Remove ClimaLandSimulations

Work in progress

[skip ci][ci skip]

Author: Sbozzolo

.buildkite/pipeline.yml

@@ -31,10 +31,6 @@ steps:
       - "julia --project=test -e 'using Pkg; Pkg.develop(;path=\".\"); Pkg.add(\"MPI\"); Pkg.add(\"CUDA\"); Pkg.instantiate(;verbose=true)'"
       - "julia --project=test -e 'using Pkg; Pkg.status()'"
 
-      - echo "--- Instantiate lib/ClimaLandSimulations"
-      - "julia --project=lib/ClimaLandSimulations -e 'using Pkg; Pkg.develop(;path=\".\"); Pkg.instantiate(;verbose=true)'"
-      - "julia --project=lib/ClimaLandSimulations -e 'using Pkg; Pkg.status()'"
-
     agents:
       slurm_gpus: 1
       # Ensures that we have all the 8 tasks on the same node
@@ -135,12 +131,6 @@ steps:
         env:
           CLIMACOMMS_DEVICE: "CUDA"
 
-  - group: "ClimaLandSimulations"
-    steps:
-      - label: "Ozark figures Makie"
-        command: "julia --color=yes --project=lib/ClimaLandSimulations lib/ClimaLandSimulations/experiments/ozark.jl"
-        artifact_paths: "figures/*pdf"
-
   - group: "CPU: global bucket"
     steps:
       - label: "Global Bucket on CPU (functional albedo)"

.github/workflows/ClimaLandSimulations.yml

@@ -2,7 +2,7 @@
 
 julia_version = "1.11.4"
 manifest_format = "2.0"
-project_hash = "53eaaa3557cec5df76ee8d7b9a7b00e0b499fc9f"
+project_hash = "9e96085ac4562c94c905e8c0b530862c4de3e77b"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "e2478490447631aedba0823d4d7a80b2cc8cdb32"
@@ -277,12 +277,6 @@ git-tree-sha1 = "535c80f1c0847a4c967ea945fca21becc9de1522"
 uuid = "0b7ba130-8d10-5ba8-a3d6-c5182647fed9"
 version = "1.21.7+0"
 
-[[deps.Bonito]]
-deps = ["Base64", "CodecZlib", "Colors", "Dates", "Deno_jll", "HTTP", "Hyperscript", "LinearAlgebra", "Markdown", "MsgPack", "Observables", "RelocatableFolders", "SHA", "Sockets", "Tables", "ThreadPools", "URIs", "UUIDs", "WidgetsBase"]
-git-tree-sha1 = "d7635780a8cfe0cb43c075276fd358c5b166695e"
-uuid = "824d6782-a2ef-11e9-3a09-e5662e0c26f8"
-version = "3.2.4"
-
 [[deps.Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
 git-tree-sha1 = "1b96ea4a01afe0ea4090c5c8039690672dd13f2e"
@@ -392,9 +386,9 @@ version = "0.14.30"
 
 [[deps.ClimaDiagnostics]]
 deps = ["Accessors", "ClimaComms", "ClimaCore", "ClimaUtilities", "Dates", "NCDatasets", "OrderedCollections", "SciMLBase"]
-git-tree-sha1 = "a67549b46bd3629a1af5739f161bc953914f9c5e"
+git-tree-sha1 = "ec2ee9e870e51a9d8b76decf941f6c9d3d3b1365"
 uuid = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f"
-version = "0.2.12"
+version = "0.2.13"
 
 [[deps.ClimaLand]]
 deps = ["ClimaComms", "ClimaCore", "ClimaDiagnostics", "ClimaUtilities", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics"]
@@ -408,10 +402,9 @@ weakdeps = ["BSON", "CSV", "ClimaParams", "DataFrames", "Flux", "HTTP", "StatsBa
     NeuralSnowExt = ["CSV", "DataFrames", "HTTP", "Flux", "StatsBase", "BSON"]
 
