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Add prescribed aerosols #2815

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Mar 27, 2024
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Add prescribed aerosols #2815

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1 change: 0 additions & 1 deletion .buildkite/pipeline.yml
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Expand Up @@ -684,7 +684,6 @@ steps:
command:
- mkdir -p gpu_aquaplanet_dyamond
- >
nsys profile --trace=nvtx,cuda --output=gpu_aquaplanet_dyamond/report
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I removed this, otherwise the job would stall.

julia --color=yes --project=examples examples/hybrid/driver.jl
--config_file ${GPU_CONFIG_PATH}gpu_aquaplanet_dyamond.yml
artifact_paths: "gpu_aquaplanet_dyamond/*"
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6 changes: 6 additions & 0 deletions Artifacts.toml
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@@ -0,0 +1,6 @@
[aerosol2005]
git-tree-sha1 = "9da4af348af2606764e5e2c94d9439714221dff1"

[[aerosol2005.download]]
sha256 = "952d723b8462439c266dc0df79d0d4e71f774559edb941e03b7979e8ad743f56"
url = "https://caltech.box.com/shared/static/chmel1vdthfvfac0yl61ayw2jqnjzr2c.gz"
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I have to learn more about Artifacts and how do they interact with extensions. Will this file be downloaded always, or only if we are running with aerosols?

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@Sbozzolo Sbozzolo Mar 27, 2024 •
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If you are using the cluster, this file is already on the cluster, so we won't have to download it.

If you are not using the cluster, this file is downloaded the first time you initialize your package.

I wrote extensive documentation on artifacts here

6 changes: 6 additions & 0 deletions NEWS.md
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Expand Up @@ -4,6 +4,12 @@ ClimaAtmos.jl Release Notes
Main
-------

- ![][badge-✨feature/enhancement]![][badge-💥breaking]. Use
[ClimaUtilities](https://github.com/CliMA/ClimaUtilities.jl) for
`TimeVaryingInputs` to read in prescribed aerosol mass concentrations. This PR
is considered breaking because it changes `AtmosCache` adding a new field,
`tracers`. PR [#2815](https://github.com/CliMA/ClimaAtmos.jl/pull/2815).

v0.22.1
-------
- ![][badge-🚀performance] Reduced the number of allocations in the NetCDF
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2 changes: 2 additions & 0 deletions Project.toml
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Expand Up @@ -13,6 +13,7 @@ ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"
ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c"
ClimaTimeSteppers = "595c0a79-7f3d-439a-bc5a-b232dc3bde79"
ClimaUtilities = "b3f4f4ca-9299-4f7f-bd9b-81e1242a7513"
CloudMicrophysics = "6a9e3e04-43cd-43ba-94b9-e8782df3c71b"
Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
Expand Down Expand Up @@ -53,6 +54,7 @@ ClimaComms = "0.5"
ClimaCore = "0.13"
ClimaParams = "0.10.4"
ClimaTimeSteppers = "0.7.18"
ClimaUtilities = "0.1.2"
CloudMicrophysics = "0.18"
Colors = "0.12"
Dates = "1"
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5 changes: 4 additions & 1 deletion config/default_configs/default_config.yml
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Expand Up @@ -141,7 +141,7 @@ bubble:
value: true
start_date:
help: "Start date of the simulation"
value: "19790101"
value: "20050117" # Where the current aerosol data begins
forcing:
help: "Forcing [`nothing` (default), `held_suarez`]"
value: ~
Expand Down Expand Up @@ -277,3 +277,6 @@ deep_atmosphere:
restart_file:
help: "Path to HDF5 file to use as simulation starting point"
value: ~
prescribed_aerosols:
help: "Which aerosols to add. List of keys from the data file (e.g., CB1, CB2)."
value: []
1 change: 1 addition & 0 deletions config/gpu_configs/gpu_aquaplanet_dyamond.yml
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Expand Up @@ -18,5 +18,6 @@ surface_setup: "DefaultMoninObukhov"
rayleigh_sponge: true
dt: "100secs"
t_end: "12hours"
prescribed_aerosols: ["CB1", "CB2", "DST01", "DST02", "DST03", "DST04", "OC1", "OC2", "SO4", "SOA", "SSLT01", "SSLT02", "SSLT03", "SSLT04"]
job_id: "gpu_aquaplanet_dyamond"
toml: [toml/longrun_aquaplanet_dyamond.toml]
1 change: 1 addition & 0 deletions config/model_configs/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.yml
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Expand Up @@ -15,5 +15,6 @@ rayleigh_sponge: true
non_orographic_gravity_wave: true
orographic_gravity_wave: "gfdl_restart"
surface_setup: "DefaultMoninObukhov"
prescribed_aerosols: ["CB1", "CB2"]
job_id: "sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res"
toml: [toml/sphere_aquaplanet_rhoe_equilmoist_allsky_gw_res.toml]
48 changes: 36 additions & 12 deletions docs/Manifest.toml
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Expand Up @@ -298,16 +298,16 @@ weakdeps = ["SparseArrays"]
ChainRulesCoreSparseArraysExt = "SparseArrays"

