(0.96.0) Move NetCDFWriter to an extension (#4239)

* start with files that don't require re-indentation

* re-format /examples

* re-format src

* re-format /test

* re-format some validation scripts

* more validation scripts

* more validation scripts

* rest of validation scripts

* fix last validation files

* re-format docs and examples

* reformat src

* reformat test

* reformat validation

* move netcdf_output_writer.jl to extension

* rename files

* move struct definition to OutputWriters

* using much more stuff

* KernelFunctinoOperation is needed

* rename test_netcdf and test_jld2 files

* include correct names

* add NCDatasets to targets

* Update OceananigansNCDatasetsExt.jl

* fix bug in JLD2_writer.jl

* fix examples

* add NCDatasets to validation scripts

* remove blank line

* Use warning instead of error

* Add output_averaging_schedule

* Import more

* using show_array_type

* fix docs/src/model_setup

* Fix lagrangian particle example

---------

Co-authored-by: Gregory L. Wagner <[email protected]>
Co-authored-by: Gregory Wagner <[email protected]>

Author: tomchor

Project.toml

@@ -22,7 +22,6 @@ KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195"
-NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
@@ -42,12 +41,14 @@ Enzyme = "7da242da-08ed-463a-9acd-ee780be4f1d9"
 Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
 MakieCore = "20f20a25-4f0e-4fdf-b5d1-57303727442b"
 Metal = "dde4c033-4e86-420c-a63e-0dd931031962"
+NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
 
 [extensions]
 OceananigansEnzymeExt = "Enzyme"
 OceananigansMakieExt = ["MakieCore", "Makie"]
 OceananigansMetalExt = "Metal"
+OceananigansNCDatasetsExt = "NCDatasets"
 OceananigansReactantExt = ["Reactant", "KernelAbstractions", "ConstructionBase"]
 
 [compat]
@@ -101,4 +102,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TimesDates = "bdfc003b-8df8-5c39-adcd-3a9087f5df4a"
 
 [targets]
-test = ["DataDeps", "SafeTestsets", "Test", "Enzyme", "Reactant", "Metal", "CUDA_Runtime_jll", "MPIPreferences", "TimesDates"]
+test = ["DataDeps", "SafeTestsets", "Test", "Enzyme", "Reactant", "Metal", "CUDA_Runtime_jll", "MPIPreferences", "TimesDates", "NCDatasets"]

docs/src/model_setup/lagrangian_particles.md

@@ -110,6 +110,7 @@ When writing to JLD2 you can pass `model.particles` as part of the named tuple o
 
 ```@setup particles
 using Oceananigans
+using NCDatasets
 grid = RectilinearGrid(size=(10, 10, 10), extent=(1, 1, 1))
 Nparticles = 3
 x₀ = zeros(Nparticles)

docs/src/model_setup/output_writers.md

@@ -52,6 +52,7 @@ Saving the u velocity field and temperature fields as full 3D fields, surface 2D
 
 ```@example netcdf1
 using Oceananigans
+using NCDatasets
 
 grid = RectilinearGrid(size=(16, 16, 16), extent=(1, 1, 1))
 
@@ -84,6 +85,7 @@ provided that their `dimensions` are provided:
 
 ```@example
 using Oceananigans
+using NCDatasets
 
 Nx, Ny, Nz = 16, 16, 16
 
@@ -128,6 +130,7 @@ to a different grid than `model.grid`. To use this functionality, include the ke
 ```@example
 using Oceananigans
 using Oceananigans.Fields: interpolate!
+using NCDatasets
 
 grid = RectilinearGrid(size=(1, 1, 8), extent=(1, 1, 1));
 model = NonhydrostaticModel(; grid)

examples/shallow_water_Bickley_jet.jl

@@ -129,7 +129,10 @@ using LinearAlgebra: norm
 perturbation_norm(args...) = norm(v)
 
 # Build the `output_writer` for the two-dimensional fields to be output.
-# Output every `t = 1.0`.
+# Output every `t = 1.0`. Note that we need `NCDatasets` to be able to use
+# the `NetCDFWriter`.
+
+using NCDatasets
 
 fields_filename = joinpath(@__DIR__, "shallow_water_Bickley_jet_fields.nc")
 simulation.output_writers[:fields] = NetCDFWriter(model, (; ω, ω′),

examples/tilted_bottom_boundary_layer.jl

@@ -187,7 +187,7 @@ simulation.callbacks[:progress] = Callback(progress_message, IterationInterval(2
 
 # ## Add outputs to the simulation
 #
-# We add outputs to our model using the `NetCDFWriter`,
+# We add outputs to our model using the `NetCDFWriter`, which needs `NCDatasets` to be loaded:
 
 u, v, w = model.velocities
 b = model.tracers.b
@@ -199,6 +199,8 @@ V = v + V∞
 
 outputs = (; u, V, w, B, ωy)
 
+using NCDatasets
+
 simulation.output_writers[:fields] = NetCDFWriter(model, outputs;
                                                   filename = joinpath(@__DIR__, "tilted_bottom_boundary_layer.nc"),
                                                   schedule = TimeInterval(20minutes),