diff --git a/Manifest.toml b/Manifest.toml
index 74690b3e58fab18085d329575fef7b50042e1397..46f7deabd22ffeb010ad88b55b91e6219e087baa 100644
--- a/Manifest.toml
+++ b/Manifest.toml
@@ -1,8 +1,8 @@
# This file is machine-generated - editing it directly is not advised
-julia_version = "1.10.0"
+julia_version = "1.10.3"
manifest_format = "2.0"
-project_hash = "34327d7ea7e42bf13c02b6c70751c90982e1f1be"
+project_hash = "cb952709b0f0743fc5b93ca3d08c93ff9353644c"
[[deps.AbstractFFTs]]
deps = ["LinearAlgebra"]
@@ -16,20 +16,26 @@ weakdeps = ["ChainRulesCore", "Test"]
AbstractFFTsTestExt = "Test"
[[deps.AbstractTrees]]
-git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c"
+git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"
uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
-version = "0.4.4"
+version = "0.4.5"
[[deps.Adapt]]
deps = ["LinearAlgebra", "Requires"]
-git-tree-sha1 = "0fb305e0253fd4e833d486914367a2ee2c2e78d0"
+git-tree-sha1 = "6a55b747d1812e699320963ffde36f1ebdda4099"
uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-version = "4.0.1"
+version = "4.0.4"
weakdeps = ["StaticArrays"]
[deps.Adapt.extensions]
AdaptStaticArraysExt = "StaticArrays"
+[[deps.AliasTables]]
+deps = ["PtrArrays", "Random"]
+git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff"
+uuid = "66dad0bd-aa9a-41b7-9441-69ab47430ed8"
+version = "1.1.3"
+
[[deps.Animations]]
deps = ["Colors"]
git-tree-sha1 = "e81c509d2c8e49592413bfb0bb3b08150056c79d"
@@ -86,10 +92,10 @@ uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82"
version = "0.5.0"
[[deps.Cairo_jll]]
-deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
-git-tree-sha1 = "4b859a208b2397a7a623a03449e4636bdb17bcf2"
+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"
uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a"
-version = "1.16.1+1"
+version = "1.18.0+2"
[[deps.Calculus]]
deps = ["LinearAlgebra"]
@@ -99,9 +105,9 @@ version = "0.5.1"
[[deps.ChainRulesCore]]
deps = ["Compat", "LinearAlgebra"]
-git-tree-sha1 = "1287e3872d646eed95198457873249bd9f0caed2"
+git-tree-sha1 = "575cd02e080939a33b6df6c5853d14924c08e35b"
uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
-version = "1.20.1"
+version = "1.23.0"
weakdeps = ["SparseArrays"]
[deps.ChainRulesCore.extensions]
@@ -109,9 +115,9 @@ weakdeps = ["SparseArrays"]
[[deps.CircularArrays]]
deps = ["OffsetArrays"]
-git-tree-sha1 = "3f7b8a37359ae592cfa7aca7f811da045deff222"
+git-tree-sha1 = "e24a6f390e5563583bb4315c73035b5b3f3e7ab4"
uuid = "7a955b69-7140-5f4e-a0ed-f168c5e2e749"
-version = "1.3.3"
+version = "1.4.0"
[[deps.CodecZlib]]
deps = ["TranscodingStreams", "Zlib_jll"]
@@ -127,15 +133,15 @@ version = "0.4.0"
[[deps.ColorSchemes]]
deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"]
-git-tree-sha1 = "67c1f244b991cad9b0aa4b7540fb758c2488b129"
+git-tree-sha1 = "4b270d6465eb21ae89b732182c20dc165f8bf9f2"
uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4"
-version = "3.24.0"
+version = "3.25.0"
[[deps.ColorTypes]]
deps = ["FixedPointNumbers", "Random"]
-git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4"
+git-tree-sha1 = "b10d0b65641d57b8b4d5e234446582de5047050d"
uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f"
-version = "0.11.4"
+version = "0.11.5"
[[deps.ColorVectorSpace]]
deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"]
@@ -145,15 +151,15 @@ version = "0.9.10"
[[deps.Colors]]
deps = ["ColorTypes", "FixedPointNumbers", "Reexport"]
-git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a"
+git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0"
uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
-version = "0.12.10"
+version = "0.12.11"
[[deps.Compat]]
deps = ["TOML", "UUIDs"]
-git-tree-sha1 = "75bd5b6fc5089df449b5d35fa501c846c9b6549b"
+git-tree-sha1 = "b1c55339b7c6c350ee89f2c1604299660525b248"
uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.12.0"
+version = "4.15.0"
weakdeps = ["Dates", "LinearAlgebra"]
[deps.Compat.extensions]
@@ -162,13 +168,13 @@ weakdeps = ["Dates", "LinearAlgebra"]
[[deps.CompilerSupportLibraries_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.0.5+1"
+version = "1.1.1+0"
[[deps.ConstructionBase]]
deps = ["LinearAlgebra"]
-git-tree-sha1 = "c53fc348ca4d40d7b371e71fd52251839080cbc9"
+git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2"
uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
-version = "1.5.4"
+version = "1.5.5"
weakdeps = ["IntervalSets", "StaticArrays"]
[deps.ConstructionBase.extensions]
@@ -176,9 +182,9 @@ weakdeps = ["IntervalSets", "StaticArrays"]
ConstructionBaseStaticArraysExt = "StaticArrays"
[[deps.Contour]]
-git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781"
+git-tree-sha1 = "439e35b0b36e2e5881738abc8857bd92ad6ff9a8"
uuid = "d38c429a-6771-53c6-b99e-75d170b6e991"
-version = "0.6.2"
+version = "0.6.3"
[[deps.DataAPI]]
git-tree-sha1 = "abe83f3a2f1b857aac70ef8b269080af17764bbe"
@@ -187,9 +193,9 @@ version = "1.16.0"
[[deps.DataStructures]]
deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "ac67408d9ddf207de5cfa9a97e114352430f01ed"
+git-tree-sha1 = "1d0a14036acb104d9e89698bd408f63ab58cdc82"
uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.18.16"
+version = "0.18.20"
[[deps.DataValueInterfaces]]
git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6"
@@ -222,10 +228,10 @@ deps = ["Random", "Serialization", "Sockets"]
uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
[[deps.Distributions]]
-deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "7c302d7a5fec5214eb8a5a4c466dcf7a51fcf169"
+deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
+git-tree-sha1 = "22c595ca4146c07b16bcf9c8bea86f731f7109d2"
uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.25.107"
+version = "0.25.108"
[deps.Distributions.extensions]
DistributionsChainRulesCoreExt = "ChainRulesCore"
@@ -268,9 +274,9 @@ version = "2.2.4+0"
[[deps.Expat_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "4558ab818dcceaab612d1bb8c19cee87eda2b83c"
+git-tree-sha1 = "1c6317308b9dc757616f0b5cb379db10494443a7"
uuid = "2e619515-83b5-522b-bb60-26c02a35a201"
-version = "2.5.0+0"
+version = "2.6.2+0"
[[deps.Extents]]
git-tree-sha1 = "2140cd04483da90b2da7f99b2add0750504fc39c"
@@ -303,18 +309,18 @@ version = "3.3.10+0"
[[deps.FileIO]]
deps = ["Pkg", "Requires", "UUIDs"]
-git-tree-sha1 = "c5c28c245101bd59154f649e19b038d15901b5dc"
+git-tree-sha1 = "82d8afa92ecf4b52d78d869f038ebfb881267322"
uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
-version = "1.16.2"
+version = "1.16.3"
[[deps.FileWatching]]
uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
[[deps.FillArrays]]
-deps = ["LinearAlgebra", "Random"]
-git-tree-sha1 = "5b93957f6dcd33fc343044af3d48c215be2562f1"
+deps = ["LinearAlgebra"]
+git-tree-sha1 = "0653c0a2396a6da5bc4766c43041ef5fd3efbe57"
uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "1.9.3"
+version = "1.11.0"
weakdeps = ["PDMats", "SparseArrays", "Statistics"]
[deps.FillArrays.extensions]
@@ -324,21 +330,26 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"]
[[deps.FixedPointNumbers]]
