Fix bug with ECCO metadata_url and urls both adding a trailing /

.gitignore

@@ -1,4 +1,5 @@
 /Manifest.toml
+docs/Manifest.toml
 
 # Files generated by invoking Julia with --code-coverage
 *.jl.cov

docs/Project.toml

@@ -6,10 +6,12 @@ Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Literate = "98b081ad-f1c9-55d3-8b20-4c87d4299306"
 Oceananigans = "9e8cae18-63c1-5223-a75c-80ca9d6e9a09"
 OrthogonalSphericalShellGrids = "c2be9673-fb75-4747-82dc-aa2bb9f4aed0"
+SeawaterPolynomials = "d496a93d-167e-4197-9f49-d3af4ff8fe40"
 
 [compat]
 CairoMakie = "0.10.12, 0.11, 0.12"
 DataDeps = "0.7"
 Documenter = "1"
-Oceananigans = "0.95.2 - 0.99"
-OrthogonalSphericalShellGrids = "0.2.0"
+Oceananigans = "0.95.4 - 0.99"
+OrthogonalSphericalShellGrids = "0.2.1"
+SeawaterPolynomials = "0.3.4"

docs/make.jl

@@ -13,7 +13,7 @@ const EXAMPLES_DIR = joinpath(@__DIR__, "..", "examples")
 const OUTPUT_DIR   = joinpath(@__DIR__, "src/literated")
 
 to_be_literated = [
-    # "ecco_inspect_temperature_salinity.jl",
+    "ecco_inspect_temperature_salinity.jl",
     "generate_bathymetry.jl",
     "generate_surface_fluxes.jl",
     "single_column_os_papa_simulation.jl",
@@ -41,7 +41,7 @@ pages = [
     "Home" => "index.md",
 
     "Examples" => [
-        # "Inspect ECCO2 data" => "literated/ecco_inspect_temperature_salinity.md",
+        "Inspect ECCO2 data" => "literated/ecco_inspect_temperature_salinity.md",
         "Generate bathymetry" => "literated/generate_bathymetry.md",
         "Surface fluxes" => "literated/generate_surface_fluxes.md",
         "Single-column simulation" => "literated/single_column_os_papa_simulation.md",
@@ -59,7 +59,7 @@ pages = [
 
 makedocs(sitename = "ClimaOcean.jl";
          format,
-         pages, 
+         pages,
          modules = [ClimaOcean],
          doctest = true,
          clean = true,

examples/ecco_inspect_temperature_salinity.jl

@@ -1,7 +1,7 @@
 using Oceananigans
 using Oceananigans.ImmersedBoundaries: mask_immersed_field!
 
-using GLMakie
+using CairoMakie
 using Printf
 using ClimaOcean
 using ClimaOcean.DataWrangling.ECCO: ECCO_field, ECCOFieldTimeSeries
@@ -32,7 +32,7 @@ T = CenterField(grid)
 S = CenterField(grid)
 
 using SeawaterPolynomials: TEOS10EquationOfState
-using Oceananigans.BuoyancyModels: buoyancy
+using Oceananigans.BuoyancyFormulations: buoyancy
 
 equation_of_state = TEOS10EquationOfState()
 sb = SeawaterBuoyancy(; equation_of_state)
@@ -83,5 +83,4 @@ Colorbar(fig[1, 2], hmT, label="Temperature (ᵒC)")
 Colorbar(fig[2, 2], hmS, label="Salinity (g kg⁻¹)")
 Colorbar(fig[3, 2], hmb, label="Buoyancy difference (m s⁻²)")
 
-display(fig)
-
+fig

examples/ecco_mixed_layer_depth.jl

@@ -2,7 +2,7 @@ using ClimaOcean
 using ClimaOcean.Diagnostics: MixedLayerDepthField
 using ClimaOcean.DataWrangling.ECCO: ECCO_field, ECCOFieldTimeSeries
 using Oceananigans
-using GLMakie
+using CairoMakie
 using Printf
 using CFTime
 using Dates
@@ -23,7 +23,7 @@ grid = LatitudeLongitudeGrid(arch; z,
                              latitude  = (-80, 80),
                              longitude = (0, 360))
 
