Add ClimaLand diagnostics

This PR adds diagnostics to ClimaLand, as a new module in /src.
This module is built on ClimaDiagnostics.jl, which is also used by
ClimaAtmos. It contains default diagnostics methods for different
ClimaLand models (for now, BucketModel and SoilCanopyModel), those
diagnostics contains metadata such as where diagnostics variables are
stored in those models, what is there names (short, long, standard)
and physical units, with additional comments. It creates a Dict of those
variables, and also default Scheduling methods, such as hourly average
or monthly maximum. Users can define their own diagnostic variables or
scheduling, and developers can add defaults. More information is
available in the documentation.

.buildkite/Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.4"
 manifest_format = "2.0"
-project_hash = "dae5b8a0ef6cad3a789e38991e9bafc7e71f7ab5"
+project_hash = "8f674e311ce137cbeb26c8e00409aca502afec54"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "fa0822e5baee6e23081c2685ae27265dabee23d8"
@@ -231,12 +231,6 @@ git-tree-sha1 = "9a9610fbe5779636f75229e423e367124034af41"
 uuid = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
 version = "0.16.43"
 
-[[deps.Blosc_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Lz4_jll", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "19b98ee7e3db3b4eff74c5c9c72bf32144e24f10"
-uuid = "0b7ba130-8d10-5ba8-a3d6-c5182647fed9"
-version = "1.21.5+0"
-
 [[deps.Bzip2_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "9e2a6b69137e6969bab0152632dcb3bc108c8bdd"
@@ -357,6 +351,20 @@ weakdeps = ["SparseArrays"]
     [deps.ChainRulesCore.extensions]
     ChainRulesCoreSparseArraysExt = "SparseArrays"
 
+[[deps.ClimaAnalysis]]
+deps = ["NCDatasets", "OrderedCollections", "Statistics"]
+git-tree-sha1 = "af5e012e13bc9609f712dea0434cb4ce2b3e709e"
+uuid = "29b5916a-a76c-4e73-9657-3c8fd22e65e6"
+version = "0.5.2"
+
+    [deps.ClimaAnalysis.extensions]
+    CairoMakieExt = "CairoMakie"
+    GeoMakieExt = "GeoMakie"
+
+    [deps.ClimaAnalysis.weakdeps]
+    CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+    GeoMakie = "db073c08-6b98-4ee5-b6a4-5efafb3259c6"
+
 [[deps.ClimaComms]]
 git-tree-sha1 = "d76590e99fa942e07f1e992a4d4a5e25121a26d6"
 uuid = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
@@ -378,8 +386,14 @@ weakdeps = ["CUDA", "Krylov"]
     ClimaCoreCUDAExt = "CUDA"
     KrylovExt = "Krylov"
 
+[[deps.ClimaDiagnostics]]
+deps = ["Accessors", "ClimaComms", "ClimaCore", "Dates", "NCDatasets", "SciMLBase"]
+git-tree-sha1 = "aff194804df0fcfcf69a80c58978b84777272619"
+uuid = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f"
+version = "0.2.2"
+
 [[deps.ClimaLand]]
-deps = ["Adapt", "ArtifactWrappers", "ClimaComms", "ClimaCore", "ClimaUtilities", "DataFrames", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "IntervalSets", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities"]
+deps = ["Adapt", "ArtifactWrappers", "ClimaComms", "ClimaCore", "ClimaDiagnostics", "ClimaUtilities", "DataFrames", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "IntervalSets", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities"]
 path = ".."
 uuid = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532"
 version = "0.12.4"
@@ -830,10 +844,10 @@ uuid = "c87230d0-a227-11e9-1b43-d7ebe4e7570a"
 version = "0.4.1"
 
 [[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 = "466d45dc38e15794ec7d5d63ec03d776a9aff36e"
+deps = ["Artifacts", "Bzip2_jll", "FreeType2_jll", "FriBidi_jll", "JLLWrappers", "LAME_jll", "Libdl", "Ogg_jll", "OpenSSL_jll", "Opus_jll", "PCRE2_jll", "Pkg", "Zlib_jll", "libaom_jll", "libass_jll", "libfdk_aac_jll", "libvorbis_jll", "x264_jll", "x265_jll"]
+git-tree-sha1 = "74faea50c1d007c85837327f6775bea60b5492dd"
 uuid = "b22a6f82-2f65-5046-a5b2-351ab43fb4e5"
-version = "4.4.4+1"
+version = "4.4.2+2"
 
 [[deps.FFTW]]
 deps = ["AbstractFFTs", "FFTW_jll", "LinearAlgebra", "MKL_jll", "Preferences", "Reexport"]
@@ -1033,11 +1047,6 @@ git-tree-sha1 = "ff38ba61beff76b8f4acad8ab0c97ef73bb670cb"
 uuid = "0656b61e-2033-5cc2-a64a-77c0f6c09b89"
 version = "3.3.9+0"
 
