diff --git a/Project.toml b/Project.toml index e6900f3f..cf9bc29f 100644 --- a/Project.toml +++ b/Project.toml @@ -11,6 +11,7 @@ FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" GPLikelihoods = "6031954c-0455-49d7-b3b9-3e1c99afaf40" +IrrationalConstants = "92d709cd-6900-40b7-9082-c6be49f344b6" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" PDMats = "90014a1f-27ba-587c-ab20-58faa44d9150" Reexport = "189a3867-3050-52da-a836-e630ba90ab69" @@ -26,6 +27,7 @@ FastGaussQuadrature = "0.4" FillArrays = "0.12" ForwardDiff = "0.10" GPLikelihoods = "0.1, 0.2" +IrrationalConstants = "0.1" PDMats = "0.11" Reexport = "1" SpecialFunctions = "1, 2" diff --git a/examples/a-regression/Manifest.toml b/examples/a-regression/Manifest.toml index 8db5fb5c..003eb0fd 100644 --- a/examples/a-regression/Manifest.toml +++ b/examples/a-regression/Manifest.toml @@ -1,16 +1,16 @@ # This file is machine-generated - editing it directly is not advised [[AbstractFFTs]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "485ee0867925449198280d4af84bdb46a2a404d0" +deps = ["ChainRulesCore", "LinearAlgebra"] +git-tree-sha1 = "6f1d9bc1c08f9f4a8fa92e3ea3cb50153a1b40d4" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.0.1" +version = "1.1.0" [[AbstractGPs]] deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "e2af18922f65ea8cee7b8cd97a1668691f76f4b2" +git-tree-sha1 = "821d37c2f571ed5f2dfa028f03e324abd12f9910" uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.3" +version = "0.5.4" [[AbstractTrees]] git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" @@ -19,24 +19,24 @@ version = "0.3.4" [[Adapt]] deps = ["LinearAlgebra"] -git-tree-sha1 = "84918055d15b3114ede17ac6a7182f68870c16f7" +git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.1" +version = "3.3.3" [[ApproximateGPs]] -deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "KLDivergences", "LinearAlgebra", "PDMats", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] +deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "IrrationalConstants", "KLDivergences", "LinearAlgebra", "PDMats", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] path = "../.." uuid = "298c2ebc-0411-48ad-af38-99e88101b606" -version = "0.2.3" +version = "0.2.6" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "e527b258413e0c6d4f66ade574744c94edef81f8" +git-tree-sha1 = "1ee88c4c76caa995a885dc2f22a5d548dfbbc0ba" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.40" +version = "3.2.2" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -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 = "2c8329f16addffd09e6ca84c556e2185a4933c64" +git-tree-sha1 = "5bd05cd090588389201f7e1c703d50ace07be861" uuid = "052768ef-5323-5732-b1bb-66c8b64840ba" -version = "3.5.0" +version = "3.6.4" [[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"] @@ -75,15 +75,21 @@ version = "1.16.1+1" [[ChainRules]] deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "RealDot", "Statistics"] -git-tree-sha1 = "035ef8a5382a614b2d8e3091b6fdbb1c2b050e11" +git-tree-sha1 = "c6366ec79d9e62cd11030bba0945712eb4013712" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.12.1" +version = "1.17.0" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "f885e7e7c124f8c92650d61b9477b9ac2ee607dd" +git-tree-sha1 = "926870acb6cbcf029396f2f2de030282b6bc1941" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.11.1" +version = "1.11.4" + +[[ChangesOfVariables]] +deps = ["ChainRulesCore", "LinearAlgebra", "Test"] +git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1" +uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" +version = "0.1.2" [[CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] @@ -117,9 +123,9 @@ 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 = "dce3e3fea680869eaa0b774b2e8343e9ff442313" +git-tree-sha1 = "44c37b4636bc54afac5c574d2d02b625349d6582" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.40.0" +version = "3.41.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -143,9 +149,9 @@ version = "1.9.0" [[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" [[DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -160,6 +166,12 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" deps = ["Mmap"] uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" +[[DensityInterface]] +deps = ["InverseFunctions", "Test"] +git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" +uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" +version = "0.4.0" + [[DiffResults]] deps = ["StaticArrays"] git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805" @@ -168,25 +180,25 @@ version = "1.0.3" [[DiffRules]] deps = ["LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "3287dacf67c3652d3fed09f4c12c187ae4dbb89a" +git-tree-sha1 = "9bc5dac3c8b6706b58ad5ce24cffd9861f07c94f" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.4.0" +version = "1.9.0" [[Distances]] -deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "837c83e5574582e07662bbbba733964ff7c26b9d" +deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.6" +version = "0.10.7" [[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 = "72dcda9e19f88d09bf21b5f9507a0bb430bce2aa" +deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] +git-tree-sha1 = "6a8dc9f82e5ce28279b6e3e2cea9421154f5bd0d" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.24" +version = "0.25.37" [[DocStringExtensions]] deps = ["LibGit2"] @@ -229,9 +241,9 @@ version = "4.4.0+0" [[FastGaussQuadrature]] deps = ["LinearAlgebra", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "5829b25887e53fb6730a9df2ff89ed24baa6abf6" +git-tree-sha1 = "58d83dd5a78a36205bdfddb82b1bb67682e64487" uuid = "442a2c76-b920-505d-bb47-c5924d526838" -version = "0.4.7" +version = "0.4.9" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] @@ -264,10 +276,10 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "ef3fec65f9db26fa2cf8f4133c697c5b7ce63c1d" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "2b72a5624e289ee18256111657663721d59c143e" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.22" +version = "0.10.24" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -293,34 +305,34 @@ uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" version = "3.3.5+1" [[GPLikelihoods]] -deps = ["Distributions", "Functors", "LinearAlgebra", "Random", "StatsFuns"] -git-tree-sha1 = "bdfe8a65b3ca3aa92812d74138264570f33aa66e" +deps = ["Distributions", "Functors", "InverseFunctions", "LinearAlgebra", "Random", "StatsFuns", "Test"] +git-tree-sha1 = "ca3cc4ca49bf8dcf3f6e92f2e2fec8bdd8e8359c" uuid = "6031954c-0455-49d7-b3b9-3e1c99afaf40" -version = "0.2.4" +version = "0.2.6" [[GPUArrays]] deps = ["Adapt", "LinearAlgebra", "Printf", "Random", "Serialization", "Statistics"] -git-tree-sha1 = "7772508f17f1d482fe0df72cabc5b55bec06bbe0" +git-tree-sha1 = "d9681e61fbce7dde48684b40bdb1a319c4083be7" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.1.2" +version = "8.1.3" [[GPUCompiler]] deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "77d915a0af27d474f0aaf12fcd46c400a552e84c" +git-tree-sha1 = "2cac236070c2c4b36de54ae9146b55ee2c34ac7a" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.13.7" +version = "0.13.10" [[GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "30f2b340c2fff8410d89bfcdc9c0a6dd661ac5f7" +git-tree-sha1 = "b9a93bcdf34618031891ee56aad94cfff0843753" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.62.1" +version = "0.63.0" [[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 = "fd75fa3a2080109a2c0ec9864a6e14c60cca3866" +git-tree-sha1 = "f97acd98255568c3c9b416c5a3cf246c1315771b" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.62.0+0" +version = "0.63.0+0" [[GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -353,9 +365,9 @@ version = "1.0.2" [[HTTP]] deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] -git-tree-sha1 = "14eece7a3308b4d8be910e265c724a6ba51a9798" +git-tree-sha1 = "0fa77022fe4b511826b39c894c90daf5fce3334a" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.9.16" +version = "0.9.17" [[HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -371,9 +383,9 @@ version = "0.2.2" [[IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "95215cd0076a150ef46ff7928892bc341864c73c" +git-tree-sha1 = "006127162a51f0effbdfaab5ac0c83f8eb7ea8f3" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.3" +version = "0.4.4" [[IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -392,9 +404,9 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "f0c6489b12d28fb4c2103073ec7452f3423bd308" +git-tree-sha1 = "a7254c0acd8e62f1ac75ad24d5db43f5f19f3c65" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.1" +version = "0.1.2" [[IrrationalConstants]] git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" @@ -402,9 +414,9 @@ uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.1.1" [[IterTools]] -git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18" +git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.3.0" +version = "1.4.0" [[IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -455,15 +467,15 @@ version = "3.100.1+0" [[LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "46092047ca4edc10720ecab437c42283cd7c44f3" +git-tree-sha1 = "f8dcd7adfda0dddaf944e62476d823164cccc217" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "4.6.0" +version = "4.7.1" [[LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6a2af408fe809c4f1a54d2b3f188fdd3698549d6" +git-tree-sha1 = "62115afed394c016c2d3096c5b85c407b48be96b" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.11+0" +version = "0.0.13+1" [[LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -564,10 +576,10 @@ uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306" version = "2.9.4" [[LogExpFunctions]] -deps = ["ChainRulesCore", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "6193c3815f13ba1b78a51ce391db8be016ae9214" +deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "e5718a00af0ab9756305a0392832c8952c7426c1" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.4" +version = "0.3.6" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -617,29 +629,29 @@ uuid = "14a3606d-f60d-562e-9121-12d972cd8159" [[NNlib]] deps = ["Adapt", "ChainRulesCore", "Compat", "LinearAlgebra", "Pkg", "Requires", "Statistics"] -git-tree-sha1 = "5203a4532ad28c44f82c76634ad621d7c90abcbd" +git-tree-sha1 = "afcfd88042cc5a62743c98ca311668ff5c03148a" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.7.29" +version = "0.7.32" [[NNlibCUDA]] deps = ["CUDA", "LinearAlgebra", "NNlib", "Random", "Statistics"] -git-tree-sha1 = "04490d5e7570c038b1cb0f5c3627597181cc15a9" +git-tree-sha1 = "a2dc748c9f6615197b6b97c10bcce829830574c9" uuid = "a00861dc-f156-4864-bf3c-e6376f28a68d" -version = "0.1.9" +version = "0.1.11" [[NaNMath]] -git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb" +git-tree-sha1 = "f755f36b19a5116bb580de457cda0c140153f283" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.5" +version = "0.3.6" [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" [[Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "7937eda4681660b4d6aeeecc2f7e1c81c8ee4e2f" +git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" -version = "1.3.5+0" +version = "1.3.5+1" [[OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -647,9 +659,9 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112" [[OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "15003dcb7d8db3c6c857fda14891a539a8f2705a" +git-tree-sha1 = "648107615c15d4e09f7eca16307bc821c1f718d8" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.10+0" +version = "1.1.13+0" [[OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -676,15 +688,15 @@ version = "8.44.0+0" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "c8b8775b2f242c80ea85c83714c64ecfa3c53355" +git-tree-sha1 = "ee26b350276c51697c9c2d88a072b339f9f03d73" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.3" +version = "0.11.5" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "ae4bbcadb2906ccc085cf52ac286dc1377dceccc" +git-tree-sha1 = "d7fa6237da8004be601e19bd6666083056649918" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.1.2" +version = "2.1.3" [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -704,21 +716,21 @@ version = "2.0.1" [[PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "b084324b4af5a438cd63619fd006614b3b20b87b" +git-tree-sha1 = "68604313ed59f0408313228ba09e79252e4b2da8" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.0.15" +version = "1.1.2" [[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", "UnicodeFun"] -git-tree-sha1 = "7dc03c2b145168f5854085a16d054429d612b637" +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", "Unzip"] +git-tree-sha1 = "68e602f447344154f3b80f7d14bfb459a0f4dadf" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.23.5" +version = "1.25.5" [[Preferences]] deps = ["TOML"] -git-tree-sha1 = "00cfd92944ca9c760982747e9a1d0d5d86ab1e5a" +git-tree-sha1 = "2cf929d64681236a2e074ffafb8d568733d2e6af" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.2.2" +version = "1.2.3" [[Printf]] deps = ["Unicode"] @@ -767,9 +779,9 @@ uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" version = "0.1.0" [[RecipesBase]] -git-tree-sha1 = "44a75aa7a527910ee3d1751d1f0e4148698add9e" +git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.1.2" +version = "1.2.1" [[RecipesPipeline]] deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] @@ -784,9 +796,9 @@ version = "1.2.2" [[Requires]] deps = ["UUIDs"] -git-tree-sha1 = "4036a3bd08ac7e968e27c203d45f5fff15020621" +git-tree-sha1 = "8f82019e525f4d5c669692772a6f4b0a58b06a6a" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.1.3" +version = "1.2.0" [[Rmath]] deps = ["Random", "Rmath_jll"] @@ -843,36 +855,36 @@ version = "1.8.1" [[Static]] deps = ["IfElse"] -git-tree-sha1 = "e7bc80dc93f50857a5d1e3c8121495852f407e6a" +git-tree-sha1 = "7f5a513baec6f122401abfc8e9c074fdac54f6c1" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.4.0" +version = "0.4.1" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "3c76dde64d03699e074ac02eb2e8ba8254d428da" +git-tree-sha1 = "88a559da57529581472320892576a486fa2377b9" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.2.13" +version = "1.3.1" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[StatsAPI]] -git-tree-sha1 = "1958272568dc176a1d881acb797beb909c785510" +git-tree-sha1 = "d88665adc9bcf45903013af0982e2fd05ae3d0a6" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.0.0" +version = "1.2.0" [[StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "eb35dcc66558b2dda84079b9a1be17557d32091a" +git-tree-sha1 = "51383f2d367eb3b444c961d485c565e4c0cf4ba0" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.12" +version = "0.33.14" [[StatsFuns]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "95072ef1a22b057b1e80f73c2a89ad238ae4cfff" +deps = ["ChainRulesCore", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "bedb3e17cc1d94ce0e6e66d3afa47157978ba404" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.12" +version = "0.9.14" [[StructArrays]] deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] @@ -896,9 +908,9 @@ version = "1.0.1" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "fed34d0e71b91734bf0a7e10eb1bb05296ddbcd0" +git-tree-sha1 = "bb1064c9a84c52e277f1096cf41434b675cd368b" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.6.0" +version = "1.6.1" [[Tar]] deps = ["ArgTools", "SHA"] @@ -916,9 +928,9 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[TimerOutputs]] deps = ["ExprTools", "Printf"] -git-tree-sha1 = "7cb456f358e8f9d102a8b25e8dfedf58fa5689bc" +git-tree-sha1 = "a5aed757f65c8a1c64503bc4035f704d24c749bf" uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.13" +version = "0.5.14" [[TranscodingStreams]] deps = ["Random", "Test"] @@ -944,6 +956,11 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" +[[Unzip]] +git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670" +uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" +version = "0.1.2" + [[Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" @@ -951,10 +968,10 @@ uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" version = "1.19.0+0" [[Wayland_protocols_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll"] -git-tree-sha1 = "2839f1c1296940218e35df0bbb220f2a79686670" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "66d72dc6fcc86352f01676e8f0f698562e60510f" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" -version = "1.18.0+4" +version = "1.23.0+0" [[XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] @@ -1112,9 +1129,9 @@ 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 = "0fc9959bcabc4668c403810b4e851f6b8962eac9" +git-tree-sha1 = "78da1a0a69bcc86b33f7cb07bc1566c926412de3" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.29" +version = "0.6.33" [[ZygoteRules]] deps = ["MacroTools"] diff --git a/examples/b-classification/Manifest.toml b/examples/b-classification/Manifest.toml index 67972d0f..b05c2b14 100644 --- a/examples/b-classification/Manifest.toml +++ b/examples/b-classification/Manifest.toml @@ -1,37 +1,37 @@ # This file is machine-generated - editing it directly is not advised [[AbstractFFTs]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "485ee0867925449198280d4af84bdb46a2a404d0" +deps = ["ChainRulesCore", "LinearAlgebra"] +git-tree-sha1 = "6f1d9bc1c08f9f4a8fa92e3ea3cb50153a1b40d4" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.0.1" +version = "1.1.0" [[AbstractGPs]] deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "e2af18922f65ea8cee7b8cd97a1668691f76f4b2" +git-tree-sha1 = "821d37c2f571ed5f2dfa028f03e324abd12f9910" uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.3" +version = "0.5.4" [[Adapt]] deps = ["LinearAlgebra"] -git-tree-sha1 = "84918055d15b3114ede17ac6a7182f68870c16f7" +git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.1" +version = "3.3.3" [[ApproximateGPs]] -deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "KLDivergences", "LinearAlgebra", "PDMats", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] +deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "IrrationalConstants", "KLDivergences", "LinearAlgebra", "PDMats", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] path = "../.." uuid = "298c2ebc-0411-48ad-af38-99e88101b606" -version = "0.2.3" +version = "0.2.6" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "e527b258413e0c6d4f66ade574744c94edef81f8" +git-tree-sha1 = "d0d82f1c0b651173a4f839d84f662d03f3417740" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.40" +version = "4.0.0" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -53,15 +53,21 @@ version = "1.16.1+1" [[ChainRules]] deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "RealDot", "Statistics"] -git-tree-sha1 = "035ef8a5382a614b2d8e3091b6fdbb1c2b050e11" +git-tree-sha1 = "c6366ec79d9e62cd11030bba0945712eb4013712" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.12.1" +version = "1.17.0" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "f885e7e7c124f8c92650d61b9477b9ac2ee607dd" +git-tree-sha1 = "926870acb6cbcf029396f2f2de030282b6bc1941" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.11.1" +version = "1.11.4" + +[[ChangesOfVariables]] +deps = ["ChainRulesCore", "LinearAlgebra", "Test"] +git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1" +uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" +version = "0.1.2" [[ColorSchemes]] deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"] @@ -89,9 +95,9 @@ 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 = "dce3e3fea680869eaa0b774b2e8343e9ff442313" +git-tree-sha1 = "44c37b4636bc54afac5c574d2d02b625349d6582" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.40.0" +version = "3.41.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -115,9 +121,9 @@ version = "1.9.0" [[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" [[DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -132,6 +138,12 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" deps = ["Mmap"] uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" +[[DensityInterface]] +deps = ["InverseFunctions", "Test"] +git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" +uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" +version = "0.4.0" + [[DiffResults]] deps = ["StaticArrays"] git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805" @@ -140,25 +152,25 @@ version = "1.0.3" [[DiffRules]] deps = ["LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "3287dacf67c3652d3fed09f4c12c187ae4dbb89a" +git-tree-sha1 = "9bc5dac3c8b6706b58ad5ce24cffd9861f07c94f" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.4.0" +version = "1.9.0" [[Distances]] -deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "837c83e5574582e07662bbbba733964ff7c26b9d" +deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.6" +version = "0.10.7" [[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 = "72dcda9e19f88d09bf21b5f9507a0bb430bce2aa" +deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] +git-tree-sha1 = "6a8dc9f82e5ce28279b6e3e2cea9421154f5bd0d" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.24" +version = "0.25.37" [[DocStringExtensions]] deps = ["LibGit2"] @@ -196,9 +208,9 @@ version = "4.4.0+0" [[FastGaussQuadrature]] deps = ["LinearAlgebra", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "5829b25887e53fb6730a9df2ff89ed24baa6abf6" +git-tree-sha1 = "58d83dd5a78a36205bdfddb82b1bb67682e64487" uuid = "442a2c76-b920-505d-bb47-c5924d526838" -version = "0.4.7" +version = "0.4.9" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] @@ -208,9 +220,9 @@ version = "0.12.7" [[FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "8b3c09b56acaf3c0e581c66638b85c8650ee9dca" +git-tree-sha1 = "b374f22e8565a01d6e5db1e8640c3c5e3fe7d564" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.8.1" +version = "2.9.0" [[FixedPointNumbers]] deps = ["Statistics"] @@ -231,10 +243,10 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "ef3fec65f9db26fa2cf8f4133c697c5b7ce63c1d" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "2b72a5624e289ee18256111657663721d59c143e" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.22" +version = "0.10.24" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -260,22 +272,22 @@ uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" version = "3.3.5+1" [[GPLikelihoods]] -deps = ["Distributions", "Functors", "LinearAlgebra", "Random", "StatsFuns"] -git-tree-sha1 = "bdfe8a65b3ca3aa92812d74138264570f33aa66e" +deps = ["Distributions", "Functors", "InverseFunctions", "LinearAlgebra", "Random", "StatsFuns", "Test"] +git-tree-sha1 = "ca3cc4ca49bf8dcf3f6e92f2e2fec8bdd8e8359c" uuid = "6031954c-0455-49d7-b3b9-3e1c99afaf40" -version = "0.2.4" +version = "0.2.6" [[GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "30f2b340c2fff8410d89bfcdc9c0a6dd661ac5f7" +git-tree-sha1 = "b9a93bcdf34618031891ee56aad94cfff0843753" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.62.1" +version = "0.63.0" [[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 = "fd75fa3a2080109a2c0ec9864a6e14c60cca3866" +git-tree-sha1 = "f97acd98255568c3c9b416c5a3cf246c1315771b" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.62.0+0" +version = "0.63.0+0" [[GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -308,9 +320,9 @@ version = "1.0.2" [[HTTP]] deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] -git-tree-sha1 = "14eece7a3308b4d8be910e265c724a6ba51a9798" +git-tree-sha1 = "0fa77022fe4b511826b39c894c90daf5fce3334a" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.9.16" +version = "0.9.17" [[HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -326,9 +338,9 @@ version = "0.2.2" [[IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "95215cd0076a150ef46ff7928892bc341864c73c" +git-tree-sha1 = "006127162a51f0effbdfaab5ac0c83f8eb7ea8f3" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.3" +version = "0.4.4" [[IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -347,9 +359,9 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "f0c6489b12d28fb4c2103073ec7452f3423bd308" +git-tree-sha1 = "a7254c0acd8e62f1ac75ad24d5db43f5f19f3c65" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.1" +version = "0.1.2" [[IrrationalConstants]] git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" @@ -357,9 +369,9 @@ uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.1.1" [[IterTools]] -git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18" +git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.3.0" +version = "1.4.0" [[IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -503,10 +515,10 @@ uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306" version = "2.9.4" [[LogExpFunctions]] -deps = ["ChainRulesCore", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "6193c3815f13ba1b78a51ce391db8be016ae9214" +deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "e5718a00af0ab9756305a0392832c8952c7426c1" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.4" +version = "0.3.6" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -555,18 +567,18 @@ uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" version = "7.8.2" [[NaNMath]] -git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb" +git-tree-sha1 = "f755f36b19a5116bb580de457cda0c140153f283" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.5" +version = "0.3.6" [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" [[Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "7937eda4681660b4d6aeeecc2f7e1c81c8ee4e2f" +git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" -version = "1.3.5+0" +version = "1.3.5+1" [[OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -574,9 +586,9 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112" [[OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "15003dcb7d8db3c6c857fda14891a539a8f2705a" +git-tree-sha1 = "648107615c15d4e09f7eca16307bc821c1f718d8" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.10+0" +version = "1.1.13+0" [[OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -586,9 +598,9 @@ version = "0.5.5+0" [[Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "35d435b512fbab1d1a29138b5229279925eba369" +git-tree-sha1 = "916077e0f0f8966eb0dc98a5c39921fdb8f49eb4" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.5.0" +version = "1.6.0" [[Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -609,15 +621,15 @@ version = "8.44.0+0" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "c8b8775b2f242c80ea85c83714c64ecfa3c53355" +git-tree-sha1 = "ee26b350276c51697c9c2d88a072b339f9f03d73" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.3" +version = "0.11.5" [[ParameterHandling]] deps = ["ChainRulesCore", "Compat", "InverseFunctions", "IterTools", "LinearAlgebra", "LogExpFunctions", "SparseArrays", "Test"] -git-tree-sha1 = "603fde842910e6d33bfce2ce7d0e0a0851d8e21e" +git-tree-sha1 = "1e38f118bf4c0428b64f39a0722446f17e95f82a" uuid = "2412ca09-6db7-441c-8e3a-88d5709968c5" -version = "0.4.0" +version = "0.4.2" [[Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -627,9 +639,9 @@ version = "0.12.3" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "ae4bbcadb2906ccc085cf52ac286dc1377dceccc" +git-tree-sha1 = "d7fa6237da8004be601e19bd6666083056649918" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.1.2" +version = "2.1.3" [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -649,15 +661,15 @@ version = "2.0.1" [[PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "b084324b4af5a438cd63619fd006614b3b20b87b" +git-tree-sha1 = "68604313ed59f0408313228ba09e79252e4b2da8" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.0.15" +version = "1.1.2" [[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", "UnicodeFun"] -git-tree-sha1 = "7dc03c2b145168f5854085a16d054429d612b637" +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", "Unzip"] +git-tree-sha1 = "68e602f447344154f3b80f7d14bfb459a0f4dadf" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.23.5" +version = "1.25.5" [[PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -667,9 +679,9 @@ version = "0.2.4" [[Preferences]] deps = ["TOML"] -git-tree-sha1 = "00cfd92944ca9c760982747e9a1d0d5d86ab1e5a" +git-tree-sha1 = "2cf929d64681236a2e074ffafb8d568733d2e6af" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.2.2" +version = "1.2.3" [[Printf]] deps = ["Unicode"] @@ -702,9 +714,9 @@ uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" version = "0.1.0" [[RecipesBase]] -git-tree-sha1 = "44a75aa7a527910ee3d1751d1f0e4148698add9e" +git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.1.2" +version = "1.2.1" [[RecipesPipeline]] deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] @@ -719,9 +731,9 @@ version = "1.2.2" [[Requires]] deps = ["UUIDs"] -git-tree-sha1 = "4036a3bd08ac7e968e27c203d45f5fff15020621" +git-tree-sha1 = "8f82019e525f4d5c669692772a6f4b0a58b06a6a" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.1.3" +version = "1.2.0" [[Rmath]] deps = ["Random", "Rmath_jll"] @@ -778,36 +790,36 @@ version = "1.8.1" [[Static]] deps = ["IfElse"] -git-tree-sha1 = "e7bc80dc93f50857a5d1e3c8121495852f407e6a" +git-tree-sha1 = "b4912cd034cdf968e06ca5f943bb54b17b97793a" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.4.0" +version = "0.5.1" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "3c76dde64d03699e074ac02eb2e8ba8254d428da" +git-tree-sha1 = "88a559da57529581472320892576a486fa2377b9" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.2.13" +version = "1.3.1" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[StatsAPI]] -git-tree-sha1 = "1958272568dc176a1d881acb797beb909c785510" +git-tree-sha1 = "d88665adc9bcf45903013af0982e2fd05ae3d0a6" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.0.0" +version = "1.2.0" [[StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "eb35dcc66558b2dda84079b9a1be17557d32091a" +git-tree-sha1 = "51383f2d367eb3b444c961d485c565e4c0cf4ba0" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.12" +version = "0.33.14" [[StatsFuns]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "95072ef1a22b057b1e80f73c2a89ad238ae4cfff" +deps = ["ChainRulesCore", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "bedb3e17cc1d94ce0e6e66d3afa47157978ba404" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.12" +version = "0.9.14" [[StructArrays]] deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] @@ -831,9 +843,9 @@ version = "1.0.1" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "fed34d0e71b91734bf0a7e10eb1bb05296ddbcd0" +git-tree-sha1 = "bb1064c9a84c52e277f1096cf41434b675cd368b" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.6.0" +version = "1.6.1" [[Tar]] deps = ["ArgTools", "SHA"] @@ -872,6 +884,11 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" +[[Unzip]] +git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670" +uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" +version = "0.1.2" + [[Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" @@ -879,10 +896,10 @@ uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" version = "1.19.0+0" [[Wayland_protocols_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll"] -git-tree-sha1 = "2839f1c1296940218e35df0bbb220f2a79686670" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "66d72dc6fcc86352f01676e8f0f698562e60510f" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" -version = "1.18.0+4" +version = "1.23.0+0" [[XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] @@ -1034,9 +1051,9 @@ 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 = "0fc9959bcabc4668c403810b4e851f6b8962eac9" +git-tree-sha1 = "78da1a0a69bcc86b33f7cb07bc1566c926412de3" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.29" +version = "0.6.33" [[ZygoteRules]] deps = ["MacroTools"] diff --git a/examples/c-comparisons/Manifest.toml b/examples/c-comparisons/Manifest.toml index de5d6de3..ee971d03 100644 --- a/examples/c-comparisons/Manifest.toml +++ b/examples/c-comparisons/Manifest.toml @@ -1,37 +1,37 @@ # This file is machine-generated - editing it directly is not advised [[AbstractFFTs]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "485ee0867925449198280d4af84bdb46a2a404d0" +deps = ["ChainRulesCore", "LinearAlgebra"] +git-tree-sha1 = "6f1d9bc1c08f9f4a8fa92e3ea3cb50153a1b40d4" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.0.1" +version = "1.1.0" [[AbstractGPs]] deps = ["ChainRulesCore", "Distributions", "FillArrays", "IrrationalConstants", "KernelFunctions", "LinearAlgebra", "Random", "RecipesBase", "Reexport", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "e2af18922f65ea8cee7b8cd97a1668691f76f4b2" +git-tree-sha1 = "821d37c2f571ed5f2dfa028f03e324abd12f9910" uuid = "99985d1d-32ba-4be9-9821-2ec096f28918" -version = "0.5.3" +version = "0.5.4" [[Adapt]] deps = ["LinearAlgebra"] -git-tree-sha1 = "84918055d15b3114ede17ac6a7182f68870c16f7" +git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.1" +version = "3.3.3" [[ApproximateGPs]] -deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "KLDivergences", "LinearAlgebra", "PDMats", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] +deps = ["AbstractGPs", "ChainRulesCore", "Distributions", "FastGaussQuadrature", "FillArrays", "ForwardDiff", "GPLikelihoods", "IrrationalConstants", "KLDivergences", "LinearAlgebra", "PDMats", "Reexport", "SpecialFunctions", "Statistics", "StatsBase"] path = "../.." uuid = "298c2ebc-0411-48ad-af38-99e88101b606" -version = "0.2.3" +version = "0.2.6" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "e527b258413e0c6d4f66ade574744c94edef81f8" +git-tree-sha1 = "d0d82f1c0b651173a4f839d84f662d03f3417740" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.40" +version = "4.0.0" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -53,15 +53,21 @@ version = "1.16.1+1" [[ChainRules]] deps = ["ChainRulesCore", "Compat", "LinearAlgebra", "Random", "RealDot", "Statistics"] -git-tree-sha1 = "035ef8a5382a614b2d8e3091b6fdbb1c2b050e11" +git-tree-sha1 = "c6366ec79d9e62cd11030bba0945712eb4013712" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.12.1" +version = "1.17.0" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "f885e7e7c124f8c92650d61b9477b9ac2ee607dd" +git-tree-sha1 = "926870acb6cbcf029396f2f2de030282b6bc1941" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.11.1" +version = "1.11.4" + +[[ChangesOfVariables]] +deps = ["ChainRulesCore", "LinearAlgebra", "Test"] +git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1" +uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" +version = "0.1.2" [[ColorSchemes]] deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"] @@ -89,9 +95,9 @@ 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 = "dce3e3fea680869eaa0b774b2e8343e9ff442313" +git-tree-sha1 = "44c37b4636bc54afac5c574d2d02b625349d6582" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.40.0" +version = "3.41.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -115,9 +121,9 @@ version = "1.9.0" [[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" [[DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -132,6 +138,12 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" deps = ["Mmap"] uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" +[[DensityInterface]] +deps = ["InverseFunctions", "Test"] +git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" +uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" +version = "0.4.0" + [[DiffResults]] deps = ["StaticArrays"] git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805" @@ -140,25 +152,25 @@ version = "1.0.3" [[DiffRules]] deps = ["LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "3287dacf67c3652d3fed09f4c12c187ae4dbb89a" +git-tree-sha1 = "9bc5dac3c8b6706b58ad5ce24cffd9861f07c94f" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.4.0" +version = "1.9.0" [[Distances]] -deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "837c83e5574582e07662bbbba733964ff7c26b9d" +deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.6" +version = "0.10.7" [[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 = "72dcda9e19f88d09bf21b5f9507a0bb430bce2aa" +deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] +git-tree-sha1 = "6a8dc9f82e5ce28279b6e3e2cea9421154f5bd0d" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.24" +version = "0.25.37" [[DocStringExtensions]] deps = ["LibGit2"] @@ -196,9 +208,9 @@ version = "4.4.0+0" [[FastGaussQuadrature]] deps = ["LinearAlgebra", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "5829b25887e53fb6730a9df2ff89ed24baa6abf6" +git-tree-sha1 = "58d83dd5a78a36205bdfddb82b1bb67682e64487" uuid = "442a2c76-b920-505d-bb47-c5924d526838" -version = "0.4.7" +version = "0.4.9" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] @@ -208,9 +220,9 @@ version = "0.12.7" [[FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "8b3c09b56acaf3c0e581c66638b85c8650ee9dca" +git-tree-sha1 = "b374f22e8565a01d6e5db1e8640c3c5e3fe7d564" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.8.1" +version = "2.9.0" [[FixedPointNumbers]] deps = ["Statistics"] @@ -231,10 +243,10 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "ef3fec65f9db26fa2cf8f4133c697c5b7ce63c1d" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "2b72a5624e289ee18256111657663721d59c143e" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.22" +version = "0.10.24" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -260,22 +272,22 @@ uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" version = "3.3.5+1" [[GPLikelihoods]] -deps = ["Distributions", "Functors", "LinearAlgebra", "Random", "StatsFuns"] -git-tree-sha1 = "bdfe8a65b3ca3aa92812d74138264570f33aa66e" +deps = ["Distributions", "Functors", "InverseFunctions", "LinearAlgebra", "Random", "StatsFuns", "Test"] +git-tree-sha1 = "ca3cc4ca49bf8dcf3f6e92f2e2fec8bdd8e8359c" uuid = "6031954c-0455-49d7-b3b9-3e1c99afaf40" -version = "0.2.4" +version = "0.2.6" [[GR]] deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "30f2b340c2fff8410d89bfcdc9c0a6dd661ac5f7" +git-tree-sha1 = "b9a93bcdf34618031891ee56aad94cfff0843753" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.62.1" +version = "0.63.0" [[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 = "fd75fa3a2080109a2c0ec9864a6e14c60cca3866" +git-tree-sha1 = "f97acd98255568c3c9b416c5a3cf246c1315771b" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.62.0+0" +version = "0.63.0+0" [[GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -308,9 +320,9 @@ version = "1.0.2" [[HTTP]] deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] -git-tree-sha1 = "14eece7a3308b4d8be910e265c724a6ba51a9798" +git-tree-sha1 = "0fa77022fe4b511826b39c894c90daf5fce3334a" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.9.16" +version = "0.9.17" [[HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -326,9 +338,9 @@ version = "0.2.2" [[IRTools]] deps = ["InteractiveUtils", "MacroTools", "Test"] -git-tree-sha1 = "95215cd0076a150ef46ff7928892bc341864c73c" +git-tree-sha1 = "006127162a51f0effbdfaab5ac0c83f8eb7ea8f3" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.3" +version = "0.4.4" [[IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -347,9 +359,9 @@ uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "f0c6489b12d28fb4c2103073ec7452f3423bd308" +git-tree-sha1 = "a7254c0acd8e62f1ac75ad24d5db43f5f19f3c65" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.1" +version = "0.1.2" [[IrrationalConstants]] git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" @@ -357,9 +369,9 @@ uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.1.1" [[IterTools]] -git-tree-sha1 = "05110a2ab1fc5f932622ffea2a003221f4782c18" +git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.3.0" +version = "1.4.0" [[IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" @@ -503,10 +515,10 @@ uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306" version = "2.9.4" [[LogExpFunctions]] -deps = ["ChainRulesCore", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "6193c3815f13ba1b78a51ce391db8be016ae9214" +deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "e5718a00af0ab9756305a0392832c8952c7426c1" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.4" +version = "0.3.6" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -555,18 +567,18 @@ uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" version = "7.8.2" [[NaNMath]] -git-tree-sha1 = "bfe47e760d60b82b66b61d2d44128b62e3a369fb" +git-tree-sha1 = "f755f36b19a5116bb580de457cda0c140153f283" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.5" +version = "0.3.6" [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" [[Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "7937eda4681660b4d6aeeecc2f7e1c81c8ee4e2f" +git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" -version = "1.3.5+0" +version = "1.3.5+1" [[OpenLibm_jll]] deps = ["Artifacts", "Libdl"] @@ -574,9 +586,9 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112" [[OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "15003dcb7d8db3c6c857fda14891a539a8f2705a" +git-tree-sha1 = "648107615c15d4e09f7eca16307bc821c1f718d8" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.10+0" +version = "1.1.13+0" [[OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -586,9 +598,9 @@ version = "0.5.5+0" [[Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "35d435b512fbab1d1a29138b5229279925eba369" +git-tree-sha1 = "916077e0f0f8966eb0dc98a5c39921fdb8f49eb4" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.5.0" +version = "1.6.0" [[Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -609,9 +621,9 @@ version = "8.44.0+0" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "c8b8775b2f242c80ea85c83714c64ecfa3c53355" +git-tree-sha1 = "ee26b350276c51697c9c2d88a072b339f9f03d73" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.3" +version = "0.11.5" [[Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -621,9 +633,9 @@ version = "0.12.3" [[Parsers]] deps = ["Dates"] -git-tree-sha1 = "ae4bbcadb2906ccc085cf52ac286dc1377dceccc" +git-tree-sha1 = "d7fa6237da8004be601e19bd6666083056649918" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.1.2" +version = "2.1.3" [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -643,15 +655,15 @@ version = "2.0.1" [[PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "b084324b4af5a438cd63619fd006614b3b20b87b" +git-tree-sha1 = "68604313ed59f0408313228ba09e79252e4b2da8" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.0.15" +version = "1.1.2" [[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", "UnicodeFun"] -git-tree-sha1 = "7dc03c2b145168f5854085a16d054429d612b637" +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", "Unzip"] +git-tree-sha1 = "68e602f447344154f3b80f7d14bfb459a0f4dadf" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.23.5" +version = "1.25.5" [[PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -661,9 +673,9 @@ version = "0.2.4" [[Preferences]] deps = ["TOML"] -git-tree-sha1 = "00cfd92944ca9c760982747e9a1d0d5d86ab1e5a" +git-tree-sha1 = "2cf929d64681236a2e074ffafb8d568733d2e6af" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.2.2" +version = "1.2.3" [[Printf]] deps = ["Unicode"] @@ -696,9 +708,9 @@ uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9" version = "0.1.0" [[RecipesBase]] -git-tree-sha1 = "44a75aa7a527910ee3d1751d1f0e4148698add9e" +git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.1.2" +version = "1.2.1" [[RecipesPipeline]] deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] @@ -713,9 +725,9 @@ version = "1.2.2" [[Requires]] deps = ["UUIDs"] -git-tree-sha1 = "4036a3bd08ac7e968e27c203d45f5fff15020621" +git-tree-sha1 = "8f82019e525f4d5c669692772a6f4b0a58b06a6a" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.1.3" +version = "1.2.0" [[Rmath]] deps = ["Random", "Rmath_jll"] @@ -772,36 +784,36 @@ version = "1.8.1" [[Static]] deps = ["IfElse"] -git-tree-sha1 = "e7bc80dc93f50857a5d1e3c8121495852f407e6a" +git-tree-sha1 = "b4912cd034cdf968e06ca5f943bb54b17b97793a" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.4.0" +version = "0.5.1" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "3c76dde64d03699e074ac02eb2e8ba8254d428da" +git-tree-sha1 = "88a559da57529581472320892576a486fa2377b9" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.2.13" +version = "1.3.1" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[StatsAPI]] -git-tree-sha1 = "1958272568dc176a1d881acb797beb909c785510" +git-tree-sha1 = "d88665adc9bcf45903013af0982e2fd05ae3d0a6" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.0.0" +version = "1.2.0" [[StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "eb35dcc66558b2dda84079b9a1be17557d32091a" +git-tree-sha1 = "51383f2d367eb3b444c961d485c565e4c0cf4ba0" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.12" +version = "0.33.14" [[StatsFuns]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "95072ef1a22b057b1e80f73c2a89ad238ae4cfff" +deps = ["ChainRulesCore", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "bedb3e17cc1d94ce0e6e66d3afa47157978ba404" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.12" +version = "0.9.14" [[StructArrays]] deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] @@ -825,9 +837,9 @@ version = "1.0.1" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "fed34d0e71b91734bf0a7e10eb1bb05296ddbcd0" +git-tree-sha1 = "bb1064c9a84c52e277f1096cf41434b675cd368b" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.6.0" +version = "1.6.1" [[Tar]] deps = ["ArgTools", "SHA"] @@ -866,6 +878,11 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" +[[Unzip]] +git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670" +uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" +version = "0.1.2" + [[Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" @@ -873,10 +890,10 @@ uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" version = "1.19.0+0" [[Wayland_protocols_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll"] -git-tree-sha1 = "2839f1c1296940218e35df0bbb220f2a79686670" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "66d72dc6fcc86352f01676e8f0f698562e60510f" uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" -version = "1.18.0+4" +version = "1.23.0+0" [[XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] @@ -1028,9 +1045,9 @@ 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 = "0fc9959bcabc4668c403810b4e851f6b8962eac9" +git-tree-sha1 = "78da1a0a69bcc86b33f7cb07bc1566c926412de3" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.29" +version = "0.6.33" [[ZygoteRules]] deps = ["MacroTools"] diff --git a/src/ApproximateGPs.jl b/src/ApproximateGPs.jl index ce26b625..20f46acf 100644 --- a/src/ApproximateGPs.jl +++ b/src/ApproximateGPs.jl @@ -12,6 +12,7 @@ using SpecialFunctions using ChainRulesCore using FillArrays using PDMats: chol_lower +using IrrationalConstants: sqrt2, invsqrtπ using AbstractGPs: AbstractGP, FiniteGP, LatentFiniteGP, ApproxPosteriorGP, At_A, diag_At_A diff --git a/src/expected_loglik.jl b/src/expected_loglik.jl index c29ff3bb..cdc9f443 100644 --- a/src/expected_loglik.jl +++ b/src/expected_loglik.jl @@ -65,6 +65,7 @@ function expected_loglik( return sum(lls) / mc.n_samples end +# Compute the expected_loglik over a collection of observations and marginal distributions function expected_loglik( gh::GaussHermite, y::AbstractVector, q_f::AbstractVector{<:Normal}, lik ) @@ -72,10 +73,27 @@ function expected_loglik( # using a reparameterisation by change of variable # (see e.g. en.wikipedia.org/wiki/Gauss%E2%80%93Hermite_quadrature) xs, ws = gausshermite(gh.n_points) - # size(fs): (length(y), n_points) - fs = √2 * std.(q_f) .* xs' .+ mean.(q_f) - lls = loglikelihood.(lik.(fs), y) - return sum((1 / √π) * lls * ws) + return sum(Broadcast.instantiate( + Broadcast.broadcasted(y, q_f) do yᵢ, q_fᵢ # Loop over every pair + # of marginal distribution q(fᵢ) and observation yᵢ + expected_loglik(gh, yᵢ, q_fᵢ, lik, (xs, ws)) + end, + )) +end + +# Compute the expected_loglik for one observation and a marginal distributions +function expected_loglik( + gh::GaussHermite, y, q_f::Normal, lik, (xs, ws)=gausshermite(gh.n_points) +) + μ = mean(q_f) + σ̃ = sqrt2 * std(q_f) + return invsqrtπ * sum(Broadcast.instantiate( + Broadcast.broadcasted(xs, ws) do x, w # Loop over every + # pair of Gauss-Hermite point x with weight w + f = σ̃ * x + μ + loglikelihood(lik(f), y) * w + end, + )) end ChainRulesCore.@non_differentiable gausshermite(n) diff --git a/test/expected_loglik.jl b/test/expected_loglik.jl index 715a595e..b8c34124 100644 --- a/test/expected_loglik.jl +++ b/test/expected_loglik.jl @@ -45,4 +45,43 @@ GaussHermite(), zeros(10), q_f, GaussianLikelihood() ) isa Real @test ApproximateGPs._default_quadrature(θ -> Normal(0, θ)) isa GaussHermite + + @testset "testing Zygote compatibility with GaussHermite" begin # see issue #82 + N = 10 + gh = GaussHermite(12) + μs = randn(rng, N) + σs = rand(rng, N) + # Test differentiation with variational parameters + for lik in likelihoods_to_test + y = rand.(rng, lik.(rand.(Normal.(μs, σs)))) + gμ, glogσ = Zygote.gradient(μs, log.(σs)) do μ, logσ + ApproximateGPs.expected_loglik(gh, y, Normal.(μ, exp.(logσ)), lik) + end + @test all(isfinite, gμ) + @test all(isfinite, glogσ) + end + # Test differentiation with likelihood parameters + # Test GaussianLikelihood parameter + σ = 1.0 + y = randn(rng, N) + glogσ = only( + Zygote.gradient(log(σ)) do x + ApproximateGPs.expected_loglik( + gh, y, Normal.(μs, σs), GaussianLikelihood(exp(x)) + ) + end, + ) + @test isfinite(glogσ) + # Test GammaLikelihood parameter + α = 2.0 + y = rand.(rng, Gamma.(α, rand(N))) + glogα = only( + Zygote.gradient(log(α)) do x + ApproximateGPs.expected_loglik( + gh, y, Normal.(μs, σs), GammaLikelihood(exp(x)) + ) + end, + ) + @test isfinite(glogα) + end end