more example in the docs

Author: Alexander-Barth

docs/src/index.md

@@ -1,15 +1,57 @@
 
 ## ZarrDatasets
 
+
+See the [documentation of JuliaGeo/CommonDataModel.jl](https://juliageo.org/CommonDataModel.jl/stable/) for the full documentation of the API. As a quick reference, here is an example how to create and read a Zarr file store as a quick reference.
+
+### Create a Zarr file store
+
+The following example create a Zarr file store in the directory `"/tmp/test-zarr"`:
+
+```julia
+using ZarrDatasets
+
+# sample data
+data = [i+j for i = 1:3, j = 1:5]
+
+directoryname = "/tmp/test-zarr4"
+mkdir(directoryname)
+
+ds = ZarrDataset(directoryname,"c")
+defDim(ds,"lon",size(data,1))
+defDim(ds,"lat",size(data,2))
+zv = defVar(ds,"varname",Int64,("lon","lat"))
+zv[:,:] = data
+zv.attrib["units"] = "m"
+close(ds)
+```
+
+### Loading a Zarr file store
+
+The data and units can be loaded by indexing the data set structure `ds`.
+
+```julia
+using ZarrDatasets
+directoryname = "/tmp/test-zarr4"
+ds = ZarrDataset(directoryname)
+data = ds["varname"][:,:]
+data_units = ds["varname"].attrib["units"]
+```
+
+
+
 ```@autodocs
 Modules = [ZarrDatasets]
 ```
 
 
+
+
+
 ### Differences between Zarr and NetCDF files
 
 * All metadata (in particular attributes) is stored in JSON files for the Zarr format with the following implications:
    * JSON does not distinguish between integers and real numbers. They are all considered as generic numbers. Whole numbers are loaded as `Int64` and real numbers `Float64`. It is not possible to store the number `1.0` as a real number.
    * The order of keys in a JSON document is undefined. It is therefore not possible to have a consistent ordering of the attributes or variables.
-   * The JSON standard does not allow the values NaN, +Inf, -Inf which is problematic for attributes ([zarr-python #412](https://github.com/zarr-developers/zarr-python/issues/412),
-   [zarr-specs #81](https://github.com/zarr-developers/zarr-specs/issues/81)). However, there is a special case for the fill-value to handle NaN, +Inf and -Inf.
+   * The JSON standard does not allow the values NaN, +Inf, -Inf which is problematic for attributes ([zarr-python #412](https://github.com/zarr-developers/zarr-python/issues/412),   [zarr-specs #81](https://github.com/zarr-developers/zarr-specs/issues/81)). However, there is a special case for the fill-value to handle NaN, +Inf and -Inf.
+   * All dimensions must be associated to Zarr variables.

src/dataset.jl

@@ -66,11 +66,16 @@ CDM.maskingvalue(ds::ZarrDataset) = ds.maskingvalue
     ZarrDataset(f::Function,url::AbstractString,mode = "r";
                      maskingvalue = missing)
 
-Open the zarr dataset at the url or path `url`. The mode can only be "r" (read-only)
-or "c" (create). `ds` supports the API of the
+Open the zarr dataset at the url or path `url`. The mode can only be `"r"` (read-only)
+or `"c"` (create). `ds` supports the API of the
 [JuliaGeo/CommonDataModel.jl](https://github.com/JuliaGeo/CommonDataModel.jl).
-The experimental `_omitcode` allows to work-around servers that return
-a HTTP error different than 404 for missing chunks.
+The experimental `_omitcode` allows to define which HTTP error code should be used
+for missing chunks. For compatibility with python's Zarr, the HTTP error 403
+(permission denied) is also used to missing chunks in addition to 404 (not
+found).
+
+The parameter `maskingvalue` allows to define which special value should be used
+as replacement for fill values. The default is `missing`.
 
 Example:
 
@@ -101,7 +106,6 @@ zos1 = ZarrDataset(url) do ds
   ds["zos"][:,:,end,1]
 end # implicit call to close(ds)
 ```
-
 """
 function ZarrDataset(url::AbstractString,mode = "r";
                      parentdataset = nothing,

src/variable.jl

@@ -58,6 +58,7 @@ function CDM.defVar(ds::ZarrDataset,name::SymbolOrString,vtype::DataType,dimensi
     if isnothing(chunksizes)
         chunksizes = _size
     end
+
     zarray = zcreate(
         vtype, ds.zgroup, name, _size...;
         chunks = chunksizes,