Consolidate Manifests

Manifests.toml are a burden to maintain and add a lot of git diff noise.
The one benefit of Manifests.toml is that they help with tracking
version dependencies.

However:
- For `docs`, the precise version of dependencies is not important,
there is pretty much no version-dependent code being executed there
- `perf` and `examples` can be consolidated into a single `.buildkite`
environment. This environment only has to have one manifest checked, the
one for which buildkite is run (and not one for each version of Julia).
- The `perf` environment can be removed all together. It is a more niche
environment: if reproducing a specific result is required, developers
can use the `.buildkite` Manifest. If not, developers can also consider
keeping the relevant tools (mainly JET) in the base environment.

This is the same pattern we have in other repos such as ClimaCore.

examples/Manifest-v1.11.toml → .buildkite/Manifest-v1.11.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.11.3"
 manifest_format = "2.0"
-project_hash = "24002e8dc6f8a8c5db6cfb0857be38051c779373"
+project_hash = "46f0a9409bb0d3c679674a0d7868d43f74e635c6"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "e1ce448a0d7f88168ffe2eeac4549c32d45a42d1"
@@ -207,6 +207,12 @@ weakdeps = ["SparseArrays"]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 version = "1.11.0"
 
+[[deps.BenchmarkTools]]
+deps = ["Compat", "JSON", "Logging", "Printf", "Profile", "Statistics", "UUIDs"]
+git-tree-sha1 = "e38fbc49a620f5d0b660d7f543db1009fe0f8336"
+uuid = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+version = "1.6.0"
+
 [[deps.BitTwiddlingConvenienceFunctions]]
 deps = ["Static"]
 git-tree-sha1 = "f21cfd4950cb9f0587d5067e69405ad2acd27b87"
@@ -305,10 +311,10 @@ uuid = "159f3aea-2a34-519c-b102-8c37f9878175"
 version = "1.1.1"
 
 [[deps.CairoMakie]]
-deps = ["CRC32c", "Cairo", "Cairo_jll", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"]
-git-tree-sha1 = "0afa2b4ac444b9412130d68493941e1af462e26a"
+deps = ["CRC32c", "Cairo", "Colors", "FileIO", "FreeType", "GeometryBasics", "LinearAlgebra", "Makie", "PrecompileTools"]
+git-tree-sha1 = "d69c7593fe9d7d617973adcbe4762028c6899b2c"
 uuid = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
-version = "0.12.18"
+version = "0.11.11"
 
 [[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"]
@@ -327,14 +333,14 @@ weakdeps = ["SparseArrays"]
     ChainRulesCoreSparseArraysExt = "SparseArrays"
 
 [[deps.ClimaAnalysis]]
-deps = ["Artifacts", "Dates", "Interpolations", "NCDatasets", "NaNStatistics", "OrderedCollections", "Reexport", "Statistics", "Unitful"]
-git-tree-sha1 = "b67f8f5f754fde6132bae1a2add06e51cf26227b"
+deps = ["Dates", "Interpolations", "NCDatasets", "NaNStatistics", "OrderedCollections", "Reexport", "Statistics"]
+git-tree-sha1 = "e13d742cd5a5ad287cf72ab22cb0927780cfe596"
 uuid = "29b5916a-a76c-4e73-9657-3c8fd22e65e6"
-version = "0.5.12"
+version = "0.5.7"
 
     [deps.ClimaAnalysis.extensions]
-    ClimaAnalysisGeoMakieExt = "GeoMakie"
-    ClimaAnalysisMakieExt = "Makie"
+    GeoMakieExt = "GeoMakie"
+    MakieExt = "Makie"
 
     [deps.ClimaAnalysis.weakdeps]
     GeoMakie = "db073c08-6b98-4ee5-b6a4-5efafb3259c6"
@@ -392,12 +398,6 @@ git-tree-sha1 = "99845c1da7e9f687180c49cf4d53140f21fc8683"
 uuid = "d934ef94-cdd4-4710-83d6-720549644b70"
 version = "0.3.18"
 
