Merge branch 'main' into dr/gpu_perf/jacobian_advection_split

Author: daverumph

.buildkite/Manifest-v1.11.toml

@@ -5,9 +5,9 @@ manifest_format = "2.0"
 project_hash = "12784bf0b21aee2b4075f2bb64383303b89e8560"
 
 [[deps.ADTypes]]
-git-tree-sha1 = "8be2ae325471fc20b11c27bb34b518541d07dd3a"
+git-tree-sha1 = "8b2b045b22740e4be20654175cc38291d48539db"
 uuid = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
-version = "1.19.0"
+version = "1.20.0"
 weakdeps = ["ChainRulesCore", "ConstructionBase", "EnzymeCore"]
 
     [deps.ADTypes.extensions]
@@ -33,9 +33,9 @@ version = "0.4.5"
 
 [[deps.Accessors]]
 deps = ["CompositionsBase", "ConstructionBase", "Dates", "InverseFunctions", "MacroTools"]
-git-tree-sha1 = "3b86719127f50670efe356bc11073d84b4ed7a5d"
+git-tree-sha1 = "856ecd7cebb68e5fc87abecd2326ad59f0f911f3"
 uuid = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"
-version = "0.1.42"
+version = "0.1.43"
 
     [deps.Accessors.extensions]
     AxisKeysExt = "AxisKeys"
@@ -129,9 +129,9 @@ version = "7.22.0"
 
 [[deps.ArrayLayouts]]
 deps = ["FillArrays", "LinearAlgebra", "StaticArrays"]
-git-tree-sha1 = "122a06c8266e00035bfa572887ab52c344526eb4"
+git-tree-sha1 = "e0b47732a192dd59b9d079a06d04235e2f833963"
 uuid = "4c555306-a7a7-4459-81d9-ec55ddd5c99a"
-version = "1.12.1"
+version = "1.12.2"
 weakdeps = ["SparseArrays"]
 
     [deps.ArrayLayouts.extensions]
@@ -260,9 +260,9 @@ version = "0.5.0"
 
 [[deps.CFTime]]
 deps = ["Dates", "Printf"]
-git-tree-sha1 = "2ed76cf4ac70526e3df565435d65e7c7b5c7a77a"
+git-tree-sha1 = "0836c647014903bedccf23ba72b5ebb8c89a7db8"
 uuid = "179af706-886a-5703-950a-314cd64e0468"
-version = "0.2.4"
+version = "0.2.5"
 
 [[deps.CPUSummary]]
 deps = ["CpuId", "IfElse", "PrecompileTools", "Preferences", "Static"]
@@ -336,9 +336,9 @@ version = "1.1.1"
 
 [[deps.CairoMakie]]
 deps = ["CRC32c", "Cairo", "Cairo_jll", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"]
-git-tree-sha1 = "f8caabc5a1c1fb88bcbf9bc4078e5656a477afd0"
+git-tree-sha1 = "5017d6849aff775febd36049f7d926a5fb6677ec"
 uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-version = "0.15.6"
+version = "0.15.8"
 
 [[deps.Cairo_jll]]
 deps = ["Artifacts", "Bzip2_jll", "CompilerSupportLibraries_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "LZO_jll", "Libdl", "Pixman_jll", "Xorg_libXext_jll", "Xorg_libXrender_jll", "Zlib_jll", "libpng_jll"]
@@ -391,7 +391,7 @@ version = "0.5.20"
 deps = ["Adapt", "ArgParse", "Artifacts", "AtmosphericProfilesLibrary", "ClimaComms", "ClimaCore", "ClimaDiagnostics", "ClimaInterpolations", "ClimaParams", "ClimaTimeSteppers", "ClimaUtilities", "CloudMicrophysics", "Dates", "ForwardDiff", "Insolation", "Interpolations", "LazyArtifacts", "LazyBroadcast", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "NullBroadcasts", "RRTMGP", "Random", "SciMLBase", "SparseMatrixColorings", "StaticArrays", "Statistics", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities", "YAML"]
 path = ".."
 uuid = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
-version = "0.31.9"
+version = "0.32.0"
 
