No ragged sequence for conversion to numpy arrays

[bnavigator]

Numpy 1.24 does not accept ragged sequences anymore.

numpy/numpy#22004

[bnavigator]

Before: #333 (comment)

[   51s] ____________________________ test_non_numpy_inputs _____________________________
[   51s] 
[   51s]     def test_non_numpy_inputs():
[   51s]         # numpy will infer a range of different shapes and dtypes for these inputs.
[   51s]         # Make sure that round-tripping through encode preserves this.
[   51s]         data = [
[   51s]             [0, 1],
[   51s]             [[0, 1], [2, 3]],
[   51s]             [[0], [1], [2, 3]],
[   51s]             [[[0, 0]], [[1, 1]], [[2, 3]]],
[   51s]             ["1"],
[   51s]             ["11", "11"],
[   51s]             ["11", "1", "1"],
[   51s]             [{}],
[   51s]             [{"key": "value"}, ["list", "of", "strings"]],
[   51s]         ]
[   51s]         for input_data in data:
[   51s]             for codec in codecs:
[   51s] >               output_data = codec.decode(codec.encode(input_data))
[   51s] 
[   51s] ../../BUILDROOT/python-numcodecs-0.11.0-0.x86_64/usr/lib64/python3.8/site-packages/numcodecs/tests/test_json.py:72: 
[   51s] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
[   51s] 
[   51s] self = JSON(encoding='utf-8', allow_nan=True, check_circular=True, ensure_ascii=True,
[   51s]      indent=None, separators=(',', ':'), skipkeys=False, sort_keys=True,
[   51s]      strict=True)
[   51s] buf = [[0], [1], [2, 3]]
[   51s] 
[   51s]     def encode(self, buf):
[   51s] >       buf = np.asarray(buf)
[   51s] E       ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (3,) + inhomogeneous part.
[   51s] 
[   51s] ../../BUILDROOT/python-numcodecs-0.11.0-0.x86_64/usr/lib64/python3.8/site-packages/numcodecs/json.py:57: ValueError
[   51s] ____________________________ test_non_numpy_inputs _____________________________
[   51s] 
[   51s]     def test_non_numpy_inputs():
[   51s]         codec = MsgPack()
[   51s]         # numpy will infer a range of different shapes and dtypes for these inputs.
[   51s]         # Make sure that round-tripping through encode preserves this.
[   51s]         data = [
[   51s]             [0, 1],
[   51s]             [[0, 1], [2, 3]],
[   51s]             [[0], [1], [2, 3]],
[   51s]             [[[0, 0]], [[1, 1]], [[2, 3]]],
[   51s]             ["1"],
[   51s]             ["11", "11"],
[   51s]             ["11", "1", "1"],
[   51s]             [{}],
[   51s]             [{"key": "value"}, ["list", "of", "strings"]],
[   51s]             [b"1"],
[   51s]             [b"11", b"11"],
[   51s]             [b"11", b"1", b"1"],
[   51s]             [{b"key": b"value"}, [b"list", b"of", b"strings"]],
[   51s]         ]
[   51s]         for input_data in data:
[   51s] >           actual = codec.decode(codec.encode(input_data))
[   51s] 
[   51s] ../../BUILDROOT/python-numcodecs-0.11.0-0.x86_64/usr/lib64/python3.8/site-packages/numcodecs/tests/test_msgpacks.py:75: 
[   51s] _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
[   51s] 
[   51s] self = MsgPack(raw=False, use_bin_type=True, use_single_float=False)
[   51s] buf = [[0], [1], [2, 3]]
[   51s] 
[   51s]     def encode(self, buf):
[   51s] >       buf = np.asarray(buf)
[   51s] E       ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (3,) + inhomogeneous part.
[   51s] 
[   51s] ../../BUILDROOT/python-numcodecs-0.11.0-0.x86_64/usr/lib64/python3.8/site-packages/numcodecs/msgpacks.py:55: ValueError

[martindurant]

numpy should be able to support these as lists within an object array, no?

x = np.array([[1], [1, 2]], dtype="object")  # ok

[bnavigator]

numpy should be able to support these as lists within an object array, no?

That is correct, but the whole point of this roundtrip test ist that an inferred dtype which is not object is preserved.