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update deps
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@olivierlabayle
olivierlabayle committed Dec 12, 2023
1 parent e94fe65 commit 3adc78a
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86 changes: 25 additions & 61 deletions Manifest.toml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
# This file is machine-generated - editing it directly is not advised

julia_version = "1.9.2"
julia_version = "1.9.4"
manifest_format = "2.0"
project_hash = "c121e046611a196881fb0b604265421386897299"
project_hash = "45039ab4ebf43a520b63a5a262a9d31cea7954b3"

[[deps.ARFFFiles]]
deps = ["CategoricalArrays", "Dates", "Parsers", "Tables"]
Expand Down Expand Up @@ -51,9 +51,9 @@ version = "0.4.4"

[[deps.Adapt]]
deps = ["LinearAlgebra", "Requires"]
git-tree-sha1 = "02f731463748db57cc2ebfbd9fbc9ce8280d3433"
git-tree-sha1 = "cde29ddf7e5726c9fb511f340244ea3481267608"
uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
version = "3.7.1"
version = "3.7.2"
weakdeps = ["StaticArrays"]

[deps.Adapt.extensions]
Expand Down Expand Up @@ -326,12 +326,6 @@ git-tree-sha1 = "8cfa272e8bdedfa88b6aefbbca7c19f1befac519"
uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb"
version = "2.3.0"

[[deps.Conda]]
deps = ["Downloads", "JSON", "VersionParsing"]
git-tree-sha1 = "51cab8e982c5b598eea9c8ceaced4b58d9dd37c9"
uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d"
version = "1.10.0"

[[deps.Configurations]]
deps = ["ExproniconLite", "OrderedCollections", "TOML"]
git-tree-sha1 = "4358750bb58a3caefd5f37a4a0c5bfdbbf075252"
Expand Down Expand Up @@ -434,9 +428,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"

[[deps.Distributions]]
deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
git-tree-sha1 = "a6c00f894f24460379cb7136633cef54ac9f6f4a"
git-tree-sha1 = "9242eec9b7e2e14f9952e8ea1c7e31a50501d587"
uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
version = "0.25.103"
version = "0.25.104"

[deps.Distributions.extensions]
DistributionsChainRulesCoreExt = "ChainRulesCore"
Expand Down Expand Up @@ -661,12 +655,6 @@ git-tree-sha1 = "abbbb9ec3afd783a7cbd82ef01dcd088ea051398"
uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
version = "1.10.1"

[[deps.HighlyAdaptiveLasso]]
deps = ["DataFrames", "MLJModelInterface", "RCall"]
git-tree-sha1 = "40f12ec0130659287a3d1b7e1a8ffc4fcf7249ba"
uuid = "c5dac772-1445-43c4-b698-9440de7877f6"
version = "0.2.0"

[[deps.Hwloc_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "ca0f6bf568b4bfc807e7537f081c81e35ceca114"
Expand Down Expand Up @@ -708,10 +696,10 @@ uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48"
version = "1.4.0"

[[deps.IntelOpenMP_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
git-tree-sha1 = "31d6adb719886d4e32e38197aae466e98881320b"
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "ad37c091f7d7daf900963171600d7c1c5c3ede32"
uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0"
version = "2024.0.0+0"
version = "2023.2.0+0"

[[deps.InteractiveUtils]]
deps = ["Markdown"]
Expand Down Expand Up @@ -839,12 +827,12 @@ version = "0.1.0"
[[deps.LibCURL]]
deps = ["LibCURL_jll", "MozillaCACerts_jll"]
uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
version = "0.6.3"
version = "0.6.4"

[[deps.LibCURL_jll]]
deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
version = "7.84.0+0"
version = "8.4.0+0"

[[deps.LibGit2]]
deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
Expand All @@ -853,7 +841,7 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
[[deps.LibSSH2_jll]]
deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
version = "1.10.2+0"
version = "1.11.0+1"

[[deps.Libdl]]
uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
Expand Down Expand Up @@ -1024,9 +1012,9 @@ version = "0.4.3"

[[deps.MPICH_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
git-tree-sha1 = "8a5b4d2220377d1ece13f49438d71ad20cf1ba83"
git-tree-sha1 = "2ee75365ca243c1a39d467e35ffd3d4d32eef11e"
uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4"
version = "4.1.2+0"
version = "4.1.2+1"

[[deps.MPIPreferences]]
deps = ["Libdl", "Preferences"]
Expand Down Expand Up @@ -1063,9 +1051,9 @@ version = "2.28.2+0"

[[deps.MetaGraphsNext]]
deps = ["Graphs", "JLD2", "SimpleTraits"]
git-tree-sha1 = "8dd4f3f8a643d53e61ff9115749f522c35a38f3f"
git-tree-sha1 = "a385fe5aa1384647e55c0c8773457b71e9b08518"
uuid = "fa8bd995-216d-47f1-8a91-f3b68fbeb377"
version = "0.6.0"
version = "0.7.0"

[[deps.MicroCollections]]
deps = ["BangBang", "InitialValues", "Setfield"]
Expand Down Expand Up @@ -1207,9 +1195,9 @@ version = "1.6.3"

[[deps.PDMats]]
deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
git-tree-sha1 = "4e5be6bb265d33669f98eb55d2a57addd1eeb72c"
git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65"
uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
version = "0.11.30"
version = "0.11.31"