 [[deps.ClimaLandSimulations]]
-deps = ["Bonito", "CairoMakie", "ClimaComms", "ClimaCore", "ClimaDiagnostics", "ClimaLand", "ClimaParams", "ClimaTimeSteppers", "ClimaUtilities", "DataFrames", "Dates", "DelimitedFiles", "Format", "HTTP", "Insolation", "Interpolations", "InverseFunctions", "JSON", "LaTeXStrings", "MutableArithmetics", "NLsolve", "PlotUtils", "RootSolvers", "SciMLBase", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "Thermodynamics", "Unitful", "UnitfulMoles", "WGLMakie"]
 path = "../lib/ClimaLandSimulations"
 uuid = "348a0bd3-1299-4261-8002-d2cd97df6055"
-version = "0.1.0"
+version = "0.0.0"
 
 [[deps.ClimaParams]]
 deps = ["TOML"]
@@ -660,12 +653,6 @@ git-tree-sha1 = "9e2f36d3c96a820c678f2f1f1782582fcf685bae"
 uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
 version = "1.9.1"
 
-[[deps.Deno_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "cd6756e833c377e0ce9cd63fb97689a255f12323"
-uuid = "04572ae6-984a-583e-9378-9577a1c2574d"
-version = "1.33.4+0"
-
 [[deps.DiffEqBase]]
 deps = ["ArrayInterface", "ConcreteStructs", "DataStructures", "DocStringExtensions", "EnumX", "EnzymeCore", "FastBroadcast", "FastClosures", "FastPower", "FunctionWrappers", "FunctionWrappersWrappers", "LinearAlgebra", "Logging", "Markdown", "MuladdMacro", "Parameters", "PrecompileTools", "Printf", "RecursiveArrayTools", "Reexport", "SciMLBase", "SciMLOperators", "SciMLStructures", "Setfield", "Static", "StaticArraysCore", "Statistics", "TruncatedStacktraces"]
 git-tree-sha1 = "e384a2cf3bb402e6dc66b1503ade22c7c1471c4d"
@@ -770,17 +757,6 @@ git-tree-sha1 = "c814502a79baa48e35afef7596c98d0d59f9e0eb"
 uuid = "3c3547ce-8d99-4f5e-a174-61eb10b00ae3"
 version = "0.4.11"
 
-[[deps.Distances]]
-deps = ["LinearAlgebra", "Statistics", "StatsAPI"]
-git-tree-sha1 = "c7e3a542b999843086e2f29dac96a618c105be1d"
-uuid = "b4f34e82-e78d-54a5-968a-f98e89d6e8f7"
-version = "0.10.12"
-weakdeps = ["ChainRulesCore", "SparseArrays"]
-
-    [deps.Distances.extensions]
-    DistancesChainRulesCoreExt = "ChainRulesCore"
-    DistancesSparseArraysExt = "SparseArrays"
-
 [[deps.Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
@@ -1288,12 +1264,6 @@ git-tree-sha1 = "68c173f4f449de5b438ee67ed0c9c748dc31a2ec"
 uuid = "34004b35-14d8-5ef3-9330-4cdb6864b03a"
 version = "0.3.28"
 
-[[deps.Hyperscript]]
-deps = ["Test"]
-git-tree-sha1 = "179267cfa5e712760cd43dcae385d7ea90cc25a4"
-uuid = "47d2ed2b-36de-50cf-bf87-49c2cf4b8b91"
-version = "0.0.5"
-
 [[deps.IOCapture]]
 deps = ["Logging", "Random"]
 git-tree-sha1 = "b6d6bfdd7ce25b0f9b2f6b3dd56b2673a66c8770"
@@ -1996,12 +1966,6 @@ version = "0.3.5"
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 version = "2023.12.12"
 
-[[deps.MsgPack]]
-deps = ["Serialization"]
-git-tree-sha1 = "f5db02ae992c260e4826fe78c942954b48e1d9c2"
-uuid = "99f44e22-a591-53d1-9472-aa23ef4bd671"
-version = "1.2.1"
-
 [[deps.MuladdMacro]]
 git-tree-sha1 = "cac9cc5499c25554cba55cd3c30543cff5ca4fab"
 uuid = "46d2c3a1-f734-5fdb-9937-b9b9aeba4221"
@@ -2037,12 +2001,6 @@ git-tree-sha1 = "1f78293864c5e48ecf97269b0e23d7be28eb1958"
 uuid = "d41bc354-129a-5804-8e4c-c37616107c6c"
 version = "7.9.0"
 
