From b7f833a6aea25b6fc0f15a7ace4922a0da78b1b6 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Tue, 7 Mar 2023 23:01:05 +0000 Subject: [PATCH 01/12] SimpleSDMLayers -> RasterDataSources --- Project.toml | 3 +- examples/InteractiveAfrica.jl | 88 +++++++++++++++-- examples/Manifest.toml | 132 ++++++++++++++++++++++---- examples/Project.toml | 3 +- examples/Worldclim_africa.jl | 38 +++++--- src/ClimatePref/ClimatePref.jl | 2 - src/ClimatePref/SimpleSDMInterface.jl | 40 -------- src/Dist.jl | 3 +- test/test_AbioticEnv.jl | 22 +++-- test/test_ReadData.jl | 43 +++++---- test/test_SimpleSDMInterface.jl | 28 ------ 11 files changed, 259 insertions(+), 143 deletions(-) delete mode 100644 src/ClimatePref/SimpleSDMInterface.jl delete mode 100644 test/test_SimpleSDMInterface.jl diff --git a/Project.toml b/Project.toml index e3a03ae0d..c87ce2d3c 100644 --- a/Project.toml +++ b/Project.toml @@ -34,9 +34,9 @@ Pluto = "c3e4b0f8-55cb-11ea-2926-15256bba5781" Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +RasterDataSources = "3cb90ccd-e1b6-4867-9617-4276c8b2ca36" Requires = "ae029012-a4dd-5104-9daa-d747884805df" SHA = "ea8e919c-243c-51af-8825-aaa63cd721ce" -SimpleSDMLayers = "2c645270-77db-11e9-22c3-0f302a89c64c" SpatialEcology = "348f2d5d-71a3-5ad4-b565-8af070f99681" Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" @@ -65,7 +65,6 @@ Optim = "0.18, 0.19, 0.20, 0.21, 0.22, 1" Phylo = "0.4.18" Plots = "0.28.4, 0.29, 1" Requires = "1" -SimpleSDMLayers = "0.7, 0.8" SpatialEcology = "0.9" StatsBase = "0.32.2, 0.33" Unitful = "1.7" diff --git a/examples/InteractiveAfrica.jl b/examples/InteractiveAfrica.jl index a970253ac..e36285345 100644 --- a/examples/InteractiveAfrica.jl +++ b/examples/InteractiveAfrica.jl @@ -1,5 +1,5 @@ ### A Pluto.jl notebook ### -# v0.19.0 +# v0.19.22 using Markdown using InteractiveUtils @@ -27,7 +27,8 @@ begin using Distributions using Diversity using SpatialEcology - using SimpleSDMLayers + using RasterDataSources + using AxisArrays end # ╔═╡ 39b75180-f384-11eb-3449-4f7c2ad25d99 @@ -37,6 +38,9 @@ Welcome to EcoSISTEM.jl! In the examples folder, you'll notice an example of run The first time round things may be a little slow - this is because Julia is compiling the code. After that, the time will whizz by!" +# ╔═╡ 1e9bcd31-9146-494b-98f5-27569c54ab0f + + # ╔═╡ e9e9065b-cf7e-4d37-8162-88f0076ad1eb begin spp_slider = @bind numSpecies html"" @@ -191,22 +195,24 @@ end # ╔═╡ 00000000-0000-0000-0000-000000000001 PLUTO_PROJECT_TOML_CONTENTS = """ [deps] +AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Diversity = "d3d5718d-52de-57ab-b67a-eca7fd6175a4" EcoSISTEM = "ed2dc23b-ada4-5fdb-a26f-56368a14ad8f" OnlineStats = "a15396b6-48d5-5d58-9928-6d29437db91e" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -SimpleSDMLayers = "2c645270-77db-11e9-22c3-0f302a89c64c" +RasterDataSources = "3cb90ccd-e1b6-4867-9617-4276c8b2ca36" SpatialEcology = "348f2d5d-71a3-5ad4-b565-8af070f99681" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [compat] +AxisArrays = "~0.4.6" Distributions = "~0.24.18" Diversity = "~0.5.6" EcoSISTEM = "~0.1.2" OnlineStats = "~1.5.11" Plots = "~0.28.4" -SimpleSDMLayers = "~0.7.0" +RasterDataSources = "~0.5.6" SpatialEcology = "~0.9.7" Unitful = "~1.9.0" """ @@ -215,6 +221,11 @@ Unitful = "~1.9.0" PLUTO_MANIFEST_TOML_CONTENTS = """ # This file is machine-generated - editing it directly is not advised +[[ASCIIrasters]] +git-tree-sha1 = "0cb0046798af8ac8561334c5a2a31f015e53c2b1" +uuid = "81770e7c-c736-4fa5-8129-46dd21831640" +version = "0.1.1" + [[AbstractTrees]] git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" @@ -234,6 +245,7 @@ version = "0.6.0" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" [[ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] @@ -258,9 +270,9 @@ version = "1.0.0" [[AxisArrays]] deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] -git-tree-sha1 = "d127d5e4d86c7680b20c35d40b503c74b9a39b5e" +git-tree-sha1 = "1dd4d9f5beebac0c03446918741b1a03dc5e5788" uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" -version = "0.4.4" +version = "0.4.6" [[Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -332,6 +344,7 @@ version = "2.2.1" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" +version = "0.5.2+0" [[ConstructionBase]] deps = ["LinearAlgebra"] @@ -439,8 +452,9 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.8.5" [[Downloads]] -deps = ["ArgTools", "LibCURL", "NetworkOptions"] +deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" +version = "1.6.0" [[EcoBase]] deps = ["RecipesBase"] @@ -478,6 +492,9 @@ git-tree-sha1 = "5a9c74bfef934bcd813570a513ccf38f25555352" uuid = "becb17da-46f6-5d3c-ad1b-1c5fe96bc73c" version = "0.5.9" +[[FileWatching]] +uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" + [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays"] git-tree-sha1 = "693210145367e7685d8604aee33d9bfb85db8b31" @@ -575,6 +592,12 @@ git-tree-sha1 = "fd83fa0bde42e01952757f01149dd968c06c4dba" uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" version = "1.12.0+1" +[[HTTP]] +deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] +git-tree-sha1 = "0fa77022fe4b511826b39c894c90daf5fce3334a" +uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" +version = "0.9.17" + [[IfElse]] git-tree-sha1 = "28e837ff3e7a6c3cdb252ce49fb412c8eb3caeef" uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" @@ -591,6 +614,11 @@ git-tree-sha1 = "f5fc07d4e706b84f72d54eedcc1c13d92fb0871c" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" version = "0.1.2" +[[IniFile]] +git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" +uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" +version = "0.5.1" + [[InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" @@ -662,10 +690,12 @@ version = "3.0.0+1" [[LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" +version = "0.6.3" [[LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" +version = "7.84.0+0" [[LibGit2]] deps = ["Base64", "NetworkOptions", "Printf", "SHA"] @@ -674,6 +704,7 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" [[LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" +version = "1.10.2+0" [[Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" @@ -697,7 +728,7 @@ uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" version = "7.1.1" [[LinearAlgebra]] -deps = ["Libdl"] +deps = ["Libdl", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[LittleCMS_jll]] @@ -737,9 +768,16 @@ version = "0.5.6" deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +[[MbedTLS]] +deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] +git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" +uuid = "739be429-bea8-5141-9913-cc70e7f3736d" +version = "1.1.7" + [[MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" +version = "2.28.0+0" [[Measures]] git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f" @@ -763,6 +801,7 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" +version = "2022.2.1" [[NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -789,6 +828,7 @@ version = "400.702.400+0" [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" +version = "1.2.0" [[OffsetArrays]] deps = ["Adapt"] @@ -808,6 +848,11 @@ git-tree-sha1 = "8efa5acf7af1623eabeebdc82ef54396adf16f71" uuid = "925886fa-5bf2-5e8e-b522-a9147a512338" version = "1.4.5" +[[OpenBLAS_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] +uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" +version = "0.3.20+0" + [[OpenJpeg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libtiff_jll", "LittleCMS_jll", "Pkg", "libpng_jll"] git-tree-sha1 = "76374b6e7f632c130e78100b166e5a48464256f8" @@ -876,6 +921,7 @@ version = "0.4.19" [[Pkg]] deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" +version = "1.8.0" [[PlotThemes]] deps = ["PlotUtils", "Requires", "Statistics"] @@ -928,7 +974,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[Random]] -deps = ["Serialization"] +deps = ["SHA", "Serialization"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[RandomBooleanMatrices]] @@ -948,6 +994,12 @@ git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5" uuid = "b3c3ace0-ae52-54e7-9d0b-2c1406fd6b9d" version = "0.3.2" +[[RasterDataSources]] +deps = ["ASCIIrasters", "Dates", "DelimitedFiles", "HTTP", "JSON", "URIs", "ZipFile"] +git-tree-sha1 = "aeb786b2cc040bc320bc97630f91fc2c33612873" +uuid = "3cb90ccd-e1b6-4867-9617-4276c8b2ca36" +version = "0.5.6" + [[Ratios]] git-tree-sha1 = "37d210f612d70f3f7d57d488cb3b6eff56ad4e41" uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" @@ -984,6 +1036,7 @@ version = "0.3.0+0" [[SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" +version = "0.7.0" [[SQLite_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -1099,6 +1152,7 @@ version = "0.3.0" [[TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" +version = "1.0.0" [[TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -1121,6 +1175,7 @@ version = "1.5.0" [[Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" +version = "1.10.0" [[Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] @@ -1137,6 +1192,11 @@ git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" version = "0.9.5" +[[URIs]] +git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" +uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" +version = "1.4.2" + [[UUIDs]] deps = ["Random", "SHA"] uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" @@ -1171,6 +1231,7 @@ version = "0.9.3" [[Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.12+3" [[Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1178,6 +1239,11 @@ git-tree-sha1 = "cc4bf3fdde8b7e3e9fa0351bdeedba1cf3b7f6e6" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" version = "1.5.0+0" +[[libblastrampoline_jll]] +deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.1.1+0" + [[libgeotiff_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libtiff_jll", "PROJ_jll", "Pkg"] git-tree-sha1 = "a5cc2e3dd7b1c1e783a61b8ab7de03eebddfed60" @@ -1193,15 +1259,19 @@ version = "1.6.38+0" [[nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.48.0+0" [[p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+0" """ # ╔═╡ Cell order: # ╟─39b75180-f384-11eb-3449-4f7c2ad25d99 # ╠═108951ec-3ecf-4f0c-b5e4-e79d00b1bfac +# ╠═5dd6e516-cfb5-4a4f-9f1c-50334c1f743f +# ╠═1e9bcd31-9146-494b-98f5-27569c54ab0f # ╠═e9e9065b-cf7e-4d37-8162-88f0076ad1eb # ╠═220e4af6-f228-4b8d-a77e-0ddbf5fc6705 # ╠═7e16f197-874b-482d-80b6-13a62ddda1f7 diff --git a/examples/Manifest.toml b/examples/Manifest.toml index e7df836b7..412d54de8 100644 --- a/examples/Manifest.toml +++ b/examples/Manifest.toml @@ -1,5 +1,10 @@ # This file is machine-generated - editing it directly is not advised +[[ASCIIrasters]] +git-tree-sha1 = "0cb0046798af8ac8561334c5a2a31f015e53c2b1" +uuid = "81770e7c-c736-4fa5-8129-46dd21831640" +version = "0.1.1" + [[AbstractTrees]] git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" @@ -19,6 +24,7 @@ version = "0.6.0" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.1" [[ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] @@ -43,9 +49,9 @@ version = "1.0.1" [[AxisArrays]] deps = ["Dates", "IntervalSets", "IterTools", "RangeArrays"] -git-tree-sha1 = "cf6875678085aed97f52bfc493baaebeb6d40bcb" +git-tree-sha1 = "1dd4d9f5beebac0c03446918741b1a03dc5e5788" uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" -version = "0.4.5" +version = "0.4.6" [[Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" @@ -68,7 +74,7 @@ uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.4.1" [[Cairo_jll]] -deps = ["Artifacts", "Bzip2_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_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" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.16.1+1" @@ -140,6 +146,13 @@ version = "3.43.0" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae" +version = "0.5.2+0" + +[[Configurations]] +deps = ["ExproniconLite", "OrderedCollections", "TOML"] +git-tree-sha1 = "62a7c76dbad02fdfdaa53608104edf760938c4ca" +uuid = "5218b696-f38b-4ac9-8b61-a12ec717816d" +version = "0.17.4" [[ConstructionBase]] deps = ["LinearAlgebra"] @@ -252,8 +265,9 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" version = "0.8.6" [[Downloads]] -deps = ["ArgTools", "LibCURL", "NetworkOptions"] +deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" +version = "1.6.0" [[EarCut_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -268,7 +282,7 @@ uuid = "a58aae7d-b440-5a11-b283-399458f99aac" version = "0.1.6" [[EcoSISTEM]] -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", "Printf", "REPL", "Random", "RecipesBase", "Requires", "SHA", "SimpleSDMLayers", "SpatialEcology", "Statistics", "StatsBase", "UUIDs", "Unitful"] +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" @@ -279,6 +293,12 @@ git-tree-sha1 = "bad72f730e9e91c08d9427d5e8db95478a3c323d" uuid = "2e619515-83b5-522b-bb60-26c02a35a201" version = "2.4.8+0" +[[ExproniconLite]] +deps = ["Pkg", "TOML"] +git-tree-sha1 = "c2eb763acf6e13e75595e0737a07a0bec0ce2147" +uuid = "55351af7-c7e9-48d6-89ff-24e801d99491" +version = "0.7.11" + [[FFMPEG]] deps = ["FFMPEG_jll"] git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" @@ -303,6 +323,9 @@ git-tree-sha1 = "80ced645013a5dbdc52cf70329399c35ce007fae" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" version = "1.13.0" +[[FileWatching]] +uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" + [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] git-tree-sha1 = "246621d23d1f43e3b9c368bf3b72b2331a27c286" @@ -361,6 +384,12 @@ version = "1.0.10+0" deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" +[[FuzzyCompletions]] +deps = ["REPL"] +git-tree-sha1 = "e16dd964b4dfaebcded16b2af32f05e235b354be" +uuid = "fb4132e2-a121-4a70-b8a1-d5b831dcdcc2" +version = "0.5.1" + [[GDAL]] deps = ["CEnum", "GDAL_jll", "NetworkOptions", "PROJ_jll"] git-tree-sha1 = "ac36f6aabae2ab70449af913f8ed60a0aecf06a8" @@ -461,6 +490,12 @@ git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" version = "2.8.1+1" +[[HypertextLiteral]] +deps = ["Tricks"] +git-tree-sha1 = "c47c5fa4c5308f27ccaac35504858d8914e102f9" +uuid = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2" +version = "0.9.4" + [[IfElse]] git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" @@ -590,10 +625,12 @@ uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" [[LibCURL]] deps = ["LibCURL_jll", "MozillaCACerts_jll"] uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" +version = "0.6.3" [[LibCURL_jll]] deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" +version = "7.84.0+0" [[LibGit2]] deps = ["Base64", "NetworkOptions", "Printf", "SHA"] @@ -602,6 +639,7 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" [[LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" +version = "1.10.2+0" [[Libdl]] uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" @@ -632,9 +670,9 @@ version = "1.42.0+0" [[Libiconv_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "42b62845d70a619f063a7da093d995ec8e15e778" +git-tree-sha1 = "c7cb1f5d892775ba13767a87c7ada0b980ea0a71" uuid = "94ce4f54-9a6c-5748-9c1c-f9c7231a4531" -version = "1.16.1+1" +version = "1.16.1+2" [[Libmount_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -667,7 +705,7 @@ uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" version = "7.1.1" [[LinearAlgebra]] -deps = ["Libdl"] +deps = ["Libdl", "libblastrampoline_jll"] uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" [[LittleCMS_jll]] @@ -685,6 +723,11 @@ version = "0.3.12" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" +[[MIMEs]] +git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" +uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" +version = "0.1.4" + [[MPI]] deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "Pkg", "Random", "Requires", "Serialization", "Sockets"] git-tree-sha1 = "d56a80d8cf8b9dc3050116346b3d83432b1912c0" @@ -692,10 +735,16 @@ uuid = "da04e1cc-30fd-572f-bb4f-1f8673147195" version = "0.19.2" [[MPICH_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3dacfc006764fe498515a022c3976b7e133c4008" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "Pkg", "TOML"] +git-tree-sha1 = "6d4fa43afab4611d090b11617ecea1a144b21d35" uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" -version = "4.0.2+0" +version = "4.0.2+5" + +[[MPIPreferences]] +deps = ["Libdl", "Preferences"] +git-tree-sha1 = "71f937129731a29eabe6969db2c90368a4408933" +uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267" +version = "0.1.7" [[MacroTools]] deps = ["Markdown", "Random"] @@ -716,6 +765,7 @@ version = "1.0.3" [[MbedTLS_jll]] deps = ["Artifacts", "Libdl"] uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" +version = "2.28.0+0" [[Measures]] git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f" @@ -739,6 +789,13 @@ uuid = "a63ad114-7e13-5084-954f-fe012c677804" [[MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" +version = "2022.2.1" + +[[MsgPack]] +deps = ["Serialization"] +git-tree-sha1 = "fc8c15ca848b902015bd4a745d350f02cf791c2a" +uuid = "99f44e22-a591-53d1-9472-aa23ef4bd671" +version = "1.2.0" [[NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] @@ -765,6 +822,7 @@ version = "400.702.402+0" [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" +version = "1.2.0" [[OffsetArrays]] deps = ["Adapt"] @@ -790,6 +848,11 @@ git-tree-sha1 = "287bd0f7ee1cc2a73f08057a7a6fcfe0c23fe4b0" uuid = "925886fa-5bf2-5e8e-b522-a9147a512338" version = "1.4.9" +[[OpenBLAS_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] +uuid = "4536629a-c528-5b80-bd46-f80d51c5b363" +version = "0.3.20+0" + [[OpenJpeg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libtiff_jll", "LittleCMS_jll", "Pkg", "libpng_jll"] git-tree-sha1 = "76374b6e7f632c130e78100b166e5a48464256f8" @@ -799,6 +862,7 @@ version = "2.4.0+0" [[OpenLibm_jll]] deps = ["Artifacts", "Libdl"] uuid = "05823500-19ac-5b8b-9628-191a04bc5112" +version = "0.8.1+0" [[OpenMPI_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] @@ -880,6 +944,7 @@ version = "0.40.1+0" [[Pkg]] deps = ["Artifacts", "Dates", "Downloads", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"] uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" +version = "1.8.0" [[PlotThemes]] deps = ["PlotUtils", "Statistics"] @@ -899,6 +964,12 @@ git-tree-sha1 = "88ee01b02fba3c771ac4dce0dfc4ecf0cb6fb772" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" version = "1.27.5" +[[Pluto]] +deps = ["Base64", "Configurations", "Dates", "Distributed", "FileWatching", "FuzzyCompletions", "HTTP", "HypertextLiteral", "InteractiveUtils", "Logging", "MIMEs", "Markdown", "MsgPack", "Pkg", "PrecompileSignatures", "REPL", "RelocatableFolders", "Sockets", "TOML", "Tables", "URIs", "UUIDs"] +git-tree-sha1 = "87b0f17b2a71eb4a20b61eed34975055fe5537dd" +uuid = "c3e4b0f8-55cb-11ea-2926-15256bba5781" +version = "0.19.9" + [[PooledArrays]] deps = ["DataAPI", "Future"] git-tree-sha1 = "28ef6c7ce353f0b35d0df0d5930e0d072c1f5b9b" @@ -911,6 +982,11 @@ git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20" uuid = "85a6dd25-e78a-55b7-8502-1745935b8125" version = "0.2.4" +[[PrecompileSignatures]] +git-tree-sha1 = "18ef344185f25ee9d51d80e179f8dad33dc48eb1" +uuid = "91cefc8d-f054-46dc-8f8c-26e11d7c5411" +version = "3.0.3" + [[Preferences]] deps = ["TOML"] git-tree-sha1 = "d3538e7f8a790dc8903519090857ef8e1283eecd" @@ -933,9 +1009,9 @@ uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79" [[Qt5Base_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Fontconfig_jll", "Glib_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "OpenSSL_jll", "Pkg", "Xorg_libXext_jll", "Xorg_libxcb_jll", "Xorg_xcb_util_image_jll", "Xorg_xcb_util_keysyms_jll", "Xorg_xcb_util_renderutil_jll", "Xorg_xcb_util_wm_jll", "Zlib_jll", "xkbcommon_jll"] -git-tree-sha1 = "ad368663a5e20dbb8d6dc2fddeefe4dae0781ae8" +git-tree-sha1 = "0c03844e2231e12fda4d0086fd7cbe4098ee8dc5" uuid = "ea2cea3b-5b76-57ae-a6ef-0a8af62496e1" -version = "5.15.3+0" +version = "5.15.3+2" [[QuadGK]] deps = ["DataStructures", "LinearAlgebra"] @@ -948,7 +1024,7 @@ deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" [[Random]] -deps = ["Serialization"] +deps = ["SHA", "Serialization"] uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" [[RandomBooleanMatrices]] @@ -968,6 +1044,12 @@ git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5" uuid = "b3c3ace0-ae52-54e7-9d0b-2c1406fd6b9d" version = "0.3.2" +[[RasterDataSources]] +deps = ["ASCIIrasters", "Dates", "DelimitedFiles", "HTTP", "JSON", "URIs", "ZipFile"] +git-tree-sha1 = "aeb786b2cc040bc320bc97630f91fc2c33612873" +uuid = "3cb90ccd-e1b6-4867-9617-4276c8b2ca36" +version = "0.5.6" + [[Ratios]] deps = ["Requires"] git-tree-sha1 = "dc84268fe0e3335a62e315a3a7cf2afa7178a734" @@ -1016,6 +1098,7 @@ version = "0.3.0+0" [[SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" +version = "0.7.0" [[SQLite_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -1042,12 +1125,6 @@ git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" -[[SimpleSDMLayers]] -deps = ["ArchGDAL", "Downloads", "RecipesBase", "Requires", "Statistics", "ZipFile"] -git-tree-sha1 = "a5f2bd0c13ae434963aadb8d1e26bf3dba81d9cc" -uuid = "2c645270-77db-11e9-22c3-0f302a89c64c" -version = "0.7.0" - [[SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" @@ -1126,6 +1203,7 @@ uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" [[TOML]] deps = ["Dates"] uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76" +version = "1.0.0" [[TableTraits]] deps = ["IteratorInterfaceExtensions"] @@ -1148,6 +1226,7 @@ version = "1.7.0" [[Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" +version = "1.10.0" [[Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] @@ -1164,6 +1243,11 @@ git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" version = "0.9.6" +[[Tricks]] +git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" +uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" +version = "0.1.6" + [[URIs]] git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" @@ -1369,6 +1453,7 @@ version = "0.9.4" [[Zlib_jll]] deps = ["Libdl"] uuid = "83775a58-1f1d-513f-b197-d71354ab007a" +version = "1.2.12+3" [[Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1382,6 +1467,11 @@ git-tree-sha1 = "5982a94fcba20f02f42ace44b9894ee2b140fe47" uuid = "0ac62f75-1d6f-5e53-bd7c-93b484bb37c0" version = "0.15.1+0" +[[libblastrampoline_jll]] +deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] +uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" +version = "5.1.1+0" + [[libfdk_aac_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "daacc84a041563f965be61859a36e17c4e4fcd55" @@ -1409,10 +1499,12 @@ version = "1.3.7+1" [[nghttp2_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d" +version = "1.48.0+0" [[p7zip_jll]] deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+0" [[x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] diff --git a/examples/Project.toml b/examples/Project.toml index c9272392a..42a56d48b 100644 --- a/examples/Project.toml +++ b/examples/Project.toml @@ -1,4 +1,5 @@ [deps] +AxisArrays = "39de3d68-74b9-583c-8d2d-e117c070f3a9" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f" Diversity = "d3d5718d-52de-57ab-b67a-eca7fd6175a4" @@ -8,6 +9,6 @@ MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" NetCDF = "30363a11-5582-574a-97bb-aa9a979735b9" OnlineStats = "a15396b6-48d5-5d58-9928-6d29437db91e" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -SimpleSDMLayers = "2c645270-77db-11e9-22c3-0f302a89c64c" +RasterDataSources = "3cb90ccd-e1b6-4867-9617-4276c8b2ca36" StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" diff --git a/examples/Worldclim_africa.jl b/examples/Worldclim_africa.jl index cfa06eb6e..5d7c12880 100644 --- a/examples/Worldclim_africa.jl +++ b/examples/Worldclim_africa.jl @@ -3,25 +3,34 @@ using EcoSISTEM using EcoSISTEM.ClimatePref using EcoSISTEM.Units -using SimpleSDMLayers +using RasterDataSources +using AxisArrays using Unitful using Unitful.DefaultSymbols using StatsBase using Plots # Download temperature and precipitation data -africa_temp = SimpleSDMPredictor(WorldClim, BioClim, 1, left = -25, right = 50, bottom = -35, top = 40) -bio_africa = Worldclim_bioclim(africa_temp, °C) -africa_water = SimpleSDMPredictor(WorldClim, BioClim, 12, left = -25, right = 50, bottom = -35, top = 40) -bio_africa_water = WaterBudget(Worldclim_bioclim(africa_water, mm)) +if !isdir("assets") + mkdir("assets") +end +ENV["RASTERDATASOURCES_PATH"] = "assets" +getraster(WorldClim{BioClim}) +world = readbioclim("assets/WorldClim/BioClim/") +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)) -plot(africa_temp) +heatmap(africa_temp') # Set up initial parameters for ecosystem -numSpecies = 1; grid = size(active); req= 10.0mm; individuals=0; area = 64e6km^2; totalK = 1000.0kJ/km^2 +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)) @@ -40,8 +49,8 @@ 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(284.0K, numSpecies) -vars = fill(4.0K, numSpecies) +opts = fill(280.0K, numSpecies) +vars = fill(10.0K, numSpecies) traits = GaussTrait(opts, vars) native = fill(true, numSpecies) abun = fill(div(individuals, numSpecies), numSpecies) @@ -85,13 +94,16 @@ 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)), +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)), +heatmap!(africa_endabun', clim = (0, maximum(abuns)), background_color = :lightblue, background_color_outside=:white, grid = false, color = cgrad(:algae, scale = :exp), subplot = 2) -plot!(africa_temp, grid = false, subplot = 3) -plot!(africa_water, grid = false, subplot = 4) + +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) diff --git a/src/ClimatePref/ClimatePref.jl b/src/ClimatePref/ClimatePref.jl index 6f1a37c3a..349efa2df 100644 --- a/src/ClimatePref/ClimatePref.jl +++ b/src/ClimatePref/ClimatePref.jl @@ -30,5 +30,3 @@ export getprofile include("PhyloModels.jl") export Brownian, Lambda, fitBrownian, fitLambda, varcovar -include("SimpleSDMInterface.jl") -export Worldclim_monthly, Worldclim_bioclim, CHELSA_bioclim, Landcover diff --git a/src/ClimatePref/SimpleSDMInterface.jl b/src/ClimatePref/SimpleSDMInterface.jl deleted file mode 100644 index 561a8348b..000000000 --- a/src/ClimatePref/SimpleSDMInterface.jl +++ /dev/null @@ -1,40 +0,0 @@ -using SimpleSDMLayers -using AxisArrays -using Unitful -using Unitful.DefaultSymbols -import AxisArrays.Axis - -function Worldclim_bioclim(sdm::SimpleSDMPredictor, units::Unitful.Units) - sdm = convert(Float64, sdm) - sdm.grid[isnothing.(sdm.grid)] .= NaN - unit_grid = sdm.grid .* units - if units == °C - unit_grid = uconvert.(K, unit_grid) - end - lat = collect(latitudes(sdm)) .* ° - lon = collect(longitudes(sdm)) .* ° - ax_array = AxisArray(unit_grid, Axis{:latitude}(lat), Axis{:longitude}(lon)) - return Worldclim_bioclim(ax_array) -end - -function CHELSA_bioclim(sdm::SimpleSDMPredictor, units::Unitful.Units) - sdm = convert(Float64, sdm) - sdm.grid[isnothing.(sdm.grid)] .= NaN - unit_grid = sdm.grid .* units - if units == °C - unit_grid = uconvert.(K, unit_grid) - end - lat = collect(latitudes(sdm)) .* ° - lon = collect(longitudes(sdm)) .* ° - ax_array = AxisArray(unit_grid, Axis{:latitude}(lat), Axis{:longitude}(lon)) - return CHELSA_bioclim(ax_array) -end - -function Landcover(sdm::SimpleSDMPredictor) - sdm = convert(Float64, sdm) - sdm.grid[isnothing.(sdm.grid)] .= NaN - lat = collect(latitudes(sdm)) .* ° - lon = collect(longitudes(sdm)) .