remove ArtifactWrappers from docs

CliMA · Jun 4, 2024 · 0db0092 · 0db0092
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diff --git a/docs/Manifest.toml b/docs/Manifest.toml
@@ -2,7 +2,7 @@
 
 julia_version = "1.10.3"
 manifest_format = "2.0"
-project_hash = "4bb6840a53a8b41815eea340f539147bec0b0ca9"
+project_hash = "bf43a7452b446a9ba967dab8eeb0bc21ba10184f"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "daf26bbdec60d9ca1c0003b70f389d821ddb4224"
@@ -271,38 +271,39 @@ version = "0.10.14"
 
 [[deps.CUDA]]
 deps = ["AbstractFFTs", "Adapt", "BFloat16s", "CEnum", "CUDA_Driver_jll", "CUDA_Runtime_Discovery", "CUDA_Runtime_jll", "Crayons", "DataFrames", "ExprTools", "GPUArrays", "GPUCompiler", "KernelAbstractions", "LLVM", "LLVMLoopInfo", "LazyArtifacts", "Libdl", "LinearAlgebra", "Logging", "NVTX", "Preferences", "PrettyTables", "Printf", "Random", "Random123", "RandomNumbers", "Reexport", "Requires", "SparseArrays", "StaticArrays", "Statistics"]
-git-tree-sha1 = "baa8ea7a1ea63316fa3feb454635215773c9c845"
+git-tree-sha1 = "6e945e876652f2003e6ca74e19a3c45017d3e9f6"
 uuid = "052768ef-5323-5732-b1bb-66c8b64840ba"
-version = "5.2.0"
-weakdeps = ["ChainRulesCore", "SpecialFunctions"]
+version = "5.4.2"
+weakdeps = ["ChainRulesCore", "EnzymeCore", "SpecialFunctions"]
 
     [deps.CUDA.extensions]
     ChainRulesCoreExt = "ChainRulesCore"
+    EnzymeCoreExt = "EnzymeCore"
     SpecialFunctionsExt = "SpecialFunctions"
 
 [[deps.CUDA_Driver_jll]]
 deps = ["Artifacts", "JLLWrappers", "LazyArtifacts", "Libdl", "Pkg"]
-git-tree-sha1 = "d01bfc999768f0a31ed36f5d22a76161fc63079c"
+git-tree-sha1 = "c48f9da18efd43b6b7adb7ee1f93fe5f2926c339"
 uuid = "4ee394cb-3365-5eb0-8335-949819d2adfc"
-version = "0.7.0+1"
+version = "0.9.0+0"
 
 [[deps.CUDA_Runtime_Discovery]]
 deps = ["Libdl"]
-git-tree-sha1 = "38f830504358e9972d2a0c3e5d51cb865e0733df"
+git-tree-sha1 = "5db9da5fdeaa708c22ba86b82c49528f402497f2"
 uuid = "1af6417a-86b4-443c-805f-a4643ffb695f"
-version = "0.2.4"
+version = "0.3.3"
 
 [[deps.CUDA_Runtime_jll]]
 deps = ["Artifacts", "CUDA_Driver_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
-git-tree-sha1 = "8e25c009d2bf16c2c31a70a6e9e8939f7325cc84"
+git-tree-sha1 = "bcba305388e16aa5c879e896726db9e71b4942c6"
 uuid = "76a88914-d11a-5bdc-97e0-2f5a05c973a2"
-version = "0.11.1+0"
+version = "0.14.0+1"
 
 [[deps.CUDNN_jll]]
 deps = ["Artifacts", "CUDA_Runtime_jll", "JLLWrappers", "LazyArtifacts", "Libdl", "TOML"]
-git-tree-sha1 = "75923dce4275ead3799b238e10178a68c07dbd3b"
+git-tree-sha1 = "cbf7d75f8c58b147bdf6acea2e5bc96cececa6d4"
 uuid = "62b44479-cb7b-5706-934f-f13b2eb2e645"
-version = "8.9.4+0"
+version = "9.0.0+1"
 
