607     Example
608     -------
609 
610     First we'll need a stored dataset:
611 
612     >>> import scanpy as sc
613     >>> import h5py
614     >>> from anndata.io import sparse_dataset
615     >>> from anndata.io import read_elem
616     >>> sc.datasets.pbmc68k_reduced().raw.to_adata().write_h5ad("pbmc.h5ad")
UNEXPECTED EXCEPTION: TypeError("h5py._hl.group.Group.create_dataset() got multiple values for keyword argument 'dtype'")
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/doctest.py", line 1368, in __run
    exec(compile(example.source, filename, "single",
  File "<doctest anndata._core.sparse_dataset.sparse_dataset[4]>", line 1, in <module>
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_core/anndata.py", line 1865, in write_h5ad
    write_h5ad(
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/h5ad.py", line 90, in write_h5ad
    write_elem(f, "X", adata.X, dataset_kwargs=dataset_kwargs)
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 488, in write_elem
    Writer(_REGISTRY).write_elem(store, k, elem, dataset_kwargs=dataset_kwargs)
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/utils.py", line 248, in func_wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 355, in write_elem
    return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 71, in wrapper
    result = func(g, k, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/methods.py", line 649, in write_sparse_compressed
    _writer.write_elem(
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/utils.py", line 248, in func_wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 355, in write_elem
    return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 71, in wrapper
    result = func(g, k, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/methods.py", line 394, in write_basic
    f.create_dataset(k, data=elem, **dataset_kwargs, dtype=dtype)
TypeError: h5py._hl.group.Group.create_dataset() got multiple values for keyword argument 'dtype'
Error raised while writing key 'indptr' of <class 'h5py._hl.group.Group'> to /X
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_core/sparse_dataset.py:616: UnexpectedException

413     >>> import tempfile
414     >>> import anndata as ad
415     >>> import zarr
416 
417     >>> tmp_path = tempfile.gettempdir()
418     >>> zarr_path = tmp_path + "/adata.zarr"
419 
420     >>> adata = pbmc3k()
421     >>> adata.layers["dense"] = adata.X.toarray()
422     >>> adata.write_zarr(zarr_path)
UNEXPECTED EXCEPTION: TypeError("zarr.hierarchy.Group.create_dataset() got multiple values for keyword argument 'dtype'")
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/doctest.py", line 1368, in __run
    exec(compile(example.source, filename, "single",
  File "<doctest anndata._io.specs.registry.read_elem_as_dask[8]>", line 1, in <module>
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_core/anndata.py", line 1928, in write_zarr
    write_zarr(store, self, chunks=chunks)
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/zarr.py", line 50, in write_zarr
    write_dispatched(f, "/", adata, callback=callback, dataset_kwargs=ds_kwargs)
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/experimental/_dispatch_io.py", line 77, in write_dispatched
    writer.write_elem(store, key, elem, dataset_kwargs=dataset_kwargs)
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/utils.py", line 248, in func_wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 356, in write_elem
    return self.callback(
           ^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/zarr.py", line 48, in callback
    func(s, k, elem, dataset_kwargs=dataset_kwargs)
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 71, in wrapper
    result = func(g, k, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/methods.py", line 277, in write_anndata
    _writer.write_elem(g, "X", adata.X, dataset_kwargs=dataset_kwargs)
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/utils.py", line 248, in func_wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 356, in write_elem
    return self.callback(
           ^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/zarr.py", line 48, in callback
    func(s, k, elem, dataset_kwargs=dataset_kwargs)
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 71, in wrapper
    result = func(g, k, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/methods.py", line 649, in write_sparse_compressed
    _writer.write_elem(
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/utils.py", line 248, in func_wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 356, in write_elem
    return self.callback(
           ^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/zarr.py", line 48, in callback
    func(s, k, elem, dataset_kwargs=dataset_kwargs)
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 71, in wrapper
    result = func(g, k, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site