 [[deps.ClimaComms]]
 deps = ["Adapt", "Logging", "LoggingExtras"]
@@ -445,9 +445,9 @@ weakdeps = ["CUDA"]
 
 [[deps.ClimaParams]]
 deps = ["Dates", "TOML"]
-git-tree-sha1 = "995991392b8bf4c8400b38ba5bcb7d3a0e7d9cce"
+git-tree-sha1 = "5ade630eb2f88bd670f316b7fb9f8001adc772c2"
 uuid = "5c42b081-d73a-476f-9059-fd94b934656c"
-version = "1.0.3"
+version = "1.0.7"
 
 [[deps.ClimaReproducibilityTests]]
 deps = ["OrderedCollections", "PrettyTables"]
@@ -590,9 +590,9 @@ weakdeps = ["InverseFunctions"]
 
 [[deps.ComputePipeline]]
 deps = ["Observables", "Preferences"]
-git-tree-sha1 = "cb1299fee09da21e65ec88c1ff3a259f8d0b5802"
+git-tree-sha1 = "76dab592fa553e378f9dd8adea16fe2591aa3daa"
 uuid = "95dc2771-c249-4cd0-9c9f-1f3b4330693c"
-version = "0.1.4"
+version = "0.1.6"
 
 [[deps.ConcreteStructs]]
 git-tree-sha1 = "f749037478283d372048690eb3b5f92a79432b34"
@@ -661,9 +661,9 @@ version = "1.11.0"
 
 [[deps.DelaunayTriangulation]]
 deps = ["AdaptivePredicates", "EnumX", "ExactPredicates", "Random"]
-git-tree-sha1 = "783b21581a051ac91a3921ee37e26a23ed7f57a6"
+git-tree-sha1 = "c55f5a9fd67bdbc8e089b5a3111fe4292986a8e8"
 uuid = "927a84f5-c5f4-47a5-9785-b46e178433df"
-version = "1.6.5"
+version = "1.6.6"
 
 [[deps.DelimitedFiles]]
 deps = ["Mmap"]
@@ -820,9 +820,9 @@ version = "0.1.6"
 
 [[deps.FFMPEG_jll]]
 deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"]
-git-tree-sha1 = "eaa040768ea663ca695d442be1bc97edfe6824f2"
+git-tree-sha1 = "ccc81ba5e42497f4e76553a5545665eed577a663"
 uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
-version = "6.1.3+0"
+version = "8.0.0+0"
 
 [[deps.FFTW]]
 deps = ["AbstractFFTs", "FFTW_jll", "Libdl", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
@@ -883,10 +883,20 @@ version = "1.17.1"
     HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 
 [[deps.FilePaths]]
-deps = ["FilePathsBase", "MacroTools", "Reexport", "Requires"]
-git-tree-sha1 = "919d9412dbf53a2e6fe74af62a73ceed0bce0629"
+deps = ["FilePathsBase", "MacroTools", "Reexport"]
+git-tree-sha1 = "a1b2fbfe98503f15b665ed45b3d149e5d8895e4c"
 uuid = "8fc22ac5-c921-52a6-82fd-178b2807b824"
-version = "0.8.3"
+version = "0.9.0"
+
+    [deps.FilePaths.extensions]
+    FilePathsGlobExt = "Glob"
+    FilePathsURIParserExt = "URIParser"
+    FilePathsURIsExt = "URIs"
+
+    [deps.FilePaths.weakdeps]
+    Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
+    URIParser = "30578b45-9adc-5946-b283-645ec420af67"
+    URIs = "5c2747f8-b7ea-4ff2-ba2e-563bfd36b1d4"
 
