From e7b3db5a4bb09e0c7dcdffc82a51461e084faa54 Mon Sep 17 00:00:00 2001 From: David Widmann Date: Wed, 8 Sep 2021 08:12:25 +0200 Subject: [PATCH] Fix order of parameters (#332) * Fix order of parameters * Add test * Bump version * Update docs/Manifest.toml --- Project.toml | 4 +- docs/Manifest.toml | 161 +++++++++++++++++++++-------------------- src/MCMCChains.jl | 2 + src/chains.jl | 2 +- test/sections_tests.jl | 6 ++ 5 files changed, 95 insertions(+), 80 deletions(-) diff --git a/Project.toml b/Project.toml index 835616a4..b9df09a8 100644 --- a/Project.toml +++ b/Project.toml @@ -3,7 +3,7 @@ uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" keywords = ["markov chain monte carlo", "probablistic programming"] license = "MIT" desc = "Chain types and utility functions for MCMC simulations." -version = "5.0.0" +version = "5.0.1" [deps] AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001" @@ -18,6 +18,7 @@ LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" MCMCDiagnosticTools = "be115224-59cd-429b-ad48-344e309966f0" MLJModelInterface = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" NaturalSort = "c020b1a1-e9b0-503a-9c33-f039bfc54a85" +OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" @@ -40,6 +41,7 @@ KernelDensity = "0.6.2" MCMCDiagnosticTools = "0.1" MLJModelInterface = "0.3.5, 0.4, 1.0" NaturalSort = "1" +OrderedCollections = "1.4" PrettyTables = "0.9, 0.10, 0.11, 0.12, 1" RecipesBase = "0.7, 0.8, 1.0" SpecialFunctions = "^0.8, 0.9, 0.10, 1.0" diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 6301fbdb..cabd983f 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -50,9 +50,9 @@ version = "3.5.0+3" [[ArrayInterface]] deps = ["IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "b6dec2ed4f10840e2cf836508525656450d4d289" +git-tree-sha1 = "019303a0f26d6012f35ecdfa4618551d145fb9f2" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.1.26" +version = "3.1.31" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -85,15 +85,15 @@ version = "0.1.1" [[Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c3598e525718abcc440f69cc6d5f60dda0a1b61e" +git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.6+5" +version = "1.0.8+0" [[Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "e2f47f6d8337369411569fd45ae5753ca10394c6" +git-tree-sha1 = "f2202b55d816427cd385a9a4f3ffb226bee80f99" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.16.0+6" +version = "1.16.1+0" [[CategoricalArrays]] deps = ["DataAPI", "Future", "JSON", "Missings", "Printf", "RecipesBase", "Statistics", "StructTypes", "Unicode"] @@ -103,9 +103,9 @@ version = "0.10.0" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "bdc0937269321858ab2a4f288486cb258b9a0af7" +git-tree-sha1 = "30ee06de5ff870b45c78f529a6b093b3323256a3" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.3.0" +version = "1.3.1" [[Clustering]] deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "SparseArrays", "Statistics", "StatsBase"] @@ -187,9 +187,9 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.0.4" [[DataAPI]] -git-tree-sha1 = "ee400abb2298bd13bfc3df1c412ed228061a2385" +git-tree-sha1 = "bec2532f8adb82005476c141ec23e921fc20971b" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.7.0" +version = "1.8.0" [[DataFrames]] deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] @@ -229,19 +229,19 @@ uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" [[Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "abe4ad222b26af3337262b8afb28fab8d215e9f8" +git-tree-sha1 = "9f46deb4d4ee4494ffb5a40a27a2aced67bdd838" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.3" +version = "0.10.4" [[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 = "f389cb8974e02d7eaa6ae2ccedbbfb43174cd8e8" +deps = ["ChainRulesCore", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns"] +git-tree-sha1 = "f4efaa4b5157e0cdb8283ae0b5428bc9208436ed" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.14" +version = "0.25.16" [[DocStringExtensions]] deps = ["LibGit2"] @@ -251,9 +251,9 @@ version = "0.8.5" [[Documenter]] deps = ["ANSIColoredPrinters", "Base64", "Dates", "DocStringExtensions", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"] -git-tree-sha1 = "350dced36c11f794c6c4da5dc6493ec894e50c16" +git-tree-sha1 = "fe0bc46b27cd3413df55859152fd70e50744025f" uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4" -version = "0.27.5" +version = "0.27.6" [[Downloads]] deps = ["ArgTools", "LibCURL", "NetworkOptions"] @@ -261,9 +261,9 @@ uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" [[EarCut_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "92d8f9f208637e8d2d28c664051a00569c01493d" +git-tree-sha1 = "3f3a2501fa7236e9b911e0f7a588c657e822bb6d" uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" -version = "2.1.5+1" +version = "2.2.3+0" [[EllipsisNotation]] deps = ["ArrayInterface"] @@ -284,10 +284,10 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" version = "0.4.1" [[FFMPEG_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "LibVPX_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "3cc57ad0a213808473eafef4845a74766242e05f" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +git-tree-sha1 = "d8a578692e3077ac998b50c0217dfd67f21d1e5f" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.3.1+4" +version = "4.4.0+0" [[FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] @@ -303,9 +303,9 @@ version = "3.3.9+8" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "7c365bdef6380b29cfc5caaf99688cd7489f9b87" +git-tree-sha1 = "a3b7b041753094f3b17ffa9d2e2e07d8cace09cd" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.12.2" +version = "0.12.3" [[FixedPointNumbers]] deps = ["Statistics"] @@ -315,9 +315,9 @@ version = "0.8.4" [[Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "35895cf184ceaab11fd778b4590144034a167a2f" +git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.1+14" +version = "2.13.93+0" [[Formatting]] deps = ["Printf"] @@ -327,9 +327,9 @@ version = "0.4.2" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "cbd58c9deb1d304f5a245a0b7eb841a2560cfec6" +git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.10.1+5" +version = "2.10.4+0" [[FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -355,9 +355,9 @@ version = "0.58.1" [[GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "d59e8320c2747553788e4fc42231489cc602fa50" +git-tree-sha1 = "ef49a187604f865f4708c90e3f431890724e9012" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.58.1+0" +version = "0.59.0+0" [[Gadfly]] deps = ["Base64", "CategoricalArrays", "Colors", "Compose", "Contour", "CoupledFields", "DataAPI", "DataStructures", "Dates", "Distributions", "DocStringExtensions", "Hexagons", "IndirectArrays", "IterTools", "JSON", "Juno", "KernelDensity", "LinearAlgebra", "Loess", "Measures", "Printf", "REPL", "Random", "Requires", "Showoff", "Statistics"] @@ -385,6 +385,12 @@ git-tree-sha1 = "7bf67e9a481712b3dbe9cb3dac852dc4b1162e02" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" version = "2.68.3+0" +[[Graphite2_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" +uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" +version = "1.3.14+0" + [[Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" @@ -392,9 +398,15 @@ version = "1.0.2" [[HTTP]] deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] -git-tree-sha1 = "44e3b40da000eab4ccb1aecdc4801c040026aeb5" +git-tree-sha1 = "60ed5f1643927479f845b0135bb369b031b541fa" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.9.13" +version = "0.9.14" + +[[HarfBuzz_jll]] +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] +git-tree-sha1 = "8a954fed8ac097d5be04921d595f741115c1b2ad" +uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" +version = "2.8.1+0" [[Hexagons]] deps = ["Test"] @@ -452,10 +464,9 @@ uuid = "8197267c-284f-5f27-9208-e0e47529a953" version = "0.5.3" [[InvertedIndices]] -deps = ["Test"] -git-tree-sha1 = "15732c475062348b0165684ffe28e85ea8396afc" +git-tree-sha1 = "bee5f1ef5bf65df56bdd2e40447590b272a5471f" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.0.0" +version = "1.1.0" [[IrrationalConstants]] git-tree-sha1 = "f76424439413893a832026ca355fe273e93bce94" @@ -556,12 +567,6 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" -[[LibVPX_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "12ee7e23fa4d18361e7c2cde8f8337d4c3101bc7" -uuid = "dd192d2f-8180-539f-9fb4-cc70b1dcf69a" -version = "1.10.0+0" - [[Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" @@ -624,10 +629,10 @@ uuid = "4345ca2d-374a-55d4-8d30-97f9976e7612" version = "0.5.3" [[LogExpFunctions]] -deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "3d682c07e6dd250ed082f883dc88aee7996bf2cc" +deps = ["ChainRulesCore", "DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "1f5097e3bce576e1cdf6dc9f051ab8c6e196b29e" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.0" +version = "0.3.1" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -645,10 +650,10 @@ uuid = "30fc2ffe-d236-52d8-8643-a9d8f7c094a7" version = "0.7.2" [[MCMCChains]] -deps = ["AbstractMCMC", "AxisArrays", "Compat", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "PrettyTables", "Random", "RecipesBase", "Serialization", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] +deps = ["AbstractMCMC", "AxisArrays", "Compat", "Dates", "Distributions", "Formatting", "IteratorInterfaceExtensions", "KernelDensity", "LinearAlgebra", "MCMCDiagnosticTools", "MLJModelInterface", "NaturalSort", "OrderedCollections", "PrettyTables", "Random", "RecipesBase", "Serialization", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "TableTraits", "Tables"] path = ".." uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "5.0.0" +version = "5.0.1" [[MCMCDiagnosticTools]] deps = ["AbstractFFTs", "DataAPI", "Distributions", "LinearAlgebra", "MLJModelInterface", "Random", "SpecialFunctions", "Statistics", "StatsBase", "Tables"] @@ -664,15 +669,15 @@ version = "2021.1.1+1" [[MLJBase]] deps = ["CategoricalArrays", "ComputationalResources", "Dates", "DelimitedFiles", "Distributed", "Distributions", "InteractiveUtils", "InvertedIndices", "LinearAlgebra", "LossFunctions", "MLJModelInterface", "Missings", "OrderedCollections", "Parameters", "PrettyTables", "ProgressMeter", "Random", "ScientificTypes", "StatisticalTraits", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "c0e721c7ab80d37e9eb87ef69361e212a12e3f37" +git-tree-sha1 = "2554ee676eb46432afa45f50ab7a131aa0d5aeeb" uuid = "a7f614a8-145f-11e9-1d2a-a57a1082229d" -version = "0.18.19" +version = "0.18.20" [[MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "0c2bcd5c5b99988bb88552a4408beb3da1f1fd4d" +git-tree-sha1 = "1b780b191a65dbefc42d2a225850d20b243dde88" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.2.0" +version = "1.3.0" [[MLJXGBoostInterface]] deps = ["MLJModelInterface", "Tables", "XGBoost"] @@ -761,9 +766,9 @@ version = "0.4.0" [[OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "c0f4a4836e5f3e0763243b8324200af6d0e0f90c" +git-tree-sha1 = "c870a0d713b51e4b49be6432eff0e26a4325afee" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.10.5" +version = "1.10.6" [[Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -846,21 +851,21 @@ version = "2.0.1" [[PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "c67334c786157d6ef091ce622b365d3d60b1e2c4" +git-tree-sha1 = "9ff1c70190c1c30aebca35dc489f7411b256cd23" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.0.12" +version = "1.0.13" [[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 = "0036d433cacff4767ff622be3cb2c281b773a2b4" +git-tree-sha1 = "2dbafeadadcf7dadff20cd60046bba416b4912be" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.21.1" +version = "1.21.3" [[PooledArrays]] deps = ["DataAPI", "Future"] -git-tree-sha1 = "cde4ce9d6f33219465b55162811d8de8139c0414" +git-tree-sha1 = "a193d6ad9c45ada72c14b731a318bedd3c2f00cf" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" -version = "1.2.1" +version = "1.3.0" [[Preferences]] deps = ["TOML"] @@ -932,9 +937,9 @@ version = "1.1.2" [[RecipesPipeline]] deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] -git-tree-sha1 = "32efa73dece357e9c834cae8af00265752c80061" +git-tree-sha1 = "1f27772b89958deed68d2709e5f08a5e5f59a5af" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.3.5" +version = "0.3.7" [[Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1031,9 +1036,9 @@ version = "0.1.13" [[Static]] deps = ["IfElse"] -git-tree-sha1 = "62701892d172a2fa41a1f829f66d2b0db94a9a63" +git-tree-sha1 = "854b024a4a81b05c0792a4b45293b85db228bd27" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.3.0" +version = "0.3.1" [[StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] @@ -1058,15 +1063,15 @@ version = "1.0.0" [[StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "fed1ec1e65749c4d96fc20dd13bea72b55457e62" +git-tree-sha1 = "8cbbc098554648c84f79a463c9ff0fd277144b6c" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.9" +version = "0.33.10" [[StatsFuns]] -deps = ["IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "20d1bb720b9b27636280f751746ba4abb465f19d" +deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "46d7ccc7104860c38b11966dd1f72ff042f382e4" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.9" +version = "0.9.10" [[StatsPlots]] deps = ["Clustering", "DataStructures", "DataValues", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] @@ -1082,9 +1087,9 @@ version = "0.6.1" [[StructTypes]] deps = ["Dates", "UUIDs"] -git-tree-sha1 = "e36adc471280e8b346ea24c5c87ba0571204be7a" +git-tree-sha1 = "8445bf99a36d703a09c601f9a57e2f83000ef2ae" uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" -version = "1.7.2" +version = "1.7.3" [[SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -1340,16 +1345,16 @@ uuid = "700de1a5-db45-46bc-99cf-38207098b444" version = "0.2.1" [[libass_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "acc685bcf777b2202a904cdcb49ad34c2fa1880c" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" -version = "0.14.0+4" +version = "0.15.1+0" [[libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "7a5780a0d9c6864184b3a2eeeb833a0c871f00ab" +git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "0.1.6+4" +version = "2.0.2+0" [[libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -1373,15 +1378,15 @@ uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" [[x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d713c1ce4deac133e3334ee12f4adff07f81778f" +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2020.7.14+2" +version = "2021.5.5+0" [[x265_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "487da2f8f2f0c8ee0e83f39d13037d6bbf0a45ab" +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.0.0+3" +version = "3.5.0+0" [[xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] diff --git a/src/MCMCChains.jl b/src/MCMCChains.jl index 65d20257..a1208466 100644 --- a/src/MCMCChains.jl +++ b/src/MCMCChains.jl @@ -13,9 +13,11 @@ using Dates using KernelDensity: kde, pdf import StatsBase: autocov, counts, sem, AbstractWeights, autocor, describe, quantile, sample, summarystats, cov + import MCMCDiagnosticTools import MLJModelInterface import NaturalSort +import OrderedCollections import PrettyTables import StatsFuns import Tables diff --git a/src/chains.jl b/src/chains.jl index 0db00f21..a4708313 100644 --- a/src/chains.jl +++ b/src/chains.jl @@ -57,7 +57,7 @@ function Chains( end # Store unassigned variables. - unassigned = Set(Symbol[]) + unassigned = OrderedCollections.OrderedSet{Symbol}() # Check that all parameters are assigned. for param in parameter_names diff --git a/test/sections_tests.jl b/test/sections_tests.jl index 5e240220..1f463073 100644 --- a/test/sections_tests.jl +++ b/test/sections_tests.jl @@ -1,5 +1,11 @@ using MCMCChains, Test +# https://github.com/TuringLang/AdvancedMH.jl/pull/63 +@testset "order of parameters" begin + chains = Chains(rand(2, 10, 4), vcat(["μ[$i]" for i in 1:9], :lp), (internals=[:lp],)) + @test names(chains, :parameters) == [Symbol("μ[$i]") for i in 1:9] +end + @testset "describe sections" begin a3d = rand(500, 9, 4)