Remove deprecated method

Add to NEWS

boundary_tags -> boundary_names kwarg

Fixes

NEWS.md

@@ -3,6 +3,7 @@ ClimaCore.jl Release Notes
 
 Main
 -------
+- ![][badge-💥breaking] support for many deprecated methods have been dropped PR [#1632](https://github.com/CliMA/ClimaCore.jl/pull/1632).
 - ![][badge-🤖precisionΔ]![][badge-🚀performance] Slight performance improvement by replacing `rdiv` with `rmul`. PR ([#1496](https://github.com/CliMA/ClimaCore.jl/pull/1496)) Machine-precision differences are expected.
 
 v0.12.1

benchmarks/3d/se_kernels.jl

@@ -81,7 +81,7 @@ function initialize_mwe(device, ::Type{FT}) where {FT}
     z_domain = Domains.IntervalDomain(
         Geometry.ZPoint(zero(z_max)),
         Geometry.ZPoint(z_max);
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     z_mesh = Meshes.IntervalMesh(z_domain, nelems = z_elem)
     z_topology = Topologies.IntervalTopology(context, z_mesh)

benchmarks/3d/vector_laplacian.jl

@@ -11,21 +11,19 @@ using ClimaCore:
     Quadratures
 using CUDA, BenchmarkTools
 
+context = ClimaComms.context()
 hdomain = Domains.SphereDomain(6.37122e6)
 hmesh = Meshes.EquiangularCubedSphere(hdomain, 30)
-htopology = Topologies.Topology2D(hmesh)
+htopology = Topologies.Topology2D(context, hmesh)
 hspace = Spaces.SpectralElementSpace2D(htopology, Quadratures.GLL{4}())
 
 vdomain = Domains.IntervalDomain(
     Geometry.ZPoint(0.0),
     Geometry.ZPoint(10e3);
-    boundary_tags = (:bottom, :top),
+    boundary_names = (:bottom, :top),
 )
 vmesh = Meshes.IntervalMesh(vdomain; nelems = 45)
-vtopology = Topologies.IntervalTopology(
-    ClimaComms.SingletonCommsContext(ClimaComms.device()),
-    vmesh,
-)
+vtopology = Topologies.IntervalTopology(context, vmesh)
 vspace = Spaces.CenterFiniteDifferenceSpace(vtopology)
 
 cspace = Spaces.ExtrudedFiniteDifferenceSpace(hspace, vspace)

benchmarks/bickleyjet/core_vs_ref.jl

@@ -30,7 +30,8 @@ for Nq in Nqs
     volume!(dydt, y0, (parameters,), 0.0)
     # TODO: move this to volume!
     dydt_data = Fields.field_values(dydt)
-    dydt_data .= RecursiveApply.rdiv.(dydt_data, space.local_geometry.WJ)
+    dydt_data .=
+        RecursiveApply.rdiv.(dydt_data, Spaces.local_geometry_data(space).WJ)
 
     # setup reference
     X = coordinates(Val(Nq), n1, n2)
@@ -83,7 +84,8 @@ for Nq in Nqs
     add_face!(dydt, y0, (parameters,), 0.0)
     # TODO: move this to volume!
     dydt_data = Fields.field_values(dydt)
-    dydt_data .= RecursiveApply.rdiv.(dydt_data, space.local_geometry.WJ)
+    dydt_data .=
+        RecursiveApply.rdiv.(dydt_data, Spaces.local_geometry_data(space).WJ)
 
     fill!(dydt_ref, 0.0)
     add_face_ref!(dydt_ref, y0_ref, (n1, n2, parameters, Val(Nq)), 0.0)

docs/src/lib/ClimaCoreTempestRemap.md

@@ -95,7 +95,7 @@ end
 
 # write out our cubed sphere mesh
 meshfile_cc = "mesh_cubedsphere.g"
-write_exodus(meshfile_cc, Spaces.horizontal_space(cspace).topology)
+write_exodus(meshfile_cc, Spaces.topology(Spaces.horizontal_space(cspace)))
 