-[[deps.GMP_jll]]
-deps = ["Artifacts", "Libdl"]
-uuid = "781609d7-10c4-51f6-84f2-b8444358ff6d"
-version = "6.2.1+6"
-
 [[deps.GPUArrays]]
 deps = ["Adapt", "GPUArraysCore", "LLVM", "LinearAlgebra", "Printf", "Random", "Reexport", "Serialization", "Statistics"]
 git-tree-sha1 = "c154546e322a9c73364e8a60430b0f79b812d320"
@@ -1103,12 +1112,6 @@ git-tree-sha1 = "7c82e6a6cd34e9d935e9aa4051b66c6ff3af59ba"
 uuid = "7746bdde-850d-59dc-9ae8-88ece973131d"
 version = "2.80.2+0"
 
-[[deps.GnuTLS_jll]]
-deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Nettle_jll", "P11Kit_jll", "Zlib_jll"]
-git-tree-sha1 = "383db7d3f900f4c1f47a8a04115b053c095e48d3"
-uuid = "0951126a-58fd-58f1-b5b3-b08c7c4a876d"
-version = "3.8.4+0"
-
 [[deps.Graphics]]
 deps = ["Colors", "LinearAlgebra", "NaNMath"]
 git-tree-sha1 = "d61890399bc535850c4bf08e4e0d3a7ad0f21cbd"
@@ -1129,9 +1132,9 @@ version = "1.11.1"
 
 [[deps.GridLayoutBase]]
 deps = ["GeometryBasics", "InteractiveUtils", "Observables"]
-git-tree-sha1 = "fc713f007cff99ff9e50accba6373624ddd33588"
+git-tree-sha1 = "6f93a83ca11346771a93bbde2bdad2f65b61498f"
 uuid = "3955a311-db13-416c-9275-1d80ed98e5e9"
-version = "0.11.0"
+version = "0.10.2"
 
 [[deps.Grisu]]
 git-tree-sha1 = "53bb909d1151e57e2484c3d1b53e19552b887fb2"
@@ -1149,10 +1152,10 @@ weakdeps = ["MPI"]
     MPIExt = "MPI"
 
 [[deps.HDF5_jll]]
-deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "OpenSSL_jll", "TOML", "Zlib_jll", "libaec_jll"]
-git-tree-sha1 = "82a471768b513dc39e471540fdadc84ff80ff997"
+deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "OpenSSL_jll", "Pkg", "Zlib_jll"]
+git-tree-sha1 = "4cc2bb72df6ff40b055295fdef6d92955f9dede8"
 uuid = "0234f1f7-429e-5d53-9886-15a909be8d59"
-version = "1.14.3+3"
+version = "1.12.2+2"
 
 [[deps.HTTP]]
 deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
@@ -1778,9 +1781,9 @@ uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
 [[deps.MathTeXEngine]]
 deps = ["AbstractTrees", "Automa", "DataStructures", "FreeTypeAbstraction", "GeometryBasics", "LaTeXStrings", "REPL", "RelocatableFolders", "UnicodeFun"]
-git-tree-sha1 = "1865d0b8a2d91477c8b16b49152a32764c7b1f5f"
+git-tree-sha1 = "96ca8a313eb6437db5ffe946c457a401bbb8ce1d"
 uuid = "0a4f8689-d25c-4efe-a92b-7142dfc1aa53"
-version = "0.6.0"
+version = "0.5.7"
 
 [[deps.MatrixFactorizations]]
 deps = ["ArrayLayouts", "LinearAlgebra", "Printf", "Random"]
@@ -1916,23 +1919,17 @@ uuid = "71a1bf82-56d0-4bbc-8a3c-48b961074391"
 version = "0.1.5"
 
 [[deps.NetCDF_jll]]
-deps = ["Artifacts", "Blosc_jll", "Bzip2_jll", "HDF5_jll", "JLLWrappers", "LazyArtifacts", "LibCURL_jll", "Libdl", "MPICH_jll", "MPIPreferences", "MPItrampoline_jll", "MicrosoftMPI_jll", "OpenMPI_jll", "TOML", "XML2_jll", "Zlib_jll", "Zstd_jll", "libzip_jll"]
-git-tree-sha1 = "4686378c4ae1d1948cfbe46c002a11a4265dcb07"
+deps = ["Artifacts", "HDF5_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Pkg", "XML2_jll", "Zlib_jll"]
+git-tree-sha1 = "072f8371f74c3b9e1b26679de7fbf059d45ea221"
 uuid = "7243133f-43d8-5620-bbf4-c2c921802cf3"
-version = "400.902.211+1"
+version = "400.902.5+1"
 
