-4096-9b7d-7a0f12cf0f6b" Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" + ReactantCore = "a3311ec8-5e00-46d5-b541-4f83e724a433" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SimpleChains = "de6bee2f-e2f4-4ec7-b6ed-219cc6f6e9e5" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" @@ -1922,9 +1904,9 @@ version = "1.2.3" [[deps.LuxCore]] deps = ["Compat", "DispatchDoctor", "Random"] -git-tree-sha1 = "9f71aea19be890e429ee21adfeda1e63d01ec610" +git-tree-sha1 = "48d45736aae190b1b41c1db5242fad955f0eff1d" uuid = "bb33d45b-7691-41d6-9220-0943567d0623" -version = "1.1.0" +version = "1.2.6" [deps.LuxCore.extensions] LuxCoreArrayInterfaceReverseDiffExt = ["ArrayInterface", "ReverseDiff"] @@ -1932,11 +1914,12 @@ version = "1.1.0" LuxCoreChainRulesCoreExt = "ChainRulesCore" LuxCoreEnzymeCoreExt = "EnzymeCore" LuxCoreFunctorsExt = "Functors" - LuxCoreMLDataDevicesExt = "MLDataDevices" + LuxCoreMLDataDevicesExt = ["Adapt", "MLDataDevices"] LuxCoreReactantExt = "Reactant" LuxCoreSetfieldExt = "Setfield" [deps.LuxCore.weakdeps] + Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" @@ -1948,10 +1931,10 @@ version = "1.1.0" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.LuxLib]] -deps = ["ArrayInterface", "ChainRulesCore", "Compat", "CpuId", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Hwloc", "KernelAbstractions", "LinearAlgebra", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Polyester", "Preferences", "Random", "Reexport", "Static", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "a9e0f1477ac91623079f7a230f4de46170dc8817" +deps = ["ArrayInterface", "CPUSummary", "ChainRulesCore", "Compat", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "KernelAbstractions", "LinearAlgebra", "LuxCore", "MLDataDevices", "Markdown", "NNlib", "Polyester", "Preferences", "Random", "Reexport", "Static", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "b06b83e48cfbfc2ea25ec673537e7eb7e69879e9" uuid = "82251201-b29d-42c6-8e01-566dec8acb11" -version = "1.3.7" +version = "1.8.0" [deps.LuxLib.extensions] LuxLibAppleAccelerateExt = "AppleAccelerate" @@ -1961,6 +1944,7 @@ version = "1.3.7" LuxLibLoopVectorizationExt = "LoopVectorization" LuxLibMKLExt = "MKL" LuxLibOctavianExt = ["Octavian", "LoopVectorization"] + LuxLibReactantExt = "Reactant" LuxLibReverseDiffExt = "ReverseDiff" LuxLibSLEEFPiratesExt = "SLEEFPirates" LuxLibTrackerAMDGPUExt = ["AMDGPU", "Tracker"] @@ -1976,6 +1960,7 @@ version = "1.3.7" LoopVectorization = "bdcacae8-1622-11e9-2a5c-532679323890" MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2" Octavian = "6fd5a793-0b7e-452c-907f-f8bfe9c57db4" + Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" SLEEFPirates = "476501e8-09a2-5ece-8869-fb82de89a1fa" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" @@ -2007,15 +1992,16 @@ version = "1.0.0" [[deps.MLDataDevices]] deps = ["Adapt", "Compat", "Functors", "Preferences", "Random"] -git-tree-sha1 = "85b47bc5a8bf0c886286638585df3bec7c9f8269" +git-tree-sha1 = "a47f08b67298dee5778cf279a9a735ca2d11a890" uuid = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40" -version = "1.5.3" +version = "1.10.0" [deps.MLDataDevices.extensions] MLDataDevicesAMDGPUExt = "AMDGPU" MLDataDevicesCUDAExt = "CUDA" MLDataDevicesChainRulesCoreExt = "ChainRulesCore" MLDataDevicesChainRulesExt = "ChainRules" + MLDataDevicesComponentArraysExt = "ComponentArrays" MLDataDevicesFillArraysExt = "FillArrays" MLDataDevicesGPUArraysExt = "GPUArrays" MLDataDevicesMLUtilsExt = "MLUtils" @@ -2035,6 +2021,7 @@ version = "1.5.3" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54" @@ -2204,14 +2191,15 @@ uuid = "78c3b35d-d492-501b-9361-3d52fe80e533" version = "0.8.1" [[deps.Mooncake]] -deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "DiffTests", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Setfield", "Test"] -git-tree-sha1 = "68c31b62f4957a76aaf379092d13475a62f7658b" +deps = ["ADTypes", "ChainRules", "ChainRulesCore", "DiffRules", "ExprTools", "FunctionWrappers", "GPUArraysCore", "Graphs", "InteractiveUtils", "LinearAlgebra", "MistyClosures", "Random", "Test"] +git-tree-sha1 = "e4811fc54aa752d4a9a5cc9bed5cd85b8ab75db0" uuid = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" -version = "0.4.104" +version = "0.4.122" [deps.Mooncake.extensions] MooncakeAllocCheckExt = "AllocCheck" MooncakeCUDAExt = "CUDA" + MooncakeFluxExt = "Flux" MooncakeJETExt = "JET" MooncakeLuxLibExt = "LuxLib" MooncakeLuxLibSLEEFPiratesExtension = ["LuxLib", "SLEEFPirates"] @@ -2221,6 +2209,7 @@ version = "0.4.104" [deps.Mooncake.weakdeps] AllocCheck = "9b6a8646-10ed-4001-bbdc-1d2f46dfbb1a" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b" LuxLib = "82251201-b29d-42c6-8e01-566dec8acb11" NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" @@ -2488,10 +2477,20 @@ version = "1.12.0" MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" [[deps.Optimisers]] -deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "c9ff5c686240c31eb8570b662dd1f66f4b183116" +deps = ["ChainRulesCore", "ConstructionBase", "Functors", "LinearAlgebra", "Random", "Statistics"] +git-tree-sha1 = "131dc319e7c58317e8c6d5170440f6bdaee0a959" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.3.4" +version = "0.4.6" + + [deps.Optimisers.extensions] + OptimisersAdaptExt = ["Adapt"] + OptimisersEnzymeCoreExt = "EnzymeCore" + OptimisersReactantExt = "Reactant" + + [deps.Optimisers.weakdeps] + Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" [[deps.Optimization]] deps = ["ADTypes", "ArrayInterface", "ConsoleProgressMonitor", "DocStringExtensions", "LBFGSB", "LinearAlgebra", "Logging", "LoggingExtras", "OptimizationBase", "Printf", "ProgressLogging", "Reexport", "SciMLBase", "SparseArrays", "TerminalLoggers"] @@ -2564,9 +2563,9 @@ 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 = "42755bd13fe56e9d9ce1bc005f8b206a6b56b731" +git-tree-sha1 = "9124a686af119063bb4d3a8f87044a8f312fcad9" uuid = "6ad6398a-0878-4a85-9266-38940aa047c8" -version = "1.5.1" +version = "1.6.0" [[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"] @@ -2586,9 +2585,9 @@ 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 = "c78060115fa4ea9d70ac47fa49496acbc630aefa" +git-tree-sha1 = "efecf0c4cc44e16251b0e718f08b0876b2a82b80" uuid = "4302a76b-040a-498a-8c04-15b101fed76b" -version = "1.9.1" +version = "1.10.0" [[deps.OrdinaryDiffEqExplicitRK]] deps = ["DiffEqBase", "FastBroadcast", "LinearAlgebra", "MuladdMacro", "OrdinaryDiffEqCore", "RecursiveArrayTools", "Reexport", "TruncatedStacktraces"] @@ -2694,9 +2693,9 @@ 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 = "063e5ff1447b3869856ed264b6dcbb21e6e8bdb0" +git-tree-sha1 = "1ce0096d920e95773220e818f29bf4b37ea2bb78" uuid = "43230ef6-c299-4910-a778-202eb28ce4ce" -version = "1.10.1" +version = "1.11.0" [[deps.OrdinaryDiffEqSDIRK]] deps = ["ADTypes", "DiffEqBase", "FastBroadcast", "LinearAlgebra", "MacroTools", "MuladdMacro", "OrdinaryDiffEqCore", "OrdinaryDiffEqDifferentiation", "OrdinaryDiffEqNonlinearSolve", "RecursiveArrayTools", "Reexport", "SciMLBase", "TruncatedStacktraces"] @@ -3121,9 +3120,9 @@ version = "0.5.0" [[deps.SciMLBase]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] -git-tree-sha1 = "ce947672206f6a3a2bee1017c690cfd5fd82d897" +git-tree-sha1 = "9efabb3d79f9076710f41af77017e42d8fa780d9" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.96.0" +version = "2.97.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3154,9 +3153,9 @@ version = "0.1.6" [[deps.SciMLOperators]] deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"] -git-tree-sha1 = "85608e4aaf758547ffc4030c908318b432114ec9" +git-tree-sha1 = "3249fe77f322fe539e935ecb388c8290cd38a3fc" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "1.3.0" +version = "1.3.1" weakdeps = ["SparseArrays", "StaticArraysCore"] [deps.SciMLOperators.extensions] @@ -3279,9 +3278,9 @@ version = "1.11.0" [[deps.SparseConnectivityTracer]] deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "fadb2d7010dd92912e5eb31a493613ad4b8c9583" +git-tree-sha1 = "2c3cbb3703f77045d4eb891b2831ca132ef4183c" uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" -version = "0.6.18" +version = "0.6.19" [deps.SparseConnectivityTracer.extensions] SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" @@ -3542,9 +3541,9 @@ version = "1.0.1" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] -git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" +git-tree-sha1 = "f2c1efbc8f3a609aadf318094f8fc5204bdaf344" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.12.0" +version = "1.12.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -3670,9 +3669,9 @@ 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 = "a22c829eaf08b3c40f7e106e81b21233c726052e" +git-tree-sha1 = "282ca358181f585fbb271eb9301e16b6fe5c80e0" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.38.4" +version = "0.39.1" weakdeps = ["DynamicHMC", "Optim"] [deps.Turing.extensions] diff --git a/Project.toml b/Project.toml index b71ab164c..a58774f97 100644 --- a/Project.toml +++ b/Project.toml @@ -13,6 +13,7 @@ DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa" Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +DistributionsAD = "ced4e74d-a319-5a8a-b0ac-84af2272839c" DynamicHMC = "bbc10e6e-7c05-544b-b16e-64fede858acb" DynamicPPL = "366bfd00-2699-11ea-058f-f148b4cae6d8" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" From 21b7cd41d4ad3050dba4d978aa725a88191cd976 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Wed, 11 Jun 2025 23:03:30 +0100 Subject: [PATCH 5/7] enable error:true for VI tutorial just so that it builds --- tutorials/variational-inference/index.qmd | 1 + 1 file changed, 1 insertion(+) diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd index 0f0cc51a5..7905cce01 100755 --- a/tutorials/variational-inference/index.qmd +++ b/tutorials/variational-inference/index.qmd @@ -3,6 +3,7 @@ title: Variational Inference engine: julia aliases: - ../09-variational-inference/index.html +error: true --- ```{julia} From 8ab5cd99011b83ab7050d10f83d0d95d06bc0404 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Thu, 12 Jun 2025 13:31:47 +0100 Subject: [PATCH 6/7] Update deps --- Manifest.toml | 150 ++++++++++++++++++++++++-------------------------- 1 file changed, 73 insertions(+), 