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20 hours ago •
pydata
pydata
🐛 compatibility issues with ArrayAPI and SparseAPI Protocols in `namedarray`
What happened?
i'm experiencing compatibility issues when using _arrayfunction_or_api and _sparsearrayfunction_or_api with the sparse arrays with dtype=object. specifically, runtime checks using isinstance with these protocols are failing, despite the sparse array object appearing to meet the necessary criteria (attributes and methods).
What did you expect to happen?
i expected that since COO arrays from the sparse library provide the necessary attributes and methods, they would pass the isinstance checks with the defined protocols.
In [56]: from xarray.namedarray._typing import _arrayfunction_or_api, _sparsearrayfunc
...: tion_or_api
In [57]: import xarray as xr, sparse, numpy as np, sparse, pandas as pd
- numeric dtypes work
In [58]: x = np.random.random((10))
In [59]: x[x < 0.9] = 0
In [60]: s = sparse.COO(x)
In [61]: isinstance(s, _arrayfunction_or_api)
Out[61]: True
In [62]: s
Out[62]: <COO: shape=(10,), dtype=float64, nnz=0, fill_value=0.0>
- string dtypes work
In [63]: p = sparse.COO(np.array(['a', 'b']))
In [64]: p
Out[64]: <COO: shape=(2,), dtype=<U1, nnz=2, fill_value=>
In [65]: isinstance(s, _arrayfunction_or_api)
Out[65]: True
- object dtype doesn't work
In [66]: q = sparse.COO(np.array(['a', 'b']).astype(object))
In [67]: isinstance(s, _arrayfunction_or_api)
Out[67]: True
In [68]: isinstance(q, _arrayfunction_or_api)
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_umath.py:606, in _Elemwise._get_func_coords_data(self, mask)
605 try:
--> 606 func_data = self.func(*func_args, dtype=self.dtype, **self.kwargs)
607 except TypeError:
TypeError: real() got an unexpected keyword argument 'dtype'
During handling of the above exception, another exception occurred:
TypeError Traceback (most recent call last)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_umath.py:611, in _Elemwise._get_func_coords_data(self, mask)
610 out = np.empty(func_args[0].shape, dtype=self.dtype)
--> 611 func_data = self.func(*func_args, out=out, **self.kwargs)
612 except TypeError:
TypeError: real() got an unexpected keyword argument 'out'
During handling of the above exception, another exception occurred:
ValueError Traceback (most recent call last)
Cell In[68], line 1
----> 1 isinstance(q, _arrayfunction_or_api)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/typing.py:1149, in _ProtocolMeta.__instancecheck__(cls, instance)
1147 return True
1148 if cls._is_protocol:
-> 1149 if all(hasattr(instance, attr) and
1150 # All *methods* can be blocked by setting them to None.
1151 (not callable(getattr(cls, attr, None)) or
1152 getattr(instance, attr) is not None)
1153 for attr in _get_protocol_attrs(cls)):
1154 return True
1155 return super().__instancecheck__(instance)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/typing.py:1149, in <genexpr>(.0)
1147 return True
1148 if cls._is_protocol:
-> 1149 if all(hasattr(instance, attr) and
1150 # All *methods* can be blocked by setting them to None.
1151 (not callable(getattr(cls, attr, None)) or
1152 getattr(instance, attr) is not None)
1153 for attr in _get_protocol_attrs(cls)):
1154 return True
1155 return super().__instancecheck__(instance)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_sparse_array.py:900, in SparseArray.real(self)
875 @property
876 def real(self):
877 """The real part of the array.
878
879 Examples
(...)
898 numpy.real : NumPy equivalent function.
899 """
--> 900 return self.__array_ufunc__(np.real, "__call__", self)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_sparse_array.py:340, in SparseArray.__array_ufunc__(self, ufunc, method, *inputs, **kwargs)
337 inputs = tuple(reversed(inputs_transformed))
339 if method == "__call__":
--> 340 result = elemwise(ufunc, *inputs, **kwargs)
341 elif method == "reduce":
342 result = SparseArray._reduce(ufunc, *inputs, **kwargs)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_umath.py:49, in elemwise(func, *args, **kwargs)
12 def elemwise(func, *args, **kwargs):
13 """
14 Apply a function to any number of arguments.
15
(...)
46 it is necessary to convert Numpy arrays to :obj:`COO` objects.
