documentation for fluxnet sites [skip ci]

Author: kmdeck

docs/Manifest-v1.11.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.11.6"
 manifest_format = "2.0"
-project_hash = "53eaaa3557cec5df76ee8d7b9a7b00e0b499fc9f"
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 [[deps.ADTypes]]
 git-tree-sha1 = "7927b9af540ee964cc5d1b73293f1eb0b761a3a1"
@@ -616,6 +616,12 @@ git-tree-sha1 = "dec769959be3af9ba94970b1f14b31c196b0fb9e"
 uuid = "f65535da-76fb-5f13-bab9-19810c17039a"
 version = "0.16.4"
 
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+
 [[deps.CpuId]]
 deps = ["Markdown"]
 git-tree-sha1 = "fcbb72b032692610bfbdb15018ac16a36cf2e406"
@@ -1199,12 +1205,72 @@ git-tree-sha1 = "294e99f19869d0b0cb71aef92f19d03649d028d5"
 uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
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+
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+
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+    GeoJSONMakieExt = "Makie"
+
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 [[deps.GeometryBasics]]
 deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"]
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+
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+    GeometryOpsDataFramesExt = "DataFrames"
+    GeometryOpsFlexiJoinsExt = "FlexiJoins"
+    GeometryOpsLibGEOSExt = "LibGEOS"
+    GeometryOpsProjExt = "Proj"
+    GeometryOpsTGGeometryExt = "TGGeometry"
+
+    [deps.GeometryOps.weakdeps]
+    DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+    FlexiJoins = "e37f2e79-19fa-4eb7-8510-b63b51fe0a37"
+    LibGEOS = "a90b1aa1-3769-5649-ba7e-abc5a9d163eb"
+    Proj = "c94c279d-25a6-4763-9509-64d165bea63e"
+    TGGeometry = "d7e755d2-3c95-4bcf-9b3c-79ab1a78647b"
+
+[[deps.GeometryOpsCore]]
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+version = "0.1.7"
+
 [[deps.GettextRuntime_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "JLLWrappers", "Libdl", "Libiconv_jll"]
 git-tree-sha1 = "45288942190db7c5f760f59c04495064eedf9340"
@@ -1803,6 +1869,12 @@ git-tree-sha1 = "da046be6d63304f7ba9c1bb04820fb306ba1ab12"
 uuid = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 version = "2.20.1"
 
+[[deps.LittleCMS_jll]]
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+
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 deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
 git-tree-sha1 = "13ca9e2586b89836fd20cccf56e57e2b9ae7f38f"
@@ -2127,6 +2199,12 @@ git-tree-sha1 = "1a0fa0e9613f46c9b8c11eee38ebb4f590013c5e"
 uuid = "71a1bf82-56d0-4bbc-8a3c-48b961074391"
 version = "0.1.5"
 
+[[deps.NaturalEarth]]
+deps = ["Downloads", "GeoJSON", "Pkg", "Scratch"]
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+uuid = "436b0209-26ab-4e65-94a9-6526d86fea76"
+version = "0.1.0"
+
 [[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", "libaec_jll", "libzip_jll"]
 git-tree-sha1 = "d574803b6055116af212434460adf654ce98e345"
@@ -2198,6 +2276,12 @@ git-tree-sha1 = "8292dd5c8a38257111ada2174000a33745b06d4e"
 uuid = "18a262bb-aa17-5467-a713-aee519bc75cb"
 version = "3.2.4+0"
 
+[[deps.OpenJpeg_jll]]
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+uuid = "643b3616-a352-519d-856d-80112ee9badc"
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+
 [[deps.OpenLibm_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "05823500-19ac-5b8b-9628-191a04bc5112"
@@ -2287,6 +2371,12 @@ git-tree-sha1 = "cf181f0b1e6a18dfeb0ee8acc4a9d1672499626c"
 uuid = "f57f5aa1-a3ce-4bc8-8ab9-96f992907883"
 version = "0.4.4"
 
+[[deps.PROJ_jll]]
+deps = ["Artifacts", "JLLWrappers", "LibCURL_jll", "Libdl", "Libtiff_jll", "SQLite_jll"]
+git-tree-sha1 = "29d4224ba271e3b679cca03a8fd72e271525c113"
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+
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 git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518"
 uuid = "65ce6f38-6b18-4e1d-a461-8949797d7930"
@@ -2399,6 +2489,12 @@ git-tree-sha1 = "36d8b4b899628fb92c2749eb488d884a926614d3"
 uuid = "2dfb63ee-cc39-5dd5-95bd-886bf059d720"
 version = "1.4.3"
 
