Merge pull request #612 from CliMA/js/deprecate

remove deprecated function calls
CliMA · Feb 10, 2024 · b88dcb8 · b88dcb8
2 parents a003ba3 + 96131d4
commit b88dcb8
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Showing 8 changed files with 11 additions and 8 deletions.
diff --git a/experiments/AMIP/cli_options.jl b/experiments/AMIP/cli_options.jl
@@ -1,7 +1,7 @@
 import ArgParse
 function argparse_settings()
     s = ArgParse.ArgParseSettings()
-    ArgParse.@add_arg_table s begin
+    ArgParse.@add_arg_table! s begin
         # ClimaCoupler flags
         "--run_name"
         help = "Name of this run."

diff --git a/experiments/AMIP/user_io/amip_visualizer.jl b/experiments/AMIP/user_io/amip_visualizer.jl
@@ -1,3 +1,4 @@
+import ClimaComms
 include("plot_helper.jl")
 
 """
@@ -77,6 +78,7 @@ function read_latest_model_data(name::Symbol, filedir::String, root::String)
     varfile_root = @sprintf "%s%s" string(name) root
     filename = glob("*" * varfile_root * "*", filedir)[end]
 
+    comms_ctx = ClimaComms.SingletonCommsContext()
     hdfreader = InputOutput.HDF5Reader(filename)
     var = InputOutput.read_field(hdfreader, string(name))
     close(hdfreader)

diff --git a/src/Regridder.jl b/src/Regridder.jl
@@ -175,7 +175,7 @@ function hdwrite_regridfile_rll_to_cgll(
     space2d_undistributed = Spaces.SpectralElementSpace2D(topology, Spaces.Quadratures.GLL{Nq}())
 
     if space isa Spaces.ExtrudedFiniteDifferenceSpace
-        vert_center_space = Spaces.CenterFiniteDifferenceSpace(space.vertical_topology.mesh)
+        vert_center_space = Spaces.CenterFiniteDifferenceSpace(Spaces.vertical_topology(space).mesh)
         space_undistributed = Spaces.ExtrudedFiniteDifferenceSpace(space2d_undistributed, vert_center_space)
     else
         space_undistributed = space2d_undistributed

diff --git a/test/TestHelper.jl b/test/TestHelper.jl
@@ -40,7 +40,7 @@ function create_space(
     mesh = Meshes.EquiangularCubedSphere(domain, ne)
 
     if comms_ctx isa ClimaComms.SingletonCommsContext
-        topology = Topologies.Topology2D(mesh, Topologies.spacefillingcurve(mesh))
+        topology = Topologies.Topology2D(comms_ctx, mesh, Topologies.spacefillingcurve(mesh))
     else
         topology = Topologies.DistributedTopology2D(comms_ctx, mesh, Topologies.spacefillingcurve(mesh))
     end

diff --git a/test/bcreader_tests.jl b/test/bcreader_tests.jl
@@ -95,7 +95,7 @@ for FT in (Float32, Float64)
         Nq = 4
         domain = Domains.SphereDomain(radius)
         mesh = Meshes.EquiangularCubedSphere(domain, 4)
-        topology = Topologies.Topology2D(mesh)
+        topology = Topologies.Topology2D(comms_ctx, mesh)
         quad = Spaces.Quadratures.GLL{Nq}()
         boundary_space_t = Spaces.SpectralElementSpace2D(topology, quad)
         monthly_fields = (zeros(boundary_space_t), ones(boundary_space_t))
@@ -349,7 +349,7 @@ for FT in (Float32, Float64)
             Nq = 4
             domain = Domains.SphereDomain(radius)
             mesh = Meshes.EquiangularCubedSphere(domain, 4)
-            topology = Topologies.Topology2D(mesh)
+            topology = Topologies.Topology2D(comms_ctx, mesh)
             quad = Spaces.Quadratures.GLL{Nq}()
             boundary_space_t = Spaces.SpectralElementSpace2D(topology, quad)
             land_fraction_t = Fields.zeros(boundary_space_t)

diff --git a/test/component_model_tests/bucket_tests.jl b/test/component_model_tests/bucket_tests.jl
@@ -4,7 +4,6 @@ using ClimaCoupler.TestHelper: create_space
 using ClimaCore: Fields, Spaces
 
 include(pkgdir(ClimaCoupler, "experiments/AMIP/components/land/bucket_init.jl"))
-include(pkgdir(ClimaCoupler, "experiments/AMIP/components/land/bucket_utils.jl"))
 
 for FT in (Float32, Float64)
     @testset "dss_state! BucketSimulation for FT=$FT" begin

diff --git a/test/experiment_tests/coupled_sims.jl b/test/experiment_tests/coupled_sims.jl
@@ -3,6 +3,7 @@ using Random
 using ClimaCoupler, Dates, Unitful
 using IntervalSets
 using ClimaCore: Domains, Meshes, Geometry, Topologies, Spaces, Fields, Operators
+using ClimaComms
 
 # Load file to test
 include("../../experiments/ClimaCore/CoupledSims/coupled_sim.jl")
@@ -40,7 +41,8 @@ function spectral_space_2D(; n1 = 1, n2 = 1, Nij = 4)
         x2boundary = (:south, :north),
     )
     mesh = Meshes.RectilinearMesh(domain, n1, n2)
-    grid_topology = Topologies.Topology2D(mesh)
+    comms_ctx = ClimaComms.SingletonCommsContext()
+    grid_topology = Topologies.Topology2D(comms_ctx, mesh)
 
     quad = Spaces.Quadratures.GLL{Nij}()
     space = Spaces.SpectralElementSpace2D(grid_topology, quad)

diff --git a/test/regridder_tests.jl b/test/regridder_tests.jl
@@ -286,7 +286,7 @@ for FT in (Float32, Float64)
             # read in data on CGLL grid from the last saved date
             date1 = TimeManager.strdate_to_datetime.(string(Int(time[end])))
             cgll_path = joinpath(REGRID_DIR, "$(hd_outfile_root)_$date1.hdf5")
-            hdfreader = InputOutput.HDF5Reader(cgll_path)
+            hdfreader = InputOutput.HDF5Reader(cgll_path, comms_ctx)
             T_cgll = InputOutput.read_field(hdfreader, varname)
             Base.close(hdfreader)