[⚡ AUTOMATED]: Pkg upgrade for 2024-11-02

Files changed:\nM	Manifest.toml

Manifest.toml

@@ -69,9 +69,9 @@ version = "7.5.1"
 
 [[ArrayLayouts]]
 deps = ["FillArrays", "LinearAlgebra", "SparseArrays"]
-git-tree-sha1 = "0dd7edaff278e346eb0ca07a7e75c9438408a3ce"
+git-tree-sha1 = "492681bc44fac86804706ddb37da10880a2bd528"
 uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
-version = "1.10.3"
+version = "1.10.4"
 
 [[Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
@@ -212,9 +212,9 @@ version = "0.9.24"
 
 [[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+2"
 
 [[CEnum]]
 git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90"
@@ -235,9 +235,9 @@ version = "0.1.1"
 
 [[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"
 
 [[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"]
@@ -247,9 +247,9 @@ version = "1.18.2+1"
 
 [[Calculus]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad"
+git-tree-sha1 = "9cb23bbb1127eefb022b022481466c0f1127d430"
 uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9"
-version = "0.5.1"
+version = "0.5.2"
 
 [[CatIndices]]
 deps = ["CustomUnitRanges", "OffsetArrays"]
@@ -549,9 +549,9 @@ version = "3.2.3"
 
 [[Distances]]
 deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "66c4c81f259586e8f002eacebc177e1fb06363b0"
+git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d"
 uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
-version = "0.10.11"
+version = "0.10.12"
 
 [[Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
@@ -713,9 +713,9 @@ version = "0.4.3"
 
 [[ForwardDiff]]
 deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"]
-git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad"
+git-tree-sha1 = "a9ce73d3c827adab2d70bf168aaece8cce196898"
 uuid = "f6369f11-7733-5829-9624-2563aa707210"
-version = "0.10.36"
+version = "0.10.37"
 
 [[FreeType2_jll]]
 deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"]
@@ -804,9 +804,9 @@ version = "0.5.4"
 
 [[GenomicAnnotations]]
 deps = ["BioGenerics", "BioSequences", "CodecZlib", "DataFrames", "TranscodingStreams"]
-git-tree-sha1 = "2568dc39310f867720a25704065bf9bc69829ef0"
+git-tree-sha1 = "244ce0dba5c6f9e63263e790f6ca4eb3ed4e29c5"
 uuid = "4f8a0a0a-376d-5ac0-ab14-e88793df67f0"
-version = "0.3.8"
+version = "0.4.0"
 
 [[GenomicFeatures]]
 deps = ["BioGenerics", "DataStructures", "IntervalTrees"]
@@ -982,15 +982,15 @@ version = "0.6.8"
 
 [[ImageMagick]]
 deps = ["FileIO", "ImageCore", "ImageMagick_jll", "InteractiveUtils"]
-git-tree-sha1 = "8e2eae13d144d545ef829324f1f0a5a4fe4340f3"
+git-tree-sha1 = "c5c5478ae8d944c63d6de961b19e6d3324812c35"
 uuid = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
-version = "1.3.1"
+version = "1.4.0"
 
 [[ImageMagick_jll]]
-deps = ["Artifacts", "Ghostscript_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "OpenJpeg_jll", "Pkg", "Zlib_jll", "libpng_jll"]
-git-tree-sha1 = "8d2e786fd090199a91ecbf4a66d03aedd0fb24d4"
+deps = ["Artifacts", "Ghostscript_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "OpenJpeg_jll", "Zlib_jll", "libpng_jll"]
+git-tree-sha1 = "fa01c98985be12e5d75301c4527fff2c46fa3e0e"
 uuid = "c73af94c-d91f-53ed-93a7-00f77d67a9d7"
-version = "6.9.11+4"
+version = "7.1.1+1"
 
 [[ImageMetadata]]
 deps = ["AxisArrays", "ImageAxes", "ImageBase", "ImageCore"]
@@ -1181,9 +1181,9 @@ version = "0.21.4"
 
 [[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"
 
 [[JavaCall]]
 deps = ["DataStructures", "Dates", "Libdl", "WinReg"]
@@ -1247,9 +1247,9 @@ version = "0.2.6"
 
 [[Krylov]]
 deps = ["LinearAlgebra", "Printf", "SparseArrays"]
-git-tree-sha1 = "267dad6b4b7b5d529c76d40ff48d33f7e94cb834"
+git-tree-sha1 = "4f20a2df85a9e5d55c9e84634bbf808ed038cabd"
 uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
-version = "0.9.6"
+version = "0.9.8"
 
 [[LAME_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1352,9 +1352,9 @@ version = "3.2.2+1"
 
 [[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"
 
 [[Libglvnd_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"]
@@ -1364,15 +1364,15 @@ version = "1.6.0+0"
 
 [[Libgpg_error_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed"
+git-tree-sha1 = "c6ce1e19f3aec9b59186bdf06cdf3c4fc5f5f3e6"
 uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8"
-version = "1.49.0+0"
+version = "1.50.0+0"
 
 [[Libiconv_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "f9557a255370125b405568f9767d6d195822a175"
+git-tree-sha1 = "61dfdba58e585066d8bce214c5a51eaa0539f269"
 uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
-version = "1.17.0+0"
+version = "1.17.0+1"
 
