From c9f7e658d586038a75afe46b1714ca0f06ae801a Mon Sep 17 00:00:00 2001 From: pat-alt Date: Thu, 12 Sep 2024 11:58:49 +0200 Subject: [PATCH 1/4] changed predict function in mljflux --- dev/Manifest.toml | 1467 ++++++++++++++++++++++++------------ dev/Project.toml | 1 + dev/issues/predict_slow.jl | 18 + src/mlj_flux.jl | 23 +- 4 files changed, 1030 insertions(+), 479 deletions(-) create mode 100644 dev/issues/predict_slow.jl diff --git a/dev/Manifest.toml b/dev/Manifest.toml index f59e8c26..c2aa14eb 100644 --- a/dev/Manifest.toml +++ b/dev/Manifest.toml @@ -1,26 +1,56 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.8.3" +julia_version = "1.10.5" manifest_format = "2.0" -project_hash = "4918aea9c4429e463b595fce940213c2d39a8299" +project_hash = "7c4391b00ad44ccd083aa89cf817ea4c83643a8f" [[deps.AbstractFFTs]] -deps = ["ChainRulesCore", "LinearAlgebra"] -git-tree-sha1 = "69f7020bd72f069c219b5e8c236c1fa90d2cb409" +deps = ["LinearAlgebra"] +git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.2.1" +version = "1.5.0" +weakdeps = ["ChainRulesCore", "Test"] + + [deps.AbstractFFTs.extensions] + AbstractFFTsChainRulesCoreExt = "ChainRulesCore" + AbstractFFTsTestExt = "Test" [[deps.Accessors]] -deps = ["Compat", "CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Requires", "StaticArrays", "Test"] -git-tree-sha1 = "f3d4132fa63a6c62ab19b5765daf87ce2d36076c" +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] +git-tree-sha1 = "f61b15be1d76846c0ce31d3fcfac5380ae53db6a" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.25" +version = "0.1.37" + + [deps.Accessors.extensions] + AccessorsAxisKeysExt = "AxisKeys" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + AccessorsUnitfulExt = "Unitful" + + [deps.Accessors.weakdeps] + AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + Requires = "ae029012-a4dd-5104-9daa-d747884805df" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Adapt]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "0310e08cb19f5da31d08341c6120c047598f5b9c" +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.5.0" +version = "4.0.4" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" + +[[deps.AliasTables]] +deps = ["PtrArrays", "Random"] +git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff" +uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8" +version = "1.1.3" [[deps.ArgCheck]] git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" @@ -34,17 +64,38 @@ version = "1.1.1" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -[[deps.BFloat16s]] -deps = ["LinearAlgebra", "Printf", "Random", "Test"] -git-tree-sha1 = "a598ecb0d717092b5539dbbe890c98bac842b072" -uuid = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" -version = "0.2.0" +[[deps.Atomix]] +deps = ["UnsafeAtomics"] +git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" +uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" +version = "0.1.0" + +[[deps.BSON]] +git-tree-sha1 = "4c3e506685c527ac6a54ccc0c8c76fd6f91b42fb" +uuid = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0" +version = "0.3.9" [[deps.BangBang]] -deps = ["Compat", "ConstructionBase", "Future", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables", "ZygoteRules"] -git-tree-sha1 = "7fe6d92c4f281cf4ca6f2fba0ce7b299742da7ca" +deps = ["Accessors", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires"] +git-tree-sha1 = "e2144b631226d9eeab2d746ca8880b7ccff504ae" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.3.37" +version = "0.4.3" + + [deps.BangBang.extensions] + BangBangChainRulesCoreExt = "ChainRulesCore" + BangBangDataFramesExt = "DataFrames" + BangBangStaticArraysExt = "StaticArrays" + BangBangStructArraysExt = "StructArrays" + BangBangTablesExt = "Tables" + BangBangTypedTablesExt = "TypedTables" + + [deps.BangBang.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" + TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -55,114 +106,168 @@ uuid = "9718e550-a3fa-408a-8086-8db961cd8217" version = "0.1.1" [[deps.BitFlags]] -git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" +git-tree-sha1 = "0691e34b3bb8be9307330f88d1a3c3f25466c24d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" -version = "0.1.7" +version = "0.1.9" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" +git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+0" +version = "1.0.8+1" [[deps.CEnum]] -git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" +git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" -version = "0.4.2" - -[[deps.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 = "6717cb9a3425ebb7b31ca4f832823615d175f64a" -uuid = "052768ef-5323-5732-b1bb-66c8b64840ba" -version = "3.13.1" +version = "0.5.0" [[deps.Cairo]] deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] -git-tree-sha1 = "d0b3f8b4ad16cb0a2988c6788646a5e6a17b6b1b" +git-tree-sha1 = "7b6ad8c35f4bc3bca8eb78127c8b99719506a5fb" uuid = "159f3aea-2a34-519c-b102-8c37f9878175" -version = "1.0.5" +version = "1.1.0" [[deps.Cairo_jll]] -deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_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 = "4b859a208b2397a7a623a03449e4636bdb17bcf2" +deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "a2f1c8c668c8e3cb4cca4e57a8efdb09067bb3fd" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.16.1+1" +version = "1.18.0+2" + +[[deps.CategoricalArrays]] +deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"] +git-tree-sha1 = "1568b28f91293458345dabba6a5ea3f183250a61" +uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597" +version = "0.10.8" + + [deps.CategoricalArrays.extensions] + CategoricalArraysJSONExt = "JSON" + CategoricalArraysRecipesBaseExt = "RecipesBase" + CategoricalArraysSentinelArraysExt = "SentinelArrays" + CategoricalArraysStructTypesExt = "StructTypes" + + [deps.CategoricalArrays.weakdeps] + JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" + RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" + SentinelArrays = "91c51154-3ec4-41a3-a24f-3f23e20d615c" + StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" + +[[deps.CategoricalDistributions]] +deps = ["CategoricalArrays", "Distributions", "Missings", "OrderedCollections", "Random", "ScientificTypes"] +git-tree-sha1 = "926862f549a82d6c3a7145bc7f1adff2a91a39f0" +uuid = "af321ab8-2d2e-40a6-b165-3d674595d28e" +version = "0.1.15" + + [deps.CategoricalDistributions.extensions] + UnivariateFiniteDisplayExt = "UnicodePlots" + + [deps.CategoricalDistributions.weakdeps] + UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228" [[deps.ChainRules]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"] -git-tree-sha1 = "c46adabdd0348f0ee8de91142cfc4a72a613ac0a" +deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] +git-tree-sha1 = "83806b5196e1e9827db0429a7579824c8b0e03ce" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.46.1" +version = "1.70.0" [[deps.ChainRulesCore]] -deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "c6d890a52d2c4d55d326439580c3b8d0875a77d9" +deps = ["Compat", "LinearAlgebra"] +git-tree-sha1 = "71acdbf594aab5bbb2cec89b208c41b4c411e49f" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.7" +version = "1.24.0" +weakdeps = ["SparseArrays"] -[[deps.ChangesOfVariables]] -deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "844b061c104c408b24537482469400af6075aae4" -uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.5" + [deps.ChainRulesCore.extensions] + ChainRulesCoreSparseArraysExt = "SparseArrays" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" +git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.1" +version = "0.7.6" [[deps.ColorSchemes]] -deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] -git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] +git-tree-sha1 = "b5278586822443594ff615963b0c09755771b3e0" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.20.0" +version = "3.26.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" +git-tree-sha1 = "b10d0b65641d57b8b4d5e234446582de5047050d" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.11.4" +version = "0.11.5" [[deps.ColorVectorSpace]] -deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] -git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" +deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "Requires", "Statistics", "TensorCore"] +git-tree-sha1 = "a1f44953f2382ebb937d60dafbe2deea4bd23249" uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" -version = "0.9.10" +version = "0.10.0" +weakdeps = ["SpecialFunctions"] + + [deps.ColorVectorSpace.extensions] + SpecialFunctionsExt = "SpecialFunctions" [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" +git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.10" +version = "0.12.11" [[deps.CommonSubexpressions]] -deps = ["MacroTools", "Test"] -git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +deps = ["MacroTools"] +git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5" uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" -version = "0.3.0" +version = "0.3.1" [[deps.Compat]] -deps = ["Dates", "LinearAlgebra", "UUIDs"] -git-tree-sha1 = "00a2cccc7f098ff3b66806862d275ca3db9e6e5a" +deps = ["TOML", "UUIDs"] +git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.5.0" +version = "4.16.0" +weakdeps = ["Dates", "LinearAlgebra"] + + [deps.Compat.extensions] + CompatLinearAlgebraExt = "LinearAlgebra" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "0.5.2+0" +version = "1.1.1+0" [[deps.CompositionsBase]] -git-tree-sha1 = "455419f7e328a1a2493cabc6428d79e951349769" +git-tree-sha1 = "802bb88cd69dfd1509f6670416bd4434015693ad" uuid = "a33af91c-f02d-484b-be07-31d278c5ca2b" -version = "0.1.1" +version = "0.1.2" +weakdeps = ["InverseFunctions"] + + [deps.CompositionsBase.extensions] + CompositionsBaseInverseFunctionsExt = "InverseFunctions" + +[[deps.ComputationalResources]] +git-tree-sha1 = "52cb3ec90e8a8bea0e62e275ba577ad0f74821f7" +uuid = "ed09eef8-17a6-5b46-8889-db040fac31e3" +version = "0.3.2" + +[[deps.ConcurrentUtilities]] +deps = ["Serialization", "Sockets"] +git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" +uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" +version = "2.4.2" [[deps.ConstructionBase]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "fb21ddd70a051d882a1686a5a550990bbe371a95" +git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.4.1" +version = "1.5.8" + + [deps.ConstructionBase.extensions] + ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseLinearAlgebraExt = "LinearAlgebra" + ConstructionBaseStaticArraysExt = "StaticArrays" + + [deps.ConstructionBase.weakdeps] + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.ContextVariablesX]] deps = ["Compat", "Logging", "UUIDs"] @@ -171,20 +276,25 @@ uuid = "6add18c4-b38d-439d-96f6-d6bc489c04c5" version = "0.1.3" [[deps.Contour]] -git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" +git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.6.2" +version = "0.6.3" + +[[deps.Crayons]] +git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" +uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" +version = "4.1.1" [[deps.DataAPI]] -git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" +git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.14.0" +version = "1.16.