From 568a9c22fab730adb9aeac58fa5405da1bacf350 Mon Sep 17 00:00:00 2001 From: AlexisRenchon Date: Thu, 29 Aug 2024 15:58:08 -0700 Subject: [PATCH] WIP --- docs/Manifest.toml | 512 +++++++++++++++++++++--------------- docs/Project.toml | 2 + docs/src/getting-started.md | 164 +++++++----- docs/src/index.md | 95 ++----- 4 files changed, 412 insertions(+), 361 deletions(-) diff --git a/docs/Manifest.toml b/docs/Manifest.toml index f6da9f57f8..8e9bfe768d 100644 --- a/docs/Manifest.toml +++ b/docs/Manifest.toml @@ -1,13 +1,13 @@ # This file is machine-generated - editing it directly is not advised -julia_version = "1.10.4" +julia_version = "1.10.5" manifest_format = "2.0" -project_hash = "6c3f79ccae513840cc13b9ac947575c2305b507f" +project_hash = "6b19e20727d983c28286d493d461a6afa5ff8e8c" [[deps.ADTypes]] -git-tree-sha1 = "7a6b285f217ba92b5b474b783b4c2e8cf8218aaa" +git-tree-sha1 = "99a6f5d0ce1c7c6afdb759daa30226f71c54f6b0" uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b" -version = "1.5.3" +version = "1.7.1" weakdeps = ["ChainRulesCore", "EnzymeCore"] [deps.ADTypes.extensions] @@ -19,6 +19,16 @@ git-tree-sha1 = "574baf8110975760d391c710b6341da1afa48d8c" uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9" version = "0.0.1" +[[deps.About]] +deps = ["InteractiveUtils", "JuliaSyntaxHighlighting", "PrecompileTools", "StyledStrings"] +git-tree-sha1 = "3a94c01a1d7678f1c29b7d97216f5046f1ed1768" +uuid = "69d22d85-9f48-4c46-bbbe-7ad8341ff72a" +version = "1.0.0" +weakdeps = ["Pkg"] + + [deps.About.extensions] + PkgExt = "Pkg" + [[deps.AbstractFFTs]] deps = ["LinearAlgebra"] git-tree-sha1 = "d92ad398961a3ed262d8bf04a1a2b8340f915fef" @@ -37,9 +47,9 @@ version = "0.4.5" [[deps.Accessors]] deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "LinearAlgebra", "MacroTools", "Markdown", "Test"] -git-tree-sha1 = "c0d491ef0b135fd7d63cbc6404286bc633329425" +git-tree-sha1 = "f61b15be1d76846c0ce31d3fcfac5380ae53db6a" uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697" -version = "0.1.36" +version = "0.1.37" [deps.Accessors.extensions] AccessorsAxisKeysExt = "AxisKeys" @@ -66,6 +76,11 @@ weakdeps = ["StaticArrays"] [deps.Adapt.extensions] AdaptStaticArraysExt = "StaticArrays" +[[deps.AdaptivePredicates]] +git-tree-sha1 = "7d5da5dd472490d048b081ca1bda4a7821b06456" +uuid = "35492f91-a3bd-45ad-95db-fcad7dcfedb7" +version = "1.1.1" + [[deps.AliasTables]] deps = ["PtrArrays", "Random"] git-tree-sha1 = "9876e1e164b144ca45e9e3198d0b689cadfed9ff" @@ -94,10 +109,10 @@ uuid = "ec485272-7323-5ecc-a04f-4719b315124d" version = "0.4.0" [[deps.ArrayInterface]] -deps = ["Adapt", "LinearAlgebra", "SparseArrays", "SuiteSparse"] -git-tree-sha1 = "5c9b74c973181571deb6442d41e5c902e6b9f38e" +deps = ["Adapt", "LinearAlgebra"] +git-tree-sha1 = "f54c23a5d304fb87110de62bace7777d59088c34" uuid = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9" -version = "7.12.0" +version = "7.15.0" [deps.ArrayInterface.extensions] ArrayInterfaceBandedMatricesExt = "BandedMatrices" @@ -107,6 +122,7 @@ version = "7.12.0" ArrayInterfaceChainRulesExt = "ChainRules" ArrayInterfaceGPUArraysCoreExt = "GPUArraysCore" ArrayInterfaceReverseDiffExt = "ReverseDiff" + ArrayInterfaceSparseArraysExt = "SparseArrays" ArrayInterfaceStaticArraysCoreExt = "StaticArraysCore" ArrayInterfaceTrackerExt = "Tracker" @@ -118,14 +134,15 @@ version = "7.12.0" ChainRules = "082447d4-558c-5d27-93f4-14fc19e9eca2" GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" [[deps.ArrayLayouts]] deps = ["FillArrays", "LinearAlgebra"] -git-tree-sha1 = "8556500c18fcad8b4c44058e23fbc4a36143f6be" +git-tree-sha1 = "0dd7edaff278e346eb0ca07a7e75c9438408a3ce" uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a" -version = "1.10.1" +version = "1.10.3" weakdeps = ["SparseArrays"] [deps.ArrayLayouts.extensions] @@ -172,9 +189,9 @@ version = "0.5.0" [[deps.BandedMatrices]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "PrecompileTools"] -git-tree-sha1 = "71f605effb24081b09cae943ba39ef9ca90c04f4" +git-tree-sha1 = "88d4a97082bc70fad702f42302a8bd21079b8963" uuid = "aae01518-5342-5314-be14-df237901396f" -version = "1.7.2" +version = "1.7.3" weakdeps = ["SparseArrays"] [deps.BandedMatrices.extensions] @@ -221,9 +238,13 @@ version = "0.1.6" [[deps.BlockArrays]] deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra"] -git-tree-sha1 = "9a9610fbe5779636f75229e423e367124034af41" +git-tree-sha1 = "5c0ffe1dff8cb7112de075f1b1cb32191675fcba" uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" -version = "0.16.43" +version = "1.1.0" +weakdeps = ["BandedMatrices"] + + [deps.BlockArrays.extensions] + BlockArraysBandedMatricesExt = "BandedMatrices" [[deps.Blosc_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Zlib_jll", "Zstd_jll"] @@ -277,9 +298,9 @@ version = "0.10.14" [[deps.CUDA]] deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CUDA_Driver_jll", "CUDA_Runtime_Discovery", "CUDA_Runtime_jll", "Crayons", "DataFrames", "ExprTools", "GPUArrays", "GPUCompiler", "KernelAbstractions", "LLVM", "LLVMLoopInfo", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "NVTX", "Preferences", "PrettyTables", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "StaticArrays", "Statistics"] -git-tree-sha1 = "6e945e876652f2003e6ca74e19a3c45017d3e9f6" +git-tree-sha1 = "fdd9dfb67dfefd548f51000cc400bb51003de247" uuid = "052768ef-5323-5732-b1bb-66c8b64840ba" -version = "5.4.2" +version = "5.4.3" weakdeps = ["ChainRulesCore", "EnzymeCore", "SpecialFunctions"] [deps.CUDA.extensions] @@ -288,10 +309,10 @@ weakdeps = ["ChainRulesCore", "EnzymeCore", "SpecialFunctions"] SpecialFunctionsExt = "SpecialFunctions" [[deps.CUDA_Driver_jll]] -deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"] -git-tree-sha1 = "97df9d4d6be8ac6270cb8fd3b8fc413690820cbd" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] +git-tree-sha1 = "325058b426c2b421e3d2df3d5fa646d72d2e3e7e" uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc" -version = "0.9.1+1" +version = "0.9.2+0" [[deps.CUDA_Runtime_Discovery]] deps = ["Libdl"] @@ -313,9 +334,9 @@ version = "9.0.0+1" [[deps.Cairo]] deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"] -git-tree-sha1 = "d0b3f8b4ad16cb0a2988c6788646a5e6a17b6b1b" +git-tree-sha1 = "7b6ad8c35f4bc3bca8eb78127c8b99719506a5fb" uuid = "159f3aea-2a34-519c-b102-8c37f9878175" -version = "1.0.5" +version = "1.1.0" [[deps.CairoMakie]] deps = ["CRC32c", "Cairo", "Cairo_jll", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"] @@ -329,12 +350,6 @@ git-tree-sha1 = "a2f1c8c668c8e3cb4cca4e57a8efdb09067bb3fd" uuid = "83423d85-b0ee-5818-9007-b63ccbeb887a" version = "1.18.0+2" -[[deps.Calculus]] -deps = ["LinearAlgebra"] -git-tree-sha1 = "f641eb0a4f00c343bbc32346e1217b86f3ce9dad" -uuid = "49dc2e85-a5d0-5ad3-a950-438e2897f1b9" -version = "0.5.1" - [[deps.ChainRules]] deps = ["Adapt", "ChainRulesCore", "Compat", "Distributed", "GPUArraysCore", "IrrationalConstants", "LinearAlgebra", "Random", "RealDot", "SparseArrays", "SparseInverseSubset", "Statistics", "StructArrays", "SuiteSparse"] git-tree-sha1 = "227985d885b4dbce5e18a96f9326ea1e836e5a03" @@ -352,9 +367,9 @@ weakdeps = ["SparseArrays"] ChainRulesCoreSparseArraysExt = "SparseArrays" [[deps.ClimaComms]] -git-tree-sha1 = "2ca8c9ca6131a7be8ca262e6db79bc7aa94ab597" +git-tree-sha1 = "ec303a4a66dc0a0ebe15a639a7e685afeaa0daef" uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d" -version = "0.6.3" +version = "0.6.4" [deps.ClimaComms.extensions] ClimaCommsCUDAExt = "CUDA" @@ -377,15 +392,15 @@ weakdeps = ["CUDA", "Krylov"] [[deps.ClimaDiagnostics]] deps = ["Accessors", "ClimaComms", "ClimaCore", "Dates", "NCDatasets", "SciMLBase"] -git-tree-sha1 = "228ff3bc4dbd7329ef054f9bfbbe34075234ca25" +git-tree-sha1 = "4f8abbf3af5a78b36bc40a33ef7e3fa1d3e8f138" uuid = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f" -version = "0.2.3" +version = "0.2.4" [[deps.ClimaLand]] -deps = ["Adapt", "ArtifactWrappers", "ClimaComms", "ClimaCore", "ClimaDiagnostics", "ClimaUtilities", "DataFrames", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "IntervalSets", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities"] +deps = ["ArtifactWrappers", "ClimaComms", "ClimaCore", "ClimaDiagnostics", "ClimaUtilities", "DataFrames", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "IntervalSets", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics"] path = ".." uuid = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532" -version = "0.14.0" +version = "0.14.2" weakdeps = ["CSV", "CUDA", "ClimaParams", "Flux", "HTTP", "StatsBase", "cuDNN"] [deps.ClimaLand.extensions] @@ -446,9 +461,9 @@ version = "0.1.13" [[deps.CodecZlib]] deps = ["TranscodingStreams", "Zlib_jll"] -git-tree-sha1 = "b8fe8546d52ca154ac556809e10c75e6e7430ac8" +git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759" uuid = "944b1d66-785c-5afd-91f1-9de20f533193" -version = "0.7.5" +version = "0.7.6" [[deps.ColorBrewer]] deps = ["Colors", "JSON", "Test"] @@ -458,9 +473,9 @@ version = "0.4.0" [[deps.ColorSchemes]] deps = ["ColorTypes", "ColorVectorSpace", "Colors", "FixedPointNumbers", "PrecompileTools", "Random"] -git-tree-sha1 = "4b270d6465eb21ae89b732182c20dc165f8bf9f2" +git-tree-sha1 = "b5278586822443594ff615963b0c09755771b3e0" uuid = "35d6a980-a343-548e-a6ea-1d62b119f2f4" -version = "3.25.0" +version = "3.26.0" [[deps.ColorTypes]] deps = ["FixedPointNumbers", "Random"] @@ -496,16 +511,21 @@ uuid = "38540f10-b2f7-11e9-35d8-d573e4eb0ff2" version = "0.2.4" [[deps.CommonSubexpressions]] -deps = ["MacroTools", "Test"] -git-tree-sha1 = "7b8a93dba8af7e3b42fecabf646260105ac373f7" +deps = ["MacroTools"] +git-tree-sha1 = "cda2cfaebb4be89c9084adaca7dd7333369715c5" uuid = "bbf7d656-a473-5ed7-a52c-81e309532950" -version = "0.3.0" +version = "0.3.1" + +[[deps.CommonWorldInvalidations]] +git-tree-sha1 = "ae52d1c52048455e85a387fbee9be553ec2b68d0" +uuid = "f70d9fcc-98c5-4d4a-abd7-e4cdeebd8ca8" +version = "1.0.0" [[deps.Compat]] deps = ["TOML", "UUIDs"] -git-tree-sha1 = "b1c55339b7c6c350ee89f2c1604299660525b248" +git-tree-sha1 = "8ae8d32e09f0dcf42a36b90d4e17f5dd2e4c4215" uuid = "34da2185-b29b-5c13-b0c7-acf172513d20" -version = "4.15.0" +version = "4.16.0" weakdeps = ["Dates", "LinearAlgebra"] [deps.Compat.extensions] @@ -538,9 +558,9 @@ version = "2.4.2" [[deps.ConstructionBase]] deps = ["LinearAlgebra"] -git-tree-sha1 = "260fd2400ed2dab602a7c15cf10c1933c59930a2" +git-tree-sha1 = "a33b7ced222c6165f624a3f2b55945fac5a598d9" uuid = "187b0558-2788-49d3-abe0-74a17ed4e7c9" -version = "1.5.5" +version = "1.5.7" weakdeps = ["IntervalSets", "StaticArrays"] [deps.ConstructionBase.extensions] @@ -601,16 +621,22 @@ version = "1.0.0" deps = ["Printf"] uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +[[deps.Dbus_jll]] +deps = ["Artifacts", "Expat_jll", "JLLWrappers", "Libdl"] +git-tree-sha1 = "fc173b380865f70627d7dd1190dc2fce6cc105af" +uuid = "ee1fde0b-3d02-5ea6-8484-8dfef6360eab" +version = "1.14.10+0" + [[deps.DefineSingletons]] git-tree-sha1 = "0fba8b706d0178b4dc7fd44a96a92382c9065c2c" uuid = "244e2a9f-e319-4986-a169-4d1fe445cd52" version = "0.1.2" [[deps.DelaunayTriangulation]] -deps = ["EnumX", "ExactPredicates", "Random"] -git-tree-sha1 = "b0cb128d2e100646573e1da8565b02491fddb5ef" +deps = ["AdaptivePredicates", "EnumX", "ExactPredicates", "Random"] +git-tree-sha1 = "b5f1c6532d2ea71e99b74231b0a3d53fba846ced" uuid = "927a84f5-c5f4-47a5-9785-b46e178433df" -version = "1.0.4" +version = "1.1.3" [[deps.DelimitedFiles]] deps = ["Mmap"] @@ -652,9 +678,9 @@ version = "6.151.5" [[deps.DiffEqCallbacks]] deps = ["DataStructures", "DiffEqBase", "ForwardDiff", "Functors", "LinearAlgebra", "Markdown", "NonlinearSolve", "Parameters", "RecipesBase", "RecursiveArrayTools", "SciMLBase", "StaticArraysCore"] -git-tree-sha1 = "c959cfd2657d16beada157a74d52269e8556500e" +git-tree-sha1 = "befc86364d9b36abc6d874f91ab5d7b4d5e6bb62" uuid = "459566f4-90b8-5000-8ac3-15dfb0a30def" -version = "3.6.2" +version = "3.8.0" [deps.DiffEqCallbacks.weakdeps] OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" @@ -674,9 +700,9 @@ version = "1.15.1" [[deps.DifferentiationInterface]] deps = ["ADTypes", "Compat", "DocStringExtensions", "FillArrays", "LinearAlgebra", "PackageExtensionCompat", "SparseArrays", "SparseMatrixColorings"] -git-tree-sha1 = "695217e97ee1ce0248f4a56c14af88ba33c585fd" +git-tree-sha1 = "06955b4e80eff01df10552ccf0226571bde94d49" uuid = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63" -version = "0.5.7" +version = "0.5.14" [deps.DifferentiationInterface.extensions] DifferentiationInterfaceChainRulesCoreExt = "ChainRulesCore" @@ -720,9 +746,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b" [[deps.Distributions]] deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"] -git-tree-sha1 = "9c405847cc7ecda2dc921ccf18b47ca150d7317e" +git-tree-sha1 = "0e0a1264b0942f1f3abb2b30891f2a590cc652ac" uuid = "31c24e10-a181-5473-b8eb-7969acd0382f" -version = "0.25.109" +version = "0.25.110" [deps.Distributions.extensions] DistributionsChainRulesCoreExt = "ChainRulesCore" @@ -751,12 +777,6 @@ deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" version = "1.6.0" -[[deps.DualNumbers]] -deps = ["Calculus", "NaNMath", "SpecialFunctions"] -git-tree-sha1 = "5837a837389fccf076445fce071c8ddaea35a566" -uuid = "fa6b7ba4-c1ee-5f82-b5fc-ecf0adba8f74" -version = "0.6.8" - [[deps.EarCut_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] git-tree-sha1 = "e3290f2d49e661fbd94046d7e3726ffcb2d41053" @@ -774,9 +794,9 @@ uuid = "4e289a0a-7415-4d19-859d-a7e5c4648b56" version = "1.0.4" [[deps.EnzymeCore]] -git-tree-sha1 = "3a3177ba05b4763234819060fb6c2e1613379ca6" +git-tree-sha1 = "8f205a601760f4798a10f138c3940f0451d95188" uuid = "f151be2c-9106-41f4-ab19-57ee4f262869" -version = "0.7.6" +version = "0.7.8" weakdeps = ["Adapt"] [deps.EnzymeCore.extensions] @@ -847,9 +867,9 @@ version = "3.3.10+0" [[deps.FLoops]] deps = ["BangBang", "Compat", "FLoopsBase", "InitialValues", "JuliaVariables", "MLStyle", "Serialization", "Setfield", "Transducers"] -git-tree-sha1 = "ffb97765602e3cbe59a0589d237bf07f245a8576" +git-tree-sha1 = "0a2e5873e9a5f54abb06418d57a8df689336a660" uuid = "cc61a311-1640-44b5-9fba-1b764f453329" -version = "0.2.1" +version = "0.2.2" [[deps.FLoopsBase]] deps = ["ContextVariablesX"] @@ -859,9 +879,9 @@ version = "0.1.1" [[deps.FastBroadcast]] deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"] -git-tree-sha1 = "bd19de6fe8a3b18888f35e79832f97544684caa7" +git-tree-sha1 = "ab1b34570bcdf272899062e1a56285a53ecaae08" uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898" -version = "0.3.4" +version = "0.3.5" [[deps.FastClosures]] git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef" @@ -903,9 +923,9 @@ uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" [[deps.FillArrays]] deps = ["LinearAlgebra"] -git-tree-sha1 = "0653c0a2396a6da5bc4766c43041ef5fd3efbe57" +git-tree-sha1 = "fd0002c0b5362d7eb952450ad5eb742443340d6e" uuid = "1a297f60-69ca-5386-bcde-b61e274b549b" -version = "1.11.0" +version = "1.12.0" weakdeps = ["PDMats", "SparseArrays", "Statistics"] [deps.FillArrays.extensions] @@ -914,10 +934,10 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"] FillArraysStatisticsExt = "Statistics" [[deps.FiniteDiff]] -deps = ["ArrayInterface", "LinearAlgebra", "Requires", "Setfield", "SparseArrays"] -git-tree-sha1 = "2de436b72c3422940cbe1367611d137008af7ec3" +deps = ["ArrayInterface", "LinearAlgebra", "Setfield", "SparseArrays"] +git-tree-sha1 = "f9219347ebf700e77ca1d48ef84e4a82a6701882" uuid = "6a86dc24-6348-571c-b903-95158fe2bd41" -version = "2.23.1" +version = "2.24.0" [deps.FiniteDiff.extensions] FiniteDiffBandedMatricesExt = "BandedMatrices" @@ -1017,19 +1037,19 @@ version = "0.1.3" [[deps.Functors]] deps = ["LinearAlgebra"] -git-tree-sha1 = "8a66c07630d6428eaab3506a0eabfcf4a9edea05" +git-tree-sha1 = "64d8e93700c7a3f28f717d265382d52fac9fa1c1" uuid = "d9f16b24-f501-4c13-a1f2-28368ffc5196" -version = "0.4.11" +version = "0.4.12" [[deps.Future]] deps = ["Random"] uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820" [[deps.GLFW_jll]] -deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "xkbcommon_jll"] -git-tree-sha1 = "3f74912a156096bd8fdbef211eff66ab446e7297" +deps = ["Artifacts", "JLLWrappers", "Libdl", "Libglvnd_jll", "Xorg_libXcursor_jll", "Xorg_libXi_jll", "Xorg_libXinerama_jll", "Xorg_libXrandr_jll", "libdecor_jll", "xkbcommon_jll"] +git-tree-sha1 = "532f9126ad901533af1d4f5c198867227a7bb077" uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89" -version = "3.4.0+0" +version = "3.4.0+1" [[deps.GMP_jll]] deps = ["Artifacts", "Libdl"] @@ -1038,9 +1058,9 @@ version = "6.2.1+6" [[deps.GPUArrays]] deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"] -git-tree-sha1 = "04661708f5301394a1f1be86a07a89e835900db6" +git-tree-sha1 = "62ee71528cca49be797076a76bdc654a170a523e" uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7" -version = "10.2.3" +version = "10.3.1" [[deps.GPUArraysCore]] deps = ["Adapt"] @@ -1049,22 +1069,22 @@ uuid = "46192b85-c4d5-4398-a991-12ede77f4527" version = "0.1.6" [[deps.GPUCompiler]] -deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"] -git-tree-sha1 = "518ebd058c9895de468a8c255797b0c53fdb44dd" +deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Preferences", "Scratch", "Serialization", "TOML", "TimerOutputs", "UUIDs"] +git-tree-sha1 = "ab29216184312f99ff957b32cd63c2fe9c928b91" uuid = "61eb1bfa-7361-4325-ad38-22787b887f55" -version = "0.26.5" +version = "0.26.7" [[deps.GR]] -deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] -git-tree-sha1 = "3e527447a45901ea392fe12120783ad6ec222803" +deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Qt6Wayland_jll", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"] +git-tree-sha1 = "629693584cef594c3f6f99e76e7a7ad17e60e8d5" uuid = "28b8d3ca-fb5f-59d9-8090-bfdbd6d07a71" -version = "0.73.6" +version = "0.73.7" [[deps.GR_jll]] deps = ["Artifacts", "Bzip2_jll", "Cairo_jll", "FFMPEG_jll", "Fontconfig_jll", "FreeType2_jll", "GLFW_jll", "JLLWrappers", "JpegTurbo_jll", "Libdl", "Libtiff_jll", "Pixman_jll", "Qt6Base_jll", "Zlib_jll", "libpng_jll"] -git-tree-sha1 = "182c478a179b267dd7a741b6f8f4c3e0803795d6" +git-tree-sha1 = "a8863b69c2a0859f2c2c87ebdc4c6712e88bdf0d" uuid = "d2c73de3-f751-5644-a686-071e5b155ba9" -version = "0.73.6+0" +version = "0.73.7+0" [[deps.GaussQuadrature]] deps = ["SpecialFunctions"] @@ -1186,15 +1206,15 @@ version = "0.1.17" [[deps.Hwloc_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "1d334207121865ac8c1c97eb7f42d0339e4635bf" +git-tree-sha1 = "5e19e1e4fa3e71b774ce746274364aef0234634e" uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8" -version = "2.11.0+0" +version = "2.11.1+0" [[deps.HypergeometricFunctions]] -deps = ["DualNumbers", "LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] -git-tree-sha1 = "f218fe3736ddf977e0e772bc9a586b2383da2685" +deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"] +git-tree-sha1 = "7c4195be1649ae622304031ed46a2f4df989f1eb" uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a" -version = "0.3.23" +version = "0.3.24" [[deps.IOCapture]] deps = ["Logging", "Random"] @@ -1265,16 +1285,17 @@ uuid = "22cec73e-a1b8-11e9-2c92-598750a2cf9c" version = "0.3.1" [[deps.InlineStrings]] -deps = ["Parsers"] -git-tree-sha1 = "86356004f30f8e737eff143d57d41bd580e437aa" +git-tree-sha1 = "45521d31238e87ee9f9732561bfee12d4eebd52d" uuid = "842dd82b-1e85-43dc-bf29-5d0ee9dffc48" -version = "1.4.1" +version = "1.4.2" [deps.InlineStrings.extensions] ArrowTypesExt = "ArrowTypes" + ParsersExt = "Parsers" [deps.InlineStrings.weakdeps] ArrowTypes = "31f734f8-188a-4ce0-8406-c8a06bd891cd" + Parsers = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0" [[deps.Insolation]] deps = ["Artifacts", "Dates", "DelimitedFiles", "Interpolations"] @@ -1288,9 +1309,9 @@ weakdeps = ["ClimaParams"] [[deps.IntelOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "be50fe8df3acbffa0274a744f1a99d29c45a57f4" +git-tree-sha1 = "14eb2b542e748570b56446f4c50fbfb2306ebc45" uuid = "1d5cc7b8-4909-519e-a0f8-d0f5ad9712d0" -version = "2024.1.0+0" +version = "2024.2.0+0" [[deps.InteractiveUtils]] deps = ["Markdown"] @@ -1324,14 +1345,14 @@ weakdeps = ["Random", "RecipesBase", "Statistics"] IntervalSetsStatisticsExt = "Statistics" [[deps.InverseFunctions]] -deps = ["Test"] -git-tree-sha1 = "e7cbed5032c4c397a6ac23d1493f3289e01231c4" +git-tree-sha1 = "2787db24f4e03daf859c6509ff87764e4182f7d1" uuid = "3587e190-3f89-42d0-90ee-14403ec27112" -version = "0.1.14" -weakdeps = ["Dates"] +version = "0.1.16" +weakdeps = ["Dates", "Test"] [deps.InverseFunctions.extensions] - DatesExt = "Dates" + InverseFunctionsDatesExt = "Dates" + InverseFunctionsTestExt = "Test" [[deps.InvertedIndices]] git-tree-sha1 = "0dc7b50b8d436461be01300fd8cd45aa0274b038" @@ -1361,9 +1382,9 @@ version = "1.0.0" [[deps.JLFzf]] deps = ["Pipe", "REPL", "Random", "fzf_jll"] -git-tree-sha1 = "a53ebe394b71470c7f97c2e7e170d51df21b17af" +git-tree-sha1 = "39d64b09147620f5ffbf6b2d3255be3c901bec63" uuid = "1019f520-868f-41f5-a6de-eb00f4b6a39c" -version = "0.1.7" +version = "0.1.8" [[deps.JLLWrappers]] deps = ["Artifacts", "Preferences"] @@ -1395,6 +1416,17 @@ git-tree-sha1 = "af433a10f3942e882d3c671aacb203e006a5808f" uuid = "9c1d0b0a-7046-5b2e-a33f-ea22f176ac7e" version = "0.2.1+0" +[[deps.JuliaSyntax]] +git-tree-sha1 = "956ac689b31cd871a48fbb70978b798c5e95018a" +uuid = "70703baa-626e-46a2-a12c-08ffd08c73b4" +version = "0.4.9" + +[[deps.JuliaSyntaxHighlighting]] +deps = ["JuliaSyntax", "StyledStrings"] +git-tree-sha1 = "19ecee1ea81c60156486a92b062e443b6bba60b7" +uuid = "ac6e5ff7-fb65-4e79-a425-ec3bc9c03011" +version = "0.1.0" + [[deps.JuliaVariables]] deps = ["MLStyle", "NameResolution"] git-tree-sha1 = "49fb3cb53362ddadb4415e9b73926d6b40709e70" @@ -1408,14 +1440,16 @@ uuid = "ef3ab10e-7fda-4108-b977-705223b18434" version = "0.6.0" [[deps.KernelAbstractions]] -deps = ["Adapt", "Atomix", "InteractiveUtils", "LinearAlgebra", "MacroTools", "PrecompileTools", "Requires", "SparseArrays", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] -git-tree-sha1 = "d0448cebd5919e06ca5edc7a264631790de810ec" +deps = ["Adapt", "Atomix", "InteractiveUtils", "MacroTools", "PrecompileTools", "Requires", "StaticArrays", "UUIDs", "UnsafeAtomics", "UnsafeAtomicsLLVM"] +git-tree-sha1 = "35ceea58aa34ad08b1ae00a52622c62d1cfb8ce2" uuid = "63c18a36-062a-441e-b654-da1e3ab1ce7c" -version = "0.9.22" -weakdeps = ["EnzymeCore"] +version = "0.9.24" +weakdeps = ["EnzymeCore", "LinearAlgebra", "SparseArrays"] [deps.KernelAbstractions.extensions] EnzymeExt = "EnzymeCore" + LinearAlgebraExt = "LinearAlgebra" + SparseArraysExt = "SparseArrays" [[deps.KernelDensity]] deps = ["Distributions", "DocStringExtensions", "FFTW", "Interpolations", "StatsBase"] @@ -1430,10 +1464,14 @@ uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7" version = "0.9.6" [[deps.KrylovKit]] -deps = ["ChainRulesCore", "GPUArraysCore", "LinearAlgebra", "Printf", "VectorInterface"] -git-tree-sha1 = "3f3a92bbe8f568b689a7f7bc193f7c717d793751" +deps = ["GPUArraysCore", "LinearAlgebra", "PackageExtensionCompat", "Printf", "VectorInterface"] +git-tree-sha1 = "3c2a016489c38f35160a246c91a3f3353c47bb68" uuid = "0b1a1467-8014-51b9-945f-bf0ae24f4b77" -version = "0.7.1" +version = "0.8.1" +weakdeps = ["ChainRulesCore"] + + [deps.KrylovKit.extensions] + KrylovKitChainRulesCoreExt = "ChainRulesCore" [[deps.LAME_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] @@ -1449,9 +1487,9 @@ version = "3.0.0+1" [[deps.LLVM]] deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"] -git-tree-sha1 = "389aea28d882a40b5e1747069af71bdbd47a1cae" +git-tree-sha1 = "2470e69781ddd70b8878491233cd09bc1bd7fc96" uuid = "929cbde3-209d-540e-8aea-75f648917ca0" -version = "7.2.1" +version = "8.1.0" weakdeps = ["BFloat16s"] [deps.LLVM.extensions] @@ -1459,9 +1497,9 @@ weakdeps = ["BFloat16s"] [[deps.LLVMExtra_jll]] deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"] -git-tree-sha1 = "88b916503aac4fb7f701bb625cd84ca5dd1677bc" +git-tree-sha1 = "597d1c758c9ae5d985ba4202386a607c675ee700" uuid = "dad2f222-ce93-54a1-a47d-0025e8a3acab" -version = "0.0.29+0" +version = "0.0.31+0" [[deps.LLVMLoopInfo]] git-tree-sha1 = "2e5c102cfc41f48ae4740c7eca7743cc7e7b75ea" @@ -1470,9 +1508,9 @@ version = "1.0.0" [[deps.LLVMOpenMP_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "d986ce2d884d49126836ea94ed5bfb0f12679713" +git-tree-sha1 = "e16271d212accd09d52ee0ae98956b8a05c4b626" uuid = "1d63c593-3942-5779-bab2-d838dc0a180e" -version = "15.0.7+0" +version = "17.0.6+0" [[deps.LRUCache]] git-tree-sha1 = "b3cc6698599b10e652832c2f23db3cab99d51b59" @@ -1496,16 +1534,18 @@ version = "1.3.1" [[deps.Latexify]] deps = ["Format", "InteractiveUtils", "LaTeXStrings", "MacroTools", "Markdown", "OrderedCollections", "Requires"] -git-tree-sha1 = "5b0d630f3020b82c0775a51d05895852f8506f50" +git-tree-sha1 = "ce5f5621cac23a86011836badfedf664a612cee4" uuid = "23fbe1c1-3f47-55db-b15f-69d7ec21a316" -version = "0.16.4" +version = "0.16.5" [deps.Latexify.extensions] DataFramesExt = "DataFrames" + SparseArraysExt = "SparseArrays" SymEngineExt = "SymEngine" [deps.Latexify.weakdeps] DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" SymEngine = "123dc426-2d89-5057-bbad-38513e3affd8" [[deps.LayoutPointers]] @@ -1520,15 +1560,23 @@ uuid = "0e77f7df-68c5-4e49-93ce-4cd80f5598bf" version = "1.2.2" [[deps.LazyArrays]] -deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "MatrixFactorizations", "SparseArrays"] -git-tree-sha1 = "35079a6a869eecace778bcda8641f9a54ca3a828" +deps = ["ArrayLayouts", "FillArrays", "LinearAlgebra", "MacroTools", "SparseArrays"] +git-tree-sha1 = "507b423197fdd9e77b74aa2532c0a05eb7eb4004" uuid = "5078a376-72f3-5289-bfd5-ec5146d43c02" -version = "1.10.0" -weakdeps = ["StaticArrays"] +version = "2.2.0" [deps.LazyArrays.extensions] + LazyArraysBandedMatricesExt = "BandedMatrices" + LazyArraysBlockArraysExt = "BlockArrays" + LazyArraysBlockBandedMatricesExt = "BlockBandedMatrices" LazyArraysStaticArraysExt = "StaticArrays" + [deps.LazyArrays.weakdeps] + BandedMatrices = "aae01518-5342-5314-be14-df237901396f" + BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e" + BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0" + StaticArrays = "90137ffa-7385-5640-81b9-e52037218182" + [[deps.LazyArtifacts]] deps = ["Artifacts", "Pkg"] uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" @@ -1615,9 +1663,9 @@ version = "2.40.1+0" [[deps.LineSearches]] deps = ["LinearAlgebra", "NLSolversBase", "NaNMath", "Parameters", "Printf"] -git-tree-sha1 = "7bbea35cec17305fc70a0e5b4641477dc0789d9d" +git-tree-sha1 = "e4c3be53733db1051cc15ecf573b1042b3a712a1" uuid = "d3d80556-e9d4-5f37-9878-2ab0fcc64255" -version = "7.2.0" +version = "7.3.0" [[deps.LinearAlgebra]] deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"] @@ -1640,10 +1688,10 @@ version = "2.8.0" LDLFactorizations = "40e66cde-538c-5869-a4ad-c39174c6795b" [[deps.LinearSolve]] -deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] -git-tree-sha1 = "7648cc20100504f4b453917aacc8520e9c0ecfb3" +deps = ["ArrayInterface", "ChainRulesCore", "ConcreteStructs", "CpuId", "DocStringExtensions", "EnumX", "FastLapackInterface", "GPUArraysCore", "InteractiveUtils", "KLU", "Krylov", "LazyArrays", "Libdl", "LinearAlgebra", "MKL_jll", "Markdown", "PrecompileTools", "Preferences", "RecursiveFactorization", "Reexport", "SciMLBase", "SciMLOperators", "Setfield", "SparseArrays", "Sparspak", "StaticArraysCore", "UnPack"] +git-tree-sha1 = "6b7011b27e35453f68a8f851776271b31fce021c" uuid = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae" -version = "2.30.1" +version = "2.33.0" [deps.LinearSolve.extensions] LinearSolveBandedMatricesExt = "BandedMatrices" @@ -1720,15 +1768,15 @@ weakdeps = ["ChainRulesCore", "ForwardDiff", "SpecialFunctions"] [[deps.Lz4_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "6c26c5e8a4203d43b5497be3ec5d4e0c3cde240a" +git-tree-sha1 = "7f26c8fc5229e68484e0b3447312c98e16207d11" uuid = "5ced341a-0733-55b8-9ab6-a4889d929147" -version = "1.9.4+0" +version = "1.10.0+0" [[deps.MKL_jll]] deps = ["Artifacts", "IntelOpenMP_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "oneTBB_jll"] -git-tree-sha1 = "80b2833b56d466b3858d565adcd16a4a05f2089b" +git-tree-sha1 = "f046ccd0c6db2832a9f639e2c669c6fe867e5f4f" uuid = "856f044c-d86e-5d09-b602-aeab76dc8ba7" -version = "2024.1.0+0" +version = "2024.2.0+0" [[deps.MLStyle]] git-tree-sha1 = "bc38dff0548128765760c79eb7388a4b37fae2c8" @@ -1743,9 +1791,9 @@ version = "0.4.4" [[deps.MPICH_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML"] -git-tree-sha1 = "4099bb6809ac109bfc17d521dad33763bcf026b7" +git-tree-sha1 = "19d4bd098928a3263693991500d05d74dbdc2004" uuid = "7cb0a576-ebde-5e09-9194-50597f1243b4" -version = "4.2.1+1" +version = "4.2.2+0" [[deps.MPIPreferences]] deps = ["Libdl", "Preferences"] @@ -1799,21 +1847,19 @@ version = "0.1.2" [[deps.MathTeXEngine]] deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "UnicodeFun"] -git-tree-sha1 = "1865d0b8a2d91477c8b16b49152a32764c7b1f5f" +git-tree-sha1 = "e1641f32ae592e415e3dbae7f4a188b5316d4b62" uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53" -version = "0.6.0" - -[[deps.MatrixFactorizations]] -deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"] -git-tree-sha1 = "6731e0574fa5ee21c02733e397beb133df90de35" -uuid = "a3b82374-2e81-5b9e-98ce-41277c0e4c87" -version = "2.2.0" +version = "0.6.1" [[deps.MaybeInplace]] -deps = ["ArrayInterface", "LinearAlgebra", "MacroTools", "SparseArrays"] -git-tree-sha1 = "1b9e613f2ca3b6cdcbfe36381e17ca2b66d4b3a1" +deps = ["ArrayInterface", "LinearAlgebra", "MacroTools"] +git-tree-sha1 = "54e2fdc38130c05b42be423e90da3bade29b74bd" uuid = "bb5d69b7-63fc-4a16-80bd-7e42200c7bdb" -version = "0.1.3" +version = "0.1.4" +weakdeps = ["SparseArrays"] + + [deps.MaybeInplace.extensions] + MaybeInplaceSparseArraysExt = "SparseArrays" [[deps.MbedTLS]] deps = ["Dates", "MbedTLS_jll", "MozillaCACerts_jll", "NetworkOptions", "Random", "Sockets"] @@ -1831,6 +1877,12 @@ git-tree-sha1 = "c13304c81eec1ed3af7fc20e75fb6b26092a1102" uuid = "442fdcdd-2543-5da2-b0f3-8c86c306513e" version = "0.3.2" +[[deps.MethodAnalysis]] +deps = ["AbstractTrees"] +git-tree-sha1 = "c2ee9b8f036c951f9ed0a47503a7f7dc0905b256" +uuid = "85b6ec6f-f7df-4429-9514-a64bcd9ee824" +version = "0.4.13" + [[deps.MicroCollections]] deps = ["BangBang", "InitialValues", "Setfield"] git-tree-sha1 = "629afd7d10dbc6935ec59b32daeb33bc4460a42e" @@ -1890,9 +1942,9 @@ version = "7.8.3" [[deps.NNlib]] deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Pkg", "Random", "Requires", "Statistics"] -git-tree-sha1 = "1288e6db94d98f7d194454452176b82edb25b32c" +git-tree-sha1 = "ae52c156a63bb647f80c26319b104e99e5977e51" uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd" -version = "0.9.19" +version = "0.9.22" [deps.NNlib.extensions] NNlibAMDGPUExt = "AMDGPU" @@ -1956,9 +2008,9 @@ version = "1.2.0" [[deps.NonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "FastBroadcast", "FastClosures", "FiniteDiff", "ForwardDiff", "LazyArrays", "LineSearches", "LinearAlgebra", "LinearSolve", "MaybeInplace", "PrecompileTools", "Preferences", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "SymbolicIndexingInterface", "TimerOutputs"] -git-tree-sha1 = "3adb1e5945b5a6b1eaee754077f25ccc402edd7f" +git-tree-sha1 = "bcd8812e751326ff1d4b2dd50764b93df51f143b" uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec" -version = "3.13.1" +version = "3.14.0" [deps.NonlinearSolve.extensions] NonlinearSolveBandedMatricesExt = "BandedMatrices" @@ -2036,9 +2088,9 @@ version = "0.8.1+2" [[deps.OpenMPI_jll]] deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"] -git-tree-sha1 = "a9de2f1fc98b92f8856c640bf4aec1ac9b2a0d86" +git-tree-sha1 = "bfce6d523861a6c562721b262c0d1aaeead2647f" uuid = "fe0851c0-eecd-5654-98d4-656369965a5c" -version = "5.0.3+0" +version = "5.0.5+0" [[deps.OpenSSL]] deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"] @@ -2118,9 +2170,9 @@ version = "0.5.12" [[deps.Pango_jll]] deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "FriBidi_jll", "Glib_jll", "HarfBuzz_jll", "JLLWrappers", "Libdl"] -git-tree-sha1 = "cb5a2ab6763464ae0f19c86c56c63d4a2b0f5bda" +git-tree-sha1 = "9dd97171646850ee607593965ce1f55063d8d3f9" uuid = "36c8627f-9965-5494-a995-c6b170f724f3" -version = "1.52.2+0" +version = "1.54.0+0" [[deps.Parameters]] deps = ["OrderedCollections", "UnPack"] @@ -2189,10 +2241,10 @@ version = "1.40.5" Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d" [[deps.Polyester]] -deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Requires", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] -git-tree-sha1 = "9ff799e8fb8ed6717710feee3be3bc20645daa97" +deps = ["ArrayInterface", "BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "ManualMemory", "PolyesterWeave", "Static", "StaticArrayInterface", "StrideArraysCore", "ThreadingUtilities"] +git-tree-sha1 = "6d38fea02d983051776a856b7df75b30cf9a3c1f" uuid = "f517fe37-dbe3-4b94-8317-1923a5111588" -version = "0.7.15" +version = "0.7.16" [[deps.PolyesterWeave]] deps = ["BitTwiddlingConvenienceFunctions", "CPUSummary", "IfElse", "Static", "ThreadingUtilities"] @@ -2213,9 +2265,9 @@ version = "1.4.3" [[deps.PreallocationTools]] deps = ["Adapt", "ArrayInterface", "ForwardDiff"] -git-tree-sha1 = "406c29a7f46706d379a3bce45671b4e3a39ddfbc" +git-tree-sha1 = "6c62ce45f268f3f958821a1e5192cf91c75ae89c" uuid = "d236fae5-4411-538c-8e31-a6e3d9e00b46" -version = "0.4.22" +version = "0.4.24" [deps.PreallocationTools.extensions] PreallocationToolsReverseDiffExt = "ReverseDiff" @@ -2264,9 +2316,9 @@ version = "0.1.4" [[deps.ProgressMeter]] deps = ["Distributed", "Printf"] -git-tree-sha1 = "763a8ceb07833dd51bb9e3bbca372de32c0605ad" +git-tree-sha1 = "8f6bc219586aef8baf0ff9a5fe16ee9c70cb65e4" uuid = "92933f4c-e287-5a05-a399-4b506db050ca" -version = "1.10.0" +version = "1.10.2" [[deps.PtrArrays]] git-tree-sha1 = "f011fbb92c4d401059b2212c05c0601b70f8b759" @@ -2285,11 +2337,29 @@ git-tree-sha1 = "492601870742dcd38f233b23c3ec629628c1d724" uuid = "c0090381-4147-56d7-9ebc-da0b1113ec56" version = "6.7.1+1" +[[deps.Qt6Declarative_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6ShaderTools_jll"] +git-tree-sha1 = "e5dd466bf2569fe08c91a2cc29c1003f4797ac3b" +uuid = "629bc702-f1f5-5709-abd5-49b8460ea067" +version = "6.7.1+2" + +[[deps.Qt6ShaderTools_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll"] +git-tree-sha1 = "1a180aeced866700d4bebc3120ea1451201f16bc" +uuid = "ce943373-25bb-56aa-8eca-768745ed7b5a" +version = "6.7.1+1" + +[[deps.Qt6Wayland_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl", "Qt6Base_jll", "Qt6Declarative_jll"] +git-tree-sha1 = "729927532d48cf79f49070341e1d918a65aba6b0" +uuid = "e99dba38-086e-5de3-a5b1-6e4c66e897c3" +version = "6.7.1+1" + [[deps.QuadGK]] deps = ["DataStructures", "LinearAlgebra"] -git-tree-sha1 = "9b23c31e76e333e6fb4c1595ae6afa74966a729e" +git-tree-sha1 = "e237232771fdafbae3db5c31275303e056afaa9f" uuid = "1fd47b50-473d-5c70-9696-f719f8f3bcdc" -version = "2.9.4" +version = "2.10.1" [[deps.REPL]] deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"] @@ -2306,10 +2376,10 @@ uuid = "74087812-796a-5b5d-8853-05524746bad3" version = "1.7.0" [[deps.RandomNumbers]] -deps = ["Random", "Requires"] -git-tree-sha1 = "043da614cc7e95c703498a491e2c21f58a2b8111" +deps = ["Random"] +git-tree-sha1 = "c6ec94d2aaba1ab2ff983052cf6a606ca5985902" uuid = "e6cf234a-135c-5ec9-84dd-332b85af5143" -version = "1.5.3" +version = "1.6.0" [[deps.RangeArrays]] git-tree-sha1 = "b9039e93773ddcfc828f12aadf7115b4b4d225f5" @@ -2345,10 +2415,10 @@ uuid = "01d81517-befc-4cb6-b9ec-a95719d0359c" version = "0.6.12" [[deps.RecursiveArrayTools]] -deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] -git-tree-sha1 = "76a35763102e16c97d7302f5dc67837d24802035" +deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"] +git-tree-sha1 = "b034171b93aebc81b3e1890a036d13a9c4a9e3e0" uuid = "731186ca-8d62-57ce-b412-fbd966d074cd" -version = "3.25.0" +version = "3.27.0" [deps.RecursiveArrayTools.extensions] RecursiveArrayToolsFastBroadcastExt = "FastBroadcast" @@ -2356,6 +2426,7 @@ version = "3.25.0" RecursiveArrayToolsMeasurementsExt = "Measurements" RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements" RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"] + RecursiveArrayToolsSparseArraysExt = ["SparseArrays"] RecursiveArrayToolsTrackerExt = "Tracker" RecursiveArrayToolsZygoteExt = "Zygote" @@ -2365,6 +2436,7 @@ version = "3.25.0" Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7" MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca" ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267" + SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf" Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" @@ -2405,9 +2477,9 @@ version = "0.7.1" [[deps.Rmath_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "d483cd324ce5cf5d61b77930f0bbd6cb61927d21" +git-tree-sha1 = "e60724fd3beea548353984dc61c943ecddb0e29a" uuid = "f50d1b31-88e8-58de-be2c-1cc44531875f" -version = "0.4.2+0" +version = "0.4.3+0" [[deps.RootSolvers]] deps = ["ForwardDiff"] @@ -2473,16 +2545,17 @@ version = "2.42.0" Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f" [[deps.SciMLOperators]] -deps = ["ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools", "Setfield", "SparseArrays", "StaticArraysCore"] -git-tree-sha1 = "10499f619ef6e890f3f4a38914481cc868689cd5" +deps = ["ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools", "Setfield", "StaticArraysCore"] +git-tree-sha1 = "23b02c588ac9a17ecb276cc62ab37f3e4fe37b32" uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961" -version = "0.3.8" +version = "0.3.9" +weakdeps = ["SparseArrays"] [[deps.SciMLStructures]] deps = ["ArrayInterface"] -git-tree-sha1 = "cfdd1200d150df1d3c055cc72ee6850742e982d7" +git-tree-sha1 = "20ad3e7c137156c50c93c888d0f2bc5b7883c729" uuid = "53ae85a6-f571-4167-b2af-e1d143709226" -version = "1.4.1" +version = "1.4.2" [[deps.Scratch]] deps = ["Dates"] @@ -2492,9 +2565,9 @@ version = "1.2.1" [[deps.SentinelArrays]] deps = ["Dates", "Random"] -git-tree-sha1 = "6bb314cb1aacfa37ef58e5a0ccf4a1ec0311f495" +git-tree-sha1 = "ff11acffdb082493657550959d4feb4b6149e73a" uuid = "91c51154-3ec4-41a3-a24f-3f23e20d615c" -version = "1.4.4" +version = "1.4.5" [[deps.Serialization]] uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b" @@ -2544,9 +2617,9 @@ version = "1.1.0" [[deps.SimpleNonlinearSolve]] deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "DiffResults", "DifferentiationInterface", "FastClosures", "FiniteDiff", "ForwardDiff", "LinearAlgebra", "MaybeInplace", "PrecompileTools", "Reexport", "SciMLBase", "Setfield", "StaticArraysCore"] -git-tree-sha1 = "58b144f34e44252b2de0acb5a9dbbb7ea5cd75d7" +git-tree-sha1 = "4d7a7c177bcb4c6dc465f09db91bfdb28c578919" uuid = "727e6d20-b764-4bd8-a329-72de5adea6c7" -version = "1.10.1" +version = "1.12.0" [deps.SimpleNonlinearSolve.extensions] SimpleNonlinearSolveChainRulesCoreExt = "ChainRulesCore" @@ -2588,9 +2661,9 @@ version = "1.10.0" [[deps.SparseDiffTools]] deps = ["ADTypes", "Adapt", "ArrayInterface", "Compat", "DataStructures", "FiniteDiff", "ForwardDiff", "Graphs", "LinearAlgebra", "PackageExtensionCompat", "Random", "Reexport", "SciMLOperators", "Setfield", "SparseArrays", "StaticArrayInterface", "StaticArrays", "Tricks", "UnPack", "VertexSafeGraphs"] -git-tree-sha1 = "469f51f8c4741ce944be2c0b65423b518b1405b0" +git-tree-sha1 = "c9e5d7ee75cf6a1ca3a22c9a6a4ef451792cf62b" uuid = "47a9eef4-7e08-11e9-0b38-333d64bd3804" -version = "2.19.0" +version = "2.20.0" [deps.SparseDiffTools.extensions] SparseDiffToolsEnzymeExt = "Enzyme" @@ -2613,10 +2686,10 @@ uuid = "dc90abb0-5640-4711-901d-7e5b23a2fada" version = "0.1.2" [[deps.SparseMatrixColorings]] -deps = ["ADTypes", "Compat", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] -git-tree-sha1 = "eed2446b3c3dd58f6ded3168998b8b2cb3fc9229" +deps = ["ADTypes", "Compat", "DataStructures", "DocStringExtensions", "LinearAlgebra", "Random", "SparseArrays"] +git-tree-sha1 = "996dff77d814c45c3f2342fa0113e4ad31e712e8" uuid = "0a514795-09f3-496d-8182-132a7b665d35" -version = "0.3.3" +version = "0.4.0" [[deps.Sparspak]] deps = ["Libdl", "LinearAlgebra", "Logging", "OffsetArrays", "Printf", "SparseArrays", "Test"] @@ -2647,16 +2720,16 @@ uuid = "cae243ae-269e-4f55-b966-ac2d0dc13c15" version = "0.1.1" [[deps.Static]] -deps = ["IfElse"] -git-tree-sha1 = "d2fdac9ff3906e27f7a618d47b676941baa6c80c" +deps = ["CommonWorldInvalidations", "IfElse", "PrecompileTools"] +git-tree-sha1 = "87d51a3ee9a4b0d2fe054bdd3fc2436258db2603" uuid = "aedffcd0-7271-4cad-89d0-dc628f76c6d3" -version = "0.8.10" +version = "1.1.1" [[deps.StaticArrayInterface]] -deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Requires", "SparseArrays", "Static", "SuiteSparse"] -git-tree-sha1 = "8963e5a083c837531298fc41599182a759a87a6d" +deps = ["ArrayInterface", "Compat", "IfElse", "LinearAlgebra", "PrecompileTools", "Static"] +git-tree-sha1 = "96381d50f1ce85f2663584c8e886a6ca97e60554" uuid = "0d7ed370-da01-4f52-bd93-41d350b8b718" -version = "1.5.1" +version = "1.8.0" weakdeps = ["OffsetArrays", "StaticArrays"] [deps.StaticArrayInterface.extensions] @@ -2732,6 +2805,12 @@ weakdeps = ["Adapt", "GPUArraysCore", "SparseArrays", "StaticArrays"] StructArraysSparseArraysExt = "SparseArrays" StructArraysStaticArraysExt = "StaticArrays" +[[deps.StyledStrings]] +deps = ["PrecompileTools", "TOML"] +git-tree-sha1 = "711c9650010c95814911c2005ea04e70e70e65ed" +uuid = "f489334b-da3d-4c2e-b8f0-e476e12c162b" +version = "1.0.3" + [[deps.SuiteSparse]] deps = ["Libdl", "LinearAlgebra", "Serialization", "SparseArrays"] uuid = "4607b0f0-06f3-5cda-b6b1-a6196a1729e9" @@ -2753,9 +2832,9 @@ weakdeps = ["ClimaParams"] [[deps.SymbolicIndexingInterface]] deps = ["Accessors", "ArrayInterface", "RuntimeGeneratedFunctions", "StaticArraysCore"] -git-tree-sha1 = "9c490ee01823dc443da25bf9225827e3cdd2d7e9" +git-tree-sha1 = "c9fce29fb41a10677e24f74421ebe31220b81ad0" uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5" -version = "0.3.26" +version = "0.3.28" [[deps.TOML]] deps = ["Dates"] @@ -2769,10 +2848,10 @@ uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c" version = "1.0.1" [[deps.Tables]] -deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "OrderedCollections", "TableTraits"] -git-tree-sha1 = "cb76cf677714c095e535e3501ac7954732aeea2d" +deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "OrderedCollections", "TableTraits"] +git-tree-sha1 = "598cd7c1f68d1e205689b1c2fe65a9f85846f297" uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c" -version = "1.11.1" +version = "1.12.0" [[deps.Tar]] deps = ["ArgTools", "SHA"] @@ -2828,13 +2907,9 @@ uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" version = "0.5.24" [[deps.TranscodingStreams]] -git-tree-sha1 = "60df3f8126263c0d6b357b9a1017bb94f53e3582" +git-tree-sha1 = "e84b3a11b9bece70d14cce63406bbc79ed3464d2" uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa" -version = "0.11.0" -weakdeps = ["Random", "Test"] - - [deps.TranscodingStreams.extensions] - TestExt = ["Test", "Random"] +version = "0.11.2" [[deps.Transducers]] deps = ["Adapt", "ArgCheck", "BangBang", "Baselet", "CompositionsBase", "ConstructionBase", "DefineSingletons", "Distributed", "InitialValues", "Logging", "Markdown", "MicroCollections", "Requires", "Setfield", "SplittablesBase", "Tables"] @@ -2863,9 +2938,9 @@ uuid = "d5829a12-d9aa-46ab-831f-fb7c9ab06edf" version = "0.2.1" [[deps.Tricks]] -git-tree-sha1 = "eae1bb484cd63b36999ee58be2de6c178105112f" +git-tree-sha1 = "7822b97e99a1672bfb1b49b668a6d46d58d8cbcb" uuid = "410a4b4d-49e4-4fbc-ab6d-cb71b17b3775" -version = "0.1.8" +version = "0.1.9" [[deps.TriplotBase]] git-tree-sha1 = "4d4ed7f294cda19382ff7de4c137d24d16adc89b" @@ -2903,9 +2978,9 @@ version = "0.4.1" [[deps.Unitful]] deps = ["Dates", "LinearAlgebra", "Random"] -git-tree-sha1 = "dd260903fdabea27d9b6021689b3cd5401a57748" +git-tree-sha1 = "d95fe458f26209c66a187b1114df96fd70839efd" uuid = "1986cc42-f94f-5a68-af5c-568840ba703d" -version = "1.20.0" +version = "1.21.0" weakdeps = ["ConstructionBase", "InverseFunctions"] [deps.Unitful.extensions] @@ -2924,11 +2999,6 @@ git-tree-sha1 = "6cc9d682755680e0f0be87c56392b7651efc2c7b" uuid = "9602ed7d-8fef-5bc8-8597-8f21381861e8" version = "0.1.5" -[[deps.UnrolledUtilities]] -git-tree-sha1 = "b73f7a7c25a2618c5052c80ed32b07e471cc6cb0" -uuid = "0fe1646c-419e-43be-ac14-22321958931b" -version = "0.1.2" - [[deps.UnsafeAtomics]] git-tree-sha1 = "6331ac3440856ea1988316b46045303bef658278" uuid = "013be700-e6cd-48c3-b4a1-df204f14c38f" @@ -2936,9 +3006,9 @@ version = "0.2.1" [[deps.UnsafeAtomicsLLVM]] deps = ["LLVM", "UnsafeAtomics"] -git-tree-sha1 = "bf2c553f25e954a9b38c9c0593a59bb13113f9e5" +git-tree-sha1 = "2d17fabcd17e67d7625ce9c531fb9f40b7c42ce4" uuid = "d80eeb9a-aca5-4d75-85e5-170c8b632249" -version = "0.1.5" +version = "0.2.1" [[deps.Unzip]] git-tree-sha1 = "ca0969166a028236229f63514992fc073799bb78" @@ -3000,9 +3070,9 @@ version = "1.6.1" [[deps.XML2_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"] -git-tree-sha1 = "d9717ce3518dc68a99e6b96300813760d887a01d" +git-tree-sha1 = "1165b0443d0eca63ac1e32b8c0eb69ed2f4f8127" uuid = "02c8fc9c-b97f-50b9-bbe4-9be30ff0a78a" -version = "2.13.1+0" +version = "2.13.3+0" [[deps.XSLT_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Libgcrypt_jll", "Libgpg_error_jll", "Libiconv_jll", "XML2_jll", "Zlib_jll"] @@ -3207,9 +3277,9 @@ version = "3.2.9+0" [[deps.fzf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl"] -git-tree-sha1 = "a68c9655fbe6dfcab3d972808f1aafec151ce3f8" +git-tree-sha1 = "936081b536ae4aa65415d869287d43ef3cb576b2" uuid = "214eeab7-80f7-51ab-84ad-2988db7cef09" -version = "0.43.0+0" +version = "0.53.0+0" [[deps.gperf_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -3244,7 +3314,13 @@ version = "0.15.1+0" [[deps.libblastrampoline_jll]] deps = ["Artifacts", "Libdl"] uuid = "8e850b90-86db-534c-a0d3-1478176c7d93" -version = "5.8.0+1" +version = "5.11.0+0" + +[[deps.libdecor_jll]] +deps = ["Artifacts", "Dbus_jll", "JLLWrappers", "Libdl", "Libglvnd_jll", "Pango_jll", "Wayland_jll", "xkbcommon_jll"] +git-tree-sha1 = "9bf7903af251d2050b467f76bdbe57ce541f7f4f" +uuid = "1183f4f0-6f2a-5f1a-908b-139f9cdfea6f" +version = "0.2.2+0" [[deps.libevdev_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"] @@ -3278,9 +3354,9 @@ version = "1.10.3+0" [[deps.libvorbis_jll]] deps = ["Artifacts", "JLLWrappers", "Libdl", "Ogg_jll", "Pkg"] -git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c" +git-tree-sha1 = "490376214c4721cdaca654041f635213c6165cb3" uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a" -version = "1.3.7+1" +version = "1.3.7+2" [[deps.libzip_jll]] deps = ["Artifacts", "Bzip2_jll", "GnuTLS_jll", "JLLWrappers", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"] diff --git a/docs/Project.toml b/docs/Project.toml index 3d599a957d..6de9a3d015 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -1,4 +1,5 @@ [deps] +About = "69d22d85-9f48-4c46-bbbe-7ad8341ff72a" AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c" CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b" CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" @@ -20,6 +21,7 @@ InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240" Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59" JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6" Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306" +MethodAnalysis = "85b6ec6f-f7df-4429-9514-a64bcd9ee824" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d" SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462" diff --git a/docs/src/getting-started.md b/docs/src/getting-started.md index c66e96c5b7..4ffbc7b6cf 100644 --- a/docs/src/getting-started.md +++ b/docs/src/getting-started.md @@ -5,7 +5,7 @@ ### Installation Installing ClimaLand in Julia is very easy. First, download and install Julia -by following the instructions at [https://julialang.org/downloads/](https://julialang.org/downloads/). +by following the instructions at [https://julialang.org/downloads/](https://julialang.org/downloads/). Then, you can add the ClimaLand package by simply doing: ```julia @@ -24,9 +24,9 @@ using ClimaLand @doc ClimaLand.Canopy.compute_GPP ``` -As you can see, our parameterisation for GPP is located in the `Canopy` Module, and requires four FT. -FT are Float (either Float32 or Float64). For example, with An = 5 µmol m⁻² s⁻¹, K = 0.5, LAI = 3 m² m⁻², -Ω = 0.7, you can compute GPP like below: +As you can see, our parameterisation for GPP is located in the `Canopy` Module, and requires four FT. +FT are Float (either Float32 or Float64). For example, with An = 5 µmol m⁻² s⁻¹, K = 0.5, LAI = 3 m² m⁻², +Ω = 0.7, you can compute GPP like below: ```@repl import ClimaLand.Canopy as canopy @@ -35,76 +35,100 @@ canopy.compute_GPP(FT(5.0), FT(0.5), FT(3.0), FT(0.7)) ``` Et voilà! -Note that our package [ParamViz](https://github.com/CliMA/ParamViz.jl) allow interactive visualisation of -our parameterisations. See examples in the standalone models pages. +Note that our package [ParamViz](https://github.com/CliMA/ParamViz.jl) allow interactive visualisation of +our parameterisations. See examples in the standalone models pages. ### ClimaLand tree ClimaLand contains multiple modules. They are listed below, as a list: -```@setup tree -function get_module_hierarchy(mod::Module, prefix="") - result = String[] - mod_name = string(nameof(mod)) - full_prefix = isempty(prefix) ? mod_name : "$prefix.$mod_name" - - for name in names(mod, all=true) - if !startswith(string(name), "#") - obj = getproperty(mod, name) - if obj isa Module && obj != mod - full_name = "$full_prefix.$name" - push!(result, full_name) - append!(result, get_module_hierarchy(obj, full_prefix)) - end - end - end - return sort(result) -end -``` - -```@example tree -using ClimaLand # hide -get_module_hierarchy(ClimaLand) # hide +```@repl +using MethodAnalysis, ClimaLand +child_modules(ClimaLand) ``` and as a tree: ```@setup climatree_md +using ClimaLand using AbstractTrees +using MethodAnalysis -# Define a simple tree node type +# Define a custom type to represent our module structure struct ModuleNode name::String children::Vector{ModuleNode} end -# Implement the required methods for AbstractTrees +# Implement the AbstractTrees interface AbstractTrees.children(node::ModuleNode) = node.children -AbstractTrees.printnode(io::IO, node::ModuleNode) = print(io, node.name) - -# Create your tree structure -climatree = ModuleNode("ClimaLand", [ - ModuleNode("Artifacts", []), - ModuleNode("Bucket", []), - ModuleNode("Canopy", [ - ModuleNode("PlantHydraulics", []) - ]), - ModuleNode("Diagnostics", []), - ModuleNode("Domains", []), - ModuleNode("Parameters", []), - ModuleNode("Pond", []), - ModuleNode("Snow", []), - ModuleNode("Soil", [ - ModuleNode("Biogeochemistry", []), - ModuleNode("Runoff", []) - ]) -]) +AbstractTrees.nodevalue(node::ModuleNode) = node.name + +# Function to build the tree structure +function build_tree(modules) + # Create a dictionary to store modules by their full path + module_dict = Dict{String, ModuleNode}() + + # First pass: create nodes for all modules + for m in modules + full_name = string(m) + parts = split(full_name, ".") + name = parts[end] # Use only the last part of the name + module_dict[full_name] = ModuleNode(name, []) + end + + # Second pass: build the tree structure + root = nothing + for (full_name, node) in module_dict + parts = split(full_name, ".") + if length(parts) == 1 + root = node + else + parent_name = join(parts[1:end-1], ".") + if haskey(module_dict, parent_name) + push!(module_dict[parent_name].children, node) + end + end + end + + return root +end + +# Custom print function to sort children +function print_sorted_tree(io::IO, tree::ModuleNode, prefix::String="") + println(io, prefix, nodevalue(tree)) + ch = sort(collect(children(tree)), by=x -> x.name) + for (i, child) in enumerate(ch) + if i == length(ch) + print_sorted_tree(io, child, prefix * "└─ ") + else + print_sorted_tree(io, child, prefix * "├─ ") + end + end +end + +# Get the modules +modules = child_modules(ClimaLand) + +# Build the tree +root = build_tree(modules) ``` ```@example climatree_md -AbstractTrees.print_tree(climatree) # hide +print_sorted_tree(stdout, root) # hide ``` +To explore what function and structure is exported in a particular module, you can use About.jl: + +```@repl +using ClimaLand +using About +about(ClimaLand.Soil.Biogeochemistry) +``` + +To see the documentation about a particular function or structure, you can use ? to go in help mode +in the REPL, or @doc as in [Parameterisation above](#Parameterisation). + #### Artifacts Artifacts contains... see ClimaArtifacts @@ -126,16 +150,16 @@ Parameters contains... see ClimaParams See page X --> this should be its own page... A ClimaLand standalone model, such as our soil hydrology model, usually advance some state -(i.e., prognostic) variable(s) (e.g., soil moisture), in time and space, and computes cache -(i.e., diagnostic) variable(s) (e.g., ). +(i.e., prognostic) variable(s) (e.g., soil moisture), in time and space, and computes cache +(i.e., diagnostic) variable(s) (e.g., ). State variables are solved via ordinary differential equations (ODEs), and require initial conditions -and a physical domain with discretized layers and boundary conditions, as well as a timestepper to -advance the state in time. +and a physical domain with discretized layers and boundary conditions, as well as a timestepper to +advance the state in