 [[deps.FilePathsBase]]
 deps = ["Compat", "Dates"]
@@ -989,10 +999,10 @@ uuid = "9fa8497b-333b-5362-9e8d-4d0656e87820"
 version = "1.11.0"
 
 [[deps.GPUArrays]]
-deps = ["Adapt", "GPUArraysCore", "KernelAbstractions", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "ScopedValues", "Serialization", "Statistics"]
-git-tree-sha1 = "8ddb438e956891a63a5367d7fab61550fc720026"
+deps = ["Adapt", "GPUArraysCore", "KernelAbstractions", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "ScopedValues", "Serialization", "SparseArrays", "Statistics"]
+git-tree-sha1 = "18da8dd0b6aded0c47184e9d2a17573ae8257f36"
 uuid = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
-version = "11.2.6"
+version = "11.3.1"
 weakdeps = ["JLD2"]
 
     [deps.GPUArrays.extensions]
@@ -1006,9 +1016,9 @@ version = "0.2.0"
 
 [[deps.GPUCompiler]]
 deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "PrecompileTools", "Preferences", "Scratch", "Serialization", "TOML", "Tracy", "UUIDs"]
-git-tree-sha1 = "90554fe518adab1b4c8f7a04d26c414482a240ca"
+git-tree-sha1 = "6e5a25bc455da8e8d88b6b7377e341e9af1929f0"
 uuid = "61eb1bfa-7361-4325-ad38-22787b887f55"
-version = "1.7.4"
+version = "1.7.5"
 
 [[deps.GPUToolbox]]
 deps = ["LLVM"]
@@ -1053,9 +1063,9 @@ version = "0.1.0"
 
 [[deps.Glib_jll]]
 deps = ["Artifacts", "GettextRuntime_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Libiconv_jll", "Libmount_jll", "PCRE2_jll", "Zlib_jll"]
-git-tree-sha1 = "50c11ffab2a3d50192a228c313f05b5b5dc5acb2"
+git-tree-sha1 = "6b4d2dc81736fe3980ff0e8879a9fc7c33c44ddf"
 uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
-version = "2.86.0+0"
+version = "2.86.2+0"
 
 [[deps.Graphics]]
 deps = ["Colors", "LinearAlgebra", "NaNMath"]
@@ -1382,9 +1392,9 @@ version = "0.6.10"
 
 [[deps.Krylov]]
 deps = ["LinearAlgebra", "Printf", "SparseArrays"]
-git-tree-sha1 = "d1fc961038207e43982851e57ee257adc37be5e8"
+git-tree-sha1 = "09895a8e17b0aa97df8964ed13c94d1b6d9de666"
 uuid = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
-version = "0.10.2"
+version = "0.10.3"
 
 [[deps.KrylovKit]]
 deps = ["LinearAlgebra", "PackageExtensionCompat", "Printf", "Random", "VectorInterface"]
@@ -1669,19 +1679,25 @@ version = "0.5.16"
 
 [[deps.Makie]]
 deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "ComputePipeline", "Contour", "Dates", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageBase", "ImageIO", "InteractiveUtils", "Interpolations", "IntervalSets", "InverseFunctions", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "PNGFiles", "Packing", "Pkg", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"]
-git-tree-sha1 = "368542cde25d381e44d84c3c4209764f05f4ef19"
+git-tree-sha1 = "d1b974f376c24dad02c873e951c5cd4e351cd7c2"
 uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
-version = "0.24.6"
+version = "0.24.8"
+
+    [deps.Makie.extensions]
+    MakieDynamicQuantitiesExt = "DynamicQuantities"
+
+    [deps.Makie.weakdeps]
+    DynamicQuantities = "06fc5a27-2a28-4c7c-a15d-362465fb6821"
 
 [[deps.ManualMemory]]
 git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd"
 uuid = "d125e4d3-2237-4719-b19c-fa641b8a4667"
 version = "0.1.8"
 