 # write out RLL mesh
 nlat = 90

docs/tutorials/introduction.jl

@@ -27,7 +27,7 @@ using ClimaComms,
 
 column_domain = ClimaCore.Domains.IntervalDomain(
     ClimaCore.Geometry.ZPoint(0.0) .. ClimaCore.Geometry.ZPoint(10.0),
-    boundary_tags = (:bottom, :top),
+    boundary_names = (:bottom, :top),
 )
 #----------------------------------------------------------------------------
 

examples/bickleyjet/bickleyjet_dg.jl

@@ -206,7 +206,8 @@ function rhs!(dydt, y, (parameters, numflux), t)
 
     # 6. Solve for final result
     dydt_data = Fields.field_values(dydt)
-    dydt_data .= RecursiveApply.rdiv.(dydt_data, space.local_geometry.WJ)
+    dydt_data .=
+        RecursiveApply.rdiv.(dydt_data, Spaces.local_geometry_data(space).WJ)
     M = Quadratures.cutoff_filter_matrix(
         Float64,
         Spaces.quadrature_style(space),

examples/common_spaces.jl

@@ -66,7 +66,7 @@ function make_hybrid_spaces(h_space, z_max, z_elem; z_stretch)
     z_domain = Domains.IntervalDomain(
         Geometry.ZPoint(zero(z_max)),
         Geometry.ZPoint(z_max);
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     z_mesh = Meshes.IntervalMesh(z_domain, z_stretch; nelems = z_elem)
     z_topology = Topologies.IntervalTopology(z_mesh)

examples/hybrid/box/bubble_3d_invariant_rhoe.jl

@@ -133,7 +133,7 @@ function hvspace_3D(
     vertdomain = Domains.IntervalDomain(
         Geometry.ZPoint{FT}(zlim[1]),
         Geometry.ZPoint{FT}(zlim[2]);
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     vertmesh = Meshes.IntervalMesh(vertdomain, nelems = zelem)
     verttopo = Topologies.IntervalTopology(

examples/hybrid/plane/isothermal_channel.jl

@@ -55,7 +55,7 @@ function hvspace_2D(
     horztopology = Topologies.IntervalTopology(horzmesh)
     quad = Quadratures.GLL{npoly + 1}()
     horzspace = Spaces.SpectralElementSpace1D(horztopology, quad)
-    z_surface = warp_fn.(Fields.coordinate_field(horzspace))
+    z_surface = Geometry.ZPoint.(warp_fn.(Fields.coordinate_field(horzspace)))
     hv_face_space = Spaces.ExtrudedFiniteDifferenceSpace(
         horzspace,
         vert_face_space,

examples/hybrid/sphere/nonhydrostatic_gravity_wave.jl

@@ -55,7 +55,7 @@ function sphere_3D(
     vertdomain = Domains.IntervalDomain(
         Geometry.ZPoint{FT}(zlim[1]),
         Geometry.ZPoint{FT}(zlim[2]);
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     vertmesh = Meshes.IntervalMesh(vertdomain, nelems = zelem)
     vert_center_space = Spaces.CenterFiniteDifferenceSpace(vertmesh)

lib/ClimaCoreMakie/test/runtests.jl

@@ -11,13 +11,11 @@ OUTPUT_DIR = mkpath(get(ENV, "CI_OUTPUT_DIR", tempname()))
 
