diff --git a/Manifest.toml b/Manifest.toml index 37fd4b5..3d6eb1c 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -51,9 +51,9 @@ version = "0.4.5" [[deps.Accessors]] deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] -git-tree-sha1 = "c0d491ef0b135fd7d63cbc6404286bc633329425" +git-tree-sha1 = "f61b15be1d76846c0ce31d3fcfac5380ae53db6a" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.36" +version = "0.1.37" [deps.Accessors.extensions] AccessorsAxisKeysExt = "AxisKeys" @@ -156,6 +156,12 @@ git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" version = "0.1.0" +[[deps.AutoHashEquals]] +deps = ["Pkg"] +git-tree-sha1 = "daaeb6f7f77b88c072a83a2451801818acb5c63b" +uuid = "15f4f7f2-30c1-5605-9d31-71845cf9641f" +version = "2.1.0" + [[deps.Automa]] deps = ["TranscodingStreams"] git-tree-sha1 = "ef9997b3d5547c48b41c7bd8899e812a917b409d" @@ -192,16 +198,17 @@ uuid = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0" version = "0.3.9" [[deps.BangBang]] -deps = ["Compat", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires", "Setfield", "Tables"] -git-tree-sha1 = "7aa7ad1682f3d5754e3491bb59b8103cae28e3a3" +deps = ["Accessors", "ConstructionBase", "InitialValues", "LinearAlgebra", "Requires"] +git-tree-sha1 = "e2144b631226d9eeab2d746ca8880b7ccff504ae" uuid = "198e06fe-97b7-11e9-32a5-e1d131e6ad66" -version = "0.3.40" +version = "0.4.3" [deps.BangBang.extensions] BangBangChainRulesCoreExt = "ChainRulesCore" BangBangDataFramesExt = "DataFrames" BangBangStaticArraysExt = "StaticArrays" BangBangStructArraysExt = "StructArrays" + BangBangTablesExt = "Tables" BangBangTypedTablesExt = "TypedTables" [deps.BangBang.weakdeps] @@ -209,6 +216,7 @@ version = "0.3.40" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" TypedTables = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" [[deps.Base64]] @@ -281,15 +289,15 @@ version = "0.10.14" [[deps.CUDA_Driver_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "c48f9da18efd43b6b7adb7ee1f93fe5f2926c339" +git-tree-sha1 = "97df9d4d6be8ac6270cb8fd3b8fc413690820cbd" uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc" -version = "0.9.0+0" +version = "0.9.1+1" [[deps.CUDA_Runtime_jll]] deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "bcba305388e16aa5c879e896726db9e71b4942c6" +git-tree-sha1 = "afea94249b821dc754a8ca6695d3daed851e1f5a" uuid = "76a88914-d11a-5bdc-97e0-2f5a05c973a2" -version = "0.14.0+1" +version = "0.14.1+0" [[deps.Cairo]] deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] @@ -342,9 +350,9 @@ version = "0.1.15" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "291821c1251486504f6bae435227907d734e94d2" +git-tree-sha1 = "227985d885b4dbce5e18a96f9326ea1e836e5a03" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.66.0" +version = "1.69.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] @@ -689,9 +697,9 @@ uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" version = "0.1.10" [[deps.ExproniconLite]] -git-tree-sha1 = "6091a6fc0f16639f43d7f78fee225ba365712612" +git-tree-sha1 = "1095361e35ea8ad9c660560df4c03c06d5244956" uuid = "55351af7-c7e9-48d6-89ff-24e801d99491" -version = "0.10.8" +version = "0.10.11" [[deps.Extents]] git-tree-sha1 = "2140cd04483da90b2da7f99b2add0750504fc39c" @@ -718,9 +726,9 @@ version = "3.3.10+0" [[deps.FLoops]] deps = ["BangBang", "Compat", "FLoopsBase", "InitialValues", "JuliaVariables", "MLStyle", "Serialization", "Setfield", "Transducers"] -git-tree-sha1 = "ffb97765602e3cbe59a0589d237bf07f245a8576" +git-tree-sha1 = "0a2e5873e9a5f54abb06418d57a8df689336a660" uuid = "cc61a311-1640-44b5-9fba-1b764f453329" -version = "0.2.1" +version = "0.2.2" [[deps.FLoopsBase]] deps = ["ContextVariablesX"] @@ -905,9 +913,9 @@ version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "4f2b57488ac7ee16124396de4f2bbdd51b2602ad" +git-tree-sha1 = "ebd18c326fa6cee1efb7da9a3b45cf69da2ed4d9" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.11.0" +version = "1.11.2" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] @@ -958,9 +966,9 @@ version = "0.1.16" [[deps.Hwloc_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "ca0f6bf568b4bfc807e7537f081c81e35ceca114" +git-tree-sha1 = "5e19e1e4fa3e71b774ce746274364aef0234634e" uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" -version = "2.10.0+0" +version = "2.11.1+0" [[deps.HypergeometricFunctions]] deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] @@ -1094,9 +1102,9 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "e7cbed5032c4c397a6ac23d1493f3289e01231c4" +git-tree-sha1 = "18c59411ece4838b18cd7f537e56cf5e41ce5bfd" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.14" +version = "0.1.15" weakdeps = ["Dates"] [deps.InverseFunctions.extensions] @@ -1194,9 +1202,9 @@ version = "0.2.4" [[deps.KernelAbstractions]] deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "db02395e4c374030c53dc28f3c1d33dec35f7272" +git-tree-sha1 = "d0448cebd5919e06ca5edc7a264631790de810ec" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.19" +version = "0.9.22" [deps.KernelAbstractions.extensions] EnzymeExt = "EnzymeCore" @@ -1353,9 +1361,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LinearMaps]] deps = ["LinearAlgebra"] -git-tree-sha1 = "9948d6f8208acfebc3e8cf4681362b2124339e7e" +git-tree-sha1 = "ee79c3208e55786de58f8dcccca098ced79f743f" uuid = "7a12625a-238d-50fd-b39a-03d52299707e" -version = "3.11.2" +version = "3.11.3" weakdeps = ["ChainRulesCore", "SparseArrays", "Statistics"] [deps.LinearMaps.extensions] @@ -1437,15 +1445,15 @@ version = "0.20.5" [[deps.MLJBalancing]] deps = ["MLJBase", "MLJModelInterface", "MLUtils", "OrderedCollections", "Random", "StatsBase"] -git-tree-sha1 = "f02e28f9f3c54a138db12a97a5d823e5e572c2d6" +git-tree-sha1 = "f707a01a92d664479522313907c07afa5d81df19" uuid = "45f359ea-796d-4f51-95a5-deb1a414c586" -version = "0.1.4" +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 = "aba2ffd56a9a97027b4102055dd9f909a6e35d12" +git-tree-sha1 = "6f45e12073bc2f2e73ed0473391db38c31e879c9" uuid = "a7f614a8-145f-11e9-1d2a-a57a1082229d" -version = "1.3.0" +version = "1.7.0" weakdeps = ["StatisticalMeasures"] [deps.MLJBase.extensions] @@ -1453,9 +1461,9 @@ weakdeps = ["StatisticalMeasures"] [[deps.MLJEnsembles]] deps = ["CategoricalArrays", "CategoricalDistributions", "ComputationalResources", "Distributed", "Distributions", "MLJModelInterface", "ProgressMeter", "Random", "ScientificTypesBase", "StatisticalMeasuresBase", "StatsBase"] -git-tree-sha1 = "d3dd87194ec96892bb243b65225a462c7ab16e66" +git-tree-sha1 = "84a5be55a364bb6b6dc7780bbd64317ebdd3ad1e" uuid = "50ed68f4-41fd-4504-931a-ed422449fee0" -version = "0.4.2" +version = "0.4.3" [[deps.MLJFlow]] deps = ["MLFlowClient", "MLJBase", "MLJModelInterface"] @@ -1471,9 +1479,9 @@ version = "0.3.7" [[deps.MLJIteration]] deps = ["IterationControl", "MLJBase", "Random", "Serialization"] -git-tree-sha1 = "1e909ee09417ebd18559c4d9c15febff887192df" +git-tree-sha1 = "f93f381a82fc1768c1a99c27a84b7ea1b1ee186d" uuid = "614be32b-d00c-4edb-bd02-1eb411ab5e55" -version = "0.6.1" +version = "0.6.2" [[deps.MLJLinearModels]] deps = ["DocStringExtensions", "IterativeSolvers", "LinearAlgebra", "LinearMaps", "MLJModelInterface", "Optim", "Parameters"] @@ -1483,9 +1491,9 @@ version = "0.10.0" [[deps.MLJModelInterface]] deps = ["Random", "ScientificTypesBase", "StatisticalTraits"] -git-tree-sha1 = "d2a45e1b5998ba3fdfb6cfe0c81096d4c7fb40e7" +git-tree-sha1 = "ceaff6618408d0e412619321ae43b33b40c1a733" uuid = "e80e1ace-859a-464e-9ed9-23947d8ae3ea" -version = "1.9.6" +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"] @@ -1495,15 +1503,15 @@ version = "0.16.17" [[deps.MLJTuning]] deps = ["ComputationalResources", "Distributed", "Distributions", "LatinHypercubeSampling", "MLJBase", "ProgressMeter", "Random", "RecipesBase", "StatisticalMeasuresBase"] -git-tree-sha1 = "efb9ec087ab9589afad0002e69fdd9cd38ef1643" +git-tree-sha1 = "38aab60b1274ce7d6da784808e3be69e585dbbf6" uuid = "03970b2e-30c4-11ea-3135-d1576263f10f" -version = "0.8.6" +version = "0.8.8" [[deps.MLJXGBoostInterface]] deps = ["MLJModelInterface", "SparseArrays", "Tables", "XGBoost"] -git-tree-sha1 = "988c399a352f0b49bc1345c509d8a4800cb468c5" +git-tree-sha1 = "25769259346a017d227c2134347db4c449d43625" uuid = "54119dfa-1dab-4055-a167-80440f4f7a91" -version = "0.3.10" +version = "0.3.11" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1518,9 +1526,9 @@ version = "0.4.4" [[deps.MPICH_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "4099bb6809ac109bfc17d521dad33763bcf026b7" +git-tree-sha1 = "19d4bd098928a3263693991500d05d74dbdc2004" uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" -version = "4.2.1+1" +version = "4.2.2+0" [[deps.MPIPreferences]] deps = ["Libdl", "Preferences"] @@ -1590,10 +1598,10 @@ uuid = "fa8bd995-216d-47f1-8a91-f3b68fbeb377" version = "0.7.0" [[deps.MicroCollections]] -deps = ["BangBang", "InitialValues", "Setfield"] -git-tree-sha1 = "629afd7d10dbc6935ec59b32daeb33bc4460a42e" +deps = ["Accessors", "BangBang", "InitialValues"] +git-tree-sha1 = "44d32db644e84c75dab479f1bc15ee76a1a3618f" uuid = "128add7d-3638-4c79-886c-908ea0c25c34" -version = "0.1.4" +version = "0.2.0" [[deps.MicrosoftMPI_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1640,20 +1648,22 @@ version = "7.8.3" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "3d4617f943afe6410206a5294a95948c8d1b35bd" +git-tree-sha1 = "190dcada8cf9520198058c4544862b1f88c6c577" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.17" +version = "0.9.21" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" NNlibCUDACUDNNExt = ["CUDA", "cuDNN"] NNlibCUDAExt = "CUDA" NNlibEnzymeCoreExt = "EnzymeCore" + NNlibFFTWExt = "FFTW" [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" cuDNN = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd" [[deps.NaNMath]] @@ -2009,9 +2019,9 @@ version = "0.4.2+0" [[deps.Roots]] deps = ["Accessors", "ChainRulesCore", "CommonSolve", "Printf"] -git-tree-sha1 = "1ab580704784260ee5f45bffac810b152922747b" +git-tree-sha1 = "3484138c9fa4296a0cf46a74ca3f97b59d12b1d0" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.1.5" +version = "2.1.6" [deps.Roots.extensions] RootsForwardDiffExt = "ForwardDiff" @@ -2265,9 +2275,9 @@ version = "0.1.1" [[deps.StatisticalTraits]] deps = ["ScientificTypesBase"] -git-tree-sha1 = "30b9236691858e13f167ce829490a68e1a597782" +git-tree-sha1 = "542d979f6e756f13f862aa00b224f04f9e445f11" uuid = "64bff920-2084-43da-a3e6-9bb72801c0c9" -version = "3.2.0" +version = "3.4.0" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -2344,12 +2354,12 @@ uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" version = "7.2.1+1" [[deps.TMLE]] -deps = ["AbstractDifferentiation", "CategoricalArrays", "Combinatorics", "DataFrames", "Dictionaries", "Distributions", "GLM", "Graphs", "HypothesisTests", "LogExpFunctions", "MLJBase", "MLJGLMInterface", "MLJModels", "MetaGraphsNext", "Missings", "PrecompileTools", "Random", "SplitApplyCombine", "Statistics", "TableOperations", "Tables", "Zygote"] -git-tree-sha1 = "c4fd98696d6db5e59544c15b6a64fed04d1cc8e2" -repo-rev = "frequency_table" +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" +repo-rev = "treatment_values" repo-url = "https://github.com/TARGENE/TMLE.jl" uuid = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf" -version = "0.16.1" +version = "0.17.0" weakdeps = ["JSON", "YAML"] [deps.TMLE.extensions] @@ -2392,8 +2402,8 @@ version = "1.10.0" [[deps.TargetedEstimation]] deps = ["ArgParse", "Arrow", "CSV", "CategoricalArrays", "Combinatorics", "Configurations", "DataFrames", "EvoTrees", "GLMNet", "HDF5", "JLD2", "JSON", "MKL", "MLJ", "MLJBase", "MLJLinearModels", "MLJModelInterface", "MLJModels", "MLJXGBoostInterface", "Mmap", "MultipleTesting", "Optim", "PackageCompiler", "Random", "Serialization", "TMLE", "Tables", "YAML"] -git-tree-sha1 = "98ae29ef85f5bbeb088b1003c58ced0e0e6104d3" -repo-rev = "agnostic_composed" +git-tree-sha1 = "c2a44b4a149c7f292fd9dcc33bb62bf55888e26e" +repo-rev = "treatment_values" repo-url = "https://github.com/TARGENE/TargetedEstimation.jl" uuid = "2573d147-4098-46ba-9db2-8608d210ccac" version = "0.9.0" @@ -2442,10 +2452,10 @@ uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" version = "0.9.13" [[deps.Transducers]] -deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] -git-tree-sha1 = "3064e780dbb8a9296ebb3af8f440f787bb5332af" +deps = ["Accessors", "Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"] +git-tree-sha1 = "5215a069867476fc8e3469602006b9670e68da23" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.80" +version = "0.4.82" [deps.Transducers.extensions] TransducersBlockArraysExt = "BlockArrays" @@ -2496,9 +2506,9 @@ version = "0.2.1" [[deps.UnsafeAtomicsLLVM]] deps = ["LLVM", "UnsafeAtomics"] -git-tree-sha1 = "d9f5962fecd5ccece07db1ff006fb0b5271bdfdd" +git-tree-sha1 = "bf2c553f25e954a9b38c9c0593a59bb13113f9e5" uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" -version = "0.1.4" +version = "0.1.5" [[deps.VariantCallFormat]] deps = ["Automa", "BGZFStreams", "BioGenerics", "BufferedStreams"] diff --git a/test/tl_inputs/loco_gwas.jl b/test/tl_inputs/loco_gwas.jl index f31f480..378aa03 100644 --- a/test/tl_inputs/loco_gwas.jl +++ b/test/tl_inputs/loco_gwas.jl @@ -23,13 +23,19 @@ function check_estimands_levels_order(estimands) for Ψ in estimands # If the two components are present, the first is the 0 -> 1 and the second is the 1 -> 2 if length(Ψ.args) == 2 - @test Ψ.args[1].treatment_values[1] == (case = 0x01, control = 0x00) - @test Ψ.args[2].treatment_values[1] == (case = 0x02, control = 0x01) + for key in keys(Ψ.args[1].treatment_values) + @test Ψ.args[1].treatment_values[key] == (control = 0x00, case = 0x01) + end + for key in keys(Ψ.args[2].treatment_values) + @test Ψ.args[2].treatment_values[key] == (control = 0x01, case = 0x02) + end else # Otherwise we check they are one or the other arg = only(Ψ.args) - @test arg.treatment_values[1]==(case = 0x01, control = 0x00) || - arg.treatment_values[1]==(case = 0x02, control = 0x01) + for key in keys(arg.treatment_values) + @test arg.treatment_values[key]==(control = 0x00, case = 0x01) || + arg.treatment_values[key]==(control = 0x01, case = 0x02) + end end end end