diff --git a/tutorials/02-logistic-regression/02_logistic-regression.jmd b/tutorials/02-logistic-regression/02_logistic-regression.jmd index 2119bc4d7..1bdab364a 100644 --- a/tutorials/02-logistic-regression/02_logistic-regression.jmd +++ b/tutorials/02-logistic-regression/02_logistic-regression.jmd @@ -131,8 +131,6 @@ n, _ = size(train) # Sample using HMC. m = logistic_regression(train, train_label, n, 1) chain = sample(m, HMC(0.05, 10), MCMCThreads(), 1_500, 3) - -describe(chain) ``` ```julia; echo=false diff --git a/tutorials/03-bayesian-neural-network/03_bayesian-neural-network.jmd b/tutorials/03-bayesian-neural-network/03_bayesian-neural-network.jmd index 0f937c897..6e249c64b 100644 --- a/tutorials/03-bayesian-neural-network/03_bayesian-neural-network.jmd +++ b/tutorials/03-bayesian-neural-network/03_bayesian-neural-network.jmd @@ -12,7 +12,13 @@ We will begin with importing the relevant libraries. ```julia # Import libraries. -using Turing, Flux, Plots, Random, ReverseDiff +using Turing +using Flux +using Plots +using ReverseDiff + +using LinearAlgebra +using Random # Hide sampling progress. Turing.setprogress!(false); @@ -87,14 +93,9 @@ length(parameters_initial) # number of paraemters in NN The probabilistic model specification below creates a `parameters` variable, which has IID normal variables. The `parameters` vector represents all parameters of our neural net (weights and biases). ```julia -# Create a regularization term and a Gaussian prior variance term. -alpha = 0.09 -sig = sqrt(1.0 / alpha) - -# Specify the probabilistic model. -@model function bayes_nn(xs, ts, nparameters, reconstruct) +@model function bayes_nn(xs, ts, nparameters, reconstruct; alpha=0.09) # Create the weight and bias vector. - parameters ~ MvNormal(zeros(nparameters), sig .* ones(nparameters)) + parameters ~ MvNormal(Zeros(nparameters), I / alpha) # Construct NN from parameters nn = reconstruct(parameters) diff --git a/tutorials/03-bayesian-neural-network/Project.toml b/tutorials/03-bayesian-neural-network/Project.toml index ad64bbcc2..7dce35a52 100644 --- a/tutorials/03-bayesian-neural-network/Project.toml +++ b/tutorials/03-bayesian-neural-network/Project.toml @@ -1,7 +1,9 @@ [deps] AdvancedVI = "b5ca4192-6429-45e5-a2d9-87aec30a685c" Bijectors = "76274a88-744f-5084-9051-94815aaf08c4" +FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" @@ -10,6 +12,7 @@ Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] AdvancedVI = "0.1" Bijectors = "0.9" +FillArrays = "0.11" Flux = "0.12" Plots = "1" ReverseDiff = "1" diff --git a/tutorials/04-hidden-markov-model/04_hidden-markov-model.jmd b/tutorials/04-hidden-markov-model/04_hidden-markov-model.jmd index b1a797e4f..ea81f4c49 100644 --- a/tutorials/04-hidden-markov-model/04_hidden-markov-model.jmd +++ b/tutorials/04-hidden-markov-model/04_hidden-markov-model.jmd @@ -131,7 +131,9 @@ g = Gibbs(HMC(0.01, 50, :m, :T), PG(120, :s)) chn = sample(BayesHmm(y, 3), g, 1000); ``` -Let's see how well our chain performed. Ordinarily, using the `describe` function from [MCMCChain](https://github.com/TuringLang/MCMCChain.jl) would be a good first step, but we have generated a lot of parameters here (`s[1]`, `s[2]`, `m[1]`, and so on). It's a bit easier to show how our model performed graphically. +Let's see how well our chain performed. +Ordinarily, using `display(chn)` would be a good first step, but we have generated a lot of parameters here (`s[1]`, `s[2]`, `m[1]`, and so on). +It's a bit easier to show how our model performed graphically. The code below generates an animation showing the graph of the data above, and the data our model generates in each sample. diff --git a/tutorials/05-linear-regression/05_linear-regression.jmd b/tutorials/05-linear-regression/05_linear-regression.jmd index 1201ed7fa..a4a110e72 100644 --- a/tutorials/05-linear-regression/05_linear-regression.jmd +++ b/tutorials/05-linear-regression/05_linear-regression.jmd @@ -28,6 +28,12 @@ using MLDataUtils: shuffleobs, splitobs, rescale! # Functionality for evaluating the model predictions. using Distances +# Functionality for constructing arrays with identical elements efficiently. +using FillArrays + +# Functionality for working with scaled identity matrices. +using LinearAlgebra + # Set a seed for reproducibility. using Random Random.seed!(0) @@ -93,24 +99,30 @@ $$ where $\alpha$ is an intercept term common to all observations, $\boldsymbol{\beta}$ is a coefficient vector, $\boldsymbol{X_i}$ is the observed data for car $i$, and $\sigma^2$ is a common variance term. -For $\sigma^2$, we assign a prior of `truncated(Normal(0, 100), 0, Inf)`. This is consistent with [Andrew Gelman's recommendations](http://www.stat.columbia.edu/%7Egelman/research/published/taumain.pdf) on noninformative priors for variance. The intercept term ($\alpha$) is assumed to be normally distributed with a mean of zero and a variance of three. This represents our assumptions that miles per gallon can be explained mostly by our assorted variables, but a high variance term indicates our uncertainty about that. Each coefficient is assumed to be normally distributed with a mean of zero and a variance of 10. We do not know that our coefficients are different from zero, and we don't know which ones are likely to be the most important, so the variance term is quite high. Lastly, each observation $y_i$ is distributed according to the calculated `mu` term given by $\alpha + \boldsymbol{\beta}^\mathsf{T}\boldsymbol{X_i}$. +For $\sigma^2$, we assign a prior of `truncated(Normal(0, 100); lower=0)`. +This is consistent with [Andrew Gelman's recommendations](http://www.stat.columbia.edu/%7Egelman/research/published/taumain.pdf) on noninformative priors for variance. +The intercept term ($\alpha$) is assumed to be normally distributed with a mean of zero and a variance of three. +This represents our assumptions that miles per gallon can be explained mostly by our assorted variables, but a high variance term indicates our uncertainty about that. +Each coefficient is assumed to be normally distributed with a mean of zero and a variance of 10. +We do not know that our coefficients are different from zero, and we don't know which ones are likely to be the most important, so the variance term is quite high. +Lastly, each observation $y_i$ is distributed according to the calculated `mu` term given by $\alpha + \boldsymbol{\beta}^\mathsf{T}\boldsymbol{X_i}$. ```julia # Bayesian linear regression. @model function linear_regression(x, y) # Set variance prior. - σ₂ ~ truncated(Normal(0, 100), 0, Inf) + σ² ~ truncated(Normal(0, 100); lower=0) # Set intercept prior. intercept ~ Normal(0, sqrt(3)) # Set the priors on our coefficients. nfeatures = size(x, 2) - coefficients ~ MvNormal(nfeatures, sqrt(10)) + coefficients ~ MvNormal(Zeros(nfeatures), 10.0 * I) # Calculate all the mu terms. mu = intercept .+ x * coefficients - return y ~ MvNormal(mu, sqrt(σ₂)) + return y ~ MvNormal(mu, σ² * I) end ``` @@ -118,20 +130,16 @@ With our model specified, we can call the sampler. We will use the No U-Turn Sam ```julia model = linear_regression(train, train_target) -chain = sample(model, NUTS(0.65), 3_000); +chain = sample(model, NUTS(0.65), 3_000) ``` -As a visual check to confirm that our coefficients have converged, we show the densities and trace plots for our parameters using the `plot` functionality. +We can also check the densities and traces of the parameters visually using the `plot` functionality. ```julia plot(chain) ``` -It looks like each of our parameters has converged. We can check our numerical esimates using `describe(chain)`, as below. - -```julia -describe(chain) -``` +It looks like all parameters have converged. ## Comparing to OLS diff --git a/tutorials/05-linear-regression/Project.toml b/tutorials/05-linear-regression/Project.toml index 13f943173..ff3c23497 100644 --- a/tutorials/05-linear-regression/Project.toml +++ b/tutorials/05-linear-regression/Project.toml @@ -3,7 +3,9 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" +FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" @@ -17,8 +19,9 @@ Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] DataFrames = "1" Distances = "0.10" -Distributions = "0.25" +Distributions = "0.25.42" FileIO = "1" +FillArrays = "0.12" GLM = "1" MCMCChains = "5" MLDataUtils = "0.5" diff --git a/tutorials/07-poisson-regression/07_poisson-regression.jmd b/tutorials/07-poisson-regression/07_poisson-regression.jmd index ffa4957dc..2176ead3e 100644 --- a/tutorials/07-poisson-regression/07_poisson-regression.jmd +++ b/tutorials/07-poisson-regression/07_poisson-regression.jmd @@ -202,19 +202,14 @@ The exponentiated mean of the coefficient `b1` is roughly half of that of `b2`. # Removing the Warmup Samples -As can be seen from the plots above, the parameters converge to their final distributions after a few iterations. These initial values during the warmup phase increase the standard deviations of the parameters and are not required after we get the desired distributions. Thus, we remove these warmup values and once again view the diagnostics. - -To remove these warmup values, we take all values except the first 200. This is because we set the second parameter of the NUTS sampler (which is the number of adaptations) to be equal to 200. `describe(chain)` is used to view the standard deviations in the estimates of the parameters. It also gives other useful information such as the means and the quantiles. - -```julia -# Note the standard deviation before removing the warmup samples -describe(chain) -``` +As can be seen from the plots above, the parameters converge to their final distributions after a few iterations. +The initial values during the warmup phase increase the standard deviations of the parameters and are not required after we get the desired distributions. +Thus, we remove these warmup values and once again view the diagnostics. +To remove these warmup values, we take all values except the first 200. +This is because we set the second parameter of the NUTS sampler (which is the number of adaptations) to be equal to 200. ```julia -# Removing the first 200 values of the chains. -chains_new = chain[201:2500, :, :] -describe(chains_new) +chains_new = chain[201:end, :, :] ``` ```julia diff --git a/tutorials/08-multinomial-logistic-regression/08_multinomial-logistic-regression.jmd b/tutorials/08-multinomial-logistic-regression/08_multinomial-logistic-regression.jmd index cb4f16e6c..20b306949 100644 --- a/tutorials/08-multinomial-logistic-regression/08_multinomial-logistic-regression.jmd +++ b/tutorials/08-multinomial-logistic-regression/08_multinomial-logistic-regression.jmd @@ -28,6 +28,12 @@ using MLDataUtils: shuffleobs, splitobs, rescale! # We need a softmax function which is provided by NNlib. using NNlib: softmax +# Functionality for constructing arrays with identical elements efficiently. +using FillArrays + +# Functionality for working with scaled identity matrices. +using LinearAlgebra + # Set a seed for reproducibility. using Random Random.seed!(0) @@ -100,8 +106,8 @@ We select the `setosa` species as the baseline class (the choice does not matter # Priors of intercepts and coefficients. intercept_versicolor ~ Normal(0, σ) intercept_virginica ~ Normal(0, σ) - coefficients_versicolor ~ MvNormal(4, σ) - coefficients_virginica ~ MvNormal(4, σ) + coefficients_versicolor ~ MvNormal(Zeros(4), σ^2 * I) + coefficients_virginica ~ MvNormal(Zeros(4), σ^2 * I) # Compute the likelihood of the observations. values_versicolor = intercept_versicolor .+ x * coefficients_versicolor diff --git a/tutorials/08-multinomial-logistic-regression/Project.toml b/tutorials/08-multinomial-logistic-regression/Project.toml index 329d3127d..4ee0fed67 100644 --- a/tutorials/08-multinomial-logistic-regression/Project.toml +++ b/tutorials/08-multinomial-logistic-regression/Project.toml @@ -1,4 +1,6 @@ [deps] +FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" MLDataUtils = "cc2ba9b6-d476-5e6d-8eaf-a92d5412d41d" NNlib = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b" @@ -7,6 +9,7 @@ StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] +FillArrays = "0.13" MLDataUtils = "0.5" NNlib = "0.7, 0.8" RDatasets = "0.7" diff --git a/tutorials/09-variational-inference/09_variational-inference.jmd b/tutorials/09-variational-inference/09_variational-inference.jmd index 044be91f3..e17bddd3d 100644 --- a/tutorials/09-variational-inference/09_variational-inference.jmd +++ b/tutorials/09-variational-inference/09_variational-inference.jmd @@ -267,9 +267,11 @@ Random.seed!(1); ``` ```julia -# Import RDatasets. +using FillArrays using RDatasets +using LinearAlgebra + # Hide the progress prompt while sampling. Turing.setprogress!(false); ``` @@ -333,17 +335,17 @@ test = Matrix(test_cut[:, remove_names]); # Bayesian linear regression. @model function linear_regression(x, y, n_obs, n_vars, ::Type{T}=Vector{Float64}) where {T} # Set variance prior. - σ₂ ~ truncated(Normal(0, 100), 0, Inf) + σ² ~ truncated(Normal(0, 100), 0, Inf) # Set intercept prior. intercept ~ Normal(0, 3) # Set the priors on our coefficients. - coefficients ~ MvNormal(zeros(n_vars), 10 * ones(n_vars)) + coefficients ~ MvNormal(Zeros(n_vars), 10.0 * I) # Calculate all the mu terms. mu = intercept .+ x * coefficients - return y ~ MvNormal(mu, σ₂) + return y ~ MvNormal(mu, σ² * I) end; ``` @@ -682,10 +684,6 @@ But using this interface it becomes trivial to go beyond the mean-field assumpti Here we'll instead consider the variational family to be a full non-diagonal multivariate Gaussian. As in the previous section we'll implement this by transforming a standard multivariate Gaussian using `Scale` and `Shift`, but now `Scale` will instead be using a lower-triangular matrix (representing the Cholesky of the covariance matrix of a multivariate normal) in contrast to the diagonal matrix we used in for the mean-field approximate posterior. -```julia -using LinearAlgebra -``` - ```julia # Using `ComponentArrays.jl` together with `UnPack.jl` makes our lives much easier. using ComponentArrays, UnPack diff --git a/tutorials/09-variational-inference/Project.toml b/tutorials/09-variational-inference/Project.toml index 6f32cf734..36312968c 100644 --- a/tutorials/09-variational-inference/Project.toml +++ b/tutorials/09-variational-inference/Project.toml @@ -3,8 +3,10 @@ Bijectors = "76274a88-744f-5084-9051-94815aaf08c4" ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" ConjugatePriors = "1624bea9-42b1-5fc1-afd3-e96f729c8d6c" FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" +FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" GLM = "38e38edf-8417-5370-95a0-9cbb8c7f171a" LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee" RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b" @@ -18,6 +20,7 @@ Bijectors = "0.9" ComponentArrays = "0.11" ConjugatePriors = "0.4" FileIO = "1.5" +FillArrays = "0.9" GLM = "1.3" LaTeXStrings = "1.2" Plots = "1.6" diff --git a/tutorials/10-bayesian-differential-equations/10_bayesian-differential-equations.jmd b/tutorials/10-bayesian-differential-equations/10_bayesian-differential-equations.jmd index 04ce045e1..20b319077 100644 --- a/tutorials/10-bayesian-differential-equations/10_bayesian-differential-equations.jmd +++ b/tutorials/10-bayesian-differential-equations/10_bayesian-differential-equations.jmd @@ -89,10 +89,10 @@ Therefore, we write the Lotka-Volterra parameter estimation problem using the Tu @model function fitlv(data, prob) # Prior distributions. σ ~ InverseGamma(2, 3) - α ~ truncated(Normal(1.5, 0.5), 0.5, 2.5) - β ~ truncated(Normal(1.2, 0.5), 0, 2) - γ ~ truncated(Normal(3.0, 0.5), 1, 4) - δ ~ truncated(Normal(1.0, 0.5), 0, 2) + α ~ truncated(Normal(1.5, 0.5); lower=0.5, upper=2.5) + β ~ truncated(Normal(1.2, 0.5); lower=0, upper=2) + γ ~ truncated(Normal(3.0, 0.5); lower=1, upper=4) + δ ~ truncated(Normal(1.0, 0.5); lower=0, upper=2) # Simulate Lotka-Volterra model. p = [α, β, γ, δ] @@ -151,10 +151,10 @@ I.e., we fit the model only to the $y$ variable of the system without providing @model function fitlv2(data::AbstractVector, prob) # Prior distributions. σ ~ InverseGamma(2, 3) - α ~ truncated(Normal(1.5, 0.5), 0.5, 2.5) - β ~ truncated(Normal(1.2, 0.5), 0, 2) - γ ~ truncated(Normal(3.0, 0.5), 1, 4) - δ ~ truncated(Normal(1.0, 0.5), 0, 2) + α ~ truncated(Normal(1.5, 0.5); lower=0.5, upper=2.5) + β ~ truncated(Normal(1.2, 0.5); lower=0, upper=2) + γ ~ truncated(Normal(3.0, 0.5); lower=1, upper=4) + δ ~ truncated(Normal(1.0, 0.5); lower=0, upper=2) # Simulate Lotka-Volterra model but save only the second state of the system (predators). p = [α, β, γ, δ] @@ -251,10 +251,10 @@ Now we define the Turing model for the Lotka-Volterra model with delay and sampl @model function fitlv_dde(data, prob) # Prior distributions. σ ~ InverseGamma(2, 3) - α ~ Truncated(Normal(1.5, 0.5), 0.5, 2.5) - β ~ Truncated(Normal(1.2, 0.5), 0, 2) - γ ~ Truncated(Normal(3.0, 0.5), 1, 4) - δ ~ Truncated(Normal(1.0, 0.5), 0, 2) + α ~ truncated(Normal(1.5, 0.5); lower=0.5, upper=2.5) + β ~ truncated(Normal(1.2, 0.5); lower=0, upper=2) + γ ~ truncated(Normal(3.0, 0.5); lower=1, upper=4) + δ ~ truncated(Normal(1.0, 0.5); lower=0, upper=2) # Simulate Lotka-Volterra model. p = [α, β, γ, δ] @@ -332,10 +332,10 @@ Here we will not choose a `sensealg` and let it use the default choice: @model function fitlv_sensealg(data, prob) # Prior distributions. σ ~ InverseGamma(2, 3) - α ~ truncated(Normal(1.5, 0.5), 0.5, 2.5) - β ~ truncated(Normal(1.2, 0.5), 0, 2) - γ ~ truncated(Normal(3.0, 0.5), 1, 4) - δ ~ truncated(Normal(1.0, 0.5), 0, 2) + α ~ truncated(Normal(1.5, 0.5); lower=0.5, upper=2.5) + β ~ truncated(Normal(1.2, 0.5); lower=0, upper=2) + γ ~ truncated(Normal(3.0, 0.5); lower=1, upper=4) + δ ~ truncated(Normal(1.0, 0.5); lower=0, upper=2) # Simulate Lotka-Volterra model and use a specific algorithm for computing sensitivities. p = [α, β, γ, δ] @@ -394,12 +394,12 @@ plot(EnsembleSummary(data)) @model function fitlv_sde(data, prob) # Prior distributions. σ ~ InverseGamma(2, 3) - α ~ truncated(Normal(1.3, 0.5), 0.5, 2.5) - β ~ truncated(Normal(1.2, 0.25), 0.5, 2) - γ ~ truncated(Normal(3.2, 0.25), 2.2, 4.0) - δ ~ truncated(Normal(1.2, 0.25), 0.5, 2.0) - ϕ1 ~ truncated(Normal(0.12, 0.3), 0.05, 0.25) - ϕ2 ~ truncated(Normal(0.12, 0.3), 0.05, 0.25) + α ~ truncated(Normal(1.3, 0.5); lower=0.5, upper=2.5) + β ~ truncated(Normal(1.2, 0.25); lower=0.5, upper=2) + γ ~ truncated(Normal(3.2, 0.25); lower=2.2, upper=4) + δ ~ truncated(Normal(1.2, 0.25); lower=0.5, upper=2) + ϕ1 ~ truncated(Normal(0.12, 0.3); lower=0.05, upper=0.25) + ϕ2 ~ truncated(Normal(0.12, 0.3); lower=0.05, upper=0.25) # Simulate stochastic Lotka-Volterra model. p = [α, β, γ, δ, ϕ1, ϕ2] diff --git a/tutorials/10-bayesian-differential-equations/Manifest.toml b/tutorials/10-bayesian-differential-equations/Manifest.toml index 7e37a666c..e07c33737 100644 --- a/tutorials/10-bayesian-differential-equations/Manifest.toml +++ b/tutorials/10-bayesian-differential-equations/Manifest.toml @@ -19,9 +19,9 @@ uuid = "7a57a42e-76ec-4ea3-a279-07e840d6d9cf" version = "0.5.2" [[AbstractTrees]] -git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" +git-tree-sha1 = "5c0b629df8a5566a06f5fef5100b53ea56e465a0" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.3.4" +version = "0.4.2" [[Adapt]] deps = ["LinearAlgebra"] @@ -31,9 +31,9 @@ version = "3.4.0" [[AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "Setfield", "Statistics", "StatsBase", "StatsFuns", "UnPack"] -git-tree-sha1 = "345effa84030f273ee86fcdd706d8484ce9a1a3c" +git-tree-sha1 = "0091e2e4d0a7125da0e3ad8c7dbff9171a921461" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.3.5" +version = "0.3.6" [[AdvancedMH]] deps = ["AbstractMCMC", "Distributions", "Random", "Requires"] @@ -81,21 +81,21 @@ version = "3.5.0+3" [[ArrayInterface]] deps = ["ArrayInterfaceCore", "Compat", "IfElse", "LinearAlgebra", "Static"] -git-tree-sha1 = "0582b5976fc76523f77056e888e454f0f7732596" +git-tree-sha1 = "d6173480145eb632d6571c148d94b9d3d773820e" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "6.0.22" +version = "6.0.23" [[ArrayInterfaceCore]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "40debc9f72d0511e12d817c7ca06a721b6423ba3" +git-tree-sha1 = "5bb0f8292405a516880a3809954cb832ae7a31c5" uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" -version = "0.1.17" +version = "0.1.20" [[ArrayInterfaceGPUArrays]] deps = ["Adapt", "ArrayInterfaceCore", "GPUArraysCore", "LinearAlgebra"] -git-tree-sha1 = "febba7add2873aecc0b6620b55969e73ec875bce" +git-tree-sha1 = "fc114f550b93d4c79632c2ada2924635aabfa5ed" uuid = "6ba088a2-8465-4c0a-af30-387133b534db" -version = "0.2.1" +version = "0.2.2" [[ArrayInterfaceOffsetArrays]] deps = ["ArrayInterface", "OffsetArrays", "Static"] @@ -144,15 +144,15 @@ version = "0.4.6" [[BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "d8da9afb97ad4a1a06650db11c8b72d9dd2f1ace" +git-tree-sha1 = "d37d493a1fc680257f424e656da06f4704c4444b" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "0.17.5" +version = "0.17.7" [[BangBang]] deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] -git-tree-sha1 = "b15a6bc52594f5e4a3b825858d1089618871bf9d" +git-tree-sha1 = "7fe6d92c4f281cf4ca6f2fba0ce7b299742da7ca" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.3.36" +version = "0.3.37" [[Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -164,9 +164,14 @@ version = "0.1.1" [[Bijectors]] deps = ["ArgCheck", "ChainRulesCore", "ChangesOfVariables", "Compat", "Distributions", "Functors", "InverseFunctions", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "Random", "Reexport", "Requires", "Roots", "SparseArrays", "Statistics"] -git-tree-sha1 = "875f3845e1256ee1d9e0c8ca3993e709b32c0ed1" +git-tree-sha1 = "a3704b8e5170f9339dff4e6cb286ad49464d3646" uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.10.3" +version = "0.10.6" + +[[BitFlags]] +git-tree-sha1 = "84259bb6172806304b9101094a7cc4bc6f56dbc6" +uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" +version = "0.1.5" [[BitTwiddlingConvenienceFunctions]] deps = ["Static"] @@ -174,18 +179,6 @@ git-tree-sha1 = "eaee37f76339077f86679787a71990c4e465477f" uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" version = "0.1.4" -[[BlockArrays]] -deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra"] -git-tree-sha1 = "0c0dd27be59bc76a3da6243d8172aeedd6420037" -uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" -version = "0.16.20" - -[[BlockBandedMatrices]] -deps = ["ArrayLayouts", "BandedMatrices", "BlockArrays", "FillArrays", "LinearAlgebra", "MatrixFactorizations", "SparseArrays", "Statistics"] -git-tree-sha1 = "e43b59446b2c10024f6b64e82e359997e7adb26b" -uuid = "ffab5731-97b5-5995-9138-79e8c1846df0" -version = "0.11.9" - [[BoundaryValueDiffEq]] deps = ["BandedMatrices", "DiffEqBase", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase", "SparseArrays"] git-tree-sha1 = "2f80b70bd3ddd9aa3ec2d77604c1121bd115650e" @@ -205,9 +198,9 @@ version = "0.4.2" [[CPUSummary]] deps = ["CpuId", "IfElse", "Static"] -git-tree-sha1 = "8a43595f7b3f7d6dd1e07ad9b94081e1975df4af" +git-tree-sha1 = "9bdd5aceea9fa109073ace6b430a24839d79315e" uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.1.25" +version = "0.1.27" [[Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] @@ -228,15 +221,15 @@ version = "0.3.10" [[ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "650415ad4c2a007b17f577cb081d9376cc908b6f" +git-tree-sha1 = "a5fd229d3569a6600ae47abe8cd48cbeb972e173" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.44.2" +version = "1.44.6" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "80ca332f6dcb2508adba68f22f551adb2d00a624" +git-tree-sha1 = "e7ff6cadf743c098e08fca25c91103ee4303c9bb" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.3" +version = "1.15.6" [[ChangesOfVariables]] deps = ["ChainRulesCore", "LinearAlgebra", "Test"] @@ -251,10 +244,10 @@ uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" version = "0.1.10" [[Clustering]] -deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "SparseArrays", "Statistics", "StatsBase"] -git-tree-sha1 = "75479b7df4167267d75294d14b58244695beb2ac" +deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "Random", "SparseArrays", "Statistics", "StatsBase"] +git-tree-sha1 = "64df3da1d2a26f4de23871cd1b6482bb68092bd5" uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5" -version = "0.14.2" +version = "0.14.3" [[CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] @@ -303,20 +296,15 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[Compat]] -deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "9be8be1d8a6f44b96482c8af52238ea7987da3e3" +deps = ["Dates", "LinearAlgebra", "UUIDs"] +git-tree-sha1 = "5856d3031cdb1f3b2b6340dfdc66b6d9a149a374" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.45.0" +version = "4.2.