-[[deps.NLsolve]]
-deps = ["Distances", "LineSearches", "LinearAlgebra", "NLSolversBase", "Printf", "Reexport"]
-git-tree-sha1 = "019f12e9a1a7880459d0173c182e6a99365d7ac1"
-uuid = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
-version = "4.5.1"
-
 [[deps.NNlib]]
 deps = ["Adapt", "Atomix", "ChainRulesCore", "GPUArraysCore", "KernelAbstractions", "LinearAlgebra", "Random", "ScopedValues", "Statistics"]
 git-tree-sha1 = "e8d4268b4a438bdad98937e4bca45881363b4767"
@@ -2986,12 +2944,6 @@ weakdeps = ["ClimaParams"]
     [deps.Thermodynamics.extensions]
     CreateParametersExt = "ClimaParams"
 
-[[deps.ThreadPools]]
-deps = ["Printf", "RecipesBase", "Statistics"]
-git-tree-sha1 = "50cb5f85d5646bc1422aa0238aa5bfca99ca9ae7"
-uuid = "b189fb0b-2eb5-4ed4-bc0c-d34c51242431"
-version = "2.1.1"
-
 [[deps.ThreadingUtilities]]
 deps = ["ManualMemory"]
 git-tree-sha1 = "eda08f7e9818eb53661b3deb74e3159460dfbc27"
@@ -3096,12 +3048,6 @@ git-tree-sha1 = "975c354fcd5f7e1ddcc1f1a23e6e091d99e99bc8"
 uuid = "45397f5d-5981-4c77-b2b3-fc36d6e9b728"
 version = "1.6.4"
 
-[[deps.UnitfulMoles]]
-deps = ["Unitful"]
-git-tree-sha1 = "cf6ae3461c3408332de9ac1253dc81600348a994"
-uuid = "999f2bd7-36bf-5ba7-9bc1-c9473aa75374"
-version = "0.1.1"
-
 [[deps.UnrolledUtilities]]
 git-tree-sha1 = "a9ebeb4308eaacfe49f71594c0fe38c0c655734f"
 uuid = "0fe1646c-419e-43be-ac14-22321958931b"
@@ -3137,12 +3083,6 @@ git-tree-sha1 = "2f0486047a07670caad3a81a075d2e518acc5c59"
 uuid = "a44049a8-05dd-5a78-86c9-5fde0876e88c"
 version = "1.3.243+0"
 
-[[deps.WGLMakie]]
-deps = ["Bonito", "Colors", "FileIO", "FreeTypeAbstraction", "GeometryBasics", "Hyperscript", "LinearAlgebra", "Makie", "Observables", "PNGFiles", "PrecompileTools", "RelocatableFolders", "ShaderAbstractions", "StaticArrays"]
-git-tree-sha1 = "676bd14390033825be847e138108a1c53701407d"
-uuid = "276b4fcb-3e11-5398-bf8b-a0c2d153d008"
-version = "0.10.18"
-
 [[deps.Wayland_jll]]
 deps = ["Artifacts", "EpollShim_jll", "Expat_jll", "JLLWrappers", "Libdl", "Libffi_jll", "Pkg", "XML2_jll"]
 git-tree-sha1 = "85c7811eddec9e7f22615371c3cc81a504c508ee"
@@ -3167,12 +3107,6 @@ git-tree-sha1 = "aa1ca3c47f119fbdae8770c29820e5e6119b83f2"
 uuid = "e3aaa7dc-3e4b-44e0-be63-ffb868ccd7c1"
 version = "0.1.3"
 