deps = ["Statistics"]
-git-tree-sha1 = "335bfdceacc84c5cdf16aadc768aa5ddfc5383cc"
+git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172"
uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
-version = "0.8.4"
+version = "0.8.5"
[[deps.Fontconfig_jll]]
-deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Pkg", "Zlib_jll"]
-git-tree-sha1 = "21efd19106a55620a188615da6d3d06cd7f6ee03"
+deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"]
+git-tree-sha1 = "db16beca600632c95fc8aca29890d83788dd8b23"
uuid = "a3f928ae-7b40-5064-980b-68af3947d34b"
-version = "2.13.93+0"
+version = "2.13.96+0"
+
+[[deps.Format]]
+git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc"
+uuid = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8"
+version = "1.3.7"
[[deps.Formatting]]
-deps = ["Printf"]
-git-tree-sha1 = "8339d61043228fdd3eb658d86c926cb282ae72a8"
+deps = ["Logging", "Printf"]
+git-tree-sha1 = "fb409abab2caf118986fc597ba84b50cbaf00b87"
uuid = "59287772-0a20-5a39-b81b-1366585eb4c0"
-version = "0.4.2"
+version = "0.4.3"
[[deps.FreeType]]
deps = ["CEnum", "FreeType2_jll"]
@@ -348,9 +359,9 @@ version = "4.1.1"
[[deps.FreeType2_jll]]
deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"]
-git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0"
+git-tree-sha1 = "5c1d8ae0efc6c2e7b1fc502cbe25def8f661b7bc"
uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7"
-version = "2.13.1+0"
+version = "2.13.2+0"
[[deps.FreeTypeAbstraction]]
deps = ["ColorVectorSpace", "Colors", "FreeType", "GeometryBasics"]
@@ -359,28 +370,22 @@ uuid = "663a7486-cb36-511b-a19d-713bb74d65c9"
version = "0.9.9"
[[deps.FriBidi_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "aa31987c2ba8704e23c6c8ba8a4f769d5d7e4f91"
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "1ed150b39aebcc805c26b93a8d0122c940f64ce2"
uuid = "559328eb-81f9-559d-9380-de523a88c83c"
-version = "1.0.10+0"
-
-[[deps.GPUArraysCore]]
-deps = ["Adapt"]
-git-tree-sha1 = "ec632f177c0d990e64d955ccc1b8c04c485a0950"
-uuid = "46192b85-c4d5-4398-a991-12ede77f4527"
-version = "0.1.6"
+version = "1.0.14+0"
[[deps.GeoInterface]]
deps = ["Extents"]
-git-tree-sha1 = "d4f85701f569584f2cff7ba67a137d03f0cfb7d0"
+git-tree-sha1 = "801aef8228f7f04972e596b09d4dba481807c913"
uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
-version = "1.3.3"
+version = "1.3.4"
[[deps.GeometryBasics]]
deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"]
-git-tree-sha1 = "5694b56ccf9d15addedc35e9a4ba9c317721b788"
+git-tree-sha1 = "b62f2b2d76cee0d61a2ef2b3118cd2a3215d3134"
uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326"
-version = "0.4.10"
+version = "0.4.11"
[[deps.Gettext_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"]
@@ -388,11 +393,17 @@ git-tree-sha1 = "9b02998aba7bf074d14de89f9d37ca24a1a0b046"
uuid = "78b55507-aeef-58d4-861c-77aaff3498b1"
version = "0.21.0+0"
+[[deps.Ghostscript_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
+git-tree-sha1 = "43ba3d3c82c18d88471cfd2924931658838c9d8f"
+uuid = "61579ee1-b43e-5ca0-a5da-69d92c66a64b"
+version = "9.55.0+4"
+
[[deps.Glib_jll]]
deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
-git-tree-sha1 = "e94c92c7bf4819685eb80186d51c43e71d4afa17"
+git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba"
uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
-version = "2.76.5+0"
+version = "2.80.2+0"
[[deps.Graphics]]
deps = ["Colors", "LinearAlgebra", "NaNMath"]
@@ -419,9 +430,9 @@ version = "1.0.2"
[[deps.HDF5]]
deps = ["Compat", "HDF5_jll", "Libdl", "MPIPreferences", "Mmap", "Preferences", "Printf", "Random", "Requires", "UUIDs"]
-git-tree-sha1 = "26407bd1c60129062cec9da63dc7d08251544d53"
+git-tree-sha1 = "e856eef26cf5bf2b0f95f8f4fc37553c72c8641c"
uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
-version = "0.17.1"
+version = "0.17.2"
[deps.HDF5.extensions]
MPIExt = "MPI"
@@ -485,21 +496,21 @@ version = "0.9.4"
[[deps.ImageIO]]
deps = ["FileIO", "IndirectArrays", "JpegTurbo", "LazyModules", "Netpbm", "OpenEXR", "PNGFiles", "QOI", "Sixel", "TiffImages", "UUIDs"]
-git-tree-sha1 = "bca20b2f5d00c4fbc192c3212da8fa79f4688009"
+git-tree-sha1 = "437abb322a41d527c197fa800455f79d414f0a3c"
uuid = "82e4d734-157c-48bb-816b-45c225c6df19"
-version = "0.6.7"
+version = "0.6.8"
[[deps.ImageMagick]]
-deps = ["FileIO", "ImageCore", "ImageMagick_jll", "InteractiveUtils"]
-git-tree-sha1 = "b0b765ff0b4c3ee20ce6740d843be8dfce48487c"
+deps = ["FileIO", "ImageCore", "ImageMagick_jll", "InteractiveUtils", "Libdl", "Pkg", "Random"]
+git-tree-sha1 = "5bc1cb62e0c5f1005868358db0692c994c3a13c6"
uuid = "6218d12a-5da1-5696-b52f-db25d2ecc6d1"
-version = "1.3.0"
+version = "1.2.1"
[[deps.ImageMagick_jll]]
-deps = ["JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pkg", "Zlib_jll", "libpng_jll"]
-git-tree-sha1 = "1c0a2295cca535fabaf2029062912591e9b61987"
+deps = ["Artifacts", "Ghostscript_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "OpenJpeg_jll", "Zlib_jll", "libpng_jll"]
+git-tree-sha1 = "d65554bad8b16d9562050c67e7223abf91eaba2f"
uuid = "c73af94c-d91f-53ed-93a7-00f77d67a9d7"
-version = "6.9.10-12+3"
+version = "6.9.13+0"
[[deps.ImageMetadata]]
deps = ["AxisArrays", "ImageAxes", "ImageBase", "ImageCore"]
@@ -509,9 +520,9 @@ version = "0.9.9"
[[deps.Imath_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "3d09a9f60edf77f8a4d99f9e015e8fbf9989605d"
+git-tree-sha1 = "0936ba688c6d201805a83da835b55c61a180db52"
uuid = "905a6f67-0a94-5f89-b386-d35d92009cd1"
-version = "3.1.7+0"
+version = "3.1.11+0"
[[deps.IndirectArrays]]
git-tree-sha1 = "012e604e1c7458645cb8b436f8fba789a51b257f"
@@ -530,9 +541,9 @@ version = "0.5.1"
[[deps.IntelOpenMP_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "5fdf2fe6724d8caabf43b557b84ce53f3b7e2f6b"
+git-tree-sha1 = "be50fe8df3acbffa0274a744f1a99d29c45a57f4"
uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0"
-version = "2024.0.2+0"
+version = "2024.1.0+0"
[[deps.InteractiveUtils]]
deps = ["Markdown"]
@@ -551,15 +562,20 @@ version = "0.15.1"
Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
[[deps.IntervalSets]]
-deps = ["Dates", "Random"]
-git-tree-sha1 = "3d8866c029dd6b16e69e0d4a939c4dfcb98fac47"
+git-tree-sha1 = "dba9ddf07f77f60450fe5d2e2beb9854d9a49bd0"
uuid = "8197267c-284f-5f27-9208-e0e47529a953"
-version = "0.7.8"
-weakdeps = ["Statistics"]
+version = "0.7.10"
[deps.IntervalSets.extensions]
+ IntervalSetsRandomExt = "Random"
+ IntervalSetsRecipesBaseExt = "RecipesBase"
IntervalSetsStatisticsExt = "Statistics"
+ [deps.IntervalSets.weakdeps]
+ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+ RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
+ Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+
[[deps.IrrationalConstants]]
git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2"
uuid = "92d709cd-6900-40b7-9082-c6be49f344b6"
@@ -619,21 +635,21 @@ version = "0.1.5"
[[deps.JpegTurbo_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "60b1194df0a3298f460063de985eae7b01bc011a"
+git-tree-sha1 = "c84a835e1a09b289ffcd2271bf2a337bbdda6637"
uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8"
