diff --git a/issues/780/Manifest.toml b/issues/780/Manifest.toml new file mode 100644 index 000000000..5b8c3b887 --- /dev/null +++ b/issues/780/Manifest.toml @@ -0,0 +1,836 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.10.4" +manifest_format = "2.0" +project_hash = "cab816fabd6dc09bb3070438342b0e3a876786b9" + +[[deps.Adapt]] +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099" +uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" +version = "4.0.4" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" + +[[deps.AliasTables]] +deps = ["PtrArrays", "Random"] +git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff" +uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8" +version = "1.1.3" + +[[deps.ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" + +[[deps.ArrayLayouts]] +deps = ["FillArrays", "LinearAlgebra"] +git-tree-sha1 = "ce2ca959f932f5dad70697dd93133d1167cf1e4e" +uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" +version = "1.10.2" +weakdeps = ["SparseArrays"] + + [deps.ArrayLayouts.extensions] + ArrayLayoutsSparseArraysExt = "SparseArrays" + +[[deps.Arrow]] +deps = ["ArrowTypes", "BitIntegers", "CodecLz4", "CodecZstd", "ConcurrentUtilities", "DataAPI", "Dates", "EnumX", "LoggingExtras", "Mmap", "PooledArrays", "SentinelArrays", "Tables", "TimeZones", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "f8d411d1b45459368567dc51f683ed78a919d795" +uuid = "69666777-d1a9-59fb-9406-91d4454c9d45" +version = "2.7.2" + +[[deps.ArrowTypes]] +deps = ["Sockets", "UUIDs"] +git-tree-sha1 = "404265cd8128a2515a81d5eae16de90fdef05101" +uuid = "31f734f8-188a-4ce0-8406-c8a06bd891cd" +version = "2.3.0" + +[[deps.Artifacts]] +uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" + +[[deps.BSplineKit]] +deps = ["ArrayLayouts", "BandedMatrices", "FastGaussQuadrature", "ForwardDiff", "LinearAlgebra", "PrecompileTools", "Random", "Reexport", "SparseArrays", "Static", "StaticArrays", "StaticArraysCore"] +git-tree-sha1 = "79dba2b0d60f225f4660075cb0e9b4da9960042a" +uuid = "093aae92-e908-43d7-9660-e50ee39d5a0a" +version = "0.17.6" + +[[deps.BandedMatrices]] +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] +git-tree-sha1 = "71f605effb24081b09cae943ba39ef9ca90c04f4" +uuid = "aae01518-5342-5314-be14-df237901396f" +version = "1.7.2" +weakdeps = ["SparseArrays"] + + [deps.BandedMatrices.extensions] + BandedMatricesSparseArraysExt = "SparseArrays" + +[[deps.Base64]] +uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" + +[[deps.BitIntegers]] +deps = ["Random"] +git-tree-sha1 = "a55462dfddabc34bc97d3a7403a2ca2802179ae6" +uuid = "c3b6d118-76ef-56ca-8cc7-ebb389d030a1" +version = "0.3.1" + +[[deps.CSV]] +deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] +git-tree-sha1 = "6c834533dc1fabd820c1db03c839bf97e45a3fab" +uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +version = "0.10.14" + +[[deps.CodecLz4]] +deps = ["Lz4_jll", "TranscodingStreams"] +git-tree-sha1 = "0db0c70ca94c0a79cadad269497f25ca88b9fa91" +uuid = "5ba52731-8f18-5e0d-9241-30f10d1ec561" +version = "0.4.5" + +[[deps.CodecZlib]] +deps = ["TranscodingStreams", "Zlib_jll"] +git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" +uuid = "944b1d66-785c-5afd-91f1-9de20f533193" +version = "0.7.6" + +[[deps.CodecZstd]] +deps = ["TranscodingStreams", "Zstd_jll"] +git-tree-sha1 = "5e41a52bec3b0881a7eb54f5391b779994504186" +uuid = "6b39b394-51ab-5f42-8807-6242bab2b4c2" +version = "0.8.5" + +[[deps.CommonSubexpressions]] +deps = ["MacroTools", "Test"] +git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" +version = "0.3.0" + +[[deps.CommonWorldInvalidations]] +git-tree-sha1 = "ae52d1c52048455e85a387fbee9be553ec2b68d0" +uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8" +version = "1.0.0" + +[[deps.Compat]] +deps = ["TOML", "UUIDs"] +git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" +uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" +version = "4.16.0" +weakdeps = ["Dates", "LinearAlgebra"] + + [deps.Compat.extensions] + CompatLinearAlgebraExt = "LinearAlgebra" + +[[deps.CompilerSupportLibraries_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" +version = "1.1.1+0" + +[[deps.ConcurrentUtilities]] +deps = ["Serialization", "Sockets"] +git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" +uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" +version = "2.4.2" + +[[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 = "1d0a14036acb104d9e89698bd408f63ab58cdc82" +uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" +version = "0.18.20" + +[[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.Dictionaries]] +deps = ["Indexing", "Random", "Serialization"] +git-tree-sha1 = "35b66b6744b2d92c778afd3a88d2571875664a2a" +uuid = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4" +version = "0.4.2" + +[[deps.DiffResults]] +deps = ["StaticArraysCore"] +git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" +uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" +version = "1.1.0" + +[[deps.DiffRules]] +deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] +git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" +uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" +version = "1.15.1" + +[[deps.Distributed]] +deps = ["Random", "Serialization", "Sockets"] +uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" + +[[deps.Distributions]] +deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] +git-tree-sha1 = "0e0a1264b0942f1f3abb2b30891f2a590cc652ac" +uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" +version = "0.25.110" + + [deps.Distributions.extensions] + DistributionsChainRulesCoreExt = "ChainRulesCore" + DistributionsDensityInterfaceExt = "DensityInterface" + DistributionsTestExt = "Test" + + [deps.Distributions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + +[[deps.DocStringExtensions]] +deps = ["LibGit2"] +git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" +uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" +version = "0.9.3" + +[[deps.Downloads]] +deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] +uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" +version = "1.6.0" + +[[deps.EnumX]] +git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" +uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" +version = "1.0.4" + +[[deps.ExprTools]] +git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" +uuid = "e2ba6199-217a-4e67-a87a-7c52f15ade04" +version = "0.1.10" + +[[deps.FastGaussQuadrature]] +deps = ["LinearAlgebra", "SpecialFunctions", "StaticArrays"] +git-tree-sha1 = "fd923962364b645f3719855c88f7074413a6ad92" +uuid = "442a2c76-b920-505d-bb47-c5924d526838" +version = "1.0.2" + +[[deps.FilePathsBase]] +deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"] +git-tree-sha1 = "9f00e42f8d99fdde64d40c8ea5d14269a2e2c1aa" +uuid = "48062228-2e41-5def-b9a4-89aafe57970f" +version = "0.9.21" + +[[deps.FileWatching]] +uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" + +[[deps.FillArrays]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "0653c0a2396a6da5bc4766c43041ef5fd3efbe57" +uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" +version = "1.11.0" +weakdeps = ["PDMats", "SparseArrays", "Statistics"] + + [deps.FillArrays.extensions] + FillArraysPDMatsExt = "PDMats" + FillArraysSparseArraysExt = "SparseArrays" + FillArraysStatisticsExt = "Statistics" + +[[deps.ForwardDiff]] +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] +git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" +uuid = "f6369f11-7733-5829-9624-2563aa707210" +version = "0.10.36" +weakdeps = ["StaticArrays"] + + [deps.ForwardDiff.extensions] + ForwardDiffStaticArraysExt = "StaticArrays" + +[[deps.Future]] +deps = ["Random"] +uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" + +[[deps.GLM]] +deps = ["Distributions", "LinearAlgebra", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "StatsModels"] +git-tree-sha1 = "273bd1cd30768a2fddfa3fd63bbc746ed7249e5f" +uuid = "38e38edf-8417-5370-95a0-9cbb8c7f171a" +version = "1.9.0" + +[[deps.HypergeometricFunctions]] +deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb" +uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" +version = "0.3.24" + +[[deps.IfElse]] +git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" +uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" +version = "0.1.1" + +[[deps.Indexing]] +git-tree-sha1 = "ce1566720fd6b19ff3411404d4b977acd4814f9f" +uuid = "313cdc1a-70c2-5d6a-ae34-0150d3930a38" +version = "1.1.1" + +[[deps.InlineStrings]] +git-tree-sha1 = "45521d31238e87ee9f9732561bfee12d4eebd52d" +uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" +version = "1.4.2" +weakdeps = ["ArrowTypes", "Parsers"] + + [deps.InlineStrings.extensions] + ArrowTypesExt = "ArrowTypes" + ParsersExt = "Parsers" + +[[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.JLLWrappers]] +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" +uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" +version = "1.5.0" + +[[deps.JSON3]] +deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] +git-tree-sha1 = "eb3edce0ed4fa32f75a0a11217433c31d56bd48b" +uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" +version = "1.14.0" +weakdeps = ["ArrowTypes"] + + [deps.JSON3.extensions] + JSON3ArrowExt = ["ArrowTypes"] + +[[deps.LaTeXStrings]] +git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" +uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" +version = "1.3.1" + +[[deps.LazyArtifacts]] +deps = ["Artifacts", "Pkg"] +uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" + +[[deps.LibCURL]] +deps = ["LibCURL_jll", "MozillaCACerts_jll"] +uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" +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 = "8.4.0+0" + +[[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 = "a2d09619db4e765091ee5c6ffe8872849de0feea" +uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" +version = "0.3.28" + + [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.LoggingExtras]] +deps = ["Dates", "Logging"] +git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" +uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" +version = "1.0.3" + +[[deps.Lz4_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "7f26c8fc5229e68484e0b3447312c98e16207d11" +uuid = "5ced341a-0733-55b8-9ab6-a4889d929147" +version = "1.10.0+0" + +[[deps.MacroTools]] +deps = ["Markdown", "Random"] +git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" +uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" +version = "0.5.13" + +[[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 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" +uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" +version = "1.2.0" + +[[deps.MixedModels]] +deps = ["Arrow", "BSplineKit", "Compat", "DataAPI", "Distributions", "GLM", "JSON3", "LinearAlgebra", "Markdown", "MixedModelsDatasets", "NLopt", "PooledArrays", "PrecompileTools", "ProgressMeter", "Random", "SparseArrays", "StaticArrays", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "StatsModels", "StructTypes", "Tables", "TypedTables"] +git-tree-sha1 = "55b9364f382b37c0794d7e8065aefceaa225c04c" +uuid = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316" +version = "4.25.3" + +[[deps.MixedModelsDatasets]] +deps = ["Arrow", "Artifacts", "LazyArtifacts"] +git-tree-sha1 = "5f508af97ecf39645febed8ba2fabf5cfdc682e0" +uuid = "7e9fb7ac-9f67-43bf-b2c8-96ba0796cbb6" +version = "0.1.1" + +[[deps.Mmap]] +uuid = "a63ad114-7e13-5084-954f-fe012c677804" + +[[deps.Mocking]] +deps = ["Compat", "ExprTools"] +git-tree-sha1 = "ead0dbb33b6808578c385ffaab20d9b57053661b" +uuid = "78c3b35d-d492-501b-9361-3d52fe80e533" +version = "0.8.0" + +[[deps.MozillaCACerts_jll]] +uuid = "14a3606d-f60d-562e-9121-12d972cd8159" +version = "2023.1.10" + +[[deps.NLopt]] +deps = ["NLopt_jll"] +git-tree-sha1 = "3b887e2ef56be3309e68d2546c6178e2d2fa9a60" +uuid = "76087f3c-5699-56af-9a33-bf431cd00edd" +version = "1.0.2" + + [deps.NLopt.extensions] + NLoptMathOptInterfaceExt = ["MathOptInterface"] + + [deps.NLopt.weakdeps] + MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee" + +[[deps.NLopt_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "3d1eefa627faeabc59ab9edbf00d17f70123ad69" +uuid = "079eb43e-fd8e-5478-9966-2cf3e3edb778" +version = "2.8.0+0" + +[[deps.NaNMath]] +deps = ["OpenLibm_jll"] +git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" +uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" +version = "1.0.2" + +[[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.OpenLibm_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "05823500-19ac-5b8b-9628-191a04bc5112" +version = "0.8.1+2" + +[[deps.OpenSpecFun_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" +uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" +version = "0.5.5+0" + +[[deps.OrderedCollections]] +git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" +uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" +version = "1.6.3" + +[[deps.PDMats]] +deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" +uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" +version = "0.11.31" + +[[deps.Parsers]] +deps = ["Dates", "PrecompileTools", "UUIDs"] +git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" +uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" +version = "2.8.1" + +[[deps.Pkg]] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" +version = "1.10.0" + +[[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 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f" +uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" +version = "1.2.1" + +[[deps.Preferences]] +deps = ["TOML"] +git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6" +uuid = "21216c6a-2e73-6563-6e65-726566657250" +version = "1.4.3" + +[[deps.PrettyTables]] +deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] +git-tree-sha1 = "66b20dd35966a748321d3b2537c4584cf40387c7" +uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" +version = "2.3.2" + +[[deps.Printf]] +deps = ["Unicode"] +uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" + +[[deps.ProgressMeter]] +deps = ["Distributed", "Printf"] +git-tree-sha1 = "8f6bc219586aef8baf0ff9a5fe16ee9c70cb65e4" +uuid = "92933f4c-e287-5a05-a399-4b506db050ca" +version = "1.10.2" + +[[deps.PtrArrays]] +git-tree-sha1 = "f011fbb92c4d401059b2212c05c0601b70f8b759" +uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" +version = "1.2.0" + +[[deps.QuadGK]] +deps = ["DataStructures", "LinearAlgebra"] +git-tree-sha1 = "e237232771fdafbae3db5c31275303e056afaa9f" +uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" +version = "2.10.1" + +[[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.Requires]] +deps = ["UUIDs"] +git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" +uuid = "ae029012-a4dd-5104-9daa-d747884805df" +version = "1.3.0" + +[[deps.Rmath]] +deps = ["Random", "Rmath_jll"] +git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" +version = "0.7.1" + +[[deps.Rmath_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e60724fd3beea548353984dc61c943ecddb0e29a" +uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" +version = "0.4.3+0" + +[[deps.SHA]] +uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" +version = "0.7.0" + +[[deps.Scratch]] +deps = ["Dates"] +git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" +uuid = "6c6a2e73-6563-6170-7368-637461726353" +version = "1.2.1" + +[[deps.SentinelArrays]] +deps = ["Dates", "Random"] +git-tree-sha1 = "ff11acffdb082493657550959d4feb4b6149e73a" +uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" +version = "1.4.5" + +[[deps.Serialization]] +uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" + +[[deps.ShiftedArrays]] +git-tree-sha1 = "503688b59397b3307443af35cd953a13e8005c16" +uuid = "1277b4bf-5013-50f5-be3d-901d8477a67a" +version = "2.0.0" + +[[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.SpecialFunctions]] +deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14" +uuid = "276daf66-3868-5448-9aa4-cd146d93841b" +version = "2.4.0" + + [deps.SpecialFunctions.extensions] + SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" + + [deps.SpecialFunctions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + +[[deps.SplitApplyCombine]] +deps = ["Dictionaries", "Indexing"] +git-tree-sha1 = "c06d695d51cfb2187e6848e98d6252df9101c588" +uuid = "03a91e81-4c3e-53e1-a0a4-9c0c8f19dd66" +version = "1.2.3" + +[[deps.Static]] +deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] +git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" +uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" +version = "1.1.1" + +[[deps.StaticArrays]] +deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] +git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50" +uuid = "90137ffa-7385-5640-81b9-e52037218182" +version = "1.9.7" + + [deps.StaticArrays.extensions] + StaticArraysChainRulesCoreExt = "ChainRulesCore" + StaticArraysStatisticsExt = "Statistics" + + [deps.StaticArrays.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" + +[[deps.StaticArraysCore]] +git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682" +uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" +version = "1.4.3" + +[[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 = "5cf7606d6cef84b543b483848d4ae08ad9832b21" +uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" +version = "0.34.3" + +[[deps.StatsFuns]] +deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" +uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" +version = "1.3.1" + + [deps.StatsFuns.extensions] + StatsFunsChainRulesCoreExt = "ChainRulesCore" + StatsFunsInverseFunctionsExt = "InverseFunctions" + + [deps.StatsFuns.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" + +[[deps.StatsModels]] +deps = ["DataAPI", "DataStructures", "LinearAlgebra", "Printf", "REPL", "ShiftedArrays", "SparseArrays", "StatsAPI", "StatsBase", "StatsFuns", "Tables"] +git-tree-sha1 = "5cf6c4583533ee38639f73b880f35fc85f2941e0" +uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" +version = "0.7.3" + +[[deps.StringManipulation]] +deps = ["PrecompileTools"] +git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" +uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" +version = "0.3.4" + +[[deps.StructTypes]] +deps = ["Dates", "UUIDs"] +git-tree-sha1 = "ca4bccb03acf9faaf4137a9abc1881ed1841aa70" +uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" +version = "1.10.0" + +[[deps.SuiteSparse]] +deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] +uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" + +[[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.TZJData]] +deps = ["Artifacts"] +git-tree-sha1 = "1607ad46cf8d642aa779a1d45af1c8620dbf6915" +uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" +version = "1.2.0+2024a" + +[[deps.TableTraits]] +deps = ["IteratorInterfaceExtensions"] +git-tree-sha1 = "c06b2f539df1c6efa794486abfb6ed2022561a39" +uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" +version = "1.0.1" + +[[deps.Tables]] +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" +uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" +version = "1.12.0" + +[[deps.Tar]] +deps = ["ArgTools", "SHA"] +uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" +version = "1.10.0" + +[[deps.Test]] +deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] +uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" + +[[deps.TimeZones]] +deps = ["Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "b92aebdd3555f3a7e3267cf17702033c2814ef48" +uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" +version = "1.18.0" + + [deps.TimeZones.extensions] + TimeZonesRecipesBaseExt = "RecipesBase" + + [deps.TimeZones.weakdeps] + RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" + +[[deps.TranscodingStreams]] +git-tree-sha1 = "d73336d81cafdc277ff45558bb7eaa2b04a8e472" +uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" +version = "0.10.10" +weakdeps = ["Random", "Test"] + + [deps.TranscodingStreams.extensions] + TestExt = ["Test", "Random"] + +[[deps.TypedTables]] +deps = ["Adapt", "Dictionaries", "Indexing", "SplitApplyCombine", "Tables", "Unicode"] +git-tree-sha1 = "84fd7dadde577e01eb4323b7e7b9cb51c62c60d4" +uuid = "9d95f2ec-7b3d-5a63-8d20-e2491e220bb9" +version = "1.4.6" + +[[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.ZipFile]] +deps = ["Libdl", "Printf", "Zlib_jll"] +git-tree-sha1 = "f492b7fe1698e623024e873244f10d89c95c340a" +uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea" +version = "0.10.1" + +[[deps.Zlib_jll]] +deps = ["Libdl"] +uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.13+1" + +[[deps.Zstd_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b" +uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" +version = "1.5.6+0" + +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.8.0+1" + +[[deps.nghttp2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.52.0+1" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+2" diff --git a/issues/780/Project.toml b/issues/780/Project.toml new file mode 100644 index 000000000..f501638da --- /dev/null +++ b/issues/780/Project.toml @@ -0,0 +1,8 @@ +[deps] +Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45" +CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6" +MixedModels = "ff71e718-51f3-5ec2-a782-8ffcbfa3c316" +Scratch = "6c6a2e73-6563-6170-7368-637461726353" +ZipFile = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea" diff --git a/issues/780/issue.jl b/issues/780/issue.jl new file mode 100644 index 000000000..83d27b871 --- /dev/null +++ b/issues/780/issue.jl @@ -0,0 +1,61 @@ +module IssueData + using Arrow + using CSV + using DataFrames + using Downloads + using Scratch + using ZipFile + + export get_data + + const CACHE = Ref("") + const URL = "https://github.com/user-attachments/files/16604579/testdataforjulia_bothcase.zip" + + function extract_csv(zipfile, fname; delim=',', header=1, kwargs...) + file = only(filter(f -> endswith(f.name, fname), zipfile.files)) + return CSV.read(file, DataFrame; delim, header, kwargs...) + end + + function get_data() + path = joinpath(CACHE[], "780.arrow") + + isfile(path) && return DataFrame(Arrow.Table(path); copycols=true) + + @info "downloading..." + data = open(Downloads.download(URL), "r") do io + zipfile = ZipFile.Reader(io) + @info "extracting..." + return extract_csv(zipfile, "testdataforjulia_bothcase.csv") + end + + Arrow.write(path, data) + return data + end + + clear_scratchspaces!() = Scratch.clear_scratchspaces!(@__MODULE__) + + function __init__() + CACHE[] = @get_scratch!("data") + return nothing + end +end + +using .IssueData +using MixedModels + +data = get_data() +m0form = @formula(case ~ 0 + Analysisclass + (1|cropyear/individual_local_identifier)) +# works +model_fast = fit(MixedModel, m0form, data, Bernoulli(); + wts=float.(data.weights), + contrasts= Dict(:Analysisclass => DummyCoding(; base="aRice_Wet_day")), + fast=true, + progress=true, + verbose=false) +# fails +model = fit(MixedModel, m0form, data, Bernoulli(); + wts=float.(data.weights), + contrasts= Dict(:Analysisclass => DummyCoding(; base="aRice_Wet_day")), + fast=false, + progress=true, + verbose=false)