diff --git a/Manifest.toml b/Manifest.toml index 1e9aea1..9b8ea89 100644 --- a/Manifest.toml +++ b/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"]