-[[deps.ClimaCoreVTK]]
-deps = ["ClimaCore", "WriteVTK"]
-git-tree-sha1 = "f23034033a0cca56f151d841a8945a75fcf4be46"
-uuid = "c8b6d40d-e815-466f-95ae-c48aefa668fa"
-version = "0.7.6"
-
 [[deps.ClimaDiagnostics]]
 deps = ["Accessors", "ClimaComms", "ClimaCore", "Dates", "NCDatasets", "OrderedCollections", "SciMLBase"]
 git-tree-sha1 = "e9ac94af815dcae2a2ab24e54b53e76cca6258b7"
@@ -421,17 +421,11 @@ deps = ["ClimaComms", "Colors", "DataStructures", "DiffEqBase", "KernelAbstracti
 git-tree-sha1 = "ff967e27a56a938d3e719bb8d2e025b086c3f808"
 uuid = "595c0a79-7f3d-439a-bc5a-b232dc3bde79"
 version = "0.7.39"
+weakdeps = ["BenchmarkTools", "CUDA", "OrderedCollections", "PrettyTables", "StatsBase"]
 
     [deps.ClimaTimeSteppers.extensions]
     ClimaTimeSteppersBenchmarkToolsExt = ["CUDA", "BenchmarkTools", "OrderedCollections", "StatsBase", "PrettyTables"]
 
-    [deps.ClimaTimeSteppers.weakdeps]
-    BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
-    CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
-    OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-    PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
-    StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-
 [[deps.ClimaUtilities]]
 deps = ["Artifacts", "ClimaComms", "Dates"]
 git-tree-sha1 = "ab44b3d5335c1a36fc9f21560a06bff373caca42"
@@ -471,12 +465,6 @@ git-tree-sha1 = "7eee164f122511d3e4e1ebadb7956939ea7e1c77"
 uuid = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2"
 version = "1.3.6"
 
-[[deps.CodecZlib]]
-deps = ["TranscodingStreams", "Zlib_jll"]
-git-tree-sha1 = "bce6804e5e6044c6daab27bb533d1295e4a2e759"
-uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
-version = "0.7.6"
-
 [[deps.ColorBrewer]]
 deps = ["Colors", "JSON"]
 git-tree-sha1 = "e771a63cc8b539eca78c85b0cabd9233d6c8f06f"
@@ -507,9 +495,9 @@ weakdeps = ["SpecialFunctions"]
 
 [[deps.Colors]]
 deps = ["ColorTypes", "FixedPointNumbers", "Reexport"]
-git-tree-sha1 = "64e15186f0aa277e174aa81798f7eb8598e0157e"
+git-tree-sha1 = "362a287c3aa50601b0bc359053d5c2468f0e7ce0"
 uuid = "5ae59095-9a9b-59fe-a467-6f913c188581"
-version = "0.13.0"
+version = "0.12.11"
 
 [[deps.Combinatorics]]
 git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860"
@@ -889,6 +877,12 @@ git-tree-sha1 = "05882d6995ae5c12bb5f36dd2ed3f61c98cbb172"
 uuid = "53c48c17-4a7d-5ca2-90c5-79b7896eea93"
 version = "0.8.5"
 
+[[deps.FlameGraphs]]
+deps = ["AbstractTrees", "Colors", "FileIO", "FixedPointNumbers", "IndirectArrays", "LeftChildRightSiblingTrees", "Profile"]
+git-tree-sha1 = "c8bb515422866a684d9e67870fc5791e3292ad01"
+uuid = "08572546-2f56-4bcf-ba4e-bab62c3a3f89"
+version = "1.0.1"
+
 [[deps.Fontconfig_jll]]
 deps = ["Artifacts", "Bzip2_jll", "Expat_jll", "FreeType2_jll", "JLLWrappers", "Libdl", "Libuuid_jll", "Zlib_jll"]
 git-tree-sha1 = "21fac3c77d7b5a9fc03b0ec503aa1a6392c34d2b"
@@ -1033,9 +1027,9 @@ version = "1.3.14+1"
 
 [[deps.GridLayoutBase]]
 deps = ["GeometryBasics", "InteractiveUtils", "Observables"]
-git-tree-sha1 = "dc6bed05c15523624909b3953686c5f5ffa10adc"
+git-tree-sha1 = "6f93a83ca11346771a93bbde2bdad2f65b61498f"
 uuid = "3955a311-db13-416c-9275-1d80ed98e5e9"
-version = "0.11.1"
+version = "0.10.2"
 
 [[deps.Grisu]]
 git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
@@ -1177,11 +1171,13 @@ deps = ["Adapt", "AxisAlgorithms", "ChainRulesCore", "LinearAlgebra", "OffsetArr
 git-tree-sha1 = "88a101217d7cb38a7b481ccd50d21876e1d1b0e0"
 uuid = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 version = "0.15.1"
-weakdeps = ["Unitful"]
 
     [deps.Interpolations.extensions]
     InterpolationsUnitfulExt = "Unitful"
 
