From becacaa3b3a23c881cd0ce59c0f5f90a1708938b Mon Sep 17 00:00:00 2001 From: ST John Date: Thu, 28 Oct 2021 13:46:42 +0300 Subject: [PATCH 01/20] return lazy Fill arrays for mean functions from #197 --- src/mean_function.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/mean_function.jl b/src/mean_function.jl index 3b16d72f..6eacec36 100644 --- a/src/mean_function.jl +++ b/src/mean_function.jl @@ -10,7 +10,7 @@ struct ZeroMean{T<:Real} <: MeanFunction end """ This is an AbstractGPs-internal workaround for AD issues; ideally we would just extend Base.map """ -_map_meanfunction(::ZeroMean{T}, x::AbstractVector) where {T} = zeros(T, length(x)) +_map_meanfunction(::ZeroMean{T}, x::AbstractVector) where {T} = Zeros{T}(length(x)) function ChainRulesCore.rrule(::typeof(_map_meanfunction), m::ZeroMean, x::AbstractVector) map_ZeroMean_pullback(Δ) = (NoTangent(), NoTangent(), ZeroTangent()) @@ -28,7 +28,7 @@ struct ConstMean{T<:Real} <: MeanFunction c::T end -_map_meanfunction(m::ConstMean, x::AbstractVector) = fill(m.c, length(x)) +_map_meanfunction(m::ConstMean, x::AbstractVector) = Fill(m.c, length(x)) """ CustomMean{Tf} <: MeanFunction From c42402b52a86f7f4313dba6881f0847ab31b30b1 Mon Sep 17 00:00:00 2001 From: ST John Date: Thu, 28 Oct 2021 13:49:02 +0300 Subject: [PATCH 02/20] replace Diagonal(Fill(...)) with PDMats.ScalMat --- Project.toml | 1 + src/AbstractGPs.jl | 1 + src/finite_gp_projection.jl | 2 +- 3 files changed, 3 insertions(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index a8882dc7..fee70307 100644 --- a/Project.toml +++ b/Project.toml @@ -10,6 +10,7 @@ FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" IrrationalConstants = "92d709cd-6900-40b7-9082-c6be49f344b6" KernelFunctions = "ec8451be-7e33-11e9-00cf-bbf324bd1392" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" Reexport = "189a3867-3050-52da-a836-e630ba90ab69" diff --git a/src/AbstractGPs.jl b/src/AbstractGPs.jl index 15b3812e..db0c09f9 100644 --- a/src/AbstractGPs.jl +++ b/src/AbstractGPs.jl @@ -4,6 +4,7 @@ using ChainRulesCore using Distributions using FillArrays using LinearAlgebra +using PDMats: ScalMat using Reexport @reexport using KernelFunctions using Random diff --git a/src/finite_gp_projection.jl b/src/finite_gp_projection.jl index 1fc98e5b..e5f2f5f2 100644 --- a/src/finite_gp_projection.jl +++ b/src/finite_gp_projection.jl @@ -17,7 +17,7 @@ end const default_σ² = 1e-18 function FiniteGP(f::AbstractGP, x::AbstractVector, σ²::Real=default_σ²) - return FiniteGP(f, x, Fill(σ², length(x))) + return FiniteGP(f, x, ScalMat(length(x), σ²)) end function FiniteGP( From 6cc507f405ec70613776484f439b6ad093215eb0 Mon Sep 17 00:00:00 2001 From: ST John Date: Thu, 28 Oct 2021 17:18:13 +0300 Subject: [PATCH 03/20] =?UTF-8?q?add=20tr=5FCf=5Finv=CE=A3y=20method=20for?= =?UTF-8?q?=20ScalMat=20&=20tests?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- src/sparse_approximations.jl | 4 ++++ test/Project.toml | 1 + test/runtests.jl | 1 + test/sparse_approximations.jl | 15 +++++++++++++++ 4 files changed, 21 insertions(+) diff --git a/src/sparse_approximations.jl b/src/sparse_approximations.jl index 2065a3f9..f173c93d 100644 --- a/src/sparse_approximations.jl +++ b/src/sparse_approximations.jl @@ -287,3 +287,7 @@ end function tr_Cf_invΣy(f::FiniteGP, Σy::Diagonal) return sum(var(f.f, f.x) ./ diag(Σy)) end + +function tr_Cf_invΣy(f::FiniteGP, Σy::ScalMat) + return sum(var(f.f, f.x) / Σy) +end diff --git a/test/Project.toml b/test/Project.toml index 3ceef702..74326ce3 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -5,6 +5,7 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" diff --git a/test/runtests.jl b/test/runtests.jl index c037ac58..f0280c93 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -31,6 +31,7 @@ using FiniteDifferences using FiniteDifferences: j′vp, to_vec using LinearAlgebra using LinearAlgebra: AbstractTriangular +using PDMats: ScalMat using Pkg using Plots using Random diff --git a/test/sparse_approximations.jl b/test/sparse_approximations.jl index 0c875120..82d3db07 100644 --- a/test/sparse_approximations.jl +++ b/test/sparse_approximations.jl @@ -115,3 +115,18 @@ @test logpdf(p_fx, y) isa T end end + +@testset "tr_Cf_invΣy" begin + N = 3 + x = rand(N) + σ² = 1.234 + Σy_Diagonal = Diagonal(Fill(σ², N)) + Σy_ScalMat = ScalMat(N, σ²) + f = GP(SqExponentialKernel()) + + for Σy in (Σy_Diagonal, Σy_ScalMat) + fx = f(x, Σy) + Cf = cov(f, x) + @test AbstractGPs.tr_Cf_invΣy(fx, Σy) ≈ tr(Cf / Matrix(Σy)) + end +end From 15143bed6c713fc1a1572f8611e2a71d4f9893d4 Mon Sep 17 00:00:00 2001 From: ST John Date: Thu, 28 Oct 2021 17:18:50 +0300 Subject: [PATCH 04/20] _cholesky for ScalMat and remove superfluous _symmetric() calls --- src/sparse_approximations.jl | 6 +++--- src/util/common_covmat_ops.jl | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/sparse_approximations.jl b/src/sparse_approximations.jl index f173c93d..eef66bf9 100644 --- a/src/sparse_approximations.jl +++ b/src/sparse_approximations.jl @@ -51,7 +51,7 @@ Intelligence and Statistics. 2009. function posterior(vfe::VFE, fx::FiniteGP, y::AbstractVector{<:Real}) @assert vfe.fz.f === fx.f - U_y = _cholesky(_symmetric(fx.Σy)).U + U_y = _cholesky(fx.Σy).U U = cholesky(_symmetric(cov(vfe.fz))).U B_εf = U' \ (U_y' \ cov(fx, vfe.fz))' @@ -85,7 +85,7 @@ function update_posterior( U = f_post_approx.data.U z = inducing_points(f_post_approx) - U_y₂ = _cholesky(_symmetric(fx.Σy)).U + U_y₂ = _cholesky(fx.Σy).U temp = zeros(size(f_post_approx.data.Σy, 1), size(fx.Σy, 2)) Σy = [f_post_approx.data.Σy temp; temp' fx.Σy] @@ -136,7 +136,7 @@ function update_posterior(f_post_approx::ApproxPosteriorGP{<:VFE}, fz::FiniteGP) Cu1f = cov(f_post_approx.prior, z_old, f_post_approx.data.x) Cu2f = cov(f_post_approx.prior, z, f_post_approx.data.x) - U_y = _cholesky(_symmetric(f_post_approx.data.Σy)).U + U_y = _cholesky(f_post_approx.data.Σy).U B_εf₂ = U22' \ (Cu2f * inv(U_y) - U12' * B_εf₁) B_εf = vcat(B_εf₁, B_εf₂) diff --git a/src/util/common_covmat_ops.jl b/src/util/common_covmat_ops.jl index 0c99beb1..7e88a3cb 100644 --- a/src/util/common_covmat_ops.jl +++ b/src/util/common_covmat_ops.jl @@ -7,7 +7,7 @@ _symmetric(X::Diagonal) = X # Small bit of indirection to work around a cholesky-related bug whereby the interaction # between `FillArrays` and `Diagonal` and `Cholesky` causes problems. _cholesky(X) = cholesky(X) -function _cholesky(X::Diagonal{<:Real,<:FillArrays.AbstractFill}) +function _cholesky(X::Union{Diagonal{<:Real,<:FillArrays.AbstractFill},ScalMat}) return cholesky(Diagonal(collect(diag(X)))) end From a95cf5486cd1802ed220d4866c60a64e4225dea0 Mon Sep 17 00:00:00 2001 From: ST John Date: Thu, 28 Oct 2021 17:19:07 +0300 Subject: [PATCH 05/20] update deprecated call --- test/latent_gp.