* ° - ax_array = AxisArray(sdm.grid, Axis{:latitude}(lat), Axis{:longitude}(lon)) - return Landcover(ax_array) -end diff --git a/src/Dist.jl b/src/Dist.jl index 7d0ae7788..a676488bc 100644 --- a/src/Dist.jl +++ b/src/Dist.jl @@ -3,7 +3,8 @@ import Random: rand using Random import Distributions: @check_args, ContinuousUnivariateDistribution, -rand, params, GLOBAL_RNG, pdf +rand, params, pdf +import Random: GLOBAL_RNG """ Trapezoid{T<:Real} <: ContinuousUnivariateDistribution diff --git a/test/test_AbioticEnv.jl b/test/test_AbioticEnv.jl index 680df1df2..a1f28c9b5 100644 --- a/test/test_AbioticEnv.jl +++ b/test/test_AbioticEnv.jl @@ -4,8 +4,14 @@ using Test using EcoSISTEM.Units using EcoSISTEM.ClimatePref using AxisArrays -using SimpleSDMLayers +using RasterDataSources +if !isdir("assets") + mkdir("assets") +end +ENV["RASTERDATASOURCES_PATH"] = "assets" + +temp = getraster(WorldClim{BioClim}, :bio1) grid = (5, 5) area = 25.0km^2 totalK = 10000.0kJ/km^2 @@ -113,19 +119,19 @@ end end @testset "Bioclim data" begin - africa_temp = SimpleSDMPredictor(WorldClim, BioClim, 1, left = -25, right = 50, bottom = -35, top = 40) - bio_africa = Worldclim_bioclim(africa_temp, °C) - active = fill(true, size(africa_temp.grid)) + bio_africa = readbioclim("assets/WorldClim/BioClim/") + bio_africa = Worldclim_bioclim(bio_africa.array[:,:,1]) + active = fill(true, size(bio_africa.array)) totalK = 1000.0kJ/km^2; area = 100.0km^2 bc = bioclimAE(bio_africa, totalK, area) @test_nowarn bioclimAE(bio_africa, totalK, area) @test_nowarn bioclimAE(bio_africa, totalK, area, active) - @test size(bc.habitat.matrix) == size(africa_temp.grid) + @test size(bc.habitat.matrix) == size(bio_africa.array) @test isapprox(EcoSISTEM.getavailableenergy(bc), totalK * area) - solar = SolarBudget(fill(10.0kJ, size(africa_temp.grid))) + solar = SolarBudget(fill(10.0kJ, size(bio_africa.array))) bc = bioclimAE(bio_africa, solar, active) end -if isdir("assets") - rm("assets", recursive = true) +if isdir("assets/WorldClim") + rm("assets/WorldClim", recursive = true) end diff --git a/test/test_ReadData.jl b/test/test_ReadData.jl index 1f32c262f..041d33379 100644 --- a/test/test_ReadData.jl +++ b/test/test_ReadData.jl @@ -2,33 +2,38 @@ using EcoSISTEM.ClimatePref using EcoSISTEM.Units using Unitful using Unitful.DefaultSymbols -using SimpleSDMLayers +using RasterDataSources using Test +if !isdir("assets") + mkdir("assets") +end +ENV["RASTERDATASOURCES_PATH"] = "assets" +# Download layers of bioclim data and test on all read functions +# (essentially all the same file type) +temp = getraster(WorldClim{BioClim}, 1:12) + @testset "Reading functions" begin - # Download layers of bioclim data and test on all read functions - # (essentially all the same file type) - temp = SimpleSDMPredictor(WorldClim, BioClim, 1:12) - @test_nowarn readbioclim("assets/WorldClim/BioClim/10/") - @test_nowarn readworldclim("assets/WorldClim/BioClim/10/") - @test_nowarn readCRUTS("assets/WorldClim/BioClim/10/", "tavg") - @test_nowarn readCHELSA_monthly("assets/WorldClim/BioClim/10/", "tavg") - @test_nowarn readCHELSA_bioclim("assets/WorldClim/BioClim/10/") - @test_nowarn readfile("assets/WorldClim/BioClim/10/wc2.1_10m_bio_1.tif") + @test_nowarn readbioclim("assets/WorldClim/BioClim/") + @test_nowarn readworldclim("assets/WorldClim/BioClim/") + @test_nowarn readCRUTS("assets/WorldClim/BioClim/", "tavg") + @test_nowarn readCHELSA_monthly("assets/WorldClim/BioClim/", "tavg") + @test_nowarn readCHELSA_bioclim("assets/WorldClim/BioClim/") + @test_nowarn readfile("assets/WorldClim/BioClim/wc2.1_10m_bio_1.tif") end @testset "Output data" begin - bc = readbioclim("assets/WorldClim/BioClim/10/") - rf = readfile("assets/WorldClim/BioClim/10/wc2.1_10m_bio_1.tif") - wc = readworldclim("assets/WorldClim/BioClim/10/") - cr = readCRUTS("assets/WorldClim/BioClim/10/", "tavg") - ch_m = readCHELSA_monthly("assets/WorldClim/BioClim/10/", "tavg") - ch_b = readCHELSA_bioclim("assets/WorldClim/BioClim/10/") + bc = readbioclim("assets/WorldClim/BioClim/") + rf = readfile("assets/WorldClim/BioClim/wc2.1_10m_bio_1.tif") + wc = readworldclim("assets/WorldClim/BioClim/") + cr = readCRUTS("assets/WorldClim/BioClim/", "tavg") + ch_m = readCHELSA_monthly("assets/WorldClim/BioClim/", "tavg") + ch_b = readCHELSA_bioclim("assets/WorldClim/BioClim/") @test unit(bc.array[1]) == unit(wc.array[1]) == unit(rf[1]) == unit(ch_b.array[1]) == NoUnits @test unit(cr.array[1]) == unit(ch_m.array[1]) == K end -if isdir("assets") - rm("assets", recursive = true) -end +if isdir("assets/WorldClim") + rm("assets/WorldClim", recursive = true) +end \ No newline at end of file diff --git a/test/test_SimpleSDMInterface.jl b/test/test_SimpleSDMInterface.jl deleted file mode 100644 index 27f9ec3f2..000000000 --- a/test/test_SimpleSDMInterface.jl +++ /dev/null @@ -1,28 +0,0 @@ -using EcoSISTEM.ClimatePref -using AxisArrays -using SimpleSDMLayers -using Unitful -using Unitful.DefaultSymbols -using Test - -@testset "Worldclim" begin - africa_temp = SimpleSDMPredictor(WorldClim, BioClim, 1, left = -25, right = 50, bottom = -35, top = 40) - bio_africa = Worldclim_bioclim(africa_temp, °C) - @test unit(bio_africa.array[1]) == K -end - -@testset "CHELSA" begin - africa_temp_chelsa = SimpleSDMPredictor(CHELSA, BioClim, 1, left = -25, right = 50, bottom = -35, top = 40) - chelsa_africa = CHELSA_bioclim(africa_temp_chelsa, °C) - @test unit(chelsa_africa.array[1]) == K -end - -@testset "Landcover" begin - africa_lc = SimpleSDMPredictor(EarthEnv, LandCover, 1, left = -25, right = 50, bottom = -35, top = 40) - lc_africa = Landcover(africa_lc) - @test unit(lc_africa.array[1]) == NoUnits -end - -if isdir("assets") - rm("assets", recursive = true) -end From 23ce696d0bf7988ce9b1380ef5ab15268201c653 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Wed, 8 Mar 2023 12:05:14 +0000 Subject: [PATCH 02/12] Add in Landcover example. --- examples/LandCover_africa.jl | 111 ++++++++++++++++++++++++++++++++ src/AbioticEnv.jl | 39 +++++++++++ src/ClimatePref/ClimatePref.jl | 6 +- src/ClimatePref/DataCleaning.jl | 47 ++++++-------- src/ClimatePref/ReadData.jl | 50 ++++++++++++++ src/EcoSISTEM.jl | 6 +- src/TraitRelationship.jl | 14 ++++ src/Traitfuns.jl | 18 ++++++ src/Traits.jl | 16 +++++ 9 files changed, 273 insertions(+), 34 deletions(-) create mode 100644 examples/LandCover_africa.jl diff --git a/examples/LandCover_africa.jl b/examples/LandCover_africa.jl new file mode 100644 index 000000000..ed3ba2ee4 --- /dev/null +++ b/examples/LandCover_africa.jl @@ -0,0 +1,111 @@ +#### 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 + +# Download landcover data +if !isdir("assets") + mkdir("assets") +end +ENV["RASTERDATASOURCES_PATH"] = "assets" +getraster(EarthEnv{LandCover}) +world = readlc("assets/EarthEnv/LandCover/without_DISCover/", -180.0°, 180.0°, -56.0°, 90.0°) +world = compressLC(world) +africa_lc = world[-25°.. 50°, -35° .. 40°] +bio_africa_lc = Landcover(africa_lc) +heatmap(africa_lc') + +getraster(WorldClim{BioClim}) +world = readbioclim("assets/WorldClim/BioClim/") +africa_water = world.array[-25°.. 50°, -35° .. 40°, 12] +africa_water = upresolution(africa_water, 2) +africa_water = Worldclim_bioclim(AxisArray(africa_water .* mm, AxisArrays.axes(africa_water))) +bio_africa_water = WaterBudget(africa_water) + +# Find which grid cells are land +active = Array{Bool, 2}(africa_lc .!= 4) + +# Set up initial parameters for ecosystem +numSpecies = 1; grid = size(active); req= 10.0mm; 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(collect(1:8), numSpecies) +traits = LCtrait(opts) +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 = lcAE(bio_africa_lc, bio_africa_water, active) + +# Set relationship between species and environment (gaussian) +rel = LCmatch{Int64}() + +# 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) + +# Create a gif (warning, slow!) +anim = @animate for i in 1:lensim + africa_abun = Float64.(abuns[:, :, i]) + africa_abun[.!(active)] .= NaN + heatmap(africa_abun, clim = (0, maximum(abuns)), + background_color = :lightblue, background_color_outside=:white, + grid = false, color = cgrad(:algae, scale = :exp)) +end +gif(anim, "examples/Africa.gif", fps = 15) + +# 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]), title = "Start abundance") +heatmap!(africa_endabun', clim = (0, maximum(abuns)), + background_color = :lightblue, background_color_outside=:white, + grid = false, color = cgrad(:algae, scale = :exp), + subplot = 2, title = "End Abundance") +africa_lc = Float64.(africa_lc.data) +africa_lc[.!active] .= NaN +heatmap!(africa_lc', grid = false, subplot = 3, title = "Land Cover") +africa_water = world.array[-25°.. 50°, -35° .. 40°, 12] +heatmap!(africa_water', grid = false, subplot = 4, title = "Precipitation") diff --git a/src/AbioticEnv.jl b/src/AbioticEnv.jl index e25654474..9f5871324 100644 --- a/src/AbioticEnv.jl +++ b/src/AbioticEnv.jl @@ -411,3 +411,42 @@ end import EcoBase.getcoords getcoords(abenv::GridAbioticEnv) = abenv.habitat + +function lcAE(lc::Landcover, maxbud::Unitful.Quantity{Float64}, area::Unitful.Area) + dimension = size(lc.array) + gridsquaresize = lc.array.axes[1].val[2] - lc.array.axes[1].val[1] + gridsquaresize = ustrip.(gridsquaresize) * 111.32km + active = fill(true, dimension) + active[isnan.(lc.array[:,:,1])] .= false + + hab = DiscreteHab(Array(lc.array), gridsquaresize, + HabitatUpdate(NoChange, 0.0/s)) + B = cancel(maxbud, area) + bud = zeros(typeof(B), dimension) + fill!(bud, B/(dimension[1]*dimension[2])) + checkbud(B) || error("Unrecognised unit in budget") + budtype = matchdict[unit(B)] + return GridAbioticEnv{typeof(hab), budtype}(hab, active, budtype(bud)) +end +function lcAE(lc::Landcover, maxbud::Unitful.Quantity{Float64}, area::Unitful.Area, active::Array{Bool, 2}) + dimension = size(lc.array)[1:2] + gridsquaresize = lc.array.axes[1].val[2] - lc.array.axes[1].val[1] + gridsquaresize = ustrip.(gridsquaresize) * 111.32km + hab = DiscreteHab(Array(lc.array), gridsquaresize, + HabitatUpdate(NoChange, 0.0/s)) + B = cancel(maxbud, area) + bud = zeros(typeof(B), dimension) + fill!(bud, B/(dimension[1]*dimension[2])) + checkbud(B) || error("Unrecognised unit in budget") + budtype = matchdict[unit(B)] + return GridAbioticEnv{typeof(hab), budtype}(hab, active, budtype(bud)) +end +function lcAE(lc::Landcover, bud::B, active::Array{Bool, 2}) where B <: AbstractBudget + dimension = size(lc.array)[1:2] + gridsquaresize = lc.array.axes[1].val[2] - lc.array.axes[1].val[1] + gridsquaresize = ustrip.(gridsquaresize) * 111.32km + hab = DiscreteHab(Array(lc.array), gridsquaresize, + HabitatUpdate(NoChange, 0.0/s)) + + return GridAbioticEnv{typeof(hab), typeof(bud)}(hab, active, bud) +end diff --git a/src/ClimatePref/ClimatePref.jl b/src/ClimatePref/ClimatePref.jl index 349efa2df..8227ba33c 100644 --- a/src/ClimatePref/ClimatePref.jl +++ b/src/ClimatePref/ClimatePref.jl @@ -12,17 +12,17 @@ end @warn "This functionality remains under development!" include("ClimateTypes.jl") -export Worldclim_monthly, Worldclim_bioclim, ERA, CERA, CRUTS, CHELSA_bioclim, CHELSA_monthly, Reference +export Worldclim_monthly, Worldclim_bioclim, ERA, CERA, CRUTS, CHELSA_bioclim, CHELSA_monthly, Reference, Landcover include("ReadData.jl") export read, searchdir, readworldclim, readbioclim, readERA, -readCERA, readfile, readCHELSA_monthly, readCHELSA_bioclim, readCRUTS +readCERA, readfile, readCHELSA_monthly, readCHELSA_bioclim, readCRUTS, readlc include("ExtractClimate.jl") export extractvalues include("DataCleaning.jl") -export create_reference, upresolution, downresolution, downresolution! +export create_reference, upresolution, downresolution, downresolution!, compressLC include("Plotting.jl") export getprofile diff --git a/src/ClimatePref/DataCleaning.jl b/src/ClimatePref/DataCleaning.jl index 589042571..c35591460 100644 --- a/src/ClimatePref/DataCleaning.jl +++ b/src/ClimatePref/DataCleaning.jl @@ -61,7 +61,7 @@ function upresolution(bc::Worldclim_bioclim, rescale::Int64) end function upresolution(aa::AxisArray{T, 3} where T, rescale::Int64) grid = size(aa) - grid = (grid[1] .* rescale, grid[2] .* rescale, grid[3]) + grid = (grid[1] * rescale -1, grid[2] * rescale - 1, grid[3]) array = Array{typeof(aa[1]), 3}(undef, grid) map(1:grid[3]) do time for x in 1:size(aa, 1) @@ -72,47 +72,28 @@ function upresolution(aa::AxisArray{T, 3} where T, rescale::Int64) end end lon = aa.axes[1].val - smallstep = (lon[2] - lon[1]) / rescale - if lon[1] == -180° - newlon = collect(lon[1]:smallstep:(lon[end]+smallstep)) - else - newlon = collect((lon[1] -smallstep):smallstep:lon[end]) - end + newlon = range(lon[1], lon[end], grid[1]) lat = aa.axes[2].val - smallstep = (lat[2] - lat[1]) / rescale - if lat[1] == -90° - newlat = collect(lat[1]:smallstep:(lat[end]+smallstep)) - else - newlat = collect((lat[1]-smallstep):smallstep:lat[end]) - end + newlat = range(lat[1], lat[end], grid[2]) return AxisArray(array, Axis{:longitude}(newlon), Axis{:latitude}(newlat), Axis{:time}(aa.axes[3].val)) end function upresolution(aa::AxisArray{T, 2} where T, rescale::Int64) - grid = size(aa) .* rescale + grid = size(aa) .* rescale .- 1 array = Array{typeof(aa[1]), 2}(undef, grid) - for x in 1:size(aa, 1) - for y in 1:size(aa, 2) + for x in 1:size(aa, 1) - 1 + for y in 1:size(aa, 2) - 1 array[(rescale*x-(rescale-1)):(rescale*x), (rescale*y-(rescale - 1)):(rescale*y)] .= aa[x, y] end end lon = aa.axes[1].val - smallstep = (lon[2] - lon[1]) / rescale - if lon[1] == -180° - newlon = collect(lon[1]:smallstep:(lon[end]+smallstep)) - else - newlon = collect((lon[1] -smallstep):smallstep:lon[end]) - end + newlon = range(lon[1], lon[end], grid[1]) lat = aa.axes[2].val - smallstep = (lat[2] - lat[1]) / rescale - if lat[1] == -90° - newlat = collect(lat[1]:smallstep:(lat[end]+smallstep)) - else - newlat = collect((lat[1]-smallstep):smallstep:lat[end]) - end + newlat = range(lat[1], lat[end], grid[2]) + return AxisArray(array, Axis{:longitude}(newlon), Axis{:latitude}(newlat)) @@ -200,3 +181,13 @@ function downresolution!(resized_array::Array{T, 3}, array::Array{T, 2}, dim::In resized_array[x, y, dim] = fn(filter(!isnan, array[xcoords, ycoords])) end end + +function compressLC(lc::AxisArray) + newLC = AxisArray(zeros(Int64, size(lc, 1), size(lc, 2)), AxisArrays.axes(lc, 1), AxisArrays.axes(lc, 2)) + for i in 1:size(lc, 1) + for j in 1:size(lc, 2) + newLC[i, j] = findmax(lc[i, j, :])[2] + end + end + return newLC +end \ No newline at end of file diff --git a/src/ClimatePref/ReadData.jl b/src/ClimatePref/ReadData.jl index b21f8c8b6..874be4826 100644 --- a/src/ClimatePref/ReadData.jl +++ b/src/ClimatePref/ReadData.jl @@ -399,3 +399,53 @@ function readCHELSA_bioclim(dir::String, CHELSA_bioclim(world) end + +""" + readlc(dir::String) + +Function to extract all raster files from a specified folder directory, +and convert into an axis array. +""" +function readlc(dir::String, xmin::Unitful.Quantity{Float64} = -180.0°, + xmax::Unitful.Quantity{Float64} = 180.0°, + ymin::Unitful.Quantity{Float64} = -90.0°, + ymax::Unitful.Quantity{Float64} = 90.0°; + res = 10, fn = x -> round(mean(x))) + files = map(searchdir(dir, ".tif")) do files + joinpath(dir, files) + end + txy = [Float32, Int32(1), Int32(1), Float64(1), ""]; + + read(files[1]) do dataset + txy[1] = AG.pixeltype(AG.getband(dataset, 1)) + txy[2] = AG.width(AG.getband(dataset, 1)) + txy[3] = AG.height(AG.getband(dataset, 1)) + txy[4] = AG.getnodatavalue(AG.getband(dataset, 1)) + txy[5] = AG.getunittype(AG.getband(dataset, 1)) + print(dataset) + end + + numfiles = length(files) + b = Array{txy[1], 3}(undef, ceil(Int64, txy[2]/res), ceil(Int64, txy[3]/res), numfiles); + a = Array{txy[1], 2}(undef, txy[2], txy[3]); + map(eachindex(files)) do count + read(files[count]) do dataset + bd = AG.getband(dataset, 1); + AG.read!(bd, a); + end; + downresolution!(b, a, count, res, fn) + end + lat, long = size(b, 1), size(b, 2); + step_lat = (xmax - xmin) / lat; + step_lon = (ymax - ymin) / long; + unit = 1.0 + world = AxisArray(b[:, long:-1:1, :] * unit, + Axis{:latitude}(xmin:step_lat:(xmax - step_lat/2.0)), + Axis{:longitude}(ymin:step_lon:(ymax - step_lon/2.0)), + Axis{:var}(1:numfiles)); + if txy[1] <: AbstractFloat + world[isapprox.