DOC: Custom ArrayArray Codecs in Zarr 3+

[dimitri-yatsenko]

Describe the issue linked to the documentation

I previously created a precompression quantization codec for multiphoton microscopy soon to be published in Nature Protocols preprint.

The Zarr V2 implementation works great and can be found here:

• https://github.com/dimitri-yatsenko/anscombe-numcodecs/tree/main
• Demo: https://github.com/dimitri-yatsenko/anscombe-numcodecs/blob/main/examples/workbook.ipynb

However, I tried following the best available instructions for an equivalent Zarr V3 implementation and have not been able to get it to work yet.

• Here is my attempt at implementing the codec: https://github.com/dimitri-yatsenko/anscombe-numcodecs/tree/zarr-ver3
• Here is an executed example with the current error is in the workbook https://github.com/dimitri-yatsenko/anscombe-numcodecs/blob/zarr-ver3/examples/workbook.ipynb

If I can figure out how to implement and use a custom codec in Zarr 3, I will write a nice tutorial.

Suggested fix for documentation

No response

[d-v-b]

thanks for the issue! I see this error in the notebook:

File ~/opt/miniconda3/envs/anscombe_numcodecs/lib/python3.11/site-packages/zarr/abc/codec.py:134, in BaseCodec._encode_single(self, chunk_data, chunk_spec)
    131 async def _encode_single(
    132     self, chunk_data: CodecInput, chunk_spec: ArraySpec
    133 ) -> CodecOutput | None:
--> 134     raise NotImplementedError

NotImplementedError: 

It looks like your codec class does not implement a require method (_encode_single). I would implement that method for your codec, along with the other methods on the codec abc.

On our end, this method should probably have been explicitly decorated as an abstract method so that subclass creation would fail, instead of the later failure we see here.

[dimitri-yatsenko]

@d-v-b Thank you.

I have updated the method name _encode_single (I had a typo previously). Here is the new error:

• Codec implementation: https://github.com/dimitri-yatsenko/anscombe-numcodecs/tree/zarr-ver3
• Notebook with new error: https://github.com/dimitri-yatsenko/anscombe-numcodecs/blob/zarr-ver3/examples/workbook.ipynb