Exceptions when creating an array that has an object

I noticed two issues:

1. Zarr raises an exception when attempting to create an array with a structured dtype that contains an object.

>>> import numcodecs
>>> import zarr
>>> foo = zarr.open('foo')
>>> foo.create('bar', dtype=[('x', float), ('y',object)],  shape=(10, 20), object_codec=numcodecs.Pickle())
TypeError                                 Traceback (most recent call last)
    ...
MetadataError: error decoding metadata: Cannot change data-type for object array.

I think that the issue is in the functions encode_fill_value and decode_fill_value. A structured dtype that contains an object reports its kind as ‘V’ so zarr encodes it using standard_b64encode, but if dtype.has_object is true then it should first pickle the fill_value and only then encode it.

1. This is a related problem to item 1. zarr essentially only supports fill-values of None for object arrays:

>>> import numpy
>>> import zarr
>>> x = zarr.open('x')
>>> y = x.create('y', shape=(2, 2), dtype='O', fill_value=zarr.Blosc, object_codec=numcodecs.Pickle())
---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
    ...
TypeError: Object of type type is not JSON serializable

• Value of zarr.__version__: 2.8.3
• Value of numcodecs.__version__: 0.6.4 – 0.8.0
• Version of Python interpreter: 3.7.4 – 3.9.6
• Operating system (Linux/Windows/Mac): Mac/Linux
• How Zarr was installed (e.g., “using pip into virtual environment”, or “using conda”): pip or conda

Edit: I cleaned up the second example (I copied and pasted an incorrect reproducer here).

[abergou]

Thanks @joshmoore !

[abergou]

Thanks for the quick reply @joshmoore!

Where do I pass in data=? I don’t see it as an argument to Group.create. If I simply pass it into foo.create then I get back the same error as before:

>>> import numcodecs
>>> import numpy
>>> import zarr
>>> foo = zarr.open('foo')
>>> foo.create('bar', dtype=[('x', float), ('y',object)],  shape=(10, 20), object_codec=numcodecs.Pickle(), data=numpy.zeros((10, 20), dtype=[('x', float), ('y', object)]))
TypeError                                 Traceback (most recent call last)
    ...
MetadataError: error decoding metadata: Cannot change data-type for object array.

Quick note: I fixed up the second reproducer I had above. I had a copy paste error that I didn’t notice before.