77 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index be908332f..7649ea370 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -106,9 +106,9 @@ version = "0.8.0" [[deps.AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "DocStringExtensions", "FillArrays", "LinearAlgebra", "LogDensityProblems", "Random", "Requires"] -git-tree-sha1 = "f3a278077383e196af143ca7daf57a303d7cac2f" +git-tree-sha1 = "0205823d612410230d18c421ed6d9d851a5451b9" uuid = "5b7e9947-ddc0-4b3f-9b55-0d8042f74170" -version = "0.8.7" +version = "0.8.8" weakdeps = ["DiffResults", "ForwardDiff", "MCMCChains", "StructArrays"] [deps.AdvancedMH.extensions] @@ -327,9 +327,9 @@ version = "0.1.6" [[deps.BoundaryValueDiffEq]] deps = ["ADTypes", "BoundaryValueDiffEqAscher", "BoundaryValueDiffEqCore", "BoundaryValueDiffEqFIRK", "BoundaryValueDiffEqMIRK", "BoundaryValueDiffEqMIRKN", "BoundaryValueDiffEqShooting", "DiffEqBase", "FastClosures", "ForwardDiff", "LinearAlgebra", "Reexport", "SciMLBase"] -git-tree-sha1 = "6606f3f7d43b038a8c34ee4cdc31bbd93b447407" +git-tree-sha1 = "d6ec33e4516b2e790a64128afdb54f3b536667a7" uuid = "764a87c0-6b3e-53db-9096-fe964310641d" -version = "5.17.0" +version = "5.18.0" [deps.BoundaryValueDiffEq.extensions] BoundaryValueDiffEqODEInterfaceExt = "ODEInterface" @@ -339,39 +339,39 @@ version = "5.17.0" [[deps.BoundaryValueDiffEqAscher]] deps = ["ADTypes", "AlmostBlockDiagonals", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield"] -git-tree-sha1 = "2e8239379bdd0f8254407ca2b2cb7b3430da687f" +git-tree-sha1 = "64a777e06d995f677c86c7ddbb85f393074a0877" uuid = "7227322d-7511-4e07-9247-ad6ff830280e" -version = "1.6.1" +version = "1.7.0" [[deps.BoundaryValueDiffEqCore]] deps = ["ADTypes", "Adapt", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "ForwardDiff", "LineSearch", "LinearAlgebra", "Logging", "NonlinearSolveFirstOrder", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings"] -git-tree-sha1 = "1e97d81b6ea5e8e938c57a3c640a5cff1e181a2f" +git-tree-sha1 = "c83bf97da90dd379b1e3f4d9c6f3d0ae48eb0b29" uuid = "56b672f2-a5fe-4263-ab2d-da677488eb3a" -version = "1.9.0" +version = "1.10.0" [[deps.BoundaryValueDiffEqFIRK]] deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] -git-tree-sha1 = "525c65da4b46271b4b5fc2178ccde16c99c21a41" +git-tree-sha1 = "e58ee9acfc6dce6dcc368fc0483952bec5625513" uuid = "85d9eb09-370e-4000-bb32-543851f73618" -version = "1.7.0" +version = "1.8.1" [[deps.BoundaryValueDiffEqMIRK]] deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] -git-tree-sha1 = "f729bdedaedb537bf7883c9f71e7577e1c7a07f6" +git-tree-sha1 = "43debeee94167e2dc744f4a385213c4f0d16b4c3" uuid = "1a22d4ce-7765-49ea-b6f2-13c8438986a6" -version = "1.7.0" +version = "1.8.1" [[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 = "1000b18a380773f049ac2f34bc12abd3d99cf21c" +git-tree-sha1 = "1d92c9f7567b627514e143a3caf93af6d235c2db" uuid = "9255f1d6-53bf-473e-b6bd-23f1ff009da4" -version = "1.6.1" +version = "1.7.1" [[deps.BoundaryValueDiffEqShooting]] deps = ["ADTypes", "ArrayInterface", "BandedMatrices", "BoundaryValueDiffEqCore", "ConcreteStructs", "DiffEqBase", "DifferentiationInterface", "FastAlmostBandedMatrices", "FastClosures", "ForwardDiff", "LinearAlgebra", "PreallocationTools", "PrecompileTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "Setfield", "SparseArrays"] -git-tree-sha1 = "255c15c2d262ea8d3c5db1e0f130f829362c0fd4" +git-tree-sha1 = "1460c449c91c9bc4c8fb08fb5e878811ab38d667" uuid = "ed55bfe0-3725-4db6-871e-a1dc9f42a757" -version = "1.7.0" +version = "1.8.1" [[deps.BracketingNonlinearSolve]] deps = ["CommonSolve", "ConcreteStructs", "NonlinearSolveBase", "PrecompileTools", "Reexport", "SciMLBase"] @@ -614,9 +614,9 @@ uuid = "88cd18e8-d9cc-4ea6-8889-5259c0d15c8b" version = "0.1.2" [[deps.ConstructionBase]] -git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" +git-tree-sha1 = "b4b092499347b18a015186eae3042f72267106cb" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.8" +version = "1.6.0" weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -704,9 +704,9 @@ 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 = "a0e5b5669df9465bc3dd32ea4a8ddeefbc0f7b5c" +git-tree-sha1 = "2d87d7bd165c1ca0d11923a9fabe90a9d71e88a6" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.175.0" +version = "6.176.0" [deps.DiffEqBase.extensions] DiffEqBaseCUDAExt = "CUDA" @@ -1253,9 +1253,9 @@ version = "0.2.0" [[deps.GPUCompiler]] deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "PrecompileTools", "Preferences", "Scratch", "Serialization", "TOML", "Tracy", "UUIDs"] -git-tree-sha1 = "fd1f587ca5dd2d52d990fbd9ff0dded736b51f1d" +git-tree-sha1 = "38e96dd44b8b1db92c81c6eb11ac39d207aa83d5" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "1.5.1" +version = "1.5.2" [[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"] @@ -1502,9 +1502,9 @@ weakdeps = ["FastBroadcast"] [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"] -git-tree-sha1 = "80d268b2f4e396edc5ea004d1e0f569231c71e9e" +git-tree-sha1 = "602c0e9efadafb8abfe8281c3fbf9cf6f406fc03" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.34" +version = "0.9.35" weakdeps = ["EnzymeCore", "LinearAlgebra", "SparseArrays"] [deps.KernelAbstractions.extensions] @@ -1758,9 +1758,9 @@ weakdeps = ["LineSearches"] [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "e4c3be53733db1051cc15ecf573b1042b3a712a1" +git-tree-sha1 = "4adee99b7262ad2a1a4bbbc59d993d24e55ea96f" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.3.0" +version = "7.4.0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] @@ -1867,9 +1867,9 @@ version = "1.1.0" [[deps.Lux]] deps = ["ADTypes", "Adapt", "ArgCheck", "ArrayInterface", "ChainRulesCore", "Compat", "ConcreteStructs", "DiffResults", "DispatchDoctor", "EnzymeCore", "FastClosures", "ForwardDiff", "Functors", "GPUArraysCore", "LinearAlgebra", "LuxCore", "LuxLib", "MLDataDevices", "MacroTools", "Markdown", "NNlib", "Optimisers", "Preferences", "Random", "Reexport", "SIMDTypes", "Setfield", "Static", "StaticArraysCore", "Statistics", "WeightInitializers"] -git-tree-sha1 = "bc06b534ec9a93815ccb86c233950c14619e5cf6" +git-tree-sha1 = "4bf87816440bec8e64b610de8724c04a58e65928" uuid = "b2108857-7c20-44ae-9111-449ecde12c47" -version = "1.13.3" +version = "1.13.4" [deps.Lux.extensions] LuxComponentArraysExt = "ComponentArrays" @@ -2239,9 +2239,9 @@ version = "0.10.3" [[deps.NLSolversBase]] deps = ["ADTypes", "DifferentiationInterface", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "b14c7be6046e7d48e9063a0053f95ee0fc954176" +git-tree-sha1 = "25a6638571a902ecfb1ae2a18fc1575f86b1d4df" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.9.1" +version = "7.10.0" [[deps.NLopt]] deps = ["CEnum", "NLopt_jll"] @@ -2466,9 +2466,9 @@ version = "0.5.6+0" [[deps.Optim]] deps = ["Compat", "EnumX", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "31b3b1b8e83ef9f1d50d74f1dd5f19a37a304a1f" +git-tree-sha1 = "68115113ff5c7e7d4985e0295f65cc53128ed6bb" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.12.0" +version = "1.13.1" [deps.Optim.extensions] OptimMOIExt = "MathOptInterface" @@ -2569,9 +2569,9 @@ version = "1.6.0" [[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 = "d29adfeb720dd7c251b216d91c4bd4fe67c087df" +git-tree-sha1 = "08dac9c6672a4548439048089bac293759a897fd" uuid = "bbf590c4-e513-4bbe-9b18-05decba2e5d8" -version = "1.26.0" +version = "1.26.1" weakdeps = ["EnzymeCore"] [deps.OrdinaryDiffEqCore.extensions] @@ -3120,9 +3120,9 @@ version = "0.5.0" [[deps.SciMLBase]] deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"] -git-tree-sha1 = "9efabb3d79f9076710f41af77017e42d8fa780d9" +git-tree-sha1 = "04bbcdc8d1f7d6f667f75fbcc68728231e21fabe" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "2.97.0" +version = "2.101.0" [deps.SciMLBase.extensions] SciMLBaseChainRulesCoreExt = "ChainRulesCore" @@ -3278,9 +3278,9 @@ version = "1.11.0" [[deps.SparseConnectivityTracer]] deps = ["ADTypes", "DocStringExtensions", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "2c3cbb3703f77045d4eb891b2831ca132ef4183c" +git-tree-sha1 = "affde0bfd920cfcaa0944d3c0eb3a573fa9c4d1e" uuid = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" -version = "0.6.19" +version = "0.6.20" [deps.SparseConnectivityTracer.extensions] SparseConnectivityTracerDataInterpolationsExt = "DataInterpolations" @@ -3705,14 +3705,16 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "d62610ec45e4efeabf7032d67de2ffdea8344bed" +git-tree-sha1 = "d2282232f8a4d71f79e85dc4dd45e5b12a6297fb" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.22.1" -weakdeps = ["ConstructionBase", "InverseFunctions"] +version = "1.23.1" +weakdeps = ["ConstructionBase", "ForwardDiff", "InverseFunctions", "Printf"] [deps.Unitful.extensions] ConstructionBaseUnitfulExt = "ConstructionBase" + ForwardDiffExt = "ForwardDiff" InverseFunctionsUnitfulExt = "InverseFunctions" + PrintfExt = "Printf" [[deps.UnitfulLatexify]] deps = ["LaTeXStrings", "Latexify", "Unitful"] @@ -3747,10 +3749,10 @@ uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" version = "1.23.1+0" [[deps.Wayland_protocols_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "5db3e9d307d32baba7067b13fc7b5aa6edd4a19a" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "54b8a029ac145ebe8299463447fd1590b2b1d92f" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" -version = "1.36.0+0" +version = "1.44.0+0" [[deps.WeakRefStrings]] deps = ["DataAPI", "InlineStrings", "Parsers"] @@ -3902,34 +3904,34 @@ uuid = "e920d4aa-a673-5f3a-b3d7-f755a4d47c43" version = "0.1.4+0" [[deps.Xorg_xcb_util_image_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_jll"] +git-tree-sha1 = "f4fc02e384b74418679983a97385644b67e1263b" uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" -version = "0.4.0+1" +version = "0.4.1+0" [[deps.Xorg_xcb_util_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] -git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll"] +git-tree-sha1 = "68da27247e7d8d8dafd1fcf0c3654ad6506f5f97" uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" -version = "0.4.0+1" +version = "0.4.1+0" [[deps.Xorg_xcb_util_keysyms_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_jll"] +git-tree-sha1 = "44ec54b0e2acd408b0fb361e1e9244c60c9c3dd4" uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" -version = "0.4.0+1" +version = "0.4.1+0" [[deps.Xorg_xcb_util_renderutil_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_jll"] +git-tree-sha1 = "5b0263b6d080716a02544c55fdff2c8d7f9a16a0" uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" -version = "0.3.9+1" +version = "0.3.10+0" [[deps.Xorg_xcb_util_wm_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_jll"] +git-tree-sha1 = "f233c83cad1fa0e70b7771e0e21b061a116f2763" uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" -version = "0.4.1+1" +version = "0.4.2+0" [[deps.Xorg_xkbcomp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"] @@ -3979,10 +3981,10 @@ uuid = "700de1a5-db45-46bc-99cf-38207098b444" version = "0.2.7" [[deps.eudev_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] -git-tree-sha1 = "431b678a28ebb559d224c0b6b6d01afce87c51ba" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "c3b0e6196d50eab0c5ed34021aaa0bb463489510" uuid = "35ca27e7-8b34-5b7f-bca9-bdc33f59eb06" -version = "3.2.9+0" +version = "3.2.14+0" [[deps.fzf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -3990,12 +3992,6 @@ git-tree-sha1 = "b6a34e0e0960190ac2a4363a1bd003504772d631" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" version = "0.61.1+0" -[[deps.gperf_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "3cad2cf2c8d80f1d17320652b3ea7778b30f473f" -uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" -version = "3.3.0+0" - [[deps.libaec_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "f5733a5a9047722470b95a81e1b172383971105c" @@ -4026,10 +4022,10 @@ uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" version = "0.2.2+0" [[deps.libevdev_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "56d643b57b188d30cccc25e331d416d3d358e557" uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" -version = "1.11.0+0" +version = "1.13.4+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -4038,10 +4034,10 @@ uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" version = "2.0.3+0" [[deps.libinput_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] -git-tree-sha1 = "ad50e5b90f222cfe78aa3d5183a20a12de1322ce" +deps = ["Artifacts", "JLLWrappers", "Libdl", "eudev_jll", "libevdev_jll", "mtdev_jll"] +git-tree-sha1 = "91d05d7f4a9f67205bd6cf395e488009fe85b499" uuid = "36db933b-70db-51c0-b978-0f229ee0e533" -version = "1.18.0+0" +version = "1.28.1+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] @@ -4056,10 +4052,10 @@ uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" version = "1.3.7+2" [[deps.mtdev_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "b4d631fd51f2e9cdd93724ae25b2efc198b059b1" uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e" -version = "1.1.6+0" +version = "1.1.7+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] From beab191d2bc46785ee272a49a3fb3f6cb5705139 Mon Sep 17 00:00:00 2001 From: Penelope Yong Date: Thu, 12 Jun 2025 15:55:56 +0100 Subject: [PATCH 7/7] Disable error=true --- tutorials/variational-inference/index.qmd | 1 - 1 file changed, 1 deletion(-) diff --git a/tutorials/variational-inference/index.qmd b/tutorials/variational-inference/index.qmd index 7905cce01..0f0cc51a5 100755 --- a/tutorials/variational-inference/index.qmd +++ b/tutorials/variational-inference/index.qmd @@ -3,7 +3,6 @@ title: Variational Inference engine: julia aliases: - ../09-variational-inference/index.html -error: true --- ```{julia}