NumPy integers not accepted in `chunks` argument to `zarr.zeros`

[mdickinson]

The following code works with zarr 2.3.2, but not with more-recently-released versions of zarr (tested on zarr 2.4.0 and zarr 2.6.1). It now gives a TypeError as a result of attempting to JSON serialize a NumPy integer.

import numpy as np
import zarr

zarr.zeros((10,), chunks=(np.int64(2),))

With zarr 2.3.2, this creates a new array, as expected. With later versions of zarr, I get the following traceback (here with zarr 2.6.1):

(seismic-zarr) mdickinson@mirzakhani temp % python bug.py             
Traceback (most recent call last):
  File "bug.py", line 4, in <module>
    zarr.zeros((10,), chunks=(np.int64(2),))
  File "/Users/mdickinson/.venvs/seismic-zarr/lib/python3.8/site-packages/zarr/creation.py", line 248, in zeros
    return create(shape=shape, fill_value=0, **kwargs)
  File "/Users/mdickinson/.venvs/seismic-zarr/lib/python3.8/site-packages/zarr/creation.py", line 121, in create
    init_array(store, shape=shape, chunks=chunks, dtype=dtype, compressor=compressor,
  File "/Users/mdickinson/.venvs/seismic-zarr/lib/python3.8/site-packages/zarr/storage.py", line 344, in init_array
    _init_array_metadata(store, shape=shape, chunks=chunks, dtype=dtype,
  File "/Users/mdickinson/.venvs/seismic-zarr/lib/python3.8/site-packages/zarr/storage.py", line 434, in _init_array_metadata
    store[key] = encode_array_metadata(meta)
  File "/Users/mdickinson/.venvs/seismic-zarr/lib/python3.8/site-packages/zarr/meta.py", line 75, in encode_array_metadata
    return json_dumps(meta)
  File "/Users/mdickinson/.venvs/seismic-zarr/lib/python3.8/site-packages/zarr/util.py", line 25, in json_dumps
    return json.dumps(o, indent=4, sort_keys=True, ensure_ascii=True,
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/__init__.py", line 234, in dumps
    return cls(
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/encoder.py", line 201, in encode
    chunks = list(chunks)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/encoder.py", line 431, in _iterencode
    yield from _iterencode_dict(o, _current_indent_level)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/encoder.py", line 325, in _iterencode_list
    yield from chunks
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/encoder.py", line 438, in _iterencode
    o = _default(o)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.8/lib/python3.8/json/encoder.py", line 179, in default
    raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type int64 is not JSON serializable

This caused a regression in some other code using zarr: tests started failing after updating zarr.

Please provide the following:

• Value of zarr.__version__: 2.6.1
• Value of numcodecs.__version__: 0.7.3
• Version of Python interpreter: 3.8.7 (from MacPorts)
• Operating system (Linux/Windows/Mac): macOS 10.15.7 (Catalina)
• How Zarr was installed (e.g., "using pip into virtual environment", or "using conda"): using pip into a venv.

NumPy version: 1.20.0 (but I was also able to reproduce with NumPy 1.16.5).

[mdickinson]

Related: https://bugs.python.org/issue24313

[mdickinson]

Still an issue with zarr 2.10.2:

(zarr) mdickinson@mirzakhani edge % python -VV 
Python 3.9.7 (default, Oct  9 2021, 07:22:04) 
[Clang 12.0.5 (clang-1205.0.22.9)]
(zarr) mdickinson@mirzakhani edge % pip list
Package    Version
---------- -------
asciitree  0.3.3
fasteners  0.16.3
numcodecs  0.9.1
numpy      1.21.3
pip        21.3.1
setuptools 57.4.0
six        1.16.0
zarr       2.10.2
(zarr) mdickinson@mirzakhani edge % python
Python 3.9.7 (default, Oct  9 2021, 07:22:04) 
[Clang 12.0.5 (clang-1205.0.22.9)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> import zarr
>>> zarr.zeros((10,), chunks=(np.int64(2),))
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/Users/mdickinson/.venvs/zarr/lib/python3.9/site-packages/zarr/creation.py", line 268, in zeros
    return create(shape=shape, fill_value=0, **kwargs)
  File "/Users/mdickinson/.venvs/zarr/lib/python3.9/site-packages/zarr/creation.py", line 138, in create
    init_array(store, shape=shape, chunks=chunks, dtype=dtype, compressor=compressor,
  File "/Users/mdickinson/.venvs/zarr/lib/python3.9/site-packages/zarr/storage.py", line 353, in init_array
    _init_array_metadata(store, shape=shape, chunks=chunks, dtype=dtype,
  File "/Users/mdickinson/.venvs/zarr/lib/python3.9/site-packages/zarr/storage.py", line 451, in _init_array_metadata
    store[key] = encode_array_metadata(meta)
  File "/Users/mdickinson/.venvs/zarr/lib/python3.9/site-packages/zarr/meta.py", line 97, in encode_array_metadata
    return json_dumps(meta)
  File "/Users/mdickinson/.venvs/zarr/lib/python3.9/site-packages/zarr/util.py", line 29, in json_dumps
    return json.dumps(o, indent=4, sort_keys=True, ensure_ascii=True,
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/__init__.py", line 234, in dumps
    return cls(
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/encoder.py", line 201, in encode
    chunks = list(chunks)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/encoder.py", line 431, in _iterencode
    yield from _iterencode_dict(o, _current_indent_level)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/encoder.py", line 325, in _iterencode_list
    yield from chunks
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/encoder.py", line 438, in _iterencode
    o = _default(o)
  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/json/encoder.py", line 179, in default
    raise TypeError(f'Object of type {o.__class__.__name__} '
TypeError: Object of type int64 is not JSON serializable

[jakirkham]

If you would like to work on a PR, that would be welcome 🙂

My guess is we can just add some logic to coerce NumPy integers to Python integers when receiving chunks (say through a utility function)