From 6a03213b8c8b267112d2047fe686f953cb191561 Mon Sep 17 00:00:00 2001 From: joshua-slaughter Date: Sun, 17 Nov 2024 23:41:43 +0000 Subject: [PATCH 01/17] GWIS configuration --- Manifest.toml | 2 +- src/inputs_from_config.jl | 42 +++++++++++- test/data/config_gwis.yaml | 10 +++ test/inputs_from_gwis_config.jl | 112 ++++++++++++++++++++++++++++++++ test/runtests.jl | 1 + 5 files changed, 164 insertions(+), 3 deletions(-) create mode 100644 test/data/config_gwis.yaml create mode 100644 test/inputs_from_gwis_config.jl diff --git a/Manifest.toml b/Manifest.toml index 5e87db8..2a3f06c 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.4" manifest_format = "2.0" -project_hash = "2b58dcc0ffd21f9ddd37c869a6c32c55af516134" +project_hash = "b1a916e4f68d2fb953c6eba21c0fc7546e7dc5c6" [[deps.ARFFFiles]] deps = ["CategoricalArrays", "Dates", "Parsers", "Tables"] diff --git a/src/inputs_from_config.jl b/src/inputs_from_config.jl index f5bc918..d2dbaa7 100644 --- a/src/inputs_from_config.jl +++ b/src/inputs_from_config.jl @@ -60,13 +60,22 @@ function estimands_from_variants( estimand_constructor, outcomes, confounders; + extra_treatments=[], outcome_extra_covariates=[], positivity_constraint=0., verbosity=1 ) estimands = [] for variant in variants - treatments = treatments_from_variant(variant, dataset) + + if isempty(extra_treatments) + treatments = treatments_from_variant(variant, dataset) + elseif length(extra_treatments) == 1 + treatments = Dict(treatments_from_variant(variant, dataset)..., treatments_from_variant(string(extra_treatments[1]), dataset)...) + else + error("GWIS mode only supports pairwise interaction with one extra treatment.") + end + local Ψ try Ψ = factorialEstimands( @@ -171,6 +180,7 @@ function treatments_from_variant(variant::String, dataset::DataFrame) end function estimands_from_gwas(dataset, variants, outcomes, confounders; + extra_treatments=extra_treatments, outcome_extra_covariates = [], positivity_constraint=0., verbosity=0 @@ -178,6 +188,7 @@ function estimands_from_gwas(dataset, variants, outcomes, confounders; variants_groups = Iterators.partition(variants, length(variants) ÷ Threads.nthreads()) estimands_tasks = map(variants_groups) do variants Threads.@spawn estimands_from_variants(variants, dataset, ATE, outcomes, confounders; + extra_treatments=extra_treatments, outcome_extra_covariates=outcome_extra_covariates, positivity_constraint=positivity_constraint, verbosity=verbosity @@ -187,6 +198,24 @@ function estimands_from_gwas(dataset, variants, outcomes, confounders; return vcat(estimands_partitions...) end +function estimands_from_gwis(dataset, variants, outcomes, confounders; + extra_treatments=extra_treatments, + outcome_extra_covariates = [], + positivity_constraint=0., + verbosity=0 + ) + variants_groups = Iterators.partition(variants, length(variants) ÷ Threads.nthreads()) + estimands_tasks = map(variants_groups) do variants + Threads.@spawn estimands_from_variants(variants, dataset, AIE, outcomes, confounders; + extra_treatments=extra_treatments, + outcome_extra_covariates=outcome_extra_covariates, + positivity_constraint=positivity_constraint, + verbosity=verbosity + ) + end + estimands_partitions = fetch.(estimands_tasks) + return vcat(estimands_partitions...) +end get_only_file_with_suffix(files, suffix) = files[only(findall(x -> endswith(x, suffix), files))] @@ -210,7 +239,7 @@ function get_genotypes_from_beds(bedprefix) end function make_genotypes(genotype_prefix, config, call_threshold) - genotypes = if config["type"] == "gwas" + genotypes = if config["type"] == "gwas"|| config["type"] == "gwis" get_genotypes_from_beds(genotype_prefix) else variants_set = Set(retrieve_variants_list(config["variants"])) @@ -263,10 +292,19 @@ function inputs_from_config(config_file, genotypes_prefix, traits_file, pcs_file elseif config_type == "gwas" variants = filter(!=("SAMPLE_ID"), names(genotypes)) estimands_from_gwas(dataset, variants, outcomes, confounders; + extra_treatments=extra_treatments, outcome_extra_covariates=outcome_extra_covariates, positivity_constraint=positivity_constraint, verbosity=verbosity ) + elseif config_type == "gwis" + variants = filter(!=("SAMPLE_ID"), names(genotypes)) + estimands_from_gwis(dataset, variants, outcomes, confounders; + extra_treatments=extra_treatments, + outcome_extra_covariates=outcome_extra_covariates, + positivity_constraint=positivity_constraint, + verbosity=verbosity + ) else throw(ArgumentError(string("Unknown extraction type: ", config_type, ", use any of: (flat, groups, gwas)"))) end diff --git a/test/data/config_gwis.yaml b/test/data/config_gwis.yaml new file mode 100644 index 0000000..36340fd --- /dev/null +++ b/test/data/config_gwis.yaml @@ -0,0 +1,10 @@ +type: gwis + +extra_treatments: + - 22001 + +outcome_extra_covariates: + - COV_1 + +extra_confounders: + - 21003 diff --git a/test/inputs_from_gwis_config.jl b/test/inputs_from_gwis_config.jl new file mode 100644 index 0000000..ad3f508 --- /dev/null +++ b/test/inputs_from_gwis_config.jl @@ -0,0 +1,112 @@ +module TestGwisEstimands + +using Test +using SnpArrays +using TargeneCore +using Arrow +using DataFrames +using Serialization +using TMLE +using CSV + +TESTDIR = joinpath(pkgdir(TargeneCore), "test") + +include(joinpath(TESTDIR, "testutils.jl")) + +function get_summary_stats(estimands) + outcomes = [TargeneCore.get_outcome(Ψ) for Ψ in estimands] + results = DataFrame(ESTIMAND = estimands, OUTCOME = outcomes) + return sort(combine(groupby(results, :OUTCOME), nrow), :OUTCOME) +end + +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 + variant = collect(keys(Ψ.args[1].treatment_values))[2] + if length(Ψ.args) == 2 + @test Ψ.args[1].treatment_values[variant] == (control = 0x00, case = 0x01) + @test Ψ.args[2].treatment_values[variant] == (control = 0x01, case = 0x02) + else + # Otherwise we check they are one or the other + arg = only(Ψ.args) + @test arg.treatment_values[variant]==(control = 0x00, case = 0x01) || + arg.treatment_values[variant]==( control = 0x01, case = 0x02) + end + end +end + +@testset "Test inputs_from_config gwas: no positivity constraint" begin + tmpdir = mktempdir() + copy!(ARGS, [ + "estimation-inputs", + joinpath(TESTDIR, "data", "config_gwis.yaml"), + string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")), + string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")), + string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")), + string("--outprefix=", joinpath(tmpdir, "final")), + "--batchsize=5", + "--verbosity=0", + "--positivity-constraint=0" + ]) + TargeneCore.julia_main() + # Check dataset + dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) + @test size(dataset) == (1940, 886) + + # Check estimands + estimands = [] + for file in readdir(tmpdir, join=true) + if endswith(file, "jls") + append!(estimands, deserialize(file).estimands) + end + end + @test all(e isa JointEstimand for e in estimands) + + # There are 875 variants in the dataset + summary_stats = get_summary_stats(estimands) + @test summary_stats == DataFrame( + OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1], + nrow = repeat([875], 5) + ) + + check_estimands_levels_order(estimands) +end + + +@testset "Test inputs_from_config gwas: positivity constraint" begin + tmpdir = mktempdir() + copy!(ARGS, [ + "estimation-inputs", + joinpath(TESTDIR, "data", "config_gwis.yaml"), + string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")), + string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")), + string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")), + string("--outprefix=", joinpath(tmpdir, "final")), + "--batchsize=5", + "--verbosity=0", + "--positivity-constraint=0.2" + ]) + TargeneCore.julia_main() + # Check dataset + dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) + @test size(dataset) == (1940, 886) + # Check estimands + estimands = [] + for file in readdir(tmpdir, join=true) + if endswith(file, "jls") + append!(estimands, deserialize(file).estimands) + end + end + # The positivity constraint reduces the number of variants + @test all(e isa JointEstimand for e in estimands) + summary_stats = get_summary_stats(estimands) + @test summary_stats == DataFrame( + OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1], + nrow = repeat([142], 5) + ) + + check_estimands_levels_order(estimands) +end + + +end \ No newline at end of file diff --git a/test/runtests.jl b/test/runtests.jl index 60adb9f..8f56e39 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -10,5 +10,6 @@ TESTDIR = joinpath(pkgdir(TargeneCore), "test") @test include(joinpath(TESTDIR, "inputs_from_estimands.jl")) @test include(joinpath(TESTDIR, "inputs_from_config.jl")) @test include(joinpath(TESTDIR, "inputs_from_gwas_config.jl")) + @test include(joinpath(TESTDIR, "inputs_from_gwis_config.jl")) @test include(joinpath(TESTDIR, "sieve_variance.jl")) end From c9ebfa5fa8d14392af644fc47436abf699a8e656 Mon Sep 17 00:00:00 2001 From: joshua-slaughter Date: Mon, 18 Nov 2024 00:42:25 +0000 Subject: [PATCH 02/17] missing true in gwis test file --- test/inputs_from_gwis_config.jl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/inputs_from_gwis_config.jl b/test/inputs_from_gwis_config.jl index ad3f508..40e98d6 100644 --- a/test/inputs_from_gwis_config.jl +++ b/test/inputs_from_gwis_config.jl @@ -109,4 +109,5 @@ end end -end \ No newline at end of file +end +true \ No newline at end of file From 4019b38e897e4cc93ba8cddaf7273c8c2e0f5289 Mon Sep 17 00:00:00 2001 From: joshua-slaughter Date: Mon, 18 Nov 2024 10:28:00 +0000 Subject: [PATCH 03/17] fixing GWIS test string output --- test/inputs_from_gwis_config.jl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/inputs_from_gwis_config.jl b/test/inputs_from_gwis_config.jl index 40e98d6..a3ed6a4 100644 --- a/test/inputs_from_gwis_config.jl +++ b/test/inputs_from_gwis_config.jl @@ -35,7 +35,7 @@ function check_estimands_levels_order(estimands) end end -@testset "Test inputs_from_config gwas: no positivity constraint" begin +@testset "Test inputs_from_config gwis: no positivity constraint" begin tmpdir = mktempdir() copy!(ARGS, [ "estimation-inputs", @@ -73,7 +73,7 @@ end end -@testset "Test inputs_from_config gwas: positivity constraint" begin +@testset "Test inputs_from_config gwis: positivity constraint" begin tmpdir = mktempdir() copy!(ARGS, [ "estimation-inputs", From f21d4d168e8df48097216ba6d647db92622dad20 Mon Sep 17 00:00:00 2001 From: Joshua Slaughter Date: Tue, 18 Mar 2025 12:37:56 +0000 Subject: [PATCH 04/17] Changes from GWIS to GWIES; Updated tests and generalized estimand creation to support higher order interactions --- Manifest.toml | 6 +- Project.toml | 3 +- src/inputs_from_config.jl | 23 +++---- test/data/config_gwis.yaml | 10 --- test/inputs_from_gwis_config.jl | 113 -------------------------------- test/runtests.jl | 2 +- 6 files changed, 18 insertions(+), 139 deletions(-) delete mode 100644 test/data/config_gwis.yaml delete mode 100644 test/inputs_from_gwis_config.jl diff --git a/Manifest.toml b/Manifest.toml index 2a3f06c..e6dafa2 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.4" manifest_format = "2.0" -project_hash = "b1a916e4f68d2fb953c6eba21c0fc7546e7dc5c6" +project_hash = "4182f1a89c1532988a40d605eeec69822a2af3fc" [[deps.ARFFFiles]] deps = ["CategoricalArrays", "Dates", "Parsers", "Tables"] @@ -1358,9 +1358,9 @@ weakdeps = ["ChainRulesCore", "SparseArrays", "Statistics"] [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "a2d09619db4e765091ee5c6ffe8872849de0feea" +git-tree-sha1 = "13ca9e2586b89836fd20cccf56e57e2b9ae7f38f" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.28" +version = "0.3.29" [deps.LogExpFunctions.extensions] LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" diff --git a/Project.toml b/Project.toml index f823dd3..f28f3ea 100644 --- a/Project.toml +++ b/Project.toml @@ -15,6 +15,7 @@ DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5" JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819" +LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2" Mmap = "a63ad114-7e13-5084-954f-fe012c677804" OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" @@ -37,12 +38,12 @@ CairoMakie = "0.12" CategoricalArrays = "0.10" Combinatorics = "1.0" DataFrames = "1.2" +MKL = "0.7" OrderedCollections = "1.6.3" PackageCompiler = "2.1.17" SnpArrays = "0.3" StableRNGs = "1.0.1" Statistics = "1.10" TMLE = "0.17" -MKL = "0.7" YAML = "0.4.9" julia = "1.10, 1" diff --git a/src/inputs_from_config.jl b/src/inputs_from_config.jl index d2dbaa7..164a36e 100644 --- a/src/inputs_from_config.jl +++ b/src/inputs_from_config.jl @@ -54,7 +54,7 @@ function try_append_new_estimands!( end end -function estimands_from_variants( +function genome_wide_estimands( variants, dataset, estimand_constructor, @@ -70,10 +70,11 @@ function estimands_from_variants( if isempty(extra_treatments) treatments = treatments_from_variant(variant, dataset) - elseif length(extra_treatments) == 1 - treatments = Dict(treatments_from_variant(variant, dataset)..., treatments_from_variant(string(extra_treatments[1]), dataset)...) else - error("GWIS mode only supports pairwise interaction with one extra treatment.") + treatments = Dict( + treatments_from_variant(variant, dataset)..., + (pair for extra in extra_treatments for pair in treatments_from_variant(string(extra), dataset))... + ) end local Ψ @@ -172,7 +173,7 @@ end """ treatment_from_variant(variant, dataset) - Generate a key-value pair (dicitionary) for treatment structs. + Generate a key-value pair (dictionary) for treatment structs. """ function treatments_from_variant(variant::String, dataset::DataFrame) variant_levels = sort(levels(dataset[!, variant], skipmissing=true)) @@ -187,7 +188,7 @@ function estimands_from_gwas(dataset, variants, outcomes, confounders; ) variants_groups = Iterators.partition(variants, length(variants) ÷ Threads.nthreads()) estimands_tasks = map(variants_groups) do variants - Threads.@spawn estimands_from_variants(variants, dataset, ATE, outcomes, confounders; + Threads.@spawn genome_wide_estimands(variants, dataset, ATE, outcomes, confounders; extra_treatments=extra_treatments, outcome_extra_covariates=outcome_extra_covariates, positivity_constraint=positivity_constraint, @@ -198,7 +199,7 @@ function estimands_from_gwas(dataset, variants, outcomes, confounders; return vcat(estimands_partitions...) end -function estimands_from_gwis(dataset, variants, outcomes, confounders; +function estimands_from_gweis(dataset, variants, outcomes, confounders; extra_treatments=extra_treatments, outcome_extra_covariates = [], positivity_constraint=0., @@ -206,7 +207,7 @@ function estimands_from_gwis(dataset, variants, outcomes, confounders; ) variants_groups = Iterators.partition(variants, length(variants) ÷ Threads.nthreads()) estimands_tasks = map(variants_groups) do variants - Threads.@spawn estimands_from_variants(variants, dataset, AIE, outcomes, confounders; + Threads.@spawn genome_wide_estimands(variants, dataset, AIE, outcomes, confounders; extra_treatments=extra_treatments, outcome_extra_covariates=outcome_extra_covariates, positivity_constraint=positivity_constraint, @@ -239,7 +240,7 @@ function get_genotypes_from_beds(bedprefix) end function make_genotypes(genotype_prefix, config, call_threshold) - genotypes = if config["type"] == "gwas"|| config["type"] == "gwis" + genotypes = if config["type"] == "gwas"|| config["type"] == "gweis" get_genotypes_from_beds(genotype_prefix) else variants_set = Set(retrieve_variants_list(config["variants"])) @@ -297,9 +298,9 @@ function inputs_from_config(config_file, genotypes_prefix, traits_file, pcs_file positivity_constraint=positivity_constraint, verbosity=verbosity ) - elseif config_type == "gwis" + elseif config_type == "gweis" variants = filter(!=("SAMPLE_ID"), names(genotypes)) - estimands_from_gwis(dataset, variants, outcomes, confounders; + estimands_from_gweis(dataset, variants, outcomes, confounders; extra_treatments=extra_treatments, outcome_extra_covariates=outcome_extra_covariates, positivity_constraint=positivity_constraint, diff --git a/test/data/config_gwis.yaml b/test/data/config_gwis.yaml deleted file mode 100644 index 36340fd..0000000 --- a/test/data/config_gwis.yaml +++ /dev/null @@ -1,10 +0,0 @@ -type: gwis - -extra_treatments: - - 22001 - -outcome_extra_covariates: - - COV_1 - -extra_confounders: - - 21003 diff --git a/test/inputs_from_gwis_config.jl b/test/inputs_from_gwis_config.jl deleted file mode 100644 index a3ed6a4..0000000 --- a/test/inputs_from_gwis_config.jl +++ /dev/null @@ -1,113 +0,0 @@ -module TestGwisEstimands - -using Test -using SnpArrays -using TargeneCore -using Arrow -using DataFrames -using Serialization -using TMLE -using CSV - -TESTDIR = joinpath(pkgdir(TargeneCore), "test") - -include(joinpath(TESTDIR, "testutils.jl")) - -function get_summary_stats(estimands) - outcomes = [TargeneCore.get_outcome(Ψ) for Ψ in estimands] - results = DataFrame(ESTIMAND = estimands, OUTCOME = outcomes) - return sort(combine(groupby(results, :OUTCOME), nrow), :OUTCOME) -end - -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 - variant = collect(keys(Ψ.args[1].treatment_values))[2] - if length(Ψ.args) == 2 - @test Ψ.args[1].treatment_values[variant] == (control = 0x00, case = 0x01) - @test Ψ.args[2].treatment_values[variant] == (control = 0x01, case = 0x02) - else - # Otherwise we check they are one or the other - arg = only(Ψ.args) - @test arg.treatment_values[variant]==(control = 0x00, case = 0x01) || - arg.treatment_values[variant]==( control = 0x01, case = 0x02) - end - end -end - -@testset "Test inputs_from_config gwis: no positivity constraint" begin - tmpdir = mktempdir() - copy!(ARGS, [ - "estimation-inputs", - joinpath(TESTDIR, "data", "config_gwis.yaml"), - string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")), - string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")), - string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")), - string("--outprefix=", joinpath(tmpdir, "final")), - "--batchsize=5", - "--verbosity=0", - "--positivity-constraint=0" - ]) - TargeneCore.julia_main() - # Check dataset - dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) - @test size(dataset) == (1940, 886) - - # Check estimands - estimands = [] - for file in readdir(tmpdir, join=true) - if endswith(file, "jls") - append!(estimands, deserialize(file).estimands) - end - end - @test all(e isa JointEstimand for e in estimands) - - # There are 875 variants in the dataset - summary_stats = get_summary_stats(estimands) - @test summary_stats == DataFrame( - OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1], - nrow = repeat([875], 5) - ) - - check_estimands_levels_order(estimands) -end - - -@testset "Test inputs_from_config gwis: positivity constraint" begin - tmpdir = mktempdir() - copy!(ARGS, [ - "estimation-inputs", - joinpath(TESTDIR, "data", "config_gwis.yaml"), - string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")), - string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")), - string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")), - string("--outprefix=", joinpath(tmpdir, "final")), - "--batchsize=5", - "--verbosity=0", - "--positivity-constraint=0.2" - ]) - TargeneCore.julia_main() - # Check dataset - dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) - @test size(dataset) == (1940, 886) - # Check estimands - estimands = [] - for file in readdir(tmpdir, join=true) - if endswith(file, "jls") - append!(estimands, deserialize(file).estimands) - end - end - # The positivity constraint reduces the number of variants - @test all(e isa JointEstimand for e in estimands) - summary_stats = get_summary_stats(estimands) - @test summary_stats == DataFrame( - OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1], - nrow = repeat([142], 5) - ) - - check_estimands_levels_order(estimands) -end - - -end -true \ No newline at end of file diff --git a/test/runtests.jl b/test/runtests.jl index 8f56e39..084c6b9 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -10,6 +10,6 @@ TESTDIR = joinpath(pkgdir(TargeneCore), "test") @test include(joinpath(TESTDIR, "inputs_from_estimands.jl")) @test include(joinpath(TESTDIR, "inputs_from_config.jl")) @test include(joinpath(TESTDIR, "inputs_from_gwas_config.jl")) - @test include(joinpath(TESTDIR, "inputs_from_gwis_config.jl")) + @test include(joinpath(TESTDIR, "inputs_from_gweis_config.jl")) @test include(joinpath(TESTDIR, "sieve_variance.jl")) end From 1b1a740e63e447a9ea662cc5fc48b0309cde9280 Mon Sep 17 00:00:00 2001 From: Joshua Slaughter Date: Tue, 18 Mar 2025 12:40:46 +0000 Subject: [PATCH 05/17] Adding unwatched files for testing GWEIS --- test/data/config_gweis_first_order.yaml | 10 ++ test/data/config_gweis_higher_order.yaml | 12 ++ test/inputs_from_gweis_config.jl | 187 +++++++++++++++++++++++ 3 files changed, 209 insertions(+) create mode 100644 test/data/config_gweis_first_order.yaml create mode 100644 test/data/config_gweis_higher_order.yaml create mode 100644 test/inputs_from_gweis_config.jl diff --git a/test/data/config_gweis_first_order.yaml b/test/data/config_gweis_first_order.yaml new file mode 100644 index 0000000..6b6ba7b --- /dev/null +++ b/test/data/config_gweis_first_order.yaml @@ -0,0 +1,10 @@ +type: gweis + +extra_treatments: + - 22001 + +outcome_extra_covariates: + - COV_1 + +extra_confounders: + - 21003 diff --git a/test/data/config_gweis_higher_order.yaml b/test/data/config_gweis_higher_order.yaml new file mode 100644 index 0000000..cafaba0 --- /dev/null +++ b/test/data/config_gweis_higher_order.yaml @@ -0,0 +1,12 @@ +type: gweis + +extra_treatments: + - 22001 + - BINARY_1 + - BINARY_2 + +outcome_extra_covariates: + - COV_1 + +extra_confounders: + - 21003 \ No newline at end of file diff --git a/test/inputs_from_gweis_config.jl b/test/inputs_from_gweis_config.jl new file mode 100644 index 0000000..4d9c6cb --- /dev/null +++ b/test/inputs_from_gweis_config.jl @@ -0,0 +1,187 @@ +module TestGweisEstimands + +using Test +using SnpArrays +using TargeneCore +using Arrow +using DataFrames +using Serialization +using TMLE +using CSV + +TESTDIR = joinpath(pkgdir(TargeneCore), "test") + +include(joinpath(TESTDIR, "testutils.jl")) + +function get_summary_stats(estimands) + outcomes = [TargeneCore.get_outcome(Ψ) for Ψ in estimands] + results = DataFrame(ESTIMAND = estimands, OUTCOME = outcomes) + return sort(combine(groupby(results, :OUTCOME), nrow), :OUTCOME) +end + +function check_estimands_levels_interactions(estimands) + for Ψ in estimands + # If the two components are present, the first is the 0 -> 1 and the second is the 1 -> 2 + # The variant should always be the last key + variant = last(collect(keys(Ψ.args[1].treatment_values))) + if length(Ψ.args) == 2 + @test Ψ.args[1].treatment_values[variant] == (control = 0x00, case = 0x01) + @test Ψ.args[2].treatment_values[variant] == (control = 0x01, case = 0x02) + else + # Otherwise we check they are one or the other + arg = only(Ψ.args) + @test arg.treatment_values[variant]==(control = 0x00, case = 0x01) || + arg.treatment_values[variant]==( control = 0x01, case = 0x02) + end + end +end + +@testset "Test inputs_from_config gweis: no positivity constraint" begin + tmpdir = mktempdir() + copy!(ARGS, [ + "estimation-inputs", + joinpath(TESTDIR, "data", "config_gweis_first_order.yaml"), + string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")), + string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")), + string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")), + string("--outprefix=", joinpath(tmpdir, "final")), + "--batchsize=5", + "--verbosity=0", + "--positivity-constraint=0" + ]) + TargeneCore.julia_main() + # Check dataset + dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) + @test size(dataset) == (1940, 886) + + # Check estimands + estimands = [] + for file in readdir(tmpdir, join=true) + if endswith(file, "jls") + append!(estimands, deserialize(file).estimands) + end + end + @test all(e isa JointEstimand for e in estimands) + + # There are 875 variants in the dataset + summary_stats = get_summary_stats(estimands) + @test summary_stats == DataFrame( + OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1], + nrow = repeat([875], 5) + ) + + check_estimands_levels_interactions(estimands) +end + + +@testset "Test inputs_from_config gweis: positivity constraint" begin + tmpdir = mktempdir() + copy!(ARGS, [ + "estimation-inputs", + joinpath(TESTDIR, "data", "config_gweis_first_order.yaml"), + string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")), + string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")), + string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")), + string("--outprefix=", joinpath(tmpdir, "final")), + "--batchsize=5", + "--verbosity=0", + "--positivity-constraint=0.2" + ]) + TargeneCore.julia_main() + # Check dataset + dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) + @test size(dataset) == (1940, 886) + # Check estimands + estimands = [] + for file in readdir(tmpdir, join=true) + if endswith(file, "jls") + append!(estimands, deserialize(file).estimands) + end + end + # The positivity constraint reduces the number of variants + @test all(e isa JointEstimand for e in estimands) + summary_stats = get_summary_stats(estimands) + @test summary_stats == DataFrame( + OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1], + nrow = repeat([142], 5) + ) + + check_estimands_levels_interactions(estimands) +end + +@testset "Test inputs_from_config gweis: no positivity constraint and four-point interaction" begin + tmpdir = mktempdir() + copy!(ARGS, [ + "estimation-inputs", + joinpath(TESTDIR, "data", "config_gweis_higher_order.yaml"), + string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")), + string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")), + string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")), + string("--outprefix=", joinpath(tmpdir, "final")), + "--batchsize=5", + "--verbosity=0", + "--positivity-constraint=0" + ]) + TargeneCore.julia_main() + # Check dataset + dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) + @test size(dataset) == (1940, 886) + + # Check estimands + estimands = [] + for file in readdir(tmpdir, join=true) + if endswith(file, "jls") + append!(estimands, deserialize(file).estimands) + end + end + @test all(e isa JointEstimand for e in estimands) + + # There are 875 variants in the dataset + summary_stats = get_summary_stats(estimands) + @test summary_stats == DataFrame( + OUTCOME = [:CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1], + nrow = repeat([875], 3) + ) + + check_estimands_levels_interactions(estimands) +end + +@testset "Test inputs_from_config gweis: positivity constraint and four-point interaction" begin + tmpdir = mktempdir() + copy!(ARGS, [ + "estimation-inputs", + joinpath(TESTDIR, "data", "config_gweis_higher_order.yaml"), + string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")), + string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")), + string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")), + string("--outprefix=", joinpath(tmpdir, "final")), + "--batchsize=5", + "--verbosity=0", + "--positivity-constraint=0.02" + ]) + TargeneCore.julia_main() + # Check dataset + dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) + @test size(dataset) == (1940, 886) + + # Check estimands + estimands = [] + for file in readdir(tmpdir, join=true) + if endswith(file, "jls") + append!(estimands, deserialize(file).estimands) + end + end + @test all(e isa JointEstimand for e in estimands) + + # There are 784 treatments in the dataset after positivity_constraint + summary_stats = get_summary_stats(estimands) + @test summary_stats == DataFrame( + OUTCOME = [:CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1], + nrow = repeat([784], 3) + ) + + check_estimands_levels_interactions(estimands) +end + +end +true \ No newline at end of file From 8d63364f3316d1d3dc316812d472890a368399e3 Mon Sep 17 00:00:00 2001 From: Joshua Slaughter Date: Tue, 18 Mar 2025 12:43:30 +0000 Subject: [PATCH 06/17] Update CI for actions --- .github/workflows/CI.