[⚡ AUTOMATED]: Pkg upgrade for 2022-07-29

Files changed:\nM	Manifest.toml

Manifest.toml

@@ -13,9 +13,9 @@ version = "0.3.4"
 
 [[Adapt]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f"
+git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f"
 uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-version = "3.3.3"
+version = "3.4.0"
 
 [[ArgParse]]
 deps = ["Logging", "TextWrap"]
@@ -173,9 +173,9 @@ version = "2.0.5"
 
 [[BioGenerics]]
 deps = ["TranscodingStreams"]
-git-tree-sha1 = "6d3f3b474b3df2e83dc67ad12ec63aee4eb5241b"
+git-tree-sha1 = "0b581906418b93231d391b5dd78831fdc2da0c82"
 uuid = "47718e42-2ac5-11e9-14af-e5595289c2ea"
-version = "0.1.1"
+version = "0.1.2"
 
 [[BioSequences]]
 deps = ["BioGenerics", "BioSymbols", "Combinatorics", "IndexableBitVectors", "Printf", "Random", "StableRNGs", "Twiddle"]
@@ -249,9 +249,9 @@ version = "0.1.1"
 
 [[CSV]]
 deps = ["CodecZlib", "Dates", "FilePathsBase", "InlineStrings", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode", "WeakRefStrings"]
-git-tree-sha1 = "49f14b6c56a2da47608fe30aed711b5882264d7a"
+git-tree-sha1 = "873fb188a4b9d76549b81465b1f75c82aaf59238"
 uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
-version = "0.9.11"
+version = "0.10.4"
 
 [[Cairo_jll]]
 deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
@@ -303,9 +303,9 @@ version = "0.14.2"
 
 [[CodeTracking]]
 deps = ["InteractiveUtils", "UUIDs"]
-git-tree-sha1 = "6d4fa04343a7fc9f9cb9cff9558929f3d2752717"
+git-tree-sha1 = "1833bda4a027f4b2a1c984baddcf755d77266818"
 uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
-version = "1.0.9"
+version = "1.1.0"
 
 [[CodecBase]]
 deps = ["TranscodingStreams"]
@@ -657,9 +657,9 @@ version = "1.1.0"
 
 [[FileIO]]
 deps = ["Pkg", "Requires", "UUIDs"]
-git-tree-sha1 = "9267e5f50b0e12fdfd5a2455534345c4cf2c7f7a"
+git-tree-sha1 = "94f5101b96d2d968ace56f7f2db19d0a5f592e28"
 uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.14.0"
+version = "1.15.0"
 
 [[FilePathsBase]]
 deps = ["Compat", "Dates", "Mmap", "Printf", "Test", "UUIDs"]
@@ -1236,9 +1236,9 @@ version = "0.2.5"
 
 [[Krylov]]
 deps = ["LinearAlgebra", "Printf", "SparseArrays"]
-git-tree-sha1 = "7f0a89bd74c30aa7ff96c4bf1bc884c39663a621"
+git-tree-sha1 = "a2327039e1c84615e22d662adb3df113caf44b70"
 uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
-version = "0.8.2"
+version = "0.8.3"
 
 [[KrylovKit]]
 deps = ["LinearAlgebra", "Printf"]
@@ -1393,9 +1393,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
 [[LinearSolve]]
 deps = ["ArrayInterfaceCore", "DocStringExtensions", "FastLapackInterface", "GPUArraysCore", "IterativeSolvers", "KLU", "Krylov", "KrylovKit", "LinearAlgebra", "RecursiveFactorization", "Reexport", "SciMLBase", "Setfield", "SparseArrays", "SuiteSparse", "UnPack"]
-git-tree-sha1 = "92cc95b66f1459d230af9e67089eeeea6c6b2ee9"
+git-tree-sha1 = "5d21d76f1d5afdfd01f910e7ff68f25d9da39ad3"
 uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
-version = "1.23.0"
+version = "1.23.1"
 
 [[LittleCMS_jll]]
 deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pkg"]
@@ -1405,9 +1405,9 @@ version = "2.12.0+0"
 
 [[LogExpFunctions]]
 deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "7c88f63f9f0eb5929f15695af9a4d7d3ed278a91"
+git-tree-sha1 = "361c2b088575b07946508f135ac556751240091c"
 uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.16"
+version = "0.3.17"
 
 [[Logging]]
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
@@ -1554,6 +1554,11 @@ git-tree-sha1 = "4e675d6e9ec02061800d6cfb695812becbd03cdf"
 uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0"
 version = "1.0.4"
 