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" +git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.13" +version = "0.18.20" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -195,6 +305,12 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +[[deps.Dbus_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" +uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" +version = "1.14.10+0" + [[deps.DefineSingletons]] git-tree-sha1 = "0fba8b706d0178b4dc7fd44a96a92382c9065c2c" uuid = "244e2a9f-e319-4986-a169-4d1fe445cd52" @@ -202,7 +318,9 @@ version = "0.1.2" [[deps.DelimitedFiles]] deps = ["Mmap"] +git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" +version = "1.9.1" [[deps.DiffResults]] deps = ["StaticArraysCore"] @@ -212,14 +330,30 @@ version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "c5b6685d53f933c11404a3ae9822afe30d522494" +git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.12.2" +version = "1.15.1" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" +[[deps.Distributions]] +deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "e6c693a0e4394f8fda0e51a5bdf5aef26f8235e9" +uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" +version = "0.25.111" + + [deps.Distributions.extensions] + DistributionsChainRulesCoreExt = "ChainRulesCore" + DistributionsDensityInterfaceExt = "DensityInterface" + DistributionsTestExt = "Test" + + [deps.Distributions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + [[deps.DocStringExtensions]] deps = ["LibGit2"] git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" @@ -231,16 +365,23 @@ deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" +[[deps.EpollShim_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8e9441ee83492030ace98f9789a654a6d0b1f643" +uuid = "2702e6a9-849d-5ed8-8c21-79e8b8f9ee43" +version = "0.0.20230411+0" + +[[deps.ExceptionUnwrapping]] +deps = ["Test"] +git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" +uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" +version = "0.1.10" + [[deps.Expat_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.4.8+0" - -[[deps.ExprTools]] -git-tree-sha1 = "56559bbef6ca5ea0c0818fa5c90320398a6fbf8d" -uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" -version = "0.1.8" +version = "2.6.2+0" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] @@ -249,16 +390,16 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" version = "0.4.1" [[deps.FFMPEG_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", 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-git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc" +git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172" uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" -version = "0.8.4" +version = "0.8.5" [[deps.Flux]] -deps = ["Adapt", "CUDA", "ChainRulesCore", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "NNlibCUDA", "OneHotArrays", "Optimisers", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Zygote"] -git-tree-sha1 = "518b553ec3776dde058aebd2750c109d04ee5593" +deps = ["Adapt", "ChainRulesCore", "Compat", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] +git-tree-sha1 = "fbf100b4bed74c9b6fac0ebd1031e04977d35b3b" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.13.11" - -[[deps.FoldsThreads]] -deps = ["Accessors", "FunctionWrappers", 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[[deps.Functors]] deps = ["LinearAlgebra"] -git-tree-sha1 = "61fa9cf802d35fe1b5b8ea9fbaac4b8f020d19b1" +git-tree-sha1 = "64d8e93700c7a3f28f717d265382d52fac9fa1c1" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.4.2" +version = "0.4.12" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GLFW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] +git-tree-sha1 = "532f9126ad901533af1d4f5c198867227a7bb077" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.8+0" +version = "3.4.0+1" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "494f1e456000c00c93dde79b38094e023f639dac" +git-tree-sha1 = "62ee71528cca49be797076a76bdc654a170a523e" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "8.6.1" +version = "10.3.1" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "57f7cde02d7a53c9d1d28443b9f11ac5fbe7ebc9" +git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.3" - -[[deps.GPUCompiler]] -deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "48832a7cacbe56e591a7bef690c78b9d00bcc692" -uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.17.1" +version = "0.1.6" [[deps.GR]] -deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "9e23bd6bb3eb4300cb567bdf63e2c14e5d2ffdbc" +deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] +git-tree-sha1 = "629693584cef594c3f6f99e76e7a7ad17e60e8d5" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.71.5" +version = "0.73.7" [[deps.GR_jll]] -deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "aa23c9f9b7c0ba6baeabe966ea1c7d2c7487ef90" +deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "a8863b69c2a0859f2c2c87ebdc4c6712e88bdf0d" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.71.5+0" +version = "0.73.7+0" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -387,10 +534,10 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.74.0+2" +version = "2.80.2+0" [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] @@ -410,27 +557,28 @@ uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "37e4657cd56b11abe3d10cd4a1ec5fbdb4180263" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.7.4" +version = "1.10.8" [[deps.HarfBuzz_jll]] -deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] -git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" +deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] +git-tree-sha1 = "401e4f3f30f43af2c8478fc008da50096ea5240f" uuid = 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"49510dfcb407e572524ba94aeae2fced1f3feb0f" +git-tree-sha1 = "2787db24f4e03daf859c6509ff87764e4182f7d1" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.8" +version = "0.1.16" +weakdeps = ["Dates", "Test"] + + [deps.InverseFunctions.extensions] + InverseFunctionsDatesExt = "Dates" + InverseFunctionsTestExt = "Test" + +[[deps.InvertedIndices]] +git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" +uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" +version = "1.3.0" [[deps.IrrationalConstants]] -git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.1" +version = "0.2.2" [[deps.IteratorInterfaceExtensions]] git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" +[[deps.JLD2]] +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Requires", "TranscodingStreams"] +git-tree-sha1 = "1dbe274ad1c199490b19a153b60a9e46c5386f8d" +uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" +version = "0.5.1" + [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "f377670cda23b6b7c1c0b3893e37451c5c1a2185" +git-tree-sha1 = "39d64b09147620f5ffbf6b2d3255be3c901bec63" uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.5" +version = "0.1.8" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.6.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" +git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.3" +version = "0.21.4" [[deps.JpegTurbo_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.2+0" +version = "3.0.3+0" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -487,17 +650,27 @@ git-tree-sha1 = "49fb3cb53362ddadb4415e9b73926d6b40709e70" uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" version = "0.2.4" -[[deps.Juno]] -deps = ["Base64", "Logging", "Media", "Profile"] -git-tree-sha1 = "07cb43290a840908a771552911a6274bc6c072c7" -uuid = "e5e0dc1b-0480-54bc-9374-aad01c23163d" -version = "0.8.4" +[[deps.KernelAbstractions]] +deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] +git-tree-sha1 = "cb1cff88ef2f3a157cbad75bbe6b229e1975e498" +uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" +version = "0.9.25" + + [deps.KernelAbstractions.extensions] + EnzymeExt = "EnzymeCore" + LinearAlgebraExt = "LinearAlgebra" + SparseArraysExt = "SparseArrays" + + [deps.KernelAbstractions.weakdeps] + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.LAME_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" -version = "3.100.1+0" +version = "3.100.2+0" [[deps.LERC_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -506,62 +679,95 @@ uuid = "88015f11-f218-50d7-93a8-a6af411a945d" version = "3.0.0+1" [[deps.LLVM]] -deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Printf", "Unicode"] -git-tree-sha1 = "b8ae281340f0d3e973aae7b96fb7502b0119b376" +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] +git-tree-sha1 = "4ad43cb0a4bb5e5b1506e1d1f48646d7e0c80363" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "4.15.0" +version = "9.1.2" + + [deps.LLVM.extensions] + BFloat16sExt = "BFloat16s" + + [deps.LLVM.weakdeps] + BFloat16s = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" [[deps.LLVMExtra_jll]] -deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg", "TOML"] -git-tree-sha1 = "771bfe376249626d3ca12bcd58ba243d3f961576" +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] +git-tree-sha1 = "05a8bd5a42309a9ec82f700876903abce1017dd3" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.16+0" +version = "0.0.34+0" + +[[deps.LLVMOpenMP_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" +uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" +version = "18.1.7+0" [[deps.LZO_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.1+0" +version = "2.10.2+0" [[deps.LaTeXStrings]] -git-tree-sha1 = "f2355693d6778a178ade15952b7ac47a4ff97996" +git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.0" +version = "1.3.1" [[deps.LaplaceRedux]] -deps = ["Flux", "LinearAlgebra", "Parameters", "Plots", "Zygote"] +deps = ["ChainRulesCore", "Compat", "ComputationalResources", "Distributions", "Flux", "LinearAlgebra", "MLJBase", "MLJFlux", "MLJModelInterface", "MLUtils", "Optimisers", "ProgressMeter", "Random", "Statistics", "Tables", "Tullio", "Zygote"] path = ".." uuid = "c52c1a26-f7c5-402b-80be-ba1e638ad478" -version = "0.1.2" +version = "1.1.0" [[deps.Latexify]] -deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", 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[[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" -version = "0.6.3" +version = "0.6.4" [[deps.LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" -version = "7.84.0+0" +version = "8.4.0+0" [[deps.LibGit2]] -deps = ["Base64", "NetworkOptions", "Printf", "SHA"] +deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +[[deps.LibGit2_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] +uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" +version = "1.6.4+0" + [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" -version = "1.10.2+0" +version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" @@ -573,10 +779,10 @@ uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" version = "3.2.2+1" [[deps.Libgcrypt_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"] -git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] +git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.7+0" +version = "1.8.11+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] @@ -585,22 +791,22 @@ uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" version = "1.6.0+0" [[deps.Libgpg_error_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.42.0+0" +version = "1.49.0+0" [[deps.Libiconv_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+2" +version = "1.17.0+0" [[deps.Libmount_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.35.0+0" +version = "2.40.1+0" [[deps.Librsvg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pango_jll", "Pkg", "gdk_pixbuf_jll"] @@ -609,121 +815,178 @@ uuid = "925c91fb-5dd6-59dd-8e8c-345e74382d89" version = "2.54.5+0" [[deps.Libtiff_jll]] -deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" +deps = ["Artifacts", "JLLWrappers", 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+git-tree-sha1 = "45cf9fd0ca5839d06ef333c8201714e888486342" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.6.11" +version = "0.6.12" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -925,9 +1256,9 @@ version = "1.2.2" [[deps.RelocatableFolders]] deps = ["SHA", "Scratch"] -git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691" +git-tree-sha1 = "ffdaf70d81cf6ff22c2b6e733c900c3321cab864" uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" -version = "1.0.0" +version = "1.0.1" [[deps.Requires]] deps = ["UUIDs"] @@ -935,6 +1266,18 @@ git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" uuid = "ae029012-a4dd-5104-9daa-d747884805df" version = "1.3.0" +[[deps.Rmath]] +deps = ["Random", "Rmath_jll"] +git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" +version = "0.7.1" + +[[deps.Rmath_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = 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-version = "1.1.1" +version = "1.2.1" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -982,30 +1336,35 @@ git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" version = "0.9.4" -[[deps.SnoopPrecompile]] -deps = ["Preferences"] -git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" -uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" -version = "1.0.3" - [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" +git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.1.0" +version = "1.2.1" [[deps.SparseArrays]] -deps = ["LinearAlgebra", "Random"] +deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" +version = "1.10.0" + +[[deps.SparseInverseSubset]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "52962839426b75b3021296f7df242e40ecfc0852" +uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" +version = "0.1.2" [[deps.SpecialFunctions]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "d75bda01f8c31ebb72df80a46c88b25d1c79c56d" +deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.1.7" +version = "2.4.0" +weakdeps = ["ChainRulesCore"] + + [deps.SpecialFunctions.extensions] + SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" [[deps.SplittablesBase]] deps = ["Setfield", "Test"] @@ -1014,42 +1373,93 @@ uuid = "171d559e-b47b-412a-8079-5efa626c420e" version = "0.1.15" [[deps.StaticArrays]] -deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = 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"SparseArrays", "StaticArrays"] + + [deps.StructArrays.extensions] + StructArraysAdaptExt = "Adapt" + StructArraysGPUArraysCoreExt = "GPUArraysCore" + StructArraysSparseArraysExt = "SparseArrays" + StructArraysStaticArraysExt = "StaticArrays" + +[[deps.SuiteSparse]] +deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] +uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" + +[[deps.SuiteSparse_jll]] +deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] +uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" +version = "7.2.1+1" [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" -version = "1.0.0" +version = "1.0.3" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -1058,15 +1468,15 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.10.0" +version = "1.12.