From 4e415fb54a1f97a351b5a2a0f3257d48eda002c4 Mon Sep 17 00:00:00 2001 From: Olivier Labayle Date: Thu, 17 Apr 2025 11:33:22 +0100 Subject: [PATCH 1/9] add new TMLE version --- Manifest.toml | 1260 +++++++++++++++++++++++++++++-------------------- Project.toml | 6 +- 2 files changed, 743 insertions(+), 523 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index e369bf9..d0b58c0 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,37 +1,25 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.10.4" +julia_version = "1.11.4" manifest_format = "2.0" -project_hash = "d053be7ce83732f6d71882679f272cdf5adc2dc6" +project_hash = "3c7db909313efc9f362b46477fcfed4c062cada1" + +[[deps.ADTypes]] +git-tree-sha1 = "e2478490447631aedba0823d4d7a80b2cc8cdb32" +uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" +version = "1.14.0" +weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] + + [deps.ADTypes.extensions] + ADTypesChainRulesCoreExt = "ChainRulesCore" + ADTypesConstructionBaseExt = "ConstructionBase" + ADTypesEnzymeCoreExt = "EnzymeCore" [[deps.ARFFFiles]] deps = ["CategoricalArrays", "Dates", "Parsers", "Tables"] -git-tree-sha1 = "e8c8e0a2be6eb4f56b1672e46004463033daa409" +git-tree-sha1 = "678eb18590a8bc6674363da4d5faa4ac09c40a18" uuid = "da404889-ca92-49ff-9e8b-0aa6b4d38dc8" -version = "1.4.1" - -[[deps.AbstractDifferentiation]] -deps = ["ExprTools", "LinearAlgebra", "Requires"] -git-tree-sha1 = "d29ce82ed1d4c37135095e1a4d799c93d7be2361" -uuid = "c29ec348-61ec-40c8-8164-b8c60e9d9f3d" -version = "0.6.2" - - [deps.AbstractDifferentiation.extensions] - AbstractDifferentiationChainRulesCoreExt = "ChainRulesCore" - AbstractDifferentiationFiniteDifferencesExt = "FiniteDifferences" - AbstractDifferentiationForwardDiffExt = ["DiffResults", "ForwardDiff"] - AbstractDifferentiationReverseDiffExt = ["DiffResults", "ReverseDiff"] - AbstractDifferentiationTrackerExt = "Tracker" - AbstractDifferentiationZygoteExt = "Zygote" - - [deps.AbstractDifferentiation.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - DiffResults = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" - FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" - ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" - Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" +version = "1.5.0" [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] @@ -50,40 +38,44 @@ uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.5" [[deps.Accessors]] -deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] -git-tree-sha1 = "f61b15be1d76846c0ce31d3fcfac5380ae53db6a" +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "MacroTools"] +git-tree-sha1 = "3b86719127f50670efe356bc11073d84b4ed7a5d" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.37" +version = "0.1.42" [deps.Accessors.extensions] - AccessorsAxisKeysExt = "AxisKeys" - AccessorsIntervalSetsExt = "IntervalSets" - AccessorsStaticArraysExt = "StaticArrays" - AccessorsStructArraysExt = "StructArrays" - AccessorsUnitfulExt = "Unitful" + AxisKeysExt = "AxisKeys" + IntervalSetsExt = "IntervalSets" + LinearAlgebraExt = "LinearAlgebra" + StaticArraysExt = "StaticArrays" + StructArraysExt = "StructArrays" + TestExt = "Test" + UnitfulExt = "Unitful" [deps.Accessors.weakdeps] AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" - Requires = "ae029012-a4dd-5104-9daa-d747884805df" + LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "cde29ddf7e5726c9fb511f340244ea3481267608" +git-tree-sha1 = "f7817e2e585aa6d924fd714df1e2a84be7896c60" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.7.2" -weakdeps = ["StaticArrays"] +version = "4.3.0" +weakdeps = ["SparseArrays", "StaticArrays"] [deps.Adapt.extensions] + AdaptSparseArraysExt = "SparseArrays" AdaptStaticArraysExt = "StaticArrays" [[deps.AdaptivePredicates]] -git-tree-sha1 = "7d5da5dd472490d048b081ca1bda4a7821b06456" +git-tree-sha1 = "7e651ea8d262d2d74ce75fdf47c4d63c07dba7a6" uuid = "35492f91-a3bd-45ad-95db-fcad7dcfedb7" -version = "1.1.1" +version = "1.2.0" [[deps.AliasTables]] deps = ["PtrArrays", "Random"] @@ -93,14 +85,14 @@ version = "1.1.3" [[deps.Animations]] deps = ["Colors"] -git-tree-sha1 = "e81c509d2c8e49592413bfb0bb3b08150056c79d" +git-tree-sha1 = "e092fa223bf66a3c41f9c022bd074d916dc303e7" uuid = "27a7e980-b3e6-11e9-2bcd-0b925532e340" -version = "0.4.1" +version = "0.4.2" [[deps.ArgCheck]] -git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" +git-tree-sha1 = "f9e9a66c9b7be1ad7372bbd9b062d9230c30c5ce" uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" -version = "2.3.0" +version = "2.5.0" [[deps.ArgParse]] deps = ["Logging", "TextWrap"] @@ -110,7 +102,7 @@ version = "1.2.0" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" -version = "1.1.1" +version = "1.1.2" [[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] @@ -119,16 +111,21 @@ uuid = "ec485272-7323-5ecc-a04f-4719b315124d" version = "0.4.0" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "c5aeb516a84459e0318a02507d2261edad97eb75" +deps = ["Adapt", "LinearAlgebra"] +git-tree-sha1 = "017fcb757f8e921fb44ee063a7aafe5f89b86dd1" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.7.1" +version = "7.18.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" + ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceReverseDiffExt = "ReverseDiff" + ArrayInterfaceSparseArraysExt = "SparseArrays" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -136,15 +133,20 @@ version = "7.7.1" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.Arrow]] -deps = ["ArrowTypes", "BitIntegers", "CodecLz4", "CodecZstd", "ConcurrentUtilities", "DataAPI", "Dates", "EnumX", "LoggingExtras", "Mmap", "PooledArrays", "SentinelArrays", "Tables", "TimeZones", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "f8d411d1b45459368567dc51f683ed78a919d795" +deps = ["ArrowTypes", "BitIntegers", "CodecLz4", "CodecZstd", "ConcurrentUtilities", "DataAPI", "Dates", "EnumX", "Mmap", "PooledArrays", "SentinelArrays", "StringViews", "Tables", "TimeZones", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "00f0b3f05bc33cc5b68db6cc22e4a7b16b65e505" uuid = "69666777-d1a9-59fb-9406-91d4454c9d45" -version = "2.7.2" +version = "2.8.0" [[deps.ArrowTypes]] deps = ["Sockets", "UUIDs"] @@ -154,18 +156,30 @@ version = "2.3.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +version = "1.11.0" [[deps.Atomix]] deps = ["UnsafeAtomics"] -git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" +git-tree-sha1 = "b5bb4dc6248fde467be2a863eb8452993e74d402" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" -version = "0.1.0" +version = "1.1.1" + + [deps.Atomix.extensions] + AtomixCUDAExt = "CUDA" + AtomixMetalExt = "Metal" + AtomixOpenCLExt = "OpenCL" + AtomixoneAPIExt = "oneAPI" + + [deps.Atomix.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + OpenCL = "08131aa3-fb12-5dee-8b74-c09406e224a2" + oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b" [[deps.AutoHashEquals]] -deps = ["Pkg"] -git-tree-sha1 = "daaeb6f7f77b88c072a83a2451801818acb5c63b" +git-tree-sha1 = "4ec6b48702dacc5994a835c1189831755e4e76ef" uuid = "15f4f7f2-30c1-5605-9d31-71845cf9641f" -version = "2.1.0" +version = "2.2.0" [[deps.Automa]] deps = ["TranscodingStreams"] @@ -203,10 +217,10 @@ uuid = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0" version = "0.3.9" [[deps.BangBang]] -deps = ["Accessors", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires"] -git-tree-sha1 = "e2144b631226d9eeab2d746ca8880b7ccff504ae" +deps = ["Accessors", "ConstructionBase", "InitialValues", "LinearAlgebra"] +git-tree-sha1 = "26f41e1df02c330c4fa1e98d4aa2168fdafc9b1f" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.4.3" +version = "0.4.4" [deps.BangBang.extensions] BangBangChainRulesCoreExt = "ChainRulesCore" @@ -226,6 +240,7 @@ version = "0.4.3" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" +version = "1.11.0" [[deps.Baselet]] git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" @@ -245,9 +260,9 @@ version = "0.1.9" [[deps.BitIntegers]] deps = ["Random"] -git-tree-sha1 = "a55462dfddabc34bc97d3a7403a2ca2802179ae6" +git-tree-sha1 = "f98cfeaba814d9746617822032d50a31c9926604" uuid = "c3b6d118-76ef-56ca-8cc7-ebb389d030a1" -version = "0.3.1" +version = "0.3.5" [[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] @@ -261,10 +276,10 @@ uuid = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d" version = "1.2.2" [[deps.Bzip2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1b96ea4a01afe0ea4090c5c8039690672dd13f2e" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+1" +version = "1.0.9+0" [[deps.CEnum]] git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" @@ -279,6 +294,7 @@ version = "0.2.6" [[deps.CRC32c]] uuid = "8bf52ea8-c179-5cab-976a-9e18b702a9bc" +version = "1.11.0" [[deps.CRlibm_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -288,39 +304,39 @@ version = "1.0.1+0" [[deps.CSV]] deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] -git-tree-sha1 = "6c834533dc1fabd820c1db03c839bf97e45a3fab" +git-tree-sha1 = "deddd8725e5e1cc49ee205a1964256043720a6c3" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.14" +version = "0.10.15" [[deps.CUDA_Driver_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "22bc8ec24f0ed05bcf8c1845ef425d8229ef6436" +git-tree-sha1 = "f69205592dbd3721a156245b6dd837206786a848" uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc" -version = "0.10.0+0" +version = "0.12.1+1" [[deps.CUDA_Runtime_jll]] deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c730797fc11265bb0940b738b3573ed38c2c8388" +git-tree-sha1 = "99f1c6b659c14bbb3492246791bb4928a40ceb84" uuid = "76a88914-d11a-5bdc-97e0-2f5a05c973a2" -version = "0.15.1+0" +version = "0.16.1+0" [[deps.Cairo]] deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] -git-tree-sha1 = "7b6ad8c35f4bc3bca8eb78127c8b99719506a5fb" +git-tree-sha1 = "71aa551c5c33f1a4415867fe06b7844faadb0ae9" uuid = "159f3aea-2a34-519c-b102-8c37f9878175" -version = "1.1.0" +version = "1.1.1" [[deps.CairoMakie]] deps = ["CRC32c", "Cairo", "Cairo_jll", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"] -git-tree-sha1 = "361dec06290d76b6d70d0c7dc888038eec9df63a" +git-tree-sha1 = "0afa2b4ac444b9412130d68493941e1af462e26a" uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" -version = "0.12.9" +version = "0.12.18" [[deps.Cairo_jll]] 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" +git-tree-sha1 = "2ac646d71d0d24b44f3f8c84da8c9f4d70fb67df" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.0+2" +version = "1.18.4+0" [[deps.CategoricalArrays]] deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"] @@ -349,15 +365,15 @@ version = "0.1.15" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "227985d885b4dbce5e18a96f9326ea1e836e5a03" +git-tree-sha1 = "a975ae558af61a2a48720a6271661bf2621e0f4e" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.69.0" +version = "1.72.3" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "71acdbf594aab5bbb2cec89b208c41b4c411e49f" +git-tree-sha1 = "1713c74e00545bfe14605d2a2be1712de8fbcb58" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.24.0" +version = "1.25.1" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -371,15 +387,15 @@ version = "0.1.13" [[deps.CodecBzip2]] deps = ["Bzip2_jll", "TranscodingStreams"] -git-tree-sha1 = "e7c529cc31bb85b97631b922fa2e6baf246f5905" +git-tree-sha1 = "84990fa864b7f2b4901901ca12736e45ee79068c" uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" -version = "0.8.4" +version = "0.8.5" [[deps.CodecLz4]] deps = ["Lz4_jll", "TranscodingStreams"] -git-tree-sha1 = "0db0c70ca94c0a79cadad269497f25ca88b9fa91" +git-tree-sha1 = "d58afcd2833601636b48ee8cbeb2edcb086522c2" uuid = "5ba52731-8f18-5e0d-9241-30f10d1ec561" -version = "0.4.5" +version = "0.4.6" [[deps.CodecXz]] deps = ["TranscodingStreams", "XZ_jll"] @@ -389,27 +405,27 @@ version = "0.7.4" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" +git-tree-sha1 = "962834c22b66e32aa10f7611c08c8ca4e20749a9" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.6" +version = "0.7.8" [[deps.CodecZstd]] deps = ["TranscodingStreams", "Zstd_jll"] -git-tree-sha1 = "5e41a52bec3b0881a7eb54f5391b779994504186" +git-tree-sha1 = "d0073f473757f0d39ac9707f1eb03b431573cbd8" uuid = "6b39b394-51ab-5f42-8807-6242bab2b4c2" -version = "0.8.5" +version = "0.8.6" [[deps.ColorBrewer]] -deps = ["Colors", "JSON", "Test"] -git-tree-sha1 = "61c5334f33d91e570e1d0c3eb5465835242582c4" +deps = ["Colors", "JSON"] +git-tree-sha1 = "e771a63cc8b539eca78c85b0cabd9233d6c8f06f" uuid = "a2cac450-b92f-5266-8821-25eda20663c8" -version = "0.4.0" +version = "0.4.1" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "b5278586822443594ff615963b0c09755771b3e0" +git-tree-sha1 = "403f2d8e209681fcbd9468a8514efff3ea08452e" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.26.0" +version = "3.29.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -429,9 +445,9 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0" +git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.11" +version = "0.13.0" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -485,9 +501,9 @@ version = "0.3.2" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" +git-tree-sha1 = "d9d26935a0bcffc87d2613ce14c527c99fc543fd" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.4.2" +version = "2.5.0" [[deps.Configurations]] deps = ["ExproniconLite", "OrderedCollections", "TOML"] @@ -496,14 +512,14 @@ uuid = "5218b696-f38b-4ac9-8b61-a12ec717816d" version = "0.17.6" [[deps.ConstructionBase]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "a33b7ced222c6165f624a3f2b55945fac5a598d9" +git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.7" -weakdeps = ["IntervalSets", "StaticArrays"] +version = "1.5.8" +weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"] [deps.ConstructionBase.extensions] ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseLinearAlgebraExt = "LinearAlgebra" ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.ContextVariablesX]] @@ -539,16 +555,16 @@ uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" version = "1.16.0" [[deps.DataFrames]] -deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "04c738083f29f86e62c8afc341f0967d8717bdb8" +deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.6.1" +version = "1.7.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" +git-tree-sha1 = "4e1fe97fdaed23e9dc21d4d664bea76b65fc50a0" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.20" +version = "0.18.22" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -558,6 +574,7 @@ version = "1.0.0" [[deps.Dates]] deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +version = "1.11.0" [[deps.DefineSingletons]] git-tree-sha1 = "0fba8b706d0178b4dc7fd44a96a92382c9065c2c" @@ -566,9 +583,9 @@ version = "0.1.2" [[deps.DelaunayTriangulation]] deps = ["AdaptivePredicates", "EnumX", "ExactPredicates", "Random"] -git-tree-sha1 = "b5f1c6532d2ea71e99b74231b0a3d53fba846ced" +git-tree-sha1 = "5620ff4ee0084a6ab7097a27ba0c19290200b037" uuid = "927a84f5-c5f4-47a5-9785-b46e178433df" -version = "1.1.3" +version = "1.6.4" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -578,9 +595,9 @@ version = "1.9.1" [[deps.Dictionaries]] deps = ["Indexing", "Random", "Serialization"] -git-tree-sha1 = "35b66b6744b2d92c778afd3a88d2571875664a2a" +git-tree-sha1 = "a86af9c4c4f33e16a2b2ff43c2113b2f390081fa" uuid = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4" -version = "0.4.2" +version = "0.4.5" [[deps.DiffResults]] deps = ["StaticArraysCore"] @@ -594,11 +611,61 @@ git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" version = "1.15.1" +[[deps.DifferentiationInterface]] +deps = ["ADTypes", "LinearAlgebra"] +git-tree-sha1 = "aa87a743e3778d35a950b76fbd2ae64f810a2bb3" +uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" +version = "0.6.52" + + [deps.DifferentiationInterface.extensions] + DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" + DifferentiationInterfaceDiffractorExt = "Diffractor" + DifferentiationInterfaceEnzymeExt = ["EnzymeCore", "Enzyme"] + DifferentiationInterfaceFastDifferentiationExt = "FastDifferentiation" + DifferentiationInterfaceFiniteDiffExt = "FiniteDiff" + DifferentiationInterfaceFiniteDifferencesExt = "FiniteDifferences" + DifferentiationInterfaceForwardDiffExt = ["ForwardDiff", "DiffResults"] + DifferentiationInterfaceGPUArraysCoreExt = "GPUArraysCore" + DifferentiationInterfaceGTPSAExt = "GTPSA" + DifferentiationInterfaceMooncakeExt = "Mooncake" + DifferentiationInterfacePolyesterForwardDiffExt = ["PolyesterForwardDiff", "ForwardDiff", "DiffResults"] + DifferentiationInterfaceReverseDiffExt = ["ReverseDiff", "DiffResults"] + DifferentiationInterfaceSparseArraysExt = "SparseArrays" + DifferentiationInterfaceSparseConnectivityTracerExt = "SparseConnectivityTracer" + DifferentiationInterfaceSparseMatrixColoringsExt = "SparseMatrixColorings" + DifferentiationInterfaceStaticArraysExt = "StaticArrays" + DifferentiationInterfaceSymbolicsExt = "Symbolics" + DifferentiationInterfaceTrackerExt = "Tracker" + DifferentiationInterfaceZygoteExt = ["Zygote", "ForwardDiff"] + + [deps.DifferentiationInterface.