-version = "3.0.1+0"
+version = "3.0.3+0"
[[deps.KernelDensity]]
deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"]
-git-tree-sha1 = "fee018a29b60733876eb557804b5b109dd3dd8a7"
+git-tree-sha1 = "7d703202e65efa1369de1279c162b915e245eed1"
uuid = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
-version = "0.6.8"
+version = "0.6.9"
[[deps.LAME_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "f6250b16881adf048549549fba48b1161acdac8c"
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "170b660facf5df5de098d866564877e119141cbd"
uuid = "c1c5ebd0-6772-5130-a774-d5fcae4a789d"
-version = "3.100.1+0"
+version = "3.100.2+0"
[[deps.LERC_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -648,10 +664,10 @@ uuid = "1d63c593-3942-5779-bab2-d838dc0a180e"
version = "15.0.7+0"
[[deps.LZO_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6"
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d"
uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac"
-version = "2.10.1+0"
+version = "2.10.2+0"
[[deps.LaTeXStrings]]
git-tree-sha1 = "50901ebc375ed41dbf8058da26f9de442febbbec"
@@ -701,16 +717,16 @@ uuid = "e9f186c6-92d2-5b65-8a66-fee21dc1b490"
version = "3.2.2+1"
[[deps.Libgcrypt_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll", "Pkg"]
-git-tree-sha1 = "64613c82a59c120435c067c2b809fc61cf5166ae"
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgpg_error_jll"]
+git-tree-sha1 = "9fd170c4bbfd8b935fdc5f8b7aa33532c991a673"
uuid = "d4300ac3-e22c-5743-9152-c294e39db1e4"
-version = "1.8.7+0"
+version = "1.8.11+0"
[[deps.Libgpg_error_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "c333716e46366857753e273ce6a69ee0945a6db9"
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "fbb1f2bef882392312feb1ede3615ddc1e9b99ed"
uuid = "7add5ba3-2f88-524e-9cd5-f83b8a55f7b8"
-version = "1.42.0+0"
+version = "1.49.0+0"
[[deps.Libiconv_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -719,32 +735,38 @@ uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531"
version = "1.17.0+0"
[[deps.Libmount_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "9c30530bf0effd46e15e0fdcf2b8636e78cbbd73"
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "0c4f9c4f1a50d8f35048fa0532dabbadf702f81e"
uuid = "4b2f31a3-9ecc-558c-b454-b3730dcb73e9"
-version = "2.35.0+0"
+version = "2.40.1+0"
[[deps.Libtiff_jll]]
-deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713"
+deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
+git-tree-sha1 = "6355fb9a4d22d867318db186fd09b09b35bd2ed7"
uuid = "89763e89-9b03-5906-acba-b20f662cd828"
-version = "4.4.0+0"
+version = "4.6.0+0"
[[deps.Libuuid_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066"
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "5ee6203157c120d79034c748a2acba45b82b8807"
uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700"
-version = "2.36.0+0"
+version = "2.40.1+0"
[[deps.LinearAlgebra]]
deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+[[deps.LittleCMS_jll]]
+deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll"]
+git-tree-sha1 = "fa7fd067dca76cadd880f1ca937b4f387975a9f5"
+uuid = "d3a379c0-f9a3-5b72-a4c0-6bf4d2e8af0f"
+version = "2.16.0+0"
+
[[deps.LogExpFunctions]]
deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
-git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa"
+git-tree-sha1 = "18144f3e9cbe9b15b070288eef858f71b291ce37"
uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
-version = "0.3.26"
+version = "0.3.27"
[deps.LogExpFunctions.extensions]
LogExpFunctionsChainRulesCoreExt = "ChainRulesCore"
@@ -761,33 +783,33 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
[[deps.MAT]]
deps = ["BufferedStreams", "CodecZlib", "HDF5", "SparseArrays"]
-git-tree-sha1 = "ed1cf0a322d78cee07718bed5fd945e2218c35a1"
+git-tree-sha1 = "1d2dd9b186742b0f317f2530ddcbf00eebb18e96"
uuid = "23992714-dd62-5051-b70f-ba57cb901cac"
-version = "0.10.6"
+version = "0.10.7"
[[deps.MKL_jll]]
-deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl"]
-git-tree-sha1 = "72dc3cf284559eb8f53aa593fe62cb33f83ed0c0"
+deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"]
+git-tree-sha1 = "80b2833b56d466b3858d565adcd16a4a05f2089b"
uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7"
-version = "2024.0.0+0"
+version = "2024.1.0+0"
[[deps.MPICH_jll]]
-deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
-git-tree-sha1 = "2ee75365ca243c1a39d467e35ffd3d4d32eef11e"
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
+git-tree-sha1 = "4099bb6809ac109bfc17d521dad33763bcf026b7"
uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4"
-version = "4.1.2+1"
+version = "4.2.1+1"
[[deps.MPIPreferences]]
deps = ["Libdl", "Preferences"]
-git-tree-sha1 = "8f6af051b9e8ec597fa09d8885ed79fd582f33c9"
+git-tree-sha1 = "c105fe467859e7f6e9a852cb15cb4301126fac07"
uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
-version = "0.1.10"
+version = "0.1.11"
[[deps.MPItrampoline_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"]
-git-tree-sha1 = "8eeb3c73bbc0ca203d0dc8dad4008350bbe5797b"
+git-tree-sha1 = "8c35d5420193841b2f367e658540e8d9e0601ed0"
uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748"
-version = "5.3.1+1"
+version = "5.4.0+0"
[[deps.MacroTools]]
deps = ["Markdown", "Random"]
@@ -847,15 +869,15 @@ version = "0.29.0"
[[deps.MicrosoftMPI_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "b01beb91d20b0d1312a9471a36017b5b339d26de"
+git-tree-sha1 = "f12a29c4400ba812841c6ace3f4efbb6dbb3ba01"
uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf"
-version = "10.1.4+1"
+version = "10.1.4+2"
[[deps.Missings]]
deps = ["DataAPI"]
-git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272"
+git-tree-sha1 = "ec4f7fbeab05d7747bdf98eb74d130a2a2ed298d"
uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
-version = "1.1.0"
+version = "1.2.0"
[[deps.Mmap]]
uuid = "a63ad114-7e13-5084-954f-fe012c677804"
@@ -912,9 +934,9 @@ uuid = "6317928a-6b1a-42e8-b853-b8e2fc3e9ca3"
version = "0.2.4"
[[deps.OffsetArrays]]
-git-tree-sha1 = "6a731f2b5c03157418a20c12195eb4b74c8f8621"
+git-tree-sha1 = "e64b4f5ea6b7389f6f046d13d4896a8f9c1ba71e"
uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
-version = "1.13.0"
+version = "1.14.0"
weakdeps = ["Adapt"]
[deps.OffsetArrays.extensions]
@@ -929,7 +951,7 @@ version = "1.3.5+1"
[[deps.OpenBLAS_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
-version = "0.3.23+2"
+version = "0.3.23+4"
[[deps.OpenEXR]]
deps = ["Colors", "FileIO", "OpenEXR_jll"]
@@ -939,9 +961,15 @@ version = "0.3.2"
[[deps.OpenEXR_jll]]
deps = ["Artifacts", "Imath_jll", "JLLWrappers", "Libdl", "Zlib_jll"]
-git-tree-sha1 = "a4ca623df1ae99d09bc9868b008262d0c0ac1e4f"
+git-tree-sha1 = "8292dd5c8a38257111ada2174000a33745b06d4e"
uuid = "18a262bb-aa17-5467-a713-aee519bc75cb"
-version = "3.1.4+0"
+version = "3.2.4+0"
+
+[[deps.OpenJpeg_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Libtiff_jll", "LittleCMS_jll", "libpng_jll"]
+git-tree-sha1 = "f4cb457ffac5f5cf695699f82c537073958a6a6c"
+uuid = "643b3616-a352-519d-856d-80112ee9badc"
