Changes to work with Zarr format v3

[tomwhite]

First go at implementing sgkit-dev/vcf-zarr-spec#41 in bio2zarr (do not merge).

[tomwhite]

Running tests locally with zarr-python 3.1.3 I get:

======================================================================= short test summary info =======================================================================
FAILED tests/test_vcf_examples.py::TestSmallExample::test_chunk_size[1-1-y_chunks0-x_chunks0] - assert ((9,),) == ((1, 1, 1, 1, 1, 1, ...),)
FAILED tests/test_vcf_examples.py::TestSmallExample::test_chunk_size[2-2-y_chunks1-x_chunks1] - assert ((9,),) == ((2, 2, 2, 2, 1),)
FAILED tests/test_vcf_examples.py::TestSmallExample::test_chunk_size[3-3-y_chunks2-x_chunks2] - assert ((9,),) == ((3, 3, 3),)
FAILED tests/test_vcf_examples.py::TestSmallExample::test_chunk_size[4-3-y_chunks3-x_chunks3] - assert ((9,),) == ((4, 4, 1),)
FAILED tests/test_vcf_hypothesis.py::test_hypothesis_generated_vcf - KeyError: 'genotypes'
FAILED tests/test_vcz.py::TestEncodeMaxMemory::test_not_enough_memory_for_two[315KiB] - ValueError: Insufficient memory to encode a partition:625 KiB > 315 KiB
FAILED tests/test_vcz.py::TestEncodeMaxMemory::test_not_enough_memory_for_two[500KiB] - ValueError: Insufficient memory to encode a partition:625 KiB > 500 KiB
FAILED tests/test_vcz.py::TestSchemaEncode::test_codec[lz4-1-0] - TypeError: `compressor` is not available for Zarr format 3 arrays.
FAILED tests/test_vcz.py::TestSchemaEncode::test_codec[zlib-7-1] - TypeError: `compressor` is not available for Zarr format 3 arrays.
FAILED tests/test_vcz.py::TestSchemaEncode::test_codec[zstd-4-2] - TypeError: `compressor` is not available for Zarr format 3 arrays.
FAILED tests/test_vcz.py::TestChunkNbytes::test_example_schema[variant_AA-72] - AssertionError: assert 144 == 72
FAILED tests/test_vcz.py::TestChunkNbytes::test_example_schema[variant_allele-288] - AssertionError: assert 576 == 288
FAILED tests/test_vcz.py::TestDefaultSchema::test_variant_contig - AssertionError: assert {'codecs': [{...iants',), ...} == {'compressor'...e': 'i1', ...}
FAILED tests/test_vcz.py::TestDefaultSchema::test_call_genotype - AssertionError: assert {'codecs': [{...ploidy'), ...} == {'compressor'...e': 'i1', ...}
FAILED tests/test_vcz.py::TestDefaultSchema::test_call_genotype_mask - AssertionError: assert {'codecs': [{...ploidy'), ...} == {'compressor'...: 'bool', ...}
FAILED tests/test_vcz.py::TestDefaultSchema::test_call_genotype_phased - AssertionError: assert {'codecs': [{...ploidy'), ...} == {'compressor'...: 'bool', ...}
FAILED tests/test_vcz.py::TestDefaultSchema::test_call_GQ - AssertionError: assert {'codecs': No...amples'), ...} == {'compressor'...e': 'i1', ...}
FAILED tests/test_vcz.py::TestLocalAllelesDefaultSchema::test_call_LA - AssertionError: assert {'codecs': No...lleles'), ...} == {'compressor'...e': 'i1', ...}
FAILED tests/test_vcz.py::TestInspect::test_vcz - AssertionError: assert ['avg_chunk_s...nchunks', ...] == ['avg_chunk_s...filters', ...]
FAILED tests/test_vcz.py::TestSchemaDefaults::test_defaults_with_encode - TypeError: `compressor` is not available for Zarr format 3 arrays.
================================================ 20 failed, 959 passed, 8 skipped, 3346 warnings in 106.72s (0:01:46) =================================================