test

Project.toml

@@ -4,15 +4,11 @@ authors = ["CliMA Contributors <clima-software@caltech.edu>"]
 version = "0.0.1"
 
 [deps]
-ClimaAtmos = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
 ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"
 ClimaCoreTempestRemap = "d934ef94-cdd4-4710-83d6-720549644b70"
-ClimaLand = "08f4d4ce-cf43-44bb-ad95-9d2d5f413532"
-ClimaParams = "5c42b081-d73a-476f-9059-fd94b934656c"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
-Insolation = "e98cc03f-d57e-4e3c-b70c-8d51efe9e0d8"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
@@ -24,15 +20,11 @@ TempestRemap_jll = "8573a8c5-1df0-515e-a024-abad257ee284"
 Thermodynamics = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
 
 [compat]
-ClimaAtmos = "0.22"
 ClimaComms = "0.5.6"
 ClimaCore = "0.13"
 ClimaCoreTempestRemap = "0.3"
-ClimaLand = "0.11"
-ClimaParams = "0.10"
 Dates = "1"
 DocStringExtensions = "0.8, 0.9"
-Insolation = "0.9.2"
 JLD2 = "0.4"
 NCDatasets = "0.11, 0.12, 0.13, 0.14.2"
 Plots = "1.39.0"

experiments/AMIP/Project.toml

@@ -51,13 +51,17 @@ ArgParse = "1.1"
 ArtifactWrappers = "0.2"
 AtmosphericProfilesLibrary = "0.1"
 ClimaAnalysis = "0.5"
+ClimaAtmos = "0.22"
 ClimaCorePlots = "0.2"
+ClimaLand = "0.11"
+ClimaParams = "0.10"
 ClimaTimeSteppers = "0.7"
 Colors = "0.12"
 Dierckx = "0.5"
 ForwardDiff = "0.10"
 Glob = "1"
 HDF5_jll = "1"
+Insolation = "0.9.2"
 IntervalSets = "0.5, 0.6, 0.7"
 JSON = "0.21"
 MPI = "0.20"

experiments/AMIP/components/atmosphere/climaatmos_extra_diags.jl

@@ -12,7 +12,7 @@ The `compute!` function is called at every atmos time step to compute the diagno
 To output these variables, short_name needs to be specified under diagnostics in the required yml file.
 """
 
-add_diagnostic_variable!(
+CAD.add_diagnostic_variable!(
     short_name = "mse",
     long_name = "Moist static energy",
     standard_name = "moist_static_energy",
@@ -32,7 +32,7 @@ add_diagnostic_variable!(
     end,
 )
 
-add_diagnostic_variable!(
+CAD.add_diagnostic_variable!(
     short_name = "lr",
     long_name = "Lapse rate",
     standard_name = "lapse_rate",
@@ -52,7 +52,7 @@ add_diagnostic_variable!(
     end,
 )
 
-add_diagnostic_variable!(
+CAD.add_diagnostic_variable!(
     short_name = "ediff",
     long_name = "Eddy diffusivity",
     standard_name = "eddy_diffusivity",

experiments/AMIP/components/ocean/eisenman_seaice.jl

@@ -17,7 +17,7 @@ import ClimaCoupler.Interfacer: get_field, update_field!, step!, reinit!
 Thermodynamic 0-layer, based on the Semtner 1979 model and later refined by
 Eisenmen 2009 and Zhang et al 2021.
 """
-struct EisenmanIceSimulation{P, Y, D, I} <: SeaIceModelSimulation
+struct EisenmanIceSimulation{P, Y, D, I} <: Interfacer.SeaIceModelSimulation
     params_ice::P
     Y_init::Y
     domain::D

experiments/AMIP/user_io/debug_plots.jl

@@ -2,16 +2,15 @@ import Plots
 import Printf
 import ClimaCore as CC
 import ClimaCorePlots
-
-using ClimaCoupler.Interfacer: ComponentModelSimulation, SurfaceModelSimulation
+import ClimaCoupler: Interfacer
 
 # plotting functions for the coupled simulation
 """
-    debug(cs::CoupledSimulation, dir = "debug", cs_fields_ref = nothing)
+    debug(cs::Interfacer.CoupledSimulation, dir = "debug", cs_fields_ref = nothing)
 
 Plot the fields of a coupled simulation and save plots to a directory.
 """
-function debug(cs::CoupledSimulation, dir = "debug", cs_fields_ref = nothing)
+function debug(cs::Interfacer.CoupledSimulation, dir = "debug", cs_fields_ref = nothing)
     mkpath(dir)
     @info "plotting debug in " * dir
     for sim in cs.model_sims
@@ -70,21 +69,21 @@ function debug(cs_fields::NamedTuple, dir, cs_fields_ref = nothing)
 end
 