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index df03723..70ea0e7 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -18,11 +18,11 @@ jobs: - x64 steps: - uses: actions/checkout@v2 - - uses: julia-actions/setup-julia@v1 + - uses: julia-actions/setup-julia@v2 with: version: ${{ matrix.version }} arch: ${{ matrix.arch }} - - uses: actions/cache@v1 + - uses: actions/cache@v4 env: cache-name: cache-artifacts with: From 5e575f762477529c1df7f63221545e232587a28b Mon Sep 17 00:00:00 2001 From: Joshua Slaughter Date: Sun, 30 Mar 2025 15:08:30 +0100 Subject: [PATCH 07/17] correct behavior to do first order interactions iteratively across listed extra_treatments --- src/inputs_from_config.jl | 24 +++++-- test/data/config_gweis_first_order.yaml | 1 + test/data/config_gweis_higher_order.yaml | 12 ---- test/inputs_from_gweis_config.jl | 92 ++++-------------------- 4 files changed, 34 insertions(+), 95 deletions(-) delete mode 100644 test/data/config_gweis_higher_order.yaml diff --git a/src/inputs_from_config.jl b/src/inputs_from_config.jl index 164a36e..c29fd6a 100644 --- a/src/inputs_from_config.jl +++ b/src/inputs_from_config.jl @@ -71,10 +71,26 @@ function genome_wide_estimands( if isempty(extra_treatments) treatments = treatments_from_variant(variant, dataset) else - treatments = Dict( - treatments_from_variant(variant, dataset)..., - (pair for extra in extra_treatments for pair in treatments_from_variant(string(extra), dataset))... - ) + for treatment in extra_treatments + treatments = Dict(treatments_from_variant(variant, dataset)..., treatments_from_variant(string(treatment), dataset)...) + local Ψ + try + Ψ = factorialEstimands( + estimand_constructor, treatments, outcomes; + confounders=confounders, + dataset=dataset, + outcome_extra_covariates=outcome_extra_covariates, + positivity_constraint=positivity_constraint, + verbosity=verbosity-1) + + catch e + if !(e == ArgumentError("No component passed the positivity constraint.")) + throw(e) + end + else + append!(estimands, Ψ) + end + end end local Ψ diff --git a/test/data/config_gweis_first_order.yaml b/test/data/config_gweis_first_order.yaml index 6b6ba7b..694d506 100644 --- a/test/data/config_gweis_first_order.yaml +++ b/test/data/config_gweis_first_order.yaml @@ -1,6 +1,7 @@ type: gweis extra_treatments: + - TREAT_1 - 22001 outcome_extra_covariates: diff --git a/test/data/config_gweis_higher_order.yaml b/test/data/config_gweis_higher_order.yaml deleted file mode 100644 index cafaba0..0000000 --- a/test/data/config_gweis_higher_order.yaml +++ /dev/null @@ -1,12 +0,0 @@ -type: gweis - -extra_treatments: - - 22001 - - BINARY_1 - - BINARY_2 - -outcome_extra_covariates: - - COV_1 - -extra_confounders: - - 21003 \ No newline at end of file diff --git a/test/inputs_from_gweis_config.jl b/test/inputs_from_gweis_config.jl index 4d9c6cb..f7c22d4 100644 --- a/test/inputs_from_gweis_config.jl +++ b/test/inputs_from_gweis_config.jl @@ -8,6 +8,7 @@ using DataFrames using Serialization using TMLE using CSV +using YAML TESTDIR = joinpath(pkgdir(TargeneCore), "test") @@ -20,10 +21,16 @@ function get_summary_stats(estimands) end function check_estimands_levels_interactions(estimands) + extra_treatments = YAML.load_file(joinpath(TESTDIR, "data", "config_gweis_first_order.yaml"))["extra_treatments"] + for (i,x) in enumerate(extra_treatments) + extra_treatments[i]=Symbol(x) + end + for Ψ in estimands # If the two components are present, the first is the 0 -> 1 and the second is the 1 -> 2 # The variant should always be the last key - variant = last(collect(keys(Ψ.args[1].treatment_values))) + treatment_set = collect(keys(Ψ.args[1].treatment_values)) + variant = setdiff(treatment_set, extra_treatments)[1] if length(Ψ.args) == 2 @test Ψ.args[1].treatment_values[variant] == (control = 0x00, case = 0x01) @test Ψ.args[2].treatment_values[variant] == (control = 0x01, case = 0x02) @@ -66,10 +73,10 @@ end # There are 875 variants in the dataset summary_stats = get_summary_stats(estimands) @test summary_stats == DataFrame( - OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1], - nrow = repeat([875], 5) + OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2], + nrow = repeat([2625], 4) ) - + println(estimands[1]) check_estimands_levels_interactions(estimands) end @@ -102,86 +109,13 @@ end @test all(e isa JointEstimand for e in estimands) summary_stats = get_summary_stats(estimands) @test summary_stats == DataFrame( - OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1], - nrow = repeat([142], 5) + OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2], + nrow = repeat([430], 4) ) check_estimands_levels_interactions(estimands) end -@testset "Test inputs_from_config gweis: no positivity constraint and four-point interaction" begin - tmpdir = mktempdir() - copy!(ARGS, [ - "estimation-inputs", - joinpath(TESTDIR, "data", "config_gweis_higher_order.yaml"), - string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")), - string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")), - string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")), - string("--outprefix=", joinpath(tmpdir, "final")), - "--batchsize=5", - "--verbosity=0", - "--positivity-constraint=0" - ]) - TargeneCore.julia_main() - # Check dataset - dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) - @test size(dataset) == (1940, 886) - - # Check estimands - estimands = [] - for file in readdir(tmpdir, join=true) - if endswith(file, "jls") - append!(estimands, deserialize(file).estimands) - end - end - @test all(e isa JointEstimand for e in estimands) - - # There are 875 variants in the dataset - summary_stats = get_summary_stats(estimands) - @test summary_stats == DataFrame( - OUTCOME = [:CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1], - nrow = repeat([875], 3) - ) - - check_estimands_levels_interactions(estimands) -end - -@testset "Test inputs_from_config gweis: positivity constraint and four-point interaction" begin - tmpdir = mktempdir() - copy!(ARGS, [ - "estimation-inputs", - joinpath(TESTDIR, "data", "config_gweis_higher_order.yaml"), - string("--traits-file=", joinpath(TESTDIR, "data", "ukbb_traits.csv")), - string("--pcs-file=", joinpath(TESTDIR, "data", "ukbb_pcs.csv")), - string("--genotypes-prefix=", joinpath(TESTDIR, "data", "ukbb", "genotypes" , "ukbb_1.")), - string("--outprefix=", joinpath(tmpdir, "final")), - "--batchsize=5", - "--verbosity=0", - "--positivity-constraint=0.02" - ]) - TargeneCore.julia_main() - # Check dataset - dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) - @test size(dataset) == (1940, 886) - - # Check estimands - estimands = [] - for file in readdir(tmpdir, join=true) - if endswith(file, "jls") - append!(estimands, deserialize(file).estimands) - end - end - @test all(e isa JointEstimand for e in estimands) - - # There are 784 treatments in the dataset after positivity_constraint - summary_stats = get_summary_stats(estimands) - @test summary_stats == DataFrame( - OUTCOME = [:CONTINUOUS_1, :CONTINUOUS_2, :TREAT_1], - nrow = repeat([784], 3) - ) - - check_estimands_levels_interactions(estimands) -end end true \ No newline at end of file From b1ef8216e53a43a536fd82d68fcba1588393d395 Mon Sep 17 00:00:00 2001 From: Joshua Slaughter Date: Sat, 12 Apr 2025 22:25:49 +0100 Subject: [PATCH 08/17] variant mapping file output; gwis is now under gwas functions specified by AIE --- .gitignore | 1 + src/inputs_from_config.jl | 109 ++++++++++-------------- test/data/config_gwas.yaml | 3 + test/data/config_gweis_first_order.yaml | 7 +- test/inputs_from_gweis_config.jl | 13 ++- 5 files changed, 60 insertions(+), 73 deletions(-) diff --git a/.gitignore b/.gitignore index 9ab9e5f..b9a423b 100644 --- a/.gitignore +++ b/.gitignore @@ -36,3 +36,4 @@ sandbox.jl src/generate_results.jl test_grid.csv test/tl_inputs/real_data.jl +test/data/scratch/ diff --git a/src/inputs_from_config.jl b/src/inputs_from_config.jl index c29fd6a..8567cea 100644 --- a/src/inputs_from_config.jl +++ b/src/inputs_from_config.jl @@ -67,10 +67,26 @@ function genome_wide_estimands( ) estimands = [] for variant in variants - - if isempty(extra_treatments) + if estimand_constructor == ATE treatments = treatments_from_variant(variant, dataset) - else + local Ψ + try + Ψ = factorialEstimands( + estimand_constructor, treatments, outcomes; + confounders=confounders, + dataset=dataset, + outcome_extra_covariates=outcome_extra_covariates, + positivity_constraint=positivity_constraint, + verbosity=verbosity-1) + + catch e + if !(e == ArgumentError("No component passed the positivity constraint.")) + throw(e) + end + else + append!(estimands, Ψ) + end + elseif estimand_constructor == AIE && !isempty(extra_treatments) for treatment in extra_treatments treatments = Dict(treatments_from_variant(variant, dataset)..., treatments_from_variant(string(treatment), dataset)...) local Ψ @@ -91,24 +107,10 @@ function genome_wide_estimands( append!(estimands, Ψ) end end - end - - local Ψ - try - Ψ = factorialEstimands( - estimand_constructor, treatments, outcomes; - confounders=confounders, - dataset=dataset, - outcome_extra_covariates=outcome_extra_covariates, - positivity_constraint=positivity_constraint, - verbosity=verbosity-1) - - catch e - if !(e == ArgumentError("No component passed the positivity constraint.")) - throw(e) - end + elseif estimand_constructor == AIE && isempty(extra_treatments) + throw(ArgumentError("Extra treatments are necessary for AIE estimands in this configuration.")) else - append!(estimands, Ψ) + throw(ArgumentError(string("Invalid estimand constructor: ", estimand_constructor))) end end return estimands @@ -196,42 +198,28 @@ function treatments_from_variant(variant::String, dataset::DataFrame) return Dict{Symbol, Vector{UInt8}}(Symbol(variant)=>variant_levels) end -function estimands_from_gwas(dataset, variants, outcomes, confounders; +function estimands_from_gwas(estimands_configs, dataset, variants, outcomes, confounders; extra_treatments=extra_treatments, outcome_extra_covariates = [], positivity_constraint=0., verbosity=0 ) - variants_groups = Iterators.partition(variants, length(variants) ÷ Threads.nthreads()) - estimands_tasks = map(variants_groups) do variants - Threads.@spawn genome_wide_estimands(variants, dataset, ATE, outcomes, confounders; - extra_treatments=extra_treatments, - outcome_extra_covariates=outcome_extra_covariates, - positivity_constraint=positivity_constraint, - verbosity=verbosity - ) - end - estimands_partitions = fetch.(estimands_tasks) - return vcat(estimands_partitions...) -end - -function estimands_from_gweis(dataset, variants, outcomes, confounders; - extra_treatments=extra_treatments, - outcome_extra_covariates = [], - positivity_constraint=0., - verbosity=0 - ) - variants_groups = Iterators.partition(variants, length(variants) ÷ Threads.nthreads()) - estimands_tasks = map(variants_groups) do variants - Threads.@spawn genome_wide_estimands(variants, dataset, AIE, outcomes, confounders; - extra_treatments=extra_treatments, - outcome_extra_covariates=outcome_extra_covariates, - positivity_constraint=positivity_constraint, - verbosity=verbosity - ) + estimands = [] + for estimands_config in estimands_configs + estimand_constructor = eval(Symbol(estimands_config["type"])) + variants_groups = Iterators.partition(variants, length(variants) ÷ Threads.nthreads()) + estimands_tasks = map(variants_groups) do variants + Threads.@spawn genome_wide_estimands(variants, dataset, estimand_constructor, outcomes, confounders; + extra_treatments=extra_treatments, + outcome_extra_covariates=outcome_extra_covariates, + positivity_constraint=positivity_constraint, + verbosity=verbosity + ) + end + estimands_partitions = fetch.(estimands_tasks) + push!(estimands, vcat(estimands_partitions...)) end - estimands_partitions = fetch.(estimands_tasks) - return vcat(estimands_partitions...) + return vcat(estimands...) end get_only_file_with_suffix(files, suffix) = files[only(findall(x -> endswith(x, suffix), files))] @@ -244,7 +232,7 @@ function read_bed_chromosome(bedprefix) return SnpData(bed_file, famnm=fam_file, bimnm=bim_file) end -function get_genotypes_from_beds(bedprefix) +function get_genotypes_from_beds(bedprefix, outprefix) snpdata = read_bed_chromosome(bedprefix) genotypes = DataFrame(convert(Matrix{UInt8}, snpdata.snparray), snpdata.snp_info."snpid") genotype_map = Union{UInt8, Missing}[0, missing, 1, 2] @@ -252,12 +240,13 @@ function get_genotypes_from_beds(bedprefix) genotypes[!, col] = [genotype_map[x+1] for x in genotypes[!, col]] end insertcols!(genotypes, 1, :SAMPLE_ID => snpdata.person_info."iid") + CSV.write(string(outprefix, ".mapping.txt"), select(snpdata.snp_info, "snpid", "allele1", "allele2")) return genotypes end -function make_genotypes(genotype_prefix, config, call_threshold) - genotypes = if config["type"] == "gwas"|| config["type"] == "gweis" - get_genotypes_from_beds(genotype_prefix) +function make_genotypes(genotype_prefix, config, call_threshold, outprefix) + genotypes = if config["type"] == "gwas" + get_genotypes_from_beds(genotype_prefix, outprefix) else variants_set = Set(retrieve_variants_list(config["variants"])) call_genotypes(genotype_prefix, variants_set, call_threshold) @@ -287,7 +276,7 @@ function inputs_from_config(config_file, genotypes_prefix, traits_file, pcs_file # Genotypes and final dataset verbosity > 0 && @info("Building and writing dataset.") - genotypes = make_genotypes(genotypes_prefix, config, call_threshold) + genotypes = make_genotypes(genotypes_prefix, config, call_threshold, outprefix) dataset = merge(traits, pcs, genotypes) Arrow.write(string(outprefix, ".data.arrow"), dataset) @@ -308,20 +297,12 @@ function inputs_from_config(config_file, genotypes_prefix, traits_file, pcs_file ) elseif config_type == "gwas" variants = filter(!=("SAMPLE_ID"), names(genotypes)) - estimands_from_gwas(dataset, variants, outcomes, confounders; + estimands_from_gwas(config["estimands"], dataset, variants, outcomes, confounders; extra_treatments=extra_treatments, outcome_extra_covariates=outcome_extra_covariates, positivity_constraint=positivity_constraint, verbosity=verbosity ) - elseif config_type == "gweis" - variants = filter(!=("SAMPLE_ID"), names(genotypes)) - estimands_from_gweis(dataset, variants, outcomes, confounders; - extra_treatments=extra_treatments, - outcome_extra_covariates=outcome_extra_covariates, - positivity_constraint=positivity_constraint, - verbosity=verbosity - ) else throw(ArgumentError(string("Unknown extraction type: ", config_type, ", use any of: (flat, groups, gwas)"))) end diff --git a/test/data/config_gwas.yaml b/test/data/config_gwas.yaml index af80bbd..4e46c3d 100644 --- a/test/data/config_gwas.yaml +++ b/test/data/config_gwas.yaml @@ -1,5 +1,8 @@ type: gwas +estimands: + - type: ATE + outcome_extra_covariates: - COV_1 diff --git a/test/data/config_gweis_first_order.yaml b/test/data/config_gweis_first_order.yaml index 694d506..db3fd5c 100644 --- a/test/data/config_gweis_first_order.yaml +++ b/test/data/config_gweis_first_order.yaml @@ -1,11 +1,14 @@ -type: gweis +type: gwas + +estimands: + - type: AIE extra_treatments: - TREAT_1 - - 22001 outcome_extra_covariates: - COV_1 extra_confounders: - 21003 + - 22001 diff --git a/test/inputs_from_gweis_config.jl b/test/inputs_from_gweis_config.jl index f7c22d4..37fe5cf 100644 --- a/test/inputs_from_gweis_config.jl +++ b/test/inputs_from_gweis_config.jl @@ -21,14 +21,14 @@ function get_summary_stats(estimands) end function check_estimands_levels_interactions(estimands) - extra_treatments = YAML.load_file(joinpath(TESTDIR, "data", "config_gweis_first_order.yaml"))["extra_treatments"] - for (i,x) in enumerate(extra_treatments) - extra_treatments[i]=Symbol(x) + string_treatments = YAML.load_file(joinpath(TESTDIR, "data", "config_gweis_first_order.yaml"))["extra_treatments"] + extra_treatments = [] + for (i,x) in enumerate(string_treatments) + push!(extra_treatments, Symbol(x)) end for Ψ in estimands # If the two components are present, the first is the 0 -> 1 and the second is the 1 -> 2 - # The variant should always be the last key treatment_set = collect(keys(Ψ.args[1].treatment_values)) variant = setdiff(treatment_set, extra_treatments)[1] if length(Ψ.args) == 2 @@ -74,9 +74,8 @@ end summary_stats = get_summary_stats(estimands) @test summary_stats == DataFrame( OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2], - nrow = repeat([2625], 4) + nrow = repeat([875], 4) ) - println(estimands[1]) check_estimands_levels_interactions(estimands) end @@ -110,7 +109,7 @@ end summary_stats = get_summary_stats(estimands) @test summary_stats == DataFrame( OUTCOME = [:BINARY_1, :BINARY_2, :CONTINUOUS_1, :CONTINUOUS_2], - nrow = repeat([430], 4) + nrow = repeat([146], 4) ) check_estimands_levels_interactions(estimands) From 04d2ac55565346a25f0460c17d4f56e7f80deb7b Mon Sep 17 00:00:00 2001 From: Joshua Slaughter Date: Sun, 13 Apr 2025 13:44:21 +0100 Subject: [PATCH 09/17] adding genotype/variant mapping for interpretability of gwas results --- Manifest.toml | 8 +++---- Project.toml | 1 + src/TargeneCore.jl | 1 + src/inputs_from_config.jl | 37 +++++++++++++++++++++++++++++++- test/inputs_from_gwas_config.jl | 3 ++- test/inputs_from_gweis_config.jl | 3 ++- 6 files changed, 46 insertions(+), 7 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index e6dafa2..a678939 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.4" manifest_format = "2.0" -project_hash = "4182f1a89c1532988a40d605eeec69822a2af3fc" +project_hash = "239580f1dc316e090dbf5ddb8739a2d1e3336f92" [[deps.ARFFFiles]] deps = ["CategoricalArrays", "Dates", "Parsers", "Tables"] @@ -2236,10 +2236,10 @@ 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" +deps = ["AliasTables", "DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "29321314c920c26684834965ec2ce0dacc9cf8e5" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.3" +version = "0.34.4" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] diff --git a/Project.toml b/Project.toml index f28f3ea..ebe1416 100644 --- a/Project.toml +++ b/Project.toml @@ -25,6 +25,7 @@ Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b" SnpArrays = "4e780e97-f5bf-4111-9dc4-b70aaf691b06" StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" TMLE = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf" TMLECLI = "2573d147-4098-46ba-9db2-8608d210ccac" YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" diff --git a/src/TargeneCore.jl b/src/TargeneCore.jl index 4434dff..a81e58d 100644 --- a/src/TargeneCore.jl +++ b/src/TargeneCore.jl @@ -25,6 +25,7 @@ using TMLECLI using HypothesisTests using OrderedCollections using Mmap +using StatsBase ############################################################################### ### INCLUDES ### diff --git a/src/inputs_from_config.jl b/src/inputs_from_config.jl index 8567cea..f6d6d6b 100644 --- a/src/inputs_from_config.jl +++ b/src/inputs_from_config.jl @@ -239,8 +239,43 @@ function get_genotypes_from_beds(bedprefix, outprefix) for col in names(genotypes) genotypes[!, col] = [genotype_map[x+1] for x in genotypes[!, col]] end + + vₘ, v₀, v₁, v₂ = [], [], [], [] + + for col in names(genotypes) + var_counts = countmap(genotypes[!, col]) + if haskey(var_counts, missing) + push!(vₘ, var_counts[missing]) + else + push!(vₘ, 0) + end + if haskey(var_counts, 0x00) + push!(v₀, var_counts[0x00]) + else + push!(v₀, 0) + end + if haskey(var_counts, 0x01) + push!(v₁, var_counts[0x01]) + else + push!(v₁, 0) + end + if haskey(var_counts, 0x02) + push!(v₂, var_counts[0x02]) + else + push!(v₂, 0) + end + end + insertcols!(genotypes, 1, :SAMPLE_ID => snpdata.person_info."iid") - CSV.write(string(outprefix, ".mapping.txt"), select(snpdata.snp_info, "snpid", "allele1", "allele2")) + + result_df = hcat(select(snpdata.snp_info, "snpid", "allele1", "allele2"), DataFrame( + vₘ = vₘ, + v₀ = v₀, + v₁ = v₁, + v₂ = v₂ + )) + + CSV.write(string(outprefix, ".mapping.txt"), result_df) return genotypes end diff --git a/test/inputs_from_gwas_config.jl b/test/inputs_from_gwas_config.jl index 919daff..a0b70e4 100644 --- a/test/inputs_from_gwas_config.jl +++ b/test/inputs_from_gwas_config.jl @@ -51,7 +51,7 @@ end # Check dataset dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) @test size(dataset) == (1940, 886) - + @test isfile(joinpath(tmpdir, "final.final.mapping.txt")) # Check estimands estimands = [] for file in readdir(tmpdir, join=true) @@ -88,6 +88,7 @@ end # Check dataset dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) @test size(dataset) == (1940, 886) + @test isfile(joinpath(tmpdir, "final.final.mapping.txt")) # Check estimands estimands = [] for file in readdir(tmpdir, join=true) diff --git a/test/inputs_from_gweis_config.jl b/test/inputs_from_gweis_config.jl index 37fe5cf..8c3011f 100644 --- a/test/inputs_from_gweis_config.jl +++ b/test/inputs_from_gweis_config.jl @@ -60,7 +60,7 @@ end # Check dataset dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) @test size(dataset) == (1940, 886) - + @test isfile(joinpath(tmpdir, "final.final.mapping.txt")) # Check estimands estimands = [] for file in readdir(tmpdir, join=true) @@ -97,6 +97,7 @@ end # Check dataset dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) @test size(dataset) == (1940, 886) + @test isfile(joinpath(tmpdir, "final.final.mapping.txt")) # Check estimands estimands = [] for file in readdir(tmpdir, join=true) From 02322ab3c8c3a171f456cef90cc608c879fa3a2b Mon Sep 17 00:00:00 2001 From: Joshua Slaughter Date: Sun, 13 Apr 2025 14:11:07 +0100 Subject: [PATCH 10/17] fix typo --- test/inputs_from_gwas_config.jl | 4 +- test/inputs_from_gweis_config.jl | 4 +- test/outputs.jl | 14 ++++ test/testutils.jl | 134 ++++++++++++++++++++++++++++--- 4 files changed, 142 insertions(+), 14 deletions(-) diff --git a/test/inputs_from_gwas_config.jl b/test/inputs_from_gwas_config.jl index a0b70e4..158c70f 100644 --- a/test/inputs_from_gwas_config.jl +++ b/test/inputs_from_gwas_config.jl @@ -51,7 +51,7 @@ end # Check dataset dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) @test size(dataset) == (1940, 886) - @test isfile(joinpath(tmpdir, "final.final.mapping.txt")) + @test isfile(joinpath(tmpdir, "final.mapping.txt")) # Check estimands estimands = [] for file in readdir(tmpdir, join=true) @@ -88,7 +88,7 @@ end # Check dataset dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) @test size(dataset) == (1940, 886) - @test isfile(joinpath(tmpdir, "final.final.mapping.txt")) + @test isfile(joinpath(tmpdir, "final.mapping.txt")) # Check estimands estimands = [] for file in readdir(tmpdir, join=true) diff --git a/test/inputs_from_gweis_config.jl b/test/inputs_from_gweis_config.jl index 8c3011f..543dbc8 100644 --- a/test/inputs_from_gweis_config.jl +++ b/test/inputs_from_gweis_config.jl @@ -60,7 +60,7 @@ end # Check dataset dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) @test size(dataset) == (1940, 886) - @test isfile(joinpath(tmpdir, "final.final.mapping.txt")) + @test isfile(joinpath(tmpdir, "final.mapping.txt")) # Check estimands estimands = [] for file in readdir(tmpdir, join=true) @@ -97,7 +97,7 @@ end # Check dataset dataset = DataFrame(Arrow.Table(joinpath(tmpdir, "final.data.arrow"))) @test size(dataset) == (1940, 886) - @test isfile(joinpath(tmpdir, "final.final.mapping.txt")) + @test isfile(joinpath(tmpdir, "final.mapping.txt")) # Check estimands estimands = [] for file in readdir(tmpdir, join=true) diff --git a/test/outputs.jl b/test/outputs.jl index 6e9d620..93bff0a 100644 --- a/test/outputs.jl +++ b/test/outputs.jl @@ -90,6 +90,20 @@ include(joinpath(TESTDIR, "testutils.jl")) @test isfile(joinpath(tmpdir, "Empty_QQ.png")) end +@testset "Test make_outputs for GWAS" begin + tmpdir = mktempdir() + input_prefix = joinpath(tmpdir, "tmle_output") + output_prefix = tmpdir + make_fake_outputs(make_gwas_estimates; prefix=input_prefix) + copy!(ARGS, [ + "make-outputs", + input_prefix, + string("--output-prefix=", output_prefix), + "--verbosity=0" + ]) + TargeneCore.julia_main() +end + end true \ No newline at end of file diff --git a/test/testutils.jl b/test/testutils.jl index 87c2fb8..5ba6048 100644 --- a/test/testutils.jl +++ b/test/testutils.jl @@ -112,17 +112,131 @@ function make_estimates() ] end +function make_gwas_estimands() + AIE₁ = AIE( + outcome = "High light scatter reticulocyte percentage", + treatment_values = ( + rs10043934 = (case=0x01, control=0x00), + Townsend_Deprivation_Index = (case=0x01, control=0x00) + ), + treatment_confounders = ( + rs10043934 = (:PC1, :PC2, :PC3, :PC4, :PC5, :PC6), + Townsend_Deprivation_Index = (:PC1, :PC2, :PC3, :PC4, :PC5, :PC6) + ), + outcome_extra_covariates = ("Age-Assessment", "Genetic-Sex") + ) + AIE₂ = AIE( + outcome = "High light scatter reticulocyte percentage", + treatment_values = ( + rs10043934 = (case=0x02, control=0x01), + Townsend_Deprivation_Index = (case=0x01, control= 0x00) + ), + treatment_confounders = ( + rs10043934 = (:PC1, :PC2, :PC3, :PC4, :PC5, :PC6), + Townsend_Deprivation_Index = (:PC1, :PC2, :PC3, :PC4, :PC5, :PC6) + ), + outcome_extra_covariates = ("Age-Assessment", "Genetic-Sex") + ) + ATE₁ = ATE( + outcome = "L50-L54 Urticaria and erythema", + treatment_values = ( + rs117913124 = (case=0x01, control=0x00), + ), + treatment_confounders = ( + rs117913124 = (:PC1, :PC2, :PC3, :PC4, :PC5, :PC6) + ), + outcome_extra_covariates = ("Age-Assessment", "Genetic-Sex") + ) + ATE₂ = ATE( + outcome = "L50-L54 Urticaria and erythema", + treatment_values = ( + rs117913124 = (case=0x02, control=0x01), + ), + treatment_confounders = ( + rs117913124 = (:PC1, :PC2, :PC3, :PC4, :PC5, :PC6), + ), + outcome_extra_covariates = ("Age-Assessment", "Genetic-Sex") + ) + jointAIE = JointEstimand(AIE₁, AIE₂) + jointATE = JointEstimand(ATE₁, ATE₂) + return (jointATE, jointAIE, AIE₁, AIE₂, ATE₁, ATE₂) +end + +function make_gwas_estimates() + jointAIE, jointATE, AIE₁, AIE₂, ATE₁, ATE₂ = make_gwas_estimands() + AIE₁ = TMLE.TMLEstimate( + estimand = AIE₁, + estimate = -1., + std = 0.003, + n = 10, + IC = [] + ) + AIE₂ = TMLE.TMLEstimate( + estimand = AIE₂, + estimate = -0.003, + std = 0.003, + n = 10, + IC = [] + ) + jointAIE = TMLE.JointEstimate( + estimand = jointAIE, + estimates = (AIE₁, AIE₂), + cov = [ + 0.003 0. + 0. 0.003 + ], + n = 10 + ) + + ATE₁ = TMLE.TMLEstimate( + estimand = ATE₁, + estimate = 0.003, + std = 0.003, + n = 20, + IC = [] + ) + ATE₂ = TMLE.TMLEstimate( + estimand = ATE₂, + estimate = 1., + std = 0.003, + n = 20, + IC = [] + ) + + jointATE = TMLE.JointEstimate( + estimand = jointATE, + estimates = (ATE₁, ATE₂), + cov = [ + 0.003 0. + 0. 0.003 + ], + n = 20 + ) + return [ + (TMLE=jointAIE, OSE=jointAIE), + (TMLE=jointATE, OSE=jointATE) + ] +end + function save(estimates; prefix="tmle_output") - # Batch 1 - outputs = TMLECLI.Outputs(hdf5=prefix*"_1.hdf5") - TMLECLI.initialize(outputs) - TMLECLI.update(outputs, estimates[1:3]) - TMLECLI.finalize(outputs) - # Batch 2 - outputs = TMLECLI.Outputs(hdf5=prefix*"_2.hdf5") - TMLECLI.initialize(outputs) - TMLECLI.update(outputs, estimates[4:end]) - TMLECLI.finalize(outputs) + # The first conditonal is to test GWAS outputs + if length(estimates) == 2 + outputs = TMLECLI.Outputs(hdf5=prefix*".hdf5") + TMLECLI.initialize(outputs) + TMLECLI.update(outputs, estimates[1:2]) + TMLECLI.finalize(outputs) + else + # Batch 1 + outputs = TMLECLI.Outputs(hdf5=prefix*"_1.hdf5") + TMLECLI.initialize(outputs) + TMLECLI.update(outputs, estimates[1:3]) + TMLECLI.finalize(outputs) + # Batch 2 + outputs = TMLECLI.Outputs(hdf5=prefix*"_2.hdf5") + TMLECLI.initialize(outputs) + TMLECLI.update(outputs, estimates[4:end]) + TMLECLI.finalize(outputs) + end end make_fake_outputs(estimates_generator=make_estimates; prefix="tmle_output") = From 79cb89595117d623f1bc60f74befeb5384aa09d6 Mon Sep 17 00:00:00 2001 From: Joshua Slaughter Date: Sun, 13 Apr 2025 14:14:28 +0100 Subject: [PATCH 11/17] Undo premature changes --- test/outputs.jl | 14 ----- test/testutils.jl | 134 ++++------------------------------------------ 2 files changed, 10 insertions(+), 138 deletions(-) diff --git a/test/outputs.jl b/test/outputs.jl index 93bff0a..6e9d620 100644 --- a/test/outputs.jl +++ b/test/outputs.jl @@ -90,20 +90,6 @@ include(joinpath(TESTDIR, "testutils.jl")) @test isfile(joinpath(tmpdir, "Empty_QQ.png")) end -@testset "Test make_outputs for GWAS" begin - tmpdir = mktempdir() - input_prefix = joinpath(tmpdir, "tmle_output") - output_prefix = tmpdir - make_fake_outputs(make_gwas_estimates; prefix=input_prefix) - copy!