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" -version = "1.10.1" +version = "1.10.0" [[deps.TensorCore]] deps = ["LinearAlgebra"] @@ -1078,28 +1488,53 @@ version = "0.1.1" deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -[[deps.TimerOutputs]] -deps = ["ExprTools", "Printf"] -git-tree-sha1 = "f2fd3f288dfc6f507b0c3a2eb3bac009251e548b" -uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" -version = "0.5.22" - [[deps.TranscodingStreams]] -deps = ["Random", "Test"] -git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" +git-tree-sha1 = "e84b3a11b9bece70d14cce63406bbc79ed3464d2" uuid = 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TransducersReferenceablesExt = "Referenceables" + + [deps.Transducers.weakdeps] + BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" + OnlineStatsBase = "925886fa-5bf2-5e8e-b522-a9147a512338" + Referenceables = "42d2dcc6-99eb-4e98-b66c-637b7d73030e" + +[[deps.Tullio]] +deps = ["DiffRules", "LinearAlgebra", "Requires"] +git-tree-sha1 = "6d476962ba4e435d7f4101a403b1d3d72afe72f3" +uuid = "bc48ee85-29a4-5162-ae0b-a64e1601d4bc" +version = "0.3.7" + + [deps.Tullio.extensions] + TullioCUDAExt = "CUDA" + TullioChainRulesCoreExt = "ChainRulesCore" + TullioFillArraysExt = "FillArrays" + TullioTrackerExt = "Tracker" + + [deps.Tullio.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.URIs]] -git-tree-sha1 = 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"91844873c4085240b95e795f692c4cec4d805f8a" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "a54ee957f4c86b526460a720dbc882fa5edcbefc" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.34+0" +version = "1.1.41+0" + +[[deps.XZ_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632" +uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" +version = "5.4.6+0" + +[[deps.Xorg_libICE_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "326b4fea307b0b39892b3e85fa451692eda8d46c" +uuid = "f67eecfb-183a-506d-b269-f58e52b52d7c" +version = "1.1.1+0" + +[[deps.Xorg_libSM_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libICE_jll"] +git-tree-sha1 = "3796722887072218eabafb494a13c963209754ce" +uuid = "c834827a-8449-5923-a945-d239c165b7dd" +version = "1.2.4+0" [[deps.Xorg_libX11_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] -git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] +git-tree-sha1 = "afead5aba5aa507ad5a3bf01f58f82c8d1403495" uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" -version = "1.6.9+4" +version = "1.8.6+0" [[deps.Xorg_libXau_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6035850dcc70518ca32f012e46015b9beeda49d8" uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.9+4" +version = "1.0.11+0" [[deps.Xorg_libXcursor_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] @@ -1167,16 +1654,16 @@ uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" version = "1.2.0+4" [[deps.Xorg_libXdmcp_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "34d526d318358a859d7de23da945578e8e8727b7" uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.3+4" +version = "1.1.4+0" [[deps.Xorg_libXext_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "d2d1a5c49fae4ba39983f63de6afcbea47194e85" uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" -version = "1.3.4+4" +version = "1.3.6+0" [[deps.Xorg_libXfixes_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] @@ -1203,28 +1690,34 @@ uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" version = "1.5.2+4" [[deps.Xorg_libXrender_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.10+4" +version = "0.9.11+0" [[deps.Xorg_libpthread_stubs_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8fdda4c692503d44d04a0603d9ac0982054635f9" uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.0+3" +version = "0.1.1+0" [[deps.Xorg_libxcb_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" +deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] +git-tree-sha1 = "bcd466676fef0878338c61e655629fa7bbc69d8e" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.13.0+3" 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-git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"] +git-tree-sha1 = "330f955bc41bb8f5270a369c473fc4a5a4e4d3cb" uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" -version = "1.4.2+4" +version = "1.4.6+0" [[deps.Xorg_xkeyboard_config_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] -git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"] +git-tree-sha1 = "691634e5453ad362044e2ad653e79f3ee3bb98c3" uuid = "33bec58e-1273-512f-9401-5d533626f822" -version = "2.27.0+4" +version = "2.39.0+0" [[deps.Xorg_xtrans_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.4.0+3" +version = "1.5.0+0" 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["Artifacts", "Libdl", "OpenBLAS_jll"] +deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.1.1+0" +version = "5.11.0+0" -[[deps.libfdk_aac_jll]] +[[deps.libdecor_jll]] +deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] +git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" +uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" +version = "0.2.2+0" + +[[deps.libevdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" +git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22" +uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" +version = "1.11.0+0" + +[[deps.libfdk_aac_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.2+0" +version = "2.0.3+0" + +[[deps.libinput_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] +git-tree-sha1 = "ad50e5b90f222cfe78aa3d5183a20a12de1322ce" +uuid = "36db933b-70db-51c0-b978-0f229ee0e533" +version = "1.18.0+0" [[deps.libpng_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.38+0" +version = "1.6.43+1" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" +git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+1" +version = "1.3.7+2" + +[[deps.mtdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11" +uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e" +version = "1.1.6+0" [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.48.0+0" +version = "1.52.0+1" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" -version = "17.4.0+0" +version = "17.4.0+2" [[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1368,6 +1907,6 @@ version = "3.5.0+0" [[deps.xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" +git-tree-sha1 = "9c304562909ab2bab0262639bd4f444d7bc2be37" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "1.4.1+0" +version = "1.4.1+1" diff --git a/dev/Project.toml b/dev/Project.toml index 2e40378a..f68c2fc8 100644 --- a/dev/Project.toml +++ b/dev/Project.toml @@ -3,6 +3,7 @@ Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" LaplaceRedux = "c52c1a26-f7c5-402b-80be-ba1e638ad478" Luxor = "ae8d54c2-7ccd-5906-9d76-62fc9837b5bc" +MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d" PlotThemes = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" diff --git a/dev/issues/predict_slow.jl b/dev/issues/predict_slow.jl new file mode 100644 index 00000000..67ae1c6f --- /dev/null +++ b/dev/issues/predict_slow.jl @@ -0,0 +1,18 @@ +using LaplaceRedux +using MLJBase + +X = MLJBase.table(rand(Float32, 100, 3)); +y = coerce(rand("abc", 100), Multiclass); +model = LaplaceClassification(); +fitresult, _, _ = MLJBase.fit(model, 0, X, y); +la = fitresult[1]; +Xmat = matrix(X) |> permutedims; + +# Single test sample: +Xtest = Xmat[:,1:10]; +Xtest_tab = MLJBase.table(Xtest'); +MLJBase.predict(model, fitresult, Xtest_tab); # warm up +LaplaceRedux.predict(la, Xmat); # warm up +@time MLJBase.predict(model, fitresult, Xtest_tab); +@time LaplaceRedux.predict(la, Xtest); +@time glm_predictive_distribution(la, Xtest); \ No newline at end of file diff --git a/src/mlj_flux.jl b/src/mlj_flux.jl index 920567ed..4df57717 100644 --- a/src/mlj_flux.jl +++ b/src/mlj_flux.jl @@ -454,21 +454,14 @@ An array of predicted class labels. """ function MLJFlux.predict(model::LaplaceClassification, fitresult, Xnew) la = fitresult[1] - Xnew = MLJBase.matrix(Xnew) - #convert in a vector of vectors because Laplace ask to do so - X_vec = collect(eachrow(Xnew)) - predictions = [ - map( - x -> LaplaceRedux.predict( - la, - x; - link_approx=model.link_approx, - predict_proba=model.predict_proba, - ret_distr=model.ret_distr, - ), - X_vec, - )..., - ] + Xnew = MLJBase.matrix(Xnew) |> permutedims + predictions = LaplaceRedux.predict( + la, + Xnew; + link_approx=model.link_approx, + predict_proba=model.predict_proba, + ret_distr=model.ret_distr, + ) return predictions end From 70e09851cf66ec74467c56c2d72dc011facbdc9e Mon Sep 17 00:00:00 2001 From: pat-alt Date: Thu, 12 Sep 2024 12:45:15 +0200 Subject: [PATCH 2/4] also changed for regression --- .github/workflows/CI.yml | 5 ++-- Project.toml | 8 ++--- dev/Manifest.toml | 4 +-- dev/Project.toml | 1 + dev/issues/predict_slow.jl | 5 ++-- src/mlj_flux.jl | 60 ++++++++++++++++---------------------- 6 files changed, 37 insertions(+), 46 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 7a2b8666..75786cb9 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -20,7 +20,6 @@ jobs: fail-fast: false matrix: version: - - '1.9' - '1.10' os: - ubuntu-latest @@ -29,10 +28,10 @@ jobs: - x64 include: - os: windows-latest - version: '1.9' + version: '1' arch: x64 - os: macOS-latest - version: '1.9' + version: '1' arch: x64 steps: - uses: actions/checkout@v2 diff --git a/Project.toml b/Project.toml index 3949c1e7..60395915 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "LaplaceRedux" uuid = "c52c1a26-f7c5-402b-80be-ba1e638ad478" authors = ["Patrick Altmeyer"] -version = "1.1.0" +version = "1.1.1" [deps] ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" @@ -36,13 +36,13 @@ MLJModelInterface = "1.8.0" MLUtils = "0.4" Optimisers = "0.2, 0.3" ProgressMeter = "1.7.2" -Random = "1.9, 1.10" +Random = "1.10" Statistics = "1" Tables = "1.10.1" -Test = "1.9, 1.10" +Test = "1.10" Tullio = "0.3.5" Zygote = "0.6" -julia = "1.9, 1.10" +julia = "1.10" [extras] Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595" diff --git a/dev/Manifest.toml b/dev/Manifest.toml index c2aa14eb..f50e0259 100644 --- a/dev/Manifest.toml +++ b/dev/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.5" manifest_format = "2.0" -project_hash = "7c4391b00ad44ccd083aa89cf817ea4c83643a8f" +project_hash = "6224e923196c94cc69f23bf59d6ea60b7ea2c919" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -717,7 +717,7 @@ version = "1.3.1" deps = ["ChainRulesCore", "Compat", "ComputationalResources", "Distributions", "Flux", "LinearAlgebra", "MLJBase", "MLJFlux", "MLJModelInterface", "MLUtils", "Optimisers", "ProgressMeter", "Random", "Statistics", "Tables", "Tullio", "Zygote"] path = ".." uuid = "c52c1a26-f7c5-402b-80be-ba1e638ad478" -version = "1.1.0" +version = "1.1.1" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] diff --git a/dev/Project.toml b/dev/Project.toml index f68c2fc8..3fb161e6 100644 --- a/dev/Project.toml +++ b/dev/Project.toml @@ -4,6 +4,7 @@ Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c" LaplaceRedux = "c52c1a26-f7c5-402b-80be-ba1e638ad478" Luxor = "ae8d54c2-7ccd-5906-9d76-62fc9837b5bc" MLJBase = "a7f614a8-145f-11e9-1d2a-a57a1082229d" +Optimisers = "3bd65402-5787-11e9-1adc-39752487f4e2" PlotThemes = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" diff --git a/dev/issues/predict_slow.jl b/dev/issues/predict_slow.jl index 67ae1c6f..ae713cbd 100644 --- a/dev/issues/predict_slow.jl +++ b/dev/issues/predict_slow.jl @@ -1,10 +1,11 @@ using LaplaceRedux using MLJBase +using Optimisers X = MLJBase.table(rand(Float32, 100, 3)); y = coerce(rand("abc", 100), Multiclass); -model = LaplaceClassification(); -fitresult, _, _ = MLJBase.fit(model, 0, X, y); +model = LaplaceClassification(optimiser=Optimisers.Adam(0.1), epochs=100); +fitresult, _, _ = MLJBase.fit(model, 2, X, y); la = fitresult[1]; Xmat = matrix(X) |> permutedims; diff --git a/src/mlj_flux.jl b/src/mlj_flux.jl index 4df57717..18890b30 100644 --- a/src/mlj_flux.jl +++ b/src/mlj_flux.jl @@ -247,21 +247,17 @@ function MLJFlux.train( push!