Custom codec information is silently dropped when writing kerchunk references

[frazane]

I encountered this bug when working on a custom GRIB parser in https://github.com/MeteoSwiss/icon-ch-vzarr.

When trying to serialize virtual datasets as kerchunk references, the custom codec information is silently dropped. The array metadata looks like this (note the codecs entry):

ArrayV3Metadata(shape=(1, 1147980),
                data_type=Float64(endianness='little'),
                chunk_grid=RegularChunkGrid(chunk_shape=(1, 1147980)),
                chunk_key_encoding=DefaultChunkKeyEncoding(name='default',
                                                           separator='/'),
                fill_value=np.float64(0.0),
                codecs=(EccodesCodec(),),
                attributes={'_earthkit': {'b64message': 'R1JJQv//AAIAAAAAAAAAqgAAABUBANcA/w8BAQfpAQEUAAABAQAAABwCAP4AB+kBARU0AwAAAAAAAAAAAAAAAAEAAAAjAwAAEYRMAAAAZQYAAAEBF2Q9oldJWbZE0lSjzW4rwAAAACIEAAAAAAAAAgCXAAAAAAAAAABnAAAAAAL///////8AAAAVBQAAAfAAAEOIgACACgAAAAAAAAAGBv8AAAAFBzc3Nzc=',
                                          'bitsPerValue': 16},
                            'long_name': '2m Temperature',
                            'standard_name': 'air_temperature',
                            'units': 'K'},
                dimension_names=('valid_time', 'values'),
                zarr_format=3,
                node_type='array',
                storage_transformers=())

but then the codecs (filter/compressors) information is not found in the references (it's null):

{"version":1,"refs":{".zgroup":"{\"zarr_format\":2}",".zattrs":"{}","T_2M\/0.0":["\/store_new\/mch\/msopr\/osm\/KENDA-CH1\/ANA25\/det\/iaf2025010120",3424926372,2296130],"T_2M\/1.0":["\/store_new\/mch\/msopr\/osm\/KENDA-CH1\/ANA25\/det\/iaf2025010121",3427222332,2296130],"T_2M\/2.0":["\/store_new\/mch\/msopr\/osm\/KENDA-CH1\/ANA25\/det\/iaf2025010122",3424926372,2296130],"T_2M\/3.0":["\/store_new\/mch\/msopr\/osm\/KENDA-CH1\/ANA25\/det\/iaf2025010123",3424926372,2296130],"T_2M\/.zarray":"{\"shape\":[4,1147980],\"chunks\":[1,1147980],\"dtype\":\"<f8\",\"fill_value\":0.0,\"order\":\"C\",\"filters\":null,\"dimension_separator\":\".\",\"compressor\":null,\"attributes\":{},\"zarr_format\":2}","T_2M\/.zattrs":"{\"standard_name\":\"air_temperature\",\"long_name\":\"2m Temperature\",\"units\":\"K\",\"_earthkit\":{\"bitsPerValue\":16,\"b64message\":\"R1JJQv\/\/AAIAAAAAAAAAqgAAABUBANcA\/w8BAQfpAQEUAAABAQAAABwCAP4AB+kBARU0AwAAAAAAAAAAAAAAAAEAAAAjAwAAEYRMAAAAZQYAAAEBF2Q9oldJWbZE0lSjzW4rwAAAACIEAAAAAAAAAgCXAAAAAAAAAABnAAAAAAL\/\/\/\/\/\/\/8AAAAVBQAAAfAAAEOIgACACgAAAAAAAAAGBv8AAAAFBzc3Nzc=\"},\"_ARRAY_DIMENSIONS\":[\"valid_time\",\"values\"]}","CLCL\/0.0":["\/store_new\/mch\/msopr\/osm\/KENDA-CH1\/ANA25\/det\/iaf2025010120",3721779870,2296130],"CLCL\/1.0":["\/store_new\/mch\/msopr\/osm\/KENDA-CH1\/ANA25\/det\/iaf2025010121",3724075830,2296130],"CLCL\/2.0":["\/store_new\/mch\/msopr\/osm\/KENDA-CH1\/ANA25\/det\/iaf2025010122",3721779870,2296130],"CLCL\/3.0":["\/store_new\/mch\/msopr\/osm\/KENDA-CH1\/ANA25\/det\/iaf2025010123",3721779870,2296130],"CLCL\/.zarray":"{\"shape\":[4,1147980],\"chunks\":[1,1147980],\"dtype\":\"<f8\",\"fill_value\":0.0,\"order\":\"C\",\"filters\":null,\"dimension_separator\":\".\",\"compressor\":null,\"attributes\":{},\"zarr_format\":2}","CLCL\/.zattrs":"{\"standard_name\":\"unknown\",\"long_name\":\"Cloud Cover (800 hPa - Soil)\",\"units\":\"%\",\"_earthkit\":{\"bitsPerValue\":16,\"b64message\":\"R1JJQv\/\/AAIAAAAAAAAAqgAAABUBANcA\/w8BAQfpAQEUAAABAQAAABwCAP4AB+kBARU0BAAAAAAAAAAAAAAAAAEAAAAjAwAAEYRMAAAAZQYAAAEBF2Q9oldJWbZE0lSjzW4rwAAAACIEAAAAAAYWAgCXAAAAAAAAAABkAAABOIABAAAAAAAAAAAVBQAAAfAAAEOIgACACgAAAAAAAAAGBv8AAAAFBzc3Nzc=\"},\"_ARRAY_DIMENSIONS\":[\"valid_time\",\"values\"]}","TOT_PREC\/0.0":["\/store_new\/mch\/msopr\/osm\/KENDA-CH1\/ANA25\/det\/iaf2025010120",3792671464,194],"TOT_PREC\/1.0":["\/store_new\/mch\/msopr\/osm\/KENDA-CH1\/ANA25\/det\/iaf2025010121",3794978942,194],"TOT_PREC\/2.0":["\/store_new\/mch\/msopr\/osm\/KENDA-CH1\/ANA25\/det\/iaf2025010122",3792683114,194],"TOT_PREC\/3.0":["\/store_new\/mch\/msopr\/osm\/KENDA-CH1\/ANA25\/det\/iaf2025010123",3792680428,194],"TOT_PREC\/.zarray":"{\"shape\":[4,1147980],\"chunks\":[1,1147980],\"dtype\":\"<f8\",\"fill_value\":0.0,\"order\":\"C\",\"filters\":null,\"dimension_separator\":\".\",\"compressor\":null,\"attributes\":{},\"zarr_format\":2}","TOT_PREC\/.zattrs":"{\"standard_name\":\"unknown\",\"long_name\":\"Total Precipitation (Accumulation)\",\"units\":\"kg m-2\",\"_earthkit\":{\"bitsPerValue\":0,\"b64message\":\"R1JJQv\/\/AAIAAAAAAAAAwgAAABUBANcA\/w8BAQfpAQEUAAABAQAAABwCAP4AB+kBARU0BQAAAAAAAAAAAAAAAAEAAAAjAwAAEYRMAAAAZQYAAAEBF2Q9oldJWbZE0lSjzW4rwAAAADoEAAAACAE0AgCXAAAAAAAAAAABAAAAAAD\/\/\/\/\/\/\/8H6QEBFAAAAQAAAAABAgAAAAAA\/wAAAAAAAAAVBQAAAfAAAEOIgACACgAAAAAAAAAGBv8AAAAFBzc3Nzc=\"},\"_ARRAY_DIMENSIONS\":[\"valid_time\",\"values\"]}","valid_time\/0":"base64:AAAAAAAAAAABAAAAAAAAAAIAAAAAAAAAAwAAAAAAAAA=","valid_time\/.zarray":"{\"shape\":[4],\"chunks\":[4],\"dtype\":\"<i8\",\"fill_value\":null,\"order\":\"C\",\"filters\":null,\"dimension_separator\":\".\",\"compressor\":null,\"attributes\":{},\"zarr_format\":2}","valid_time\/.zattrs":"{\"units\":\"hours since 2025-01-01 20:00:00\",\"calendar\":\"proleptic_gregorian\",\"_ARRAY_DIMENSIONS\":[\"valid_time\"]}"}}