(ARGS, [ - "make-outputs", - input_prefix, - string("--output-prefix=", output_prefix), - "--verbosity=0" - ]) - TargeneCore.julia_main() -end - end true \ No newline at end of file diff --git a/test/testutils.jl b/test/testutils.jl index 5ba6048..87c2fb8 100644 --- a/test/testutils.jl +++ b/test/testutils.jl @@ -112,131 +112,17 @@ function make_estimates() ] end -function make_gwas_estimands() - AIE₁ = AIE( - outcome = "High light scatter reticulocyte percentage", - treatment_values = ( - rs10043934 = (case=0x01, control=0x00), - Townsend_Deprivation_Index = (case=0x01, control=0x00) - ), - treatment_confounders = ( - rs10043934 = (:PC1, :PC2, :PC3, :PC4, :PC5, :PC6), - Townsend_Deprivation_Index = (:PC1, :PC2, :PC3, :PC4, :PC5, :PC6) - ), - outcome_extra_covariates = ("Age-Assessment", "Genetic-Sex") - ) - AIE₂ = AIE( - outcome = "High light scatter reticulocyte percentage", - treatment_values = ( - rs10043934 = (case=0x02, control=0x01), - Townsend_Deprivation_Index = (case=0x01, control= 0x00) - ), - treatment_confounders = ( - rs10043934 = (:PC1, :PC2, :PC3, :PC4, :PC5, :PC6), - Townsend_Deprivation_Index = (:PC1, :PC2, :PC3, :PC4, :PC5, :PC6) - ), - outcome_extra_covariates = ("Age-Assessment", "Genetic-Sex") - ) - ATE₁ = ATE( - outcome = "L50-L54 Urticaria and erythema", - treatment_values = ( - rs117913124 = (case=0x01, control=0x00), - ), - treatment_confounders = ( - rs117913124 = (:PC1, :PC2, :PC3, :PC4, :PC5, :PC6) - ), - outcome_extra_covariates = ("Age-Assessment", "Genetic-Sex") - ) - ATE₂ = ATE( - outcome = "L50-L54 Urticaria and erythema", - treatment_values = ( - rs117913124 = (case=0x02, control=0x01), - ), - treatment_confounders = ( - rs117913124 = (:PC1, :PC2, :PC3, :PC4, :PC5, :PC6), - ), - outcome_extra_covariates = ("Age-Assessment", "Genetic-Sex") - ) - jointAIE = JointEstimand(AIE₁, AIE₂) - jointATE = JointEstimand(ATE₁, ATE₂) - return (jointATE, jointAIE, AIE₁, AIE₂, ATE₁, ATE₂) -end - -function make_gwas_estimates() - jointAIE, jointATE, AIE₁, AIE₂, ATE₁, ATE₂ = make_gwas_estimands() - AIE₁ = TMLE.TMLEstimate( - estimand = AIE₁, - estimate = -1., - std = 0.003, - n = 10, - IC = [] - ) - AIE₂ = TMLE.TMLEstimate( - estimand = AIE₂, - estimate = -0.003, - std = 0.003, - n = 10, - IC = [] - ) - jointAIE = TMLE.JointEstimate( - estimand = jointAIE, - estimates = (AIE₁, AIE₂), - cov = [ - 0.003 0. - 0. 0.003 - ], - n = 10 - ) - - ATE₁ = TMLE.TMLEstimate( - estimand = ATE₁, - estimate = 0.003, - std = 0.003, - n = 20, - IC = [] - ) - ATE₂ = TMLE.TMLEstimate( - estimand = ATE₂, - estimate = 1., - std = 0.003, - n = 20, - IC = [] - ) - - jointATE = TMLE.JointEstimate( - estimand = jointATE, - estimates = (ATE₁, ATE₂), - cov = [ - 0.003 0. - 0. 0.003 - ], - n = 20 - ) - return [ - (TMLE=jointAIE, OSE=jointAIE), - (TMLE=jointATE, OSE=jointATE) - ] -end - function save(estimates; prefix="tmle_output") - # The first conditonal is to test GWAS outputs - if length(estimates) == 2 - outputs = TMLECLI.Outputs(hdf5=prefix*".hdf5") - TMLECLI.initialize(outputs) - TMLECLI.update(outputs, estimates[1:2]) - TMLECLI.finalize(outputs) - else - # Batch 1 - outputs = TMLECLI.Outputs(hdf5=prefix*"_1.hdf5") - TMLECLI.initialize(outputs) - TMLECLI.update(outputs, estimates[1:3]) - TMLECLI.finalize(outputs) - # Batch 2 - outputs = TMLECLI.Outputs(hdf5=prefix*"_2.hdf5") - TMLECLI.initialize(outputs) - TMLECLI.update(outputs, estimates[4:end]) - TMLECLI.finalize(outputs) - end + # Batch 1 + outputs = TMLECLI.Outputs(hdf5=prefix*"_1.hdf5") + TMLECLI.initialize(outputs) + TMLECLI.update(outputs, estimates[1:3]) + TMLECLI.finalize(outputs) + # Batch 2 + outputs = TMLECLI.Outputs(hdf5=prefix*"_2.hdf5") + TMLECLI.initialize(outputs) + TMLECLI.update(outputs, estimates[4:end]) + TMLECLI.finalize(outputs) end make_fake_outputs(estimates_generator=make_estimates; prefix="tmle_output") = From 1c3453f17ac4c919e390cc43021ea3f0433bf44d Mon Sep 17 00:00:00 2001 From: joshua-slaughter Date: Wed, 23 Apr 2025 10:58:30 +0100 Subject: [PATCH 12/17] up manifest --- Manifest.toml | 1185 ++++++++++++++++++++++++++++++++++--------------- Project.toml | 16 +- 2 files changed, 840 insertions(+), 361 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 2a3f06c..38cda90 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,14 +1,14 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.10.4" +julia_version = "1.11.4" manifest_format = "2.0" -project_hash = "b1a916e4f68d2fb953c6eba21c0fc7546e7dc5c6" +project_hash = "f0fd0a5f42e7f0463412b8be589f8914c9a7c555" [[deps.ARFFFiles]] deps = ["CategoricalArrays", "Dates", "Parsers", "Tables"] -git-tree-sha1 = "e8c8e0a2be6eb4f56b1672e46004463033daa409" +git-tree-sha1 = "678eb18590a8bc6674363da4d5faa4ac09c40a18" uuid = "da404889-ca92-49ff-9e8b-0aa6b4d38dc8" -version = "1.4.1" +version = "1.5.0" [[deps.AbstractDifferentiation]] deps = ["ExprTools", "LinearAlgebra", "Requires"] @@ -50,40 +50,44 @@ uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.5" [[deps.Accessors]] -deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] -git-tree-sha1 = "f61b15be1d76846c0ce31d3fcfac5380ae53db6a" +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "MacroTools"] +git-tree-sha1 = "0ba8f4c1f06707985ffb4804fdad1bf97b233897" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.37" +version = "0.1.41" [deps.Accessors.extensions] - AccessorsAxisKeysExt = "AxisKeys" - AccessorsIntervalSetsExt = "IntervalSets" - AccessorsStaticArraysExt = "StaticArrays" - AccessorsStructArraysExt = "StructArrays" - AccessorsUnitfulExt = "Unitful" + AxisKeysExt = "AxisKeys" + IntervalSetsExt = "IntervalSets" + LinearAlgebraExt = "LinearAlgebra" + StaticArraysExt = "StaticArrays" + StructArraysExt = "StructArrays" + TestExt = "Test" + UnitfulExt = "Unitful" [deps.Accessors.weakdeps] AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Requires = "ae029012-a4dd-5104-9daa-d747884805df" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" + Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "cde29ddf7e5726c9fb511f340244ea3481267608" +git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.7.2" +version = "4.1.1" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] AdaptStaticArraysExt = "StaticArrays" [[deps.AdaptivePredicates]] -git-tree-sha1 = "7d5da5dd472490d048b081ca1bda4a7821b06456" +git-tree-sha1 = "7e651ea8d262d2d74ce75fdf47c4d63c07dba7a6" uuid = "35492f91-a3bd-45ad-95db-fcad7dcfedb7" -version = "1.1.1" +version = "1.2.0" [[deps.AliasTables]] deps = ["PtrArrays", "Random"] @@ -93,14 +97,14 @@ version = "1.1.3" [[deps.Animations]] deps = ["Colors"] -git-tree-sha1 = "e81c509d2c8e49592413bfb0bb3b08150056c79d" +git-tree-sha1 = "e092fa223bf66a3c41f9c022bd074d916dc303e7" uuid = "27a7e980-b3e6-11e9-2bcd-0b925532e340" -version = "0.4.1" +version = "0.4.2" [[deps.ArgCheck]] -git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" +git-tree-sha1 = "680b3b8759bd4c54052ada14e52355ab69e07876" uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" -version = "2.3.0" +version = "2.4.0" [[deps.ArgParse]] deps = ["Logging", "TextWrap"] @@ -110,7 +114,7 @@ version = "1.2.0" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" -version = "1.1.1" +version = "1.1.2" [[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] @@ -118,17 +122,34 @@ git-tree-sha1 = "d57bd3762d308bded22c3b82d033bff85f6195c6" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" version = "0.4.0" +[[deps.Arpack]] +deps = ["Arpack_jll", "Libdl", "LinearAlgebra", "Logging"] +git-tree-sha1 = "9b9b347613394885fd1c8c7729bfc60528faa436" +uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97" +version = "0.5.4" + +[[deps.Arpack_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg"] +git-tree-sha1 = "5ba6c757e8feccf03a1554dfaf3e26b3cfc7fd5e" +uuid = "68821587-b530-5797-8361-c406ea357684" +version = "3.5.1+1" + [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "c5aeb516a84459e0318a02507d2261edad97eb75" +deps = ["Adapt", "LinearAlgebra"] +git-tree-sha1 = "017fcb757f8e921fb44ee063a7aafe5f89b86dd1" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.7.1" +version = "7.18.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceCUDSSExt = "CUDSS" + ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" + ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceReverseDiffExt = "ReverseDiff" + ArrayInterfaceSparseArraysExt = "SparseArrays" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -136,15 +157,20 @@ version = "7.7.1" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" + ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.Arrow]] -deps = ["ArrowTypes", "BitIntegers", "CodecLz4", "CodecZstd", "ConcurrentUtilities", "DataAPI", "Dates", "EnumX", "LoggingExtras", "Mmap", "PooledArrays", "SentinelArrays", "Tables", "TimeZones", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "4ece4573f169d64b1508b0c8dd38c7919ae7a907" +deps = ["ArrowTypes", "BitIntegers", "CodecLz4", "CodecZstd", "ConcurrentUtilities", "DataAPI", "Dates", "EnumX", "Mmap", "PooledArrays", "SentinelArrays", "StringViews", "Tables", "TimeZones", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "00f0b3f05bc33cc5b68db6cc22e4a7b16b65e505" uuid = "69666777-d1a9-59fb-9406-91d4454c9d45" -version = "2.7.3" +version = "2.8.0" [[deps.ArrowTypes]] deps = ["Sockets", "UUIDs"] @@ -154,18 +180,28 @@ version = "2.3.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +version = "1.11.0" [[deps.Atomix]] deps = ["UnsafeAtomics"] -git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" +git-tree-sha1 = "c3b238aa28c1bebd4b5ea4988bebf27e9a01b72b" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" -version = "0.1.0" +version = "1.0.1" + + [deps.Atomix.extensions] + AtomixCUDAExt = "CUDA" + AtomixMetalExt = "Metal" + AtomixoneAPIExt = "oneAPI" + + [deps.Atomix.weakdeps] + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + Metal = "dde4c033-4e86-420c-a63e-0dd931031962" + oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b" [[deps.AutoHashEquals]] -deps = ["Pkg"] -git-tree-sha1 = "daaeb6f7f77b88c072a83a2451801818acb5c63b" +git-tree-sha1 = "4ec6b48702dacc5994a835c1189831755e4e76ef" uuid = "15f4f7f2-30c1-5605-9d31-71845cf9641f" -version = "2.1.0" +version = "2.2.0" [[deps.Automa]] deps = ["TranscodingStreams"] @@ -226,6 +262,7 @@ version = "0.4.3" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" +version = "1.11.0" [[deps.Baselet]] git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" @@ -245,9 +282,9 @@ version = "0.1.9" [[deps.BitIntegers]] deps = ["Random"] -git-tree-sha1 = "a55462dfddabc34bc97d3a7403a2ca2802179ae6" +git-tree-sha1 = "6158239ac409f960abbc232a9b24c00f5cce3108" uuid = "c3b6d118-76ef-56ca-8cc7-ebb389d030a1" -version = "0.3.1" +version = "0.3.2" [[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] @@ -262,9 +299,9 @@ version = "1.2.2" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" +git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+1" +version = "1.0.8+4" [[deps.CEnum]] git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" @@ -279,6 +316,7 @@ version = "0.2.6" [[deps.CRC32c]] uuid = "8bf52ea8-c179-5cab-976a-9e18b702a9bc" +version = "1.11.0" [[deps.CRlibm_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -288,39 +326,39 @@ version = "1.0.1+0" [[deps.CSV]] deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] -git-tree-sha1 = "6c834533dc1fabd820c1db03c839bf97e45a3fab" +git-tree-sha1 = "deddd8725e5e1cc49ee205a1964256043720a6c3" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.14" +version = "0.10.15" [[deps.CUDA_Driver_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "22bc8ec24f0ed05bcf8c1845ef425d8229ef6436" +git-tree-sha1 = "14996d716a2eaaeccfc8d7bc854dd87fde720ac1" uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc" -version = "0.10.0+0" +version = "0.10.4+0" [[deps.CUDA_Runtime_jll]] deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "c730797fc11265bb0940b738b3573ed38c2c8388" +git-tree-sha1 = "17f1536c600133f7c4113bae0a2d98dbf27c7ebc" uuid = "76a88914-d11a-5bdc-97e0-2f5a05c973a2" -version = "0.15.1+0" +version = "0.15.5+0" [[deps.Cairo]] deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] -git-tree-sha1 = "7b6ad8c35f4bc3bca8eb78127c8b99719506a5fb" +git-tree-sha1 = "71aa551c5c33f1a4415867fe06b7844faadb0ae9" uuid = "159f3aea-2a34-519c-b102-8c37f9878175" -version = "1.1.0" +version = "1.1.1" [[deps.CairoMakie]] deps = ["CRC32c", "Cairo", "Cairo_jll", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"] -git-tree-sha1 = "361dec06290d76b6d70d0c7dc888038eec9df63a" +git-tree-sha1 = "0afa2b4ac444b9412130d68493941e1af462e26a" uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" -version = "0.12.9" +version = "0.12.18" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "a2f1c8c668c8e3cb4cca4e57a8efdb09067bb3fd" +git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.0+2" +version = "1.18.2+1" [[deps.CategoricalArrays]] deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"] @@ -349,15 +387,15 @@ version = "0.1.15" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "227985d885b4dbce5e18a96f9326ea1e836e5a03" +git-tree-sha1 = "4312d7869590fab4a4f789e97bd82f0a04eaaa05" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.69.0" +version = "1.72.2" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "71acdbf594aab5bbb2cec89b208c41b4c411e49f" +git-tree-sha1 = "1713c74e00545bfe14605d2a2be1712de8fbcb58" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.24.0" +version = "1.25.1" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -369,11 +407,17 @@ git-tree-sha1 = "05ba0d07cd4fd8b7a39541e31a7b0254704ea581" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" version = "0.1.13" +[[deps.Clustering]] +deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "Random", "SparseArrays", "Statistics", "StatsBase"] +git-tree-sha1 = "3e22db924e2945282e70c33b75d4dde8bfa44c94" +uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5" +version = "0.15.8" + [[deps.CodecBzip2]] deps = ["Bzip2_jll", "TranscodingStreams"] -git-tree-sha1 = "e7c529cc31bb85b97631b922fa2e6baf246f5905" +git-tree-sha1 = "84990fa864b7f2b4901901ca12736e45ee79068c" uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" -version = "0.8.4" +version = "0.8.5" [[deps.CodecLz4]] deps = ["Lz4_jll", "TranscodingStreams"] @@ -395,21 +439,21 @@ version = "0.7.6" [[deps.CodecZstd]] deps = ["TranscodingStreams", "Zstd_jll"] -git-tree-sha1 = "5e41a52bec3b0881a7eb54f5391b779994504186" +git-tree-sha1 = "d0073f473757f0d39ac9707f1eb03b431573cbd8" uuid = "6b39b394-51ab-5f42-8807-6242bab2b4c2" -version = "0.8.5" +version = "0.8.6" [[deps.ColorBrewer]] -deps = ["Colors", "JSON", "Test"] -git-tree-sha1 = "61c5334f33d91e570e1d0c3eb5465835242582c4" +deps = ["Colors", "JSON"] +git-tree-sha1 = "e771a63cc8b539eca78c85b0cabd9233d6c8f06f" uuid = "a2cac450-b92f-5266-8821-25eda20663c8" -version = "0.4.0" +version = "0.4.1" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "b5278586822443594ff615963b0c09755771b3e0" +git-tree-sha1 = "26ec26c98ae1453c692efded2b17e15125a5bea1" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.26.0" +version = "3.28.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -429,9 +473,9 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0" +git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.11" +version = "0.13.0" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -485,9 +529,9 @@ version = "0.3.2" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" +git-tree-sha1 = "f36e5e8fdffcb5646ea5da81495a5a7566005127" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.4.2" +version = "2.4.3" [[deps.Configurations]] deps = ["ExproniconLite", "OrderedCollections", "TOML"] @@ -539,10 +583,10 @@ 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" +deps = ["Compat", "DataAPI", "DataStructures", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrecompileTools", "PrettyTables", "Printf", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.6.1" +version = "1.7.0" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -558,6 +602,13 @@ version = "1.0.0" [[deps.Dates]] deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +version = "1.11.0" + +[[deps.Dbus_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" +uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" +version = "1.14.10+0" [[deps.DefineSingletons]] git-tree-sha1 = "0fba8b706d0178b4dc7fd44a96a92382c9065c2c" @@ -566,9 +617,9 @@ version = "0.1.2" [[deps.DelaunayTriangulation]] deps = ["AdaptivePredicates", "EnumX", "ExactPredicates", "Random"] -git-tree-sha1 = "46f12daa85e5acc0ea5d5f9f8c3f1fc679e0f7e5" +git-tree-sha1 = "5620ff4ee0084a6ab7097a27ba0c19290200b037" uuid = "927a84f5-c5f4-47a5-9785-b46e178433df" -version = "1.2.0" +version = "1.6.4" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -578,9 +629,9 @@ version = "1.9.1" [[deps.Dictionaries]] deps = ["Indexing", "Random", "Serialization"] -git-tree-sha1 = "35b66b6744b2d92c778afd3a88d2571875664a2a" +git-tree-sha1 = "61ab242274c0d44412d8eab38942a49aa46de9d0" uuid = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4" -version = "0.4.2" +version = "0.4.3" [[deps.DiffResults]] deps = ["StaticArraysCore"] @@ -596,9 +647,9 @@ version = "1.15.1" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" +git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.11" +version = "0.10.12" weakdeps = ["ChainRulesCore", "SparseArrays"] [deps.Distances.extensions] @@ -608,12 +659,13 @@ weakdeps = ["ChainRulesCore", "SparseArrays"] [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" +version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "e6c693a0e4394f8fda0e51a5bdf5aef26f8235e9" +git-tree-sha1 = "03aa5d44647eaec98e1920635cdfed5d5560a8b9" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.111" +version = "0.25.117" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -653,11 +705,17 @@ git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" +[[deps.EpollShim_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8a4be429317c42cfae6a7fc03c31bad1970c310d" +uuid = "2702e6a9-849d-5ed8-8c21-79e8b8f9ee43" +version = "0.0.20230411+1" + [[deps.EvoTrees]] deps = ["BSON", "CategoricalArrays", "Distributions", "MLJModelInterface", "NetworkLayout", "Random", "RecipesBase", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "92d1f78f95f4794bf29bd972dacfa37ea1fec9f4" +git-tree-sha1 = "1692b52f3e8e2d25b41b837d3a32710979761e9b" uuid = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5" -version = "0.16.7" +version = "0.16.8" [deps.EvoTrees.extensions] EvoTreesCUDAExt = "CUDA" @@ -673,15 +731,15 @@ version = "2.2.8" [[deps.ExceptionUnwrapping]] deps = ["Test"] -git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" +git-tree-sha1 = "d36f682e590a83d63d1c7dbd287573764682d12a" uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" -version = "0.1.10" +version = "0.1.11" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" +git-tree-sha1 = "e51db81749b0777b2147fbe7b783ee79045b8e99" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.6.2+0" +version = "2.6.4+3" [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" @@ -694,15 +752,21 @@ uuid = "55351af7-c7e9-48d6-89ff-24e801d99491" version = "0.10.13" [[deps.Extents]] -git-tree-sha1 = "81023caa0021a41712685887db1fc03db26f41f5" +git-tree-sha1 = "063512a13dbe9c40d999c439268539aa552d1ae6" uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" -version = "0.1.4" +version = "0.1.5" + +[[deps.FFMPEG]] +deps = ["FFMPEG_jll"] +git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00" +uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" +version = "0.4.2" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "8cc47f299902e13f90405ddb5bf87e5d474c0d38" +git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "6.1.2+0" +version = "4.4.4+1" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] @@ -712,9 +776,9 @@ version = "1.8.0" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" +git-tree-sha1 = "4d81ed14783ec49ce9f2e168208a12ce1815aa25" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = "3.3.10+0" +version = "3.3.10+3" [[deps.FLoops]] deps = ["BangBang", "Compat", "FLoopsBase", "InitialValues", "JuliaVariables", "MLStyle", "Serialization", "Setfield", "Transducers"] @@ -736,9 +800,13 @@ version = "0.2.2" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322" +git-tree-sha1 = "2dd20384bf8c6d411b5c7370865b1e9b26cb2ea3" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.3" +version = "1.16.6" +weakdeps = ["HTTP"] + + [deps.FileIO.extensions] + HTTPExt = "HTTP" [[deps.FilePaths]] deps = ["FilePathsBase", "MacroTools", "Reexport", "Requires"] @@ -759,6 +827,7 @@ weakdeps = ["Mmap", "Test"] [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" +version = "1.11.0" [[deps.FillArrays]] deps = ["LinearAlgebra"] @@ -773,19 +842,21 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] FillArraysStatisticsExt = "Statistics" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Setfield", "SparseArrays"] -git-tree-sha1 = "f9219347ebf700e77ca1d48ef84e4a82a6701882" +deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] +git-tree-sha1 = "84e3a47db33be7248daa6274b287507dd6ff84e8" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.24.0" +version = "2.26.2" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" + FiniteDiffSparseArraysExt = "SparseArrays" FiniteDiffStaticArraysExt = "StaticArrays" [deps.FiniteDiff.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FixedPointNumbers]] @@ -796,9 +867,9 @@ version = "0.8.5" [[deps.Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] -git-tree-sha1 = "db16beca600632c95fc8aca29890d83788dd8b23" +git-tree-sha1 = "21fac3c77d7b5a9fc03b0ec503aa1a6392c34d2b" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.13.96+0" +version = "2.15.0+0" [[deps.Format]] git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" @@ -807,9 +878,9 @@ version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" +git-tree-sha1 = "a2df1b776752e3f344e5116c06d75a10436ab853" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.36" +version = "0.10.38" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -823,25 +894,32 @@ version = "4.1.1" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "5c1d8ae0efc6c2e7b1fc502cbe25def8f661b7bc" +git-tree-sha1 = "786e968a8d2fb167f2e4880baba62e0e26bd8e4e" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.13.2+0" +version = "2.13.3+1" [[deps.FreeTypeAbstraction]] deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"] -git-tree-sha1 = "2493cdfd0740015955a8e46de4ef28f49460d8bc" +git-tree-sha1 = "d52e255138ac21be31fa633200b65e4e71d26802" uuid = "663a7486-cb36-511b-a19d-713bb74d65c9" -version = "0.10.3" +version = "0.10.6" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" +git-tree-sha1 = "846f7026a9decf3679419122b49f8a1fdb48d2d5" uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.14+0" +version = "1.0.16+0" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" +version = "1.11.0" + +[[deps.GLFW_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] +git-tree-sha1 = "fcb0584ff34e25155876418979d4c8971243bb89" +uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" +version = "3.4.0+2" [[deps.GLM]] deps = ["Distributions", "LinearAlgebra", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "StatsModels"] @@ -851,21 +929,33 @@ version = "1.9.0" [[deps.GLMNet]] deps = ["DataFrames", "Distributed", "Distributions", "Printf", "Random", "SparseArrays", "StatsBase", "glmnet_jll"] -git-tree-sha1 = "7ea4e2bbb84183fe52a488d05e16c152b2387b95" +git-tree-sha1 = "b873c384d3490304c18224b1d5554cdebaafb60b" uuid = "8d5ece8b-de18-5317-b113-243142960cc6" -version = "0.7.2" +version = "0.7.4" [[deps.GPUArrays]] -deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "85d7fb51afb3def5dcb85ad31c3707795c8bccc1" +deps = ["Adapt", "GPUArraysCore", "KernelAbstractions", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "ScopedValues", "Serialization", "Statistics"] +git-tree-sha1 = "0ef97e93edced3d0e713f4cfd031cc9020e022b0" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "9.1.0" +version = "11.2.1" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" +git-tree-sha1 = "83cf05ab16a73219e5f6bd1bdfa9848fa24ac627" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.1.5" +version = "0.2.0" + +[[deps.GR]] +deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] +git-tree-sha1 = "9bf00ba4c45867c86251a7fd4cb646dcbeb41bf0" +uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" +version = "0.73.12" + +[[deps.GR_jll]] +deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] +git-tree-sha1 = "36d5430819123553bf31dfdceb3653ca7d9e62d7" +uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" +version = "0.73.12+0" [[deps.GeneticVariantBase]] deps = ["StatsBase"] @@ -874,15 +964,15 @@ uuid = "2447270c-d849-4bf9-ac0d-b5c0b265991c" version = "0.1.2" [[deps.GeoFormatTypes]] -git-tree-sha1 = "59107c179a586f0fe667024c5eb7033e81333271" +git-tree-sha1 = "8e233d5167e63d708d41f87597433f59a0f213fe" uuid = "68eda718-8dee-11e9-39e7-89f7f65f511f" -version = "0.4.2" +version = "0.4.4" [[deps.GeoInterface]] -deps = ["Extents", "GeoFormatTypes"] -git-tree-sha1 = "5921fc0704e40c024571eca551800c699f86ceb4" +deps = ["DataAPI", "Extents", "GeoFormatTypes"] +git-tree-sha1 = "294e99f19869d0b0cb71aef92f19d03649d028d5" uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" -version = "1.3.6" +version = "1.4.1" [[deps.GeometryBasics]] deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -896,11 +986,17 @@ git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" +[[deps.Giflib_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6570366d757b50fabae9f4315ad74d2e40c0560a" +uuid = "59f7168a-df46-5410-90c8-f2779963d0ec" +version = "5.2.3+0" + [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba" +git-tree-sha1 = "b0036b392358c80d2d2124746c2bf3d48d457938" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.80.2+0" +version = "2.82.4+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -909,27 +1005,27 @@ version = "1.3.1" [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] -git-tree-sha1 = "d61890399bc535850c4bf08e4e0d3a7ad0f21cbd" +git-tree-sha1 = "a641238db938fff9b2f60d08ed9030387daf428c" uuid = "a2bd30eb-e257-5431-a919-1863eab51364" -version = "1.1.2" +version = "1.1.3" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" +git-tree-sha1 = "01979f9b37367603e2848ea225918a3b3861b606" uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" -version = "1.3.14+0" +version = "1.3.14+1" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "ebd18c326fa6cee1efb7da9a3b45cf69da2ed4d9" +git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.11.2" +version = "1.12.0" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] -git-tree-sha1 = "fc713f007cff99ff9e50accba6373624ddd33588" +git-tree-sha1 = "dc6bed05c15523624909b3953686c5f5ffa10adc" uuid = "3955a311-db13-416c-9275-1d80ed98e5e9" -version = "0.11.0" +version = "0.11.1" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -937,16 +1033,21 @@ uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "c67b33b085f6e2faf8bf79a61962e7339a81129c" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.8" +version = "1.10.15" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] -git-tree-sha1 = "401e4f3f30f43af2c8478fc008da50096ea5240f" +git-tree-sha1 = "55c53be97790242c29031e5cd45e8ac296dadda3" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "8.3.1+0" +version = "8.5.0+0" + +[[deps.HashArrayMappedTries]] +git-tree-sha1 = "2eaa69a7cab70a52b9687c8bf950a5a93ec895ae" +uuid = "076d061b-32b6-4027-95e0-9a2c6f6d7e74" +version = "0.2.0" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] @@ -956,15 +1057,15 @@ version = "0.1.17" [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb" +git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.24" +version = "0.3.25" [[deps.HypothesisTests]] deps = ["Combinatorics", "Distributions", "LinearAlgebra", "Printf", "Random", "Rmath", "Roots", "Statistics", "StatsAPI", "StatsBase"] -git-tree-sha1 = "4b5d5ba51f5f473737ed9de6d8a7aa190ad8c72f" +git-tree-sha1 = "6c3ce99fdbaf680aa6716f4b919c19e902d67c9c" uuid = "09f84164-cd44-5f33-b23f-e6b0d136a0d5" -version = "0.11.0" +version = "0.11.3" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools"] @@ -979,9 +1080,9 @@ version = "0.1.1" [[deps.ImageAxes]] deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"] -git-tree-sha1 = "2e4520d67b0cef90865b3ef727594d2a58e0e1f8" +git-tree-sha1 = "e12629406c6c4442539436581041d372d69c55ba" uuid = "2803e5a7-5153-5ecf-9a86-9b4c37f5f5ac" -version = "0.6.11" +version = "0.6.12" [[deps.ImageBase]] deps = ["ImageCore", "Reexport"] @@ -991,21 +1092,21 @@ version = "0.1.7" [[deps.ImageCore]] deps = ["ColorVectorSpace", "Colors", "FixedPointNumbers", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "PrecompileTools", "Reexport"] -git-tree-sha1 = "b2a7eaa169c13f5bcae8131a83bc30eff8f71be0" +git-tree-sha1 = "8c193230235bbcee22c8066b0374f63b5683c2d3" uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534" -version = "0.10.2" +version = "0.10.5" [[deps.ImageIO]] -deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs"] -git-tree-sha1 = "437abb322a41d527c197fa800455f79d414f0a3c" +deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs", "WebP"] +git-tree-sha1 = "696144904b76e1ca433b886b4e7edd067d76cbf7" uuid = "82e4d734-157c-48bb-816b-45c225c6df19" -version = "0.6.8" +version = "0.6.9" [[deps.ImageMetadata]] deps = ["AxisArrays", "ImageAxes", "ImageBase", "ImageCore"] -git-tree-sha1 = "355e2b974f2e3212a75dfb60519de21361ad3cb7" +git-tree-sha1 = "2a81c3897be6fbcde0802a0ebe6796d0562f63ec" uuid = "bc367c6b-8a6b-528e-b4bd-a4b897500b49" -version = "0.9.9" +version = "0.9.10" [[deps.Imath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1052,6 +1153,7 @@ version = "2024.2.1+0" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" +version = "1.11.0" [[deps.Interpolations]] deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] @@ -1064,17 +1166,17 @@ weakdeps = ["Unitful"] InterpolationsUnitfulExt = "Unitful" [[deps.IntervalArithmetic]] -deps = ["CRlibm_jll", "MacroTools", "RoundingEmulator"] -git-tree-sha1 = "01fa84a20be8c7c867edf3b9ef33ac15f4089c1a" +deps = ["CRlibm_jll", "LinearAlgebra", "MacroTools", "RoundingEmulator"] +git-tree-sha1 = "ffb76d09ab0dc9f5a27edac2acec13c74a876cc6" uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" -version = "0.22.15" +version = "0.22.21" weakdeps = ["DiffRules", "ForwardDiff", "IntervalSets", "RecipesBase"] [deps.IntervalArithmetic.extensions] IntervalArithmeticDiffRulesExt = "DiffRules" IntervalArithmeticForwardDiffExt = "ForwardDiff" + IntervalArithmeticIntervalSetsExt = "IntervalSets" IntervalArithmeticRecipesBaseExt = "RecipesBase" - IntervalArithmeticsIntervalSetsExt = "IntervalSets" [[deps.IntervalSets]] git-tree-sha1 = "dba9ddf07f77f60450fe5d2e2beb9854d9a49bd0" @@ -1088,9 +1190,9 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] IntervalSetsStatisticsExt = "Statistics" [[deps.InverseFunctions]] -git-tree-sha1 = "2787db24f4e03daf859c6509ff87764e4182f7d1" +git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.16" +version = "0.1.17" weakdeps = ["Dates", "Test"] [deps.InverseFunctions.extensions] @@ -1098,9 +1200,9 @@ weakdeps = ["Dates", "Test"] InverseFunctionsTestExt = "Test" [[deps.InvertedIndices]] -git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" +git-tree-sha1 = "6da3c4316095de0f5ee2ebd875df8721e7e0bdbe" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.3.0" +version = "1.3.1" [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" @@ -1141,11 +1243,17 @@ git-tree-sha1 = "a0746c21bdc986d0dc293efa6b1faee112c37c28" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" version = "0.4.53" +[[deps.JLFzf]] +deps = ["Pipe", "REPL", "Random", "fzf_jll"] +git-tree-sha1 = "71b48d857e86bf7a1838c4736545699974ce79a2" +uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" +version = "0.1.9" + [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40" +git-tree-sha1 = "a007feb38b422fbdab534406aeca1b86823cb4d6" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.6.0" +version = "1.7.