 [[deps.Cairo]]
 deps = ["Cairo_jll", "Colors", "Glib_jll", "Graphics", "Libdl", "Pango_jll"]
@@ -823,9 +824,9 @@ version = "0.1.1"
 
 [[deps.FastBroadcast]]
 deps = ["ArrayInterface", "LinearAlgebra", "Polyester", "Static", "StaticArrayInterface", "StrideArraysCore"]
-git-tree-sha1 = "a6e756a880fc419c8b41592010aebe6a5ce09136"
+git-tree-sha1 = "699c2556ecdf3b5913c7a57769f8975adf48cf8e"
 uuid = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
-version = "0.2.8"
+version = "0.3.0"
 
 [[deps.FastClosures]]
 git-tree-sha1 = "acebe244d53ee1b461970f8910c235b259e772ef"
@@ -1008,9 +1009,9 @@ version = "0.1.6"
 
 [[deps.GPUCompiler]]
 deps = ["ExprTools", "InteractiveUtils", "LLVM", "Libdl", "Logging", "Scratch", "TimerOutputs", "UUIDs"]
-git-tree-sha1 = "a846f297ce9d09ccba02ead0cae70690e072a119"
+git-tree-sha1 = "518ebd058c9895de468a8c255797b0c53fdb44dd"
 uuid = "61eb1bfa-7361-4325-ad38-22787b887f55"
-version = "0.25.0"
+version = "0.26.5"
 
 [[deps.GR]]
 deps = ["Artifacts", "Base64", "DelimitedFiles", "Downloads", "GR_jll", "HTTP", "JSON", "Libdl", "LinearAlgebra", "Preferences", "Printf", "Random", "Serialization", "Sockets", "TOML", "Tar", "Test", "p7zip_jll"]
@@ -1383,9 +1384,9 @@ version = "3.0.0+1"
 
 [[deps.LLVM]]
 deps = ["CEnum", "LLVMExtra_jll", "Libdl", "Preferences", "Printf", "Requires", "Unicode"]
-git-tree-sha1 = "839c82932db86740ae729779e610f07a1640be9a"
+git-tree-sha1 = "065c36f95709dd4a676dc6839a35d6fa6f192f24"
 uuid = "929cbde3-209d-540e-8aea-75f648917ca0"
-version = "6.6.3"
+version = "7.1.0"
 weakdeps = ["BFloat16s"]
 
     [deps.LLVM.extensions]
@@ -2176,9 +2177,9 @@ version = "0.6.12"
 
 [[deps.RecursiveArrayTools]]
 deps = ["Adapt", "ArrayInterface", "DocStringExtensions", "GPUArraysCore", "IteratorInterfaceExtensions", "LinearAlgebra", "RecipesBase", "SparseArrays", "StaticArraysCore", "Statistics", "SymbolicIndexingInterface", "Tables"]
-git-tree-sha1 = "758bc86b90e9fee2edc4af2a750b0d3f2d5c02c5"
+git-tree-sha1 = "d0f8d22294f932efb1617d669aff73a5c97d38ff"
 uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
-version = "3.19.0"
+version = "3.20.0"
 
     [deps.RecursiveArrayTools.extensions]
     RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
@@ -2938,9 +2939,9 @@ version = "0.2.5"
 
 [[deps.cuDNN]]
 deps = ["CEnum", "CUDA", "CUDA_Runtime_Discovery", "CUDNN_jll"]
-git-tree-sha1 = "d433ec29756895512190cac9c96666d879f07b92"
+git-tree-sha1 = "4909e87d6d62c29a897d54d9001c63932e41cb0e"
 uuid = "02a925ec-e4fe-4b08-9a7e-0d78e3d38ccd"
-version = "1.3.0"
+version = "1.3.2"
 
 [[deps.eudev_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg", "gperf_jll"]

