From eacc25fb096c8a0b26b86abea30ad28e744a0681 Mon Sep 17 00:00:00 2001 From: Philip Swannell <18028484+PGS62@users.noreply.github.com> Date: Sat, 6 Apr 2024 16:26:38 +0100 Subject: [PATCH] Compatibility with Julia 1.4 --- src/corkendall_fromfile.jl | 2 +- test/Manifest.toml | 347 -------------------------------- test/compare_implementations.jl | 8 +- test/naive_implementations.jl | 12 +- test/rankcorr.jl | 2 +- 5 files changed, 12 insertions(+), 359 deletions(-) delete mode 100644 test/Manifest.toml diff --git a/src/corkendall_fromfile.jl b/src/corkendall_fromfile.jl index f34d681..5d28f06 100644 --- a/src/corkendall_fromfile.jl +++ b/src/corkendall_fromfile.jl @@ -92,7 +92,7 @@ function csvread(filename::String, ignorefirstrow::Bool, ignorefirstcol::Bool; types = Union{Missing,Float64} strict = true - filedata = File(filename; header, drop, missingstring, types, strict) + filedata = File(filename; header=header, drop=drop, missingstring=missingstring, types=types, strict=strict) data = matrix(filedata) #Convert to Array{Float64} if there are in fact no missings diff --git a/test/Manifest.toml b/test/Manifest.toml deleted file mode 100644 index 2ccaf0e..0000000 --- a/test/Manifest.toml +++ /dev/null @@ -1,347 +0,0 @@ -# This file is machine-generated - editing it directly is not advised - -julia_version = "1.10.2" -manifest_format = "2.0" -project_hash = "2fb9fc3e929e222826103eced966184d9c664dd2" - -[[deps.Artifacts]] -uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" - -[[deps.Base64]] -uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" - -[[deps.CSV]] -deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] -git-tree-sha1 = "679e69c611fff422038e9e21e270c4197d49d918" -uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.12" - -[[deps.CodecZlib]] -deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73" -uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.4" - -[[deps.Compat]] -deps = ["TOML", "UUIDs"] -git-tree-sha1 = "c955881e3c981181362ae4088b35995446298b80" -uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.14.0" -weakdeps = ["Dates", "LinearAlgebra"] - - [deps.Compat.extensions] - CompatLinearAlgebraExt = "LinearAlgebra" - -[[deps.CompilerSupportLibraries_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "1.1.0+0" - -[[deps.Crayons]] -git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" -uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" -version = "4.1.1" - -[[deps.DataAPI]] -git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe" -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" -uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.6.1" - -[[deps.DataStructures]] -deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "1fb174f0d48fe7d142e1109a10636bc1d14f5ac2" -uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.17" - -[[deps.DataValueInterfaces]] -git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" -uuid = "e2d170a0-9d28-54be-80f0-106bbe20a464" -version = "1.0.0" - -[[deps.Dates]] -deps = ["Printf"] -uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" - -[[deps.DocStringExtensions]] -deps = ["LibGit2"] -git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" -uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.9.3" - -[[deps.FilePathsBase]] -deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] -git-tree-sha1 = "9f00e42f8d99fdde64d40c8ea5d14269a2e2c1aa" -uuid = "48062228-2e41-5def-b9a4-89aafe57970f" -version = "0.9.21" - -[[deps.Future]] -deps = ["Random"] -uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" - -[[deps.InlineStrings]] -deps = ["Parsers"] -git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461" -uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.4.0" - -[[deps.InteractiveUtils]] -deps = ["Markdown"] -uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" - -[[deps.InvertedIndices]] -git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" -uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.3.0" - -[[deps.IrrationalConstants]] -git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" -uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.2.2" - -[[deps.IteratorInterfaceExtensions]] -git-tree-sha1 = "a3f24677c21f5bbe9d2a714f95dcd58337fb2856" -uuid = "82899510-4779-5014-852e-03e436cf321d" -version = "1.0.0" - -[[deps.LaTeXStrings]] -git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" -uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.1" - -[[deps.LibGit2]] -deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] -uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" - -[[deps.LibGit2_jll]] -deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] -uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" -version = "1.6.4+0" - -[[deps.LibSSH2_jll]] -deps = ["Artifacts", "Libdl", "MbedTLS_jll"] -uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" -version = "1.11.0+1" - -[[deps.Libdl]] -uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" - -[[deps.LinearAlgebra]] -deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] -uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" - -[[deps.LogExpFunctions]] -deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "18144f3e9cbe9b15b070288eef858f71b291ce37" -uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.27" - - [deps.LogExpFunctions.extensions] - LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" - LogExpFunctionsChangesOfVariablesExt = "ChangesOfVariables" - LogExpFunctionsInverseFunctionsExt = "InverseFunctions" - - [deps.LogExpFunctions.