---

Issue seems to be here: https://github.com/zarr-developers/VirtualiZarr/blob/f3149d6464fa2e88c01c71d03170993f93bb3e8c/virtualizarr/utils.py#L138 if my custom codec is a subclass of ArrayBytesCodec it will be excluded. There's also a TODO left there which may refer to this.

---

I added a reproducible example here (run it with uv run virtualize_kenda.py): https://gist.github.com/frazane/d26fd8925aea11cadf5bb012d81c5c2e

[TomNicholas]

Thanks for raising this @frazane !

We clearly need to pass this information in.

Just to clarify - it looks like the part of the VirtualiZarr code you're referring to is for non-virtual variables (i.e. not ManifestArrays). Is that what you meant?

The next step here would be to create a minimum reproducible example, ideally by just artificially creating some data with a single compressor or filter.

[frazane]

@TomNicholas

Just to clarify - it looks like the part of the VirtualiZarr code you're referring to is for non-virtual variables (i.e. not ManifestArrays). Is that what you meant?

Ops, no, that was a mistake. The issue is elsewhere, likely here https://github.com/zarr-developers/VirtualiZarr/blob/f3149d6464fa2e88c01c71d03170993f93bb3e8c/virtualizarr/utils.py#L138

I added a "minimal" reproducible example here: https://gist.github.com/frazane/d26fd8925aea11cadf5bb012d81c5c2e. You can run it directly with uv run virtualize_kenda.py.

[TomNicholas]

When I try to run that example I get this error:

  File "/Users/tom/.cache/uv/environments-v2/virtualize-kenda-kerchunk-fffb73731867bdee/lib/python3.12/site-packages/zarr/codecs/_v2.py", line 51, in _decode_single
    chunk = chunk.view(chunk_spec.dtype.to_native_dtype())
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ValueError: When changing to a larger dtype, its size must be a divisor of the total size in bytes of the last axis of the array.

Is that what you expect me to see?

[TomNicholas]

FYI @frazane I would like to fix this but I'm going to release VZ now without this fix just because there are multiple other important fixes to get out there.

[frazane]

Is that what you expect me to see?

Yes, that is the same exception I get.

[frazane]

Hi @TomNicholas, are there any news regarding this issue? (I am not in need of an urgent fix, just happened to remember about it)