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update deps
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@olivierlabayle
olivierlabayle committed Aug 21, 2024
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154 changes: 74 additions & 80 deletions Manifest.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

julia_version = "1.10.4"
manifest_format = "2.0"
project_hash = "b62f3762a6535538ed6b74bdb53c6ce6255c32d6"
project_hash = "5f0a91ea516a5a3c8c559534896b38da912db764"

[[deps.ARFFFiles]]
deps = ["CategoricalArrays", "Dates", "Parsers", "Tables"]
Expand Down Expand Up @@ -222,22 +222,16 @@ uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
version = "0.10.14"

[[deps.CUDA_Driver_jll]]
deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"]
git-tree-sha1 = "97df9d4d6be8ac6270cb8fd3b8fc413690820cbd"
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "22bc8ec24f0ed05bcf8c1845ef425d8229ef6436"
uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc"
version = "0.9.1+1"
version = "0.10.0+0"

[[deps.CUDA_Runtime_jll]]
deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
git-tree-sha1 = "afea94249b821dc754a8ca6695d3daed851e1f5a"
git-tree-sha1 = "c730797fc11265bb0940b738b3573ed38c2c8388"
uuid = "76a88914-d11a-5bdc-97e0-2f5a05c973a2"
version = "0.14.1+0"

[[deps.Calculus]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad"
uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
version = "0.5.1"
version = "0.15.1+0"

[[deps.CategoricalArrays]]
deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"]
Expand Down Expand Up @@ -282,21 +276,21 @@ weakdeps = ["SparseArrays"]

[[deps.CodecLz4]]
deps = ["Lz4_jll", "TranscodingStreams"]
git-tree-sha1 = "42494e2756fe6f775d6da57aac6762d2e11a95ce"
git-tree-sha1 = "0db0c70ca94c0a79cadad269497f25ca88b9fa91"
uuid = "5ba52731-8f18-5e0d-9241-30f10d1ec561"
version = "0.4.4"
version = "0.4.5"

[[deps.CodecZlib]]
deps = ["TranscodingStreams", "Zlib_jll"]
git-tree-sha1 = "b8fe8546d52ca154ac556809e10c75e6e7430ac8"
git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759"
uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
version = "0.7.5"
version = "0.7.6"

[[deps.CodecZstd]]
deps = ["TranscodingStreams", "Zstd_jll"]
git-tree-sha1 = "ed0be9a9c1a6b6dec7aac15f8977f16ad6a9796c"
git-tree-sha1 = "5e41a52bec3b0881a7eb54f5391b779994504186"
uuid = "6b39b394-51ab-5f42-8807-6242bab2b4c2"
version = "0.8.4"
version = "0.8.5"

[[deps.ColorTypes]]
deps = ["FixedPointNumbers", "Random"]
Expand All @@ -315,16 +309,16 @@ uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2"
version = "0.2.4"

[[deps.CommonSubexpressions]]
deps = ["MacroTools", "Test"]
git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7"
deps = ["MacroTools"]
git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5"
uuid = "bbf7d656-a473-5ed7-a52c-81e309532950"
version = "0.3.0"
version = "0.3.1"

[[deps.Compat]]
deps = ["TOML", "UUIDs"]
git-tree-sha1 = "b1c55339b7c6c350ee89f2c1604299660525b248"
git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215"
uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
version = "4.15.0"
version = "4.16.0"
weakdeps = ["Dates", "LinearAlgebra"]

[deps.Compat.extensions]
Expand Down Expand Up @@ -363,9 +357,9 @@ version = "0.17.6"

[[deps.ConstructionBase]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "d8a9c0b6ac2d9081bf76324b39c78ca3ce4f0c98"
git-tree-sha1 = "a33b7ced222c6165f624a3f2b55945fac5a598d9"
uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
version = "1.5.6"
version = "1.5.7"

[deps.ConstructionBase.extensions]
ConstructionBaseIntervalSetsExt = "IntervalSets"
Expand Down Expand Up @@ -458,9 +452,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"

[[deps.Distributions]]
deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
git-tree-sha1 = "9c405847cc7ecda2dc921ccf18b47ca150d7317e"
git-tree-sha1 = "0e0a1264b0942f1f3abb2b30891f2a590cc652ac"
uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
version = "0.25.109"
version = "0.25.110"

