(0.5.1) Metadata for JRA55 (#286)

* start modifying the data structure

* going on...

* comment

* add some changes

* in their folder

* modernize

* start changing stuff

* starting a bit

* let's go

* correct alias

* correct dates

* syntax

* more updates

* all this should work?

* clear comments

* vestigial code

* works

* veeery much simplified

* this part is already done

* back to working

* works

* improve show method

* change names

* remove vestigial code

* tests should pass

* no bang for download_dataset

* fix tests

* fixed all tests?

* more usefull comments

* fix a couple of stuff

* probably correct now

* last fix

* remove extra line

* add a default architecture

* correct default

* fixed all tests

* another bugfix

* churning on

* this should be ready to merge

* add correct tests

* fix tests

* fix tests

* updTE CLIMA COMMON

* Update metadata.jl

* fix delta

* fix bugs

* rivers and icebergs should be fixed

* chnage to DateTime

* bugfix

* bugfix

* bugfix

* some fixes

* correct examples

* more bugfixing

* bugfix

* fix examples

* export Metadata

* update compats

* fix typo in comment

* fix stray spaces

* add .vscode

* add Oceananigans.defaults.FloatType = Float32 in example

* infer FT in SimilarityTheoryFluxes from ocean_grid

* remove spaces

* slice times

* unify interfaces

* export all_dates

* export all_dates

* formatting fixes

* scalar indexing error

* pass the grid

* change version to dataset

* add start_date end_date

* fix example

* bugfix

* bugfix

* bump up

---------

Co-authored-by: Navid C. Constantinou <[email protected]>

Author: simone-silvestri

.buildkite/pipeline.yml

@@ -34,9 +34,9 @@ steps:
   - wait
 
   - label: "CPU JRA55 tests"
-    key: "cpu_jra55_tests"
+    key: "cpu_JRA55_tests"
     env:
-      TEST_GROUP: "jra55"
+      TEST_GROUP: "JRA55"
     commands:
       - "julia --project -e 'using Pkg; Pkg.test()'"
     agents:
@@ -78,9 +78,9 @@ steps:
       slurm_ntasks: 1
 
   - label: "GPU JRA55 tests"
-    key: "gpu_jra55_tests"
+    key: "gpu_JRA55_tests"
     env:
-      TEST_GROUP: "jra55"
+      TEST_GROUP: "JRA55"
       GPU_TEST: "true"
     commands:
       - "julia --project -e 'using Pkg; Pkg.test()'"

.gitignore

@@ -21,7 +21,7 @@ docs/build/
 docs/site/
 docs/src/literated/
 
-# Output files 
+# Output files
 *.nc
 *.jld2
 *.mp4
@@ -57,3 +57,6 @@ docs/src/literated/
 *.tls
 *.tpc
 *.txt
+
+# vscode
+.vscode

Project.toml

@@ -2,7 +2,7 @@ name = "ClimaOcean"
 uuid = "0376089a-ecfe-4b0e-a64f-9c555d74d754"
 license = "MIT"
 authors = ["Climate Modeling Alliance and contributors"]
-version = "0.5.0"
+version = "0.5.1"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

docs/src/index.md

@@ -49,7 +49,7 @@ grid = ImmersedBoundaryGrid(grid, GridFittedBottom(bathymetry))
 
 # Build an ocean simulation initialized to the ECCO state estimate on Jan 1, 1993
 ocean = ClimaOcean.ocean_simulation(grid)
-date  = DateTimeProlepticGregorian(1993, 1, 1)
+date  = DateTime(1993, 1, 1)
 set!(ocean.model, T = ClimaOcean.ECCOMetadata(:temperature; date),
                   S = ClimaOcean.ECCOMetadata(:salinity; date))
 

examples/ecco_inspect_temperature_salinity.jl

@@ -4,7 +4,7 @@ using Oceananigans.ImmersedBoundaries: mask_immersed_field!
 using CairoMakie
 using Printf
 using ClimaOcean
-using ClimaOcean.DataWrangling.ECCO: ECCO_field, ECCOFieldTimeSeries
+using ClimaOcean.DataWrangling.ECCO: ECCO_field, ECCOFieldTimeSeries, ECCO4Monthly
 using CFTime
 using Dates
 
@@ -39,12 +39,12 @@ sb = SeawaterBuoyancy(; equation_of_state)
 tracers = (T=T, S=S)
 b = Field(buoyancy(sb, grid, tracers))
 
-start = DateTimeProlepticGregorian(1993, 1, 1)
-stop  = DateTimeProlepticGregorian(1999, 1, 1)
+start = DateTime(1993, 1, 1)
+stop  = DateTime(1999, 1, 1)
 dates = range(start; stop, step=Month(1))
 
-Tmeta = ECCOMetadata(:temperature; dates)
-Smeta = ECCOMetadata(:salinity; dates)
+Tmeta = Metadata(:temperature; dates, dataset=ECCO4Monthly())
+Smeta = Metadata(:salinity; dates, dataset=ECCO4Monthly())
 
