From 5e546f0b138dfd3f4cdb5f559e8bd30928169284 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Mon, 28 Aug 2023 10:51:13 +0100 Subject: [PATCH 1/7] Update tools - ecmwfapi no longer exists! Set up as 1.9 extension to package --- Project.toml | 13 +- examples/Manifest.toml | 755 ++++++++++++------ examples/Project.toml | 4 +- ext/DataTools.jl | 21 + ext/ERATools.jl | 100 +++ src/ClimatePref/ClimatePref.jl | 25 +- src/ClimatePref/ECMWF_tools.jl | 54 -- .../{ERA_interim_tools.jl => ERA5_tools.jl} | 29 +- src/ClimatePref/Extensions.jl | 7 + src/Traits.jl | 3 - 10 files changed, 661 insertions(+), 350 deletions(-) create mode 100644 ext/DataTools.jl create mode 100644 ext/ERATools.jl delete mode 100644 src/ClimatePref/ECMWF_tools.jl rename src/ClimatePref/{ERA_interim_tools.jl => ERA5_tools.jl} (63%) create mode 100644 src/ClimatePref/Extensions.jl diff --git a/Project.toml b/Project.toml index 97c385c63..fa7f63dfb 100644 --- a/Project.toml +++ b/Project.toml @@ -8,6 +8,7 @@ ArchGDAL = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3" AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9" Calculus = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" +DataPipeline = "9ced6f0a-eb77-43a8-bbd1-bbf3031b0d12" Dates = "ade2ca70-3891-5945-98fb-dc099432e06a" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Diversity = "d3d5718d-52de-57ab-b67a-eca7fd6175a4" @@ -32,6 +33,7 @@ Phylo = "aea672f4-3940-5932-aa44-993d1c3ff149" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781" Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" +PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" RasterDataSources = "3cb90ccd-e1b6-4867-9617-4276c8b2ca36" @@ -43,11 +45,20 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" +[weakdeps] +DataPipeline = "9ced6f0a-eb77-43a8-bbd1-bbf3031b0d12" +PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" + +[extensions] +DataTools = "DataPipeline" +ERATools = "PyCall" + [compat] ArchGDAL = "0.6, 0.7, 0.8, 0.9, 0.10" AxisArrays = "0.4.3" Calculus = "0.4.1, 0.5" DataFrames = "0.21.8, 0.22, 1.0" +DataPipeline = "0.53" Distributions = "0.24.15, 0.25" Diversity = "0.5.6" EcoBase = "0.1.3" @@ -70,7 +81,7 @@ Requires = "1" SpatialEcology = "0.9" StatsBase = "0.32.2, 0.33" Unitful = "1.7" -julia = "1.6, 1.8" +julia = "1.9" [extras] MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" diff --git a/examples/Manifest.toml b/examples/Manifest.toml index d04b9b046..1d5a23272 100644 --- a/examples/Manifest.toml +++ b/examples/Manifest.toml @@ -1,8 +1,8 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.8.0" +julia_version = "1.9.2" manifest_format = "2.0" -project_hash = "c0e516f61644651e06acb8acd91b717e6cd3a7bd" +project_hash = "4f156d9c7e48ef361d27dcb4a23a19d047370b4c" [[deps.ASCIIrasters]] git-tree-sha1 = "0cb0046798af8ac8561334c5a2a31f015e53c2b1" @@ -10,10 +10,15 @@ uuid = "81770e7c-c736-4fa5-8129-46dd21831640" version = "0.1.1" [[deps.AbstractFFTs]] -deps = ["ChainRulesCore", "LinearAlgebra"] -git-tree-sha1 = "16b6dbc4cf7caee4e1e75c49485ec67b667098a0" +deps = ["LinearAlgebra"] +git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" -version = "1.3.1" +version = "1.5.0" +weakdeps = ["ChainRulesCore", "Test"] + + [deps.AbstractFFTs.extensions] + AbstractFFTsChainRulesCoreExt = "ChainRulesCore" + AbstractFFTsTestExt = "Test" [[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" @@ -22,15 +27,19 @@ version = "0.4.4" [[deps.Adapt]] deps = ["LinearAlgebra", "Requires"] -git-tree-sha1 = "cc37d689f599e8df4f464b2fa3870ff7db7492ef" +git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.6.1" +version = "3.6.2" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" [[deps.ArchGDAL]] deps = ["CEnum", "ColorTypes", "Dates", "DiskArrays", "Extents", "GDAL", "GeoFormatTypes", "GeoInterface", "GeoInterfaceRecipes", "ImageCore", "Tables"] -git-tree-sha1 = "ef43020f8b69ed20439a10a5690d07bf6cbc7ee8" +git-tree-sha1 = "0ca60eb1896df6ca2f2a856faf287c0dd6f27a32" uuid = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3" -version = "0.10.0" +version = "0.10.1" [[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" @@ -38,15 +47,31 @@ version = "1.1.1" [[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] -git-tree-sha1 = "f87e559f87a45bece9c9ed97458d3afe98b1ebb9" +git-tree-sha1 = "62e51b39331de8911e4a7ff6f5aaf38a5f4cc0ae" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" -version = "0.1.0" +version = "0.2.0" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "a89acc90c551067cd84119ff018619a1a76c6277" +deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "f83ec24f76d4c8f525099b2ac475fc098138ec31" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.2.1" +version = "7.4.11" + + [deps.ArrayInterface.extensions] + ArrayInterfaceBandedMatricesExt = "BandedMatrices" + ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" + ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" + ArrayInterfaceTrackerExt = "Tracker" + + [deps.ArrayInterface.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.Arrow_jll]] deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Lz4_jll", "Pkg", "Thrift_jll", "Zlib_jll", "boost_jll", "snappy_jll"] @@ -94,6 +119,12 @@ git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.4.2" +[[deps.CSV]] +deps = ["Dates", "Mmap", "Parsers", "PooledArrays", "SentinelArrays", "Tables", "Unicode"] +git-tree-sha1 = "b83aa3f513be680454437a0eee21001607e5d983" +uuid = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" +version = "0.8.5" + [[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" @@ -108,9 +139,21 @@ version = "0.5.1" [[deps.CategoricalArrays]] deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"] -git-tree-sha1 = "5084cc1a28976dd1642c9f337b28a3cb03e0f7d2" +git-tree-sha1 = "1568b28f91293458345dabba6a5ea3f183250a61" uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597" -version = "0.10.7" +version = "0.10.8" + + [deps.CategoricalArrays.extensions] + CategoricalArraysJSONExt = "JSON" + CategoricalArraysRecipesBaseExt = "RecipesBase" + CategoricalArraysSentinelArraysExt = "SentinelArrays" + CategoricalArraysStructTypesExt = "StructTypes" + + [deps.CategoricalArrays.weakdeps] + JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" + RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" + SentinelArrays = "91c51154-3ec4-41a3-a24f-3f23e20d615c" + StructTypes = "856f2bd8-1eba-4b0a-8007-ebc267875bd4" [[deps.Chain]] git-tree-sha1 = "339237319ef4712e6e5df7758d0bccddf5c237d9" @@ -119,27 +162,21 @@ version = "0.4.10" [[deps.ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "c6d890a52d2c4d55d326439580c3b8d0875a77d9" +git-tree-sha1 = "e30f2f4e20f7f186dc36529910beaedc60cfa644" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.15.7" - -[[deps.ChangesOfVariables]] -deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "485193efd2176b88e6622a39a246f8c5b600e74e" -uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.6" +version = "1.16.0" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" +git-tree-sha1 = "02aa26a4cf76381be7f66e020a3eddeb27b0a092" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.1" +version = "0.7.2" [[deps.ColorSchemes]] -deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] -git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] +git-tree-sha1 = "d9a8f86737b665e15a9641ecbac64deef9ce6724" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.20.0" +version = "3.23.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -171,27 +208,42 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[deps.Compat]] -deps = ["Dates", "LinearAlgebra", "UUIDs"] -git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957" +deps = ["UUIDs"] +git-tree-sha1 = "e460f044ca8b99be31d35fe54fc33a5c33dd8ed7" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.6.1" +version = "4.9.0" +weakdeps = ["Dates", "LinearAlgebra"] + + [deps.Compat.extensions] + CompatLinearAlgebraExt = "LinearAlgebra" [[deps.CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" -version = "0.5.2+0" +version = "1.0.5+0" + +[[deps.ConcurrentUtilities]] +deps = ["Serialization", "Sockets"] +git-tree-sha1 = "5372dbbf8f0bdb8c700db5367132925c0771ef7e" +uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb" +version = "2.2.1" [[deps.Configurations]] deps = ["ExproniconLite", "OrderedCollections", "TOML"] -git-tree-sha1 = "62a7c76dbad02fdfdaa53608104edf760938c4ca" +git-tree-sha1 = "434f446dbf89d08350e83bf57c0fc86f5d3ffd4e" uuid = "5218b696-f38b-4ac9-8b61-a12ec717816d" -version = "0.17.4" +version = "0.17.5" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "89a9db8d28102b094992472d333674bd1a83ce2a" +git-tree-sha1 = "fe2838a593b5f776e1597e086dcd47560d94e816" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.1" +version = "1.5.3" +weakdeps = ["IntervalSets", "StaticArrays"] + + [deps.ConstructionBase.extensions] + ConstructionBaseIntervalSetsExt = "IntervalSets" + ConstructionBaseStaticArraysExt = "StaticArrays" [[deps.Contour]] git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" @@ -203,16 +255,21 @@ git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" +[[deps.DBInterface]] +git-tree-sha1 = "9b0dc525a052b9269ccc5f7f04d5b3639c65bca5" +uuid = "a10d1c49-ce27-4219-8d33-6db1a4562965" +version = "2.5.0" + [[deps.DataAPI]] -git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" +git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.14.0" +version = "1.15.0" [[deps.DataFrames]] -deps = ["Compat", "DataAPI", "Future", "InlineStrings", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SentinelArrays", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "aa51303df86f8626a962fccb878430cdb0a97eee" +deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Random", "Reexport", "SnoopPrecompile", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] +git-tree-sha1 = "d4f69885afa5e6149d0cab3818491565cf41446d" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.5.0" +version = "1.4.4" [[deps.DataFramesMeta]] deps = ["Chain", "DataFrames", "MacroTools", "Reexport"] @@ -220,11 +277,17 @@ git-tree-sha1 = "29e71b438935977f8905c0cb3a8a84475fc70101" uuid = "1313f7d8-7da2-5740-9ea0-a2ca25f37964" version = "0.9.1" +[[deps.DataPipeline]] +deps = ["AxisArrays", "CSV", "DataFrames", "Dates", "FTPClient", "HDF5", "HTTP", "JSON", "NetCDF", "Plots", "PrettyTables", "SHA", "SQLite", "TOML", "URIs", "UnicodePlots", "YAML"] +git-tree-sha1 = "9002581ac7bb2b9944cf598d09622997b3cd83ed" +uuid = "9ced6f0a-eb77-43a8-bbd1-bbf3031b0d12" +version = "0.53.2" + [[deps.DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" +git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.13" +version = "0.18.15" [[deps.DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -243,13 +306,9 @@ uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" [[deps.DelimitedFiles]] deps = ["Mmap"] +git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae" uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab" - -[[deps.DensityInterface]] -deps = ["InverseFunctions", "Test"] -git-tree-sha1 = "80c3e8639e3353e5d2912fb3a1916b8455e2494b" -uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" -version = "0.4.0" +version = "1.9.1" [[deps.DiffResults]] deps = ["StaticArraysCore"] @@ -259,32 +318,44 @@ version = "1.1.0" [[deps.DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "a4ad7ef19d2cdc2eff57abbbe68032b1cd0bd8f8" +git-tree-sha1 = "23163d55f885173722d1e4cf0f6110cdbaf7e272" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.13.0" +version = "1.15.1" [[deps.DiskArrays]] deps = ["OffsetArrays"] -git-tree-sha1 = "3f87990e0882e44c0f4e5c9699d09a0edbfa25c8" +git-tree-sha1 = "7e8dcba9d1d1ba8aa576f7d899d42e04d76431b2" uuid = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3" -version = "0.3.9" +version = "0.3.15" [[deps.Distances]] -deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "49eba9ad9f7ead780bfb7ee319f962c811c6d3b2" +deps = ["LinearAlgebra", "Statistics", "StatsAPI"] +git-tree-sha1 = "b6def76ffad15143924a2199f72a5cd883a2e8a9" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.8" +version = "0.10.9" +weakdeps = ["SparseArrays"] + + [deps.Distances.extensions] + DistancesSparseArraysExt = "SparseArrays" [[deps.Distributed]] deps = ["Random", "Serialization", "Sockets"] uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] -deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] +deps = ["FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] git-tree-sha1 = "da9e1a9058f8d3eec3a8c9fe4faacfb89180066b" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" version = "0.25.86" + [deps.Distributions.extensions] + DistributionsChainRulesCoreExt = "ChainRulesCore" + DistributionsDensityInterfaceExt = "DensityInterface" + + [deps.Distributions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + DensityInterface = "b429d917-457f-4dbc-8f4c-0cc954292b1d" + [[deps.Diversity]] deps = ["AxisArrays", "DataFrames", "EcoBase", "InteractiveUtils", "LinearAlgebra", "Missings", "RecipesBase", "Requires", "Statistics"] git-tree-sha1 = "819eb004d95692407c7ab5f4638607a998c50118" @@ -318,19 +389,33 @@ version = "0.1.6" deps = ["ArchGDAL", "AxisArrays", "Calculus", "DataFrames", "Dates", "Distributions", "Diversity", "EcoBase", "Feather", "HCubature", "IndexedTables", "Interpolations", "JLD2", "LibGit2", "Libdl", "LinearAlgebra", "Logging", "MPI", "Markdown", "Measures", "Missings", "NetCDF", "OnlineStats", "Optim", "Phylo", "Plots", "Pluto", "Printf", "REPL", "Random", "RasterDataSources", "Requires", "SHA", "SpatialEcology", "Statistics", "StatsBase", "UUIDs", "Unitful"] path = ".." uuid = "ed2dc23b-ada4-5fdb-a26f-56368a14ad8f" -version = "0.1.3" +version = "0.1.4" + + [deps.EcoSISTEM.extensions] + DataTools = "DataPipeline" + ERATools = "PyCall" + + [deps.EcoSISTEM.weakdeps] + DataPipeline = "9ced6f0a-eb77-43a8-bbd1-bbf3031b0d12" + PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0" + +[[deps.ExceptionUnwrapping]] +deps = ["Test"] +git-tree-sha1 = "e90caa41f5a86296e014e148ee061bd6c3edec96" +uuid = "460bff9d-24e4-43bc-9d9f-a8973cb893f4" +version = "0.1.9" [[deps.Expat_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "4558ab818dcceaab612d1bb8c19cee87eda2b83c" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" -version = "2.4.8+0" +version = "2.5.0+0" [[deps.ExproniconLite]] deps = ["Pkg", "TOML"] -git-tree-sha1 = "c2eb763acf6e13e75595e0737a07a0bec0ce2147" +git-tree-sha1 = "d80b5d5990071086edf5de9018c6c69c83937004" uuid = "55351af7-c7e9-48d6-89ff-24e801d99491" -version = "0.7.11" +version = "0.10.3" [[deps.Extents]] git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" @@ -349,6 +434,12 @@ git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" version = "4.4.2+2" +[[deps.FTPClient]] +deps = ["LibCURL", "URIParser"] +git-tree-sha1 = "fcdcac297167852b23bae6d7bb3bf82a726ff70c" +uuid = "01fcc997-4f28-56b8-8a06-30002c134abb" +version = "1.2.1" + [[deps.Feather]] deps = ["CategoricalArrays", "DataFrames", "Dates", "FlatBuffers", "Mmap", "Tables"] git-tree-sha1 = "d2755da2b5cdc90586764f24c2de9267464b7ed0" @@ -357,24 +448,34 @@ version = "0.5.10" [[deps.FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "7be5f99f7d15578798f338f5433b6c432ea8037b" +git-tree-sha1 = "299dc33549f68299137e51e6d49a13b5b1da9673" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.16.0" +version = "1.16.1" [[deps.FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "d3ba08ab64bdfd27234d3f61956c966266757fe6" +git-tree-sha1 = "7072f1e3e5a8be51d525d64f63d3ec1287ff2790" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.7" +version = "0.13.11" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "ed1b56934a2f7a65035976985da71b6a65b4f2cf" +deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] +git-tree-sha1 = "c6e4a1fbe73b31a3dea94b1da449503b8830c306" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.18.0" +version = "2.21.1" + + [deps.FiniteDiff.extensions] + FiniteDiffBandedMatricesExt = "BandedMatrices" + FiniteDiffBlockBandedMatricesExt = "BlockBandedMatrices" + FiniteDiffStaticArraysExt = "StaticArrays" + + [deps.FiniteDiff.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" [[deps.FixedPointNumbers]] deps = ["Statistics"] @@ -401,16 +502,20 @@ uuid = "59287772-0a20-5a39-b81b-1366585eb4c0" version = "0.4.2" [[deps.ForwardDiff]] -deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" +deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"] +git-tree-sha1 = "cf0fe81336da9fb90944683b8c41984b08793dad" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.35" +version = "0.10.36" +weakdeps = ["StaticArrays"] + + [deps.ForwardDiff.extensions] + ForwardDiffStaticArraysExt = "StaticArrays" [[deps.FreeType2_jll]] -deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "87eb71354d8ec1a96d4a7636bd57a7347dde3ef9" +deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "d8db6a5a2fe1381c1ea4ef2cab7c69c2de7f9ea0" uuid = "d7e528f0-a631-5988-bf34-fe36492bcfd7" -version = "2.10.4+0" +version = "2.13.1+0" [[deps.FriBidi_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -430,9 +535,9 @@ version = "0.5.1" [[deps.GDAL]] deps = ["CEnum", "GDAL_jll", "NetworkOptions", "PROJ_jll"] -git-tree-sha1 = "aa6f8ca2f7a0eb46f4d8353eb725c717de40da6e" +git-tree-sha1 = "41ce0b68c058822c465e5f4a71d9249887e05a2f" uuid = "add2ef01-049f-52c4-9ee2-e494f65e021a" -version = "1.5.1" +version = "1.6.0" [[deps.GDAL_jll]] deps = ["Arrow_jll", "Artifacts", "Expat_jll", "GEOS_jll", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "LibPQ_jll", "Libdl", "Libtiff_jll", "NetCDF_jll", "OpenJpeg_jll", "PROJ_jll", "Pkg", "SQLite_jll", "Zlib_jll", "Zstd_jll", "libgeotiff_jll"] @@ -441,10 +546,10 @@ uuid = "a7073274-a066-55f0-b90d-d619367d196c" version = "301.600.200+0" [[deps.GEOS_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "f4c0cafb093b62d5a5d8447a9b2306555385c0d9" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "818ab247de98d8848a022c7be084b1283d912326" uuid = "d604d12d-fa86-5845-992e-78dc15976526" -version = "3.11.0+0" +version = "3.11.2+0" [[deps.GLFW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] @@ -454,15 +559,15 @@ version = "3.3.8+0" [[deps.GR]] deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "UUIDs", "p7zip_jll"] -git-tree-sha1 = "660b2ea2ec2b010bb02823c6d0ff6afd9bdc5c16" +git-tree-sha1 = "4423d87dc2d3201f3f1768a29e807ddc8cc867ef" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.71.7" +version = "0.71.8" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "d5e1fd17ac7f3aa4c5287a61ee28d4f8b8e98873" +git-tree-sha1 = "3657eb348d44575cc5560c80d7e55b812ff6ffe1" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.71.7+0" +version = "0.71.8+0" [[deps.GeoFormatTypes]] git-tree-sha1 = "434166198434a5c2fcc0a1a59d22c3b0ad460889" @@ -471,15 +576,15 @@ version = "0.4.1" [[deps.GeoInterface]] deps = ["Extents"] -git-tree-sha1 = "e07a1b98ed72e3cdd02c6ceaab94b8a606faca40" +git-tree-sha1 = "bb198ff907228523f3dee1070ceee63b9359b6ab" uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" -version = "1.2.1" +version = "1.3.1" [[deps.GeoInterfaceRecipes]] deps = ["GeoInterface", "RecipesBase"] -git-tree-sha1 = "29e1ec25cfb6762f503a19495aec347acf867a9e" +git-tree-sha1 = "0e26e1737e94de57c858649dc28e482b6c87d341" uuid = "0329782f-3d07-4b52-b9f6-d3137cf03c7a" -version = "1.0.0" +version = "1.0.1" [[deps.Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -505,6 +610,12 @@ git-tree-sha1 = "344bf40dcab1073aca04aa0df4fb092f920e4011" uuid = "3b182d85-2403-5c21-9c21-1e1f0cc25472" version = "1.3.14+0" +[[deps.Graphs]] +deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] +git-tree-sha1 = "1cf1d7dcb4bc32d7b4a5add4232db3750c27ecb4" +uuid = "86223c79-3864-5bf0-83f7-82e725a168b6" +version = "1.8.0" + [[deps.Grisu]] git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2" uuid = "42e2da0e-8278-4e71-bc24-59509adca0fe" @@ -516,6 +627,12 @@ git-tree-sha1 = "e95b36755023def6ebc3d269e6483efa8b2f7f65" uuid = "19dc6840-f33b-545b-b366-655c7e3ffd49" version = "1.5.1" +[[deps.HDF5]] +deps = ["Compat", "HDF5_jll", "Libdl", "Mmap", "Printf", "Random", "Requires", "UUIDs"] +git-tree-sha1 = "114e20044677badbc631ee6fdc80a67920561a29" +uuid = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f" +version = "0.16.16" + [[deps.HDF5_jll]] deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"] git-tree-sha1 = "4cc2bb72df6ff40b055295fdef6d92955f9dede8" @@ -523,10 +640,10 @@ uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" version = "1.12.2+2" [[deps.HTTP]] -deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] -git-tree-sha1 = "37e4657cd56b11abe3d10cd4a1ec5fbdb4180263" +deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "cb56ccdd481c0dd7f975ad2b3b62d9eda088f7e2" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "1.7.4" +version = "1.9.14" [[deps.HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -535,10 +652,10 @@ uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" version = "2.8.1+1" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] -git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" +deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.11" +version = "0.3.23" [[deps.HypertextLiteral]] deps = ["Tricks"] @@ -563,17 +680,6 @@ git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" version = "0.1.3" -[[deps.IniFile]] -git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" -uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" -version = "0.5.1" - -[[deps.InlineStrings]] -deps = ["Parsers"] -git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461" -uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.4.0" - [[deps.InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" @@ -585,21 +691,19 @@ uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" version = "0.14.7" [[deps.IntervalSets]] -deps = ["Dates", "Random", "Statistics"] -git-tree-sha1 = "16c0cc91853084cb5f58a78bd209513900206ce6" +deps = ["Dates", "Random"] +git-tree-sha1 = "8e59ea773deee525c99a8018409f64f19fb719e6" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.7.4" +version = "0.7.7" +weakdeps = ["Statistics"] -[[deps.InverseFunctions]] -deps = ["Test"] -git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" -uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.8" + [deps.IntervalSets.extensions] + IntervalSetsStatisticsExt = "Statistics" [[deps.InvertedIndices]] -git-tree-sha1 = "82aec7a3dd64f4d9584659dc0b62ef7db2ef3e19" +git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.2.0" +version = "1.3.0" [[deps.IrrationalConstants]] git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" @@ -607,9 +711,9 @@ uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" version = "0.2.2" [[deps.IterTools]] -git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" +git-tree-sha1 = "4ced6667f9974fc5c5943fa5e2ef1ca43ea9e450" uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e" -version = "1.4.0" +version = "1.8.0" [[deps.IterableTables]] deps = ["DataValues", "IteratorInterfaceExtensions", "Requires", "TableTraits", "TableTraitsUtils"] @@ -624,9 +728,9 @@ version = "1.0.0" [[deps.JLD2]] deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "42c17b18ced77ff0be65957a591d34f4ed57c631" +git-tree-sha1 = "aa6ffef1fd85657f4999030c52eaeec22a279738" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.31" +version = "0.4.33" [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] @@ -635,16 +739,16 @@ uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" version = "0.1.5" [[deps.JLLWrappers]] -deps = ["Preferences"] -git-tree-sha1 = "abc9885a7ca2052a736a600f7fa66209f96506e1" +deps = ["Artifacts", "Preferences"] +git-tree-sha1 = "7e5d6779a1e09a36db2a7b6cff50942a0a7d0fca" uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210" -version = "1.4.1" +version = "1.5.0" [[deps.JSON]] deps = ["Dates", "Mmap", "Parsers", "Unicode"] -git-tree-sha1 = "3c837543ddb02250ef42f4738347454f95079d4e" +git-tree-sha1 = "31e996f0a15c7b280ba9f76636b3ff9e2ae58c9a" uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" -version = "0.21.3" +version = "0.21.4" [[deps.JpegTurbo_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -670,6 +774,12 @@ git-tree-sha1 = "bf36f528eec6634efc60d7ec062008f171071434" uuid = "88015f11-f218-50d7-93a8-a6af411a945d" version = "3.0.0+1" +[[deps.LLVMOpenMP_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "f689897ccbe049adb19a065c495e75f372ecd42b" +uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" +version = "15.0.4+0" + [[deps.LZO_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "e5b909bcf985c5e2605737d2ce278ed791b89be6" @@ -683,9 +793,21 @@ version = "1.3.0" [[deps.Latexify]] deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] -git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" +git-tree-sha1 = "8c57307b5d9bb3be1ff2da469063628631d4d51e" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.18" +version = "0.15.21" + + [deps.Latexify.extensions] + DataFramesExt = "DataFrames" + DiffEqBiologicalExt = "DiffEqBiological" + ParameterizedFunctionsExt = "DiffEqBase" + SymEngineExt = "SymEngine" + + [deps.Latexify.weakdeps] + DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" + DiffEqBiological = "eb300fae-53e8-50a0-950c-e21f52c2b7e0" + SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" [[deps.LazilyInitializedFields]] git-tree-sha1 = "410fe4739a4b092f2ffe36fcb0dcc3ab12648ce1" @@ -772,12 +894,6 @@ git-tree-sha1 = "7f3efec06033682db852f8b3bc3c1d2b0a0ab066" uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700" version = "2.36.0+0" -[[deps.LightGraphs]] -deps = ["ArnoldiMethod", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"] -git-tree-sha1 = "432428df5f360964040ed60418dd5601ecd240b6" -uuid = "093fc24a-ae57-5d10-9952-331d41423f4d" -version = "1.3.5" - [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" @@ -785,7 +901,7 @@ uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" version = "7.2.0" [[deps.LinearAlgebra]] -deps = ["Libdl", "libblastrampoline_jll"] +deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[deps.LittleCMS_jll]] @@ -795,19 +911,29 @@ uuid = "d3a379c0-f9a3-5b72-a4c0-6bf4d2e8af0f" version = "2.12.0+0" [[deps.LogExpFunctions]] -deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "0a1b7c2863e44523180fdb3146534e265a91870b" +deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"] +git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.23" +version = "0.3.26" + + [deps.LogExpFunctions.extensions] + LogExpFunctionsChainRulesCoreExt = "ChainRulesCore" + LogExpFunctionsChangesOfVariablesExt = "ChangesOfVariables" + LogExpFunctionsInverseFunctionsExt = "InverseFunctions" + + [deps.LogExpFunctions.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" [[deps.Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" [[deps.LoggingExtras]] deps = ["Dates", "Logging"] -git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +git-tree-sha1 = "a03c77519ab45eb9a34d3cfe2ca223d79c064323" uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" -version = "1.0.0" +version = "1.0.1" [[deps.Lz4_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -828,32 +954,38 @@ version = "0.20.8" [[deps.MPICH_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "7ec808cad4f3940316c015cb16608e4e632c2c89" +git-tree-sha1 = "8a5b4d2220377d1ece13f49438d71ad20cf1ba83" uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" -version = "4.1.0+1" +version = "4.1.2+0" [[deps.MPIPreferences]] deps = ["Libdl", "Preferences"] -git-tree-sha1 = "71f937129731a29eabe6969db2c90368a4408933" +git-tree-sha1 = "781916a2ebf2841467cda03b6f1af43e23839d85" uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267" -version = "0.1.7" +version = "0.1.9" [[deps.MPItrampoline_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "Pkg", "TOML"] -git-tree-sha1 = "b3f9e42685b4ad614eca0b44bd863cd41b1c86ea" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "6979eccb6a9edbbb62681e158443e79ecc0d056a" uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" -version = "5.0.2+1" +version = "5.3.1+0" [[deps.MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" +git-tree-sha1 = "9ee1618cbf5240e6d4e0371d6f24065083f60c48" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.10" +version = "0.5.11" [[deps.MappedArrays]] -git-tree-sha1 = "e8b359ef06ec72e8c030463fe02efe5527ee5142" +git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e" uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" -version = "0.4.1" +version = "0.4.2" + +[[deps.MarchingCubes]] +deps = ["PrecompileTools", "StaticArrays"] +git-tree-sha1 = "c8e29e2bacb98c9b6f10445227a8b0402f2f173a" +uuid = "299715c1-40a9-479a-aaf9-4a633d36f717" +version = "0.1.8" [[deps.Markdown]] deps = ["Base64"] @@ -868,7 +1000,7 @@ version = "1.1.7" [[deps.MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" -version = "2.28.0+0" +version = "2.28.2+0" [[deps.Measures]] git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" @@ -877,9 +1009,9 @@ version = "0.3.2" [[deps.MicrosoftMPI_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "a16aa086d335ed7e0170c5265247db29172af2f9" +git-tree-sha1 = "a8027af3d1743b3bfae34e54872359fdebb31422" uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf" -version = "10.1.3+2" +version = "10.1.3+4" [[deps.Missings]] deps = ["DataAPI"] @@ -898,7 +1030,7 @@ version = "0.3.4" [[deps.MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" -version = "2022.2.1" +version = "2022.10.11" [[deps.MsgPack]] deps = ["Serialization"] @@ -925,10 +1057,10 @@ uuid = "30363a11-5582-574a-97bb-aa9a979735b9" version = "0.11.7" [[deps.NetCDF_jll]] -deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Pkg", "XML2_jll", "Zlib_jll"] -git-tree-sha1 = "072f8371f74c3b9e1b26679de7fbf059d45ea221" +deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "7f5a03e6712f5447c9c344430b8d1927a4777483" uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3" -version = "400.902.5+1" +version = "400.902.206+0" [[deps.NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" @@ -936,9 +1068,9 @@ version = "1.2.0" [[deps.OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "82d7c9e310fe55aa54996e6f7f94674e2a38fcb4" +git-tree-sha1 = "2ac17d29c523ce1cd38e27785a7d23024853a4bb" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.12.9" +version = "1.12.10" [[deps.Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -954,14 +1086,14 @@ version = "1.5.14" [[deps.OnlineStatsBase]] deps = ["AbstractTrees", "Dates", "LinearAlgebra", "OrderedCollections", "Statistics", "StatsBase"] -git-tree-sha1 = "60e587c99ea261d1c452d2acb1f3a481e772660c" +git-tree-sha1 = "790f151a4650b77850ec2313eae034e99823dafe" uuid = "925886fa-5bf2-5e8e-b522-a9147a512338" -version = "1.5.0" +version = "1.6.1" [[deps.OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" -version = "0.3.20+0" +version = "0.3.21+4" [[deps.OpenJpeg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libtiff_jll", "LittleCMS_jll", "Pkg", "libpng_jll"] @@ -982,15 +1114,15 @@ version = "4.1.5+0" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] -git-tree-sha1 = "6503b77492fd7fcb9379bf73cd31035670e3c509" +git-tree-sha1 = "51901a49222b09e3743c65b8847687ae5fc78eb2" uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" -version = "1.3.3" +version = "1.4.1" [[deps.OpenSSL_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "9ff31d101d987eb9d66bd8b176ac7c277beccd09" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "bbb5c2115d63c2f1451cb70e5ef75e8fe4707019" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.20+0" +version = "1.1.22+0" [[deps.OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -1000,9 +1132,9 @@ version = "0.5.5+0" [[deps.Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "1903afc76b7d01719d9c30d3c7d501b61db96721" +git-tree-sha1 = "963b004d15216f8129f6c0f7d187efa136570be0" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.7.4" +version = "1.7.7" [[deps.Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1011,14 +1143,14 @@ uuid = "91d4177d-7536-5919-b921-800302f37372" version = "1.3.2+0" [[deps.OrderedCollections]] -git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" +git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" -version = "1.4.1" +version = "1.6.2" [[deps.PCRE2_jll]] deps = ["Artifacts", "Libdl"] uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" -version = "10.40.0+0" +version = "10.42.0+0" [[deps.PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] @@ -1034,9 +1166,9 @@ version = "900.100.0+0" [[deps.PaddedViews]] deps = ["OffsetArrays"] -git-tree-sha1 = "03a7a85b76381a3d04c7a1656039197e70eda03d" +git-tree-sha1 = "0fac6313486baae819364c52b4f483450a9d793f" uuid = "5432bcbf-9aad-5242-b902-cca2824c8663" -version = "0.5.11" +version = "0.5.12" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -1045,16 +1177,16 @@ uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" version = "0.12.3" [[deps.Parsers]] -deps = ["Dates", "SnoopPrecompile"] -git-tree-sha1 = "478ac6c952fddd4399e71d4779797c538d0ff2bf" +deps = ["Dates"] +git-tree-sha1 = "bfd7d8c7fd87f04543810d9cbd3995972236ba1b" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.5.8" +version = "1.1.2" [[deps.Phylo]] -deps = ["AxisArrays", "DataFrames", "DataStructures", "Distributions", "IterableTables", "LightGraphs", "Missings", "Printf", "Random", "RecipesBase", "Requires", "SimpleTraits", "Statistics", "Tokenize", "Unitful"] -git-tree-sha1 = "fe4370547df637e4b6dfd6446ec227a4fd780cad" +deps = ["AxisArrays", "DataFrames", "DataStructures", "Distributions", "Graphs", "IterableTables", "Missings", "Printf", "Random", "RecipesBase", "Requires", "SimpleTraits", "Statistics", "Tokenize", "Unitful"] +git-tree-sha1 = "b01925c56e4c76004bddeb229fe4aa16d5aa9144" uuid = "aea672f4-3940-5932-aa44-993d1c3ff149" -version = "0.4.21" +version = "0.4.23" [[deps.Pipe]] git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" @@ -1062,15 +1194,15 @@ uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" version = "1.3.0" [[deps.Pixman_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LLVMOpenMP_jll", "Libdl"] +git-tree-sha1 = "64779bc4c9784fee475689a1752ef4d5747c5e87" uuid = "30392449-352a-5448-841d-b1acce4e97dc" -version = "0.40.1+0" +version = "0.42.2+0" [[deps.Pkg]] -deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" -version = "1.8.0" +version = "1.9.2" [[deps.PlotThemes]] deps = ["PlotUtils", "Statistics"] @@ -1079,10 +1211,10 @@ uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" version = "3.1.0" [[deps.PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] -git-tree-sha1 = "c95373e73290cf50a8a22c3375e4625ded5c5280" +deps = ["ColorSchemes", "Colors", "Dates", "PrecompileTools", "Printf", "Random", "Reexport", "Statistics"] +git-tree-sha1 = "f92e1315dadf8c46561fb9396e525f7200cdc227" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.3.4" +version = "1.3.5" [[deps.Plots]] deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "JLFzf", "JSON", "LaTeXStrings", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Preferences", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "RelocatableFolders", "Requires", "Scratch", "Showoff", "SnoopPrecompile", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] @@ -1090,11 +1222,25 @@ git-tree-sha1 = "cfcd24ebf8b066b4f8e42bade600c8558212ed83" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" version = "1.38.7" + [deps.Plots.extensions] + FileIOExt = "FileIO" + GeometryBasicsExt = "GeometryBasics" + IJuliaExt = "IJulia" + ImageInTerminalExt = "ImageInTerminal" + UnitfulExt = "Unitful" + + [deps.Plots.weakdeps] + FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" + GeometryBasics = "5c1252a2-5f33-56bf-86c9-59e7332b4326" + IJulia = "7073ff75-c697-5162-941a-fcdaad2a7d2a" + ImageInTerminal = "d8c32880-2388-543b-8c61-d9f865259254" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" + [[deps.Pluto]] -deps = ["Base64", "Configurations", "Dates", "Distributed", "FileWatching", "FuzzyCompletions", "HTTP", "HypertextLiteral", "InteractiveUtils", "Logging", "MIMEs", "Markdown", "MsgPack", "Pkg", "PrecompileSignatures", "REPL", "RegistryInstances", "RelocatableFolders", "SnoopPrecompile", "Sockets", "TOML", "Tables", "URIs", "UUIDs"] -git-tree-sha1 = "0ee5bd226e5b95e2232229f7c4a97309ccd8158b" +deps = ["Base64", "Configurations", "Dates", "Distributed", "FileWatching", "FuzzyCompletions", "HTTP", "HypertextLiteral", "InteractiveUtils", "Logging", "LoggingExtras", "MIMEs", "Markdown", "MsgPack", "Pkg", "PrecompileSignatures", "PrecompileTools", "REPL", "RegistryInstances", "RelocatableFolders", "Sockets", "TOML", "Tables", "URIs", "UUIDs"] +git-tree-sha1 = "06fec2244568a4641e3352d20d0a0a608df6fa92" uuid = "c3e4b0f8-55cb-11ea-2926-15256bba5781" -version = "0.19.22" +version = "0.19.27" [[deps.PooledArrays]] deps = ["DataAPI", "Future"] @@ -1113,17 +1259,23 @@ git-tree-sha1 = "18ef344185f25ee9d51d80e179f8dad33dc48eb1" uuid = "91cefc8d-f054-46dc-8f8c-26e11d7c5411" version = "3.0.3" +[[deps.PrecompileTools]] +deps = ["Preferences"] +git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f" +uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a" +version = "1.2.0" + [[deps.Preferences]] deps = ["TOML"] -git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" +git-tree-sha1 = "7eb1686b4f04b82f96ed7a4ea5890a4f0c7a09f1" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.3.0" +version = "1.4.0" [[deps.PrettyTables]] -deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"] -git-tree-sha1 = "96f6db03ab535bdb901300f88335257b0018689d" +deps = ["Crayons", "LaTeXStrings", "Markdown", "Printf", "Reexport", "StringManipulation", "Tables"] +git-tree-sha1 = "ee094908d720185ddbdc58dbe0c1cbe35453ec7a" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "2.2.2" +version = "2.2.7" [[deps.Printf]] deps = ["Unicode"] @@ -1141,9 +1293,9 @@ version = "5.15.3+2" [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "786efa36b7eff813723c4849c90456609cf06661" +git-tree-sha1 = "6ec7ac8412e83d57e313393220879ede1740f9ee" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.8.1" +version = "2.8.2" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -1178,21 +1330,25 @@ version = "0.5.6" [[deps.Ratios]] deps = ["Requires"] -git-tree-sha1 = "dc84268fe0e3335a62e315a3a7cf2afa7178a734" +git-tree-sha1 = "1342a47bf3260ee108163042310d26f2be5ec90b" uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" -version = "0.4.3" +version = "0.4.5" +weakdeps = ["FixedPointNumbers"] + + [deps.Ratios.extensions] + RatiosFixedPointNumbersExt = "FixedPointNumbers" [[deps.RecipesBase]] -deps = ["SnoopPrecompile"] -git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" +deps = ["PrecompileTools"] +git-tree-sha1 = "5c3d09cc4f31f5fc6af001c250bf1278733100ff" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.3.3" +version = "1.3.4" [[deps.RecipesPipeline]] -deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"] -git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f" +deps = ["Dates", "NaNMath", "PlotUtils", "PrecompileTools", "RecipesBase"] +git-tree-sha1 = "45cf9fd0ca5839d06ef333c8201714e888486342" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.6.11" +version = "0.6.12" [[deps.Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" @@ -1233,11 +1389,17 @@ version = "0.4.0+0" uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" +[[deps.SQLite]] +deps = ["DBInterface", "Random", "SQLite_jll", "Serialization", "Tables", "WeakRefStrings"] +git-tree-sha1 = "eb9a473c9b191ced349d04efa612ec9f39c087ea" +uuid = "0aa819cd-b072-5ff4-a722-6bc24af294d9" +version = "1.6.0" + [[deps.SQLite_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] -git-tree-sha1 = "54d66b0f69f4578f4988fc08d579783fcdcd764f" +git-tree-sha1 = "4619dd3363610d94fb42a95a6dc35b526a26d0ef" uuid = "76ed43ae-9a5d-5a62-8c75-30186b810ce8" -version = "3.41.0+0" +version = "3.42.0+0" [[deps.Scratch]] deps = ["Dates"] @@ -1247,9 +1409,9 @@ version = "1.2.0" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "77d3c4726515dca71f6d80fbb5e251088defe305" +git-tree-sha1 = "04bdff0b09c65ff3e06a05e3eb7b120223da3d39" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.3.18" +version = "1.4.0" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -1292,12 +1454,12 @@ uuid = "6462fe0b-24de-5631-8697-dd941f90decc" [[deps.SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" +git-tree-sha1 = "c60ec5c62180f27efea3ba2908480f8055e17cee" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.1.0" +version = "1.1.1" [[deps.SparseArrays]] -deps = ["LinearAlgebra", "Random"] +deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"] uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" [[deps.SpatialEcology]] @@ -1307,10 +1469,14 @@ uuid = "348f2d5d-71a3-5ad4-b565-8af070f99681" version = "0.9.15" [[deps.SpecialFunctions]] -deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" +deps = ["IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] +git-tree-sha1 = "e2cfc4012a19088254b3950b85c3c1d8882d864d" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.2.0" +version = "2.3.1" +weakdeps = ["ChainRulesCore"] + + [deps.SpecialFunctions.extensions] + SpecialFunctionsChainRulesCoreExt = "ChainRulesCore" [[deps.StackViews]] deps = ["OffsetArrays"] @@ -1319,25 +1485,30 @@ uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15" version = "0.1.1" [[deps.StaticArrays]] -deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] -git-tree-sha1 = "2d7d9e1ddadc8407ffd460e24218e37ef52dd9a3" +deps = ["LinearAlgebra", "Random", "StaticArraysCore"] +git-tree-sha1 = "9cabadf6e7cd2349b6cf49f1915ad2028d65e881" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.5.16" +version = "1.6.2" +weakdeps = ["Statistics"] + + [deps.StaticArrays.extensions] + StaticArraysStatisticsExt = "Statistics" [[deps.StaticArraysCore]] -git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" +git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d" uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" -version = "1.4.0" +version = "1.4.2" [[deps.Statistics]] deps = ["LinearAlgebra", "SparseArrays"] uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" +version = "1.9.0" [[deps.StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" +git-tree-sha1 = "45a7769a04a3cf80da1c1c7c60caf932e6f4c9f7" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.5.0" +version = "1.6.0" [[deps.StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] @@ -1346,11 +1517,25 @@ uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" version = "0.33.21" [[deps.StatsFuns]] -deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" version = "1.3.0" + [deps.StatsFuns.extensions] + StatsFunsChainRulesCoreExt = "ChainRulesCore" + StatsFunsInverseFunctionsExt = "InverseFunctions" + + [deps.StatsFuns.weakdeps] + ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" + InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112" + +[[deps.StringEncodings]] +deps = ["Libiconv_jll"] +git-tree-sha1 = "b765e46ba27ecf6b44faf70df40c57aa3a547dcb" +uuid = "69024149-9ee7-55f6-a4c4-859efe599b68" +version = "0.3.7" + [[deps.StringManipulation]] git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" @@ -1366,10 +1551,15 @@ version = "0.4.2" deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" +[[deps.SuiteSparse_jll]] +deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"] +uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c" +version = "5.10.1+6" + [[deps.TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" -version = "1.0.0" +version = "1.0.3" [[deps.TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -1385,9 +1575,9 @@ version = "1.0.2" [[deps.Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" +git-tree-sha1 = "1544b926975372da01227b382066ab70e574a3ec" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.10.0" +version = "1.10.1" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -1417,19 +1607,25 @@ version = "0.5.25" [[deps.TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" +git-tree-sha1 = "9a6ae7ed916312b41236fcef7e0af564ef934769" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.11" +version = "0.9.13" [[deps.Tricks]] -git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" +git-tree-sha1 = "aadb748be58b492045b4f56166b5188aa63ce549" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.6" +version = "0.1.7" + +[[deps.URIParser]] +deps = ["Unicode"] +git-tree-sha1 = "53a9f49546b8d2dd2e688d216421d050c9a31d0d" +uuid = "30578b45-9adc-5946-b283-645ec420af67" +version = "0.4.1" [[deps.URIs]] -git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" +git-tree-sha1 = "b7a5e99f24892b6824a954199a45e9ffcc1c70f0" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.4.2" +version = "1.5.0" [[deps.UUIDs]] deps = ["Random", "SHA"] @@ -1449,6 +1645,27 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf" uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1" version = "0.4.1" +[[deps.UnicodePlots]] +deps = ["ColorSchemes", "ColorTypes", "Contour", "Crayons", "Dates", "LinearAlgebra", "MarchingCubes", "NaNMath", "PrecompileTools", "Printf", "Requires", "SparseArrays", "StaticArrays", "StatsBase"] +git-tree-sha1 = "b96de03092fe4b18ac7e4786bee55578d4b75ae8" +uuid = "b8865327-cd53-5732-bb35-84acbb429228" +version = "3.6.0" + + [deps.UnicodePlots.extensions] + FreeTypeExt = ["FileIO", "FreeType"] + ImageInTerminalExt = "ImageInTerminal" + IntervalSetsExt = "IntervalSets" + TermExt = "Term" + UnitfulExt = "Unitful" + + [deps.UnicodePlots.weakdeps] + FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" + FreeType = "b38be410-82b0-50bf-ab77-7b57e271db43" + ImageInTerminal = "d8c32880-2388-543b-8c61-d9f865259254" + IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953" + Term = "22787eb5-b846-44ae-b979-8e399b8463ab" + Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" + [[deps.Unitful]] deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"] git-tree-sha1 = "bb37ed24f338bc59b83e3fc9f32dd388e5396c53" @@ -1497,16 +1714,16 @@ uuid = "aed1982a-8fda-507f-9586-7b0439959a61" version = "1.1.34+0" [[deps.Xorg_libX11_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] -git-tree-sha1 = "5be649d550f3f4b95308bf0183b82e2582876527" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxcb_jll", "Xorg_xtrans_jll"] +git-tree-sha1 = "afead5aba5aa507ad5a3bf01f58f82c8d1403495" uuid = "4f6342f7-b3d2-589e-9d20-edeb45f2b2bc" -version = "1.6.9+4" +version = "1.8.6+0" [[deps.Xorg_libXau_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4e490d5c960c314f33885790ed410ff3a94ce67e" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6035850dcc70518ca32f012e46015b9beeda49d8" uuid = "0c0b7dd1-d40b-584c-a123-a41640f87eec" -version = "1.0.9+4" +version = "1.0.11+0" [[deps.Xorg_libXcursor_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libXfixes_jll", "Xorg_libXrender_jll"] @@ -1515,10 +1732,10 @@ uuid = "935fb764-8cf2-53bf-bb30-45bb1f8bf724" version = "1.2.0+4" [[deps.Xorg_libXdmcp_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "4fe47bd2247248125c428978740e18a681372dd4" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "34d526d318358a859d7de23da945578e8e8727b7" uuid = "a3789734-cfe1-5b06-b2d0-1dd0d9d62d05" -version = "1.1.3+4" +version = "1.1.4+0" [[deps.Xorg_libXext_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] @@ -1557,22 +1774,22 @@ uuid = "ea2f1a96-1ddc-540d-b46f-429655e07cfa" version = "0.9.10+4" [[deps.Xorg_libpthread_stubs_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "8fdda4c692503d44d04a0603d9ac0982054635f9" uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" -version = "0.1.0+3" +version = "0.1.1+0" [[deps.Xorg_libxcb_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] -git-tree-sha1 = "daf17f441228e7a3833846cd048892861cff16d6" +deps = ["Artifacts", "JLLWrappers", "Libdl", "XSLT_jll", "Xorg_libXau_jll", "Xorg_libXdmcp_jll", "Xorg_libpthread_stubs_jll"] +git-tree-sha1 = "b4bfde5d5b652e22b9c790ad00af08b6d042b97d" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" -version = "1.13.0+3" +version = "1.15.0+0" [[deps.Xorg_libxkbfile_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] -git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libX11_jll"] +git-tree-sha1 = "730eeca102434283c50ccf7d1ecdadf521a765a4" uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" -version = "1.1.0+4" +version = "1.1.2+0" [[deps.Xorg_xcb_util_image_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] @@ -1605,22 +1822,28 @@ uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" version = "0.4.1+1" [[deps.Xorg_xkbcomp_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] -git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_libxkbfile_jll"] +git-tree-sha1 = "330f955bc41bb8f5270a369c473fc4a5a4e4d3cb" uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" -version = "1.4.2+4" +version = "1.4.6+0" [[deps.Xorg_xkeyboard_config_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] -git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Xorg_xkbcomp_jll"] +git-tree-sha1 = "691634e5453ad362044e2ad653e79f3ee3bb98c3" uuid = "33bec58e-1273-512f-9401-5d533626f822" -version = "2.27.0+4" +version = "2.39.0+0" [[deps.Xorg_xtrans_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "e92a1a012a10506618f10b7047e478403a046c77" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.4.0+3" +version = "1.5.0+0" + +[[deps.YAML]] +deps = ["Base64", "Dates", "Printf", "StringEncodings"] +git-tree-sha1 = "e6330e4b731a6af7959673621e91645eb1356884" +uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6" +version = "0.4.9" [[deps.ZipFile]] deps = ["Libdl", "Printf", "Zlib_jll"] @@ -1631,13 +1854,13 @@ version = "0.9.4" [[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.12+3" +version = "1.2.13+0" [[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "c6edfe154ad7b313c01aceca188c05c835c67360" +git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.4+0" +version = "1.5.5+0" [[deps.boost_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -1664,9 +1887,9 @@ uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" [[deps.libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.1.1+0" +version = "5.8.0+0" [[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] diff --git a/examples/Project.toml b/examples/Project.toml index c0458211e..710f3849b 100644 --- a/examples/Project.toml +++ b/examples/Project.toml @@ -1,6 +1,7 @@ [deps] AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" +DataPipeline = "9ced6f0a-eb77-43a8-bbd1-bbf3031b0d12" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Diversity = "d3d5718d-52de-57ab-b67a-eca7fd6175a4" EcoBase = "a58aae7d-b440-5a11-b283-399458f99aac" @@ -16,6 +17,7 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [compat] AxisArrays = "0.4.6" BenchmarkTools = "1.3.2" +DataPipeline = "0.53" Distributions = "0.25.86" Diversity = "0.5.6" EcoBase = "0.1.6" @@ -25,4 +27,4 @@ OnlineStats = "1.5.14" Plots = "1.38.7" RasterDataSources = "0.5.6" StatsBase = "0.33.21" -Unitful = "1.12.4" \ No newline at end of file +Unitful = "1.12.4" diff --git a/ext/DataTools.jl b/ext/DataTools.jl new file mode 100644 index 000000000..fd39ffc12 --- /dev/null +++ b/ext/DataTools.jl @@ -0,0 +1,21 @@ +module DataTools + +if isdefined(Base, :get_extension) + using DataPipeline +else + using ..DataPipeline +end + +println("Creating data pipeline interface ...") + +using EcoSISTEM +using EcoSISTEM.ClimatePref + +function EcoSISTEM.ClimatePref.unzip(path::String) + newpath = joinpath(splitpath(path)[1:end-1]) + run(`tar xvf $path -C $newpath`) + println("Unzipped to $newpath") + return newpath +end + +end \ No newline at end of file diff --git a/ext/ERATools.jl b/ext/ERATools.jl new file mode 100644 index 000000000..8420b69c7 --- /dev/null +++ b/ext/ERATools.jl @@ -0,0 +1,100 @@ +module ERATools + +if isdefined(Base, :get_extension) + using PyCall +else + using ..PyCall +end + +# Install python api for Climate Data Store +run(`$(PyCall.python) -m pip install cdsapi`) + +println("Creating ECMWF interface ...") + +using EcoSISTEM +using EcoSISTEM.ClimatePref + +py""" +from math import floor +import cdsapi + +server = cdsapi.Client() + +def retrieve_era5(param, from_year, to_year, filename, **kwargs): + + months = range(1, 13) + years = range(from_year, to_year + 1) + decades = sorted({floor(y / 10) * 10 for y in years}) + + # Loop through decades and create a request list for all months/years + for d in decades: + # Filter for years within the decade + years_in_decade = list(filter(lambda y: floor(y / 10) * 10 == d, years)) + # Set up all request months per decade in correct format + request_dates = "/".join([f'{y}{m:02}01' for y in years_in_decade for m in months]) + # Create target file + target = f'{filename}_{d}' + print(f'Years: {years_in_decade}\nOutput file: {target}') + era5_request(param, request_dates, d, target, **kwargs) + +def era5_request( + param, request_dates, decade, target, + stream='moda', modeltype='an', levtype='sfc', + grid='0.75/0.75', format='netcdf', step='0-12'): + + server.retrieve('reanalysis-era5-complete', { + "dataset": "era5", + 'stream': stream, + 'type': modeltype, + 'levtype': levtype, + 'param': param, + 'grid': grid, + 'format': format, + 'date': request_dates, + 'decade': decade, + 'target': target, + 'step': step + }) +""" + +function EcoSISTEM.ClimatePref.retrieve_era5(param::String, from_year::Int64, to_year::Int64, filename::String = "era5"; kws...) + py""" + from math import floor + import cdsapi + server = cdsapi.Client() + def retrieve_era5(param, from_year, to_year, filename, **kwargs): + months = range(1, 13) + years = range(from_year, to_year + 1) + decades = sorted({floor(y / 10) * 10 for y in years}) + # Loop through decades and create a request list for all months/years + for d in decades: + # Filter for years within the decade + years_in_decade = list(filter(lambda y: floor(y / 10) * 10 == d, years)) + # Set up all request months per decade in correct format + request_dates = "/".join([f'{y}{m:02}01' for y in years_in_decade for m in months]) + # Create target file + target = f'{filename}_{d}' + print(f'Years: {years_in_decade}\nOutput file: {target}') + era5_request(param, request_dates, d, target, **kwargs) + def era5_request( + param, request_dates, decade, target, + stream='moda', modeltype='an', levtype='sfc', + grid='0.75/0.75', format='netcdf', step='0-12'): + + server.retrieve('reanalysis-era5-complete', { + "class": "ea", + "dataset": "era5", + "expver": "1", + 'stream': stream, + 'type': modeltype, + 'levtype': levtype, + 'param': param, + 'format': format, + 'date': request_dates, + 'decade': decade, + }, target) + """ + py"retrieve_era5"(param, from_year, to_year, filename; kws...) +end + +end \ No newline at end of file diff --git a/src/ClimatePref/ClimatePref.jl b/src/ClimatePref/ClimatePref.jl index 8227ba33c..d06cf41a0 100644 --- a/src/ClimatePref/ClimatePref.jl +++ b/src/ClimatePref/ClimatePref.jl @@ -1,16 +1,27 @@ -using Requires +if !isdefined(Base, :get_extension) + using Requires +end + function __init__() - @require PyCall="438e738f-606a-5dbb-bf0a-cddfbfd45ab0" begin - println("Creating ECMWF interface ...") - include("ERA_interim_tools.jl") - export retrieve_era_interim - include("ECMWF_tools.jl") - export retrieve_ECMWF + @static if !isdefined(Base, :get_extension) + @require PyCall="438e738f-606a-5dbb-bf0a-cddfbfd45ab0" begin + println("Creating ECMWF interface ...") + include("ERA5_tools.jl") + export retrieve_era5 + end + @require DataPipeline = "9ced6f0a-eb77-43a8-bbd1-bbf3031b0d12" begin + println("Creating data pipeline interface ...") + include("Pipeline.jl") + export unzip + end end end @warn "This functionality remains under development!" +include("Extensions.jl") +export unzip, retrieve_era5 + include("ClimateTypes.jl") export Worldclim_monthly, Worldclim_bioclim, ERA, CERA, CRUTS, CHELSA_bioclim, CHELSA_monthly, Reference, Landcover diff --git a/src/ClimatePref/ECMWF_tools.jl b/src/ClimatePref/ECMWF_tools.jl deleted file mode 100644 index 5fb60a577..000000000 --- a/src/ClimatePref/ECMWF_tools.jl +++ /dev/null @@ -1,54 +0,0 @@ -using .PyCall -py""" -from math import floor -from ecmwfapi import ECMWFDataServer - -server = ECMWFDataServer() - - -def retrieve_ECMWF(param, from_year, to_year, filename, **kwargs): - - months = range(1, 13) - years = range(from_year, to_year + 1) - decades = sorted({floor(y / 10) * 10 for y in years}) - - # Loop through decades and create a request list for all months/years - for d in decades: - # Filter for years within the decade - years_in_decade = list(filter(lambda y: floor(y / 10) * 10 == d, years)) - - # Set up all request months per decade in correct format - request_dates = "/".join([f'{y}{m:02}01' for y in years_in_decade for m in months]) - - # Create target file - target = f'{filename}_{d}' - print(f'Years: {years_in_decade}\nOutput file: {target}') - ECMWF_request(param, request_dates, d, target, **kwargs) - - -def ECMWF_request( - param, request_dates, decade, target, - eclass = 'ei', dataset = 'interim', stream='moda', modeltype='an', levtype='sfc', grid='0.75/0.75', format='netcdf', step='0-12', num = '0' -): - - server.retrieve({ - 'class': eclass, - 'dataset': dataset, - 'expver': '1', - 'stream': stream, - 'number': num, - 'type': modeltype, - 'levtype': levtype, - 'param': param, - 'grid': grid, - 'format': format, - 'date': request_dates, - 'decade': decade, - 'target': target, - 'step': step - }) -""" - -function retrieve_ECMWF(param::String, from_year::Int64, to_year::Int64, filename::String = "era_interim"; kws...) - py"retrieve_ECMWF"(param, from_year, to_year, filename; kws...) -end diff --git a/src/ClimatePref/ERA_interim_tools.jl b/src/ClimatePref/ERA5_tools.jl similarity index 63% rename from src/ClimatePref/ERA_interim_tools.jl rename to src/ClimatePref/ERA5_tools.jl index faafe0542..9128e8290 100644 --- a/src/ClimatePref/ERA_interim_tools.jl +++ b/src/ClimatePref/ERA5_tools.jl @@ -1,12 +1,11 @@ -using .PyCall +# using .PyCall py""" from math import floor -from ecmwfapi import ECMWFDataServer +import cdsapi -server = ECMWFDataServer() +server = cdsapi.Client() - -def retrieve_era_interim(param, from_year, to_year, filename, **kwargs): +def retrieve_era5(param, from_year, to_year, filename, **kwargs): months = range(1, 13) years = range(from_year, to_year + 1) @@ -16,26 +15,20 @@ def retrieve_era_interim(param, from_year, to_year, filename, **kwargs): for d in decades: # Filter for years within the decade years_in_decade = list(filter(lambda y: floor(y / 10) * 10 == d, years)) - # Set up all request months per decade in correct format request_dates = "/".join([f'{y}{m:02}01' for y in years_in_decade for m in months]) - # Create target file target = f'{filename}_{d}' print(f'Years: {years_in_decade}\nOutput file: {target}') - era_interim_request(param, request_dates, d, target, **kwargs) - + era5_request(param, request_dates, d, target, **kwargs) -def era_interim_request( +def era5_request( param, request_dates, decade, target, stream='moda', modeltype='an', levtype='sfc', - grid='0.75/0.75', format='netcdf', step='0-12' -): + grid='0.75/0.75', format='netcdf', step='0-12'): - server.retrieve({ - "class": "ei", - "dataset": "interim", - 'expver': '1', + server.retrieve('reanalysis-era5-complete', { + "dataset": "era5", 'stream': stream, 'type': modeltype, 'levtype': levtype, @@ -49,6 +42,6 @@ def era_interim_request( }) """ -function retrieve_era_interim(param::String, from_year::Int64, to_year::Int64, filename::String = "era_interim"; kws...) - py"retrieve_era_interim"(param, from_year, to_year, filename; kws...) +function retrieve_era5(param::String, from_year::Int64, to_year::Int64, filename::String = "era5"; kws...) + py"retrieve_era5"(param, from_year, to_year, filename; kws...) end diff --git a/src/ClimatePref/Extensions.jl b/src/ClimatePref/Extensions.jl new file mode 100644 index 000000000..3d76a2294 --- /dev/null +++ b/src/ClimatePref/Extensions.jl @@ -0,0 +1,7 @@ +function retrieve_era5() + "Please install `PyCall` for this functionality" +end + +function unzip() + "Please install `DataPipeline` for this functionality" +end diff --git a/src/Traits.jl b/src/Traits.jl index 409df18c2..166a6050f 100644 --- a/src/Traits.jl +++ b/src/Traits.jl @@ -32,9 +32,6 @@ mutable struct LCtrait{D <: Number} <: AbstractTraits{D} return LCtrait{typeof(1.0)}(vals) end - iscontinuous(tr::multiplicativeTR3{TR1, TR2, TR3} ) where {TR1, TR2, TR3} = - [iscontinuous(tr.tr1), iscontinuous(tr.tr2), iscontinuous(tr.tr3)] - """ DiscreteEvolve(numTraits::Int64, tree::BinaryTree) From fb13f2794d5dd50ace2d8e801c42d9d64da06fd7 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Mon, 28 Aug 2023 10:53:28 +0100 Subject: [PATCH 2/7] Add DataPipeline run to examples --- docs/make.jl | 1 + docs/src/pipeline.md | 18 ++++++ examples/pipeline/AfricaRun.jl | 105 +++++++++++++++++++++++++++++++ examples/pipeline/AfricaRun.yaml | 37 +++++++++++ 4 files changed, 161 insertions(+) create mode 100644 docs/src/pipeline.md create mode 100644 examples/pipeline/AfricaRun.jl create mode 100644 examples/pipeline/AfricaRun.yaml diff --git a/docs/make.jl b/docs/make.jl index f51b8e9ba..4a2556db7 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -14,6 +14,7 @@ makedocs( "Diversity" => "diversity.md", "Examples" => "examples.md", "Africa" => "africa.md" + "Data Pipeline" => "pipeline.md" ] ], strict=true, diff --git a/docs/src/pipeline.md b/docs/src/pipeline.md new file mode 100644 index 000000000..ea3e671e5 --- /dev/null +++ b/docs/src/pipeline.md @@ -0,0 +1,18 @@ +# Data pipeline + +**DataPipeline.jl** is a [Julia](https://github.com/FAIRDataPipeline/DataPipeline.jl) package that provides functionality for the [FAIR Data Pipeline](https://www.fairdatapipeline.org/). The pipeline is intended to enable tracking of provenance of FAIR (findable, accessible, interoperable and reusable) data. We use it in examples under the `pipeline` folder for a run of a single species in Africa. + +See [here](https://www.fairdatapipeline.org/docs/data_registry/installation/) for details on what to install to set up the Data Pipeline. Once installed, the workflow is to initialise the pipeline in the repository, pull in the external data needed for the simulation (as described in the `AfricaRun.yaml`) and run the simulation. The output is also described in the `AfricaRun.yaml`, which is produced from the corresponding run file `AfricaRun.jl`. The output and provenance can then be pushed back to the online [data registry](https://data.fairdatapipeline.org/) to be inspected further. + +``` +## Initialise the data pipeline in the git repository +fair init +# Pull in any external data described in the yaml +fair pull .