 [[Libmount_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1499,9 +1499,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
 [[MathOptInterface]]
 deps = ["BenchmarkTools", "CodecBzip2", "CodecZlib", "DataStructures", "ForwardDiff", "JSON", "LinearAlgebra", "MutableArithmetics", "NaNMath", "OrderedCollections", "PrecompileTools", "Printf", "SparseArrays", "SpecialFunctions", "Test", "Unicode"]
-git-tree-sha1 = "5b246fca5420ae176d65ed43a2d0ee5897775216"
+git-tree-sha1 = "9a9905be768c496fb2f2c5fe34e2c9fe44b86e7a"
 uuid = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
-version = "1.31.2"
+version = "1.33.0"
 
 [[MbedTLS]]
 deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"]
@@ -1573,9 +1573,9 @@ version = "1.0.20"
 
 [[MutableArithmetics]]
 deps = ["LinearAlgebra", "SparseArrays", "Test"]
-git-tree-sha1 = "7768a4e5f2b372777a90c1758809333081a096a8"
+git-tree-sha1 = "90077f1e79de8c9c7c8a90644494411111f4e07b"
 uuid = "d8a4904e-b15c-11e9-3269-09a3773c0cb0"
-version = "1.5.1"
+version = "1.5.2"
 
 [[MyterialColors]]
 git-tree-sha1 = "01d8466fb449436348999d7c6ad740f8f853a579"
@@ -1753,9 +1753,9 @@ version = "0.11.31"
 
 [[PGFPlots]]
 deps = ["ColorBrewer", "ColorSchemes", "Colors", "Contour", "DataFrames", "DelimitedFiles", "Discretizers", "Distributed", "ImageMagick", "Images", "Printf", "Requires", "StatsBase", "TikzPictures"]
-git-tree-sha1 = "9c047c45b5c256a284b2d7a9d24aeacc44d32f3d"
+git-tree-sha1 = "5dbc6e27694edf02db5141fa5b06b3a64d5b07c0"
 uuid = "3b7a836e-365b-5785-a47d-02c71176b4aa"
-version = "3.4.5"
+version = "3.4.6"
 
 [[PNGFiles]]
 deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"]
@@ -1828,15 +1828,15 @@ version = "0.3.3"
 
 [[PlotThemes]]
 deps = ["PlotUtils", "Statistics"]
-git-tree-sha1 = "6e55c6841ce3411ccb3457ee52fc48cb698d6fb0"
+git-tree-sha1 = "41031ef3a1be6f5bbbf3e8073f210556daeae5ca"
 uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a"
-version = "3.2.0"
+version = "3.3.0"
 
 [[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"
 
 [[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"]
@@ -2167,9 +2167,9 @@ version = "1.2.1"
 
 [[SentinelArrays]]
 deps = ["Dates", "Random"]
-git-tree-sha1 = "ff11acffdb082493657550959d4feb4b6149e73a"
+git-tree-sha1 = "305becf8af67eae1dbc912ee9097f00aeeabb8d5"
 uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c"
-version = "1.4.5"
+version = "1.4.6"
 
 [[SequenceVariation]]
 deps = ["BioAlignments", "BioGenerics", "BioSequences", "BioSymbols"]
@@ -2267,6 +2267,12 @@ git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14"
 uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
 version = "2.4.0"
 
+[[StableRNGs]]
+deps = ["Random"]
+git-tree-sha1 = "83e6cce8324d49dfaf9ef059227f91ed4441a8e5"
+uuid = "860ef19b-820b-49d6-a774-d7a799459cd3"
+version = "1.0.2"
+
 [[StackViews]]
 deps = ["OffsetArrays"]
 git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c"
@@ -2287,9 +2293,9 @@ version = "1.6.0"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore", "Statistics"]
-git-tree-sha1 = "eeafab08ae20c62c44c8399ccb9354a04b80db50"
+git-tree-sha1 = "777657803913ffc7e8cc20f0fd04b634f871af8f"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.9.7"
+version = "1.9.8"
 
 [[StaticArraysCore]]
 git-tree-sha1 = "192954ef1208c7019899fbf8049e717f92959682"
@@ -2580,9 +2586,9 @@ version = "0.5.6"
 
 [[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"
 
 [[VertexSafeGraphs]]
 deps = ["Graphs"]
@@ -2657,9 +2663,9 @@ version = "0.3.1"
 
 [[XML2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
-git-tree-sha1 = "1165b0443d0eca63ac1e32b8c0eb69ed2f4f8127"
+git-tree-sha1 = "6a451c6f33a176150f315726eba8b92fbfdb9ae7"
 uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
-version = "2.13.3+0"
+version = "2.13.4+0"
 
 [[XMLDict]]
 deps = ["EzXML", "IterTools", "OrderedCollections"]
@@ -2675,9 +2681,9 @@ version = "1.1.41+0"
 
 [[XZ_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632"
+git-tree-sha1 = "15e637a697345f6743674f1322beefbc5dcd5cfc"
 uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800"
-version = "5.4.6+0"
+version = "5.6.3+0"
 
 [[Xorg_libX11_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"]
@@ -2819,9 +2825,9 @@ version = "1.3.0"
 
 [[ZeroMQ_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "libsodium_jll"]
-git-tree-sha1 = "42f97fb27394378591666ab0e9cee369e6d0e1f9"
+git-tree-sha1 = "f02ce8f0fda1ed40f4d0d59a2ad05e35e8ac9b0e"
 uuid = "8f1865be-045e-5c20-9c9f-bfbfb0764568"
-version = "4.3.5+0"
+version = "4.3.5+1"
 
 [[Zlib_jll]]
 deps = ["Libdl"]