avoid non-standard indexing

src/NCODV.jl

@@ -334,7 +334,7 @@ function load(T, fname, long_name; qv_flags = ["good_value", "probably_good_valu
             ncvar_LOCAL_CDI_ID = varbyattrib_first(ds, long_name = "LOCAL_CDI_ID")
 
             if ndims(ncvar_LOCAL_CDI_ID) == 2
-                LOCAL_CDI_ID = chararray2strings(ncvar_LOCAL_CDI_ID.var[:])
+                LOCAL_CDI_ID = chararray2strings(Array(ncvar_LOCAL_CDI_ID.var))
             else
                 @warn """The variable with the long_name attribute \'LOCAL_CDI_ID\' is expected to have two dimensions. For example the output of 'ncdump -h' of $fname should contain:
 [...]
@@ -348,13 +348,13 @@ We use the empty string for LOCAL_CDI_ID instead.
         end
 
         EDMO_CODE = if length(varbyattrib(ds; long_name = "EDMO_code")) > 0
-            varbyattrib_first(ds, long_name = "EDMO_code")[:]
+            Array(varbyattrib_first(ds, long_name = "EDMO_code"))
         else
-            varbyattrib_first(ds, long_name = "EDMO_CODE")[:]
+            Array(varbyattrib_first(ds, long_name = "EDMO_CODE"))
         end
 
-        obsproflon = varbyattrib_first(ds, standard_name = "longitude")[:]
-        obsproflat = varbyattrib_first(ds, standard_name = "latitude")[:]
+        obsproflon = Array(varbyattrib_first(ds, standard_name = "longitude"))
+        obsproflat = Array(varbyattrib_first(ds, standard_name = "latitude"))
 
         # time for time series
         ncvar_time = nothing
@@ -369,7 +369,7 @@ We use the empty string for LOCAL_CDI_ID instead.
             @assert ndims(ncvar_time) == 2
         else
             # profile
-            obsproftime = varbyattrib_first(ds, standard_name = "time")[:]
+            obsproftime = Array(varbyattrib_first(ds, standard_name = "time"))
             @assert ndims(obsproftime) == 1
         end
 

src/NCSDN.jl

@@ -61,11 +61,11 @@ function loadvar(
         return T[]
     end
 
-    dataarray = ds[param][:]
+    dataarray = Array(ds[param])
     data = nomissing(dataarray, fillvalue)
 
     if qfname in ds
-        qf = ds[qfname].var[:]
+        qf = Array(ds[qfname].var)
 
         keep_data = falses(size(qf))
 
@@ -176,7 +176,7 @@ function load(
     )
 
     if ndims(lon) == 1
-        #@show fname,param,size(lon),size(data)
+        @debug "check size",fname,param,size(lon),size(data)
         @assert size(lon, 1) == size(data, 2)
         lon = repeat(reshape(lon, 1, size(lon, 1)), inner = (size(data, 1), 1))
     end
@@ -207,8 +207,8 @@ function load(
         time = repeat(reshape(time, 1, size(time, 1)), inner = (size(data, 1), 1))
     end
 
-    edmo = ds["SDN_EDMO_CODE"][:]
-    cdiid = ds["SDN_LOCAL_CDI_ID"][:]
+    edmo = Array(ds["SDN_EDMO_CODE"])
+    cdiid = Array(ds["SDN_LOCAL_CDI_ID"])
 
     @assert size(edmo, 1) == size(data, 2)
     @assert size(cdiid, 2) == size(data, 2)

test/test_ncodv.jl

@@ -375,14 +375,14 @@ obsvalue,obslon,obslat,obsdepth,obstime,obsids = NCODV.load(T,fname_TS,long_name
 almostgood(qf) = !ismissing(qf) && ((qf == 49) || (qf == 50))
 
 nc = NCDataset(fname_TS)
-ox = nc["var3"][:];
-ox_qf = nc["var3_qc"][:];
+ox = nc["var3"][:,:];
+ox_qf = nc["var3_qc"][:,:];
 
-z = nc["var2"][:];
-z_qf = nc["var2_qc"][:];
+z = nc["var2"][:,:];
+z_qf = nc["var2_qc"][:,:];
 
-time = nc["var1_qc"].var[:];
-time_qf = nc["var1_qc"][:];
+time = nc["var1_qc"].var[:,:];
+time_qf = nc["var1_qc"][:,:];
 
 good = almostgood.(ox_qf) .& .!ismissing.(ox) .& almostgood.(z_qf) .& .!ismissing.(z) .& almostgood.(time_qf) .& .!ismissing.(time)
 

test/test_save.jl

@@ -21,7 +21,7 @@ relerr = rand(T, sz)
 DIVAnd.save(filename, xyi, fi, varname; type_save = T, relerr = relerr)
 
 ds = Dataset(filename)
-fi2 = ds[varname][:]
+fi2 = ds[varname][:,:,:,:]
 close(ds)
 
 @test fi2[mask] == fi[mask]