 [[deps.MappedArrays]]
-git-tree-sha1 = "2dab0221fe2b0f2cb6754eaa743cc266339f527e"
+git-tree-sha1 = "0ee4497a4e80dbd29c058fcee6493f5219556f40"
 uuid = "dbb5928d-eab1-5f90-85c2-b9b0edb7c900"
-version = "0.4.2"
+version = "0.4.3"
 
 [[deps.Markdown]]
 deps = ["Base64"]
@@ -1864,7 +1880,7 @@ version = "2.5.5+0"
 [[deps.OpenLibm_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
-version = "0.8.1+4"
+version = "0.8.5+0"
 
 [[deps.OpenMPI_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Hwloc_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "MPIPreferences", "TOML", "Zlib_jll"]
@@ -2076,9 +2092,9 @@ version = "1.3.0"
 
 [[deps.QOI]]
 deps = ["ColorTypes", "FileIO", "FixedPointNumbers"]
-git-tree-sha1 = "8b3fc30bc0390abdce15f8822c889f669baed73d"
+git-tree-sha1 = "472daaa816895cb7aee81658d4e7aec901fa1106"
 uuid = "4b34888f-f399-49d4-9bb3-47ed5cae4e65"
-version = "1.0.1"
+version = "1.0.2"
 
 [[deps.QuadGK]]
 deps = ["DataStructures", "LinearAlgebra"]
@@ -2282,9 +2298,9 @@ version = "2.112.0"
 
 [[deps.SciMLOperators]]
 deps = ["Accessors", "ArrayInterface", "DocStringExtensions", "LinearAlgebra", "MacroTools"]
-git-tree-sha1 = "a1e12aee1eb7e6f957e8483eeebf9a98f3e135d6"
+git-tree-sha1 = "9deb07bb4e6f95712bda5617a717caed701fbe4b"
 uuid = "c0aeaf25-5076-4817-a8d5-81caf7dfa961"
-version = "1.13.0"
+version = "1.14.0"
 weakdeps = ["SparseArrays", "StaticArraysCore"]
 
     [deps.SciMLOperators.extensions]
@@ -2490,15 +2506,15 @@ weakdeps = ["SparseArrays"]
 
 [[deps.StatsAPI]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "9d72a13a3f4dd3795a195ac5a44d7d6ff5f552ff"
+git-tree-sha1 = "178ed29fd5b2a2cfc3bd31c13375ae925623ff36"
 uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
-version = "1.7.1"
+version = "1.8.0"
 
 [[deps.StatsBase]]
 deps = ["AliasTables", "DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
-git-tree-sha1 = "064b532283c97daae49e544bb9cb413c26511f8c"
+git-tree-sha1 = "be5733d4a2b03341bdcab91cea6caa7e31ced14b"
 uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.34.8"
+version = "0.34.9"
 
 [[deps.StatsFuns]]
 deps = ["HypergeometricFunctions", "IrrationalConstants", "LogExpFunctions", "Reexport", "Rmath", "SpecialFunctions"]
@@ -2525,9 +2541,9 @@ version = "0.3.7"
 
 [[deps.StringManipulation]]
 deps = ["PrecompileTools"]
-git-tree-sha1 = "725421ae8e530ec29bcbdddbe91ff8053421d023"
+git-tree-sha1 = "a3c1536470bf8c5e02096ad4853606d7c8f62721"
 uuid = "892a3eda-7b42-436c-8928-eab12a02cf0e"
-version = "0.4.1"
+version = "0.4.2"
 
 [[deps.StructArrays]]
 deps = ["ConstructionBase", "DataAPI", "Tables"]
@@ -2614,9 +2630,9 @@ version = "1.10.0"
 
 [[deps.TaylorSeries]]
 deps = ["LinearAlgebra", "Markdown", "SparseArrays"]
-git-tree-sha1 = "dbb2073ed3d0b356405abb7562bfb3326f9cb5fe"
+git-tree-sha1 = "4a5ddc4036946d3a7900b5776b0872e36d848a29"
 uuid = "6aa5eb33-94cf-58f4-a9d0-e4b2c4fc25ea"
-version = "0.20.9"
+version = "0.20.10"
 weakdeps = ["IntervalArithmetic", "JLD2", "RecursiveArrayTools", "StaticArrays"]
 