+version = "2.5.2+0"
[[deps.OpenLibm_jll]]
deps = ["Artifacts", "Libdl"]
@@ -949,16 +977,16 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
version = "0.8.1+2"
[[deps.OpenMPI_jll]]
-deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "PMIx_jll", "TOML", "Zlib_jll", "libevent_jll", "prrte_jll"]
-git-tree-sha1 = "1d1421618bab0e820bdc7ae1a2b46ce576981273"
+deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"]
+git-tree-sha1 = "a9de2f1fc98b92f8856c640bf4aec1ac9b2a0d86"
uuid = "fe0851c0-eecd-5654-98d4-656369965a5c"
-version = "5.0.1+0"
+version = "5.0.3+0"
[[deps.OpenSSL_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "60e3045590bd104a16fefb12836c00c0ef8c7f8c"
+git-tree-sha1 = "3da7367955dcc5c54c1ba4d402ccdc09a1a3e046"
uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
-version = "3.0.13+0"
+version = "3.0.13+1"
[[deps.OpenSpecFun_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"]
@@ -988,12 +1016,6 @@ git-tree-sha1 = "949347156c25054de2db3b166c52ac4728cbad65"
uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
version = "0.11.31"
-[[deps.PMIx_jll]]
-deps = ["Artifacts", "Hwloc_jll", "JLLWrappers", "Libdl", "Zlib_jll", "libevent_jll"]
-git-tree-sha1 = "8b3b19351fa24791f94d7ae85faf845ca1362541"
-uuid = "32165bc3-0280-59bc-8c0b-c33b6203efab"
-version = "4.2.7+0"
-
[[deps.PNGFiles]]
deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"]
git-tree-sha1 = "67186a2bc9a90f9f85ff3cc8277868961fb57cbd"
@@ -1020,9 +1042,9 @@ version = "2.8.1"
[[deps.Pixman_jll]]
deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"]
-git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87"
+git-tree-sha1 = "35621f10a7531bc8fa58f74610b1bfb70a3cfc6b"
uuid = "30392449-352a-5448-841d-b1acce4e97dc"
-version = "0.42.2+0"
+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"]
@@ -1045,9 +1067,9 @@ version = "0.16.0"
[[deps.PlotUtils]]
deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"]
-git-tree-sha1 = "862942baf5663da528f66d24996eb6da85218e76"
+git-tree-sha1 = "7b1a9df27f072ac4c9c7cbe5efb198489258d1f5"
uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043"
-version = "1.4.0"
+version = "1.4.1"
[[deps.PolygonOps]]
git-tree-sha1 = "77b3d3605fc1cd0b42d95eba87dfcd2bf67d5ff6"
@@ -1056,15 +1078,15 @@ version = "0.1.2"
[[deps.PrecompileTools]]
deps = ["Preferences"]
-git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f"
+git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f"
uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
-version = "1.2.0"
+version = "1.2.1"
[[deps.Preferences]]
deps = ["TOML"]
-git-tree-sha1 = "00805cd429dcb4870060ff49ef443486c262e38e"
+git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6"
uuid = "21216c6a-2e73-6563-6e65-726566657250"
-version = "1.4.1"
+version = "1.4.3"
[[deps.Printf]]
deps = ["Unicode"]
@@ -1072,9 +1094,14 @@ uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
[[deps.ProgressMeter]]
deps = ["Distributed", "Printf"]
-git-tree-sha1 = "00099623ffee15972c16111bcf84c58a0051257c"
+git-tree-sha1 = "763a8ceb07833dd51bb9e3bbca372de32c0605ad"
uuid = "92933f4c-e287-5a05-a399-4b506db050ca"
-version = "1.9.0"
+version = "1.10.0"
+
+[[deps.PtrArrays]]
+git-tree-sha1 = "f011fbb92c4d401059b2212c05c0601b70f8b759"
+uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d"
+version = "1.2.0"
[[deps.QOI]]
deps = ["ColorTypes", "FileIO", "FixedPointNumbers"]
@@ -1090,9 +1117,9 @@ version = "2.9.4"
[[deps.Quaternions]]
deps = ["LinearAlgebra", "Random", "RealDot"]
-git-tree-sha1 = "9a46862d248ea548e340e30e2894118749dc7f51"
+git-tree-sha1 = "994cc27cdacca10e68feb291673ec3a76aa2fae9"
uuid = "94ee1d12-ae83-5a48-8b1c-48b8ff168ae0"
-version = "0.7.5"
+version = "0.7.6"
[[deps.REPL]]
deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
@@ -1147,21 +1174,33 @@ uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa"
version = "0.7.1"
[[deps.Rmath_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da"
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "d483cd324ce5cf5d61b77930f0bbd6cb61927d21"
uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f"
-version = "0.4.0+0"
+version = "0.4.2+0"
[[deps.Rotations]]
deps = ["LinearAlgebra", "Quaternions", "Random", "StaticArrays"]
-git-tree-sha1 = "792d8fd4ad770b6d517a13ebb8dadfcac79405b8"
+git-tree-sha1 = "5680a9276685d392c87407df00d57c9924d9f11e"
uuid = "6038ab10-8711-5258-84ad-4b1120ba62dc"
-version = "1.6.1"
+version = "1.7.1"
+
+ [deps.Rotations.extensions]
+ RotationsRecipesBaseExt = "RecipesBase"
+
+ [deps.Rotations.weakdeps]
+ RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
[[deps.SHA]]
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
version = "0.7.0"
+[[deps.SIMD]]
+deps = ["PrecompileTools"]
+git-tree-sha1 = "2803cab51702db743f3fda07dd1745aadfbf43bd"
+uuid = "fdea26ae-647d-5447-a871-4b548cad5224"
+version = "3.5.0"
+
[[deps.Scratch]]
deps = ["Dates"]
git-tree-sha1 = "3bac05bc7e74a75fd9cba4295cde4045d9fe2386"
@@ -1221,9 +1260,9 @@ version = "1.10.0"
[[deps.SpecialFunctions]]
deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"]
-git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d"
+git-tree-sha1 = "2f5d4697f21388cbe1ff299430dd169ef97d7e14"
uuid = "276daf66-3868-5448-9aa4-cd146d93841b"
-version = "2.3.1"
+version = "2.4.0"
weakdeps = ["ChainRulesCore"]
[deps.SpecialFunctions.extensions]
@@ -1237,9 +1276,9 @@ version = "0.1.1"
[[deps.StaticArrays]]
deps = ["LinearAlgebra", "PrecompileTools", "Random", "StaticArraysCore"]
-git-tree-sha1 = "7b0e9c14c624e435076d19aea1e5cbdec2b9ca37"
+git-tree-sha1 = "9ae599cd7529cfce7fea36cf00a62cfc56f0f37c"
uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "1.9.2"
+version = "1.9.4"
weakdeps = ["ChainRulesCore", "Statistics"]
[deps.StaticArrays.extensions]
@@ -1270,9 +1309,9 @@ version = "0.33.21"
[[deps.StatsFuns]]
deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
-git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a"
+git-tree-sha1 = "cef0472124fab0695b58ca35a77c6fb942fdab8a"
uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c"
-version = "1.3.0"
+version = "1.3.1"
[deps.StatsFuns.extensions]
StatsFunsChainRulesCoreExt = "ChainRulesCore"
@@ -1283,10 +1322,22 @@ version = "1.3.0"
InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"
[[deps.StructArrays]]
-deps = ["Adapt", "ConstructionBase", "DataAPI", "GPUArraysCore", "StaticArraysCore", "Tables"]
-git-tree-sha1 = "1b0b1205a56dc288b71b1961d48e351520702e24"
+deps = ["ConstructionBase", "DataAPI", "Tables"]
+git-tree-sha1 = "f4dc295e983502292c4c3f951dbb4e985e35b3be"
uuid = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
-version = "0.6.17"
+version = "0.6.18"
+
+ [deps.StructArrays.extensions]
+ StructArraysAdaptExt = "Adapt"
+ StructArraysGPUArraysCoreExt = "GPUArraysCore"
+ StructArraysSparseArraysExt = "SparseArrays"
+ StructArraysStaticArraysExt = "StaticArrays"
+
+ [deps.StructArrays.weakdeps]
+ Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
+ GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
+ SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
[[deps.StructTypes]]