 [[deps.Netpbm]]
 deps = ["FileIO", "ImageCore", "ImageMetadata"]
 git-tree-sha1 = "d92b107dbb887293622df7697a2223f9f8176fcd"
 uuid = "f09324ee-3d7c-5217-9330-fc30815ba969"
 version = "1.1.1"
 
-[[deps.Nettle_jll]]
-deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "eca63e3847dad608cfa6a3329b95ef674c7160b4"
-uuid = "4c82536e-c426-54e4-b420-14f461c4ed8b"
-version = "3.7.2+0"
-
 [[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 version = "1.2.0"
@@ -2058,12 +2055,6 @@ git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 version = "1.6.3"
 
-[[deps.P11Kit_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "2cd396108e178f3ae8dedbd8e938a18726ab2fbf"
-uuid = "c2071276-7c44-58a7-b746-946036e04d0a"
-version = "0.24.1+0"
-
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "efcefdf7-47ab-520b-bdef-62a2eaa19f15"
@@ -3215,12 +3206,6 @@ git-tree-sha1 = "51b5eeb3f98367157a7a12a1fb0aa5328946c03c"
 uuid = "9a68df92-36a6-505f-a73e-abb412b6bfb4"
 version = "0.2.3+0"
 
-[[deps.libaec_jll]]
-deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "46bf7be2917b59b761247be3f317ddf75e50e997"
-uuid = "477f73a3-ac25-53e9-8cc3-50b2fa2566f0"
-version = "1.1.2+0"
-
 [[deps.libaom_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
 git-tree-sha1 = "1827acba325fdcdf1d2647fc8d5301dd9ba43a9d"
@@ -3274,12 +3259,6 @@ git-tree-sha1 = "b910cb81ef3fe6e78bf6acee440bda86fd6ae00c"
 uuid = "f27f6e37-5d2b-51aa-960f-b287f2bc3b7a"
 version = "1.3.7+1"
 
-[[deps.libzip_jll]]
-deps = ["Artifacts", "Bzip2_jll", "GnuTLS_jll", "JLLWrappers", "Libdl", "XZ_jll", "Zlib_jll", "Zstd_jll"]
-git-tree-sha1 = "3282b7d16ae7ac3e57ec2f3fa8fafb564d8f9f7f"
-uuid = "337d8026-41b4-5cde-a456-74a10e5b31d1"
-version = "1.10.1+0"
-
 [[deps.mtdev_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
 git-tree-sha1 = "814e154bdb7be91d78b6802843f76b6ece642f11"

.buildkite/Project.toml

@@ -5,8 +5,10 @@ BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+ClimaAnalysis = "29b5916a-a76c-4e73-9657-3c8fd22e65e6"
 ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"
+ClimaDiagnostics = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f"
 ClimaLand = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532"
 ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c"
 ClimaTimeSteppers = "595c0a79-7f3d-439a-bc5a-b232dc3bde79"

.buildkite/pipeline.yml

@@ -137,7 +137,9 @@ steps:
       - label: "Global Bucket on CPU (functional albedo)"
         key: "global_bucket_function_cpu"
         command: "julia --color=yes --project=.buildkite experiments/standalone/Bucket/global_bucket_function.jl"
-        artifact_paths: "experiments/standalone/Bucket/artifacts/*cpu*"
+        artifact_paths:
+          - "experiments/standalone/Bucket/artifacts/*cpu*"
+          - "experiments/global_bucket_function/output_active/*.png"
 
       - label: "Global Bucket on CPU (static map albedo)"
         key: "global_bucket_staticmap_cpu"

.github/workflows/ClimaLandSimulations.yml

@@ -19,13 +19,14 @@ jobs:
       - uses: julia-actions/setup-julia@latest
         with:
           version: '1.10'
-      - uses: julia-actions/cache@v2
+#  julia-actions/cache@v2 did not seem to invalidate cache correctly...
+#    - uses: julia-actions/cache@v2
       - name: Install Julia dependencies
         run: >
-          julia --project= -e 'using Pkg; Pkg.develop(path="$(pwd())"); Pkg.develop(path="$(pwd())/lib/ClimaLandSimulations")'
+          julia --project=lib/ClimaLandSimulations -e 'using Pkg; Pkg.develop(path=".")'
       - name: Run the tests
         continue-on-error: true
         env:
             CI_OUTPUT_DIR: output
         run: >
-          julia --project= -e 'using Pkg; Pkg.test("ClimaLandSimulations")'
+          julia --project=lib/ClimaLandSimulations -e 'using Pkg; Pkg.test("ClimaLandSimulations")'

Artifacts.toml

@@ -1,9 +1,9 @@
+[era5_land_forcing_data2021]
+git-tree-sha1 = "ec424296df6b60cfe273ac8f981701fbbed0bd8a"
+
 [soil_params_Gupta2020_2022]
 git-tree-sha1 = "8e28b4274b10020b6cdd54b8e7585221379d9d33"
 