+[[MyterialColors]]
+git-tree-sha1 = "01d8466fb449436348999d7c6ad740f8f853a579"
+uuid = "1c23619d-4212-4747-83aa-717207fae70f"
+version = "0.3.0"
+
 [[NLSolversBase]]
 deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"]
 git-tree-sha1 = "50310f934e55e5ca3912fb941dec199b49ca9b68"
@@ -1583,6 +1588,12 @@ git-tree-sha1 = "b086b7ea07f8e38cf122f5016af580881ac914fe"
 uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
 version = "0.3.7"
 
+[[NamedArrays]]
+deps = ["Combinatorics", "DataStructures", "DelimitedFiles", "InvertedIndices", "LinearAlgebra", "Random", "Requires", "SparseArrays", "Statistics"]
+git-tree-sha1 = "2fd5787125d1a93fbe30961bd841707b8a80d75b"
+uuid = "86f7a689-2022-50b4-a561-43c23ac3c673"
+version = "0.9.6"
+
 [[NearestNeighbors]]
 deps = ["Distances", "StaticArrays"]
 git-tree-sha1 = "0e353ed734b1747fc20cd4cba0edd9ac027eff6a"
@@ -1825,22 +1836,22 @@ uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 version = "1.4.2"
 
 [[PopGen]]
-deps = ["Clustering", "DataFrames", "Distributions", "MultipleTesting", "MultivariateStats", "PooledArrays", "PopGenCore", "ProgressMeter", "Random", "Reexport", "StatsBase"]
-git-tree-sha1 = "f696f6c338adc3d328cd8e9b52fabb2c84fe5db3"
+deps = ["Clustering", "DataFrames", "Distances", "Distributions", "MultipleTesting", "MultivariateStats", "NamedArrays", "OnlineStats", "PooledArrays", "PopGenCore", "Random", "Reexport", "StatsBase", "TSne", "Term"]
+git-tree-sha1 = "fefba180135f55d6568702ee2605756ed6b16d4c"
 uuid = "af524d12-c74b-11e9-22a8-3b091653023f"
-version = "0.8.0"
+version = "0.9.0"
 
 [[PopGenCore]]
 deps = ["CSV", "CodecZlib", "DataFrames", "PooledArrays", "Random", "StaticArrays", "StatsBase", "VariantCallFormat"]
-git-tree-sha1 = "e107a2412c47098cfe23d0726962d03c3ed64495"
+git-tree-sha1 = "6f1106fd0ea9b61efc7b937b2896e2c6013a1507"
 uuid = "45b36091-5ef7-4b08-b448-aaf24c763a14"
-version = "0.5.1"
+version = "0.7.1"
 
 [[Poppler_jll]]
 deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "OpenJpeg_jll", "Pkg", "libpng_jll"]
-git-tree-sha1 = "02148a0cb2532f22c0589ceb75c110e168fb3d1f"
+git-tree-sha1 = "e11443687ac151ac6ef6699eb75f964bed8e1faa"
 uuid = "9c32591e-4766-534b-9725-b71a8799265b"
-version = "21.9.0+0"
+version = "0.87.0+2"
 
 [[PositiveFactorizations]]
 deps = ["LinearAlgebra"]
@@ -1880,6 +1891,12 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 deps = ["Printf"]
 uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
 
+[[ProgressLogging]]
+deps = ["Logging", "SHA", "UUIDs"]
+git-tree-sha1 = "80d919dee55b9c50e8d9e2da5eeafff3fe58b539"
+uuid = "33c8b6b6-d38a-422a-b730-caa89a2f386c"
+version = "0.1.4"
+
 [[ProgressMeter]]
 deps = ["Distributed", "Printf"]
 git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9"
@@ -1932,9 +1949,9 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [[Random123]]
 deps = ["Random", "RandomNumbers"]
-git-tree-sha1 = "afeacaecf4ed1649555a19cb2cad3c141bbc9474"
+git-tree-sha1 = "7a1a306b72cfa60634f03a911405f4e64d1b718b"
 uuid = "74087812-796a-5b5d-8853-05524746bad3"
-version = "1.5.0"
+version = "1.6.0"
 
 [[RandomNumbers]]
 deps = ["Random", "Requires"]
@@ -1972,9 +1989,9 @@ version = "1.2.1"
 