[[deps.PMIx_jll]]
deps = ["Artifacts", "Hwloc_jll", "JLLWrappers", "Libdl", "Zlib_jll", "libevent_jll"]
Expand Down Expand Up @@ -1296,12 +1284,6 @@ git-tree-sha1 = "9ebcd48c498668c7fa0e97a9cae873fbee7bfee1"
uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
version = "2.9.1"

[[deps.RCall]]
deps = ["CategoricalArrays", "Conda", "DataFrames", "DataStructures", "Dates", "Libdl", "Missings", "REPL", "Random", "Requires", "StatsModels", "WinReg"]
git-tree-sha1 = "3084689b18f9e5e817a6ce9a83a7654d8ad0f2f6"
uuid = "6f49c342-dc21-5d91-9882-a32aef131414"
version = "0.13.18"

[[deps.REPL]]
deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
Expand Down Expand Up @@ -1608,23 +1590,15 @@ version = "5.10.1+6"

[[deps.TMLE]]
deps = ["AbstractDifferentiation", "CategoricalArrays", "Combinatorics", "Distributions", "GLM", "Graphs", "HypothesisTests", "LogExpFunctions", "MLJBase", "MLJGLMInterface", "MLJModels", "MetaGraphsNext", "Missings", "PrecompileTools", "PrettyTables", "Random", "Statistics", "TableOperations", "Tables", "Zygote"]
git-tree-sha1 = "b051714cef808de23bc928f2277cbb1e3c8a1f47"
repo-rev = "cvtmle"
repo-url = "https://github.com/TARGENE/TMLE.jl.git"
git-tree-sha1 = "e66fe5f9cfdfb69f8fb8f870a89b5ce151789ae9"
uuid = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf"
version = "0.12.0"
version = "0.12.1"
weakdeps = ["JSON", "YAML"]

[deps.TMLE.extensions]
GraphMakieExt = ["GraphMakie", "CairoMakie"]
JSONExt = "JSON"
YAMLExt = "YAML"

[deps.TMLE.weakdeps]
CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"

[[deps.TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
Expand Down Expand Up @@ -1660,10 +1634,10 @@ uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
version = "1.10.0"

[[deps.TargetedEstimation]]
deps = ["Arrow", "CSV", "CategoricalArrays", "Combinatorics", "Comonicon", "Configurations", "DataFrames", "EvoTrees", "GLMNet", "HDF5", "HighlyAdaptiveLasso", "JLD2", "JSON", "MKL", "MLJ", "MLJBase", "MLJLinearModels", "MLJModelInterface", "MLJModels", "MLJXGBoostInterface", "Mmap", "MultipleTesting", "Optim", "Random", "Serialization", "TMLE", "Tables", "YAML"]
git-tree-sha1 = "e9cb946be5497f0c390b1dc6a286ab8a84c8709a"
deps = ["Arrow", "CSV", "CategoricalArrays", "Combinatorics", "Comonicon", "Configurations", "DataFrames", "EvoTrees", "GLMNet", "HDF5", "JLD2", "JSON", "MKL", "MLJ", "MLJBase", "MLJLinearModels", "MLJModelInterface", "MLJModels", "MLJXGBoostInterface", "Mmap", "MultipleTesting", "Optim", "Random", "Serialization", "TMLE", "Tables", "YAML"]
git-tree-sha1 = "94334dd6c98f3a4ae10143d0d85e3f99383b69be"
repo-rev = "cv_tmle"
repo-url = "https://github.com/TARGENE/TargetedEstimation.jl"
repo-url = "https://github.com/TARGENE/TargetedEstimation.jl.git"
uuid = "2573d147-4098-46ba-9db2-8608d210ccac"
version = "0.7.4"

Expand Down Expand Up @@ -1740,22 +1714,12 @@ git-tree-sha1 = "323e3d0acf5e78a56dfae7bd8928c989b4f3083e"
uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249"
version = "0.1.3"

[[deps.VersionParsing]]
git-tree-sha1 = "58d6e80b4ee071f5efd07fda82cb9fbe17200868"
uuid = "81def892-9a0e-5fdd-b105-ffc91e053289"
version = "1.3.0"

[[deps.WeakRefStrings]]
deps = ["DataAPI", "InlineStrings", "Parsers"]
git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23"
uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5"
version = "1.4.2"

[[deps.WinReg]]
git-tree-sha1 = "cd910906b099402bcc50b3eafa9634244e5ec83b"
uuid = "1b915085-20d7-51cf-bf83-8f477d6f5128"
version = "1.0.0"

[[deps.WorkerUtilities]]
git-tree-sha1 = "cd1659ba0d57b71a464a29e64dbc67cfe83d54e7"
uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60"
Expand Down Expand Up @@ -1846,7 +1810,7 @@ version = "2.1.13+1"
[[deps.nghttp2_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.48.0+0"
version = "1.52.0+1"

[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
Expand Down
1 change: 1 addition & 0 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -30,4 +30,5 @@ DataFrames = "1.5.0"
HTTP = "1.8.0"
JSON = "0.21.4"
StableRNGs = "1.0.0"
TMLE = "0.12.1"
julia = "1"
9 changes: 4 additions & 5 deletions test/permutation_test.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -132,11 +132,10 @@ end

# Clean
clean()
for file in readdir()
if startswith(file, "permutation_")
rm(file)
end
end
rm("permutation_estimands_1.yaml")
rm("permutation_estimands_2.yaml")
rm("permutation_estimands_3.yaml")
rm("permutation_dataset.arrow")
end

end
Expand Down

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