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1155,9 +1263,9 @@ version = "0.21.4" [[deps.JSON3]] deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] -git-tree-sha1 = "eb3edce0ed4fa32f75a0a11217433c31d56bd48b" +git-tree-sha1 = "1d322381ef7b087548321d3f878cb4c9bd8f8f9b" uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -version = "1.14.0" +version = "1.14.1" weakdeps = ["ArrowTypes"] [deps.JSON3.extensions] @@ -1171,9 +1279,9 @@ version = "0.1.5" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637" +git-tree-sha1 = "eac1206917768cb54957c65a615460d87b455fc1" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.0.3+0" +version = "3.1.1+0" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -1182,10 +1290,10 @@ uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" version = "0.2.4" [[deps.KernelAbstractions]] -deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "cb1cff88ef2f3a157cbad75bbe6b229e1975e498" +deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"] +git-tree-sha1 = "019e9de20154148a4937965ec43084435e946450" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.25" +version = "0.9.32" [deps.KernelAbstractions.extensions] EnzymeExt = "EnzymeCore" @@ -1209,11 +1317,17 @@ git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" version = "3.100.2+0" +[[deps.LERC_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "aaafe88dccbd957a8d82f7d05be9b69172e0cee3" +uuid = "88015f11-f218-50d7-93a8-a6af411a945d" +version = "4.0.1+0" + [[deps.LLVM]] -deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] -git-tree-sha1 = "839c82932db86740ae729779e610f07a1640be9a" +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"] +git-tree-sha1 = "5fcfea6df2ff3e4da708a40c969c3812162346df" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "6.6.3" +version = "9.2.0" [deps.LLVM.extensions] BFloat16sExt = "BFloat16s" @@ -1223,26 +1337,42 @@ version = "6.6.3" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "88b916503aac4fb7f701bb625cd84ca5dd1677bc" +git-tree-sha1 = "4b5ad6a4ffa91a00050a964492bc4f86bb48cea0" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.29+0" +version = "0.0.35+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e16271d212accd09d52ee0ae98956b8a05c4b626" +git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "17.0.6+0" +version = "18.1.7+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d" +git-tree-sha1 = "1c602b1127f4751facb671441ca72715cc95938a" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.2+0" +version = "2.10.3+0" [[deps.LaTeXStrings]] -git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" +git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.3.1" +version = "1.4.0" + +[[deps.Latexify]] +deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] +git-tree-sha1 = "ce5f5621cac23a86011836badfedf664a612cee4" +uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" +version = "0.16.5" + + [deps.Latexify.extensions] + DataFramesExt = "DataFrames" + SparseArraysExt = "SparseArrays" + SymEngineExt = "SymEngine" + + [deps.Latexify.weakdeps] + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" + SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" [[deps.LatinHypercubeSampling]] deps = ["Random", "StableRNGs", "StatsBase", "Test"] @@ -1259,6 +1389,7 @@ version = "0.1.17" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" +version = "1.11.0" [[deps.LazyModules]] git-tree-sha1 = "a560dd966b386ac9ae60bdd3a3d3a326062d3c3e" @@ -1279,16 +1410,17 @@ 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" +version = "8.6.0+0" [[deps.LibGit2]] deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +version = "1.11.0" [[deps.LibGit2_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" -version = "1.6.4+0" +version = "1.7.2+0" [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] @@ -1297,42 +1429,55 @@ version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" +version = "1.11.0" [[deps.Libffi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" +git-tree-sha1 = "27ecae93dd25ee0909666e6835051dd684cc035e" uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" -version = "3.2.2+1" +version = "3.2.2+2" [[deps.Libgcrypt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] -git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673" +git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.8.11+0" +version = "1.11.0+0" + +[[deps.Libglvnd_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll", "Xorg_libXext_jll"] +git-tree-sha1 = "ff3b4b9d35de638936a525ecd36e86a8bb919d11" +uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" +version = "1.7.0+0" [[deps.Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed" +git-tree-sha1 = "df37206100d39f79b3376afb6b9cee4970041c61" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.49.0+0" +version = "1.51.1+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" +git-tree-sha1 = "be484f5c92fad0bd8acfef35fe017900b0b73809" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.17.0+0" +version = "1.18.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e" +git-tree-sha1 = "89211ea35d9df5831fca5d33552c02bd33878419" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.40.1+0" +version = "2.40.3+0" + +[[deps.Libtiff_jll]] +deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] +git-tree-sha1 = "4ab7581296671007fc33f07a721631b8855f4b1d" +uuid = "89763e89-9b03-5906-acba-b20f662cd828" +version = "4.7.1+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" +git-tree-sha1 = "e888ad02ce716b319e6bdb985d2ef300e7089889" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.40.1+0" +version = "2.40.3+0" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] @@ -1343,6 +1488,7 @@ version = "7.3.0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" +version = "1.11.0" [[deps.LinearMaps]] deps = ["LinearAlgebra"] @@ -1358,9 +1504,9 @@ weakdeps = ["ChainRulesCore", "SparseArrays", "Statistics"] [[deps.LogExpFunctions]] deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "a2d09619db4e765091ee5c6ffe8872849de0feea" +git-tree-sha1 = "13ca9e2586b89836fd20cccf56e57e2b9ae7f38f" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.28" +version = "0.3.29" [deps.LogExpFunctions.extensions] LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" @@ -1374,12 +1520,13 @@ version = "0.3.28" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" +version = "1.11.0" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" +git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.3" +version = "1.1.0" [[deps.LoopVectorization]] deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] @@ -1394,9 +1541,9 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [[deps.Lz4_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "7f26c8fc5229e68484e0b3447312c98e16207d11" +git-tree-sha1 = "191686b1ac1ea9c89fc52e996ad15d1d241d1e33" uuid = "5ced341a-0733-55b8-9ab6-a4889d929147" -version = "1.10.0+0" +version = "1.10.1+0" [[deps.MKL]] deps = ["Artifacts", "Libdl", "LinearAlgebra", "Logging", "MKL_jll"] @@ -1458,9 +1605,9 @@ version = "0.3.7" [[deps.MLJIteration]] deps = ["IterationControl", "MLJBase", "Random", "Serialization"] -git-tree-sha1 = "f93f381a82fc1768c1a99c27a84b7ea1b1ee186d" +git-tree-sha1 = "ad16cfd261e28204847f509d1221a581286448ae" uuid = "614be32b-d00c-4edb-bd02-1eb411ab5e55" -version = "0.6.2" +version = "0.6.3" [[deps.MLJLinearModels]] deps = ["DocStringExtensions", "IterativeSolvers", "LinearAlgebra", "LinearMaps", "MLJModelInterface", "Optim", "Parameters"] @@ -1476,9 +1623,9 @@ 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"] -git-tree-sha1 = "c1b1f72379d15079d2c97937d9c1ed38f9ab4679" +git-tree-sha1 = "9dbbe1e9a8ba1fd60fefb5e39dd9a070bbda9c79" uuid = "d491faf4-2d78-11e9-2867-c94bc002c0b7" -version = "0.17.4" +version = "0.17.6" [[deps.MLJTuning]] deps = ["ComputationalResources", "Distributed", "Distributions", "LatinHypercubeSampling", "MLJBase", "ProgressMeter", "Random", "RecipesBase", "StatisticalMeasuresBase"] @@ -1488,9 +1635,9 @@ version = "0.8.8" [[deps.MLJXGBoostInterface]] deps = ["MLJModelInterface", "SparseArrays", "Tables", "XGBoost"] -git-tree-sha1 = "25769259346a017d227c2134347db4c449d43625" +git-tree-sha1 = "385031c897e822755e7d194b0f9745fb20129972" uuid = "54119dfa-1dab-4055-a167-80440f4f7a91" -version = "0.3.11" +version = "0.3.12" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1499,27 +1646,26 @@ version = "0.4.17" [[deps.MLUtils]] deps = ["ChainRulesCore", "Compat", "DataAPI", "DelimitedFiles", "FLoops", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] -git-tree-sha1 = "b45738c2e3d0d402dffa32b2c1654759a2ac35a4" +git-tree-sha1 = "7940c0af802586b97009f254aa6065000a16fa1d" uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" -version = "0.4.4" +version = "0.4.5" [[deps.MacroTools]] -deps = ["Markdown", "Random"] -git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" +git-tree-sha1 = "72aebe0b5051e5143a079a4685a46da330a40472" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.13" +version = "0.5.15" [[deps.Makie]] -deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"] -git-tree-sha1 = "204f06860af9008fa08b3a4842f48116e1209a2c" +deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageBase", "ImageIO", "InteractiveUtils", "Interpolations", "IntervalSets", "InverseFunctions", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"] +git-tree-sha1 = "be3051d08b78206fb5e688e8d70c9e84d0264117" uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" -version = "0.21.9" +version = "0.21.18" [[deps.MakieCore]] deps = ["ColorTypes", "GeometryBasics", "IntervalSets", "Observables"] -git-tree-sha1 = "b0e2e3473af351011e598f9219afb521121edd2b" +git-tree-sha1 = "9019b391d7d086e841cbeadc13511224bd029ab3" uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b" -version = "0.8.6" +version = "0.8.12" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -1534,6 +1680,7 @@ version = "0.4.2" [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +version = "1.11.0" [[deps.MathTeXEngine]] deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "Test", "UnicodeFun"] @@ -1550,13 +1697,18 @@ version = "1.1.9" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.2+1" +version = "2.28.6+0" + +[[deps.Measures]] +git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" +uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" +version = "0.3.2" [[deps.MetaGraphsNext]] deps = ["Graphs", "JLD2", "SimpleTraits"] -git-tree-sha1 = "a385fe5aa1384647e55c0c8773457b71e9b08518" +git-tree-sha1 = "d2ecf4a20f4ac694987dd08ac489b7f7ff805f35" uuid = "fa8bd995-216d-47f1-8a91-f3b68fbeb377" -version = "0.7.0" +version = "0.7.1" [[deps.MicroCollections]] deps = ["Accessors", "BangBang", "InitialValues"] @@ -1572,6 +1724,7 @@ version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" +version = "1.11.0" [[deps.Mocking]] deps = ["Compat", "ExprTools"] @@ -1587,7 +1740,19 @@ version = "0.3.4" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2023.1.10" +version = "2023.12.12" + +[[deps.MultipleTesting]] +deps = ["Distributions", "SpecialFunctions", "StatsBase"] +git-tree-sha1 = "1e98f8f732e7035c4333135b75605b74f3462b9b" +uuid = "f8716d33-7c4a-5097-896f-ce0ecbd3ef6b" +version = "0.6.0" + +[[deps.MultivariateStats]] +deps = ["Arpack", "Distributions", "LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI", "StatsBase"] +git-tree-sha1 = "816620e3aac93e5b5359e4fdaf23ca4525b00ddf" +uuid = "6f286f6a-111f-5878-ab1e-185364afe411" +version = "0.10.3" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1597,9 +1762,9 @@ version = "7.8.3" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "4a83c2e01027a0bfcea28589222f2df60b2e20cb" +git-tree-sha1 = "bdc9d30f151590aca0af22690f5ab7dc18a551cb" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.23" +version = "0.9.27" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1619,9 +1784,9 @@ version = "0.9.23" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" +git-tree-sha1 = "030ea22804ef91648f29b7ad3fc15fa49d0e6e71" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.2" +version = "1.0.3" [[deps.NameResolution]] deps = ["PrettyPrint"] @@ -1629,6 +1794,12 @@ git-tree-sha1 = "1a0fa0e9613f46c9b8c11eee38ebb4f590013c5e" uuid = "71a1bf82-56d0-4bbc-8a3c-48b961074391" version = "0.1.5" +[[deps.NearestNeighbors]] +deps = ["Distances", "StaticArrays"] +git-tree-sha1 = "8a3271d8309285f4db73b4f662b1b290c715e85e" +uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" +version = "0.4.21" + [[deps.Netpbm]] deps = ["FileIO", "ImageCore", "ImageMetadata"] git-tree-sha1 = "d92b107dbb887293622df7697a2223f9f8176fcd" @@ -1637,9 +1808,9 @@ version = "1.1.1" [[deps.NetworkLayout]] deps = ["GeometryBasics", "LinearAlgebra", "Random", "Requires", "StaticArrays"] -git-tree-sha1 = "91bb2fedff8e43793650e7a677ccda6e6e6e166b" +git-tree-sha1 = "ef79ce223dddbdaf709779842211d6d6e85c1514" uuid = "46757867-2c16-5918-afeb-47bfcb05e46a" -version = "0.4.6" +version = "0.4.9" weakdeps = ["Graphs"] [deps.NetworkLayout.extensions] @@ -1655,9 +1826,9 @@ uuid = "510215fc-4207-5dde-b226-833fc4488ee2" version = "0.5.5" [[deps.OffsetArrays]] -git-tree-sha1 = "1a27764e945a152f7ca7efa04de513d473e9542e" +git-tree-sha1 = "5e1897147d1ff8d98883cda2be2187dcf57d8f0c" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.14.1" +version = "1.15.0" weakdeps = ["Adapt"] [deps.OffsetArrays.extensions] @@ -1672,13 +1843,13 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.23+4" +version = "0.3.27+1" [[deps.OpenEXR]] deps = ["Colors", "FileIO", "OpenEXR_jll"] -git-tree-sha1 = "327f53360fdb54df7ecd01e96ef1983536d1e633" +git-tree-sha1 = "97db9e07fe2091882c765380ef58ec553074e9c7" uuid = "52e1d378-f018-4a11-a4be-720524705ac7" -version = "0.3.2" +version = "0.3.3" [[deps.OpenEXR_jll]] deps = ["Artifacts", "Imath_jll", "JLLWrappers", "Libdl", "Zlib_jll"] @@ -1689,13 +1860,13 @@ version = "3.2.4+0" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+2" +version = "0.8.1+4" [[deps.OpenML]] deps = ["ARFFFiles", "HTTP", "JSON", "Markdown", "Pkg", "Scratch"] -git-tree-sha1 = "6efb039ae888699d5a74fb593f6f3e10c7193e33" +git-tree-sha1 = "63603b2b367107e87dbceda4e33c67aed17e50e0" uuid = "8b6db2d4-7670-4922-a472-f9537c81ab66" -version = "0.3.1" +version = "0.3.2" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] @@ -1705,21 +1876,21 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a028ee3cb5641cccc4c24e90c36b0a4f7707bdf5" +git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.14+0" +version = "3.0.15+3" [[deps.OpenSpecFun_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "1346c9208249809840c91b26703912dff463d335" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" -version = "0.5.5+0" +version = "0.5.6+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89" +git-tree-sha1 = "ab7edad78cdef22099f43c54ef77ac63c2c9cc64" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.9.4" +version = "1.10.0" [deps.Optim.extensions] OptimMOIExt = "MathOptInterface" @@ -1734,9 +1905,9 @@ uuid = "91d4177d-7536-5919-b921-800302f37372" version = "1.3.3+0" [[deps.OrderedCollections]] -git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" +git-tree-sha1 = "12f1439c4f986bb868acda6ea33ebc78e19b95ad" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.6.3" +version = "1.7.0" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1745,9 +1916,9 @@ version = "10.42.0+1" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" +git-tree-sha1 = "966b85253e959ea89c53a9abebbf2e964fbf593b" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.31" +version = "0.11.32" [[deps.PNGFiles]] deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] @@ -1757,15 +1928,15 @@ version = "0.4.3" [[deps.PackageCompiler]] deps = ["Artifacts", "Glob", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "48d4429862157ad5500c4f61444db1b8c32e0a2b" +git-tree-sha1 = "5d13e5b70011762b74f86fc08385303589f80272" uuid = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d" -version = "2.1.17" +version = "2.2.0" [[deps.Packing]] deps = ["GeometryBasics"] -git-tree-sha1 = "ec3edfe723df33528e085e632414499f26650501" +git-tree-sha1 = "bc5bf2ea3d5351edf285a06b0016788a121ce92c" uuid = "19eb6ba3-879d-56ad-ad62-d5c202156566" -version = "0.5.0" +version = "0.5.1" [[deps.PaddedViews]] deps = ["OffsetArrays"] @@ -1775,9 +1946,9 @@ version = "0.5.12" [[deps.Pango_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e127b609fb9ecba6f201ba7ab753d5a605d53801" +git-tree-sha1 = "ed6834e95bd326c52d5675b4181386dfbe885afb" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.54.1+0" +version = "1.55.5+0" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -1791,6 +1962,11 @@ git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" version = "2.8.1" +[[deps.Pipe]] +git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" +uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" +version = "1.3.0" + [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b" @@ -1798,9 +1974,13 @@ uuid = "30392449-352a-5448-841d-b1acce4e97dc" version = "0.43.4+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.10.0" +version = "1.11.0" +weakdeps = ["REPL"] + + [deps.Pkg.extensions] + REPLExt = "REPL" [[deps.PkgVersion]] deps = ["Pkg"] @@ -1808,11 +1988,37 @@ git-tree-sha1 = "f9501cc0430a26bc3d156ae1b5b0c1b47af4d6da" uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688" version = "0.3.3" +[[deps.PlotThemes]] +deps = ["PlotUtils", "Statistics"] +git-tree-sha1 = "41031ef3a1be6f5bbbf3e8073f210556daeae5ca" +uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" +version = "3.3.0" + [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "7b1a9df27f072ac4c9c7cbe5efb198489258d1f5" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"] +git-tree-sha1 = "3ca9a356cd2e113c420f2c13bea19f8d3fb1cb18" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.4.1" +version = "1.4.3" + +[[deps.Plots]] +deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] +git-tree-sha1 = "dae01f8c2e069a683d3a6e17bbae5070ab94786f" +uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" +version = "1.40.9" + + [deps.Plots.extensions] + FileIOExt = "FileIO" + GeometryBasicsExt = "GeometryBasics" + IJuliaExt = "IJulia" + ImageInTerminalExt = "ImageInTerminal" + UnitfulExt = "Unitful" + + [deps.Plots.weakdeps] + FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" + GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326" + IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a" + ImageInTerminal = "d8c32880-2388-543b-8c61-d9f865259254" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] @@ -1861,13 +2067,14 @@ version = "0.4.2" [[deps.PrettyTables]] deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "66b20dd35966a748321d3b2537c4584cf40387c7" +git-tree-sha1 = "1101cd475833706e4d0e7b122218257178f48f34" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.3.2" +version = "2.4.0" [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" +version = "1.11.0" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] @@ -1876,21 +2083,45 @@ uuid = "92933f4c-e287-5a05-a399-4b506db050ca" version = "1.10.2" [[deps.PtrArrays]] -git-tree-sha1 = "77a42d78b6a92df47ab37e177b2deac405e1c88f" +git-tree-sha1 = "1d36ef11a9aaf1e8b74dacc6a731dd1de8fd493d" uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" -version = "1.2.1" +version = "1.3.0" [[deps.QOI]] deps = ["ColorTypes", "FileIO", "FixedPointNumbers"] -git-tree-sha1 = "18e8f4d1426e965c7b532ddd260599e1510d26ce" +git-tree-sha1 = "8b3fc30bc0390abdce15f8822c889f669baed73d" uuid = "4b34888f-f399-49d4-9bb3-47ed5cae4e65" -version = "1.0.0" +version = "1.0.1" + +[[deps.Qt6Base_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"] +git-tree-sha1 = "492601870742dcd38f233b23c3ec629628c1d724" +uuid = "c0090381-4147-56d7-9ebc-da0b1113ec56" +version = "6.7.1+1" + +[[deps.Qt6Declarative_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6ShaderTools_jll"] +git-tree-sha1 = "e5dd466bf2569fe08c91a2cc29c1003f4797ac3b" +uuid = "629bc702-f1f5-5709-abd5-49b8460ea067" +version = "6.7.1+2" + +[[deps.Qt6ShaderTools_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll"] +git-tree-sha1 = "1a180aeced866700d4bebc3120ea1451201f16bc" +uuid = "ce943373-25bb-56aa-8eca-768745ed7b5a" +version = "6.7.1+1" + +[[deps.Qt6Wayland_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6Declarative_jll"] +git-tree-sha1 = "729927532d48cf79f49070341e1d918a65aba6b0" +uuid = "e99dba38-086e-5de3-a5b1-6e4c66e897c3" +version = "6.7.1+1" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "1d587203cf851a51bf1ea31ad7ff89eff8d625ea" +git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.11.0" +version = "2.11.1" [deps.QuadGK.extensions] QuadGKEnzymeExt = "Enzyme" @@ -1899,12 +2130,14 @@ version = "2.11.0" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" [[deps.REPL]] -deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] +deps = ["InteractiveUtils", "Markdown", "Sockets", "StyledStrings", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" +version = "1.11.0" [[deps.Random]] deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +version = "1.11.0" [[deps.RangeArrays]] git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5" @@ -1933,6 +2166,12 @@ git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" version = "1.3.4" +[[deps.RecipesPipeline]] +deps = ["Dates", "NaNMath", "PlotUtils", "PrecompileTools", "RecipesBase"] +git-tree-sha1 = "45cf9fd0ca5839d06ef333c8201714e888486342" +uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" +version = "0.6.12" + [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" @@ -1952,29 +2191,31 @@ version = "1.3.0" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" +git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.1" +version = "0.8.0" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e60724fd3beea548353984dc61c943ecddb0e29a" +git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.3+0" +version = "0.5.1+0" [[deps.Roots]] -deps = ["Accessors", "ChainRulesCore", "CommonSolve", "Printf"] -git-tree-sha1 = "12e0a0e549c8545db615a2ec48664d56e1aad44d" +deps = ["Accessors", "CommonSolve", "Printf"] +git-tree-sha1 = "f233e0a3de30a6eed170b8e1be0440f732fdf456" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.1.7" +version = "2.2.4" [deps.Roots.extensions] + RootsChainRulesCoreExt = "ChainRulesCore" RootsForwardDiffExt = "ForwardDiff" RootsIntervalRootFindingExt = "IntervalRootFinding" RootsSymPyExt = "SymPy" RootsSymPyPythonCallExt = "SymPyPythonCall" [deps.Roots.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807" SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" @@ -1991,9 +2232,9 @@ version = "0.7.0" [[deps.SIMD]] deps = ["PrecompileTools"] -git-tree-sha1 = "2803cab51702db743f3fda07dd1745aadfbf43bd" +git-tree-sha1 = "fea870727142270bdf7624ad675901a1ee3b4c87" uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.5.0" +version = "3.7.1" [[deps.SIMDTypes]] git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" @@ -2014,9 +2255,9 @@ version = "1.6.1" [[deps.SQLite_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "004fffbe2711abdc7263a980bbb1af9620781dd9" +git-tree-sha1 = "e84fab7d16107342d7638fbd519151d9a0d80720" uuid = "76ed43ae-9a5d-5a62-8c75-30186b810ce8" -version = "3.45.3+0" +version = "3.47.2+2" [[deps.ScientificTypes]] deps = ["CategoricalArrays", "ColorTypes", "Dates", "Distributions", "PrettyTables", "Reexport", "ScientificTypesBase", "StatisticalTraits", "Tables"] @@ -2029,6 +2270,12 @@ git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" uuid = "30f210dd-8aff-4c5f-94ba-8e64358c1161" version = "3.0.0" +[[deps.ScopedValues]] +deps = ["HashArrayMappedTries", "Logging"] +git-tree-sha1 = "1147f140b4c8ddab224c94efa9569fc23d63ab44" +uuid = "7e506255-f358-4e82-b7e4-beb19740aa63" +version = "1.3.0" + [[deps.Scratch]] deps = ["Dates"] git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" @@ -2037,12 +2284,13 @@ version = "1.2.1" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "ff11acffdb082493657550959d4feb4b6149e73a" +git-tree-sha1 = "712fb0231ee6f9120e005ccd56297abbc053e7e0" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.4.5" +version = "1.4.8" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" +version = "1.11.0" [[deps.Setfield]] deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] @@ -2059,6 +2307,7 @@ version = "0.4.1" [[deps.SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" +version = "1.11.0" [[deps.ShiftedArrays]] git-tree-sha1 = "503688b59397b3307443af35cd953a13e8005c16" @@ -2083,9 +2332,9 @@ uuid = "73760f76-fbc4-59ce-8f25-708e95d2df96" version = "0.4.0" [[deps.SimpleBufferStream]] -git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.1.0" +version = "1.2.0" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -2101,12 +2350,13 @@ version = "0.1.3" [[deps.SnpArrays]] deps = ["Adapt", "CSV", "CodecBzip2", "CodecXz", "CodecZlib", "CodecZstd", "DataFrames", "DelimitedFiles", "Glob", "LinearAlgebra", "LoopVectorization", "Missings", "Mmap", "Printf", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Tables", "TranscodingStreams", "VariantCallFormat", "VectorizationBase"] -git-tree-sha1 = "d81de62a0acdbfd7d7ff3d64403eccf06c2fe986" +git-tree-sha1 = "810c0a75a336d63cb2b51561f1c1e3ccf6dbc2ad" uuid = "4e780e97-f5bf-4111-9dc4-b70aaf691b06" -version = "0.3.21" +version = "0.3.22" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" +version = "1.11.