[deps.Distributions.extensions]
DistributionsChainRulesCoreExt = "ChainRulesCore"
Expand All @@ -483,12 +477,6 @@ deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
version = "1.6.0"

[[deps.DualNumbers]]
deps = ["Calculus", "NaNMath", "SpecialFunctions"]
git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566"
uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74"
version = "0.6.8"

[[deps.EarCut_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "e3290f2d49e661fbd94046d7e3726ffcb2d41053"
Expand Down Expand Up @@ -530,9 +518,9 @@ uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
version = "0.1.10"

[[deps.ExproniconLite]]
git-tree-sha1 = "1095361e35ea8ad9c660560df4c03c06d5244956"
git-tree-sha1 = "4c9ed87a6b3cd90acf24c556f2119533435ded38"
uuid = "55351af7-c7e9-48d6-89ff-24e801d99491"
version = "0.10.11"
version = "0.10.13"

[[deps.Extents]]
git-tree-sha1 = "94997910aca72897524d2237c41eb852153b0f65"
Expand All @@ -551,6 +539,12 @@ git-tree-sha1 = "656f7a6859be8673bf1f35da5670246b923964f7"
uuid = "b9860ae5-e623-471e-878b-f6a53c775ea6"
version = "0.1.1"

[[deps.FeatureSelection]]
deps = ["MLJModelInterface", "ScientificTypesBase", "Tables"]
git-tree-sha1 = "d78c565b6296e161193eb0f053bbcb3f1a82091d"
uuid = "33837fe5-dbff-4c9e-8c2f-c5612fe2b8b6"
version = "0.2.2"

[[deps.FileIO]]
deps = ["Pkg", "Requires", "UUIDs"]
git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322"
Expand All @@ -568,9 +562,9 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"

[[deps.FillArrays]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "0653c0a2396a6da5bc4766c43041ef5fd3efbe57"
git-tree-sha1 = "fd0002c0b5362d7eb952450ad5eb742443340d6e"
uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
version = "1.11.0"
version = "1.12.0"
weakdeps = ["PDMats", "SparseArrays", "Statistics"]

[deps.FillArrays.extensions]
Expand All @@ -579,10 +573,10 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"]
FillArraysStatisticsExt = "Statistics"

[[deps.FiniteDiff]]
deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"]
git-tree-sha1 = "2de436b72c3422940cbe1367611d137008af7ec3"
deps = ["ArrayInterface", "LinearAlgebra", "Setfield", "SparseArrays"]
git-tree-sha1 = "f9219347ebf700e77ca1d48ef84e4a82a6701882"
uuid = "6a86dc24-6348-571c-b903-95158fe2bd41"
version = "2.23.1"
version = "2.24.0"

[deps.FiniteDiff.extensions]
FiniteDiffBandedMatricesExt = "BandedMatrices"
Expand Down Expand Up @@ -692,10 +686,10 @@ uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8"
version = "2.11.1+0"

[[deps.HypergeometricFunctions]]
deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685"
deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb"
uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a"
version = "0.3.23"
version = "0.3.24"

[[deps.HypothesisTests]]
deps = ["Combinatorics", "Distributions", "LinearAlgebra", "Printf", "Random", "Rmath", "Roots", "Statistics", "StatsAPI", "StatsBase"]
Expand Down Expand Up @@ -745,14 +739,14 @@ deps = ["Markdown"]
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"

[[deps.InverseFunctions]]
deps = ["Test"]
git-tree-sha1 = "18c59411ece4838b18cd7f537e56cf5e41ce5bfd"
git-tree-sha1 = "2787db24f4e03daf859c6509ff87764e4182f7d1"
uuid = "3587e190-3f89-42d0-90ee-14403ec27112"
version = "0.1.15"
weakdeps = ["Dates"]
version = "0.1.16"
weakdeps = ["Dates", "Test"]

[deps.InverseFunctions.extensions]
DatesExt = "Dates"
InverseFunctionsDatesExt = "Dates"
InverseFunctionsTestExt = "Test"

[[deps.InvertedIndices]]
git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038"
Expand Down Expand Up @@ -822,9 +816,9 @@ version = "0.2.4"