47 """
---> 49 return _Elemwise(func, *args, **kwargs).get_result()
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_umath.py:480, in _Elemwise.get_result(self)
477 if not any(mask):
478 continue
--> 480 r = self._get_func_coords_data(mask)
482 if r is not None:
483 coords_list.append(r[0])
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_umath.py:613, in _Elemwise._get_func_coords_data(self, mask)
611 func_data = self.func(*func_args, out=out, **self.kwargs)
612 except TypeError:
--> 613 func_data = self.func(*func_args, **self.kwargs).astype(self.dtype)
615 unmatched_mask = ~equivalent(func_data, self.fill_value)
617 if not unmatched_mask.any():
ValueError: invalid literal for int() with base 10: 'a'
In [69]: q
Out[69]: <COO: shape=(2,), dtype=object, nnz=2, fill_value=0>
the failing case appears to be a well know issue
- https://github.com/pydata/sparse/issues/104
Minimal Complete Verifiable Example
In [69]: q
Out[69]: <COO: shape=(2,), dtype=object, nnz=2, fill_value=0>
In [70]: n = xr.NamedArray(data=q, dims=['x'])
MVCE confirmation
- [ ] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
- [ ] Complete example — the example is self-contained, including all data and the text of any traceback.
- [ ] Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
- [ ] New issue — a search of GitHub Issues suggests this is not a duplicate.
- [ ] Recent environment — the issue occurs with the latest version of xarray and its dependencies.
Relevant log output
In [71]: n.data
Out[71]: <COO: shape=(2,), dtype=object, nnz=2, fill_value=0>
In [72]: n
Out[72]: ---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_umath.py:606, in _Elemwise._get_func_coords_data(self, mask)
605 try:
--> 606 func_data = self.func(*func_args, dtype=self.dtype, **self.kwargs)
607 except TypeError:
TypeError: real() got an unexpected keyword argument 'dtype'
During handling of the above exception, another exception occurred:
TypeError Traceback (most recent call last)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_umath.py:611, in _Elemwise._get_func_coords_data(self, mask)
610 out = np.empty(func_args[0].shape, dtype=self.dtype)
--> 611 func_data = self.func(*func_args, out=out, **self.kwargs)
612 except TypeError:
TypeError: real() got an unexpected keyword argument 'out'
During handling of the above exception, another exception occurred:
ValueError Traceback (most recent call last)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/IPython/core/formatters.py:708, in PlainTextFormatter.__call__(self, obj)
701 stream = StringIO()
702 printer = pretty.RepresentationPrinter(stream, self.verbose,
703 self.max_width, self.newline,
704 max_seq_length=self.max_seq_length,
705 singleton_pprinters=self.singleton_printers,
706 type_pprinters=self.type_printers,
707 deferred_pprinters=self.deferred_printers)
--> 708 printer.pretty(obj)
709 printer.flush()
710 return stream.getvalue()
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/IPython/lib/pretty.py:410, in RepresentationPrinter.pretty(self, obj)
407 return meth(obj, self, cycle)
408 if cls is not object \
409 and callable(cls.__dict__.get('__repr__')):
--> 410 return _repr_pprint(obj, self, cycle)
412 return _default_pprint(obj, self, cycle)
413 finally:
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/IPython/lib/pretty.py:778, in _repr_pprint(obj, p, cycle)
776 """A pprint that just redirects to the normal repr function."""
777 # Find newlines and replace them with p.break_()
--> 778 output = repr(obj)
779 lines = output.splitlines()
780 with p.group():
File ~/devel/pydata/xarray/xarray/namedarray/core.py:987, in NamedArray.__repr__(self)
986 def __repr__(self) -> str:
--> 987 return formatting.array_repr(self)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/reprlib.py:21, in recursive_repr.<locals>.decorating_function.<locals>.wrapper(self)
19 repr_running.add(key)
20 try:
---> 21 result = user_function(self)
22 finally:
23 repr_running.discard(key)
File ~/devel/pydata/xarray/xarray/core/formatting.py:665, in array_repr(arr)
658 name_str = ""
660 if (
661 isinstance(arr, Variable)
662 or _get_boolean_with_default("display_expand_data", default=True)
663 or isinstance(arr.variable._data, MemoryCachedArray)
664 ):
--> 665 data_repr = short_data_repr(arr)
666 else:
667 data_repr = inline_variable_array_repr(arr.variable, OPTIONS["display_width"])
File ~/devel/pydata/xarray/xarray/core/formatting.py:633, in short_data_repr(array)
631 if isinstance(array, np.ndarray):
632 return short_array_repr(array)
--> 633 elif isinstance(internal_data, _arrayfunction_or_api):
634 return limit_lines(repr(array.data), limit=40)
635 elif getattr(array, "_in_memory", None):
File ~/mambaforge/envs/xarray-tests/lib/python3.9/typing.py:1149, in _ProtocolMeta.__instancecheck__(cls, instance)
1147 return True
1148 if cls._is_protocol:
-> 1149 if all(hasattr(instance, attr) and
1150 # All *methods* can be blocked by setting them to None.
1151 (not callable(getattr(cls, attr, None)) or
1152 getattr(instance, attr) is not None)
1153 for attr in _get_protocol_attrs(cls)):
1154 return True
1155 return super().__instancecheck__(instance)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/typing.py:1149, in <genexpr>(.0)
1147 return True
1148 if cls._is_protocol:
-> 1149 if all(hasattr(instance, attr) and
1150 # All *methods* can be blocked by setting them to None.
1151 (not callable(getattr(cls, attr, None)) or
1152 getattr(instance, attr) is not None)
1153 for attr in _get_protocol_attrs(cls)):
1154 return True
1155 return super().__instancecheck__(instance)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_sparse_array.py:900, in SparseArray.real(self)
875 @property
876 def real(self):
877 """The real part of the array.
878
879 Examples
(...)
898 numpy.real : NumPy equivalent function.
899 """
--> 900 return self.__array_ufunc__(np.real, "__call__", self)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_sparse_array.py:340, in SparseArray.__array_ufunc__(self, ufunc, method, *inputs, **kwargs)
337 inputs = tuple(reversed(inputs_transformed))
339 if method == "__call__":
--> 340 result = elemwise(ufunc, *inputs, **kwargs)
341 elif method == "reduce":
342 result = SparseArray._reduce(ufunc, *inputs, **kwargs)
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_umath.py:49, in elemwise(func, *args, **kwargs)
12 def elemwise(func, *args, **kwargs):
13 """
14 Apply a function to any number of arguments.
15
(...)
46 it is necessary to convert Numpy arrays to :obj:`COO` objects.
47 """
---> 49 return _Elemwise(func, *args, **kwargs).get_result()
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_umath.py:480, in _Elemwise.get_result(self)
477 if not any(mask):
478 continue
--> 480 r = self._get_func_coords_data(mask)
482 if r is not None:
483 coords_list.append(r[0])
File ~/mambaforge/envs/xarray-tests/lib/python3.9/site-packages/sparse/_umath.py:613, in _Elemwise._get_func_coords_data(self, mask)
611 func_data = self.func(*func_args, out=out, **self.kwargs)
612 except TypeError:
--> 613 func_data = self.func(*func_args, **self.kwargs).astype(self.dtype)
615 unmatched_mask = ~equivalent(func_data, self.fill_value)
617 if not unmatched_mask.any():
ValueError: invalid literal for int() with base 10: 'a'
Anything else we need to know?
i was trying to replace instances of is_duck_array with the protocol runtime checks (as part of https://github.com/pydata/xarray/pull/8319), and i've come to a realization that these runtime checks are rigid to accommodate the diverse behaviors of different array types, and is_duck_array() the function-based approach might be more manageable.
@Illviljan, are there any changes that could be made to both protocols without making them too complex?
Environment
INSTALLED VERSIONS
------------------
commit: 541049f45edeb518a767cb3b23fa53f6045aa508
python: 3.9.18 | packaged by conda-forge | (main, Dec 23 2023, 16:35:41)
[Clang 16.0.6 ]
python-bits: 64
OS: Darwin
OS-release: 23.2.0
machine: arm64
processor: arm
byteorder: little
LC_ALL: None
LANG: en_US.UTF-8
LOCALE: ('en_US', 'UTF-8')
libhdf5: 1.14.3
libnetcdf: 4.9.2
xarray: 2024.1.2.dev50+g78dec61f
pandas: 2.2.0
numpy: 1.26.3
scipy: 1.12.0
netCDF4: 1.6.5
pydap: installed
h5netcdf: 1.3.0
h5py: 3.10.0
Nio: None
zarr: 2.16.1
cftime: 1.6.3
nc_time_axis: 1.4.1
iris: 3.7.0
bottleneck: 1.3.7
dask: 2024.1.1
distributed: 2024.1.1
matplotlib: 3.8.2
cartopy: 0.22.0
seaborn: 0.13.2
numbagg: 0.7.1
fsspec: 2023.12.2
cupy: None
pint: 0.23
sparse: 0.15.1
flox: 0.9.0
numpy_groupies: 0.9.22
setuptools: 67.7.2
pip: 23.3.2
conda: None
pytest: 8.0.0
mypy: 1.8.0
IPython: 8.14.0
sphinx: None
Note that on python 3.12 and higher this will actually start to work because it will not use hasattr anymore (which, by calling getattr, evaluates properties / descriptors).
See also #8605
Isn't this a bug in sparse?
import numpy as np
import numpy.array_api as xp
import sparse
a_np = np.array(['a', 'b']).astype(object)
a_sparse = sparse.COO(a_np)
print(a_np.real) # works
print(a_sparse.real) # ValueError: invalid literal for int() with base 10: 'a'
a_xp = xp.asarray(a_np) # TypeError: The array_api namespace does not support the dtype 'object'
is_duck_array looks like this:
https://github.com/pydata/xarray/blob/c9ba2be2690564594a89eb93fb5d5c4ae7a9253c/xarray/core/utils.py#L262-L273
It is simply not true that namedarray only needs these for everything to work as namedarray use .real, .imag etc.
The true minimum requirement is _arrayfunction_or_api.
By using _arrayfunction_or_api you will guarantee that mypy finds places where namedarray uses more methods than the requirement and this happens quite often as there are many places where we assume (incorrectly?) numpy arrays are used.
