diff --git a/Project.toml b/Project.toml index 442f998a..197e6b3a 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "ArviZ" uuid = "131c737c-5715-5e2e-ad31-c244f01c1dc7" authors = ["Seth Axen "] -version = "0.3.1" +version = "0.3.2" [deps] Conda = "8f4d0f93-b110-5947-807f-2305c1781a2d" @@ -17,7 +17,7 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" [compat] CmdStan = "5.2.3, 6.0" Conda = "1.0" -MCMCChains = "0.3.15, 0.4.2, 1.0, 2.0" +MCMCChains = "0.3.15, 0.4.2, 1.0, 2.0, 3.0" MonteCarloMeasurements = "0.6.4, 0.7, 0.8" NamedTupleTools = "0.11.0, 0.12" Pandas = "1.3.0" diff --git a/docs/Manifest.toml b/docs/Manifest.toml index ac499143..2c74e7fe 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -19,9 +19,9 @@ uuid = "0bf59076-c3b1-5ca4-86bd-e02cd72cde3d" version = "0.2.7" [[ArgCheck]] -git-tree-sha1 = "e14de95bcfacd85e00f5369958a38bb72827bce2" +git-tree-sha1 = "59c256cf71c3982484ae4486ee86a3d7da891dea" uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" -version = "1.1.0" +version = "2.0.0" [[Arpack]] deps = ["Arpack_jll", "Libdl", "LinearAlgebra"] @@ -47,12 +47,6 @@ git-tree-sha1 = "bc779df8d73be70e4e05a63727d3a4dfb4c52b1f" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" version = "0.1.5" -[[ArviZ]] -deps = ["Markdown", "NamedTupleTools", "Pandas", "PyCall", "PyPlot", "REPL", "Requires", "StatsBase"] -path = "/Users/saxen/projects/ArviZ.jl" -uuid = "131c737c-5715-5e2e-ad31-c244f01c1dc7" -version = "0.2.5-DEV" - [[AxisArrays]] deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] git-tree-sha1 = "04f979dd266c708f478334e0a85785eab0558740" @@ -63,10 +57,10 @@ version = "0.4.2" uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[BenchmarkTools]] -deps = ["JSON", "Printf", "Statistics"] -git-tree-sha1 = "90b73db83791c5f83155016dd1cc1f684d4e1361" +deps = ["JSON", "Logging", "Printf", "Statistics", "UUIDs"] +git-tree-sha1 = "9e62e66db34540a0c919d72172cc2f642ac71260" uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "0.4.3" +version = "0.5.0" [[BinaryProvider]] deps = ["Libdl", "SHA"] @@ -98,18 +92,6 @@ git-tree-sha1 = "f81ec2bc1e4cbb95d65e04bd2cf621e1a0d32d06" uuid = "593b3428-ca2f-500c-ae53-031589ec8ddd" version = "6.0.2" -[[ColorTypes]] -deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "b9de8dc6106e09c79f3f776c27c62360d30e5eb8" -uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.9.1" - -[[Colors]] -deps = ["ColorTypes", "FixedPointNumbers", "InteractiveUtils", "Printf", "Reexport"] -git-tree-sha1 = "177d8b959d3c103a6d57574c38ee79c81059c31b" -uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.11.2" - [[Combinatorics]] deps = ["LinearAlgebra", "Polynomials", "Test"] git-tree-sha1 = "50b3ae4d643dc27eaff69fb6be06ee094d5500c9" @@ -156,12 +138,6 @@ git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464" version = "1.0.0" -[[DataValues]] -deps = ["DataValueInterfaces", "Dates"] -git-tree-sha1 = "d88a19299eba280a6d062e135a43f00323ae70bf" -uuid = "e7dc6d0d-1eca-5fa6-8ad6-5aecde8b7ea5" -version = "0.4.13" - [[Dates]] deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" @@ -206,9 +182,9 @@ version = "0.24.5" [[DynamicHMC]] deps = ["ArgCheck", "DocStringExtensions", "LinearAlgebra", "LogDensityProblems", "NLSolversBase", "Optim", "Parameters", "Random", "Statistics"] -git-tree-sha1 = "faed3874fcc953857edefbdd0e72cf6ad484cb17" +git-tree-sha1 = "970309540e8e8c30831c191f7967d2b64b050e2c" uuid = "bbc10e6e-7c05-544b-b16e-64fede858acb" -version = "2.1.4" +version = "2.1.5" [[EllipsisNotation]] git-tree-sha1 = "65dad386e877850e6fce4fc77f60fe75a468ce9d" @@ -223,20 +199,15 @@ version = "0.7.0" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "fec413d4fc547992eb62a5c544cedb6d7853c1f5" +git-tree-sha1 = "85c6b57e2680fa28d5c8adc798967377646fbf66" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.8.4" +version = "0.8.5" [[FiniteDiff]] deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "eb90294af97b564e6036b49296479d7f667763c0" +git-tree-sha1 = "aa78e468afa6a0fde472c3dba0782d1ab60b203d" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.2.0" - -[[FixedPointNumbers]] -git-tree-sha1 = "4aaea64dd0c30ad79037084f8ca2b94348e65eaa" -uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" -version = "0.7.1" +version = "2.2.1" [[FlexLinearAlgebra]] deps = ["LinearAlgebra", "Test"] @@ -244,6 +215,12 @@ git-tree-sha1 = "f2340868b95891c36bb643387326a7e336184ee4" uuid = "b67e1e5a-d13e-5892-ad81-fb75f5903773" version = "0.0.3" +[[Formatting]] +deps = ["Printf"] +git-tree-sha1 = "a0c901c29c0e7c763342751c0a94211d56c0de5c" +uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" +version = "0.4.1" + [[ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "NaNMath", "Random", "SpecialFunctions", "StaticArrays"] git-tree-sha1 = "88b082d492be6b63f967b6c96b352e25ced1a34c" @@ -322,18 +299,6 @@ git-tree-sha1 = "8868479ff35ab98588ed0a529a9c2a4f8bda3bd6" uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" version = "0.2.0" -[[LaTeXStrings]] -deps = ["Compat"] -git-tree-sha1 = "7ab9b8788cfab2bdde22adf9004bda7ad9954b6c" -uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.0.3" - -[[Lazy]] -deps = ["MacroTools"] -git-tree-sha1 = "0bd934e15f5df97414aa81abf74ba8a2d5042964" -uuid = "50d2b5c4-7a5e-59d5-8109-a42b560f39c0" -version = "0.15.0" - [[LazyArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "StaticArrays"] git-tree-sha1 = "6e818d550c2158def13c236c3b825fc14995160c" @@ -364,18 +329,18 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[LogDensityProblems]] deps = ["ArgCheck", "BenchmarkTools", "DiffResults", "DocStringExtensions", "Parameters", "Random", "Requires", "TransformVariables"] -git-tree-sha1 = "76f423d36cd44773b7e16d802da172a74c8fe2c4" +git-tree-sha1 = "77ac6c4bb1eae4072a5d0fcfba621020f7802cc2" uuid = "6fdf6af0-433a-55f7-b3ed-c6c6e0b8df7c" -version = "0.10.1" +version = "0.10.3" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[MCMCChains]] -deps = ["AbstractMCMC", "AxisArrays", "DataFrames", "Distributions", "LinearAlgebra", "Random", "RecipesBase", "Serialization", "SpecialFunctions", "Statistics", "StatsBase"] -git-tree-sha1 = "921ca164a84fa7b62721aeb1105c114dbc25dd4a" +deps = ["AbstractMCMC", "AxisArrays", "Distributions", "Formatting", "LinearAlgebra", "Random", "RecipesBase", "Requires", "Serialization", "SpecialFunctions", "Statistics", "StatsBase"] +git-tree-sha1 = "1c91ed3149171f326aa80816f229f7517ba32c5e" uuid = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" -version = "2.0.0" +version = "3.0.0" [[MLStyle]] git-tree-sha1 = "67f9a88611bc79f992aa705d9bbc833a2547dec7" @@ -403,9 +368,9 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[MonteCarloMeasurements]] deps = ["Distributed", "Distributions", "GenericLinearAlgebra", "LinearAlgebra", "MacroTools", "Random", "RecipesBase", "Requires", "StaticArrays", "Statistics", "StatsBase", "Test"] -git-tree-sha1 = "788251645c61fb8f144ddc87d59fa903c4453d1d" +git-tree-sha1 = "338a8bab4507c6b467c387570ecd24fe705f6afc" uuid = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" -version = "0.8.0" +version = "0.8.2" [[NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -459,12 +424,6 @@ git-tree-sha1 = "5f303510529486bb02ac4d70da8295da38302194" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" version = "0.9.11" -[[Pandas]] -deps = ["Compat", "DataValues", "IteratorInterfaceExtensions", "Lazy", "Pkg", "PyCall", "Statistics", "TableTraits", "TableTraitsUtils", "Test"] -git-tree-sha1 = "40b84de2260989a63792704014b99a86bb8f1425" -uuid = "eadc2687-ae89-51f9-a5d9-86b5a6373a9c" -version = "1.4.0" - [[Parameters]] deps = ["OrderedCollections"] git-tree-sha1 = "b62b2558efb1eef1fa44e4be5ff58a515c287e38" @@ -532,12 +491,6 @@ git-tree-sha1 = "ce0780857d129208c4e5a6d722486fb40ce11bf8" uuid = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" version = "1.91.3" -[[PyPlot]] -deps = ["Colors", "LaTeXStrings", "PyCall", "Sockets", "Test", "VersionParsing"] -git-tree-sha1 = "ccecc72cf5b41a5de686bd76999040050a8a3472" -uuid = "d330b81b-6aea-500a-939a-2ce795aea3ee" -version = "2.8.2" - [[QuadGK]] deps = ["DataStructures", "LinearAlgebra"] git-tree-sha1 = "dc84e810393cfc6294248c9032a9cdacc14a3db4" @@ -637,7 +590,7 @@ version = "0.3.1" [[Soss]] deps = ["AdvancedHMC", "DiffResults", "Distributions", "DynamicHMC", "FillArrays", "ForwardDiff", "GeneralizedGenerated", "Graphs", "IterTools", "LazyArrays", "LogDensityProblems", "MLStyle", "MacroTools", "MonteCarloMeasurements", "NamedTupleTools", "Printf", "PyCall", "Random", "RecipesBase", "Reexport", "ResumableFunctions", "ReverseDiff", "SimpleGraphs", "SimplePartitions", "SimplePosets", "SpecialFunctions", "Statistics", "StatsFuns", "SymPy", "TransformVariables"] -git-tree-sha1 = "49952b80168c0e10a85e9ce41f59b8f74f8a2774" +git-tree-sha1 = "2d4c3b3874d43060d400d9bbab4bcca9fe15b0d9" repo-rev = "master" repo-url = "https://github.com/cscherrer/Soss.jl.git" uuid = "8ce77f84-9b61-11e8-39ff-d17a774bf41c" @@ -665,9 +618,9 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics"] -git-tree-sha1 = "c53e809e63fe5cf5de13632090bc3520649c9950" +git-tree-sha1 = "be5c7d45daa449d12868f4466dbf5882242cf2d9" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.32.0" +version = "0.32.1" [[StatsFuns]] deps = ["Rmath", "SpecialFunctions"] @@ -681,9 +634,9 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[SymPy]] deps = ["LinearAlgebra", "PyCall", "RecipesBase", "SpecialFunctions"] -git-tree-sha1 = "75ecb5af3b7de5f72389bc4210107f66a158ee6e" +git-tree-sha1 = "05021fea82b12f1037a73cf72520ab325874488b" uuid = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" -version = "1.0.7" +version = "1.0.16" [[TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -691,17 +644,11 @@ git-tree-sha1 = "b1ad568ba658d8cbb3b892ed5380a6f3e781a81e" uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.0" -[[TableTraitsUtils]] -deps = ["DataValues", "IteratorInterfaceExtensions", "Missings", "TableTraits"] -git-tree-sha1 = "8fc12ae66deac83e44454e61b02c37b326493233" -uuid = "382cd787-c1b6-5bf2-a167-d5b971a19bda" -version = "1.0.1" - [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "22eea0f6619df63954b9404c8d47cd42c5d529f9" +git-tree-sha1 = "a54b8ce702aa863eced47bade03123d4dca0db84" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.0.1" +version = "1.0.2" [[Test]] deps = ["Distributed", "InteractiveUtils", "Logging", "Random"] @@ -709,9 +656,9 @@ uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[TransformVariables]] deps = ["ArgCheck", "DocStringExtensions", "ForwardDiff", "LinearAlgebra", "MacroTools", "Parameters", "Pkg", "Random"] -git-tree-sha1 = "dd4c257cb7a997bcabb5c5afbe62e544c1a750ce" +git-tree-sha1 = "df748ba8b73996f2b46fe9103b45f75a4a5561e0" uuid = "84d833dd-6860-57f9-a1a7-6da5db126cff" -version = "0.3.9" +version = "0.3.8" [[UUIDs]] deps = ["Random", "SHA"] diff --git a/docs/Project.toml b/docs/Project.toml index e9edfa15..4db9424d 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -5,3 +5,6 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" NamedTupleTools = "d9ec5142-1e00-5aa0-9d6a-321866360f50" Soss = "8ce77f84-9b61-11e8-39ff-d17a774bf41c" + +[compat] +MCMCChains = "3.0" diff --git a/docs/src/assets/turing_centered_eight_chains.jls b/docs/src/assets/turing_centered_eight_chains.jls index 457a9581..d77c5809 100644 Binary files a/docs/src/assets/turing_centered_eight_chains.jls and b/docs/src/assets/turing_centered_eight_chains.jls differ diff --git a/docs/src/quickstart.md b/docs/src/quickstart.md index 8498c97b..df1a720c 100644 --- a/docs/src/quickstart.md +++ b/docs/src/quickstart.md @@ -111,12 +111,13 @@ end param_mod = turing_model(J, y, σ) sampler = NUTS(nwarmup, 0.8) +rng = Random.MersenneTwister(5130) turing_chns = psample( param_mod, sampler, nwarmup + nsamples, nchains; - progress = true, + progress = false, ); ```