diff --git a/Manifest.toml b/Manifest.toml index 4758c942b153ce03879d40868de40321bd467397..f2ee5f976ec38d9753442ab7f7f8ac8a877974a7 100644 --- a/Manifest.toml +++ b/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.7.0" +julia_version = "1.7.1" manifest_format = "2.0" [[deps.AbstractFFTs]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "485ee0867925449198280d4af84bdb46a2a404d0" +deps = ["ChainRulesCore", "LinearAlgebra"] +git-tree-sha1 = "6f1d9bc1c08f9f4a8fa92e3ea3cb50153a1b40d4" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.0.1" +version = "1.1.0" [[deps.AbstractTrees]] git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" @@ -16,9 +16,9 @@ version = "0.3.4" [[deps.Adapt]] deps = ["LinearAlgebra"] -git-tree-sha1 = "9faf218ea18c51fcccaf956c8d39614c9d30fe8b" +git-tree-sha1 = "af92965fb30777147966f58acb05da51c5616b5f" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.3.2" +version = "3.3.3" [[deps.Animations]] deps = ["Colors"] @@ -31,9 +31,9 @@ uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" [[deps.ArrayInterface]] deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "1ee88c4c76caa995a885dc2f22a5d548dfbbc0ba" +git-tree-sha1 = "c933ce606f6535a7c7b98e1d86d5d1014f730596" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "3.2.2" +version = "5.0.7" [[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -78,15 +78,15 @@ version = "1.16.1+1" [[deps.CategoricalArrays]] deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"] -git-tree-sha1 = "c308f209870fdbd84cb20332b6dfaf14bf3387f8" +git-tree-sha1 = "109664d3a6f2202b1225478335ea8fea3cd8706b" uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597" -version = "0.10.2" +version = "0.10.5" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "d711603452231bad418bd5e0c91f1abd650cba71" +git-tree-sha1 = "9950387274246d08af38f6eef8cb5480862a435f" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.11.3" +version = "1.14.0" [[deps.ChangesOfVariables]] deps = ["ChainRulesCore", "LinearAlgebra", "Test"] @@ -114,9 +114,9 @@ version = "0.4.0" [[deps.ColorSchemes]] deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"] -git-tree-sha1 = "a851fec56cb73cfdf43762999ec72eff5b86882a" +git-tree-sha1 = "12fc73e5e0af68ad3137b886e3f7c1eacfca2640" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.15.0" +version = "3.17.1" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -138,9 +138,9 @@ version = "0.12.8" [[deps.Compat]] deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "44c37b4636bc54afac5c574d2d02b625349d6582" +git-tree-sha1 = "96b0bc6c52df76506efc8a441c6cf1adcb1babc4" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.41.0" +version = "3.42.0" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -153,9 +153,9 @@ uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" version = "0.5.7" [[deps.Crayons]] -git-tree-sha1 = "3f71217b538d7aaee0b69ab47d9b7724ca8afa0d" +git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" -version = "4.0.4" +version = "4.1.1" [[deps.DataAPI]] git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8" @@ -199,9 +199,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "6a8dc9f82e5ce28279b6e3e2cea9421154f5bd0d" +git-tree-sha1 = "5a4168170ede913a2cd679e53c2123cb4b889795" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.37" +version = "0.25.53" [[deps.DocStringExtensions]] deps = ["LibGit2"] @@ -221,15 +221,15 @@ version = "2.2.3+0" [[deps.EllipsisNotation]] deps = ["ArrayInterface"] -git-tree-sha1 = "3fe985505b4b667e1ae303c9ca64d181f09d5c05" +git-tree-sha1 = "d064b0340db45d48893e7604ec95e7a2dc9da904" uuid = "da5c29d0-fa7d-589e-88eb-ea29b0a81949" -version = "1.1.3" +version = "1.5.0" [[deps.Expat_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b3bfd02e98aedfa5cf885665493c5598c350cd2f" +git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.2.10+0" +version = "2.4.8+0" [[deps.FFMPEG]] deps = ["FFMPEG_jll"] @@ -245,9 +245,9 @@ version = "4.4.0+0" [[deps.FFTW]] deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"] -git-tree-sha1 = "463cb335fa22c4ebacfd1faba5fde14edb80d96c" +git-tree-sha1 = "505876577b5481e50d089c1c68899dfb6faebc62" uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341" -version = "1.4.5" +version = "1.4.6" [[deps.FFTW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -257,15 +257,15 @@ version = "3.3.10+0" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "67551df041955cc6ee2ed098718c8fcd7fc7aebe" +git-tree-sha1 = "80ced645013a5dbdc52cf70329399c35ce007fae" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.12.0" +version = "1.13.0" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "8756f9935b7ccc9064c6eef0bff0ad643df733a3" +git-tree-sha1 = "246621d23d1f43e3b9c368bf3b72b2331a27c286" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.12.7" +version = "0.13.2" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -298,10 +298,10 @@ uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" version = "2.10.4+0" [[deps.FreeTypeAbstraction]] -deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics", "StaticArrays"] -git-tree-sha1 = "770050893e7bc8a34915b4b9298604a3236de834" +deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"] +git-tree-sha1 = "b5c7fe9cea653443736d264b85466bad8c574f4a" uuid = "663a7486-cb36-511b-a19d-713bb74d65c9" -version = "0.9.5" +version = "0.9.9" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -315,9 +315,9 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GeometryBasics]] deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "58bcdf5ebc057b085e58d95c138725628dd7453c" +git-tree-sha1 = "83ea630384a13fc4f002b77690bc0afeb4255ac9" uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.4.1" +version = "0.4.2" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -351,9 +351,9 @@ version = "1.3.14+0" [[deps.GridLayoutBase]] deps = ["GeometryBasics", "InteractiveUtils", "Observables"] -git-tree-sha1 = "70938436e2720e6cb8a7f2ca9f1bbdbf40d7f5d0" +git-tree-sha1 = "169c3dc5acae08835a573a8a3e25c62f689f8b5c" uuid = "3955a311-db13-416c-9275-1d80ed98e5e9" -version = "0.6.4" +version = "0.6.5" [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" @@ -362,9 +362,9 @@ version = "1.0.2" [[deps.HDF5]] deps = ["Compat", "HDF5_jll", "Libdl", "Mmap", "Random", "Requires"] -git-tree-sha1 = "36df177c1ce5f399a8de959e5f4b75216fe6c834" +git-tree-sha1 = "cdd249512de03cbf8370365a0a08b9a24955dca9" uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" -version = "0.16.7" +version = "0.16.6" [[deps.HDF5_jll]] deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"] @@ -436,10 +436,9 @@ uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" version = "0.1.2" [[deps.IniFile]] -deps = ["Test"] -git-tree-sha1 = "098e4d2c533924c921f9f9847274f2ad89e018b8" +git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" -version = "0.5.0" +version = "0.5.1" [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -459,15 +458,15 @@ version = "0.13.5" [[deps.IntervalSets]] deps = ["Dates", "EllipsisNotation", "Statistics"] -git-tree-sha1 = "3cc368af3f110a767ac786560045dceddfc16758" +git-tree-sha1 = "bcf640979ee55b652f3b01650444eb7bbe3ea837" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.5.3" +version = "0.5.4" [[deps.InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "a7254c0acd8e62f1ac75ad24d5db43f5f19f3c65" +git-tree-sha1 = "91b5dcf362c5add98049e6c29ee756910b03051d" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.2" +version = "0.1.3" [[deps.IrrationalConstants]] git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" @@ -492,15 +491,15 @@ version = "1.0.0" [[deps.JLLWrappers]] deps = ["Preferences"] -git-tree-sha1 = "642a199af8b68253517b80bd3bfd17eb4e84df6e" +git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.3.0" +version = "1.4.1" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "8076680b162ada2a031f707ac7b4953e30667a37" +git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.2" +version = "0.21.3" [[deps.JSON3]] deps = ["Dates", "Mmap", "Parsers", "StructTypes", "UUIDs"] @@ -516,9 +515,9 @@ version = "1.2.4" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "d735490ac75c5cb9f1b00d8b5509c11984dc6943" +git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.0+0" +version = "2.1.2+0" [[deps.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] @@ -620,9 +619,9 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "e5718a00af0ab9756305a0392832c8952c7426c1" +git-tree-sha1 = "58f25e56b706f95125dcb796f39e1fb01d913a71" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.6" +version = "0.3.10" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" @@ -635,9 +634,9 @@ version = "0.10.3" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "5455aef09b40e5020e1520f551fa3135040d4ed0" +git-tree-sha1 = "e595b205efd49508358f7dc670a940c790204629" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2021.1.1+2" +version = "2022.0.0+0" [[deps.MacroTools]] deps = ["Markdown", "Random"] @@ -718,15 +717,15 @@ uuid = "99f44e22-a591-53d1-9472-aa23ef4bd671" version = "1.1.0" [[deps.NaNMath]] -git-tree-sha1 = "f755f36b19a5116bb580de457cda0c140153f283" +git-tree-sha1 = "b086b7ea07f8e38cf122f5016af580881ac914fe" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.6" +version = "0.3.7" [[deps.NearestNeighbors]] deps = ["Distances", "StaticArrays"] -git-tree-sha1 = "16baacfdc8758bc374882566c9187e785e85c2f0" +git-tree-sha1 = "ded92de95031d4a8c61dfb6ba9adb6f1d8016ddd" uuid = "b8a86587-4115-5ab1-83bc-aa920d37bbce" -version = "0.4.9" +version = "0.4.10" [[deps.Netpbm]] deps = ["FileIO", "ImageCore"] @@ -784,9 +783,9 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112" [[deps.OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "15003dcb7d8db3c6c857fda14891a539a8f2705a" +git-tree-sha1 = "ab05aa4cc89736e95915b01e7279e61b1bfe33b8" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.10+0" +version = "1.1.14+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -813,15 +812,15 @@ version = "8.44.0+0" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "ee26b350276c51697c9c2d88a072b339f9f03d73" +git-tree-sha1 = "e8185b83b9fc56eb6456200e873ce598ebc7f262" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.5" +version = "0.11.7" [[deps.PNGFiles]] deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"] -git-tree-sha1 = "6d105d40e30b635cfed9d52ec29cf456e27d38f8" +git-tree-sha1 = "eb4dbb8139f6125471aa3da98fb70f02dc58e49c" uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883" -version = "0.3.12" +version = "0.3.14" [[deps.Packing]] deps = ["GeometryBasics"] @@ -837,9 +836,9 @@ version = "0.5.11" [[deps.Parsers]] deps = ["Dates"] -git-tree-sha1 = "d7fa6237da8004be601e19bd6666083056649918" +git-tree-sha1 = "621f4f3b4977325b9128d5fae7a8b4829a0c2222" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.1.3" +version = "2.2.4" [[deps.Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -859,15 +858,17 @@ version = "0.1.1" [[deps.PlanarLarvae]] deps = ["DelimitedFiles", "JSON3", "MAT", "Meshes", "OrderedCollections", "SHA", "StaticArrays", "StructTypes"] -path = "../PlanarLarvae" +git-tree-sha1 = "34279a2e3f91bc7dff05d7d02c8710eadd76fdaf" +repo-rev = "dev" +repo-url = "https://gitlab.pasteur.fr/nyx/planarlarvae.jl" uuid = "c2615984-ef14-4d40-b148-916c85b43307" version = "0.4.0" [[deps.PlotUtils]] deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "68604313ed59f0408313228ba09e79252e4b2da8" +git-tree-sha1 = "bb16469fd5224100e422f0b027d26c5a25de1200" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.1.2" +version = "1.2.0" [[deps.PolygonOps]] git-tree-sha1 = "77b3d3605fc1cd0b42d95eba87dfcd2bf67d5ff6" @@ -876,9 +877,9 @@ version = "0.1.2" [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "2cf929d64681236a2e074ffafb8d568733d2e6af" +git-tree-sha1 = "d3538e7f8a790dc8903519090857ef8e1283eecd" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.2.3" +version = "1.2.5" [[deps.Printf]] deps = ["Unicode"] @@ -886,9 +887,9 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "afadeba63d90ff223a6a48d2009434ecee2ec9e8" +git-tree-sha1 = "d7a7aef8f8f2d537104f170139553b14dfe39fe9" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.7.1" +version = "1.7.2" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] @@ -906,9 +907,9 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[deps.Ratios]] deps = ["Requires"] -git-tree-sha1 = "01d341f502250e81f6fec0afe662aa861392a3aa" +git-tree-sha1 = "dc84268fe0e3335a62e315a3a7cf2afa7178a734" uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" -version = "0.4.2" +version = "0.4.3" [[deps.RecipesBase]] git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" @@ -934,9 +935,9 @@ version = "0.1.3" [[deps.Requires]] deps = ["UUIDs"] -git-tree-sha1 = "8f82019e525f4d5c669692772a6f4b0a58b06a6a" +git-tree-sha1 = "838a3a4188e2ded87a4f9f184b4b0d78a1e91cb7" uuid = "ae029012-a4dd-5104-9daa-d747884805df" -version = "1.2.0" +version = "1.3.0" [[deps.Rmath]] deps = ["Random", "Rmath_jll"] @@ -954,9 +955,9 @@ version = "0.3.0+0" uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" [[deps.SIMD]] -git-tree-sha1 = "9ba33637b24341aba594a2783a502760aa0bff04" +git-tree-sha1 = "7dbc15af7ed5f751a82bf3ed37757adf76c32402" uuid = "fdea26ae-647d-5447-a871-4b548cad5224" -version = "3.3.1" +version = "3.4.1" [[deps.ScanByte]] deps = ["Libdl", "SIMD"] @@ -1016,9 +1017,9 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpecialFunctions]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "e08890d19787ec25029113e88c34ec20cac1c91e" +git-tree-sha1 = "5ba658aeecaaf96923dce0da9e703bd1fe7666f9" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.0.0" +version = "2.1.4" [[deps.StackViews]] deps = ["OffsetArrays"] @@ -1028,9 +1029,9 @@ version = "0.1.1" [[deps.Static]] deps = ["IfElse"] -git-tree-sha1 = "7f5a513baec6f122401abfc8e9c074fdac54f6c1" +git-tree-sha1 = "87e9954dfa33fd145694e42337bdd3d5b07021a6" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.4.1" +version = "0.6.0" [[deps.StaticArrays]] deps = ["LinearAlgebra", "Random", "Statistics"] @@ -1043,27 +1044,28 @@ deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[deps.StatsAPI]] -git-tree-sha1 = "d88665adc9bcf45903013af0982e2fd05ae3d0a6" +deps = ["LinearAlgebra"] +git-tree-sha1 = "c3d8ba7f3fa0625b062b82853a7d5229cb728b6b" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.2.0" +version = "1.2.1" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "51383f2d367eb3b444c961d485c565e4c0cf4ba0" +git-tree-sha1 = "8977b17906b0a1cc74ab2e3a05faa16cf08a8291" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.14" +version = "0.33.16" [[deps.StatsFuns]] deps = ["ChainRulesCore", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "bedb3e17cc1d94ce0e6e66d3afa47157978ba404" +git-tree-sha1 = "5950925ff997ed6fb3e985dcce8eb1ba42a0bbe7" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.14" +version = "0.9.18" [[deps.StructArrays]] deps = ["Adapt", "DataAPI", "StaticArrays", "Tables"] -git-tree-sha1 = "2ce41e0d042c60ecd131e9fb7154a3bfadbf50d3" +git-tree-sha1 = "57617b34fa34f91d536eb265df67c2d4519b8b98" uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a" -version = "0.6.3" +version = "0.6.5" [[deps.StructTypes]] deps = ["Dates", "UUIDs"] @@ -1086,10 +1088,10 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"] -git-tree-sha1 = "bb1064c9a84c52e277f1096cf41434b675cd368b" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] +git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.6.1" +version = "1.7.