chore: upgrade to zarr v3 sharding default

[ilan-gold]

If this goes in, we will start raising warnings in a "backport" PR for the current default settings

• Closes #
• Tests added

• Release note not necessary because:

[codecov]

❌ 2 Tests Failed:

Tests completed	Failed	Passed	Skipped
8	2	6	1

View the top 2 failed test(s) by shortest run time

tests.test_dask::test_dask_to_disk_view[zarr2-jax_array]

Stack Traces | 0.001s run time

request = <SubRequest 'diskfmt' for <Function test_dask_to_disk_view[zarr2-jax_array]>>

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.fixture(#x1B[90m#x1B[39;49;00m
        params=[(#x1B[33m"#x1B[39;49;00m#x1B[33mh5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94mNone#x1B[39;49;00m), (#x1B[33m"#x1B[39;49;00m#x1B[33mzarr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m2#x1B[39;49;00m), (#x1B[33m"#x1B[39;49;00m#x1B[33mzarr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m3#x1B[39;49;00m)],#x1B[90m#x1B[39;49;00m
        ids=[#x1B[33m"#x1B[39;49;00m#x1B[33mh5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mzarr2#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mzarr3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
    )#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mdiskfmt#x1B[39;49;00m(#x1B[90m#x1B[39;49;00m
        request: pytest.FixtureRequest,#x1B[90m#x1B[39;49;00m
    ) -> Generator[Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mh5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mzarr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m], #x1B[94mNone#x1B[39;49;00m, #x1B[94mNone#x1B[39;49;00m]:#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m (fmt := request.param[#x1B[94m0#x1B[39;49;00m]) == #x1B[33m"#x1B[39;49;00m#x1B[33mh5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94myield#x1B[39;49;00m fmt#x1B[90m#x1B[39;49;00m
        #x1B[94melse#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>           #x1B[94mwith#x1B[39;49;00m ad.settings.override(#x1B[90m#x1B[39;49;00m
                auto_shard_zarr_v3=request.param[#x1B[94m1#x1B[39;49;00m] == #x1B[94m3#x1B[39;49;00m, zarr_write_format=request.param[#x1B[94m1#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
            ):#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/conftest.py#x1B[0m:46: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../...../_temp/uv-python-dir/cpython-3.14.3-linux-x86_64-gnu/lib/python3.14/contextlib.py#x1B[0m:141: in __enter__
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m #x1B[96mnext#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m.gen)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/anndata/_settings.py#x1B[0m:376: in override
    #x1B[0m#x1B[96msetattr#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, k, overrides.get(k))#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/anndata/_settings.py#x1B[0m:315: in __setattr__
    #x1B[0mregistered_option.validate(val, #x1B[96mself#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

format = 2
settings = SettingsManager(
	remove_unused_categories=True,
	check_uniqueness=True,
	allow_write_nullable_strings=None,
	zarr_wri..._h5ad=False,
	write_csr_csc_indices_with_min_possible_dtype=False,
	auto_shard_zarr_v3=True,
	copy_on_write_X=False,

)

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mvalidate_zarr_write_format#x1B[39;49;00m(#x1B[96mformat#x1B[39;49;00m: #x1B[96mint#x1B[39;49;00m, settings: SettingsManager):#x1B[90m#x1B[39;49;00m
        validate_int(#x1B[96mformat#x1B[39;49;00m, settings)#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[96mformat#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m #x1B[95min#x1B[39;49;00m {#x1B[94m2#x1B[39;49;00m, #x1B[94m3#x1B[39;49;00m}:#x1B[90m#x1B[39;49;00m
            msg = #x1B[33m"#x1B[39;49;00m#x1B[33mnon-v2 zarr on-disk format not supported#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mraise#x1B[39;49;00m #x1B[96mValueError#x1B[39;49;00m(msg)#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[96mformat#x1B[39;49;00m == #x1B[94m2#x1B[39;49;00m #x1B[95mand#x1B[39;49;00m #x1B[96mgetattr#x1B[39;49;00m(settings, #x1B[33m"#x1B[39;49;00m#x1B[33mauto_shard_zarr_v3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94mFalse#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
            msg = #x1B[33m"#x1B[39;49;00m#x1B[33mCannot set `zarr_write_format` to 2 with autosharding on.  Please set to `False` `anndata.settings.auto_shard_zarr_v3`#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
>           #x1B[94mraise#x1B[39;49;00m #x1B[96mValueError#x1B[39;49;00m(msg)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE           ValueError: Cannot set `zarr_write_format` to 2 with autosharding on.  Please set to `False` `anndata.settings.auto_shard_zarr_v3`#x1B[0m