[[deps.ClimaAtmos]]
deps = ["Adapt", "ArgParse", "ArtifactWrappers", "Artifacts", "AtmosphericProfilesLibrary", "ClimaComms", "ClimaCore", "ClimaParams", "ClimaTimeSteppers", "CloudMicrophysics", "Colors", "Dates", "Dierckx", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FastGaussQuadrature", "Insolation", "Interpolations", "IntervalSets", "Krylov", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "Pkg", "Printf", "RRTMGP", "Random", "RootSolvers", "SciMLBase", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "Thermodynamics", "YAML"]
deps = ["Adapt", "ArgParse", "ArtifactWrappers", "Artifacts", "AtmosphericProfilesLibrary", "ClimaComms", "ClimaCore", "ClimaParams", "ClimaTimeSteppers", "ClimaUtilities", "CloudMicrophysics", "Colors", "Dates", "Dierckx", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FastGaussQuadrature", "Insolation", "Interpolations", "IntervalSets", "Krylov", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "Pkg", "Printf", "RRTMGP", "Random", "RootSolvers", "SciMLBase", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "Thermodynamics", "YAML"]
path = ".."
uuid = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
version = "0.22.1"

[[deps.ClimaComms]]
deps = ["CUDA", "MPI"]
git-tree-sha1 = "f0350e34c91c8f3b5a11b5e39990439303d727b1"
git-tree-sha1 = "ef5d206be51fdf62cd0cbd63058e237128652cf7"
uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
version = "0.5.7"
version = "0.5.8"

[[deps.ClimaCore]]
deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "KrylovKit", "LinearAlgebra", "PkgVersion", "RecursiveArrayTools", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "Unrolled"]
Expand All @@ -331,6 +331,30 @@ git-tree-sha1 = "9c203f39784c968700c55f555754a7771b3410df"
uuid = "595c0a79-7f3d-439a-bc5a-b232dc3bde79"
version = "0.7.19"

[[deps.ClimaUtilities]]
deps = ["Artifacts", "CFTime", "Dates"]
git-tree-sha1 = "2b42b44a95245e2920bbb3ec4b5ca643a5f13b9a"
uuid = "b3f4f4ca-9299-4f7f-bd9b-81e1242a7513"
version = "0.1.2"

[deps.ClimaUtilities.extensions]
ClimaArtifactsExt = ["ClimaComms"]
DataHandlingExt = ["ClimaCore", "NCDatasets"]
InterpolationsRegridderExt = ["Interpolations", "ClimaCore"]
NCFileReaderExt = "NCDatasets"
SpaceVaryingInputsExt = ["ClimaCore", "NCDatasets"]
TempestRegridderExt = "ClimaCoreTempestRemap"
TimeVaryingInputs0DExt = "ClimaCore"
TimeVaryingInputsExt = ["ClimaCore", "NCDatasets"]

[deps.ClimaUtilities.weakdeps]
Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"
ClimaCoreTempestRemap = "d934ef94-cdd4-4710-83d6-720549644b70"
Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"

[[deps.CloseOpenIntervals]]
deps = ["Static", "StaticArrayInterface"]
git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1"
Expand Down Expand Up @@ -776,9 +800,9 @@ uuid = "a3f928ae-7b40-5064-980b-68af3947d34b"
version = "2.13.93+0"

[[deps.Format]]
git-tree-sha1 = "f3cf88025f6d03c194d73f5d13fee9004a108329"
git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc"
uuid = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8"
version = "1.3.6"
version = "1.3.7"

[[deps.ForwardDiff]]
deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"]
Expand Down Expand Up @@ -1912,9 +1936,9 @@ version = "1.3.4"

[[deps.RecursiveArrayTools]]
deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
git-tree-sha1 = "a94d22ca9ad49a7a169ecbc5419c59b9793937cc"
git-tree-sha1 = "d8f131090f2e44b145084928856a561c83f43b27"
uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
version = "3.12.0"
version = "3.13.0"

[deps.RecursiveArrayTools.extensions]
RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
Expand Down Expand Up @@ -2003,9 +2027,9 @@ version = "0.1.0"