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] @@ -2117,7 +2367,7 @@ version = "1.2.1" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -version = "1.10.0" +version = "1.11.0" [[deps.SparseInverseSubset]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] @@ -2127,15 +2377,15 @@ version = "0.1.2" [[deps.SparseMatricesCSR]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "38677ca58e80b5cad2382e5a1848f93b054ad28d" +git-tree-sha1 = "6bc0c4cca30222586bde1ec5a0d9a3c6aaa51833" uuid = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1" -version = "0.6.7" +version = "0.6.8" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14" +git-tree-sha1 = "64cca0c26b4f31ba18f13f6c12af7c85f478cfde" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.4.0" +version = "2.5.0" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -2184,9 +2434,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50" +git-tree-sha1 = "47091a0340a675c738b1304b58161f3b0839d454" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.7" +version = "1.9.10" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -2200,9 +2450,9 @@ version = "1.4.3" [[deps.StatisticalMeasures]] deps = ["CategoricalArrays", "CategoricalDistributions", "Distributions", "LearnAPI", "LinearAlgebra", "MacroTools", "OrderedCollections", "PrecompileTools", "ScientificTypesBase", "StatisticalMeasuresBase", "Statistics", "StatsBase"] -git-tree-sha1 = "8b5a165b0ee2b361d692636bfb423b19abfd92b3" +git-tree-sha1 = "c1d4318fa41056b839dfbb3ee841f011fa6e8518" uuid = "a19d573c-0a75-4610-95b3-7071388c7541" -version = "0.1.6" +version = "0.1.7" [deps.StatisticalMeasures.extensions] LossFunctionsExt = "LossFunctions" @@ -2225,9 +2475,14 @@ uuid = "64bff920-2084-43da-a3e6-9bb72801c0c9" version = "3.4.0" [[deps.Statistics]] -deps = ["LinearAlgebra", "SparseArrays"] +deps = ["LinearAlgebra"] +git-tree-sha1 = "ae3bb1eb3bba077cd276bc5cfc337cc65c3075c0" uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.10.0" +version = "1.11.1" +weakdeps = ["SparseArrays"] + + [deps.Statistics.extensions] + SparseArraysExt = ["SparseArrays"] [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -2236,16 +2491,16 @@ 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" +deps = ["AliasTables", "DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] +git-tree-sha1 = "29321314c920c26684834965ec2ce0dacc9cf8e5" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.34.3" +version = "0.34.4" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" +git-tree-sha1 = "b423576adc27097764a90e163157bcfc9acf0f46" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.1" +version = "1.3.2" weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] @@ -2258,6 +2513,12 @@ git-tree-sha1 = "9022bcaa2fc1d484f1326eaa4db8db543ca8c66d" uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" version = "0.7.4" +[[deps.StatsPlots]] +deps = ["AbstractFFTs", "Clustering", "DataStructures", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] +git-tree-sha1 = "3b1dcbf62e469a67f6733ae493401e53d92ff543" +uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" +version = "0.15.7" + [[deps.StringEncodings]] deps = ["Libiconv_jll"] git-tree-sha1 = "b765e46ba27ecf6b44faf70df40c57aa3a547dcb" @@ -2266,20 +2527,26 @@ version = "0.3.7" [[deps.StringManipulation]] deps = ["PrecompileTools"] -git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" +git-tree-sha1 = "a6b1675a536c5ad1a60e5a5153e1fee12eb146e3" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.3.4" +version = "0.4.0" + +[[deps.StringViews]] +git-tree-sha1 = "ec4bf39f7d25db401bcab2f11d2929798c0578e5" +uuid = "354b36f9-a18e-4713-926e-db85100087ba" +version = "1.3.4" [[deps.StructArrays]] deps = ["ConstructionBase", "DataAPI", "Tables"] -git-tree-sha1 = "f4dc295e983502292c4c3f951dbb4e985e35b3be" +git-tree-sha1 = "9537ef82c42cdd8c5d443cbc359110cbb36bae10" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.18" -weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"] +version = "0.6.21" +weakdeps = ["Adapt", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "SparseArrays", "StaticArrays"] [deps.StructArrays.extensions] StructArraysAdaptExt = "Adapt" - StructArraysGPUArraysCoreExt = "GPUArraysCore" + StructArraysGPUArraysCoreExt = ["GPUArraysCore", "KernelAbstractions"] + StructArraysLinearAlgebraExt = "LinearAlgebra" StructArraysSparseArraysExt = "SparseArrays" StructArraysStaticArraysExt = "StaticArrays" @@ -2289,6 +2556,10 @@ git-tree-sha1 = "159331b30e94d7b11379037feeb9b690950cace8" uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" version = "1.11.0" +[[deps.StyledStrings]] +uuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b" +version = "1.11.0" + [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" @@ -2296,7 +2567,7 @@ 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" +version = "7.7.0+0" [[deps.TMLE]] deps = ["AbstractDifferentiation", "AutoHashEquals", "CategoricalArrays", "Combinatorics", "Distributions", "GLM", "Graphs", "HypothesisTests", "LogExpFunctions", "MLJBase", "MLJGLMInterface", "MLJModels", "MetaGraphsNext", "Missings", "OrderedCollections", "PrecompileTools", "Random", "SplitApplyCombine", "Statistics", "TableOperations", "Tables", "Zygote"] @@ -2322,9 +2593,9 @@ version = "1.0.3" [[deps.TZJData]] deps = ["Artifacts"] -git-tree-sha1 = "1607ad46cf8d642aa779a1d45af1c8620dbf6915" +git-tree-sha1 = "006a327222dda856e2304959e566ff0104ac8594" uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" -version = "1.2.0+2024a" +version = "1.3.1+2024b" [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] @@ -2358,6 +2629,7 @@ version = "0.1.1" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +version = "1.11.0" [[deps.TextWrap]] git-tree-sha1 = "43044b737fa70bc12f6105061d3da38f881a3e3c" @@ -2372,15 +2644,15 @@ version = "0.5.2" [[deps.TiffImages]] deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "SIMD", "UUIDs"] -git-tree-sha1 = "bc7fd5c91041f44636b2c134041f7e5263ce58ae" +git-tree-sha1 = "3c0faa42f2bd3c6d994b06286bba2328eae34027" uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" -version = "0.10.0" +version = "0.11.2" [[deps.TimeZones]] -deps = ["Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] -git-tree-sha1 = "b92aebdd3555f3a7e3267cf17702033c2814ef48" +deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "fcbcffdc11524d08523e92ae52214b29d90b50bb" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.18.0" +version = "1.20.0" weakdeps = ["RecipesBase"] [deps.TimeZones.extensions] @@ -2393,12 +2665,13 @@ uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" version = "0.9.13" [[deps.Transducers]] -deps = ["Accessors", "Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"] -git-tree-sha1 = "5215a069867476fc8e3469602006b9670e68da23" +deps = ["Accessors", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"] +git-tree-sha1 = "7deeab4ff96b85c5f72c824cae53a1398da3d1cb" uuid = "28d57a85-8fef-5791-bfe6-a80928e7c999" -version = "0.4.82" +version = "0.4.84" [deps.Transducers.extensions] + TransducersAdaptExt = "Adapt" TransducersBlockArraysExt = "BlockArrays" TransducersDataFramesExt = "DataFrames" TransducersLazyArraysExt = "LazyArrays" @@ -2406,6 +2679,7 @@ version = "0.4.82" TransducersReferenceablesExt = "Referenceables" [deps.Transducers.weakdeps] + Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" @@ -2425,6 +2699,7 @@ version = "1.5.1" [[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" +version = "1.11.0" [[deps.UnPack]] git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" @@ -2433,6 +2708,7 @@ version = "1.0.2" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" +version = "1.11.0" [[deps.UnicodeFun]] deps = ["REPL"] @@ -2442,25 +2718,34 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" +git-tree-sha1 = "c0667a8e676c53d390a09dc6870b3d8d6650e2bf" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.21.0" +version = "1.22.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] ConstructionBaseUnitfulExt = "ConstructionBase" InverseFunctionsUnitfulExt = "InverseFunctions" +[[deps.UnitfulLatexify]] +deps = ["LaTeXStrings", "Latexify", "Unitful"] +git-tree-sha1 = "975c354fcd5f7e1ddcc1f1a23e6e091d99e99bc8" +uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" +version = "1.6.4" + [[deps.UnsafeAtomics]] -git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" +git-tree-sha1 = "b13c4edda90890e5b04ba24e20a310fbe6f249ff" uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" -version = "0.2.1" +version = "0.3.0" +weakdeps = ["LLVM"] -[[deps.UnsafeAtomicsLLVM]] -deps = ["LLVM", "UnsafeAtomics"] -git-tree-sha1 = "bf2c553f25e954a9b38c9c0593a59bb13113f9e5" -uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" -version = "0.1.5" + [deps.UnsafeAtomics.extensions] + UnsafeAtomicsLLVM = ["LLVM"] + +[[deps.Unzip]] +git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" +uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" +version = "0.2.0" [[deps.VariantCallFormat]] deps = ["Automa", "BGZFStreams", "BioGenerics", "BufferedStreams"] @@ -2470,9 +2755,27 @@ version = "0.5.6" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "e7f5b81c65eb858bed630fe006837b935518aca5" +git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.70" +version = "0.21.71" + +[[deps.Vulkan_Loader_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Wayland_jll", "Xorg_libX11_jll", "Xorg_libXrandr_jll", "xkbcommon_jll"] +git-tree-sha1 = "2f0486047a07670caad3a81a075d2e518acc5c59" +uuid = "a44049a8-05dd-5a78-86c9-5fde0876e88c" +version = "1.3.243+0" + +[[deps.Wayland_jll]] +deps = ["Artifacts", "EpollShim_jll", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] +git-tree-sha1 = "85c7811eddec9e7f22615371c3cc81a504c508ee" +uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" +version = "1.21.0+2" + +[[deps.Wayland_protocols_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "5db3e9d307d32baba7067b13fc7b5aa6edd4a19a" +uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" +version = "1.36.0+0" [[deps.WeakRefStrings]] deps = ["DataAPI", "InlineStrings", "Parsers"] @@ -2480,6 +2783,18 @@ git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" version = "1.4.2" +[[deps.WebP]] +deps = ["CEnum", "ColorTypes", "FileIO", "FixedPointNumbers", "ImageCore", "libwebp_jll"] +git-tree-sha1 = "aa1ca3c47f119fbdae8770c29820e5e6119b83f2" +uuid = "e3aaa7dc-3e4b-44e0-be63-ffb868ccd7c1" +version = "0.1.3" + +[[deps.Widgets]] +deps = ["Colors", "Dates", "Observables", "OrderedCollections"] +git-tree-sha1 = "e9aeb174f95385de31e70bd15fa066a505ea82b9" +uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62" +version = "0.6.7" + [[deps.WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] git-tree-sha1 = "c1a7aa6219628fcd757dede0ca95e245c5cd9511" @@ -2513,69 +2828,165 @@ version = "2.0.1+0" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "1165b0443d0eca63ac1e32b8c0eb69ed2f4f8127" +git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.13.3+0" +version = "2.13.5+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "a54ee957f4c86b526460a720dbc882fa5edcbefc" +git-tree-sha1 = "7d1671acbe47ac88e981868a078bd6b4e27c5191" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.41+0" +version = "1.1.42+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632" +git-tree-sha1 = "beef98d5aad604d9e7d60b2ece5181f7888e2fd6" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.4.6+0" +version = "5.6.4+0" + +[[deps.Xorg_libICE_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "326b4fea307b0b39892b3e85fa451692eda8d46c" +uuid = "f67eecfb-183a-506d-b269-f58e52b52d7c" +version = "1.1.1+0" + +[[deps.Xorg_libSM_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libICE_jll"] +git-tree-sha1 = "3796722887072218eabafb494a13c963209754ce" +uuid = "c834827a-8449-5923-a945-d239c165b7dd" +version = "1.2.4+0" [[deps.Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] -git-tree-sha1 = "afead5aba5aa507ad5a3bf01f58f82c8d1403495" +git-tree-sha1 = "9dafcee1d24c4f024e7edc92603cedba72118283" uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" -version = "1.8.6+0" +version = "1.8.6+3" [[deps.Xorg_libXau_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6035850dcc70518ca32f012e46015b9beeda49d8" +git-tree-sha1 = "e9216fdcd8514b7072b43653874fd688e4c6c003" uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.11+0" +version = "1.0.12+0" + +[[deps.Xorg_libXcursor_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] +git-tree-sha1 = "807c226eaf3651e7b2c468f687ac788291f9a89b" +uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" +version = "1.2.3+0" [[deps.Xorg_libXdmcp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "34d526d318358a859d7de23da945578e8e8727b7" +git-tree-sha1 = "89799ae67c17caa5b3b5a19b8469eeee474377db" uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.4+0" +version = "1.1.5+0" [[deps.Xorg_libXext_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "d2d1a5c49fae4ba39983f63de6afcbea47194e85" +git-tree-sha1 = "d7155fea91a4123ef59f42c4afb5ab3b4ca95058" uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" -version = "1.3.6+0" +version = "1.3.6+3" + +[[deps.Xorg_libXfixes_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "6fcc21d5aea1a0b7cce6cab3e62246abd1949b86" +uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" +version = "6.0.0+0" + +[[deps.Xorg_libXi_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] +git-tree-sha1 = "984b313b049c89739075b8e2a94407076de17449" +uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" +version = "1.8.2+0" + +[[deps.Xorg_libXinerama_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXext_jll"] +git-tree-sha1 = "a1a7eaf6c3b5b05cb903e35e8372049b107ac729" +uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" +version = "1.1.5+0" + +[[deps.Xorg_libXrandr_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXext_jll", "Xorg_libXrender_jll"] +git-tree-sha1 = "b6f664b7b2f6a39689d822a6300b14df4668f0f4" +uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" +version = "1.5.4+0" [[deps.Xorg_libXrender_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" +git-tree-sha1 = "a490c6212a0e90d2d55111ac956f7c4fa9c277a6" uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.11+0" +version = "0.9.11+1" [[deps.Xorg_libpthread_stubs_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8fdda4c692503d44d04a0603d9ac0982054635f9" +git-tree-sha1 = "c57201109a9e4c0585b208bb408bc41d205ac4e9" uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.1+0" +version = "0.1.2+0" [[deps.Xorg_libxcb_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "bcd466676fef0878338c61e655629fa7bbc69d8e" +git-tree-sha1 = "1a74296303b6524a0472a8cb12d3d87a78eb3612" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.17.0+0" +version = "1.17.0+3" + +[[deps.Xorg_libxkbfile_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "dbc53e4cf7701c6c7047c51e17d6e64df55dca94" +uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" +version = "1.1.2+1" + +[[deps.Xorg_xcb_util_cursor_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_jll", "Xorg_xcb_util_renderutil_jll"] +git-tree-sha1 = "04341cb870f29dcd5e39055f895c39d016e18ccd" +uuid = "e920d4aa-a673-5f3a-b3d7-f755a4d47c43" +version = "0.1.4+0" + +[[deps.Xorg_xcb_util_image_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" +uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" +version = "0.4.0+1" + +[[deps.Xorg_xcb_util_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] +git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" +uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" +version = "0.4.0+1" + +[[deps.Xorg_xcb_util_keysyms_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" +uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" +version = "0.4.0+1" + +[[deps.Xorg_xcb_util_renderutil_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" +uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" +version = "0.3.9+1" + +[[deps.Xorg_xcb_util_wm_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] +git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" +uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" +version = "0.4.1+1" + +[[deps.Xorg_xkbcomp_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"] +git-tree-sha1 = "ab2221d309eda71020cdda67a973aa582aa85d69" +uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" +version = "1.4.6+1" + +[[deps.Xorg_xkeyboard_config_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"] +git-tree-sha1 = "691634e5453ad362044e2ad653e79f3ee3bb98c3" +uuid = "33bec58e-1273-512f-9401-5d533626f822" +version = "2.39.0+0" [[deps.Xorg_xtrans_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" +git-tree-sha1 = "6dba04dbfb72ae3ebe5418ba33d087ba8aa8cb00" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.5.0+0" +version = "1.5.1+0" [[deps.YAML]] deps = ["Base64", "Dates", "Printf", "StringEncodings"] @@ -2590,15 +3001,15 @@ version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b" +git-tree-sha1 = "622cf78670d067c738667aaa96c553430b65e269" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.6+0" +version = "1.5.7+0" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "19c586905e78a26f7e4e97f81716057bd6b1bc54" +git-tree-sha1 = "0b3c944f5d2d8b466c5d20a84c229c17c528f49e" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.70" +version = "0.6.75" [deps.Zygote.extensions] ZygoteColorsExt = "Colors" @@ -2612,9 +3023,21 @@ version = "0.6.70" [[deps.ZygoteRules]] deps = ["ChainRulesCore", "MacroTools"] -git-tree-sha1 = "27798139afc0a2afa7b1824c206d5e87ea587a00" +git-tree-sha1 = "434b3de333c75fc446aa0d19fc394edafd07ab08" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.5" +version = "0.2.7" + +[[deps.eudev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] +git-tree-sha1 = "431b678a28ebb559d224c0b6b6d01afce87c51ba" +uuid = "35ca27e7-8b34-5b7f-bca9-bdc33f59eb06" +version = "3.2.9+0" + +[[deps.fzf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6e50f145003024df4f5cb96c7fce79466741d601" +uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" +version = "0.56.3+0" [[deps.glmnet_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -2622,6 +3045,12 @@ git-tree-sha1 = "31adae3b983b579a1fbd7cfd43a4bc0d224c2f5a" uuid = "78c6b45d-5eaf-5d68-bcfb-a5a2cb06c27f" version = "2.0.13+0" +[[deps.gperf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "0ba42241cb6809f1a278d0bcb976e0483c3f1f2d" +uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" +version = "3.1.1+1" + [[deps.isoband_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c" @@ -2630,9 +3059,9 @@ version = "0.2.3+0" [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" +git-tree-sha1 = "522c1df09d05a71785765d19c9524661234738e9" uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.9.0+0" +version = "3.11.0+0" [[deps.libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] @@ -2643,7 +3072,19 @@ version = "0.15.2+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+1" +version = "5.11.0+0" + +[[deps.libdecor_jll]] +deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] +git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" +uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" +version = "0.2.2+0" + +[[deps.libevdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22" +uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" +version = "1.11.0+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2651,17 +3092,23 @@ git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" version = "2.0.3+0" +[[deps.libinput_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] +git-tree-sha1 = "ad50e5b90f222cfe78aa3d5183a20a12de1322ce" +uuid = "36db933b-70db-51c0-b978-0f229ee0e533" +version = "1.18.0+0" + [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" +git-tree-sha1 = "d7b5bbf1efbafb5eca466700949625e07533aff2" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.43+1" +version = "1.6.45+1" [[deps.libsixel_jll]] -deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"] -git-tree-sha1 = "d4f63314c8aa1e48cd22aa0c17ed76cd1ae48c3c" +deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "libpng_jll"] +git-tree-sha1 = "c1733e347283df07689d71d61e14be986e49e47a" uuid = "075b6546-f08a-558a-be8f-8157d0f608a5" -version = "1.10.3+0" +version = "1.10.5+0" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] @@ -2669,10 +3116,22 @@ git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" version = "1.3.7+2" +[[deps.libwebp_jll]] +deps = ["Artifacts", "Giflib_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libglvnd_jll", "Libtiff_jll", "libpng_jll"] +git-tree-sha1 = "d2408cac540942921e7bd77272c32e58c33d8a77" +uuid = "c5f90fcd-3b7e-5836-afba-fc50a0988cb2" +version = "1.5.0+0" + +[[deps.mtdev_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11" +uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e" +version = "1.1.6+0" + [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.52.0+1" +version = "1.59.0+0" [[deps.oneTBB_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -2686,13 +3145,19 @@ uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" version = "17.4.0+2" [[deps.x264_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "35976a1216d6c066ea32cba2150c4fa682b276fc" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "10164.0.0+0" +version = "2021.5.5+0" [[deps.x265_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "dcc541bb19ed5b0ede95581fb2e41ecf179527d2" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.6.0+0" +version = "3.5.0+0" + +[[deps.xkbcommon_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] +git-tree-sha1 = "63406453ed9b33a0df95d570816d5366c92b7809" +uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" +version = "1.4.1+2" diff --git a/Project.toml b/Project.toml index f823dd3..586cf04 100644 --- a/Project.toml +++ b/Project.toml @@ -13,17 +13,24 @@ CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597" Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +Glob = "c27321d9-0574-5035-807b-f59d2c89b15c" +HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3" HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5" JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819" +JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2" Mmap = "a63ad114-7e13-5084-954f-fe012c677804" +MultipleTesting = "f8716d33-7c4a-5097-896f-ce0ecbd3ef6b" OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" PackageCompiler = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d" +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b" SnpArrays = "4e780e97-f5bf-4111-9dc4-b70aaf691b06" StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" +StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" TMLE = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf" TMLECLI = "2573d147-4098-46ba-9db2-8608d210ccac" YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" @@ -37,12 +44,19 @@ CairoMakie = "0.12" CategoricalArrays = "0.10" Combinatorics = "1.0" DataFrames = "1.2" +Glob = "1.3.1" +HTTP = "1.10.15" +JSON3 = "1.14.1" +MKL = "0.7" +MultipleTesting = "0.6.0" OrderedCollections = "1.6.3" PackageCompiler = "2.1.17" +Plots = "1.40.9" SnpArrays = "0.3" StableRNGs = "1.0.1" Statistics = "1.10" +StatsBase = "0.34.4" +StatsPlots = "0.15.7" TMLE = "0.17" -MKL = "0.7" YAML = "0.4.9" julia = "1.10, 1" From 99976c1f9299946a7eff4c19ac66046a71849e9a Mon Sep 17 00:00:00 2001 From: joshua-slaughter Date: Wed, 23 Apr 2025 11:02:16 +0100 Subject: [PATCH 13/17] Errors in Project.toml --- Project.toml | 2 -- 1 file changed, 2 deletions(-) diff --git a/Project.toml b/Project.toml index 4a20155..281c38c 100644 --- a/Project.toml +++ b/Project.toml @@ -32,7 +32,6 @@ StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" -StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" TMLE = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf" TMLECLI = "2573d147-4098-46ba-9db2-8608d210ccac" YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" @@ -51,7 +50,6 @@ HTTP = "1.10.15" JSON3 = "1.14.1" MKL = "0.7" MultipleTesting = "0.6.0" -MKL = "0.7" OrderedCollections = "1.6.3" PackageCompiler = "2.1.17" Plots = "1.40.9" From e01696430c359b39fd9e63711101f0047f9d94fc Mon Sep 17 00:00:00 2001 From: Joshua Slaughter Date: Mon, 12 May 2025 11:45:39 +0100 Subject: [PATCH 14/17] allow duplicate variant names for estimation --- Manifest.toml | 77 ++++++++++++++++++++++++++++++++++++--- Project.toml | 1 + src/inputs_from_config.jl | 2 +- 3 files changed, 73 insertions(+), 7 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index a678939..e4c5124 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -2,7 +2,7 @@ julia_version = "1.10.4" manifest_format = "2.0" -project_hash = "239580f1dc316e090dbf5ddb8739a2d1e3336f92" +project_hash = "026a4a228f2fe6f789f0bbad2d45493e7ed45f99" [[deps.ARFFFiles]] deps = ["CategoricalArrays", "Dates", "Parsers", "Tables"] @@ -936,6 +936,24 @@ git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" version = "1.0.2" +[[deps.HDF5]] +deps = ["Compat", "HDF5_jll", "Libdl", "MPIPreferences", "Mmap", "Preferences", "Printf", "Random", "Requires", "UUIDs"] +git-tree-sha1 = "e856eef26cf5bf2b0f95f8f4fc37553c72c8641c" +uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" +version = "0.17.2" + + [deps.HDF5.extensions] + MPIExt = "MPI" + + [deps.HDF5.weakdeps] + MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" + +[[deps.HDF5_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"] +git-tree-sha1 = "82a471768b513dc39e471540fdadc84ff80ff997" +uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" +version = "1.14.3+3" + [[deps.HTTP]] deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" @@ -954,6 +972,12 @@ git-tree-sha1 = "8e070b599339d622e9a081d17230d74a5c473293" uuid = "3e5b6fbb-0976-4d2c-9146-d79de83f2fb0" version = "0.1.17" +[[deps.Hwloc_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "50aedf345a709ab75872f80a2779568dc0bb461b" +uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" +version = "2.11.2+3" + [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb" @@ -1137,9 +1161,9 @@ version = "1.0.0" [[deps.JLD2]] deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "PrecompileTools", "Requires", "TranscodingStreams"] -git-tree-sha1 = "a0746c21bdc986d0dc293efa6b1faee112c37c28" +git-tree-sha1 = "89e1e5c3d43078d42eed2306cab2a11b13e5c6ae" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.53" +version = "0.4.54" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] @@ -1503,6 +1527,24 @@ git-tree-sha1 = "b45738c2e3d0d402dffa32b2c1654759a2ac35a4" uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" version = "0.4.4" +[[deps.MPICH_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "7715e65c47ba3941c502bffb7f266a41a7f54423" +uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" +version = "4.2.3+0" + +[[deps.MPIPreferences]] +deps = ["Libdl", "Preferences"] +git-tree-sha1 = "c105fe467859e7f6e9a852cb15cb4301126fac07" +uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267" +version = "0.1.11" + +[[deps.MPItrampoline_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "70e830dab5d0775183c99fc75e4c24c614ed7142" +uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" +version = "5.5.1+2" + [[deps.MacroTools]] deps = ["Markdown", "Random"] git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" @@ -1564,6 +1606,12 @@ git-tree-sha1 = "44d32db644e84c75dab479f1bc15ee76a1a3618f" uuid = "128add7d-3638-4c79-886c-908ea0c25c34" version = "0.2.0" +[[deps.MicrosoftMPI_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "bc95bf4149bf535c09602e3acdf950d9b4376227" +uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf" +version = "10.1.4+3" + [[deps.Missings]] deps = ["DataAPI"] git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d" @@ -1697,6 +1745,12 @@ git-tree-sha1 = "6efb039ae888699d5a74fb593f6f3e10c7193e33" uuid = "8b6db2d4-7670-4922-a472-f9537c81ab66" version = "0.3.1" +[[deps.OpenMPI_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "e25c1778a98e34219a00455d6e4384e017ea9762" +uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" +version = "4.1.6+0" + [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] git-tree-sha1 = "38cb508d080d21dc1128f7fb04f20387ed4c0af4" @@ -2300,15 +2354,20 @@ version = "7.2.1+1" [[deps.TMLE]] 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 = "2928dc0b1c3e26d8dcaaa7585dedefe33f687020" +git-tree-sha1 = "01d5f62021293388d0d7a1fb6b3618312d543a33" uuid = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf" -version = "0.17.0" -weakdeps = ["JSON", "YAML"] +version = "0.17.1" [deps.TMLE.extensions] + CausalTablesExt = "CausalTables" JSONExt = "JSON" YAMLExt = "YAML" + [deps.TMLE.weakdeps] + CausalTables = "6af48e0c-efc2-4bf7-a92f-a553ccf79fd6" + JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" + YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" + [[deps.TMLECLI]] deps = ["ArgParse", "Arrow", "CSV", "CategoricalArrays", "Combinatorics", "Configurations", "DataFrames", "EvoTrees", "GLMNet", "JLD2", "JSON", "MKL", "MLJ", "MLJBase", "MLJLinearModels", "MLJModelInterface", "MLJModels", "MLJXGBoostInterface", "Mmap", "PackageCompiler", "Random", "Serialization", "TMLE", "Tables", "YAML"] git-tree-sha1 = "eb8a7aa2a17c0dd2fb165dd79a860c1aea0df55a" @@ -2628,6 +2687,12 @@ git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c" uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4" version = "0.2.3+0" +[[deps.libaec_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "46bf7be2917b59b761247be3f317ddf75e50e997" +uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0" +version = "1.1.2+2" + [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" diff --git a/Project.toml b/Project.toml index ebe1416..cdac9ef 100644 --- a/Project.toml +++ b/Project.toml @@ -13,6 +13,7 @@ CategoricalArrays = "324d7699-5711-5eae-9e2f-1d82baa6b597" Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" +HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5" JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819" LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" diff --git a/src/inputs_from_config.jl b/src/inputs_from_config.jl index f6d6d6b..3d638c0 100644 --- a/src/inputs_from_config.jl +++ b/src/inputs_from_config.jl @@ -234,7 +234,7 @@ end function get_genotypes_from_beds(bedprefix, outprefix) snpdata = read_bed_chromosome(bedprefix) - genotypes = DataFrame(convert(Matrix{UInt8}, snpdata.snparray), snpdata.snp_info."snpid") + genotypes = DataFrame(convert(Matrix{UInt8}, snpdata.snparray), snpdata.snp_info."snpid", makeunique=true) genotype_map = Union{UInt8, Missing}[0, missing, 1, 2] for col in names(genotypes) genotypes[!, col] = [genotype_map[x+1] for x in genotypes[!, col]] From 5ede1f05505044748ec8dd02a5b978b92b53db8e Mon Sep 17 00:00:00 2001 From: Joshua Slaughter Date: Mon, 12 May 2025 16:44:09 +0100 Subject: [PATCH 15/17] Revert "Merge branch 'gwis' of github.com:TARGENE/TargeneCore.jl into gwis" This reverts commit 4516d04838b6ce13be8ac2a2f49a42c188e31277, reversing changes made to e01696430c359b39fd9e63711101f0047f9d94fc. --- Manifest.toml | 1163 +++++++++++++++---------------------------------- Project.toml | 11 - 2 files changed, 352 insertions(+), 822 deletions(-) diff --git a/Manifest.toml b/Manifest.toml index 61d5d57..e4c5124 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,14 +1,14 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.11.4" +julia_version = "1.10.4" manifest_format = "2.0" project_hash = "026a4a228f2fe6f789f0bbad2d45493e7ed45f99" [[deps.ARFFFiles]] deps = ["CategoricalArrays", "Dates", "Parsers", "Tables"] -git-tree-sha1 = "678eb18590a8bc6674363da4d5faa4ac09c40a18" +git-tree-sha1 = "e8c8e0a2be6eb4f56b1672e46004463033daa409" uuid = "da404889-ca92-49ff-9e8b-0aa6b4d38dc8" -version = "1.5.0" +version = "1.4.1" [[deps.AbstractDifferentiation]] deps = ["ExprTools", "LinearAlgebra", "Requires"] @@ -50,44 +50,40 @@ uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.5" [[deps.Accessors]] -deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "MacroTools"] -git-tree-sha1 = "0ba8f4c1f06707985ffb4804fdad1bf97b233897" +deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] +git-tree-sha1 = "f61b15be1d76846c0ce31d3fcfac5380ae53db6a" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.41" +version = "0.1.37" [deps.Accessors.extensions] - AxisKeysExt = "AxisKeys" - IntervalSetsExt = "IntervalSets" - LinearAlgebraExt = "LinearAlgebra" - StaticArraysExt = "StaticArrays" - StructArraysExt = "StructArrays" - TestExt = "Test" - UnitfulExt = "Unitful" + AccessorsAxisKeysExt = "AxisKeys" + AccessorsIntervalSetsExt = "IntervalSets" + AccessorsStaticArraysExt = "StaticArrays" + AccessorsStructArraysExt = "StructArrays" + AccessorsUnitfulExt = "Unitful" [deps.Accessors.weakdeps] AxisKeys = "94b1ba4f-4ee9-5380-92f1-94cde586c3c5" IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" - LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" Requires = "ae029012-a4dd-5104-9daa-d747884805df" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" - Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "50c3c56a52972d78e8be9fd135bfb91c9574c140" +git-tree-sha1 = "cde29ddf7e5726c9fb511f340244ea3481267608" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "4.1.1" +version = "3.7.2" weakdeps = ["StaticArrays"] [deps.Adapt.extensions] AdaptStaticArraysExt = "StaticArrays" [[deps.AdaptivePredicates]] -git-tree-sha1 = "7e651ea8d262d2d74ce75fdf47c4d63c07dba7a6" +git-tree-sha1 = "7d5da5dd472490d048b081ca1bda4a7821b06456" uuid = "35492f91-a3bd-45ad-95db-fcad7dcfedb7" -version = "1.2.0" +version = "1.1.1" [[deps.AliasTables]] deps = ["PtrArrays", "Random"] @@ -97,14 +93,14 @@ version = "1.1.3" [[deps.Animations]] deps = ["Colors"] -git-tree-sha1 = "e092fa223bf66a3c41f9c022bd074d916dc303e7" +git-tree-sha1 = "e81c509d2c8e49592413bfb0bb3b08150056c79d" uuid = "27a7e980-b3e6-11e9-2bcd-0b925532e340" -version = "0.4.2" +version = "0.4.1" [[deps.ArgCheck]] -git-tree-sha1 = "680b3b8759bd4c54052ada14e52355ab69e07876" +git-tree-sha1 = "a3a402a35a2f7e0b87828ccabbd5ebfbebe356b4" uuid = "dce04be8-c92d-5529-be00-80e4d2c0e197" -version = "2.4.0" +version = "2.3.0" [[deps.ArgParse]] deps = ["Logging", "TextWrap"] @@ -114,7 +110,7 @@ version = "1.2.0" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" -version = "1.1.2" +version = "1.1.1" [[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] @@ -122,34 +118,17 @@ git-tree-sha1 = "d57bd3762d308bded22c3b82d033bff85f6195c6" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" version = "0.4.0" -[[deps.Arpack]] -deps = ["Arpack_jll", "Libdl", "LinearAlgebra", "Logging"] -git-tree-sha1 = "9b9b347613394885fd1c8c7729bfc60528faa436" -uuid = "7d9fca2a-8960-54d3-9f78-7d1dccf2cb97" -version = "0.5.4" - -[[deps.Arpack_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "OpenBLAS_jll", "Pkg"] -git-tree-sha1 = "5ba6c757e8feccf03a1554dfaf3e26b3cfc7fd5e" -uuid = "68821587-b530-5797-8361-c406ea357684" -version = "3.5.1+1" - [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra"] -git-tree-sha1 = "017fcb757f8e921fb44ee063a7aafe5f89b86dd1" +deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "c5aeb516a84459e0318a02507d2261edad97eb75" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.18.0" +version = "7.7.1" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" ArrayInterfaceCUDAExt = "CUDA" - ArrayInterfaceCUDSSExt = "CUDSS" - ArrayInterfaceChainRulesCoreExt = "ChainRulesCore" - ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" - ArrayInterfaceReverseDiffExt = "ReverseDiff" - ArrayInterfaceSparseArraysExt = "SparseArrays" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -157,20 +136,15 @@ version = "7.18.0" BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - CUDSS = "45b445bb-4962-46a0-9369-b4df9d0f772e" - ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" - ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" - SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.Arrow]] -deps = ["ArrowTypes", "BitIntegers", "CodecLz4", "CodecZstd", "ConcurrentUtilities", "DataAPI", "Dates", "EnumX", "Mmap", "PooledArrays", "SentinelArrays", "StringViews", "Tables", "TimeZones", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "00f0b3f05bc33cc5b68db6cc22e4a7b16b65e505" +deps = ["ArrowTypes", "BitIntegers", "CodecLz4", "CodecZstd", "ConcurrentUtilities", "DataAPI", "Dates", "EnumX", "LoggingExtras", "Mmap", "PooledArrays", "SentinelArrays", "Tables", "TimeZones", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "4ece4573f169d64b1508b0c8dd38c7919ae7a907" uuid = "69666777-d1a9-59fb-9406-91d4454c9d45" -version = "2.8.0" +version = "2.7.3" [[deps.ArrowTypes]] deps = ["Sockets", "UUIDs"] @@ -180,28 +154,18 @@ version = "2.3.0" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -version = "1.11.0" [[deps.Atomix]] deps = ["UnsafeAtomics"] -git-tree-sha1 = "c3b238aa28c1bebd4b5ea4988bebf27e9a01b72b" +git-tree-sha1 = "c06a868224ecba914baa6942988e2f2aade419be" uuid = "a9b6321e-bd34-4604-b9c9-b65b8de01458" -version = "1.0.1" - - [deps.Atomix.extensions] - AtomixCUDAExt = "CUDA" - AtomixMetalExt = "Metal" - AtomixoneAPIExt = "oneAPI" - - [deps.Atomix.weakdeps] - CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" - Metal = "dde4c033-4e86-420c-a63e-0dd931031962" - oneAPI = "8f75cd03-7ff8-4ecb-9b8f-daf728133b1b" +version = "0.1.0" [[deps.AutoHashEquals]] -git-tree-sha1 = "4ec6b48702dacc5994a835c1189831755e4e76ef" +deps = ["Pkg"] +git-tree-sha1 = "daaeb6f7f77b88c072a83a2451801818acb5c63b" uuid = "15f4f7f2-30c1-5605-9d31-71845cf9641f" -version = "2.2.0" +version = "2.1.0" [[deps.Automa]] deps = ["TranscodingStreams"] @@ -262,7 +226,6 @@ version = "0.4.3" [[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -version = "1.11.0" [[deps.Baselet]] git-tree-sha1 = "aebf55e6d7795e02ca500a689d326ac979aaf89e" @@ -282,9 +245,9 @@ version = "0.1.9" [[deps.BitIntegers]] deps = ["Random"] -git-tree-sha1 = "6158239ac409f960abbc232a9b24c00f5cce3108" +git-tree-sha1 = "a55462dfddabc34bc97d3a7403a2ca2802179ae6" uuid = "c3b6d118-76ef-56ca-8cc7-ebb389d030a1" -version = "0.3.2" +version = "0.3.1" [[deps.BitTwiddlingConvenienceFunctions]] deps = ["Static"] @@ -299,9 +262,9 @@ version = "1.2.2" [[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "8873e196c2eb87962a2048b3b8e08946535864a1" +git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" -version = "1.0.8+4" +version = "1.0.8+1" [[deps.CEnum]] git-tree-sha1 = "389ad5c84de1ae7cf0e28e381131c98ea87d54fc" @@ -316,7 +279,6 @@ version = "0.2.6" [[deps.CRC32c]] uuid = "8bf52ea8-c179-5cab-976a-9e18b702a9bc" -version = "1.11.0" [[deps.CRlibm_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -326,39 +288,39 @@ version = "1.0.1+0" [[deps.CSV]] deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "PrecompileTools", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings", "WorkerUtilities"] -git-tree-sha1 = "deddd8725e5e1cc49ee205a1964256043720a6c3" +git-tree-sha1 = "6c834533dc1fabd820c1db03c839bf97e45a3fab" uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" -version = "0.10.15" +version = "0.10.14" [[deps.CUDA_Driver_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "14996d716a2eaaeccfc8d7bc854dd87fde720ac1" +git-tree-sha1 = "22bc8ec24f0ed05bcf8c1845ef425d8229ef6436" uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc" -version = "0.10.4+0" +version = "0.10.0+0" [[deps.CUDA_Runtime_jll]] deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "17f1536c600133f7c4113bae0a2d98dbf27c7ebc" +git-tree-sha1 = "c730797fc11265bb0940b738b3573ed38c2c8388" uuid = "76a88914-d11a-5bdc-97e0-2f5a05c973a2" -version = "0.15.5+0" +version = "0.15.1+0" [[deps.Cairo]] deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] -git-tree-sha1 = "71aa551c5c33f1a4415867fe06b7844faadb0ae9" +git-tree-sha1 = "7b6ad8c35f4bc3bca8eb78127c8b99719506a5fb" uuid = "159f3aea-2a34-519c-b102-8c37f9878175" -version = "1.1.1" +version = "1.1.0" [[deps.CairoMakie]] deps = ["CRC32c", "Cairo", "Cairo_jll", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"] -git-tree-sha1 = "0afa2b4ac444b9412130d68493941e1af462e26a" +git-tree-sha1 = "361dec06290d76b6d70d0c7dc888038eec9df63a" uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" -version = "0.12.18" +version = "0.12.9" [[deps.Cairo_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "009060c9a6168704143100f36ab08f06c2af4642" +git-tree-sha1 = "a2f1c8c668c8e3cb4cca4e57a8efdb09067bb3fd" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" -version = "1.18.2+1" +version = "1.18.0+2" [[deps.CategoricalArrays]] deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"] @@ -387,15 +349,15 @@ version = "0.1.15" [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] -git-tree-sha1 = "4312d7869590fab4a4f789e97bd82f0a04eaaa05" +git-tree-sha1 = "227985d885b4dbce5e18a96f9326ea1e836e5a03" uuid = "082447d4-558c-5d27-93f4-14fc19e9eca2" -version = "1.72.2" +version = "1.69.0" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra"] -git-tree-sha1 = "1713c74e00545bfe14605d2a2be1712de8fbcb58" +git-tree-sha1 = "71acdbf594aab5bbb2cec89b208c41b4c411e49f" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.25.1" +version = "1.24.0" weakdeps = ["SparseArrays"] [deps.ChainRulesCore.extensions] @@ -407,17 +369,11 @@ git-tree-sha1 = "05ba0d07cd4fd8b7a39541e31a7b0254704ea581" uuid = "fb6a15b2-703c-40df-9091-08a04967cfa9" version = "0.1.13" -[[deps.Clustering]] -deps = ["Distances", "LinearAlgebra", "NearestNeighbors", "Printf", "Random", "SparseArrays", "Statistics", "StatsBase"] -git-tree-sha1 = "3e22db924e2945282e70c33b75d4dde8bfa44c94" -uuid = "aaaa29a8-35af-508c-8bc3-b662a17a0fe5" -version = "0.15.8" - [[deps.CodecBzip2]] deps = ["Bzip2_jll", "TranscodingStreams"] -git-tree-sha1 = "84990fa864b7f2b4901901ca12736e45ee79068c" +git-tree-sha1 = "e7c529cc31bb85b97631b922fa2e6baf246f5905" uuid = "523fee87-0ab8-5b00-afb7-3ecf72e48cfd" -version = "0.8.5" +version = "0.8.4" [[deps.CodecLz4]] deps = ["Lz4_jll", "TranscodingStreams"] @@ -439,21 +395,21 @@ version = "0.7.6" [[deps.CodecZstd]] deps = ["TranscodingStreams", "Zstd_jll"] -git-tree-sha1 = "d0073f473757f0d39ac9707f1eb03b431573cbd8" +git-tree-sha1 = "5e41a52bec3b0881a7eb54f5391b779994504186" uuid = "6b39b394-51ab-5f42-8807-6242bab2b4c2" -version = "0.8.6" +version = "0.8.5" [[deps.ColorBrewer]] -deps = ["Colors", "JSON"] -git-tree-sha1 = "e771a63cc8b539eca78c85b0cabd9233d6c8f06f" +deps = ["Colors", "JSON", "Test"] +git-tree-sha1 = "61c5334f33d91e570e1d0c3eb5465835242582c4" uuid = "a2cac450-b92f-5266-8821-25eda20663c8" -version = "0.4.1" +version = "0.4.0" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "26ec26c98ae1453c692efded2b17e15125a5bea1" +git-tree-sha1 = "b5278586822443594ff615963b0c09755771b3e0" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.28.0" +version = "3.26.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -473,9 +429,9 @@ weakdeps = ["SpecialFunctions"] [[deps.Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e" +git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.13.0" +version = "0.12.11" [[deps.Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -529,9 +485,9 @@ version = "0.3.2" [[deps.ConcurrentUtilities]] deps = ["Serialization", "Sockets"] -git-tree-sha1 = "f36e5e8fdffcb5646ea5da81495a5a7566005127" +git-tree-sha1 = "ea32b83ca4fefa1768dc84e504cc0a94fb1ab8d1" uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" -version = "2.4.3" +version = "2.4.2" [[deps.Configurations]] deps = ["ExproniconLite", "OrderedCollections", "TOML"] @@ -583,10 +539,10 @@ 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", "Random", "Reexport", "SentinelArrays", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "fb61b4812c49343d7ef0b533ba982c46021938a6" +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 = "1.7.0" +version = "1.6.1" [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] @@ -602,13 +558,6 @@ version = "1.0.0" [[deps.Dates]] deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" -version = "1.11.0" - -[[deps.Dbus_jll]] -deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" -uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" -version = "1.14.10+0" [[deps.DefineSingletons]] git-tree-sha1 = "0fba8b706d0178b4dc7fd44a96a92382c9065c2c" @@ -617,9 +566,9 @@ version = "0.1.2" [[deps.DelaunayTriangulation]] deps = ["AdaptivePredicates", "EnumX", "ExactPredicates", "Random"] -git-tree-sha1 = "5620ff4ee0084a6ab7097a27ba0c19290200b037" +git-tree-sha1 = "46f12daa85e5acc0ea5d5f9f8c3f1fc679e0f7e5" uuid = "927a84f5-c5f4-47a5-9785-b46e178433df" -version = "1.6.4" +version = "1.2.0" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -629,9 +578,9 @@ version = "1.9.1" [[deps.Dictionaries]] deps = ["Indexing", "Random", "Serialization"] -git-tree-sha1 = "61ab242274c0d44412d8eab38942a49aa46de9d0" +git-tree-sha1 = "35b66b6744b2d92c778afd3a88d2571875664a2a" uuid = "85a47980-9c8c-11e8-2b9f-f7ca1fa99fb4" -version = "0.4.3" +version = "0.4.2" [[deps.DiffResults]] deps = ["StaticArraysCore"] @@ -647,9 +596,9 @@ version = "1.15.1" [[deps.Distances]] deps = ["LinearAlgebra", "Statistics", "StatsAPI"] -git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d" +git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.12" +version = "0.10.11" weakdeps = ["ChainRulesCore", "SparseArrays"] [deps.Distances.extensions] @@ -659,13 +608,12 @@ weakdeps = ["ChainRulesCore", "SparseArrays"] [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" -version = "1.11.0" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "03aa5d44647eaec98e1920635cdfed5d5560a8b9" +git-tree-sha1 = "e6c693a0e4394f8fda0e51a5bdf5aef26f8235e9" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.117" +version = "0.25.111" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -705,17 +653,11 @@ git-tree-sha1 = "bdb1942cd4c45e3c678fd11569d5cccd80976237" uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" -[[deps.EpollShim_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "8a4be429317c42cfae6a7fc03c31bad1970c310d" -uuid = "2702e6a9-849d-5ed8-8c21-79e8b8f9ee43" -version = "0.0.20230411+1" - [[deps.EvoTrees]] deps = ["BSON", "CategoricalArrays", "Distributions", "MLJModelInterface", "NetworkLayout", "Random", "RecipesBase", "Statistics", "StatsBase", "Tables"] -git-tree-sha1 = "1692b52f3e8e2d25b41b837d3a32710979761e9b" +git-tree-sha1 = "92d1f78f95f4794bf29bd972dacfa37ea1fec9f4" uuid = "f6006082-12f8-11e9-0c9c-0d5d367ab1e5" -version = "0.16.8" +version = "0.16.7" [deps.EvoTrees.extensions] EvoTreesCUDAExt = "CUDA" @@ -731,15 +673,15 @@ version = "2.2.8" [[deps.ExceptionUnwrapping]] deps = ["Test"] -git-tree-sha1 = "d36f682e590a83d63d1c7dbd287573764682d12a" +git-tree-sha1 = "dcb08a0d93ec0b1cdc4af184b26b591e9695423a" uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" -version = "0.1.11" +version = "0.1.10" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e51db81749b0777b2147fbe7b783ee79045b8e99" +git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.6.4+3" +version = "2.6.2+0" [[deps.ExprTools]] git-tree-sha1 = "27415f162e6028e81c72b82ef756bf321213b6ec" @@ -752,21 +694,15 @@ uuid = "55351af7-c7e9-48d6-89ff-24e801d99491" version = "0.10.13" [[deps.Extents]] -git-tree-sha1 = "063512a13dbe9c40d999c439268539aa552d1ae6" +git-tree-sha1 = "81023caa0021a41712685887db1fc03db26f41f5" uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" -version = "0.1.5" - -[[deps.FFMPEG]] -deps = ["FFMPEG_jll"] -git-tree-sha1 = "53ebe7511fa11d33bec688a9178fac4e49eeee00" -uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" -version = "0.4.2" +version = "0.1.4" [[deps.FFMPEG_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e" +git-tree-sha1 = "8cc47f299902e13f90405ddb5bf87e5d474c0d38" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.4+1" +version = "6.1.2+0" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] @@ -776,9 +712,9 @@ version = "1.8.0" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4d81ed14783ec49ce9f2e168208a12ce1815aa25" +git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea" uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a" -version = "3.3.10+3" +version = "3.3.10+0" [[deps.FLoops]] deps = ["BangBang", "Compat", "FLoopsBase", "InitialValues", "JuliaVariables", "MLStyle", "Serialization", "Setfield", "Transducers"] @@ -800,13 +736,9 @@ version = "0.2.2" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "2dd20384bf8c6d411b5c7370865b1e9b26cb2ea3" +git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.6" -weakdeps = ["HTTP"] - - [deps.FileIO.extensions] - HTTPExt = "HTTP" +version = "1.16.3" [[deps.FilePaths]] deps = ["FilePathsBase", "MacroTools", "Reexport", "Requires"] @@ -827,7 +759,6 @@ weakdeps = ["Mmap", "Test"] [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" -version = "1.11.0" [[deps.FillArrays]] deps = ["LinearAlgebra"] @@ -842,21 +773,19 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] FillArraysStatisticsExt = "Statistics" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Setfield"] -git-tree-sha1 = "84e3a47db33be7248daa6274b287507dd6ff84e8" +deps = ["ArrayInterface", "LinearAlgebra", "Setfield", "SparseArrays"] +git-tree-sha1 = "f9219347ebf700e77ca1d48ef84e4a82a6701882" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.26.2" +version = "2.24.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" - FiniteDiffSparseArraysExt = "SparseArrays" FiniteDiffStaticArraysExt = "StaticArrays" [deps.FiniteDiff.weakdeps] BandedMatrices = "aae01518-5342-5314-be14-df237901396f" BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" - SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FixedPointNumbers]] @@ -867,9 +796,9 @@ version = "0.8.5" [[deps.Fontconfig_jll]] deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"] -git-tree-sha1 = "21fac3c77d7b5a9fc03b0ec503aa1a6392c34d2b" +git-tree-sha1 = "db16beca600632c95fc8aca29890d83788dd8b23" uuid = "a3f928ae-7b40-5064-980b-68af3947d34b" -version = "2.15.0+0" +version = "2.13.96+0" [[deps.Format]] git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc" @@ -878,9 +807,9 @@ version = "1.3.7" [[deps.ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] -git-tree-sha1 = "a2df1b776752e3f344e5116c06d75a10436ab853" +git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.38" +version = "0.10.36" weakdeps = ["StaticArrays"] [deps.ForwardDiff.extensions] @@ -894,32 +823,25 @@ version = "4.1.1" [[deps.FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "786e968a8d2fb167f2e4880baba62e0e26bd8e4e" +git-tree-sha1 = "5c1d8ae0efc6c2e7b1fc502cbe25def8f661b7bc" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.13.3+1" +version = "2.13.2+0" [[deps.FreeTypeAbstraction]] deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"] -git-tree-sha1 = "d52e255138ac21be31fa633200b65e4e71d26802" +git-tree-sha1 = "2493cdfd0740015955a8e46de4ef28f49460d8bc" uuid = "663a7486-cb36-511b-a19d-713bb74d65c9" -version = "0.10.6" +version = "0.10.3" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "846f7026a9decf3679419122b49f8a1fdb48d2d5" +git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2" uuid = "559328eb-81f9-559d-9380-de523a88c83c" -version = "1.0.16+0" +version = "1.0.14+0" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" -version = "1.11.0" - -[[deps.GLFW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] -git-tree-sha1 = "fcb0584ff34e25155876418979d4c8971243bb89" -uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.4.0+2" [[deps.GLM]] deps = ["Distributions", "LinearAlgebra", "Printf", "Reexport", "SparseArrays", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns", "StatsModels"] @@ -929,33 +851,21 @@ version = "1.9.0" [[deps.GLMNet]] deps = ["DataFrames", "Distributed", "Distributions", "Printf", "Random", "SparseArrays", "StatsBase", "glmnet_jll"] -git-tree-sha1 = "b873c384d3490304c18224b1d5554cdebaafb60b" +git-tree-sha1 = "7ea4e2bbb84183fe52a488d05e16c152b2387b95" uuid = "8d5ece8b-de18-5317-b113-243142960cc6" -version = "0.7.4" +version = "0.7.2" [[deps.GPUArrays]] -deps = ["Adapt", "GPUArraysCore", "KernelAbstractions", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "ScopedValues", "Serialization", "Statistics"] -git-tree-sha1 = "0ef97e93edced3d0e713f4cfd031cc9020e022b0" +deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] +git-tree-sha1 = "85d7fb51afb3def5dcb85ad31c3707795c8bccc1" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "11.2.1" +version = "9.1.0" [[deps.GPUArraysCore]] deps = ["Adapt"] -git-tree-sha1 = "83cf05ab16a73219e5f6bd1bdfa9848fa24ac627" +git-tree-sha1 = "2d6ca471a6c7b536127afccfa7564b5b39227fe0" uuid = "46192b85-c4d5-4398-a991-12ede77f4527" -version = "0.2.0" - -[[deps.GR]] -deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] -git-tree-sha1 = "9bf00ba4c45867c86251a7fd4cb646dcbeb41bf0" -uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.12" - -[[deps.GR_jll]] -deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "36d5430819123553bf31dfdceb3653ca7d9e62d7" -uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.12+0" +version = "0.1.5" [[deps.GeneticVariantBase]] deps = ["StatsBase"] @@ -964,15 +874,15 @@ uuid = "2447270c-d849-4bf9-ac0d-b5c0b265991c" version = "0.1.2" [[deps.GeoFormatTypes]] -git-tree-sha1 = "8e233d5167e63d708d41f87597433f59a0f213fe" +git-tree-sha1 = "59107c179a586f0fe667024c5eb7033e81333271" uuid = "68eda718-8dee-11e9-39e7-89f7f65f511f" -version = "0.4.4" +version = "0.4.2" [[deps.GeoInterface]] -deps = ["DataAPI", "Extents", "GeoFormatTypes"] -git-tree-sha1 = "294e99f19869d0b0cb71aef92f19d03649d028d5" +deps = ["Extents", "GeoFormatTypes"] +git-tree-sha1 = "5921fc0704e40c024571eca551800c699f86ceb4" uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" -version = "1.4.1" +version = "1.3.6" [[deps.GeometryBasics]] deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] @@ -986,17 +896,11 @@ git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046" uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" -[[deps.Giflib_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6570366d757b50fabae9f4315ad74d2e40c0560a" -uuid = "59f7168a-df46-5410-90c8-f2779963d0ec" -version = "5.2.3+0" - [[deps.Glib_jll]] deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"] -git-tree-sha1 = "b0036b392358c80d2d2124746c2bf3d48d457938" +git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.82.4+0" +version = "2.80.2+0" [[deps.Glob]] git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" @@ -1005,27 +909,27 @@ version = "1.3.1" [[deps.Graphics]] deps = ["Colors", "LinearAlgebra", "NaNMath"] -git-tree-sha1 = "a641238db938fff9b2f60d08ed9030387daf428c" +git-tree-sha1 = "d61890399bc535850c4bf08e4e0d3a7ad0f21cbd" uuid = "a2bd30eb-e257-5431-a919-1863eab51364" -version = "1.1.3" +version = "1.1.2" [[deps.Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "01979f9b37367603e2848ea225918a3b3861b606" +git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" -version = "1.3.14+1" +version = "1.3.14+0" [[deps.Graphs]] deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780" +git-tree-sha1 = "ebd18c326fa6cee1efb7da9a3b45cf69da2ed4d9" uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" -version = "1.12.0" +version = "1.11.2" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] -git-tree-sha1 = "dc6bed05c15523624909b3953686c5f5ffa10adc" +git-tree-sha1 = "fc713f007cff99ff9e50accba6373624ddd33588" uuid = "3955a311-db13-416c-9275-1d80ed98e5e9" -version = "0.11.1" +version = "0.11.0" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -1051,21 +955,16 @@ uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" version = "1.14.3+3" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "PrecompileTools", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "c67b33b085f6e2faf8bf79a61962e7339a81129c" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "d1d712be3164d61d1fb98e7ce9bcbc6cc06b45ed" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.10.15" +version = "1.10.8" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll"] -git-tree-sha1 = "55c53be97790242c29031e5cd45e8ac296dadda3" +git-tree-sha1 = "401e4f3f30f43af2c8478fc008da50096ea5240f" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" -version = "8.5.0+0" - -[[deps.HashArrayMappedTries]] -git-tree-sha1 = "2eaa69a7cab70a52b9687c8bf950a5a93ec895ae" -uuid = "076d061b-32b6-4027-95e0-9a2c6f6d7e74" -version = "0.2.0" +version = "8.3.1+0" [[deps.HostCPUFeatures]] deps = ["BitTwiddlingConvenienceFunctions", "IfElse", "Libdl", "Static"] @@ -1081,15 +980,15 @@ version = "2.11.2+3" [[deps.HypergeometricFunctions]] deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "b1c2585431c382e3fe5805874bda6aea90a95de9" +git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.25" +version = "0.3.24" [[deps.HypothesisTests]] deps = ["Combinatorics", "Distributions", "LinearAlgebra", "Printf", "Random", "Rmath", "Roots", "Statistics", "StatsAPI", "StatsBase"] -git-tree-sha1 = "6c3ce99fdbaf680aa6716f4b919c19e902d67c9c" +git-tree-sha1 = "4b5d5ba51f5f473737ed9de6d8a7aa190ad8c72f" uuid = "09f84164-cd44-5f33-b23f-e6b0d136a0d5" -version = "0.11.3" +version = "0.11.0" [[deps.IRTools]] deps = ["InteractiveUtils", "MacroTools"] @@ -1104,9 +1003,9 @@ version = "0.1.1" [[deps.ImageAxes]] deps = ["AxisArrays", "ImageBase", "ImageCore", "Reexport", "SimpleTraits"] -git-tree-sha1 = "e12629406c6c4442539436581041d372d69c55ba" +git-tree-sha1 = "2e4520d67b0cef90865b3ef727594d2a58e0e1f8" uuid = "2803e5a7-5153-5ecf-9a86-9b4c37f5f5ac" -version = "0.6.12" +version = "0.6.11" [[deps.ImageBase]] deps = ["ImageCore", "Reexport"] @@ -1116,21 +1015,21 @@ version = "0.1.7" [[deps.ImageCore]] deps = ["ColorVectorSpace", "Colors", "FixedPointNumbers", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "PrecompileTools", "Reexport"] -git-tree-sha1 = "8c193230235bbcee22c8066b0374f63b5683c2d3" +git-tree-sha1 = "b2a7eaa169c13f5bcae8131a83bc30eff8f71be0" uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534" -version = "0.10.5" +version = "0.10.2" [[deps.ImageIO]] -deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs", "WebP"] -git-tree-sha1 = "696144904b76e1ca433b886b4e7edd067d76cbf7" +deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs"] +git-tree-sha1 = "437abb322a41d527c197fa800455f79d414f0a3c" uuid = "82e4d734-157c-48bb-816b-45c225c6df19" -version = "0.6.9" +version = "0.6.8" [[deps.ImageMetadata]] deps = ["AxisArrays", "ImageAxes", "ImageBase", "ImageCore"] -git-tree-sha1 = "2a81c3897be6fbcde0802a0ebe6796d0562f63ec" +git-tree-sha1 = "355e2b974f2e3212a75dfb60519de21361ad3cb7" uuid = "bc367c6b-8a6b-528e-b4bd-a4b897500b49" -version = "0.9.10" +version = "0.9.9" [[deps.Imath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1177,7 +1076,6 @@ version = "2024.2.1+0" [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" -version = "1.11.0" [[deps.Interpolations]] deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] @@ -1190,17 +1088,17 @@ weakdeps = ["Unitful"] InterpolationsUnitfulExt = "Unitful" [[deps.IntervalArithmetic]] -deps = ["CRlibm_jll", "LinearAlgebra", "MacroTools", "RoundingEmulator"] -git-tree-sha1 = "ffb76d09ab0dc9f5a27edac2acec13c74a876cc6" +deps = ["CRlibm_jll", "MacroTools", "RoundingEmulator"] +git-tree-sha1 = "01fa84a20be8c7c867edf3b9ef33ac15f4089c1a" uuid = "d1acc4aa-44c8-5952-acd4-ba5d80a2a253" -version = "0.22.21" +version = "0.22.15" weakdeps = ["DiffRules", "ForwardDiff", "IntervalSets", "RecipesBase"] [deps.IntervalArithmetic.extensions] IntervalArithmeticDiffRulesExt = "DiffRules" IntervalArithmeticForwardDiffExt = "ForwardDiff" - IntervalArithmeticIntervalSetsExt = "IntervalSets" IntervalArithmeticRecipesBaseExt = "RecipesBase" + IntervalArithmeticsIntervalSetsExt = "IntervalSets" [[deps.IntervalSets]] git-tree-sha1 = "dba9ddf07f77f60450fe5d2e2beb9854d9a49bd0" @@ -1214,9 +1112,9 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] IntervalSetsStatisticsExt = "Statistics" [[deps.InverseFunctions]] -git-tree-sha1 = "a779299d77cd080bf77b97535acecd73e1c5e5cb" +git-tree-sha1 = "2787db24f4e03daf859c6509ff87764e4182f7d1" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.17" +version = "0.1.16" weakdeps = ["Dates", "Test"] [deps.InverseFunctions.extensions] @@ -1224,9 +1122,9 @@ weakdeps = ["Dates", "Test"] InverseFunctionsTestExt = "Test" [[deps.InvertedIndices]] -git-tree-sha1 = "6da3c4316095de0f5ee2ebd875df8721e7e0bdbe" +git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.3.1" +version = "1.3.0" [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" @@ -1269,9 +1167,9 @@ version = "0.4.54" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] -git-tree-sha1 = "a007feb38b422fbdab534406aeca1b86823cb4d6" +git-tree-sha1 = "f389674c99bfcde17dc57454011aa44d5a260a40" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.7.0" +version = "1.6.