Merge 100f834 into 8c09c37

gaelforget · Mar 21, 2020 · 4031e97 · 4031e97
2 parents 8c09c37 + 100f834
commit 4031e97
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Showing 3 changed files with 36 additions and 88 deletions.
diff --git a/src/write.jl b/src/write.jl
@@ -405,8 +405,8 @@ function createfile(filename, field::Union{NCvar,Dict}, rdm="";
     if ~isnothing(attribs)
         fillval = pop!(attribs,"_FillValue",NaN)
         missingval = pop!(attribs,"missing_value",NaN)
-        itile = pop!(attribs,"itile",1)
-        ntile = pop!(attribs,"ntile",1)
+        haskey(attribs,"itile") ? itile = pop!(attribs,"itile") : nothing
+        haskey(attribs,"ntile") ? ntile = pop!(attribs,"ntile") : nothing
         description = [pop!(attribs,k,"") for k in ["description","A","B","C","D","E","F","G","H","I","J"]]
         description = description[.~isempty.(description)]
         if isempty(README)

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -15,22 +15,11 @@ ncfilnc2d,tmp = mktemp()
 ncfilnc3d,tmp = mktemp()
 ncfiltile2d,tmp = mktemp()
 
-ncfilarray2d_hl,tmp = mktemp()
-ncfilarray3d_hl,tmp = mktemp()
-ncfilbin2d_hl,tmp = mktemp()
-ncfilbin3d_hl,tmp = mktemp()
-ncfilnc2d_hl,tmp = mktemp()
-ncfilnc3d_hl,tmp = mktemp()
-ncfiltile2d_hl,tmp = mktemp()
-
 tempfiles = vcat(testvars["fnames2d"], testvars["fnames3d"],
                     testvars["tile_ex"]["fnamestile2d"],
                     ncfilarray2d, ncfilarray3d,
                     ncfilbin2d, ncfilbin3d,
-                    ncfilnc2d, ncfilnc3d,
-                    ncfilarray2d_hl, ncfilarray3d_hl,
-                    ncfilbin2d_hl, ncfilbin3d_hl,
-                    ncfilnc2d_hl, ncfilnc3d_hl)
+                    ncfilnc2d, ncfilnc3d)
 
 @testset "NCtiles Tests" begin
 
@@ -39,17 +28,11 @@ tempfiles = vcat(testvars["fnames2d"], testvars["fnames3d"],
         fld2d = NCvar("data2d",testvars["units"],[testvars["dims"][1:2]; testvars["dims"][4]],testvars["data2d"],Dict("long_name" =>testvars["longname2d"]),NCDatasets)
         fld3d = NCvar("data3d",testvars["units"],testvars["dims"],testvars["data3d"],Dict("long_name" =>testvars["longname3d"]),NCDatasets)
 
-        writetestfile(ncfilarray2d,fld2d,NCDatasets)
-        writetestfile(ncfilarray3d,fld3d,NCDatasets)
+        write(fld2d,ncfilarray2d)
+        write(fld3d,ncfilarray3d)
 
         @test testfile(ncfilarray2d,fld2d)
         @test testfile(ncfilarray3d,fld3d)
-
-        write(fld2d,ncfilarray2d_hl)
-        write(fld3d,ncfilarray3d_hl)
-
-        @test testfile(ncfilarray2d_hl,fld2d)
-        @test testfile(ncfilarray3d_hl,fld3d)
     end
 
     # Test BinData write
@@ -60,17 +43,11 @@ tempfiles = vcat(testvars["fnames2d"], testvars["fnames3d"],
         bfld2d = NCvar("data2d",testvars["units"],[testvars["dims"][1:2]; testvars["dims"][4]],bdatafld2d,Dict("long_name" =>testvars["longname2d"]),NCDatasets)
         bfld3d = NCvar("data3d",testvars["units"],testvars["dims"],bdatafld3d,Dict("long_name" =>testvars["longname3d"]),NCDatasets)
 
-        writetestfile(ncfilbin2d,bfld2d,NCDatasets)
-        writetestfile(ncfilbin3d,bfld3d,NCDatasets)
+        write(bfld2d,ncfilbin2d)
+        write(bfld3d,ncfilbin3d)
 
         @test testfile(ncfilbin2d,bfld2d)
         @test testfile(ncfilbin3d,bfld3d)
-
-        write(bfld2d,ncfilbin2d_hl)
-        write(bfld3d,ncfilbin3d_hl)
-
-        @test testfile(ncfilbin2d_hl,bfld2d)
-        @test testfile(ncfilbin3d_hl,bfld3d)
     end
 
     #Test NCData write
@@ -81,17 +58,11 @@ tempfiles = vcat(testvars["fnames2d"], testvars["fnames3d"],
         ncfld2d = NCvar("data2d",testvars["units"],[testvars["dims"][1:2]; testvars["dims"][4]],ncdatafld2d,Dict("long_name" =>testvars["longname2d"]),NCDatasets)
         ncfld3d = NCvar("data3d",testvars["units"],testvars["dims"],ncdatafld3d,Dict("long_name" =>testvars["longname3d"]),NCDatasets)
 
-        writetestfile(ncfilnc2d,ncfld2d,NCDatasets)
-        writetestfile(ncfilnc3d,ncfld3d,NCDatasets)
+        write(ncfld2d,ncfilnc2d)
+        write(ncfld3d,ncfilnc3d)
 