deps = ["Dates", "UUIDs"]
@@ -1344,10 +1395,10 @@ uuid = "c8131bbd-73a8-4254-a42d-d5d4c5febb31"
version = "0.1.1"
[[deps.TiffImages]]
-deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "UUIDs"]
-git-tree-sha1 = "34cc045dd0aaa59b8bbe86c644679bc57f1d5bd0"
+deps = ["ColorTypes", "DataStructures", "DocStringExtensions", "FileIO", "FixedPointNumbers", "IndirectArrays", "Inflate", "Mmap", "OffsetArrays", "PkgVersion", "ProgressMeter", "SIMD", "UUIDs"]
+git-tree-sha1 = "bc7fd5c91041f44636b2c134041f7e5263ce58ae"
uuid = "731e570b-9d59-4bfa-96dc-6df516fadf69"
-version = "0.6.8"
+version = "0.10.0"
[[deps.TranscodingStreams]]
deps = ["Random", "Test"]
@@ -1405,9 +1456,9 @@ version = "1.0.0"
[[deps.XML2_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
-git-tree-sha1 = "801cbe47eae69adc50f36c3caec4758d2650741b"
+git-tree-sha1 = "52ff2af32e591541550bd753c0da8b9bc92bb9d9"
uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a"
-version = "2.12.2+0"
+version = "2.12.7+0"
[[deps.XSLT_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"]
@@ -1415,6 +1466,12 @@ git-tree-sha1 = "91844873c4085240b95e795f692c4cec4d805f8a"
uuid = "aed1982a-8fda-507f-9586-7b0439959a61"
version = "1.1.34+0"
+[[deps.XZ_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "ac88fb95ae6447c8dda6a5503f3bafd496ae8632"
+uuid = "ffd25f8a-64ca-5728-b0f7-c24cf3aae800"
+version = "5.4.6+0"
+
[[deps.Xorg_libX11_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"]
git-tree-sha1 = "afead5aba5aa507ad5a3bf01f58f82c8d1403495"
@@ -1434,16 +1491,16 @@ uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05"
version = "1.1.4+0"
[[deps.Xorg_libXext_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"]
-git-tree-sha1 = "b7c0aa8c376b31e4852b360222848637f481f8c3"
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"]
+git-tree-sha1 = "d2d1a5c49fae4ba39983f63de6afcbea47194e85"
uuid = "1082639a-0dae-5f34-9b06-72781eeb8cb3"
-version = "1.3.4+4"
+version = "1.3.6+0"
[[deps.Xorg_libXrender_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"]
-git-tree-sha1 = "19560f30fd49f4d4efbe7002a1037f8c43d43b96"
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"]
+git-tree-sha1 = "47e45cd78224c53109495b3e324df0c37bb61fbe"
uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa"
-version = "0.9.10+4"
+version = "0.9.11+0"
[[deps.Xorg_libpthread_stubs_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
@@ -1470,9 +1527,9 @@ version = "1.2.13+1"
[[deps.Zstd_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c"
+git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b"
uuid = "3161d3a3-bdf6-5164-811a-617609db77b4"
-version = "1.5.5+0"
+version = "1.5.6+0"
[[deps.isoband_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -1482,15 +1539,15 @@ version = "0.2.3+0"
[[deps.libaec_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "eddd19a8dea6b139ea97bdc8a0e2667d4b661720"
+git-tree-sha1 = "46bf7be2917b59b761247be3f317ddf75e50e997"
uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0"
-version = "1.0.6+1"
+version = "1.1.2+0"
[[deps.libaom_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4"
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d"
uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b"
-version = "3.4.0+0"
+version = "3.9.0+0"
[[deps.libass_jll]]
deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"]
@@ -1503,12 +1560,6 @@ deps = ["Artifacts", "Libdl"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
version = "5.8.0+1"
-[[deps.libevent_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "OpenSSL_jll"]
-git-tree-sha1 = "f04ec6d9a186115fb38f858f05c0c4e1b7fc9dcb"
-uuid = "1080aeaf-3a6a-583e-a51c-c537b09f60ec"
-version = "2.1.13+1"
-
[[deps.libfdk_aac_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55"
@@ -1517,9 +1568,9 @@ version = "2.0.2+0"
[[deps.libpng_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
-git-tree-sha1 = "93284c28274d9e75218a416c65ec49d0e0fcdf3d"
+git-tree-sha1 = "d7015d2e18a5fd9a4f47de711837e980519781a4"
uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f"
-version = "1.6.40+0"
+version = "1.6.43+1"
[[deps.libsixel_jll]]
deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Pkg", "libpng_jll"]
@@ -1538,17 +1589,17 @@ deps = ["Artifacts", "Libdl"]
uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
version = "1.52.0+1"
+[[deps.oneTBB_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl"]
+git-tree-sha1 = "7d0ea0f4895ef2f5cb83645fa689e52cb55cf493"
+uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e"
+version = "2021.12.0+0"
+
[[deps.p7zip_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
version = "17.4.0+2"
-[[deps.prrte_jll]]
-deps = ["Artifacts", "Hwloc_jll", "JLLWrappers", "Libdl", "PMIx_jll", "libevent_jll"]
-git-tree-sha1 = "5adb2d7a18a30280feb66cad6f1a1dfdca2dc7b0"
-uuid = "eb928a42-fffd-568d-ab9c-3f5d54fc65b9"
-version = "3.0.2+0"
-
[[deps.x264_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2"
diff --git a/Project.toml b/Project.toml
index f68dc9b94e69cb353cb5a6024506178afcadc2ad..9d6f12c1137bd1f09584dd4e1e8028942745784a 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,13 +1,13 @@
name = "LarvaTagger"
uuid = "8b3b36f1-dfed-446e-8561-ea19fe966a4d"
authors = ["François Laurent", "Institut Pasteur"]
-version = "0.18.1"
+version = "0.18.3"
[deps]
Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
DocOpt = "968ba79b-81e4-546f-ab3a-2eecfa62a9db"
-Formatting = "59287772-0a20-5a39-b81b-1366585eb4c0"
+Format = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8"
JSServe = "824d6782-a2ef-11e9-3a09-e5662e0c26f9"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
diff --git a/README.md b/README.md
index ec5ec0cf975d31337f6564c26e95d4e3b1d96f42..5636442e7d09ab77e21cb0b498b7f0100701e828 100644
--- a/README.md
+++ b/README.md
@@ -90,11 +90,33 @@ Alternatively, tags can be similarly *un*assigned at individual time steps or ov
## Installing
-[Using the *Docker* image](https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/tree/main/recipes) is recommended, as it ships *LarvaTagger* with the default *MaggotUBA*-based tagger as a standalone package and is easier to update.
+[Using the *Docker* image](https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/tree/main/recipes) may come handy, as it ships *LarvaTagger* with the default *MaggotUBA*-based tagger as a standalone package and is easier to update.
-To natively run *LarvaTagger.jl* instead, you will need [`julia>=1.7`](https://julialang.org/downloads/).
+### Using the *scripts/install.sh* script
-If you are not familiar with installing *Julia*, you may appreciate installation helpers such as [*Juliaup*](https://github.com/JuliaLang/juliaup) or [*jill*](https://pypi.org/project/jill/) (preferred).
+On macOS, Linux and WSL, a [script](https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/blob/dev/scripts/install.sh?ref_type=heads) is provided to automate the installation process from source. This script installs LarvaTagger.jl and Julia if missing. It also adds the *larvatagger* command to the user's path variable.