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] @@ -1281,9 +1179,9 @@ version = "0.21.4" [[deps.JSON3]] deps = ["Dates", "Mmap", "Parsers", "PrecompileTools", "StructTypes", "UUIDs"] -git-tree-sha1 = "1d322381ef7b087548321d3f878cb4c9bd8f8f9b" +git-tree-sha1 = "eb3edce0ed4fa32f75a0a11217433c31d56bd48b" uuid = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" -version = "1.14.1" +version = "1.14.0" weakdeps = ["ArrowTypes"] [deps.JSON3.extensions] @@ -1297,9 +1195,9 @@ version = "0.1.5" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "eac1206917768cb54957c65a615460d87b455fc1" +git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "3.1.1+0" +version = "3.0.3+0" [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] @@ -1308,10 +1206,10 @@ uuid = "b14d175d-62b4-44ba-8fb7-3064adc8c3ec" version = "0.2.4" [[deps.KernelAbstractions]] -deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs"] -git-tree-sha1 = "019e9de20154148a4937965ec43084435e946450" +deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] +git-tree-sha1 = "cb1cff88ef2f3a157cbad75bbe6b229e1975e498" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.32" +version = "0.9.25" [deps.KernelAbstractions.extensions] EnzymeExt = "EnzymeCore" @@ -1335,17 +1233,11 @@ git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd" uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d" version = "3.100.2+0" -[[deps.LERC_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "aaafe88dccbd957a8d82f7d05be9b69172e0cee3" -uuid = "88015f11-f218-50d7-93a8-a6af411a945d" -version = "4.0.1+0" - [[deps.LLVM]] -deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Unicode"] -git-tree-sha1 = "5fcfea6df2ff3e4da708a40c969c3812162346df" +deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] +git-tree-sha1 = "839c82932db86740ae729779e610f07a1640be9a" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "9.2.0" +version = "6.6.3" [deps.LLVM.extensions] BFloat16sExt = "BFloat16s" @@ -1355,42 +1247,26 @@ version = "9.2.0" [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "4b5ad6a4ffa91a00050a964492bc4f86bb48cea0" +git-tree-sha1 = "88b916503aac4fb7f701bb625cd84ca5dd1677bc" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.35+0" +version = "0.0.29+0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "78211fb6cbc872f77cad3fc0b6cf647d923f4929" +git-tree-sha1 = "e16271d212accd09d52ee0ae98956b8a05c4b626" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "18.1.7+0" +version = "17.0.6+0" [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1c602b1127f4751facb671441ca72715cc95938a" +git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d" uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac" -version = "2.10.3+0" +version = "2.10.2+0" [[deps.LaTeXStrings]] -git-tree-sha1 = "dda21b8cbd6a6c40d9d02a73230f9d70fed6918c" +git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec" uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" -version = "1.4.0" - -[[deps.Latexify]] -deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "ce5f5621cac23a86011836badfedf664a612cee4" -uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.5" - - [deps.Latexify.extensions] - DataFramesExt = "DataFrames" - SparseArraysExt = "SparseArrays" - SymEngineExt = "SymEngine" - - [deps.Latexify.weakdeps] - DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" - SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" - SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" +version = "1.3.1" [[deps.LatinHypercubeSampling]] deps = ["Random", "StableRNGs", "StatsBase", "Test"] @@ -1407,7 +1283,6 @@ version = "0.1.17" [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" -version = "1.11.0" [[deps.LazyModules]] git-tree-sha1 = "a560dd966b386ac9ae60bdd3a3d3a326062d3c3e" @@ -1428,17 +1303,16 @@ 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 = "8.6.0+0" +version = "8.4.0+0" [[deps.LibGit2]] deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" -version = "1.11.0" [[deps.LibGit2_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" -version = "1.7.2+0" +version = "1.6.4+0" [[deps.LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] @@ -1447,55 +1321,42 @@ version = "1.11.0+1" [[deps.Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" -version = "1.11.0" [[deps.Libffi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "27ecae93dd25ee0909666e6835051dd684cc035e" +git-tree-sha1 = "0b4a5d71f3e5200a7dff793393e09dfc2d874290" uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490" -version = "3.2.2+2" +version = "3.2.2+1" [[deps.Libgcrypt_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"] -git-tree-sha1 = "8be878062e0ffa2c3f67bb58a595375eda5de80b" +git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673" uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4" -version = "1.11.0+0" - -[[deps.Libglvnd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll", "Xorg_libXext_jll"] -git-tree-sha1 = "ff3b4b9d35de638936a525ecd36e86a8bb919d11" -uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" -version = "1.7.0+0" +version = "1.8.11+0" [[deps.Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "df37206100d39f79b3376afb6b9cee4970041c61" +git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed" uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8" -version = "1.51.1+0" +version = "1.49.0+0" [[deps.Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "be484f5c92fad0bd8acfef35fe017900b0b73809" +git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.18.0+0" +version = "1.17.0+0" [[deps.Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "89211ea35d9df5831fca5d33552c02bd33878419" +git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e" uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9" -version = "2.40.3+0" - -[[deps.Libtiff_jll]] -deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "4ab7581296671007fc33f07a721631b8855f4b1d" -uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.7.1+0" +version = "2.40.1+0" [[deps.Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e888ad02ce716b319e6bdb985d2ef300e7089889" +git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" -version = "2.40.3+0" +version = "2.40.1+0" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] @@ -1506,7 +1367,6 @@ version = "7.3.0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" -version = "1.11.0" [[deps.LinearMaps]] deps = ["LinearAlgebra"] @@ -1538,13 +1398,12 @@ version = "0.3.29" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" -version = "1.11.0" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "f02b56007b064fbfddb4c9cd60161b6dd0f40df3" +git-tree-sha1 = "c1dd6d7978c12545b4179fb6153b9250c96b0075" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.1.0" +version = "1.0.3" [[deps.LoopVectorization]] deps = ["ArrayInterface", "CPUSummary", "CloseOpenIntervals", "DocStringExtensions", "HostCPUFeatures", "IfElse", "LayoutPointers", "LinearAlgebra", "OffsetArrays", "PolyesterWeave", "PrecompileTools", "SIMDTypes", "SLEEFPirates", "Static", "StaticArrayInterface", "ThreadingUtilities", "UnPack", "VectorizationBase"] @@ -1559,9 +1418,9 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [[deps.Lz4_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "191686b1ac1ea9c89fc52e996ad15d1d241d1e33" +git-tree-sha1 = "7f26c8fc5229e68484e0b3447312c98e16207d11" uuid = "5ced341a-0733-55b8-9ab6-a4889d929147" -version = "1.10.1+0" +version = "1.10.0+0" [[deps.MKL]] deps = ["Artifacts", "Libdl", "LinearAlgebra", "Logging", "MKL_jll"] @@ -1623,9 +1482,9 @@ version = "0.3.7" [[deps.MLJIteration]] deps = ["IterationControl", "MLJBase", "Random", "Serialization"] -git-tree-sha1 = "ad16cfd261e28204847f509d1221a581286448ae" +git-tree-sha1 = "f93f381a82fc1768c1a99c27a84b7ea1b1ee186d" uuid = "614be32b-d00c-4edb-bd02-1eb411ab5e55" -version = "0.6.3" +version = "0.6.2" [[deps.MLJLinearModels]] deps = ["DocStringExtensions", "IterativeSolvers", "LinearAlgebra", "LinearMaps", "MLJModelInterface", "Optim", "Parameters"] @@ -1641,9 +1500,9 @@ 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"] -git-tree-sha1 = "9dbbe1e9a8ba1fd60fefb5e39dd9a070bbda9c79" +git-tree-sha1 = "c1b1f72379d15079d2c97937d9c1ed38f9ab4679" uuid = "d491faf4-2d78-11e9-2867-c94bc002c0b7" -version = "0.17.6" +version = "0.17.4" [[deps.MLJTuning]] deps = ["ComputationalResources", "Distributed", "Distributions", "LatinHypercubeSampling", "MLJBase", "ProgressMeter", "Random", "RecipesBase", "StatisticalMeasuresBase"] @@ -1653,9 +1512,9 @@ version = "0.8.8" [[deps.MLJXGBoostInterface]] deps = ["MLJModelInterface", "SparseArrays", "Tables", "XGBoost"] -git-tree-sha1 = "385031c897e822755e7d194b0f9745fb20129972" +git-tree-sha1 = "25769259346a017d227c2134347db4c449d43625" uuid = "54119dfa-1dab-4055-a167-80440f4f7a91" -version = "0.3.12" +version = "0.3.11" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1664,7 +1523,7 @@ version = "0.4.17" [[deps.MLUtils]] deps = ["ChainRulesCore", "Compat", "DataAPI", "DelimitedFiles", "FLoops", "NNlib", "Random", "ShowCases", "SimpleTraits", "Statistics", "StatsBase", "Tables", "Transducers"] -git-tree-sha1 = "7940c0af802586b97009f254aa6065000a16fa1d" +git-tree-sha1 = "b45738c2e3d0d402dffa32b2c1654759a2ac35a4" uuid = "f1d291b0-491e-4a28-83b9-f70985020b54" version = "0.4.4" @@ -1687,21 +1546,22 @@ uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" version = "5.5.1+2" [[deps.MacroTools]] -git-tree-sha1 = "72aebe0b5051e5143a079a4685a46da330a40472" +deps = ["Markdown", "Random"] +git-tree-sha1 = "2fa9ee3e63fd3a4f7a9a4f4744a52f4856de82df" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.15" +version = "0.5.13" [[deps.Makie]] -deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageBase", "ImageIO", "InteractiveUtils", "Interpolations", "IntervalSets", "InverseFunctions", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"] -git-tree-sha1 = "be3051d08b78206fb5e688e8d70c9e84d0264117" +deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"] +git-tree-sha1 = "204f06860af9008fa08b3a4842f48116e1209a2c" uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" -version = "0.21.18" +version = "0.21.9" [[deps.MakieCore]] deps = ["ColorTypes", "GeometryBasics", "IntervalSets", "Observables"] -git-tree-sha1 = "9019b391d7d086e841cbeadc13511224bd029ab3" +git-tree-sha1 = "b0e2e3473af351011e598f9219afb521121edd2b" uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b" -version = "0.8.12" +version = "0.8.6" [[deps.ManualMemory]] git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd" @@ -1716,7 +1576,6 @@ version = "0.4.2" [[deps.Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" -version = "1.11.0" [[deps.MathTeXEngine]] deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "Test", "UnicodeFun"] @@ -1733,18 +1592,13 @@ version = "1.1.9" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.6+0" - -[[deps.Measures]] -git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" -uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" -version = "0.3.2" +version = "2.28.2+1" [[deps.MetaGraphsNext]] deps = ["Graphs", "JLD2", "SimpleTraits"] -git-tree-sha1 = "d2ecf4a20f4ac694987dd08ac489b7f7ff805f35" +git-tree-sha1 = "a385fe5aa1384647e55c0c8773457b71e9b08518" uuid = "fa8bd995-216d-47f1-8a91-f3b68fbeb377" -version = "0.7.1" +version = "0.7.0" [[deps.MicroCollections]] deps = ["Accessors", "BangBang", "InitialValues"] @@ -1766,7 +1620,6 @@ version = "1.2.0" [[deps.Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" -version = "1.11.0" [[deps.Mocking]] deps = ["Compat", "ExprTools"] @@ -1782,19 +1635,7 @@ version = "0.3.4" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2023.12.12" - -[[deps.MultipleTesting]] -deps = ["Distributions", "SpecialFunctions", "StatsBase"] -git-tree-sha1 = "1e98f8f732e7035c4333135b75605b74f3462b9b" -uuid = "f8716d33-7c4a-5097-896f-ce0ecbd3ef6b" -version = "0.6.0" - -[[deps.MultivariateStats]] -deps = ["Arpack", "Distributions", "LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI", "StatsBase"] -git-tree-sha1 = "816620e3aac93e5b5359e4fdaf23ca4525b00ddf" -uuid = "6f286f6a-111f-5878-ab1e-185364afe411" -version = "0.10.3" +version = "2023.1.10" [[deps.NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -1804,9 +1645,9 @@ version = "7.8.3" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "bdc9d30f151590aca0af22690f5ab7dc18a551cb" +git-tree-sha1 = "4a83c2e01027a0bfcea28589222f2df60b2e20cb" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.27" +version = "0.9.23" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1826,9 +1667,9 @@ version = "0.9.27" [[deps.NaNMath]] deps = ["OpenLibm_jll"] -git-tree-sha1 = "030ea22804ef91648f29b7ad3fc15fa49d0e6e71" +git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "1.0.3" +version = "1.0.2" [[deps.NameResolution]] deps = ["PrettyPrint"] @@ -1836,12 +1677,6 @@ git-tree-sha1 = "1a0fa0e9613f46c9b8c11eee38ebb4f590013c5e" uuid = "71a1bf82-56d0-4bbc-8a3c-48b961074391" version = "0.1.5" -[[deps.NearestNeighbors]] -deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "8a3271d8309285f4db73b4f662b1b290c715e85e" -uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.21" - [[deps.Netpbm]] deps = ["FileIO", "ImageCore", "ImageMetadata"] git-tree-sha1 = "d92b107dbb887293622df7697a2223f9f8176fcd" @@ -1850,9 +1685,9 @@ version = "1.1.1" [[deps.NetworkLayout]] deps = ["GeometryBasics", "LinearAlgebra", "Random", "Requires", "StaticArrays"] -git-tree-sha1 = "ef79ce223dddbdaf709779842211d6d6e85c1514" +git-tree-sha1 = "91bb2fedff8e43793650e7a677ccda6e6e6e166b" uuid = "46757867-2c16-5918-afeb-47bfcb05e46a" -version = "0.4.9" +version = "0.4.6" weakdeps = ["Graphs"] [deps.NetworkLayout.extensions] @@ -1868,9 +1703,9 @@ uuid = "510215fc-4207-5dde-b226-833fc4488ee2" version = "0.5.5" [[deps.OffsetArrays]] -git-tree-sha1 = "5e1897147d1ff8d98883cda2be2187dcf57d8f0c" +git-tree-sha1 = "1a27764e945a152f7ca7efa04de513d473e9542e" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.15.0" +version = "1.14.1" weakdeps = ["Adapt"] [deps.OffsetArrays.extensions] @@ -1885,13 +1720,13 @@ version = "1.3.5+1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.27+1" +version = "0.3.23+4" [[deps.OpenEXR]] deps = ["Colors", "FileIO", "OpenEXR_jll"] -git-tree-sha1 = "97db9e07fe2091882c765380ef58ec553074e9c7" +git-tree-sha1 = "327f53360fdb54df7ecd01e96ef1983536d1e633" uuid = "52e1d378-f018-4a11-a4be-720524705ac7" -version = "0.3.3" +version = "0.3.2" [[deps.OpenEXR_jll]] deps = ["Artifacts", "Imath_jll", "JLLWrappers", "Libdl", "Zlib_jll"] @@ -1902,11 +1737,11 @@ version = "3.2.4+0" [[deps.OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" -version = "0.8.1+4" +version = "0.8.1+2" [[deps.OpenML]] deps = ["ARFFFiles", "HTTP", "JSON", "Markdown", "Pkg", "Scratch"] -git-tree-sha1 = "63603b2b367107e87dbceda4e33c67aed17e50e0" +git-tree-sha1 = "6efb039ae888699d5a74fb593f6f3e10c7193e33" uuid = "8b6db2d4-7670-4922-a472-f9537c81ab66" version = "0.3.1" @@ -1924,21 +1759,21 @@ version = "1.4.3" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "7493f61f55a6cce7325f197443aa80d32554ba10" +git-tree-sha1 = "a028ee3cb5641cccc4c24e90c36b0a4f7707bdf5" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "3.0.15+3" +version = "3.0.14+0" [[deps.OpenSpecFun_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1346c9208249809840c91b26703912dff463d335" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "13652491f6856acfd2db29360e1bbcd4565d04f1" uuid = "efe28fd5-8261-553b-a9e1-b2916fc3738e" -version = "0.5.6+0" +version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "ab7edad78cdef22099f43c54ef77ac63c2c9cc64" +git-tree-sha1 = "d9b79c4eed437421ac4285148fcadf42e0700e89" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.10.0" +version = "1.9.4" [deps.Optim.extensions] OptimMOIExt = "MathOptInterface" @@ -1953,9 +1788,9 @@ uuid = "91d4177d-7536-5919-b921-800302f37372" version = "1.3.3+0" [[deps.OrderedCollections]] -git-tree-sha1 = "12f1439c4f986bb868acda6ea33ebc78e19b95ad" +git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.7.0" +version = "1.6.3" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] @@ -1964,9 +1799,9 @@ version = "10.42.0+1" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "966b85253e959ea89c53a9abebbf2e964fbf593b" +git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.32" +version = "0.11.31" [[deps.PNGFiles]] deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] @@ -1976,15 +1811,15 @@ version = "0.4.3" [[deps.PackageCompiler]] deps = ["Artifacts", "Glob", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "5d13e5b70011762b74f86fc08385303589f80272" +git-tree-sha1 = "48d4429862157ad5500c4f61444db1b8c32e0a2b" uuid = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d" -version = "2.2.0" +version = "2.1.17" [[deps.Packing]] deps = ["GeometryBasics"] -git-tree-sha1 = "bc5bf2ea3d5351edf285a06b0016788a121ce92c" +git-tree-sha1 = "ec3edfe723df33528e085e632414499f26650501" uuid = "19eb6ba3-879d-56ad-ad62-d5c202156566" -version = "0.5.1" +version = "0.5.0" [[deps.PaddedViews]] deps = ["OffsetArrays"] @@ -1994,9 +1829,9 @@ version = "0.5.12" [[deps.Pango_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "ed6834e95bd326c52d5675b4181386dfbe885afb" +git-tree-sha1 = "e127b609fb9ecba6f201ba7ab753d5a605d53801" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.55.5+0" +version = "1.54.1+0" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -2010,11 +1845,6 @@ git-tree-sha1 = "8489905bcdbcfac64d1daa51ca07c0d8f0283821" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" version = "2.8.1" -[[deps.Pipe]] -git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" -uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" -version = "1.3.0" - [[deps.Pixman_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b" @@ -2022,13 +1852,9 @@ uuid = "30392449-352a-5448-841d-b1acce4e97dc" version = "0.43.4+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"] +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 = "1.11.0" -weakdeps = ["REPL"] - - [deps.Pkg.extensions] - REPLExt = "REPL" +version = "1.10.0" [[deps.PkgVersion]] deps = ["Pkg"] @@ -2036,37 +1862,11 @@ git-tree-sha1 = "f9501cc0430a26bc3d156ae1b5b0c1b47af4d6da" uuid = "eebad327-c553-4316-9ea0-9fa01ccd7688" version = "0.3.3" -[[deps.PlotThemes]] -deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "41031ef3a1be6f5bbbf3e8073f210556daeae5ca" -uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" -version = "3.3.0" - [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "StableRNGs", "Statistics"] -git-tree-sha1 = "3ca9a356cd2e113c420f2c13bea19f8d3fb1cb18" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] +git-tree-sha1 = "7b1a9df27f072ac4c9c7cbe5efb198489258d1f5" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.4.3" - -[[deps.Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "PrecompileTools", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "TOML", "UUIDs", "UnicodeFun", "UnitfulLatexify", "Unzip"] -git-tree-sha1 = "dae01f8c2e069a683d3a6e17bbae5070ab94786f" -uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.40.9" - - [deps.Plots.extensions] - FileIOExt = "FileIO" - GeometryBasicsExt = "GeometryBasics" - IJuliaExt = "IJulia" - ImageInTerminalExt = "ImageInTerminal" - UnitfulExt = "Unitful" - - [deps.Plots.weakdeps] - FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" - GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326" - IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a" - ImageInTerminal = "d8c32880-2388-543b-8c61-d9f865259254" - Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" +version = "1.4.1" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] @@ -2115,14 +1915,13 @@ version = "0.4.2" [[deps.PrettyTables]] deps = ["Crayons", "LaTeXStrings", "Markdown", "PrecompileTools", "Printf", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "1101cd475833706e4d0e7b122218257178f48f34" +git-tree-sha1 = "66b20dd35966a748321d3b2537c4584cf40387c7" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.4.0" +version = "2.3.2" [[deps.Printf]] deps = ["Unicode"] uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" -version = "1.11.0" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] @@ -2131,45 +1930,21 @@ uuid = "92933f4c-e287-5a05-a399-4b506db050ca" version = "1.10.2" [[deps.PtrArrays]] -git-tree-sha1 = "1d36ef11a9aaf1e8b74dacc6a731dd1de8fd493d" +git-tree-sha1 = "77a42d78b6a92df47ab37e177b2deac405e1c88f" uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d" -version = "1.3.0" +version = "1.2.1" [[deps.QOI]] deps = ["ColorTypes", "FileIO", "FixedPointNumbers"] -git-tree-sha1 = "8b3fc30bc0390abdce15f8822c889f669baed73d" +git-tree-sha1 = "18e8f4d1426e965c7b532ddd260599e1510d26ce" uuid = "4b34888f-f399-49d4-9bb3-47ed5cae4e65" -version = "1.0.1" - -[[deps.Qt6Base_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Vulkan_Loader_jll", "Xorg_libSM_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_cursor_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "libinput_jll", "xkbcommon_jll"] -git-tree-sha1 = "492601870742dcd38f233b23c3ec629628c1d724" -uuid = "c0090381-4147-56d7-9ebc-da0b1113ec56" -version = "6.7.1+1" - -[[deps.Qt6Declarative_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6ShaderTools_jll"] -git-tree-sha1 = "e5dd466bf2569fe08c91a2cc29c1003f4797ac3b" -uuid = "629bc702-f1f5-5709-abd5-49b8460ea067" -version = "6.7.1+2" - -[[deps.Qt6ShaderTools_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll"] -git-tree-sha1 = "1a180aeced866700d4bebc3120ea1451201f16bc" -uuid = "ce943373-25bb-56aa-8eca-768745ed7b5a" -version = "6.7.1+1" - -[[deps.Qt6Wayland_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6Declarative_jll"] -git-tree-sha1 = "729927532d48cf79f49070341e1d918a65aba6b0" -uuid = "e99dba38-086e-5de3-a5b1-6e4c66e897c3" -version = "6.7.1+1" +version = "1.0.0" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "cda3b045cf9ef07a08ad46731f5a3165e56cf3da" +git-tree-sha1 = "1d587203cf851a51bf1ea31ad7ff89eff8d625ea" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.11.1" +version = "2.11.0" [deps.QuadGK.extensions] QuadGKEnzymeExt = "Enzyme" @@ -2178,14 +1953,12 @@ version = "2.11.1" Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9" [[deps.REPL]] -deps = ["InteractiveUtils", "Markdown", "Sockets", "StyledStrings", "Unicode"] +deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" -version = "1.11.0" [[deps.Random]] deps = ["SHA"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" -version = "1.11.0" [[deps.RangeArrays]] git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5" @@ -2214,12 +1987,6 @@ git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" version = "1.3.4" -[[deps.RecipesPipeline]] -deps = ["Dates", "NaNMath", "PlotUtils", "PrecompileTools", "RecipesBase"] -git-tree-sha1 = "45cf9fd0ca5839d06ef333c8201714e888486342" -uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.6.12" - [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" @@ -2239,31 +2006,29 @@ version = "1.3.0" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "852bd0f55565a9e973fcfee83a84413270224dc4" +git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.8.0" +version = "0.7.1" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "58cdd8fb2201a6267e1db87ff148dd6c1dbd8ad8" +git-tree-sha1 = "e60724fd3beea548353984dc61c943ecddb0e29a" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.5.1+0" +version = "0.4.3+0" [[deps.Roots]] -deps = ["Accessors", "CommonSolve", "Printf"] -git-tree-sha1 = "f233e0a3de30a6eed170b8e1be0440f732fdf456" +deps = ["Accessors", "ChainRulesCore", "CommonSolve", "Printf"] +git-tree-sha1 = "12e0a0e549c8545db615a2ec48664d56e1aad44d" uuid = "f2b01f46-fcfa-551c-844a-d8ac1e96c665" -version = "2.2.4" +version = "2.1.7" [deps.Roots.extensions] - RootsChainRulesCoreExt = "ChainRulesCore" RootsForwardDiffExt = "ForwardDiff" RootsIntervalRootFindingExt = "IntervalRootFinding" RootsSymPyExt = "SymPy" RootsSymPyPythonCallExt = "SymPyPythonCall" [deps.Roots.weakdeps] - ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" IntervalRootFinding = "d2bf35a9-74e0-55ec-b149-d360ff49b807" SymPy = "24249f21-da20-56a4-8eb1-6a02cf4ae2e6" @@ -2280,9 +2045,9 @@ version = "0.7.0" [[deps.SIMD]] deps = ["PrecompileTools"] -git-tree-sha1 = "fea870727142270bdf7624ad675901a1ee3b4c87" +git-tree-sha1 = "2803cab51702db743f3fda07dd1745aadfbf43bd" uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.7.1" +version = "3.5.0" [[deps.SIMDTypes]] git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c" @@ -2303,9 +2068,9 @@ version = "1.6.1" [[deps.SQLite_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "e84fab7d16107342d7638fbd519151d9a0d80720" +git-tree-sha1 = "004fffbe2711abdc7263a980bbb1af9620781dd9" uuid = "76ed43ae-9a5d-5a62-8c75-30186b810ce8" -version = "3.47.2+2" +version = "3.45.3+0" [[deps.ScientificTypes]] deps = ["CategoricalArrays", "ColorTypes", "Dates", "Distributions", "PrettyTables", "Reexport", "ScientificTypesBase", "StatisticalTraits", "Tables"] @@ -2318,12 +2083,6 @@ git-tree-sha1 = "a8e18eb383b5ecf1b5e6fc237eb39255044fd92b" uuid = "30f210dd-8aff-4c5f-94ba-8e64358c1161" version = "3.0.0" -[[deps.ScopedValues]] -deps = ["HashArrayMappedTries", "Logging"] -git-tree-sha1 = "1147f140b4c8ddab224c94efa9569fc23d63ab44" -uuid = "7e506255-f358-4e82-b7e4-beb19740aa63" -version = "1.3.0" - [[deps.Scratch]] deps = ["Dates"] git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386" @@ -2332,13 +2091,12 @@ version = "1.2.1" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "712fb0231ee6f9120e005ccd56297abbc053e7e0" +git-tree-sha1 = "ff11acffdb082493657550959d4feb4b6149e73a" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.4.8" +version = "1.4.5" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" -version = "1.11.0" [[deps.Setfield]] deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] @@ -2355,7 +2113,6 @@ version = "0.4.1" [[deps.SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" -version = "1.11.0" [[deps.ShiftedArrays]] git-tree-sha1 = "503688b59397b3307443af35cd953a13e8005c16" @@ -2380,9 +2137,9 @@ uuid = "73760f76-fbc4-59ce-8f25-708e95d2df96" version = "0.4.0" [[deps.SimpleBufferStream]] -git-tree-sha1 = "f305871d2f381d21527c770d4788c06c097c9bc1" +git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" -version = "1.2.0" +version = "1.1.0" [[deps.SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] @@ -2398,13 +2155,12 @@ version = "0.1.3" [[deps.SnpArrays]] deps = ["Adapt", "CSV", "CodecBzip2", "CodecXz", "CodecZlib", "CodecZstd", "DataFrames", "DelimitedFiles", "Glob", "LinearAlgebra", "LoopVectorization", "Missings", "Mmap", "Printf", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "Tables", "TranscodingStreams", "VariantCallFormat", "VectorizationBase"] -git-tree-sha1 = "810c0a75a336d63cb2b51561f1c1e3ccf6dbc2ad" +git-tree-sha1 = "d81de62a0acdbfd7d7ff3d64403eccf06c2fe986" uuid = "4e780e97-f5bf-4111-9dc4-b70aaf691b06" -version = "0.3.22" +version = "0.3.21" [[deps.Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" -version = "1.11.0" [[deps.SortingAlgorithms]] deps = ["DataStructures"] @@ -2415,7 +2171,7 @@ version = "1.2.1" [[deps.SparseArrays]] deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" -version = "1.11.0" +version = "1.10.0" [[deps.SparseInverseSubset]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] @@ -2425,15 +2181,15 @@ version = "0.1.2" [[deps.SparseMatricesCSR]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "6bc0c4cca30222586bde1ec5a0d9a3c6aaa51833" +git-tree-sha1 = "38677ca58e80b5cad2382e5a1848f93b054ad28d" uuid = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1" -version = "0.6.8" +version = "0.6.7" [[deps.SpecialFunctions]] deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "64cca0c26b4f31ba18f13f6c12af7c85f478cfde" +git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.5.0" +version = "2.4.0" weakdeps = ["ChainRulesCore"] [deps.SpecialFunctions.extensions] @@ -2482,9 +2238,9 @@ weakdeps = ["OffsetArrays", "StaticArrays"] [[deps.StaticArrays]] deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"] -git-tree-sha1 = "47091a0340a675c738b1304b58161f3b0839d454" +git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.9.10" +version = "1.9.7" weakdeps = ["ChainRulesCore", "Statistics"] [deps.StaticArrays.extensions] @@ -2498,9 +2254,9 @@ version = "1.4.3" [[deps.StatisticalMeasures]] deps = ["CategoricalArrays", "CategoricalDistributions", "Distributions", "LearnAPI", "LinearAlgebra", "MacroTools", "OrderedCollections", "PrecompileTools", "ScientificTypesBase", "StatisticalMeasuresBase", "Statistics", "StatsBase"] -git-tree-sha1 = "c1d4318fa41056b839dfbb3ee841f011fa6e8518" +git-tree-sha1 = "8b5a165b0ee2b361d692636bfb423b19abfd92b3" uuid = "a19d573c-0a75-4610-95b3-7071388c7541" -version = "0.1.7" +version = "0.1.6" [deps.StatisticalMeasures.extensions] LossFunctionsExt = "LossFunctions" @@ -2523,14 +2279,9 @@ uuid = "64bff920-2084-43da-a3e6-9bb72801c0c9" version = "3.4.0" [[deps.Statistics]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "ae3bb1eb3bba077cd276bc5cfc337cc65c3075c0" +deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" -version = "1.11.1" -weakdeps = ["SparseArrays"] - - [deps.Statistics.extensions] - SparseArraysExt = ["SparseArrays"] +version = "1.10.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] @@ -2546,9 +2297,9 @@ version = "0.34.4" [[deps.StatsFuns]] deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "b423576adc27097764a90e163157bcfc9acf0f46" +git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "1.3.2" +version = "1.3.1" weakdeps = ["ChainRulesCore", "InverseFunctions"] [deps.StatsFuns.extensions] @@ -2561,12 +2312,6 @@ git-tree-sha1 = "9022bcaa2fc1d484f1326eaa4db8db543ca8c66d" uuid = "3eaba693-59b7-5ba5-a881-562e759f1c8d" version = "0.7.4" -[[deps.StatsPlots]] -deps = ["AbstractFFTs", "Clustering", "DataStructures", "Distributions", "Interpolations", "KernelDensity", "LinearAlgebra", "MultivariateStats", "NaNMath", "Observables", "Plots", "RecipesBase", "RecipesPipeline", "Reexport", "StatsBase", "TableOperations", "Tables", "Widgets"] -git-tree-sha1 = "3b1dcbf62e469a67f6733ae493401e53d92ff543" -uuid = "f3b207a7-027a-5e70-b257-86293d7955fd" -version = "0.15.7" - [[deps.StringEncodings]] deps = ["Libiconv_jll"] git-tree-sha1 = "b765e46ba27ecf6b44faf70df40c57aa3a547dcb" @@ -2575,26 +2320,20 @@ version = "0.3.7" [[deps.StringManipulation]] deps = ["PrecompileTools"] -git-tree-sha1 = "a6b1675a536c5ad1a60e5a5153e1fee12eb146e3" +git-tree-sha1 = "a04cabe79c5f01f4d723cc6704070ada0b9d46d5" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" -version = "0.4.0" - -[[deps.StringViews]] -git-tree-sha1 = "ec4bf39f7d25db401bcab2f11d2929798c0578e5" -uuid = "354b36f9-a18e-4713-926e-db85100087ba" -version = "1.3.4" +version = "0.3.4" [[deps.StructArrays]] deps = ["ConstructionBase", "DataAPI", "Tables"] -git-tree-sha1 = "9537ef82c42cdd8c5d443cbc359110cbb36bae10" +git-tree-sha1 = "f4dc295e983502292c4c3f951dbb4e985e35b3be" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.21" -weakdeps = ["Adapt", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "SparseArrays", "StaticArrays"] +version = "0.6.18" +weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"] [deps.StructArrays.extensions] StructArraysAdaptExt = "Adapt" - StructArraysGPUArraysCoreExt = ["GPUArraysCore", "KernelAbstractions"] - StructArraysLinearAlgebraExt = "LinearAlgebra" + StructArraysGPUArraysCoreExt = "GPUArraysCore" StructArraysSparseArraysExt = "SparseArrays" StructArraysStaticArraysExt = "StaticArrays" @@ -2604,10 +2343,6 @@ git-tree-sha1 = "159331b30e94d7b11379037feeb9b690950cace8" uuid = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" version = "1.11.0" -[[deps.StyledStrings]] -uuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b" -version = "1.11.0" - [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" @@ -2615,7 +2350,7 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[deps.SuiteSparse_jll]] deps = ["Artifacts", "Libdl", "libblastrampoline_jll"] uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" -version = "7.7.0+0" +version = "7.2.1+1" [[deps.TMLE]] deps = ["AbstractDifferentiation", "AutoHashEquals", "CategoricalArrays", "Combinatorics", "Distributions", "GLM", "Graphs", "HypothesisTests", "LogExpFunctions", "MLJBase", "MLJGLMInterface", "MLJModels", "MetaGraphsNext", "Missings", "OrderedCollections", "PrecompileTools", "Random", "SplitApplyCombine", "Statistics", "TableOperations", "Tables", "Zygote"] @@ -2646,9 +2381,9 @@ version = "1.0.3" [[deps.TZJData]] deps = ["Artifacts"] -git-tree-sha1 = "006a327222dda856e2304959e566ff0104ac8594" +git-tree-sha1 = "1607ad46cf8d642aa779a1d45af1c8620dbf6915" uuid = "dc5dba14-91b3-4cab-a142-028a31da12f7" -version = "1.3.1+2024b" +version = "1.2.0+2024a" [[deps.TableOperations]] deps = ["SentinelArrays", "Tables", "Test"] @@ -2682,7 +2417,6 @@ version = "0.1.1" [[deps.Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" -version = "1.11.0" [[deps.TextWrap]] git-tree-sha1 = "43044b737fa70bc12f6105061d3da38f881a3e3c" @@ -2697,15 +2431,15 @@ version = "0.5.2" [[deps.TiffImages]] deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "SIMD", "UUIDs"] -git-tree-sha1 = "3c0faa42f2bd3c6d994b06286bba2328eae34027" +git-tree-sha1 = "bc7fd5c91041f44636b2c134041f7e5263ce58ae" uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" -version = "0.11.2" +version = "0.10.0" [[deps.TimeZones]] -deps = ["Artifacts", "Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] -git-tree-sha1 = "fcbcffdc11524d08523e92ae52214b29d90b50bb" +deps = ["Dates", "Downloads", "InlineStrings", "Mocking", "Printf", "Scratch", "TZJData", "Unicode", "p7zip_jll"] +git-tree-sha1 = "b92aebdd3555f3a7e3267cf17702033c2814ef48" uuid = "f269a46b-ccf7-5d73-abea-4c690281aa53" -version = "1.20.0" +version = "1.18.0" weakdeps = ["RecipesBase"] [deps.TimeZones.extensions] @@ -2718,13 +2452,12 @@ uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" version = "0.9.13" [[deps.Transducers]] -deps = ["Accessors", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "SplittablesBase", "Tables"] -git-tree-sha1 = "7deeab4ff96b85c5f72c824cae53a1398da3d1cb" +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 = "0.4.84" +version = "0.4.82" [deps.Transducers.extensions] - TransducersAdaptExt = "Adapt" TransducersBlockArraysExt = "BlockArrays" TransducersDataFramesExt = "DataFrames" TransducersLazyArraysExt = "LazyArrays" @@ -2732,7 +2465,6 @@ version = "0.4.84" TransducersReferenceablesExt = "Referenceables" [deps.Transducers.weakdeps] - Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" LazyArrays = "5078a376-72f3-5289-bfd5-ec5146d43c02" @@ -2752,7 +2484,6 @@ version = "1.5.1" [[deps.UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" -version = "1.11.0" [[deps.UnPack]] git-tree-sha1 = "387c1f73762231e86e0c9c5443ce3b4a0a9a0c2b" @@ -2761,7 +2492,6 @@ version = "1.0.2" [[deps.Unicode]] uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5" -version = "1.11.0" [[deps.UnicodeFun]] deps = ["REPL"] @@ -2771,34 +2501,25 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "c0667a8e676c53d390a09dc6870b3d8d6650e2bf" +git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.22.0" +version = "1.21.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] ConstructionBaseUnitfulExt = "ConstructionBase" InverseFunctionsUnitfulExt = "InverseFunctions" -[[deps.UnitfulLatexify]] -deps = ["LaTeXStrings", "Latexify", "Unitful"] -git-tree-sha1 = "975c354fcd5f7e1ddcc1f1a23e6e091d99e99bc8" -uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728" -version = "1.6.4" - [[deps.UnsafeAtomics]] -git-tree-sha1 = "b13c4edda90890e5b04ba24e20a310fbe6f249ff" +git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" -version = "0.3.0" -weakdeps = ["LLVM"] - - [deps.UnsafeAtomics.extensions] - UnsafeAtomicsLLVM = ["LLVM"] +version = "0.2.1" -[[deps.Unzip]] -git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" -uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" -version = "0.2.0" +[[deps.UnsafeAtomicsLLVM]] +deps = ["LLVM", "UnsafeAtomics"] +git-tree-sha1 = "bf2c553f25e954a9b38c9c0593a59bb13113f9e5" +uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" +version = "0.1.5" [[deps.VariantCallFormat]] deps = ["Automa", "BGZFStreams", "BioGenerics", "BufferedStreams"] @@ -2808,27 +2529,9 @@ version = "0.5.6" [[deps.VectorizationBase]] deps = ["ArrayInterface", "CPUSummary", "HostCPUFeatures", "IfElse", "LayoutPointers", "Libdl", "LinearAlgebra", "SIMDTypes", "Static", "StaticArrayInterface"] -git-tree-sha1 = "4ab62a49f1d8d9548a1c8d1a75e5f55cf196f64e" +git-tree-sha1 = "e7f5b81c65eb858bed630fe006837b935518aca5" uuid = "3d5dd08c-fd9d-11e8-17fa-ed2836048c2f" -version = "0.21.71" - -[[deps.Vulkan_Loader_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Wayland_jll", "Xorg_libX11_jll", "Xorg_libXrandr_jll", "xkbcommon_jll"] -git-tree-sha1 = "2f0486047a07670caad3a81a075d2e518acc5c59" -uuid = "a44049a8-05dd-5a78-86c9-5fde0876e88c" -version = "1.3.243+0" - -[[deps.Wayland_jll]] -deps = ["Artifacts", "EpollShim_jll", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "85c7811eddec9e7f22615371c3cc81a504c508ee" -uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" -version = "1.21.0+2" - -[[deps.Wayland_protocols_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "5db3e9d307d32baba7067b13fc7b5aa6edd4a19a" -uuid = "2381bf8a-dfd0-557d-9999-79630e7b1b91" -version = "1.36.0+0" +version = "0.21.70" [[deps.WeakRefStrings]] deps = ["DataAPI", "InlineStrings", "Parsers"] @@ -2836,18 +2539,6 @@ git-tree-sha1 = "b1be2855ed9ed8eac54e5caff2afcdb442d52c23" uuid = "ea10d353-3f73-51f8-a26c-33c1cb351aa5" version = "1.4.2" -[[deps.WebP]] -deps = ["CEnum", "ColorTypes", "FileIO", "FixedPointNumbers", "ImageCore", "libwebp_jll"] -git-tree-sha1 = "aa1ca3c47f119fbdae8770c29820e5e6119b83f2" -uuid = "e3aaa7dc-3e4b-44e0-be63-ffb868ccd7c1" -version = "0.1.3" - -[[deps.Widgets]] -deps = ["Colors", "Dates", "Observables", "OrderedCollections"] -git-tree-sha1 = "e9aeb174f95385de31e70bd15fa066a505ea82b9" -uuid = "cc8bc4a8-27d6-5769-a93b-9d913e69aa62" -version = "0.6.7" - [[deps.WoodburyMatrices]] deps = ["LinearAlgebra", "SparseArrays"] git-tree-sha1 = "c1a7aa6219628fcd757dede0ca95e245c5cd9511" @@ -2881,165 +2572,69 @@ version = "2.0.1+0" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6" +git-tree-sha1 = "1165b0443d0eca63ac1e32b8c0eb69ed2f4f8127" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.13.5+0" +version = "2.13.3+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "7d1671acbe47ac88e981868a078bd6b4e27c5191" +git-tree-sha1 = "a54ee957f4c86b526460a720dbc882fa5edcbefc" uuid = "aed1982a-8fda-507f-9586-7b0439959a61" -version = "1.1.42+0" +version = "1.1.41+0" [[deps.XZ_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "beef98d5aad604d9e7d60b2ece5181f7888e2fd6" +git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632" uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800" -version = "5.6.4+0" - -[[deps.Xorg_libICE_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "326b4fea307b0b39892b3e85fa451692eda8d46c" -uuid = "f67eecfb-183a-506d-b269-f58e52b52d7c" -version = "1.1.1+0" - -[[deps.Xorg_libSM_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libICE_jll"] -git-tree-sha1 = "3796722887072218eabafb494a13c963209754ce" -uuid = "c834827a-8449-5923-a945-d239c165b7dd" -version = "1.2.4+0" +version = "5.4.6+0" [[deps.Xorg_libX11_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] -git-tree-sha1 = "9dafcee1d24c4f024e7edc92603cedba72118283" +git-tree-sha1 = "afead5aba5aa507ad5a3bf01f58f82c8d1403495" uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" -version = "1.8.6+3" +version = "1.8.6+0" [[deps.Xorg_libXau_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "e9216fdcd8514b7072b43653874fd688e4c6c003" +git-tree-sha1 = "6035850dcc70518ca32f012e46015b9beeda49d8" uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.12+0" - -[[deps.Xorg_libXcursor_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] -git-tree-sha1 = "807c226eaf3651e7b2c468f687ac788291f9a89b" -uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" -version = "1.2.3+0" +version = "1.0.11+0" [[deps.Xorg_libXdmcp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "89799ae67c17caa5b3b5a19b8469eeee474377db" +git-tree-sha1 = "34d526d318358a859d7de23da945578e8e8727b7" uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.5+0" +version = "1.1.4+0" [[deps.Xorg_libXext_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "d7155fea91a4123ef59f42c4afb5ab3b4ca95058" +git-tree-sha1 = "d2d1a5c49fae4ba39983f63de6afcbea47194e85" uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3" -version = "1.3.6+3" - -[[deps.Xorg_libXfixes_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "6fcc21d5aea1a0b7cce6cab3e62246abd1949b86" -uuid = "d091e8ba-531a-589c-9de9-94069b037ed8" -version = "6.0.0+0" - -[[deps.Xorg_libXi_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXext_jll", "Xorg_libXfixes_jll"] -git-tree-sha1 = "984b313b049c89739075b8e2a94407076de17449" -uuid = "a51aa0fd-4e3c-5386-b890-e753decda492" -version = "1.8.2+0" - -[[deps.Xorg_libXinerama_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXext_jll"] -git-tree-sha1 = "a1a7eaf6c3b5b05cb903e35e8372049b107ac729" -uuid = "d1454406-59df-5ea1-beac-c340f2130bc3" -version = "1.1.5+0" - -[[deps.Xorg_libXrandr_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libXext_jll", "Xorg_libXrender_jll"] -git-tree-sha1 = "b6f664b7b2f6a39689d822a6300b14df4668f0f4" -uuid = "ec84b674-ba8e-5d96-8ba1-2a689ba10484" -version = "1.5.4+0" +version = "1.3.6+0" [[deps.Xorg_libXrender_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "a490c6212a0e90d2d55111ac956f7c4fa9c277a6" +git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe" uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" -version = "0.9.11+1" +version = "0.9.11+0" [[deps.Xorg_libpthread_stubs_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "c57201109a9e4c0585b208bb408bc41d205ac4e9" +git-tree-sha1 = "8fdda4c692503d44d04a0603d9ac0982054635f9" uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.2+0" +version = "0.1.1+0" [[deps.Xorg_libxcb_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "1a74296303b6524a0472a8cb12d3d87a78eb3612" +git-tree-sha1 = "bcd466676fef0878338c61e655629fa7bbc69d8e" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.17.0+3" - -[[deps.Xorg_libxkbfile_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] -git-tree-sha1 = "dbc53e4cf7701c6c7047c51e17d6e64df55dca94" -uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" -version = "1.1.2+1" - -[[deps.Xorg_xcb_util_cursor_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_jll", "Xorg_xcb_util_renderutil_jll"] -git-tree-sha1 = "04341cb870f29dcd5e39055f895c39d016e18ccd" -uuid = "e920d4aa-a673-5f3a-b3d7-f755a4d47c43" -version = "0.1.4+0" - -[[deps.Xorg_xcb_util_image_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" -uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" -version = "0.4.0+1" - -[[deps.Xorg_xcb_util_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] -git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" -uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" -version = "0.4.0+1" - -[[deps.Xorg_xcb_util_keysyms_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" -uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" -version = "0.4.0+1" - -[[deps.Xorg_xcb_util_renderutil_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" -uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" -version = "0.3.9+1" - -[[deps.Xorg_xcb_util_wm_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] -git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" -uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" -version = "0.4.1+1" - -[[deps.Xorg_xkbcomp_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"] -git-tree-sha1 = "ab2221d309eda71020cdda67a973aa582aa85d69" -uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" -version = "1.4.6+1" - -[[deps.Xorg_xkeyboard_config_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"] -git-tree-sha1 = "691634e5453ad362044e2ad653e79f3ee3bb98c3" -uuid = "33bec58e-1273-512f-9401-5d533626f822" -version = "2.39.0+0" +version = "1.17.0+0" [[deps.Xorg_xtrans_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6dba04dbfb72ae3ebe5418ba33d087ba8aa8cb00" +git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.5.1+0" +version = "1.5.0+0" [[deps.YAML]] deps = ["Base64", "Dates", "Printf", "StringEncodings"] @@ -3054,15 +2649,15 @@ version = "1.2.13+1" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "622cf78670d067c738667aaa96c553430b65e269" +git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.7+0" +version = "1.5.6+0" [[deps.Zygote]] deps = ["AbstractFFTs", "ChainRules", "ChainRulesCore", "DiffRules", "Distributed", "FillArrays", "ForwardDiff", "GPUArrays", "GPUArraysCore", "IRTools", "InteractiveUtils", "LinearAlgebra", "LogExpFunctions", "MacroTools", "NaNMath", "PrecompileTools", "Random", "Requires", "SparseArrays", "SpecialFunctions", "Statistics", "ZygoteRules"] -git-tree-sha1 = "0b3c944f5d2d8b466c5d20a84c229c17c528f49e" +git-tree-sha1 = "19c586905e78a26f7e4e97f81716057bd6b1bc54" uuid = "e88e6eb3-aa80-5325-afca-941959d7151f" -version = "0.6.75" +version = "0.6.70" [deps.Zygote.extensions] ZygoteColorsExt = "Colors" @@ -3076,21 +2671,9 @@ version = "0.6.75" [[deps.ZygoteRules]] deps = ["ChainRulesCore", "MacroTools"] -git-tree-sha1 = "434b3de333c75fc446aa0d19fc394edafd07ab08" +git-tree-sha1 = "27798139afc0a2afa7b1824c206d5e87ea587a00" uuid = "700de1a5-db45-46bc-99cf-38207098b444" -version = "0.2.7" - -[[deps.eudev_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"] -git-tree-sha1 = "431b678a28ebb559d224c0b6b6d01afce87c51ba" -uuid = "35ca27e7-8b34-5b7f-bca9-bdc33f59eb06" -version = "3.2.9+0" - -[[deps.fzf_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6e50f145003024df4f5cb96c7fce79466741d601" -uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.56.3+0" +version = "0.2.5" [[deps.glmnet_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -3098,12 +2681,6 @@ git-tree-sha1 = "31adae3b983b579a1fbd7cfd43a4bc0d224c2f5a" uuid = "78c6b45d-5eaf-5d68-bcfb-a5a2cb06c27f" version = "2.0.13+0" -[[deps.gperf_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "0ba42241cb6809f1a278d0bcb976e0483c3f1f2d" -uuid = "1a1c6b14-54f6-533d-8383-74cd7377aa70" -version = "3.1.1+1" - [[deps.isoband_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c" @@ -3118,9 +2695,9 @@ version = "1.1.2+2" [[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "522c1df09d05a71785765d19c9524661234738e9" +git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d" uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" -version = "3.11.0+0" +version = "3.9.0+0" [[deps.libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Zlib_jll"] @@ -3131,19 +2708,7 @@ version = "0.15.2+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.11.0+0" - -[[deps.libdecor_jll]] -deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] -git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" -uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" -version = "0.2.2+0" - -[[deps.libevdev_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "141fe65dc3efabb0b1d5ba74e91f6ad26f84cc22" -uuid = "2db6ffa8-e38f-5e21-84af-90c45d0032cc" -version = "1.11.0+0" +version = "5.8.0+1" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -3151,23 +2716,17 @@ git-tree-sha1 = "8a22cf860a7d27e4f3498a0fe0811a7957badb38" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" version = "2.0.3+0" -[[deps.libinput_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "eudev_jll", "libevdev_jll", "mtdev_jll"] -git-tree-sha1 = "ad50e5b90f222cfe78aa3d5183a20a12de1322ce" -uuid = "36db933b-70db-51c0-b978-0f229ee0e533" -version = "1.18.0+0" - [[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "d7b5bbf1efbafb5eca466700949625e07533aff2" +git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" -version = "1.6.45+1" +version = "1.6.43+1" [[deps.libsixel_jll]] -deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "libpng_jll"] -git-tree-sha1 = "c1733e347283df07689d71d61e14be986e49e47a" +deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"] +git-tree-sha1 = "d4f63314c8aa1e48cd22aa0c17ed76cd1ae48c3c" uuid = "075b6546-f08a-558a-be8f-8157d0f608a5" -version = "1.10.5+0" +version = "1.10.3+0" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] @@ -3175,22 +2734,10 @@ git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" version = "1.3.7+2" -[[deps.libwebp_jll]] -deps = ["Artifacts", "Giflib_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libglvnd_jll", "Libtiff_jll", "libpng_jll"] -git-tree-sha1 = "d2408cac540942921e7bd77272c32e58c33d8a77" -uuid = "c5f90fcd-3b7e-5836-afba-fc50a0988cb2" -version = "1.5.0+0" - -[[deps.mtdev_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11" -uuid = "009596ad-96f7-51b1-9f1b-5ce2d5e8a71e" -version = "1.1.6+0" - [[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" -version = "1.59.0+0" +version = "1.52.0+1" [[deps.oneTBB_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -3204,19 +2751,13 @@ uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" version = "17.4.0+2" [[deps.x264_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "35976a1216d6c066ea32cba2150c4fa682b276fc" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" -version = "2021.5.5+0" +version = "10164.0.0+0" [[deps.x265_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "dcc541bb19ed5b0ede95581fb2e41ecf179527d2" uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" -version = "3.5.0+0" - -[[deps.xkbcommon_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "63406453ed9b33a0df95d570816d5366c92b7809" -uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "1.4.1+2" +version = "3.6.0+0" diff --git a/Project.toml b/Project.toml index e9fc3f9..cdac9ef 100644 --- a/Project.toml +++ b/Project.toml @@ -16,21 +16,17 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5" JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -JSON3 = "0f8b85d8-7281-11e9-16c2-39a750bddbf1" LogExpFunctions = "2ab3a3ac-af41-5b50-aa03-7779005ae688" MKL = "33e6dc65-8f57-5167-99aa-e5a354878fb2" Mmap = "a63ad114-7e13-5084-954f-fe012c677804" -MultipleTesting = "f8716d33-7c4a-5097-896f-ce0ecbd3ef6b" OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" PackageCompiler = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d" -Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b" SnpArrays = "4e780e97-f5bf-4111-9dc4-b70aaf691b06" StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -StatsPlots = "f3b207a7-027a-5e70-b257-86293d7955fd" TMLE = "8afdd2fb-6e73-43df-8b62-b1650cd9c8cf" TMLECLI = "2573d147-4098-46ba-9db2-8608d210ccac" YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" @@ -44,19 +40,12 @@ CairoMakie = "0.12" CategoricalArrays = "0.10" Combinatorics = "1.0" DataFrames = "1.2" -Glob = "1.3.1" -HTTP = "1.10.15" -JSON3 = "1.14.1" MKL = "0.7" -MultipleTesting = "0.6.0" OrderedCollections = "1.6.3" PackageCompiler = "2.1.17" -Plots = "1.40.9" SnpArrays = "0.3" StableRNGs = "1.0.1" Statistics = "1.10" -StatsBase = "0.34.4" -StatsPlots = "0.15.7" TMLE = "0.17" YAML = "0.4.9" julia = "1.10, 1" From abef21034f4577bd214b98b525b6855ce832a639 Mon Sep 17 00:00:00 2001 From: Joshua Slaughter Date: Mon, 26 May 2025 12:10:40 +0100 Subject: [PATCH 16/17] harmonization of estimands; 0x00 will be encoded as major-major relative to the observed population --- src/inputs_from_config.jl | 68 ++++++++++++++++----------------------- 1 file changed, 28 insertions(+), 40 deletions(-) diff --git a/src/inputs_from_config.jl b/src/inputs_from_config.jl index 3d638c0..9990df6 100644 --- a/src/inputs_from_config.jl +++ b/src/inputs_from_config.jl @@ -233,49 +233,37 @@ function read_bed_chromosome(bedprefix) end function get_genotypes_from_beds(bedprefix, outprefix) - snpdata = read_bed_chromosome(bedprefix) - genotypes = DataFrame(convert(Matrix{UInt8}, snpdata.snparray), snpdata.snp_info."snpid", makeunique=true) - genotype_map = Union{UInt8, Missing}[0, missing, 1, 2] - for col in names(genotypes) - genotypes[!, col] = [genotype_map[x+1] for x in genotypes[!, col]] - end - - vₘ, v₀, v₁, v₂ = [], [], [], [] - - for col in names(genotypes) - var_counts = countmap(genotypes[!, col]) - if haskey(var_counts, missing) - push!(vₘ, var_counts[missing]) - else - push!(vₘ, 0) - end - if haskey(var_counts, 0x00) - push!(v₀, var_counts[0x00]) - else - push!(v₀, 0) - end - if haskey(var_counts, 0x01) - push!(v₁, var_counts[0x01]) - else - push!(v₁, 0) - end - if haskey(var_counts, 0x02) - push!(v₂, var_counts[0x02]) - else - push!(v₂, 0) + snpdata = read_bed_chromosome(bedprefix) + code_map = Union{UInt8,Missing}[0, missing, 1, 2] + geno_mat = map(x -> code_map[x+1], snpdata.snparray) + genotypes = DataFrame(geno_mat, snpdata.snp_info.snpid; makeunique=true) + insertcols!(genotypes, 1, :SAMPLE_ID => snpdata.person_info.iid) + counts = countmap.(eachcol(select(genotypes, Not(:SAMPLE_ID)))) + + mapping_df = DataFrame( + snpid = snpdata.snp_info.snpid, + allele1 = snpdata.snp_info.allele1, + allele2 = snpdata.snp_info.allele2, + vₘ = get.(counts, missing, 0), + v₀ = get.(counts, UInt8(0), 0), + v₁ = get.(counts, UInt8(1), 0), + v₂ = get.(counts, UInt8(2), 0), + ) + mapping_df.n = mapping_df.v₀ .+ mapping_df.v₁ .+ mapping_df.v₂ + + # if v₀ < v₂, swap all 0↔2 so that 0 always marks the major homozygote + for (i, snpid) in enumerate(mapping_df.snpid) + if mapping_df.v₀[i] < mapping_df.v₂[i] + col = Symbol(snpid) + genotypes[!, col] = map(x -> x === UInt8(0) ? UInt8(2) : x === UInt8(2) ? UInt8(0) : x, genotypes[!, col]) + x = mapping_df.v₀[i] + mapping_df.v₀[i] = mapping_df.v₂[i] + mapping_df.v₂[i] = x end end + mapping_df.MAF = (mapping_df.v₁ .+ (2 .* mapping_df.v₂)) ./ (2 .* (mapping_df.v₀ .+ mapping_df.v₁ .+ mapping_df.v₂)) + CSV.write("$(outprefix).mapping.txt", mapping_df) - insertcols!(genotypes, 1, :SAMPLE_ID => snpdata.person_info."iid") - - result_df = hcat(select(snpdata.snp_info, "snpid", "allele1", "allele2"), DataFrame( - vₘ = vₘ, - v₀ = v₀, - v₁ = v₁, - v₂ = v₂ - )) - - CSV.write(string(outprefix, ".mapping.txt"), result_df) return genotypes end From 086ee830e3750871a793ad4ea83cd31366f4a5a4 Mon Sep 17 00:00:00 2001 From: Joshua Slaughter Date: Mon, 26 May 2025 12:15:13 +0100 Subject: [PATCH 17/17] allele orientation fix --- src/inputs_from_config.jl | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/src/inputs_from_config.jl b/src/inputs_from_config.jl index 9990df6..171bce8 100644 --- a/src/inputs_from_config.jl +++ b/src/inputs_from_config.jl @@ -256,9 +256,15 @@ function get_genotypes_from_beds(bedprefix, outprefix) if mapping_df.v₀[i] < mapping_df.v₂[i] col = Symbol(snpid) genotypes[!, col] = map(x -> x === UInt8(0) ? UInt8(2) : x === UInt8(2) ? UInt8(0) : x, genotypes[!, col]) - x = mapping_df.v₀[i] + + # Swap alleles and counts respectively + allele2 = mapping_df.allele2[i] + mapping_df.allele2[i] = mapping_df.allele1[i] + mapping_df.allele1[i] = allele2 + + v₂ = mapping_df.v₀[i] mapping_df.v₀[i] = mapping_df.v₂[i] - mapping_df.v₂[i] = x + mapping_df.v₂[i] = v₂ end end mapping_df.MAF = (mapping_df.v₁ .+ (2 .* mapping_df.v₂)) ./ (2 .* (mapping_df.v₀ .+ mapping_df.v₁ .+ mapping_df.v₂))