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -1115,9 +1117,9 @@ version = "0.1.0" [[deps.TiffImages]] deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "OffsetArrays", "PkgVersion", "ProgressMeter", "UUIDs"] -git-tree-sha1 = "991d34bbff0d9125d93ba15887d6594e8e84b305" +git-tree-sha1 = "aaa19086bc282630d82f818456bc40b4d314307d" uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69" -version = "0.5.3" +version = "0.5.4" [[deps.TranscodingStreams]] deps = ["Random", "Test"] @@ -1233,15 +1235,15 @@ uuid = "83775a58-1f1d-513f-b197-d71354ab007a" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "cc4bf3fdde8b7e3e9fa0351bdeedba1cf3b7f6e6" +git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.0+0" +version = "1.5.2+0" [[deps.isoband_jll]] -deps = ["Libdl", "Pkg"] -git-tree-sha1 = "a1ac99674715995a536bbce674b068ec1b7d893d" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c" uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4" -version = "0.2.2+0" +version = "0.2.3+0" [[deps.libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] diff --git a/src/LarvaTagger.jl b/src/LarvaTagger.jl index 3f32d4c64d8e6ac545ec565d122ecaec7c2e399e..a2423378dda39adb91f4edfa0bd6e302ef334bf4 100644 --- a/src/LarvaTagger.jl +++ b/src/LarvaTagger.jl @@ -1,6 +1,6 @@ module LarvaTagger -using PlanarLarvae, PlanarLarvae.Datasets, PlanarLarvae.Loaders +using PlanarLarvae, PlanarLarvae.Datasets, PlanarLarvae.Formats using ObservationPolicies using TidyObservables diff --git a/src/files.jl b/src/files.jl index 118030a6f0936e7efe9043c3792143b0b3b08405..80dc877957a2f2e8e09be62d6b1793e582a4f813 100644 --- a/src/files.jl +++ b/src/files.jl @@ -147,20 +147,22 @@ function tryopenfile(controller, path; reload::Bool=false) end function loadfile(path) - file = Loaders.load(path) + file = Formats.load(path) data = isempty(file.run) ? file.timeseries : file.run # tracks times = PlanarLarvae.times(data) - if data isa PlanarLarvae.LarvaBase.Larvae - tracks = [LarvaModel(id, ts, times) for (id, ts) in pairs(data)] + if file isa Formats.FIMTrack + tracks = [LarvaModel(track, times) for track in values(getrun(file))] else - tracks = [LarvaModel(track, times) for track in values(data)] + tracks = [LarvaModel(id, ts, times) for (id, ts) in pairs(gettimeseries(file))] end # dataset metadata = getmetadata(file) if isempty(metadata) metadata = extract_metadata_from_filepath(path) run = get!(metadata, :date_time, "NA") + else + run = file.run.id end output = Dataset([Run(run; metadata...)]) # diff --git a/src/models.jl b/src/models.jl index f8578e92e04c8f9777e2379be4fac0fd497d3e40..fc0f7e3daf1d96a3257a0ca938e8dada2fba9b26 100644 --- a/src/models.jl +++ b/src/models.jl @@ -213,7 +213,7 @@ end function LarvaModel(id::LarvaID, timeseries::PlanarLarvae.TimeSeries{<:NamedTuple}, times::Vector{PlanarLarvae.Time}) alignedsteps = map(timeseries) do (t, _) - findfirst(≈(t), times) + findfirst(t′-> abs(t - t′) < TIME_PRECISION, times) end path = coordinates.(larvatrack(timeseries)) usertags = Observable(Dict{TimeStep, UserTags}()) @@ -222,7 +222,7 @@ end function LarvaModel(track::Track, times::Vector{PlanarLarvae.Time}) alignedsteps = map(track.timestamps) do t - findfirst(≈(t), times) + findfirst(t′-> abs(t - t′) < TIME_PRECISION, times) end path = coordinates.(larvatrack(track[:spine])) usertags = Observable(Dict{TimeStep, UserTags}())