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DiffResults = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" + Diffractor = "9f5e2b26-1114-432f-b630-d3fe2085c51c" + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + FastDifferentiation = "eb9bf01b-bf85-4b60-bf87-ee5de06c00be" + FiniteDiff = "6a86dc24-6348-571c-b903-95158fe2bd41" + FiniteDifferences = "26cc04aa-876d-5657-8c51-4c34ba976000" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + GTPSA = "b27dd330-f138-47c5-815b-40db9dd9b6e8" + Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6" + PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SparseConnectivityTracer = "9f842d2f-2579-4b1d-911e-f412cf18a3f5" + SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" +git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.11" +version = "0.10.12" weakdeps = ["ChainRulesCore", "SparseArrays"] [deps.Distances.extensions] @@ -608,12 +675,13 @@ weakdeps = ["ChainRulesCore", "SparseArrays"] [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" +version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "0e0a1264b0942f1f3abb2b30891f2a590cc652ac" +git-tree-sha1 = "6d8b535fd38293bc54b88455465a1386f8ac1c3c" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.110" +version = "0.25.119" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -626,10 +694,9 @@ version = "0.25.110" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.DocStringExtensions]] -deps = ["LibGit2"] -git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" +git-tree-sha1 = "e7b7e6f178525d17c720ab9c081e4ef04429f860" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.9.3" +version = "0.9.4" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] @@ -649,15 +716,24 @@ uuid = "792122b4-ca99-40de-a6bc-6742525f08b6" version = "0.3.0" [[deps.EnumX]] -git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" +git-tree-sha1 = "bddad79635af6aec424f53ed8aad5d7555dc6f00" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" -version = "1.0.4" +version = "1.0.5" + +[[deps.EnzymeCore]] +git-tree-sha1 = "0cdb7af5c39e92d78a0ee8d0a447d32f7593137e" +uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" +version = "0.8.8" +weakdeps = ["Adapt"] + + [deps.EnzymeCore.extensions] + AdaptExt = "Adapt" [[deps.EvoTrees]] deps = ["BSON", "CategoricalArrays", "Distributions", "MLJModelInterface", "NetworkLayout", "Random", "RecipesBase", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "92d1f78f95f4794bf29bd972dacfa37ea1fec9f4" +git-tree-sha1 = "79a4d55fb2aed62053dd85961278b8090c972367" uuid = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5" -version = "0.16.7" +version = "0.17.2" [deps.EvoTrees.extensions] EvoTreesCUDAExt = "CUDA" @@ -673,15 +749,15 @@ version = "2.2.8" [[deps.ExceptionUnwrapping]] deps = ["Test"] -git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" +git-tree-sha1 = "d36f682e590a83d63d1c7dbd287573764682d12a" uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" -version = "0.1.10" +version = "0.1.11" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" +git-tree-sha1 = "d55dffd9ae73ff72f1c0482454dcf2ec6c6c4a63" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.6.2+0" +version = "2.6.5+0" [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" @@ -689,14 +765,14 @@ uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.10" [[deps.ExproniconLite]] -git-tree-sha1 = "4c9ed87a6b3cd90acf24c556f2119533435ded38" +git-tree-sha1 = "c13f0b150373771b0fdc1713c97860f8df12e6c2" uuid = "55351af7-c7e9-48d6-89ff-24e801d99491" -version = "0.10.13" +version = "0.10.14" [[deps.Extents]] -git-tree-sha1 = "81023caa0021a41712685887db1fc03db26f41f5" +git-tree-sha1 = "063512a13dbe9c40d999c439268539aa552d1ae6" uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" -version = "0.1.4" +version = "0.1.5" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] @@ -706,15 +782,15 @@ version = "6.1.2+0" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "4820348781ae578893311153d69049a93d05f39d" +git-tree-sha1 = "7de7c78d681078f027389e067864a8d53bd7c3c9" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.8.0" +version = "1.8.1" [[deps.FFTW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6d6219a004b8cf1e0b4dbe27a2860b8e04eba0be" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = "3.3.10+0" +version = "3.3.11+0" [[deps.FLoops]] deps = ["BangBang", "Compat", "FLoopsBase", "InitialValues", "JuliaVariables", "MLStyle", "Serialization", "Setfield", "Transducers"] @@ -736,9 +812,13 @@ version = "0.2.2" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322" +git-tree-sha1 = "b66970a70db13f45b7e57fbda1736e1cf72174ea" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.3" +version = "1.17.0" +weakdeps = ["HTTP"] + + [deps.FileIO.extensions] + HTTPExt = "HTTP" [[deps.FilePaths]] deps = ["FilePathsBase", "MacroTools", "Reexport", "Requires"] @@ -747,19 +827,25 @@ uuid = "8fc22ac5-c921-52a6-82fd-178b2807b824" version = "0.8.3" [[deps.FilePathsBase]] -deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] -git-tree-sha1 = "9f00e42f8d99fdde64d40c8ea5d14269a2e2c1aa" +deps = ["Compat", "Dates"] +git-tree-sha1 = "3bab2c5aa25e7840a4b065805c0cdfc01f3068d2" uuid = "48062228-2e41-5def-b9a4-89aafe57970f" -version = "0.9.21" +version = "0.9.24" +weakdeps = ["Mmap", "Test"] + + [deps.FilePathsBase.extensions] + FilePathsBaseMmapExt = "Mmap" + FilePathsBaseTestExt = "Test" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" +version = "1.11.0" [[deps.FillArrays]] deps = ["LinearAlgebra"] -git-tree-sha1 = "fd0002c0b5362d7eb952450ad5eb742443340d6e" +git-tree-sha1 = "6a70198746448456524cb442b8af316927ff3e1a" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.12.0" +version = "1.13.0" weakdeps = ["PDMats", "SparseArrays", "Statistics"] [deps.FillArrays.extensions] @@ -768,19 +854,21 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] FillArraysStatisticsExt = "Statistics" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Setfield", "SparseArrays"] -git-tree-sha1 = "f9219347ebf700e77ca1d48ef84e4a82a6701882" +deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] +git-tree-sha1 = "f089ab1f834470c525562030c8cfde4025d5e915" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.24.0" +version = "2.27.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" + FiniteDiffSparseArraysExt = "SparseArrays" FiniteDiffStaticArraysExt = "StaticArrays" [deps.FiniteDiff.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FixedPointNumbers]] @@ -790,30 +878,32 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.5" [[deps.Flux]] -deps = ["Adapt", "ChainRulesCore", "Compat", "Functors", "LinearAlgebra", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] -git-tree-sha1 = "fbf100b4bed74c9b6fac0ebd1031e04977d35b3b" +deps = ["Adapt", "ChainRulesCore", "Compat", "EnzymeCore", "Functors", "LinearAlgebra", "MLDataDevices", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "Setfield", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] +git-tree-sha1 = "49d213a90b159c74e9fc2b53162b5f699b6f3516" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.14.19" +version = "0.16.3" [deps.Flux.extensions] FluxAMDGPUExt = "AMDGPU" FluxCUDAExt = "CUDA" FluxCUDAcuDNNExt = ["CUDA", "cuDNN"] FluxEnzymeExt = "Enzyme" - FluxMetalExt = "Metal" + FluxMPIExt = "MPI" + FluxMPINCCLExt = ["CUDA", "MPI", "NCCL"] [deps.Flux.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" - Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" + NCCL = "3fe64909-d7a1-4096-9b7d-7a0f12cf0f6b" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" [[deps.Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] -git-tree-sha1 = "db16beca600632c95fc8aca29890d83788dd8b23" +git-tree-sha1 = "301b5d5d731a0654825f1f2e906990f7141a106b" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.96+0" +version = "2.16.0+0" [[deps.Format]] git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" @@ -822,9 +912,9 @@ version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" +git-tree-sha1 = "910febccb28d493032495b7009dce7d7f7aee554" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.36" +version = "1.0.1" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -838,31 +928,32 @@ version = "4.1.1" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "5c1d8ae0efc6c2e7b1fc502cbe25def8f661b7bc" +git-tree-sha1 = "2c5512e11c791d1baed2049c5652441b28fc6a31" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.13.2+0" +version = "2.13.4+0" [[deps.FreeTypeAbstraction]] deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"] -git-tree-sha1 = "2493cdfd0740015955a8e46de4ef28f49460d8bc" +git-tree-sha1 = "d52e255138ac21be31fa633200b65e4e71d26802" uuid = "663a7486-cb36-511b-a19d-713bb74d65c9" -version = "0.10.3" +version = "0.10.6" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" +git-tree-sha1 = "7a214fdac5ed5f59a22c2d9a885a16da1c74bbc7" uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.14+0" +version = "1.0.17+0" [[deps.Functors]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "64d8e93700c7a3f28f717d265382d52fac9fa1c1" +deps = ["Compat", "ConstructionBase", "LinearAlgebra", "Random"] +git-tree-sha1 = "60a0339f28a233601cb74468032b5c302d5067de" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.4.12" +version = "0.5.2" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" +version = "1.11.0" [[deps.GLM]] deps = ["Distributions", "LinearAlgebra", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "StatsModels"] @@ -872,21 +963,15 @@ version = "1.9.0" [[deps.GLMNet]] deps = ["DataFrames", "Distributed", "Distributions", "Printf", "Random", "SparseArrays", "StatsBase", "glmnet_jll"] -git-tree-sha1 = "7ea4e2bbb84183fe52a488d05e16c152b2387b95" +git-tree-sha1 = "b873c384d3490304c18224b1d5554cdebaafb60b" uuid = "8d5ece8b-de18-5317-b113-243142960cc6" -version = "0.7.2" - -[[deps.GPUArrays]] -deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "85d7fb51afb3def5dcb85ad31c3707795c8bccc1" -uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "9.1.0" +version = "0.7.4" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" +git-tree-sha1 = "83cf05ab16a73219e5f6bd1bdfa9848fa24ac627" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.5" +version = "0.2.0" [[deps.GeneticVariantBase]] deps = ["StatsBase"] @@ -894,11 +979,16 @@ git-tree-sha1 = "e7ae81f2cf78f499553630ab9f26357e23a7ad1d" uuid = "2447270c-d849-4bf9-ac0d-b5c0b265991c" version = "0.1.2" +[[deps.GeoFormatTypes]] +git-tree-sha1 = "8e233d5167e63d708d41f87597433f59a0f213fe" +uuid = "68eda718-8dee-11e9-39e7-89f7f65f511f" +version = "0.4.4" + [[deps.GeoInterface]] -deps = ["Extents"] -git-tree-sha1 = "9fff8990361d5127b770e3454488360443019bb3" +deps = ["DataAPI", "Extents", "GeoFormatTypes"] +git-tree-sha1 = "294e99f19869d0b0cb71aef92f19d03649d028d5" uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" -version = "1.3.5" +version = "1.4.1" [[deps.GeometryBasics]] deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -912,11 +1002,17 @@ git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" +[[deps.Giflib_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6570366d757b50fabae9f4315ad74d2e40c0560a" +uuid = "59f7168a-df46-5410-90c8-f2779963d0ec" +version = "5.2.3+0" + [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba" +git-tree-sha1 = "b0036b392358c80d2d2124746c2bf3d48d457938" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.80.2+0" +version = "2.82.4+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -925,27 +1021,27 @@ version = "1.3.1" [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] -git-tree-sha1 = "d61890399bc535850c4bf08e4e0d3a7ad0f21cbd" +git-tree-sha1 = "a641238db938fff9b2f60d08ed9030387daf428c" uuid = "a2bd30eb-e257-5431-a919-1863eab51364" -version = "1.1.2" +version = "1.1.3" [[deps.Graphite2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a6dbda1fd736d60cc477d99f2e7a042acfa46e8" uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" -version = "1.3.14+0" +version = "1.3.15+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "ebd18c326fa6cee1efb7da9a3b45cf69da2ed4d9" +git-tree-sha1 = "3169fd3440a02f35e549728b0890904cfd4ae58a" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.11.2" +version = "1.12.1" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] -git-tree-sha1 = "fc713f007cff99ff9e50accba6373624ddd33588" +git-tree-sha1 = "dc6bed05c15523624909b3953686c5f5ffa10adc" uuid = "3955a311-db13-416c-9275-1d80ed98e5e9" -version = "0.11.0" +version = "0.11.1" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -953,16 +1049,21 @@ uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "f93655dc73d7a0b4a368e3c0bce296ae035ad76e" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.8" +version = "1.10.16" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] -git-tree-sha1 = "401e4f3f30f43af2c8478fc008da50096ea5240f" +git-tree-sha1 = "55c53be97790242c29031e5cd45e8ac296dadda3" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "8.3.1+0" +version = "8.5.0+0" + +[[deps.HashArrayMappedTries]] +git-tree-sha1 = "2eaa69a7cab70a52b9687c8bf950a5a93ec895ae" +uuid = "076d061b-32b6-4027-95e0-9a2c6f6d7e74" +version = "0.2.0" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] @@ -972,15 +1073,15 @@ version = "0.1.17" [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb" +git-tree-sha1 = "68c173f4f449de5b438ee67ed0c9c748dc31a2ec" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.24" +version = "0.3.28" [[deps.HypothesisTests]] -deps = ["Combinatorics", "Distributions", "LinearAlgebra", "Printf", "Random", "Rmath", "Roots", "Statistics", "StatsAPI", "StatsBase"] -git-tree-sha1 = "4b5d5ba51f5f473737ed9de6d8a7aa190ad8c72f" +deps = ["Combinatorics", "Distributions", "LinearAlgebra", "Printf", "Random", "Roots", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "15319d5a767eb386bc4b702d5e025a0be62be293" uuid = "09f84164-cd44-5f33-b23f-e6b0d136a0d5" -version = "0.11.0" +version = "0.11.5" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools"] @@ -995,9 +1096,9 @@ version = "0.1.1" [[deps.ImageAxes]] deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"] -git-tree-sha1 = "2e4520d67b0cef90865b3ef727594d2a58e0e1f8" +git-tree-sha1 = "e12629406c6c4442539436581041d372d69c55ba" uuid = "2803e5a7-5153-5ecf-9a86-9b4c37f5f5ac" -version = "0.6.11" +version = "0.6.12" [[deps.ImageBase]] deps = ["ImageCore", "Reexport"] @@ -1007,21 +1108,21 @@ version = "0.1.7" [[deps.ImageCore]] deps = ["ColorVectorSpace", "Colors", "FixedPointNumbers", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "PrecompileTools", "Reexport"] -git-tree-sha1 = "b2a7eaa169c13f5bcae8131a83bc30eff8f71be0" +git-tree-sha1 = "8c193230235bbcee22c8066b0374f63b5683c2d3" uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534" -version = "0.10.2" +version = "0.10.5" [[deps.ImageIO]] -deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs"] -git-tree-sha1 = "437abb322a41d527c197fa800455f79d414f0a3c" +deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs", "WebP"] +git-tree-sha1 = "696144904b76e1ca433b886b4e7edd067d76cbf7" uuid = "82e4d734-157c-48bb-816b-45c225c6df19" -version = "0.6.8" +version = "0.6.9" [[deps.ImageMetadata]] deps = ["AxisArrays", "ImageAxes", "ImageBase", "ImageCore"] -git-tree-sha1 = "355e2b974f2e3212a75dfb60519de21361ad3cb7" +git-tree-sha1 = "2a81c3897be6fbcde0802a0ebe6796d0562f63ec" uuid = "bc367c6b-8a6b-528e-b4bd-a4b897500b49" -version = "0.9.9" +version = "0.9.10" [[deps.Imath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1050,9 +1151,9 @@ uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" version = "0.3.1" [[deps.InlineStrings]] -git-tree-sha1 = "45521d31238e87ee9f9732561bfee12d4eebd52d" +git-tree-sha1 = "6a9fde685a7ac1eb3495f8e812c5a7c3711c2d5e" uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.4.2" +version = "1.4.3" weakdeps = ["ArrowTypes", "Parsers"] [deps.InlineStrings.extensions] @@ -1060,14 +1161,15 @@ weakdeps = ["ArrowTypes", "Parsers"] ParsersExt = "Parsers" [[deps.IntelOpenMP_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "14eb2b542e748570b56446f4c50fbfb2306ebc45" +deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl"] +git-tree-sha1 = "0f14a5456bdc6b9731a5682f439a672750a09e48" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2024.2.0+0" +version = "2025.0.4+0" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" +version = "1.11.0" [[deps.Interpolations]] deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] @@ -1080,15 +1182,16 @@ weakdeps = ["Unitful"] InterpolationsUnitfulExt = "Unitful" [[deps.IntervalArithmetic]] -deps = ["CRlibm_jll", "MacroTools", "RoundingEmulator"] -git-tree-sha1 = "433b0bb201cd76cb087b017e49244f10394ebe9c" +deps = ["CRlibm_jll", "LinearAlgebra", "MacroTools", "OpenBLASConsistentFPCSR_jll", "RoundingEmulator"] +git-tree-sha1 = "2c337f943879911c74bb62c927b65b9546552316" uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" -version = "0.22.14" -weakdeps = ["DiffRules", "ForwardDiff", "RecipesBase"] +version = "0.22.29" +weakdeps = ["DiffRules", "ForwardDiff", "IntervalSets", "RecipesBase"] [deps.IntervalArithmetic.extensions] IntervalArithmeticDiffRulesExt = "DiffRules" IntervalArithmeticForwardDiffExt = "ForwardDiff" + IntervalArithmeticIntervalSetsExt = "IntervalSets" IntervalArithmeticRecipesBaseExt = "RecipesBase" [[deps.IntervalSets]] @@ -1103,9 +1206,9 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] IntervalSetsStatisticsExt = "Statistics" [[deps.InverseFunctions]] -git-tree-sha1 = "2787db24f4e03daf859c6509ff87764e4182f7d1" +git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.16" +version = "0.1.17" weakdeps = ["Dates", "Test"] [deps.InverseFunctions.extensions] @@ -1113,14 +1216,14 @@ weakdeps = ["Dates", "Test"] InverseFunctionsTestExt = "Test" [[deps.InvertedIndices]] -git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" +git-tree-sha1 = "6da3c4316095de0f5ee2ebd875df8721e7e0bdbe" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.3.0" +version = "1.3.1" [[deps.IrrationalConstants]] -git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" +git-tree-sha1 = "e2222959fbc6c19554dc15174c81bf7bf3aa691c" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.2.2" +version = "0.2.4" [[deps.Isoband]] deps = ["isoband_jll"] @@ -1151,16 +1254,16 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLD2]] -deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Reexport", "Requires", "TranscodingStreams", "UUIDs", "Unicode"] -git-tree-sha1 = "67d4690d32c22e28818a434b293a374cc78473d3" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Requires", "TranscodingStreams"] +git-tree-sha1 = "1059c071429b4753c0c869b75c859c44ba09a526" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.51" +version = "0.5.12" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" +git-tree-sha1 = "a007feb38b422fbdab534406aeca1b86823cb4d6" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.5.0" +version = "1.7.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1170,9 +1273,9 @@ version = "0.21.4" [[deps.JSON3]] deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] -git-tree-sha1 = "eb3edce0ed4fa32f75a0a11217433c31d56bd48b" +git-tree-sha1 = "196b41e5a854b387d99e5ede2de3fcb4d0422aae" uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -version = "1.14.0" +version = "1.14.2" weakdeps = ["ArrowTypes"] [deps.JSON3.extensions] @@ -1180,15 +1283,15 @@ weakdeps = ["ArrowTypes"] [[deps.JpegTurbo]] deps = ["CEnum", "FileIO", "ImageCore", "JpegTurbo_jll", "TOML"] -git-tree-sha1 = "fa6d0bcff8583bac20f1ffa708c3913ca605c611" +git-tree-sha1 = "9496de8fb52c224a2e3f9ff403947674517317d9" uuid = "b835a17e-a41a-41e7-81f0-2f016b05efe0" -version = "0.1.5" +version = "0.1.6" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637" +git-tree-sha1 = "eac1206917768cb54957c65a615460d87b455fc1" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.0.3+0" +version = "3.1.1+0" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -1197,21 +1300,17 @@ uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" version = "0.2.4" [[deps.KernelAbstractions]] -deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "35ceea58aa34ad08b1ae00a52622c62d1cfb8ce2" +deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"] +git-tree-sha1 = "80d268b2f4e396edc5ea004d1e0f569231c71e9e" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.24" +version = "0.9.34" +weakdeps = ["EnzymeCore", "LinearAlgebra", "SparseArrays"] [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.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] git-tree-sha1 = "7d703202e65efa1369de1279c162b915e245eed1" @@ -1224,40 +1323,28 @@ git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" version = "3.100.2+0" -[[deps.LLVM]] -deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] -git-tree-sha1 = "839c82932db86740ae729779e610f07a1640be9a" -uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.6.3" - - [deps.LLVM.extensions] - BFloat16sExt = "BFloat16s" - - [deps.LLVM.weakdeps] - BFloat16s = "ab4f0b2a-ad5b-11e8-123f-65d77653426b" - -[[deps.LLVMExtra_jll]] -deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "88b916503aac4fb7f701bb625cd84ca5dd1677bc" -uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.29+0" +[[deps.LERC_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "aaafe88dccbd957a8d82f7d05be9b69172e0cee3" +uuid = "88015f11-f218-50d7-93a8-a6af411a945d" +version = "4.0.1+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e16271d212accd09d52ee0ae98956b8a05c4b626" +git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "17.0.6+0" +version = "18.1.7+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d" +git-tree-sha1 = "1c602b1127f4751facb671441ca72715cc95938a" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.2+0" +version = "2.10.3+0" [[deps.LaTeXStrings]] -git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" +git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.1" +version = "1.4.0" [[deps.LatinHypercubeSampling]] deps = ["Random", "StableRNGs", "StatsBase", "Test"] @@ -1274,6 +1361,7 @@ version = "0.1.17" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" +version = "1.11.0" [[deps.LazyModules]] git-tree-sha1 = "a560dd966b386ac9ae60bdd3a3d3a326062d3c3e" @@ -1294,16 +1382,17 @@ 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 = "8.4.0+0" +version = "8.6.0+0" [[deps.LibGit2]] deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +version = "1.11.0" [[deps.LibGit2_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" -version = "1.6.4+0" +version = "1.7.2+0" [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] @@ -1312,42 +1401,43 @@ version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" +version = "1.11.0" [[deps.Libffi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" +git-tree-sha1 = "27ecae93dd25ee0909666e6835051dd684cc035e" uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" -version = "3.2.2+1" +version = "3.2.2+2" -[[deps.Libgcrypt_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] -git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673" -uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.11+0" - -[[deps.Libgpg_error_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed" -uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.49.0+0" +[[deps.Libglvnd_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll", "Xorg_libXext_jll"] +git-tree-sha1 = "ff3b4b9d35de638936a525ecd36e86a8bb919d11" +uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" +version = "1.7.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" +git-tree-sha1 = "be484f5c92fad0bd8acfef35fe017900b0b73809" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.17.0+0" +version = "1.18.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e" +git-tree-sha1 = "a31572773ac1b745e0343fe5e2c8ddda7a37e997" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.40.1+0" +version = "2.41.0+0" + +[[deps.Libtiff_jll]] +deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] +git-tree-sha1 = "4ab7581296671007fc33f07a721631b8855f4b1d" +uuid = "89763e89-9b03-5906-acba-b20f662cd828" +version = "4.7.1+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" +git-tree-sha1 = "321ccef73a96ba828cd51f2ab5b9f917fa73945a" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.40.1+0" +version = "2.41.0+0" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] @@ -1358,12 +1448,13 @@ version = "7.3.0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +version = "1.11.0" [[deps.LinearMaps]] deps = ["LinearAlgebra"] -git-tree-sha1 = "ee79c3208e55786de58f8dcccca098ced79f743f" +git-tree-sha1 = "7f6be2e4cdaaf558623d93113d6ddade7b916209" uuid = "7a12625a-238d-50fd-b39a-03d52299707e" -version = "3.11.3" +version = "3.11.4" weakdeps = ["ChainRulesCore", "SparseArrays", "Statistics"] [deps.LinearMaps.extensions] @@ -1373,9 +1464,9 @@ weakdeps = ["ChainRulesCore", "SparseArrays", "Statistics"] [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "a2d09619db4e765091ee5c6ffe8872849de0feea" +git-tree-sha1 = "13ca9e2586b89836fd20cccf56e57e2b9ae7f38f" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.28" +version = "0.3.29" [deps.LogExpFunctions.extensions] LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" @@ -1389,18 +1480,19 @@ version = "0.3.28" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" +version = "1.11.0" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" +git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.3" +version = "1.1.0" [[deps.LoopVectorization]] deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] -git-tree-sha1 = "8084c25a250e00ae427a379a5b607e7aed96a2dd" +git-tree-sha1 = "e5afce7eaf5b5ca0d444bcb4dc4fd78c54cbbac0" uuid = "bdcacae8-1622-11e9-2a5c-532679323890" -version = "0.12.171" +version = "0.12.172" weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [deps.LoopVectorization.extensions] @@ -1409,21 +1501,73 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [[deps.Lz4_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "7f26c8fc5229e68484e0b3447312c98e16207d11" +git-tree-sha1 = "191686b1ac1ea9c89fc52e996ad15d1d241d1e33" uuid = "5ced341a-0733-55b8-9ab6-a4889d929147" -version = "1.10.0+0" +version = "1.10.1+0" [[deps.MKL]] deps = ["Artifacts", "Libdl", "LinearAlgebra", "Logging", "MKL_jll"] -git-tree-sha1 = "18b02c359c1150bf182978e18dbd9ce7ccc860af" +git-tree-sha1 = "39fd578c295085e77aedec501149a63f9ab0c0b6" uuid = "33e6dc65-8f57-5167-99aa-e5a354878fb2" -version = "0.7.0" +version = "0.8.0" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] -git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f" +git-tree-sha1 = "5de60bc6cb3899cd318d80d627560fae2e2d99ae" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2024.2.0+0" +version = "2025.0.1+1" + +[[deps.MLCore]] +deps = ["DataAPI", "SimpleTraits", "Tables"] +git-tree-sha1 = "73907695f35bc7ffd9f11f6c4f2ee8c1302084be" +uuid = "c2834f40-e789-41da-a90e-33b280584a8c" +version = "1.0.0" + +[[deps.MLDataDevices]] +deps = ["Adapt", "Compat", "Functors", "Preferences", "Random"] +git-tree-sha1 = "1326836c4c845cfabc542b658c8686f0c31a9911" +uuid = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40" +version = "1.9.1" + + [deps.MLDataDevices.extensions] + MLDataDevicesAMDGPUExt = "AMDGPU" + MLDataDevicesCUDAExt = "CUDA" + MLDataDevicesChainRulesCoreExt = "ChainRulesCore" + MLDataDevicesChainRulesExt = "ChainRules" + MLDataDevicesComponentArraysExt = "ComponentArrays" + MLDataDevicesFillArraysExt = "FillArrays" + MLDataDevicesGPUArraysExt = "GPUArrays" + MLDataDevicesMLUtilsExt = "MLUtils" + MLDataDevicesMetalExt = ["GPUArrays", "Metal"] + MLDataDevicesOneHotArraysExt = "OneHotArrays" + MLDataDevicesReactantExt = "Reactant" + MLDataDevicesRecursiveArrayToolsExt = "RecursiveArrayTools" + MLDataDevicesReverseDiffExt = "ReverseDiff" + MLDataDevicesSparseArraysExt = "SparseArrays" + MLDataDevicesTrackerExt = "Tracker" + MLDataDevicesZygoteExt = "Zygote" + MLDataDevicescuDNNExt = ["CUDA", "cuDNN"] + MLDataDevicesoneAPIExt = ["GPUArrays", "oneAPI"] + + [deps.MLDataDevices.weakdeps] + AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ComponentArrays = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66" + FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" + GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" + MLUtils = "f1d291b0-491e-4a28-83b9-f70985020b54" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + OneHotArrays = "0b1bfda6-eb8a-41d2-88d8-f5af5cad476f" + Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" + RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" + cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" + oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b" [[deps.MLFlowClient]] deps = ["Dates", "FilePathsBase", "HTTP", "JSON", "ShowCases", "URIs", "UUIDs"] @@ -1473,9 +1617,9 @@ version = "0.3.7" [[deps.MLJIteration]] deps = ["IterationControl", "MLJBase", "Random", "Serialization"] -git-tree-sha1 = "f93f381a82fc1768c1a99c27a84b7ea1b1ee186d" +git-tree-sha1 = "ad16cfd261e28204847f509d1221a581286448ae" uuid = "614be32b-d00c-4edb-bd02-1eb411ab5e55" -version = "0.6.2" +version = "0.6.3" [[deps.MLJLinearModels]] deps = ["DocStringExtensions", "IterativeSolvers", "LinearAlgebra", "LinearMaps", "MLJModelInterface", "Optim", "Parameters"] @@ -1491,9 +1635,9 @@ version = "1.11.0" [[deps.MLJModels]] deps = ["CategoricalArrays", "CategoricalDistributions", "Combinatorics", "Dates", "Distances", "Distributions", "InteractiveUtils", "LinearAlgebra", "MLJModelInterface", "Markdown", "OrderedCollections", "Parameters", "Pkg", "PrettyPrinting", "REPL", "Random", "RelocatableFolders", "ScientificTypes", "StatisticalTraits", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "c1b1f72379d15079d2c97937d9c1ed38f9ab4679" +git-tree-sha1 = "09381923be5ed34416ed77badbc26e1adf295492" uuid = "d491faf4-2d78-11e9-2867-c94bc002c0b7" -version = "0.17.4" +version = "0.17.9" [[deps.MLJTuning]] deps = ["ComputationalResources", "Distributed", "Distributions", "LatinHypercubeSampling", "MLJBase", "ProgressMeter", "Random", "RecipesBase", "StatisticalMeasuresBase"] @@ -1503,9 +1647,9 @@ version = "0.8.8" [[deps.MLJXGBoostInterface]] deps = ["MLJModelInterface", "SparseArrays", "Tables", "XGBoost"] -git-tree-sha1 = "25769259346a017d227c2134347db4c449d43625" +git-tree-sha1 = "385031c897e822755e7d194b0f9745fb20129972" uuid = "54119dfa-1dab-4055-a167-80440f4f7a91" -version = "0.3.11" +version = "0.3.12" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1513,28 +1657,27 @@ uuid = "d8e11817-5142-5d16-987a-aa16d5891078" version = "0.4.17" [[deps.MLUtils]] -deps = ["ChainRulesCore", "Compat", "DataAPI", "DelimitedFiles", "FLoops", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] -git-tree-sha1 = "b45738c2e3d0d402dffa32b2c1654759a2ac35a4" +deps = ["ChainRulesCore", "Compat", "DataAPI", "DelimitedFiles", "FLoops", "MLCore", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] +git-tree-sha1 = "a772d8d1987433538a5c226f79393324b55f7846" uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" -version = "0.4.4" +version = "0.4.8" [[deps.MacroTools]] -deps = ["Markdown", "Random"] -git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" +git-tree-sha1 = "72aebe0b5051e5143a079a4685a46da330a40472" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.13" +version = "0.5.15" [[deps.Makie]] -deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"] -git-tree-sha1 = "204f06860af9008fa08b3a4842f48116e1209a2c" +deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageBase", "ImageIO", "InteractiveUtils", "Interpolations", "IntervalSets", "InverseFunctions", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"] +git-tree-sha1 = "be3051d08b78206fb5e688e8d70c9e84d0264117" uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" -version = "0.21.9" +version = "0.21.18" [[deps.MakieCore]] deps = ["ColorTypes", "GeometryBasics", "IntervalSets", "Observables"] -git-tree-sha1 = "b0e2e3473af351011e598f9219afb521121edd2b" +git-tree-sha1 = "9019b391d7d086e841cbeadc13511224bd029ab3" uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b" -version = "0.8.6" +version = "0.8.12" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -1549,6 +1692,7 @@ version = "0.4.2" [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +version = "1.11.0" [[deps.MathTeXEngine]] deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "Test", "UnicodeFun"] @@ -1565,13 +1709,13 @@ version = "1.1.9" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+1" +version = "2.28.6+0" [[deps.MetaGraphsNext]] deps = ["Graphs", "JLD2", "SimpleTraits"] -git-tree-sha1 = "a385fe5aa1384647e55c0c8773457b71e9b08518" +git-tree-sha1 = "1e3b196ecbbf221d4d3696ea9de4288bea4c39f9" uuid = "fa8bd995-216d-47f1-8a91-f3b68fbeb377" -version = "0.7.0" +version = "0.7.3" [[deps.MicroCollections]] deps = ["Accessors", "BangBang", "InitialValues"] @@ -1587,6 +1731,7 @@ version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" +version = "1.11.0" [[deps.Mocking]] deps = ["Compat", "ExprTools"] @@ -1602,19 +1747,19 @@ version = "0.3.4" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2023.1.10" +version = "2023.12.12" [[deps.NLSolversBase]] -deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" +deps = ["ADTypes", "DifferentiationInterface", "Distributed", "FiniteDiff", "ForwardDiff"] +git-tree-sha1 = "b14c7be6046e7d48e9063a0053f95ee0fc954176" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.8.3" +version = "7.9.1" [[deps.NNlib]] -deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "ae52c156a63bb647f80c26319b104e99e5977e51" +deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "ScopedValues", "Statistics"] +git-tree-sha1 = "4abc63cdd8dd9dd925d8e879cda280bedc8013ca" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.22" +version = "0.9.30" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1622,19 +1767,23 @@ version = "0.9.22" NNlibCUDAExt = "CUDA" NNlibEnzymeCoreExt = "EnzymeCore" NNlibFFTWExt = "FFTW" + NNlibForwardDiffExt = "ForwardDiff" + NNlibSpecialFunctionsExt = "SpecialFunctions" [deps.NNlib.weakdeps] AMDGPU = "21141c5a-9bdb-4563-92ae-f87d6854732e" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" +git-tree-sha1 = "9b8215b1ee9e78a293f99797cd31375471b2bcae" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.2" +version = "1.1.3" [[deps.NameResolution]] deps = ["PrettyPrint"] @@ -1650,9 +1799,9 @@ version = "1.1.1" [[deps.NetworkLayout]] deps = ["GeometryBasics", "LinearAlgebra", "Random", "Requires", "StaticArrays"] -git-tree-sha1 = "91bb2fedff8e43793650e7a677ccda6e6e6e166b" +git-tree-sha1 = "f7466c23a7c5029dc99e8358e7ce5d81a117c364" uuid = "46757867-2c16-5918-afeb-47bfcb05e46a" -version = "0.4.6" +version = "0.4.10" weakdeps = ["Graphs"] [deps.NetworkLayout.extensions] @@ -1668,9 +1817,9 @@ uuid = "510215fc-4207-5dde-b226-833fc4488ee2" version = "0.5.5" [[deps.OffsetArrays]] -git-tree-sha1 = "1a27764e945a152f7ca7efa04de513d473e9542e" +git-tree-sha1 = "117432e406b5c023f665fa73dc26e79ec3630151" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.14.1" +version = "1.17.0" weakdeps = ["Adapt"] [deps.OffsetArrays.extensions] @@ -1684,20 +1833,26 @@ version = "1.3.5+1" [[deps.OneHotArrays]] deps = ["Adapt", "ChainRulesCore", "Compat", "GPUArraysCore", "LinearAlgebra", "NNlib"] -git-tree-sha1 = "963a3f28a2e65bb87a68033ea4a616002406037d" +git-tree-sha1 = "ec127b6ef91de07a48ed9db251d63b0a46490b90" uuid = "0b1bfda6-eb8a-41d2-88d8-f5af5cad476f" -version = "0.2.5" +version = "0.2.7" + +[[deps.OpenBLASConsistentFPCSR_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "567515ca155d0020a45b05175449b499c63e7015" +uuid = "6cdc7f73-28fd-5e50-80fb-958a8875b1af" +version = "0.3.29+0" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.23+4" +version = "0.3.27+1" [[deps.OpenEXR]] deps = ["Colors", "FileIO", "OpenEXR_jll"] -git-tree-sha1 = "327f53360fdb54df7ecd01e96ef1983536d1e633" +git-tree-sha1 = "97db9e07fe2091882c765380ef58ec553074e9c7" uuid = "52e1d378-f018-4a11-a4be-720524705ac7" -version = "0.3.2" +version = "0.3.3" [[deps.OpenEXR_jll]] deps = ["Artifacts", "Imath_jll", "JLLWrappers", "Libdl", "Zlib_jll"] @@ -1708,13 +1863,13 @@ version = "3.2.4+0" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+2" +version = "0.8.1+4" [[deps.OpenML]] deps = ["ARFFFiles", "HTTP", "JSON", "Markdown", "Pkg", "Scratch"] -git-tree-sha1 = "6efb039ae888699d5a74fb593f6f3e10c7193e33" +git-tree-sha1 = "63603b2b367107e87dbceda4e33c67aed17e50e0" uuid = "8b6db2d4-7670-4922-a472-f9537c81ab66" -version = "0.3.1" +version = "0.3.2" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] @@ -1724,21 +1879,21 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a028ee3cb5641cccc4c24e90c36b0a4f7707bdf5" +git-tree-sha1 = "a9697f1d06cc3eb3fb3ad49cc67f2cfabaac31ea" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.14+0" +version = "3.0.16+0" [[deps.OpenSpecFun_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1346c9208249809840c91b26703912dff463d335" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" -version = "0.5.5+0" +version = "0.5.6+0" [[deps.Optim]] -deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89" +deps = ["Compat", "EnumX", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] +git-tree-sha1 = "31b3b1b8e83ef9f1d50d74f1dd5f19a37a304a1f" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.9.4" +version = "1.12.0" [deps.Optim.extensions] OptimMOIExt = "MathOptInterface" @@ -1747,10 +1902,20 @@ version = "1.9.4" MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" [[deps.Optimisers]] -deps = ["ChainRulesCore", "Functors", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "6572fe0c5b74431aaeb0b18a4aa5ef03c84678be" +deps = ["ChainRulesCore", "ConstructionBase", "Functors", "LinearAlgebra", "Random", "Statistics"] +git-tree-sha1 = "131dc319e7c58317e8c6d5170440f6bdaee0a959" uuid = "3bd65402-5787-11e9-1adc-39752487f4e2" -version = "0.3.3" +version = "0.4.6" + + [deps.Optimisers.extensions] + OptimisersAdaptExt = ["Adapt"] + OptimisersEnzymeCoreExt = "EnzymeCore" + OptimisersReactantExt = "Reactant" + + [deps.Optimisers.weakdeps] + Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" + EnzymeCore = "f151be2c-9106-41f4-ab19-57ee4f262869" + Reactant = "3c362404-f566-11ee-1572-e11a4b42c853" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1759,9 +1924,9 @@ uuid = "91d4177d-7536-5919-b921-800302f37372" version = "1.3.3+0" [[deps.OrderedCollections]] -git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" +git-tree-sha1 = "cc4054e898b852042d7b503313f7ad03de99c3dd" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.3" +version = "1.8.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1770,27 +1935,27 @@ version = "10.42.0+1" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" +git-tree-sha1 = "0e1340b5d98971513bddaa6bbed470670cebbbfe" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.31" +version = "0.11.34" [[deps.PNGFiles]] deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] -git-tree-sha1 = "67186a2bc9a90f9f85ff3cc8277868961fb57cbd" +git-tree-sha1 = "cf181f0b1e6a18dfeb0ee8acc4a9d1672499626c" uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883" -version = "0.4.3" +version = "0.4.4" [[deps.PackageCompiler]] deps = ["Artifacts", "Glob", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "48d4429862157ad5500c4f61444db1b8c32e0a2b" +git-tree-sha1 = "5d13e5b70011762b74f86fc08385303589f80272" uuid = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d" -version = "2.1.17" +version = "2.2.0" [[deps.Packing]] deps = ["GeometryBasics"] -git-tree-sha1 = "ec3edfe723df33528e085e632414499f26650501" +git-tree-sha1 = "bc5bf2ea3d5351edf285a06b0016788a121ce92c" uuid = "19eb6ba3-879d-56ad-ad62-d5c202156566" -version = "0.5.0" +version = "0.5.1" [[deps.PaddedViews]] deps = ["OffsetArrays"] @@ -1800,9 +1965,9 @@ version = "0.5.12" [[deps.Pango_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e127b609fb9ecba6f201ba7ab753d5a605d53801" +git-tree-sha1 = "3b31172c032a1def20c98dae3f2cdc9d10e3b561" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.54.1+0" +version = "1.56.1+0" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -1812,20 +1977,24 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" +git-tree-sha1 = "44f6c1f38f77cafef9450ff93946c53bd9ca16ff" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.8.1" +version = "2.8.2" [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] -git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b" +git-tree-sha1 = "db76b1ecd5e9715f3d043cec13b2ec93ce015d53" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.43.4+0" +version = "0.44.2+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.10.0" +version = "1.11.0" +weakdeps = ["REPL"] + + [deps.Pkg.extensions] + REPLExt = "REPL" [[deps.PkgVersion]] deps = ["Pkg"] @@ -1834,10 +2003,10 @@ uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688" version = "0.3.3" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "7b1a9df27f072ac4c9c7cbe5efb198489258d1f5" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"] +git-tree-sha1 = "3ca9a356cd2e113c420f2c13bea19f8d3fb1cb18" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.4.1" +version = "1.4.3" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] @@ -1886,13 +2055,14 @@ version = "0.4.2" [[deps.PrettyTables]] deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "66b20dd35966a748321d3b2537c4584cf40387c7" +git-tree-sha1 = "1101cd475833706e4d0e7b122218257178f48f34" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.3.2" +version = "2.4.0" [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" +version = "1.11.0" [[deps.ProgressLogging]] deps = ["Logging", "SHA", "UUIDs"] @@ -1902,34 +2072,42 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "8f6bc219586aef8baf0ff9a5fe16ee9c70cb65e4" +git-tree-sha1 = "13c5103482a8ed1536a54c08d0e742ae3dca2d42" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.10.2" +version = "1.10.4" [[deps.PtrArrays]] -git-tree-sha1 = "f011fbb92c4d401059b2212c05c0601b70f8b759" +git-tree-sha1 = "1d36ef11a9aaf1e8b74dacc6a731dd1de8fd493d" uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" -version = "1.2.0" +version = "1.3.0" [[deps.QOI]] deps = ["ColorTypes", "FileIO", "FixedPointNumbers"] -git-tree-sha1 = "18e8f4d1426e965c7b532ddd260599e1510d26ce" +git-tree-sha1 = "8b3fc30bc0390abdce15f8822c889f669baed73d" uuid = "4b34888f-f399-49d4-9bb3-47ed5cae4e65" -version = "1.0.0" +version = "1.0.1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "e237232771fdafbae3db5c31275303e056afaa9f" +git-tree-sha1 = "9da16da70037ba9d701192e27befedefb91ec284" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.10.1" +version = "2.11.2" + + [deps.QuadGK.extensions] + QuadGKEnzymeExt = "Enzyme" + + [deps.QuadGK.weakdeps] + Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" [[deps.REPL]] -deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] +deps = ["InteractiveUtils", "Markdown", "Sockets", "StyledStrings", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" +version = "1.11.0" [[deps.Random]] deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +version = "1.11.0" [[deps.RangeArrays]] git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5" @@ -1971,35 +2149,37 @@ version = "1.0.1" [[deps.Requires]] deps = ["UUIDs"] -git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" +git-tree-sha1 = "62389eeff14780bfe55195b7204c0d8738436d64" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.3.0" +version = "1.3.1" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.1" +version = "0.8.0" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e60724fd3beea548353984dc61c943ecddb0e29a" +git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.3+0" +version = "0.5.1+0" [[deps.Roots]] -deps = ["Accessors", "ChainRulesCore", "CommonSolve", "Printf"] -git-tree-sha1 = "3484138c9fa4296a0cf46a74ca3f97b59d12b1d0" +deps = ["Accessors", "CommonSolve", "Printf"] +git-tree-sha1 = "3ac13765751ffc81e3531223782d9512f6023f71" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.1.6" +version = "2.2.7" [deps.Roots.extensions] + RootsChainRulesCoreExt = "ChainRulesCore" RootsForwardDiffExt = "ForwardDiff" RootsIntervalRootFindingExt = "IntervalRootFinding" RootsSymPyExt = "SymPy" RootsSymPyPythonCallExt = "SymPyPythonCall" [deps.Roots.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807" SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" @@ -2016,9 +2196,9 @@ version = "0.7.0" [[deps.SIMD]] deps = ["PrecompileTools"] -git-tree-sha1 = "2803cab51702db743f3fda07dd1745aadfbf43bd" +git-tree-sha1 = "fea870727142270bdf7624ad675901a1ee3b4c87" uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.5.0" +version = "3.7.1" [[deps.SIMDTypes]] git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" @@ -2039,21 +2219,27 @@ version = "1.6.1" [[deps.SQLite_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "004fffbe2711abdc7263a980bbb1af9620781dd9" +git-tree-sha1 = "9a325057cdb9b066f1f96dc77218df60fe3007cb" uuid = "76ed43ae-9a5d-5a62-8c75-30186b810ce8" -version = "3.45.3+0" +version = "3.48.0+0" [[deps.ScientificTypes]] deps = ["CategoricalArrays", "ColorTypes", "Dates", "Distributions", "PrettyTables", "Reexport", "ScientificTypesBase", "StatisticalTraits", "Tables"] -git-tree-sha1 = "75ccd10ca65b939dab03b812994e571bf1e3e1da" +git-tree-sha1 = "4d083ffec53dbd5097a6723b0699b175be2b61fb" uuid = "321657f4-b219-11e9-178b-2701a2544e81" -version = "3.0.2" +version = "3.1.0" [[deps.ScientificTypesBase]] git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" uuid = "30f210dd-8aff-4c5f-94ba-8e64358c1161" version = "3.0.0" +[[deps.ScopedValues]] +deps = ["HashArrayMappedTries", "Logging"] +git-tree-sha1 = "1147f140b4c8ddab224c94efa9569fc23d63ab44" +uuid = "7e506255-f358-4e82-b7e4-beb19740aa63" +version = "1.3.0" + [[deps.Scratch]] deps = ["Dates"] git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" @@ -2062,18 +2248,19 @@ version = "1.2.1" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "ff11acffdb082493657550959d4feb4b6149e73a" +git-tree-sha1 = "712fb0231ee6f9120e005ccd56297abbc053e7e0" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.4.5" +version = "1.4.8" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" +version = "1.11.0" [[deps.Setfield]] deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] -git-tree-sha1 = "e2cc6d8c88613c05e1defb55170bf5ff211fbeac" +git-tree-sha1 = "c5391c6ace3bc430ca630251d02ea9687169ca68" uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" -version = "1.1.1" +version = "1.1.2" [[deps.ShaderAbstractions]] deps = ["ColorTypes", "FixedPointNumbers", "GeometryBasics", "LinearAlgebra", "Observables", "StaticArrays", "StructArrays", "Tables"] @@ -2084,6 +2271,7 @@ version = "0.4.1" [[deps.SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" +version = "1.11.0" [[deps.ShiftedArrays]] git-tree-sha1 = "503688b59397b3307443af35cd953a13e8005c16" @@ -2108,9 +2296,9 @@ uuid = "73760f76-fbc4-59ce-8f25-708e95d2df96" version = "0.4.0" [[deps.SimpleBufferStream]] -git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.1.0" +version = "1.2.0" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -2126,12 +2314,13 @@ version = "0.1.3" [[deps.SnpArrays]] deps = ["Adapt", "CSV", "CodecBzip2", "CodecXz", "CodecZlib", "CodecZstd", "DataFrames", "DelimitedFiles", "Glob", "LinearAlgebra", "LoopVectorization", "Missings", "Mmap", "Printf", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Tables", "TranscodingStreams", "VariantCallFormat", "VectorizationBase"] -git-tree-sha1 = "d81de62a0acdbfd7d7ff3d64403eccf06c2fe986" +git-tree-sha1 = "810c0a75a336d63cb2b51561f1c1e3ccf6dbc2ad" uuid = "4e780e97-f5bf-4111-9dc4-b70aaf691b06" -version = "0.3.21" +version = "0.3.22" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" +version = "1.11.