 @testset "spectral element 2D cubed-sphere" begin
     R = 6.37122e6
+    context = ClimaComms.SingletonCommsContext()
 
     domain = ClimaCore.Domains.SphereDomain(R)
     mesh = ClimaCore.Meshes.EquiangularCubedSphere(domain, 6)
-    grid_topology = ClimaCore.Topologies.Topology2D(
-        ClimaComms.SingletonCommsContext(),
-        mesh,
-    )
+    grid_topology = ClimaCore.Topologies.Topology2D(context, mesh)
     quad = ClimaCore.Quadratures.GLL{5}()
     space = ClimaCore.Spaces.SpectralElementSpace2D(grid_topology, quad)
     coords = ClimaCore.Fields.coordinate_field(space)
@@ -75,6 +73,7 @@ end
 
 @testset "extruded" begin
 
+    context = ClimaComms.context()
     domain = ClimaCore.Domains.IntervalDomain(
         ClimaCore.Geometry.XPoint(-1000.0),
         ClimaCore.Geometry.XPoint(1000.0),
@@ -87,16 +86,17 @@ end
     horz_coords = ClimaCore.Fields.coordinate_field(horz_space)
 
     z_surface = map(horz_coords) do coord
-        100 * exp(-(coord.x / 100)^2)
+        Geometry.ZPoint(100 * exp(-(coord.x / 100)^2))
     end
 
     vert_domain = ClimaCore.Domains.IntervalDomain(
         ClimaCore.Geometry.ZPoint(0.0),
         ClimaCore.Geometry.ZPoint(1000.0);
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     vert_mesh = ClimaCore.Meshes.IntervalMesh(vert_domain, nelems = 36)
-    vert_center_space = ClimaCore.Spaces.CenterFiniteDifferenceSpace(vert_mesh)
+    vtopology = Topologies.IntervalTopology(context, vert_mesh)
+    vert_center_space = ClimaCore.Spaces.CenterFiniteDifferenceSpace(vtopology)
     vert_face_space =
         ClimaCore.Spaces.FaceFiniteDifferenceSpace(vert_center_space)
 

lib/ClimaCorePlots/test/runtests.jl

@@ -13,7 +13,7 @@ OUTPUT_DIR = mkpath(get(ENV, "CI_OUTPUT_DIR", tempname()))
 @testset "spectral element 1D" begin
     domain = ClimaCore.Domains.IntervalDomain(
         ClimaCore.Geometry.XPoint(0.0) .. ClimaCore.Geometry.XPoint(π),
-        boundary_tags = (:left, :right),
+        boundary_names = (:left, :right),
     )
     mesh = ClimaCore.Meshes.IntervalMesh(domain; nelems = 5)
     grid_topology = ClimaCore.Topologies.IntervalTopology(mesh)
@@ -109,7 +109,7 @@ end
     vertdomain = ClimaCore.Domains.IntervalDomain(
         ClimaCore.Geometry.ZPoint{FT}(0),
         ClimaCore.Geometry.ZPoint{FT}(1000);
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     vertmesh = ClimaCore.Meshes.IntervalMesh(vertdomain, nelems = velem)
     vert_center_space = ClimaCore.Spaces.CenterFiniteDifferenceSpace(vertmesh)
@@ -197,7 +197,7 @@ end
     vertdomain = ClimaCore.Domains.IntervalDomain(
         ClimaCore.Geometry.ZPoint{FT}(0),
         ClimaCore.Geometry.ZPoint{FT}(1000);
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     vertmesh = ClimaCore.Meshes.IntervalMesh(vertdomain, nelems = velem)
     vert_center_space = ClimaCore.Spaces.CenterFiniteDifferenceSpace(vertmesh)
@@ -246,7 +246,7 @@ end
     vertdomain = ClimaCore.Domains.IntervalDomain(
         ClimaCore.Geometry.ZPoint{FT}(0),
         ClimaCore.Geometry.ZPoint{FT}(1000);
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     vertmesh = ClimaCore.Meshes.IntervalMesh(vertdomain, nelems = velem)
     vert_center_space = ClimaCore.Spaces.CenterFiniteDifferenceSpace(vertmesh)