time. -ClimaLand domains are X, and timestepper are Y. +ClimaLand domains are X, and timestepper are Y. -## For Developers +## For Developers Note: This should be a separate page... to do, WIP @@ -145,21 +169,21 @@ explain FT explain AbstractModel and why, etc. Existing Earth System Models and Land Surface Models are monolythique and the scientific community -has asked for modularity in those models for a long time, as currently making modifications in -existing models is a task requiring a lot of time and money. +has asked for modularity in those models for a long time, as currently making modifications in +existing models is a task requiring a lot of time and money. -ClimaLand takes advantage of Julia multiple dispatch to build a modular model. +ClimaLand takes advantage of Julia multiple dispatch to build a modular model. You can find detailed explanation on Julia multiple dispatch here, but I will give a brief overview -and explain how we use it to build a modular land model in ClimaLand. +and explain how we use it to build a modular land model in ClimaLand. -The core idea is that functions can have multiple methods depending on their arguments number or type. +The core idea is that functions can have multiple methods depending on their arguments number or type. -For example, leaf transpiration is a function of stomatal conductance. Many models exists for stomatal conductance, +For example, leaf transpiration is a function of stomatal conductance. Many models exists for stomatal conductance, such as the Medlyn optimality model or the Ball-Berry model. We are going to create a new type, that we call "Abstract" type because it is not a fundamental type -(Number, Real, Float, Integer...), but a subtype. For example: +(Number, Real, Float, Integer...), but a subtype. For example: ```jl abstract type AbstractStomatalConductanceModel{FT} <: AbstractModel{FT} end @@ -167,12 +191,12 @@ abstract type MedlynConductanceModel <: AbstractStomatalConductanceModel{FT} end abstract type BallBerryConductanceModel <: AbstractStomatalConductanceModel{FT} end ``` -now, when we call the function `function leaf_transpiration(conductance::AbstractStomatalConductanceModel)`, -conductance can be either Medlyn of BallBerry. +now, when we call the function `function leaf_transpiration(conductance::AbstractStomatalConductanceModel)`, +conductance can be either Medlyn of BallBerry. -ClimaLand does this at multiple level, for example, our AbstractCanopyModel is made of photosynthesis, conductance, hydraulics, etc. -Similarly to AbstractConductanceModel, the AbstractCanopyModel can have multiple configurations that the rest of the model can dispatch -on, without changing anything. +ClimaLand does this at multiple level, for example, our AbstractCanopyModel is made of photosynthesis, conductance, hydraulics, etc. +Similarly to AbstractConductanceModel, the AbstractCanopyModel can have multiple configurations that the rest of the model can dispatch +on, without changing anything. -This approach allow us to build ClimaLand as a puzzle, where we assemble pieces of many sizes, and can swap them easily. +This approach allow us to build ClimaLand as a puzzle, where we assemble pieces of many sizes, and can swap them easily. diff --git a/docs/src/index.md b/docs/src/index.md index ed7d4e1a15..4e064583c5 100644 --- a/docs/src/index.md +++ b/docs/src/index.md @@ -3,103 +3,52 @@ using Pkg io = IOBuffer() v = Pkg.installed()["ClimaLand"] print(io, """ - # ClimaLand $(v) Documentation - - Welcome to the documentation for ClimaLand $(v). + # ClimaLand.jl Documentation (v$(v)) """) import Markdown Markdown.parse(String(take!(io))) ``` -Please read the [release notes](https://github.com/CliMA/ClimaLand.jl/blob/main/NEWS.md) to see what has changed since the last release. ## Introduction -ClimaLand is the Land model of the CliMA Earth System Model, which -also contains other components ([atmosphere](https://github.com/CliMA/ClimaAtmos.jl), [ocean](https://github.com/CliMA/ClimaOcean.jl), [sea-ice](https://github.com/CliMA/ClimaSeaIce.jl)). +ClimaLand is the Land model of the Climate Modeling Alliance (CliMA) Earth System Model, which +also contains other components ([atmosphere](https://github.com/CliMA/ClimaAtmos.jl), [ocean](https://github.com/CliMA/ClimaOcean.jl), [sea-ice](https://github.com/CliMA/ClimaSeaIce.jl)). -ClimaLand can be run coupled (or "online") with these other components via [ClimaCoupler](https://github.com/CliMA/ClimaCoupler.jl), -or it can be run as a standalone, via prescribed meteorological data ("offline"). +ClimaLand can be run coupled (or "online") with these other components via [ClimaCoupler](https://github.com/CliMA/ClimaCoupler.jl), +or it can be run as a standalone, via prescribed meteorological data ("offline"). -ClimaLand library, described in this documentation, is written in the Julia -programming language. It aims to be fast and have a clear syntax. ClimaLand +ClimaLand library, described in this documentation, is written in the Julia +programming language. It aims to be fast and have a clear syntax. ClimaLand can run on CPU or GPU, it has a modular design, and is flexible in many ways. This documentation will expand on each of these elements. ## Important Links - [CliMA Homepage](https://clima.caltech.edu/) -- [CliMA GitHub Org](https://github.com/CliMA) +- [CliMA GitHub Organisation](https://github.com/CliMA) - [ClimaCoupler](https://github.com/CliMA/ClimaCoupler.jl) - [ClimaAnalysis](https://github.com/CliMA/ClimaAnalysis.jl) - [Julia Homepage](https://julialang.org) ## Documentation for Users and Developers -ClimaLand has documentation for both users and developers. The documentation for users is aimed at scientists who wants -to run simulations using ClimaLand, whereas the documentation for developers is aimed at contributors of the ClimaLand -code library. As such, users can skip reading the docs for developers, and vice-versa. +ClimaLand has documentation for both users and developers. The documentation for users is aimed at scientists who wants +to run simulations using ClimaLand, whereas the documentation for developers is aimed at contributors of the ClimaLand +code library. As such, users can skip reading the docs for developers, and vice-versa. ## Physical units Note that CliMA, in all its repositories, uses Standard Units, reminded below -```@setup PTSI -using PrettyTables - -Quantity = [ - "Length", - "Mass", - "Time", - "Temperature", - "Amount of Substance", - "Energy", - "Power", - "Pressure", - "Frequency" -] - -UnitName = [ - "Meter", - "Kilogram", - "Second", - "Kelvin", - "Mole", - "Joule", - "Watt", - "Pascal", - "Hertz" -] - -UnitSymbol = [ - "m", - "kg", - "s", - "K", - "mol", - "J", - "W", - "Pa", - "Hz" -] - -SIUnitEquivalent = [ - "1 m", - "1 kg", - "1 s", - "1 K", - "1 mol", - "1 J = 1 N·m", - "1 W = 1 J/s", - "1 Pa = 1 N/m²", - "1 Hz = 1 s⁻¹" -] - -table_data = hcat(Quantity, UnitName, UnitSymbol, SIUnitEquivalent); -header = ["Quantity", "Unit Name", "SI Symbol", "SI Unit Equivalent"]; -tableSI = pretty_table(table_data, header = header) -``` - -```@example PTSI -pretty_table(table_data, header = header) # hide -``` +| Quantity | Unit Name | SI Symbol | SI Unit Equivalent | +|:----------------------|:----------|:----------|:--------------------| +| Length | Meter | m | 1 m | +| Mass | Kilogram | kg | 1 kg | +| Time | Second | s | 1 s | +| Temperature | Kelvin | K | 1 K | +| Amount of Substance | Mole | mol | 1 mol | +| Energy | Joule | J | 1 J = 1 N·m | +| Power | Watt | W | 1 W = 1 J/s | +| Pressure | Pascal | Pa | 1 Pa = 1 N/m² | +| Frequency | Hertz | Hz | 1 Hz = 1 s⁻¹ |