515     ...         for data in r.iter_bytes():
516     ...             f.write(data)
517     ...     return out_path
518     >>> path_b_cells = get_cellxgene_data('a93eab58-3d82-4b61-8a2f-d7666dcdb7c4')
519     >>> path_fetal = get_cellxgene_data('d170ff04-6da0-4156-a719-f8e1bbefbf53')
520 
521     Now we can concatenate them on-disk:
522 
523     >>> import anndata as ad
524     >>> ad.experimental.concat_on_disk(
UNEXPECTED EXCEPTION: TypeError("h5py._hl.group.Group.create_dataset() got multiple values for keyword argument 'dtype'")
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/doctest.py", line 1368, in __run
    exec(compile(example.source, filename, "single",
  File "<doctest anndata.experimental.merge.concat_on_disk[7]>", line 1, in <module>
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/experimental/merge.py", line 634, in concat_on_disk
    _write_concat_arrays(
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/experimental/merge.py", line 300, in _write_concat_arrays
    write_concat_sparse(
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/experimental/merge.py", line 226, in write_concat_sparse
    write_elem(
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 488, in write_elem
    Writer(_REGISTRY).write_elem(store, k, elem, dataset_kwargs=dataset_kwargs)
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/utils.py", line 248, in func_wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 355, in write_elem
    return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 71, in wrapper
    result = func(g, k, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/methods.py", line 649, in write_sparse_compressed
    _writer.write_elem(
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/utils.py", line 248, in func_wrapper
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 355, in write_elem
    return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py", line 71, in wrapper
    result = func(g, k, *args, **kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/methods.py", line 394, in write_basic
    f.create_dataset(k, data=elem, **dataset_kwargs, dtype=dtype)
TypeError: h5py._hl.group.Group.create_dataset() got multiple values for keyword argument 'dtype'
Error raised while writing key 'indptr' of <class 'h5py._hl.group.Group'> to /X
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/experimental/merge.py:524: UnexpectedException

tmp_path = PosixPath('/tmp/pytest-of-vsts/pytest-0/test_awkward_io_view0')

    def test_awkward_io_view(tmp_path):
        """Check that views are converted to actual arrays on save, i.e. the _view_args and __list__ parameters are removed"""
        adata = gen_adata((3, 3), varm_types=(), obsm_types=(AwkArray,), layers_types=())
    
        v = adata[1:]
        adata_path = tmp_path / "adata.h5ad"
>       v.write_h5ad(adata_path)

tests/test_awkward.py:259: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_core/anndata.py:1865: in write_h5ad
    write_h5ad(
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/h5ad.py:90: in write_h5ad
    write_elem(f, "X", adata.X, dataset_kwargs=dataset_kwargs)
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py:488: in write_elem
    Writer(_REGISTRY).write_elem(store, k, elem, dataset_kwargs=dataset_kwargs)
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/utils.py:248: in func_wrapper
    return func(*args, **kwargs)
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py:355: in write_elem
    return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py:71: in wrapper
    result = func(g, k, *args, **kwargs)
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/methods.py:649: in write_sparse_compressed
    _writer.write_elem(
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/utils.py:248: in func_wrapper
    return func(*args, **kwargs)
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py:355: in write_elem
    return write_func(store, k, elem, dataset_kwargs=dataset_kwargs)
/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/registry.py:71: in wrapper
    result = func(g, k, *args, **kwargs)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

f = <Closed HDF5 group>, k = '/X/indptr', elem = array([0, 3, 4], dtype=int32)

    @_REGISTRY.register_write(H5Group, views.ArrayView, IOSpec("array", "0.2.0"))
    @_REGISTRY.register_write(H5Group, np.ndarray, IOSpec("array", "0.2.0"))
    @_REGISTRY.register_write(H5Group, np.ma.MaskedArray, IOSpec("array", "0.2.0"))
    @_REGISTRY.register_write(ZarrGroup, views.ArrayView, IOSpec("array", "0.2.0"))
    @_REGISTRY.register_write(ZarrGroup, np.ndarray, IOSpec("array", "0.2.0"))
    @_REGISTRY.register_write(ZarrGroup, np.ma.MaskedArray, IOSpec("array", "0.2.0"))
    @_REGISTRY.register_write(ZarrGroup, ZarrArray, IOSpec("array", "0.2.0"))
    @_REGISTRY.register_write(ZarrGroup, H5Array, IOSpec("array", "0.2.0"))
    def write_basic(
        f: GroupStorageType,
        k: str,
        elem: views.ArrayView | np.ndarray | h5py.Dataset | np.ma.MaskedArray | ZarrArray,
        *,
        _writer: Writer,
        dataset_kwargs: Mapping[str, Any] = MappingProxyType({}),
    ):
        """Write methods which underlying library handles natively."""
        dtype = dataset_kwargs.get("dtype", elem.dtype)
>       f.create_dataset(k, data=elem, **dataset_kwargs, dtype=dtype)
E       TypeError: h5py._hl.group.Group.create_dataset() got multiple values for keyword argument 'dtype'
E       Error raised while writing key 'indptr' of <class 'h5py._hl.group.Group'> to /X

/opt/hostedtoolcache/Python/3.12.7/x64/lib/python3.12/site-packages/anndata/_io/specs/methods.py:394: TypeError