+The *scripts/install.sh* script can be run with:
+```
+/bin/bash -c "$(curl -sSL "https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/raw/dev/scripts/install.sh?ref_type=heads&inline=false")"
+```
+To install the full LarvaTagger suite (Linux and WSL only!), run instead:
+```
+curl -sSL "https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/raw/dev/scripts/install.sh?ref_type=heads&inline=false" | /bin/bash -s -- --with-default-backend
+```
+
+In the latter case, the script may install several extra dependencies, but not all of them.
+In particular, Python is required; either 3.8 with `--with-default-backend`, or 3.11 with `--with-backend --experimental`.
+If `pyenv` is available, the script will use this tool to install Python.
+Otherwise, `python3.8` and `python3.8-venv` may have to be manually installed.
+On WSL, the script will attempt to install `pyenv` and Python (tested with Ubuntu 20.04).
+
+This script can also uninstall LarvaTagger (if installed with the same script) with: `curl -sSL "https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/raw/dev/scripts/install.sh?ref_type=heads&inline=false" | /bin/bash -s -- --uninstall` which can be useful for example prior to reinstalling after failure.
+
+### Manually from source
+
+To natively run *LarvaTagger.jl* instead, you will need [*julia>=1.7*](https://julialang.org/downloads/).
+
+If you are not familiar with installing *Julia*, you may appreciate installation helpers such as [*Juliaup*](https://github.com/JuliaLang/juliaup) or [*jill*](https://pypi.org/project/jill/).
```
git clone https://gitlab.pasteur.fr/nyx/larvatagger.jl LarvaTagger
@@ -102,6 +124,12 @@ cd LarvaTagger
julia --project=. -e 'using Pkg; Pkg.instantiate()'
```
+In May 2024, the gitlab.pasteur.fr server began to request an authentication token on cloning public repositories.
+If the `git clone` command requests an authentication token you do not have, do instead:
+```
+curl -sSL https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/archive/main/larvatagger.jl-main.tar.gz | tar zxv && mv larvatagger.jl-main LarvaTagger
+```
+
Calling `Pkg.instantiate` in a copy of the project is preferred over using `Pkg.add`,
because *LarvaTagger.jl* depends on several unregistered packages.
@@ -123,7 +151,11 @@ The `--project=.` option will make the newly created *LarvaTagger* directory a n
### Upgrading
-From a local copy of the git repository, be sure to be on the appropriate branch (in most cases the *main* branch) and update (*git pull*) it:
+Using the Docker image, run `scripts/larvatagger.sh --update`.
+
+Using the *scripts/install.sh* script, upgrading is done uninstalling and installing LarvaTagger again.
+
+Using a local copy of the git repository, go to that repository, be sure to be on the appropriate branch (in most cases the *main* branch) and update (*git pull*) it:
```
git checkout main
git pull
@@ -150,6 +182,11 @@ If you cloned the repository, we recommend you run *LarvaTagger* using the *larv
scripts/larvatagger open path/to/data/file --browser
```
+If LarvaTagger was installed using the *scripts/install.sh* script, the *larvatagger* script should be in the user's path environment variable and, as a consequence, available from everywhere in the commandline:
+```
+larvatagger open path/to/data/file --browser
+```
+
The script will actually open a *Julia* interpreter, and give some guidance on how to exit the interpreter.
> For now, `larvatagger open` cannot be run with no input arguments. A track data file is required.
@@ -180,7 +217,7 @@ Feel free to adjust the value if the 2D view is too small or large.
## Automatic tagging
-*LarvaTagger.jl* comes with no automatic tagger per default.
+*LarvaTagger.jl* comes with no automatic tagger per default, unless installed with the *scripts/install.sh* script and the `--with-default-backend` option.
To extend the editor with *MaggotUBA*-based automatic tagging, see the [recommended installation steps for *TaggingBackends* and *MaggotUBA*](https://gitlab.pasteur.fr/nyx/TaggingBackends#recommended-installation).
diff --git a/recipes/Dockerfile b/recipes/Dockerfile
index c09163d71126f2024fcf6912d9d8f9814eb87c0b..f52fe0e29a60577e1a60844e16d33dee7ccc7aad 100644
--- a/recipes/Dockerfile
+++ b/recipes/Dockerfile
@@ -1,4 +1,4 @@
-FROM julia:1.10.0-bullseye AS base
+FROM julia:1.10.4-bullseye AS base
ARG PROJECT_DIR=/app
ARG BRANCH=main
@@ -15,12 +15,11 @@ RUN apt-get update \
&& ln -s "$JULIA_PROJECT/scripts/larvatagger" /bin \
&& mkdir -p "$JULIA_DEPOT_PATH/logs" && rm -f "$JULIA_DEPOT_PATH/logs/manifest_usage.toml" && ln -s /dev/null "$JULIA_DEPOT_PATH/logs/manifest_usage.toml"
-#RUN $JULIA_PROJECT/test/precompile.sh --shallow \
-# && mv larvatagger.so /lib/ \
-# && rm -rf $JULIA_PROJECT/test/data
+RUN $JULIA_PROJECT/test/precompile.sh --shallow \
+ && mv larvatagger.so /lib/ \
+ && rm -rf $JULIA_PROJECT/test/data
-ENTRYPOINT ["/app/scripts/larvatagger"]
-#, "-J/lib/larvatagger.so"]
+ENTRYPOINT ["/app/scripts/larvatagger", "-J/lib/larvatagger.so"]
FROM base AS prebuild
diff --git a/recipes/README.md b/recipes/README.md
index d13b72db0b1b1172fbff13c419ee060b7ca702cd..4259994144c7f0c6582e969aedabba0550729c37 100644
--- a/recipes/README.md
+++ b/recipes/README.md
@@ -149,6 +149,10 @@ Optionally, you can also get the default backend (currently *20230311*) with:
```
scripts/larvatagger.sh build --with-default-backend
```
+Currently, Docker images on Docker Hub are built with:
+```
+scripts/larvatagger.sh --target confusion build --with-default-backend
+```
If you want another tagger, *e.g.* the *20230129* tagger implemented by the *20230129* branch of the *MaggotUBA-adapter* repository, do:
```
diff --git a/scripts/install.sh b/scripts/install.sh
new file mode 100755
index 0000000000000000000000000000000000000000..af1f164f583f0d90ed1d8c1454c416a5ac2fd915
--- /dev/null
+++ b/scripts/install.sh
@@ -0,0 +1,238 @@
+#!/usr/bin/env bash
+
+[ -d "`pwd`" ] || cd
+
+if [ -z "$BIN_DIR" ]; then
+ BIN_DIR=~/.local/bin
+fi
+if [ -z "$LARVATAGGER_PATH" ]; then
+ LARVATAGGER_PATH=~/.local/share/larvatagger
+fi
+
+if [ "$1" = "--uninstall" ]; then
+ for pkg in MaggotUBA TaggingBackends; do
+ if [ -d "$LARVATAGGER_PATH/$pkg" ]; then
+ env=$(cd "$LARVATAGGER_PATH/$pkg" && poetry env info -p)
+ [ -d "$env" ] && rm -rf "$env"
+ fi
+ done
+ rm -rf "$BIN_DIR/larvatagger"
+ rm -rf "$LARVATAGGER_PATH"
+else
+
+PYTHON_VERSION=3.8
+for arg in "$@"; do