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -1,5 +1,4 @@
 [deps]
-ArtifactWrappers = "a14bc488-3040-4b00-9dc1-f6467924858a"
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"

diff --git a/docs/src/APIs/Bucket.md b/docs/src/APIs/Bucket.md
@@ -19,8 +19,3 @@ ClimaLand.Bucket.surface_albedo
 ClimaLand.Bucket.beta_factor
 ```
 
-## Artifact Path Functions
-
-```@docs
-ClimaLand.Bucket.cesm2_albedo_dataset_path
-```
diff --git a/docs/tutorials/standalone/Soil/evaporation.jl b/docs/tutorials/standalone/Soil/evaporation.jl
@@ -13,7 +13,6 @@ import ClimaParams as CP
 using SurfaceFluxes
 using StaticArrays
 using Dates
-using ArtifactWrappers
 using DelimitedFiles: readdlm
 
 using ClimaLand
@@ -208,17 +207,9 @@ evap = [
     )[1] for k in 1:length(sol.t)
 ]
 savepath = joinpath(pkgdir(ClimaLand), "docs/tutorials/standalone/Soil/")
-evap_dataset = ArtifactWrapper(
-    @__DIR__,
-    "lehmann2008_fig8_evaporation",
-    ArtifactFile[ArtifactFile(
-        url = "https://caltech.box.com/shared/static/cgppw3tx6zdz7h02yt28ri44g1j088ju.csv",
-        filename = "lehmann2008_fig8_evaporation.csv",
-    ),],
-)
-evap_datapath = get_data_folder(evap_dataset)
-ref_soln_E =
-    readdlm(joinpath(evap_datapath, "lehmann2008_fig8_evaporation.csv"), ',')
+evaporation_data =
+    ClimaLand.Artifacts.lehmann_assouline_or2008_evaporation_data();
+ref_soln_E = readdlm(evaporation_data, ',')
 ref_soln_E_350mm = ref_soln_E[2:end, 1:2]
 data_dates = ref_soln_E_350mm[:, 1]
 data_e = ref_soln_E_350mm[:, 2];

diff --git a/docs/tutorials/standalone/Soil/evaporation_gilat_loess.jl b/docs/tutorials/standalone/Soil/evaporation_gilat_loess.jl
@@ -22,7 +22,6 @@ import ClimaParams as CP
 using SurfaceFluxes
 using StaticArrays
 using Dates
-using ArtifactWrappers
 using DelimitedFiles: readdlm
 
 using ClimaLand

diff --git a/docs/tutorials/standalone/Soil/freezing_front.jl b/docs/tutorials/standalone/Soil/freezing_front.jl
@@ -74,7 +74,6 @@
 # # Import necessary modules
 import SciMLBase
 import ClimaTimeSteppers as CTS
-using ArtifactWrappers
 using DelimitedFiles
 using CairoMakie
 
@@ -219,14 +218,8 @@ sol = SciMLBase.solve(prob, ode_algo; dt = dt, saveat = 0:3600:tf);
 # This data was obtained by us from the figures of Hansson et al. (2004), but was originally obtained
 # by Mizoguchi (1990). No error bars were reported, and we haven't quantified the error in our
 # estimation of the data from images.
-af = ArtifactFile(
-    url = "https://caltech.box.com/shared/static/3xbo4rlam8u390vmucc498cao6wmqlnd.csv",
-    filename = "mizoguchi_all_data.csv",
-)
-dataset = ArtifactWrapper(@__DIR__, "mizoguchi", ArtifactFile[af]);
-dataset_path = get_data_folder(dataset);
-data = joinpath(dataset_path, "mizoguchi_all_data.csv")
-ds = readdlm(data, ',')
+dataset_path = ClimaLand.Artifacts.mizoguchi1990_soil_freezing_data();
+ds = readdlm(dataset_path, ',')
 hours = ds[:, 1][2:end]
 vwc = ds[:, 2][2:end] ./ 100.0
 depth = ds[:, 3][2:end]

diff --git a/docs/tutorials/standalone/Soil/layered_soil.jl b/docs/tutorials/standalone/Soil/layered_soil.jl
@@ -4,7 +4,7 @@
 # Can. J. Soil Sci. (2011) 91: 169183 doi:10.4141/CJSS09118,
 # which measured the infiltration of layered soil in Fort McMurray,
 # Alberta, Canada. We thank Mingbin Huang and S. Lee Barbour for
-# correspondence and support, including sharing of data, with us
