Small tidyups, remove CommonDataModel extension

Move CommonDataModel extension changes to a separate PR

Project cdm.toml

@@ -0,0 +1,71 @@
+name = "PALEOboxes"
+uuid = "804b410e-d900-4b2a-9ecd-f5a06d4c1fd4"
+authors = ["Stuart Daines <[email protected]>"]
+version = "0.22.0"
+
+[deps]
+Atomix = "a9b6321e-bd34-4604-b9c9-b65b8de01458"
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
+DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+Infiltrator = "5903a43b-9cc3-4c30-8d17-598619ec4e9b"
+InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
+Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
+MAT = "23992714-dd62-5051-b70f-ba57cb901cac"
+NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
+OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
+PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
+Preferences = "21216c6a-2e73-6563-6e65-726566657250"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
+SIMD = "fdea26ae-647d-5447-a871-4b548cad5224"
+SLEEF_jll = "63e82ce6-3d80-5af4-a84c-484b71ab98bb"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
+StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
+TestEnv = "1e6cf692-eddd-4d53-88a5-2d735e33781b"
+TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
+YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
+
+[weakdeps]
+CommonDataModel = "1fbeeb36-5f17-413c-809b-666fb144f157"
+
+[extensions]
+CommonDataModelExt = "CommonDataModel"
+
+[compat]
+Atomix = "0.1, 1.0"
+BenchmarkTools = "1.0"
+CommonDataModel = "0.3.7"
+DataFrames = "1.1"
+DocStringExtensions = "0.8, 0.9"
+Documenter = "1"
+Graphs = "1.4"
+Infiltrator = "1.0"
+Interpolations = "0.13, 0.14, 0.15"
+MAT = "0.10"
+NCDatasets = "0.12, 0.13, 0.14"
+OrderedCollections = "1.4"
+PrecompileTools = "1.0"
+Preferences = "1.2"
+Revise = "3.1"
+SIMD = "3.3"
+SLEEF_jll = "3.4"
+StaticArrays = "1.4"
+StructArrays = "0.6, 0.7"
+TestEnv = "1.0"
+TimerOutputs = "0.5"
+YAML = "0.4.7"
+julia = "1.10"
+
+[extras]
+CommonDataModel = "1fbeeb36-5f17-413c-809b-666fb144f157"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[targets]
+test = ["CommonDataModel", "Documenter", "Logging", "Test"]

src/CoordsDims.jl

@@ -16,7 +16,11 @@ struct NamedDimension
 end
 
 function Base.show(io::IO, nd::NamedDimension)
-    print(io, "NamedDimension(name=", nd.name, ", size=", nd.size, ")")
+    if get(io, :typeinfo, nothing) === NamedDimension
+        print(io, "(name=", nd.name, ", size=", nd.size, ")")
+    else
+        print(io, "NamedDimension(name=", nd.name, ", size=", nd.size, ")")
+    end
     return nothing
 end
 

src/Grids.jl

@@ -684,24 +684,25 @@ function CartesianGrid(
 end
 
 """
-    CartesianGrid(GridType, ncfilename::AbstractString, dimnames::Vector{<:AbstractString}; equalspacededges=false) -
-        > grid::GridType, coord_vars, coord_edges_vars
+    CartesianGrid(GridType, ncfilename::AbstractString, dimnames::Vector{<:AbstractString};
+        equalspacededges=false, convert_edges_to_bounds=false) -> grid::GridType, coord_vars, coord_edges_bounds_vars
 
 Read a netcdf file with CF1.0 coordinates, and create corresponding a CartesianLinearGrid or CartesianArrayGrid from dimensions `dimnames`.
-`coord_vars` and optional `coord_edges_vars` are Vectors of `coorddimname=>values` for creating coordinate variables.
+`coord_vars` and optional `coord_edges_bounds_vars` are Vectors of `coorddimname => values` for creating coordinate variables.
 """
 function CartesianGrid(
     GridType::Type{<:Union{CartesianLinearGrid, CartesianArrayGrid}},
     ncfilename::AbstractString, 
     dimnames::Vector{<:AbstractString};
-    equalspacededges=false
+    equalspacededges=false,
+    convert_edges_to_bounds=false,
 )   
     @info "CartesianGrid creating $GridType{$(length(dimnames))} from dimnames=$dimnames in netcdf file $(ncfilename)"
 
     grid = GridType{length(dimnames)}()
 
     coord_vars = []
-    coord_edges_vars = []
+    coord_edges_bounds_vars = []
 