+ if [ "$arg" = "--with-default-backend" ]; then
+ WITH_BACKEND=1
+ MAGGOTUBA_CORE_BRANCH=
+ MAGGOTUBA_ADAPTER_BRANCH=
+ break
+ elif [ "$arg" = "--with-backend" ]; then
+ WITH_BACKEND=1
+ elif [ "$arg" = "--experimental" ]; then
+ MAGGOTUBA_CORE_BRANCH=
+ MAGGOTUBA_ADAPTER_BRANCH=torch2
+ PYTHON_VERSION=3.11
+ fi
+done
+
+if ! command -v curl >/dev/null; then
+ if command -v brew >/dev/null; then
+ # macOS users are not given the choice as they usually do not care about freedom
+ brew install curl
+ fi
+fi
+if ! command -v curl >/dev/null; then
+ echo "Command curl required; aborting"
+else
+
+check_brew() {
+ if [ "`uname`" = "Darwin" ]; then
+ # macOS
+ if ! command -v brew >/dev/null; then
+ echo "Installing Homebrew; admin rights will be requested"
+ /bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"
+ fi
+ fi
+}
+
+if ! command -v realpath >/dev/null; then
+ # macOS
+ check_brew
+ if command -v brew >/dev/null; then
+ brew install coreutils
+ fi
+fi
+
+if ! command -v julia >/dev/null; then
+ if [ -z "$JULIA_INSTALL_ARGS" ]; then
+ JULIA_INSTALL_ARGS=-y
+ fi
+ curl -fsSL https://install.julialang.org | sh -s -- $JULIA_INSTALL_ARGS
+ if [ -f ~/.bashrc ]; then
+ source ~/.bashrc
+ elif [ -f ~/.bash_profile ]; then
+ source ~/.bash_profile
+ fi
+fi
+
+if [ -n "$WITH_BACKEND" ]; then
+ if [ "`uname`" = "Darwin" ]; then
+ echo "WARNING: the default tagging backend is not supported by macOS"
+ fi
+ if ! command -v python$PYTHON_VERSION >/dev/null; then
+ if command -v pyenv >/dev/null; then
+ [ `pyenv versions | grep $PYTHON_VERSION` ] || pyenv install $PYTHON_VERSION
+ elif [[ "`uname -r`" =~ "-microsoft-standard-WSL2" ]]; then
+ echo
+ echo "INFO: installing pyenv and its dependencies"
+ echo
+ if ! [ -d ~/.pyenv ]; then
+ sudo apt-get update
+ sudo apt-get install --no-install-recommends curl build-essential libssl-dev zlib1g-dev libbz2-dev libreadline-dev libsqlite3-dev llvm libncurses5-dev xz-utils libxml2-dev libxmlsec1-dev libffi-dev liblzma-dev #tk-dev
+ curl https://pyenv.run | bash
+ fi
+ export PATH=~/.pyenv/bin:$PATH
+ eval "$(~/.pyenv/bin/pyenv init -)"
+ cat <<"EOF" >>~/.bashrc
+
+command -v pyenv >/dev/null || export PATH=~/.pyenv/bin:$PATH
+eval "$(~/.pyenv/bin/pyenv init -)"
+EOF
+ pyenv install $PYTHON_VERSION
+ else
+ check_brew
+ if command -v brew >/dev/null; then
+ brew install python@$PYTHON_VERSION
+ else
+ echo "WARNING: command python$PYTHON_VERSION not found"
+ fi
+ fi
+ fi
+ if ! command -v poetry >/dev/null; then
+ if command -v pipx >/dev/null; then
+ pipx install poetry
+ else
+ curl -fsSL https://install.python-poetry.org | python3 -
+ fi
+ fi
+fi
+
+mkdir -p "$LARVATAGGER_PATH" && pushd $_
+##
+
+if [ -d PlanarLarvae ]; then
+ echo "PlanarLarvae.jl installation found; skipping"
+else
+ if [ -z "$PLANARLARVAE_BRANCH" ]; then
+ PLANARLARVAE_BRANCH=main
+ else
+ curl -fsSL https://gitlab.pasteur.fr/nyx/planarlarvae.jl/-/archive/${PLANARLARVAE_BRANCH}/planarlarvae.jl-${PLANARLARVAE_BRANCH}.tar.gz | tar zxv
+ mv planarlarvae.jl-${PLANARLARVAE_BRANCH} PlanarLarvae
+ fi
+fi
+
+if [ -d LarvaTagger.jl ]; then
+ echo "LarvaTagger.jl installation found; skipping"
+else
+ if [ -z "$LARVATAGGER_BRANCH" ]; then
+ LARVATAGGER_BRANCH=dev
+ fi
+ curl -fsSL https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/archive/${LARVATAGGER_BRANCH}/larvatagger.jl-${LARVATAGGER_BRANCH}.tar.gz | tar zxv
+ mv larvatagger.jl-${LARVATAGGER_BRANCH} LarvaTagger.jl
+fi
+(cd LarvaTagger.jl && julia --project=. -e 'using Pkg; Pkg.instantiate()')
+[ -d PlanarLarvae ] && (cd LarvaTagger.jl && julia --project=. -e 'using Pkg; Pkg.develop(path="../PlanarLarvae")')
+
+if [ -z "$WITH_BACKEND" ]; then
+
+mkdir -p "$BIN_DIR"
+cat <<EOF >"$BIN_DIR"/larvatagger
+#!/usr/bin/env bash
+
+OPEN_BROWSER=1 "$LARVATAGGER_PATH/LarvaTagger.jl/scripts/larvatagger" \$@
+EOF
+
+else
+
+activate() {
+ # pyenv activation is necessary on WSL
+ command -v pyenv >/dev/null && pyenv local $PYTHON_VERSION
+ poetry env use $PYTHON_VERSION
+}
+
+if [ -d TaggingBackends ]; then
+ echo "TaggingBackends installation found; skipping"
+else
+ if [ -z "$TAGGINGBACKENDS_BRANCH" ]; then
+ TAGGINGBACKENDS_BRANCH=main
+ fi
+ curl -fsSL https://gitlab.pasteur.fr/nyx/TaggingBackends/-/archive/${TAGGINGBACKENDS_BRANCH}/TaggingBackends-${TAGGINGBACKENDS_BRANCH}.tar.gz | tar zxv
+ mv TaggingBackends-${TAGGINGBACKENDS_BRANCH} TaggingBackends
+fi
+(cd TaggingBackends && julia --project=. -e 'using Pkg; Pkg.instantiate()')
+[ -d PlanarLarvae ] && (cd TaggingBackends && julia --project=. -e 'using Pkg; Pkg.develop(path="../PlanarLarvae")')
+(cd TaggingBackends && activate && JULIA_PROJECT=$(pwd) poetry install)
+
+if [ -d MaggotUBA-core ]; then
+ echo "MaggotUBA-core installation found; skipping"
+else
+ if [ -z "$MAGGOTUBA_CORE_BRANCH" ]; then
+ MAGGOTUBA_CORE_BRANCH=main
+ else
+ curl -fsSL https://gitlab.pasteur.fr/nyx/maggotuba-core/-/archive/${MAGGOTUBA_CORE_BRANCH}/maggotuba-core-${MAGGOTUBA_CORE_BRANCH}.tar.gz | tar zxv
+ mv maggotuba-core-${MAGGOTUBA_CORE_BRANCH} MaggotUBA-core
+ fi
+fi
+
+if [ -d MaggotUBA ]; then
+ echo "MaggotUBA installation found; skipping"
+else
+ if [ -z "$MAGGOTUBA_ADAPTER_BRANCH" ]; then
+ MAGGOTUBA_ADAPTER_BRANCH=main
+ fi
+ curl -fsSL https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter/-/archive/${MAGGOTUBA_ADAPTER_BRANCH}/MaggotUBA-adapter-${MAGGOTUBA_ADAPTER_BRANCH}.tar.gz | tar zxv
+ mv MaggotUBA-adapter-${MAGGOTUBA_ADAPTER_BRANCH} MaggotUBA #-adapter
+ #ln -s $(realpath MaggotUBA-adapter) MaggotUBA
+fi
+# setting JULIA_PROJECT may not be necessary at this point
+export JULIA_PROJECT=$(realpath TaggingBackends)
+(cd MaggotUBA && activate && (cat requirements.txt | xargs -I % sh -c 'poetry add "%"' || true) && poetry install -v)
+[ -d TaggingBackends ] && (cd MaggotUBA && activate && poetry remove taggingbackends && poetry add ../TaggingBackends)
+[ -d MaggotUBA-core ] && (cd MaggotUBA && activate && poetry remove maggotuba-core && poetry add ../MaggotUBA-core)
+(cd MaggotUBA && scripts/make_models.jl default)
+
+mkdir -p "$BIN_DIR"
+cat <<EOF >"$BIN_DIR"/larvatagger
+#!/usr/bin/env bash
+
+JULIA_PROJECT="$(realpath "$LARVATAGGER_PATH/TaggingBackends")" BACKENDS_PATH="$LARVATAGGER_PATH" OPEN_BROWSER=1 "$LARVATAGGER_PATH/LarvaTagger.jl/scripts/larvatagger" \$@
+EOF
+
+fi
+
+chmod a+x "$BIN_DIR/larvatagger"
+
+if ! command -v larvatagger >/dev/null; then
+ # ~/.local/bin not in $PATH?