     [[soil_params_Gupta2020_2022.download]]
     sha256 = "97dcf1158cba03b1fd397262bdfaf85a523f57038c337bcce163e32664d3616b"
     url = "https://caltech.box.com/shared/static/f2y23qx0lggjskftzgh7ht7fsbh36gmm.gz"
-
-[era5_land_forcing_data2021]
-git-tree-sha1 = "ec424296df6b60cfe273ac8f981701fbbed0bd8a"

Project.toml

@@ -8,6 +8,7 @@ Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 ArtifactWrappers = "a14bc488-3040-4b00-9dc1-f6467924858a"
 ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"
+ClimaDiagnostics = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f"
 ClimaUtilities = "b3f4f4ca-9299-4f7f-bd9b-81e1242a7513"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
@@ -44,6 +45,7 @@ CSV = "0.10"
 CUDA = "5.3"
 ClimaComms = "0.5.6, 0.6"
 ClimaCore = "0.13.2, 0.14"
+ClimaDiagnostics = "0.2"
 ClimaParams = "0.10.2"
 ClimaUtilities = "0.1.2"
 DataFrames = "1"

README.md

@@ -8,6 +8,7 @@
 component) or standalone (single component) modes.  </strong>
 </p>
 
+[![Downloads](https://img.shields.io/badge/dynamic/json?url=http%3A%2F%2Fjuliapkgstats.com%2Fapi%2Fv1%2Ftotal_downloads%2FClimaLand&query=total_requests&suffix=%2Ftotal&label=Downloads)](http://juliapkgstats.com/pkg/ClimaLand)
 
 Recommended Julia Version: Stable release v1.10.0. CI no longer tests earlier
 versions of Julia.

docs/Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.4"
 manifest_format = "2.0"
-project_hash = "bf43a7452b446a9ba967dab8eeb0bc21ba10184f"
+project_hash = "6c3f79ccae513840cc13b9ac947575c2305b507f"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "fa0822e5baee6e23081c2685ae27265dabee23d8"
@@ -375,8 +375,14 @@ weakdeps = ["CUDA", "Krylov"]
     ClimaCoreCUDAExt = "CUDA"
     KrylovExt = "Krylov"
 
+[[deps.ClimaDiagnostics]]
+deps = ["Accessors", "ClimaComms", "ClimaCore", "Dates", "NCDatasets", "SciMLBase"]
+git-tree-sha1 = "aff194804df0fcfcf69a80c58978b84777272619"
+uuid = "1ecacbb8-0713-4841-9a07-eb5aa8a2d53f"
+version = "0.2.2"
+
 [[deps.ClimaLand]]
-deps = ["Adapt", "ArtifactWrappers", "ClimaComms", "ClimaCore", "ClimaUtilities", "DataFrames", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "IntervalSets", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities"]
+deps = ["Adapt", "ArtifactWrappers", "ClimaComms", "ClimaCore", "ClimaDiagnostics", "ClimaUtilities", "DataFrames", "Dates", "DocStringExtensions", "Insolation", "Interpolations", "IntervalSets", "LazyArtifacts", "LinearAlgebra", "NCDatasets", "SciMLBase", "StaticArrays", "SurfaceFluxes", "Thermodynamics", "UnrolledUtilities"]
 path = ".."
 uuid = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532"
 version = "0.12.4"

docs/Project.toml

@@ -20,6 +20,7 @@ Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"

docs/list_diagnostics.jl

@@ -0,0 +1,5 @@
+diagnostics = [
+    "Available diagnostics" => "diagnostics/available_diagnostics.md",
+    "For developers" => "diagnostics/developers_diagnostics.md",
+    "For users" => "diagnostics/users_diagnostics.md",
+]

docs/make.jl

@@ -84,13 +84,15 @@ ext_jl2md(x) = joinpath(basename(GENERATED_DIR), replace(x, ".jl" => ".md"))
 tutorials = transform_second(x -> ext_jl2md(x), tutorials)
 include("list_of_apis.jl")
 include("list_standalone_models.jl")
+include("list_diagnostics.jl")
 pages = Any[
     "Home" => "index.md",
     "APIs" => apis,
     "Contribution guide" => "Contributing.md",
     "Tutorials" => tutorials,
     "Repository structure" => "folderstructure.md",
     "Standalone models" => standalone_models,
+    "Diagnostics" => diagnostics,
 ]
 
 

docs/src/diagnostics/available_diagnostics.md

@@ -0,0 +1,6 @@
+# Available diagnostic variables
+
+Autogenerate table of available diagnostics:
+```@example
+include("make_diagnostic_table.jl")
+```