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/latent_gp.jl b/test/latent_gp.jl index 506dcf92..1645f2b8 100644 --- a/test/latent_gp.jl +++ b/test/latent_gp.jl @@ -3,7 +3,7 @@ x = rand(10) y = rand(10) - lgp = LatentGP(gp, x -> MvNormal(x, 0.1), 1e-5) + lgp = LatentGP(gp, x -> MvNormal(x, 0.01 * I), 1e-5) @test lgp isa LatentGP @test lgp.f isa AbstractGPs.AbstractGP @test lgp.Σy isa Real From 8159debb4c41f8578d82339ec2940253fececaa5 Mon Sep 17 00:00:00 2001 From: ST John Date: Thu, 28 Oct 2021 18:02:33 +0300 Subject: [PATCH 06/20] standard fallback for ScalMat --- src/util/common_covmat_ops.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/util/common_covmat_ops.jl b/src/util/common_covmat_ops.jl index 7e88a3cb..0c99beb1 100644 --- a/src/util/common_covmat_ops.jl +++ b/src/util/common_covmat_ops.jl @@ -7,7 +7,7 @@ _symmetric(X::Diagonal) = X # Small bit of indirection to work around a cholesky-related bug whereby the interaction # between `FillArrays` and `Diagonal` and `Cholesky` causes problems. _cholesky(X) = cholesky(X) -function _cholesky(X::Union{Diagonal{<:Real,<:FillArrays.AbstractFill},ScalMat}) +function _cholesky(X::Diagonal{<:Real,<:FillArrays.AbstractFill}) return cholesky(Diagonal(collect(diag(X)))) end From aec60e26a05c1c380c7d2c81abbecbb0cc1ba3c9 Mon Sep 17 00:00:00 2001 From: ST John Date: Fri, 29 Oct 2021 08:43:48 +0300 Subject: [PATCH 07/20] update Manifests --- docs/Manifest.toml | 109 +++++++++++---------- examples/regression-1d/Manifest.toml | 140 ++++++++++++++------------- 2 files changed, 132 insertions(+), 117 deletions(-) diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 457db8cc..900ac8d0 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -6,10 +6,10 @@ uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" version = "0.0.1" [[AbstractGPs]] -deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] +deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "PDMats", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] path = ".." uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.4.0" +version = "0.5.3" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" @@ -22,15 +22,15 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "bdc0937269321858ab2a4f288486cb258b9a0af7" +git-tree-sha1 = "3533f5a691e60601fe60c90d8bc47a27aa2907ec" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.3.0" +version = "1.11.0" [[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 = "727e463cfebd0c7b999bbf3e9e7e16f254b94193" +git-tree-sha1 = "31d0151f5716b655421d9d75b7fa74cc4e744df2" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.34.0" +version = "3.39.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -42,9 +42,9 @@ uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" version = "0.1.1" [[DataAPI]] -git-tree-sha1 = "ee400abb2298bd13bfc3df1c412ed228061a2385" +git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.7.0" +version = "1.9.0" [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -62,31 +62,31 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" [[Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "abe4ad222b26af3337262b8afb28fab8d215e9f8" +git-tree-sha1 = "09d9eaef9ef719d2cd5d928a191dc95be2ec8059" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.3" +version = "0.10.5" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[Distributions]] -deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "3889f646423ce91dd1055a76317e9a1d3a23fff1" +deps = ["ChainRulesCore", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"] +git-tree-sha1 = "d249ebaa67716b39f91cf6052daf073634013c0f" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.11" +version = "0.25.23" [[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 = "350dced36c11f794c6c4da5dc6493ec894e50c16" +git-tree-sha1 = "f425293f7e0acaf9144de6d731772de156676233" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.27.5" +version = "0.27.10" [[Downloads]] deps = ["ArgTools", "LibCURL", "NetworkOptions"] @@ -94,15 +94,14 @@ uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "7c365bdef6380b29cfc5caaf99688cd7489f9b87" +git-tree-sha1 = "8756f9935b7ccc9064c6eef0bff0ad643df733a3" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.12.2" +version = "0.12.7" [[Functors]] -deps = ["MacroTools"] -git-tree-sha1 = "4cd9e70bf8fce05114598b663ad79dfe9ae432b3" +git-tree-sha1 = "e4768c3b7f597d5a352afa09874d16e3c3f6ead2" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.2.3" +version = "0.2.7" [[IOCapture]] deps = ["Logging", "Random"] @@ -114,10 +113,16 @@ 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"] @@ -133,9 +138,9 @@ version = "0.21.2" [[KernelFunctions]] deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "Random", "Requires", "SpecialFunctions", "StatsBase", "TensorCore", "Test", "ZygoteRules"] -git-tree-sha1 = "6f46fb7fa868699dfbb6ae7973ba2825d3558ade" +git-tree-sha1 = "9c3d38dafc02feae68a4747813b8b0205fd03da5" uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" -version = "0.10.16" +version = "0.10.26" [[LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] @@ -161,19 +166,19 @@ deps = ["Libdl"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[LogExpFunctions]] -deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "3d682c07e6dd250ed082f883dc88aee7996bf2cc" +deps = ["ChainRulesCore", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "6193c3815f13ba1b78a51ce391db8be016ae9214" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.0" +version = "0.3.4" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "0fb723cd8c45858c22169b2e42269e53271a6df7" +git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.7" +version = "0.5.9" [[Markdown]] deps = ["Base64"] @@ -185,9 +190,9 @@ uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" [[Missings]] deps = ["DataAPI"] -git-tree-sha1 = "2ca267b08821e86c5ef4376cffed98a46c2cb205" +git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.0.1" +version = "1.0.2" [[Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" @@ -198,6 +203,10 @@ uuid = "14a3606d-f60d-562e-9121-12d972cd8159" [[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" @@ -217,9 +226,9 @@ version = "0.11.1" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "438d35d2d95ae2c5e8780b330592b6de8494e779" +git-tree-sha1 = "d911b6a12ba974dabe2291c6d450094a7226b372" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.0.3" +version = "2.1.1" [[Pkg]] deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] @@ -237,9 +246,9 @@ 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"] @@ -255,9 +264,9 @@ uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" version = "1.1.2" [[Reexport]] -git-tree-sha1 = "5f6c21241f0f655da3952fd60aa18477cf96c220" +git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" -version = "1.1.0" +version = "1.2.2" [[Requires]] deps = ["UUIDs"] @@ -301,10 +310,10 @@ 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" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -316,16 +325,16 @@ 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 = "fed1ec1e65749c4d96fc20dd13bea72b55457e62" +deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "eb35dcc66558b2dda84079b9a1be17557d32091a" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.9" +version = "0.33.12" [[StatsFuns]] -deps = ["IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "20d1bb720b9b27636280f751746ba4abb465f19d" +deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "95072ef1a22b057b1e80f73c2a89ad238ae4cfff" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.9" +version = "0.9.12" [[SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -362,9 +371,9 @@ 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/examples/regression-1d/Manifest.toml b/examples/regression-1d/Manifest.toml index 1ad33fe8..9c645dc6 100644 --- a/examples/regression-1d/Manifest.toml +++ b/examples/regression-1d/Manifest.toml @@ -1,10 +1,10 @@ # This file is machine-generated - editing it directly is not advised [[AbstractGPs]] -deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] +deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "PDMats", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] path = "../.." uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.2" +version = "0.5.3" [[AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] @@ -25,9 +25,9 @@ version = "3.3.1" [[AdvancedHMC]] deps = ["AbstractMCMC", "ArgCheck", "DocStringExtensions", "InplaceOps", "LinearAlgebra", "ProgressMeter", "Random", "Requires", "Setfield", "Statistics", "StatsBase", "StatsFuns", "UnPack"] -git-tree-sha1 = "c71d9da0b0e5183a3410066e6b85670b0ae2bdbe" +git-tree-sha1 = "0a655e9a59ee1c8bafc3af18e96d90f980b08600" uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" -version = "0.3.1" +version = "0.3.2" [[ArgCheck]] git-tree-sha1 = "dedbbb2ddb876f899585c4ec4433265e3017215a" @@ -39,9 +39,9 @@ uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "b8d49c34c3da35f220e7295659cd0bab8e739fed" +git-tree-sha1 = "a8101545d6b15ff1ebc927e877e28b0ab4bc4f16" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.33" +version = "3.1.36" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -80,9 +80,9 @@ version = "1.16.1+0" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "e8a30e8019a512e4b6c56ccebc065026624660e8" +git-tree-sha1 = "3533f5a691e60601fe60c90d8bc47a27aa2907ec" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.7.0" +version = "1.11.0" [[ColorSchemes]] deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"] @@ -184,9 +184,9 @@ version = "1.3.1" [[Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "9f46deb4d4ee4494ffb5a40a27a2aced67bdd838" +git-tree-sha1 = "09d9eaef9ef719d2cd5d928a191dc95be2ec8059" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.4" +version = "0.10.5" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -194,15 +194,15 @@ 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 = "d249ebaa67716b39f91cf6052daf073634013c0f" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.16" +version = "0.25.23" [[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"] @@ -210,9 +210,9 @@ uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" [[DynamicHMC]] deps = ["ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "Parameters", "ProgressMeter", "Random", "Statistics"] -git-tree-sha1 = "b60dcde7440787fb21cd8347edc5623cb89aace8" +git-tree-sha1 = "2222e7aa89dcc6d5df239417da1e65bfa6d5a638" uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb" -version = "3.1.0" +version = "3.1.1" [[EarCut_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -246,9 +246,9 @@ version = "4.4.0+0" [[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"] @@ -275,10 +275,10 @@ 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 = "63777916efbcb0ab6173d09a658fb7f2783de485" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.19" +version = "0.10.21" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -293,9 +293,9 @@ 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" [[Future]] deps = ["Random"] @@ -303,21 +303,21 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[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" [[GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "c2178cfbc0a5a552e16d097fae508f2024de61a3" +git-tree-sha1 = "d189c6d2004f63fd3c91748c458b09f26de0efaa" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.59.0" +version = "0.61.0" [[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 = "cafe0823979a5c9bff86224b3b8de29ea5a44b2e" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.59.0+0" +version = "0.61.0+0" [[GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -367,9 +367,9 @@ uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89" version = "0.2.2" [[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"] @@ -392,10 +392,16 @@ version = "0.3.0" 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" @@ -427,9 +433,9 @@ version = "2.1.0+0" [[KernelFunctions]] deps = ["ChainRulesCore", "Compat", "CompositionsBase", "Distances", "FillArrays", "Functors", "IrrationalConstants", "LinearAlgebra", "LogExpFunctions", "Random", "Requires", "SpecialFunctions", "StatsBase", "TensorCore", "Test", "ZygoteRules"] -git-tree-sha1 = "8be72e5494ee98ac1fc24f9e7db28508d030af3b" +git-tree-sha1 = "9c3d38dafc02feae68a4747813b8b0205fd03da5" uuid = "ec8451be-7e33-11e9-00cf-bbf324bd1392" -version = "0.10.20" +version = "0.10.26" [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -450,9 +456,9 @@ version = "1.2.1" [[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" [[LeftChildRightSiblingTrees]] deps = ["AbstractTrees"] @@ -539,9 +545,9 @@ 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" [[LogDensityProblems]] deps = ["ArgCheck", "BenchmarkTools", "DiffResults", "DocStringExtensions", "Random", "Requires", "TransformVariables", "UnPack"] @@ -550,10 +556,10 @@ uuid = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c" version = "0.10.6" [[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" @@ -566,9 +572,9 @@ version = "0.4.7" [[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"] @@ -680,9 +686,9 @@ version = "0.12.3" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "9d8c00ef7a8d110787ff6f170579846f776133a9" +git-tree-sha1 = "d911b6a12ba974dabe2291c6d450094a7226b372" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.0.4" +version = "2.1.1" [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -702,15 +708,15 @@ 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" +git-tree-sha1 = "ca7d534a27b1c279f05cd094196cb70c35e3d892" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.22.3" +version = "1.23.2" [[PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -808,9 +814,9 @@ uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" [[Setfield]] deps = ["ConstructionBase", "Future", "MacroTools", "Requires"] -git-tree-sha1 = "fca29e68c5062722b5b4435594c3d1ba557072a3" +git-tree-sha1 = "def0718ddbabeb5476e51e5a43609bee889f285d" uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" -version = "0.7.1" +version = "0.8.0" [[SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] @@ -837,9 +843,9 @@ 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" [[SplittablesBase]] deps = ["Setfield", "Test"] @@ -849,15 +855,15 @@ version = "0.1.14" [[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"] @@ -869,10 +875,10 @@ 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"] @@ -902,9 +908,9 @@ 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"] @@ -928,9 +934,9 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] -git-tree-sha1 = "dec7b7839f23efe21770b3b1307ca77c13ed631d" +git-tree-sha1 = "bccb153150744d476a6a8d4facf5299325d5a442" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.66" +version = "0.4.67" [[TransformVariables]] deps = ["ArgCheck", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "Pkg", "Random", "UnPack"] @@ -1117,9 +1123,9 @@ version = "1.5.0+0" [[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"] From 30a20b5bda3c080e6ffb2f042a33a5346f97a6c5 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 30 Mar 2022 10:21:06 +0300 Subject: [PATCH 08/20] revert change that is separated into #239 --- src/sparse_approximations.jl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/sparse_approximations.jl b/src/sparse_approximations.jl index 202e6821..984132a4 100644 --- a/src/sparse_approximations.jl +++ b/src/sparse_approximations.jl @@ -51,7 +51,7 @@ Intelligence and Statistics. 2009. function posterior(vfe::VFE, fx::FiniteGP, y::AbstractVector{<:Real}) @assert vfe.fz.f === fx.f - U_y = _cholesky(fx.Σy).U + U_y = _cholesky(_symmetric(fx.Σy)).U U = cholesky(_symmetric(cov(vfe.fz))).U B_εf = U' \ (U_y' \ cov(fx, vfe.fz))' @@ -85,7 +85,7 @@ function update_posterior( U = f_post_approx.data.U z = inducing_points(f_post_approx) - U_y₂ = _cholesky(fx.Σy).U + U_y₂ = _cholesky(_symmetric(fx.Σy)).U temp = zeros(size(f_post_approx.data.Σy, 1), size(fx.Σy, 2)) Σy = [f_post_approx.data.Σy temp; temp' fx.Σy] @@ -136,7 +136,7 @@ function update_posterior(f_post_approx::ApproxPosteriorGP{<:VFE}, fz::FiniteGP) Cu1f = cov(f_post_approx.prior, z_old, f_post_approx.data.x) Cu2f = cov(f_post_approx.prior, z, f_post_approx.data.x) - U_y = _cholesky(f_post_approx.data.Σy).U + U_y = _cholesky(_symmetric(f_post_approx.data.Σy)).U B_εf₂ = U22' \ (Cu2f * inv(U_y) - U12' * B_εf₁) B_εf = vcat(B_εf₁, B_εf₂) From 694fd36a8d0e16b11bb4db8631c3671be68b1843 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 30 Mar 2022 10:37:56 +0300 Subject: [PATCH 09/20] _symmetric(X::AbstractPDMat) = X --- src/util/common_covmat_ops.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/util/common_covmat_ops.jl b/src/util/common_covmat_ops.jl index b93be14d..b4218896 100644 --- a/src/util/common_covmat_ops.jl +++ b/src/util/common_covmat_ops.jl @@ -5,6 +5,7 @@ _symmetric(X) = Symmetric(X) _symmetric(X::Diagonal) = X _symmetric(X::Cholesky) = X +_symmetric(X::AbstractPDMat) = X # Small bit of indirection to work around a cholesky-related bug whereby the interaction # between `FillArrays` and `Diagonal` and `Cholesky` causes problems. From d41a59b249cae9e8e7a96f046393855a16dc1e1c Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 30 Mar 2022 10:40:13 +0300 Subject: [PATCH 10/20] restrict type parameter --- src/finite_gp_projection.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/finite_gp_projection.jl b/src/finite_gp_projection.jl index 6b9933c0..0e9e9d90 100644 --- a/src/finite_gp_projection.jl +++ b/src/finite_gp_projection.jl @@ -4,7 +4,7 @@ The finite-dimensional projection of the AbstractGP `f` at `x`. Assumed to be observed under Gaussian noise with zero mean and covariance matrix `Σy` """ -struct FiniteGP{Tf<:AbstractGP,Tx<:AbstractVector,TΣ} <: AbstractMvNormal +struct FiniteGP{Tf<:AbstractGP,Tx<:AbstractVector,TΣ<:AbstractMatrix} <: AbstractMvNormal f::Tf x::Tx Σy::TΣ From a0ae96d05c1fd83dda6cded1e4c4cbb32d81c905 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 30 Mar 2022 10:41:11 +0300 Subject: [PATCH 11/20] restrict further --- src/finite_gp_projection.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/finite_gp_projection.jl b/src/finite_gp_projection.jl index 0e9e9d90..fe2efd03 100644 --- a/src/finite_gp_projection.jl +++ b/src/finite_gp_projection.jl @@ -4,7 +4,7 @@ The finite-dimensional projection of the AbstractGP `f` at `x`. Assumed to be observed under Gaussian noise with zero mean and covariance matrix `Σy` """ -struct FiniteGP{Tf<:AbstractGP,Tx<:AbstractVector,TΣ<:AbstractMatrix} <: AbstractMvNormal +struct FiniteGP{Tf<:AbstractGP,Tx<:AbstractVector,TΣ<:AbstractMatrix{<:Real}} <: AbstractMvNormal f::Tf x::Tx Σy::TΣ From 03c46a5e8b957b5fe8db211f86d0e377e52083c0 Mon Sep 17 00:00:00 2001 From: st-- Date: Wed, 30 Mar 2022 14:17:05 +0300 Subject: [PATCH 12/20] Update src/finite_gp_projection.jl Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --- src/finite_gp_projection.jl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/finite_gp_projection.jl b/src/finite_gp_projection.jl index fe2efd03..4b396604 100644 --- a/src/finite_gp_projection.jl +++ b/src/finite_gp_projection.jl @@ -4,7 +4,8 @@ The finite-dimensional projection of the AbstractGP `f` at `x`. Assumed to be observed under Gaussian noise with zero mean and covariance matrix `Σy` """ -struct FiniteGP{Tf<:AbstractGP,Tx<:AbstractVector,TΣ<:AbstractMatrix{<:Real}} <: AbstractMvNormal +struct FiniteGP{Tf<:AbstractGP,Tx<:AbstractVector,TΣ<:AbstractMatrix{<:Real}} <: + AbstractMvNormal f::Tf x::Tx Σy::TΣ From 7127868a4a54814b6b59eb0cc539d070ce7cfdbe Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 30 Mar 2022 14:18:07 +0300 Subject: [PATCH 13/20] compat --- Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/Project.toml b/Project.toml index c88126ac..4de5b84f 100644 --- a/Project.toml +++ b/Project.toml @@ -24,6 +24,7 @@ Distributions = "0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25" FillArrays = "0.7, 0.8, 0.9, 0.10, 0.11, 0.12, 0.13" IrrationalConstants = "0.1" KernelFunctions = "0.9, 0.10" +PDMats = "0.11" RecipesBase = "1" Reexport = "0.2, 1" StatsBase = "0.33" From ab2c0a16f2da51dbba759ed784b2c9f20f4d8749 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 30 Mar 2022 14:19:48 +0300 Subject: [PATCH 14/20] compat --- test/Project.toml | 1 + 1 file changed, 1 insertion(+) diff --git a/test/Project.toml b/test/Project.toml index ccb51d1b..57222240 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -19,6 +19,7 @@ Distributions = "0.19, 0.20, 0.21, 0.22, 0.23, 0.24, 0.25" Documenter = "0.24, 0.25, 0.26, 0.27" FillArrays = "0.11, 0.12, 0.13" FiniteDifferences = "0.9.6, 0.10, 0.11, 0.12" +PDMats = "0.11" Plots = "1" Zygote = "0.5, 0.6" julia = "1.3" From de926ce1c43e79f646828795d08ac66e76281f0e Mon Sep 17 00:00:00 2001 From: st-- Date: Wed, 30 Mar 2022 14:24:22 +0300 Subject: [PATCH 15/20] Update src/sparse_approximations.jl Co-authored-by: David Widmann --- src/sparse_approximations.