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -[[CompositeTypes]] -git-tree-sha1 = "d5b014b216dc891e81fea299638e4c10c657b582" -uuid = "b152e2b5-7a66-4b01-a709-34e65c35f657" -version = "0.1.2" - [[CompositionsBase]] git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" @@ -330,9 +318,9 @@ version = "0.1.2" [[ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "59d00b3139a9de4eb961057eabb65ac6522be954" +git-tree-sha1 = "fb21ddd70a051d882a1686a5a550990bbe371a95" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.4.0" +version = "1.4.1" [[Contour]] git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" @@ -351,9 +339,9 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[DataAPI]] -git-tree-sha1 = "fb5f5316dd3fd4c5e7c30a24d50643b73e37cd40" +git-tree-sha1 = "46d2680e618f8abd007bce0c3026cb0c4a8f2032" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.10.0" +version = "1.12.0" [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -383,9 +371,9 @@ version = "0.1.2" [[DelayDiffEq]] deps = ["ArrayInterface", "DataStructures", "DiffEqBase", "LinearAlgebra", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "UnPack"] -git-tree-sha1 = "078f21d61a6f43a7b3eab4620ac958183e44cee2" +git-tree-sha1 = "5acc7807b906d6a938dfeb965a6ea931260f054e" uuid = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb" -version = "5.37.0" +version = "5.38.0" [[DelimitedFiles]] deps = ["Mmap"] @@ -398,46 +386,40 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[DiffEqBase]] -deps = ["ArrayInterfaceCore", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "Logging", "MuladdMacro", "NonlinearSolve", "Parameters", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "StaticArrays", "Statistics", "ZygoteRules"] -git-tree-sha1 = "fb4d56afb939f233e2abf964e619ef069a021e26" +deps = ["ArrayInterfaceCore", "ChainRulesCore", "DataStructures", "Distributions", "DocStringExtensions", "FastBroadcast", "ForwardDiff", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "MuladdMacro", "NonlinearSolve", "Parameters", "Printf", "RecursiveArrayTools", "Reexport", "Requires", "SciMLBase", "Setfield", "SparseArrays", "Static", "StaticArrays", "Statistics", "Tricks", "ZygoteRules"] +git-tree-sha1 = "0f9f82671406d21f6275cb6e9336259f062e81fa" uuid = "2b5f629d-d688-5b77-993f-72d75c75574e" -version = "6.95.2" +version = "6.105.0" [[DiffEqCallbacks]] deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "LinearAlgebra", "Markdown", "NLsolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArrays"] -git-tree-sha1 = "d1a99f72b7596fcd55f3cbaeb91332af17581ede" +git-tree-sha1 = "f8cc1ad62a87988225a07524ef84c7df7264c232" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "2.24.0" +version = "2.24.1" [[DiffEqNoiseProcess]] deps = ["DiffEqBase", "Distributions", "GPUArraysCore", "LinearAlgebra", "Markdown", "Optim", "PoissonRandom", "QuadGK", "Random", "Random123", "RandomNumbers", "RecipesBase", "RecursiveArrayTools", "ResettableStacks", "SciMLBase", "StaticArrays", "Statistics"] -git-tree-sha1 = "baddd892e9a5dec5ccd3d8e71ec198251d3c5522" +git-tree-sha1 = "8ba7a8913dc57c087d3cdc9b67eb1c9d760125bc" uuid = "77a26b50-5914-5dd7-bc55-306e6241c503" -version = "5.12.1" - -[[DiffEqOperators]] -deps = ["BandedMatrices", "BlockBandedMatrices", "DiffEqBase", "DomainSets", "ForwardDiff", "LazyArrays", "LazyBandedMatrices", "LinearAlgebra", "LoopVectorization", "NNlib", "NonlinearSolve", "Requires", "RuntimeGeneratedFunctions", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrays", "SuiteSparse"] -git-tree-sha1 = "403d101caee42ba504f2ee74ae6e8413b765605b" -uuid = "9fdde737-9c7f-55bf-ade8-46b3f136cc48" -version = "4.43.1" +version = "5.13.0" [[DiffResults]] -deps = ["StaticArrays"] -git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805" +deps = ["StaticArraysCore"] +git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" -version = "1.0.3" +version = "1.1.0" [[DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "28d605d9a0ac17118fe2c5e9ce0fbb76c3ceb120" +git-tree-sha1 = "992a23afdb109d0d2f8802a30cf5ae4b1fe7ea68" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.11.0" +version = "1.11.1" [[DifferentialEquations]] -deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] -git-tree-sha1 = "0ccc4356a8f268d5eee641f0944074560c45267a" +deps = ["BoundaryValueDiffEq", "DelayDiffEq", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "JumpProcesses", "LinearAlgebra", "LinearSolve", "OrdinaryDiffEq", "Random", "RecursiveArrayTools", "Reexport", "SciMLBase", "SteadyStateDiffEq", "StochasticDiffEq", "Sundials"] +git-tree-sha1 = "f6b75cc940e8791b5cef04d29eb88731955e759c" uuid = "0c46a032-eb83-5123-abaf-570d42b7fbaa" -version = "7.2.0" +version = "7.5.0" [[Distances]] deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] @@ -451,15 +433,15 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[Distributions]] deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "6180800cebb409d7eeef8b2a9a562107b9705be5" +git-tree-sha1 = "0d7d213133d948c56e8c2d9f4eab0293491d8e4a" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.67" +version = "0.25.75" [[DistributionsAD]] deps = ["Adapt", "ChainRules", "ChainRulesCore", "Compat", "DiffRules", "Distributions", "FillArrays", "LinearAlgebra", "NaNMath", "PDMats", "Random", "Requires", "SpecialFunctions", "StaticArrays", "StatsBase", "StatsFuns", "ZygoteRules"] -git-tree-sha1 = "74dd5dac82812af7041ae322584d5c2181dead5c" +git-tree-sha1 = "0c139e48a8cea06c6ecbbec19d3ebc5dcbd7870d" uuid = "ced4e74d-a319-5a8a-b0ac-84af2272839c" -version = "0.6.42" +version = "0.6.43" [[DocStringExtensions]] deps = ["LibGit2"] @@ -467,12 +449,6 @@ git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.8.6" -[[DomainSets]] -deps = ["CompositeTypes", "IntervalSets", "LinearAlgebra", "StaticArrays", "Statistics"] -git-tree-sha1 = "ac425eea956013b51e7891bef3c33684b7d37029" -uuid = "5b8099bc-c8ec-5219-889f-1d9e522a28bf" -version = "0.5.11" - [[Downloads]] deps = ["ArgTools", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" @@ -484,16 +460,10 @@ uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" version = "0.6.8" [[DynamicPPL]] -deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "MacroTools", "Random", "Setfield", "Test", "ZygoteRules"] -git-tree-sha1 = "b1d485d5e92a16545d14775d08eb22ca7a840515" +deps = ["AbstractMCMC", "AbstractPPL", "BangBang", "Bijectors", "ChainRulesCore", "ConstructionBase", "Distributions", "DocStringExtensions", "LinearAlgebra", "MacroTools", "OrderedCollections", "Random", "Setfield", "Test", "ZygoteRules"] +git-tree-sha1 = "7bc3920ba1e577ad3d7ebac75602ab42b557e28e" uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8" -version = "0.20.0" - -[[EarCut_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3f3a2501fa7236e9b911e0f7a588c657e822bb6d" -uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" -version = "2.2.3+0" +version = "0.20.2" [[EllipsisNotation]] deps = ["ArrayInterface"] @@ -509,15 +479,15 @@ version = "1.0.0" [[Enzyme]] deps = ["Adapt", "CEnum", "Enzyme_jll", "GPUCompiler", "LLVM", "Libdl", "LinearAlgebra", "ObjectFile", "Printf", "Random"] -git-tree-sha1 = "8ab9eb44fbcfc9161b3f81be7814a7618f2a3460" +git-tree-sha1 = "f546203984c47932b1d8710c3967af873e02fd4a" uuid = "7da242da-08ed-463a-9acd-ee780be4f1d9" -version = "0.10.4" +version = "0.10.6" [[Enzyme_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg", "TOML"] -git-tree-sha1 = "722aa3b554e883118e0e3111629ec40e176cee2c" +git-tree-sha1 = "16f787c10928af62b0782c67abf4cfe43ba67674" uuid = "7cc45869-7501-5eee-bdea-0790c847d4ef" -version = "0.0.33+0" +version = "0.0.38+0" [[Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -527,20 +497,15 @@ version = "2.4.8+0" [[ExponentialUtilities]] deps = ["ArrayInterfaceCore", "GPUArraysCore", "GenericSchur", "LinearAlgebra", "Printf", "SparseArrays", "libblastrampoline_jll"] -git-tree-sha1 = "b40c9037e1a33990466bc5d224ced34b34eebdb0" +git-tree-sha1 = "b19c3f5001b11b71d0f970f354677d604f3a1a97" uuid = "d4d017d3-3776-5f7e-afef-a10c40355c18" -version = "1.18.0" +version = "1.19.0" [[ExprTools]] git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d" uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.8" -[[Extents]] -git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" -uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" -version = "0.1.1" - [[FFMPEG]] deps = ["FFMPEG_jll"] git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" @@ -548,10 +513,10 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" version = "0.4.1" [[FFMPEG_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "ccd479984c7838684b3ac204b716c89955c76623" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.2+0" +version = "4.4.2+2" [[FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] @@ -578,15 +543,15 @@ version = "0.3.2" [[FastLapackInterface]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f2f624311f5e3e74c0d7f8d17ec280d867cd342f" +git-tree-sha1 = "14a6f7a21125f715d935fe8f83560ee833f7d79d" uuid = "29a986be-02c6-4525-aec4-84b980013641" -version = "1.2.2" +version = "1.2.7" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "246621d23d1f43e3b9c368bf3b72b2331a27c286" +git-tree-sha1 = "87519eb762f85534445f5cda35be12e32759ee14" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.2" +version = "0.13.4" [[FiniteDiff]] deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] @@ -631,14 +596,21 @@ uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.10+0" [[FunctionWrappers]] -git-tree-sha1 = "241552bc2209f0fa068b6415b1942cc0aa486bcc" +git-tree-sha1 = "d62485945ce5ae9c0c48f124a84998d755bae00e" uuid = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e" -version = "1.1.2" +version = "1.1.3" + +[[FunctionWrappersWrappers]] +deps = ["FunctionWrappers"] +git-tree-sha1 = "a5e6e7f12607e90d71b09e6ce2c965e41b337968" +uuid = "77dc65aa-8811-40c2-897b-53d922fa7daf" +version = "0.1.1" [[Functors]] -git-tree-sha1 = "223fffa49ca0ff9ce4f875be001ffe173b2b7de4" +deps = ["LinearAlgebra"] +git-tree-sha1 = "a2657dd0f3e8a61dbe70fc7c122038bd33790af5" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.2.8" +version = "0.3.0" [[Future]] deps = ["Random"] @@ -652,33 +624,33 @@ version = "3.3.8+0" [[GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "73145f1d724b5ee0e90098aec39a65e9697429a6" +git-tree-sha1 = "45d7deaf05cbb44116ba785d147c518ab46352d7" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.4.2" +version = "8.5.0" [[GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "d88b17a38322e153c519f5a9ed8d91e9baa03d8f" +git-tree-sha1 = "6872f5ec8fd1a38880f027a26739d42dcda6691f" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.1" +version = "0.1.2" [[GPUCompiler]] deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "122d7bcc92abf94cf1a86281ad7a4d0e838ab9e0" +git-tree-sha1 = "ebb892e1df16040a845e1d11087e4fbfe10323a8" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.16.3" +version = "0.16.4" [[GR]] -deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "cf0a9940f250dc3cb6cc6c6821b4bf8a4286cf9c" +deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] +git-tree-sha1 = "a9ec6a35bc5ddc3aeb8938f800dc599e652d0029" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.66.2" +version = "0.69.3" [[GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "c8ab731c9127cd931c93221f65d6a1008dad7256" +git-tree-sha1 = "bc9f7725571ddb4ab2c4bc74fa397c1c5ad08943" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.66.0+0" +version = "0.69.1+0" [[GenericSchur]] deps = ["LinearAlgebra", "Printf"] @@ -686,18 +658,6 @@ git-tree-sha1 = "fb69b2a645fa69ba5f474af09221b9308b160ce6" uuid = "c145ed77-6b09-5dd9-b285-bf645a82121e" version = "0.5.3" -[[GeoInterface]] -deps = ["Extents"] -git-tree-sha1 = "fb28b5dc239d0174d7297310ef7b84a11804dfab" -uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" -version = "1.0.1" - -[[GeometryBasics]] -deps = ["EarCut_jll", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "a7a97895780dab1085a97769316aa348830dc991" -uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.4.3" - [[Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" @@ -705,10 +665,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] +git-tree-sha1 = "fb83fbe02fe57f2c068013aa94bcdf6760d3a7a7" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.68.3+2" +version = "2.74.0+1" [[Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -718,9 +678,9 @@ version = "1.3.14+0" [[Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "db5c7e27c0d46fd824d470a3c32a4fc6c935fa96" +git-tree-sha1 = "ba2d094a88b6b287bd25cfa86f301e7693ffae2f" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.7.1" +version = "1.7.4" [[Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -728,10 +688,10 @@ uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" [[HTTP]] -deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "f0956f8d42a92816d2bf062f8a6a6a0ad7f9b937" +deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "4abede886fcba15cd5fd041fef776b230d004cee" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.2.1" +version = "1.4.0" [[HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -763,9 +723,9 @@ uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" version = "0.1.1" [[Inflate]] -git-tree-sha1 = "f5fc07d4e706b84f72d54eedcc1c13d92fb0871c" +git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.2" +version = "0.1.3" [[IniFile]] git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" @@ -795,21 +755,21 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[Interpolations]] deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] -git-tree-sha1 = "64f138f9453a018c8f3562e7bae54edc059af249" +git-tree-sha1 = "f67b55b6447d36733596aea445a9f119e83498b6" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.14.4" +version = "0.14.5" [[IntervalSets]] deps = ["Dates", "Random", "Statistics"] -git-tree-sha1 = "57af5939800bce15980bddd2426912c4f83012d8" +git-tree-sha1 = "3f91cd3f56ea48d4d2a75c2a65455c5fc74fa347" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.1" +version = "0.7.3" [[InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "b3364212fb5d870f724876ffcd34dd8ec6d98918" +git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.7" +version = "0.1.8" [[InvertedIndices]] git-tree-sha1 = "bee5f1ef5bf65df56bdd2e40447590b272a5471f" @@ -837,6 +797,12 @@ git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" +[[JLFzf]] +deps = ["Pipe", "REPL", "Random", "fzf_jll"] +git-tree-sha1 = "f377670cda23b6b7c1c0b3893e37451c5c1a2185" +uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" +version = "0.1.5" + [[JLLWrappers]] deps = ["Preferences"] git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" @@ -857,9 +823,9 @@ version = "2.1.2+0" [[JumpProcesses]] deps = ["ArrayInterfaceCore", "DataStructures", "DiffEqBase", "DocStringExtensions", "FunctionWrappers", "Graphs", "LinearAlgebra", "Markdown", "PoissonRandom", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "StaticArrays", "TreeViews", "UnPack"] -git-tree-sha1 = "065462b4dcf2ca4de9701cc86e20f24570ae4bac" +git-tree-sha1 = "5a6e6c522e8a7b39b24be8eebcc13cc7885c6f2c" uuid = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5" -version = "9.1.0" +version = "9.2.0" [[KLU]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse_jll"] @@ -875,9 +841,9 @@ version = "0.6.5" [[Krylov]] deps = ["LinearAlgebra", "Printf", "SparseArrays"] -git-tree-sha1 = "a2327039e1c84615e22d662adb3df113caf44b70" +git-tree-sha1 = "92256444f81fb094ff5aa742ed10835a621aef75" uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" -version = "0.8.3" +version = "0.8.4" [[KrylovKit]] deps = ["LinearAlgebra", "Printf"] @@ -926,10 +892,10 @@ uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" version = "1.3.0" [[Latexify]] -deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "1a43be956d433b5d0321197150c2f94e16c0aaa0" +deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] +git-tree-sha1 = "ab9aa169d2160129beb241cb2750ca499b4e90e9" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.16" +version = "0.15.17" [[LayoutPointers]] deps = ["ArrayInterface", "ArrayInterfaceOffsetArrays", "ArrayInterfaceStaticArrays", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static"] @@ -937,27 +903,15 @@ git-tree-sha1 = "b67e749fb35530979839e7b4b606a97105fe4f1c" uuid = "10f19ff3-798f-405d-979b-55457f8fc047" version = "0.1.10" -[[LazyArrays]] -deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "MatrixFactorizations", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "d9a962fac652cc6b0224622b18199f0ed46d316a" -uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "0.22.11" - [[LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" -[[LazyBandedMatrices]] -deps = ["ArrayLayouts", "BandedMatrices", "BlockArrays", "BlockBandedMatrices", "FillArrays", "LazyArrays", "LinearAlgebra", "MatrixFactorizations", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "034d371419140f14a986ab7325d11f90f30b0c6d" -uuid = "d7e5e226-e90b-4449-9968-0f923699bf6f" -version = "0.7.17" - [[LeftChildRightSiblingTrees]] deps = ["AbstractTrees"] -git-tree-sha1 = "b864cb409e8e445688bc478ef87c0afe4f6d1f8d" +git-tree-sha1 = "fb6803dafae4a5d62ea5cab204b1e657d9737e7f" uuid = "1d6d02ad-be62-4b6b-8a6d-2f90e265016e" -version = "0.1.3" +version = "0.2.0" [[LevyArea]] deps = ["LinearAlgebra", "Random", "SpecialFunctions"] @@ -1040,9 +994,9 @@ version = "2.36.0+0" [[LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "f27132e551e959b3667d8c93eae90973225032dd" +git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.1.1" +version = "7.2.0" [[LinearAlgebra]] deps = ["Libdl"] @@ -1050,15 +1004,21 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[LinearSolve]] deps = ["ArrayInterfaceCore", "DocStringExtensions", "FastLapackInterface", "GPUArraysCore", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SuiteSparse", "UnPack"] -git-tree-sha1 = "c48c190442b22c94499a446b8b452f16d04a258c" +git-tree-sha1 = "c17007396b2ae56b8496f5a9857326dea0b7bb7b" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "1.23.3" +version = "1.26.0" + +[[LogDensityProblems]] +deps = ["ArgCheck", "DocStringExtensions", "Random", "Requires", "UnPack"] +git-tree-sha1 = "408a29d70f8032b50b22155e6d7776715144b761" +uuid = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c" +version = "1.0.2" [[LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "361c2b088575b07946508f135ac556751240091c" +git-tree-sha1 = "94d9c52ca447e23eac0c0f074effbcd38830deb5" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.17" +version = "0.3.18" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -1071,15 +1031,15 @@ version = "0.4.9" [[LoopVectorization]] deps = ["ArrayInterface", "ArrayInterfaceCore", "ArrayInterfaceOffsetArrays", "ArrayInterfaceStaticArrays", "CPUSummary", "ChainRulesCore", "CloseOpenIntervals", "DocStringExtensions", "ForwardDiff", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "SIMDDualNumbers", "SIMDTypes", "SLEEFPirates", "SnoopPrecompile", "SpecialFunctions", "Static", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "91368447f98b0d0cbc31c089e27a07f281db741d" +git-tree-sha1 = "c38ab7b38df71346dc181f1a9d8dc455387f018b" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.122" +version = "0.12.132" [[MCMCChains]] deps = ["AbstractMCMC", "AxisArrays", "Compat", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Serialization", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] -git-tree-sha1 = "8cb9b8fb081afd7728f5de25b9025bff97cb5c7a" +git-tree-sha1 = "0995883c615e93187e8365e35af771afcf74da03" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "5.3.1" +version = "5.4.0" [[MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "Tables"] @@ -1089,21 +1049,21 @@ version = "0.1.4" [[MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "e595b205efd49508358f7dc670a940c790204629" +git-tree-sha1 = "41d162ae9c868218b1f3fe78cba878aa348c2d26" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2022.0.0+0" +version = "2022.1.0+0" [[MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "16fa7c2e14aa5b3854bc77ab5f1dbe2cdc488903" +git-tree-sha1 = "0a36882e73833d60dac49b00d203f73acfd50b85" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.6.0" +version = "1.7.0" [[MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" +git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.9" +version = "0.5.10" [[ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -1119,17 +1079,11 @@ version = "0.4.1" deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -[[MatrixFactorizations]] -deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] -git-tree-sha1 = "2320f1e1d87c98693df7fd30c2adcfca923f42da" -uuid = "a3b82374-2e81-5b9e-98ce-41277c0e4c87" -version = "0.9.2" - [[MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] -git-tree-sha1 = "d9ab10da9de748859a7780338e1d6566993d1f25" +git-tree-sha1 = "6872f9594ff273da6d13c7c1a1545d5a8c7d0c1c" uuid = "739be429-bea8-5141-9913-cc70e7f3736d" -version = "1.1.3" +version = "1.1.6" [[MbedTLS_jll]] deps = ["Artifacts", "Libdl"] @@ -1165,9 +1119,9 @@ version = "0.2.2" [[MultivariateStats]] deps = ["Arpack", "LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI", "StatsBase"] -git-tree-sha1 = "7008a3412d823e29d370ddc77411d593bd8a3d03" +git-tree-sha1 = "efe9c8ecab7a6311d4b91568bd6c88897822fabe" uuid = "6f286f6a-111f-5878-ab1e-185364afe411" -version = "0.9.1" +version = "0.10.0" [[NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1188,9 +1142,10 @@ uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" version = "0.8.9" [[NaNMath]] -git-tree-sha1 = "b086b7ea07f8e38cf122f5016af580881ac914fe" +deps = ["OpenLibm_jll"] +git-tree-sha1 = "a7c3d1da1189a1c2fe843a3bfa04d18d20eb3211" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.7" +version = "1.0.1" [[NamedArrays]] deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"] @@ -1205,9 +1160,9 @@ version = "1.0.0" [[NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "0e353ed734b1747fc20cd4cba0edd9ac027eff6a" +git-tree-sha1 = "440165bf08bc500b8fe4a7be2dc83271a00c0716" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.11" +version = "0.4.12" [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" @@ -1225,9 +1180,9 @@ uuid = "d8793406-e978-5875-9003-1fc021f44a92" version = "0.3.7" [[Observables]] -git-tree-sha1 = "dfd8d34871bc3ad08cd16026c1828e271d554db9" +git-tree-sha1 = "5a9ea4b9430d511980c01e9f7173739595bbd335" uuid = "510215fc-4207-5dde-b226-833fc4488ee2" -version = "0.5.1" +version = "0.5.2" [[OffsetArrays]] deps = ["Adapt"] @@ -1249,6 +1204,12 @@ uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" +[[OpenSSL]] +deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] +git-tree-sha1 = "ebe81469e9d7b471d7ddb611d9e147ea16de0add" +uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" +version = "1.2.1" + [[OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "e60321e3f2616584ff98f0a4f18d98ae6f89bbb3" @@ -1263,9 +1224,15 @@ version = "0.5.5+0" [[Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "7351d1daa3dad1bcf67c79d1ba34dd3f6136c9aa" +git-tree-sha1 = "b9fe76d1a39807fdcf790b991981a922de0c3050" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.7.1" +version = "1.7.3" + +[[Optimisers]] +deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] +git-tree-sha1 = "1ef34738708e3f31994b52693286dabcb3d29f6b" +uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" +version = "0.2.9" [[Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1279,16 +1246,14 @@ uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.4.1" [[OrdinaryDiffEq]] -deps = ["Adapt", "ArrayInterface", "ArrayInterfaceGPUArrays", "ArrayInterfaceStaticArrays", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "6be470b4eb54a4f7c46bc3e0c7bd77f9113d787f" +deps = ["Adapt", "ArrayInterface", "ArrayInterfaceGPUArrays", "ArrayInterfaceStaticArrays", "DataStructures", "DiffEqBase", "DocStringExtensions", "ExponentialUtilities", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "LinearAlgebra", "LinearSolve", "Logging", "LoopVectorization", "MacroTools", "MuladdMacro", "NLsolve", "NonlinearSolve", "Polyester", "PreallocationTools", "Preferences", "RecursiveArrayTools", "Reexport", "SciMLBase", "SnoopPrecompile", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] +git-tree-sha1 = "06dbf3ab4f2530d5c5464f78c9aba4cc300ed069" uuid = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" -version = "6.20.0" +version = "6.28.0" -[[PCRE_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b2a7af664e098055a7529ad1a900ded962bca488" -uuid = "2f80f16e-611a-54ab-bc61-aa92de5b98fc" -version = "8.44.0+0" +[[PCRE2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] @@ -1304,9 +1269,14 @@ version = "0.12.3" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "0044b23da09b5608b4ecacb4e5e6c6332f833a7e" +git-tree-sha1 = "3d5bf43e3e8b412656404ed9466f1dcbf7c50269" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.3.2" +version = "2.4.0" + +[[Pipe]] +git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" +uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" +version = "1.3.0" [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1325,16 +1295,16 @@ uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" version = "3.0.0" [[PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "9888e59493658e476d3073f1ce24348bdc086660" +deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] +git-tree-sha1 = "21303256d239f6b484977314674aef4bb1fe4420" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.0" +version = "1.3.1" [[Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "a19652399f43938413340b2068e11e55caa46b65" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] +git-tree-sha1 = "65451f70d8d71bd9d06821c7a53adbed162454c9" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.31.7" +version = "1.35.2" [[PoissonRandom]] deps = ["Random"] @@ -1344,15 +1314,15 @@ version = "0.4.1" [[Polyester]] deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "94e20822bd7427b1b1b843a3980003f5d5e8696b" +git-tree-sha1 = "6ee5518f7baa05e154757a003bfb6936a174dbad" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.6.14" +version = "0.6.15" [[PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] -git-tree-sha1 = "cf8155767df6ec8fd21b49e81ec8a8099e1a5f96" +git-tree-sha1 = "b42fb2292fbbaed36f25d33a15c8cc0b4f287fcf" uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" -version = "0.1.8" +version = "0.1.10" [[PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -1361,10 +1331,10 @@ uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" [[PreallocationTools]] -deps = ["Adapt", "ArrayInterfaceCore", "ForwardDiff", "ReverseDiff"] -git-tree-sha1 = "5c076a409ec8d2a86d3685a7e4fed330cd489889" +deps = ["Adapt", "ArrayInterfaceCore", "ForwardDiff"] +git-tree-sha1 = "3953d18698157e1d27a51678c89c88d53e071a42" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.2" +version = "0.4.4" [[Preferences]] deps = ["TOML"] @@ -1402,9 +1372,9 @@ version = "5.15.3+1" [[QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "78aadffb3efd2155af139781b8a8df1ef279ea39" +git-tree-sha1 = "3c009334f45dfd546a16a57960a821a1a023d241" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.4.2" +version = "2.5.0" [[REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -1444,15 +1414,16 @@ uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" version = "0.1.0" [[RecipesBase]] -git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" +deps = ["SnoopPrecompile"] +git-tree-sha1 = "612a4d76ad98e9722c8ba387614539155a59e30c" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.2.1" +version = "1.3.0" [[RecipesPipeline]] deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] -git-tree-sha1 = "e7eac76a958f8664f2718508435d058168c7953d" +git-tree-sha1 = "017f217e647cf20b0081b9be938b78c3443356a0" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.6.3" +version = "0.6.6" [[RecursiveArrayTools]] deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "Tables", "ZygoteRules"] @@ -1461,10 +1432,10 @@ uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" version = "2.32.0" [[RecursiveFactorization]] -deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "StrideArraysCore", "TriangularSolve"] -git-tree-sha1 = "3ee71214057e29a8466f5d70cfe745236aa1d9d7" +deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "StrideArraysCore", "TriangularSolve"] +git-tree-sha1 = "0a2dfb3358fcde3676beb75405e782faa8c9aded" uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" -version = "0.2.11" +version = "0.2.12" [[Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1473,9 +1444,9 @@ version = "1.2.2" [[RelocatableFolders]] deps = ["SHA", "Scratch"] -git-tree-sha1 = "22c5201127d7b243b9ee1de3b43c408879dff60f" +git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691" uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" -version = "0.3.0" +version = "1.0.0" [[Requires]] deps = ["UUIDs"] @@ -1491,9 +1462,9 @@ version = "1.1.1" [[ReverseDiff]] deps = ["ChainRulesCore", "DiffResults", "DiffRules", "ForwardDiff", "FunctionWrappers", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "SpecialFunctions", "StaticArrays", "Statistics"] -git-tree-sha1 = "b8e2eb3d8e1530acb73d8949eab3cedb1d43f840" +git-tree-sha1 = "af3dcf5c1ba51a671db61789fff2534c58eb50f5" uuid = "37e2e3b7-166d-5795-8a7a-e32c996b4267" -version = "1.14.1" +version = "1.14.3" [[Rmath]] deps = ["Random", "Rmath_jll"] @@ -1508,16 +1479,10 @@ uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" version = "0.3.0+0" [[Roots]] -deps = ["CommonSolve", "Printf", "Setfield"] -git-tree-sha1 = "50f945fb7d7fdece03bbc76ff1ab96170f64a892" +deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"] +git-tree-sha1 = "422c880f74967af5a8db5702c6df9a03b465202e" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.0.2" - -[[RuntimeGeneratedFunctions]] -deps = ["ExprTools", "SHA", "Serialization"] -git-tree-sha1 = "cdc1e4278e91a6ad530770ebb327f9ed83cf10c4" -uuid = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47" -version = "0.5.3" +version = "2.0.7" [[SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" @@ -1535,21 +1500,21 @@ version = "0.1.0" [[SLEEFPirates]] deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "7ee0e13ac7cd77f2c0e93bff8c40c45f05c77a5a" +git-tree-sha1 = "938c9ecffb28338a6b8b970bda0f3806a65e7906" uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.33" +version = "0.6.36" [[SciMLBase]] -deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "RecipesBase", "RecursiveArrayTools", "StaticArraysCore", "Statistics", "Tables"] -git-tree-sha1 = "bcbc793b4006179c5a146d3d6afa9c699a14d03c" +deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Preferences", "RecipesBase", "RecursiveArrayTools", "StaticArraysCore", "Statistics", "Tables"] +git-tree-sha1 = "2c7b9be95f91c971ae4e4a6e3a0556b839874f2b" uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.48.1" +version = "1.59.4" [[SciMLSensitivity]] -deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceTracker", "Cassette", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffEqOperators", "DiffRules", "Distributions", "EllipsisNotation", "Enzyme", "FiniteDiff", "ForwardDiff", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEq", "Parameters", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "StaticArrays", "Statistics", "StochasticDiffEq", "Tracker", "Zygote", "ZygoteRules"] -git-tree-sha1 = "b66b34cab572b442bf8410e3dd56b0b64b131403" +deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceTracker", "Cassette", "ChainRulesCore", "DiffEqBase", "DiffEqCallbacks", "DiffEqNoiseProcess", "DiffRules", "Distributions", "EllipsisNotation", "Enzyme", "FiniteDiff", "ForwardDiff", "FunctionWrappersWrappers", "GPUArraysCore", "LinearAlgebra", "LinearSolve", "Markdown", "OrdinaryDiffEq", "Parameters", "PreallocationTools", "QuadGK", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "ReverseDiff", "SciMLBase", "StaticArrays", "Statistics", "StochasticDiffEq", "Tracker", "Zygote", "ZygoteRules"] +git-tree-sha1 = "f38a497ca34d491c1888496fc699afcd0a1577a6" uuid = "1ed8b502-d754-442c-8d5d-10ac956f44a1" -version = "7.4.0" +version = "7.10.0" [[ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" @@ -1564,9 +1529,9 @@ version = "1.1.1" [[SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "db8481cf5d6278a121184809e9eb1628943c7704" +git-tree-sha1 = "c0f56940fc967f3d5efed58ba829747af5f8b586" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.3.13" +version = "1.3.15" [[Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1599,9 +1564,9 @@ uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" version = "0.9.4" [[SnoopPrecompile]] -git-tree-sha1 = "3841791b9d1a4d5a4394d7eb4c43f42303a20e0c" +git-tree-sha1 = "f604441450a3c0569830946e5b33b78c928e1a85" uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" -version = "1.0.0" +version = "1.0.1" [[Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" @@ -1618,9 +1583,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[SparseDiffTools]] deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArrays", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays", "VertexSafeGraphs"] -git-tree-sha1 = "9287f8a1831e7b978f609a4c52c8b94ba6e863ad" +git-tree-sha1 = "5fb8ba9180f467885e87a2c99cae178b67934be1" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "1.25.1" +version = "1.26.2" [[SpecialFunctions]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] @@ -1636,20 +1601,20 @@ version = "0.1.14" [[Static]] deps = ["IfElse"] -git-tree-sha1 = "f94f9d627ba3f91e41a815b9f9f977d729e2e06f" +git-tree-sha1 = "de4f0a4f049a4c87e4948c04acff37baf1be01a6" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.7.6" +version = "0.7.7" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "8803c6dea034ab8cd988abe4a91e5589d61c7416" +git-tree-sha1 = "f86b3a049e5d05227b10e15dbb315c5b90f14988" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.4" +version = "1.5.9" [[StaticArraysCore]] -git-tree-sha1 = "5b413a57dd3cea38497d745ce088ac8592fbb5be" +git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.1.0" +version = "1.4.0" [[StatisticalTraits]] deps = ["ScientificTypesBase"] @@ -1663,9 +1628,9 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "8d7530a38dbd2c397be7ddd01a424e4f411dcc41" +git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.2.2" +version = "1.5.0" [[StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1680,10 +1645,10 @@ uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" version = "1.0.1" [[StatsPlots]] -deps = ["AbstractFFTs", "Clustering", "DataStructures", "DataValues", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] -git-tree-sha1 = "2b35ba790f1f823872dcf378a6d3c3b520092eac" +deps = ["AbstractFFTs", "Clustering", "DataStructures", "DataValues", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] +git-tree-sha1 = "3e59e005c5caeb1a57a90b17f582cbfc2c8da8f7" uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" -version = "0.15.1" +version = "0.15.3" [[SteadyStateDiffEq]] deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"] @@ -1693,9 +1658,9 @@ version = "1.9.0" [[StochasticDiffEq]] deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"] -git-tree-sha1 = "a13569d9c5b2a7b35ce0462864138383fceab26f" +git-tree-sha1 = "8062351f645bb23725c494be74619ef802a2ffa8" uuid = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0" -version = "6.52.0" +version = "6.54.0" [[StrideArraysCore]] deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "SIMDTypes", "Static", "ThreadingUtilities"] @@ -1704,10 +1669,10 @@ uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" version = "0.3.15" [[StructArrays]] -deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] -git-tree-sha1 = "ec47fb6069c57f1cee2f67541bf8f23415146de7" +deps = ["Adapt", "DataAPI", "StaticArraysCore", "Tables"] +git-tree-sha1 = "8c6ac65ec9ab781af05b08ff305ddc727c25f680" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.11" +version = "0.6.12" [[StructIO]] deps = ["Test"] @@ -1724,10 +1689,10 @@ deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" [[Sundials]] -deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "Reexport", "SparseArrays", "Sundials_jll"] -git-tree-sha1 = "6549d3b1b5cf86446949c62616675588159ea2fb" +deps = ["CEnum", "DataStructures", "DiffEqBase", "Libdl", "LinearAlgebra", "Logging", "Reexport", "SnoopPrecompile", "SparseArrays", "Sundials_jll"] +git-tree-sha1 = "5717b2c13ddc167d7db931bfdd1a94133ee1d4f0" uuid = "c3572dad-4567-51f8-b174-8c6c989267f4" -version = "4.9.4" +version = "4.10.1" [[Sundials_jll]] deps = ["CompilerSupportLibraries_jll", "Libdl", "OpenBLAS_jll", "Pkg", "SuiteSparse_jll"] @@ -1753,9 +1718,9 @@ version = "1.0.1" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1" +git-tree-sha1 = "2d7164f7b8a066bcfa6224e67736ce0eb54aef5b" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.7.0" +version = "1.9.0" [[Tar]] deps = ["ArgTools", "SHA"] @@ -1769,9 +1734,9 @@ version = "0.1.1" [[TerminalLoggers]] deps = ["LeftChildRightSiblingTrees", "Logging", "Markdown", "Printf", "ProgressLogging", "UUIDs"] -git-tree-sha1 = "62846a48a6cd70e63aa29944b8c4ef704360d72f" +git-tree-sha1 = "f53e34e784ae771eb9ccde4d72e578aa453d0554" uuid = "5d786b92-1e48-4d6f-9151-6b4477ca9bed" -version = "0.1.5" +version = "0.1.6" [[Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] @@ -1785,21 +1750,21 @@ version = "0.5.0" [[TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "464d64b2510a25e6efe410e7edab14fffdc333df" +git-tree-sha1 = "9dfcb767e17b0849d6aaf85997c98a5aea292513" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.20" +version = "0.5.21" [[Tracker]] -deps = ["Adapt", "DiffRules", "ForwardDiff", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] -git-tree-sha1 = "0874c1b5de1b5529b776cfeca3ec0acfada97b1b" +deps = ["Adapt", "DiffRules", "ForwardDiff", "Functors", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NNlib", "NaNMath", "Optimisers", "Printf", "Random", "Requires", "SpecialFunctions", "Statistics"] +git-tree-sha1 = "d963aad627fd7af56fbbfee67703c2f7bfee9dd7" uuid = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" -version = "0.2.20" +version = "0.2.22" [[TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c" +git-tree-sha1 = "8a75929dcd3c38611db2f8d08546decb514fcadf" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.6" +version = "0.9.9" [[Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] @@ -1815,15 +1780,20 @@ version = "0.3.0" [[TriangularSolve]] deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "SnoopPrecompile", "Static", "VectorizationBase"] -git-tree-sha1 = "8987cf4a0f8d6c375e4ab1438a048e0a185151e4" +git-tree-sha1 = "fdddcf6b2c7751cd97de69c18157aacc18fbc660" uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.1.13" +version = "0.1.14" + +[[Tricks]] +git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" +uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" +version = "0.1.6" [[Turing]] -deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "DiffResults", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker", "ZygoteRules"] -git-tree-sha1 = "c43c5b5e2c6dcebee8705c25dbf22f4411e992ab" +deps = ["AbstractMCMC", "AdvancedHMC", "AdvancedMH", "AdvancedPS", "AdvancedVI", "BangBang", "Bijectors", "DataStructures", "Distributions", "DistributionsAD", "DocStringExtensions", "DynamicPPL", "EllipticalSliceSampling", "ForwardDiff", "Libtask", "LinearAlgebra", "LogDensityProblems", "MCMCChains", "NamedArrays", "Printf", "Random", "Reexport", "Requires", "SciMLBase", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Tracker"] +git-tree-sha1 = "68fb67dab0c11de2bb1d761d7a742b965a9bc875" uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" -version = "0.21.10" +version = "0.21.12" [[URIs]] git-tree-sha1 = "e59ecc5a41b000fa94423a578d29290c7266fc10" @@ -1855,9 +1825,9 @@ version = "0.1.2" [[VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static"] -git-tree-sha1 = "a0b74e8247f30420ba25c8fcfc1c69cb84ff8cff" +git-tree-sha1 = "3bc5ea8fbf25f233c4c49c0a75f14b276d2f9a69" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.46" +version = "0.21.51" [[VertexSafeGraphs]] deps = ["Graphs"] @@ -2039,9 +2009,9 @@ version = "1.5.2+0" [[Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "8ac61a92a33b3fd2a4cbf92951817831e313a004" +git-tree-sha1 = "66cc604b9a27a660e25a54e408b4371123a186a6" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.44" +version = "0.6.49" [[ZygoteRules]] deps = ["MacroTools"] @@ -2049,6 +2019,12 @@ git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" uuid = "700de1a5-db45-46bc-99cf-38207098b444" version = "0.2.2" +[[fzf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" +uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" +version = "0.29.0+0" + [[libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" diff --git a/tutorials/12-gaussian-process/12_gaussian-process.jmd b/tutorials/12-gaussian-process/12_gaussian-process.jmd index a1166b893..4aba18105 100644 --- a/tutorials/12-gaussian-process/12_gaussian-process.jmd +++ b/tutorials/12-gaussian-process/12_gaussian-process.jmd @@ -20,11 +20,16 @@ Let's start by loading some dependencies. ```julia using Turing -using AbstractGPs, Random +using AbstractGPs +using DataFrames +using FillArrays +using RDatasets +using StatsBase +using StatsPlots +using VegaLite using LinearAlgebra -using VegaLite, DataFrames, StatsPlots, StatsBase -using RDatasets +using Random Random.seed!(1789); ``` @@ -97,7 +102,7 @@ We create separate models for the two types of kernel. noise = 1e-3 # Priors - α ~ MvLogNormal(MvNormal(zeros(K), I)) + α ~ MvLogNormal(MvNormal(Zeros(K), I)) Z ~ filldist(Normal(), K, N) mu ~ filldist(Normal(), N) @@ -117,7 +122,7 @@ end; noise = 1e-3 # Priors - α ~ MvLogNormal(MvNormal(zeros(K), I)) + α ~ MvLogNormal(MvNormal(Zeros(K), I)) σ ~ LogNormal(0.0, 1.0) Z ~ filldist(Normal(), K, N) mu ~ filldist(Normal(), N) @@ -244,7 +249,7 @@ using Stheno noise = 1e-3 # Priors - α ~ MvLogNormal(MvNormal(zeros(K), I)) + α ~ MvLogNormal(MvNormal(Zeros(K), I)) σ ~ LogNormal(1.0, 1.0) Z ~ filldist(Normal(), K, N) mu ~ filldist(Normal(), N) diff --git a/tutorials/12-gaussian-process/Project.toml b/tutorials/12-gaussian-process/Project.toml index d3d3f4cca..8e1804d1b 100644 --- a/tutorials/12-gaussian-process/Project.toml +++ b/tutorials/12-gaussian-process/Project.toml @@ -1,6 +1,7 @@ [deps] AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" RDatasets = "ce6b1742-4840-55fa-b093-852dadbb1d8b" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" @@ -13,6 +14,7 @@ VegaLite = "112f6efa-9a02-5b7d-90c0-432ed331239a" [compat] AbstractGPs = "0.5" DataFrames = "1" +FillArrays = "0.13" RDatasets = "0.7" StatsBase = "0.33" StatsPlots = "0.14" diff --git a/tutorials/13-seasonal-time-series/13_seasonal_time_series.jmd b/tutorials/13-seasonal-time-series/13_seasonal_time_series.jmd index 6b3b1df75..3dd46e4ed 100644 --- a/tutorials/13-seasonal-time-series/13_seasonal_time_series.jmd +++ b/tutorials/13-seasonal-time-series/13_seasonal_time_series.jmd @@ -30,8 +30,16 @@ and *cyclic effects* which contribute oscillating effects around the trend. Let us simulate some data with an additive linear trend and oscillating effects. ```julia -using StatsPlots, Turing, Statistics, LinearAlgebra, Random +using Turing +using FillArrays +using StatsPlots + +using LinearAlgebra +using Random +using Statistics + Random.seed!(12345) + true_sin_freq = 2 true_sin_amp = 5 true_cos_freq = 7 @@ -130,7 +138,7 @@ Finally, we plot prior predictive samples to make sure our priors make sense. @model function decomp_model(t, c, op) α ~ Normal(0, 10) βt ~ Normal(0, 2) - βc ~ MvNormal(zeros(size(c, 2)), I) + βc ~ MvNormal(Zeros(size(c, 2)), I) σ ~ truncated(Normal(0, 0.1); lower=0) cyclic = c * βc diff --git a/tutorials/13-seasonal-time-series/Project.toml b/tutorials/13-seasonal-time-series/Project.toml index b27721272..b16ec8779 100644 --- a/tutorials/13-seasonal-time-series/Project.toml +++ b/tutorials/13-seasonal-time-series/Project.toml @@ -1,7 +1,10 @@ [deps] +FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" +LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" Turing = "fce5fe82-541a-59a6-adf8-730c64b5f9a0" [compat] +FillArrays = "0.13" StatsPlots = "0.15" Turing = "0.21"