-bottom_height = regrid_bathymetry(grid; 
+bottom_height = regrid_bathymetry(grid;
                                   minimum_depth = 10,
                                   interpolation_passes = 5,
                                   major_basins = 1)
@@ -73,7 +73,9 @@ Label(fig[1, 1], str, tellwidth=false)
 hn = @lift ht[$n]
 hm = heatmap!(axh, hn, colorrange=(0, 500), colormap=:magma, nan_color=:lightgray)
 Colorbar(fig[2, 2], hm, label="Mixed layer depth (m)")
-display(fig)
+fig
+
+# And record a movie
 
 record(fig, "ecco_mld.mp4", 1:Nt-1, framerate=4) do nn
     @info "Drawing frame $nn of $Nt..."

src/DataWrangling/ECCO/ECCO_metadata.jl

@@ -197,24 +197,36 @@ ECCO_location = Dict(
 )
 
 # URLs for the ECCO datasets specific to each version
-urls(::ECCOMetadata{<:Any, <:ECCO2Monthly}) = "https://ecco.jpl.nasa.gov/drive/files/ECCO2/cube92_latlon_quart_90S90N/monthly/"
-urls(::ECCOMetadata{<:Any, <:ECCO2Daily})   = "https://ecco.jpl.nasa.gov/drive/files/ECCO2/cube92_latlon_quart_90S90N/daily/"
-urls(::ECCOMetadata{<:Any, <:ECCO4Monthly}) = "https://ecco.jpl.nasa.gov/drive/files/Version4/Release4/interp_monthly/"
+urls(::ECCOMetadata{<:Any, <:ECCO2Monthly}) = "https://ecco.jpl.nasa.gov/drive/files/ECCO2/cube92_latlon_quart_90S90N/monthly"
+urls(::ECCOMetadata{<:Any, <:ECCO2Daily})   = "https://ecco.jpl.nasa.gov/drive/files/ECCO2/cube92_latlon_quart_90S90N/daily"
+urls(::ECCOMetadata{<:Any, <:ECCO4Monthly}) = "https://ecco.jpl.nasa.gov/drive/files/Version4/Release4/interp_monthly"
 
 """
     download_dataset(metadata::ECCOMetadata; url = urls(metadata))
 
-Download the dataset specified by `ECCOMetadata`. If `ECCOMetadata.dates` is a single date, 
+Download the dataset specified by `ECCOMetadata`. If `ECCOMetadata.dates` is a single date,
 the dataset is downloaded directly. If `ECCOMetadata.dates` is a vector of dates, each date
 is downloaded individually.
+
 The data download requires a username and password to be provided in the `ECCO_USERNAME` and
 `ECCO_PASSWORD` environment variables. This can be done by exporting the environment variables
-in the shell before running the script, or by launching julia with 
+in the shell before running the script, or by launching julia with
 
 ```
-ECCO_USERNAME=myusername ECCO_PASSWORD=mypassword julia 
+ECCO_USERNAME=myusername ECCO_PASSWORD=mypassword julia
+```
+
+or by invoking
+
+```julia
+julia> ENV["ECCO_USERNAME"] = "myusername"
+
+julia> ENV["ECCO_PASSWORD"] = "mypassword"
 ```
 
+within julia.
+
+
 Arguments
 =========
 - `metadata::ECCOMetadata`: The metadata specifying the dataset to be downloaded.
@@ -223,7 +235,7 @@ function download_dataset(metadata::ECCOMetadata; url = urls(metadata))
     username = get(ENV, "ECCO_USERNAME", nothing)
     password = get(ENV, "ECCO_PASSWORD", nothing)
     dir = metadata.dir
-    
+
     # Create a temporary directory to store the .netrc file
     # The directory will be deleted after the download is complete
     @root mktempdir(dir) do tmp
@@ -254,6 +266,6 @@ function download_dataset(metadata::ECCOMetadata; url = urls(metadata))
             end
         end
     end
-    
+
     return nothing
 end