+    [deps.Interpolations.weakdeps]
+    Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+
 [[deps.IntervalArithmetic]]
 deps = ["CRlibm", "FastRounding", "LinearAlgebra", "Markdown", "Random", "RecipesBase", "RoundingEmulator", "SetRounding", "StaticArrays"]
 git-tree-sha1 = "5ab7744289be503d76a944784bac3f2df7b809af"
@@ -1405,6 +1401,12 @@ git-tree-sha1 = "a560dd966b386ac9ae60bdd3a3d3a326062d3c3e"
 uuid = "8cdb02fc-e678-4876-92c5-9defec4f444e"
 version = "0.3.1"
 
+[[deps.LeftChildRightSiblingTrees]]
+deps = ["AbstractTrees"]
+git-tree-sha1 = "fb6803dafae4a5d62ea5cab204b1e657d9737e7f"
+uuid = "1d6d02ad-be62-4b6b-8a6d-2f90e265016e"
+version = "0.2.0"
+
 [[deps.LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]
 uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
@@ -1482,12 +1484,6 @@ git-tree-sha1 = "e888ad02ce716b319e6bdb985d2ef300e7089889"
 uuid = "38a345b3-de98-5d2b-a5d3-14cd9215e700"
 version = "2.40.3+0"
 
-[[deps.LightXML]]
-deps = ["Libdl", "XML2_jll"]
-git-tree-sha1 = "3a994404d3f6709610701c7dabfc03fed87a81f8"
-uuid = "9c8b4983-aa76-5018-a973-4c85ecc9e179"
-version = "0.9.1"
-
 [[deps.LinearAlgebra]]
 deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
 uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -1602,16 +1598,16 @@ uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 version = "0.5.15"
 
 [[deps.Makie]]
-deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "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", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun", "Unitful"]
-git-tree-sha1 = "be3051d08b78206fb5e688e8d70c9e84d0264117"
+deps = ["Animations", "Base64", "CRC32c", "ColorBrewer", "ColorSchemes", "ColorTypes", "Colors", "Contour", "DelaunayTriangulation", "Distributions", "DocStringExtensions", "Downloads", "FFMPEG_jll", "FileIO", "FilePaths", "FixedPointNumbers", "Format", "FreeType", "FreeTypeAbstraction", "GeometryBasics", "GridLayoutBase", "ImageIO", "InteractiveUtils", "IntervalSets", "Isoband", "KernelDensity", "LaTeXStrings", "LinearAlgebra", "MacroTools", "MakieCore", "Markdown", "MathTeXEngine", "Observables", "OffsetArrays", "Packing", "PlotUtils", "PolygonOps", "PrecompileTools", "Printf", "REPL", "Random", "RelocatableFolders", "Scratch", "ShaderAbstractions", "Showoff", "SignedDistanceFields", "SparseArrays", "Statistics", "StatsBase", "StatsFuns", "StructArrays", "TriplotBase", "UnicodeFun"]
+git-tree-sha1 = "4d49c9ee830eec99d3e8de2425ff433ece7cc1bc"
 uuid = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
-version = "0.21.18"
+version = "0.20.10"
 
 [[deps.MakieCore]]
-deps = ["ColorTypes", "GeometryBasics", "IntervalSets", "Observables"]
-git-tree-sha1 = "9019b391d7d086e841cbeadc13511224bd029ab3"
+deps = ["Observables", "REPL"]
+git-tree-sha1 = "248b7a4be0f92b497f7a331aed02c1e9a878f46b"
 uuid = "20f20a25-4f0e-4fdf-b5d1-57303727442b"
-version = "0.8.12"
+version = "0.7.3"
 
 [[deps.ManualMemory]]
 git-tree-sha1 = "bcaef4fc7a0cfe2cba636d84cda54b5e4e4ca3cd"
@@ -1630,9 +1626,9 @@ version = "1.11.0"
 
 [[deps.MathTeXEngine]]
 deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "UnicodeFun"]
-git-tree-sha1 = "f45c8916e8385976e1ccd055c9874560c257ab13"
+git-tree-sha1 = "96ca8a313eb6437db5ffe946c457a401bbb8ce1d"
 uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53"
-version = "0.6.2"
+version = "0.5.7"
 
 [[deps.MbedTLS_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -1962,6 +1958,12 @@ version = "1.11.0"
 uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
 version = "1.11.0"
 