\examples\pipeline\AfricaRun.yaml +# Run the simulation described in the yaml +fair run .\examples\pipeline\AfricaRun.yaml +# Stage the code run using the unique identifier +fair add +# Push the run and corresponding metadata back to the online registry +fair push +``` diff --git a/examples/pipeline/AfricaRun.jl b/examples/pipeline/AfricaRun.jl new file mode 100644 index 000000000..800a2e57f --- /dev/null +++ b/examples/pipeline/AfricaRun.jl @@ -0,0 +1,105 @@ +#### SINGLE SPECIES #### +# Code to run single species across Africa with WorldClim data. +using EcoSISTEM +using EcoSISTEM.ClimatePref +using EcoSISTEM.Units +using RasterDataSources +using AxisArrays +using Unitful +using Unitful.DefaultSymbols +using StatsBase +using Plots +using DataPipeline + +# Initialise datapipeline +handle = DataPipeline.initialise() + +# Download temperature and precipitation data +path = link_read!(handle, "AfricaModel/WorldClim") +newpath = unzip(path) +world = readbioclim(newpath) +africa_temp = world.array[-25°.. 50°, -35° .. 40°, 1] +bio_africa = uconvert.(K, africa_temp .* °C) +bio_africa = Worldclim_bioclim(AxisArray(bio_africa, AxisArrays.axes(africa_temp))) +africa_water = world.array[-25°.. 50°, -35° .. 40°, 12] .* mm +africa_water = Worldclim_bioclim(AxisArray(africa_water, AxisArrays.axes(africa_temp))) +bio_africa_water = WaterBudget(africa_water) + +# Find which grid cells are land +active = Array{Bool, 2}(.!isnan.(bio_africa.array)) + +heatmap(africa_temp') + +# Set up initial parameters for ecosystem +numSpecies = 1; grid = size(active); req= 0.1mm; individuals=0; area = 64e6km^2; totalK = 1000.0kJ/km^2 + +# Set up how much water each species consumes +energy_vec = WaterRequirement(fill(req, numSpecies)) + +# Set rates for birth and death +birth = 0.6/year +death = 0.6/year +longevity = 1.0 +survival = 0.2 +boost = 1.0 +# Collect model parameters together +param = EqualPop(birth, death, longevity, survival, boost) + +# Create kernel for movement +kernel = fill(GaussianKernel(15.0km, 10e-10), numSpecies) +movement = AlwaysMovement(kernel, Torus()) + +# Create species list, including their temperature preferences, seed abundance and native status +opts = fill(280.0K, numSpecies) +vars = fill(10.0K, numSpecies) +traits = GaussTrait(opts, vars) +native = fill(true, numSpecies) +abun = fill(div(individuals, numSpecies), numSpecies) +sppl = SpeciesList(numSpecies, traits, abun, energy_vec, + movement, param, native) + +# Create abiotic environment - with temperature and water resource +abenv = bioclimAE(bio_africa, bio_africa_water, active) + +# Set relationship between species and environment (gaussian) +rel = Gauss{typeof(1.0K)}() + +# Create ecosystem and fill every active grid square with an individual +eco = Ecosystem(sppl, abenv, rel) +rand_start = findall(active) +for i in rand_start + eco.abundances.grid[1, i[1], i[2]] += 1 +end + +# Run simulation +times = 10years; timestep = 1month; record_interval = 1month; repeats = 1 +lensim = length(0years:record_interval:times) +abuns = zeros(Int64, numSpecies, prod(grid), lensim) +@time simulate_record!(abuns, eco, times, record_interval, timestep); + +# Reshape abundances for plotting +abuns = reshape(abuns[1, :, :, 1], grid[1], grid[2], lensim) + +# Plot start and end abundances, next to temperature and rainfall +africa_startabun = Float64.(abuns[:, :, 1]) +africa_startabun[.!(active)] .= NaN +africa_endabun = Float64.(abuns[:, :, end]) +africa_endabun[.!(active)] .= NaN +heatmap(africa_startabun', clim = (0, maximum(abuns)), + background_color = :lightblue, background_color_outside=:white, + grid = false, color = cgrad(:algae, scale = :exp), + layout = (@layout [a b; c d])) +heatmap!(africa_endabun', clim = (0, maximum(abuns)), + background_color = :lightblue, background_color_outside=:white, + grid = false, color = cgrad(:algae, scale = :exp), + subplot = 2) + +africa_temp = world.array[-25°.. 50°, -35° .. 40°, 1] +africa_water = world.array[-25°.. 50°, -35° .. 40°, 12] +heatmap!(africa_temp', grid = false, subplot = 3) +heatmap!(africa_water', grid = false, subplot = 4) + +path = link_write!(handle, "Africa-plot") +Plots.pdf(path) + +DataPipeline.finalise(handle) \ No newline at end of file diff --git a/examples/pipeline/AfricaRun.yaml b/examples/pipeline/AfricaRun.yaml new file mode 100644 index 000000000..94cf6e847 --- /dev/null +++ b/examples/pipeline/AfricaRun.yaml @@ -0,0 +1,37 @@ +run_metadata: + default_input_namespace: claireh93 + description: Africa model inputs + script: | + julia --project=examples examples/pipeline/AfricaRun.jl + +register: +- namespace: UCDavis + full_name: University of California Davis + website: https://ror.org/05rrcem69 +- namespace: GBIF + full_name: Global Biodiversity Information Facility + website: https://ror.org/05fjyn938 + +- external_object: AfricaModel/WorldClim + namespace_name: UCDavis + root: https://biogeo.ucdavis.edu/ + path: data/worldclim/v2.1/base/wc2.1_10m_bio.zip + title: WorldClim Bioclimatic variables + description: Bioclimatic variables are derived from the monthly temperature and rainfall values in order to generate more biologically meaningful variables. + identifier: https://doi.org/10.1002/joc.5086 + file_type: zip + release_date: 2017-03-28T12:00 + version: "1.0.0" + primary: True + authors: + - https://ror.org/05rrcem69 + +write: +- data_product: Africa-plot + description: Plot start and end abundances, next to temperature and rainfall + file_type: pdf + use: + data_product: AfricaModel/Africa-plot + + + From 61c063ce1cba82a8c0150547a822b5d76c016fc6 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Mon, 28 Aug 2023 11:44:36 +0100 Subject: [PATCH 3/7] Update distributions. --- src/Dist.jl | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/Dist.jl b/src/Dist.jl index a676488bc..b35635c5a 100644 --- a/src/Dist.jl +++ b/src/Dist.jl @@ -17,14 +17,12 @@ struct Trapezoid{T<:Real} <: ContinuousUnivariateDistribution c::T d::T - Trapezoid{T}(a::T, b::T, c::T, d::T) where {T} = new{T}(a, b, c, d) + Trapezoid{T}(a::T, b::T, c::T, d::T) where {T <: Real} = new{T}(a, b, c, d) end -function Trapezoid{T}(a::T, b::T, c::T, d::T; check_args::Bool = true) where {T} +function Trapezoid(a::T, b::T, c::T, d::T; check_args::Bool = true) where {T <: Real} @check_args Trapezoid (a < d) return Trapezoid{T}(a, b, c, d) end - -Trapezoid(a::T, b::T, c::T, d::T; check_args::Bool = true) where {T<:Real} = Trapezoid{T}(a, b, c, d; check_args=check_args) Trapezoid(a::Real, b::Real, c::Real, d::Real; check_args::Bool = true) = Trapezoid(promote(a, b, c, d)...; check_args=check_args) Trapezoid(a::Integer, b::Integer, c::Integer, d::Integer; check_args::Bool = true) = Trapezoid(Float64(a), Float64(b), Float64(c), Float64(d); check_args=check_args) From cfc2688965a0bb9552dab027a1676b55fd80f45c Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Mon, 28 Aug 2023 13:49:59 +0100 Subject: [PATCH 4/7] Update pipeline for tests --- .github/workflows/testing.yaml | 1 + ext/ERATools.jl | 43 ---------------------------------- src/ClimatePref/Pipeline.jl | 6 +++++ 3 files changed, 7 insertions(+), 43 deletions(-) create mode 100644 src/ClimatePref/Pipeline.jl diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml index 7ffa9e8ba..d0f7a6e86 100644 --- a/.github/workflows/testing.yaml +++ b/.github/workflows/testing.yaml @@ -17,6 +17,7 @@ jobs: matrix: julia-version: - '1.8' + - '1.9' os: - ubuntu-latest - macOS-10.15 diff --git a/ext/ERATools.jl b/ext/ERATools.jl index 8420b69c7..bbf4536e3 100644 --- a/ext/ERATools.jl +++ b/ext/ERATools.jl @@ -14,49 +14,6 @@ println("Creating ECMWF interface ...") using EcoSISTEM using EcoSISTEM.ClimatePref -py""" -from math import floor -import cdsapi - -server = cdsapi.Client() - -def retrieve_era5(param, from_year, to_year, filename, **kwargs): - - months = range(1, 13) - years = range(from_year, to_year + 1) - decades = sorted({floor(y / 10) * 10 for y in years}) - - # Loop through decades and create a request list for all months/years - for d in decades: - # Filter for years within the decade - years_in_decade = list(filter(lambda y: floor(y / 10) * 10 == d, years)) - # Set up all request months per decade in correct format - request_dates = "/".join([f'{y}{m:02}01' for y in years_in_decade for m in months]) - # Create target file - target = f'{filename}_{d}' - print(f'Years: {years_in_decade}\nOutput file: {target}') - era5_request(param, request_dates, d, target, **kwargs) - -def era5_request( - param, request_dates, decade, target, - stream='moda', modeltype='an', levtype='sfc', - grid='0.75/0.75', format='netcdf', step='0-12'): - - server.retrieve('reanalysis-era5-complete', { - "dataset": "era5", - 'stream': stream, - 'type': modeltype, - 'levtype': levtype, - 'param': param, - 'grid': grid, - 'format': format, - 'date': request_dates, - 'decade': decade, - 'target': target, - 'step': step - }) -""" - function EcoSISTEM.ClimatePref.retrieve_era5(param::String, from_year::Int64, to_year::Int64, filename::String = "era5"; kws...) py""" from math import floor diff --git a/src/ClimatePref/Pipeline.jl b/src/ClimatePref/Pipeline.jl new file mode 100644 index 000000000..7684e28e7 --- /dev/null +++ b/src/ClimatePref/Pipeline.jl @@ -0,0 +1,6 @@ +function unzip(path::String) + newpath = joinpath(splitpath(path)[1:end-1]) + run(`tar xvf $path -C $newpath`) + println("Unzipped to $newpath") + return newpath +end From f9796c4d3548abdb910ce86a9244dd25a6dcc4fe Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Mon, 28 Aug 2023 14:34:21 +0100 Subject: [PATCH 5/7] Fix docs --- docs/Manifest.toml | 1625 +++++++++++++++++++++++++++----------------- docs/src/basics.md | 3 +- 2 files changed, 1006 insertions(+), 622 deletions(-) diff --git a/docs/Manifest.toml b/docs/Manifest.toml index 0abe92caa..85181f506 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,1519 +1,1902 @@ # This file is machine-generated - editing it directly is not advised -[[AbstractTrees]] -git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" -uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.3.4" +julia_version = "1.9.2" +manifest_format = "2.0" +project_hash = "6d7c963ed7c56b3292608f9e1dcaf8657213c9e8" + +[[deps.ASCIIrasters]] +git-tree-sha1 = "0cb0046798af8ac8561334c5a2a31f015e53c2b1" +uuid = "81770e7c-c736-4fa5-8129-46dd21831640" +version = "0.1.1" -[[Adapt]] +[[deps.AbstractFFTs]] deps = ["LinearAlgebra"] -git-tree-sha1 = "195c5505521008abea5aee4f96930717958eac6f" +git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "1.5.0" +weakdeps = ["ChainRulesCore", "Test"] + + [deps.AbstractFFTs.extensions] + AbstractFFTsChainRulesCoreExt = "ChainRulesCore" + AbstractFFTsTestExt = "Test" + +[[deps.AbstractTrees]] +git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" +uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" +version = "0.4.4" + +[[deps.Adapt]] +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "76289dc51920fdc6e0013c872ba9551d54961c24" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "3.4.0" +version = "3.6.2" +weakdeps = ["StaticArrays"] + + [deps.Adapt.extensions] + AdaptStaticArraysExt = "StaticArrays" -[[ArchGDAL]] -deps = ["Dates", "DiskArrays", "GDAL", "GeoFormatTypes", "GeoInterface", "Tables"] -git-tree-sha1 = "ac9a3bdf0b1cc5bd276c530b645194bf57373ecf" +[[deps.ArchGDAL]] +deps = ["CEnum", "ColorTypes", "Dates", "DiskArrays", "Extents", "GDAL", "GeoFormatTypes", "GeoInterface", "GeoInterfaceRecipes", "ImageCore", "Tables"] +git-tree-sha1 = "0ca60eb1896df6ca2f2a856faf287c0dd6f27a32" uuid = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3" -version = "0.6.0" +version = "0.10.1" -[[ArgTools]] +[[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" -[[ArnoldiMethod]] +[[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] -git-tree-sha1 = "f87e559f87a45bece9c9ed97458d3afe98b1ebb9" +git-tree-sha1 = "62e51b39331de8911e4a7ff6f5aaf38a5f4cc0ae" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" -version = "0.1.0" - -[[ArrayInterfaceCore]] -deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "5bb0f8292405a516880a3809954cb832ae7a31c5" -uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" -version = "0.1.20" +version = "0.2.0" -[[Artifacts]] +[[deps.ArrayInterface]] +deps = ["Adapt", "LinearAlgebra", "Requires", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "f83ec24f76d4c8f525099b2ac475fc098138ec31" +uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" +version = "7.4.11" + + [deps.ArrayInterface.extensions] + ArrayInterfaceBandedMatricesExt = "BandedMatrices" + ArrayInterfaceBlockBandedMatricesExt = "BlockBandedMatrices" + ArrayInterfaceCUDAExt = "CUDA" + ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" + ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" + ArrayInterfaceTrackerExt = "Tracker" + + [deps.ArrayInterface.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba" + GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" + StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" + Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" + +[[deps.Arrow_jll]] +deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Lz4_jll", "Pkg", "Thrift_jll", "Zlib_jll", "boost_jll", "snappy_jll"] +git-tree-sha1 = "d64cb60c0e6a138fbe5ea65bcbeea47813a9a700" +uuid = "8ce61222-c28f-5041-a97a-c2198fb817bf" +version = "10.0.0+1" + +[[deps.Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" -[[AxisAlgorithms]] +[[deps.AxisAlgorithms]] deps = ["LinearAlgebra", "Random", "SparseArrays", "WoodburyMatrices"] git-tree-sha1 = "66771c8d21c8ff5e3a93379480a2307ac36863f7" uuid = "13072b0f-2c55-5437-9ae7-d433b7a33950" version = "1.0.1" -[[AxisArrays]] +[[deps.AxisArrays]] deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] -git-tree-sha1 = "1dd4d9f5beebac0c03446918741b1a03dc5e5788" +git-tree-sha1 = "16351be62963a67ac4083f748fdb3cca58bfd52f" uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" -version = "0.4.6" +version = "0.4.7" -[[Base64]] +[[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -[[Bzip2_jll]] +[[deps.BitFlags]] +git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" +uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" +version = "0.1.7" + +[[deps.Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "19a35467a82e236ff51bc17a3a44b69ef35185a2" uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.8+0" -[[CEnum]] +[[deps.CEnum]] git-tree-sha1 = 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"c5fb5394-a638-5e4d-96e5-b29de1b5cf10" -version = "1.4.0+3" +version = "1.5.0+0" -[[ZipFile]] +[[deps.ZipFile]] deps = ["Libdl", "Printf", "Zlib_jll"] git-tree-sha1 = "3593e69e469d2111389a9bd06bac1f3d730ac6de" uuid = "a5390f91-8eb1-5f08-bee0-b1d1ffed6cea" version = "0.9.4" -[[Zlib_jll]] +[[deps.Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" -version = "1.2.12+3" +version = "1.2.13+0" -[[Zstd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" +[[deps.Zstd_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "49ce682769cd5de6c72dcf1b94ed7790cd08974c" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.2+0" +version = "1.5.5+0" -[[libaom_jll]] +[[deps.boost_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "7a89efe0137720ca82f99e8daa526d23120d0d37" +uuid = "28df3c45-c428-5900-9ff8-a3135698ca75" +version = "1.76.0+1" + +[[deps.fzf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" +uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" +version = "0.29.0+0" + +[[deps.libaom_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "3a2ea60308f0996d26f1e5354e10c24e9ef905d4" uuid = "a4ae2306-e953-59d6-aa16-d00cac43593b" version = "3.4.0+0" -[[libass_jll]] +[[deps.libass_jll]] deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" -[[libblastrampoline_jll]] -deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +[[deps.libblastrampoline_jll]] +deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.1.1+0" +version = "5.8.0+0" -[[libfdk_aac_jll]] +[[deps.libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" uuid = "f638f0a6-7fb0-5443-88ba-1cc74229b280" version = "2.0.2+0" -[[libgeotiff_jll]] +[[deps.libgeotiff_jll]] deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "Libtiff_jll", "PROJ_jll", "Pkg"] git-tree-sha1 = "13dfba87a1fe301c4b40f991d0ec990bbee59bbe" uuid = "06c338fa-64ff-565b-ac2f-249532af990e" version = "100.700.100+0" -[[libpng_jll]] +[[deps.libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] git-tree-sha1 = "94d180a6d2b5e55e447e2d27a29ed04fe79eb30c" uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f" version = "1.6.38+0" -[[libvorbis_jll]] +[[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" version = "1.3.7+1" -[[nghttp2_jll]] +[[deps.nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" version = "1.48.0+0" -[[p7zip_jll]] +[[deps.p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" version = "17.4.0+0" -[[x264_jll]] +[[deps.snappy_jll]] +deps = ["Artifacts", "JLLWrappers", "LZO_jll", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "985c1da710b0e43f7c52f037441021dfd0e3be14" +uuid = "fe1e1685-f7be-5f59-ac9f-4ca204017dfd" +version = "1.1.9+1" + +[[deps.x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" uuid = "1270edf5-f2f9-52d2-97e9-ab00b5d0237a" version = "2021.5.5+0" -[[x265_jll]] +[[deps.x265_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "ee567a171cce03570d77ad3a43e90218e38937a9" uuid = "dfaa095f-4041-5dcd-9319-2fabd8486b76" version = "3.5.0+0" -[[xkbcommon_jll]] +[[deps.xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" diff --git a/docs/src/basics.md b/docs/src/basics.md index 67998e091..4ec7a2393 100644 --- a/docs/src/basics.md +++ b/docs/src/basics.md @@ -3,7 +3,8 @@ ## Install ```julia -]add EcoSISTEM +using Pkg +Pkg.add("EcoSISTEM") ``` ## Setting up an ecosystem From 5c2ad99b2879afc231f251a4f8d115f5e2ddf68d Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Mon, 28 Aug 2023 15:49:54 +0100 Subject: [PATCH 6/7] Fix docs --- docs/make.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/make.jl b/docs/make.jl index 4a2556db7..d783c5964 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -13,7 +13,7 @@ makedocs( "Basics" => "basics.md", "Diversity" => "diversity.md", "Examples" => "examples.md", - "Africa" => "africa.md" + "Africa" => "africa.md", "Data Pipeline" => "pipeline.md" ] ], From 78225d6cf992d8704183b66506e7b621e56da2e2 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Tue, 29 Aug 2023 09:42:01 +0100 Subject: [PATCH 7/7] Fix MPI testing and try upgrading to Mac-latest --- .github/workflows/testing.yaml | 2 +- test/SmallMPItest.jl | 3 +++ test/test_MPI.jl | 2 +- 3 files changed, 5 insertions(+), 2 deletions(-) diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml index d0f7a6e86..ecc50251f 100644 --- a/.github/workflows/testing.yaml +++ b/.github/workflows/testing.yaml @@ -20,7 +20,7 @@ jobs: - '1.9' os: - ubuntu-latest - - macOS-10.15 + - macOS-latest - windows-latest R-version: - 'release' diff --git a/test/SmallMPItest.jl b/test/SmallMPItest.jl index 87bcc8774..38b28a8e2 100644 --- a/test/SmallMPItest.jl +++ b/test/SmallMPItest.jl @@ -1,5 +1,8 @@ ## Small scale test for MPI Ecosystems ## Set random number seeds for reproducible results +using Pkg +Pkg.activate("..") +Pkg.instantiate() using EcoSISTEM using EcoSISTEM.Units diff --git a/test/test_MPI.jl b/test/test_MPI.jl index 2b0a048aa..b2b810e7a 100644 --- a/test/test_MPI.jl +++ b/test/test_MPI.jl @@ -79,7 +79,7 @@ using JLD2 end # Only test on linux for now - bug in Windows machine testing -if !Sys.iswindows() +if Sys.islinux() @testset "mpirun" begin # Keep outputs all one folder isdir("data") || mkdir("data")