Write to Zarr store using h5py-like interface

[magland]

This PR adds support for writing to Zarr stores using the h5py-like interface.

See https://github.com/NeurodataWithoutBorders/lindi/blob/write/tests/test_zarr_write.py

and

https://github.com/NeurodataWithoutBorders/lindi/blob/write/examples/example_create_zarr_nwb.py

[codecov-commenter]

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[oruebel]

Just to clarify, if I understand this correctly, lindi.LindiH5pyFile is here backed by a Zarr store, i.e., it is representing a Zarr file as if it where h5py and as such, pynwb.NWBHDF5IO is here actually writing to Zarr. I.e., in some sense this would be in a form a replacement forZarrIO in hdmf_zarr.

lindi/examples/example_create_zarr_nwb.py

Lines 16 to 20 in 0f6814a

	store = zarr.DirectoryStore(zarr_dirname)
	zarr.group(store=store) # create a root group
	with lindi.LindiH5pyFile.from_zarr_store(store, mode='a') as client:
	with pynwb.NWBHDF5IO(file=client, mode='r+') as io:
	io.write(nwbfile) # type: ignore

[magland]

Just to clarify, if I understand this correctly, lindi.LindiH5pyFile is here backed by a Zarr store, i.e., it is representing a Zarr file as if it where h5py and as such, pynwb.NWBHDF5IO is here actually writing to Zarr. I.e., in some sense this would be in a form a replacement forZarrIO in hdmf_zarr.

lindi/examples/example_create_zarr_nwb.py

Lines 16 to 20 in 0f6814a

	store = zarr.DirectoryStore(zarr_dirname)
	zarr.group(store=store) # create a root group
	with lindi.LindiH5pyFile.from_zarr_store(store, mode='a') as client:
	with pynwb.NWBHDF5IO(file=client, mode='r+') as io:
	io.write(nwbfile) # type: ignore

@oruebel Yes that's right.

[rly]

The suggested changes around np.float128/np.complex256 and the change of mode="a" to mode="r+" were necessary to make examples/example_create_zarr_nwb.py run on my machine.

[rly]

I did not do heavy testing of this PR, but I read through it all, and as far as I can tell, it makes sense and looks good. Nicely done!

HDMF supports a lot of weird edge cases. I'll see if I can think up more tests to what you already have here.

[magland]

I did not do heavy testing of this PR, but I read through it all, and as far as I can tell, it makes sense and looks good. Nicely done!

HDMF supports a lot of weird edge cases. I'll see if I can think up more tests to what you already have here.

Thanks Ryan!