Distributed writing for H5ad format due to h5py objects being unserializable

[selmanozleyen]

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• I have checked that this issue has not already been reported.
• I have confirmed this bug exists on the latest version of anndata.
• (optional) I have confirmed this bug exists on the master branch of anndata.

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This is the code that will fail.

import anndata as ad
import dask.array as da
import dask.distributed as dd

with dd.LocalCluster(n_workers=1,threads_per_worker=1) as cluster:
    with dd.Client(cluster) as client:
        adata = ad.AnnData(da.random.random((100, 100), chunks=(10, 10)))
        adata.write_h5ad("test.h5ad")

Usually the same code used to fail for both zarr and h5ad, but this PR will fix the issue with zarr #1079. For h5ad serialization of h5py might be overcome by whatever Xarray does as mentioned in this issue pydata/xarray#4242

Traceback:

023-08-25 11:17:10,491 - distributed.protocol.pickle - ERROR - Failed to serialize <ToPickle: HighLevelGraph with 1 layers.
<dask.highlevelgraph.HighLevelGraph object at 0x7f6ae131c700>
 0. 140097021523072
>.
Traceback (most recent call last):
  File "/home/sel/mambaforge/envs/dask/lib/python3.9/site-packages/distributed/protocol/pickle.py", line 63, in dumps
    result = pickle.dumps(x, **dump_kwargs)
  File "/home/sel/mambaforge/envs/dask/lib/python3.9/site-packages/h5py/_hl/base.py", line 368, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/sel/mambaforge/envs/dask/lib/python3.9/site-packages/distributed/protocol/pickle.py", line 68, in dumps
    pickler.dump(x)
  File "/home/sel/mambaforge/envs/dask/lib/python3.9/site-packages/distributed/protocol/pickle.py", line 29, in reducer_override
    return deserialize, serialize(obj)
  File "/home/sel/mambaforge/envs/dask/lib/python3.9/site-packages/distributed/protocol/h5py.py", line 24, in serialize_h5py_dataset
    header, _ = serialize_h5py_file(x.file)
  File "/home/sel/mambaforge/envs/dask/lib/python3.9/site-packages/distributed/protocol/h5py.py", line 11, in serialize_h5py_file
    raise ValueError("Can only serialize read-only h5py files")
ValueError: Can only serialize read-only h5py files

During handling of the above exception, another exception occurred:
...
    return Pickler.dump(self, obj)
  File "/home/sel/mambaforge/envs/dask/lib/python3.9/site-packages/h5py/_hl/base.py", line 368, in __getnewargs__
    raise TypeError("h5py objects cannot be pickled")
TypeError: h5py objects cannot be pickled

Versions

-----
anndata             0.10.0.dev198+ga61d5d4
dask                2023.7.1
distributed         2023.7.1
numpy               1.22.4
pandas              2.0.0
scipy               1.9.3
session_info        1.0.0
zarr                2.13.3
-----
PIL                 9.2.0
asciitree           NA
asttokens           NA
attr                23.1.0
awkward             2.1.0
awkward_cpp         NA
backcall            0.2.0
bokeh               2.4.3
cffi                1.15.1
click               8.1.3
cloudpickle         2.2.0
colorama            0.4.6
comm                0.1.1
cython_runtime      NA
cytoolz             0.12.0
...
Python 3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 15:55:03) [GCC 10.4.0]
Linux-6.1.44-1-MANJARO-x86_64-with-glibc2.38
-----

Session information updated at 2023-08-25 11:18

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