+[[deps.Poppler_jll]]
+deps = ["Artifacts", "Cairo_jll", "Fontconfig_jll", "FreeType2_jll", "Glib_jll", "JLLWrappers", "JpegTurbo_jll", "LibCURL_jll", "Libdl", "Libtiff_jll", "OpenJpeg_jll", "libpng_jll"]
+git-tree-sha1 = "7dbfb7f61c3aa5def7b7dad3fa344c1c2858a83b"
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+
 [[deps.PositiveFactorizations]]
 deps = ["LinearAlgebra"]
 git-tree-sha1 = "17275485f373e6673f7e7f97051f703ed5b15b20"
@@ -2449,6 +2545,12 @@ git-tree-sha1 = "13c5103482a8ed1536a54c08d0e742ae3dca2d42"
 uuid = "92933f4c-e287-5a05-a399-4b506db050ca"
 version = "1.10.4"
 
+[[deps.Proj]]
+deps = ["CEnum", "CoordinateTransformations", "GeoFormatTypes", "GeoInterface", "NetworkOptions", "PROJ_jll"]
+git-tree-sha1 = "61188669db4f5b400173e4ec60da8bcb72d6e749"
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+version = "1.9.0"
+
 [[deps.PtrArrays]]
 git-tree-sha1 = "1d36ef11a9aaf1e8b74dacc6a731dd1de8fd493d"
 uuid = "43287f4e-b6f4-7ad1-bb20-aadabca52c3d"
@@ -2676,6 +2778,12 @@ git-tree-sha1 = "330289636fb8107c5f32088d2741e9fd7a061a5c"
 uuid = "94e857df-77ce-4151-89e5-788b33177be4"
 version = "0.1.0"
 
+[[deps.SQLite_jll]]
+deps = ["Artifacts", "JLLWrappers", "Libdl", "Zlib_jll"]
+git-tree-sha1 = "9a325057cdb9b066f1f96dc77218df60fe3007cb"
+uuid = "76ed43ae-9a5d-5a62-8c75-30186b810ce8"
+version = "3.48.0+0"
+
 [[deps.SciMLBase]]
 deps = ["ADTypes", "Accessors", "Adapt", "ArrayInterface", "CommonSolve", "ConstructionBase", "Distributed", "DocStringExtensions", "EnumX", "FunctionWrappersWrappers", "IteratorInterfaceExtensions", "LinearAlgebra", "Logging", "Markdown", "Moshi", "PrecompileTools", "Preferences", "Printf", "RecipesBase", "RecursiveArrayTools", "Reexport", "RuntimeGeneratedFunctions", "SciMLOperators", "SciMLStructures", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface"]
 git-tree-sha1 = "04bbcdc8d1f7d6f667f75fbcc68728231e21fabe"
@@ -2797,6 +2905,12 @@ version = "0.1.5"
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 version = "1.11.0"
 
+[[deps.SortTileRecursiveTree]]
+deps = ["AbstractTrees", "Extents", "GeoInterface"]
+git-tree-sha1 = "f9aa6616a9b3bd01f93f27c010f1d25fc5a094a9"
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+
 [[deps.SortingAlgorithms]]
 deps = ["DataStructures"]
 git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085"
@@ -2836,6 +2950,11 @@ git-tree-sha1 = "95af145932c2ed859b63329952ce8d633719f091"
 uuid = "860ef19b-820b-49d6-a774-d7a799459cd3"
 version = "1.0.3"
 