lib/ClimaCoreTempestRemap/src/onlineremap.jl

@@ -244,7 +244,8 @@ function generate_map(
 
     if target_space_distr != nothing
         # Create map from unique (TempestRemap convention) to local element indices
-        target_local_elem_gidx = target_space_distr.topology.local_elem_gidx # gidx = local_elem_gidx[lidx]
+        target_local_elem_gidx =
+            Spaces.topology(target_space_distr).local_elem_gidx # gidx = local_elem_gidx[lidx]
         target_global_elem_lidx = Dict{Int, Int}() # inverse of local_elem_gidx: lidx = global_elem_lidx[gidx]
         for (lidx, gidx) in enumerate(target_local_elem_gidx)
             target_global_elem_lidx[gidx] = lidx

lib/ClimaCoreTempestRemap/test/netcdf.jl

@@ -98,7 +98,7 @@ end
     vdomain = Domains.IntervalDomain(
         Geometry.ZPoint(0.0),
         Geometry.ZPoint(50.0);
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     vmesh = Meshes.IntervalMesh(vdomain, nelems = nlevels)
     vspace = Spaces.CenterFiniteDifferenceSpace(vmesh)
@@ -181,7 +181,7 @@ end
     vdomain = Domains.IntervalDomain(
         Geometry.ZPoint(0.0),
         Geometry.ZPoint(50.0);
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     vmesh = Meshes.IntervalMesh(vdomain, nelems = nlevels)
     vspace = Spaces.CenterFiniteDifferenceSpace(vmesh)
@@ -316,11 +316,11 @@ end
     vdomain = Domains.IntervalDomain(
         Geometry.ZPoint(0.0),
         Geometry.ZPoint(50.0);
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     vmesh = Meshes.IntervalMesh(vdomain, nelems = nlevels)
     vfspace = Spaces.FaceFiniteDifferenceSpace(vmesh)
-    z_surface = test_warp.(Fields.coordinate_field(hspace))
+    z_surface = Geometry.ZPoint.(test_warp.(Fields.coordinate_field(hspace)))
     fhvspace = Spaces.ExtrudedFiniteDifferenceSpace(
         hspace,
         vfspace,
@@ -425,7 +425,7 @@ end
     vdomain = Domains.IntervalDomain(
         Geometry.ZPoint(0.0),
         Geometry.ZPoint(50.0);
-        boundary_tags = (:bottom, :top),
+        boundary_names = (:bottom, :top),
     )
     vmesh = Meshes.IntervalMesh(vdomain, nelems = nlevels)
     vspace = Spaces.CenterFiniteDifferenceSpace(vmesh)

lib/ClimaCoreVTK/src/ClimaCoreVTK.jl

@@ -156,12 +156,4 @@ function writepvd(basename::String, times, fields::NamedTuple; vtkargs...)
     end
 end
 
-Base.@deprecate writevtk(basename::String, times, fields; vtkargs...) writepvd(
-    basename,
-    times,
-    fields;
-    vtkargs...,
-)
-
-
 end # module

src/DataLayouts/broadcast.jl

@@ -538,9 +538,6 @@ function Base.copyto!(
     dest::VIFH{S, Ni},
     bc::Base.Broadcast.Broadcasted{VIFHStyle{Ni, A}},
 ) where {S, Ni, A}
-    # if enable_threading()
-    #     return _threaded_copyto!(dest, bc)
-    # end
     return _serial_copyto!(dest, bc)
 end
 