         @test testfile(ncfilnc2d,ncfld2d)
         @test testfile(ncfilnc3d,ncfld3d)
-
-        write(ncfld2d,ncfilnc2d_hl) 
-        write(ncfld3d,ncfilnc3d_hl)
-
-        @test testfile(ncfilnc2d_hl,ncfld2d)
-        @test testfile(ncfilnc3d_hl,ncfld3d)
     end
 
     @testset "Tile Data" begin
@@ -119,20 +90,16 @@ tempfiles = vcat(testvars["fnames2d"], testvars["fnames3d"],
                     "area" => NCvar("area","m^2",dims[1:2],tilarea,Dict(["long_name" => "grid cell area", "standard_name" => "cell_area"]),NCDatasets),
                     "land" => NCvar("land","1",dims[1:3],tilland,Dict(["long_name" => "land mask", "standard_name" => "land_binary_mask"]),NCDatasets),
                     "thic" => NCvar("thic","m",dims[3],thic,Dict("standard_name" => "cell_thickness"),NCDatasets)
-        ]) 
-        writetestfile(ncfiltile2d,flds,NCDatasets)
-        write(flds, ncfiltile2d_hl)
+        ])
+        write(flds, ncfiltile2d)
         savenames = joinpath.(ncfiltile2d*".".*lpad.(string.(1:tilfld2d.numtiles),4,"0").*".nc")
-        savenames_hl = joinpath.(ncfiltile2d_hl*".".*lpad.(string.(1:tilfld2d.numtiles),4,"0").*".nc")
         for k in keys(flds)
             if k != "thic" && k != "land" && isa(flds[k].values,MeshArray)
                 applylandmask(flds[k],land)
             end
         end
         @test all([testfile(fname,flds[fld]) for fname in savenames for fld in keys(flds)])
-        #@test all([testfile(fname,flds[fld]) for fname in savenames_hl for fld in keys(flds)])
         rm.(savenames)
-        rm.(savenames_hl)
     end
 
 end

diff --git a/test/testutils.jl b/test/testutils.jl
@@ -1,51 +1,17 @@
 using NCTiles, NCDatasets, MeshArrays, Dates
 
-function writetestfile(fname,field,package)
-
-    if isfile(fname)
-        rm(fname)
-    end
-
-    README = ["This file is written as a test for NCTiles.jl."]
-    if isa(field,Dict) # TileData Example
-        savenames = joinpath.(ncfiltile2d*".".*lpad.(string.(1:field["data2d"].values.numtiles),4,"0").*".nc")
-        dims = unique(vcat([field[v].dims for v in keys(field)]...))
-        datasets = [createfile(savenames[tidx],field,README,ntile = length(savenames), itile = tidx) for tidx in 1:length(savenames)]
-
-        ds = [x[1] for x in datasets]
-        fldvars = [x[2] for x in datasets]
-        #dims = [x[3] for x in datasets]
-
-        for k in keys(field)
-            if isa(field[k].values,TileData)
-                addData(fldvars,field[k])
-            else
-                tmpfldvars = [fv[findfirst(isequal(k),name.(fv))] for fv in fldvars]
-                addData.(tmpfldvars,Ref(field[k]))
-            end
-        end
-
-        for dim in dims
-            addDimData.(ds,Ref(dim))
-        end
-        close.(ds)
-
-    else
-        ds,fldvar,dimlist = createfile(fname,field,README)
-
-        addData(fldvar,field)
-        if package == NCDatasets
-            addDimData.(Ref(ds),field.dims)
-        end
-        # Close the file
-        close(ds)
-    end
-end
+"""
+    testfile(fname,checkfld)
 
+Perform various checks on a netcdf file (fname) variable (checkfld).
+"""
 function testfile(fname,checkfld)
     pass = true
     ds = Dataset(fname)
+    dsvar = ds[checkfld.name]
     varcheck = Dict()
+
+    #1. checks on dimensions
     varcheck["dims"] = Dict()
     for d in checkfld.dims
         fildim = ds[d.name]
@@ -76,8 +42,7 @@ function testfile(fname,checkfld)
         varcheck["dims"][d.name] = dimcheck
     end
 
-    dsvar = ds[checkfld.name]
-
+    #2. checks on units
     for k in keys(dsvar.attrib)
         if k == "units"
             varcheck["units"] = dsvar.attrib[k] == checkfld.units
@@ -88,7 +53,7 @@ function testfile(fname,checkfld)
         end
     end
 
-    # Check values of test data
+    #3. checks on values
     varcheck["values"] = false
     if isa(checkfld.values,Array)
         varcheck["values"] = true
@@ -166,6 +131,7 @@ function testfile(fname,checkfld)
     end
     pass = pass && varcheck["values"]
 
+    #4. printout message if >0 test failed
     if ~pass
         missmatchstring = ""
         for k in keys(varcheck)
@@ -188,6 +154,11 @@ function testfile(fname,checkfld)
     return pass
 end
 
+"""
+    applylandmask(data,land)
+
+Apply land mask either lazily (NCvar) or eagerly (other input types).
+"""
 function applylandmask(data,land)
     if isa(data,NCvar)
         if length(data.dims) == 2
@@ -209,6 +180,11 @@ function applylandmask(data,land)
     return dataout
 end
 
+"""
+    maketestdata()
+
+Create test data on a simple, coarse-grained Earth grid.
+"""
 function maketestdata()
     lon=-180:20:180; lat=-90:20:90;
     depth = 5:10:100
@@ -269,6 +245,11 @@ function maketestdata()
 
 end
 
+"""
+    getgrid()
+
+Download (if not already done) real ocean model grid (GRID_CS32) for testing pkg.
+"""
 function getgrid()
 
     testdir = abspath(joinpath(dirname(pathof(NCTiles)),"..","test"))