[[deps.KernelAbstractions]]
deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"]
git-tree-sha1 = "d0448cebd5919e06ca5edc7a264631790de810ec"
git-tree-sha1 = "0fac59881e91c7233a9b0d47f4b7d9432e534f0f"
uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
version = "0.9.22"
version = "0.9.23"

[deps.KernelAbstractions.extensions]
EnzymeExt = "EnzymeCore"
Expand All @@ -834,9 +828,9 @@ version = "0.9.22"

[[deps.LLVM]]
deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"]
git-tree-sha1 = "020abd49586480c1be84f57da0017b5d3db73f7c"
git-tree-sha1 = "2470e69781ddd70b8878491233cd09bc1bd7fc96"
uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
version = "8.0.0"
version = "8.1.0"

[deps.LLVM.extensions]
BFloat16sExt = "BFloat16s"
Expand All @@ -846,15 +840,15 @@ version = "8.0.0"

[[deps.LLVMExtra_jll]]
deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
git-tree-sha1 = "c2636c264861edc6d305e6b4d528f09566d24c5e"
git-tree-sha1 = "597d1c758c9ae5d985ba4202386a607c675ee700"
uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab"
version = "0.0.30+0"
version = "0.0.31+0"

[[deps.LLVMOpenMP_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "d986ce2d884d49126836ea94ed5bfb0f12679713"
git-tree-sha1 = "e16271d212accd09d52ee0ae98956b8a05c4b626"
uuid = "1d63c593-3942-5779-bab2-d838dc0a180e"
version = "15.0.7+0"
version = "17.0.6+0"

[[deps.LaTeXStrings]]
git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec"
Expand Down Expand Up @@ -912,9 +906,9 @@ version = "1.17.0+0"

[[deps.LineSearches]]
deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"]
git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d"
git-tree-sha1 = "e4c3be53733db1051cc15ecf573b1042b3a712a1"
uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255"
version = "7.2.0"
version = "7.3.0"

[[deps.LinearAlgebra]]
deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
Expand Down Expand Up @@ -965,9 +959,9 @@ version = "1.10.0+0"

[[deps.MKL]]
deps = ["Artifacts", "Libdl", "LinearAlgebra", "Logging", "MKL_jll"]
git-tree-sha1 = "17f06b6fb5198b757413d8379bfa62246c5da5a3"
git-tree-sha1 = "18b02c359c1150bf182978e18dbd9ce7ccc860af"
uuid = "33e6dc65-8f57-5167-99aa-e5a354878fb2"
version = "0.6.3"
version = "0.7.0"

[[deps.MKL_jll]]
deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"]
Expand All @@ -982,10 +976,10 @@ uuid = "64a0f543-368b-4a9a-827a-e71edb2a0b83"
version = "0.5.1"

[[deps.MLJ]]
deps = ["CategoricalArrays", "ComputationalResources", "Distributed", "Distributions", "LinearAlgebra", "MLJBalancing", "MLJBase", "MLJEnsembles", "MLJFlow", "MLJIteration", "MLJModels", "MLJTuning", "OpenML", "Pkg", "ProgressMeter", "Random", "Reexport", "ScientificTypes", "StatisticalMeasures", "Statistics", "StatsBase", "Tables"]
git-tree-sha1 = "bd2072e9cd65be0a3cb841f3d8cda1d2cacfe5db"
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"
uuid = "add582a8-e3ab-11e8-2d5e-e98b27df1bc7"
version = "0.20.5"
version = "0.20.7"

[[deps.MLJBalancing]]
deps = ["MLJBase", "MLJModelInterface", "MLUtils", "OrderedCollections", "Random", "StatsBase"]
Expand Down Expand Up @@ -1041,9 +1035,9 @@ 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 = "410da88e0e6ece5467293d2c76b51b7c6df7d072"
git-tree-sha1 = "c1b1f72379d15079d2c97937d9c1ed38f9ab4679"
uuid = "d491faf4-2d78-11e9-2867-c94bc002c0b7"
version = "0.16.17"
version = "0.17.4"