@@ -588,8 +585,5 @@ function Base.copyto!(
     dest::VIJFH{S, Nij},
     bc::Base.Broadcast.Broadcasted{VIJFHStyle{Nij, A}},
 ) where {S, Nij, A}
-    # if enable_threading()
-    #     return _threaded_copyto!(dest, bc)
-    # end
     return _serial_copyto!(dest, bc)
 end

src/Domains/Domains.jl

@@ -51,8 +51,7 @@ function IntervalDomain(
     coord_min::Geometry.Abstract1DPoint,
     coord_max::Geometry.Abstract1DPoint;
     periodic = false,
-    boundary_tags = nothing, # TODO: deprecate this
-    boundary_names::BCTagType = boundary_tags,
+    boundary_names::BCTagType = nothing,
 )
     if !periodic && isnothing(boundary_names)
         throw(

src/Fields/Fields.jl

@@ -331,9 +331,6 @@ local_geometry_field(space::AbstractSpace) =
     Field(Spaces.local_geometry_data(space), space)
 local_geometry_field(field::Field) = local_geometry_field(axes(field))
 
-Base.@deprecate dz_field(space::AbstractSpace) Δz_field(space) false
-Base.@deprecate dz_field(field::Field) Δz_field(field) false
-
 """
     Δz_field(field::Field)
     Δz_field(space::AbstractSpace)
@@ -457,22 +454,6 @@ function Spaces.weighted_dss!(
     return nothing
 end
 
-# Add definitions for backward compatibility
-Spaces.weighted_dss2!(
-    field::Field,
-    dss_buffer = Spaces.create_dss_buffer(field),
-) = Spaces.weighted_dss!(field, dss_buffer)
-
-Spaces.weighted_dss_start2!(field::Field, ghost_buffer) =
-    Spaces.weighted_dss_start!(field, ghost_buffer)
-
-Spaces.weighted_dss_internal2!(field::Field, ghost_buffer) =
-    Spaces.weighted_dss_internal!(field, ghost_buffer)
-
-Spaces.weighted_dss_ghost2!(field, ghost_buffer) =
-    Spaces.weighted_dss_ghost!(field, ghost_buffer)
-
-
 """
     Spaces.create_dss_buffer(field::Field)
 

src/Fields/broadcast.jl

@@ -420,12 +420,3 @@ function Base.Broadcast.copyto!(field::Field, nt::NamedTuple)
         ),
     )
 end
-
-
-# TODO: deprecate these
-
-allow_mismatched_diagonalized_spaces() = false
-
-is_diagonalized_spaces(::Type{S}, ::Type{S}) where {S <: AbstractSpace} = true
-
-is_diagonalized_spaces(::Type, ::Type) = false

src/Hypsography/Hypsography.jl

@@ -79,13 +79,6 @@ of the domain, using the method of [GalChen1975](@cite).
 """
 struct LinearAdaption{F <: Fields.Field} <: HypsographyAdaption
     surface::F
-    function LinearAdaption(surface::Fields.Field)
-        if eltype(surface) <: Real
-            @warn "`LinearAdaptation`: `surface` argument scalar field has been deprecated. Use a field `ZPoint`s."
-            surface = Geometry.ZPoint.(surface)
-        end
-        new{typeof(surface)}(surface)
-    end
 end
 
 Adapt.adapt_structure(to, adaption::LinearAdaption) =
@@ -132,10 +125,6 @@ struct SLEVEAdaption{F <: Fields.Field, FT <: Real} <: HypsographyAdaption
     ) where {FT <: Real}
         @assert 0 <= ηₕ <= 1
         @assert s >= 0
-        if eltype(surface) <: Real
-            @warn "`SLEVEAdaption`: `surface` argument scalar field has been deprecated. Use a field `ZPoint`s."
-            surface = Geometry.ZPoint.(surface)
-        end
         new{typeof(surface), FT}(surface, ηₕ, s)
     end
 end

src/InputOutput/readers.jl

@@ -88,11 +88,6 @@ struct HDF5Reader{C <: ClimaComms.AbstractCommsContext}
     grid_cache::Dict{Any, Any}
 end
 
-@deprecate HDF5Reader(filename::AbstractString) HDF5Reader(
-    filename,
-    ClimaComms.SingletonCommsContext(),
-)
-
 function HDF5Reader(
     filename::AbstractString,
     context::ClimaComms.AbstractCommsContext,