-[[deps.WidgetsBase]]
-deps = ["Observables"]
-git-tree-sha1 = "30a1d631eb06e8c868c559599f915a62d55c2601"
-uuid = "eead4739-05f7-45a1-878c-cee36b57321c"
-version = "0.1.4"
-
 [[deps.WoodburyMatrices]]
 deps = ["LinearAlgebra", "SparseArrays"]
 git-tree-sha1 = "c1a7aa6219628fcd757dede0ca95e245c5cd9511"

docs/Manifest-v1.11.toml

@@ -3,7 +3,9 @@ AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"
+ClimaDiagnostics = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f"
 ClimaLand = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532"
 ClimaLandSimulations = "348a0bd3-1299-4261-8002-d2cd97df6055"
 ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c"

docs/Project.toml

@@ -6,7 +6,6 @@
 - experiments: contains simple runs of `ClimaLand` models. Most of these experiments is run as part of our CI.
 - src: contains the code of `ClimaLand` models.
 - ext: contains a package extension for Neural Snow and an extension with constructors for model parameters
-- lib: contains two packages that extend ClimaLand functionality: ClimaLandSimulations and ClimaLandDashboards
 - test: contains [unit tests](https://en.wikipedia.org/wiki/Unit_testing), which are meant to ensure small pieces of ClimaLand source code work as intended before merging pull requests.
 
 and 3 GitHub actions folders. GitHub actions are `.yml` files that define workflows that are run at each pull request.
@@ -84,20 +83,6 @@ As well as two files:
 - ClimaLand.jl: This file is the main Julia module of `ClimaLand.jl` repository. It contains all functions defined in `/src` in a nested way, for example `ClimaLand.X`, `ClimaLand.Soil.X`, `ClimaLand.Canopy.X`, etc. When a Julia user install and uses ClimaLand via `]add ClimaLand, using ClimaLand`, they are loading those functions, and are ready to use ClimaLand codebase.
 - Artifacts.jl: Contains functions that return the path of the given artifact name in the current context
 
-## /lib folder
-
-This folder contains a subfolder, `/ClimaLandSimulations`, which contains a library of methods
-to easily and conveniently run ClimaLand at a variety of sites and globally. There are 3 subfolders:
-
-- experiments: This folder contains scripts to run ClimaLand at a fluxnet site using ClimaLandSimulations
-- src: Contains source code for the ClimaLandSimulations package. There are 3 subfolders and
-1 file.
-  - Dashboards: Contains scripts to create dashboards for running simulations at fluxnet sites
-  - Fluxnet: Contains scripts to setup a ClimaLand simulation at a fluxnet site
-  - utilities: Contains utilities used in setup of ClimaLand simulation at a fluxnet sites
-
-- test: Contains tests for the ClimaLandSimulations package
-
 ## /ext folder
 This folder has one subfolder, `/neural_snow`, which contains tools to create the neural network
 for snow and process its data. There are also two files
@@ -121,4 +106,4 @@ subfolders:
 - aqua.jl: Contains code quality assurance tests tha use Aqua.jl
 - Project.toml: Specifies dependencies needed for testing
 - runtests.jl: When `test` is ran from the package manager, this file is ran. It can also be
-manually ran using the `test` environment. This file runs all the other test scripts.
+manually ran using the `test` environment. This file runs all the other test scripts.

docs/src/folderstructure.md

@@ -23,6 +23,8 @@ import Random # to use the same seed each run in the tutorial, optional
 import Logging
 Logging.disable_logging(Logging.Warn); # hide julia warnings
 
+include("run_fluxnet.jl")
+
 # ## Write a function returning our model LHF output given the parameters to calibrate
 function Ozark_LatentHeatFlux(params) # params is a 2 element Array
     g1, g0 = params

docs/src/standalone/apps.jl

@@ -12,12 +12,13 @@
 # 3. The prior distribution of these parameters.
 
 # ## Load packages
-import ClimaLandSimulations.Fluxnet as CLS # to run the model
 import EnsembleKalmanProcesses as EKP # to perform the calibration
 import Random # to use the same seed each run in the tutorial, optional
 import Logging
 Logging.disable_logging(Logging.Warn); # hide julia warnings
 
+include("run_fluxnet.jl")
+
 # ## Write a function returning our model LHF output given the parameters to calibrate
 function Ozark_LHF(params) # params is a 2 element Array
     g1, sc, pc = params