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] @@ -2142,7 +2331,7 @@ version = "1.2.1" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -version = "1.10.0" +version = "1.11.0" [[deps.SparseInverseSubset]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] @@ -2152,15 +2341,15 @@ version = "0.1.2" [[deps.SparseMatricesCSR]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "38677ca58e80b5cad2382e5a1848f93b054ad28d" +git-tree-sha1 = "cc05d16e340aecfa0e4cf4616194abc894cd0bca" uuid = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1" -version = "0.6.7" +version = "0.6.9" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14" +git-tree-sha1 = "41852b8679f78c8d8961eeadc8f62cef861a52e3" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.4.0" +version = "2.5.1" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -2192,9 +2381,9 @@ version = "0.1.1" [[deps.Static]] deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] -git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" +git-tree-sha1 = "f737d444cb0ad07e61b3c1bef8eb91203c321eff" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "1.1.1" +version = "1.2.0" [[deps.StaticArrayInterface]] deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Static"] @@ -2209,9 +2398,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50" +git-tree-sha1 = "0feb6b9031bd5c51f9072393eb5ab3efd31bf9e4" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.7" +version = "1.9.13" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -2225,9 +2414,9 @@ version = "1.4.3" [[deps.StatisticalMeasures]] deps = ["CategoricalArrays", "CategoricalDistributions", "Distributions", "LearnAPI", "LinearAlgebra", "MacroTools", "OrderedCollections", "PrecompileTools", "ScientificTypesBase", "StatisticalMeasuresBase", "Statistics", "StatsBase"] -git-tree-sha1 = "8b5a165b0ee2b361d692636bfb423b19abfd92b3" +git-tree-sha1 = "c1d4318fa41056b839dfbb3ee841f011fa6e8518" uuid = "a19d573c-0a75-4610-95b3-7071388c7541" -version = "0.1.6" +version = "0.1.7" [deps.StatisticalMeasures.extensions] LossFunctionsExt = "LossFunctions" @@ -2239,9 +2428,9 @@ version = "0.1.6" [[deps.StatisticalMeasuresBase]] deps = ["CategoricalArrays", "InteractiveUtils", "MLUtils", "MacroTools", "OrderedCollections", "PrecompileTools", "ScientificTypesBase", "Statistics"] -git-tree-sha1 = "17dfb22e2e4ccc9cd59b487dce52883e0151b4d3" +git-tree-sha1 = "e4f508cf3b3253f3eb357274fe36fb3332ca9896" uuid = "c062fc1d-0d66-479b-b6ac-8b44719de4cc" -version = "0.1.1" +version = "0.1.2" [[deps.StatisticalTraits]] deps = ["ScientificTypesBase"] @@ -2250,9 +2439,14 @@ uuid = "64bff920-2084-43da-a3e6-9bb72801c0c9" version = "3.4.0" [[deps.Statistics]] -deps = ["LinearAlgebra", "SparseArrays"] +deps = ["LinearAlgebra"] +git-tree-sha1 = "ae3bb1eb3bba077cd276bc5cfc337cc65c3075c0" uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.10.0" +version = "1.11.1" +weakdeps = ["SparseArrays"] + + [deps.Statistics.extensions] + SparseArraysExt = ["SparseArrays"] [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -2261,16 +2455,16 @@ uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" version = "1.7.0" [[deps.StatsBase]] -deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "5cf7606d6cef84b543b483848d4ae08ad9832b21" +deps = ["AliasTables", "DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "29321314c920c26684834965ec2ce0dacc9cf8e5" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.3" +version = "0.34.4" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" +git-tree-sha1 = "35b09e80be285516e52c9054792c884b9216ae3c" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.1" +version = "1.4.0" weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] @@ -2291,28 +2485,38 @@ version = "0.3.7" [[deps.StringManipulation]] deps = ["PrecompileTools"] -git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" +git-tree-sha1 = "725421ae8e530ec29bcbdddbe91ff8053421d023" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.4" +version = "0.4.1" + +[[deps.StringViews]] +git-tree-sha1 = "ec4bf39f7d25db401bcab2f11d2929798c0578e5" +uuid = "354b36f9-a18e-4713-926e-db85100087ba" +version = "1.3.4" [[deps.StructArrays]] deps = ["ConstructionBase", "DataAPI", "Tables"] -git-tree-sha1 = "f4dc295e983502292c4c3f951dbb4e985e35b3be" +git-tree-sha1 = "9537ef82c42cdd8c5d443cbc359110cbb36bae10" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.18" -weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"] +version = "0.6.21" +weakdeps = ["Adapt", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "SparseArrays", "StaticArrays"] [deps.StructArrays.extensions] StructArraysAdaptExt = "Adapt" - StructArraysGPUArraysCoreExt = "GPUArraysCore" + StructArraysGPUArraysCoreExt = ["GPUArraysCore", "KernelAbstractions"] + StructArraysLinearAlgebraExt = "LinearAlgebra" StructArraysSparseArraysExt = "SparseArrays" StructArraysStaticArraysExt = "StaticArrays" [[deps.StructTypes]] deps = ["Dates", "UUIDs"] -git-tree-sha1 = "ca4bccb03acf9faaf4137a9abc1881ed1841aa70" +git-tree-sha1 = "159331b30e94d7b11379037feeb9b690950cace8" uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" -version = "1.10.0" +version = "1.11.0" + +[[deps.StyledStrings]] +uuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b" +version = "1.11.0" [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] @@ -2321,24 +2525,29 @@ 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" +version = "7.7.0+0" [[deps.TMLE]] -deps = ["AbstractDifferentiation", "AutoHashEquals", "CategoricalArrays", "Combinatorics", "Distributions", "GLM", "Graphs", "HypothesisTests", "LogExpFunctions", "MLJBase", "MLJGLMInterface", "MLJModels", "MetaGraphsNext", "Missings", "OrderedCollections", "PrecompileTools", "Random", "SplitApplyCombine", "Statistics", "TableOperations", "Tables", "Zygote"] -git-tree-sha1 = "2928dc0b1c3e26d8dcaaa7585dedefe33f687020" +deps = ["AutoHashEquals", "CategoricalArrays", "Combinatorics", "DifferentiationInterface", "Distributions", "GLM", "Graphs", "HypothesisTests", "LogExpFunctions", "MLJBase", "MLJGLMInterface", "MLJModels", "MetaGraphsNext", "Missings", "OrderedCollections", "Random", "SplitApplyCombine", "Statistics", "TableOperations", "Tables", "Zygote"] +git-tree-sha1 = "d951eb4c5bf2985f2b286f84ceba6ab28a3b32da" uuid = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf" -version = "0.17.0" -weakdeps = ["JSON", "YAML"] +version = "0.18.1" [deps.TMLE.extensions] + CausalTablesExt = "CausalTables" JSONExt = "JSON" YAMLExt = "YAML" + [deps.TMLE.weakdeps] + CausalTables = "6af48e0c-efc2-4bf7-a92f-a553ccf79fd6" + JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" + YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" + [[deps.TMLECLI]] -deps = ["ArgParse", "Arrow", "CSV", "CategoricalArrays", "Combinatorics", "Configurations", "DataFrames", "EvoTrees", "GLMNet", "JLD2", "JSON", "MKL", "MLJ", "MLJBase", "MLJLinearModels", "MLJModelInterface", "MLJModels", "MLJXGBoostInterface", "Mmap", "PackageCompiler", "Random", "Serialization", "TMLE", "Tables", "YAML"] -git-tree-sha1 = "eb8a7aa2a17c0dd2fb165dd79a860c1aea0df55a" +deps = ["ArgParse", "Arrow", "CSV", "CategoricalArrays", "Combinatorics", "Configurations", "DataFrames", "EvoTrees", "GLMNet", "JLD2", "JSON", "MLJ", "MLJBase", "MLJLinearModels", "MLJModelInterface", "MLJModels", "MLJXGBoostInterface", "PackageCompiler", "Random", "Serialization", "TMLE", "Tables", "YAML"] +git-tree-sha1 = "a26b409928eeae05f99138e19162316e1c0f0a87" uuid = "2573d147-4098-46ba-9db2-8608d210ccac" -version = "0.9.1" +version = "0.10.2" [[deps.TOML]] deps = ["Dates"] @@ -2347,9 +2556,9 @@ version = "1.0.3" [[deps.TZJData]] deps = ["Artifacts"] -git-tree-sha1 = "1607ad46cf8d642aa779a1d45af1c8620dbf6915" +git-tree-sha1 = "72df96b3a595b7aab1e101eb07d2a435963a97e2" uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" -version = "1.2.0+2024a" +version = "1.5.0+2025b" [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] @@ -2375,9 +2584,9 @@ uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" version = "1.10.0" [[deps.TargeneCore]] -deps = ["ArgParse", "Arrow", "BGEN", "CSV", "CairoMakie", "CategoricalArrays", "Combinatorics", "DataFrames", "Distributions", "HypothesisTests", "JLD2", "PackageCompiler", "Random", "Serialization", "SnpArrays", "StableRNGs", "Statistics", "TMLE", "TMLECLI", "YAML"] -git-tree-sha1 = "73699459340c54c18633fad5f77d5c0a5ac676f3" -repo-rev = "v0.9.0" +deps = ["ArgParse", "Arrow", "BGEN", "CSV", "CairoMakie", "CategoricalArrays", "Combinatorics", "DataFrames", "Distributions", "HypothesisTests", "JLD2", "MKL", "Mmap", "OrderedCollections", "PackageCompiler", "Random", "Serialization", "SnpArrays", "StableRNGs", "Statistics", "TMLE", "TMLECLI", "YAML"] +git-tree-sha1 = "6f5dfa4c302dab2e30e12bd4cfc1de1ac1fa1e93" +repo-rev = "extra_treatment_covariates_ol" repo-url = "https://github.com/TARGENE/TargeneCore.jl" uuid = "3aa9512e-41c2-4133-bfaa-ba71048dd391" version = "0.9.0" @@ -2391,6 +2600,7 @@ version = "0.1.1" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +version = "1.11.0" [[deps.TextWrap]] git-tree-sha1 = "43044b737fa70bc12f6105061d3da38f881a3e3c" @@ -2399,21 +2609,21 @@ version = "1.0.2" [[deps.ThreadingUtilities]] deps = ["ManualMemory"] -git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27" +git-tree-sha1 = "18ad3613e129312fe67789a71720c3747e598a61" uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" -version = "0.5.2" +version = "0.5.3" [[deps.TiffImages]] deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "SIMD", "UUIDs"] -git-tree-sha1 = "bc7fd5c91041f44636b2c134041f7e5263ce58ae" +git-tree-sha1 = "f21231b166166bebc73b99cea236071eb047525b" uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" -version = "0.10.0" +version = "0.11.3" [[deps.TimeZones]] -deps = ["Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] -git-tree-sha1 = "b92aebdd3555f3a7e3267cf17702033c2814ef48" +deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "2c705e96825b66c4a3f25031a683c06518256dd3" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.18.0" +version = "1.21.3" weakdeps = ["RecipesBase"] [deps.TimeZones.extensions] @@ -2426,12 +2636,13 @@ uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" version = "0.9.13" [[deps.Transducers]] -deps = ["Accessors", "Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"] -git-tree-sha1 = "5215a069867476fc8e3469602006b9670e68da23" +deps = ["Accessors", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"] +git-tree-sha1 = "7deeab4ff96b85c5f72c824cae53a1398da3d1cb" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.82" +version = "0.4.84" [deps.Transducers.extensions] + TransducersAdaptExt = "Adapt" TransducersBlockArraysExt = "BlockArrays" TransducersDataFramesExt = "DataFrames" TransducersLazyArraysExt = "LazyArrays" @@ -2439,6 +2650,7 @@ version = "0.4.82" TransducersReferenceablesExt = "Referenceables" [deps.Transducers.weakdeps] + Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" @@ -2451,13 +2663,14 @@ uuid = "981d1d27-644d-49a2-9326-4793e63143c3" version = "0.1.0" [[deps.URIs]] -git-tree-sha1 = "67db6cc7b3821e19ebe75791a9dd19c9b1188f2b" +git-tree-sha1 = "cbbebadbcc76c5ca1cc4b4f3b0614b3e603b5000" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.5.1" +version = "1.5.2" [[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" +version = "1.11.0" [[deps.UnPack]] git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" @@ -2466,6 +2679,7 @@ version = "1.0.2" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" +version = "1.11.0" [[deps.UnicodeFun]] deps = ["REPL"] @@ -2475,9 +2689,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" +git-tree-sha1 = "c0667a8e676c53d390a09dc6870b3d8d6650e2bf" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.21.0" +version = "1.22.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -2485,15 +2699,15 @@ weakdeps = ["ConstructionBase", "InverseFunctions"] InverseFunctionsUnitfulExt = "InverseFunctions" [[deps.UnsafeAtomics]] -git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" +git-tree-sha1 = "b13c4edda90890e5b04ba24e20a310fbe6f249ff" uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" -version = "0.2.1" +version = "0.3.0" -[[deps.UnsafeAtomicsLLVM]] -deps = ["LLVM", "UnsafeAtomics"] -git-tree-sha1 = "bf2c553f25e954a9b38c9c0593a59bb13113f9e5" -uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" -version = "0.1.5" + [deps.UnsafeAtomics.extensions] + UnsafeAtomicsLLVM = ["LLVM"] + + [deps.UnsafeAtomics.weakdeps] + LLVM = "929cbde3-209d-540e-8aea-75f648917ca0" [[deps.VariantCallFormat]] deps = ["Automa", "BGZFStreams", "BioGenerics", "BufferedStreams"] @@ -2503,9 +2717,9 @@ version = "0.5.6" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "e7f5b81c65eb858bed630fe006837b935518aca5" +git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.70" +version = "0.21.71" [[deps.WeakRefStrings]] deps = ["DataAPI", "InlineStrings", "Parsers"] @@ -2513,6 +2727,12 @@ git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" version = "1.4.2" +[[deps.WebP]] +deps = ["CEnum", "ColorTypes", "FileIO", "FixedPointNumbers", "ImageCore", "libwebp_jll"] +git-tree-sha1 = "aa1ca3c47f119fbdae8770c29820e5e6119b83f2" +uuid = "e3aaa7dc-3e4b-44e0-be63-ffb868ccd7c1" +version = "0.1.3" + [[deps.WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] git-tree-sha1 = "c1a7aa6219628fcd757dede0ca95e245c5cd9511" @@ -2546,75 +2766,63 @@ version = "2.0.1+0" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "1165b0443d0eca63ac1e32b8c0eb69ed2f4f8127" +git-tree-sha1 = "b8b243e47228b4a3877f1dd6aee0c5d56db7fcf4" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.13.3+0" - -[[deps.XSLT_jll]] -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 = "1.1.41+0" +version = "2.13.6+1" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632" +git-tree-sha1 = "fee71455b0aaa3440dfdd54a9a36ccef829be7d4" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.4.6+0" +version = "5.8.1+0" [[deps.Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] -git-tree-sha1 = "afead5aba5aa507ad5a3bf01f58f82c8d1403495" +git-tree-sha1 = "b5899b25d17bf1889d25906fb9deed5da0c15b3b" uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" -version = "1.8.6+0" +version = "1.8.12+0" [[deps.Xorg_libXau_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6035850dcc70518ca32f012e46015b9beeda49d8" +git-tree-sha1 = "aa1261ebbac3ccc8d16558ae6799524c450ed16b" uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.11+0" +version = "1.0.13+0" [[deps.Xorg_libXdmcp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "34d526d318358a859d7de23da945578e8e8727b7" +git-tree-sha1 = "52858d64353db33a56e13c341d7bf44cd0d7b309" uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.4+0" +version = "1.1.6+0" [[deps.Xorg_libXext_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "d2d1a5c49fae4ba39983f63de6afcbea47194e85" +git-tree-sha1 = "a4c0ee07ad36bf8bbce1c3bb52d21fb1e0b987fb" uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" -version = "1.3.6+0" +version = "1.3.7+0" [[deps.Xorg_libXrender_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" +git-tree-sha1 = "7ed9347888fac59a618302ee38216dd0379c480d" uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.11+0" - -[[deps.Xorg_libpthread_stubs_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8fdda4c692503d44d04a0603d9ac0982054635f9" -uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.1+0" +version = "0.9.12+0" [[deps.Xorg_libxcb_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "bcd466676fef0878338c61e655629fa7bbc69d8e" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXau_jll", "Xorg_libXdmcp_jll"] +git-tree-sha1 = "bfcaf7ec088eaba362093393fe11aa141fa15422" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.17.0+0" +version = "1.17.1+0" [[deps.Xorg_xtrans_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" +git-tree-sha1 = "a63799ff68005991f9d9491b6e95bd3478d783cb" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.5.0+0" +version = "1.6.0+0" [[deps.YAML]] deps = ["Base64", "Dates", "Printf", "StringEncodings"] -git-tree-sha1 = "dea63ff72079443240fbd013ba006bcbc8a9ac00" +git-tree-sha1 = "b46894beba6c05cd185d174654479aaec09ea6b1" uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" -version = "0.4.12" +version = "0.4.13" [[deps.Zlib_jll]] deps = ["Libdl"] @@ -2623,31 +2831,33 @@ version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b" +git-tree-sha1 = "446b23e73536f84e8037f5dce465e92275f6a308" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.6+0" +version = "1.5.7+1" [[deps.Zygote]] -deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "19c586905e78a26f7e4e97f81716057bd6b1bc54" +deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] +git-tree-sha1 = "207d714f3514b0d564e3a08f9e9f753bf6566c2d" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.70" +version = "0.7.6" [deps.Zygote.extensions] + ZygoteAtomExt = "Atom" ZygoteColorsExt = "Colors" ZygoteDistancesExt = "Distances" ZygoteTrackerExt = "Tracker" [deps.Zygote.weakdeps] + Atom = "c52e3926-4ff0-5f6e-af25-54175e0327b1" Colors = "5ae59095-9a9b-59fe-a467-6f913c188581" Distances = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ZygoteRules]] deps = ["ChainRulesCore", "MacroTools"] -git-tree-sha1 = "27798139afc0a2afa7b1824c206d5e87ea587a00" +git-tree-sha1 = "434b3de333c75fc446aa0d19fc394edafd07ab08" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.5" +version = "0.2.7" [[deps.glmnet_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -2663,9 +2873,9 @@ version = "0.2.3+0" [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" +git-tree-sha1 = "522c1df09d05a71785765d19c9524661234738e9" uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.9.0+0" +version = "3.11.0+0" [[deps.libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] @@ -2676,7 +2886,7 @@ version = "0.15.2+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+1" +version = "5.11.0+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2686,15 +2896,15 @@ version = "2.0.3+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" +git-tree-sha1 = "068dfe202b0a05b8332f1e8e6b4080684b9c7700" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.43+1" +version = "1.6.47+0" [[deps.libsixel_jll]] -deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"] -git-tree-sha1 = "d4f63314c8aa1e48cd22aa0c17ed76cd1ae48c3c" +deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "libpng_jll"] +git-tree-sha1 = "c1733e347283df07689d71d61e14be986e49e47a" uuid = "075b6546-f08a-558a-be8f-8157d0f608a5" -version = "1.10.3+0" +version = "1.10.5+0" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] @@ -2702,16 +2912,22 @@ git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" version = "1.3.7+2" +[[deps.libwebp_jll]] +deps = ["Artifacts", "Giflib_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libglvnd_jll", "Libtiff_jll", "libpng_jll"] +git-tree-sha1 = "d2408cac540942921e7bd77272c32e58c33d8a77" +uuid = "c5f90fcd-3b7e-5836-afba-fc50a0988cb2" +version = "1.5.0+0" + [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.52.0+1" +version = "1.59.0+0" [[deps.oneTBB_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493" +git-tree-sha1 = "d5a767a3bb77135a99e433afe0eb14cd7f6914c3" uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" -version = "2021.12.0+0" +version = "2022.0.0+0" [[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] @@ -2720,9 +2936,9 @@ version = "17.4.0+2" [[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "35976a1216d6c066ea32cba2150c4fa682b276fc" +git-tree-sha1 = "14cc7083fc6dff3cc44f2bc435ee96d06ed79aa7" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "10164.0.0+0" +version = "10164.0.1+0" [[deps.x265_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] diff --git a/Project.toml b/Project.toml index a8872ac..71073d1 100644 --- a/Project.toml +++ b/Project.toml @@ -36,7 +36,11 @@ YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] -julia = "1.10" +JLD2 = "0.5" +TMLE = "0.18.1" +TMLECLI = "0.10.2" +TargeneCore = "0.9.0" +julia = "1.10, 1.11" [extras] Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" From 4c795004d6707e5f4c6de39ac88577c5406f5e37 Mon Sep 17 00:00:00 2001 From: Olivier Labayle Date: Sun, 27 Apr 2025 12:16:59 +0100 Subject: [PATCH 2/9] temporarily point to BGEN commit --- Manifest.toml | 12 +++++++----- Project.toml | 1 + 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index d0b58c0..78b2633 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,8 +1,8 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.11.4" +julia_version = "1.11.5" manifest_format = "2.0" -project_hash = "3c7db909313efc9f362b46477fcfed4c062cada1" +project_hash = "70c23d5346be58f89169899026704a4e60bb5c64" [[deps.ADTypes]] git-tree-sha1 = "e2478490447631aedba0823d4d7a80b2cc8cdb32" @@ -201,9 +201,11 @@ version = "0.4.7" [[deps.BGEN]] deps = ["CodecZlib", "CodecZstd", "GeneticVariantBase", "Printf", "SIMD", "SQLite", "SpecialFunctions", "Statistics", "Tables", "TranscodingStreams"] -git-tree-sha1 = "6512022b637fc17c297bb3050ba2e6cdd50b6fa0" +git-tree-sha1 = "aaf4444997470744c956a24bf83987918a7ed48a" +repo-rev = "075607d10cf8509910d9c62a837796105b47107c" +repo-url = "https://github.com/OpenMendel/BGEN.jl.git" uuid = "6db4b851-9beb-4b83-9d64-eb1cfb37721d" -version = "0.2.1" +version = "0.2.2" [[deps.BGZFStreams]] deps = ["CodecZlib"] @@ -1863,7 +1865,7 @@ version = "3.2.4+0" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+4" +version = "0.8.5+0" [[deps.OpenML]] deps = ["ARFFFiles", "HTTP", "JSON", "Markdown", "Pkg", "Scratch"] diff --git a/Project.toml b/Project.toml index 71073d1..5687d47 100644 --- a/Project.toml +++ b/Project.toml @@ -36,6 +36,7 @@ YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [compat] +BGEN = "0.2.2" JLD2 = "0.5" TMLE = "0.18.1" TMLECLI = "0.10.2" From 58e023cadd501f4489f3c77a8c4bc76c3b81bc0a Mon Sep 17 00:00:00 2001 From: Olivier Labayle Date: Sun, 27 Apr 2025 12:24:13 +0100 Subject: [PATCH 3/9] update CI actions --- .github/workflows/CI.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 5c132ca..578bc20 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -27,11 +27,11 @@ jobs: - x64 steps: - uses: actions/checkout@v4 - - uses: julia-actions/setup-julia@v1 + - uses: julia-actions/setup-julia@v2 with: version: ${{ matrix.version }} arch: ${{ matrix.arch }} - - uses: julia-actions/cache@v1 + - uses: julia-actions/cache@v2 - uses: julia-actions/julia-buildpkg@v1 - uses: julia-actions/julia-runtest@v1 - uses: julia-actions/julia-processcoverage@v1 From a96dbefd8966b75a60629495ce78913e45ba815f Mon Sep 17 00:00:00 2001 From: Olivier Labayle Date: Mon, 28 Apr 2025 10:19:52 +0100 Subject: [PATCH 4/9] update dependencies and fix tests --- Manifest.toml | 60 +++++++++++++++++----------- docker/Dockerfile | 2 +- src/density_estimation/neural_net.jl | 2 +- src/realistic_simulation_inputs.jl | 4 +- test/realistic_simulation_inputs.jl | 18 ++++----- 5 files changed, 49 insertions(+), 37 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 78b2633..6e2ee9b 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -298,6 +298,12 @@ version = "0.2.6" uuid = "8bf52ea8-c179-5cab-976a-9e18b702a9bc" version = "1.11.0" +[[deps.CRlibm]] +deps = ["CRlibm_jll"] +git-tree-sha1 = "66188d9d103b92b6cd705214242e27f5737a1e5e" +uuid = "96374032-68de-5a5b-8d9e-752f78720389" +version = "1.0.2" + [[deps.CRlibm_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "e329286945d0cfc04456972ea732551869af1cfc" @@ -1184,22 +1190,24 @@ weakdeps = ["Unitful"] InterpolationsUnitfulExt = "Unitful" [[deps.IntervalArithmetic]] -deps = ["CRlibm_jll", "LinearAlgebra", "MacroTools", "OpenBLASConsistentFPCSR_jll", "RoundingEmulator"] -git-tree-sha1 = "2c337f943879911c74bb62c927b65b9546552316" +deps = ["CRlibm", "MacroTools", "OpenBLASConsistentFPCSR_jll", "RoundingEmulator"] +git-tree-sha1 = "e9c16669687ce0a6af7a136a8774bf9633026e7c" uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" -version = "0.22.29" -weakdeps = ["DiffRules", "ForwardDiff", "IntervalSets", "RecipesBase"] +version = "0.22.30" +weakdeps = ["DiffRules", "ForwardDiff", "IntervalSets", "LinearAlgebra", "RecipesBase", "SparseArrays"] [deps.IntervalArithmetic.extensions] IntervalArithmeticDiffRulesExt = "DiffRules" IntervalArithmeticForwardDiffExt = "ForwardDiff" IntervalArithmeticIntervalSetsExt = "IntervalSets" + IntervalArithmeticLinearAlgebraExt = "LinearAlgebra" IntervalArithmeticRecipesBaseExt = "RecipesBase" + IntervalArithmeticSparseArraysExt = "SparseArrays" [[deps.IntervalSets]] -git-tree-sha1 = "dba9ddf07f77f60450fe5d2e2beb9854d9a49bd0" +git-tree-sha1 = "5fbb102dcb8b1a858111ae81d56682376130517d" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.10" +version = "0.7.11" weakdeps = ["Random", "RecipesBase", "Statistics"] [deps.IntervalSets.extensions] @@ -1256,10 +1264,14 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLD2]] -deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Requires", "TranscodingStreams"] -git-tree-sha1 = "1059c071429b4753c0c869b75c859c44ba09a526" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "TranscodingStreams"] +git-tree-sha1 = "8e071648610caa2d3a5351aba03a936a0c37ec61" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.5.12" +version = "0.5.13" +weakdeps = ["UnPack"] + + [deps.JLD2.extensions] + UnPackExt = "UnPack" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] @@ -1333,9 +1345,9 @@ version = "4.0.1+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" +git-tree-sha1 = "eb62a3deb62fc6d8822c0c4bef73e4412419c5d8" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "18.1.7+0" +version = "18.1.8+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1413,9 +1425,9 @@ version = "3.2.2+2" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll", "Xorg_libXext_jll"] -git-tree-sha1 = "ff3b4b9d35de638936a525ecd36e86a8bb919d11" +git-tree-sha1 = "d36c21b9e7c172a44a10484125024495e2625ac0" uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" -version = "1.7.0+0" +version = "1.7.1+1" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1630,10 +1642,10 @@ uuid = "6ee0df7b-362f-4a72-a706-9e79364fb692" version = "0.10.0" [[deps.MLJModelInterface]] -deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "ceaff6618408d0e412619321ae43b33b40c1a733" +deps = ["REPL", "Random", "ScientificTypesBase", "StatisticalTraits"] +git-tree-sha1 = "66626f80d5807921045d539b4f7153b1d47c5f8a" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.11.0" +version = "1.11.1" [[deps.MLJModels]] deps = ["CategoricalArrays", "CategoricalDistributions", "Combinatorics", "Dates", "Distances", "Distributions", "InteractiveUtils", "LinearAlgebra", "MLJModelInterface", "Markdown", "OrderedCollections", "Parameters", "Pkg", "PrettyPrinting", "REPL", "Random", "RelocatableFolders", "ScientificTypes", "StatisticalTraits", "Statistics", "StatsBase", "Tables"] @@ -1665,9 +1677,9 @@ uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" version = "0.4.8" [[deps.MacroTools]] -git-tree-sha1 = "72aebe0b5051e5143a079a4685a46da330a40472" +git-tree-sha1 = "1e0228a030642014fe5cfe68c2c0a818f9e3f522" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.15" +version = "0.5.16" [[deps.Makie]] deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageBase", "ImageIO", "InteractiveUtils", "Interpolations", "IntervalSets", "InverseFunctions", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"] @@ -1881,9 +1893,9 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a9697f1d06cc3eb3fb3ad49cc67f2cfabaac31ea" +git-tree-sha1 = "9216a80ff3682833ac4b733caa8c00390620ba5d" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.16+0" +version = "3.5.0+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] @@ -1979,9 +1991,9 @@ version = "0.12.3" [[deps.Parsers]] deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "44f6c1f38f77cafef9450ff93946c53bd9ca16ff" +git-tree-sha1 = "7d2f8f21da5db6a806faf7b9b292296da42b2810" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.8.2" +version = "2.8.3" [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] @@ -2587,8 +2599,8 @@ version = "1.10.0" [[deps.TargeneCore]] deps = ["ArgParse", "Arrow", "BGEN", "CSV", "CairoMakie", "CategoricalArrays", "Combinatorics", "DataFrames", "Distributions", "HypothesisTests", "JLD2", "MKL", "Mmap", "OrderedCollections", "PackageCompiler", "Random", "Serialization", "SnpArrays", "StableRNGs", "Statistics", "TMLE", "TMLECLI", "YAML"] -git-tree-sha1 = "6f5dfa4c302dab2e30e12bd4cfc1de1ac1fa1e93" -repo-rev = "extra_treatment_covariates_ol" +git-tree-sha1 = "12a14ca3993f895f2622a97dd0ef6dd5de382f86" +repo-rev = "update_deps" repo-url = "https://github.com/TARGENE/TargeneCore.jl" uuid = "3aa9512e-41c2-4133-bfaa-ba71048dd391" version = "0.9.0" diff --git a/docker/Dockerfile b/docker/Dockerfile index afc3c14..ee09dc5 100644 --- a/docker/Dockerfile +++ b/docker/Dockerfile @@ -1,4 +1,4 @@ -FROM julia:1.10-bullseye +FROM julia:1.11-bullseye ARG DEBIAN_FRONTEND=noninteractive diff --git a/src/density_estimation/neural_net.jl b/src/density_estimation/neural_net.jl index 358df74..5c2445a 100644 --- a/src/density_estimation/neural_net.jl +++ b/src/density_estimation/neural_net.jl @@ -198,7 +198,7 @@ end mutable struct NeuralNetworkEstimator model encoder::MLJBase.Machine - optimiser::Flux.Optimise.AbstractOptimiser + optimiser::Flux.AbstractRule resampling::MLJBase.ResamplingStrategy batchsize::Int patience::Int diff --git a/src/realistic_simulation_inputs.jl b/src/realistic_simulation_inputs.jl index 1972c7f..f00d2b7 100644 --- a/src/realistic_simulation_inputs.jl +++ b/src/realistic_simulation_inputs.jl @@ -210,7 +210,7 @@ end function write_densities(output_prefix, trait_to_variants, estimands) # Initialise densities from trait_to_variants - conditional_densities = Dict(outcome => Set(variants) for (outcome, variants) in trait_to_variants) + conditional_densities = Dict(outcome => unique(variants) for (outcome, variants) in trait_to_variants) for Ψ ∈ estimands # Update outcome's parents list outcome = get_outcome(Ψ) @@ -227,7 +227,7 @@ function write_densities(output_prefix, trait_to_variants, estimands) # Add treatment mechanism if not already present for treatment in treatments if !haskey(conditional_densities, treatment) - conditional_densities[string.(treatment)] = Set(string.(get_confounders(Ψ, treatment))) + conditional_densities[string.(treatment)] = sort(unique(string.(get_confounders(Ψ, treatment)))) end end end diff --git a/test/realistic_simulation_inputs.jl b/test/realistic_simulation_inputs.jl index 589debc..655d5ef 100644 --- a/test/realistic_simulation_inputs.jl +++ b/test/realistic_simulation_inputs.jl @@ -126,17 +126,17 @@ end conditional_densities = Set([JSON.parsefile(f) for f in TargeneCore.files_matching_prefix(string(output_prefix, ".conditional_density"))]) @test conditional_densities == Set([ # Treatment mechanisms - Dict("parents" => ["PC2", "PC1"], "outcome" => "TREAT_1"), - Dict("parents" => ["PC2", "PC1"], "outcome" => "RSID_2"), - Dict("parents" => ["PC2", "PC1"], "outcome" => "RSID_198"), + Dict("parents" => ["PC1", "PC2"], "outcome" => "TREAT_1"), + Dict("parents" => ["PC1", "PC2"], "outcome" => "RSID_2"), + Dict("parents" => ["PC1", "PC2"], "outcome" => "RSID_198"), # Outcome mechanisms: inferred from ATE with ALL - Dict("parents" => ["TREAT_1", "RSID_2", "22001", "PC2", "PC1"], "outcome" => "BINARY_2"), - Dict("parents" => ["TREAT_1", "RSID_2", "22001", "PC2", "PC1"], "outcome" => "COV_1"), - Dict("parents" => ["TREAT_1", "RSID_2", "22001", "PC2", "PC1"], "outcome" => "CONTINUOUS_2"), - Dict("parents" => ["TREAT_1", "RSID_2", "22001", "PC2", "PC1"], "outcome" => "21003"), - Dict("parents" => ["TREAT_1", "RSID_2", "22001", "PC2", "PC1"], "outcome" => "CONTINUOUS_1"), + Dict("parents" => ["RSID_2", "22001", "TREAT_1", "PC1", "PC2"], "outcome" => "BINARY_2"), + Dict("parents" => ["RSID_2", "22001", "TREAT_1", "PC1", "PC2"], "outcome" => "COV_1"), + Dict("parents" => ["RSID_2", "22001", "TREAT_1", "PC1", "PC2"], "outcome" => "CONTINUOUS_2"), + Dict("parents" => ["RSID_2", "22001", "TREAT_1", "PC1", "PC2"], "outcome" => "21003"), + Dict("parents" => ["RSID_2", "22001", "TREAT_1", "PC1", "PC2"], "outcome" => "CONTINUOUS_1"), # Outcome mechanisms: from both JointEstimand and ATE with ALL, note the presence of TREAT_1 in the parents - Dict("parents" => ["TREAT_1", "RSID_2", "22001", "PC2", "RSID_198", "PC1"], "outcome" => "BINARY_1") + Dict("parents" => ["RSID_2", "RSID_198", "22001","TREAT_1", "PC1", "PC2"], "outcome" => "BINARY_1") ]) # Check dataset dataset = Arrow.Table(string(output_prefix, ".data.arrow")) |> DataFrame From 2268e6880ef13adfe8cba84d56dcc75f3edb214d Mon Sep 17 00:00:00 2001 From: Olivier Labayle Date: Mon, 28 Apr 2025 17:24:46 +0100 Subject: [PATCH 5/9] update targenecore dep once more --- Manifest.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 6e2ee9b..ef81fc4 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2476,9 +2476,9 @@ version = "0.34.4" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "35b09e80be285516e52c9054792c884b9216ae3c" +git-tree-sha1 = "8e45cecc66f3b42633b8ce14d431e8e57a3e242e" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.4.0" +version = "1.5.0" weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] @@ -2599,7 +2599,7 @@ version = "1.10.0" [[deps.TargeneCore]] deps = ["ArgParse", "Arrow", "BGEN", "CSV", "CairoMakie", "CategoricalArrays", "Combinatorics", "DataFrames", "Distributions", "HypothesisTests", "JLD2", "MKL", "Mmap", "OrderedCollections", "PackageCompiler", "Random", "Serialization", "SnpArrays", "StableRNGs", "Statistics", "TMLE", "TMLECLI", "YAML"] -git-tree-sha1 = "12a14ca3993f895f2622a97dd0ef6dd5de382f86" +git-tree-sha1 = "e73fdbb1065d6749c88abc3f84aba574ca6026dd" repo-rev = "update_deps" repo-url = "https://github.com/TARGENE/TargeneCore.jl" uuid = "3aa9512e-41c2-4133-bfaa-ba71048dd391" From fdfd1504920efd55b740c39125c8b1e742755b45 Mon Sep 17 00:00:00 2001 From: Olivier Labayle Date: Tue, 29 Apr 2025 10:18:39 +0100 Subject: [PATCH 6/9] fix call_genotypes call --- src/realistic_simulation_inputs.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/realistic_simulation_inputs.jl b/src/realistic_simulation_inputs.jl index f00d2b7..66b84b6 100644 --- a/src/realistic_simulation_inputs.jl +++ b/src/realistic_simulation_inputs.jl @@ -390,7 +390,7 @@ function realistic_simulation_inputs( # Call variants from BGEN & Merge all data sources verbosity > 0 && @info("Calling genotypes from BGEN files.") variants_set = Set(string.