[[deps.MLJTuning]]
deps = ["ComputationalResources", "Distributed", "Distributions", "LatinHypercubeSampling", "MLJBase", "ProgressMeter", "Random", "RecipesBase", "StatisticalMeasuresBase"]
Expand Down Expand Up @@ -1136,9 +1130,9 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804"

[[deps.Mocking]]
deps = ["Compat", "ExprTools"]
git-tree-sha1 = "c74e5e7c5f83ccb0bca0377d316d966d296106d4"
git-tree-sha1 = "2c140d60d7cb82badf06d8783800d0bcd1a7daa2"
uuid = "78c3b35d-d492-501b-9361-3d52fe80e533"
version = "0.7.9"
version = "0.8.1"

[[deps.MozillaCACerts_jll]]
uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
Expand All @@ -1158,9 +1152,9 @@ version = "7.8.3"

[[deps.NNlib]]
deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"]
git-tree-sha1 = "190dcada8cf9520198058c4544862b1f88c6c577"
git-tree-sha1 = "ae52c156a63bb647f80c26319b104e99e5977e51"
uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
version = "0.9.21"
version = "0.9.22"

[deps.NNlib.extensions]
NNlibAMDGPUExt = "AMDGPU"
Expand Down Expand Up @@ -1220,9 +1214,9 @@ version = "0.3.1"

[[deps.OpenMPI_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"]
git-tree-sha1 = "2f0a1d8c79bc385ec3fcda12830c9d0e72b30e71"
git-tree-sha1 = "bfce6d523861a6c562721b262c0d1aaeead2647f"
uuid = "fe0851c0-eecd-5654-98d4-656369965a5c"
version = "5.0.4+0"
version = "5.0.5+0"

[[deps.OpenSSL]]
deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"]
Expand Down Expand Up @@ -1394,9 +1388,9 @@ version = "0.7.1"

[[deps.Rmath_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "d483cd324ce5cf5d61b77930f0bbd6cb61927d21"
git-tree-sha1 = "e60724fd3beea548353984dc61c943ecddb0e29a"
uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f"
version = "0.4.2+0"
version = "0.4.3+0"

[[deps.Roots]]
deps = ["Accessors", "ChainRulesCore", "CommonSolve", "Printf"]
Expand Down Expand Up @@ -1603,9 +1597,9 @@ weakdeps = ["ChainRulesCore", "InverseFunctions"]

[[deps.StatsModels]]
deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsAPI", "StatsBase", "StatsFuns", "Tables"]
git-tree-sha1 = "5cf6c4583533ee38639f73b880f35fc85f2941e0"
git-tree-sha1 = "9022bcaa2fc1d484f1326eaa4db8db543ca8c66d"
uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
version = "0.7.3"
version = "0.7.4"

[[deps.StringEncodings]]
deps = ["Libiconv_jll"]
Expand Down Expand Up @@ -1649,7 +1643,7 @@ version = "7.2.1+1"

[[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 = "aa8e553a2601eec43fbbb273acde056dcf3258a0"
git-tree-sha1 = "9e2f702a8dc2ffa850901ebf32d2ef1d69982f1e"
repo-rev = "treatment_values"
repo-url = "https://github.com/TARGENE/TMLE.jl"
uuid = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf"
Expand Down Expand Up @@ -1705,9 +1699,9 @@ version = "1.0.2"

[[deps.TimeZones]]
deps = ["Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"]
git-tree-sha1 = "a6ae8d7a27940c33624f8c7bde5528de21ba730d"
git-tree-sha1 = "b92aebdd3555f3a7e3267cf17702033c2814ef48"
uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53"
version = "1.17.0"
version = "1.18.0"
weakdeps = ["RecipesBase"]

[deps.TimeZones.extensions]
Expand Down Expand Up @@ -1766,9 +1760,9 @@ version = "0.2.1"

[[deps.UnsafeAtomicsLLVM]]
deps = ["LLVM", "UnsafeAtomics"]
git-tree-sha1 = "bf2c553f25e954a9b38c9c0593a59bb13113f9e5"
git-tree-sha1 = "4073c836c2befcb041e5fe306cb6abf621eb3140"
uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249"
version = "0.1.5"
version = "0.2.0"

[[deps.WeakRefStrings]]
deps = ["DataAPI", "InlineStrings", "Parsers"]
Expand Down
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