[[deps.SciMLBase]]
deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
git-tree-sha1 = "3daaea955c0905200943175637f184a968574a2d"
git-tree-sha1 = "d15c65e25615272e1b1c5edb1d307484c7942824"
uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
version = "2.30.3"
version = "2.31.0"

[deps.SciMLBase.extensions]
SciMLBaseChainRulesCoreExt = "ChainRulesCore"
Expand Down Expand Up @@ -2278,10 +2302,10 @@ weakdeps = ["ClimaParams"]
CreateParametersExt = "ClimaParams"

[[deps.SymbolicIndexingInterface]]
deps = ["MacroTools", "RuntimeGeneratedFunctions"]
git-tree-sha1 = "f7b1fc9fc2bc938436b7684c243be7d317919056"
deps = ["ArrayInterface", "MacroTools", "RuntimeGeneratedFunctions", "StaticArraysCore"]
git-tree-sha1 = "dd94edee1542e9da422cb2f12494ef09ea823e48"
uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
version = "0.3.11"
version = "0.3.13"

[[deps.TOML]]
deps = ["Dates"]
Expand Down
47 changes: 32 additions & 15 deletions examples/Manifest.toml
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Expand Up @@ -2,7 +2,7 @@

julia_version = "1.10.2"
manifest_format = "2.0"
project_hash = "f5b1fcb410aed0e48423c671cbcacf28aec0e1d1"
project_hash = "60f53d07d79df5008ec331956e3787f67e499da0"

[[deps.ADTypes]]
git-tree-sha1 = "016833eb52ba2d6bea9fcb50ca295980e728ee24"
Expand Down Expand Up @@ -286,16 +286,16 @@ weakdeps = ["CairoMakie"]
CairoMakieExt = "CairoMakie"

[[deps.ClimaAtmos]]
deps = ["Adapt", "ArgParse", "ArtifactWrappers", "Artifacts", "AtmosphericProfilesLibrary", "ClimaComms", "ClimaCore", "ClimaParams", "ClimaTimeSteppers", "CloudMicrophysics", "Colors", "Dates", "Dierckx", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FastGaussQuadrature", "Insolation", "Interpolations", "IntervalSets", "Krylov", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "Pkg", "Printf", "RRTMGP", "Random", "RootSolvers", "SciMLBase", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "Thermodynamics", "YAML"]
deps = ["Adapt", "ArgParse", "ArtifactWrappers", "Artifacts", "AtmosphericProfilesLibrary", "ClimaComms", "ClimaCore", "ClimaParams", "ClimaTimeSteppers", "ClimaUtilities", "CloudMicrophysics", "Colors", "Dates", "Dierckx", "DiffEqBase", "DiffEqCallbacks", "DocStringExtensions", "FastGaussQuadrature", "Insolation", "Interpolations", "IntervalSets", "Krylov", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "Pkg", "Printf", "RRTMGP", "Random", "RootSolvers", "SciMLBase", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "Thermodynamics", "YAML"]
path = ".."
uuid = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
version = "0.22.1"

[[deps.ClimaComms]]
deps = ["CUDA", "MPI"]
git-tree-sha1 = "f0350e34c91c8f3b5a11b5e39990439303d727b1"
git-tree-sha1 = "ef5d206be51fdf62cd0cbd63058e237128652cf7"
uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
version = "0.5.7"
version = "0.5.8"

[[deps.ClimaCore]]
deps = ["Adapt", "BandedMatrices", "BlockArrays", "CUDA", "ClimaComms", "CubedSphere", "DataStructures", "DocStringExtensions", "ForwardDiff", "GaussQuadrature", "GilbertCurves", "HDF5", "InteractiveUtils", "IntervalSets", "KrylovKit", "LinearAlgebra", "PkgVersion", "RecursiveArrayTools", "RootSolvers", "SparseArrays", "Static", "StaticArrays", "Statistics", "Unrolled"]
Expand Down Expand Up @@ -349,6 +349,23 @@ git-tree-sha1 = "9c203f39784c968700c55f555754a7771b3410df"
uuid = "595c0a79-7f3d-439a-bc5a-b232dc3bde79"
version = "0.7.19"

[[deps.ClimaUtilities]]
deps = ["Artifacts", "CFTime", "Dates"]
git-tree-sha1 = "2b42b44a95245e2920bbb3ec4b5ca643a5f13b9a"
uuid = "b3f4f4ca-9299-4f7f-bd9b-81e1242a7513"
version = "0.1.2"
weakdeps = ["Adapt", "ClimaComms", "ClimaCore", "ClimaCoreTempestRemap", "Interpolations", "NCDatasets"]

