Up_tmle_dep (#180)

* working state from_param_files

* working tmle inputs tests

* update from actors mode

* remove old param files

* rename batchsize parameter

* up manifest

* update option name

* up TMLE to 0.11

Author: olivierlabayle

Manifest.toml

@@ -108,6 +108,12 @@ git-tree-sha1 = "c700cce799b51c9045473de751e9319bdd1c6e94"
 uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 version = "0.10.9"
 
+[[deps.Calculus]]
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad"
+uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
+version = "0.5.1"
+
 [[deps.CategoricalArrays]]
 deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"]
 git-tree-sha1 = "5084cc1a28976dd1642c9f337b28a3cb03e0f7d2"
@@ -122,9 +128,9 @@ version = "0.1.10"
 
 [[deps.ChainRules]]
 deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "Statistics", "StructArrays"]
-git-tree-sha1 = "7d20c2fb8ab838e41069398685e7b6b5f89ed85b"
+git-tree-sha1 = "8bae903893aeeb429cf732cf1888490b93ecf265"
 uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2"
-version = "1.48.0"
+version = "1.49.0"
 
 [[deps.ChainRulesCore]]
 deps = ["Compat", "LinearAlgebra", "SparseArrays"]
@@ -169,10 +175,10 @@ uuid = "6b39b394-51ab-5f42-8807-6242bab2b4c2"
 version = "0.7.2"
 
 [[deps.ColorSchemes]]
-deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"]
-git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3"
+deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"]
+git-tree-sha1 = "be6ab11021cd29f0344d5c4357b163af05a48cba"
 uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
-version = "3.20.0"
+version = "3.21.0"
 
 [[deps.ColorTypes]]
 deps = ["FixedPointNumbers", "Random"]
@@ -224,6 +230,12 @@ git-tree-sha1 = "52cb3ec90e8a8bea0e62e275ba577ad0f74821f7"
 uuid = "ed09eef8-17a6-5b46-8889-db040fac31e3"
 version = "0.3.2"
 
+[[deps.Configurations]]
+deps = ["ExproniconLite", "OrderedCollections", "TOML"]
+git-tree-sha1 = "62a7c76dbad02fdfdaa53608104edf760938c4ca"
+uuid = "5218b696-f38b-4ac9-8b61-a12ec717816d"
+version = "0.17.4"
+
 [[deps.ConstructionBase]]
 deps = ["LinearAlgebra"]
 git-tree-sha1 = "89a9db8d28102b094992472d333674bd1a83ce2a"
@@ -326,11 +338,23 @@ 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.ExprTools]]
 git-tree-sha1 = "c1d06d129da9f55715c6c212866f5b1bddc5fa00"
 uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
 version = "0.1.9"
 
+[[deps.ExproniconLite]]
+deps = ["Pkg", "TOML"]
+git-tree-sha1 = "c2eb763acf6e13e75595e0737a07a0bec0ce2147"
+uuid = "55351af7-c7e9-48d6-89ff-24e801d99491"
+version = "0.7.11"
+
 [[deps.FilePathsBase]]
 deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"]
 git-tree-sha1 = "e27c4ebe80e8699540f2d6c805cc12203b614f12"
@@ -369,10 +393,10 @@ deps = ["Random"]
 uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 
 [[deps.GLM]]
-deps = ["Distributions", "LinearAlgebra", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "StatsModels"]
-git-tree-sha1 = "92b8d38886445d6d06e5f13201e57d018c4ff880"
+deps = ["Distributions", "LinearAlgebra", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "StatsModels"]
+git-tree-sha1 = "cd3e314957dc11c4c905d54d1f5a65c979e4748a"
 uuid = "38e38edf-8417-5370-95a0-9cbb8c7f171a"
-version = "1.7.0"
+version = "1.8.2"
 
 [[deps.GPUArrays]]
 deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"]
@@ -397,6 +421,12 @@ git-tree-sha1 = "734fd90dd2f920a2f1921d5388dcebe805b262dc"
 uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0"
 version = "0.1.14"
 
+[[deps.HypergeometricFunctions]]
+deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
+git-tree-sha1 = "432b5b03176f8182bd6841fbfc42c718506a2d5f"
+uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a"
+version = "0.3.15"
+
 [[deps.HypothesisTests]]
 deps = ["Combinatorics", "Distributions", "LinearAlgebra", "Random", "Rmath", "Roots", "Statistics", "StatsBase"]
 git-tree-sha1 = "ae3b6964d58df11984d22644ce5546eaf20fe95d"
@@ -436,9 +466,9 @@ uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f"
 version = "1.3.0"
 
 [[deps.IrrationalConstants]]
-git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151"
+git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2"
 uuid = "92d709cd-6900-40b7-9082-c6be49f344b6"
-version = "0.1.1"
+version = "0.2.2"
 
 [[deps.IteratorInterfaceExtensions]]
 git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856"
@@ -526,22 +556,22 @@ uuid = "bdcacae8-1622-11e9-2a5c-532679323890"
 version = "0.12.157"
 