 """
-    debug(sim::ComponentModelSimulation, dir)
+    debug(sim::Interfacer.ComponentModelSimulation, dir)
 
 Plot the fields of a component model simulation and save plots to a directory.
 """
-function debug(sim::ComponentModelSimulation, dir)
+function debug(sim::Interfacer.ComponentModelSimulation, dir)
 
     field_names = plot_field_names(sim)
 
     all_plots = []
     for field_name in field_names
-        field = get_field(sim, Val(field_name))
+        field = Interfacer.get_field(sim, Val(field_name))
         push!(all_plots, Plots.plot(field, title = string(field_name) * print_extrema(field)))
     end
     fig = Plots.plot(all_plots..., size = (1500, 800))
-    Plots.png(joinpath(dir, "debug_$(name(sim))"))
+    Plots.png(joinpath(dir, "debug_$(Interfacer.name(sim))"))
 
 end
 
@@ -117,7 +116,7 @@ get_field(sim::BucketSimulation, ::Val{:Ws}) = sim.integrator.u.bucket.Ws
 get_field(sim::BucketSimulation, ::Val{:W}) = sim.integrator.u.bucket.W
 
 # currently selected plot fields
-plot_field_names(sim::SurfaceModelSimulation) = (:area_fraction, :surface_temperature, :surface_humidity)
+plot_field_names(sim::Interfacer.SurfaceModelSimulation) = (:area_fraction, :surface_temperature, :surface_humidity)
 plot_field_names(sim::BucketSimulation) =
     (:area_fraction, :surface_temperature, :surface_humidity, :air_density, :σS, :Ws, :W)
 plot_field_names(sim::ClimaAtmosSimulation) = (:w, :ρq_tot, :ρe_tot, :liquid_precipitation, :snow_precipitation)

experiments/ClimaCore/Project.toml

@@ -17,6 +17,7 @@ TerminalLoggers = "5d786b92-1e48-4d6f-9151-6b4477ca9bed"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
+ClimaParams = "0.10"
 ClimaTimeSteppers = "0.7"
 DifferentialEquations = "7.10"
 FileIO = "1.16"

perf/Project.toml

@@ -47,13 +47,17 @@ YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 ArgParse = "1.1"
 ArtifactWrappers = "0.2"
 AtmosphericProfilesLibrary = "0.1"
+ClimaAtmos = "0.22"
 ClimaCorePlots = "0.2"
+ClimaLand = "0.11"
+ClimaParams = "0.10"
 ClimaTimeSteppers = "0.7"
 Colors = "0.12"
 Dierckx = "0.5"
 ForwardDiff = "0.10"
 Glob = "1"
 HDF5_jll = "1"
+Insolation = "0.9.2"
 IntervalSets = "0.5, 0.6, 0.7"
 JSON = "0.21"
 MPI = "0.20"

src/Regridder.jl

@@ -370,8 +370,8 @@ function write_datafile_cc(datafile_cc, field, name)
     space = axes(field)
     # write data
     NCD.NCDataset(datafile_cc, "c") do nc
-        def_space_coord(nc, space; type = "cgll")
-        nc_field = defVar(nc, name, Float64, space)
+        CCTR.def_space_coord(nc, space; type = "cgll")
+        nc_field = NCD.defVar(nc, name, Float64, space)
         nc_field[:, 1] = field
 
         nothing
@@ -486,7 +486,7 @@ function land_fraction(
     ClimaComms.barrier(comms_ctx)
     file_dates = JLD2.load(joinpath(REGRID_DIR, outfile_root * "_times.jld2"), "times")
     fraction = read_from_hdf5(REGRID_DIR, outfile_root, file_dates[1], varname, comms_ctx)
-    fraction = swap_space!(zeros(boundary_space), fraction) # needed if we are reading from previous run
+    fraction = Utilities.swap_space!(zeros(boundary_space), fraction) # needed if we are reading from previous run
     return mono ? fraction : binary_mask.(fraction, threshold)
 end
 
@@ -629,7 +629,7 @@ Regrids a field from CGLL to an RLL array using TempestRemap. It can hanlde mult
 """
 function cgll2latlonz(field; DIR = "cgll2latlonz_dir", nlat = 360, nlon = 720, clean_dir = true)
     isdir(DIR) ? nothing : mkpath(DIR)
-    datafile_latlon = DIR * "/remapped_" * string(name) * ".nc"
+    datafile_latlon = DIR * "/remapped_" * string(Interfacer.name) * ".nc"
     remap_field_cgll_to_rll(:var, field, DIR, datafile_latlon, nlat = nlat, nlon = nlon)
     new_data, coords = read_remapped_field(:var, datafile_latlon)
     clean_dir ? rm(DIR; recursive = true) : nothing

