diff --git a/.github/workflows/Docs.yml b/.github/workflows/Docs.yml index de2bb0e3..0400696b 100644 --- a/.github/workflows/Docs.yml +++ b/.github/workflows/Docs.yml @@ -16,8 +16,10 @@ jobs: - uses: julia-actions/setup-julia@v1 with: version: '1' - - run: julia --project=docs -e 'using Pkg; Pkg.instantiate()' - - run: julia --project=docs docs/make.jl + - name: Install dependencies + run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()' + - name: Build and deploy + run: julia --project=docs docs/make.jl env: GKSwstype: nul GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} diff --git a/docs/Manifest.toml b/docs/Manifest.toml deleted file mode 100644 index cabd983f..00000000 --- a/docs/Manifest.toml +++ /dev/null @@ -1,1395 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -[[ANSIColoredPrinters]] -git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" -uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" -version = "0.0.1" - 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-[[XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "1acf5bdf07aa0907e0a37d3718bb88d4b687b74a" -uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.9.12+0" - -[[XSLT_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a" -uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.34+0" - -[[Xorg_libX11_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] -git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" -uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" -version = "1.6.9+4" - -[[Xorg_libXau_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" -uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.9+4" - -[[Xorg_libXcursor_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] -git-tree-sha1 = "12e0eb3bc634fa2080c1c37fccf56f7c22989afd" -uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" -version = "1.2.0+4" - -[[Xorg_libXdmcp_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" -uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.3+4" - -[[Xorg_libXext_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" -uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" -version = "1.3.4+4" - -[[Xorg_libXfixes_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "0e0dc7431e7a0587559f9294aeec269471c991a4" -uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" -version = "5.0.3+4" - -[[Xorg_libXi_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] -git-tree-sha1 = "89b52bc2160aadc84d707093930ef0bffa641246" -uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" -version = "1.7.10+4" - -[[Xorg_libXinerama_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll"] -git-tree-sha1 = "26be8b1c342929259317d8b9f7b53bf2bb73b123" -uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" -version = "1.1.4+4" - -[[Xorg_libXrandr_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll"] -git-tree-sha1 = "34cea83cb726fb58f325887bf0612c6b3fb17631" -uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" -version = "1.5.2+4" - -[[Xorg_libXrender_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" -uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.10+4" - -[[Xorg_libpthread_stubs_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" -uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.0+3" - -[[Xorg_libxcb_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" -uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.13.0+3" - -[[Xorg_libxkbfile_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" -uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" -version = "1.1.0+4" - -[[Xorg_xcb_util_image_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" -uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" -version = "0.4.0+1" - -[[Xorg_xcb_util_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] -git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" -uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" -version = "0.4.0+1" - -[[Xorg_xcb_util_keysyms_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" -uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" -version = "0.4.0+1" - -[[Xorg_xcb_util_renderutil_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" -uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" -version = "0.3.9+1" - -[[Xorg_xcb_util_wm_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" -uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" -version = "0.4.1+1" - -[[Xorg_xkbcomp_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] -git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" -uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" -version = "1.4.2+4" - -[[Xorg_xkeyboard_config_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] -git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" -uuid = "33bec58e-1273-512f-9401-5d533626f822" -version = "2.27.0+4" - -[[Xorg_xtrans_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" -uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.4.0+3" - -[[Zlib_jll]] -deps = ["Libdl"] -uuid = "83775a58-1f1d-513f-b197-d71354ab007a" - -[[Zstd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "cc4bf3fdde8b7e3e9fa0351bdeedba1cf3b7f6e6" -uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.0+0" - -[[ZygoteRules]] -deps = ["MacroTools"] -git-tree-sha1 = "9e7a1e8ca60b742e508a315c17eef5211e7fbfd7" -uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.1" - -[[libass_jll]] -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 = "0.15.1+0" - -[[libfdk_aac_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" -uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.2+0" - -[[libpng_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" -uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.38+0" - -[[libvorbis_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "c45f4e40e7aafe9d086379e5578947ec8b95a8fb" -uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+0" - -[[nghttp2_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" - -[[p7zip_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" - -[[x264_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" -uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2021.5.5+0" - -[[x265_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" -uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.5.0+0" - -[[xkbcommon_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6" -uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "0.9.1+5" diff --git a/docs/Project.toml b/docs/Project.toml index d665a5d7..f53dbe5a 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -5,16 +5,16 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" Gadfly = "c91e804a-d5a3-530f-b6f0-dfbca275c004" MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d" -MLJXGBoostInterface = "54119dfa-1dab-4055-a167-80440f4f7a91" +MLJDecisionTreeInterface = "c6f25543-311c-4c74-83dc-3ea6d1015661" StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" [compat] CategoricalArrays = "0.8, 0.9, 0.10" DataFrames = "0.22, 1" Documenter = "0.26, 0.27" -Gadfly = "1.3" +Gadfly = "1.3.4" MCMCChains = "5" MLJBase = "0.18" -MLJXGBoostInterface = "0.1" +MLJDecisionTreeInterface = "0.1.3" StatsPlots = "0.14" -julia = "1.3" +julia = "1.7" diff --git a/docs/make.jl b/docs/make.jl index e9279243..a4b2b865 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -29,12 +29,6 @@ makedocs( modules = [MCMCChains], strict = true, checkdocs = :exports, - # https://github.com/JuliaLang/julia/pull/37085#issuecomment-683356098 - doctestfilters = [ - r"{([a-zA-Z0-9]+,\s?)+[a-zA-Z0-9]+}", - r"(Array{[a-zA-Z0-9]+,\s?1}|Vector{[a-zA-Z0-9]+})", - r"(Array{[a-zA-Z0-9]+,\s?2}|Matrix{[a-zA-Z0-9]+})", - ] ) deploydocs(repo = "github.com/TuringLang/MCMCChains.jl.git", push_preview=true) diff --git a/src/chains.jl b/src/chains.jl index a4708313..583aaf6e 100644 --- a/src/chains.jl +++ b/src/chains.jl @@ -210,10 +210,10 @@ Passing `flatten=true` will return a `NamedTuple` with keys ungrouped. julia> chn = Chains([1:2 3:4]); julia> get(chn, :param_1) -(param_1 = [1; 2],) +(param_1 = [1; 2;;],) julia> get(chn, [:param_2]) -(param_2 = [3; 4],) +(param_2 = [3; 4;;],) julia> get(chn, :param_1; flatten=true) (param_1 = 1,) @@ -258,10 +258,10 @@ Passing `flatten=true` will return a `NamedTuple` with keys ungrouped. julia> chn = Chains([1:2 3:4], [:a, :b], Dict(:internals => [:a])); julia> get(chn; section=:parameters) -(b = [3; 4],) +(b = [3; 4;;],) julia> get(chn; section=[:internals]) -(a = [1; 2],) +(a = [1; 2;;],) ``` """ function Base.get( diff --git a/src/rstar.jl b/src/rstar.jl index ba4340e8..e0ce9e1d 100644 --- a/src/rstar.jl +++ b/src/rstar.jl @@ -8,8 +8,8 @@ and chain indices. # Examples -```jldoctest rstar; setup = :(using Random; Random.seed!