Merge pull request #247 from meggart/fg/diskarrays_04

Update to Diskarrays 0.4

.github/workflows/ci.yml

@@ -10,7 +10,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
+          - 'lts'
           - '1'
           #- '~1.8.0-0'
           - 'nightly'

Project.toml

@@ -19,7 +19,7 @@ Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 CFTime = "0.1.1"
 CommonDataModel = "0.3.4"
 DataStructures = "0.17, 0.18"
-DiskArrays = "0.3.22"
+DiskArrays = "0.4.5"
 NetCDF_jll = "=400.701.400, =400.702.400, =400.902.5, =400.902.208, =400.902.209, =400.902.211"
 NetworkOptions = "1.2"
 julia = "1.6"

src/variable.jl

@@ -443,7 +443,8 @@ function eachchunk(v::Variable)
         return DiskArrays.GridChunks(v, chunksizes)
     end
 end
-haschunks(v::Variable) = (_chunking(v)[1] == :contiguous ? DiskArrays.Unchunked() : DiskArrays.Chunked())
+haschunks(v::Variable) = (_chunking(v)[1] == :contiguous ? DiskArrays.Unchunked(DiskArrays.SubRanges(DiskArrays.CanStepRange(),1.0)) : 
+    DiskArrays.Chunked(DiskArrays.SubRanges(DiskArrays.CanStepRange(),1.0)))
 
 eachchunk(v::CFVariable{T,N,<:Variable}) where {T,N} = eachchunk(v.var)
 haschunks(v::CFVariable{T,N,<:Variable}) where {T,N} = haschunks(v.var)
@@ -537,38 +538,3 @@ function _range_indices_dest(of,v,rest...)
 end
 range_indices_dest(ri...) = _range_indices_dest((),ri...)
 
-function _batchgetindex(
-    v::Variable{T},
-    indices::Union{<:Integer,Colon,AbstractRange{<:Integer},AbstractVector{<:Integer}}...) where T
-
-    @debug "transform vector of indices to ranges"
-
-    sz_source = size(v)
-    ri = to_range_list.(indices,sz_source)
-    sz_dest = size_getindex(v,indices...)
-
-    N = length(indices)
-
-    ri_dest = range_indices_dest(ri...)
-    @debug "ri_dest $ri_dest"
-    @debug "ri $ri"
-
-    if all(==(1),length.(ri))
-        # single chunk
-        R = first(CartesianIndices(length.(ri)))
-        ind_source = ntuple(i -> ri[i][R[i]],N)
-        ind_dest = ntuple(i -> ri_dest[i][R[i]],length(ri_dest))
-        return v[ind_source...]
-    end
-
-    dest = Array{eltype(v),length(sz_dest)}(undef,sz_dest)
-    for R in CartesianIndices(length.(ri))
-        ind_source = ntuple(i -> ri[i][R[i]],N)
-        ind_dest = ntuple(i -> ri_dest[i][R[i]],length(ri_dest))
-        dest[ind_dest...] = v[ind_source...]
-    end
-    return dest
-end
-
-DiskArrays.batchgetindex(v::Variable,indices::Union{<:Integer,Colon,AbstractRange{<:Integer},AbstractVector{<:Integer}}...) = _batchgetindex(v,indices...)
-DiskArrays.batchgetindex(v::Variable,index::AbstractVector{Int}) = _batchgetindex(v,index)

test/test_check_size.jl

@@ -33,10 +33,10 @@ ds["w"][:,1:15] = ones(10,15)
 @test size(ds["w"]) == (10,15)
 
 # w cannot grow along a fixed dimension
-@test_throws DimensionMismatch ds["w"][:,:] = ones(11,15)
+@test_throws Union{NCDatasets.NetCDFError,DimensionMismatch} ds["w"][:, :] = ones(11, 15)
 
 # NetCDF: Index exceeds dimension bound
-@test_throws NCDatasets.NetCDFError ds["u"][100,100]
+@test_throws Union{NCDatasets.NetCDFError,BoundsError} ds["u"][100,100]
 close(ds)
 rm(filename)
 

test/test_variable.jl

@@ -20,7 +20,7 @@ NCDataset(filename,"c") do ds
 
     v = defVar(ds,"small",Float64,("lon","lat"))
 #    @test_throws Union{NCDatasets.NetCDFError,DimensionMismatch} v[:] = zeros(sz[1]+1,sz[2])
-    @test_throws DimensionMismatch v[1:sz[1],1:sz[2]] = zeros(sz[1]+1,sz[2])
+    @test_throws Union{NCDatasets.NetCDFError,DimensionMismatch} v[1:sz[1],1:sz[2]] = zeros(sz[1]+1,sz[2])
     @test_throws NCDatasets.NetCDFError v[sz[1]+1,1] = 1
     @test_throws NCDatasets.NetCDFError v[-1,1] = 1