test/Project.toml

@@ -14,7 +14,6 @@ ClimaTimeSteppers = "595c0a79-7f3d-439a-bc5a-b232dc3bde79"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
 GeoMakie = "db073c08-6b98-4ee5-b6a4-5efafb3259c6"
-Insolation = "e98cc03f-d57e-4e3c-b70c-8d51efe9e0d8"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -38,6 +37,9 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 [compat]
 Aqua = "0.8"
 ArtifactWrappers = "0.2"
+ClimaAtmos = "0.22"
+ClimaLand = "0.11"
+ClimaParams = "0.10"
 Dates = "1"
 Downloads = "1"
 IntervalSets = "0.5, 0.6, 0.7"

test/TestHelper.jl

@@ -6,9 +6,9 @@ various files in the test folder.
 =#
 module TestHelper
 
-using ClimaCore: Geometry, Meshes, Domains, Topologies, Spaces, Fields, InputOutput
-using ClimaComms
-using NCDatasets
+import ClimaCore as CC
+import ClimaComms
+import NCDatasets as NCD
 
 export create_space, gen_ncdata
 
@@ -36,25 +36,28 @@ function create_space(
     polynomial_degree = 3,
     nz = 1,
 )
-    domain = Domains.SphereDomain(R)
-    mesh = Meshes.EquiangularCubedSphere(domain, ne)
+    domain = CC.Domains.SphereDomain(R)
+    mesh = CC.Meshes.EquiangularCubedSphere(domain, ne)
 
     if comms_ctx isa ClimaComms.SingletonCommsContext
-        topology = Topologies.Topology2D(comms_ctx, mesh, Topologies.spacefillingcurve(mesh))
+        topology = CC.Topologies.Topology2D(comms_ctx, mesh, CC.Topologies.spacefillingcurve(mesh))
     else
-        topology = Topologies.DistributedTopology2D(comms_ctx, mesh, Topologies.spacefillingcurve(mesh))
+        topology = CC.Topologies.DistributedTopology2D(comms_ctx, mesh, CC.Topologies.spacefillingcurve(mesh))
     end
 
     Nq = polynomial_degree + 1
-    quad = Spaces.Quadratures.GLL{Nq}()
-    sphere_space = Spaces.SpectralElementSpace2D(topology, quad)
+    quad = CC.Spaces.Quadratures.GLL{Nq}()
+    sphere_space = CC.Spaces.SpectralElementSpace2D(topology, quad)
 
     if nz > 1
-        vertdomain =
-            Domains.IntervalDomain(Geometry.ZPoint{FT}(0), Geometry.ZPoint{FT}(100); boundary_names = (:bottom, :top))
-        vertmesh = Meshes.IntervalMesh(vertdomain, nelems = nz)
-        vert_center_space = Spaces.CenterFiniteDifferenceSpace(vertmesh)
-        return Spaces.ExtrudedFiniteDifferenceSpace(sphere_space, vert_center_space)
+        vertdomain = CC.Domains.IntervalDomain(
+            CC.Geometry.ZPoint{FT}(0),
+            CC.Geometry.ZPoint{FT}(100);
+            boundary_names = (:bottom, :top),
+        )
+        vertmesh = CC.Meshes.IntervalMesh(vertdomain, nelems = nz)
+        vert_center_space = CC.Spaces.CenterFiniteDifferenceSpace(vertmesh)
+        return CC.Spaces.ExtrudedFiniteDifferenceSpace(sphere_space, vert_center_space)
     else
         return sphere_space
     end
@@ -76,17 +79,17 @@ function gen_ncdata(FT, path, varname, val)
     isfile(path) ? rm(path) : nothing
 
     # Create dataset of all ones
-    nc = NCDataset(path, "c")
+    nc = NCD.NCDataset(path, "c")
 
     # Define dataset information
-    defDim(nc, "lon", 64)
-    defDim(nc, "lat", 32)
+    NCD.defDim(nc, "lon", 64)
+    NCD.defDim(nc, "lat", 32)
     nc.attrib["title"] = "this is an NCDataset containing all 1s on a lat/lon grid"
 
     # Define variables
-    lon = defVar(nc, "lon", FT, ("lon",))
-    lat = defVar(nc, "lat", FT, ("lat",))
-    v = defVar(nc, varname, FT, ("lon", "lat"))
+    lon = NCD.defVar(nc, "lon", FT, ("lon",))
+    lat = NCD.defVar(nc, "lat", FT, ("lat",))
+    v = NCD.defVar(nc, varname, FT, ("lon", "lat"))
 
     # Populate lon and lat
     lon[:] = [i for i in 0.0:(360 / 64):(360 - (360 / 64))]

test/aqua.jl

@@ -1,6 +1,6 @@
-using Test
-using ClimaCoupler
-using Aqua
+import Test: @test, @testset
+import ClimaCoupler
+import Aqua
 
 @testset "Aqua tests (performance)" begin
     # This tests that we don't accidentally run into