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/sparse_approximations.jl b/src/sparse_approximations.jl index 984132a4..5393a35f 100644 --- a/src/sparse_approximations.jl +++ b/src/sparse_approximations.jl @@ -290,5 +290,5 @@ function tr_Cf_invΣy(f::FiniteGP, Σy::Diagonal) end function tr_Cf_invΣy(f::FiniteGP, Σy::ScalMat) - return sum(var(f.f, f.x) / Σy) + return sum(var(f.f, f.x)) / Σy.value end From 569718c54af40187cf51ff18f7a9a6402ff7231d Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 30 Mar 2022 14:31:28 +0300 Subject: [PATCH 16/20] version bump --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 4de5b84f..930864b0 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "AbstractGPs" uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" authors = ["JuliaGaussianProcesses Team"] -version = "0.5.9" +version = "0.5.10" [deps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" From 3576ab3ae6449c6ab46a7e291de88b4158e2cf85 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 30 Mar 2022 14:31:56 +0300 Subject: [PATCH 17/20] fix Manifest --- examples/0-intro-1d/Manifest.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/examples/0-intro-1d/Manifest.toml b/examples/0-intro-1d/Manifest.toml index f1f9cb0e..8d4f1d31 100644 --- a/examples/0-intro-1d/Manifest.toml +++ b/examples/0-intro-1d/Manifest.toml @@ -4,10 +4,10 @@ julia_version = "1.7.1" manifest_format = "2.0" [[deps.AbstractGPs]] -deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "9a86aff5babfe1e4dbd79be47d7a9dfd141e11af" +deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "PDMats", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] +path = "../.." uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.9" +version = "0.5.10" [[deps.AbstractMCMC]] deps = ["BangBang", "ConsoleProgressMonitor", "Distributed", "Logging", "LoggingExtras", "ProgressLogging", "Random", "StatsBase", "TerminalLoggers", "Transducers"] From eeaee743b0cf3a45e05f01b13d51ef9e987b94dd Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 30 Mar 2022 15:01:03 +0300 Subject: [PATCH 18/20] remove "breaking" change, someone else can handle this elsewhere --- src/AbstractGPs.jl | 2 +- src/finite_gp_projection.jl | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/src/AbstractGPs.jl b/src/AbstractGPs.jl index 7279f94a..9792cbea 100644 --- a/src/AbstractGPs.jl +++ b/src/AbstractGPs.jl @@ -4,7 +4,7 @@ using ChainRulesCore using Distributions using FillArrays using LinearAlgebra -using PDMats: ScalMat +using PDMats: AbstractPDMat, ScalMat using Reexport @reexport using KernelFunctions using Random diff --git a/src/finite_gp_projection.jl b/src/finite_gp_projection.jl index 4b396604..6b9933c0 100644 --- a/src/finite_gp_projection.jl +++ b/src/finite_gp_projection.jl @@ -4,8 +4,7 @@ The finite-dimensional projection of the AbstractGP `f` at `x`. Assumed to be observed under Gaussian noise with zero mean and covariance matrix `Σy` """ -struct FiniteGP{Tf<:AbstractGP,Tx<:AbstractVector,TΣ<:AbstractMatrix{<:Real}} <: - AbstractMvNormal +struct FiniteGP{Tf<:AbstractGP,Tx<:AbstractVector,TΣ} <: AbstractMvNormal f::Tf x::Tx Σy::TΣ From 9321393e383f0d61226e57094f7605f40cd5efc7 Mon Sep 17 00:00:00 2001 From: ST John Date: Wed, 30 Mar 2022 22:44:17 +0300 Subject: [PATCH 19/20] update docs/Manifest --- docs/Manifest.toml | 310 ++++++++++++++++++++++++++------------------- 1 file changed, 178 insertions(+), 132 deletions(-) diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 900ac8d0..89f93bc1 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,384 +1,430 @@ # This file is machine-generated - editing it directly is not advised -[[ANSIColoredPrinters]] +manifest_format = "2.0" + +[[deps.ANSIColoredPrinters]] git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" version = "0.0.1" -[[AbstractGPs]] +[[deps.AbstractGPs]] deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "PDMats", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] path = ".." uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.3" +version = "0.5.10" -[[ArgTools]] +[[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" -[[Artifacts]] +[[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -[[Base64]] +[[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -[[ChainRulesCore]] +[[deps.Calculus]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" +uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" +version = "0.5.1" + +[[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "3533f5a691e60601fe60c90d8bc47a27aa2907ec" +git-tree-sha1 = "9950387274246d08af38f6eef8cb5480862a435f" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.11.0" +version = "1.14.0" -[[Compat]] +[[deps.ChangesOfVariables]] +deps = ["ChainRulesCore", "LinearAlgebra", "Test"] +git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1" +uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" +version = "0.1.2" + +[[deps.