+# correspondence and support, including sharing of data, with us.
 # Note that all data used in this tutorial is available in their
 # publication.
 
@@ -15,7 +15,6 @@ import SciMLBase
 import ClimaTimeSteppers as CTS
 using ClimaCore
 import ClimaParams as CP
-using ArtifactWrappers
 using DelimitedFiles: readdlm
 
 using ClimaLand
@@ -41,14 +40,8 @@ soil_domain = Column(; zlim = (zmin, zmax), nelements = nelems);
 # Infiltration and drainage processes in multi-layered coarse soils
 # Mingbin Huang et. al.
 # Can. J. Soil Sci. (2011) 91: 169183 doi:10.4141/CJSS09118
-af = ArtifactFile(
-    url = "https://caltech.box.com/shared/static/qvbt37xkwz8gveyi6tzzbs0e18trpcsq.csv",
-    filename = "sv_62.csv",
-)
-dataset = ArtifactWrapper(@__DIR__, "sv62", ArtifactFile[af]);
-dataset_path = get_data_folder(dataset);
-data = joinpath(dataset_path, af.filename)
-parameter_data = readdlm(data, ',');
+data_file = ClimaLand.Artifacts.huang_et_al2011_soil_van_genuchten_data();
+parameter_data = readdlm(data_file, ',');
 # Our model treats z as increasing in the upwards direction.
 # Values below the surface are negative.
 # Because of this, we convert the (positive-valued) depth

diff --git a/docs/tutorials/standalone/Soil/sublimation.jl b/docs/tutorials/standalone/Soil/sublimation.jl
@@ -12,7 +12,6 @@ import ClimaParams as CP
 using SurfaceFluxes
 using StaticArrays
 using Dates
-using ArtifactWrappers
 using DelimitedFiles: readdlm
 
 using ClimaLand

diff --git a/src/Artifacts.jl b/src/Artifacts.jl
@@ -221,6 +221,137 @@ function topmodel_data_path(; context = nothing)
     )
     path = joinpath(get_data_folder(topmodel_dataset), "means_2.5_new.nc")
     return path
+
+end
+
+"""
+    lehmann_assouline_or2008_evaporation_data(; context=nothing)
+
+Local path to file containing measured evaporation rate as a function of time
+for bare soil.
+
+Data was originally collected by Lehmann, Peter, Shmuel Assouline, 
+and Dani Or. "Characteristic lengths affecting evaporative drying of 
+porous media." Physical Review E 77.5 (2008): 056309 and presented
+in Figure 8 of that work.
+
+https://doi.org/10.1103/PhysRevE.77.056309
+"""
+function lehmann_assouline_or2008_evaporation_data(; context = nothing)
+    dir = joinpath(@__DIR__, "../")
+    evap_dataset = ArtifactWrapper(
+        dir,
+        "lehmann2008_fig8_evaporation",
+        ArtifactFile[ArtifactFile(
+            url = "https://caltech.box.com/shared/static/cgppw3tx6zdz7h02yt28ri44g1j088ju.csv",
+            filename = "lehmann2008_fig8_evaporation.csv",
+        ),],
+    )
+    evap_datapath = get_data_folder(evap_dataset)
+    return joinpath(evap_datapath, "lehmann2008_fig8_evaporation.csv")
+end
+
+"""
+    huang_et_al2011_soil_van_genuchten_data(; context=nothing)
+
+Local path to file containing soil van Genuchten parameters as a 
+function of depth for soil
+from site SV62 in Fort McMurray, Alberta, Canada.
+
+Data was originally collected by Huang, Mingbin, et al. 
+"Infiltration and drainage processes in multi-layered coarse soils." 
+Canadian Journal of Soil Science 91.2 (2011): 169-183 
+and presented in Table 1b of that work.
