From a361401cbc3dadd76f0b79418f0ebd4cfd0d8d92 Mon Sep 17 00:00:00 2001 From: Ross Viljoen Date: Thu, 4 Nov 2021 23:09:34 +0000 Subject: [PATCH 1/7] Rename `SVGP` to `StochasticVariationalApproximation` --- examples/a-regression/script.jl | 12 ++++---- examples/b-classification/script.jl | 11 +++++-- src/ApproximateGPs.jl | 4 +-- src/elbo.jl | 26 ++++++++-------- src/{svgp.jl => stochastic_variational.jl} | 34 ++++++++++----------- test/elbo.jl | 8 ++--- test/equivalences.jl | 8 ++--- test/runtests.jl | 4 +-- test/{svgp.jl => stochastic_variational.jl} | 0 9 files changed, 56 insertions(+), 51 deletions(-) rename src/{svgp.jl => stochastic_variational.jl} (57%) rename test/{svgp.jl => stochastic_variational.jl} (100%) diff --git a/examples/a-regression/script.jl b/examples/a-regression/script.jl index 2f0fa289..5f29e71f 100644 --- a/examples/a-regression/script.jl +++ b/examples/a-regression/script.jl @@ -84,8 +84,8 @@ lik_noise = 0.3 jitter = 1e-5; # Next, we define some useful functions on the model - creating the prior GP -# under the model, as well as the `SVGP` struct needed to create the posterior -# approximation and to compute the ELBO. +# under the model, as well as the `StochasticVariationalApproximation` struct +# needed to create the posterior approximation and to compute the ELBO. function prior(m::SVGPModel) kernel = make_kernel(m.k) @@ -104,7 +104,7 @@ function make_approx(m::SVGPModel, prior) S = PDMat(Cholesky(LowerTriangular(m.A))) q = MvNormal(m.m, S) fz = prior(m.z, jitter) - return SVGP(fz, q) + return StochasticVariationalApproximation(fz, q) end; # Create the approximate posterior GP under the model. @@ -123,9 +123,9 @@ function (m::SVGPModel)(x) return post(x) end; -# Return the loss given data - for the SVGP, the loss used is the negative ELBO -# (also known as the Variational Free Energy). `num_data` is required for -# minibatching used below. +# Return the loss given data - for the StochasticVariationalApproximation, the +# loss used is the negative ELBO (also known as the Variational Free Energy). +# `num_data` is required for minibatching used below. function loss(m::SVGPModel, x, y; num_data=length(y)) f = prior(m) diff --git a/examples/b-classification/script.jl b/examples/b-classification/script.jl index 7214b536..56fdc446 100644 --- a/examples/b-classification/script.jl +++ b/examples/b-classification/script.jl @@ -102,8 +102,13 @@ raw_initial_params = ( flat_init_params, unflatten = ParameterHandling.flatten(raw_initial_params) unpack = ParameterHandling.value ∘ unflatten; -# Now, we define a function to build the SVGP model from the constrained -# parameters as well as a loss function - in this case the negative ELBO. +# Now, we define a function to build everything needed for an SVGP model from +# the constrained parameters. The two necessary components are the `LatentGP` +# which we are trying to approximate and the +# `StochasticVariationalApproximation` struct. This struct takes as arguments +# the inducing points as a `FiniteGP`, `fz`, and the variational posterior +# distribution `q`. These elements can then be passed to the loss function (the +# `elbo`) along with the data `x` and `y`. lik = BernoulliLikelihood() jitter = 1e-3 # added to aid numerical stability @@ -113,7 +118,7 @@ function build_SVGP(params::NamedTuple) f = LatentGP(GP(kernel), lik, jitter) q = MvNormal(params.m, params.A) fz = f(params.z).fx - return SVGP(fz, q), f + return StochasticVariationalApproximation(fz, q), f end function loss(params::NamedTuple) diff --git a/src/ApproximateGPs.jl b/src/ApproximateGPs.jl index 589b423e..78c17351 100644 --- a/src/ApproximateGPs.jl +++ b/src/ApproximateGPs.jl @@ -15,10 +15,10 @@ using KLDivergences using AbstractGPs: AbstractGP, FiniteGP, LatentFiniteGP, ApproxPosteriorGP, At_A, diag_At_A -export SVGP, DefaultQuadrature, Analytic, GaussHermite, MonteCarlo +export SparseVariationalApproximation, DefaultQuadrature, Analytic, GaussHermite, MonteCarlo include("utils.jl") -include("svgp.jl") +include("stochastic_variational.jl") include("expected_loglik.jl") include("elbo.jl") diff --git a/src/elbo.jl b/src/elbo.jl index 4a896879..01e83afd 100644 --- a/src/elbo.jl +++ b/src/elbo.jl @@ -1,5 +1,5 @@ """ - elbo(svgp::SVGP, fx::FiniteGP, y::AbstractVector{<:Real}; num_data=length(y), quadrature=DefaultQuadrature()) + elbo(svgp::SparseVariationalApproximation, fx::FiniteGP, y::AbstractVector{<:Real}; num_data=length(y), quadrature=DefaultQuadrature()) Compute the Evidence Lower BOund from [1] for the process `f = fx.f == svgp.fz.f` where `y` are observations of `fx`, pseudo-inputs are given by `z = @@ -20,53 +20,53 @@ variational Gaussian process classification." Artificial Intelligence and Statistics. PMLR, 2015. """ function AbstractGPs.elbo( - svgp::SVGP, + sva::SparseVariationalApproximation, fx::FiniteGP{<:AbstractGP,<:AbstractVector,<:Diagonal{<:Real,<:Fill}}, y::AbstractVector{<:Real}; num_data=length(y), quadrature=DefaultQuadrature(), ) - @assert svgp.fz.f === fx.f - return _elbo(quadrature, svgp, fx, y, GaussianLikelihood(fx.Σy[1]), num_data) + @assert sva.fz.f === fx.f + return _elbo(quadrature, sva, fx, y, GaussianLikelihood(fx.Σy[1]), num_data) end -function AbstractGPs.elbo(::SVGP, ::FiniteGP, ::AbstractVector; kwargs...) +function AbstractGPs.elbo(::SparseVariationalApproximation, ::FiniteGP, ::AbstractVector; kwargs...) return error( "The observation noise fx.Σy must be homoscedastic.\n To avoid this error, construct fx using: f = GP(kernel); fx = f(x, σ²)", ) end """ - elbo(svgp, ::SVGP, lfx::LatentFiniteGP, y::AbstractVector; num_data=length(y), quadrature=DefaultQuadrature()) + elbo(svgp, ::SparseVariationalApproximation, lfx::LatentFiniteGP, y::AbstractVector; num_data=length(y), quadrature=DefaultQuadrature()) Compute the ELBO for a LatentGP with a possibly non-conjugate likelihood. """ function AbstractGPs.elbo( - svgp::SVGP, + sva::SparseVariationalApproximation, lfx::LatentFiniteGP, y::AbstractVector; num_data=length(y), quadrature=DefaultQuadrature(), ) - @assert svgp.fz.f === lfx.fx.f - return _elbo(quadrature, svgp, lfx.fx, y, lfx.lik, num_data) + @assert sva.fz.f === lfx.fx.f + return _elbo(quadrature, sva, lfx.fx, y, lfx.lik, num_data) end # Compute the common elements of the ELBO function _elbo( quadrature::QuadratureMethod, - svgp::SVGP, + sva::SparseVariationalApproximation, fx::FiniteGP, y::AbstractVector, lik, num_data::Integer, ) - @assert svgp.fz.f === fx.f - post = posterior(svgp) + @assert sva.fz.f === fx.f + post = posterior(sva) q_f = marginals(post(fx.x)) variational_exp = expected_loglik(quadrature, y, q_f, lik) - kl_term = KL(svgp.q, svgp.fz) + kl_term = KL(sva.q, sva.fz) n_batch = length(y) scale = num_data / n_batch diff --git a/src/svgp.jl b/src/stochastic_variational.jl similarity index 57% rename from src/svgp.jl rename to src/stochastic_variational.jl index 766f97a0..0e84fa00 100644 --- a/src/svgp.jl +++ b/src/stochastic_variational.jl @@ -1,14 +1,14 @@ -struct SVGP{Tfz<:FiniteGP,Tq<:AbstractMvNormal} +struct SparseVariationalApproximation{Tfz<:FiniteGP,Tq<:AbstractMvNormal} fz::Tfz q::Tq end raw""" - posterior(svgp::SVGP) + posterior(sva::SparseVariationalApproximation) Compute the approximate posterior [1] over the process `f = -svgp.fz.f`, given inducing inputs `z = svgp.fz.x` and a variational -distribution over inducing points `svgp.q` (which represents ``q(u)`` +sva.fz.f`, given inducing inputs `z = sva.fz.x` and a variational +distribution over inducing points `sva.q` (which represents ``q(u)`` where `u = f(z)`). The approximate posterior at test points ``x^*`` where ``f^* = f(x^*)`` is then given by: @@ -21,38 +21,38 @@ which can be found in closed form. variational Gaussian process classification." Artificial Intelligence and Statistics. PMLR, 2015. """ -function AbstractGPs.posterior(svgp::SVGP) - q, fz = svgp.q, svgp.fz +function AbstractGPs.posterior(sva::SparseVariationalApproximation) + q, fz = sva.q, sva.fz m, S = mean(q), _chol_cov(q) Kuu = _chol_cov(fz) B = Kuu.L \ S.L α = Kuu \ (m - mean(fz)) data = (S=S, m=m, Kuu=Kuu, B=B, α=α) - return ApproxPosteriorGP(svgp, fz.f, data) + return ApproxPosteriorGP(sva, fz.f, data) end -function AbstractGPs.posterior(svgp::SVGP, fx::FiniteGP, ::AbstractVector) - @assert svgp.fz.f === fx.f - return posterior(svgp) +function AbstractGPs.posterior(sva::SparseVariationalApproximation, fx::FiniteGP, ::AbstractVector) + @assert sva.fz.f === fx.f + return posterior(sva) end -function Statistics.mean(f::ApproxPosteriorGP{<:SVGP}, x::AbstractVector) +function Statistics.mean(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector) return mean(f.prior, x) + cov(f.prior, x, inducing_points(f)) * f.data.α end -function Statistics.cov(f::ApproxPosteriorGP{<:SVGP}, x::AbstractVector) +function Statistics.cov(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector) Cux = cov(f.prior, inducing_points(f), x) D = f.data.Kuu.L \ Cux return cov(f.prior, x) - At_A(D) + At_A(f.data.B' * D) end -function Statistics.var(f::ApproxPosteriorGP{<:SVGP}, x::AbstractVector) +function Statistics.var(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector) Cux = cov(f.prior, inducing_points(f), x) D = f.data.Kuu.L \ Cux return var(f.prior, x) - diag_At_A(D) + diag_At_A(f.data.B' * D) end -function Statistics.cov(f::ApproxPosteriorGP{<:SVGP}, x::AbstractVector, y::AbstractVector) +function Statistics.cov(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector, y::AbstractVector) B = f.data.B Cxu = cov(f.prior, x, inducing_points(f)) Cuy = cov(f.prior, inducing_points(f), y) @@ -61,7 +61,7 @@ function Statistics.cov(f::ApproxPosteriorGP{<:SVGP}, x::AbstractVector, y::Abst return cov(f.prior, x, y) - (E * D) + (E * B * B' * D) end -function StatsBase.mean_and_cov(f::ApproxPosteriorGP{<:SVGP}, x::AbstractVector) +function StatsBase.mean_and_cov(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector) Cux = cov(f.prior, inducing_points(f), x) D = f.data.Kuu.L \ Cux μ = Cux' * f.data.α @@ -69,7 +69,7 @@ function StatsBase.mean_and_cov(f::ApproxPosteriorGP{<:SVGP}, x::AbstractVector) return μ, Σ end -function StatsBase.mean_and_var(f::ApproxPosteriorGP{<:SVGP}, x::AbstractVector) +function StatsBase.mean_and_var(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector) Cux = cov(f.prior, inducing_points(f), x) D = f.data.Kuu.L \ Cux μ = Cux' * f.data.α @@ -77,7 +77,7 @@ function StatsBase.mean_and_var(f::ApproxPosteriorGP{<:SVGP}, x::AbstractVector) return μ, Σ_diag end -inducing_points(f::ApproxPosteriorGP{<:SVGP}) = f.approx.fz.x +inducing_points(f::ApproxPosteriorGP{<:SparseVariationalApproximation}) = f.approx.fz.x _chol_cov(q::AbstractMvNormal) = cholesky(Symmetric(cov(q))) _chol_cov(q::MvNormal) = cholesky(q.