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" - ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" - InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" - -[[deps.Logging]] -uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" - -[[deps.Markdown]] -deps = ["Base64"] -uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" - -[[deps.MbedTLS_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+1" - -[[deps.Missings]] -deps = ["DataAPI"] -git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" -uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.1.0" - -[[deps.Mmap]] -uuid = "a63ad114-7e13-5084-954f-fe012c677804" - -[[deps.NetworkOptions]] -uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" -version = "1.2.0" - -[[deps.OpenBLAS_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] -uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.23+4" - -[[deps.OrderedCollections]] -git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" -uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.3" - -[[deps.Parsers]] -deps = ["Dates", "PrecompileTools", "UUIDs"] -git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" -uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.8.1" - -[[deps.PooledArrays]] -deps = ["DataAPI", "Future"] -git-tree-sha1 = "36d8b4b899628fb92c2749eb488d884a926614d3" -uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" -version = "1.4.3" - -[[deps.PrecompileTools]] -deps = ["Preferences"] -git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" -uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" -version = "1.2.0" - -[[deps.Preferences]] -deps = ["TOML"] -git-tree-sha1 = "00805cd429dcb4870060ff49ef443486c262e38e" -uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.4.1" - -[[deps.PrettyTables]] -deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "88b895d13d53b5577fd53379d913b9ab9ac82660" -uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.3.1" - -[[deps.Printf]] -deps = ["Unicode"] -uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" - -[[deps.REPL]] -deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] -uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" - -[[deps.Random]] -deps = ["SHA"] -uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" - -[[deps.Reexport]] -git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" -uuid = "189a3867-3050-52da-a836-e630ba90ab69" -version = "1.2.2" - -[[deps.SHA]] -uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" -version = "0.7.0" - -[[deps.SentinelArrays]] -deps = ["Dates", "Random"] -git-tree-sha1 = "0e7508ff27ba32f26cd459474ca2ede1bc10991f" -uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.4.1" - -[[deps.Serialization]] -uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" - -[[deps.Sockets]] -uuid = "6462fe0b-24de-5631-8697-dd941f90decc" - -[[deps.SortingAlgorithms]] -deps = ["DataStructures"] -git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085" -uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.2.1" - -[[deps.SparseArrays]] -deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] -uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -version = "1.10.0" - -[[deps.Statistics]] -deps = ["LinearAlgebra", "SparseArrays"] -uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.10.0" - -[[deps.StatsAPI]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed" -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 = "1d77abd07f617c4868c33d4f5b9e1dbb2643c9cf" -uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.2" - -[[deps.StringManipulation]] -deps = ["PrecompileTools"] -git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" -uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.4" - -[[deps.SuiteSparse_jll]] -deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] -uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "7.2.1+1" - -[[deps.TOML]] -deps = ["Dates"] -uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" -version = "1.0.3" - -[[deps.TableTraits]] -deps = ["IteratorInterfaceExtensions"] -git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" -uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" -version = "1.0.1" - -[[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] -git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d" -uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.11.1" - -[[deps.Test]] -deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] -uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" - -[[deps.TranscodingStreams]] -git-tree-sha1 = "54194d92959d8ebaa8e26227dbe3cdefcdcd594f" -uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.10.3" -weakdeps = ["Random", "Test"] - - [deps.TranscodingStreams.extensions] - TestExt = ["Test", "Random"] - -[[deps.UUIDs]] -deps = ["Random", "SHA"] -uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" - -[[deps.Unicode]] -uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" - -[[deps.WeakRefStrings]] -deps = ["DataAPI", "InlineStrings", "Parsers"] -git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" -uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" -version = "1.4.2" - -[[deps.WorkerUtilities]] -git-tree-sha1 = "cd1659ba0d57b71a464a29e64dbc67cfe83d54e7" -uuid = "76eceee3-57b5-4d4a-8e66-0e911cebbf60" -version = "1.6.1" - -[[deps.Zlib_jll]] -deps = ["Libdl"] -uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.13+1" - -[[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl"] -uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+1" diff --git a/test/compare_implementations.jl b/test/compare_implementations.jl index 9bd94d8..797624e 100644 --- a/test/compare_implementations.jl +++ b/test/compare_implementations.jl @@ -153,7 +153,7 @@ function compare_implementations(fn1::Function=corkendall, fn2::Function=corkend if j <= 3 if fns_handle_missing - res1 = fn1(arg1; skipmissing) + res1 = fn1(arg1; skipmissing=skipmissing) else res1 = fn1(arg1) end @@ -162,7 +162,7 @@ function compare_implementations(fn1::Function=corkendall, fn2::Function=corkend @error("Detected that function $fn1name mutated its argument, $casedesc") if fns_handle_missing - res2 = fn2(arg1; skipmissing) + res2 = fn2(arg1; skipmissing=skipmissing) else res2 = fn2(arg1) end @@ -172,7 +172,7 @@ function compare_implementations(fn1::Function=corkendall, fn2::Function=corkend else arg2_backup = copy(arg2) if fns_handle_missing - res1 = fn1(arg1, arg2; skipmissing) + res1 = fn1(arg1, arg2; skipmissing=skipmissing) else res1 = fn1(arg1, arg2) end @@ -180,7 +180,7 @@ function compare_implementations(fn1::Function=corkendall, fn2::Function=corkend (myisequal(arg1, arg1_backup) && myisequal(arg2, arg2_backup)) || @error("Detected that function $fn1name mutated one of its argument, $casedesc") if fns_handle_missing - res2 = fn2(arg1, arg2; skipmissing) + res2 = fn2(arg1, arg2; skipmissing=skipmissing) else res2 = fn2(arg1, arg2) end diff --git a/test/naive_implementations.jl b/test/naive_implementations.jl index b771419..bfee33b 100644 --- a/test/naive_implementations.jl +++ b/test/naive_implementations.jl @@ -29,7 +29,7 @@ function corkendall_naive(x::AbstractMatrix, y::AbstractMatrix=x; else dest = ones(Float64, nr, nc) end - return _corkendall_naive(x, y; dest, skipmissing) + return _corkendall_naive(x, y; dest=dest, skipmissing=skipmissing) end @@ -70,11 +70,11 @@ function corkendall_naive(x::AbstractVector, y::AbstractVector; skipmissing::Sym end function corkendall_naive(x::AbstractMatrix, y::AbstractVector; skipmissing::Symbol=:none) - return vec(corkendall_naive(x, reshape(y, (length(y), 1)); skipmissing)) + return vec(corkendall_naive(x, reshape(y, (length(y), 1)); skipmissing=skipmissing)) end function corkendall_naive(x::AbstractVector, y::AbstractMatrix; skipmissing::Symbol=:none) - return corkendall_naive(reshape(x, (length(x), 1)), y; skipmissing) + return corkendall_naive(reshape(x, (length(x), 1)), y; skipmissing=skipmissing) end function corkendall_naive_kernel!(x, y, skipmissing::Symbol) @@ -162,7 +162,7 @@ function corspearman_naive(x::AbstractMatrix, y::AbstractMatrix=x; else dest = ones(Float64, nr, nc) end - return _corspearman_naive(x, y; dest, skipmissing) + return _corspearman_naive(x, y; dest=dest, skipmissing=skipmissing) end @@ -204,11 +204,11 @@ function corspearman_naive(x::AbstractVector, y::AbstractVector; skipmissing::Sy end function corspearman_naive(x::AbstractMatrix, y::AbstractVector; skipmissing::Symbol=:none) - return corspearman_naive(x, reshape(y, (length(y), 1)); skipmissing) + return corspearman_naive(x, reshape(y, (length(y), 1)); skipmissing=skipmissing) end function corspearman_naive(x::AbstractVector, y::AbstractMatrix; skipmissing::Symbol=:none) - return corspearman_naive(reshape(x, (length(x), 1)), y; skipmissing) + return corspearman_naive(reshape(x, (length(x), 1)), y; skipmissing=skipmissing) end function corspearman_naive_kernel!(x, y, skipmissing::Symbol) diff --git a/test/rankcorr.jl b/test/rankcorr.jl index 32c3d40..d74b8c6 100644 --- a/test/rankcorr.jl +++ b/test/rankcorr.jl @@ -341,7 +341,7 @@ end if !((arg1 isa Vector) && (arg2 isa Vector) && skipmissing == :listwise) copy1 = copy(arg1) copy2 = copy(arg2) - res = f(arg1, arg2; skipmissing) + res = f(arg1, arg2; skipmissing=skipmissing) @test isequal(arg1, copy1) @test isequal(arg2, copy2) end