Dependency Issue for Kerchunk -> Icechunk via Virtualizarr

[dwest77a]

Hi all, I'm relatively new to using virtualizarr but have been developing tools using Kerchunk for some time, specifically a package around large-scale conversions in parallel for thousands of datasets in our data archives.

I'm attempting to use the Virtualizarr library to concatenate some NetCDF4 data into a virtual dataset, then write out as an Icechunk store to disk. My issue is that it seems Icechunk requires the new zarr v3 pre-release, but Kerchunk (used to create the virtual dataset) needs Zarr < 3. I've so far been unable to resolve this dependency issue. Any suggestions for how to go about solving this would be appreciated, thanks!

My example code:

from virtualizarr import open_virtual_dataset
vds = [open_virtual_dataset(f, indexes={}) for f in files]

import xarray as xr
combined_vds = xr.concat(vds, dim='time', coords='minimal', compat='override')

from icechunk import IcechunkStore, StorageConfig, StoreConfig, VirtualRefConfig
storage = StorageConfig.filesystem(str('combined'))
store = IcechunkStore.create(storage=storage, mode="w", config=StoreConfig(
    virtual_ref_config=VirtualRefConfig.s3_anonymous(region='us-east-1'),
))

combined_vds.virtualize.to_icechunk(store)

I either get an issue importing kerchunk (if I uninstall that to reinstall the zarr v3 pre-release) or an issue with zarr when trying to create the Icechunk store.

[maxrjones]

Matthew Iannucci has been helpfully tracking the compatibility between Icechunk, VirtualiZarr, and Kerchunk in earth-mover/icechunk#197. The tl;dr is that until fsspec/kerchunk#516 is completed/merged to add Zarr-Python v3 compatibility in Kerchunk one would need to work off Matt's fork and branch to use these libraries in the same environment, since icechunk requires Zarr-Python v3.

[TomNicholas]

@maxrjones is correct that we're waiting on kerchunk to support zarr-python v3, and as icechunk requires zarr-python v3 currently the released versions of kerchunk and icechunk are incompatible. But as you're working with netCDF4 data you actually have a few different options:

1. As Max mentioned use the fork of kerchunk that Matt is maintaining for now (but some parts of kerchunk might not work on that branch yet). This is recommended for now if you want to try putting virtual datasets in Icechunk.
2. Try using @sharkinsspatial's non-kerchunk alternative HDF reader (Non-kerchunk backend for HDF5/netcdf4 files. #87), which should be able to read netCDF4 files. This doesn't require kerchunk to be installed so I think should work with zarr-python v3 (?) It is very new and experimental though. You have to explicitly opt in to using it via

   from virtualizarr.readers.hdf import HDFVirtualBackend
   
   vds = open_virtual_dataset('file.nc', backend=HDFVirtualBackend)

3. Have 2 environments, one with kerchunk and zarr-python v2, and one with icechunk and zarr-python v3. You use the first to open and concatenate the files, then save them to disk using vds.virtualize.to_kerchunk('refs.json'). Then in the second environment you use open_virtual_dataset(refs.json, filetype='kerchunk'), then save that into icechunk. It's janky but it should work, because open_virtual_dataset(refs.json, filetype='kerchunk') doesn't actually require the kerchunk package as a dependency.
4. Just wait a few weeks and hopefully kerchunk will be updated, then you should be able to just use the released versions of everything together.

[dwest77a]

Hi both, thanks very much for the suggestions! I will attempt both the first and second solutions in the next few days, I'm just trying to get a picture of how it all works for now. Solution 3 suggested above has an additional issue that it can't be used where some variables/dimensions are written inline in the kerchunk file (i.e base64 encoded) - this is listed as a ToDo in the error message. Most of the kerchunk files we've produced have inline components for some dimensions as this is more performant than having to make many very small requests to compose a dimension.

Thanks again for the suggestions!

[TomNicholas]

This was closed by release v1.3.0!