Fill value fixes for V3

[rabernat]

This gets many of the backend tests passing against V3. Still some work to go.

Main issues addressed:

• only use fill_value for signaling missing data in V2 data via use_zarr_fill_value_as_mask parameter
• add new Numpy2StringDTypeCoder to deal with StringDType data coming out of Zarr

Summary of failures (many V2 due to zarr-developers/zarr-python#2315)

$ pytest -v xarray/tests/test_backends.py::TestZarrDictStore
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_roundtrip_object_dtype[2] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_roundtrip_empty_vlen_string_array[2] - AssertionError: assert dtype('<U') == dtype('<U1')
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_write_persistence_modes[2-None] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_write_persistence_modes[2-group1] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_check_encoding_is_consistent_after_append[2] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_append_with_new_variable[2] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_append_with_append_dim_no_overwrite[2] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_to_zarr_append_compute_false_roundtrip[2] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_roundtrip_bytes_with_fill_value[3] - TypeError: Invalid attribute in Dataset.attrs.
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_roundtrip_endian[3] - KeyError: '>i2'
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_default_fill_value[3] - TypeError: must be real number, not str
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_explicitly_omit_fill_value_via_encoding_kwarg[3] - ValueError: unexpected encoding parameters for zarr backend:  ['_FillValue']
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_explicitly_omit_fill_value_in_coord_via_encoding_kwarg[3] - ValueError: unexpected encoding parameters for zarr backend:  ['_FillValue']
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_append_string_length_mismatch_raises[3-U] - Failed: DID NOT RAISE <class 'ValueError'>
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_append_string_length_mismatch_raises[3-S] - Failed: DID NOT RAISE <class 'ValueError'>
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_check_encoding_is_consistent_after_append[3] - AttributeError: 'list' object has no attribute 'get_config'

[rabernat]

In 34c4c24 I added some custom encoding / decoding for _FillValue which mostly makes things work in V3.

Latest list of failing tests

FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_roundtrip_object_dtype[2] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_roundtrip_empty_vlen_string_array[2] - AssertionError: assert dtype('<U') == dtype('<U1')
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_write_persistence_modes[2-None] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_write_persistence_modes[2-group1] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_check_encoding_is_consistent_after_append[2] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_append_with_new_variable[2] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_append_with_append_dim_no_overwrite[2] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_to_zarr_append_compute_false_roundtrip[2] - ValueError: When changing to a smaller dtype, its size must be a divisor of the size of original dtype
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_roundtrip_endian[3] - KeyError: '>i2'
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_explicitly_omit_fill_value_via_encoding_kwarg[3] - ValueError: unexpected encoding parameters for zarr backend:  ['_FillValue']
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_explicitly_omit_fill_value_in_coord_via_encoding_kwarg[3] - ValueError: unexpected encoding parameters for zarr backend:  ['_FillValue']
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_append_string_length_mismatch_raises[3-U] - Failed: DID NOT RAISE <class 'ValueError'>
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_append_string_length_mismatch_raises[3-S] - Failed: DID NOT RAISE <class 'ValueError'>
FAILED xarray/tests/test_backends.py::TestZarrDictStore::test_check_encoding_is_consistent_after_append[3] - AttributeError: 'list' object has no attribute 'get_config'

The roundtrip_endian is related to zarr-developers/zarr-python#2324

[TomAugspurger]

Looks good, thanks. There's a merge conflict now that I added the zarr_format / zarr_version deprecation to this branch. LMK if you want me to resolve the conflicts.

[TomAugspurger]

Actually I'm fixing some merge conflicts in other spots right now and will handle this quick.