#x1B[1m#x1B[31msrc/anndata/_settings.py#x1B[0m:461: ValueError

tests.test_readwrite::test_readwrite_roundtrip[zarr2-jax.array]

Stack Traces | 0.001s run time

request = <SubRequest 'diskfmt' for <Function test_readwrite_roundtrip[zarr2-jax.array]>>

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.fixture(#x1B[90m#x1B[39;49;00m
        params=[(#x1B[33m"#x1B[39;49;00m#x1B[33mh5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94mNone#x1B[39;49;00m), (#x1B[33m"#x1B[39;49;00m#x1B[33mzarr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m2#x1B[39;49;00m), (#x1B[33m"#x1B[39;49;00m#x1B[33mzarr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94m3#x1B[39;49;00m)],#x1B[90m#x1B[39;49;00m
        ids=[#x1B[33m"#x1B[39;49;00m#x1B[33mh5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mzarr2#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mzarr3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
    )#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mdiskfmt#x1B[39;49;00m(#x1B[90m#x1B[39;49;00m
        request: pytest.FixtureRequest,#x1B[90m#x1B[39;49;00m
    ) -> Generator[Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mh5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mzarr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m], #x1B[94mNone#x1B[39;49;00m, #x1B[94mNone#x1B[39;49;00m]:#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m (fmt := request.param[#x1B[94m0#x1B[39;49;00m]) == #x1B[33m"#x1B[39;49;00m#x1B[33mh5ad#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94myield#x1B[39;49;00m fmt#x1B[90m#x1B[39;49;00m
        #x1B[94melse#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>           #x1B[94mwith#x1B[39;49;00m ad.settings.override(#x1B[90m#x1B[39;49;00m
                auto_shard_zarr_v3=request.param[#x1B[94m1#x1B[39;49;00m] == #x1B[94m3#x1B[39;49;00m, zarr_write_format=request.param[#x1B[94m1#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
            ):#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/conftest.py#x1B[0m:46: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../...../_temp/uv-python-dir/cpython-3.14.3-linux-x86_64-gnu/lib/python3.14/contextlib.py#x1B[0m:141: in __enter__
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m #x1B[96mnext#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m.gen)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/anndata/_settings.py#x1B[0m:376: in override
    #x1B[0m#x1B[96msetattr#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, k, overrides.get(k))#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31msrc/anndata/_settings.py#x1B[0m:315: in __setattr__
    #x1B[0mregistered_option.validate(val, #x1B[96mself#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

format = 2
settings = SettingsManager(
	remove_unused_categories=True,
	check_uniqueness=True,
	allow_write_nullable_strings=None,
	zarr_wri..._h5ad=False,
	write_csr_csc_indices_with_min_possible_dtype=False,
	auto_shard_zarr_v3=True,
	copy_on_write_X=False,

)

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mvalidate_zarr_write_format#x1B[39;49;00m(#x1B[96mformat#x1B[39;49;00m: #x1B[96mint#x1B[39;49;00m, settings: SettingsManager):#x1B[90m#x1B[39;49;00m
        validate_int(#x1B[96mformat#x1B[39;49;00m, settings)#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[96mformat#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m #x1B[95min#x1B[39;49;00m {#x1B[94m2#x1B[39;49;00m, #x1B[94m3#x1B[39;49;00m}:#x1B[90m#x1B[39;49;00m
            msg = #x1B[33m"#x1B[39;49;00m#x1B[33mnon-v2 zarr on-disk format not supported#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            #x1B[94mraise#x1B[39;49;00m #x1B[96mValueError#x1B[39;49;00m(msg)#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[96mformat#x1B[39;49;00m == #x1B[94m2#x1B[39;49;00m #x1B[95mand#x1B[39;49;00m #x1B[96mgetattr#x1B[39;49;00m(settings, #x1B[33m"#x1B[39;49;00m#x1B[33mauto_shard_zarr_v3#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[94mFalse#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
            msg = #x1B[33m"#x1B[39;49;00m#x1B[33mCannot set `zarr_write_format` to 2 with autosharding on.  Please set to `False` `anndata.settings.auto_shard_zarr_v3`#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
>           #x1B[94mraise#x1B[39;49;00m #x1B[96mValueError#x1B[39;49;00m(msg)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE           ValueError: Cannot set `zarr_write_format` to 2 with autosharding on.  Please set to `False` `anndata.settings.auto_shard_zarr_v3`#x1B[0m

#x1B[1m#x1B[31msrc/anndata/_settings.py#x1B[0m:461: ValueError

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