(world, txy[4])] *= NaN; + end; + + return world +end diff --git a/src/EcoSISTEM.jl b/src/EcoSISTEM.jl index a23a5ed3b..a70b64a8a 100644 --- a/src/EcoSISTEM.jl +++ b/src/EcoSISTEM.jl @@ -17,7 +17,7 @@ export assign_traits!, get_traits, resettraits!, reroot! include("TraitRelationship.jl") export TraitRelationship,multiplicativeTR2, multiplicativeTR3, Gauss, Match, NoRelContinuous, NoRelDiscrete, Trapeze, Unif, - additiveTR2, additiveTR3 + additiveTR2, additiveTR3, LCmatch include("Habitats.jl") export ContinuousHab,ContinuousTimeHab, DiscreteHab, HabitatCollection2, HabitatCollection3, tempgrad, raingrad @@ -26,7 +26,7 @@ include("Energy.jl") export SimpleRequirement, SizeRequirement, SolarRequirement, WaterRequirement, VolWaterRequirement, SimpleBudget, SolarBudget, SolarTimeBudget, WaterBudget, VolWaterBudget, WaterTimeBudget, VolWaterTimeBudget, ReqCollection2, BudgetCollection2 include("AbioticEnv.jl") -export GridAbioticEnv, simplenicheAE, tempgradAE, raingradAE, peakedgradAE, simplehabitatAE, degradedhabitatAE, eraAE, worldclimAE, bioclimAE +export GridAbioticEnv, simplenicheAE, tempgradAE, raingradAE, peakedgradAE, simplehabitatAE, degradedhabitatAE, eraAE, worldclimAE, bioclimAE, lcAE include("Movement.jl") export GaussianKernel, LongTailKernel, BirthOnlyMovement, AlwaysMovement, NoMovement, getkernel, Torus, Cylinder, NoBoundary @@ -34,7 +34,7 @@ export GaussianKernel, LongTailKernel, BirthOnlyMovement, AlwaysMovement, NoMove include("Traits.jl") export GaussTrait, DiscreteTrait, TempBin,RainBin, TraitCollection2, TraitCollection3,DiscreteEvolve, -ContinuousEvolve +ContinuousEvolve, LCtrait include("Demographics.jl") export PopGrowth, EqualPop, NoGrowth diff --git a/src/TraitRelationship.jl b/src/TraitRelationship.jl index 4b118c7f5..3f6099c5f 100644 --- a/src/TraitRelationship.jl +++ b/src/TraitRelationship.jl @@ -88,6 +88,20 @@ function eltype(tr::Match{TR}) where TR return TR end +mutable struct LCmatch{TR} <: AbstractTraitRelationship{TR} +end +function (::LCmatch{TR})(niche::TR, pref::Vector{TR}) where TR + if niche in pref + return 1.0 + else + return 0.0 + end +end +iscontinuous(tr::LCmatch{TR}) where TR = false +function eltype(tr::LCmatch{TR}) where TR + return TR +end + """ NoRelContinuous{TR} <: AbstractTraitRelationship{TR} diff --git a/src/Traitfuns.jl b/src/Traitfuns.jl index 7c9ba8f3c..e644a8767 100644 --- a/src/Traitfuns.jl +++ b/src/Traitfuns.jl @@ -46,6 +46,24 @@ function _traitfun(hab::DiscreteHab, trts::DiscreteTrait, preference = getpref(trts, sp) return rel(currentniche, preference) end +function _traitfun(hab::HabitatCollection3, trts::TraitCollection3, rel::R, pos::Int64, spp::Int64) where R <: AbstractTraitRelationship + res1 = _traitfun(hab.h1, trts.t1, rel.tr1, pos, spp) + res2 = _traitfun(hab.h2, trts.t2, rel.tr2, pos, spp) + res3 = _traitfun(hab.h3, trts.t3, rel.tr3, pos, spp) + return combineTR(rel)(res1, res2, res3) +end + +function _traitfun(hab::DiscreteHab, trts::LCtrait, + rel::R, pos::Int64, spp::Int64) where R <: AbstractTraitRelationship + h = gethabitat(hab, pos) + vals = getpref(trts, spp) + return rel(h, vals) +end + +function getpref(traits::LCtrait, spp::Int64) + return traits.vals[spp] +end + function getpref(traits::GaussTrait, sp::Int64) return traits.mean[sp], traits.var[sp] diff --git a/src/Traits.jl b/src/Traits.jl index a9de24def..409df18c2 100644 --- a/src/Traits.jl +++ b/src/Traits.jl @@ -19,6 +19,22 @@ function eltype(trait::DiscreteTrait{D}) where D return D end +mutable struct LCtrait{D <: Number} <: AbstractTraits{D} + vals::Array{Array{D, 1}, 1} + end + + iscontinuous(trait::LCtrait{D}) where D = false + function eltype(trait::LCtrait{D}) where D + return D + end + + function LCtrait(vals::Array{Array{D, 1}, 1}) where D <: AbstractFloat + 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 78650997749cf0837f08fc68f9b017d1a937c50b Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Wed, 8 Mar 2023 12:29:43 +0000 Subject: [PATCH 03/12] Add tests. --- test/test_AbioticEnv.jl | 19 +++++++++++++++++++ test/test_ReadData.jl | 5 ++++- 2 files changed, 23 insertions(+), 1 deletion(-) diff --git a/test/test_AbioticEnv.jl b/test/test_AbioticEnv.jl index a1f28c9b5..a5cfbcbe3 100644 --- a/test/test_AbioticEnv.jl +++ b/test/test_AbioticEnv.jl @@ -12,6 +12,7 @@ end ENV["RASTERDATASOURCES_PATH"] = "assets" temp = getraster(WorldClim{BioClim}, :bio1) +getraster(EarthEnv{LandCover}) grid = (5, 5) area = 25.0km^2 totalK = 10000.0kJ/km^2 @@ -132,6 +133,24 @@ end bc = bioclimAE(bio_africa, solar, active) end +@testset "Lancover data" begin + world = readlc("assets/EarthEnv/LandCover/without_DISCover/") + world_lc = compressLC(world) + world_lc = Landcover(world_lc) + active = fill(true, size(world_lc.array)) + totalK = 1000.0kJ/km^2; area = 100.0km^2 + lc = lcAE(world_lc, totalK, area) + @test_nowarn lcAE(world_lc, totalK, area) + @test_nowarn lcAE(world_lc, totalK, area, active) + @test size(lc.habitat.matrix) == size(world_lc.array) + @test isapprox(EcoSISTEM.getavailableenergy(lc), totalK * area) + solar = SolarBudget(fill(10.0kJ, size(world_lc.array))) + lc = lcAE(world_lc, solar, active) +end + if isdir("assets/WorldClim") rm("assets/WorldClim", recursive = true) end +if isdir("assets/EarthEnv") + rm("assets/EarthEnv", recursive = true) +end \ No newline at end of file diff --git a/test/test_ReadData.jl b/test/test_ReadData.jl index 041d33379..17d90ff18 100644 --- a/test/test_ReadData.jl +++ b/test/test_ReadData.jl @@ -12,6 +12,7 @@ ENV["RASTERDATASOURCES_PATH"] = "assets" # Download layers of bioclim data and test on all read functions # (essentially all the same file type) temp = getraster(WorldClim{BioClim}, 1:12) +lc = getraster(EarthEnv{LandCover}) @testset "Reading functions" begin @test_nowarn readbioclim("assets/WorldClim/BioClim/") @@ -19,6 +20,7 @@ temp = getraster(WorldClim{BioClim}, 1:12) @test_nowarn readCRUTS("assets/WorldClim/BioClim/", "tavg") @test_nowarn readCHELSA_monthly("assets/WorldClim/BioClim/", "tavg") @test_nowarn readCHELSA_bioclim("assets/WorldClim/BioClim/") + @test_nowarn readlc("assets/EarthEnv/LandCover/without_DISCover/") @test_nowarn readfile("assets/WorldClim/BioClim/wc2.1_10m_bio_1.tif") end @@ -29,8 +31,9 @@ end cr = readCRUTS("assets/WorldClim/BioClim/", "tavg") ch_m = readCHELSA_monthly("assets/WorldClim/BioClim/", "tavg") ch_b = readCHELSA_bioclim("assets/WorldClim/BioClim/") + lc = readlc("assets/EarthEnv/LandCover/without_DISCover/") - @test unit(bc.array[1]) == unit(wc.array[1]) == unit(rf[1]) == unit(ch_b.array[1]) == NoUnits + @test unit(bc.array[1]) == unit(wc.array[1]) == unit(rf[1]) == unit(ch_b.array[1]) == unit(lc[1])== NoUnits @test unit(cr.array[1]) == unit(ch_m.array[1]) == K end From 23c3f204d2312e46f5cd7de4f3f5470cdecdcd75 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Wed, 8 Mar 2023 12:36:47 +0000 Subject: [PATCH 04/12] Update pluto notebook. --- examples/InteractiveAfrica.jl | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/examples/InteractiveAfrica.jl b/examples/InteractiveAfrica.jl index e36285345..eabdf3b52 100644 --- a/examples/InteractiveAfrica.jl +++ b/examples/InteractiveAfrica.jl @@ -119,20 +119,20 @@ end # ╔═╡ 7e16f197-874b-482d-80b6-13a62ddda1f7 begin - temperature = SimpleSDMPredictor(WorldClim, BioClim, 1) - africa_temp = temperature[left = -25.0, right = 50.0, bottom = -35.0, top = 40.0] + if !isdir("assets") + mkdir("assets") + end + ENV["RASTERDATASOURCES_PATH"] = "assets" + getraster(WorldClim{BioClim}) + world = readbioclim("assets/WorldClim/BioClim/") + africa_temp = world.array[-25°.. 50°, -35° .. 40°, 1] plot(africa_temp) end -# ╔═╡ 03ade0dc-271d-407c-a0f1-583007b168d8 -begin - temp = Worldclim_bioclim(africa_temp, °C) - meantemp = mean(temp.array[.!isnan.(temp.array)]) -end - # ╔═╡ ee925e21-b0b6-478e-a3a0-573e8497b9f6 begin - africa_new = Worldclim_bioclim(africa_temp, K) + temp = uconvert.(K, africa_temp .* °C) + africa_new = Worldclim_bioclim(AxisArray(temp, AxisArrays.axes(africa_temp))) active_new = Array{Bool, 2}(.!isnan.(africa)) # Set up initial parameters for ecosystem grd_new = size(africa_new.array); req_new= 10.0kJ; individuals_new=3*10^8; area_new = 64e6km^2; totalK_new = 1000.0kJ/km^2 From f81fefbcb1e9eb1ff33f2f3eac10cb304e1d0a7c Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Wed, 8 Mar 2023 12:39:20 +0000 Subject: [PATCH 05/12] Allow NetCDF to update. --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index c87ce2d3c..3eaeeb4e1 100644 --- a/Project.toml +++ b/Project.toml @@ -59,7 +59,7 @@ JLD2 = "0.4.3" MPI = "0.17.2, 0.18, 0.19, 0.20" Measures = "0.3.1" Missings = "0.4.5, 1.0" -NetCDF = "0.11.3" +NetCDF = "0.11" OnlineStats = "1.5.8" Optim = "0.18, 0.19, 0.20, 0.21, 0.22, 1" Phylo = "0.4.18" From 193e6f89a1a06eeab0b7267981a3cc8d37f583cc Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Wed, 8 Mar 2023 12:56:42 +0000 Subject: [PATCH 06/12] Move notebooks into their own folder --- {examples => notebooks}/InteractiveAfrica.jl | 0 {examples => notebooks}/Introduction.jl | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename {examples => notebooks}/InteractiveAfrica.jl (100%) rename {examples => notebooks}/Introduction.jl (100%) diff --git a/examples/InteractiveAfrica.jl b/notebooks/InteractiveAfrica.jl similarity index 100% rename from examples/InteractiveAfrica.jl rename to notebooks/InteractiveAfrica.jl diff --git a/examples/Introduction.jl b/notebooks/Introduction.jl similarity index 100% rename from examples/Introduction.jl rename to notebooks/Introduction.jl From f72bea42b138cc0f655396508ad9e515dc649443 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Wed, 8 Mar 2023 15:04:52 +0000 Subject: [PATCH 07/12] Reduce memory load for testing --- test/test_ReadData.jl | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/test/test_ReadData.jl b/test/test_ReadData.jl index 17d90ff18..a0b7b6637 100644 --- a/test/test_ReadData.jl +++ b/test/test_ReadData.jl @@ -28,12 +28,16 @@ end bc = readbioclim("assets/WorldClim/BioClim/") rf = readfile("assets/WorldClim/BioClim/wc2.1_10m_bio_1.tif") wc = readworldclim("assets/WorldClim/BioClim/") - cr = readCRUTS("assets/WorldClim/BioClim/", "tavg") - ch_m = readCHELSA_monthly("assets/WorldClim/BioClim/", "tavg") ch_b = readCHELSA_bioclim("assets/WorldClim/BioClim/") lc = readlc("assets/EarthEnv/LandCover/without_DISCover/") @test unit(bc.array[1]) == unit(wc.array[1]) == unit(rf[1]) == unit(ch_b.array[1]) == unit(lc[1])== NoUnits +end + +@testset "Output data 2" begin + cr = readCRUTS("assets/WorldClim/BioClim/", "tavg") + ch_m = readCHELSA_monthly("assets/WorldClim/BioClim/", "tavg") + @test unit(cr.array[1]) == unit(ch_m.array[1]) == K end From 52aaab6448b4a90e0dcab5c5c41139fb0346b696 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Thu, 9 Mar 2023 12:23:15 +0000 Subject: [PATCH 08/12] Add in compat for examples folder --- examples/Manifest.toml | 736 ++++++++++++++++++++++++++--------------- examples/Project.toml | 14 + 2 files changed, 481 insertions(+), 269 deletions(-) diff --git a/examples/Manifest.toml b/examples/Manifest.toml index 412d54de8..3c453b4b6 100644 --- a/examples/Manifest.toml +++ b/examples/Manifest.toml @@ -5,10 +5,16 @@ git-tree-sha1 = "0cb0046798af8ac8561334c5a2a31f015e53c2b1" uuid = "81770e7c-c736-4fa5-8129-46dd21831640" version = "0.1.1" +[[AbstractFFTs]] +deps = ["ChainRulesCore", "LinearAlgebra"] +git-tree-sha1 = "16b6dbc4cf7caee4e1e75c49485ec67b667098a0" +uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" +version = "1.3.1" + [[AbstractTrees]] -git-tree-sha1 = "03e0550477d86222521d254b741d470ba17ea0b5" +git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" -version = "0.3.4" +version = "0.4.4" [[Adapt]] deps = ["LinearAlgebra"] @@ -17,10 +23,10 @@ uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" version = "2.4.0" [[ArchGDAL]] -deps = ["Dates", "DiskArrays", "GDAL", "GeoFormatTypes", "GeoInterface", "Tables"] -git-tree-sha1 = "ac9a3bdf0b1cc5bd276c530b645194bf57373ecf" +deps = ["CEnum", "ColorTypes", "Dates", "DiskArrays", "Extents", "GDAL", "GeoFormatTypes", "GeoInterface", "GeoInterfaceRecipes", "ImageCore", "Tables"] +git-tree-sha1 = "ef43020f8b69ed20439a10a5690d07bf6cbc7ee8" uuid = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3" -version = "0.6.0" +version = "0.10.0" [[ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" @@ -32,11 +38,17 @@ git-tree-sha1 = "f87e559f87a45bece9c9ed97458d3afe98b1ebb9" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" version = "0.1.0" -[[ArrayInterface]] -deps = ["Compat", "IfElse", "LinearAlgebra", "Requires", "SparseArrays", "Static"] -git-tree-sha1 = "c933ce606f6535a7c7b98e1d86d5d1014f730596" -uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "5.0.7" +[[ArrayInterfaceCore]] +deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "e5f08b5689b1aad068e01751889f2f615c7db36d" +uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" +version = "0.1.29" + +[[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" [[Artifacts]] uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" @@ -58,9 +70,14 @@ uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" [[BenchmarkTools]] deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] -git-tree-sha1 = "4c10eee4af024676200bc7752e536f858c6b8f93" +git-tree-sha1 = "d9a9701b899b30332bbcb3e1679c41cce81fb0e8" uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" -version = "1.3.1" +version = "1.3.2" + +[[BitFlags]] +git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" +uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" +version = "0.1.7" [[Bzip2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -69,9 +86,9 @@ uuid = "6e34b625-4abd-537c-b88f-471c36dfa7a0" version = "1.0.8+0" [[CEnum]] -git-tree-sha1 = "215a9aa4a1f23fbd05b92769fdd62559488d70e9" +git-tree-sha1 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" -version = "0.4.1" +version = "0.4.2" [[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"] @@ -87,9 +104,9 @@ version = "0.5.1" [[CategoricalArrays]] deps = ["DataAPI", "Future", "Missings", "Printf", "Requires", "Statistics", "Unicode"] -git-tree-sha1 = "109664d3a6f2202b1225478335ea8fea3cd8706b" +git-tree-sha1 = "5084cc1a28976dd1642c9f337b28a3cb03e0f7d2" uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597" -version = "0.10.5" +version = "0.10.7" [[Chain]] git-tree-sha1 = "339237319ef4712e6e5df7758d0bccddf5c237d9" @@ -98,33 +115,45 @@ version = "0.4.10" [[ChainRulesCore]] deps = ["Compat", "LinearAlgebra", "SparseArrays"] -git-tree-sha1 = "9950387274246d08af38f6eef8cb5480862a435f" +git-tree-sha1 = "c6d890a52d2c4d55d326439580c3b8d0875a77d9" uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4" -version = "1.14.0" +version = "1.15.7" [[ChangesOfVariables]] deps = ["ChainRulesCore", "LinearAlgebra", "Test"] -git-tree-sha1 = "bf98fa45a0a4cee295de98d4c1462be26345b9a1" +git-tree-sha1 = "485193efd2176b88e6622a39a246f8c5b600e74e" uuid = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0" -version = "0.1.2" +version = "0.1.6" + +[[CodecZlib]] +deps = ["TranscodingStreams", "Zlib_jll"] +git-tree-sha1 = "9c209fb7536406834aa938fb149964b985de6c83" +uuid = "944b1d66-785c-5afd-91f1-9de20f533193" +version = "0.7.1" [[ColorSchemes]] -deps = ["ColorTypes", "Colors", "FixedPointNumbers", "Random"] -git-tree-sha1 = "12fc73e5e0af68ad3137b886e3f7c1eacfca2640" +deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Random", "SnoopPrecompile"] +git-tree-sha1 = "aa3edc8f8dea6cbfa176ee12f7c2fc82f0608ed3" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.17.1" +version = "3.20.0" [[ColorTypes]] deps = ["FixedPointNumbers", "Random"] -git-tree-sha1 = "024fe24d83e4a5bf5fc80501a314ce0d1aa35597" +git-tree-sha1 = "eb7f0f8307f71fac7c606984ea5fb2817275d6e4" uuid = "3da002f7-5984-5a60-b8a6-cbb66c0b333f" -version = "0.11.0" +version = "0.11.4" + +[[ColorVectorSpace]] +deps = ["ColorTypes", "FixedPointNumbers", "LinearAlgebra", "SpecialFunctions", "Statistics", "TensorCore"] +git-tree-sha1 = "600cc5508d66b78aae350f7accdb58763ac18589" +uuid = "c3611d14-8923-5661-9e6a-0046d554d3a4" +version = "0.9.10" [[Colors]] deps = ["ColorTypes", "FixedPointNumbers", "Reexport"] -git-tree-sha1 = "417b0ed7b8b838aa6ca0a87aadf1bb9eb111ce40" +git-tree-sha1 = "fc08e5930ee9a4e03f84bfb5211cb54e7769758a" uuid = "5ae59095-9a9b-59fe-a467-6f913c188581" -version = "0.12.8" +version = "0.12.10" [[Combinatorics]] git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860" @@ -138,10 +167,10 @@ uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" version = "0.3.0" [[Compat]] -deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"] -git-tree-sha1 = "b153278a25dd42c65abbf4e62344f9d22e59191b" +deps = ["Dates", "LinearAlgebra", "UUIDs"] +git-tree-sha1 = "7a60c856b9fa189eb34f5f8a6f6b5529b7942957" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "3.43.0" +version = "4.6.1" [[CompilerSupportLibraries_jll]] deps = ["Artifacts", "Libdl"] @@ -156,15 +185,14 @@ version = "0.17.4" [[ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "f74e9d5388b8620b4cee35d4c5a618dd4dc547f4" +git-tree-sha1 = "89a9db8d28102b094992472d333674bd1a83ce2a" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.3.0" +version = "1.5.1" [[Contour]] -deps = ["StaticArrays"] -git-tree-sha1 = "9f02045d934dc030edad45944ea80dbd1f0ebea7" +git-tree-sha1 = "d05d9e7b7aedff4e5b51a029dced05cfb6125781" uuid = "d38c429a-6771-53c6-b99e-75d170b6e991" -version = "0.5.7" +version = "0.6.2" [[Crayons]] git-tree-sha1 = "249fe38abf76d48563e2f4556bebd215aa317e15" @@ -172,15 +200,15 @@ uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f" version = "4.1.1" [[DataAPI]] -git-tree-sha1 = "cc70b17275652eb47bc9e5f81635981f13cea5c8" +git-tree-sha1 = "e8119c1a33d267e16108be441a287a6981ba1630" uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a" -version = "1.9.0" +version = "1.14.0" [[DataFrames]] -deps = ["Compat", "DataAPI", "Future", "InvertedIndices", "IteratorInterfaceExtensions", "LinearAlgebra", "Markdown", "Missings", "PooledArrays", "PrettyTables", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"] -git-tree-sha1 = "6c19003824cbebd804a51211fd3bbd81bf1ecad5" +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" uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" -version = "1.3.3" +version = "1.5.0" [[DataFramesMeta]] deps = ["Chain", "DataFrames", "MacroTools", "Reexport"] @@ -190,9 +218,9 @@ version = "0.9.1" [[DataStructures]] deps = ["Compat", "InteractiveUtils", "OrderedCollections"] -git-tree-sha1 = "3daef5523dd2e769dad2365274f760ff5f282c7d" +git-tree-sha1 = "d1fff3a548102f48987a52a2e0d114fa97d730f0" uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" -version = "0.18.11" +version = "0.18.13" [[DataValueInterfaces]] git-tree-sha1 = "bfc1187b79289637fa0ef6d4436ebdfe6905cbd6" @@ -220,27 +248,28 @@ uuid = "b429d917-457f-4dbc-8f4c-0cc954292b1d" version = "0.4.0" [[DiffResults]] -deps = ["StaticArrays"] -git-tree-sha1 = "c18e98cba888c6c25d1c3b048e4b3380ca956805" +deps = ["StaticArraysCore"] +git-tree-sha1 = "782dd5f4561f5d267313f23853baaaa4c52ea621" uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5" -version = "1.0.3" +version = "1.1.0" [[DiffRules]] deps = ["IrrationalConstants", "LogExpFunctions", "NaNMath", "Random", "SpecialFunctions"] -git-tree-sha1 = "dd933c4ef7b4c270aacd4eb88fa64c147492acf0" +git-tree-sha1 = "a4ad7ef19d2cdc2eff57abbbe68032b1cd0bd8f8" uuid = "b552c78f-8df3-52c6-915a-8e097449b14b" -version = "1.10.0" +version = "1.13.0" [[DiskArrays]] -git-tree-sha1 = "cfca3b5d0df57f6315b5187482ab8eae4a5beb0e" +deps = ["OffsetArrays"] +git-tree-sha1 = "3f87990e0882e44c0f4e5c9699d09a0edbfa25c8" uuid = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3" -version = "0.2.13" +version = "0.3.9" [[Distances]] deps = ["LinearAlgebra", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "3258d0659f812acde79e8a74b11f17ac06d0ca04" +git-tree-sha1 = "49eba9ad9f7ead780bfb7ee319f962c811c6d3b2" uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7" -version = "0.10.7" +version = "0.10.8" [[Distributed]] deps = ["Random", "Serialization", "Sockets"] @@ -248,9 +277,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[Distributions]] deps = ["ChainRulesCore", "DensityInterface", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SparseArrays", "SpecialFunctions", "Statistics", "StatsBase", "StatsFuns", "Test"] -git-tree-sha1 = "5a4168170ede913a2cd679e53c2123cb4b889795" +git-tree-sha1 = "da9e1a9058f8d3eec3a8c9fe4faacfb89180066b" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.53" +version = "0.25.86" [[Diversity]] deps = ["AxisArrays", "DataFrames", "EcoBase", "InteractiveUtils", "LinearAlgebra", "Missings", "RecipesBase", "Requires", "Statistics"] @@ -260,20 +289,20 @@ version = "0.5.6" [[DocStringExtensions]] deps = ["LibGit2"] -git-tree-sha1 = "b19534d1895d702889b219c382a6e18010797f0b" +git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d" uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae" -version = "0.8.6" +version = "0.9.3" [[Downloads]] deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" -[[EarCut_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "3f3a2501fa7236e9b911e0f7a588c657e822bb6d" -uuid = "5ae413db-bbd1-5e63-b57d-d24a61df00f5" -version = "2.2.3+0" +[[DualNumbers]] +deps = ["Calculus", "NaNMath", "SpecialFunctions"] +git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" +uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" +version = "0.6.8" [[EcoBase]] deps = ["RecipesBase"] @@ -299,6 +328,11 @@ git-tree-sha1 = "c2eb763acf6e13e75595e0737a07a0bec0ce2147" uuid = "55351af7-c7e9-48d6-89ff-24e801d99491" version = "0.7.11" +[[Extents]] +git-tree-sha1 = "5e1e4c53fa39afe63a7d356e30452249365fba99" +uuid = "411431e0-e8b7-467b-b5e0-f676ba4f2910" +version = "0.1.1" + [[FFMPEG]] deps = ["FFMPEG_jll"] git-tree-sha1 = "b57e3acbe22f8484b4b5ff66a7499717fe1a9cc8" @@ -306,10 +340,10 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" version = "0.4.1" [[FFMPEG_jll]] -deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "Pkg", "Zlib_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] -git-tree-sha1 = "d8a578692e3077ac998b50c0217dfd67f21d1e5f" +deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"] +git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd" uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5" -version = "4.4.0+0" +version = "4.4.2+2" [[Feather]] deps = ["CategoricalArrays", "DataFrames", "Dates", "FlatBuffers", "Mmap", "Tables"] @@ -319,24 +353,24 @@ version = "0.5.10" [[FileIO]] deps = ["Pkg", "Requires", "UUIDs"] -git-tree-sha1 = "80ced645013a5dbdc52cf70329399c35ce007fae" +git-tree-sha1 = "7be5f99f7d15578798f338f5433b6c432ea8037b" uuid = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549" -version = "1.13.0" +version = "1.16.0" [[FileWatching]] uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[FillArrays]] deps = ["LinearAlgebra", "Random", "SparseArrays", "Statistics"] -git-tree-sha1 = "246621d23d1f43e3b9c368bf3b72b2331a27c286" +git-tree-sha1 = "d3ba08ab64bdfd27234d3f61956c966266757fe6" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "0.13.2" +version = "0.13.7" [[FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "SparseArrays", "StaticArrays"] -git-tree-sha1 = "56956d1e4c1221000b7781104c58c34019792951" +deps = ["ArrayInterfaceCore", "LinearAlgebra", "Requires", "Setfield", "SparseArrays", "StaticArrays"] +git-tree-sha1 = "04ed1f0029b6b3af88343e439b995141cb0d0b8d" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.11.0" +version = "2.17.0" [[FixedPointNumbers]] deps = ["Statistics"] @@ -364,9 +398,9 @@ version = "0.4.2" [[ForwardDiff]] deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions", "StaticArrays"] -git-tree-sha1 = "1bd6fc0c344fc0cbee1f42f8d2e7ec8253dda2d2" +git-tree-sha1 = "00e252f4d706b3d55a8863432e742bf5717b498d" uuid = "f6369f11-7733-5829-9624-2563aa707210" -version = "0.10.25" +version = "0.10.35" [[FreeType2_jll]] deps = ["Artifacts", "Bzip2_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -392,56 +426,56 @@ version = "0.5.1" [[GDAL]] deps = ["CEnum", "GDAL_jll", "NetworkOptions", "PROJ_jll"] -git-tree-sha1 = "ac36f6aabae2ab70449af913f8ed60a0aecf06a8" +git-tree-sha1 = "aa6f8ca2f7a0eb46f4d8353eb725c717de40da6e" uuid = "add2ef01-049f-52c4-9ee2-e494f65e021a" -version = "1.3.0" +version = "1.5.1" [[GDAL_jll]] -deps = ["Artifacts", "Expat_jll", "GEOS_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libtiff_jll", "OpenJpeg_jll", "PROJ_jll", "Pkg", "SQLite_jll", "Zlib_jll", "Zstd_jll", "libgeotiff_jll"] -git-tree-sha1 = "5272b856ca84a20871858b46a1f3b529e12c38a7" +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"] +git-tree-sha1 = "aa913bff49c25482fe3db2c357cb5f8127a6d2ba" uuid = "a7073274-a066-55f0-b90d-d619367d196c" -version = "300.400.100+0" +version = "301.600.200+0" [[GEOS_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "07f6426d716d0d110cdede90ebd3bbb2f3be0d8c" +git-tree-sha1 = "f4c0cafb093b62d5a5d8447a9b2306555385c0d9" uuid = "d604d12d-fa86-5845-992e-78dc15976526" -version = "3.10.0+0" +version = "3.11.0+0" [[GLFW_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pkg", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll"] -git-tree-sha1 = "51d2dfe8e590fbd74e7a842cf6d13d8a2f45dc01" +git-tree-sha1 = "d972031d28c8c8d9d7b41a536ad7bb0c2579caca" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.3.6+0" +version = "3.3.8+0" [[GR]] -deps = ["Base64", "DelimitedFiles", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Pkg", "Printf", "Random", "RelocatableFolders", "Serialization", "Sockets", "Test", "UUIDs"] -git-tree-sha1 = "af237c08bda486b74318c8070adb96efa6952530" +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" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.64.2" +version = "0.71.7" [[GR_jll]] -deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Pkg", "Qt5Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "cd6efcf9dc746b06709df14e462f0a3fe0786b1e" +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" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.64.2+0" +version = "0.71.7+0" [[GeoFormatTypes]] -git-tree-sha1 = "bb75ce99c9d6fb2edd8ef8ee474991cdacf12221" +git-tree-sha1 = "434166198434a5c2fcc0a1a59d22c3b0ad460889" uuid = "68eda718-8dee-11e9-39e7-89f7f65f511f" -version = "0.3.0" +version = "0.4.1" [[GeoInterface]] -deps = ["RecipesBase"] -git-tree-sha1 = "6b1a29c757f56e0ae01a35918a2c39260e2c4b98" +deps = ["Extents"] +git-tree-sha1 = "e07a1b98ed72e3cdd02c6ceaab94b8a606faca40" uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f" -version = "0.5.7" +version = "1.2.1" -[[GeometryBasics]] -deps = ["EarCut_jll", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"] -git-tree-sha1 = "82853ebc70db4f5a3084853738c68fd497b22c7c" -uuid = "5c1252a2-5f33-56bf-86c9-59e7332b4326" -version = "0.3.10" +[[GeoInterfaceRecipes]] +deps = ["GeoInterface", "RecipesBase"] +git-tree-sha1 = "29e1ec25cfb6762f503a19495aec347acf867a9e" +uuid = "0329782f-3d07-4b52-b9f6-d3137cf03c7a" +version = "1.0.0" [[Gettext_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "XML2_jll"] @@ -450,10 +484,16 @@ uuid = "78b55507-aeef-58d4-861c-77aaff3498b1" version = "0.21.0+0" [[Glib_jll]] -deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "a32d672ac2c967f3deb8a81d828afc739c838a06" +deps = ["Artifacts", "Gettext_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Pkg", "Zlib_jll"] +git-tree-sha1 = "d3b3624125c1474292d0d8ed0f65554ac37ddb23" uuid = "7746bdde-850d-59dc-9ae8-88ece973131d" -version = "2.68.3+2" +version = "2.74.0+2" + +[[Graphics]] +deps = ["Colors", "LinearAlgebra", "NaNMath"] +git-tree-sha1 = "d61890399bc535850c4bf08e4e0d3a7ad0f21cbd" +uuid = "a2bd30eb-e257-5431-a919-1863eab51364" +version = "1.1.2" [[Graphite2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -468,21 +508,21 @@ version = "1.0.2" [[HCubature]] deps = ["Combinatorics", "DataStructures", "LinearAlgebra", "QuadGK", "StaticArrays"] -git-tree-sha1 = "134af3b940d1ca25b19bc9740948157cee7ff8fa" +git-tree-sha1 = "e95b36755023def6ebc3d269e6483efa8b2f7f65" uuid = "19dc6840-f33b-545b-b366-655c7e3ffd49" -version = "1.5.0" +version = "1.5.1" [[HDF5_jll]] deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "bab67c0d1c4662d2c4be8c6007751b0b6111de5c" +git-tree-sha1 = "4cc2bb72df6ff40b055295fdef6d92955f9dede8" uuid = "0234f1f7-429e-5d53-9886-15a909be8d59" -version = "1.12.1+0" +version = "1.12.2+2" [[HTTP]] -deps = ["Base64", "Dates", "IniFile", "Logging", "MbedTLS", "NetworkOptions", "Sockets", "URIs"] -git-tree-sha1 = "0fa77022fe4b511826b39c894c90daf5fce3334a" +deps = ["Base64", "CodecZlib", "Dates", "IniFile", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"] +git-tree-sha1 = "37e4657cd56b11abe3d10cd4a1ec5fbdb4180263" uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3" -version = "0.9.17" +version = "1.7.4" [[HarfBuzz_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "Graphite2_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg"] @@ -490,16 +530,23 @@ git-tree-sha1 = "129acf094d168394e80ee1dc4bc06ec835e510a3" uuid = "2e76f6c2-a576-52d4-95c1-20adfe4de566" version = "2.8.1+1" +[[HypergeometricFunctions]] +deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions", "Test"] +git-tree-sha1 = "709d864e3ed6e3545230601f94e11ebc65994641" +uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" +version = "0.3.11" + [[HypertextLiteral]] deps = ["Tricks"] git-tree-sha1 = "c47c5fa4c5308f27ccaac35504858d8914e102f9" uuid = "ac1192a8-f4b3-4bfe-ba22-af5b92cd3ab2" version = "0.9.4" -[[IfElse]] -git-tree-sha1 = "debdd00ffef04665ccbb3e150747a77560e8fad1" -uuid = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173" -version = "0.1.1" +[[ImageCore]] +deps = ["AbstractFFTs", "ColorVectorSpace", "Colors", "FixedPointNumbers", "Graphics", "MappedArrays", "MosaicViews", "OffsetArrays", "PaddedViews", "Reexport"] +git-tree-sha1 = "acf614720ef026d38400b3817614c45882d75500" +uuid = "a09fc81d-aa75-5fe9-8630-4744c3626534" +version = "0.9.4" [[IndexedTables]] deps = ["DataAPI", "DataValues", "Distributed", "InvertedIndices", "IteratorInterfaceExtensions", "OnlineStatsBase", "PooledArrays", "SparseArrays", "Statistics", "StatsBase", "StructArrays", "TableTraits", "TableTraitsUtils", "Tables", "WeakRefStrings"] @@ -508,46 +555,52 @@ uuid = "6deec6e2-d858-57c5-ab9b-e6ca5bd20e43" version = "1.0.0" [[Inflate]] -git-tree-sha1 = "f5fc07d4e706b84f72d54eedcc1c13d92fb0871c" +git-tree-sha1 = "5cd07aab533df5170988219191dfad0519391428" uuid = "d25df0c9-e2be-5dd7-82c8-3ad0b3e990b9" -version = "0.1.2" +version = "0.1.3" [[IniFile]] git-tree-sha1 = "f550e6e32074c939295eb5ea6de31849ac2c9625" uuid = "83e8ac13-25f8-5344-8a64-a9f2b223428f" version = "0.5.1" +[[InlineStrings]] +deps = ["Parsers"] +git-tree-sha1 = "9cc2baf75c6d09f9da536ddf58eb2f29dedaf461" +uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" +version = "1.4.0" + [[InteractiveUtils]] deps = ["Markdown"] uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240" [[Interpolations]] -deps = ["AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] -git-tree-sha1 = "b7bc05649af456efc75d178846f47006c2c4c3c7" +deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArrays", "Random", "Ratios", "Requires", "SharedArrays", "SparseArrays", "StaticArrays", "WoodburyMatrices"] +git-tree-sha1 = "721ec2cf720536ad005cb38f50dbba7b02419a15" uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" -version = "0.13.6" +version = "0.14.7" [[IntervalSets]] -deps = ["Dates", "Statistics"] -git-tree-sha1 = "eb381d885e30ef859068fce929371a8a5d06a914" +deps = ["Dates", "Random", "Statistics"] +git-tree-sha1 = "16c0cc91853084cb5f58a78bd209513900206ce6" uuid = "8197267c-284f-5f27-9208-e0e47529a953" -version = "0.6.1" +version = "0.7.4" [[InverseFunctions]] deps = ["Test"] -git-tree-sha1 = "91b5dcf362c5add98049e6c29ee756910b03051d" +git-tree-sha1 = "49510dfcb407e572524ba94aeae2fced1f3feb0f" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.3" +version = "0.1.8" [[InvertedIndices]] -git-tree-sha1 = "bee5f1ef5bf65df56bdd2e40447590b272a5471f" +git-tree-sha1 = "82aec7a3dd64f4d9584659dc0b62ef7db2ef3e19" uuid = "41ab1584-1d38-5bbf-9106-f11c6c58b48f" -version = "1.1.0" +version = "1.2.0" [[IrrationalConstants]] -git-tree-sha1 = "7fd44fd4ff43fc60815f8e764c0f352b83c49151" +git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2" uuid = "92d709cd-6900-40b7-9082-c6be49f344b6" -version = "0.1.1" +version = "0.2.2" [[IterTools]] git-tree-sha1 = "fa6287a4469f5e048d763df38279ee729fbd44e5" @@ -566,10 +619,16 @@ uuid = "82899510-4779-5014-852e-03e436cf321d" version = "1.0.0" [[JLD2]] -deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "TranscodingStreams", "UUIDs"] -git-tree-sha1 = "81b9477b49402b47fbe7f7ae0b252077f53e4a08" +deps = ["FileIO", "MacroTools", "Mmap", "OrderedCollections", "Pkg", "Printf", "Reexport", "Requires", "TranscodingStreams", "UUIDs"] +git-tree-sha1 = "42c17b18ced77ff0be65957a591d34f4ed57c631" uuid = "033835bb-8acc-5ee8-8aae-3f567f8a3819" -version = "0.4.22" +version = "0.4.31" + +[[JLFzf]] +deps = ["Pipe", "REPL", "Random", "fzf_jll"] +git-tree-sha1 = "f377670cda23b6b7c1c0b3893e37451c5c1a2185" +uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" +version = "0.1.5" [[JLLWrappers]] deps = ["Preferences"] @@ -584,10 +643,16 @@ uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" version = "0.21.3" [[JpegTurbo_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b53380851c6e6664204efb2e62cd24fa5c47e4ba" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "6f2675ef130a300a112286de91973805fcc5ffbc" uuid = "aacddb02-875f-59d6-b918-886e6ef4fbf8" -version = "2.1.2+0" +version = "2.1.91+0" + +[[Kerberos_krb5_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "60274b4ab38e8d1248216fe6b6ace75ae09b0502" +uuid = "b39eb1a6-c29a-53d7-8c32-632cd16f18da" +version = "1.19.3+0" [[LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -613,10 +678,15 @@ uuid = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f" version = "1.3.0" [[Latexify]] -deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "Printf", "Requires"] -git-tree-sha1 = "6f14549f7760d84b2db7a9b10b88cd3cc3025730" +deps = ["Formatting", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Printf", "Requires"] +git-tree-sha1 = "2422f47b34d4b127720a18f86fa7b1aa2e141f29" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.15.14" +version = "0.15.18" + +[[LazilyInitializedFields]] +git-tree-sha1 = "410fe4739a4b092f2ffe36fcb0dcc3ab12648ce1" +uuid = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf" +version = "1.2.1" [[LazyArtifacts]] deps = ["Artifacts", "Pkg"] @@ -636,6 +706,12 @@ version = "7.84.0+0" deps = ["Base64", "NetworkOptions", "Printf", "SHA"] uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +[[LibPQ_jll]] +deps = ["Artifacts", "JLLWrappers", "Kerberos_krb5_jll", "Libdl", "OpenSSL_jll", "Pkg"] +git-tree-sha1 = "a299629703a93d8efcefccfc16b18ad9a073d131" +uuid = "08be9ffa-1c94-5ee5-a977-46a84ec9b350" +version = "14.3.0+1" + [[LibSSH2_jll]] deps = ["Artifacts", "Libdl", "MbedTLS_jll"] uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" @@ -658,9 +734,9 @@ version = "1.8.7+0" [[Libglvnd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll", "Xorg_libXext_jll"] -git-tree-sha1 = "7739f837d6447403596a75d19ed01fd08d6f56bf" +git-tree-sha1 = "6f73d1dd803986947b2c750138528a999a6c7733" uuid = "7e76a0d4-f3c7-5321-8279-8d96eeed0f29" -version = "1.3.0+3" +version = "1.6.0+0" [[Libgpg_error_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -682,9 +758,9 @@ version = "2.35.0+0" [[Libtiff_jll]] deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "LERC_jll", "Libdl", "Pkg", "Zlib_jll", "Zstd_jll"] -git-tree-sha1 = "c9551dd26e31ab17b86cbd00c2ede019c08758eb" +git-tree-sha1 = "3eb79b0ca5764d4799c06699573fd8f533259713" uuid = "89763e89-9b03-5906-acba-b20f662cd828" -version = "4.3.0+1" +version = "4.4.0+0" [[Libuuid_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -700,9 +776,9 @@ version = "1.3.5" [[LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "f27132e551e959b3667d8c93eae90973225032dd" +git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.1.1" +version = "7.2.0" [[LinearAlgebra]] deps = ["Libdl", "libblastrampoline_jll"] @@ -716,29 +792,41 @@ version = "2.12.0+0" [[LogExpFunctions]] deps = ["ChainRulesCore", "ChangesOfVariables", "DocStringExtensions", "InverseFunctions", "IrrationalConstants", "LinearAlgebra"] -git-tree-sha1 = "a970d55c2ad8084ca317a4658ba6ce99b7523571" +git-tree-sha1 = "0a1b7c2863e44523180fdb3146534e265a91870b" uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688" -version = "0.3.12" +version = "0.3.23" [[Logging]] uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" +[[LoggingExtras]] +deps = ["Dates", "Logging"] +git-tree-sha1 = "cedb76b37bc5a6c702ade66be44f831fa23c681e" +uuid = "e6f89c97-d47a-5376-807f-9c37f3926c36" +version = "1.0.0" + +[[Lz4_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "5d494bc6e85c4c9b626ee0cab05daa4085486ab1" +uuid = "5ced341a-0733-55b8-9ab6-a4889d929147" +version = "1.9.3+0" + [[MIMEs]] git-tree-sha1 = "65f28ad4b594aebe22157d6fac869786a255b7eb" uuid = "6c6e2e6c-3030-632d-7369-2d6c69616d65" version = "0.1.4" [[MPI]] -deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "Pkg", "Random", "Requires", "Serialization", "Sockets"] -git-tree-sha1 = "d56a80d8cf8b9dc3050116346b3d83432b1912c0" +deps = ["Distributed", "DocStringExtensions", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "Requires", "Serialization", "Sockets"] +git-tree-sha1 = "6d72bafd3960f9c119ceb8f034fef28346490fe5" uuid = "da04e1cc-30fd-572f-bb4f-1f8673147195" -version = "0.19.2" +version = "0.20.8" [[MPICH_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "Pkg", "TOML"] -git-tree-sha1 = "6d4fa43afab4611d090b11617ecea1a144b21d35" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "7ec808cad4f3940316c015cb16608e4e632c2c89" uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" -version = "4.0.2+5" +version = "4.1.0+1" [[MPIPreferences]] deps = ["Libdl", "Preferences"] @@ -746,21 +834,32 @@ git-tree-sha1 = "71f937129731a29eabe6969db2c90368a4408933" uuid = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267" version = "0.1.7" +[[MPItrampoline_jll]] +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "Pkg", "TOML"] +git-tree-sha1 = "b3f9e42685b4ad614eca0b44bd863cd41b1c86ea" +uuid = "f1f71cc9-e9ae-5b93-9b94-4fe0e1ad3748" +version = "5.0.2+1" + [[MacroTools]] deps = ["Markdown", "Random"] -git-tree-sha1 = "3d3e902b31198a27340d0bf00d6ac452866021cf" +git-tree-sha1 = "42324d08725e200c23d4dfb549e0d5d89dede2d2" uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09" -version = "0.5.9" +version = "0.5.10" + +[[MappedArrays]] +git-tree-sha1 = "e8b359ef06ec72e8c030463fe02efe5527ee5142" +uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900" +version = "0.4.1" [[Markdown]] deps = ["Base64"] uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" [[MbedTLS]] -deps = ["Dates", "MbedTLS_jll", "Random", "Sockets"] -git-tree-sha1 = "1c38e51c3d08ef2278062ebceade0e46cefc96fe" +deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "Random", "Sockets"] +git-tree-sha1 = "03a9b9718f5682ecb107ac9f7308991db4ce395b" uuid = "739be429-bea8-5141-9913-cc70e7f3736d" -version = "1.0.3" +version = "1.1.7" [[MbedTLS_jll]] deps = ["Artifacts", "Libdl"] @@ -768,9 +867,9 @@ uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" version = "2.28.0+0" [[Measures]] -git-tree-sha1 = "e498ddeee6f9fdb4551ce855a46f54dbd900245f" +git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" -version = "0.3.1" +version = "0.3.2" [[MicrosoftMPI_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -780,13 +879,19 @@ version = "10.1.3+2" [[Missings]] deps = ["DataAPI"] -git-tree-sha1 = "bf210ce90b6c9eed32d25dbcae1ebc565df2687f" +git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272" uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28" -version = "1.0.2" +version = "1.1.0" [[Mmap]] uuid = "a63ad114-7e13-5084-954f-fe012c677804" +[[MosaicViews]] +deps = ["MappedArrays", "OffsetArrays", "PaddedViews", "StackViews"] +git-tree-sha1 = "7b86a5d4d70a9f5cdf2dacb3cbe6d251d1a61dbe" +uuid = "e94cdb99-869f-56ef-bcf0-1ae2bcbe0389" +version = "0.3.4" + [[MozillaCACerts_jll]] uuid = "14a3606d-f60d-562e-9121-12d972cd8159" version = "2022.2.1" @@ -799,26 +904,27 @@ version = "1.2.0" [[NLSolversBase]] deps = ["DiffResults", "Distributed", "FiniteDiff", "ForwardDiff"] -git-tree-sha1 = "50310f934e55e5ca3912fb941dec199b49ca9b68" +git-tree-sha1 = "a0b464d183da839699f4c79e7606d9d186ec172c" uuid = "d41bc354-129a-5804-8e4c-c37616107c6c" -version = "7.8.2" +version = "7.8.3" [[NaNMath]] -git-tree-sha1 = "b086b7ea07f8e38cf122f5016af580881ac914fe" +deps = ["OpenLibm_jll"] +git-tree-sha1 = "0877504529a3e5c3343c6f8b4c0381e57e4387e4" uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3" -version = "0.3.7" +version = "1.0.2" [[NetCDF]] deps = ["DiskArrays", "Formatting", "NetCDF_jll"] -git-tree-sha1 = "8aca90c1a0f6c3bb65be11d307d8aad6b200087b" +git-tree-sha1 = "328178762645783b20495d408ab317b4c2d25b1a" uuid = "30363a11-5582-574a-97bb-aa9a979735b9" -version = "0.11.4" +version = "0.11.7" [[NetCDF_jll]] -deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Pkg", "Zlib_jll", "nghttp2_jll"] -git-tree-sha1 = "598f1a5e9829b3e57f233f98b34a22b376dff373" +deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Pkg", "XML2_jll", "Zlib_jll"] +git-tree-sha1 = "072f8371f74c3b9e1b26679de7fbf059d45ea221" uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3" -version = "400.702.402+0" +version = "400.902.5+1" [[NetworkOptions]] uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" @@ -826,9 +932,9 @@ version = "1.2.0" [[OffsetArrays]] deps = ["Adapt"] -git-tree-sha1 = "043017e0bdeff61cfbb7afeb558ab29536bbb5ed" +git-tree-sha1 = "82d7c9e310fe55aa54996e6f7f94674e2a38fcb4" uuid = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" -version = "1.10.8" +version = "1.12.9" [[Ogg_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -838,15 +944,15 @@ version = "1.3.5+1" [[OnlineStats]] deps = ["AbstractTrees", "Dates", "LinearAlgebra", "OnlineStatsBase", "OrderedCollections", "Random", "RecipesBase", "Statistics", "StatsBase"] -git-tree-sha1 = "78feae582915781a235912de43280f98e6962a78" +git-tree-sha1 = "e81f7f4179becdb6c365fb5a44042cfe7d50b77a" uuid = "a15396b6-48d5-5d58-9928-6d29437db91e" -version = "1.5.13" +version = "1.5.14" [[OnlineStatsBase]] deps = ["AbstractTrees", "Dates", "LinearAlgebra", "OrderedCollections", "Statistics", "StatsBase"] -git-tree-sha1 = "287bd0f7ee1cc2a73f08057a7a6fcfe0c23fe4b0" +git-tree-sha1 = "60e587c99ea261d1c452d2acb1f3a481e772660c" uuid = "925886fa-5bf2-5e8e-b522-a9147a512338" -version = "1.4.9" +version = "1.5.0" [[OpenBLAS_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"] @@ -865,16 +971,22 @@ uuid = "05823500-19ac-5b8b-9628-191a04bc5112" version = "0.8.1+0" [[OpenMPI_jll]] -deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "6340586e076b2abd41f5ba1a3b9c774ec6b30fde" +deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] +git-tree-sha1 = "f3080f4212a8ba2ceb10a34b938601b862094314" uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" -version = "4.1.2+0" +version = "4.1.5+0" + +[[OpenSSL]] +deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] +git-tree-sha1 = "6503b77492fd7fcb9379bf73cd31035670e3c509" +uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c" +version = "1.3.3" [[OpenSSL_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "ab05aa4cc89736e95915b01e7279e61b1bfe33b8" +git-tree-sha1 = "9ff31d101d987eb9d66bd8b176ac7c277beccd09" uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95" -version = "1.1.14+0" +version = "1.1.20+0" [[OpenSpecFun_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Pkg"] @@ -884,9 +996,9 @@ version = "0.5.5+0" [[Optim]] deps = ["Compat", "FillArrays", "ForwardDiff", "LineSearches", "LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "PositiveFactorizations", "Printf", "SparseArrays", "StatsBase"] -git-tree-sha1 = "bc0a748740e8bc5eeb9ea6031e6f050de1fc0ba2" +git-tree-sha1 = "1903afc76b7d01719d9c30d3c7d501b61db96721" uuid = "429524aa-4258-5aef-a3af-852621145aeb" -version = "1.6.2" +version = "1.7.4" [[Opus_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -899,23 +1011,28 @@ git-tree-sha1 = "85f8e6578bf1f9ee0d11e7bb1b1456435479d47c" uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" version = "1.4.1" -[[PCRE_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "b2a7af664e098055a7529ad1a900ded962bca488" -uuid = "2f80f16e-611a-54ab-bc61-aa92de5b98fc" -version = "8.44.0+0" +[[PCRE2_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15" +version = "10.40.0+0" [[PDMats]] deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "e8185b83b9fc56eb6456200e873ce598ebc7f262" +git-tree-sha1 = "67eae2738d63117a196f497d7db789821bce61d1" uuid = "90014a1f-27ba-587c-ab20-58faa44d9150" -version = "0.11.7" +version = "0.11.17" [[PROJ_jll]] deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "Libtiff_jll", "Pkg", "SQLite_jll"] -git-tree-sha1 = "59c43648bf081f732eae1e44b8883f713d2ca1b6" +git-tree-sha1 = "fcb3f39ae1184a056ecc415863d46d2109aa6947" uuid = "58948b4f-47e0-5654-a9ad-f609743f8632" -version = "800.200.100+0" +version = "900.100.0+0" + +[[PaddedViews]] +deps = ["OffsetArrays"] +git-tree-sha1 = "03a7a85b76381a3d04c7a1656039197e70eda03d" +uuid = "5432bcbf-9aad-5242-b902-cca2824c8663" +version = "0.5.11" [[Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -924,10 +1041,10 @@ uuid = "d96e819e-fc66-5662-9728-84c9c7592b0a" version = "0.12.3" [[Parsers]] -deps = ["Dates"] -git-tree-sha1 = "621f4f3b4977325b9128d5fae7a8b4829a0c2222" +deps = ["Dates", "SnoopPrecompile"] +git-tree-sha1 = "478ac6c952fddd4399e71d4779797c538d0ff2bf" uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" -version = "2.2.4" +version = "2.5.8" [[Phylo]] deps = ["AxisArrays", "DataFrames", "DataStructures", "Distributions", "IterableTables", "LightGraphs", "Missings", "Printf", "Random", "RecipesBase", "Requires", "SimpleTraits", "Statistics", "Tokenize", "Unitful"] @@ -935,6 +1052,11 @@ git-tree-sha1 = "fe4370547df637e4b6dfd6446ec227a4fd780cad" uuid = "aea672f4-3940-5932-aa44-993d1c3ff149" version = "0.4.21" +[[Pipe]] +git-tree-sha1 = "6842804e7867b115ca9de748a0cf6b364523c16d" +uuid = "b98c9c47-44ae-5843-9183-064241ee97a0" +version = "1.3.0" + [[Pixman_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "b4f5d02549a10e20780a24fce72bea96b6329e29" @@ -948,33 +1070,33 @@ version = "1.8.0" [[PlotThemes]] deps = ["PlotUtils", "Statistics"] -git-tree-sha1 = "8162b2f8547bc23876edd0c5181b27702ae58dce" +git-tree-sha1 = "1f03a2d339f42dca4a4da149c7e15e9b896ad899" uuid = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a" -version = "3.0.0" +version = "3.1.0" [[PlotUtils]] -deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "Statistics"] -git-tree-sha1 = "bb16469fd5224100e422f0b027d26c5a25de1200" +deps = ["ColorSchemes", "Colors", "Dates", "Printf", "Random", "Reexport", "SnoopPrecompile", "Statistics"] +git-tree-sha1 = "c95373e73290cf50a8a22c3375e4625ded5c5280" uuid = "995b91a9-d308-5afd-9ec6-746e21dbc043" -version = "1.2.0" +version = "1.3.4" [[Plots]] -deps = ["Base64", "Contour", "Dates", "Downloads", "FFMPEG", "FixedPointNumbers", "GR", "GeometryBasics", "JSON", "Latexify", "LinearAlgebra", "Measures", "NaNMath", "Pkg", "PlotThemes", "PlotUtils", "Printf", "REPL", "Random", "RecipesBase", "RecipesPipeline", "Reexport", "Requires", "Scratch", "Showoff", "SparseArrays", "Statistics", "StatsBase", "UUIDs", "UnicodeFun", "Unzip"] -git-tree-sha1 = "88ee01b02fba3c771ac4dce0dfc4ecf0cb6fb772" +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"] +git-tree-sha1 = "cfcd24ebf8b066b4f8e42bade600c8558212ed83" uuid = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" -version = "1.27.5" +version = "1.38.7" [[Pluto]] -deps = ["Base64", "Configurations", "Dates", "Distributed", "FileWatching", "FuzzyCompletions", "HTTP", "HypertextLiteral", "InteractiveUtils", "Logging", "MIMEs", "Markdown", "MsgPack", "Pkg", "PrecompileSignatures", "REPL", "RelocatableFolders", "Sockets", "TOML", "Tables", "URIs", "UUIDs"] -git-tree-sha1 = "87b0f17b2a71eb4a20b61eed34975055fe5537dd" +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" uuid = "c3e4b0f8-55cb-11ea-2926-15256bba5781" -version = "0.19.9" +version = "0.19.22" [[PooledArrays]] deps = ["DataAPI", "Future"] -git-tree-sha1 = "28ef6c7ce353f0b35d0df0d5930e0d072c1f5b9b" +git-tree-sha1 = "a6062fe4063cdafe78f4a0a81cfffb89721b30e7" uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720" -version = "1.4.1" +version = "1.4.2" [[PositiveFactorizations]] deps = ["LinearAlgebra"] @@ -989,15 +1111,15 @@ version = "3.0.3" [[Preferences]] deps = ["TOML"] -git-tree-sha1 = "d3538e7f8a790dc8903519090857ef8e1283eecd" +git-tree-sha1 = "47e5f437cc0e7ef2ce8406ce1e7e24d44915f88d" uuid = "21216c6a-2e73-6563-6e65-726566657250" -version = "1.2.5" +version = "1.3.0" [[PrettyTables]] -deps = ["Crayons", "Formatting", "Markdown", "Reexport", "Tables"] -git-tree-sha1 = "dfb54c4e414caa595a1f2ed759b160f5a3ddcba5" +deps = ["Crayons", "Formatting", "LaTeXStrings", "Markdown", "Reexport", "StringManipulation", "Tables"] +git-tree-sha1 = "96f6db03ab535bdb901300f88335257b0018689d" uuid = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" -version = "1.3.1" +version = "2.2.2" [[Printf]] deps = ["Unicode"] @@ -1015,9 +1137,9 @@ version = "5.15.3+2" [[QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "78aadffb3efd2155af139781b8a8df1ef279ea39" +git-tree-sha1 = "786efa36b7eff813723c4849c90456609cf06661" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.4.2" +version = "2.8.1" [[REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -1057,26 +1179,33 @@ uuid = "c84ed2f1-dad5-54f0-aa8e-dbefe2724439" version = "0.4.3" [[RecipesBase]] -git-tree-sha1 = "6bf3f380ff52ce0832ddd3a2a7b9538ed1bcca7d" +deps = ["SnoopPrecompile"] +git-tree-sha1 = "261dddd3b862bd2c940cf6ca4d1c8fe593e457c8" uuid = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" -version = "1.2.1" +version = "1.3.3" [[RecipesPipeline]] -deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase"] -git-tree-sha1 = "dc1e451e15d90347a7decc4221842a022b011714" +deps = ["Dates", "NaNMath", "PlotUtils", "RecipesBase", "SnoopPrecompile"] +git-tree-sha1 = "e974477be88cb5e3040009f3767611bc6357846f" uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" -version = "0.5.2" +version = "0.6.11" [[Reexport]] git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b" uuid = "189a3867-3050-52da-a836-e630ba90ab69" version = "1.2.2" +[[RegistryInstances]] +deps = ["LazilyInitializedFields", "Pkg", "TOML", "Tar"] +git-tree-sha1 = "ffd19052caf598b8653b99404058fce14828be51" +uuid = "2792f1a3-b283-48e8-9a74-f99dce5104f3" +version = "0.1.0" + [[RelocatableFolders]] deps = ["SHA", "Scratch"] -git-tree-sha1 = "cdbd3b1338c72ce29d9584fdbe9e9b70eeb5adca" +git-tree-sha1 = "90bc7a7c96410424509e4263e277e43250c05691" uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" -version = "0.1.3" +version = "1.0.0" [[Requires]] deps = ["UUIDs"] @@ -1086,35 +1215,47 @@ version = "1.3.0" [[Rmath]] deps = ["Random", "Rmath_jll"] -git-tree-sha1 = "bf3188feca147ce108c76ad82c2792c57abe7b1f" +git-tree-sha1 = "f65dcb5fa46aee0cf9ed6274ccbd597adc49aa7b" uuid = "79098fc4-a85e-5d69-aa6a-4863f24498fa" -version = "0.7.0" +version = "0.7.1" [[Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "68db32dff12bb6127bac73c209881191bf0efbb7" +git-tree-sha1 = "6ed52fdd3382cf21947b15e8870ac0ddbff736da" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.3.0+0" +version = "0.4.0+0" [[SHA]] uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce" version = "0.7.0" [[SQLite_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] -git-tree-sha1 = "f79c1c58951ea4f5bb63bb96b99bf7f440a3f774" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"] +git-tree-sha1 = "54d66b0f69f4578f4988fc08d579783fcdcd764f" uuid = "76ed43ae-9a5d-5a62-8c75-30186b810ce8" -version = "3.38.0+0" +version = "3.41.0+0" [[Scratch]] deps = ["Dates"] -git-tree-sha1 = "0b4b7f1393cff97c33891da2a0bf69c6ed241fda" +git-tree-sha1 = "30449ee12237627992a99d5e30ae63e4d78cd24a" uuid = "6c6a2e73-6563-6170-7368-637461726353" -version = "1.1.0" +version = "1.2.0" + +[[SentinelArrays]] +deps = ["Dates", "Random"] +git-tree-sha1 = "77d3c4726515dca71f6d80fbb5e251088defe305" +uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" +version = "1.3.18" [[Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" +[[Setfield]] +deps = ["ConstructionBase", "Future", "MacroTools", "StaticArraysCore"] +git-tree-sha1 = "e2cc6d8c88613c05e1defb55170bf5ff211fbeac" +uuid = "efcf1570-3423-57d1-acb7-fd33fddbac46" +version = "1.1.1" + [[SharedArrays]] deps = ["Distributed", "Mmap", "Random", "Serialization"] uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383" @@ -1125,20 +1266,31 @@ git-tree-sha1 = "91eddf657aca81df9ae6ceb20b959ae5653ad1de" uuid = "992d4aef-0814-514b-bc4d-f2e9a6c4116f" version = "1.0.3" +[[SimpleBufferStream]] +git-tree-sha1 = "874e8867b33a00e784c8a7e4b60afe9e037b74e1" +uuid = "777ac1f9-54b0-4bf8-805c-2214025038e7" +version = "1.1.0" + [[SimpleTraits]] deps = ["InteractiveUtils", "MacroTools"] git-tree-sha1 = "5d7e3f4e11935503d3ecaf7186eac40602e7d231" uuid = "699a6c99-e7fa-54fc-8d76-47d257e15c1d" version = "0.9.4" +[[SnoopPrecompile]] +deps = ["Preferences"] +git-tree-sha1 = "e760a70afdcd461cf01a575947738d359234665c" +uuid = "66db9d55-30c0-4569-8b51-7e840670fc0c" +version = "1.0.3" + [[Sockets]] uuid = "6462fe0b-24de-5631-8697-dd941f90decc" [[SortingAlgorithms]] deps = ["DataStructures"] -git-tree-sha1 = "b3363d7460f7d098ca0912c69b082f75625d7508" +git-tree-sha1 = "a4ada03f999bd01b3a25dcaa30b2d929fe537e00" uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c" -version = "1.0.1" +version = "1.1.0" [[SparseArrays]] deps = ["LinearAlgebra", "Random"] @@ -1152,21 +1304,26 @@ version = "0.9.15" [[SpecialFunctions]] deps = ["ChainRulesCore", "IrrationalConstants", "LogExpFunctions", "OpenLibm_jll", "OpenSpecFun_jll"] -git-tree-sha1 = "5ba658aeecaaf96923dce0da9e703bd1fe7666f9" +git-tree-sha1 = "ef28127915f4229c971eb43f3fc075dd3fe91880" uuid = "276daf66-3868-5448-9aa4-cd146d93841b" -version = "2.1.4" +version = "2.2.0" -[[Static]] -deps = ["IfElse"] -git-tree-sha1 = "87e9954dfa33fd145694e42337bdd3d5b07021a6" -uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.6.0" +[[StackViews]] +deps = ["OffsetArrays"] +git-tree-sha1 = "46e589465204cd0c08b4bd97385e4fa79a0c770c" +uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15" +version = "0.1.1" [[StaticArrays]] -deps = ["LinearAlgebra", "Random", "Statistics"] -git-tree-sha1 = "4f6ec5d99a28e1a749559ef7dd518663c5eca3d5" +deps = ["LinearAlgebra", "Random", "StaticArraysCore", "Statistics"] +git-tree-sha1 = "2d7d9e1ddadc8407ffd460e24218e37ef52dd9a3" uuid = "90137ffa-7385-5640-81b9-e52037218182" -version = "1.4.3" +version = "1.5.16" + +[[StaticArraysCore]] +git-tree-sha1 = "6b7ba252635a5eff6a0b0664a41ee140a1c9e72a" +uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" +version = "1.4.0" [[Statistics]] deps = ["LinearAlgebra", "SparseArrays"] @@ -1174,21 +1331,26 @@ uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2" [[StatsAPI]] deps = ["LinearAlgebra"] -git-tree-sha1 = "8d7530a38dbd2c397be7ddd01a424e4f411dcc41" +git-tree-sha1 = "f9af7f195fb13589dd2e2d57fdb401717d2eb1f6" uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0" -version = "1.2.2" +version = "1.5.0" [[StatsBase]] deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"] -git-tree-sha1 = "8977b17906b0a1cc74ab2e3a05faa16cf08a8291" +git-tree-sha1 = "d1bf48bfcc554a3761a133fe3a9bb01488e06916" uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" -version = "0.33.16" +version = "0.33.21" [[StatsFuns]] -deps = ["ChainRulesCore", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] -git-tree-sha1 = "5950925ff997ed6fb3e985dcce8eb1ba42a0bbe7" +deps = ["ChainRulesCore", "HypergeometricFunctions", "InverseFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"] +git-tree-sha1 = "f625d686d5a88bcd2b15cd81f18f98186fdc0c9a" uuid = "4c63d2b9-4356-54db-8cca-17b64c39e42c" -version = "0.9.18" +version = "1.3.0" + +[[StringManipulation]] +git-tree-sha1 = "46da2434b41f41ac3594ee9816ce5541c6096123" +uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e" +version = "0.3.0" [[StructArrays]] deps = ["Adapt", "DataAPI", "Tables"] @@ -1219,29 +1381,41 @@ version = "1.0.2" [[Tables]] deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits", "Test"] -git-tree-sha1 = "5ce79ce186cc678bbb5c5681ca3379d1ddae11a1" +git-tree-sha1 = "c79322d36826aa2f4fd8ecfa96ddb47b174ac78d" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.7.0" +version = "1.10.0" [[Tar]] deps = ["ArgTools", "SHA"] uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e" version = "1.10.0" +[[TensorCore]] +deps = ["LinearAlgebra"] +git-tree-sha1 = "1feb45f88d133a655e001435632f019a9a1bcdb6" +uuid = "62fd8b95-f654-4bbd-a8a5-9c27f68ccd50" +version = "0.1.1" + [[Test]] deps = ["InteractiveUtils", "Logging", "Random", "Serialization"] uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40" +[[Thrift_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "boost_jll"] +git-tree-sha1 = "fd7da49fae680c18aa59f421f0ba468e658a2d7a" +uuid = "e0b8ae26-5307-5830-91fd-398402328850" +version = "0.16.0+0" + [[Tokenize]] -git-tree-sha1 = "0952c9cee34988092d73a5708780b3917166a0dd" +git-tree-sha1 = "90538bf898832b6ebd900fa40f223e695970e3a5" uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624" -version = "0.5.21" +version = "0.5.25" [[TranscodingStreams]] deps = ["Random", "Test"] -git-tree-sha1 = "216b95ea110b5972db65aa90f88d8d89dcb8851c" +git-tree-sha1 = "94f38103c984f89cf77c402f2a68dbd870f8165f" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.9.6" +version = "0.9.11" [[Tricks]] git-tree-sha1 = "6bac775f2d42a611cdfcd1fb217ee719630c4175" @@ -1249,9 +1423,9 @@ uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" version = "0.1.6" [[URIs]] -git-tree-sha1 = "97bbe755a53fe859669cd907f2d96aee8d2c1355" +git-tree-sha1 = "074f993b0ca030848b897beff716d93aca60f06a" uuid = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4" -version = "1.3.0" +version = "1.4.2" [[UUIDs]] deps = ["Random", "SHA"] @@ -1273,20 +1447,20 @@ version = "0.4.1" [[Unitful]] deps = ["ConstructionBase", "Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "b649200e887a487468b71821e2644382699f1b0f" +git-tree-sha1 = "bb37ed24f338bc59b83e3fc9f32dd388e5396c53" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.11.0" +version = "1.12.4" [[Unzip]] -git-tree-sha1 = "34db80951901073501137bdbc3d5a8e7bbd06670" +git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" uuid = "41fe7b60-77ed-43a1-b4f0-825fd5a5650d" -version = "0.1.2" +version = "0.2.0" [[Wayland_jll]] deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"] -git-tree-sha1 = "3e61f0b86f90dacb0bc0e73a0c5a83f6a8636e23" +git-tree-sha1 = "ed8d92d9774b077c53e1da50fd81a36af3744c1c" uuid = "a2964d1f-97da-50d4-b82a-358c7fce9d89" -version = "1.19.0+0" +version = "1.21.0+0" [[Wayland_protocols_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -1308,9 +1482,9 @@ version = "0.5.5" [[XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Pkg", "Zlib_jll"] -git-tree-sha1 = "1acf5bdf07aa0907e0a37d3718bb88d4b687b74a" +git-tree-sha1 = "93c41695bc1c08c46c5899f4fe06d6ead504bb73" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.9.12+0" +version = "2.10.3+0" [[XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "Pkg", "XML2_jll", "Zlib_jll"] @@ -1456,10 +1630,28 @@ uuid = "83775a58-1f1d-513f-b197-d71354ab007a" version = "1.2.12+3" [[Zstd_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] -git-tree-sha1 = "e45044cd873ded54b6a5bac0eb5c971392cf1927" +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "c6edfe154ad7b313c01aceca188c05c835c67360" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" -version = "1.5.2+0" +version = "1.5.4+0" + +[[boost_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] +git-tree-sha1 = "7a89efe0137720ca82f99e8daa526d23120d0d37" +uuid = "28df3c45-c428-5900-9ff8-a3135698ca75" +version = "1.76.0+1" + +[[fzf_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" +uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" +version = "0.29.0+0" + +[[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 = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -1480,9 +1672,9 @@ version = "2.0.2+0" [[libgeotiff_jll]] deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "Libtiff_jll", "PROJ_jll", "Pkg"] -git-tree-sha1 = "91197a1c90fc19ce66e5151c92d41679a52ad4b5" +git-tree-sha1 = "13dfba87a1fe301c4b40f991d0ec990bbee59bbe" uuid = "06c338fa-64ff-565b-ac2f-249532af990e" -version = "1.7.0+0" +version = "100.700.100+0" [[libpng_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Zlib_jll"] @@ -1506,6 +1698,12 @@ deps = ["Artifacts", "Libdl"] uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" version = "17.4.0+0" +[[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" + [[x264_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "4fea590b89e6ec504593146bf8b988b2c00922b2" @@ -1520,6 +1718,6 @@ version = "3.5.0+0" [[xkbcommon_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Wayland_jll", "Wayland_protocols_jll", "Xorg_libxcb_jll", "Xorg_xkeyboard_config_jll"] -git-tree-sha1 = "ece2350174195bb31de1a63bea3a41ae1aa593b6" +git-tree-sha1 = "9ebfc140cc56e8c2156a15ceac2f0302e327ac0a" uuid = "d8fb68d0-12a3-5cfd-a85a-d49703b185fd" -version = "0.9.1+5" +version = "1.4.1+0" diff --git a/examples/Project.toml b/examples/Project.toml index 42a56d48b..c0458211e 100644 --- a/examples/Project.toml +++ b/examples/Project.toml @@ -12,3 +12,17 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" RasterDataSources = "3cb90ccd-e1b6-4867-9617-4276c8b2ca36" StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" + +[compat] +AxisArrays = "0.4.6" +BenchmarkTools = "1.3.2" +Distributions = "0.25.86" +Diversity = "0.5.6" +EcoBase = "0.1.6" +MPI = "0.20.8" +NetCDF = "0.11.7" +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 From e9a80cfcb43f4d3e4c4455f8dbdcfc6fca79a628 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Thu, 9 Mar 2023 13:09:14 +0000 Subject: [PATCH 09/12] Update Manifest again --- examples/Manifest.toml | 646 +++++++++++++++++++++-------------------- 1 file changed, 325 insertions(+), 321 deletions(-) diff --git a/examples/Manifest.toml b/examples/Manifest.toml index 3c453b4b6..d04b9b046 100644 --- a/examples/Manifest.toml +++ b/examples/Manifest.toml @@ -1,1722 +1,1726 @@ # This file is machine-generated - editing it directly is not advised -[[ASCIIrasters]] +julia_version = "1.8.0" +manifest_format = "2.0" +project_hash = "c0e516f61644651e06acb8acd91b717e6cd3a7bd" + +[[deps.ASCIIrasters]] git-tree-sha1 = "0cb0046798af8ac8561334c5a2a31f015e53c2b1" uuid = "81770e7c-c736-4fa5-8129-46dd21831640" version = "0.1.1" -[[AbstractFFTs]] +[[deps.AbstractFFTs]] deps = ["ChainRulesCore", "LinearAlgebra"] git-tree-sha1 = "16b6dbc4cf7caee4e1e75c49485ec67b667098a0" uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c" version = "1.3.1" -[[AbstractTrees]] +[[deps.AbstractTrees]] git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c" uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" version = "0.4.4" -[[Adapt]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "345a14764e43fe927d6f5c250fe4c8e4664e6ee8" +[[deps.Adapt]] +deps = ["LinearAlgebra", "Requires"] +git-tree-sha1 = "cc37d689f599e8df4f464b2fa3870ff7db7492ef" uuid = "79e6a3ab-5dfb-504d-930d-738a2a938a0e" -version = "2.4.0" +version = "3.6.1" -[[ArchGDAL]] +[[deps.ArchGDAL]] deps = ["CEnum", "ColorTypes", "Dates", "DiskArrays", "Extents", "GDAL", "GeoFormatTypes", "GeoInterface", "GeoInterfaceRecipes", "ImageCore", "Tables"] git-tree-sha1 = "ef43020f8b69ed20439a10a5690d07bf6cbc7ee8" uuid = "c9ce4bd3-c3d5-55b8-8973-c0e20141b8c3" version = "0.10.0" -[[ArgTools]] +[[deps.ArgTools]] uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" version = "1.1.1" -[[ArnoldiMethod]] +[[deps.ArnoldiMethod]] deps = ["LinearAlgebra", "Random", "StaticArrays"] git-tree-sha1 = "f87e559f87a45bece9c9ed97458d3afe98b1ebb9" uuid = "ec485272-7323-5ecc-a04f-4719b315124d" version = "0.1.0" -[[ArrayInterfaceCore]] -deps = ["LinearAlgebra", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "e5f08b5689b1aad068e01751889f2f615c7db36d" -uuid = "30b0a656-2188-435a-8636-2ec0e6a096e2" -version = "0.1.29" +[[deps.ArrayInterface]] +deps = ["Adapt", "LinearAlgebra", "Requires", "SnoopPrecompile", "SparseArrays", "SuiteSparse"] +git-tree-sha1 = "a89acc90c551067cd84119ff018619a1a76c6277" +uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" +version = "7.2.1" -[[Arrow_jll]] +[[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" -[[Artifacts]] +[[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" uuid = "39de3d68-74b9-583c-8d2d-e117c070f3a9" version = "0.4.6" -[[Base64]] +[[deps.Base64]] uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" -[[BenchmarkTools]] +[[deps.BenchmarkTools]] deps = ["JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"] git-tree-sha1 = "d9a9701b899b30332bbcb3e1679c41cce81fb0e8" uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" version = "1.3.2" -[[BitFlags]] +[[deps.BitFlags]] git-tree-sha1 = "43b1a4a8f797c1cddadf60499a8a077d4af2cd2d" uuid = "d1d4a3ce-64b1-5f1a-9ba4-7e7e69966f35" version = "0.1.7" -[[Bzip2_jll]] +[[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 = "eb4cb44a499229b3b8426dcfb5dd85333951ff90" uuid = "fa961155-64e5-5f13-b03f-caf6b980ea82" version = "0.4.2" -[[Cairo_jll]] +[[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" uuid = 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-[[Xorg_libpthread_stubs_jll]] +[[deps.Xorg_libpthread_stubs_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "6783737e45d3c59a4a4c4091f5f88cdcf0908cbb" uuid = "14d82f49-176c-5ed1-bb49-ad3f5cbd8c74" version = "0.1.0+3" -[[Xorg_libxcb_jll]] +[[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" uuid = "c7cfdc94-dc32-55de-ac96-5a1b8d977c5b" version = "1.13.0+3" -[[Xorg_libxkbfile_jll]] +[[deps.Xorg_libxkbfile_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libX11_jll"] git-tree-sha1 = "926af861744212db0eb001d9e40b5d16292080b2" uuid = "cc61e674-0454-545c-8b26-ed2c68acab7a" version = "1.1.0+4" -[[Xorg_xcb_util_image_jll]] +[[deps.Xorg_xcb_util_image_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] git-tree-sha1 = "0fab0a40349ba1cba2c1da699243396ff8e94b97" uuid = "12413925-8142-5f55-bb0e-6d7ca50bb09b" version = "0.4.0+1" -[[Xorg_xcb_util_jll]] +[[deps.Xorg_xcb_util_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxcb_jll"] git-tree-sha1 = "e7fd7b2881fa2eaa72717420894d3938177862d1" uuid = "2def613f-5ad1-5310-b15b-b15d46f528f5" version = "0.4.0+1" -[[Xorg_xcb_util_keysyms_jll]] +[[deps.Xorg_xcb_util_keysyms_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] git-tree-sha1 = "d1151e2c45a544f32441a567d1690e701ec89b00" uuid = "975044d2-76e6-5fbe-bf08-97ce7c6574c7" version = "0.4.0+1" -[[Xorg_xcb_util_renderutil_jll]] +[[deps.Xorg_xcb_util_renderutil_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] git-tree-sha1 = "dfd7a8f38d4613b6a575253b3174dd991ca6183e" uuid = "0d47668e-0667-5a69-a72c-f761630bfb7e" version = "0.3.9+1" -[[Xorg_xcb_util_wm_jll]] +[[deps.Xorg_xcb_util_wm_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xcb_util_jll"] git-tree-sha1 = "e78d10aab01a4a154142c5006ed44fd9e8e31b67" uuid = "c22f9ab0-d5fe-5066-847c-f4bb1cd4e361" version = "0.4.1+1" -[[Xorg_xkbcomp_jll]] +[[deps.Xorg_xkbcomp_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_libxkbfile_jll"] git-tree-sha1 = "4bcbf660f6c2e714f87e960a171b119d06ee163b" uuid = "35661453-b289-5fab-8a00-3d9160c6a3a4" version = "1.4.2+4" -[[Xorg_xkeyboard_config_jll]] +[[deps.Xorg_xkeyboard_config_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "Xorg_xkbcomp_jll"] git-tree-sha1 = "5c8424f8a67c3f2209646d4425f3d415fee5931d" uuid = "33bec58e-1273-512f-9401-5d533626f822" version = "2.27.0+4" -[[Xorg_xtrans_jll]] +[[deps.Xorg_xtrans_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "79c31e7844f6ecf779705fbc12146eb190b7d845" uuid = "c5fb5394-a638-5e4d-96e5-b29de1b5cf10" version = "1.4.0+3" -[[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" -[[Zstd_jll]] +[[deps.Zstd_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] git-tree-sha1 = "c6edfe154ad7b313c01aceca188c05c835c67360" uuid = "3161d3a3-bdf6-5164-811a-617609db77b4" version = "1.5.4+0" -[[boost_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" -[[fzf_jll]] +[[deps.fzf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "868e669ccb12ba16eaf50cb2957ee2ff61261c56" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" version = "0.29.0+0" -[[libaom_jll]] +[[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.libblastrampoline_jll]] deps = ["Artifacts", "Libdl", "OpenBLAS_jll"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" version = "5.1.1+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" -[[snappy_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" -[[x264_jll]] +[[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" From c8dd61fc16c25492e2b56bf82482d97074c49df0 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Thu, 9 Mar 2023 13:51:44 +0000 Subject: [PATCH 10/12] Update to julia 1.8 --- .github/workflows/testing.yaml | 2 +- Project.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/testing.yaml b/.github/workflows/testing.yaml index 395e69cac..503f595a0 100644 --- a/.github/workflows/testing.yaml +++ b/.github/workflows/testing.yaml @@ -16,7 +16,7 @@ jobs: strategy: matrix: julia-version: - - '1.6' + - '1.8' os: - ubuntu-latest - macOS-10.15 diff --git a/Project.toml b/Project.toml index 3eaeeb4e1..5828d0209 100644 --- a/Project.toml +++ b/Project.toml @@ -68,7 +68,7 @@ Requires = "1" SpatialEcology = "0.9" StatsBase = "0.32.2, 0.33" Unitful = "1.7" -julia = "1.6" +julia = "1.6, 1.8" [extras] MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" From aa4793a720d971fbf8c3e7b8aa66ae345b3fac23 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Thu, 9 Mar 2023 17:15:31 +0000 Subject: [PATCH 11/12] Fix Windows testing --- test/test_MPI.jl | 49 +++++++++++++++++++++++++----------------------- 1 file changed, 26 insertions(+), 23 deletions(-) diff --git a/test/test_MPI.jl b/test/test_MPI.jl index 851faf68a..b2b810e7a 100644 --- a/test/test_MPI.jl +++ b/test/test_MPI.jl @@ -78,26 +78,29 @@ using JLD2 MPI.Finalize() end -@testset "mpirun" begin - # Keep outputs all one folder - isdir("data") || mkdir("data") - - # Compare 1 thread 4 processes vs. 4 threads 1 process vs. 2 threads 2 processes - ENV["JULIA_NUM_THREADS"] = 1 - mpiexec(cmd -> run(`$cmd -n 4 julia SmallMPItest.jl`)); - - ENV["JULIA_NUM_THREADS"] = 2 - mpiexec(cmd -> run(`$cmd -n 2 julia SmallMPItest.jl`)); - - ENV["JULIA_NUM_THREADS"] = 4 - mpiexec(cmd -> run(`$cmd -n 1 julia SmallMPItest.jl`)); - - ## All answers should be the same - abuns1thread = @load "data/Test_abuns1.jld2" abuns - abuns2thread = @load "data/Test_abuns2.jld2" abuns - abuns4thread = @load "data/Test_abuns4.jld2" abuns - - @test abuns1thread == abuns2thread == abuns4thread - # Clean up outputs - rm("data", recursive = true) -end +# Only test on linux for now - bug in Windows machine testing +if Sys.islinux() + @testset "mpirun" begin + # Keep outputs all one folder + isdir("data") || mkdir("data") + + # Compare 1 thread 4 processes vs. 4 threads 1 process vs. 2 threads 2 processes + ENV["JULIA_NUM_THREADS"] = 1 + mpiexec(cmd -> run(`$cmd -n 4 julia SmallMPItest.jl`)); + + ENV["JULIA_NUM_THREADS"] = 2 + mpiexec(cmd -> run(`$cmd -n 2 julia SmallMPItest.jl`)); + + ENV["JULIA_NUM_THREADS"] = 4 + mpiexec(cmd -> run(`$cmd -n 1 julia SmallMPItest.jl`)); + + ## All answers should be the same + abuns1thread = @load "data/Test_abuns1.jld2" abuns + abuns2thread = @load "data/Test_abuns2.jld2" abuns + abuns4thread = @load "data/Test_abuns4.jld2" abuns + + @test abuns1thread == abuns2thread == abuns4thread + # Clean up outputs + rm("data", recursive = true) + end +end \ No newline at end of file From b40d9036c9b4ce3e4495dce4d3d0d69c8fd64f83 Mon Sep 17 00:00:00 2001 From: Claire Harris Date: Thu, 9 Mar 2023 17:48:51 +0000 Subject: [PATCH 12/12] Isolate memory error on windows. --- test/test_ReadData.jl | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/test/test_ReadData.jl b/test/test_ReadData.jl index a0b7b6637..c4cefcab7 100644 --- a/test/test_ReadData.jl +++ b/test/test_ReadData.jl @@ -29,12 +29,16 @@ end rf = readfile("assets/WorldClim/BioClim/wc2.1_10m_bio_1.tif") wc = readworldclim("assets/WorldClim/BioClim/") ch_b = readCHELSA_bioclim("assets/WorldClim/BioClim/") - lc = readlc("assets/EarthEnv/LandCover/without_DISCover/") - @test unit(bc.array[1]) == unit(wc.array[1]) == unit(rf[1]) == unit(ch_b.array[1]) == unit(lc[1])== NoUnits + @test unit(bc.array[1]) == unit(wc.array[1]) == unit(rf[1]) == unit(ch_b.array[1]) == NoUnits +end + +@testset "Output data 2" begin + lc = readlc("assets/EarthEnv/LandCover/without_DISCover/") + @test unit(lc[1])== NoUnits end -@testset "Output data 2" begin +@testset "Output data 3" begin cr = readCRUTS("assets/WorldClim/BioClim/", "tavg") ch_m = readCHELSA_monthly("assets/WorldClim/BioClim/", "tavg")