+[[deps.StableTasks]]
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+
 [[deps.StackViews]]
 deps = ["OffsetArrays"]
 git-tree-sha1 = "be1cf4eb0ac528d96f5115b4ed80c26a8d8ae621"

docs/Project.toml

@@ -4,6 +4,7 @@ BSON = "fbb218c0-5317-5bc6-957e-2ee96dd4b1f0"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 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"
@@ -17,6 +18,7 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 EnsembleKalmanProcesses = "aa8a2aa5-91d8-4396-bcef-d4f2ec43552d"
 Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 Format = "1fa38f19-a742-5d3f-a2b9-30dd87b9d5f8"
+GeoMakie = "db073c08-6b98-4ee5-b6a4-5efafb3259c6"
 HTTP = "cd3eb016-35fb-5094-929b-558a96fad6f3"
 Insolation = "e98cc03f-d57e-4e3c-b70c-8d51efe9e0d8"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
@@ -25,6 +27,7 @@ JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 MethodAnalysis = "85b6ec6f-f7df-4429-9514-a64bcd9ee824"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
+Poppler_jll = "9c32591e-4766-534b-9725-b71a8799265b"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
 Roots = "f2b01f46-fcfa-551c-844a-d8ac1e96c665"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"

docs/list_tutorials.jl

@@ -1,19 +1,20 @@
 tutorials = [
-    "Running land simulations" => [
-        "Bucket LSM" => [
+    "Running Fluxnet simulations" => [
+        "Canopy and soil" => "integrated/soil_canopy_fluxnet_tutorial.jl",
+        "Canopy, soil, and snow" => "integrated/snowy_land_fluxnet_tutorial.jl",
+        "Data processing" =>
+            "Fluxnet forcing and comparison data" => "integrated/fluxnet_data.jl",
+        "Visualization" =>
+            "Fluxnet simulation visualization" => "integrated/fluxnet_vis.jl",
+    ],
+    "Running global simulations" => [
+        "Bucket land model" => [
             "standalone/Bucket/bucket_tutorial.jl",
             "standalone/Bucket/coupled_bucket.jl",
         ],
-        "Integrated soil+canopy modeling" => [
-            "Coupled Canopy and Soil" => "integrated/soil_canopy_tutorial.jl",
-        ],
-        "Handling interactions between model components" => [
-            "Adjusting boundary conditions for the soil" => "integrated/handling_soil_fluxes.jl",
-            "Adjusting boundary conditions for the snow" => "integrated/handling_snow_fluxes.jl",
-        ],
     ],
     "Running standalone component simulations" => [
-        "Soil modeling" => [
+        "Soil" => [
             "Boundary conditions" => "standalone/Soil/boundary_conditions.jl",
             "Richards Equation" => "standalone/Soil/richards_equation.jl",
             "Energy and Hydrology" => "standalone/Soil/soil_energy_hydrology.jl",
@@ -26,21 +27,25 @@ tutorials = [
             "Gilat Loess Evaporation" => "standalone/Soil/evaporation_gilat_loess.jl",
             "Bare soil site" => "standalone/Soil/sublimation.jl",
         ],
-        "Canopy modeling" => [
+        "Canopy" => [
             "Standalone Canopy" => "standalone/Canopy/canopy_tutorial.jl",
         ],
-        "Snow Modeling" => [
+        "Snow" => [
             "standalone/Snow/base_tutorial.jl",
             "standalone/Snow/data_tutorial.jl",
         ],
     ],
-    "Calibrating your ClimaLand model" => [
+    "Calibrating a ClimaLand model" => [
         "Single site perfect model" => "calibration/minimal_working_example.jl",
         "Single site observations" => "calibration/minimal_working_example_obs.jl",
     ],
     "For model developers" => [
         "Intro to standalone models" => "standalone/Usage/model_tutorial.jl",
-        "Intro to multi-component models" => "standalone/Usage/LSM_single_column_tutorial.jl",
+        "Intro to multi-component models" => [
+            "Blah" => "standalone/Usage/LSM_single_column_tutorial.jl",
+            "Adjusting boundary conditions for the soil" => "integrated/handling_soil_fluxes.jl",
+            "Adjusting boundary conditions for the snow" => "integrated/handling_snow_fluxes.jl",
+        ],
         "Intro to ClimaLand Domains" => "standalone/Usage/domain_tutorial.jl",
         "Intro to forced site-level runs" => "shared_utilities/driver_tutorial.jl",
         "Intro to implicit/explicit timestepping" => "shared_utilities/timestepping.jl",

docs/src/tutorials/integrated/fluxnet_data.jl

@@ -0,0 +1 @@
+# # Fluxnet forcing data: LAI, radiation, and atmospheric variables

docs/src/tutorials/integrated/fluxnet_vis.jl

@@ -0,0 +1 @@
+# # Visualizing the output of a Fluxnet simulation