Support for the array API standard#
Note
Array API standard support is still experimental and hidden behind an environment variable. Only a small part of the public API is covered right now.
This guide describes how to use and add support for the Python array API standard. This standard allows users to use any array API compatible array library with SciPy out of the box.
The RFC defines how SciPy implements support for the standard, with the main principle being “array type in equals array type out”. In addition, the implementation does more strict validation of allowed array-like inputs, e.g. rejecting numpy matrix and masked array instances, and arrays with object dtype.
In the following, an array API compatible namespace is noted as xp.
Using array API standard support#
To enable the array API standard support, an environment variable must be set before importing SciPy:
export SCIPY_ARRAY_API=1
This both enables array API standard support and the more strict input validation for array-like arguments. Note that this environment variable is meant to be temporary, as a way to make incremental changes and merge them into ``main`` without affecting backwards compatibility immediately. We do not intend to keep this environment variable around long-term.
This clustering example shows usage with PyTorch tensors as inputs and return values:
>>> import torch
>>> from scipy.cluster.vq import vq
>>> code_book = torch.tensor([[1., 1., 1.],
... [2., 2., 2.]])
>>> features = torch.tensor([[1.9, 2.3, 1.7],
... [1.5, 2.5, 2.2],
... [0.8, 0.6, 1.7]])
>>> code, dist = vq(features, code_book)
>>> code
tensor([1, 1, 0], dtype=torch.int32)
>>> dist
tensor([0.4359, 0.7348, 0.8307])
Note that the above example works for PyTorch CPU tensors. For GPU tensors or
CuPy arrays, the expected result for vq is a TypeError, because vq
is not a pure Python function and hence won’t work on GPU.
More strict array input validation will reject np.matrix and
np.ma.MaskedArray instances, as well as arrays with object dtype:
>>> import numpy as np
>>> from scipy.cluster.vq import vq
>>> code_book = np.array([[1., 1., 1.],
... [2., 2., 2.]])
>>> features = np.array([[1.9, 2.3, 1.7],
... [1.5, 2.5, 2.2],
... [0.8, 0.6, 1.7]])
>>> vq(features, code_book)
(array([1, 1, 0], dtype=int32), array([0.43588989, 0.73484692, 0.83066239]))
>>> # The above uses numpy arrays; trying to use np.matrix instances or object
>>> # arrays instead will yield an exception with `SCIPY_ARRAY_API=1`:
>>> vq(np.asmatrix(features), code_book)
...
TypeError: 'numpy.matrix' are not supported
>>> vq(np.ma.asarray(features), code_book)
...
TypeError: 'numpy.ma.MaskedArray' are not supported
>>> vq(features.astype(np.object_), code_book)
...
TypeError: object arrays are not supported
Currently supported functionality#
The following modules provide array API standard support when the environment variable is set:
Support is provided in scipy.special for the following functions:
scipy.special.log_ndtr, scipy.special.ndtr, scipy.special.ndtri,
scipy.special.erf, scipy.special.erfc, scipy.special.i0,
scipy.special.i0e, scipy.special.i1, scipy.special.i1e,
scipy.special.gammaln, scipy.special.gammainc, scipy.special.gammaincc,
scipy.special.logit, scipy.special.expit, scipy.special.entr,
scipy.special.rel_entr, scipy.special.rel_entr, scipy.special.xlogy,
and scipy.special.chdtrc.
Support is provided in scipy.stats for the following functions:
scipy.stats.describe, scipy.stats.moment, scipy.stats.skew,
scipy.stats.kurtosis, scipy.stats.kstat, scipy.stats.kstatvar,
scipy.stats.circmean, scipy.stats.circvar, scipy.stats.circstd,
scipy.stats.entropy, scipy.stats.variation , scipy.stats.sem,
scipy.stats.ttest_1samp, scipy.stats.pearsonr, scipy.stats.chisquare,
scipy.stats.skewtest, scipy.stats.kurtosistest, scipy.stats.normaltest,
scipy.stats.jarque_bera, scipy.stats.bartlett, scipy.stats.power_divergence,
and scipy.stats.monte_carlo_test.