 Tt = ECCOFieldTimeSeries(Tmeta, grid; time_indices_in_memory=length(dates))
 St = ECCOFieldTimeSeries(Smeta, grid; time_indices_in_memory=length(dates))

examples/ecco_mixed_layer_depth.jl

@@ -1,6 +1,6 @@
 using ClimaOcean
 using ClimaOcean.Diagnostics: MixedLayerDepthField
-using ClimaOcean.DataWrangling.ECCO: ECCO_field, ECCOFieldTimeSeries
+using ClimaOcean.DataWrangling.ECCO: ECCO_field, ECCOFieldTimeSeries, ECCO4Monthly
 using Oceananigans
 using CairoMakie
 using Printf
@@ -34,8 +34,8 @@ start = DateTimeProlepticGregorian(1993, 1, 1)
 stop  = DateTimeProlepticGregorian(2003, 1, 1)
 dates = range(start; stop, step=Month(1))
 
-Tmeta = ECCOMetadata(:temperature; dates)
-Smeta = ECCOMetadata(:salinity; dates)
+Tmeta = Metadata(:temperature; dates, dataset=ECCO4Monthly())
+Smeta = Metadata(:salinity; dates, dataset=ECCO4Monthly())
 
 Tt = ECCOFieldTimeSeries(Tmeta, grid; time_indices_in_memory=2)
 St = ECCOFieldTimeSeries(Smeta, grid; time_indices_in_memory=2)

examples/generate_atmos_dataset.jl

@@ -43,19 +43,19 @@ save("ECCO_continents.png", fig) #hide
 # - downwelling shortwave radiation
 # - downwelling longwave radiation
 #
-# We invoke the constructor with only the first two time indices, corresponding to 
-# January 1st (at 00:00 AM and 03:00 AM).
+# We load in memory only the first two time indices, corresponding to January 1st
+# (at 00:00 AM and 03:00 AM), by using `JRA55NetCDFBackend(2)`.
 
-atmosphere = JRA55PrescribedAtmosphere(1:2; backend = InMemory())
+atmosphere = JRA55PrescribedAtmosphere(; backend = JRA55NetCDFBackend(2))
 ocean = ocean_simulation(grid, closure=nothing)
 
 # Now that we have an atmosphere and ocean, we `set!` the ocean temperature and salinity
 # to the ECCO2 data by first creating T, S metadata objects,
 
-T_metadata = ECCOMetadata(:temperature)
-S_metadata = ECCOMetadata(:salinity)
+T_metadata = Metadata(:temperature; dataset=ECCO4Monthly())
+S_metadata = Metadata(:salinity; dataset=ECCO4Monthly())
 
-# Note that if a date is not provided to `ECCOMetadata`, then the default Jan 1st, 1992 is used.
+# Note that if a date is not provided to `Metadata`, then the default Jan 1st, 1992 is used.
 # To copy the ECCO state into `ocean.model`, we use `set!`,
 
 set!(ocean.model; T=T_metadata, S=S_metadata)
@@ -65,7 +65,7 @@ set!(ocean.model; T=T_metadata, S=S_metadata)
 # uses the two-band shortwave (visible and UV) + longwave (mid and far infrared)
 # decomposition of the radiation spectrum.
 
-coupled_model = OceanSeaIceModel(ocean; atmosphere, radiation=Radiation())
+coupled_model = OceanSeaIceModel(ocean; atmosphere, radiation=Radiation(eltype))
 
 # # Now that the surface fluxes are computed, we can extract and visualize them.
 # # The turbulent fluxes are stored in `coupled_modelinterfaces.atmosphere_ocean_interface.fluxes`.
@@ -91,4 +91,5 @@ ax = Axis(fig[3, 1], title = "Water vapor flux (kg m⁻² s⁻¹)", xlabel = "Lo
 heatmap!(ax, λ, φ, interior(fluxes.water_vapor, :, :, 1); colormap = :bwr)
 
 save("fluxes.png", fig)
-![](fluxes.png)
+
+# ![](fluxes.png)

examples/generate_surface_fluxes.jl

@@ -4,9 +4,8 @@ using Oceananigans
 using Oceananigans.Units
 using Printf
 
-time_indices = Colon()
-Qswt = ClimaOcean.JRA55.JRA55_field_time_series(:downwelling_shortwave_radiation; time_indices)
-rht = ClimaOcean.JRA55.JRA55_field_time_series(:relative_humidity; time_indices)
+Qswt = ClimaOcean.JRA55.JRA55FieldTimeSeries(:downwelling_shortwave_radiation)
+rht  = ClimaOcean.JRA55.JRA55FieldTimeSeries(:relative_humidity)
 
 function lonlat2xyz(lons::AbstractVector, lats::AbstractVector)
     x = [cosd(lat) * cosd(lon) for lon in lons, lat in lats]

examples/inspect_JRA55_data.jl

@@ -75,8 +75,8 @@ grid = ImmersedBoundaryGrid(grid, GridFittedBottom(bottom_height))
 
 dates = DateTimeProlepticGregorian(1993, 1, 1) : Month(1) : DateTimeProlepticGregorian(1993, 12, 1)
 
-temperature = ECCOMetadata(:temperature, dates, ECCO4Monthly())
-salinity    = ECCOMetadata(:salinity,    dates, ECCO4Monthly())
+temperature = Metadata(:temperature; dates, dataset=ECCO4Monthly())
+salinity    = Metadata(:salinity;    dates, dataset=ECCO4Monthly())
 
 FT = ECCO_restoring_forcing(temperature; architecture = GPU(), timescale = 2days)
 FS = ECCO_restoring_forcing(salinity;    architecture = GPU(), timescale = 2days)