Fixes for Oceananigans v0.102 (#705)

* fixes for Oceananigans v0.102

* bump patch release

* revert

* some more updates to OS Papa exampe

* remove ClimaOcean

* back to n = Observable(1)

* fix doctests

* remove redundancy

Author: navidcy

Project.toml

@@ -1,7 +1,7 @@
 name = "ClimaOcean"
 uuid = "0376089a-ecfe-4b0e-a64f-9c555d74d754"
 license = "MIT"
-version = "0.8.9"
+version = "0.8.10"
 authors = ["Climate Modeling Alliance and contributors"]
 
 [deps]

docs/Project.toml

@@ -16,5 +16,5 @@ XESMF = "2e0b0046-e7a1-486f-88de-807ee8ffabe5"
 [compat]
 Documenter = "1"
 DocumenterCitations = "1.3"
-XESMF = "0.1.6"
 Literate = "2.2"
+XESMF = "0.1.6"

docs/make.jl

@@ -17,13 +17,17 @@ bib = CitationBibliography(bib_filepath, style=:authoryear)
 const EXAMPLES_DIR = joinpath(@__DIR__, "..", "examples")
 const OUTPUT_DIR   = joinpath(@__DIR__, "src/literated")
 
-to_be_literated = [
-    "single_column_os_papa_simulation.jl",
-    "one_degree_simulation.jl",
-    "near_global_ocean_simulation.jl",
-    "global_climate_simulation.jl",
+ examples_pages = [
+    "Single-column ocean simulation" => "literated/single_column_os_papa_simulation.md",
+    "One-degree ocean--sea ice simulation" => "literated/one_degree_simulation.md",
+    "Near-global ocean simulation" => "literated/near_global_ocean_simulation.md",
+    "Global climate simulation" => "literated/global_climate_simulation.md",
 ]
 
+to_be_literated = map(examples_pages) do (_, mdpath)
+    replace(basename(mdpath), ".md" => ".jl")
+end
+
 for file in to_be_literated
     filepath = joinpath(EXAMPLES_DIR, file)
     withenv("JULIA_DEBUG" => "Literate") do
@@ -44,12 +48,7 @@ format = Documenter.HTML(collapselevel = 2,
 pages = [
     "Home" => "index.md",
 
-    "Examples" => [
-        "Single-column ocean simulation" => "literated/single_column_os_papa_simulation.md",
-        "One-degree ocean--sea ice simulation" => "literated/one_degree_simulation.md",
-        "Near-global ocean simulation" => "literated/near_global_ocean_simulation.md",
-        "Global climate simulation" => "literated/global_climate_simulation.md",
-        ],
+    "Examples" => examples_pages,
 
     "Vertical grids" => "vertical_grids.md",
 

examples/single_column_os_papa_simulation.jl

@@ -3,21 +3,21 @@
 # In this example, we simulate the evolution of an ocean water column
 # forced by an atmosphere derived from the JRA55 re-analysis.
 # The simulated column is located at ocean station
-# Papa (144.9ᵒ W and 50.1ᵒ N)
+# Papa (144.9ᵒ W and 50.1ᵒ N).
 #
 # ## Install dependencies
 #
 # First let's make sure we have all required packages installed.
 
 # ```julia
 # using Pkg
-# pkg"add Oceananigans, ClimaOcean, CairoMakie"
+# pkg"add Oceananigans, ClimaOcean, Dates, CairoMakie"
 # ```
 
 using ClimaOcean
 using Oceananigans
 using Oceananigans.Units
-using Oceananigans.BuoyancyFormulations: buoyancy_frequency
+using Oceananigans.Models: buoyancy_frequency
 using Dates
 using Printf
 
@@ -54,7 +54,7 @@ set!(ocean.model, T=Metadatum(:temperature, dataset=ECCO4Monthly()),
 
 # # A prescribed atmosphere based on JRA55 re-analysis
 #
-# We build a PrescribedAtmosphere at the same location as the single-colunm grid
+# We build a `JRA55PrescribedAtmosphere` at the same location as the single-colunm grid
 # which is based on the JRA55 reanalysis.
 
 atmosphere = JRA55PrescribedAtmosphere(longitude = λ★,
@@ -72,7 +72,7 @@ ua = interior(atmosphere.velocities.u, 1, 1, 1, :)
 va = interior(atmosphere.velocities.v, 1, 1, 1, :)
 Ta = interior(atmosphere.tracers.T, 1, 1, 1, :)
 qa = interior(atmosphere.tracers.q, 1, 1, 1, :)
-t_days = atmosphere.times[1:length(ua)] / days
+t_days = atmosphere.times / days
 
 using CairoMakie
 
@@ -169,6 +169,8 @@ simulation.output_writers[:jld2] = JLD2Writer(ocean.model, outputs; filename,
 
 run!(simulation)
 