 [[deps.LossFunctions]]
-deps = ["InteractiveUtils", "Markdown", "RecipesBase"]
-git-tree-sha1 = "f27330f931944ecee340f004302db724c1985955"
+deps = ["CategoricalArrays", "Markdown"]
+git-tree-sha1 = "d4c7ff8c7281943371e1725000fd538a699024d0"
 uuid = "30fc2ffe-d236-52d8-8643-a9d8f7c094a7"
-version = "0.8.1"
+version = "0.9.0"
 
 [[deps.MLJBase]]
 deps = ["CategoricalArrays", "CategoricalDistributions", "ComputationalResources", "Dates", "DelimitedFiles", "Distributed", "Distributions", "InteractiveUtils", "InvertedIndices", "LinearAlgebra", "LossFunctions", "MLJModelInterface", "Missings", "OrderedCollections", "Parameters", "PrettyTables", "ProgressMeter", "Random", "ScientificTypes", "Serialization", "StatisticalTraits", "Statistics", "StatsBase", "Tables"]
-git-tree-sha1 = "37a311b0cd581764fc460f6632e6219dc32f9427"
+git-tree-sha1 = "e99e84c7ca1696b38e2a8823f53ac9cc775599dd"
 uuid = "a7f614a8-145f-11e9-1d2a-a57a1082229d"
-version = "0.21.8"
+version = "0.21.9"
 
 [[deps.MLJGLMInterface]]
-deps = ["Distributions", "GLM", "MLJModelInterface", "Tables"]
-git-tree-sha1 = "87b665f79b082e15acb8def31ede049386dcb0c6"
+deps = ["Distributions", "GLM", "MLJModelInterface", "StatsModels", "Tables"]
+git-tree-sha1 = "06aba1c96b19f31744f7e97d96fcf66b79739e05"
 uuid = "caf8df21-4939-456d-ac9c-5fefbfb04c0c"
-version = "0.3.4"
+version = "0.3.5"
 
 [[deps.MLJModelInterface]]
 deps = ["Random", "ScientificTypesBase", "StatisticalTraits"]
@@ -567,10 +597,10 @@ uuid = "d125e4d3-2237-4719-b19c-fa641b8a4667"
 version = "0.1.8"
 
 [[deps.MarchingCubes]]
-deps = ["SnoopPrecompile", "StaticArrays"]
-git-tree-sha1 = "b198463d1a631e8771709bc8e011ba329da9ad38"
+deps = ["PrecompileTools", "StaticArrays"]
+git-tree-sha1 = "c8e29e2bacb98c9b6f10445227a8b0402f2f173a"
 uuid = "299715c1-40a9-479a-aaf9-4a633d36f717"
-version = "0.1.7"
+version = "0.1.8"
 
 [[deps.Markdown]]
 deps = ["Base64"]
@@ -666,6 +696,12 @@ git-tree-sha1 = "a6062fe4063cdafe78f4a0a81cfffb89721b30e7"
 uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 version = "1.4.2"
 
+[[deps.PrecompileTools]]
+deps = ["Preferences"]
+git-tree-sha1 = "2e47054ffe7d0a8872e977c0d09eb4b3d162ebde"
+uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
+version = "1.0.2"
+
 [[deps.Preferences]]
 deps = ["TOML"]
 git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d"
@@ -713,12 +749,6 @@ git-tree-sha1 = "9f0a1b71baaf7650f4fa8a1d168c7fb6ee41f0c9"
 uuid = "c1ae055f-0cd5-4b69-90a6-9a35b1a98df9"
 version = "0.1.0"
 
-[[deps.RecipesBase]]
-deps = ["SnoopPrecompile"]
-git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8"
-uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
-version = "1.3.3"
-
 [[deps.Reexport]]
 git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
 uuid = "189a3867-3050-52da-a836-e630ba90ab69"
@@ -750,9 +780,9 @@ version = "0.4.0+0"
 
 [[deps.Roots]]
 deps = ["ChainRulesCore", "CommonSolve", "Printf", "Setfield"]
-git-tree-sha1 = "b45deea4566988994ebb8fb80aa438a295995a6e"
+git-tree-sha1 = "82362f2a4f756951f21ebb3ac2aed094c46a5109"
 uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
-version = "2.0.10"
+version = "2.0.12"
 
 [[deps.SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
@@ -869,15 +899,15 @@ version = "0.8.6"
 
 [[deps.StaticArrayInterface]]
 deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "Static", "SuiteSparse"]
-git-tree-sha1 = "fd5f417fd7e103c121b0a0b4a6902f03991111f4"
+git-tree-sha1 = "33040351d2403b84afce74dae2e22d3f5b18edcb"
 uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718"
-version = "1.3.0"
+version = "1.4.0"
 
 [[deps.StaticArrays]]
 deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"]
-git-tree-sha1 = "b8d897fe7fa688e93aef573711cb207c08c9e11e"
+git-tree-sha1 = "fd9a77cfd87116a27b2121c1988045f428b35a36"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.5.19"
+version = "1.5.22"
 