(100)) -julia> using MLJBase, MLJXGBoostInterface, Statistics +```jldoctest rstar; setup = :(using Random; Random.seed!(200)) +julia> using MLJBase, MLJDecisionTreeInterface, Statistics julia> chains = Chains(fill(4.0, 100, 2, 3)); ``` @@ -17,7 +17,7 @@ julia> chains = Chains(fill(4.0, 100, 2, 3)); One can compute the distribution of the ``R^*`` statistic with the probabilistic classifier. ```jldoctest rstar -julia> distribution = rstar(XGBoostClassifier(), chains); +julia> distribution = rstar(DecisionTreeClassifier(), chains); julia> isapprox(mean(distribution), 1; atol=0.1) true @@ -26,9 +26,9 @@ true For deterministic classifiers, a single ``R^*`` statistic is returned. ```jldoctest rstar -julia> @pipeline XGBoostClassifier name = XGBoostDeterministic operation = predict_mode; +julia> @pipeline DecisionTreeClassifier name = DecisionTreeDeterministic operation = predict_mode; -julia> value = rstar(XGBoostDeterministic(), chains); +julia> value = rstar(DecisionTreeDeterministic(), chains); julia> isapprox(value, 1; atol=0.2) true diff --git a/test/Project.toml b/test/Project.toml index 7d9f27d2..c9c10608 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -9,6 +9,8 @@ IteratorInterfaceExtensions = "82899510-4779-5014-852e-03e436cf321d" KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b" Logging = "56ddb016-857b-54e1-b83d-db4d58db5568" MCMCChains = "c7f686f2-ff18-58e9-bc7b-31028e88f75d" +MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d" +MLJDecisionTreeInterface = "c6f25543-311c-4c74-83dc-3ea6d1015661" Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -29,6 +31,8 @@ FFTW = "1.1" IteratorInterfaceExtensions = "1" KernelDensity = "0.6.2" MCMCChains = "5" +MLJBase = "0.18" +MLJDecisionTreeInterface = "0.1.3" StatsBase = "0.33.2" StatsPlots = "0.14.17" TableTraits = "1" diff --git a/test/rstar_tests.jl b/test/rstar_tests.jl index cc4f7dd4..4b190ab6 100644 --- a/test/rstar_tests.jl +++ b/test/rstar_tests.jl @@ -1,6 +1,6 @@ using MCMCChains using MLJBase -using MLJXGBoostInterface +using MLJDecisionTreeInterface using Test N = 1000 @@ -9,7 +9,7 @@ colnames = ["a", "b", "c", "d", "e", "f", "g", "h"] internal_colnames = ["c", "d", "e", "f", "g", "h"] chn = Chains(val, colnames, Dict(:internals => internal_colnames)) -classif = XGBoostClassifier() +classif = DecisionTreeClassifier() @testset "R star test" begin # Compute R* statistic for a mixed chain. diff --git a/test/runtests.jl b/test/runtests.jl index 5ac95d30..eefadadf 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,7 +1,6 @@ -using Pkg - # Activate test environment on older Julia versions if VERSION < v"1.2" + using Pkg Pkg.activate(@__DIR__) Pkg.develop(PackageSpec(path=dirname(@__DIR__))) Pkg.instantiate() @@ -17,33 +16,6 @@ using Random Random.seed!(0) @testset "MCMCChains" begin - # MLJXGBoostInterface requires Julia >= 1.3 - # XGBoost errors on 32bit systems: https://github.com/dmlc/XGBoost.jl/issues/92 - if VERSION >= v"1.3" && VERSION < v"1.7" && Sys.WORD_SIZE == 64 - # run tests related to rstar statistic - println("Rstar") - Pkg.add("MLJBase") - Pkg.add("MLJXGBoostInterface") - @time include("rstar_tests.jl") - - DocMeta.setdocmeta!( - MCMCChains, - :DocTestSetup, - :(using MCMCChains); - recursive=true - ) - - doctest( - MCMCChains; - # https://github.com/JuliaLang/julia/pull/37085#issuecomment-683356098 - doctestfilters = [ - r"{([a-zA-Z0-9]+,\s?)+[a-zA-Z0-9]+}", - r"(Array{[a-zA-Z0-9]+,\s?1}|Vector{[a-zA-Z0-9]+})", - r"(Array{[a-zA-Z0-9]+,\s?2}|Matrix{[a-zA-Z0-9]+})", - ], - ) - end - # run tests for effective sample size println("ESS") @time include("ess_tests.jl") @@ -96,4 +68,19 @@ Random.seed!(0) println("Concatenation") @time include("concatenation_tests.jl") + # run tests related to rstar statistic + println("Rstar") + @time include("rstar_tests.jl") + + # Array printing depends on Julia version and architecture, + # therefore we only run doctests with Julia >= 1.7 and on 64bit where `Int === Int64` + if VERSION >= v"1.7" && Sys.WORD_SIZE == 64 + DocMeta.setdocmeta!( + MCMCChains, + :DocTestSetup, + :(using MCMCChains); + recursive = true + ) + doctest(MCMCChains) + end end