     [deps.TaylorSeries.extensions]
@@ -2649,9 +2665,9 @@ version = "1.0.2"
 
 [[deps.Thermodynamics]]
 deps = ["DocStringExtensions", "ForwardDiff", "KernelAbstractions", "Random", "RootSolvers"]
-git-tree-sha1 = "bae39665e42c36e2e6bf5b814631915ec7d90232"
+git-tree-sha1 = "b8203ebbcf1dd74ee13d84c52819fb159ac44b93"
 uuid = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
-version = "0.15.0"
+version = "0.15.2"
 weakdeps = ["ClimaParams"]
 
     [deps.Thermodynamics.extensions]
@@ -2729,15 +2745,16 @@ version = "0.4.1"
 
 [[deps.Unitful]]
 deps = ["Dates", "LinearAlgebra", "Random"]
-git-tree-sha1 = "83360bda12f61c250835830cc40b64f487cc2230"
+git-tree-sha1 = "c25751629f5baaa27fef307f96536db62e1d754e"
 uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
-version = "1.25.1"
+version = "1.27.0"
 
     [deps.Unitful.extensions]
     ConstructionBaseUnitfulExt = "ConstructionBase"
     ForwardDiffExt = "ForwardDiff"
     InverseFunctionsUnitfulExt = "InverseFunctions"
     LatexifyExt = ["Latexify", "LaTeXStrings"]
+    NaNMathExt = "NaNMath"
     PrintfExt = "Printf"
 
     [deps.Unitful.weakdeps]
@@ -2746,6 +2763,7 @@ version = "1.25.1"
     InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"
     LaTeXStrings = "b964fa9f-0449-5b57-a5c2-d3ea65f4040f"
     Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
+    NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
     Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
 [[deps.UnrolledUtilities]]
@@ -2904,9 +2922,9 @@ version = "2.0.4+0"
 
 [[deps.libpng_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
-git-tree-sha1 = "07b6a107d926093898e82b3b1db657ebe33134ec"
+git-tree-sha1 = "de8ab4f01cb2d8b41702bab9eaad9e8b7d352f73"
 uuid = "b53b4c65-9356-5827-b1ea-8c7a1a84506f"
-version = "1.6.50+0"
+version = "1.6.53+0"
 
 [[deps.libsixel_jll]]
 deps = ["Artifacts", "JLLWrappers", "JpegTurbo_jll", "Libdl", "libpng_jll"]

NEWS.md

@@ -4,9 +4,32 @@ ClimaAtmos.jl Release Notes
 main
 -------
 
-PR [#4021](https://github.com/CliMA/ClimaAtmos.jl/pull/4021) uses ClimaCore
+
+v0.32.0
+-------
+- ![][badge-💥breaking] Remove the options `co2_model` and `prescribe_ozone`.
+These are both fixed by default now, and can be set to time-varying by
+including one or both in the option `time_varying_trace_gases: ["CO2", "O3]`.
+
+- PR [#4162](https://github.com/CliMA/ClimaAtmos.jl/pull/4162) adds an option for
+reproducible restart. It is set to false by default. This shouldn't affect restart
+in the coupler as the coupler save the cache for restarting.
+
+- PR [#4021](https://github.com/CliMA/ClimaAtmos.jl/pull/4021) uses ClimaCore
 convenience constructors to create spaces without an AtmosConfig.
 
+v0.31.9
+-------
+
+v0.31.8
+-------
+
+v0.31.7
+-------
+
+v0.31.6
+-------
+
 v0.31.5
 -------
 PR [#3975](https://github.com/CliMA/ClimaAtmos.jl/pull/3975) updates the pressure gradient formulation to subtract a reference state and use the Exner pressure.