 [[deps.StaticArraysCore]]
 git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a"
@@ -907,16 +937,16 @@ uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 version = "0.33.21"
 
 [[deps.StatsFuns]]
-deps = ["ChainRulesCore", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
-git-tree-sha1 = "5950925ff997ed6fb3e985dcce8eb1ba42a0bbe7"
+deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
+git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a"
 uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "0.9.18"
+version = "1.3.0"
 
 [[deps.StatsModels]]
 deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsBase", "StatsFuns", "Tables"]
-git-tree-sha1 = "a5e15f27abd2692ccb61a99e0854dfb7d48017db"
+git-tree-sha1 = "51cdf1afd9d78552e7a08536930d7abc3b288a5c"
 uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d"
-version = "0.6.33"
+version = "0.7.1"
 
 [[deps.StringEncodings]]
 deps = ["Libiconv_jll"]
@@ -940,12 +970,10 @@ deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"]
 uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9"
 
 [[deps.TMLE]]
-deps = ["AbstractDifferentiation", "CategoricalArrays", "Distributions", "GLM", "HypothesisTests", "LogExpFunctions", "MLJBase", "MLJGLMInterface", "MLJModels", "Missings", "PrettyTables", "Statistics", "TableOperations", "Tables", "YAML", "Zygote"]
-git-tree-sha1 = "ea4ed14ea78402bcc29ff201644467a854315daa"
-repo-rev = "73fc566cbad8c4e0e8c96d73b3ed602ba3699e48"
-repo-url = "https://github.com/olivierlabayle/TMLE.jl.git"
+deps = ["AbstractDifferentiation", "CategoricalArrays", "Configurations", "Distributions", "GLM", "HypothesisTests", "LogExpFunctions", "MLJBase", "MLJGLMInterface", "MLJModels", "Missings", "PrettyTables", "Statistics", "TableOperations", "Tables", "YAML", "Zygote"]
+git-tree-sha1 = "cd8e0284a7d805d8a1ea749a9290d6799dfc19fe"
 uuid = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf"
-version = "0.10.0"
+version = "0.11.0"
 
 [[deps.TOML]]
 deps = ["Dates"]
@@ -1015,10 +1043,10 @@ version = "1.0.2"
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [[deps.UnicodePlots]]
-deps = ["ColorSchemes", "ColorTypes", "Contour", "Crayons", "Dates", "LinearAlgebra", "MarchingCubes", "NaNMath", "Printf", "Requires", "SnoopPrecompile", "SparseArrays", "StaticArrays", "StatsBase"]
-git-tree-sha1 = "2825e58f6ec3cab889dfa2c824f8d89b9f7ee731"
+deps = ["ColorSchemes", "ColorTypes", "Contour", "Crayons", "Dates", "LinearAlgebra", "MarchingCubes", "NaNMath", "PrecompileTools", "Printf", "Requires", "SparseArrays", "StaticArrays", "StatsBase"]
+git-tree-sha1 = "9fbe3fb6c4bbe4cafb5ce4d15bbec82f0077e1d5"
 uuid = "b8865327-cd53-5732-bb35-84acbb429228"
-version = "3.5.1"
+version = "3.5.2"
 
 [[deps.VariantCallFormat]]
 deps = ["Automa", "BGZFStreams", "BioCore", "BufferedStreams"]

Project.toml

@@ -24,3 +24,4 @@ Combinatorics = "1.0"
 DataFrames = "1.2"
 SnpArrays = "0.3"
 YAML = "0.4"
+TMLE = "0.11"

bin/tmle_inputs.jl

@@ -11,7 +11,7 @@ function parse_commandline()
                    "baal-nf pipeline (https://git.ecdf.ed.ac.uk/oalmelid/baal-nf), trans-actors "*
                    " and potential additional exposures from an external trait dataset."
 
-        "from-param-files"
+        "from-param-file"
             action = :command
             help = "Will assume Parameter files (see README.md) to be given."
 
@@ -41,12 +41,10 @@ function parse_commandline()
             required = true
             help = "Path to a genetic confounders file"
 
-        "--phenotype-batch-size"
+        "--batch-size"
             arg_type = Int
             required = false
-            help = "Further performance may be obtained by batching phenotypes in a"*
-                   " single Targeted Estimation run. If not specified, all phenotypes "*
-                   "constitute a batch."
+            help = "To split parameters in multiple files of size batch-size"
 
         "--positivity-constraint"
             arg_type = Float64
@@ -90,10 +88,10 @@ function parse_commandline()
             help = "If true, genotypes are encoded as the number of minor alleles."
     end
 
-    @add_arg_table s["from-param-files"] begin
-        "param-prefix"
+    @add_arg_table s["from-param-file"] begin
+        "paramfile"
             arg_type = String
-            help = "Prefix to parameter files"
+            help = "Parameter file"
     end
 
     return parse_args(s)