Σ) diff --git a/test/elbo.jl b/test/elbo.jl index 6ca06762..428d81e9 100644 --- a/test/elbo.jl +++ b/test/elbo.jl @@ -10,12 +10,12 @@ fz = f(z) q_ex = exact_variational_posterior(fz, fx, y) - svgp = SVGP(fz, q_ex) - @test elbo(svgp, fx, y) isa Real - @test elbo(svgp, fx, y) ≤ logpdf(fx, y) + sva = StochasticVariationalApproximation(fz, q_ex) + @test elbo(sva, fx, y) isa Real + @test elbo(sva, fx, y) ≤ logpdf(fx, y) fx_bad = f(x, fill(0.1, N)) - @test_throws ErrorException elbo(svgp, fx_bad, y) + @test_throws ErrorException elbo(sva, fx_bad, y) # Test that the various methods of computing expectations return the same # result. diff --git a/test/equivalences.jl b/test/equivalences.jl index 0cda5af0..593aa1e2 100644 --- a/test/equivalences.jl +++ b/test/equivalences.jl @@ -11,7 +11,7 @@ @testset "exact posterior" begin # There is a closed form optimal solution for the variational posterior # q(u) (e.g. # https://krasserm.github.io/2020/12/12/gaussian-processes-sparse/ - # equations (11) & (12)). The SVGP posterior with this optimal q(u) + # equations (11) & (12)). The StochasticVariationalApproximation posterior with this optimal q(u) # should therefore be equivalent to the sparse GP (Titsias) posterior # and exact GP regression (when z == x). @@ -23,7 +23,7 @@ gpr_post = posterior(fx, y) # Exact GP regression vfe_post = posterior(VFE(fz), fx, y) # Titsias posterior - svgp_post = posterior(SVGP(fz, q_ex)) # Hensman (2013) exact posterior + svgp_post = posterior(StochasticVariationalApproximation(fz, q_ex)) # Hensman (2013) exact posterior @test mean(gpr_post, x) ≈ mean(svgp_post, x) atol = 1e-10 @test cov(gpr_post, x) ≈ cov(svgp_post, x) atol = 1e-10 @@ -31,7 +31,7 @@ @test mean(vfe_post, x) ≈ mean(svgp_post, x) atol = 1e-10 @test cov(vfe_post, x) ≈ cov(svgp_post, x) atol = 1e-10 - @test elbo(SVGP(fz, q_ex), fx, y) ≈ logpdf(fx, y) atol = 1e-6 + @test elbo(StochasticVariationalApproximation(fz, q_ex), fx, y) ≈ logpdf(fx, y) atol = 1e-6 end @testset "optimised posterior" begin @@ -55,7 +55,7 @@ S = PDMat(Cholesky(LowerTriangular(m.A))) q = MvNormal(m.m, S) - return SVGP(fz, q), fx + return StochasticVariationalApproximation(fz, q), fx end m, A = zeros(N), Matrix{Float64}(I, N, N) # initialise the variational parameters diff --git a/test/runtests.jl b/test/runtests.jl index ae6801a0..0a858106 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -25,8 +25,8 @@ include("test_utils.jl") println(" ") @info "Ran expected_loglik tests" - @testset "SVGP" begin - include("svgp.jl") + @testset "StochasticVariationalApproximation" begin + include("stochastic_variational.jl") println(" ") @info "Ran svgp tests" diff --git a/test/svgp.jl b/test/stochastic_variational.jl similarity index 100% rename from test/svgp.jl rename to test/stochastic_variational.jl From 25105c2054546882a63858c9d3177598fb3cf2b5 Mon Sep 17 00:00:00 2001 From: Ross Viljoen Date: Thu, 4 Nov 2021 23:17:26 +0000 Subject: [PATCH 2/7] Stochastic -> sparse --- examples/a-regression/script.jl | 6 +++--- examples/b-classification/script.jl | 10 +++++----- src/ApproximateGPs.jl | 2 +- ...stochastic_variational.jl => sparse_variational.jl} | 0 test/elbo.jl | 2 +- test/equivalences.jl | 8 ++++---- test/runtests.jl | 4 ++-- ...stochastic_variational.jl => sparse_variational.jl} | 2 +- 8 files changed, 17 insertions(+), 17 deletions(-) rename src/{stochastic_variational.jl => sparse_variational.jl} (100%) rename test/{stochastic_variational.jl => sparse_variational.jl} (87%) diff --git a/examples/a-regression/script.jl b/examples/a-regression/script.jl index 5f29e71f..1899aeb0 100644 --- a/examples/a-regression/script.jl +++ b/examples/a-regression/script.jl @@ -84,7 +84,7 @@ lik_noise = 0.3 jitter = 1e-5; # Next, we define some useful functions on the model - creating the prior GP -# under the model, as well as the `StochasticVariationalApproximation` struct +# under the model, as well as the `SparseVariationalApproximation` struct # needed to create the posterior approximation and to compute the ELBO. function prior(m::SVGPModel) @@ -104,7 +104,7 @@ function make_approx(m::SVGPModel, prior) S = PDMat(Cholesky(LowerTriangular(m.A))) q = MvNormal(m.m, S) fz = prior(m.z, jitter) - return StochasticVariationalApproximation(fz, q) + return SparseVariationalApproximation(fz, q) end; # Create the approximate posterior GP under the model. @@ -123,7 +123,7 @@ function (m::SVGPModel)(x) return post(x) end; -# Return the loss given data - for the StochasticVariationalApproximation, the +# Return the loss given data - for the SparseVariationalApproximation, the # loss used is the negative ELBO (also known as the Variational Free Energy). # `num_data` is required for minibatching used below. diff --git a/examples/b-classification/script.jl b/examples/b-classification/script.jl index 56fdc446..58163518 100644 --- a/examples/b-classification/script.jl +++ b/examples/b-classification/script.jl @@ -105,10 +105,10 @@ unpack = ParameterHandling.value ∘ unflatten; # Now, we define a function to build everything needed for an SVGP model from # the constrained parameters. The two necessary components are the `LatentGP` # which we are trying to approximate and the -# `StochasticVariationalApproximation` struct. This struct takes as arguments -# the inducing points as a `FiniteGP`, `fz`, and the variational posterior -# distribution `q`. These elements can then be passed to the loss function (the -# `elbo`) along with the data `x` and `y`. +# `SparseVariationalApproximation` struct. This struct takes as arguments +# the inducing points `fz`, and the variational posterior distribution `q`. +# These elements can then be passed to the loss function (the `elbo`) along with +# the data `x` and `y`. lik = BernoulliLikelihood() jitter = 1e-3 # added to aid numerical stability @@ -118,7 +118,7 @@ function build_SVGP(params::NamedTuple) f = LatentGP(GP(kernel), lik, jitter) q = MvNormal(params.m, params.A) fz = f(params.z).fx - return StochasticVariationalApproximation(fz, q), f + return SparseVariationalApproximation(fz, q), f end function loss(params::NamedTuple) diff --git a/src/ApproximateGPs.jl b/src/ApproximateGPs.jl index 78c17351..1e291412 100644 --- a/src/ApproximateGPs.jl +++ b/src/ApproximateGPs.jl @@ -18,7 +18,7 @@ using AbstractGPs: AbstractGP, FiniteGP, LatentFiniteGP, ApproxPosteriorGP, At_A export SparseVariationalApproximation, DefaultQuadrature, Analytic, GaussHermite, MonteCarlo include("utils.jl") -include("stochastic_variational.jl") +include("sparse_variational.jl") include("expected_loglik.jl") include("elbo.jl") diff --git a/src/stochastic_variational.jl b/src/sparse_variational.jl similarity index 100% rename from src/stochastic_variational.jl rename to src/sparse_variational.jl diff --git a/test/elbo.jl b/test/elbo.jl index 428d81e9..d372d2ab 100644 --- a/test/elbo.jl +++ b/test/elbo.jl @@ -10,7 +10,7 @@ fz = f(z) q_ex = exact_variational_posterior(fz, fx, y) - sva = StochasticVariationalApproximation(fz, q_ex) + sva = SparseVariationalApproximation(fz, q_ex) @test elbo(sva, fx, y) isa Real @test elbo(sva, fx, y) ≤ logpdf(fx, y) diff --git a/test/equivalences.jl b/test/equivalences.jl index 593aa1e2..9d4e9159 100644 --- a/test/equivalences.jl +++ b/test/equivalences.jl @@ -11,7 +11,7 @@ @testset "exact posterior" begin # There is a closed form optimal solution for the variational posterior # q(u) (e.g. # https://krasserm.github.io/2020/12/12/gaussian-processes-sparse/ - # equations (11) & (12)). The StochasticVariationalApproximation posterior with this optimal q(u) + # equations (11) & (12)). The SparseVariationalApproximation posterior with this optimal q(u) # should therefore be equivalent to the sparse GP (Titsias) posterior # and exact GP regression (when z == x). @@ -23,7 +23,7 @@ gpr_post = posterior(fx, y) # Exact GP regression vfe_post = posterior(VFE(fz), fx, y) # Titsias posterior - svgp_post = posterior(StochasticVariationalApproximation(fz, q_ex)) # Hensman (2013) exact posterior + svgp_post = posterior(SparseVariationalApproximation(fz, q_ex)) # Hensman (2013) exact posterior @test mean(gpr_post, x) ≈ mean(svgp_post, x) atol = 1e-10 @test cov(gpr_post, x) ≈ cov(svgp_post, x) atol = 1e-10 @@ -31,7 +31,7 @@ @test mean(vfe_post, x) ≈ mean(svgp_post, x) atol = 1e-10 @test cov(vfe_post, x) ≈ cov(svgp_post, x) atol = 1e-10 - @test elbo(StochasticVariationalApproximation(fz, q_ex), fx, y) ≈ logpdf(fx, y) atol = 1e-6 + @test elbo(SparseVariationalApproximation(fz, q_ex), fx, y) ≈ logpdf(fx, y) atol = 1e-6 end @testset "optimised posterior" begin @@ -55,7 +55,7 @@ S = PDMat(Cholesky(LowerTriangular(m.A))) q = MvNormal(m.m, S) - return StochasticVariationalApproximation(fz, q), fx + return SparseVariationalApproximation(fz, q), fx end m, A = zeros(N), Matrix{Float64}(I, N, N) # initialise the variational parameters diff --git a/test/runtests.jl b/test/runtests.jl index 0a858106..744be20f 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -25,8 +25,8 @@ include("test_utils.jl") println(" ") @info "Ran expected_loglik tests" - @testset "StochasticVariationalApproximation" begin - include("stochastic_variational.jl") + @testset "SparseVariationalApproximation" begin + include("sparse_variational.jl") println(" ") @info "Ran svgp tests" diff --git a/test/stochastic_variational.jl b/test/sparse_variational.jl similarity index 87% rename from test/stochastic_variational.jl rename to test/sparse_variational.jl index a0901051..a4ed8a0a 100644 --- a/test/stochastic_variational.jl +++ b/test/sparse_variational.jl @@ -12,7 +12,7 @@ y = rand(rng, fx) q = exact_variational_posterior(fx, fx, y) - f_approx_post = posterior(SVGP(fx, q)) + f_approx_post = posterior(SparseVariationalApproximation(fx, q)) a = collect(range(-1.0, 1.0; length=N_a)) b = randn(rng, N_b) From 5fc5b67b9345b6ac4c32028f2f8f0808a49b0950 Mon Sep 17 00:00:00 2001 From: Ross Viljoen Date: Thu, 4 Nov 2021 23:19:09 +0000 Subject: [PATCH 3/7] Formatting --- src/elbo.jl | 4 +++- src/sparse_variational.jl | 30 +++++++++++++++++++++++------- test/equivalences.jl | 3 ++- 3 files changed, 28 insertions(+), 9 deletions(-) diff --git a/src/elbo.jl b/src/elbo.jl index 01e83afd..e22bd428 100644 --- a/src/elbo.jl +++ b/src/elbo.jl @@ -30,7 +30,9 @@ function AbstractGPs.elbo( return _elbo(quadrature, sva, fx, y, GaussianLikelihood(fx.Σy[1]), num_data) end -function AbstractGPs.elbo(::SparseVariationalApproximation, ::FiniteGP, ::AbstractVector; kwargs...) +function AbstractGPs.elbo( + ::SparseVariationalApproximation, ::FiniteGP, ::AbstractVector; kwargs... +) return error( "The observation noise fx.Σy must be homoscedastic.\n To avoid this error, construct fx using: f = GP(kernel); fx = f(x, σ²)", ) diff --git a/src/sparse_variational.jl b/src/sparse_variational.jl index 0e84fa00..c8585a0a 100644 --- a/src/sparse_variational.jl +++ b/src/sparse_variational.jl @@ -31,28 +31,40 @@ function AbstractGPs.posterior(sva::SparseVariationalApproximation) return ApproxPosteriorGP(sva, fz.f, data) end -function AbstractGPs.posterior(sva::SparseVariationalApproximation, fx::FiniteGP, ::AbstractVector) +function AbstractGPs.posterior( + sva::SparseVariationalApproximation, fx::FiniteGP, ::AbstractVector +) @assert sva.fz.f === fx.f return posterior(sva) end -function Statistics.mean(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector) +function Statistics.mean( + f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector +) return mean(f.prior, x) + cov(f.prior, x, inducing_points(f)) * f.data.α end -function Statistics.cov(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector) +function Statistics.cov( + f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector +) Cux = cov(f.prior, inducing_points(f), x) D = f.data.Kuu.L \ Cux return cov(f.prior, x) - At_A(D) + At_A(f.data.B' * D) end -function Statistics.var(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector) +function Statistics.var( + f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector +) Cux = cov(f.prior, inducing_points(f), x) D = f.data.Kuu.L \ Cux return var(f.prior, x) - diag_At_A(D) + diag_At_A(f.data.B' * D) end -function Statistics.cov(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector, y::AbstractVector) +function Statistics.cov( + f::ApproxPosteriorGP{<:SparseVariationalApproximation}, + x::AbstractVector, + y::AbstractVector, +) B = f.data.B Cxu = cov(f.prior, x, inducing_points(f)) Cuy = cov(f.prior, inducing_points(f), y) @@ -61,7 +73,9 @@ function Statistics.cov(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, return cov(f.prior, x, y) - (E * D) + (E * B * B' * D) end -function StatsBase.mean_and_cov(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector) +function StatsBase.mean_and_cov( + f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector +) Cux = cov(f.prior, inducing_points(f), x) D = f.data.Kuu.L \ Cux μ = Cux' * f.data.