+[[deps.ProfileCanvas]]
+deps = ["Base64", "JSON", "Pkg", "Profile", "REPL"]
+git-tree-sha1 = "e42571ce9a614c2fbebcaa8aab23bbf8865c624e"
+uuid = "efd6af41-a80b-495e-886c-e51b0c7d77a3"
+version = "0.1.6"
+
 [[deps.ProgressLogging]]
 deps = ["Logging", "SHA", "UUIDs"]
 git-tree-sha1 = "80d919dee55b9c50e8d9e2da5eeafff3fe58b539"
@@ -2250,6 +2252,30 @@ git-tree-sha1 = "2da10356e31327c7096832eb9cd86307a50b1eb6"
 uuid = "45858cf5-a6b0-47a3-bbea-62219f50df47"
 version = "0.1.3"
 
+[[deps.SnoopCompile]]
+deps = ["AbstractTrees", "FlameGraphs", "InteractiveUtils", "OrderedCollections", "Pkg", "Printf", "Profile", "Serialization", "SnoopCompileCore", "YAML"]
+git-tree-sha1 = "52e1d0d595362c1512b90c00aef642c152a73185"
+uuid = "aa65fe97-06da-5843-b5b1-d5d13cad87d2"
+version = "3.0.2"
+
+    [deps.SnoopCompile.extensions]
+    CthulhuExt = "Cthulhu"
+    JETExt = ["JET", "Cthulhu"]
+    SCPrettyTablesExt = "PrettyTables"
+    SCPyPlotExt = "PyPlot"
+
+    [deps.SnoopCompile.weakdeps]
+    Cthulhu = "f68482b8-f384-11e8-15f7-abe071a5a75f"
+    JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+    PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
+    PyPlot = "d330b81b-6aea-500a-939a-2ce795aea3ee"
+
+[[deps.SnoopCompileCore]]
+deps = ["Serialization"]
+git-tree-sha1 = "32d1b8d669ee7a7d8ecb6bc2046d6e019f1e0571"
+uuid = "e2b509da-e806-4183-be48-004708413034"
+version = "3.0.0"
+
 [[deps.Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 version = "1.11.0"
@@ -2535,17 +2561,6 @@ git-tree-sha1 = "53915e50200959667e78a92a418594b428dffddf"
 uuid = "1cfade01-22cf-5700-b092-accc4b62d6e1"
 version = "0.4.1"
 
-[[deps.Unitful]]
-deps = ["Dates", "LinearAlgebra", "Random"]
-git-tree-sha1 = "c0667a8e676c53d390a09dc6870b3d8d6650e2bf"
-uuid = "1986cc42-f94f-5a68-af5c-568840ba703d"
-version = "1.22.0"
-weakdeps = ["ConstructionBase", "InverseFunctions"]
-
-    [deps.Unitful.extensions]
-    ConstructionBaseUnitfulExt = "ConstructionBase"
-    InverseFunctionsUnitfulExt = "InverseFunctions"
-
 [[deps.Unrolled]]
 deps = ["MacroTools"]
 git-tree-sha1 = "6cc9d682755680e0f0be87c56392b7651efc2c7b"
@@ -2570,11 +2585,6 @@ weakdeps = ["LLVM"]
     [deps.UnsafeAtomics.extensions]
     UnsafeAtomicsLLVM = ["LLVM"]
 
-[[deps.VTKBase]]
-git-tree-sha1 = "c2d0db3ef09f1942d08ea455a9e252594be5f3b6"
-uuid = "4004b06d-e244-455f-a6ce-a5f9919cc534"
-version = "1.0.1"
-
 [[deps.VectorInterface]]
 deps = ["LinearAlgebra"]
 git-tree-sha1 = "9166406dedd38c111a6574e9814be83d267f8aec"
@@ -2593,12 +2603,6 @@ git-tree-sha1 = "c1a7aa6219628fcd757dede0ca95e245c5cd9511"
 uuid = "efce3f68-66dc-5838-9240-27a6d6f5f9b6"
 version = "1.0.0"
 
-[[deps.WriteVTK]]
-deps = ["Base64", "CodecZlib", "FillArrays", "LightXML", "TranscodingStreams", "VTKBase"]
-git-tree-sha1 = "1d8042d58334ab7947ce505709df7009da6f3375"
-uuid = "64499a7a-5c06-52f2-abe2-ccb03c286192"
-version = "1.21.1"
-
 [[deps.XML2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Libiconv_jll", "Zlib_jll"]
 git-tree-sha1 = "a2fccc6559132927d4c5dc183e3e01048c6dcbd6"