workaround for meggart/DiskArrays.jl#131

src/NCDatasets.jl

@@ -45,11 +45,12 @@ import CommonDataModel: AbstractDataset, AbstractVariable,
     chunking, deflate, checksum, fillmode,
     iswritable, sync, CatArrays,
     SubDataset,
-    @select, select, Near, coordinate_value, coordinate_names, split_by_and
+    @select, select, Near, coordinate_value, coordinate_names, split_by_and,
+    chunking, deflate, checksum
+
 
 import DiskArrays
-import DiskArrays: readblock!, writeblock!, eachchunk, haschunks
-using DiskArrays: @implement_diskarray
+import DiskArrays: readblock!, writeblock!, eachchunk, haschunks, batchgetindex
 
 function __init__()
     NetCDF_jll.is_available() && init_certificate_authority()
@@ -73,7 +74,8 @@ include("multifile.jl")
 include("ncgen.jl")
 include("precompile.jl")
 
-@implement_diskarray NCDatasets.Variable
+DiskArrays.@implement_diskarray NCDatasets.Variable
+
 
 export CatArrays
 export CFTime

src/variable.jl

@@ -498,7 +498,6 @@ end
 end
 
 
-#=
 
 # indexing with vector of integers
 
@@ -549,7 +548,10 @@ function _range_indices_dest(of,v,rest...)
 end
 range_indices_dest(ri...) = _range_indices_dest((),ri...)
 
-function Base.getindex(v::Union{MFVariable,SubVariable},indices::Union{Int,Colon,AbstractRange{<:Integer},Vector{<:Integer}}...)
+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)
@@ -574,15 +576,10 @@ function Base.getindex(v::Union{MFVariable,SubVariable},indices::Union{Int,Colon
     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...]
-        if hasproperty(v,:var)
-            buffer = Array{eltype(v.var),length(ind_dest)}(undef,length.(ind_dest))
-            load!(v,view(dest,ind_dest...),buffer,ind_source...)
-        else
-            dest[ind_dest...] = v[ind_source...]
-        end
+        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_bounds.jl

@@ -30,7 +30,7 @@ nctime_bounds[:,:] = time_bounds
 close(ds)
 
 
-# issue 170
+# NCDatasets issue 170
 
 fname = tempname()
 ds = NCDataset(fname,"c")

test/test_select.jl

@@ -247,32 +247,32 @@ i = findmin(x -> abs.(DateTime(2000,1,3,1) - x),time)[2]
 v = NCDatasets.@select(ds["SST"],30 <= lon <= 60 && 40 <= lat <= 90)
 
 # # https://github.com/meggart/DiskArrays.jl/issues/131
-# ilon = findall(x -> 30 <= x <= 60,ds["lon"])
-# ilat = findall(x -> 40 <= x <= 90,ds["lat"])
-# v2 = ds["SST"][ilon,ilat,:]
-# @test_broken v == v2
-
-
-# lonr = 30..60
-# latr = ClosedInterval(40, 90) # latitude range
-# v = NCDatasets.@select(ds["SST"], lon ∈ $lonr && lat in $latr)
-# ilon = findall(x -> 30 <= x <= 60,ds["lon"])
-# ilat = findall(x -> 40 <= x <= 90,ds["lat"])
-# v2 = ds["SST"][ilon,ilat,:]
-# @test_broken v == v2
-
-# v = NCDatasets.@select(ds["SST"], lon ∈ $(30..60) && lat ∈ $(65 ± 25))
-# ilon = findall(x -> 30 <= x <= 60,ds["lon"])
-# ilat = findall(x -> 40 <= x <= 90,ds["lat"])
-# v2 = ds["SST"][ilon,ilat,:]
-# @test_broken v == v2
-
-
-# v = NCDatasets.@select(ds["SST"], lon ∈ 30..60 && lat ∈ 65 ± 25)
-# ilon = findall(x -> 30 <= x <= 60,ds["lon"])
-# ilat = findall(x -> 40 <= x <= 90,ds["lat"])
-# v2 = ds["SST"][ilon,ilat,:]
-# @test_broken v == v2
+ilon = findall(x -> 30 <= x <= 60,ds["lon"])
+ilat = findall(x -> 40 <= x <= 90,ds["lat"])
+v2 = ds["SST"][ilon,ilat,:]
+@test v == v2
+
+
+lonr = 30..60
+latr = ClosedInterval(40, 90) # latitude range
+v = NCDatasets.@select(ds["SST"], lon ∈ $lonr && lat in $latr)
+ilon = findall(x -> 30 <= x <= 60,ds["lon"])
+ilat = findall(x -> 40 <= x <= 90,ds["lat"])
+v2 = ds["SST"][ilon,ilat,:]
+@test v == v2
+
+v = NCDatasets.@select(ds["SST"], lon ∈ $(30..60) && lat ∈ $(65 ± 25))
+ilon = findall(x -> 30 <= x <= 60,ds["lon"])
+ilat = findall(x -> 40 <= x <= 90,ds["lat"])
+v2 = ds["SST"][ilon,ilat,:]
+@test v == v2
+
+
+v = NCDatasets.@select(ds["SST"], lon ∈ 30..60 && lat ∈ 65 ± 25)
+ilon = findall(x -> 30 <= x <= 60,ds["lon"])
+ilat = findall(x -> 40 <= x <= 90,ds["lat"])
+v2 = ds["SST"][ilon,ilat,:]
+@test v == v2
 
 
 in_lon_range(lon) = 30 <= lon <= 60

test/test_variable.jl

@@ -268,14 +268,11 @@ close(ds_src)
 close(ds_dest)
 
 # issue 209
-# broken
-# maybe related to
-# https://github.com/meggart/DiskArrays.jl/issues/131
 filename_src = tempname()
 ds = NCDataset(filename_src, "c")
 data = [1,2,3]
 ncv = defVar(ds,"data",data,("data",))
-@test_broken isempty(ncv[Int[]])
+@test isempty(ncv[Int[]])
 close(ds)
 
 # issue 211