+# Now let's load the saved output and visualise.
+
 filename *= ".jld2"
 
 u  = FieldTimeSeries(filename, "u")
@@ -208,14 +210,14 @@ Qlwt = zeros(Nt)
 Pt   = zeros(Nt)
 
 for n = 1:Nt
-    t = times[n]
-    uat[n]  =  ua[1, 1, 1, Time(t)]
-    vat[n]  =  va[1, 1, 1, Time(t)]
-    Tat[n]  =  Ta[1, 1, 1, Time(t)]
-    qat[n]  =  qa[1, 1, 1, Time(t)]
-    Qswt[n] = Qsw[1, 1, 1, Time(t)]
-    Qlwt[n] = Qlw[1, 1, 1, Time(t)]
-    Pt[n]   =  Pr[1, 1, 1, Time(t)] + Ps[1, 1, 1, Time(t)]
+    t = Oceananigans.Units.Time(times[n])
+    uat[n]  =  ua[1, 1, 1, t]
+    vat[n]  =  va[1, 1, 1, t]
+    Tat[n]  =  Ta[1, 1, 1, t]
+    qat[n]  =  qa[1, 1, 1, t]
+    Qswt[n] = Qsw[1, 1, 1, t]
+    Qlwt[n] = Qlw[1, 1, 1, t]
+    Pt[n]   =  Pr[1, 1, 1, t] + Ps[1, 1, 1, t]
 end
 
 fig = Figure(size=(1800, 1800))
@@ -281,44 +283,40 @@ axislegend(axF)
 lines!(axS, times, interior(S, 1, 1, Nz, :))
 vlines!(axS, tn, linewidth=4, color=(:black, 0.5))
 
-zc = znodes(T)
-zf = znodes(κ)
-un  = @lift interior(u[$n],  1, 1, :)
-vn  = @lift interior(v[$n],  1, 1, :)
-Tn  = @lift interior(T[$n],  1, 1, :)
-Sn  = @lift interior(S[$n],  1, 1, :)
-κn  = @lift interior(κ[$n],  1, 1, :)
-en  = @lift interior(e[$n],  1, 1, :)
-N²n = @lift interior(N²[$n], 1, 1, :)
-
-scatterlines!(axuz, un,  zc, label="u")
-scatterlines!(axuz, vn,  zc, label="v")
-scatterlines!(axTz, Tn,  zc)
-scatterlines!(axSz, Sn,  zc)
-scatterlines!(axez, en,  zc)
-scatterlines!(axNz, N²n, zf)
-scatterlines!(axκz, κn,  zf)
+un  = @lift u[$n]
+vn  = @lift v[$n]
+Tn  = @lift T[$n]
+Sn  = @lift S[$n]
+κn  = @lift κ[$n]
+en  = @lift e[$n]
+N²n = @lift N²[$n]
+
+scatterlines!(axuz, un, label="u")
+scatterlines!(axuz, vn, label="v")
+scatterlines!(axTz, Tn)
+scatterlines!(axSz, Sn)
+scatterlines!(axez, en)
+scatterlines!(axNz, N²n)
+scatterlines!(axκz, κn)
 
 axislegend(axuz)
 
 ulim = max(maximum(abs, u), maximum(abs, v))
 xlims!(axuz, -ulim, ulim)
 
-Tmax = maximum(interior(T))
-Tmin = minimum(interior(T))
+Tmin, Tmax = extrema(T)
 xlims!(axTz, Tmin - 0.1, Tmax + 0.1)
 
-Nmax = maximum(interior(N²))
+Nmax = maximum(N²)
 xlims!(axNz, -Nmax/10, Nmax * 1.05)
 
-κmax = maximum(interior(κ))
+κmax = maximum(κ)
 xlims!(axκz, 1e-9, κmax * 1.1)
 
-emax = maximum(interior(e))
+emax = maximum(e)
 xlims!(axez, 1e-11, emax * 1.1)
 
-Smax = maximum(interior(S))
-Smin = minimum(interior(S))
+Smin, Smax = extrema(S)
 xlims!(axSz, Smin - 0.2, Smax + 0.2)
 
 CairoMakie.record(fig, "single_column_profiles.mp4", 1:Nt, framerate=24) do nn

src/OceanSeaIceModels/InterfaceComputations/coefficient_based_turbulent_fluxes.jl

@@ -71,8 +71,8 @@ interfaces = ComponentInterfaces(nothing, ocean; atmosphere_ocean_fluxes=ao_flux
 
 # output
 ┌ Warning: Split barotropic-baroclinic time stepping with SplitRungeKutta3TimeStepper is experimental.
-│ Use at own risk, and report any issues encountered at [https://github.com/CliMA/Oceananigans.jl/issues](https://github.com/CliMA/Oceananigans.jl/issues).
-└ @ Oceananigans.TimeSteppers ~/.julia/packages/Oceananigans/fI8pm/src/TimeSteppers/split_hydrostatic_runge_kutta_3.jl:59
+│ Use at own risk, and report any issues encountered at https://github.com/CliMA/Oceananigans.jl/issues.
+└ @ Oceananigans.TimeSteppers ~/.julia/packages/Oceananigans/cQglC/src/TimeSteppers/split_hydrostatic_runge_kutta_3.jl:59
 ComponentInterfaces
 ```
 """

src/OceanSeaIceModels/ocean_sea_ice_model.jl

@@ -138,8 +138,8 @@ model = OceanSeaIceModel(ocean; interfaces)
 
 # output
 ┌ Warning: Split barotropic-baroclinic time stepping with SplitRungeKutta3TimeStepper is experimental.
-│ Use at own risk, and report any issues encountered at [https://github.com/CliMA/Oceananigans.jl/issues](https://github.com/CliMA/Oceananigans.jl/issues).
-└ @ Oceananigans.TimeSteppers ~/.julia/packages/Oceananigans/fI8pm/src/TimeSteppers/split_hydrostatic_runge_kutta_3.jl:59
+│ Use at own risk, and report any issues encountered at https://github.com/CliMA/Oceananigans.jl/issues.
+└ @ Oceananigans.TimeSteppers ~/.julia/packages/Oceananigans/cQglC/src/TimeSteppers/split_hydrostatic_runge_kutta_3.jl:59
 OceanSeaIceModel{CPU}(time = 0 seconds, iteration = 0)
 ├── ocean: HydrostaticFreeSurfaceModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
 ├── atmosphere: Nothing