(history, current_loss) end - if !isa(chain, AbstractLaplace) - la = LaplaceRedux.Laplace( - chain; - likelihood=:regression, - subset_of_weights=model.subset_of_weights, - subnetwork_indices=model.subnetwork_indices, - hessian_structure=model.hessian_structure, - backend=model.backend, - σ=model.σ, - μ₀=model.μ₀, - P₀=model.P₀, - ) - else - la = chain - end + la = LaplaceRedux.Laplace( + chain; + likelihood=:regression, + subset_of_weights=model.subset_of_weights, + subnetwork_indices=model.subnetwork_indices, + hessian_structure=model.hessian_structure, + backend=model.backend, + σ=model.σ, + μ₀=model.μ₀, + P₀=model.P₀, + ) # fit the Laplace model: LaplaceRedux.fit!(la, zip(X, y)) @@ -285,12 +281,9 @@ Predict the output for new input data using a Laplace regression model. """ function MLJFlux.predict(model::LaplaceRegression, fitresult, Xnew) - Xnew = MLJBase.matrix(Xnew) + Xnew = MLJBase.matrix(Xnew) |> permutedims la = fitresult[1] - #convert in a vector of vectors because MLJ ask to do so - X_vec = collect(eachrow(Xnew)) - # Predict using Laplace and collect the predictions - yhat = [map(x -> LaplaceRedux.predict(la, x; ret_distr=model.ret_distr), X_vec)...] + yhat = LaplaceRedux.predict(la, Xnew; ret_distr=model.ret_distr) return yhat end @@ -416,21 +409,18 @@ function MLJFlux.train( push!(history, current_loss) end - if !isa(chain, AbstractLaplace) - la = LaplaceRedux.Laplace( - chain; - likelihood=:classification, - subset_of_weights=model.subset_of_weights, - subnetwork_indices=model.subnetwork_indices, - hessian_structure=model.hessian_structure, - backend=model.backend, - σ=model.σ, - μ₀=model.μ₀, - P₀=model.P₀, - ) - else - la = chain - end + la = LaplaceRedux.Laplace( + chain; + likelihood=:classification, + subset_of_weights=model.subset_of_weights, + subnetwork_indices=model.subnetwork_indices, + hessian_structure=model.hessian_structure, + backend=model.backend, + σ=model.σ, + μ₀=model.μ₀, + P₀=model.P₀, + ) + # fit the Laplace model: LaplaceRedux.fit!(la, zip(X, y)) optimize_prior!(la; verbose=verbose_laplace, n_steps=model.fit_prior_nsteps) From 98b2f67036661e1a056677caa563d7a2fdda4e04 Mon Sep 17 00:00:00 2001 From: pat-alt Date: Thu, 12 Sep 2024 12:54:11 +0200 Subject: [PATCH 3/4] do we need the if statement after all? --- src/mlj_flux.jl | 52 ++++++++++++++++++++++++++++--------------------- 1 file changed, 30 insertions(+), 22 deletions(-) diff --git a/src/mlj_flux.jl b/src/mlj_flux.jl index 18890b30..0b1fa68f 100644 --- a/src/mlj_flux.jl +++ b/src/mlj_flux.jl @@ -247,17 +247,21 @@ function MLJFlux.train( push!(history, current_loss) end - la = LaplaceRedux.Laplace( - chain; - likelihood=:regression, - subset_of_weights=model.subset_of_weights, - subnetwork_indices=model.subnetwork_indices, - hessian_structure=model.hessian_structure, - backend=model.backend, - σ=model.σ, - μ₀=model.μ₀, - P₀=model.P₀, - ) + if !isa(chain, AbstractLaplace) + la = LaplaceRedux.Laplace( + chain; + likelihood=:regression, + subset_of_weights=model.subset_of_weights, + subnetwork_indices=model.subnetwork_indices, + hessian_structure=model.hessian_structure, + backend=model.backend, + σ=model.σ, + μ₀=model.μ₀, + P₀=model.P₀, + ) + else + la = chain + end # fit the Laplace model: LaplaceRedux.fit!(la, zip(X, y)) @@ -409,17 +413,21 @@ function MLJFlux.train( push!(history, current_loss) end - la = LaplaceRedux.Laplace( - chain; - likelihood=:classification, - subset_of_weights=model.subset_of_weights, - subnetwork_indices=model.subnetwork_indices, - hessian_structure=model.hessian_structure, - backend=model.backend, - σ=model.σ, - μ₀=model.μ₀, - P₀=model.P₀, - ) + if !isa(chain, AbstractLaplace) + la = LaplaceRedux.Laplace( + chain; + likelihood=:regression, + subset_of_weights=model.subset_of_weights, + subnetwork_indices=model.subnetwork_indices, + hessian_structure=model.hessian_structure, + backend=model.backend, + σ=model.σ, + μ₀=model.μ₀, + P₀=model.P₀, + ) + else + la = chain + end # fit the Laplace model: LaplaceRedux.fit!(la, zip(X, y)) From 9873c55b045d9bed6f858ab2689fb214d66d6aa7 Mon Sep 17 00:00:00 2001 From: pat-alt Date: Thu, 12 Sep 2024 13:29:16 +0200 Subject: [PATCH 4/4] updated changelog --- CHANGELOG.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index e62d9bd0..09586163 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -6,6 +6,12 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/), *Note*: We try to adhere to these practices as of version [v0.2.1]. +## Version [1.1.1] - 2024-09-12 + +### Changed + +- Fixed an issue in MLJFlux implementation that led to long compute times for predictions. [#122] + ## Version [1.1.0] - 2024-09-03 ### Changed