α @@ -69,7 +83,9 @@ function StatsBase.mean_and_cov(f::ApproxPosteriorGP{<:SparseVariationalApproxim return μ, Σ end -function StatsBase.mean_and_var(f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector) +function StatsBase.mean_and_var( + f::ApproxPosteriorGP{<:SparseVariationalApproximation}, x::AbstractVector +) Cux = cov(f.prior, inducing_points(f), x) D = f.data.Kuu.L \ Cux μ = Cux' * f.data.α diff --git a/test/equivalences.jl b/test/equivalences.jl index 9d4e9159..b5248d9c 100644 --- a/test/equivalences.jl +++ b/test/equivalences.jl @@ -31,7 +31,8 @@ @test mean(vfe_post, x) ≈ mean(svgp_post, x) atol = 1e-10 @test cov(vfe_post, x) ≈ cov(svgp_post, x) atol = 1e-10 - @test elbo(SparseVariationalApproximation(fz, q_ex), fx, y) ≈ logpdf(fx, y) atol = 1e-6 + @test elbo(SparseVariationalApproximation(fz, q_ex), fx, y) ≈ logpdf(fx, y) atol = + 1e-6 end @testset "optimised posterior" begin From 3bfa589aada8a5bbe9f3c58603494e929efd76df Mon Sep 17 00:00:00 2001 From: Ross Viljoen Date: Fri, 5 Nov 2021 10:49:38 +0000 Subject: [PATCH 4/7] Apply suggestions from code review Co-authored-by: st-- --- examples/a-regression/script.jl | 2 +- test/equivalences.jl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/examples/a-regression/script.jl b/examples/a-regression/script.jl index 1899aeb0..762b0e8b 100644 --- a/examples/a-regression/script.jl +++ b/examples/a-regression/script.jl @@ -123,7 +123,7 @@ function (m::SVGPModel)(x) return post(x) end; -# Return the loss given data - for the SparseVariationalApproximation, the +# Return the loss given data - for the SVGP model as constructed using `SparseVariationalApproximation`, the # loss used is the negative ELBO (also known as the Variational Free Energy). # `num_data` is required for minibatching used below. diff --git a/test/equivalences.jl b/test/equivalences.jl index b5248d9c..26c2b58d 100644 --- a/test/equivalences.jl +++ b/test/equivalences.jl @@ -11,7 +11,7 @@ @testset "exact posterior" begin # There is a closed form optimal solution for the variational posterior # q(u) (e.g. # https://krasserm.github.io/2020/12/12/gaussian-processes-sparse/ - # equations (11) & (12)). The SparseVariationalApproximation posterior with this optimal q(u) + # equations (11) & (12)). The SVGP posterior with this optimal q(u) # should therefore be equivalent to the sparse GP (Titsias) posterior # and exact GP regression (when z == x). From 32436849b597f5460aae26d1b6ef86f858e97036 Mon Sep 17 00:00:00 2001 From: Ross Viljoen Date: Fri, 5 Nov 2021 11:02:13 +0000 Subject: [PATCH 5/7] Add SVGP deprecation --- src/ApproximateGPs.jl | 5 ++++- src/deprecations.jl | 1 + 2 files changed, 5 insertions(+), 1 deletion(-) create mode 100644 src/deprecations.jl diff --git a/src/ApproximateGPs.jl b/src/ApproximateGPs.jl index 1e291412..83cb797e 100644 --- a/src/ApproximateGPs.jl +++ b/src/ApproximateGPs.jl @@ -15,7 +15,8 @@ using KLDivergences using AbstractGPs: AbstractGP, FiniteGP, LatentFiniteGP, ApproxPosteriorGP, At_A, diag_At_A -export SparseVariationalApproximation, DefaultQuadrature, Analytic, GaussHermite, MonteCarlo +export SparseVariationalApproximation +export DefaultQuadrature, Analytic, GaussHermite, MonteCarlo include("utils.jl") include("sparse_variational.jl") @@ -29,4 +30,6 @@ export build_laplace_objective, build_laplace_objective! export approx_lml # TODO move to AbstractGPs, see https://github.com/JuliaGaussianProcesses/AbstractGPs.jl/issues/221 include("laplace.jl") +include("deprecations.jl") + end diff --git a/src/deprecations.jl b/src/deprecations.jl new file mode 100644 index 00000000..fab42428 --- /dev/null +++ b/src/deprecations.jl @@ -0,0 +1 @@ +@deprecate SVGP SparseVariationalApproximation From 42fb670f6c1cae8c004aa88cc40af03b8bda92e9 Mon Sep 17 00:00:00 2001 From: Ross Viljoen Date: Fri, 5 Nov 2021 11:12:50 +0000 Subject: [PATCH 6/7] Patch bump and change author --- Project.toml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Project.toml b/Project.toml index e7f9e1b4..2e59f4b6 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "ApproximateGPs" uuid = "298c2ebc-0411-48ad-af38-99e88101b606" -authors = ["Ross Viljoen "] -version = "0.1.2" +authors = ["JuliaGaussianProcesses Team"] +version = "0.2.0" [deps] AbstractGPs = "99985d1d-32ba-4be9-9821-2ec096f28918" From 20114d639de517da7de52f4f10bfd66c3bbb3445 Mon Sep 17 00:00:00 2001 From: Ross Viljoen Date: Fri, 5 Nov 2021 11:24:13 +0000 Subject: [PATCH 7/7] Update test, docs & examples Projects and Manifests --- docs/Manifest.toml | 141 +++++---- docs/Project.toml | 2 +- examples/a-regression/Manifest.toml | 220 +++++++------- examples/b-classification/Manifest.toml | 381 +++++++----------------- examples/c-comparisons/Manifest.toml | 190 ++++++------ test/Project.toml | 2 +- 6 files changed, 425 insertions(+), 511 deletions(-) diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 5fa60165..0ced0e9b 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -7,15 +7,15 @@ version = "0.0.1" [[AbstractGPs]] deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "80b6c9734d00ae7518e65a0e1063772a050d04a0" +git-tree-sha1 = "e2af18922f65ea8cee7b8cd97a1668691f76f4b2" uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.1" +version = "0.5.3" [[ApproximateGPs]] -deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "GPLikelihoods", "KLDivergences", "LinearAlgebra", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] +deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "KLDivergences", "LinearAlgebra", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] path = ".." uuid = "298c2ebc-0411-48ad-af38-99e88101b606" -version = "0.1.0" +version = "0.2.0" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" @@ -28,15 +28,21 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "4ce9393e871aca86cc457d9f66976c3da6902ea7" +git-tree-sha1 = "f885e7e7c124f8c92650d61b9477b9ac2ee607dd" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.4.0" +version = "1.11.1" + +[[CommonSubexpressions]] +deps = ["MacroTools", "Test"] +git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +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 = "4866e381721b30fac8dda4c8cb1d9db45c8d2994" +git-tree-sha1 = "dce3e3fea680869eaa0b774b2e8343e9ff442313" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.37.0" +version = "3.40.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -48,9 +54,9 @@ uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" version = "0.1.1" [[DataAPI]] -git-tree-sha1 = "bec2532f8adb82005476c141ec23e921fc20971b" +git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.8.0" +version = "1.9.0" [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -66,11 +72,23 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" deps = ["Mmap"] uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" +[[DiffResults]] +deps = ["StaticArrays"] +git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805" +uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" +version = "1.0.3" + +[[DiffRules]] +deps = ["LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] +git-tree-sha1 = "3287dacf67c3652d3fed09f4c12c187ae4dbb89a" +uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" +version = "1.4.0" + [[Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "9f46deb4d4ee4494ffb5a40a27a2aced67bdd838" +git-tree-sha1 = "837c83e5574582e07662bbbba733964ff7c26b9d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.4" +version = "0.10.6" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -78,21 +96,21 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[Distributions]] deps = ["ChainRulesCore", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "f4efaa4b5157e0cdb8283ae0b5428bc9208436ed" +git-tree-sha1 = "72dcda9e19f88d09bf21b5f9507a0bb430bce2aa" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.16" +version = "0.25.24" [[DocStringExtensions]] deps = ["LibGit2"] -git-tree-sha1 = "a32185f5428d3986f47c2ab78b1f216d5e6cc96f" +git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.8.5" +version = "0.8.6" [[Documenter]] deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] -git-tree-sha1 = "fe0bc46b27cd3413df55859152fd70e50744025f" +git-tree-sha1 = "f425293f7e0acaf9144de6d731772de156676233" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.27.6" +version = "0.27.10" [[Downloads]] deps = ["ArgTools", "LibCURL", "NetworkOptions"] @@ -106,20 +124,26 @@ version = "0.4.7" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "caf289224e622f518c9dbfe832cdafa17d7c80a6" +git-tree-sha1 = "8756f9935b7ccc9064c6eef0bff0ad643df733a3" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.12.4" +version = "0.12.7" + +[[ForwardDiff]] +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "ef3fec65f9db26fa2cf8f4133c697c5b7ce63c1d" +uuid = "f6369f11-7733-5829-9624-2563aa707210" +version = "0.10.22" [[Functors]] -git-tree-sha1 = "e2727f02325451f6b24445cd83bfa9aaac19cbe7" +git-tree-sha1 = "e4768c3b7f597d5a352afa09874d16e3c3f6ead2" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.2.5" +version = "0.2.7" [[GPLikelihoods]] deps = ["Distributions", "Functors", "LinearAlgebra", "Random", "StatsFuns"] -git-tree-sha1 = "e07acc5ca79ead40c8cf0338c9357fc7fb90eea1" +git-tree-sha1 = "bdfe8a65b3ca3aa92812d74138264570f33aa66e" uuid = "6031954c-0455-49d7-b3b9-3e1c99afaf40" -version = "0.2.0" +version = "0.2.4" [[IOCapture]] deps = ["Logging", "Random"] @@ -131,10 +155,16 @@ version = "0.2.2" deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" +[[InverseFunctions]] +deps = ["Test"] +git-tree-sha1 = "f0c6489b12d28fb4c2103073ec7452f3423bd308" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.1" + [[IrrationalConstants]] -git-tree-sha1 = "f76424439413893a832026ca355fe273e93bce94" +git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.0" +version = "0.1.1" [[JLLWrappers]] deps = ["Preferences"] @@ -156,9 +186,9 @@ version = "0.2.1" [[KernelFunctions]] deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "Random", "Requires", "SpecialFunctions", "StatsBase", "TensorCore", "Test", "ZygoteRules"] -git-tree-sha1 = "3b7fceeab37b650c280eb072ffe2b868b03a5423" +git-tree-sha1 = "9c3d38dafc02feae68a4747813b8b0205fd03da5" uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" -version = "0.10.17" +version = "0.10.26" [[LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] @@ -184,19 +214,19 @@ deps = ["Libdl"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[LogExpFunctions]] -deps = ["ChainRulesCore", "DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "34dc30f868e368f8a17b728a1238f3fcda43931a" +deps = ["ChainRulesCore", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "6193c3815f13ba1b78a51ce391db8be016ae9214" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.3" +version = "0.3.4" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "5a5bc6bf062f0f95e62d0fe0a2d99699fed82dd9" +git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.8" +version = "0.5.9" [[Markdown]] deps = ["Base64"] @@ -218,9 +248,18 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" +[[NaNMath]] +git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb" +uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" +version = "0.3.5" + [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" +[[OpenLibm_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "05823500-19ac-5b8b-9628-191a04bc5112" + [[OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" @@ -234,15 +273,15 @@ version = "1.4.1" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "4dd403333bcf0909341cfe57ec115152f937d7d8" +git-tree-sha1 = "c8b8775b2f242c80ea85c83714c64ecfa3c53355" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.1" +version = "0.11.3" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "438d35d2d95ae2c5e8780b330592b6de8494e779" +git-tree-sha1 = "ae4bbcadb2906ccc085cf52ac286dc1377dceccc" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.0.3" +version = "2.1.2" [[Pkg]] deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] @@ -260,9 +299,9 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" [[QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "12fbe86da16df6679be7521dfb39fbc861e1dc7b" +git-tree-sha1 = "78aadffb3efd2155af139781b8a8df1ef279ea39" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.4.1" +version = "2.4.2" [[REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -324,16 +363,16 @@ deps = ["LinearAlgebra", "Random"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[SpecialFunctions]] -deps = ["ChainRulesCore", "LogExpFunctions", "OpenSpecFun_jll"] -git-tree-sha1 = "a322a9493e49c5f3a10b50df3aedaf1cdb3244b7" +deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "f0bccf98e16759818ffc5d97ac3ebf87eb950150" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "1.6.1" +version = "1.8.1" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "3240808c6d463ac46f1c1cd7638375cd22abbccb" +git-tree-sha1 = "3c76dde64d03699e074ac02eb2e8ba8254d428da" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.2.12" +version = "1.2.13" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -345,16 +384,16 @@ uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" version = "1.0.0" [[StatsBase]] -deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "8cbbc098554648c84f79a463c9ff0fd277144b6c" +deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "eb35dcc66558b2dda84079b9a1be17557d32091a" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.10" +version = "0.33.12" [[StatsFuns]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "46d7ccc7104860c38b11966dd1f72ff042f382e4" +git-tree-sha1 = "95072ef1a22b057b1e80f73c2a89ad238ae4cfff" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.10" +version = "0.9.12" [[SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -391,9 +430,9 @@ uuid = "83775a58-1f1d-513f-b197-d71354ab007a" [[ZygoteRules]] deps = ["MacroTools"] -git-tree-sha1 = "9e7a1e8ca60b742e508a315c17eef5211e7fbfd7" +git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.1" +version = "0.2.2" [[nghttp2_jll]] deps = ["Artifacts", "Libdl"] diff --git a/docs/Project.toml b/docs/Project.toml index 3b7fa1dd..3589ff2f 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -3,5 +3,5 @@ ApproximateGPs = "298c2ebc-0411-48ad-af38-99e88101b606" Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" [compat] -ApproximateGPs = "0.1" +ApproximateGPs = "0.2" Documenter = "0.27" diff --git a/examples/a-regression/Manifest.toml b/examples/a-regression/Manifest.toml index bf1717ca..cd42657c 100644 --- a/examples/a-regression/Manifest.toml +++ b/examples/a-regression/Manifest.toml @@ -8,9 +8,9 @@ version = "1.0.1" [[AbstractGPs]] deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "80b6c9734d00ae7518e65a0e1063772a050d04a0" +git-tree-sha1 = "e2af18922f65ea8cee7b8cd97a1668691f76f4b2" uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.1" +version = "0.5.3" [[AbstractTrees]] git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" @@ -24,28 +24,28 @@ uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" version = "3.3.1" [[ApproximateGPs]] -deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "KLDivergences", "LinearAlgebra", "QuadGK", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] +deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "KLDivergences", "LinearAlgebra", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] path = "../.." uuid = "298c2ebc-0411-48ad-af38-99e88101b606" -version = "0.1.1" +version = "0.2.0" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "b8d49c34c3da35f220e7295659cd0bab8e739fed" +git-tree-sha1 = "e527b258413e0c6d4f66ade574744c94edef81f8" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.33" +version = "3.1.40" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" [[BFloat16s]] -deps = ["LinearAlgebra", "Test"] -git-tree-sha1 = "4af69e205efc343068dc8722b8dfec1ade89254a" +deps = ["LinearAlgebra", "Printf", "Random", "Test"] +git-tree-sha1 = "a598ecb0d717092b5539dbbe890c98bac842b072" uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" -version = "0.1.0" +version = "0.2.0" [[Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -63,9 +63,9 @@ version = "0.4.1" [[CUDA]] deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CompilerSupportLibraries_jll", "ExprTools", "GPUArrays", "GPUCompiler", "LLVM", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "SpecialFunctions", "TimerOutputs"] -git-tree-sha1 = "335b3d2373733919b4972a51215a6840c7a33828" +git-tree-sha1 = "2c8329f16addffd09e6ca84c556e2185a4933c64" uuid = "052768ef-5323-5732-b1bb-66c8b64840ba" -version = "3.4.2" +version = "3.5.0" [[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"] @@ -74,16 +74,16 @@ uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.16.1+0" [[ChainRules]] -deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "d88340ab502af66cfffc821e70ae72f7dbdce645" +deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "RealDot", "Statistics"] +git-tree-sha1 = "035ef8a5382a614b2d8e3091b6fdbb1c2b050e11" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.11.5" +version = "1.12.1" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "bd4afa1fdeec0c8b89dad3c6e92bc6e3b0fec9ce" +git-tree-sha1 = "f885e7e7c124f8c92650d61b9477b9ac2ee607dd" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.6.0" +version = "1.11.1" [[CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] @@ -93,9 +93,9 @@ version = "0.7.0" [[ColorSchemes]] deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"] -git-tree-sha1 = "9995eb3977fbf67b86d0a0a0508e83017ded03f2" +git-tree-sha1 = "a851fec56cb73cfdf43762999ec72eff5b86882a" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.14.0" +version = "3.15.0" [[ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -117,9 +117,9 @@ 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 = "1a90210acd935f222ea19657f143004d2c2a1117" +git-tree-sha1 = "dce3e3fea680869eaa0b774b2e8343e9ff442313" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.38.0" +version = "3.40.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -167,16 +167,16 @@ uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" version = "1.0.3" [[DiffRules]] -deps = ["NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "7220bc21c33e990c14f4a9a319b1d242ebc5b269" +deps = ["LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] +git-tree-sha1 = "3287dacf67c3652d3fed09f4c12c187ae4dbb89a" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.3.1" +version = "1.4.0" [[Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "9f46deb4d4ee4494ffb5a40a27a2aced67bdd838" +git-tree-sha1 = "837c83e5574582e07662bbbba733964ff7c26b9d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.4" +version = "0.10.6" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -184,15 +184,15 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[Distributions]] deps = ["ChainRulesCore", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "f4efaa4b5157e0cdb8283ae0b5428bc9208436ed" +git-tree-sha1 = "72dcda9e19f88d09bf21b5f9507a0bb430bce2aa" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.16" +version = "0.25.24" [[DocStringExtensions]] deps = ["LibGit2"] -git-tree-sha1 = "a32185f5428d3986f47c2ab78b1f216d5e6cc96f" +git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.8.5" +version = "0.8.6" [[Downloads]] deps = ["ArgTools", "LibCURL", "NetworkOptions"] @@ -235,9 +235,9 @@ version = "0.4.7" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "7f6ad1a7f4621b4ab8e554133dade99ebc6e7221" +git-tree-sha1 = "8756f9935b7ccc9064c6eef0bff0ad643df733a3" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.12.5" +version = "0.12.7" [[FixedPointNumbers]] deps = ["Statistics"] @@ -246,10 +246,10 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.4" [[Flux]] -deps = ["AbstractTrees", "Adapt", "ArrayInterface", "CUDA", "CodecZlib", "Colors", "DelimitedFiles", "Functors", "Juno", "LinearAlgebra", "MacroTools", "NNlib", "NNlibCUDA", "Pkg", "Printf", "Random", "Reexport", "SHA", "Statistics", "StatsBase", "Test", "ZipFile", "Zygote"] -git-tree-sha1 = "1286e5dd0b4c306108747356a7a5d39a11dc4080" +deps = ["AbstractTrees", "Adapt", "ArrayInterface", "CUDA", "CodecZlib", "Colors", "DelimitedFiles", "Functors", "Juno", "LinearAlgebra", "MacroTools", "NNlib", "NNlibCUDA", "Pkg", "Printf", "Random", "Reexport", "SHA", "SparseArrays", "Statistics", "StatsBase", "Test", "ZipFile", "Zygote"] +git-tree-sha1 = "e8b37bb43c01eed0418821d1f9d20eca5ba6ab21" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.12.6" +version = "0.12.8" [[Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] @@ -264,10 +264,10 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "b5e930ac60b613ef3406da6d4f42c35d8dc51419" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "ef3fec65f9db26fa2cf8f4133c697c5b7ce63c1d" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.19" +version = "0.10.22" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -282,45 +282,45 @@ uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.10+0" [[Functors]] -git-tree-sha1 = "e2727f02325451f6b24445cd83bfa9aaac19cbe7" +git-tree-sha1 = "e4768c3b7f597d5a352afa09874d16e3c3f6ead2" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.2.5" +version = "0.2.7" [[GLFW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "dba1e8614e98949abfa60480b13653813d8f0157" +git-tree-sha1 = "0c603255764a1fa0b61752d2bec14cfbd18f7fe8" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.5+0" +version = "3.3.5+1" [[GPLikelihoods]] deps = ["Distributions", "Functors", "LinearAlgebra", "Random", "StatsFuns"] -git-tree-sha1 = "e07acc5ca79ead40c8cf0338c9357fc7fb90eea1" +git-tree-sha1 = "bdfe8a65b3ca3aa92812d74138264570f33aa66e" uuid = "6031954c-0455-49d7-b3b9-3e1c99afaf40" -version = "0.2.0" +version = "0.2.4" [[GPUArrays]] deps = ["Adapt", "LinearAlgebra", "Printf", "Random", "Serialization", "Statistics"] -git-tree-sha1 = "7c39d767a9c55fafd01f7bc8b3fd0adf175fbc97" +git-tree-sha1 = "7772508f17f1d482fe0df72cabc5b55bec06bbe0" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.1.0" +version = "8.1.2" [[GPUCompiler]] deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "4ed2616d5e656c8716736b64da86755467f26cf5" +git-tree-sha1 = "77d915a0af27d474f0aaf12fcd46c400a552e84c" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.12.9" +version = "0.13.7" [[GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "c2178cfbc0a5a552e16d097fae508f2024de61a3" +git-tree-sha1 = "30f2b340c2fff8410d89bfcdc9c0a6dd661ac5f7" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.59.0" +version = "0.62.1" [[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 = "ef49a187604f865f4708c90e3f431890724e9012" +git-tree-sha1 = "fd75fa3a2080109a2c0ec9864a6e14c60cca3866" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.59.0+0" +version = "0.62.0+0" [[GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -353,9 +353,9 @@ version = "1.0.2" [[HTTP]] deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] -git-tree-sha1 = "60ed5f1643927479f845b0135bb369b031b541fa" +git-tree-sha1 = "14eece7a3308b4d8be910e265c724a6ba51a9798" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.9.14" +version = "0.9.16" [[HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -376,9 +376,9 @@ uuid = "7869d1d1-7146-5819-86e3-90919afe41df" version = "0.4.3" [[IfElse]] -git-tree-sha1 = "28e837ff3e7a6c3cdb252ce49fb412c8eb3caeef" +git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" -version = "0.1.0" +version = "0.1.1" [[IniFile]] deps = ["Test"] @@ -390,10 +390,16 @@ version = "0.5.0" deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" +[[InverseFunctions]] +deps = ["Test"] +git-tree-sha1 = "f0c6489b12d28fb4c2103073ec7452f3423bd308" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.1" + [[IrrationalConstants]] -git-tree-sha1 = "f76424439413893a832026ca355fe273e93bce94" +git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.0" +version = "0.1.1" [[IterTools]] git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18" @@ -437,9 +443,9 @@ version = "0.2.1" [[KernelFunctions]] deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "Random", "Requires", "SpecialFunctions", "StatsBase", "TensorCore", "Test", "ZygoteRules"] -git-tree-sha1 = "3b7fceeab37b650c280eb072ffe2b868b03a5423" +git-tree-sha1 = "9c3d38dafc02feae68a4747813b8b0205fd03da5" uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" -version = "0.10.17" +version = "0.10.26" [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -449,15 +455,15 @@ version = "3.100.1+0" [[LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "36d95ecdfbc3240d728f68d73064d5b097fbf2ef" +git-tree-sha1 = "46092047ca4edc10720ecab437c42283cd7c44f3" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "4.5.2" +version = "4.6.0" [[LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9c360e5ce980b88bb31a7b086dbb19469008154b" +git-tree-sha1 = "6a2af408fe809c4f1a54d2b3f188fdd3698549d6" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.10+0" +version = "0.0.11+0" [[LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -466,15 +472,15 @@ uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" version = "2.10.1+0" [[LaTeXStrings]] -git-tree-sha1 = "c7f1c695e06c01b95a67f0cd1d34994f3e7db104" +git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.2.1" +version = "1.3.0" [[Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "a4b12a1bd2ebade87891ab7e36fdbce582301a92" +git-tree-sha1 = "a8f4f279b6fa3c3c4f1adadd78a621b13a506bce" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.6" +version = "0.15.9" [[LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -553,24 +559,24 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[Literate]] deps = ["Base64", "IOCapture", "JSON", "REPL"] -git-tree-sha1 = "bbebc3c14dbfbe76bfcbabf0937481ac84dc86ef" +git-tree-sha1 = "d3493acfb9e6aa0cff46b09773fc2342327b0feb" uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306" -version = "2.9.3" +version = "2.9.4" [[LogExpFunctions]] -deps = ["ChainRulesCore", "DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "34dc30f868e368f8a17b728a1238f3fcda43931a" +deps = ["ChainRulesCore", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "6193c3815f13ba1b78a51ce391db8be016ae9214" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.3" +version = "0.3.4" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "5a5bc6bf062f0f95e62d0fe0a2d99699fed82dd9" +git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.8" +version = "0.5.9" [[Markdown]] deps = ["Base64"] @@ -670,15 +676,15 @@ version = "8.44.0+0" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "4dd403333bcf0909341cfe57ec115152f937d7d8" +git-tree-sha1 = "c8b8775b2f242c80ea85c83714c64ecfa3c53355" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.1" +version = "0.11.3" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "9d8c00ef7a8d110787ff6f170579846f776133a9" +git-tree-sha1 = "ae4bbcadb2906ccc085cf52ac286dc1377dceccc" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.0.4" +version = "2.1.2" [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -698,15 +704,15 @@ version = "2.0.1" [[PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "2537ed3c0ed5e03896927187f5f2ee6a4ab342db" +git-tree-sha1 = "b084324b4af5a438cd63619fd006614b3b20b87b" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.0.14" +version = "1.0.15" [[Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"] -git-tree-sha1 = "457b13497a3ea4deb33d273a6a5ea15c25c0ebd9" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun"] +git-tree-sha1 = "7dc03c2b145168f5854085a16d054429d612b637" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.22.2" +version = "1.23.5" [[Preferences]] deps = ["TOML"] @@ -754,6 +760,12 @@ git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" version = "1.5.3" +[[RealDot]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "9f0a1b71baaf7650f4fa8a1d168c7fb6ee41f0c9" +uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" +version = "0.1.0" + [[RecipesBase]] git-tree-sha1 = "44a75aa7a527910ee3d1751d1f0e4148698add9e" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" @@ -824,22 +836,22 @@ deps = ["LinearAlgebra", "Random"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[SpecialFunctions]] -deps = ["ChainRulesCore", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "ad42c30a6204c74d264692e633133dcea0e8b14e" +deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "f0bccf98e16759818ffc5d97ac3ebf87eb950150" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "1.6.2" +version = "1.8.1" [[Static]] deps = ["IfElse"] -git-tree-sha1 = "a8f30abc7c64a39d389680b74e749cf33f872a70" +git-tree-sha1 = "e7bc80dc93f50857a5d1e3c8121495852f407e6a" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.3.3" +version = "0.4.0" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "3240808c6d463ac46f1c1cd7638375cd22abbccb" +git-tree-sha1 = "3c76dde64d03699e074ac02eb2e8ba8254d428da" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.2.12" +version = "1.2.13" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -851,16 +863,16 @@ uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" version = "1.0.0" [[StatsBase]] -deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "8cbbc098554648c84f79a463c9ff0fd277144b6c" +deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "eb35dcc66558b2dda84079b9a1be17557d32091a" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.10" +version = "0.33.12" [[StatsFuns]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "46d7ccc7104860c38b11966dd1f72ff042f382e4" +git-tree-sha1 = "95072ef1a22b057b1e80f73c2a89ad238ae4cfff" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.10" +version = "0.9.12" [[StructArrays]] deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] @@ -884,9 +896,9 @@ version = "1.0.1" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "1162ce4a6c4b7e31e0e6b14486a6986951c73be9" +git-tree-sha1 = "fed34d0e71b91734bf0a7e10eb1bb05296ddbcd0" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.5.2" +version = "1.6.0" [[Tar]] deps = ["ArgTools", "SHA"] @@ -926,6 +938,12 @@ uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" [[Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" +[[UnicodeFun]] +deps = ["REPL"] +git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" +uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" +version = "0.4.1" + [[Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" @@ -1094,15 +1112,15 @@ version = "1.5.0+0" [[Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "4b799addc63aa77ad4112cede8086564d9068511" +git-tree-sha1 = "0fc9959bcabc4668c403810b4e851f6b8962eac9" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.22" +version = "0.6.29" [[ZygoteRules]] deps = ["MacroTools"] -git-tree-sha1 = "9e7a1e8ca60b742e508a315c17eef5211e7fbfd7" +git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.1" +version = "0.2.2" [[libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] diff --git a/examples/b-classification/Manifest.toml b/examples/b-classification/Manifest.toml index c596c51e..a8b06699 100644 --- a/examples/b-classification/Manifest.toml +++ b/examples/b-classification/Manifest.toml @@ -8,9 +8,9 @@ version = "1.0.1" [[AbstractGPs]] deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "80b6c9734d00ae7518e65a0e1063772a050d04a0" +git-tree-sha1 = "e2af18922f65ea8cee7b8cd97a1668691f76f4b2" uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.1" +version = "0.5.3" [[Adapt]] deps = ["LinearAlgebra"] @@ -19,24 +19,19 @@ uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" version = "3.3.1" [[ApproximateGPs]] -deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "KLDivergences", "LinearAlgebra", "QuadGK", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] +deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "KLDivergences", "LinearAlgebra", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] path = "../.." uuid = "298c2ebc-0411-48ad-af38-99e88101b606" -version = "0.1.1" - -[[ArgCheck]] -git-tree-sha1 = "dedbbb2ddb876f899585c4ec4433265e3017215a" -uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" -version = "2.1.0" +version = "0.2.0" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "b8d49c34c3da35f220e7295659cd0bab8e739fed" +git-tree-sha1 = "e527b258413e0c6d4f66ade574744c94edef81f8" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.33" +version = "3.1.40" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -44,30 +39,12 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" [[Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -[[Bijectors]] -deps = ["ArgCheck", "ChainRulesCore", "Compat", "Distributions", "Functors", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "MappedArrays", "NonlinearSolve", "Random", "Reexport", "Requires", "SparseArrays", "Statistics"] -git-tree-sha1 = "dca5e02c9426b2f8ce86d8e723d0702ff33df234" -uuid = "76274a88-744f-5084-9051-94815aaf08c4" -version = "0.9.8" - -[[BitTwiddlingConvenienceFunctions]] -deps = ["Static"] -git-tree-sha1 = "652aab0fc0d6d4db4cc726425cadf700e9f473f1" -uuid = "62783981-4cbd-42fc-bca8-16325de8dc4b" -version = "0.1.0" - [[Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.8+0" -[[CPUSummary]] -deps = ["Hwloc", "IfElse", "Static"] -git-tree-sha1 = "ed720e2622820bf584d4ad90e6fcb93d95170b44" -uuid = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9" -version = "0.1.3" - [[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"] git-tree-sha1 = "f2202b55d816427cd385a9a4f3ffb226bee80f99" @@ -75,28 +52,22 @@ uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.16.1+0" [[ChainRules]] -deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "d88340ab502af66cfffc821e70ae72f7dbdce645" +deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "RealDot", "Statistics"] +git-tree-sha1 = "035ef8a5382a614b2d8e3091b6fdbb1c2b050e11" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.11.5" +version = "1.12.1" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "bd4afa1fdeec0c8b89dad3c6e92bc6e3b0fec9ce" +git-tree-sha1 = "f885e7e7c124f8c92650d61b9477b9ac2ee607dd" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.6.0" - -[[CloseOpenIntervals]] -deps = ["ArrayInterface", "Static"] -git-tree-sha1 = "ce9c0d07ed6e1a4fecd2df6ace144cbd29ba6f37" -uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" -version = "0.1.2" +version = "1.11.1" [[ColorSchemes]] deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"] -git-tree-sha1 = "9995eb3977fbf67b86d0a0a0508e83017ded03f2" +git-tree-sha1 = "a851fec56cb73cfdf43762999ec72eff5b86882a" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.14.0" +version = "3.15.0" [[ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -110,11 +81,6 @@ git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" version = "0.12.8" -[[CommonSolve]] -git-tree-sha1 = "68a0743f578349ada8bc911a5cbd5a2ef6ed6d1f" -uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" -version = "0.2.0" - [[CommonSubexpressions]] deps = ["MacroTools", "Test"] git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" @@ -123,9 +89,9 @@ 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 = "1a90210acd935f222ea19657f143004d2c2a1117" +git-tree-sha1 = "dce3e3fea680869eaa0b774b2e8343e9ff442313" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.38.0" +version = "3.40.