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 = "96b0bc6c52df76506efc8a441c6cf1adcb1babc4" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.39.0" +version = "3.42.0" -[[CompilerSupportLibraries_jll]] +[[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -[[CompositionsBase]] +[[deps.CompositionsBase]] git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" version = "0.1.1" -[[DataAPI]] +[[deps.DataAPI]] git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" version = "1.9.0" -[[DataStructures]] +[[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "7d9d316f04214f7efdbb6398d545446e246eff02" +git-tree-sha1 = "3daef5523dd2e769dad2365274f760ff5f282c7d" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.10" +version = "0.18.11" -[[Dates]] +[[deps.Dates]] deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -[[DelimitedFiles]] +[[deps.DelimitedFiles]] deps = ["Mmap"] uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" -[[Distances]] -deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "09d9eaef9ef719d2cd5d928a191dc95be2ec8059" +[[deps.DensityInterface]] +deps = ["InverseFunctions", "Test"] +git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" +uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" +version = "0.4.0" + +[[deps.Distances]] +deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.5" +version = "0.10.7" -[[Distributed]] +[[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" -[[Distributions]] -deps = ["ChainRulesCore", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"] -git-tree-sha1 = "d249ebaa67716b39f91cf6052daf073634013c0f" +[[deps.Distributions]] +deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] +git-tree-sha1 = 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+version = "0.11.7" -[[Parsers]] +[[deps.Parsers]] deps = ["Dates"] -git-tree-sha1 = "d911b6a12ba974dabe2291c6d450094a7226b372" +git-tree-sha1 = "85b5da0fa43588c75bb1ff986493443f821c70b7" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.1.1" +version = "2.2.3" -[[Pkg]] +[[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -[[Preferences]] +[[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "00cfd92944ca9c760982747e9a1d0d5d86ab1e5a" +git-tree-sha1 = "d3538e7f8a790dc8903519090857ef8e1283eecd" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.2.2" +version = "1.2.5" -[[Printf]] +[[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -[[QuadGK]] +[[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] git-tree-sha1 = "78aadffb3efd2155af139781b8a8df1ef279ea39" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" version = "2.4.2" -[[REPL]] +[[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -[[Random]] -deps = ["Serialization"] +[[deps.Random]] +deps = ["SHA", "Serialization"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -[[RecipesBase]] -git-tree-sha1 = "44a75aa7a527910ee3d1751d1f0e4148698add9e" +[[deps.RecipesBase]] +git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.1.2" +version = "1.2.1" -[[Reexport]] +[[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" version = "1.2.2" -[[Requires]] +[[deps.Requires]] deps = ["UUIDs"] -git-tree-sha1 = "4036a3bd08ac7e968e27c203d45f5fff15020621" +git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.1.3" +version = "1.3.0" -[[Rmath]] +[[deps.Rmath]] deps = ["Random", "Rmath_jll"] git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" version = "0.7.0" -[[Rmath_jll]] +[[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" version = "0.3.0+0" -[[SHA]] +[[deps.SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" -[[Serialization]] +[[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -[[SharedArrays]] +[[deps.SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" -[[Sockets]] +[[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -[[SortingAlgorithms]] +[[deps.SortingAlgorithms]] deps = ["DataStructures"] git-tree-sha1 = "b3363d7460f7d098ca0912c69b082f75625d7508" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" version = "1.0.1" -[[SparseArrays]] +[[deps.SparseArrays]] deps = ["LinearAlgebra", "Random"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -[[SpecialFunctions]] +[[deps.SpecialFunctions]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "f0bccf98e16759818ffc5d97ac3ebf87eb950150" +git-tree-sha1 = "5ba658aeecaaf96923dce0da9e703bd1fe7666f9" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "1.8.1" +version = "2.1.4" -[[Statistics]] +[[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -[[StatsAPI]] -git-tree-sha1 = "1958272568dc176a1d881acb797beb909c785510" +[[deps.StatsAPI]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "c3d8ba7f3fa0625b062b82853a7d5229cb728b6b" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.0.0" +version = "1.2.1" -[[StatsBase]] +[[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "eb35dcc66558b2dda84079b9a1be17557d32091a" +git-tree-sha1 = "8977b17906b0a1cc74ab2e3a05faa16cf08a8291" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.12" +version = "0.33.16" -[[StatsFuns]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "95072ef1a22b057b1e80f73c2a89ad238ae4cfff" +[[deps.StatsFuns]] +deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "25405d7016a47cf2bd6cd91e66f4de437fd54a07" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.12" +version = "0.9.16" -[[SuiteSparse]] +[[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" -[[TOML]] +[[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" -[[Tar]] +[[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" -[[TensorCore]] +[[deps.TensorCore]] deps = ["LinearAlgebra"] git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" version = "0.1.1" -[[Test]] +[[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -[[UUIDs]] +[[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -[[Unicode]] +[[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -[[Zlib_jll]] +[[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -[[ZygoteRules]] +[[deps.ZygoteRules]] deps = ["MacroTools"] git-tree-sha1 = "8c1a8e4dfacb1fd631745552c8db35d0deb09ea0" uuid = "700de1a5-db45-46bc-99cf-38207098b444" version = "0.2.2" -[[nghttp2_jll]] +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" + +[[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -[[p7zip_jll]] +[[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" From 9568b1a8360190fe207ed16cdd7e6360a4531080 Mon Sep 17 00:00:00 2001 From: ST John Date: Thu, 31 Mar 2022 10:49:00 +0300 Subject: [PATCH 20/20] update Manifests --- docs/Manifest.toml | 5 +- examples/0-intro-1d/Manifest.toml | 8 +- examples/1-mauna-loa/Manifest.toml | 12 +-- examples/2-deep-kernel-learning/Manifest.toml | 52 ++++++------- .../Manifest.toml | 76 +++++++++---------- 5 files changed, 77 insertions(+), 76 deletions(-) diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 89f93bc1..9c0b2bb0 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,5 +1,6 @@ # This file is machine-generated - editing it directly is not advised +julia_version = "1.7.1" manifest_format = "2.0" [[deps.ANSIColoredPrinters]] @@ -267,9 +268,9 @@ version = "0.11.7" [[deps.Parsers]] deps = ["Dates"] -git-tree-sha1 = "85b5da0fa43588c75bb1ff986493443f821c70b7" +git-tree-sha1 = "621f4f3b4977325b9128d5fae7a8b4829a0c2222" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.2.3" +version = "2.2.4" [[deps.Pkg]] deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] diff --git a/examples/0-intro-1d/Manifest.toml b/examples/0-intro-1d/Manifest.toml index 8d4f1d31..0eb89f79 100644 --- a/examples/0-intro-1d/Manifest.toml +++ b/examples/0-intro-1d/Manifest.toml @@ -722,9 +722,9 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates"] -git-tree-sha1 = "85b5da0fa43588c75bb1ff986493443f821c70b7" +git-tree-sha1 = "621f4f3b4977325b9128d5fae7a8b4829a0c2222" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.2.3" +version = "2.2.4" [[deps.Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -750,9 +750,9 @@ version = "1.2.0" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "5f6e1309595e95db24342e56cd4dabd2159e0b79" +git-tree-sha1 = "edec0846433f1c1941032385588fd57380b62b59" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.27.3" +version = "1.27.4" [[deps.PositiveFactorizations]] deps = ["LinearAlgebra"] diff --git a/examples/1-mauna-loa/Manifest.toml b/examples/1-mauna-loa/Manifest.toml index da0a8b73..bc35e6c8 100644 --- a/examples/1-mauna-loa/Manifest.toml +++ b/examples/1-mauna-loa/Manifest.toml @@ -44,9 +44,9 @@ version = "1.0.8+0" [[deps.CSV]] deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings"] -git-tree-sha1 = "9310d9495c1eb2e4fa1955dd478660e2ecab1fbb" +git-tree-sha1 = "873fb188a4b9d76549b81465b1f75c82aaf59238" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.3" +version = "0.10.4" [[deps.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"] @@ -689,9 +689,9 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates"] -git-tree-sha1 = "85b5da0fa43588c75bb1ff986493443f821c70b7" +git-tree-sha1 = "621f4f3b4977325b9128d5fae7a8b4829a0c2222" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.2.3" +version = "2.2.4" [[deps.Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -717,9 +717,9 @@ version = "1.2.0" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "5f6e1309595e95db24342e56cd4dabd2159e0b79" +git-tree-sha1 = "edec0846433f1c1941032385588fd57380b62b59" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.27.3" +version = "1.27.4" [[deps.PooledArrays]] deps = ["DataAPI", "Future"] diff --git a/examples/2-deep-kernel-learning/Manifest.toml b/examples/2-deep-kernel-learning/Manifest.toml index 7a756609..9aaaf40a 100644 --- a/examples/2-deep-kernel-learning/Manifest.toml +++ b/examples/2-deep-kernel-learning/Manifest.toml @@ -10,10 +10,10 @@ uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" version = "1.1.0" [[deps.AbstractGPs]] -deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] +deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "PDMats", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] path = "../.." uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.7" +version = "0.5.10" [[deps.AbstractTrees]] git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" @@ -84,9 +84,9 @@ version = "1.28.1" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "c9a6160317d1abe9c44b3beb367fd448117679ca" +git-tree-sha1 = "9950387274246d08af38f6eef8cb5480862a435f" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.13.0" +version = "1.14.0" [[deps.ChangesOfVariables]] deps = ["ChainRulesCore", "LinearAlgebra", "Test"] @@ -210,9 +210,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "c43e992f186abaf9965cc45e372f4693b7754b22" +git-tree-sha1 = "5a4168170ede913a2cd679e53c2123cb4b889795" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.52" +version = "0.25.53" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -226,9 +226,9 @@ uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" [[deps.DualNumbers]] deps = ["Calculus", "NaNMath", "SpecialFunctions"] -git-tree-sha1 = "90b158083179a6ccbce2c7eb1446d5bf9d7ae571" +git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" -version = "0.6.7" +version = "0.6.8" [[deps.EarCut_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -238,9 +238,9 @@ version = "2.2.3+0" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ae13fcbc7ab8f16b0856729b050ef0c446aa3492" +git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.4.4+0" +version = "2.4.8+0" [[deps.ExprTools]] git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d" @@ -336,15 +336,15 @@ version = "0.13.14" [[deps.GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "9f836fb62492f4b0f0d3b06f55983f2704ed0883" +git-tree-sha1 = "df5f5b0450c489fe6ed59a6c0a9804159c22684d" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.64.0" +version = "0.64.1" [[deps.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 = "a6c850d77ad5118ad3be4bd188919ce97fffac47" +git-tree-sha1 = "83578392343a7885147726712523c39edc714956" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.64.0+0" +version = "0.64.1+0" [[deps.GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -512,9 +512,9 @@ version = "1.3.0" [[deps.Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "4f00cc36fede3c04b8acf9b2e2763decfdcecfa6" +git-tree-sha1 = "6f14549f7760d84b2db7a9b10b88cd3cc3025730" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.13" +version = "0.15.14" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -749,9 +749,9 @@ version = "0.11.7" [[deps.Parsers]] deps = ["Dates"] -git-tree-sha1 = "85b5da0fa43588c75bb1ff986493443f821c70b7" +git-tree-sha1 = "621f4f3b4977325b9128d5fae7a8b4829a0c2222" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.2.3" +version = "2.2.4" [[deps.Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -777,15 +777,15 @@ version = "1.2.0" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "1690b713c3b460c955a2957cd7487b1b725878a7" +git-tree-sha1 = "edec0846433f1c1941032385588fd57380b62b59" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.27.1" +version = "1.27.4" [[deps.PooledArrays]] deps = ["DataAPI", "Future"] -git-tree-sha1 = "db3a23166af8aebf4db5ef87ac5b00d36eb771e2" +git-tree-sha1 = "28ef6c7ce353f0b35d0df0d5930e0d072c1f5b9b" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" -version = "1.4.0" +version = "1.4.1" [[deps.Preferences]] deps = ["TOML"] @@ -852,9 +852,9 @@ version = "1.2.1" [[deps.RecipesPipeline]] deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] -git-tree-sha1 = "995a812c6f7edea7527bb570f0ac39d0fb15663c" +git-tree-sha1 = "dc1e451e15d90347a7decc4221842a022b011714" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.5.1" +version = "0.5.2" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -934,9 +934,9 @@ version = "0.5.6" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "6976fab022fea2ffea3d945159317556e5dad87c" +git-tree-sha1 = "4f6ec5d99a28e1a749559ef7dd518663c5eca3d5" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.4.2" +version = "1.4.3" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] diff --git a/examples/3-parametric-heteroscedastic/Manifest.toml b/examples/3-parametric-heteroscedastic/Manifest.toml index c2e76c3c..1fc9e923 100644 --- a/examples/3-parametric-heteroscedastic/Manifest.toml +++ b/examples/3-parametric-heteroscedastic/Manifest.toml @@ -11,9 +11,9 @@ version = "1.1.0" [[deps.AbstractGPs]] deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "8706d50694fd8b12b331195d151575c3e5a0d9f7" +git-tree-sha1 = "9a86aff5babfe1e4dbd79be47d7a9dfd141e11af" uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.7" +version = "0.5.9" [[deps.AbstractGPsMakie]] deps = ["AbstractGPs", "LinearAlgebra", "Makie"] @@ -43,9 +43,9 @@ uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[deps.ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "d49f55ff9c7ee06930b0f65b1df2bfa811418475" +git-tree-sha1 = "6e8fada11bb015ecf9263f64b156f98b546918c7" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "4.0.4" +version = "5.0.5" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -84,9 +84,9 @@ version = "1.0.5" [[deps.CairoMakie]] deps = ["Base64", "Cairo", "Colors", "FFTW", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "SHA", "StaticArrays"] -git-tree-sha1 = "aedc7c910713eb616391cf95218277b714a7913f" +git-tree-sha1 = "4a0de4f5aa2d5d27a1efa293aeabb1a081e46b2b" uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" -version = "0.7.4" +version = "0.7.5" [[deps.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"] @@ -102,15 +102,15 @@ version = "0.5.1" [[deps.ChainRules]] deps = ["ChainRulesCore", "Compat", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics"] -git-tree-sha1 = "8aa3851bfd1e5fc9c584afe4fe6ebd3d440deddb" +git-tree-sha1 = "8b887daa6af5daf705081061e36386190204ac87" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.28.0" +version = "1.28.1" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "c9a6160317d1abe9c44b3beb367fd448117679ca" +git-tree-sha1 = "9950387274246d08af38f6eef8cb5480862a435f" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.13.0" +version = "1.14.0" [[deps.ChangesOfVariables]] deps = ["ChainRulesCore", "LinearAlgebra", "Test"] @@ -229,9 +229,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "9d3c0c762d4666db9187f363a76b47f7346e673b" +git-tree-sha1 = "5a4168170ede913a2cd679e53c2123cb4b889795" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.49" +version = "0.25.53" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -245,9 +245,9 @@ uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" [[deps.DualNumbers]] deps = ["Calculus", "NaNMath", "SpecialFunctions"] -git-tree-sha1 = "90b158083179a6ccbce2c7eb1446d5bf9d7ae571" +git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" -version = "0.6.7" +version = "0.6.8" [[deps.EarCut_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -257,15 +257,15 @@ version = "2.2.3+0" [[deps.EllipsisNotation]] deps = ["ArrayInterface"] -git-tree-sha1 = "d7ab55febfd0907b285fbf8dc0c73c0825d9d6aa" +git-tree-sha1 = "d064b0340db45d48893e7604ec95e7a2dc9da904" uuid = "da5c29d0-fa7d-589e-88eb-ea29b0a81949" -version = "1.3.0" +version = "1.5.0" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ae13fcbc7ab8f16b0856729b050ef0c446aa3492" +git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.4.4+0" +version = "2.4.8+0" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] @@ -299,9 +299,9 @@ version = "1.13.0" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "0dbc5b9683245f905993b51d2814202d75b34f1a" +git-tree-sha1 = "246621d23d1f43e3b9c368bf3b72b2331a27c286" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.1" +version = "0.13.2" [[deps.FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] @@ -347,9 +347,9 @@ version = "2.10.4+0" [[deps.FreeTypeAbstraction]] deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics", "StaticArrays"] -git-tree-sha1 = "770050893e7bc8a34915b4b9298604a3236de834" +git-tree-sha1 = "8e76bcd47f98ee25c8f8be4b9a1c60f48efa4f9e" uuid = "663a7486-cb36-511b-a19d-713bb74d65c9" -version = "0.9.5" +version = "0.9.7" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -478,9 +478,9 @@ version = "0.13.5" [[deps.IntervalSets]] deps = ["Dates", "EllipsisNotation", "Statistics"] -git-tree-sha1 = "3cc368af3f110a767ac786560045dceddfc16758" +git-tree-sha1 = "bcf640979ee55b652f3b01650444eb7bbe3ea837" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.5.3" +version = "0.5.4" [[deps.InverseFunctions]] deps = ["Test"] @@ -660,9 +660,9 @@ version = "0.5.9" [[deps.Makie]] deps = ["Animations", "Base64", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Distributions", "DocStringExtensions", "FFMPEG", "FileIO", "FixedPointNumbers", "Formatting", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MakieCore", "Markdown", "Match", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "Printf", "Random", "RelocatableFolders", "Serialization", "Showoff", "SignedDistanceFields", "SparseArrays", "StaticArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "UnicodeFun"] -git-tree-sha1 = "cd0fd02ab0d129f03515b7b68ca77fb670ef2e61" +git-tree-sha1 = "63de3b8a5c1f764e4e3a036c7752a632b4f0b8d1" uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" -version = "0.16.5" +version = "0.16.6" [[deps.MakieCore]] deps = ["Observables"] @@ -771,9 +771,9 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "648107615c15d4e09f7eca16307bc821c1f718d8" +git-tree-sha1 = "ab05aa4cc89736e95915b01e7279e61b1bfe33b8" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.13+0" +version = "1.1.14+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -848,9 +848,9 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates"] -git-tree-sha1 = "85b5da0fa43588c75bb1ff986493443f821c70b7" +git-tree-sha1 = "621f4f3b4977325b9128d5fae7a8b4829a0c2222" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.2.3" +version = "2.2.4" [[deps.Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -897,9 +897,9 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "afadeba63d90ff223a6a48d2009434ecee2ec9e8" +git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.1" +version = "1.7.2" [[deps.QOI]] deps = ["ColorTypes", "FileIO", "FixedPointNumbers"] @@ -1039,15 +1039,15 @@ version = "0.1.1" [[deps.Static]] deps = ["IfElse"] -git-tree-sha1 = "65068e4b4d10f3c31aaae2e6cb92b6c6cedca610" +git-tree-sha1 = "87e9954dfa33fd145694e42337bdd3d5b07021a6" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.5.6" +version = "0.6.0" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "74fb527333e72ada2dd9ef77d98e4991fb185f04" +git-tree-sha1 = "4f6ec5d99a28e1a749559ef7dd518663c5eca3d5" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.4.1" +version = "1.4.3" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -1213,9 +1213,9 @@ uuid = "83775a58-1f1d-513f-b197-d71354ab007a" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NaNMath", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "bf526aa30677f1dde58febc67cb9021aab5eb396" +git-tree-sha1 = "52adc0a505b6421a8668f13dcdb0c4cb498bd72c" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.36" +version = "0.6.37" [[deps.ZygoteRules]] deps = ["MacroTools"]