+
+https://doi.org/10.4141/cjss09118
+"""
+function huang_et_al2011_soil_van_genuchten_data(; context = nothing)
+    dir = joinpath(@__DIR__, "../")
+    af = ArtifactFile(
+        url = "https://caltech.box.com/shared/static/qvbt37xkwz8gveyi6tzzbs0e18trpcsq.csv",
+        filename = "sv_62.csv",
+    )
+    dataset = ArtifactWrapper(dir, "sv62", ArtifactFile[af])
+    dataset_path = get_data_folder(dataset)
+    return joinpath(dataset_path, af.filename)
+end
+
+"""
+    mizoguchi1990_soil_freezing_data(; context=nothing)
+
+Local path to file containing soil volumetric content as a function 
+of depth and time during a freezing 
+soil column experiment.
+
+Data was originally collected in Mizoguchi, M. 1990. Water, heat and 
+salt transport in freezing soil, Ph.D. thesis. (In Japanese.) 
+University of Tokyo, Tokyo.
+
+Data was obtained by us from Figure 4 of Hansson, Klas, et al. 
+"Water flow and heat transport in frozen soil: Numerical solution 
+and freeze–thaw applications." Vadose Zone Journal 3.2 (2004): 693-704 
+using a plot digitizer; we did not quantify uncertainties introduced 
+in this process.
+"""
+function mizoguchi1990_soil_freezing_data(; context = nothing)
+    dir = joinpath(@__DIR__, "../")
+    af = ArtifactFile(
+        url = "https://caltech.box.com/shared/static/3xbo4rlam8u390vmucc498cao6wmqlnd.csv",
+        filename = "mizoguchi_all_data.csv",
+    )
+    dataset = ArtifactWrapper(dir, "mizoguchi", ArtifactFile[af])
+    dataset_path = joinpath(get_data_folder(dataset), "mizoguchi_all_data.csv")
+    return dataset_path
+end
+
+"""
+    cesm2_albedo_dataset_path()
+
+Triggers the download of the CESM2 land albedo dataset, if not
+already downloaded, using Julia Artifacts, and returns the path to
+this file.
+
+This dataset contains monthly albedo data from 15/01/1850
+to 15/12/2014.
+"""
+function cesm2_albedo_dataset_path(; context = nothing)
+    dir = joinpath(@__DIR__, "../")
+    land_albedo_dataset = ArtifactWrapper(
+        dir,
+        "land_albedo",
+        ArtifactFile[ArtifactFile(
+            url = "https://caltech.box.com/shared/static/eesee8iv3c21z3pysizcgnuncfp5xykv.nc",
+            filename = "esw_albedo_Amon_CESM2_historical_r1i1p1f1_gn_185001-201412_v2.nc",
+        ),],
+    )
+    path = get_data_folder(land_albedo_dataset)
+    return joinpath(
+        path,
+        "esw_albedo_Amon_CESM2_historical_r1i1p1f1_gn_185001-201412_v2.nc",
+    )
+end
+
+"""
+    bareground_albedo_dataset_path()
+
+Triggers the download of the average bareground land albedo dataset, if not
+already downloaded, using Julia Artifacts, and returns the path to
+this file.
+
+This dataset does not contain a time component.
+"""
+function bareground_albedo_dataset_path(; context = nothing)
+    dir = joinpath(@__DIR__, "../")
+    bareground_albedo_dataset = ArtifactWrapper(
+        dir,
+        "bareground_albedo",
+        ArtifactFile[ArtifactFile(
+            url = "https://caltech.box.com/shared/static/ga9385kyl82t955dylsbnn4x51b412md.nc",
+            filename = "bareground_albedo.nc",
+        ),],
+    )
+    path = get_data_folder(bareground_albedo_dataset)
+    return joinpath(path, "bareground_albedo.nc")
 end
 
 end