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -136,12 +102,6 @@ git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" version = "0.1.1" -[[ConstructionBase]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "f74e9d5388b8620b4cee35d4c5a618dd4dc547f4" -uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.3.0" - [[Contour]] deps = ["StaticArrays"] git-tree-sha1 = "9f02045d934dc030edad45944ea80dbd1f0ebea7" @@ -179,16 +139,16 @@ uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" version = "1.0.3" [[DiffRules]] -deps = ["NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "7220bc21c33e990c14f4a9a319b1d242ebc5b269" +deps = ["LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] +git-tree-sha1 = "3287dacf67c3652d3fed09f4c12c187ae4dbb89a" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.3.1" +version = "1.4.0" [[Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "9f46deb4d4ee4494ffb5a40a27a2aced67bdd838" +git-tree-sha1 = "837c83e5574582e07662bbbba733964ff7c26b9d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.4" +version = "0.10.6" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -196,15 +156,15 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[Distributions]] deps = ["ChainRulesCore", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "f4efaa4b5157e0cdb8283ae0b5428bc9208436ed" +git-tree-sha1 = "72dcda9e19f88d09bf21b5f9507a0bb430bce2aa" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.16" +version = "0.25.24" [[DocStringExtensions]] deps = ["LibGit2"] -git-tree-sha1 = "a32185f5428d3986f47c2ab78b1f216d5e6cc96f" +git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.8.5" +version = "0.8.6" [[Downloads]] deps = ["ArgTools", "LibCURL", "NetworkOptions"] @@ -242,9 +202,9 @@ version = "0.4.7" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "7f6ad1a7f4621b4ab8e554133dade99ebc6e7221" +git-tree-sha1 = "8756f9935b7ccc9064c6eef0bff0ad643df733a3" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.12.5" +version = "0.12.7" [[FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] @@ -271,10 +231,10 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "b5e930ac60b613ef3406da6d4f42c35d8dc51419" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "ef3fec65f9db26fa2cf8f4133c697c5b7ce63c1d" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.19" +version = "0.10.22" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -289,37 +249,33 @@ uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.10+0" [[Functors]] -git-tree-sha1 = "e2727f02325451f6b24445cd83bfa9aaac19cbe7" +git-tree-sha1 = "e4768c3b7f597d5a352afa09874d16e3c3f6ead2" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.2.5" - -[[Future]] -deps = ["Random"] -uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" +version = "0.2.7" [[GLFW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "dba1e8614e98949abfa60480b13653813d8f0157" +git-tree-sha1 = "0c603255764a1fa0b61752d2bec14cfbd18f7fe8" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.5+0" +version = "3.3.5+1" [[GPLikelihoods]] deps = ["Distributions", "Functors", "LinearAlgebra", "Random", "StatsFuns"] -git-tree-sha1 = "e07acc5ca79ead40c8cf0338c9357fc7fb90eea1" +git-tree-sha1 = "bdfe8a65b3ca3aa92812d74138264570f33aa66e" uuid = "6031954c-0455-49d7-b3b9-3e1c99afaf40" -version = "0.2.0" +version = "0.2.4" [[GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "c2178cfbc0a5a552e16d097fae508f2024de61a3" +git-tree-sha1 = "30f2b340c2fff8410d89bfcdc9c0a6dd661ac5f7" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.59.0" +version = "0.62.1" [[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 = "ef49a187604f865f4708c90e3f431890724e9012" +git-tree-sha1 = "fd75fa3a2080109a2c0ec9864a6e14c60cca3866" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.59.0+0" +version = "0.62.0+0" [[GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -352,9 +308,9 @@ version = "1.0.2" [[HTTP]] deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] -git-tree-sha1 = "60ed5f1643927479f845b0135bb369b031b541fa" +git-tree-sha1 = "14eece7a3308b4d8be910e265c724a6ba51a9798" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.9.14" +version = "0.9.16" [[HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -362,24 +318,6 @@ git-tree-sha1 = "8a954fed8ac097d5be04921d595f741115c1b2ad" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" version = "2.8.1+0" -[[HostCPUFeatures]] -deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] -git-tree-sha1 = "3169c8b31863f9a409be1d17693751314241e3eb" -uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" -version = "0.1.4" - -[[Hwloc]] -deps = ["Hwloc_jll"] -git-tree-sha1 = "92d99146066c5c6888d5a3abc871e6a214388b91" -uuid = "0e44f5e4-bd66-52a0-8798-143a42290a1d" -version = "2.0.0" - -[[Hwloc_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3395d4d4aeb3c9d31f5929d32760d8baeee88aaf" -uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" -version = "2.5.0+0" - [[IOCapture]] deps = ["Logging", "Random"] git-tree-sha1 = "f7be53659ab06ddc986428d3a9dcc95f6fa6705a" @@ -393,9 +331,9 @@ uuid = "7869d1d1-7146-5819-86e3-90919afe41df" version = "0.4.3" [[IfElse]] -git-tree-sha1 = "28e837ff3e7a6c3cdb252ce49fb412c8eb3caeef" +git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" -version = "0.1.0" +version = "0.1.1" [[IniFile]] deps = ["Test"] @@ -407,22 +345,22 @@ version = "0.5.0" deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" +[[InverseFunctions]] +deps = ["Test"] +git-tree-sha1 = "f0c6489b12d28fb4c2103073ec7452f3423bd308" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.1" + [[IrrationalConstants]] -git-tree-sha1 = "f76424439413893a832026ca355fe273e93bce94" +git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.0" +version = "0.1.1" [[IterTools]] git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" version = "1.3.0" -[[IterativeSolvers]] -deps = ["LinearAlgebra", "Printf", "Random", "RecipesBase", "SparseArrays"] -git-tree-sha1 = "1a8c6237e78b714e901e406c096fc8a65528af7d" -uuid = "42fd0dbc-a981-5370-80f2-aaf504508153" -version = "0.9.1" - [[IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" uuid = "82899510-4779-5014-852e-03e436cf321d" @@ -454,9 +392,9 @@ version = "0.2.1" [[KernelFunctions]] deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "Random", "Requires", "SpecialFunctions", "StatsBase", "TensorCore", "Test", "ZygoteRules"] -git-tree-sha1 = "3b7fceeab37b650c280eb072ffe2b868b03a5423" +git-tree-sha1 = "9c3d38dafc02feae68a4747813b8b0205fd03da5" uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" -version = "0.10.17" +version = "0.10.26" [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -471,21 +409,15 @@ uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" version = "2.10.1+0" [[LaTeXStrings]] -git-tree-sha1 = "c7f1c695e06c01b95a67f0cd1d34994f3e7db104" +git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.2.1" +version = "1.3.0" [[Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "a4b12a1bd2ebade87891ab7e36fdbce582301a92" +git-tree-sha1 = "a8f4f279b6fa3c3c4f1adadd78a621b13a506bce" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.6" - -[[LayoutPointers]] -deps = ["ArrayInterface", "LinearAlgebra", "ManualMemory", "SIMDTypes", "Static"] -git-tree-sha1 = "d2bda6aa0b03ce6f141a2dc73d0bcb7070131adc" -uuid = "10f19ff3-798f-405d-979b-55457f8fc047" -version = "0.1.3" +version = "0.15.9" [[LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] @@ -566,40 +498,24 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[Literate]] deps = ["Base64", "IOCapture", "JSON", "REPL"] -git-tree-sha1 = "bbebc3c14dbfbe76bfcbabf0937481ac84dc86ef" +git-tree-sha1 = "d3493acfb9e6aa0cff46b09773fc2342327b0feb" uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306" -version = "2.9.3" +version = "2.9.4" [[LogExpFunctions]] -deps = ["ChainRulesCore", "DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "34dc30f868e368f8a17b728a1238f3fcda43931a" +deps = ["ChainRulesCore", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "6193c3815f13ba1b78a51ce391db8be016ae9214" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.3" +version = "0.3.4" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -[[LoopVectorization]] -deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "Requires", "SLEEFPirates", "Static", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "4804192466f4d370ca19c9957dfb3d919e6ef77e" -uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.77" - [[MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "5a5bc6bf062f0f95e62d0fe0a2d99699fed82dd9" +git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.8" - -[[ManualMemory]] -git-tree-sha1 = "9cb207b18148b2199db259adfa923b45593fe08e" -uuid = "d125e4d3-2237-4719-b19c-fa641b8a4667" -version = "0.1.6" - -[[MappedArrays]] -git-tree-sha1 = "e8b359ef06ec72e8c030463fe02efe5527ee5142" -uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" -version = "0.4.1" +version = "0.5.9" [[Markdown]] deps = ["Base64"] @@ -634,9 +550,9 @@ uuid = "14a3606d-f60d-562e-9121-12d972cd8159" [[NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "144bab5b1443545bc4e791536c9f1eacb4eed06a" +git-tree-sha1 = "50310f934e55e5ca3912fb941dec199b49ca9b68" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.8.1" +version = "7.8.2" [[NaNMath]] git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb" @@ -646,18 +562,6 @@ version = "0.3.5" [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" -[[NonlinearSolve]] -deps = ["ArrayInterface", "FiniteDiff", "ForwardDiff", "IterativeSolvers", "LinearAlgebra", "RecursiveArrayTools", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "StaticArrays", "UnPack"] -git-tree-sha1 = "e9ffc92217b8709e0cf7b8808f6223a4a0936c95" -uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "0.3.11" - -[[OffsetArrays]] -deps = ["Adapt"] -git-tree-sha1 = "c0e9e582987d36d5a61e650e6e543b9e44d9914b" -uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.10.7" - [[Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "7937eda4681660b4d6aeeecc2f7e1c81c8ee4e2f" @@ -681,10 +585,10 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.5+0" [[Optim]] -deps = ["Compat", "FillArrays", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "7863df65dbb2a0fa8f85fcaf0a41167640d2ebed" +deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] +git-tree-sha1 = "35d435b512fbab1d1a29138b5229279925eba369" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.4.1" +version = "1.5.0" [[Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -705,15 +609,15 @@ version = "8.44.0+0" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "4dd403333bcf0909341cfe57ec115152f937d7d8" +git-tree-sha1 = "c8b8775b2f242c80ea85c83714c64ecfa3c53355" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.1" +version = "0.11.3" [[ParameterHandling]] -deps = ["Bijectors", "ChainRulesCore", "Compat", "IterTools", "LinearAlgebra", "SparseArrays", "Test"] -git-tree-sha1 = "b454231b4559c118fe3522734c71555592445843" +deps = ["ChainRulesCore", "Compat", "InverseFunctions", "IterTools", "LinearAlgebra", "LogExpFunctions", "SparseArrays", "Test"] +git-tree-sha1 = "603fde842910e6d33bfce2ce7d0e0a0851d8e21e" uuid = "2412ca09-6db7-441c-8e3a-88d5709968c5" -version = "0.3.8" +version = "0.4.0" [[Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -723,9 +627,9 @@ version = "0.12.3" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "9d8c00ef7a8d110787ff6f170579846f776133a9" +git-tree-sha1 = "ae4bbcadb2906ccc085cf52ac286dc1377dceccc" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.0.4" +version = "2.1.2" [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -745,27 +649,15 @@ version = "2.0.1" [[PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "2537ed3c0ed5e03896927187f5f2ee6a4ab342db" +git-tree-sha1 = "b084324b4af5a438cd63619fd006614b3b20b87b" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.0.14" +version = "1.0.15" [[Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"] -git-tree-sha1 = "457b13497a3ea4deb33d273a6a5ea15c25c0ebd9" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun"] +git-tree-sha1 = "7dc03c2b145168f5854085a16d054429d612b637" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.22.2" - -[[Polyester]] -deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "74d358e649e0450cb5d3ff54ca7c8d806ed62765" -uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.5.1" - -[[PolyesterWeave]] -deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] -git-tree-sha1 = "371a19bb801c1b420b29141750f3a34d6c6634b9" -uuid = "1d0040c9-8b98-4ee7-8388-3f51789ca0ad" -version = "0.1.0" +version = "1.23.5" [[PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -803,6 +695,12 @@ uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" deps = ["Serialization"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +[[RealDot]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "9f0a1b71baaf7650f4fa8a1d168c7fb6ee41f0c9" +uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" +version = "0.1.0" + [[RecipesBase]] git-tree-sha1 = "44a75aa7a527910ee3d1751d1f0e4148698add9e" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" @@ -814,18 +712,6 @@ git-tree-sha1 = "7ad0dfa8d03b7bcf8c597f59f5292801730c55b8" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.4.1" -[[RecursiveArrayTools]] -deps = ["ArrayInterface", "ChainRulesCore", "DocStringExtensions", "LinearAlgebra", "RecipesBase", "Requires", "StaticArrays", "Statistics", "ZygoteRules"] -git-tree-sha1 = "00bede2eb099dcc1ddc3f9ec02180c326b420ee2" -uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "2.17.2" - -[[RecursiveFactorization]] -deps = ["LinearAlgebra", "LoopVectorization", "Polyester", "StrideArraysCore", "TriangularSolve"] -git-tree-sha1 = "575c18c6b00ce409f75d96fefe33ebe01575457a" -uuid = "f2c3362d-daeb-58d1-803e-2bc74f2840b4" -version = "0.2.4" - [[Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" @@ -852,23 +738,6 @@ version = "0.3.0+0" [[SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" -[[SIMDTypes]] -git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" -uuid = "94e857df-77ce-4151-89e5-788b33177be4" -version = "0.1.0" - -[[SLEEFPirates]] -deps = ["IfElse", "Static", "VectorizationBase"] -git-tree-sha1 = "2e8150c7d2a14ac68537c7aac25faa6577aff046" -uuid = "476501e8-09a2-5ece-8869-fb82de89a1fa" -version = "0.6.27" - -[[SciMLBase]] -deps = ["ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "RecipesBase", "RecursiveArrayTools", "StaticArrays", "Statistics", "Tables", "TreeViews"] -git-tree-sha1 = "91e29a2bb257a4b992c48f35084064578b87d364" -uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462" -version = "1.19.0" - [[Scratch]] deps = ["Dates"] git-tree-sha1 = "0b4b7f1393cff97c33891da2a0bf69c6ed241fda" @@ -878,12 +747,6 @@ version = "1.1.0" [[Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -[[Setfield]] -deps = ["ConstructionBase", "Future", "MacroTools", "Requires"] -git-tree-sha1 = "def0718ddbabeb5476e51e5a43609bee889f285d" -uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" -version = "0.8.0" - [[SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" @@ -908,22 +771,22 @@ deps = ["LinearAlgebra", "Random"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[SpecialFunctions]] -deps = ["ChainRulesCore", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "ad42c30a6204c74d264692e633133dcea0e8b14e" +deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "f0bccf98e16759818ffc5d97ac3ebf87eb950150" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "1.6.2" +version = "1.8.1" [[Static]] deps = ["IfElse"] -git-tree-sha1 = "a8f30abc7c64a39d389680b74e749cf33f872a70" +git-tree-sha1 = "e7bc80dc93f50857a5d1e3c8121495852f407e6a" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.3.3" +version = "0.4.0" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "3240808c6d463ac46f1c1cd7638375cd22abbccb" +git-tree-sha1 = "3c76dde64d03699e074ac02eb2e8ba8254d428da" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.2.12" +version = "1.2.13" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -935,22 +798,16 @@ uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" version = "1.0.0" [[StatsBase]] -deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "8cbbc098554648c84f79a463c9ff0fd277144b6c" +deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "eb35dcc66558b2dda84079b9a1be17557d32091a" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.10" +version = "0.33.12" [[StatsFuns]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "46d7ccc7104860c38b11966dd1f72ff042f382e4" +git-tree-sha1 = "95072ef1a22b057b1e80f73c2a89ad238ae4cfff" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.10" - -[[StrideArraysCore]] -deps = ["ArrayInterface", "CloseOpenIntervals", "IfElse", "LayoutPointers", "ManualMemory", "Requires", "SIMDTypes", "Static", "ThreadingUtilities"] -git-tree-sha1 = "1258e25e171aec339866f283a11e7d75867e77d7" -uuid = "7792a7ef-975c-4747-a70f-980b88e8d1da" -version = "0.2.4" +version = "0.9.12" [[StructArrays]] deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] @@ -974,9 +831,9 @@ version = "1.0.1" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "1162ce4a6c4b7e31e0e6b14486a6986951c73be9" +git-tree-sha1 = "fed34d0e71b91734bf0a7e10eb1bb05296ddbcd0" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.5.2" +version = "1.6.0" [[Tar]] deps = ["ArgTools", "SHA"] @@ -992,24 +849,6 @@ version = "0.1.1" deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -[[ThreadingUtilities]] -deps = ["ManualMemory"] -git-tree-sha1 = "03013c6ae7f1824131b2ae2fc1d49793b51e8394" -uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" -version = "0.4.6" - -[[TreeViews]] -deps = ["Test"] -git-tree-sha1 = "8d0d7a3fe2f30d6a7f833a5f19f7c7a5b396eae6" -uuid = "a2a6695c-b41b-5b7d-aed9-dbfdeacea5d7" -version = "0.3.0" - -[[TriangularSolve]] -deps = ["CloseOpenIntervals", "IfElse", "LayoutPointers", "LinearAlgebra", "LoopVectorization", "Polyester", "Static", "VectorizationBase"] -git-tree-sha1 = "ed55426a514db35f58d36c3812aae89cfc057401" -uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" -version = "0.1.6" - [[URIs]] git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" @@ -1027,11 +866,11 @@ version = "1.0.2" [[Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -[[VectorizationBase]] -deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "Hwloc", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static"] -git-tree-sha1 = "3e2385f4ec895e694c24a1d5aba58cb6d27cf8b6" -uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.10" +[[UnicodeFun]] +deps = ["REPL"] +git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" +uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" +version = "0.4.1" [[Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] @@ -1195,15 +1034,15 @@ version = "1.5.0+0" [[Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "4b799addc63aa77ad4112cede8086564d9068511" +git-tree-sha1 = "0fc9959bcabc4668c403810b4e851f6b8962eac9" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.22" +version = "0.6.29" [[ZygoteRules]] deps = ["MacroTools"] -git-tree-sha1 = "9e7a1e8ca60b742e508a315c17eef5211e7fbfd7" +git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.1" +version = "0.2.2" [[libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] diff --git a/examples/c-comparisons/Manifest.toml b/examples/c-comparisons/Manifest.toml index 2e5e8962..66937125 100644 --- a/examples/c-comparisons/Manifest.toml +++ b/examples/c-comparisons/Manifest.toml @@ -8,9 +8,9 @@ version = "1.0.1" [[AbstractGPs]] deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "80b6c9734d00ae7518e65a0e1063772a050d04a0" +git-tree-sha1 = "e2af18922f65ea8cee7b8cd97a1668691f76f4b2" uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.1" +version = "0.5.3" [[Adapt]] deps = ["LinearAlgebra"] @@ -22,16 +22,16 @@ version = "3.3.1" deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "KLDivergences", "LinearAlgebra", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] path = "../.." uuid = "298c2ebc-0411-48ad-af38-99e88101b606" -version = "0.1.2" +version = "0.2.0" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "b8d49c34c3da35f220e7295659cd0bab8e739fed" +git-tree-sha1 = "e527b258413e0c6d4f66ade574744c94edef81f8" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.33" +version = "3.1.40" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -52,16 +52,16 @@ uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.16.1+0" [[ChainRules]] -deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "74c737978316e19e0706737542037c468b21a8d9" +deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "RealDot", "Statistics"] +git-tree-sha1 = "035ef8a5382a614b2d8e3091b6fdbb1c2b050e11" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.11.6" +version = "1.12.1" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "e8a30e8019a512e4b6c56ccebc065026624660e8" +git-tree-sha1 = "f885e7e7c124f8c92650d61b9477b9ac2ee607dd" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.7.0" +version = "1.11.1" [[ColorSchemes]] deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"] @@ -89,9 +89,9 @@ 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 = "31d0151f5716b655421d9d75b7fa74cc4e744df2" +git-tree-sha1 = "dce3e3fea680869eaa0b774b2e8343e9ff442313" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.39.0" +version = "3.40.