 [[RecipesPipeline]]
 deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"]
-git-tree-sha1 = "2690681814016887462cf5ac37102b51cd9ec781"
+git-tree-sha1 = "e7eac76a958f8664f2718508435d058168c7953d"
 uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c"
-version = "0.6.2"
+version = "0.6.3"
 
 [[RecursiveArrayTools]]
 deps = ["Adapt", "ArrayInterfaceCore", "ArrayInterfaceStaticArraysCore", "ChainRulesCore", "DocStringExtensions", "FillArrays", "GPUArraysCore", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "ZygoteRules"]
@@ -2074,9 +2091,9 @@ version = "0.3.3"
 
 [[SciMLBase]]
 deps = ["ArrayInterfaceCore", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "RecipesBase", "RecursiveArrayTools", "StaticArraysCore", "Statistics", "Tables"]
-git-tree-sha1 = "d48bd7ac5500dd45aac2d4a2bd1da8baedb4a7e1"
+git-tree-sha1 = "7cb46ff55af945a8b68e148bf22f9325f7221d8d"
 uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-version = "1.44.1"
+version = "1.45.0"
 
 [[ScikitLearnBase]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
@@ -2234,9 +2251,9 @@ version = "0.15.0"
 
 [[SteadyStateDiffEq]]
 deps = ["DiffEqBase", "DiffEqCallbacks", "LinearAlgebra", "NLsolve", "Reexport", "SciMLBase"]
-git-tree-sha1 = "fa04638e98850332978467a085e58aababfa203a"
+git-tree-sha1 = "f4492f790434f405139eb3a291fdbb45997857c6"
 uuid = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
-version = "1.8.0"
+version = "1.9.0"
 
 [[StochasticDiffEq]]
 deps = ["Adapt", "ArrayInterface", "DataStructures", "DiffEqBase", "DiffEqNoiseProcess", "DocStringExtensions", "FillArrays", "FiniteDiff", "ForwardDiff", "JumpProcesses", "LevyArea", "LinearAlgebra", "Logging", "MuladdMacro", "NLsolve", "OrdinaryDiffEq", "Random", "RandomNumbers", "RecursiveArrayTools", "Reexport", "SciMLBase", "SparseArrays", "SparseDiffTools", "StaticArrays", "UnPack"]
@@ -2298,6 +2315,12 @@ version = "5.2.0+1"
 deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 
+[[TSne]]
+deps = ["Distances", "LinearAlgebra", "Printf", "ProgressMeter", "Statistics"]
+git-tree-sha1 = "6f1dfbf9dad6958439816fa9c5fa20898203fdf4"
+uuid = "24678dba-d5e9-5843-a4c6-250288b04835"
+version = "1.3.0"
+
 [[TableOperations]]
 deps = ["SentinelArrays", "Tables", "Test"]
 git-tree-sha1 = "e383c87cf2a1dc41fa30c093b2a19877c83e1bc1"
@@ -2320,12 +2343,24 @@ version = "1.7.0"
 deps = ["ArgTools", "SHA"]
 uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
 
+[[Tectonic]]
+deps = ["Pkg"]
+git-tree-sha1 = "0b3881685ddb3ab066159b2ce294dc54fcf3b9ee"
+uuid = "9ac5f52a-99c6-489f-af81-462ef484790f"
+version = "0.8.0"
+
 [[TensorCore]]
 deps = ["LinearAlgebra"]
 git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6"
 uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50"
 version = "0.1.1"
 
+[[Term]]
+deps = ["Dates", "Highlights", "InteractiveUtils", "Logging", "Markdown", "MyterialColors", "OrderedCollections", "Parameters", "ProgressLogging", "Tables", "UUIDs", "UnicodeFun"]
+git-tree-sha1 = "e4ccdfbdc073f71109c5fe0af7239c43714997d3"
+uuid = "22787eb5-b846-44ae-b979-8e399b8463ab"
+version = "1.0.2"
+
 [[Test]]
 deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
@@ -2348,10 +2383,10 @@ uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69"
 version = "0.6.0"
 
 [[TikzPictures]]
-deps = ["LaTeXStrings", "Poppler_jll"]
-git-tree-sha1 = "40d1559df48a5316eb66ad29ac734db6829e433d"
+deps = ["LaTeXStrings", "Poppler_jll", "Requires", "Tectonic"]
+git-tree-sha1 = "4e75374d207fefb21105074100034236fceed7cb"
 uuid = "37f6aa50-8035-52d0-81c2-5a1d08754b2d"
-version = "3.2.0"
+version = "3.4.2"
 
 [[TiledIteration]]
 deps = ["OffsetArrays"]