     NCDatasets.Dataset(ncfilename) do ds
         # read dimensions and coordinates
@@ -713,20 +714,43 @@ function CartesianGrid(
             grid.dimensions[i] = PB.NamedDimension(dimname, dim)
             v_cf = ds[dimname]
             coord_vals = Array(v_cf)
+            @assert ndims(coord_vals) == 1
+            coord_vals = [cv for cv in coord_vals] # narrow type to eliminate unnecessary Missing
             push!(coord_vars, dimname=>coord_vals)
             if haskey(v_cf.attrib, "edges")
                 edgesname = v_cf.attrib["edges"]
-                edgesdim = ds.dim[edgesname]
+                edgesdim = ds.dim[edgesname]            
                 @info "  reading coordinate edges from $edgesname = $edgesdim"
-                push!(grid.dimensions_extra,  PB.NamedDimension(edgesname, edgesdim))
-                push!(coord_edges_vars, edgesname=>Array(ds[edgesname]))
+                edges_vals = Array(ds[edgesname])              
+                @assert size(edges_vals) == (edgesdim, )
+                edges_vals = [ev for ev in edges_vals]
+                if convert_edges_to_bounds
+                    boundsname = dimname*"_bnds"
+                    @info "    converting edges to bounds $boundsname"
+                    coord_bounds = similar(coord_vals, eltype(coord_vals), 2, length(coord_vals))
+                    coord_bounds[1, :] = edges_vals[1:end-1]
+                    coord_bounds[2, :] = edges_vals[2:end]
+                    push!(coord_edges_bounds_vars, boundsname => coord_bounds)
+                else
+                    push!(grid.dimensions_extra,  PB.NamedDimension(edgesname, edgesdim))
+                    push!(coord_edges_bounds_vars, edgesname => edges_vals)
+                end
             elseif equalspacededges
-                edgesname = dimname*"_edges"
                 ew = coord_vals[2] - coord_vals[1]
-                edgesvals = [coord_vals .- ew/2.0; coord_vals[end] + ew/2.0 ]
-                @info "  assuming equal spacing $ew to calculate coordinate edges $edgesname"
-                push!(grid.dimensions_extra,  PB.NamedDimension(edgesname, dim+1))
-                push!(coord_edges_vars, edgesname=>edgesvals)
+                if convert_edges_to_bounds
+                    boundsname = dimname*"_bnds"
+                    @info "  assuming equal spacing $ew to calculate coordinate bounds $boundsname"
+                    coord_bounds = similar(coord_vals, eltype(coord_vals), 2, length(coord_vals))
+                    coord_bounds[1, :] = coord_vals .- ew/2.0
+                    coord_bounds[2, :] = coord_vals .+ ew/2.0
+                    push!(coord_edges_bounds_vars, boundsname => coord_bounds)
+                else
+                    edgesname = dimname*"_edges"
+                    @info "  assuming equal spacing $ew to calculate coordinate edges $edgesname"
+                    edges_vals = [coord_vals .- ew/2.0; coord_vals[end] + ew/2.0 ]
+                    push!(grid.dimensions_extra,  PB.NamedDimension(edgesname, dim + 1))
+                    push!(coord_edges_bounds_vars, edgesname => edges_vals)
+                end
             else
                 @info "   no edges attribute and equalspacededges=false"
             end
@@ -760,7 +784,7 @@ function CartesianGrid(
         grid.ncells = prod(grid_size)
     end
 
-    return grid, coord_vars, coord_edges_vars
+    return grid, coord_vars, coord_edges_bounds_vars
 end
 
 """