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -139,16 +139,16 @@ uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" version = "1.0.3" [[DiffRules]] -deps = ["NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "7220bc21c33e990c14f4a9a319b1d242ebc5b269" +deps = ["LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] +git-tree-sha1 = "3287dacf67c3652d3fed09f4c12c187ae4dbb89a" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.3.1" +version = "1.4.0" [[Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "9f46deb4d4ee4494ffb5a40a27a2aced67bdd838" +git-tree-sha1 = "837c83e5574582e07662bbbba733964ff7c26b9d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.4" +version = "0.10.6" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -156,15 +156,15 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[Distributions]] deps = ["ChainRulesCore", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "f4efaa4b5157e0cdb8283ae0b5428bc9208436ed" +git-tree-sha1 = "72dcda9e19f88d09bf21b5f9507a0bb430bce2aa" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.16" +version = "0.25.24" [[DocStringExtensions]] deps = ["LibGit2"] -git-tree-sha1 = "a32185f5428d3986f47c2ab78b1f216d5e6cc96f" +git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.8.5" +version = "0.8.6" [[Downloads]] deps = ["ArgTools", "LibCURL", "NetworkOptions"] @@ -202,9 +202,9 @@ version = "0.4.7" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "29890dfbc427afa59598b8cfcc10034719bd7744" +git-tree-sha1 = "8756f9935b7ccc9064c6eef0bff0ad643df733a3" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.12.6" +version = "0.12.7" [[FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] @@ -231,10 +231,10 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "b5e930ac60b613ef3406da6d4f42c35d8dc51419" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "ef3fec65f9db26fa2cf8f4133c697c5b7ce63c1d" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.19" +version = "0.10.22" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -249,33 +249,33 @@ uuid = "559328eb-81f9-559d-9380-de523a88c83c" version = "1.0.10+0" [[Functors]] -git-tree-sha1 = "e2727f02325451f6b24445cd83bfa9aaac19cbe7" +git-tree-sha1 = "e4768c3b7f597d5a352afa09874d16e3c3f6ead2" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.2.5" +version = "0.2.7" [[GLFW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "dba1e8614e98949abfa60480b13653813d8f0157" +git-tree-sha1 = "0c603255764a1fa0b61752d2bec14cfbd18f7fe8" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.5+0" +version = "3.3.5+1" [[GPLikelihoods]] deps = ["Distributions", "Functors", "LinearAlgebra", "Random", "StatsFuns"] -git-tree-sha1 = "e07acc5ca79ead40c8cf0338c9357fc7fb90eea1" +git-tree-sha1 = "bdfe8a65b3ca3aa92812d74138264570f33aa66e" uuid = "6031954c-0455-49d7-b3b9-3e1c99afaf40" -version = "0.2.0" +version = "0.2.4" [[GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "c2178cfbc0a5a552e16d097fae508f2024de61a3" +git-tree-sha1 = "30f2b340c2fff8410d89bfcdc9c0a6dd661ac5f7" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.59.0" +version = "0.62.1" [[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 = "ef49a187604f865f4708c90e3f431890724e9012" +git-tree-sha1 = "fd75fa3a2080109a2c0ec9864a6e14c60cca3866" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.59.0+0" +version = "0.62.0+0" [[GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -308,9 +308,9 @@ version = "1.0.2" [[HTTP]] deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] -git-tree-sha1 = "24675428ca27678f003414a98c9e473e45fe6a21" +git-tree-sha1 = "14eece7a3308b4d8be910e265c724a6ba51a9798" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.9.15" +version = "0.9.16" [[HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -331,9 +331,9 @@ uuid = "7869d1d1-7146-5819-86e3-90919afe41df" version = "0.4.3" [[IfElse]] -git-tree-sha1 = "28e837ff3e7a6c3cdb252ce49fb412c8eb3caeef" +git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" -version = "0.1.0" +version = "0.1.1" [[IniFile]] deps = ["Test"] @@ -345,10 +345,16 @@ version = "0.5.0" deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" +[[InverseFunctions]] +deps = ["Test"] +git-tree-sha1 = "f0c6489b12d28fb4c2103073ec7452f3423bd308" +uuid = "3587e190-3f89-42d0-90ee-14403ec27112" +version = "0.1.1" + [[IrrationalConstants]] -git-tree-sha1 = "f76424439413893a832026ca355fe273e93bce94" +git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.0" +version = "0.1.1" [[IterTools]] git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18" @@ -386,9 +392,9 @@ version = "0.2.1" [[KernelFunctions]] deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "Random", "Requires", "SpecialFunctions", "StatsBase", "TensorCore", "Test", "ZygoteRules"] -git-tree-sha1 = "88506985f762e63e5cab00d5d90cacf86c05fa7b" +git-tree-sha1 = "9c3d38dafc02feae68a4747813b8b0205fd03da5" uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" -version = "0.10.18" +version = "0.10.26" [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -403,15 +409,15 @@ uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" version = "2.10.1+0" [[LaTeXStrings]] -git-tree-sha1 = "c7f1c695e06c01b95a67f0cd1d34994f3e7db104" +git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.2.1" +version = "1.3.0" [[Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "a4b12a1bd2ebade87891ab7e36fdbce582301a92" +git-tree-sha1 = "a8f4f279b6fa3c3c4f1adadd78a621b13a506bce" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.6" +version = "0.15.9" [[LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] @@ -492,24 +498,24 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[Literate]] deps = ["Base64", "IOCapture", "JSON", "REPL"] -git-tree-sha1 = "bbebc3c14dbfbe76bfcbabf0937481ac84dc86ef" +git-tree-sha1 = "d3493acfb9e6aa0cff46b09773fc2342327b0feb" uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306" -version = "2.9.3" +version = "2.9.4" [[LogExpFunctions]] -deps = ["ChainRulesCore", "DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "34dc30f868e368f8a17b728a1238f3fcda43931a" +deps = ["ChainRulesCore", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "6193c3815f13ba1b78a51ce391db8be016ae9214" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.3" +version = "0.3.4" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "5a5bc6bf062f0f95e62d0fe0a2d99699fed82dd9" +git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.8" +version = "0.5.9" [[Markdown]] deps = ["Base64"] @@ -544,9 +550,9 @@ uuid = "14a3606d-f60d-562e-9121-12d972cd8159" [[NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "144bab5b1443545bc4e791536c9f1eacb4eed06a" +git-tree-sha1 = "50310f934e55e5ca3912fb941dec199b49ca9b68" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.8.1" +version = "7.8.2" [[NaNMath]] git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb" @@ -579,10 +585,10 @@ uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" version = "0.5.5+0" [[Optim]] -deps = ["Compat", "FillArrays", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "7863df65dbb2a0fa8f85fcaf0a41167640d2ebed" +deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] +git-tree-sha1 = "35d435b512fbab1d1a29138b5229279925eba369" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.4.1" +version = "1.5.0" [[Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -603,9 +609,9 @@ version = "8.44.0+0" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "4dd403333bcf0909341cfe57ec115152f937d7d8" +git-tree-sha1 = "c8b8775b2f242c80ea85c83714c64ecfa3c53355" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.1" +version = "0.11.3" [[Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -615,9 +621,9 @@ version = "0.12.3" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "9d8c00ef7a8d110787ff6f170579846f776133a9" +git-tree-sha1 = "ae4bbcadb2906ccc085cf52ac286dc1377dceccc" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.0.4" +version = "2.1.2" [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -637,15 +643,15 @@ version = "2.0.1" [[PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "2537ed3c0ed5e03896927187f5f2ee6a4ab342db" +git-tree-sha1 = "b084324b4af5a438cd63619fd006614b3b20b87b" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.0.14" +version = "1.0.15" [[Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs"] -git-tree-sha1 = "cfbd033def161db9494f86c5d18fbf874e09e514" +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun"] +git-tree-sha1 = "7dc03c2b145168f5854085a16d054429d612b637" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.22.3" +version = "1.23.5" [[PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -683,6 +689,12 @@ uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" deps = ["Serialization"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +[[RealDot]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "9f0a1b71baaf7650f4fa8a1d168c7fb6ee41f0c9" +uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" +version = "0.1.0" + [[RecipesBase]] git-tree-sha1 = "44a75aa7a527910ee3d1751d1f0e4148698add9e" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" @@ -754,21 +766,21 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[SpecialFunctions]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "793793f1df98e3d7d554b65a107e9c9a6399a6ed" +git-tree-sha1 = "f0bccf98e16759818ffc5d97ac3ebf87eb950150" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "1.7.0" +version = "1.8.1" [[Static]] deps = ["IfElse"] -git-tree-sha1 = "a8f30abc7c64a39d389680b74e749cf33f872a70" +git-tree-sha1 = "e7bc80dc93f50857a5d1e3c8121495852f407e6a" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.3.3" +version = "0.4.0" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "3240808c6d463ac46f1c1cd7638375cd22abbccb" +git-tree-sha1 = "3c76dde64d03699e074ac02eb2e8ba8254d428da" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.2.12" +version = "1.2.13" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -780,16 +792,16 @@ uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" version = "1.0.0" [[StatsBase]] -deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "8cbbc098554648c84f79a463c9ff0fd277144b6c" +deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "eb35dcc66558b2dda84079b9a1be17557d32091a" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.10" +version = "0.33.12" [[StatsFuns]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "46d7ccc7104860c38b11966dd1f72ff042f382e4" +git-tree-sha1 = "95072ef1a22b057b1e80f73c2a89ad238ae4cfff" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.10" +version = "0.9.12" [[StructArrays]] deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] @@ -813,9 +825,9 @@ version = "1.0.1" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "1162ce4a6c4b7e31e0e6b14486a6986951c73be9" +git-tree-sha1 = "fed34d0e71b91734bf0a7e10eb1bb05296ddbcd0" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.5.2" +version = "1.6.0" [[Tar]] deps = ["ArgTools", "SHA"] @@ -848,6 +860,12 @@ version = "1.0.2" [[Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" +[[UnicodeFun]] +deps = ["REPL"] +git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" +uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" +version = "0.4.1" + [[Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" @@ -1010,15 +1028,15 @@ version = "1.5.0+0" [[Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "2c18495c33331497f147b21e7c65c3246cdb59cc" +git-tree-sha1 = "0fc9959bcabc4668c403810b4e851f6b8962eac9" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.23" +version = "0.6.29" [[ZygoteRules]] deps = ["MacroTools"] -git-tree-sha1 = "9e7a1e8ca60b742e508a315c17eef5211e7fbfd7" +git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.1" +version = "0.2.2" [[libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] diff --git a/test/Project.toml b/test/Project.toml index f8c698e4..9326a1dc 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -17,7 +17,7 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] AbstractGPs = "0.4, 0.5" -ApproximateGPs = "0.1" +ApproximateGPs = "0.2" ChainRulesCore = "1" ChainRulesTestUtils = "1.2.3" Distributions = "0.25"