(union(values(traits_to_variants)...))) - genotypes = TargeneCore.call_genotypes( + genotypes, _ = TargeneCore.call_genotypes( bgen_prefix, variants_set, call_threshold From 500f00e0e3839d06e79af164312603242739238a Mon Sep 17 00:00:00 2001 From: Olivier Labayle Date: Thu, 10 Jul 2025 11:16:39 +0100 Subject: [PATCH 7/9] update manifest --- Manifest.toml | 339 ++++++++++++++++++++++++++------------------------ 1 file changed, 173 insertions(+), 166 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index ef81fc4..7105d09 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -5,9 +5,9 @@ manifest_format = "2.0" project_hash = "70c23d5346be58f89169899026704a4e60bb5c64" [[deps.ADTypes]] -git-tree-sha1 = "e2478490447631aedba0823d4d7a80b2cc8cdb32" +git-tree-sha1 = "be7ae030256b8ef14a441726c4c37766b90b93a3" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.14.0" +version = "1.15.0" weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"] [deps.ADTypes.extensions] @@ -112,9 +112,9 @@ version = "0.4.0" [[deps.ArrayInterface]] deps = ["Adapt", "LinearAlgebra"] -git-tree-sha1 = "017fcb757f8e921fb44ee063a7aafe5f89b86dd1" +git-tree-sha1 = "9606d7832795cbef89e06a550475be300364a8aa" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.18.0" +version = "7.19.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" @@ -201,9 +201,7 @@ version = "0.4.7" [[deps.BGEN]] deps = ["CodecZlib", "CodecZstd", "GeneticVariantBase", "Printf", "SIMD", "SQLite", "SpecialFunctions", "Statistics", "Tables", "TranscodingStreams"] -git-tree-sha1 = "aaf4444997470744c956a24bf83987918a7ed48a" -repo-rev = "075607d10cf8509910d9c62a837796105b47107c" -repo-url = "https://github.com/OpenMendel/BGEN.jl.git" +git-tree-sha1 = "82151c26443f27213cdd32b0bd29b13c7518ffa0" uuid = "6db4b851-9beb-4b83-9d64-eb1cfb37721d" version = "0.2.2" @@ -244,6 +242,11 @@ version = "0.4.4" uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" version = "1.11.0" +[[deps.BaseDirs]] +git-tree-sha1 = "0b3c211ec48050496075523ea7ee045db9341a42" +uuid = "18cc8868-cbac-4acf-b575-c8ff214dc66f" +version = "1.3.1" + [[deps.Baselet]] git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" uuid = "9718e550-a3fa-408a-8086-8db961cd8217" @@ -318,15 +321,15 @@ version = "0.10.15" [[deps.CUDA_Driver_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f69205592dbd3721a156245b6dd837206786a848" +git-tree-sha1 = "21ce786b1616c0f5f7c00331ae11fa59713654f7" uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc" -version = "0.12.1+1" +version = "12.9.0+0" [[deps.CUDA_Runtime_jll]] deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "99f1c6b659c14bbb3492246791bb4928a40ceb84" +git-tree-sha1 = "1b476b62a462e7ee17d33c0aca03415c9c17f8c9" uuid = "76a88914-d11a-5bdc-97e0-2f5a05c973a2" -version = "0.16.1+0" +version = "0.18.0+0" [[deps.Cairo]] deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] @@ -342,9 +345,9 @@ version = "0.12.18" [[deps.Cairo_jll]] 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 = "2ac646d71d0d24b44f3f8c84da8c9f4d70fb67df" +git-tree-sha1 = "fde3bf89aead2e723284a8ff9cdf5b551ed700e8" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.4+0" +version = "1.18.5+0" [[deps.CategoricalArrays]] deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"] @@ -373,15 +376,15 @@ version = "0.1.15" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "a975ae558af61a2a48720a6271661bf2621e0f4e" +git-tree-sha1 = "224f9dc510986549c8139def08e06f78c562514d" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.72.3" +version = "1.72.5" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "1713c74e00545bfe14605d2a2be1712de8fbcb58" +git-tree-sha1 = "06ee8d1aa558d2833aa799f6f0b31b30cada405f" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.25.1" +version = "1.25.2" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -431,9 +434,9 @@ version = "0.4.1" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "403f2d8e209681fcbd9468a8514efff3ea08452e" +git-tree-sha1 = "a656525c8b46aa6a1c76891552ed5381bb32ae7b" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.29.0" +version = "3.30.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -453,14 +456,14 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e" +git-tree-sha1 = "37ea44092930b1811e666c3bc38065d7d87fcc74" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.13.0" +version = "0.13.1" [[deps.Combinatorics]] -git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" +git-tree-sha1 = "8010b6bb3388abe68d95743dcbea77650bb2eddf" uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" -version = "1.0.2" +version = "1.0.3" [[deps.CommonSolve]] git-tree-sha1 = "0eee5eb66b1cf62cd6ad1b460238e60e4b09400c" @@ -480,9 +483,9 @@ version = "1.0.0" [[deps.Compat]] deps = ["TOML", "UUIDs"] -git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" +git-tree-sha1 = "3a3dfb30697e96a440e4149c8c51bf32f818c0f3" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.16.0" +version = "4.17.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -520,9 +523,9 @@ uuid = "5218b696-f38b-4ac9-8b61-a12ec717816d" version = "0.17.6" [[deps.ConstructionBase]] -git-tree-sha1 = "76219f1ed5771adbb096743bff43fb5fdd4c1157" +git-tree-sha1 = "b4b092499347b18a015186eae3042f72267106cb" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.8" +version = "1.6.0" weakdeps = ["IntervalSets", "LinearAlgebra", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -621,9 +624,9 @@ version = "1.15.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "LinearAlgebra"] -git-tree-sha1 = "aa87a743e3778d35a950b76fbd2ae64f810a2bb3" +git-tree-sha1 = "c8d85ecfcbaef899308706bebdd8b00107f3fb43" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.6.52" +version = "0.6.54" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -687,9 +690,9 @@ version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "6d8b535fd38293bc54b88455465a1386f8ac1c3c" +git-tree-sha1 = "3e6d038b77f22791b8e3472b7c633acea1ecac06" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.119" +version = "0.25.120" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -702,9 +705,9 @@ version = "0.25.119" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [[deps.DocStringExtensions]] -git-tree-sha1 = "e7b7e6f178525d17c720ab9c081e4ef04429f860" +git-tree-sha1 = "7442a5dfe1ebb773c29cc2962a8980f47221d76c" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.9.4" +version = "0.9.5" [[deps.Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] @@ -729,9 +732,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.5" [[deps.EnzymeCore]] -git-tree-sha1 = "0cdb7af5c39e92d78a0ee8d0a447d32f7593137e" +git-tree-sha1 = "8272a687bca7b5c601c0c24fc0c71bff10aafdfd" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.8.8" +version = "0.8.12" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -739,9 +742,9 @@ weakdeps = ["Adapt"] [[deps.EvoTrees]] deps = ["BSON", "CategoricalArrays", "Distributions", "MLJModelInterface", "NetworkLayout", "Random", "RecipesBase", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "79a4d55fb2aed62053dd85961278b8090c972367" +git-tree-sha1 = "0762caa55dd94403bc9d434eb609c3f9ce3d4dc9" uuid = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5" -version = "0.17.2" +version = "0.17.3" [deps.EvoTrees.extensions] EvoTreesCUDAExt = "CUDA" @@ -778,9 +781,9 @@ uuid = "55351af7-c7e9-48d6-89ff-24e801d99491" version = "0.10.14" [[deps.Extents]] -git-tree-sha1 = "063512a13dbe9c40d999c439268539aa552d1ae6" +git-tree-sha1 = "b309b36a9e02fe7be71270dd8c0fd873625332b4" uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" -version = "0.1.5" +version = "0.1.6" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] @@ -790,9 +793,9 @@ version = "6.1.2+0" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "7de7c78d681078f027389e067864a8d53bd7c3c9" +git-tree-sha1 = "797762812ed063b9b94f6cc7742bc8883bb5e69e" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.8.1" +version = "1.9.0" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -886,10 +889,10 @@ uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93" version = "0.8.5" [[deps.Flux]] -deps = ["Adapt", "ChainRulesCore", "Compat", "EnzymeCore", "Functors", "LinearAlgebra", "MLDataDevices", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "Setfield", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] -git-tree-sha1 = "49d213a90b159c74e9fc2b53162b5f699b6f3516" +deps = ["Adapt", "ChainRulesCore", "Compat", "EnzymeCore", "Functors", "LinearAlgebra", "MLCore", "MLDataDevices", "MLUtils", "MacroTools", "NNlib", "OneHotArrays", "Optimisers", "Preferences", "ProgressLogging", "Random", "Reexport", "Setfield", "SparseArrays", "SpecialFunctions", "Statistics", "Zygote"] +git-tree-sha1 = "2c35003ec8dafabdc48549102208b1b15552cb33" uuid = "587475ba-b771-5e3f-ad9e-33799f191a9c" -version = "0.16.3" +version = "0.16.4" [deps.Flux.extensions] FluxAMDGPUExt = "AMDGPU" @@ -941,10 +944,10 @@ uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" version = "2.13.4+0" [[deps.FreeTypeAbstraction]] -deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"] -git-tree-sha1 = "d52e255138ac21be31fa633200b65e4e71d26802" +deps = ["BaseDirs", "ColorVectorSpace", "Colors", "FreeType", "GeometryBasics", "Mmap"] +git-tree-sha1 = "4ebb930ef4a43817991ba35db6317a05e59abd11" uuid = "663a7486-cb36-511b-a19d-713bb74d65c9" -version = "0.10.6" +version = "0.10.8" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1004,11 +1007,11 @@ git-tree-sha1 = "b62f2b2d76cee0d61a2ef2b3118cd2a3215d3134" uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" version = "0.4.11" -[[deps.Gettext_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" -uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" -version = "0.21.0+0" +[[deps.GettextRuntime_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll"] +git-tree-sha1 = "45288942190db7c5f760f59c04495064eedf9340" +uuid = "b0724c58-0f36-5564-988d-3bb0596ebc4a" +version = "0.22.4+0" [[deps.Giflib_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1017,10 +1020,10 @@ uuid = "59f7168a-df46-5410-90c8-f2779963d0ec" version = "5.2.3+0" [[deps.Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "b0036b392358c80d2d2124746c2bf3d48d457938" +deps = ["Artifacts", "GettextRuntime_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] +git-tree-sha1 = "35fbd0cefb04a516104b8e183ce0df11b70a3f1a" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.82.4+0" +version = "2.84.3+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -1040,10 +1043,10 @@ uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" version = "1.3.15+0" [[deps.Graphs]] -deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "3169fd3440a02f35e549728b0890904cfd4ae58a" +deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] +git-tree-sha1 = "c5abfa0ae0aaee162a3fbb053c13ecda39be545b" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.12.1" +version = "1.13.0" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] @@ -1058,15 +1061,15 @@ version = "1.0.2" [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "f93655dc73d7a0b4a368e3c0bce296ae035ad76e" +git-tree-sha1 = "ed5e9c58612c4e081aecdb6e1a479e18462e041e" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.16" +version = "1.10.17" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] -git-tree-sha1 = "55c53be97790242c29031e5cd45e8ac296dadda3" +git-tree-sha1 = "f923f9a774fcf3f5cb761bfa43aeadd689714813" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "8.5.0+0" +version = "8.5.1+0" [[deps.HashArrayMappedTries]] git-tree-sha1 = "2eaa69a7cab70a52b9687c8bf950a5a93ec895ae" @@ -1093,9 +1096,9 @@ version = "0.11.5" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools"] -git-tree-sha1 = "950c3717af761bc3ff906c2e8e52bd83390b6ec2" +git-tree-sha1 = "57e9ce6cf68d0abf5cb6b3b4abf9bedf05c939c0" uuid = "7869d1d1-7146-5819-86e3-90919afe41df" -version = "0.4.14" +version = "0.4.15" [[deps.IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" @@ -1159,9 +1162,9 @@ uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" version = "0.3.1" [[deps.InlineStrings]] -git-tree-sha1 = "6a9fde685a7ac1eb3495f8e812c5a7c3711c2d5e" +git-tree-sha1 = "8594fac023c5ce1ef78260f24d1ad18b4327b420" uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.4.3" +version = "1.4.4" weakdeps = ["ArrowTypes", "Parsers"] [deps.InlineStrings.extensions] @@ -1190,13 +1193,13 @@ weakdeps = ["Unitful"] InterpolationsUnitfulExt = "Unitful" [[deps.IntervalArithmetic]] -deps = ["CRlibm", "MacroTools", "OpenBLASConsistentFPCSR_jll", "RoundingEmulator"] -git-tree-sha1 = "e9c16669687ce0a6af7a136a8774bf9633026e7c" +deps = ["CRlibm", "MacroTools", "OpenBLASConsistentFPCSR_jll", "Random", "RoundingEmulator"] +git-tree-sha1 = "79342df41c3c24664e5bf29395cfdf2f2a599412" uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" -version = "0.22.30" -weakdeps = ["DiffRules", "ForwardDiff", "IntervalSets", "LinearAlgebra", "RecipesBase", "SparseArrays"] +version = "0.22.36" [deps.IntervalArithmetic.extensions] + IntervalArithmeticArblibExt = "Arblib" IntervalArithmeticDiffRulesExt = "DiffRules" IntervalArithmeticForwardDiffExt = "ForwardDiff" IntervalArithmeticIntervalSetsExt = "IntervalSets" @@ -1204,6 +1207,15 @@ weakdeps = ["DiffRules", "ForwardDiff", "IntervalSets", "LinearAlgebra", "Recipe IntervalArithmeticRecipesBaseExt = "RecipesBase" IntervalArithmeticSparseArraysExt = "SparseArrays" + [deps.IntervalArithmetic.weakdeps] + Arblib = "fb37089c-8514-4489-9461-98f9c8763369" + DiffRules = "b552c78f-8df3-52c6-915a-8e097449b14b" + ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" + RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + [[deps.IntervalSets]] git-tree-sha1 = "5fbb102dcb8b1a858111ae81d56682376130517d" uuid = "8197267c-284f-5f27-9208-e0e47529a953" @@ -1264,10 +1276,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[deps.JLD2]] -deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "TranscodingStreams"] -git-tree-sha1 = "8e071648610caa2d3a5351aba03a936a0c37ec61" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "ScopedValues", "TranscodingStreams"] +git-tree-sha1 = "d97791feefda45729613fafeccc4fbef3f539151" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.5.13" +version = "0.5.15" weakdeps = ["UnPack"] [deps.JLD2.extensions] @@ -1287,9 +1299,9 @@ version = "0.21.4" [[deps.JSON3]] deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] -git-tree-sha1 = "196b41e5a854b387d99e5ede2de3fcb4d0422aae" +git-tree-sha1 = "411eccfe8aba0814ffa0fdf4860913ed09c34975" uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -version = "1.14.2" +version = "1.14.3" weakdeps = ["ArrowTypes"] [deps.JSON3.extensions] @@ -1315,9 +1327,9 @@ version = "0.2.4" [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"] -git-tree-sha1 = "80d268b2f4e396edc5ea004d1e0f569231c71e9e" +git-tree-sha1 = "4efa9cec6f308e0f492ea635421638bff81cf6f8" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.34" +version = "0.9.36" weakdeps = ["EnzymeCore", "LinearAlgebra", "SparseArrays"] [deps.KernelAbstractions.extensions] @@ -1333,9 +1345,9 @@ version = "0.6.9" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" +git-tree-sha1 = "059aabebaa7c82ccb853dd4a0ee9d17796f7e1bc" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" -version = "3.100.2+0" +version = "3.100.3+0" [[deps.LERC_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1383,10 +1395,9 @@ uuid = "8cdb02fc-e678-4876-92c5-9defec4f444e" version = "0.3.1" [[deps.LearnAPI]] -deps = ["InteractiveUtils", "Statistics"] -git-tree-sha1 = "ec695822c1faaaa64cee32d0b21505e1977b4809" +git-tree-sha1 = "c276ed13346953f3035a6d35519ec816b820cd44" uuid = "92ad9a40-7767-427a-9ee6-6e577f1266cb" -version = "0.1.0" +version = "1.0.1" [[deps.LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] @@ -1418,10 +1429,10 @@ uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" version = "1.11.0" [[deps.Libffi_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "27ecae93dd25ee0909666e6835051dd684cc035e" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "c8da7e6a91781c41a863611c7e966098d783c57a" uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" -version = "3.2.2+2" +version = "3.4.7+0" [[deps.Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll", "Xorg_libXext_jll"] @@ -1455,9 +1466,9 @@ version = "2.41.0+0" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "e4c3be53733db1051cc15ecf573b1042b3a712a1" +git-tree-sha1 = "4adee99b7262ad2a1a4bbbc59d993d24e55ea96f" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.3.0" +version = "7.4.0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] @@ -1539,9 +1550,9 @@ version = "1.0.0" [[deps.MLDataDevices]] deps = ["Adapt", "Compat", "Functors", "Preferences", "Random"] -git-tree-sha1 = "1326836c4c845cfabc542b658c8686f0c31a9911" +git-tree-sha1 = "209390b236bb04b289c708054fe1df06a4b314b5" uuid = "7e8f7934-dd98-4c1a-8fe8-92b47a384d40" -version = "1.9.1" +version = "1.11.0" [deps.MLDataDevices.extensions] MLDataDevicesAMDGPUExt = "AMDGPU" @@ -1591,9 +1602,9 @@ version = "0.5.1" [[deps.MLJ]] deps = ["CategoricalArrays", "ComputationalResources", "Distributed", "Distributions", "FeatureSelection", "LinearAlgebra", "MLJBalancing", "MLJBase", "MLJEnsembles", "MLJFlow", "MLJIteration", "MLJModels", "MLJTuning", "OpenML", "Pkg", "ProgressMeter", "Random", "Reexport", "ScientificTypes", "StatisticalMeasures", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "521eec7a22417d54fdc66f5dc0b7dc9628931c54" +git-tree-sha1 = "65f2031dbd48117062c23931f243a0f8666535a1" uuid = "add582a8-e3ab-11e8-2d5e-e98b27df1bc7" -version = "0.20.7" +version = "0.20.8" [[deps.MLJBalancing]] deps = ["MLJBase", "MLJModelInterface", "MLUtils", "OrderedCollections", "Random", "StatsBase"] @@ -1603,9 +1614,9 @@ version = "0.1.5" [[deps.MLJBase]] deps = ["CategoricalArrays", "CategoricalDistributions", "ComputationalResources", "Dates", "DelimitedFiles", "Distributed", "Distributions", "InteractiveUtils", "InvertedIndices", "LearnAPI", "LinearAlgebra", "MLJModelInterface", "Missings", "OrderedCollections", "Parameters", "PrettyTables", "ProgressMeter", "Random", "RecipesBase", "Reexport", "ScientificTypes", "Serialization", "StatisticalMeasuresBase", "StatisticalTraits", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "6f45e12073bc2f2e73ed0473391db38c31e879c9" +git-tree-sha1 = "05b91197e791cd1410aad3e421e9e47b27e9ce31" uuid = "a7f614a8-145f-11e9-1d2a-a57a1082229d" -version = "1.7.0" +version = "1.8.1" weakdeps = ["StatisticalMeasures"] [deps.MLJBase.extensions] @@ -1637,9 +1648,9 @@ version = "0.6.3" [[deps.MLJLinearModels]] deps = ["DocStringExtensions", "IterativeSolvers", "LinearAlgebra", "LinearMaps", "MLJModelInterface", "Optim", "Parameters"] -git-tree-sha1 = "7f517fd840ca433a8fae673edb31678ff55d969c" +git-tree-sha1 = "d23c53a454f01c03780621477000f03bae487a9a" uuid = "6ee0df7b-362f-4a72-a706-9e79364fb692" -version = "0.10.0" +version = "0.10.1" [[deps.MLJModelInterface]] deps = ["REPL", "Random", "ScientificTypesBase", "StatisticalTraits"] @@ -1765,9 +1776,9 @@ version = "2023.12.12" [[deps.NLSolversBase]] deps = ["ADTypes", "DifferentiationInterface", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "b14c7be6046e7d48e9063a0053f95ee0fc954176" +git-tree-sha1 = "25a6638571a902ecfb1ae2a18fc1575f86b1d4df" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.9.1" +version = "7.10.0" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "ScopedValues", "Statistics"] @@ -1840,16 +1851,16 @@ weakdeps = ["Adapt"] OffsetArraysAdaptExt = "Adapt" [[deps.Ogg_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "887579a3eb005446d514ab7aeac5d1d027658b8f" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "b6aa4566bb7ae78498a5e68943863fa8b5231b59" uuid = "e7412a2a-1a6e-54c0-be00-318e2571c051" -version = "1.3.5+1" +version = "1.3.6+0" [[deps.OneHotArrays]] deps = ["Adapt", "ChainRulesCore", "Compat", "GPUArraysCore", "LinearAlgebra", "NNlib"] -git-tree-sha1 = "ec127b6ef91de07a48ed9db251d63b0a46490b90" +git-tree-sha1 = "bfe8e84c71972f77e775f75e6d8048ad3fdbe8bc" uuid = "0b1bfda6-eb8a-41d2-88d8-f5af5cad476f" -version = "0.2.7" +version = "0.2.10" [[deps.OpenBLASConsistentFPCSR_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] @@ -1887,15 +1898,15 @@ version = "0.3.2" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "38cb508d080d21dc1128f7fb04f20387ed4c0af4" +git-tree-sha1 = "f1a7e086c677df53e064e0fdd2c9d0b0833e3f6e" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.4.3" +version = "1.5.0" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "9216a80ff3682833ac4b733caa8c00390620ba5d" +git-tree-sha1 = "87510f7292a2b21aeff97912b0898f9553cc5c2c" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.5.0+0" +version = "3.5.1+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] @@ -1905,9 +1916,9 @@ version = "0.5.6+0" [[deps.Optim]] deps = ["Compat", "EnumX", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "31b3b1b8e83ef9f1d50d74f1dd5f19a37a304a1f" +git-tree-sha1 = "61942645c38dd2b5b78e2082c9b51ab315315d10" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.12.0" +version = "1.13.2" [deps.Optim.extensions] OptimMOIExt = "MathOptInterface" @@ -1933,14 +1944,14 @@ version = "0.4.6" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6703a85cb3781bd5909d48730a67205f3f31a575" +git-tree-sha1 = "c392fc5dd032381919e3b22dd32d6443760ce7ea" uuid = "91d4177d-7536-5919-b921-800302f37372" -version = "1.3.3+0" +version = "1.5.2+0" [[deps.OrderedCollections]] -git-tree-sha1 = "cc4054e898b852042d7b503313f7ad03de99c3dd" +git-tree-sha1 = "05868e21324cede2207c6f0f466b4bfef6d5e7ee" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.8.0" +version = "1.8.1" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1949,9 +1960,9 @@ version = "10.42.0+1" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "0e1340b5d98971513bddaa6bbed470670cebbbfe" +git-tree-sha1 = "f07c06228a1c670ae4c87d1276b92c7c597fdda0" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.34" +version = "0.11.35" [[deps.PNGFiles]] deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] @@ -1961,9 +1972,9 @@ version = "0.4.4" [[deps.PackageCompiler]] deps = ["Artifacts", "Glob", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "5d13e5b70011762b74f86fc08385303589f80272" +git-tree-sha1 = "d6fdae30c99917e01b7a3776e9bfd5b32f0665cc" uuid = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d" -version = "2.2.0" +version = "2.2.1" [[deps.Packing]] deps = ["GeometryBasics"] @@ -1979,9 +1990,9 @@ version = "0.5.12" [[deps.Pango_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "3b31172c032a1def20c98dae3f2cdc9d10e3b561" +git-tree-sha1 = "275a9a6d85dc86c24d03d1837a0010226a96f540" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.56.1+0" +version = "1.56.3+0" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -2080,9 +2091,9 @@ version = "1.11.0" [[deps.ProgressLogging]] deps = ["Logging", "SHA", "UUIDs"] -git-tree-sha1 = "80d919dee55b9c50e8d9e2da5eeafff3fe58b539" +git-tree-sha1 = "d95ed0324b0799843ac6f7a6a85e65fe4e5173f0" uuid = "33c8b6b6-d38a-422a-b730-caa89a2f386c" -version = "0.1.4" +version = "0.1.5" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] @@ -2181,9 +2192,9 @@ version = "0.5.1+0" [[deps.Roots]] deps = ["Accessors", "CommonSolve", "Printf"] -git-tree-sha1 = "3ac13765751ffc81e3531223782d9512f6023f71" +git-tree-sha1 = "668e411c0616a70860249b4c96e5d35296631a1d" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.2.7" +version = "2.2.8" [deps.Roots.extensions] RootsChainRulesCoreExt = "ChainRulesCore" @@ -2256,9 +2267,9 @@ version = "1.3.0" [[deps.Scratch]] deps = ["Dates"] -git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" +git-tree-sha1 = "9b81b8393e50b7d4e6d0a9f14e192294d3b7c109" uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.2.1" +version = "1.3.0" [[deps.SentinelArrays]] deps = ["Dates", "Random"] @@ -2322,9 +2333,9 @@ version = "0.9.4" [[deps.Sixel]] deps = ["Dates", "FileIO", "ImageCore", "IndirectArrays", "OffsetArrays", "REPL", "libsixel_jll"] -git-tree-sha1 = "2da10356e31327c7096832eb9cd86307a50b1eb6" +git-tree-sha1 = "0494aed9501e7fb65daba895fb7fd57cc38bc743" uuid = "45858cf5-a6b0-47a3-bbea-62219f50df47" -version = "0.1.3" +version = "0.1.5" [[deps.SnpArrays]] deps = ["Adapt", "CSV", "CodecBzip2", "CodecXz", "CodecZlib", "CodecZstd", "DataFrames", "DelimitedFiles", "Glob", "LinearAlgebra", "LoopVectorization", "Missings", "Mmap", "Printf", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Tables", "TranscodingStreams", "VariantCallFormat", "VectorizationBase"] @@ -2383,15 +2394,15 @@ version = "0.1.15" [[deps.StableRNGs]] deps = ["Random"] -git-tree-sha1 = "83e6cce8324d49dfaf9ef059227f91ed4441a8e5" +git-tree-sha1 = "95af145932c2ed859b63329952ce8d633719f091" uuid = "860ef19b-820b-49d6-a774-d7a799459cd3" -version = "1.0.2" +version = "1.0.3" [[deps.StackViews]] deps = ["OffsetArrays"] -git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c" +git-tree-sha1 = "be1cf4eb0ac528d96f5115b4ed80c26a8d8ae621" uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15" -version = "0.1.1" +version = "0.1.2" [[deps.Static]] deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] @@ -2428,9 +2439,9 @@ version = "1.4.3" [[deps.StatisticalMeasures]] deps = ["CategoricalArrays", "CategoricalDistributions", "Distributions", "LearnAPI", "LinearAlgebra", "MacroTools", "OrderedCollections", "PrecompileTools", "ScientificTypesBase", "StatisticalMeasuresBase", "Statistics", "StatsBase"] -git-tree-sha1 = "c1d4318fa41056b839dfbb3ee841f011fa6e8518" +git-tree-sha1 = "d15f71761dce0a2833d458824e6b60edbfd4f138" uuid = "a19d573c-0a75-4610-95b3-7071388c7541" -version = "0.1.7" +version = "0.2.1" [deps.StatisticalMeasures.extensions] LossFunctionsExt = "LossFunctions" @@ -2464,15 +2475,15 @@ weakdeps = ["SparseArrays"] [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" +git-tree-sha1 = "9d72a13a3f4dd3795a195ac5a44d7d6ff5f552ff" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.7.0" +version = "1.7.1" [[deps.StatsBase]] deps = ["AliasTables", "DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "29321314c920c26684834965ec2ce0dacc9cf8e5" +git-tree-sha1 = "b81c5035922cc89c2d9523afc6c54be512411466" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.4" +version = "0.34.5" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] @@ -2588,9 +2599,9 @@ version = "1.0.1" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] -git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" +git-tree-sha1 = "f2c1efbc8f3a609aadf318094f8fc5204bdaf344" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.12.0" +version = "1.12.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -2599,7 +2610,7 @@ version = "1.10.0" [[deps.TargeneCore]] deps = ["ArgParse", "Arrow", "BGEN", "CSV", "CairoMakie", "CategoricalArrays", "Combinatorics", "DataFrames", "Distributions", "HypothesisTests", "JLD2", "MKL", "Mmap", "OrderedCollections", "PackageCompiler", "Random", "Serialization", "SnpArrays", "StableRNGs", "Statistics", "TMLE", "TMLECLI", "YAML"] -git-tree-sha1 = "e73fdbb1065d6749c88abc3f84aba574ca6026dd" +git-tree-sha1 = "be1463012a37c5ecda514c5e5b07381f36451bb1" repo-rev = "update_deps" repo-url = "https://github.com/TARGENE/TargeneCore.jl" uuid = "3aa9512e-41c2-4133-bfaa-ba71048dd391" @@ -2623,15 +2634,15 @@ version = "1.0.2" [[deps.ThreadingUtilities]] deps = ["ManualMemory"] -git-tree-sha1 = "18ad3613e129312fe67789a71720c3747e598a61" +git-tree-sha1 = "d969183d3d244b6c33796b5ed01ab97328f2db85" uuid = "8290d209-cae3-49c0-8002-c8c24d57dab5" -version = "0.5.3" +version = "0.5.5" [[deps.TiffImages]] -deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "SIMD", "UUIDs"] -git-tree-sha1 = "f21231b166166bebc73b99cea236071eb047525b" +deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "PrecompileTools", "ProgressMeter", "SIMD", "UUIDs"] +git-tree-sha1 = "02aca429c9885d1109e58f400c333521c13d48a0" uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" -version = "0.11.3" +version = "0.11.4" [[deps.TimeZones]] deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] @@ -2677,9 +2688,9 @@ uuid = "981d1d27-644d-49a2-9326-4793e63143c3" version = "0.1.0" [[deps.URIs]] -git-tree-sha1 = "cbbebadbcc76c5ca1cc4b4f3b0614b3e603b5000" +git-tree-sha1 = "bef26fb046d031353ef97a82e3fdb6afe7f21b1a" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.5.2" +version = "1.6.1" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -2703,14 +2714,16 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "c0667a8e676c53d390a09dc6870b3d8d6650e2bf" +git-tree-sha1 = "d2282232f8a4d71f79e85dc4dd45e5b12a6297fb" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.22.0" -weakdeps = ["ConstructionBase", "InverseFunctions"] +version = "1.23.1" +weakdeps = ["ConstructionBase", "ForwardDiff", "InverseFunctions", "Printf"] [deps.Unitful.extensions] ConstructionBaseUnitfulExt = "ConstructionBase" + ForwardDiffExt = "ForwardDiff" InverseFunctionsUnitfulExt = "InverseFunctions" + PrintfExt = "Printf" [[deps.UnsafeAtomics]] git-tree-sha1 = "b13c4edda90890e5b04ba24e20a310fbe6f249ff" @@ -2778,12 +2791,6 @@ git-tree-sha1 = "1c0aa2390a7ebb28a3d6c214f64e57a24091fbd7" uuid = "a5c6f535-4255-5ca2-a466-0e519f119c46" version = "2.0.1+0" -[[deps.XML2_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "b8b243e47228b4a3877f1dd6aee0c5d56db7fcf4" -uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.13.6+1" - [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "fee71455b0aaa3440dfdd54a9a36ccef829be7d4" @@ -2834,9 +2841,9 @@ version = "1.6.0+0" [[deps.YAML]] deps = ["Base64", "Dates", "Printf", "StringEncodings"] -git-tree-sha1 = "b46894beba6c05cd185d174654479aaec09ea6b1" +git-tree-sha1 = "2f58ac39f64b41fb812340347525be3b590cce3b" uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" -version = "0.4.13" +version = "0.4.14" [[deps.Zlib_jll]] deps = ["Libdl"] @@ -2851,9 +2858,9 @@ version = "1.5.7+1" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "207d714f3514b0d564e3a08f9e9f753bf6566c2d" +git-tree-sha1 = "a29cbf3968d36022198bcc6f23fdfd70f7caf737" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.7.6" +version = "0.7.10" [deps.Zygote.extensions] ZygoteAtomExt = "Atom" @@ -2904,15 +2911,15 @@ version = "5.11.0+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" +git-tree-sha1 = "646634dd19587a56ee2f1199563ec056c5f228df" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" -version = "2.0.3+0" +version = "2.0.4+0" [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "068dfe202b0a05b8332f1e8e6b4080684b9c7700" +git-tree-sha1 = "07b6a107d926093898e82b3b1db657ebe33134ec" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.47+0" +version = "1.6.50+0" [[deps.libsixel_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "libpng_jll"] @@ -2921,10 +2928,10 @@ uuid = "075b6546-f08a-558a-be8f-8157d0f608a5" version = "1.10.5+0" [[deps.libvorbis_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll"] +git-tree-sha1 = "11e1772e7f3cc987e9d3de991dd4f6b2602663a5" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+2" +version = "1.3.8+0" [[deps.libwebp_jll]] deps = ["Artifacts", "Giflib_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libglvnd_jll", "Libtiff_jll", "libpng_jll"] From 6274ef402eb9dacebed3a8ea9f8caaeddce2feff Mon Sep 17 00:00:00 2001 From: Olivier Labayle Date: Thu, 10 Jul 2025 14:34:42 +0100 Subject: [PATCH 8/9] updtate targene core version --- Manifest.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Manifest.toml b/Manifest.toml index 7105d09..51c5d16 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2611,7 +2611,7 @@ version = "1.10.0" [[deps.TargeneCore]] deps = ["ArgParse", "Arrow", "BGEN", "CSV", "CairoMakie", "CategoricalArrays", "Combinatorics", "DataFrames", "Distributions", "HypothesisTests", "JLD2", "MKL", "Mmap", "OrderedCollections", "PackageCompiler", "Random", "Serialization", "SnpArrays", "StableRNGs", "Statistics", "TMLE", "TMLECLI", "YAML"] git-tree-sha1 = "be1463012a37c5ecda514c5e5b07381f36451bb1" -repo-rev = "update_deps" +repo-rev = "v0.11.0" repo-url = "https://github.com/TARGENE/TargeneCore.jl" uuid = "3aa9512e-41c2-4133-bfaa-ba71048dd391" version = "0.9.0" From d678c60ccc7d8d387eab3fb882a8467f88acca08 Mon Sep 17 00:00:00 2001 From: Olivier Labayle Date: Thu, 10 Jul 2025 14:37:29 +0100 Subject: [PATCH 9/9] update CI julia version tested and project version --- .github/workflows/CI.yml | 1 + Project.toml | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index 578bc20..ef99d4c 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -21,6 +21,7 @@ jobs: matrix: version: - '1.10' + - '1' os: - ubuntu-latest arch: diff --git a/Project.toml b/Project.toml index 5687d47..38da06e 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Simulations" uuid = "d443f30a-01cc-4ad2-ad2b-7e2d1cb5fd9b" authors = ["Olivier Labayle and contributors"] -version = "0.0.1" +version = "0.1.0" [deps] ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"