Implementation notes#
A key part of the support for the array API standard and specific compatibility
functions for Numpy, CuPy and PyTorch is provided through
array-api-compat.
This package is included in the SciPy code base via a git submodule (under
scipy/_lib), so no new dependencies are introduced.
array-api-compat provides generic utility functions and adds aliases such
as xp.concat (which, for numpy, maps to np.concatenate). This allows
using a uniform API across NumPy, PyTorch, CuPy and JAX (with other libraries,
such as Dask, coming in the future).
When the environment variable isn’t set and hence array API standard support in
SciPy is disabled, we still use the “augmented” version of the NumPy namespace,
which is array_api_compat.numpy. That should not change behavior of SciPy
functions, it’s effectively the existing numpy namespace with a number of
aliases added and a handful of functions amended/added for array API standard
support. When support is enabled, depending on the type of arrays, xp will
return the standard-compatible namespace matching the input array type to a
function (e.g., if the input to cluster.vq.kmeans is a PyTorch array, then
xp is array_api_compat.torch).
Adding array API standard support to a SciPy function#
As much as possible, new code added to SciPy should try to follow as closely as possible the array API standard (these functions typically are best-practice idioms for NumPy usage as well). By following the standard, effectively adding support for the array API standard is typically straightforward, and we ideally don’t need to maintain any customization.
Three helper functions are available:
array_namespace: return the namespace based on input arrays and do some input validation (like refusing to work with masked arrays, please see the RFC.)_asarray: a drop-in replacement forasarraywith the additional parameterscheck_finiteandorder. As stated above, try to limit the use of non-standard features. In the end we would want to upstream our needs to the compatibility library. Passingxp=xpavoids duplicate calls ofarray_namespaceinternally.copy: an alias for_asarray(x, copy=True). Thecopyparameter was only introduced tonp.asarrayin NumPy 2.0, so use of the helper is needed to support<2.0. Passingxp=xpavoids duplicate calls ofarray_namespaceinternally.
To add support to a SciPy function which is defined in a .py file, what you
have to change is:
Input array validation,
Using
xprathernpfunctions,When calling into compiled code, convert the array to a NumPy array before and convert it back to the input array type after.
Input array validation uses the following pattern:
xp = array_namespace(arr) # where arr is the input array
# alternatively, if there are multiple array inputs, include them all:
xp = array_namespace(arr1, arr2)
# uses of non-standard parameters of np.asarray can be replaced with _asarray
arr = _asarray(arr, order='C', dtype=xp.float64, xp=xp)
Note that if one input is a non-numpy array type, all array-like inputs have to be of that type; trying to mix non-numpy arrays with lists, Python scalars or other arbitrary Python objects will raise an exception. For NumPy arrays, those types will continue to be accepted for backwards compatibility reasons.
If a function calls into a compiled code just once, use the following pattern:
x = np.asarray(x) # convert to numpy right before compiled call(s)
y = _call_compiled_code(x)
y = xp.asarray(y) # convert back to original array type
If there are multiple calls to compiled code, ensure doing the conversion just once to avoid too much overhead.
Here is an example for a hypothetical public SciPy function toto:
def toto(a, b):
a = np.asarray(a)
b = np.asarray(b, copy=True)
c = np.sum(a) - np.prod(b)
# this is some C or Cython call
d = cdist(c)
return d
You would convert this like so:
def toto(a, b):
xp = array_namespace(a, b)
a = xp.asarray(a)
b = copy(b, xp=xp) # our custom helper is needed for copy
c = xp.sum(a) - xp.prod(b)
# this is some C or Cython call
c = np.asarray(c)
d = cdist(c)
d = xp.asarray(d)
return d
Going through compiled code requires going back to a NumPy array, because SciPy’s extension modules only work with NumPy arrays (or memoryviews in the case of Cython), but not with other array types. For arrays on CPU, the conversions should be zero-copy, while on GPU and other devices the attempt at conversion will raise an exception. The reason for that is that silent data transfer between devices is considered bad practice, as it is likely to be a large and hard-to-detect performance bottleneck.