+ if [ "$SHELL" = "/bin/zsh" ]; then
+ rcfile=~/.zshrc
+ elif [ "$SHELL" = "/bin/bash" ]; then
+ if [ -f ~/.bashrc ]; then
+ rcfile=~/.bashrc
+ elif [ -f ~/.bash_profile ]; then
+ rcfile=~/.bash_profile
+ fi
+ fi
+ cat <<"EOF" >>$rcfile
+
+export PATH=$PATH:~/.local/bin
+EOF
+ export PATH=$PATH:~/.local/bin
+fi
+
+##
+popd
+
+fi
+fi
diff --git a/scripts/larvatagger b/scripts/larvatagger
index d9a475be6a19e7f2cab8feccfc1feea31bd87bf4..91c4d7f2df592049367abc46c40ab0d0de2ebf72 100755
--- a/scripts/larvatagger
+++ b/scripts/larvatagger
@@ -17,11 +17,32 @@ fi
case $cmd in
open)
shift
- $currentdir/larvatagger-gui.jl $@
+ datapath=$1
+ shift
+ args=
+ if [ -n "$BACKENDS_PATH" ]; then
+ args="--backends=\"$BACKENDS_PATH\" $args"
+ fi
+ if [ -n "$OPEN_BROWSER" ]; then
+ args="--browser $args"
+ fi
+ eval "\"$currentdir/larvatagger-gui.jl\" \"$datapath\" $args$@"
+ ;;
+
+train|predict)
+ if [ -n "$BACKENDS_PATH" -a -n "$2" -a -d "$BACKENDS_PATH/$2" ]; then
+ cmd=$1
+ shift
+ backend=$1
+ shift
+ "$currentdir/larvatagger-toolkit.jl" $cmd "$BACKENDS_PATH/$backend" $@
+ else
+ "$currentdir/larvatagger-toolkit.jl" $@
+ fi
;;
-import|merge|train|predict|--version|-V)
- $currentdir/larvatagger-toolkit.jl $@
+import|merge|--version|-V)
+ "$currentdir/larvatagger-toolkit.jl" $@
;;
*)
diff --git a/src/LarvaTagger.jl b/src/LarvaTagger.jl
index f500ba120d11daf1153ed13a5d394dfbf20b2d04..337a0e34b730e13913282b2b9573437d5405a88c 100644
--- a/src/LarvaTagger.jl
+++ b/src/LarvaTagger.jl
@@ -7,7 +7,7 @@ using TidyObservables
using JSServe, WGLMakie
using JSServe: evaljs, onjs
using Makie
-using Formatting
+using Format
using Colors
using StaticArrays
using Statistics
diff --git a/src/cli_open.jl b/src/cli_open.jl
index d62d3740648b993fe875adc55966d5bc49f32709..f46a52a26e98d40c4effd6775a2c873f2ffbf8aa 100644
--- a/src/cli_open.jl
+++ b/src/cli_open.jl
@@ -76,7 +76,8 @@ function main(args=ARGS; exit_on_error=false)
server = Server(app, "0.0.0.0", port)
if parsed_args["--browser"]
JSServe.openurl("http://127.0.0.1:$(port)")
- elseif verbose
+ end
+ if verbose
@info "The server is ready at http://127.0.0.1:$(port)"
end
if verbose
diff --git a/src/wgl.jl b/src/wgl.jl
index a162e970af2959e4a33ef4c4a138a26324cc52d3..66408bbd99a3ed35ee7d82005f1836f9672c153d 100644
--- a/src/wgl.jl
+++ b/src/wgl.jl
@@ -321,7 +321,8 @@ end
timelabel(master::TimeController; kwargs...) = timelabel(master.time; kwargs...)
function JSServe.jsrender(session::Session, tl::TimeLabel)
- formatter = generate_formatter("t=% .$(tl.ndecimals)f s")
+ fmt = FormatExpr("t={: .$(tl.ndecimals)f} s")
+ formatter = t -> format(fmt, t)
r(session,
DOM.label(lift(formatter, tl.time);
tl.attributes...))
diff --git a/test/deploy_and_test.sh b/test/deploy_and_test.sh
index 45c5a8dfc874ddd2bea4c00bff80eb3f06db634f..42a2db685c2f28bdff0a97d47ef549c181182743 100755
--- a/test/deploy_and_test.sh
+++ b/test/deploy_and_test.sh
@@ -68,13 +68,18 @@ if [ -z "$(which shunit2)" ]; then
git clone -c advice.detachedHead=false -b v2.1.8 https://github.com/kward/shunit2
fi
-# comment out the below line to build a development environment
-CLONE_OPTS=" --depth 1 --no-tags --single-branch -b dev"
-git clone$CLONE_OPTS https://gitlab.pasteur.fr/nyx/planarlarvae.jl PlanarLarvae
-git clone$CLONE_OPTS https://gitlab.pasteur.fr/nyx/LarvaTagger.jl
+## comment out the below line to build a development environment
+#CLONE_OPTS=" --depth 1 --no-tags --single-branch -b dev"
+#git clone$CLONE_OPTS https://gitlab.pasteur.fr/nyx/planarlarvae.jl PlanarLarvae
+#git clone$CLONE_OPTS https://gitlab.pasteur.fr/nyx/LarvaTagger.jl
+BRANCH=dev
+wget -O- https://gitlab.pasteur.fr/nyx/planarlarvae.jl/-/archive/${BRANCH}/planarlarvae.jl-${BRANCH}.tar.gz | tar zxv && mv planarlarvae.jl-${BRANCH} PlanarLarvae
+wget -O- https://gitlab.pasteur.fr/nyx/larvatagger.jl/-/archive/${BRANCH}/larvatagger.jl-${BRANCH}.tar.gz | tar zxv && mv larvatagger.jl-${BRANCH} LarvaTagger.jl
ln -s $(realpath LarvaTagger.jl) LarvaTagger
-git clone$CLONE_OPTS https://gitlab.pasteur.fr/nyx/TaggingBackends
-git clone$CLONE_OPTS https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter
+#git clone$CLONE_OPTS https://gitlab.pasteur.fr/nyx/TaggingBackends
+#git clone$CLONE_OPTS https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter
+wget -O- https://gitlab.pasteur.fr/nyx/TaggingBackends/-/archive/${BRANCH}/TaggingBackends-${BRANCH}.tar.gz | tar zxv && mv TaggingBackends-${BRANCH} TaggingBackends
+wget -O- https://gitlab.pasteur.fr/nyx/MaggotUBA-adapter/-/archive/${BRANCH}/MaggotUBA-adapter-${BRANCH}.tar.gz | tar zxv && mv MaggotUBA-adapter-${BRANCH} MaggotUBA-adapter
ln -s $(realpath MaggotUBA-adapter) MaggotUBA
# the poetry install step may not be necessary
@@ -103,7 +108,8 @@ if [ -f ../../LarvaTagger_test_data.tgz ]; then
tar zxvf ../../LarvaTagger_test_data.tgz
else
# Not recommended; reproducibility is not guarantee across hosts or architectures yet
- wget -O- https://dl.pasteur.fr/fop/8MvgygD4/LarvaTagger_test_data.tgz | tar zxv
+ #wget -O- https://dl.pasteur.fr/fop/8MvgygD4/LarvaTagger_test_data.tgz | tar zxv
+ wget -O- https://dl.pasteur.fr/fop/WdnyHdKR/240208_LarvaTagger_test_data.tgz | tar zxv
fi
if [ "$LOCAL_SCENARII" = "1" ]; then