[deps.ClimaUtilities.extensions]
ClimaArtifactsExt = ["ClimaComms"]
DataHandlingExt = ["ClimaCore", "NCDatasets"]
InterpolationsRegridderExt = ["Interpolations", "ClimaCore"]
NCFileReaderExt = "NCDatasets"
SpaceVaryingInputsExt = ["ClimaCore", "NCDatasets"]
TempestRegridderExt = "ClimaCoreTempestRemap"
TimeVaryingInputs0DExt = "ClimaCore"
TimeVaryingInputsExt = ["ClimaCore", "NCDatasets"]

[[deps.CloseOpenIntervals]]
deps = ["Static", "StaticArrayInterface"]
git-tree-sha1 = "70232f82ffaab9dc52585e0dd043b5e0c6b714f1"
Expand Down Expand Up @@ -788,9 +805,9 @@ uuid = "a3f928ae-7b40-5064-980b-68af3947d34b"
version = "2.13.93+0"

[[deps.Format]]
git-tree-sha1 = "f3cf88025f6d03c194d73f5d13fee9004a108329"
git-tree-sha1 = "9c68794ef81b08086aeb32eeaf33531668d5f5fc"
uuid = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8"
version = "1.3.6"
version = "1.3.7"

[[deps.ForwardDiff]]
deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "LinearAlgebra", "LogExpFunctions", "NaNMath", "Preferences", "Printf", "Random", "SpecialFunctions"]
Expand Down Expand Up @@ -1148,9 +1165,9 @@ version = "3.0.2+0"

[[deps.JuliaInterpreter]]
deps = ["CodeTracking", "InteractiveUtils", "Random", "UUIDs"]
git-tree-sha1 = "0015726aa3eb28973fbbdbb7ca2ed6396ffe3a23"
git-tree-sha1 = "e9648d90370e2d0317f9518c9c6e0841db54a90b"
uuid = "aa1ae85d-cabe-5617-a682-6adf51b2e16a"
version = "0.9.30"
version = "0.9.31"

[[deps.JuliaNVTXCallbacks_jll]]
deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
Expand Down Expand Up @@ -1964,9 +1981,9 @@ version = "1.3.4"

[[deps.RecursiveArrayTools]]
deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
git-tree-sha1 = "a94d22ca9ad49a7a169ecbc5419c59b9793937cc"
git-tree-sha1 = "d8f131090f2e44b145084928856a561c83f43b27"
uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
version = "3.12.0"
version = "3.13.0"

[deps.RecursiveArrayTools.extensions]
RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
Expand Down Expand Up @@ -2055,9 +2072,9 @@ version = "0.1.0"

[[deps.SciMLBase]]
deps = ["ADTypes", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
git-tree-sha1 = "3daaea955c0905200943175637f184a968574a2d"
git-tree-sha1 = "d15c65e25615272e1b1c5edb1d307484c7942824"
uuid = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
version = "2.30.3"
version = "2.31.0"

[deps.SciMLBase.extensions]
SciMLBaseChainRulesCoreExt = "ChainRulesCore"
Expand Down Expand Up @@ -2324,10 +2341,10 @@ weakdeps = ["ClimaParams"]
CreateParametersExt = "ClimaParams"

[[deps.SymbolicIndexingInterface]]
deps = ["MacroTools", "RuntimeGeneratedFunctions"]
git-tree-sha1 = "f7b1fc9fc2bc938436b7684c243be7d317919056"
deps = ["ArrayInterface", "MacroTools", "RuntimeGeneratedFunctions", "StaticArraysCore"]
git-tree-sha1 = "dd94edee1542e9da422cb2f12494ef09ea823e48"
uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
version = "0.3.11"
version = "0.3.13"

[[deps.TOML]]
deps = ["Dates"]
Expand Down
1 change: 1 addition & 0 deletions examples/Project.toml
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Expand Up @@ -17,6 +17,7 @@ ClimaCoreTempestRemap = "d934ef94-cdd4-4710-83d6-720549644b70"
ClimaCoreVTK = "c8b6d40d-e815-466f-95ae-c48aefa668fa"
ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c"
ClimaTimeSteppers = "595c0a79-7f3d-439a-bc5a-b232dc3bde79"
ClimaUtilities = "b3f4f4ca-9299-4f7f-bd9b-81e1242a7513"
CloudMicrophysics = "6a9e3e04-43cd-43ba-94b9-e8782df3c71b"
Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
Expand Down
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