Adding tests#
The following pytest markers are available:
array_api_compatible -> xp: use a parametrisation to run a test on multiple array backends.skip_xp_backends(*backends, reasons=None, np_only=False, cpu_only=False): skip certain backends and/or devices.np_onlyskips tests for all backends other than the default NumPy backend.@pytest.mark.usefixtures("skip_xp_backends")must be used alongside this marker for the skipping to apply.skip_xp_invalid_argis used to skip tests that use arguments which are invalid whenSCIPY_ARRAY_APIis used. For instance, some tests ofscipy.statsfunctions pass masked arrays to the function being tested, but masked arrays are incompatible with the array API. Use of theskip_xp_invalid_argdecorator allows these tests to protect against regressions whenSCIPY_ARRAY_APIis not used without resulting in failures whenSCIPY_ARRAY_APIis used. In time, we will want these functions to emit deprecation warnings when they receive array API invalid input, and this decorator will check that the deprecation warning is emitted without it causing the test to fail. WhenSCIPY_ARRAY_API=1behavior becomes the default and only behavior, these tests (and the decorator itself) will be removed.
The following is an example using the markers:
from scipy.conftest import array_api_compatible, skip_xp_invalid_arg
...
@pytest.mark.skip_xp_backends(np_only=True,
reasons=['skip reason'])
@pytest.mark.usefixtures("skip_xp_backends")
@array_api_compatible
def test_toto1(self, xp):
a = xp.asarray([1, 2, 3])
b = xp.asarray([0, 2, 5])
toto(a, b)
...
@pytest.mark.skip_xp_backends('array_api_strict', 'cupy',
reasons=['skip reason 1',
'skip reason 2',])
@pytest.mark.usefixtures("skip_xp_backends")
@array_api_compatible
def test_toto2(self, xp):
a = xp.asarray([1, 2, 3])
b = xp.asarray([0, 2, 5])
toto(a, b)
...
# Do not run when SCIPY_ARRAY_API is used
@skip_xp_invalid_arg
def test_toto_masked_array(self):
a = np.ma.asarray([1, 2, 3])
b = np.ma.asarray([0, 2, 5])
toto(a, b)
Passing a custom reason to reasons when cpu_only=True is unsupported
since cpu_only=True can be used alongside passing backends. Also,
the reason for using cpu_only is likely just that compiled code is used
in the function(s) being tested.
When every test function in a file has been updated for array API
compatibility, one can reduce verbosity by telling pytest to apply the
markers to every test function using pytestmark:
from scipy.conftest import array_api_compatible
pytestmark = [array_api_compatible, pytest.mark.usefixtures("skip_xp_backends")]
skip_xp_backends = pytest.mark.skip_xp_backends
...
@skip_xp_backends(np_only=True, reasons=['skip reason'])
def test_toto1(self, xp):
a = xp.asarray([1, 2, 3])
b = xp.asarray([0, 2, 5])
toto(a, b)
After applying these markers, dev.py test can be used with the new option
-b or --array-api-backend:
python dev.py test -b numpy -b pytorch -s cluster
This automatically sets SCIPY_ARRAY_API appropriately. To test a library
that has multiple devices with a non-default device, a second environment
variable (SCIPY_DEVICE, only used in the test suite) can be set. Valid
values depend on the array library under test, e.g. for PyTorch (currently the
only library with multi-device support that is known to work) valid values are
"cpu", "cuda", "mps". So to run the test suite with the PyTorch MPS
backend, use: SCIPY_DEVICE=mps python dev.py test -b pytorch.
Note that there is a GitHub Actions workflow which runs pytorch-cpu.
Additional information#
Here are some additional resources which motivated some design decisions and helped during the development phase: