From 5cd2dbc254aae30b5d8b4785f6e2531192cec4d3 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Sun, 11 May 2025 23:29:45 +0100 Subject: [PATCH 001/104] DEV: bump version to 0.8.0.dev0 (#292) --- pixi.lock | 114 ++++++++++----------- src/array_api_extra/__init__.py | 2 +- src/array_api_extra/_lib/_utils/_compat.py | 1 + src/array_api_extra/_lib/_utils/_typing.py | 2 +- 4 files changed, 60 insertions(+), 59 deletions(-) diff --git a/pixi.lock b/pixi.lock index ac0d48f9..c154cfdb 100644 --- a/pixi.lock +++ b/pixi.lock @@ -97,7 +97,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/alabaster-1.0.0-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.11.2-pyh29332c3_0.conda - conda: https://prefix.dev/conda-forge/noarch/array-api-strict-2.3.1-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/astroid-3.3.9-py310hff52083_0.conda + - conda: https://prefix.dev/conda-forge/linux-64/astroid-3.3.10-py310hff52083_0.conda - conda: https://prefix.dev/conda-forge/noarch/asttokens-3.0.0-pyhd8ed1ab_1.conda - 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python >=3.10,<3.11.0a0 - python_abi 3.10.* *_cp310 - - typing_extensions >=4.0.0 + - typing_extensions >=4 license: LGPL-2.1-or-later license_family: LGPL purls: - pkg:pypi/astroid?source=hash-mapping - size: 399061 - timestamp: 1741614789905 -- conda: https://prefix.dev/conda-forge/win-64/astroid-3.3.9-py313hfa70ccb_0.conda - sha256: 09fbd82a58a6e67baf39f1ae8c4824925623ff9656d952743b508ec8724de6c8 - md5: e0ed4cbb6c5e410b0673d33202ed96e2 + size: 398834 + timestamp: 1746997190828 +- conda: https://prefix.dev/conda-forge/win-64/astroid-3.3.10-py313hfa70ccb_0.conda + sha256: f32b9bfdb515db963ed5e6b3c92d499c8537c6c2070810c533cf3bdeb5325b5f + md5: 94ccfd2c342d01a5d9f574fdbdddbfd2 depends: - python >=3.13,<3.14.0a0 - python_abi 3.13.* *_cp313 @@ -5403,8 +5403,8 @@ packages: license_family: LGPL purls: - pkg:pypi/astroid?source=hash-mapping - size: 513721 - timestamp: 1741614789100 + size: 516241 + timestamp: 1746997224346 - conda: https://prefix.dev/conda-forge/noarch/asttokens-3.0.0-pyhd8ed1ab_1.conda sha256: 93b14414b3b3ed91e286e1cbe4e7a60c4e1b1c730b0814d1e452a8ac4b9af593 md5: 8f587de4bcf981e26228f268df374a9b diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index aa833bcf..1c55a6d1 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -16,7 +16,7 @@ ) from ._lib._lazy import lazy_apply -__version__ = "0.7.2" +__version__ = "0.8.0.dev0" # pylint: disable=duplicate-code __all__ = [ diff --git a/src/array_api_extra/_lib/_utils/_compat.py b/src/array_api_extra/_lib/_utils/_compat.py index c6eec4cd..82ce76b8 100644 --- a/src/array_api_extra/_lib/_utils/_compat.py +++ b/src/array_api_extra/_lib/_utils/_compat.py @@ -2,6 +2,7 @@ # Allow packages that vendor both `array-api-extra` and # `array-api-compat` to override the import location +# pylint: disable=duplicate-code try: from ...._array_api_compat_vendor import ( array_namespace, diff --git a/src/array_api_extra/_lib/_utils/_typing.py b/src/array_api_extra/_lib/_utils/_typing.py index d32a3a07..8204be47 100644 --- a/src/array_api_extra/_lib/_utils/_typing.py +++ b/src/array_api_extra/_lib/_utils/_typing.py @@ -1,5 +1,5 @@ # numpydoc ignore=GL08 -# pylint: disable=missing-module-docstring +# pylint: disable=missing-module-docstring,duplicate-code Array = object DType = object From 09e0eca700069c2ee3916a87c9a3be884ae6bdc8 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sun, 11 May 2025 22:36:59 +0000 Subject: [PATCH 002/104] deps: Update dask to >=2025.4.1 (#290) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pixi.lock b/pixi.lock index c154cfdb..0187c5ba 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5286,7 +5286,7 @@ packages: - pypi: . name: array-api-extra version: 0.8.0.dev0 - sha256: eb518a1094740e5a41c947fb7b93845d39c8c52fd03755313440f3771ecad7f6 + sha256: 79190d03eb04cf8aca45f95ee9fdccc3a4e817a2b140a6c7910f465abee077b5 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index cba9c4cf..ca346fed 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -65,7 +65,7 @@ array-api-strict = ">=2.3.1" numpy = ">=2.1.3" pytest = ">=8.3.5" hypothesis = ">=6.131.8" -dask-core = ">=2025.3.0" # No distributed, tornado, etc. +dask-core = ">=2025.4.1" # No distributed, tornado, etc. # NOTE: don't add jax, pytorch, sparse, cupy here # as they slow down mypy and are not portable across target OSs @@ -105,7 +105,7 @@ myst-parser = ">=4.0.1" sphinx-copybutton = ">=0.5.2" sphinx-autodoc-typehints = ">=1.25.3" # Needed to import parsed modules with autodoc -dask-core = ">=2025.3.0" +dask-core = ">=2025.4.1" pytest = ">=8.3.5" typing-extensions = ">=4.13.2" numpy = ">=2.1.3" @@ -135,7 +135,7 @@ numpy = "=1.22.0" # Note: JAX and PyTorch will install CPU variants. [tool.pixi.feature.backends.dependencies] pytorch = ">=2.6.0" -dask = ">=2025.3.0" +dask = ">=2025.4.1" numba = ">=0.61.2" # sparse dependency llvmlite = ">=0.44.0" # sparse dependency From c9204ea5a960605a7f5382b6662b3eb5f0ee5859 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Mon, 12 May 2025 00:21:12 +0000 Subject: [PATCH 003/104] deps: Update dependency basedpyright to >=1.29.1 (#291) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 0187c5ba..5213bb47 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5286,7 +5286,7 @@ packages: - pypi: . name: array-api-extra version: 0.8.0.dev0 - sha256: 79190d03eb04cf8aca45f95ee9fdccc3a4e817a2b140a6c7910f465abee077b5 + sha256: 4b8857cf2ae805c43d808b860046f8bad5a0324267b804fd8617978694893c0b requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index ca346fed..0c032896 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ typing-extensions = ">=4.13.2" pre-commit = ">=4.2.0" pylint = ">=3.3.6" basedmypy = ">=2.10.0" -basedpyright = ">=1.28.5" +basedpyright = ">=1.29.1" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1" From 82db3bf2847e0a002d8859ef9baa556b02c302cf Mon Sep 17 00:00:00 2001 From: Matt Haberland Date: Mon, 12 May 2025 08:12:16 -0700 Subject: [PATCH 004/104] ENH/TST: `xp_assert_` enhancements (#267) * WIP: xp_assert enhancements * ENH: add xp_assert_less * Rework prepare_for_test (#2) * Fix failures in #267 * Update tests/test_testing.py [skip ci] Co-authored-by: Lucas Colley * Update _testing.py --------- Co-authored-by: Guido Imperiale Co-authored-by: Lucas Colley --- src/array_api_extra/_lib/_testing.py | 223 +++++++++++++++++---------- tests/test_funcs.py | 1 - tests/test_testing.py | 92 ++++++++++- 3 files changed, 224 insertions(+), 92 deletions(-) diff --git a/src/array_api_extra/_lib/_testing.py b/src/array_api_extra/_lib/_testing.py index 301a851f..c60cf466 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -5,10 +5,13 @@ See also ..testing for public testing utilities. """ +from __future__ import annotations + import math from types import ModuleType -from typing import cast +from typing import Any, cast +import numpy as np import pytest from ._utils._compat import ( @@ -16,16 +19,23 @@ is_array_api_strict_namespace, is_cupy_namespace, is_dask_namespace, + is_jax_namespace, + is_numpy_namespace, is_pydata_sparse_namespace, is_torch_namespace, + to_device, ) -from ._utils._typing import Array +from ._utils._typing import Array, Device -__all__ = ["xp_assert_close", "xp_assert_equal"] +__all__ = ["as_numpy_array", "xp_assert_close", "xp_assert_equal", "xp_assert_less"] def _check_ns_shape_dtype( - actual: Array, desired: Array + actual: Array, + desired: Array, + check_dtype: bool, + check_shape: bool, + check_scalar: bool, ) -> ModuleType: # numpydoc ignore=RT03 """ Assert that namespace, shape and dtype of the two arrays match. @@ -36,6 +46,11 @@ def _check_ns_shape_dtype( The array produced by the tested function. desired : Array The expected array (typically hardcoded). + check_dtype, check_shape : bool, default: True + Whether to check agreement between actual and desired dtypes and shapes + check_scalar : bool, default: False + NumPy only: whether to check agreement between actual and desired types - + 0d array vs scalar. Returns ------- @@ -47,43 +62,67 @@ def _check_ns_shape_dtype( msg = f"namespaces do not match: {actual_xp} != f{desired_xp}" assert actual_xp == desired_xp, msg - actual_shape = actual.shape - desired_shape = desired.shape - if is_dask_namespace(desired_xp): - # Dask uses nan instead of None for unknown shapes - if any(math.isnan(i) for i in cast(tuple[float, ...], actual_shape)): - actual_shape = actual.compute().shape # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] - if any(math.isnan(i) for i in cast(tuple[float, ...], desired_shape)): - desired_shape = desired.compute().shape # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] - - msg = f"shapes do not match: {actual_shape} != f{desired_shape}" - assert actual_shape == desired_shape, msg - - msg = f"dtypes do not match: {actual.dtype} != {desired.dtype}" - assert actual.dtype == desired.dtype, msg + if check_shape: + actual_shape = actual.shape + desired_shape = desired.shape + if is_dask_namespace(desired_xp): + # Dask uses nan instead of None for unknown shapes + if any(math.isnan(i) for i in cast(tuple[float, ...], actual_shape)): + actual_shape = actual.compute().shape # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + if any(math.isnan(i) for i in cast(tuple[float, ...], desired_shape)): + desired_shape = desired.compute().shape # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + + msg = f"shapes do not match: {actual_shape} != f{desired_shape}" + assert actual_shape == desired_shape, msg + + if check_dtype: + msg = f"dtypes do not match: {actual.dtype} != {desired.dtype}" + assert actual.dtype == desired.dtype, msg + + if is_numpy_namespace(actual_xp) and check_scalar: + # only NumPy distinguishes between scalars and arrays; we do if check_scalar. + _msg = ( + "array-ness does not match:\n Actual: " + f"{type(actual)}\n Desired: {type(desired)}" + ) + assert np.isscalar(actual) == np.isscalar(desired), _msg return desired_xp -def _prepare_for_test(array: Array, xp: ModuleType) -> Array: +def as_numpy_array(array: Array, *, xp: ModuleType) -> np.typing.NDArray[Any]: # type: ignore[explicit-any] """ - Ensure that the array can be compared with xp.testing or np.testing. - - This involves transferring it from GPU to CPU memory, densifying it, etc. + Convert array to NumPy, bypassing GPU-CPU transfer guards and densification guards. """ - if is_torch_namespace(xp): - return array.cpu() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + if is_cupy_namespace(xp): + return xp.asnumpy(array) if is_pydata_sparse_namespace(xp): return array.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + + if is_torch_namespace(xp): + array = to_device(array, "cpu") if is_array_api_strict_namespace(xp): - # Note: we deliberately did not add a `.to_device` method in _typing.pyi - # even if it is required by the standard as many backends don't support it - return array.to_device(xp.Device("CPU_DEVICE")) # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] - # Note: nothing to do for CuPy, because it uses a bespoke test function - return array + cpu: Device = xp.Device("CPU_DEVICE") + array = to_device(array, cpu) + if is_jax_namespace(xp): + import jax + # Note: only needed if the transfer guard is enabled + cpu = cast(Device, jax.devices("cpu")[0]) + array = to_device(array, cpu) -def xp_assert_equal(actual: Array, desired: Array, err_msg: str = "") -> None: + return np.asarray(array) + + +def xp_assert_equal( + actual: Array, + desired: Array, + *, + err_msg: str = "", + check_dtype: bool = True, + check_shape: bool = True, + check_scalar: bool = False, +) -> None: """ Array-API compatible version of `np.testing.assert_array_equal`. @@ -95,34 +134,56 @@ def xp_assert_equal(actual: Array, desired: Array, err_msg: str = "") -> None: The expected array (typically hardcoded). err_msg : str, optional Error message to display on failure. + check_dtype, check_shape : bool, default: True + Whether to check agreement between actual and desired dtypes and shapes + check_scalar : bool, default: False + NumPy only: whether to check agreement between actual and desired types - + 0d array vs scalar. See Also -------- xp_assert_close : Similar function for inexact equality checks. numpy.testing.assert_array_equal : Similar function for NumPy arrays. """ - xp = _check_ns_shape_dtype(actual, desired) - actual = _prepare_for_test(actual, xp) - desired = _prepare_for_test(desired, xp) + xp = _check_ns_shape_dtype(actual, desired, check_dtype, check_shape, check_scalar) + actual_np = as_numpy_array(actual, xp=xp) + desired_np = as_numpy_array(desired, xp=xp) + np.testing.assert_array_equal(actual_np, desired_np, err_msg=err_msg) - if is_cupy_namespace(xp): - xp.testing.assert_array_equal(actual, desired, err_msg=err_msg) - elif is_torch_namespace(xp): - # PyTorch recommends using `rtol=0, atol=0` like this - # to test for exact equality - xp.testing.assert_close( - actual, - desired, - rtol=0, - atol=0, - equal_nan=True, - check_dtype=False, - msg=err_msg or None, - ) - else: - import numpy as np # pylint: disable=import-outside-toplevel - np.testing.assert_array_equal(actual, desired, err_msg=err_msg) +def xp_assert_less( + x: Array, + y: Array, + *, + err_msg: str = "", + check_dtype: bool = True, + check_shape: bool = True, + check_scalar: bool = False, +) -> None: + """ + Array-API compatible version of `np.testing.assert_array_less`. + + Parameters + ---------- + x, y : Array + The arrays to compare according to ``x < y`` (elementwise). + err_msg : str, optional + Error message to display on failure. + check_dtype, check_shape : bool, default: True + Whether to check agreement between actual and desired dtypes and shapes + check_scalar : bool, default: False + NumPy only: whether to check agreement between actual and desired types - + 0d array vs scalar. + + See Also + -------- + xp_assert_close : Similar function for inexact equality checks. + numpy.testing.assert_array_equal : Similar function for NumPy arrays. + """ + xp = _check_ns_shape_dtype(x, y, check_dtype, check_shape, check_scalar) + x_np = as_numpy_array(x, xp=xp) + y_np = as_numpy_array(y, xp=xp) + np.testing.assert_array_less(x_np, y_np, err_msg=err_msg) def xp_assert_close( @@ -132,6 +193,9 @@ def xp_assert_close( rtol: float | None = None, atol: float = 0, err_msg: str = "", + check_dtype: bool = True, + check_shape: bool = True, + check_scalar: bool = False, ) -> None: """ Array-API compatible version of `np.testing.assert_allclose`. @@ -148,6 +212,11 @@ def xp_assert_close( Absolute tolerance. Default: 0. err_msg : str, optional Error message to display on failure. + check_dtype, check_shape : bool, default: True + Whether to check agreement between actual and desired dtypes and shapes + check_scalar : bool, default: False + NumPy only: whether to check agreement between actual and desired types - + 0d array vs scalar. See Also -------- @@ -159,40 +228,26 @@ def xp_assert_close( ----- The default `atol` and `rtol` differ from `xp.all(xpx.isclose(a, b))`. """ - xp = _check_ns_shape_dtype(actual, desired) - - floating = xp.isdtype(actual.dtype, ("real floating", "complex floating")) - if rtol is None and floating: - # multiplier of 4 is used as for `np.float64` this puts the default `rtol` - # roughly half way between sqrt(eps) and the default for - # `numpy.testing.assert_allclose`, 1e-7 - rtol = xp.finfo(actual.dtype).eps ** 0.5 * 4 - elif rtol is None: - rtol = 1e-7 - - actual = _prepare_for_test(actual, xp) - desired = _prepare_for_test(desired, xp) - - if is_cupy_namespace(xp): - xp.testing.assert_allclose( - actual, desired, rtol=rtol, atol=atol, err_msg=err_msg - ) - elif is_torch_namespace(xp): - xp.testing.assert_close( - actual, desired, rtol=rtol, atol=atol, equal_nan=True, msg=err_msg or None - ) - else: - import numpy as np # pylint: disable=import-outside-toplevel - - # JAX/Dask arrays work directly with `np.testing` - assert isinstance(rtol, float) - np.testing.assert_allclose( # type: ignore[call-overload] # pyright: ignore[reportCallIssue] - actual, # pyright: ignore[reportArgumentType] - desired, # pyright: ignore[reportArgumentType] - rtol=rtol, - atol=atol, - err_msg=err_msg, - ) + xp = _check_ns_shape_dtype(actual, desired, check_dtype, check_shape, check_scalar) + + if rtol is None: + if xp.isdtype(actual.dtype, ("real floating", "complex floating")): + # multiplier of 4 is used as for `np.float64` this puts the default `rtol` + # roughly half way between sqrt(eps) and the default for + # `numpy.testing.assert_allclose`, 1e-7 + rtol = xp.finfo(actual.dtype).eps ** 0.5 * 4 + else: + rtol = 1e-7 + + actual_np = as_numpy_array(actual, xp=xp) + desired_np = as_numpy_array(desired, xp=xp) + np.testing.assert_allclose( # pyright: ignore[reportCallIssue] + actual_np, + desired_np, + rtol=rtol, # pyright: ignore[reportArgumentType] + atol=atol, + err_msg=err_msg, + ) def xfail( diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 0cee0b4d..5f34bd60 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -196,7 +196,6 @@ def test_device(self, xp: ModuleType, device: Device): y = apply_where(x % 2 == 0, x, self.f1, fill_value=x) assert get_device(y) == device - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") @pytest.mark.filterwarnings("ignore::RuntimeWarning") # overflows, etc. @hypothesis.settings( # The xp and library fixtures are not regenerated between hypothesis iterations diff --git a/tests/test_testing.py b/tests/test_testing.py index fb9ba581..adb77d20 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -1,4 +1,5 @@ from collections.abc import Callable +from contextlib import nullcontext from types import ModuleType from typing import cast @@ -6,13 +7,18 @@ import pytest from array_api_extra._lib._backends import Backend -from array_api_extra._lib._testing import xp_assert_close, xp_assert_equal +from array_api_extra._lib._testing import ( + as_numpy_array, + xp_assert_close, + xp_assert_equal, + xp_assert_less, +) from array_api_extra._lib._utils._compat import ( array_namespace, is_dask_namespace, is_jax_namespace, ) -from array_api_extra._lib._utils._typing import Array +from array_api_extra._lib._utils._typing import Array, Device from array_api_extra.testing import lazy_xp_function # mypy: disable-error-code=decorated-any @@ -22,15 +28,25 @@ "func", [ xp_assert_equal, + xp_assert_less, pytest.param( xp_assert_close, - marks=pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype"), + marks=pytest.mark.xfail_xp_backend( + Backend.SPARSE, reason="no isdtype", strict=False + ), ), ], ) -@param_assert_equal_close +def test_as_numpy_array(xp: ModuleType, device: Device): + x = xp.asarray([1, 2, 3], device=device) + y = as_numpy_array(x, xp=xp) + assert isinstance(y, np.ndarray) + + +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype", strict=False) +@pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close]) def test_assert_close_equal_basic(xp: ModuleType, func: Callable[..., None]): # type: ignore[explicit-any] func(xp.asarray(0), xp.asarray(0)) func(xp.asarray([1, 2]), xp.asarray([1, 2])) @@ -50,8 +66,8 @@ def test_assert_close_equal_basic(xp: ModuleType, func: Callable[..., None]): # @pytest.mark.skip_xp_backend(Backend.NUMPY, reason="test other ns vs. numpy") @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="test other ns vs. numpy") -@pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close]) -def test_assert_close_equal_namespace(xp: ModuleType, func: Callable[..., None]): # type: ignore[explicit-any] +@pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) +def test_assert_close_equal_less_namespace(xp: ModuleType, func: Callable[..., None]): # type: ignore[explicit-any] with pytest.raises(AssertionError, match="namespaces do not match"): func(xp.asarray(0), np.asarray(0)) with pytest.raises(TypeError, match="Unrecognized array input"): @@ -60,6 +76,59 @@ def test_assert_close_equal_namespace(xp: ModuleType, func: Callable[..., None]) func(xp.asarray([0]), [0]) +@param_assert_equal_close +@pytest.mark.parametrize("check_shape", [False, True]) +def test_assert_close_equal_less_shape( # type: ignore[explicit-any] + xp: ModuleType, + func: Callable[..., None], + check_shape: bool, +): + context = ( + pytest.raises(AssertionError, match="shapes do not match") + if check_shape + else nullcontext() + ) + with context: + # note: NaNs are handled by all 3 checks + func(xp.asarray([xp.nan, xp.nan]), xp.asarray(xp.nan), check_shape=check_shape) + + +@param_assert_equal_close +@pytest.mark.parametrize("check_dtype", [False, True]) +def test_assert_close_equal_less_dtype( # type: ignore[explicit-any] + xp: ModuleType, + func: Callable[..., None], + check_dtype: bool, +): + context = ( + pytest.raises(AssertionError, match="dtypes do not match") + if check_dtype + else nullcontext() + ) + with context: + func( + xp.asarray(xp.nan, dtype=xp.float32), + xp.asarray(xp.nan, dtype=xp.float64), + check_dtype=check_dtype, + ) + + +@pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) +@pytest.mark.parametrize("check_scalar", [False, True]) +def test_assert_close_equal_less_scalar( # type: ignore[explicit-any] + xp: ModuleType, + func: Callable[..., None], + check_scalar: bool, +): + context = ( + pytest.raises(AssertionError, match="array-ness does not match") + if check_scalar + else nullcontext() + ) + with context: + func(np.asarray(xp.nan), np.asarray(xp.nan)[()], check_scalar=check_scalar) + + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") def test_assert_close_tolerance(xp: ModuleType): xp_assert_close(xp.asarray([100.0]), xp.asarray([102.0]), rtol=0.03) @@ -71,9 +140,18 @@ def test_assert_close_tolerance(xp: ModuleType): xp_assert_close(xp.asarray([100.0]), xp.asarray([102.0]), atol=1) -@param_assert_equal_close +def test_assert_less_basic(xp: ModuleType): + xp_assert_less(xp.asarray(-1), xp.asarray(0)) + xp_assert_less(xp.asarray([1, 2]), xp.asarray([2, 3])) + with pytest.raises(AssertionError): + xp_assert_less(xp.asarray([1, 1]), xp.asarray([2, 1])) + with pytest.raises(AssertionError, match="hello"): + xp_assert_less(xp.asarray([1, 1]), xp.asarray([2, 1]), err_msg="hello") + + @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="index by sparse array") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="boolean indexing") +@pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close]) def test_assert_close_equal_none_shape(xp: ModuleType, func: Callable[..., None]): # type: ignore[explicit-any] """On Dask and other lazy backends, test that a shape with NaN's or None's can be compared to a real shape. From 84b1f0b0c0eb11c3b1acd2bb9aa3f70bac429a37 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 15 May 2025 04:20:58 +0000 Subject: [PATCH 005/104] deps: Update gha (#293) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/cd.yml | 4 ++-- .github/workflows/ci.yml | 10 +++++----- .github/workflows/docs-build.yml | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 13411752..c57eeb4d 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -34,13 +34,13 @@ jobs: if: github.event_name == 'release' && github.event.action == 'published' steps: - - uses: actions/download-artifact@95815c38cf2ff2164869cbab79da8d1f422bc89e # v4.2.1 + - uses: actions/download-artifact@d3f86a106a0bac45b974a628896c90dbdf5c8093 # v4.3.0 with: name: Packages path: dist - name: Generate artifact attestation for sdist and wheel - uses: actions/attest-build-provenance@c074443f1aee8d4aeeae555aebba3282517141b2 # v2.2.3 + uses: actions/attest-build-provenance@db473fddc028af60658334401dc6fa3ffd8669fd # v2.3.0 with: subject-path: "dist/*" diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d030beff..73ab37e1 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -27,13 +27,13 @@ jobs: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 with: fetch-depth: 0 - - uses: actions/setup-python@8d9ed9ac5c53483de85588cdf95a591a75ab9f55 # v5.5.0 + - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0 with: - python-version: "3.13.2" + python-version: "3.13.3" - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 with: extra_args: --hook-stage manual --all-files - - uses: prefix-dev/setup-pixi@dbaed5efa0bd33d6bd6d162bec8a06d8fc43c807 # v0.8.5 + - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 with: pixi-version: v0.42.1 cache: true @@ -59,7 +59,7 @@ jobs: with: fetch-depth: 0 - - uses: prefix-dev/setup-pixi@dbaed5efa0bd33d6bd6d162bec8a06d8fc43c807 # v0.8.5 + - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 with: pixi-version: v0.42.1 cache: true @@ -69,6 +69,6 @@ jobs: run: pixi run -e ${{ matrix.environment }} tests-ci - name: Upload coverage report - uses: codecov/codecov-action@0565863a31f2c772f9f0395002a31e3f06189574 # v5.4.0 + uses: codecov/codecov-action@ad3126e916f78f00edff4ed0317cf185271ccc2d # v5.4.2 with: token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index edf949c7..e9da16ec 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -10,7 +10,7 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 - - uses: prefix-dev/setup-pixi@dbaed5efa0bd33d6bd6d162bec8a06d8fc43c807 # v0.8.5 + - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 with: pixi-version: v0.42.1 cache: true From 5bcd66d447ee540805bc53bd2eb9298249ab19a2 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Fri, 16 May 2025 11:10:05 +0100 Subject: [PATCH 006/104] MAINT: test against Dask 2025.5 --- pixi.lock | 9449 ++++++++++-------------------------------------- pyproject.toml | 18 +- 2 files changed, 1883 insertions(+), 7584 deletions(-) diff --git a/pixi.lock b/pixi.lock index 5213bb47..5159c189 100644 --- a/pixi.lock +++ b/pixi.lock @@ -100,30 +100,11 @@ environments: - 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[tool.pixi.feature.backends.dependencies] pytorch = ">=2.6.0" -dask = ">=2025.4.1" -numba = ">=0.61.2" # sparse dependency -llvmlite = ">=0.44.0" # sparse dependency - -[tool.pixi.feature.backends.pypi-dependencies] -sparse = { version = ">=0.16.0" } +dask-core = ">=2025.5.0" # No distributed, tornado, etc. +sparse = ">=0.16.0" [tool.pixi.feature.backends.target.linux-64.dependencies] jax = ">=0.5.2" @@ -237,8 +233,8 @@ disallow_any_expr = false disable_error_code = ["redundant-expr", "unreachable", "no-any-return"] [[tool.mypy.overrides]] -# slow/unavailable on Windows; do not add to the lint env -module = ["dask.*", "jax.*", "torch.*"] +# slow or unavailable on Windows; do not add to the lint env +module = ["cupy.*", "jax.*", "sparse.*", "torch.*"] ignore_missing_imports = true # pyright From ad55fea063ab412af0861bca4567574368030b3d Mon Sep 17 00:00:00 2001 From: crusaderky Date: Fri, 16 May 2025 11:02:22 +0100 Subject: [PATCH 007/104] MAINT: `reshape` does not accept int --- src/array_api_extra/_lib/_funcs.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index e552392b..bb39775f 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -725,7 +725,8 @@ def nunique(x: Array, /, *, xp: ModuleType | None = None) -> Array: return xp.asarray(n, device=_compat.device(x)) # xp does not have unique_counts; O(n*logn) complexity - x = xp.sort(xp.reshape(x, -1)) + x = xp.reshape(x, (-1,)) + x = xp.sort(x) mask = x != xp.roll(x, -1) default_int = xp.__array_namespace_info__().default_dtypes( device=_compat.device(x) From 197476f9062f581a6a419c174a92e3924a0d9de1 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Fri, 16 May 2025 11:19:33 +0100 Subject: [PATCH 008/104] MAINT: upgrade to array-api-compat >=1.12 --- pixi.lock | 105 ++++++++++---------- pyproject.toml | 4 +- src/array_api_extra/_lib/_utils/_helpers.py | 8 +- 3 files changed, 56 insertions(+), 61 deletions(-) diff --git a/pixi.lock b/pixi.lock index 5159c189..a95291d1 100644 --- a/pixi.lock +++ b/pixi.lock @@ -9,7 +9,7 @@ environments: linux-64: - conda: https://prefix.dev/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2 - conda: https://prefix.dev/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.11.2-pyh29332c3_0.conda + - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.12.0-pyhe01879c_0.conda - 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- python >=3.9 + - python >=3.10 - python license: MIT - license_family: MIT purls: - pkg:pypi/array-api-compat?source=hash-mapping - size: 41599 - timestamp: 1742509526028 + size: 45821 + timestamp: 1747403732947 - pypi: . name: array-api-extra version: 0.8.0.dev0 - sha256: e3263c30289d66eb33e78df344e50a1a93db11b5207e317c541c3bb52ba56b4a + sha256: ef4f51355b324b4797283953199955b2c7cdd6afa4a187ddd10e663e9ab0de59 requires_dist: - - array-api-compat>=1.11.2,<2 + - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' editable: true - conda: https://prefix.dev/conda-forge/noarch/array-api-strict-2.3.1-pyhd8ed1ab_0.conda diff --git a/pyproject.toml b/pyproject.toml index 13e5672b..f692c801 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,7 +26,7 @@ classifiers = [ "Typing :: Typed", ] dynamic = ["version"] -dependencies = ["array-api-compat>=1.11.2,<2"] +dependencies = ["array-api-compat>=1.12.0,<2"] [project.urls] Homepage = "https://github.com/data-apis/array-api-extra" @@ -48,7 +48,7 @@ platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"] [tool.pixi.dependencies] python = ">=3.10,<3.14" -array-api-compat = ">=1.11.2,<2" +array-api-compat = ">=1.12.0,<2" [tool.pixi.pypi-dependencies] array-api-extra = { path = ".", editable = true } diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 64006270..1a04fc8b 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -296,13 +296,9 @@ def capabilities(xp: ModuleType) -> dict[str, int]: # No __array_namespace_info__(); no indexing by sparse arrays return {"boolean indexing": False, "data-dependent shapes": True} out = xp.__array_namespace_info__().capabilities() - if is_jax_namespace(xp): + if is_jax_namespace(xp) and out["boolean indexing"]: # FIXME https://github.com/jax-ml/jax/issues/27418 + # Fixed in jax >=0.6.0 out = out.copy() out["boolean indexing"] = False - if is_dask_namespace(xp): - # FIXME https://github.com/data-apis/array-api-compat/pull/290 - out = out.copy() - out["boolean indexing"] = True - out["data-dependent shapes"] = True return out From 28a364d961dfe506877bd111f9d4e503a9fafa16 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Fri, 16 May 2025 22:04:34 +0100 Subject: [PATCH 009/104] Merge pull request #284 from crusaderky/autojit ENH: `jax_autojit` --- src/array_api_extra/_lib/_utils/_helpers.py | 263 +++++++++++++++++++- src/array_api_extra/testing.py | 85 ++++--- tests/conftest.py | 41 ++- tests/test_at.py | 22 +- tests/test_funcs.py | 20 +- tests/test_helpers.py | 199 ++++++++++++++- tests/test_lazy.py | 6 +- tests/test_testing.py | 96 +++++-- 8 files changed, 628 insertions(+), 104 deletions(-) diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 1a04fc8b..99fcf65a 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -2,10 +2,24 @@ from __future__ import annotations +import io import math -from collections.abc import Generator, Iterable +import pickle +import types +from collections.abc import Callable, Generator, Iterable +from functools import wraps from types import ModuleType -from typing import TYPE_CHECKING, cast +from typing import ( + TYPE_CHECKING, + Any, + ClassVar, + Generic, + Literal, + ParamSpec, + TypeAlias, + TypeVar, + cast, +) from . import _compat from ._compat import ( @@ -19,8 +33,16 @@ from ._typing import Array if TYPE_CHECKING: # pragma: no cover - # TODO import from typing (requires Python >=3.13) - from typing_extensions import TypeIs + # TODO import from typing (requires Python >=3.12 and >=3.13) + from typing_extensions import TypeIs, override +else: + + def override(func): + return func + + +P = ParamSpec("P") +T = TypeVar("T") __all__ = [ @@ -29,8 +51,11 @@ "eager_shape", "in1d", "is_python_scalar", + "jax_autojit", "mean", "meta_namespace", + "pickle_flatten", + "pickle_unflatten", ] @@ -302,3 +327,233 @@ def capabilities(xp: ModuleType) -> dict[str, int]: out = out.copy() out["boolean indexing"] = False return out + + +_BASIC_PICKLED_TYPES = frozenset(( + bool, int, float, complex, str, bytes, bytearray, + list, tuple, dict, set, frozenset, range, slice, + types.NoneType, types.EllipsisType, +)) # fmt: skip +_BASIC_REST_TYPES = frozenset(( + type, types.BuiltinFunctionType, types.FunctionType, types.ModuleType +)) # fmt: skip + +FlattenRest: TypeAlias = tuple[object, ...] + + +def pickle_flatten( + obj: object, cls: type[T] | tuple[type[T], ...] +) -> tuple[list[T], FlattenRest]: + """ + Use the pickle machinery to extract objects out of an arbitrary container. + + Unlike regular ``pickle.dumps``, this function always succeeds. + + Parameters + ---------- + obj : object + The object to pickle. + cls : type | tuple[type, ...] + One or multiple classes to extract from the object. + The instances of these classes inside ``obj`` will not be pickled. + + Returns + ------- + instances : list[cls] + All instances of ``cls`` found inside ``obj`` (not pickled). + rest + Opaque object containing the pickled bytes plus all other objects where + ``__reduce__`` / ``__reduce_ex__`` is either not implemented or raised. + These are unpickleable objects, types, modules, and functions. + + This object is *typically* hashable save for fairly exotic objects + that are neither pickleable nor hashable. + + This object is pickleable if everything except ``instances`` was pickleable + in the input object. + + See Also + -------- + pickle_unflatten : Reverse function. + + Examples + -------- + >>> class A: + ... def __repr__(self): + ... return "" + >>> class NS: + ... def __repr__(self): + ... return "" + ... def __reduce__(self): + ... assert False, "not serializable" + >>> obj = {1: A(), 2: [A(), NS(), A()]} + >>> instances, rest = pickle_flatten(obj, A) + >>> instances + [, , ] + >>> pickle_unflatten(instances, rest) + {1: , 2: [, , ]} + + This can be also used to swap inner objects; the only constraint is that + the number of objects in and out must be the same: + + >>> pickle_unflatten(["foo", "bar", "baz"], rest) + {1: "foo", 2: ["bar", , "baz"]} + """ + instances: list[T] = [] + rest: list[object] = [] + + class Pickler(pickle.Pickler): # numpydoc ignore=GL08 + """ + Use the `pickle.Pickler.persistent_id` hook to extract objects. + """ + + @override + def persistent_id(self, obj: object) -> Literal[0, 1, None]: # pyright: ignore[reportIncompatibleMethodOverride] # numpydoc ignore=GL08 + if isinstance(obj, cls): + instances.append(obj) # type: ignore[arg-type] + return 0 + + typ_ = type(obj) + if typ_ in _BASIC_PICKLED_TYPES: # No subclasses! + # If obj is a collection, recursively descend inside it + return None + if typ_ in _BASIC_REST_TYPES: + rest.append(obj) + return 1 + + try: + # Note: a class that defines __slots__ without defining __getstate__ + # cannot be pickled with __reduce__(), but can with __reduce_ex__(5) + _ = obj.__reduce_ex__(pickle.HIGHEST_PROTOCOL) + except Exception: # pylint: disable=broad-exception-caught + rest.append(obj) + return 1 + + # Object can be pickled. Let the Pickler recursively descend inside it. + return None + + f = io.BytesIO() + p = Pickler(f, protocol=pickle.HIGHEST_PROTOCOL) + p.dump(obj) + return instances, (f.getvalue(), *rest) + + +def pickle_unflatten(instances: Iterable[object], rest: FlattenRest) -> Any: # type: ignore[explicit-any] + """ + Reverse of ``pickle_flatten``. + + Parameters + ---------- + instances : Iterable + Inner objects to be reinserted into the flattened container. + rest : FlattenRest + Extra bits, as returned by ``pickle_flatten``. + + Returns + ------- + object + The outer object originally passed to ``pickle_flatten`` after a + pickle->unpickle round-trip. + + See Also + -------- + pickle_flatten : Serializing function. + pickle.loads : Standard unpickle function. + + Notes + ----- + The `instances` iterable must yield at least the same number of elements as the ones + returned by ``pickle_without``, but the elements do not need to be the same objects + or even the same types of objects. Excess elements, if any, will be left untouched. + """ + iters = iter(instances), iter(rest) + pik = cast(bytes, next(iters[1])) + + class Unpickler(pickle.Unpickler): # numpydoc ignore=GL08 + """Mirror of the overridden Pickler in pickle_flatten.""" + + @override + def persistent_load(self, pid: Literal[0, 1]) -> object: # pyright: ignore[reportIncompatibleMethodOverride] # numpydoc ignore=GL08 + try: + return next(iters[pid]) + except StopIteration as e: + msg = "Not enough objects to unpickle" + raise ValueError(msg) from e + + f = io.BytesIO(pik) + return Unpickler(f).load() + + +class _AutoJITWrapper(Generic[T]): # numpydoc ignore=PR01 + """ + Helper of :func:`jax_autojit`. + + Wrap arbitrary inputs and outputs of the jitted function and + convert them to/from PyTrees. + """ + + obj: T + _registered: ClassVar[bool] = False + __slots__: tuple[str, ...] = ("obj",) + + def __init__(self, obj: T) -> None: # numpydoc ignore=GL08 + self._register() + self.obj = obj + + @classmethod + def _register(cls): # numpydoc ignore=SS06 + """ + Register upon first use instead of at import time, to avoid + globally importing JAX. + """ + if not cls._registered: + import jax + + jax.tree_util.register_pytree_node( + cls, + lambda obj: pickle_flatten(obj, jax.Array), # pyright: ignore[reportUnknownArgumentType] + lambda aux_data, children: pickle_unflatten(children, aux_data), # pyright: ignore[reportUnknownArgumentType] + ) + cls._registered = True + + +def jax_autojit( + func: Callable[P, T], +) -> Callable[P, T]: # numpydoc ignore=PR01,RT01,SS03 + """ + Wrap `func` with ``jax.jit``, with the following differences: + + - Python scalar arguments and return values are not automatically converted to + ``jax.Array`` objects. + - All non-array arguments are automatically treated as static. + Unlike ``jax.jit``, static arguments must be either hashable or serializable with + ``pickle``. + - Unlike ``jax.jit``, non-array arguments and return values are not limited to + tuple/list/dict, but can be any object serializable with ``pickle``. + - Automatically descend into non-array arguments and find ``jax.Array`` objects + inside them, then rebuild the arguments when entering `func`, swapping the JAX + concrete arrays with tracer objects. + - Automatically descend into non-array return values and find ``jax.Array`` objects + inside them, then rebuild them downstream of exiting the JIT, swapping the JAX + tracer objects with concrete arrays. + + See Also + -------- + jax.jit : JAX JIT compilation function. + """ + import jax + + @jax.jit # type: ignore[misc] # pyright: ignore[reportUntypedFunctionDecorator] + def inner( # type: ignore[decorated-any,explicit-any] # numpydoc ignore=GL08 + wargs: _AutoJITWrapper[Any], + ) -> _AutoJITWrapper[T]: + args, kwargs = wargs.obj + res = func(*args, **kwargs) # pyright: ignore[reportCallIssue] + return _AutoJITWrapper(res) + + @wraps(func) + def outer(*args: P.args, **kwargs: P.kwargs) -> T: # numpydoc ignore=GL08 + wargs = _AutoJITWrapper((args, kwargs)) + return inner(wargs).obj + + return outer diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index 37e8e69e..c14e9a22 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -7,12 +7,15 @@ from __future__ import annotations import contextlib -from collections.abc import Callable, Iterable, Iterator, Sequence +import enum +import warnings +from collections.abc import Callable, Iterator, Sequence from functools import wraps from types import ModuleType from typing import TYPE_CHECKING, Any, ParamSpec, TypeVar, cast from ._lib._utils._compat import is_dask_namespace, is_jax_namespace +from ._lib._utils._helpers import jax_autojit, pickle_flatten, pickle_unflatten __all__ = ["lazy_xp_function", "patch_lazy_xp_functions"] @@ -26,7 +29,7 @@ # Sphinx hacks SchedulerGetCallable = object - def override(func: object) -> object: + def override(func): return func @@ -36,13 +39,22 @@ def override(func: object) -> object: _ufuncs_tags: dict[object, dict[str, Any]] = {} # type: ignore[explicit-any] +class Deprecated(enum.Enum): + """Unique type for deprecated parameters.""" + + DEPRECATED = 1 + + +DEPRECATED = Deprecated.DEPRECATED + + def lazy_xp_function( # type: ignore[explicit-any] func: Callable[..., Any], *, allow_dask_compute: bool | int = False, jax_jit: bool = True, - static_argnums: int | Sequence[int] | None = None, - static_argnames: str | Iterable[str] | None = None, + static_argnums: Deprecated = DEPRECATED, + static_argnames: Deprecated = DEPRECATED, ) -> None: # numpydoc ignore=GL07 """ Tag a function to be tested on lazy backends. @@ -82,16 +94,30 @@ def lazy_xp_function( # type: ignore[explicit-any] Default: False, meaning that `func` must be fully lazy and never materialize the graph. jax_jit : bool, optional - Set to True to replace `func` with ``jax.jit(func)`` after calling the - :func:`patch_lazy_xp_functions` test helper with ``xp=jax.numpy``. Set to False - if `func` is only compatible with eager (non-jitted) JAX. Default: True. - static_argnums : int | Sequence[int], optional - Passed to jax.jit. Positional arguments to treat as static (compile-time - constant). Default: infer from `static_argnames` using - `inspect.signature(func)`. - static_argnames : str | Iterable[str], optional - Passed to jax.jit. Named arguments to treat as static (compile-time constant). - Default: infer from `static_argnums` using `inspect.signature(func)`. + Set to True to replace `func` with a smart variant of ``jax.jit(func)`` after + calling the :func:`patch_lazy_xp_functions` test helper with ``xp=jax.numpy``. + Set to False if `func` is only compatible with eager (non-jitted) JAX. + + Unlike with vanilla ``jax.jit``, all arguments and return types that are not JAX + arrays are treated as static; the function can accept and return arbitrary + wrappers around JAX arrays. This difference is because, in real life, most users + won't wrap the function directly with ``jax.jit`` but rather they will use it + within their own code, which is itself then wrapped by ``jax.jit``, and + internally consume the function's outputs. + + In other words, the pattern that is being tested is:: + + >>> @jax.jit + ... def user_func(x): + ... y = user_prepares_inputs(x) + ... z = func(y, some_static_arg=True) + ... return user_consumes(z) + + Default: True. + static_argnums : + Deprecated; ignored + static_argnames : + Deprecated; ignored See Also -------- @@ -108,7 +134,7 @@ def lazy_xp_function( # type: ignore[explicit-any] def test_myfunc(xp): a = xp.asarray([1, 2]) - # When xp=jax.numpy, this is the same as `b = jax.jit(myfunc)(a)` + # When xp=jax.numpy, this is similar to `b = jax.jit(myfunc)(a)` # When xp=dask.array, crash on compute() or persist() b = myfunc(a) @@ -168,12 +194,20 @@ def test_myfunc(xp): b = mymodule.myfunc(a) # This is wrapped when xp=jax.numpy or xp=dask.array c = naked.myfunc(a) # This is not """ + if static_argnums is not DEPRECATED or static_argnames is not DEPRECATED: + warnings.warn( + ( + "The `static_argnums` and `static_argnames` parameters are deprecated " + "and ignored. They will be removed in a future version." + ), + DeprecationWarning, + stacklevel=2, + ) tags = { "allow_dask_compute": allow_dask_compute, "jax_jit": jax_jit, - "static_argnums": static_argnums, - "static_argnames": static_argnames, } + try: func._lazy_xp_function = tags # type: ignore[attr-defined] # pylint: disable=protected-access # pyright: ignore[reportFunctionMemberAccess] except AttributeError: # @cython.vectorize @@ -247,19 +281,9 @@ def iter_tagged() -> ( # type: ignore[explicit-any] monkeypatch.setattr(mod, name, wrapped) elif is_jax_namespace(xp): - import jax - for mod, name, func, tags in iter_tagged(): if tags["jax_jit"]: - # suppress unused-ignore to run mypy in -e lint as well as -e dev - wrapped = cast( # type: ignore[explicit-any] - Callable[..., Any], - jax.jit( - func, - static_argnums=tags["static_argnums"], - static_argnames=tags["static_argnames"], - ), - ) + wrapped = jax_autojit(func) monkeypatch.setattr(mod, name, wrapped) @@ -308,6 +332,7 @@ def _dask_wrap( After the function returns, materialize the graph in order to re-raise exceptions. """ import dask + import dask.array as da func_name = getattr(func, "__name__", str(func)) n_str = f"only up to {n}" if n else "no" @@ -327,6 +352,8 @@ def wrapper(*args: P.args, **kwargs: P.kwargs) -> T: # numpydoc ignore=GL08 # Block until the graph materializes and reraise exceptions. This allows # `pytest.raises` and `pytest.warns` to work as expected. Note that this would # not work on scheduler='distributed', as it would not block. - return dask.persist(out, scheduler="threads")[0] # type: ignore[attr-defined,no-untyped-call,func-returns-value,index] # pyright: ignore[reportPrivateImportUsage] + arrays, rest = pickle_flatten(out, da.Array) + arrays = dask.persist(arrays, scheduler="threads")[0] # type: ignore[attr-defined,no-untyped-call,func-returns-value,index] # pyright: ignore[reportPrivateImportUsage] + return pickle_unflatten(arrays, rest) # pyright: ignore[reportUnknownArgumentType] return wrapper diff --git a/tests/conftest.py b/tests/conftest.py index 5676cc0d..372f9960 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -148,19 +148,7 @@ def xp( patch_lazy_xp_functions(request, monkeypatch, xp=xp) if library.like(Backend.JAX): - import jax - - # suppress unused-ignore to run mypy in -e lint as well as -e dev - jax.config.update("jax_enable_x64", True) # type: ignore[no-untyped-call,unused-ignore] - - if library == Backend.JAX_GPU: - try: - device = jax.devices("cuda")[0] - except RuntimeError: - pytest.skip("no CUDA device available") - else: - device = jax.devices("cpu")[0] - jax.config.update("jax_default_device", device) + _setup_jax(library) elif library == Backend.TORCH_GPU: import torch.cuda @@ -175,6 +163,22 @@ def xp( yield xp +def _setup_jax(library: Backend) -> None: + import jax + + # suppress unused-ignore to run mypy in -e lint as well as -e dev + jax.config.update("jax_enable_x64", True) # type: ignore[no-untyped-call,unused-ignore] + + if library == Backend.JAX_GPU: + try: + device = jax.devices("cuda")[0] + except RuntimeError: + pytest.skip("no CUDA device available") + else: + device = jax.devices("cpu")[0] + jax.config.update("jax_default_device", device) + + @pytest.fixture(params=[Backend.DASK]) # Can select the test with `pytest -k dask` def da( request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch @@ -186,6 +190,17 @@ def da( return xp +@pytest.fixture(params=[Backend.JAX, Backend.JAX_GPU]) +def jnp( + request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch +) -> ModuleType: # numpydoc ignore=PR01,RT01 + """Variant of the `xp` fixture that only yields jax.numpy.""" + xp = pytest.importorskip("jax.numpy") + _setup_jax(request.param) + patch_lazy_xp_functions(request, monkeypatch, xp=xp) + return xp + + @pytest.fixture def device( library: Backend, xp: ModuleType diff --git a/tests/test_at.py b/tests/test_at.py index fa9bcdc8..7294a7c4 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -1,5 +1,4 @@ import math -import pickle from collections.abc import Callable, Generator from contextlib import contextmanager from types import ModuleType @@ -41,28 +40,11 @@ def at_op( just a workaround for when one wants to apply jax.jit to `at()` directly, which is not a common use case. """ - if isinstance(idx, (slice | tuple)): - return _at_op(x, None, pickle.dumps(idx), op, y, copy=copy, xp=xp) - return _at_op(x, idx, None, op, y, copy=copy, xp=xp) - - -def _at_op( - x: Array, - idx: SetIndex | None, - idx_pickle: bytes | None, - op: _AtOp, - y: Array | object, - copy: bool | None, - xp: ModuleType | None = None, -) -> Array: - """jitted helper of at_op""" - if idx_pickle: - idx = pickle.loads(idx_pickle) - meth = cast(Callable[..., Array], getattr(at(x, cast(SetIndex, idx)), op.value)) # type: ignore[explicit-any] + meth = cast(Callable[..., Array], getattr(at(x, idx), op.value)) # type: ignore[explicit-any] return meth(y, copy=copy, xp=xp) -lazy_xp_function(_at_op, static_argnames=("op", "idx_pickle", "copy", "xp")) +lazy_xp_function(at_op) @contextmanager diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 5f34bd60..4cd1718c 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -37,17 +37,17 @@ # some xp backends are untyped # mypy: disable-error-code=no-untyped-def -lazy_xp_function(apply_where, static_argnums=(2, 3), static_argnames="xp") -lazy_xp_function(atleast_nd, static_argnames=("ndim", "xp")) -lazy_xp_function(cov, static_argnames="xp") -lazy_xp_function(create_diagonal, static_argnames=("offset", "xp")) -lazy_xp_function(expand_dims, static_argnames=("axis", "xp")) -lazy_xp_function(kron, static_argnames="xp") -lazy_xp_function(nunique, static_argnames="xp") -lazy_xp_function(pad, static_argnames=("pad_width", "mode", "constant_values", "xp")) +lazy_xp_function(apply_where) +lazy_xp_function(atleast_nd) +lazy_xp_function(cov) +lazy_xp_function(create_diagonal) +lazy_xp_function(expand_dims) +lazy_xp_function(kron) +lazy_xp_function(nunique) +lazy_xp_function(pad) # FIXME calls in1d which calls xp.unique_values without size -lazy_xp_function(setdiff1d, jax_jit=False, static_argnames=("assume_unique", "xp")) -lazy_xp_function(sinc, static_argnames="xp") +lazy_xp_function(setdiff1d, jax_jit=False) +lazy_xp_function(sinc) class TestApplyWhere: diff --git a/tests/test_helpers.py b/tests/test_helpers.py index a104e93c..d2068f13 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -1,5 +1,5 @@ from types import ModuleType -from typing import cast +from typing import TYPE_CHECKING, Generic, TypeVar, cast import numpy as np import pytest @@ -13,18 +13,31 @@ capabilities, eager_shape, in1d, + jax_autojit, meta_namespace, ndindex, + pickle_flatten, + pickle_unflatten, ) from array_api_extra._lib._utils._typing import Array, Device, DType from array_api_extra.testing import lazy_xp_function from .conftest import np_compat +if TYPE_CHECKING: + # TODO import from typing (requires Python >=3.12) + from typing_extensions import override +else: + + def override(func): + return func + # mypy: disable-error-code=no-untyped-usage +T = TypeVar("T") + # FIXME calls xp.unique_values without size -lazy_xp_function(in1d, jax_jit=False, static_argnames=("assume_unique", "invert", "xp")) +lazy_xp_function(in1d, jax_jit=False) @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no unique_inverse") @@ -204,3 +217,185 @@ def test_capabilities(xp: ModuleType): if xp.__array_api_version__ >= "2024.12": expect.add("max dimensions") assert capabilities(xp).keys() == expect + + +class Wrapper(Generic[T]): + """Trivial opaque wrapper. Must be pickleable.""" + + x: T + # __slots__ make this object serializable with __reduce_ex__(5), + # but not with __reduce__ + __slots__: tuple[str, ...] = ("x",) + + def __init__(self, x: T): + self.x = x + + # Note: this makes the object not hashable + @override + def __eq__(self, other: object) -> bool: + return isinstance(other, Wrapper) and self.x == other.x + + +class TestPickleFlatten: + def test_roundtrip(self): + class NotSerializable: + @override + def __reduce__(self) -> tuple[object, ...]: + raise NotImplementedError() + + # Note: NotHashable() instances can be reduced to an + # unserializable local class + class NotHashable: + @override + def __eq__(self, other: object) -> bool: + return isinstance(other, type(self)) and other.__dict__ == self.__dict__ + + with pytest.raises(TypeError): + _ = hash(NotHashable()) + + # Extracted objects need be neither pickleable nor serializable + class C(NotSerializable, NotHashable): + x: int + + def __init__(self, x: int): + self.x = x + + class D(C): + pass + + c1 = C(1) + c2 = C(2) + d3 = D(3) + + # An assorted bunch of opaque containers, standard containers, + # non-serializable objects, and non-hashable objects (but not at the same time) + obj = Wrapper([1, c1, {2: (c2, {NotSerializable()})}, NotHashable(), d3]) + instances, rest = pickle_flatten(obj, C) + + assert instances == [c1, c2, d3] + obj2 = pickle_unflatten(instances, rest) + assert obj2 == obj + + def test_swap_objects(self): + class C: + pass + + obj = [1, C(), {2: (C(), {C()})}] + _, rest = pickle_flatten(obj, C) + obj2 = pickle_unflatten(["foo", "bar", "baz"], rest) + assert obj2 == [1, "foo", {2: ("bar", {"baz"})}] + + def test_multi_class(self): + class C: + pass + + class D: + pass + + c, d = C(), D() + instances, _ = pickle_flatten([c, d], (C, D)) + assert len(instances) == 2 + assert instances[0] is c + assert instances[1] is d + + def test_no_class(self): + obj = {1: "foo", 2: (3, 4)} + instances, rest = pickle_flatten(obj, ()) # type: ignore[var-annotated] + assert instances == [] + obj2 = pickle_unflatten([], rest) + assert obj2 == obj + + def test_flattened_stream(self): + """ + Test that multiple calls to flatten() can feed into the same stream of instances + """ + obj1 = Wrapper(1) + obj2 = [Wrapper(2), Wrapper(3)] + instances1, rest1 = pickle_flatten(obj1, Wrapper) + instances2, rest2 = pickle_flatten(obj2, Wrapper) + it = iter(instances1 + instances2 + [Wrapper(4)]) # pyright: ignore[reportUnknownArgumentType] + assert pickle_unflatten(it, rest1) == obj1 # pyright: ignore[reportUnknownArgumentType] + assert pickle_unflatten(it, rest2) == obj2 # pyright: ignore[reportUnknownArgumentType] + assert list(it) == [Wrapper(4)] # pyright: ignore[reportUnknownArgumentType] + + def test_too_short(self): + obj = [Wrapper(1), Wrapper(2)] + instances, rest = pickle_flatten(obj, Wrapper) + with pytest.raises(ValueError, match="Not enough"): + pickle_unflatten(instances[:1], rest) # pyright: ignore[reportUnknownArgumentType] + + def test_recursion(self): + obj: list[object] = [Wrapper(1)] + obj.append(obj) + + instances, rest = pickle_flatten(obj, Wrapper) + assert instances == [Wrapper(1)] + + obj2 = pickle_unflatten(instances, rest) # pyright: ignore[reportUnknownArgumentType] + assert len(obj2) == 2 + assert obj2[0] is obj[0] + assert obj2[1] is obj2 + + +class TestJAXAutoJIT: + def test_basic(self, jnp: ModuleType): + @jax_autojit + def f(x: Array, k: object = False) -> Array: + return x + 1 if k else x - 1 + + # Basic recognition of static_argnames + xp_assert_equal(f(jnp.asarray([1, 2])), jnp.asarray([0, 1])) + xp_assert_equal(f(jnp.asarray([1, 2]), False), jnp.asarray([0, 1])) + xp_assert_equal(f(jnp.asarray([1, 2]), True), jnp.asarray([2, 3])) + xp_assert_equal(f(jnp.asarray([1, 2]), 1), jnp.asarray([2, 3])) + + # static argument is not an ArrayLike + xp_assert_equal(f(jnp.asarray([1, 2]), "foo"), jnp.asarray([2, 3])) + + # static argument is not hashable, but serializable + xp_assert_equal(f(jnp.asarray([1, 2]), ["foo"]), jnp.asarray([2, 3])) + + def test_wrapper(self, jnp: ModuleType): + @jax_autojit + def f(w: Wrapper[Array]) -> Wrapper[Array]: + return Wrapper(w.x + 1) + + inp = Wrapper(jnp.asarray([1, 2])) + out = f(inp).x + xp_assert_equal(out, jnp.asarray([2, 3])) + + def test_static_hashable(self, jnp: ModuleType): + """Static argument/return value is hashable, but not serializable""" + + class C: + def __reduce__(self) -> object: # type: ignore[explicit-override,override] # pyright: ignore[reportIncompatibleMethodOverride,reportImplicitOverride] + raise Exception() + + @jax_autojit + def f(x: object) -> object: + return x + + inp = C() + out = f(inp) + assert out is inp + + # Serializable opaque input contains non-serializable object plus array + inp = Wrapper((C(), jnp.asarray([1, 2]))) + out = f(inp) + assert isinstance(out, Wrapper) + assert out.x[0] is inp.x[0] + assert out.x[1] is not inp.x[1] + xp_assert_equal(out.x[1], inp.x[1]) # pyright: ignore[reportUnknownArgumentType] + + def test_arraylikes_are_static(self): + pytest.importorskip("jax") + + @jax_autojit + def f(x: list[int]) -> list[int]: + assert isinstance(x, list) + assert x == [1, 2] + return [3, 4] + + out = f([1, 2]) + assert isinstance(out, list) + assert out == [3, 4] diff --git a/tests/test_lazy.py b/tests/test_lazy.py index f40df277..aef73301 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -15,9 +15,7 @@ from array_api_extra._lib._utils._typing import Array, Device from array_api_extra.testing import lazy_xp_function -lazy_xp_function( - lazy_apply, static_argnames=("func", "shape", "dtype", "as_numpy", "xp") -) +lazy_xp_function(lazy_apply) as_numpy = pytest.mark.parametrize( "as_numpy", @@ -386,7 +384,7 @@ def eager( ) -lazy_xp_function(check_lazy_apply_kwargs, static_argnames=("expect_cls", "as_numpy")) +lazy_xp_function(check_lazy_apply_kwargs) @as_numpy diff --git a/tests/test_testing.py b/tests/test_testing.py index adb77d20..51a7775e 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -263,32 +263,24 @@ def static_params(x: Array, n: int, flag: bool = False) -> Array: return x * 3.0 -def static_params1(x: Array, n: int, flag: bool = False) -> Array: - return static_params(x, n, flag) +lazy_xp_function(static_params) -def static_params2(x: Array, n: int, flag: bool = False) -> Array: - return static_params(x, n, flag) - - -def static_params3(x: Array, n: int, flag: bool = False) -> Array: - return static_params(x, n, flag) - - -lazy_xp_function(static_params1, static_argnums=(1, 2)) -lazy_xp_function(static_params2, static_argnames=("n", "flag")) -lazy_xp_function(static_params3, static_argnums=1, static_argnames="flag") +def test_lazy_xp_function_static_params(xp: ModuleType): + x = xp.asarray([1.0, 2.0]) + xp_assert_equal(static_params(x, 1), xp.asarray([3.0, 6.0])) + xp_assert_equal(static_params(x, 1, True), xp.asarray([2.0, 4.0])) + xp_assert_equal(static_params(x, 1, False), xp.asarray([3.0, 6.0])) + xp_assert_equal(static_params(x, 0, False), xp.asarray([3.0, 6.0])) + xp_assert_equal(static_params(x, 1, flag=True), xp.asarray([2.0, 4.0])) + xp_assert_equal(static_params(x, n=1, flag=True), xp.asarray([2.0, 4.0])) -@pytest.mark.parametrize("func", [static_params1, static_params2, static_params3]) -def test_lazy_xp_function_static_params(xp: ModuleType, func: Callable[..., Array]): # type: ignore[explicit-any] - x = xp.asarray([1.0, 2.0]) - xp_assert_equal(func(x, 1), xp.asarray([3.0, 6.0])) - xp_assert_equal(func(x, 1, True), xp.asarray([2.0, 4.0])) - xp_assert_equal(func(x, 1, False), xp.asarray([3.0, 6.0])) - xp_assert_equal(func(x, 0, False), xp.asarray([3.0, 6.0])) - xp_assert_equal(func(x, 1, flag=True), xp.asarray([2.0, 4.0])) - xp_assert_equal(func(x, n=1, flag=True), xp.asarray([2.0, 4.0])) +def test_lazy_xp_function_deprecated_static_argnames(): + with pytest.warns(DeprecationWarning, match="static_argnames"): + lazy_xp_function(static_params, static_argnames=["flag"]) # type: ignore[arg-type] # pyright: ignore[reportArgumentType] + with pytest.warns(DeprecationWarning, match="static_argnums"): + lazy_xp_function(static_params, static_argnums=[1]) # type: ignore[arg-type] # pyright: ignore[reportArgumentType] try: @@ -351,6 +343,66 @@ def test_lazy_xp_function_eagerly_raises(da: ModuleType): _ = dask_raises(x) +class Wrapper: + """Trivial opaque wrapper. Must be pickleable.""" + + x: Array + + def __init__(self, x: Array): + self.x = x + + +def check_opaque_wrapper(w: Wrapper, xp: ModuleType) -> Wrapper: + assert isinstance(w, Wrapper) + assert array_namespace(w.x) == xp + return Wrapper(w.x + 1) + + +lazy_xp_function(check_opaque_wrapper) + + +def test_lazy_xp_function_opaque_wrappers(xp: ModuleType): + """ + Test that function input and output can be wrapped into arbitrary + serializable Python objects, even if jax.jit does not support them. + """ + x = xp.asarray([1, 2]) + xp2 = array_namespace(x) # Revert NUMPY_READONLY to array_api_compat.numpy + res = check_opaque_wrapper(Wrapper(x), xp2) + xp_assert_equal(res.x, xp.asarray([2, 3])) + + +def test_lazy_xp_function_opaque_wrappers_eagerly_raise(da: ModuleType): + """ + Like `test_lazy_xp_function_eagerly_raises`, but the returned object is + wrapped in an opaque wrapper. + """ + x = da.arange(3) + with pytest.raises(ValueError, match="Hello world"): + _ = Wrapper(dask_raises(x)) + + +def check_recursive(x: list[object]) -> list[object]: + assert isinstance(x, list) + assert x[1] is x + y: list[object] = [cast(Array, x[0]) + 1] + y.append(y) + return y + + +lazy_xp_function(check_recursive) + + +def test_lazy_xp_function_recursive(xp: ModuleType): + """Test that inputs and outputs can be recursive data structures.""" + x: list[object] = [xp.asarray([1, 2])] + x.append(x) + y = check_recursive(x) + assert isinstance(y, list) + xp_assert_equal(cast(Array, y[0]), xp.asarray([2, 3])) + assert y[1] is y + + wrapped = ModuleType("wrapped") naked = ModuleType("naked") From 4d8953dc25aa8ef000b34651c5b10fb1c86205b5 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Sat, 17 May 2025 12:33:54 +0100 Subject: [PATCH 010/104] DOC: `autojit` notes (#297) --- src/array_api_extra/_lib/_utils/_helpers.py | 21 ++++++++++++++++++++- src/array_api_extra/testing.py | 1 + 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 99fcf65a..b856eb41 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -463,7 +463,7 @@ def pickle_unflatten(instances: Iterable[object], rest: FlattenRest) -> Any: # Notes ----- The `instances` iterable must yield at least the same number of elements as the ones - returned by ``pickle_without``, but the elements do not need to be the same objects + returned by ``pickle_flatten``, but the elements do not need to be the same objects or even the same types of objects. Excess elements, if any, will be left untouched. """ iters = iter(instances), iter(rest) @@ -540,6 +540,25 @@ def jax_autojit( See Also -------- jax.jit : JAX JIT compilation function. + + Notes + ----- + These are useful choices *for testing purposes only*, which is how this function is + intended to be used. The output of ``jax.jit`` is a C++ level callable, that + directly dispatches to the compiled kernel after the initial call. In comparison, + ``jax_autojit`` incurs a much higher dispatch time. + + Additionally, consider:: + + def f(x: Array, y: float, plus: bool) -> Array: + return x + y if plus else x - y + + j1 = jax.jit(f, static_argnames="plus") + j2 = jax_autojit(f) + + In the above example, ``j2`` requires a lot less setup to be tested effectively than + ``j1``, but on the flip side it means that it will be re-traced for every different + value of ``y``, which likely makes it not fit for purpose in production. """ import jax diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index c14e9a22..3979f9dd 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -96,6 +96,7 @@ def lazy_xp_function( # type: ignore[explicit-any] jax_jit : bool, optional Set to True to replace `func` with a smart variant of ``jax.jit(func)`` after calling the :func:`patch_lazy_xp_functions` test helper with ``xp=jax.numpy``. + This is the default behaviour. Set to False if `func` is only compatible with eager (non-jitted) JAX. Unlike with vanilla ``jax.jit``, all arguments and return types that are not JAX From e4ecb82cad8b22bd58f1808ee1021793adc354f8 Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Sat, 17 May 2025 13:14:55 +0100 Subject: [PATCH 011/104] docs: add pearu as a contributor for review (#298) * docs: update README.md * docs: update CONTRIBUTORS.md * docs: update .all-contributorsrc --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> --- .all-contributorsrc | 9 +++++++++ CONTRIBUTORS.md | 1 + README.md | 1 + 3 files changed, 11 insertions(+) diff --git a/.all-contributorsrc b/.all-contributorsrc index 5e5e6b0b..561259e2 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -239,6 +239,15 @@ "bug", "tool" ] + }, + { + "login": "pearu", + "name": "Pearu Peterson", + "avatar_url": "https://avatars.githubusercontent.com/u/402156?v=4", + "profile": "https://github.com/pearu", + "contributions": [ + "review" + ] } ] } diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index 36d50b0d..b0f2ffb6 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -37,6 +37,7 @@ This project exists thanks to the following contributors Thomas Li
Thomas Li
🐛 🔧 + Pearu Peterson
Pearu Peterson
👀 diff --git a/README.md b/README.md index 3fe7e3eb..65d19699 100644 --- a/README.md +++ b/README.md @@ -92,6 +92,7 @@ This project exists thanks to the following contributors Thomas Li
Thomas Li
🐛 🔧 + Pearu Peterson
Pearu Peterson
👀 From 11b535c944d5e70186028837cebe226d452ffa60 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Sun, 18 May 2025 12:49:18 +0100 Subject: [PATCH 012/104] TST: rework tests for xp_assert_equal --- tests/test_testing.py | 271 ++++++++++++++++++++---------------------- 1 file changed, 132 insertions(+), 139 deletions(-) diff --git a/tests/test_testing.py b/tests/test_testing.py index 51a7775e..0cd117c2 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -1,5 +1,4 @@ from collections.abc import Callable -from contextlib import nullcontext from types import ModuleType from typing import cast @@ -21,23 +20,9 @@ from array_api_extra._lib._utils._typing import Array, Device from array_api_extra.testing import lazy_xp_function -# mypy: disable-error-code=decorated-any +# mypy: disable-error-code="decorated-any, explicit-any" # pyright: reportUnknownParameterType=false,reportMissingParameterType=false -param_assert_equal_close = pytest.mark.parametrize( - "func", - [ - xp_assert_equal, - xp_assert_less, - pytest.param( - xp_assert_close, - marks=pytest.mark.xfail_xp_backend( - Backend.SPARSE, reason="no isdtype", strict=False - ), - ), - ], -) - def test_as_numpy_array(xp: ModuleType, device: Device): x = xp.asarray([1, 2, 3], device=device) @@ -45,136 +30,144 @@ def test_as_numpy_array(xp: ModuleType, device: Device): assert isinstance(y, np.ndarray) -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype", strict=False) -@pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close]) -def test_assert_close_equal_basic(xp: ModuleType, func: Callable[..., None]): # type: ignore[explicit-any] - func(xp.asarray(0), xp.asarray(0)) - func(xp.asarray([1, 2]), xp.asarray([1, 2])) - - with pytest.raises(AssertionError, match="shapes do not match"): - func(xp.asarray([0]), xp.asarray([[0]])) - - with pytest.raises(AssertionError, match="dtypes do not match"): - func(xp.asarray(0, dtype=xp.float32), xp.asarray(0, dtype=xp.float64)) - - with pytest.raises(AssertionError): - func(xp.asarray([1, 2]), xp.asarray([1, 3])) - - with pytest.raises(AssertionError, match="hello"): - func(xp.asarray([1, 2]), xp.asarray([1, 3]), err_msg="hello") - - -@pytest.mark.skip_xp_backend(Backend.NUMPY, reason="test other ns vs. numpy") -@pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="test other ns vs. numpy") -@pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) -def test_assert_close_equal_less_namespace(xp: ModuleType, func: Callable[..., None]): # type: ignore[explicit-any] - with pytest.raises(AssertionError, match="namespaces do not match"): - func(xp.asarray(0), np.asarray(0)) - with pytest.raises(TypeError, match="Unrecognized array input"): - func(xp.asarray(0), 0) - with pytest.raises(TypeError, match="list is not a supported array type"): - func(xp.asarray([0]), [0]) - - -@param_assert_equal_close -@pytest.mark.parametrize("check_shape", [False, True]) -def test_assert_close_equal_less_shape( # type: ignore[explicit-any] - xp: ModuleType, - func: Callable[..., None], - check_shape: bool, -): - context = ( - pytest.raises(AssertionError, match="shapes do not match") - if check_shape - else nullcontext() - ) - with context: - # note: NaNs are handled by all 3 checks - func(xp.asarray([xp.nan, xp.nan]), xp.asarray(xp.nan), check_shape=check_shape) - - -@param_assert_equal_close -@pytest.mark.parametrize("check_dtype", [False, True]) -def test_assert_close_equal_less_dtype( # type: ignore[explicit-any] - xp: ModuleType, - func: Callable[..., None], - check_dtype: bool, -): - context = ( - pytest.raises(AssertionError, match="dtypes do not match") - if check_dtype - else nullcontext() - ) - with context: - func( - xp.asarray(xp.nan, dtype=xp.float32), - xp.asarray(xp.nan, dtype=xp.float64), - check_dtype=check_dtype, - ) - - -@pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) -@pytest.mark.parametrize("check_scalar", [False, True]) -def test_assert_close_equal_less_scalar( # type: ignore[explicit-any] - xp: ModuleType, - func: Callable[..., None], - check_scalar: bool, -): - context = ( - pytest.raises(AssertionError, match="array-ness does not match") - if check_scalar - else nullcontext() +class TestAssertEqualCloseLess: + pr_assert_close = pytest.param( # pyright: ignore[reportUnannotatedClassAttribute] + xp_assert_close, + marks=pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype"), ) - with context: - func(np.asarray(xp.nan), np.asarray(xp.nan)[()], check_scalar=check_scalar) + @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close]) + def test_assert_equal_close_basic(self, xp: ModuleType, func: Callable[..., None]): + func(xp.asarray(0), xp.asarray(0)) + func(xp.asarray([1, 2]), xp.asarray([1, 2])) -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") -def test_assert_close_tolerance(xp: ModuleType): - xp_assert_close(xp.asarray([100.0]), xp.asarray([102.0]), rtol=0.03) - with pytest.raises(AssertionError): - xp_assert_close(xp.asarray([100.0]), xp.asarray([102.0]), rtol=0.01) + with pytest.raises(AssertionError, match="Mismatched elements"): + func(xp.asarray([1, 2]), xp.asarray([2, 1])) - xp_assert_close(xp.asarray([100.0]), xp.asarray([102.0]), atol=3) - with pytest.raises(AssertionError): - xp_assert_close(xp.asarray([100.0]), xp.asarray([102.0]), atol=1) + with pytest.raises(AssertionError, match="hello"): + func(xp.asarray([1, 2]), xp.asarray([2, 1]), err_msg="hello") + @pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) + def test_shape_dtype(self, xp: ModuleType, func: Callable[..., None]): + with pytest.raises(AssertionError, match="shapes do not match"): + func(xp.asarray([0]), xp.asarray([[0]])) -def test_assert_less_basic(xp: ModuleType): - xp_assert_less(xp.asarray(-1), xp.asarray(0)) - xp_assert_less(xp.asarray([1, 2]), xp.asarray([2, 3])) - with pytest.raises(AssertionError): - xp_assert_less(xp.asarray([1, 1]), xp.asarray([2, 1])) - with pytest.raises(AssertionError, match="hello"): - xp_assert_less(xp.asarray([1, 1]), xp.asarray([2, 1]), err_msg="hello") + with pytest.raises(AssertionError, match="dtypes do not match"): + func(xp.asarray(0, dtype=xp.float32), xp.asarray(0, dtype=xp.float64)) - -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="index by sparse array") -@pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="boolean indexing") -@pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close]) -def test_assert_close_equal_none_shape(xp: ModuleType, func: Callable[..., None]): # type: ignore[explicit-any] - """On Dask and other lazy backends, test that a shape with NaN's or None's - can be compared to a real shape. - """ - a = xp.asarray([1, 2]) - a = a[a > 1] - - func(a, xp.asarray([2])) - with pytest.raises(AssertionError): - func(a, xp.asarray([2, 3])) - with pytest.raises(AssertionError): - func(a, xp.asarray(2)) - with pytest.raises(AssertionError): - func(a, xp.asarray([3])) - - # Swap actual and desired - func(xp.asarray([2]), a) - with pytest.raises(AssertionError): - func(xp.asarray([2, 3]), a) - with pytest.raises(AssertionError): - func(xp.asarray(2), a) - with pytest.raises(AssertionError): - func(xp.asarray([3]), a) + @pytest.mark.skip_xp_backend(Backend.NUMPY, reason="test other ns vs. numpy") + @pytest.mark.skip_xp_backend( + Backend.NUMPY_READONLY, reason="test other ns vs. numpy" + ) + @pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) + def test_namespace(self, xp: ModuleType, func: Callable[..., None]): + with pytest.raises(AssertionError, match="namespaces do not match"): + func(xp.asarray(0), np.asarray(0)) + with pytest.raises(TypeError, match="Unrecognized array input"): + func(xp.asarray(0), 0) + with pytest.raises(TypeError, match="list is not a supported array type"): + func(xp.asarray([0]), [0]) + + @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close, xp_assert_less]) + def test_check_shape(self, xp: ModuleType, func: Callable[..., None]): + a = xp.asarray([1] if func is xp_assert_less else [2]) + b = xp.asarray(2) + c = xp.asarray(0) + d = xp.asarray([2, 2]) + + with pytest.raises(AssertionError, match="shapes do not match"): + func(a, b) + func(a, b, check_shape=False) + with pytest.raises(AssertionError, match="Mismatched elements"): + func(a, c, check_shape=False) + with pytest.raises(AssertionError, match=r"shapes \(1,\), \(2,\) mismatch"): + func(a, d, check_shape=False) + + @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close, xp_assert_less]) + def test_check_dtype(self, xp: ModuleType, func: Callable[..., None]): + a = xp.asarray(1 if func is xp_assert_less else 2) + b = xp.asarray(2, dtype=xp.int16) + c = xp.asarray(0, dtype=xp.int16) + + with pytest.raises(AssertionError, match="dtypes do not match"): + func(a, b) + func(a, b, check_dtype=False) + with pytest.raises(AssertionError, match="Mismatched elements"): + func(a, c, check_dtype=False) + + @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close, xp_assert_less]) + @pytest.mark.xfail_xp_backend( + Backend.SPARSE, reason="sparse [()] returns np.generic" + ) + def test_check_scalar( + self, xp: ModuleType, library: Backend, func: Callable[..., None] + ): + a = xp.asarray(1 if func is xp_assert_less else 2) + b = xp.asarray(2)[()] # Note: only makes a difference on NumPy + c = xp.asarray(0) + + func(a, b) + if library.like(Backend.NUMPY): + with pytest.raises(AssertionError, match="array-ness does not match"): + func(a, b, check_scalar=True) + else: + func(a, b, check_scalar=True) + with pytest.raises(AssertionError, match="Mismatched elements"): + func(a, c, check_scalar=True) + + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") + @pytest.mark.parametrize("dtype", ["int64", "float64"]) + def test_assert_close_tolerance(self, dtype: str, xp: ModuleType): + a = xp.asarray([100], dtype=getattr(xp, dtype)) + b = xp.asarray([102], dtype=getattr(xp, dtype)) + + with pytest.raises(AssertionError, match="Mismatched elements"): + xp_assert_close(a, b) + + xp_assert_close(a, b, rtol=0.03) + with pytest.raises(AssertionError, match="Mismatched elements"): + xp_assert_close(a, b, rtol=0.01) + + xp_assert_close(a, b, atol=3) + with pytest.raises(AssertionError, match="Mismatched elements"): + xp_assert_close(a, b, atol=1) + + def test_assert_less(self, xp: ModuleType): + xp_assert_less(xp.asarray(-1), xp.asarray(0)) + xp_assert_less(xp.asarray([1, 2]), xp.asarray([2, 3])) + with pytest.raises(AssertionError, match="Mismatched elements"): + xp_assert_less(xp.asarray([1, 1]), xp.asarray([2, 1])) + + @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close, xp_assert_less]) + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="index by sparse array") + @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="boolean indexing") + def test_none_shape(self, xp: ModuleType, func: Callable[..., None]): + """On Dask and other lazy backends, test that a shape with NaN's or None's + can be compared to a real shape. + """ + # actual has shape=(None, ) + a = xp.asarray([1] if func is xp_assert_less else [2]) + a = a[a > 0] + + func(a, xp.asarray([2])) + with pytest.raises(AssertionError, match="shapes do not match"): + func(a, xp.asarray(2)) + with pytest.raises(AssertionError, match="shapes do not match"): + func(a, xp.asarray([2, 3])) + with pytest.raises(AssertionError, match="Mismatched elements"): + func(a, xp.asarray([0])) + + # desired has shape=(None, ) + a = xp.asarray([3] if func is xp_assert_less else [2]) + a = a[a > 0] + + func(xp.asarray([2]), a) + with pytest.raises(AssertionError, match="shapes do not match"): + func(xp.asarray(2), a) + with pytest.raises(AssertionError, match="shapes do not match"): + func(xp.asarray([2, 3]), a) + with pytest.raises(AssertionError, match="Mismatched elements"): + func(xp.asarray([4]), a) def good_lazy(x: Array) -> Array: From e2762f5f3db5e07a1ddd6e1d4473bd72aa09cb2d Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Mon, 19 May 2025 04:29:35 +0000 Subject: [PATCH 013/104] deps: Update dependency pylint to >=3.3.7 (#302) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 92 +++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 47 insertions(+), 47 deletions(-) diff --git a/pixi.lock b/pixi.lock index a95291d1..c58f985a 100644 --- a/pixi.lock +++ b/pixi.lock @@ -30,7 +30,7 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda - conda: https://prefix.dev/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda - conda: 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".", editable = true } [tool.pixi.feature.lint.dependencies] typing-extensions = ">=4.13.2" pre-commit = ">=4.2.0" -pylint = ">=3.3.6" +pylint = ">=3.3.7" basedmypy = ">=2.10.0" basedpyright = ">=1.29.1" numpydoc = ">=1.8.0,<2" From 27fbd9c6262ed7c547f17e247e9e21eaddf89576 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Mon, 19 May 2025 08:52:22 +0100 Subject: [PATCH 014/104] ENH: support PyTorch `device='meta'` (#300) --- src/array_api_extra/_lib/_funcs.py | 4 +- src/array_api_extra/_lib/_testing.py | 44 ++++++++++++++++----- src/array_api_extra/_lib/_utils/_helpers.py | 14 ++++++- tests/conftest.py | 8 ++-- tests/test_funcs.py | 6 +-- tests/test_helpers.py | 30 +++++++++++--- tests/test_lazy.py | 3 ++ tests/test_testing.py | 31 ++++++++++++--- 8 files changed, 111 insertions(+), 29 deletions(-) diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index bb39775f..645f7a1b 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -153,7 +153,7 @@ def _apply_where( # type: ignore[explicit-any] # numpydoc ignore=PR01,RT01 ) -> Array: """Helper of `apply_where`. On Dask, this runs on a single chunk.""" - if not capabilities(xp)["boolean indexing"]: + if not capabilities(xp, device=_compat.device(cond))["boolean indexing"]: # jax.jit does not support assignment by boolean mask return xp.where(cond, f1(*args), f2(*args) if f2 is not None else fill_value) @@ -716,7 +716,7 @@ def nunique(x: Array, /, *, xp: ModuleType | None = None) -> Array: # 2. backend has unique_counts and it returns a None-sized array; # e.g. Dask, ndonnx # 3. backend does not have unique_counts; e.g. wrapped JAX - if capabilities(xp)["data-dependent shapes"]: + if capabilities(xp, device=_compat.device(x))["data-dependent shapes"]: # xp has unique_counts; O(n) complexity _, counts = xp.unique_counts(x) n = _compat.size(counts) diff --git a/src/array_api_extra/_lib/_testing.py b/src/array_api_extra/_lib/_testing.py index c60cf466..16a9d102 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -22,6 +22,7 @@ is_jax_namespace, is_numpy_namespace, is_pydata_sparse_namespace, + is_torch_array, is_torch_namespace, to_device, ) @@ -62,18 +63,28 @@ def _check_ns_shape_dtype( msg = f"namespaces do not match: {actual_xp} != f{desired_xp}" assert actual_xp == desired_xp, msg - if check_shape: - actual_shape = actual.shape - desired_shape = desired.shape - if is_dask_namespace(desired_xp): - # Dask uses nan instead of None for unknown shapes - if any(math.isnan(i) for i in cast(tuple[float, ...], actual_shape)): - actual_shape = actual.compute().shape # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] - if any(math.isnan(i) for i in cast(tuple[float, ...], desired_shape)): - desired_shape = desired.compute().shape # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + # Dask uses nan instead of None for unknown shapes + actual_shape = cast(tuple[float, ...], actual.shape) + desired_shape = cast(tuple[float, ...], desired.shape) + assert None not in actual_shape # Requires explicit support + assert None not in desired_shape + if is_dask_namespace(desired_xp): + if any(math.isnan(i) for i in actual_shape): + actual_shape = actual.compute().shape # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + if any(math.isnan(i) for i in desired_shape): + desired_shape = desired.compute().shape # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + if check_shape: msg = f"shapes do not match: {actual_shape} != f{desired_shape}" assert actual_shape == desired_shape, msg + else: + # Ignore shape, but check flattened size. This is normally done by + # np.testing.assert_array_equal etc even when strict=False, but not for + # non-materializable arrays. + actual_size = math.prod(actual_shape) # pyright: ignore[reportUnknownArgumentType] + desired_size = math.prod(desired_shape) # pyright: ignore[reportUnknownArgumentType] + msg = f"sizes do not match: {actual_size} != f{desired_size}" + assert actual_size == desired_size, msg if check_dtype: msg = f"dtypes do not match: {actual.dtype} != {desired.dtype}" @@ -90,6 +101,15 @@ def _check_ns_shape_dtype( return desired_xp +def _is_materializable(x: Array) -> bool: + """ + Return True if you can call `as_numpy_array(x)`; False otherwise. + """ + # Important: here we assume that we're not tracing - + # e.g. we're not inside `jax.jit`` nor `cupy.cuda.Stream.begin_capture`. + return not is_torch_array(x) or x.device.type != "meta" # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + + def as_numpy_array(array: Array, *, xp: ModuleType) -> np.typing.NDArray[Any]: # type: ignore[explicit-any] """ Convert array to NumPy, bypassing GPU-CPU transfer guards and densification guards. @@ -146,6 +166,8 @@ def xp_assert_equal( numpy.testing.assert_array_equal : Similar function for NumPy arrays. """ xp = _check_ns_shape_dtype(actual, desired, check_dtype, check_shape, check_scalar) + if not _is_materializable(actual): + return actual_np = as_numpy_array(actual, xp=xp) desired_np = as_numpy_array(desired, xp=xp) np.testing.assert_array_equal(actual_np, desired_np, err_msg=err_msg) @@ -181,6 +203,8 @@ def xp_assert_less( numpy.testing.assert_array_equal : Similar function for NumPy arrays. """ xp = _check_ns_shape_dtype(x, y, check_dtype, check_shape, check_scalar) + if not _is_materializable(x): + return x_np = as_numpy_array(x, xp=xp) y_np = as_numpy_array(y, xp=xp) np.testing.assert_array_less(x_np, y_np, err_msg=err_msg) @@ -229,6 +253,8 @@ def xp_assert_close( The default `atol` and `rtol` differ from `xp.all(xpx.isclose(a, b))`. """ xp = _check_ns_shape_dtype(actual, desired, check_dtype, check_shape, check_scalar) + if not _is_materializable(actual): + return if rtol is None: if xp.isdtype(actual.dtype, ("real floating", "complex floating")): diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index b856eb41..f4997dd3 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -29,8 +29,9 @@ is_jax_namespace, is_numpy_array, is_pydata_sparse_namespace, + is_torch_namespace, ) -from ._typing import Array +from ._typing import Array, Device if TYPE_CHECKING: # pragma: no cover # TODO import from typing (requires Python >=3.12 and >=3.13) @@ -300,7 +301,7 @@ def meta_namespace( return array_namespace(*metas) -def capabilities(xp: ModuleType) -> dict[str, int]: +def capabilities(xp: ModuleType, *, device: Device | None = None) -> dict[str, int]: """ Return patched ``xp.__array_namespace_info__().capabilities()``. @@ -311,6 +312,8 @@ def capabilities(xp: ModuleType) -> dict[str, int]: ---------- xp : array_namespace The standard-compatible namespace. + device : Device, optional + The device to use. Returns ------- @@ -326,6 +329,13 @@ def capabilities(xp: ModuleType) -> dict[str, int]: # Fixed in jax >=0.6.0 out = out.copy() out["boolean indexing"] = False + if is_torch_namespace(xp): + # FIXME https://github.com/data-apis/array-api/issues/945 + device = xp.get_default_device() if device is None else xp.device(device) + if device.type == "meta": # type: ignore[union-attr] # pyright: ignore[reportAttributeAccessIssue,reportOptionalMemberAccess] + out = out.copy() + out["boolean indexing"] = False + out["data-dependent shapes"] = False return out diff --git a/tests/conftest.py b/tests/conftest.py index 372f9960..bb72139b 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -211,7 +211,9 @@ def device( Where possible, return a device that is not the default one. """ if library == Backend.ARRAY_API_STRICT: - d = xp.Device("device1") - assert get_device(xp.empty(0)) != d - return d + return xp.Device("device1") + if library == Backend.TORCH: + return xp.device("meta") + if library == Backend.TORCH_GPU: + return xp.device("cpu") return get_device(xp.empty(0)) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 4cd1718c..7c138442 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -731,9 +731,6 @@ def test_device(self, xp: ModuleType, device: Device, equal_nan: bool): b = xp.asarray([1e-9, 1e-4, xp.nan], device=device) res = isclose(a, b, equal_nan=equal_nan) assert get_device(res) == device - xp_assert_equal( - isclose(a, b, equal_nan=equal_nan), xp.asarray([True, False, equal_nan]) - ) class TestKron: @@ -996,6 +993,9 @@ def test_all_python_scalars(self, assume_unique: bool): _ = setdiff1d(0, 0, assume_unique=assume_unique) @assume_unique + @pytest.mark.skip_xp_backend( + Backend.TORCH, reason="device='meta' does not support unknown shapes" + ) def test_device(self, xp: ModuleType, device: Device, assume_unique: bool): x1 = xp.asarray([3, 8, 20], device=device) x2 = xp.asarray([2, 3, 4], device=device) diff --git a/tests/test_helpers.py b/tests/test_helpers.py index d2068f13..b1b6ddba 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -212,11 +212,31 @@ def test_xp(self, xp: ModuleType): assert meta_namespace(*args, xp=xp) in (xp, np_compat) -def test_capabilities(xp: ModuleType): - expect = {"boolean indexing", "data-dependent shapes"} - if xp.__array_api_version__ >= "2024.12": - expect.add("max dimensions") - assert capabilities(xp).keys() == expect +class TestCapabilities: + def test_basic(self, xp: ModuleType): + expect = {"boolean indexing", "data-dependent shapes"} + if xp.__array_api_version__ >= "2024.12": + expect.add("max dimensions") + assert capabilities(xp).keys() == expect + + def test_device(self, xp: ModuleType, library: Backend, device: Device): + expect_keys = {"boolean indexing", "data-dependent shapes"} + if xp.__array_api_version__ >= "2024.12": + expect_keys.add("max dimensions") + assert capabilities(xp, device=device).keys() == expect_keys + + if library.like(Backend.TORCH): + # The output of capabilities is device-specific. + + # Test that device=None gets the current default device. + expect = capabilities(xp, device=device) + with xp.device(device): + actual = capabilities(xp) + assert actual == expect + + # Test that we're accepting anything that is accepted by the + # device= parameter in other functions + actual = capabilities(xp, device=device.type) # type: ignore[attr-defined] # pyright: ignore[reportUnknownArgumentType,reportAttributeAccessIssue] class Wrapper(Generic[T]): diff --git a/tests/test_lazy.py b/tests/test_lazy.py index aef73301..f97062f0 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -278,6 +278,9 @@ def test_lazy_apply_none_shape_broadcast(xp: ModuleType): Backend.ARRAY_API_STRICT, reason="device->host copy" ), pytest.mark.skip_xp_backend(Backend.CUPY, reason="device->host copy"), + pytest.mark.skip_xp_backend( + Backend.TORCH, reason="materialize 'meta' device" + ), pytest.mark.skip_xp_backend( Backend.TORCH_GPU, reason="device->host copy" ), diff --git a/tests/test_testing.py b/tests/test_testing.py index 0cd117c2..b195a65b 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -24,10 +24,17 @@ # pyright: reportUnknownParameterType=false,reportMissingParameterType=false -def test_as_numpy_array(xp: ModuleType, device: Device): - x = xp.asarray([1, 2, 3], device=device) - y = as_numpy_array(x, xp=xp) - assert isinstance(y, np.ndarray) +class TestAsNumPyArray: + def test_basic(self, xp: ModuleType): + x = xp.asarray([1, 2, 3]) + y = as_numpy_array(x, xp=xp) + xp_assert_equal(y, np.asarray([1, 2, 3])) # type: ignore[arg-type] # pyright: ignore[reportArgumentType] + + @pytest.mark.skip_xp_backend(Backend.TORCH, reason="materialize 'meta' device") + def test_device(self, xp: ModuleType, device: Device): + x = xp.asarray([1, 2, 3], device=device) + y = as_numpy_array(x, xp=xp) + xp_assert_equal(y, np.asarray([1, 2, 3])) # type: ignore[arg-type] # pyright: ignore[reportArgumentType] class TestAssertEqualCloseLess: @@ -80,7 +87,7 @@ def test_check_shape(self, xp: ModuleType, func: Callable[..., None]): func(a, b, check_shape=False) with pytest.raises(AssertionError, match="Mismatched elements"): func(a, c, check_shape=False) - with pytest.raises(AssertionError, match=r"shapes \(1,\), \(2,\) mismatch"): + with pytest.raises(AssertionError, match="sizes do not match"): func(a, d, check_shape=False) @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close, xp_assert_less]) @@ -169,6 +176,20 @@ def test_none_shape(self, xp: ModuleType, func: Callable[..., None]): with pytest.raises(AssertionError, match="Mismatched elements"): func(xp.asarray([4]), a) + @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close, xp_assert_less]) + def test_device(self, xp: ModuleType, device: Device, func: Callable[..., None]): + a = xp.asarray([1] if func is xp_assert_less else [2], device=device) + b = xp.asarray([2], device=device) + c = xp.asarray([2, 2], device=device) + + func(a, b) + with pytest.raises(AssertionError, match="shapes do not match"): + func(a, c) + # This is normally performed by np.testing.assert_array_equal etc. + # but in case of torch device='meta' we have to do it manually + with pytest.raises(AssertionError, match="sizes do not match"): + func(a, c, check_shape=False) + def good_lazy(x: Array) -> Array: """A function that behaves well in Dask and jax.jit""" From 0979f26900990f12fdb681e0326a0de5f07f3725 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 29 May 2025 18:15:29 +0100 Subject: [PATCH 015/104] deps: Update dependency pytorch to >=2.7.0 (#299) --- pixi.lock | 192 ++++++++++++++++++++++++++----------------------- pyproject.toml | 6 +- 2 files changed, 105 insertions(+), 93 deletions(-) diff --git a/pixi.lock b/pixi.lock index c58f985a..29340074 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1334,7 +1334,7 @@ environments: - conda: https://prefix.dev/conda-forge/win-64/cuda-cupti-12.9.19-he0c23c2_0.conda - conda: https://prefix.dev/conda-forge/win-64/cuda-nvrtc-12.9.41-he0c23c2_0.conda - conda: https://prefix.dev/conda-forge/noarch/cuda-version-12.9-h4f385c5_3.conda - - conda: https://prefix.dev/conda-forge/win-64/cudnn-9.10.0.56-hffc9a7f_0.conda + - conda: https://prefix.dev/conda-forge/win-64/cudnn-9.10.1.4-h1361d0a_0.conda - conda: https://prefix.dev/conda-forge/win-64/cupy-13.4.1-py310h1203e13_0.conda - conda: https://prefix.dev/conda-forge/win-64/cupy-core-13.4.1-py310h9d4bcf3_0.conda - conda: https://prefix.dev/conda-forge/noarch/dask-core-2025.5.0-pyhd8ed1ab_0.conda @@ -1366,8 +1366,8 @@ environments: - conda: https://prefix.dev/conda-forge/win-64/libblas-3.9.0-31_h641d27c_mkl.conda - conda: https://prefix.dev/conda-forge/win-64/libcblas-3.9.0-31_h5e41251_mkl.conda - conda: https://prefix.dev/conda-forge/win-64/libcublas-12.9.0.13-he0c23c2_0.conda - - conda: https://prefix.dev/conda-forge/win-64/libcudnn-9.10.0.56-hffc9a7f_0.conda - 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pkg:pypi/torch?source=hash-mapping - size: 23555333 - timestamp: 1746268961298 + size: 23684707 + timestamp: 1748513257167 - conda: https://prefix.dev/conda-forge/noarch/pytz-2025.2-pyhd8ed1ab_0.conda sha256: 8d2a8bf110cc1fc3df6904091dead158ba3e614d8402a83e51ed3a8aa93cdeb0 md5: bc8e3267d44011051f2eb14d22fb0960 diff --git a/pyproject.toml b/pyproject.toml index 3d3e22e1..485b0816 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -134,7 +134,7 @@ numpy = "=1.22.0" # Backends that can run on CPU-only hosts # Note: JAX and PyTorch will install CPU variants. [tool.pixi.feature.backends.dependencies] -pytorch = ">=2.6.0" +pytorch = ">=2.7.0" dask-core = ">=2025.5.0" # No distributed, tornado, etc. sparse = ">=0.16.0" @@ -162,7 +162,7 @@ system-requirements = { cuda = "12" } [tool.pixi.feature.cuda-backends.target.linux-64.dependencies] cupy = ">=13.4.1" jaxlib = { version = ">=0.5.2", build = "cuda12*" } -pytorch = { version = ">=2.6.0", build = "cuda12*" } +pytorch = { version = ">=2.7.0", build = "cuda12*" } [tool.pixi.feature.cuda-backends.target.osx-64.dependencies] # cupy = "*" # unavailable @@ -177,7 +177,7 @@ pytorch = { version = ">=2.6.0", build = "cuda12*" } [tool.pixi.feature.cuda-backends.target.win-64.dependencies] cupy = ">=13.4.1" # jaxlib = { version = "*", build = "cuda12*" } # unavailable -pytorch = { version = ">=2.6.0", build = "cuda12*" } +pytorch = { version = ">=2.7.0", build = "cuda12*" } [tool.pixi.environments] default = { features = ["py313"], solve-group = "py313" } From dd7650aa737f4ded37e5d406067f117e05035ec3 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sat, 31 May 2025 20:20:56 +0000 Subject: [PATCH 016/104] deps: Update dependency jaxlib to >=0.5.3 (#309) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 105 +++++++++++++++++++++++++++++-------------------- pyproject.toml | 2 +- 2 files changed, 63 insertions(+), 44 deletions(-) diff --git a/pixi.lock b/pixi.lock index 29340074..3ce120cf 100644 --- a/pixi.lock +++ b/pixi.lock @@ -794,7 +794,7 @@ environments: - 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conda: https://prefix.dev/conda-forge/linux-64/numba-0.61.2-py310h699fe88_0.conda @@ -3915,7 +3915,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.0.dev0 - sha256: 3a4a70c9c4bbfdc6af7247ea160a1cd6eb9d0ece6b59f6a4acdf82fef1414af4 + sha256: a3296bd31e0640360736388accc9305ee606fe6cafb22b8fdd7492fa96a57cf8 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' @@ -4956,21 +4956,21 @@ packages: purls: [] size: 21578 timestamp: 1746134436166 -- conda: https://prefix.dev/conda-forge/linux-64/cudnn-9.10.0.56-hcd2ec93_0.conda - sha256: 77ad964a70402885989a32824c5d626b78978a0d0b9a2453f350d3a57fada44f - md5: 5539c6138d1cb5f91acb1da3673b9e88 +- conda: https://prefix.dev/conda-forge/linux-64/cudnn-9.10.1.4-h7646684_0.conda + sha256: 746cfa7c0e9b9eba3429465cf9a70786a63da2f4b2c322c33d74b5ff2db6d8ae + md5: 5aa5b04b995ebe10fe44de6fe93b1850 depends: - __glibc >=2.28,<3.0.a0 - cuda-version >=12,<13.0a0 - - libcudnn-dev 9.10.0.56 hcd2ec93_0 + - libcudnn-dev 9.10.1.4 hcd2ec93_0 - libgcc >=13 - libstdcxx >=13 constrains: - cudnn-jit <0a license: LicenseRef-cuDNN-Software-License-Agreement purls: [] - size: 19362 - timestamp: 1747077048802 + size: 19516 + timestamp: 1747774432049 - conda: https://prefix.dev/conda-forge/win-64/cudnn-9.10.1.4-h1361d0a_0.conda sha256: 55d225f9012cd145c5ccb9a1d72b9070d303b9657b8fd4c12fa5071e5ed118fa md5: faf9d123cfd4cd6d6b18484380cdbfb6 @@ -5546,6 +5546,25 @@ packages: - pkg:pypi/jax?source=hash-mapping size: 1556886 timestamp: 1741182198677 +- conda: https://prefix.dev/conda-forge/noarch/jax-0.6.0-pyhd8ed1ab_0.conda + sha256: 573a5582dfba84a8f67c351b6218cb9579cb8d0f6d4b4186a806852111d4a6f1 + md5: bd364feb12c744cf5c60e1e5b586171b + depends: + - importlib-metadata >=4.6 + - jaxlib >=0.6.0,<=0.6.0 + - ml_dtypes >=0.5.0 + - numpy >=1.25 + - opt_einsum + - python >=3.10 + - scipy >=1.11.1 + constrains: + - cudnn >=9.8,<10.0 + license: Apache-2.0 + license_family: APACHE + purls: + - pkg:pypi/jax?source=hash-mapping + size: 1538293 + timestamp: 1748688029463 - conda: https://prefix.dev/conda-forge/linux-64/jaxlib-0.5.2-cpu_py310hc96afab_2.conda sha256: bc9fc4a0bc9b43b0799c3320b62bd5e486e57ac70396ee5236a70a87018723b6 md5: 2bbb84513ad8ff868dd21ef5e5661aaa @@ -5571,9 +5590,9 @@ packages: - pkg:pypi/jaxlib?source=hash-mapping size: 69060155 timestamp: 1747094262205 -- conda: https://prefix.dev/conda-forge/linux-64/jaxlib-0.5.2-cuda126py310hec873cc_202.conda - sha256: 227dac171d747f378ac1e0b14722f72bc7ab56976ea07d487bd796976ea0780e - md5: 9bf2096fc296cd6cc3392e00cea59b64 +- conda: https://prefix.dev/conda-forge/linux-64/jaxlib-0.6.0-cuda126py310hec873cc_200.conda + sha256: 5a52619f5e6d40d5c8e8223a5ec113d5bb097456656bc5668ab24df6b75f69ae + md5: 1b39986ae9b1bcfddc720ef10bb67420 depends: - __cuda - __glibc >=2.17,<3.0.a0 @@ -5583,6 +5602,7 @@ packages: - cuda-nvcc-tools - cuda-nvtx >=12.6.77,<13.0a0 - cuda-version >=12.6,<13 + - cudnn >=9.10.1.4,<10.0a0 - libabseil * cxx17* - libabseil >=20250127.1,<20250128.0a0 - libcublas >=12.6.4.1,<13.0a0 @@ -5600,22 +5620,21 @@ packages: - libstdcxx >=13 - libzlib >=1.3.1,<2.0a0 - ml_dtypes >=0.2.0 - - nccl >=2.26.5.1,<3.0a0 + - nccl >=2.26.6.1,<3.0a0 - numpy >=1.19,<3 - openssl >=3.5.0,<4.0a0 - python >=3.10,<3.11.0a0 - python_abi 3.10.* *_cp310 - scipy >=1.9 constrains: - - jax >=0.5.2 + - jax >=0.6.0 license: Apache-2.0 - license_family: APACHE purls: - pkg:pypi/jax-cuda12-pjrt?source=hash-mapping - pkg:pypi/jax-cuda12-plugin?source=hash-mapping - pkg:pypi/jaxlib?source=hash-mapping - size: 150779832 - timestamp: 1747101156606 + size: 146820753 + timestamp: 1748663708635 - conda: https://prefix.dev/conda-forge/osx-64/jaxlib-0.5.2-cpu_py310h22b337c_2.conda sha256: bb292699e4523002e868c9b56379574c74ef82f718ef574d27fefa0a882ae0e0 md5: 2f10f0eb0ddf22befa0d8c750d2df551 @@ -6013,9 +6032,9 @@ packages: purls: [] size: 91998 timestamp: 1746203009003 -- conda: https://prefix.dev/conda-forge/linux-64/libcudnn-9.10.0.56-h4840ae0_0.conda - sha256: 5fee28ef7842402757b61263c9c2fc3757358b2ba81bec38eae60c9d1f629b7d - md5: df5d2581c6b951715b345495e37cafcd +- conda: https://prefix.dev/conda-forge/linux-64/libcudnn-9.10.1.4-h4840ae0_0.conda + sha256: 5f21148b7bdfbcf5e40b4debaccd6d36b8a75405fdef1c66d75059a12d43bd0e + md5: c19f7281266ca77da5458d2ccf17ba82 depends: - __glibc >=2.28,<3.0.a0 - cuda-nvrtc @@ -6028,8 +6047,8 @@ packages: - libcudnn-jit <0a license: LicenseRef-cuDNN-Software-License-Agreement purls: [] - size: 526869792 - timestamp: 1747076587395 + size: 527020675 + timestamp: 1747773945760 - conda: https://prefix.dev/conda-forge/win-64/libcudnn-9.10.1.4-hffc9a7f_0.conda sha256: 26d399ecad571797b2600b0c6c955a6ce2f3372d71cca0c148c5867a4a52a377 md5: 5f3f28dcfb3f8c8cc6f826079923377f @@ -6046,21 +6065,21 @@ packages: purls: [] size: 509841043 timestamp: 1747774328068 -- conda: https://prefix.dev/conda-forge/linux-64/libcudnn-dev-9.10.0.56-hcd2ec93_0.conda - sha256: 655b21a1f32b82cd70bc2fcb0cc2b971cabe6ccce3cf328b96c110f2f5e69912 - md5: c0f9074c58fa2a1aa32856076b626b22 +- conda: https://prefix.dev/conda-forge/linux-64/libcudnn-dev-9.10.1.4-hcd2ec93_0.conda + sha256: 34fb3c9fa9b67a18fd0b4d28518fdacf11dbed3ad3fbf24aec341d1b8490d3c0 + md5: bce8ec010b35f2c1e5db441f3f396754 depends: - __glibc >=2.28,<3.0.a0 - cuda-version >=12,<13.0a0 - - libcudnn 9.10.0.56 h4840ae0_0 + - libcudnn 9.10.1.4 h4840ae0_0 - libgcc >=13 - libstdcxx >=13 constrains: - libcudnn-jit-dev <0a license: LicenseRef-cuDNN-Software-License-Agreement purls: [] - size: 43729 - timestamp: 1747077027897 + size: 44217 + timestamp: 1747774406255 - conda: https://prefix.dev/conda-forge/win-64/libcudnn-dev-9.10.1.4-hffc9a7f_0.conda sha256: 66ea382c3fa5b3a5fa448166865b154a7d6d263f981243a96ddb045278a75bb2 md5: 81ae4771239f63d4f0aebad63de544f6 @@ -8046,9 +8065,9 @@ packages: - pkg:pypi/myst-parser?source=hash-mapping size: 73074 timestamp: 1739381945342 -- conda: https://prefix.dev/conda-forge/linux-64/nccl-2.26.5.1-ha44e49d_0.conda - sha256: 3a715dab311d045ecd5811b06012ebc7a1b8ce9c899d40952d834bd713fe9ac9 - md5: 45823c363ce0803d29c4a444e4309634 +- conda: https://prefix.dev/conda-forge/linux-64/nccl-2.26.6.1-ha44e49d_0.conda + sha256: b6a54445f2326b27707851ea590dae2ebcd1492ca41d039ddca3ec305d2189e2 + md5: 62f23f8be42626cc7c15553a9e2e0ab8 depends: - __glibc >=2.17,<3.0.a0 - cuda-version >=12,<13.0a0 @@ -8057,8 +8076,8 @@ packages: license: BSD-3-Clause license_family: BSD purls: [] - size: 180506014 - timestamp: 1746010496065 + size: 180500682 + timestamp: 1747783682945 - conda: https://prefix.dev/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda sha256: 3fde293232fa3fca98635e1167de6b7c7fda83caf24b9d6c91ec9eefb4f4d586 md5: 47e340acb35de30501a76c7c799c41d7 diff --git a/pyproject.toml b/pyproject.toml index 485b0816..b710e5d2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -161,7 +161,7 @@ system-requirements = { cuda = "12" } [tool.pixi.feature.cuda-backends.target.linux-64.dependencies] cupy = ">=13.4.1" -jaxlib = { version = ">=0.5.2", build = "cuda12*" } +jaxlib = { version = ">=0.5.3", build = "cuda12*" } pytorch = { version = ">=2.7.0", build = "cuda12*" } [tool.pixi.feature.cuda-backends.target.osx-64.dependencies] From 87c24899af5b43a55b9b1a7d80d7af5e85906819 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Tue, 3 Jun 2025 08:38:33 +0100 Subject: [PATCH 017/104] ENH: New function `default_dtype` (#310) * default_dtype * tweak comment in conftest --- docs/api-reference.md | 1 + src/array_api_extra/__init__.py | 2 ++ src/array_api_extra/_lib/_funcs.py | 46 ++++++++++++++++++++++++++---- tests/conftest.py | 39 ++++++++++++++++++------- tests/test_funcs.py | 34 ++++++++++++++++++++++ 5 files changed, 107 insertions(+), 15 deletions(-) diff --git a/docs/api-reference.md b/docs/api-reference.md index ee33a819..8e9375d0 100644 --- a/docs/api-reference.md +++ b/docs/api-reference.md @@ -12,6 +12,7 @@ broadcast_shapes cov create_diagonal + default_dtype expand_dims isclose kron diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 1c55a6d1..5cfe8594 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -8,6 +8,7 @@ broadcast_shapes, cov, create_diagonal, + default_dtype, expand_dims, kron, nunique, @@ -27,6 +28,7 @@ "broadcast_shapes", "cov", "create_diagonal", + "default_dtype", "expand_dims", "isclose", "kron", diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 645f7a1b..be703fb5 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -4,7 +4,7 @@ import warnings from collections.abc import Callable, Sequence from types import ModuleType, NoneType -from typing import cast, overload +from typing import Literal, cast, overload from ._at import at from ._utils import _compat, _helpers @@ -16,7 +16,7 @@ meta_namespace, ndindex, ) -from ._utils._typing import Array +from ._utils._typing import Array, Device, DType __all__ = [ "apply_where", @@ -438,6 +438,44 @@ def create_diagonal( return xp.reshape(diag, (*batch_dims, n, n)) +def default_dtype( + xp: ModuleType, + kind: Literal[ + "real floating", "complex floating", "integral", "indexing" + ] = "real floating", + *, + device: Device | None = None, +) -> DType: + """ + Return the default dtype for the given namespace and device. + + This is a convenience shorthand for + ``xp.__array_namespace_info__().default_dtypes(device=device)[kind]``. + + Parameters + ---------- + xp : array_namespace + The standard-compatible namespace for which to get the default dtype. + kind : {'real floating', 'complex floating', 'integral', 'indexing'}, optional + The kind of dtype to return. Default is 'real floating'. + device : Device, optional + The device for which to get the default dtype. Default: current device. + + Returns + ------- + dtype + The default dtype for the given namespace, kind, and device. + """ + dtypes = xp.__array_namespace_info__().default_dtypes(device=device) + try: + return dtypes[kind] + except KeyError as e: + domain = ("real floating", "complex floating", "integral", "indexing") + assert set(dtypes) == set(domain), f"Non-compliant namespace: {dtypes}" + msg = f"Unknown kind '{kind}'. Expected one of {domain}." + raise ValueError(msg) from e + + def expand_dims( a: Array, /, *, axis: int | tuple[int, ...] = (0,), xp: ModuleType | None = None ) -> Array: @@ -728,9 +766,7 @@ def nunique(x: Array, /, *, xp: ModuleType | None = None) -> Array: x = xp.reshape(x, (-1,)) x = xp.sort(x) mask = x != xp.roll(x, -1) - default_int = xp.__array_namespace_info__().default_dtypes( - device=_compat.device(x) - )["integral"] + default_int = default_dtype(xp, "integral", device=_compat.device(x)) return xp.maximum( # Special cases: # - array is size 0 diff --git a/tests/conftest.py b/tests/conftest.py index bb72139b..82a0acbb 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -149,16 +149,8 @@ def xp( if library.like(Backend.JAX): _setup_jax(library) - - elif library == Backend.TORCH_GPU: - import torch.cuda - - if not torch.cuda.is_available(): - pytest.skip("no CUDA device available") - xp.set_default_device("cuda") - - elif library == Backend.TORCH: # CPU - xp.set_default_device("cpu") + elif library.like(Backend.TORCH): + _setup_torch(library) yield xp @@ -179,6 +171,24 @@ def _setup_jax(library: Backend) -> None: jax.config.update("jax_default_device", device) +def _setup_torch(library: Backend) -> None: + import torch + + # This is already the default, but some tests or env variables may change it. + # TODO test both float32 and float64, like in scipy. + torch.set_default_dtype(torch.float32) + + if library == Backend.TORCH_GPU: + import torch.cuda + + if not torch.cuda.is_available(): + pytest.skip("no CUDA device available") + torch.set_default_device("cuda") + else: + assert library == Backend.TORCH + torch.set_default_device("cpu") + + @pytest.fixture(params=[Backend.DASK]) # Can select the test with `pytest -k dask` def da( request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch @@ -201,6 +211,15 @@ def jnp( return xp +@pytest.fixture(params=[Backend.TORCH, Backend.TORCH_GPU]) +def torch(request: pytest.FixtureRequest) -> ModuleType: # numpydoc ignore=PR01,RT01 + """Variant of the `xp` fixture that only yields torch.""" + xp = pytest.importorskip("torch") + xp = array_namespace(xp.empty(0)) + _setup_torch(request.param) + return xp + + @pytest.fixture def device( library: Backend, xp: ModuleType diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 7c138442..b89c7441 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -17,6 +17,7 @@ broadcast_shapes, cov, create_diagonal, + default_dtype, expand_dims, isclose, kron, @@ -517,6 +518,39 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(y, xp.asarray([[1, 0], [0, 2]])) +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no __array_namespace_info__") +class TestDefaultDType: + def test_basic(self, xp: ModuleType): + assert default_dtype(xp) == xp.empty(0).dtype + + def test_kind(self, xp: ModuleType): + assert default_dtype(xp, "real floating") == xp.empty(0).dtype + assert default_dtype(xp, "complex floating") == (xp.empty(0) * 1j).dtype + assert default_dtype(xp, "integral") == xp.int64 + assert default_dtype(xp, "indexing") == xp.int64 + + with pytest.raises(ValueError, match="Unknown kind"): + _ = default_dtype(xp, "foo") # type: ignore[arg-type] # pyright: ignore[reportArgumentType] + + def test_device(self, xp: ModuleType, device: Device): + # Note: at the moment there are no known namespaces with + # device-specific default dtypes. + assert default_dtype(xp, device=None) == xp.empty(0).dtype + assert default_dtype(xp, device=device) == xp.empty(0).dtype + + def test_torch(self, torch: ModuleType): + xp = torch + xp.set_default_dtype(xp.float64) + assert default_dtype(xp) == xp.float64 + assert default_dtype(xp, "real floating") == xp.float64 + assert default_dtype(xp, "complex floating") == xp.complex128 + + xp.set_default_dtype(xp.float32) + assert default_dtype(xp) == xp.float32 + assert default_dtype(xp, "real floating") == xp.float32 + assert default_dtype(xp, "complex floating") == xp.complex64 + + class TestExpandDims: def test_single_axis(self, xp: ModuleType): """Trivial case where xpx.expand_dims doesn't add anything to xp.expand_dims""" From a0ff73363514d91091191a684e3eef3d19fcd1a1 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 3 Jun 2025 08:29:09 +0000 Subject: [PATCH 018/104] deps: Update dependency jax to >=0.5.3 (#311) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 97 ++++++++++++++++++++------------------------------ pyproject.toml | 6 ++-- 2 files changed, 42 insertions(+), 61 deletions(-) diff --git a/pixi.lock b/pixi.lock index 3ce120cf..76ae4833 100644 --- a/pixi.lock +++ b/pixi.lock @@ -142,8 +142,8 @@ environments: - 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libabseil * cxx17* @@ -5583,13 +5564,13 @@ packages: - python_abi 3.10.* *_cp310 - scipy >=1.9 constrains: - - jax >=0.5.2 + - jax >=0.6.0 license: Apache-2.0 license_family: APACHE purls: - pkg:pypi/jaxlib?source=hash-mapping - size: 69060155 - timestamp: 1747094262205 + size: 60603285 + timestamp: 1748663385056 - conda: https://prefix.dev/conda-forge/linux-64/jaxlib-0.6.0-cuda126py310hec873cc_200.conda sha256: 5a52619f5e6d40d5c8e8223a5ec113d5bb097456656bc5668ab24df6b75f69ae md5: 1b39986ae9b1bcfddc720ef10bb67420 @@ -5635,9 +5616,9 @@ packages: - pkg:pypi/jaxlib?source=hash-mapping size: 146820753 timestamp: 1748663708635 -- conda: https://prefix.dev/conda-forge/osx-64/jaxlib-0.5.2-cpu_py310h22b337c_2.conda - sha256: bb292699e4523002e868c9b56379574c74ef82f718ef574d27fefa0a882ae0e0 - md5: 2f10f0eb0ddf22befa0d8c750d2df551 +- conda: https://prefix.dev/conda-forge/osx-64/jaxlib-0.6.0-cpu_py310h22b337c_0.conda + sha256: 1ea4b15f45eeecd939270d93675f7b7361c9a6cd7a830d361920855a10573b59 + md5: 25c084b06a0c200d1cc095b59f24a757 depends: - __osx >=10.15 - libabseil * cxx17* @@ -5652,16 +5633,16 @@ packages: - python_abi 3.10.* *_cp310 - scipy >=1.9 constrains: - - jax >=0.5.2 + - jax >=0.6.0 license: Apache-2.0 license_family: APACHE purls: - pkg:pypi/jaxlib?source=hash-mapping - size: 66014116 - timestamp: 1747095379031 -- conda: https://prefix.dev/conda-forge/osx-arm64/jaxlib-0.5.2-cpu_py310h2c532f2_2.conda - sha256: f4d9d8e57db13d09eb3f83f3c57bceef327689075b434dff44137045dd43da33 - md5: e9f65c12435b42a8094701861d02f25b + size: 62834580 + timestamp: 1748654408664 +- conda: https://prefix.dev/conda-forge/osx-arm64/jaxlib-0.6.0-cpu_py310h2c532f2_0.conda + sha256: a35d81d3ac366fcff2d5cba19ae5452b9aa8fd87ea4ace34a737f2fa88a85826 + md5: 1ab7fe4ca08fb32518bdeea813ef6bef depends: - __osx >=11.0 - libabseil * cxx17* @@ -5677,13 +5658,13 @@ packages: - python_abi 3.10.* *_cp310 - scipy >=1.9 constrains: - - jax >=0.5.2 + - jax >=0.6.0 license: Apache-2.0 license_family: APACHE purls: - pkg:pypi/jaxlib?source=hash-mapping - size: 54831498 - timestamp: 1747096397162 + size: 51702562 + timestamp: 1748652584379 - conda: https://prefix.dev/conda-forge/noarch/jedi-0.19.2-pyhd8ed1ab_1.conda sha256: 92c4d217e2dc68983f724aa983cca5464dcb929c566627b26a2511159667dba8 md5: a4f4c5dc9b80bc50e0d3dc4e6e8f1bd9 diff --git a/pyproject.toml b/pyproject.toml index b710e5d2..84dc07b8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -139,13 +139,13 @@ dask-core = ">=2025.5.0" # No distributed, tornado, etc. sparse = ">=0.16.0" [tool.pixi.feature.backends.target.linux-64.dependencies] -jax = ">=0.5.2" +jax = ">=0.5.3" [tool.pixi.feature.backends.target.osx-64.dependencies] -jax = ">=0.5.2" +jax = ">=0.5.3" [tool.pixi.feature.backends.target.osx-arm64.dependencies] -jax = ">=0.5.2" +jax = ">=0.5.3" [tool.pixi.feature.backends.target.win-64.dependencies] # jax = "*" # unavailable From 61b512ee25679eab3c409b5be209d35dae41f8cb Mon Sep 17 00:00:00 2001 From: Neil Girdhar Date: Tue, 3 Jun 2025 05:46:19 -0400 Subject: [PATCH 019/104] ENH: add new function `one_hot` (#306) Co-authored-by: Guido Imperiale --- docs/api-reference.md | 1 + src/array_api_extra/__init__.py | 3 +- src/array_api_extra/_delegation.py | 82 +++++++++++++++++++++++++- src/array_api_extra/_lib/_funcs.py | 17 ++++++ tests/test_funcs.py | 94 ++++++++++++++++++++++++++++++ 5 files changed, 194 insertions(+), 3 deletions(-) diff --git a/docs/api-reference.md b/docs/api-reference.md index 8e9375d0..38d0d26e 100644 --- a/docs/api-reference.md +++ b/docs/api-reference.md @@ -17,6 +17,7 @@ isclose kron nunique + one_hot pad setdiff1d sinc diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 5cfe8594..ba9de3b4 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -1,6 +1,6 @@ """Extra array functions built on top of the array API standard.""" -from ._delegation import isclose, pad +from ._delegation import isclose, one_hot, pad from ._lib._at import at from ._lib._funcs import ( apply_where, @@ -34,6 +34,7 @@ "kron", "lazy_apply", "nunique", + "one_hot", "pad", "setdiff1d", "sinc", diff --git a/src/array_api_extra/_delegation.py b/src/array_api_extra/_delegation.py index b52c23ae..756841c8 100644 --- a/src/array_api_extra/_delegation.py +++ b/src/array_api_extra/_delegation.py @@ -14,10 +14,11 @@ is_pydata_sparse_namespace, is_torch_namespace, ) +from ._lib._utils._compat import device as get_device from ._lib._utils._helpers import asarrays -from ._lib._utils._typing import Array +from ._lib._utils._typing import Array, DType -__all__ = ["isclose", "pad"] +__all__ = ["isclose", "one_hot", "pad"] def isclose( @@ -112,6 +113,83 @@ def isclose( return _funcs.isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan, xp=xp) +def one_hot( + x: Array, + /, + num_classes: int, + *, + dtype: DType | None = None, + axis: int = -1, + xp: ModuleType | None = None, +) -> Array: + """ + One-hot encode the given indices. + + Each index in the input `x` is encoded as a vector of zeros of length `num_classes` + with the element at the given index set to one. + + Parameters + ---------- + x : array + An array with integral dtype whose values are between `0` and `num_classes - 1`. + num_classes : int + Number of classes in the one-hot dimension. + dtype : DType, optional + The dtype of the return value. Defaults to the default float dtype (usually + float64). + axis : int, optional + Position in the expanded axes where the new axis is placed. Default: -1. + xp : array_namespace, optional + The standard-compatible namespace for `x`. Default: infer. + + Returns + ------- + array + An array having the same shape as `x` except for a new axis at the position + given by `axis` having size `num_classes`. If `axis` is unspecified, it + defaults to -1, which appends a new axis. + + If ``x < 0`` or ``x >= num_classes``, then the result is undefined, may raise + an exception, or may even cause a bad state. `x` is not checked. + + Examples + -------- + >>> import array_api_extra as xpx + >>> import array_api_strict as xp + >>> xpx.one_hot(xp.asarray([1, 2, 0]), 3) + Array([[0., 1., 0.], + [0., 0., 1.], + [1., 0., 0.]], dtype=array_api_strict.float64) + """ + # Validate inputs. + if xp is None: + xp = array_namespace(x) + if not xp.isdtype(x.dtype, "integral"): + msg = "x must have an integral dtype." + raise TypeError(msg) + if dtype is None: + dtype = _funcs.default_dtype(xp, device=get_device(x)) + # Delegate where possible. + if is_jax_namespace(xp): + from jax.nn import one_hot as jax_one_hot + + return jax_one_hot(x, num_classes, dtype=dtype, axis=axis) + if is_torch_namespace(xp): + from torch.nn.functional import one_hot as torch_one_hot + + x = xp.astype(x, xp.int64) # PyTorch only supports int64 here. + try: + out = torch_one_hot(x, num_classes) + except RuntimeError as e: + raise IndexError from e + else: + out = _funcs.one_hot(x, num_classes, xp=xp) + out = xp.astype(out, dtype, copy=False) + if axis != -1: + out = xp.moveaxis(out, -1, axis) + return out + + def pad( x: Array, pad_width: int | tuple[int, int] | Sequence[tuple[int, int]], diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index be703fb5..69dfe6a4 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -375,6 +375,23 @@ def cov(m: Array, /, *, xp: ModuleType | None = None) -> Array: return xp.squeeze(c, axis=axes) +def one_hot( + x: Array, + /, + num_classes: int, + *, + xp: ModuleType, +) -> Array: # numpydoc ignore=PR01,RT01 + """See docstring in `array_api_extra._delegation.py`.""" + # TODO: Benchmark whether this is faster on the NumPy backend: + # if is_numpy_array(x): + # out = xp.zeros((x.size, num_classes), dtype=dtype) + # out[xp.arange(x.size), xp.reshape(x, (-1,))] = 1 + # return xp.reshape(out, (*x.shape, num_classes)) + range_num_classes = xp.arange(num_classes, dtype=x.dtype, device=_compat.device(x)) + return x[..., xp.newaxis] == range_num_classes + + def create_diagonal( x: Array, /, *, offset: int = 0, xp: ModuleType | None = None ) -> Array: diff --git a/tests/test_funcs.py b/tests/test_funcs.py index b89c7441..c8bea859 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -22,6 +22,7 @@ isclose, kron, nunique, + one_hot, pad, setdiff1d, sinc, @@ -45,6 +46,7 @@ lazy_xp_function(expand_dims) lazy_xp_function(kron) lazy_xp_function(nunique) +lazy_xp_function(one_hot) lazy_xp_function(pad) # FIXME calls in1d which calls xp.unique_values without size lazy_xp_function(setdiff1d, jax_jit=False) @@ -449,6 +451,98 @@ def test_xp(self, xp: ModuleType): ) +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="backend doesn't have arange") +class TestOneHot: + @pytest.mark.parametrize("n_dim", range(4)) + @pytest.mark.parametrize("num_classes", [1, 3, 10]) + def test_dims_and_classes(self, xp: ModuleType, n_dim: int, num_classes: int): + shape = tuple(range(2, 2 + n_dim)) + rng = np.random.default_rng(2347823) + np_x = rng.integers(num_classes, size=shape) + x = xp.asarray(np_x) + y = one_hot(x, num_classes) + assert y.shape == (*x.shape, num_classes) + for *i_list, j in ndindex(*shape, num_classes): + i = tuple(i_list) + assert float(y[(*i, j)]) == (int(x[i]) == j) + + def test_basic(self, xp: ModuleType): + actual = one_hot(xp.asarray([0, 1, 2]), 3) + expected = xp.asarray([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]) + xp_assert_equal(actual, expected) + + actual = one_hot(xp.asarray([1, 2, 0]), 3) + expected = xp.asarray([[0.0, 1.0, 0.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0]]) + xp_assert_equal(actual, expected) + + def test_2d(self, xp: ModuleType): + actual = one_hot(xp.asarray([[2, 1, 0], [1, 0, 2]]), 3, axis=1) + expected = xp.asarray( + [ + [[0.0, 0.0, 1.0], [0.0, 1.0, 0.0], [1.0, 0.0, 0.0]], + [[0.0, 1.0, 0.0], [1.0, 0.0, 0.0], [0.0, 0.0, 1.0]], + ] + ) + xp_assert_equal(actual, expected) + + @pytest.mark.skip_xp_backend( + Backend.ARRAY_API_STRICTEST, reason="backend doesn't support Boolean indexing" + ) + def test_abstract_size(self, xp: ModuleType): + x = xp.arange(5) + x = x[x > 2] + actual = one_hot(x, 5) + expected = xp.asarray([[0.0, 0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 0.0, 1.0]]) + xp_assert_equal(actual, expected) + + @pytest.mark.skip_xp_backend( + Backend.TORCH_GPU, reason="Puts Pytorch into a bad state." + ) + def test_out_of_bound(self, xp: ModuleType): + # Undefined behavior. Either return zero, or raise. + try: + actual = one_hot(xp.asarray([-1, 3]), 3) + except IndexError: + return + expected = xp.asarray([[0.0, 0.0, 0.0], [0.0, 0.0, 0.0]]) + xp_assert_equal(actual, expected) + + @pytest.mark.parametrize( + "int_dtype", + ["int8", "int16", "int32", "int64", "uint8", "uint16", "uint32", "uint64"], + ) + def test_int_types(self, xp: ModuleType, int_dtype: str): + dtype = getattr(xp, int_dtype) + x = xp.asarray([0, 1, 2], dtype=dtype) + actual = one_hot(x, 3) + expected = xp.asarray([[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0]]) + xp_assert_equal(actual, expected) + + def test_custom_dtype(self, xp: ModuleType): + actual = one_hot(xp.asarray([0, 1, 2], dtype=xp.int32), 3, dtype=xp.bool) + expected = xp.asarray( + [[True, False, False], [False, True, False], [False, False, True]] + ) + xp_assert_equal(actual, expected) + + def test_axis(self, xp: ModuleType): + expected = xp.asarray([[0.0, 1.0, 0.0], [0.0, 0.0, 1.0], [1.0, 0.0, 0.0]]).T + actual = one_hot(xp.asarray([1, 2, 0]), 3, axis=0) + xp_assert_equal(actual, expected) + + actual = one_hot(xp.asarray([1, 2, 0]), 3, axis=-2) + xp_assert_equal(actual, expected) + + def test_non_integer(self, xp: ModuleType): + with pytest.raises(TypeError): + _ = one_hot(xp.asarray([1.0]), 3) + + def test_device(self, xp: ModuleType, device: Device): + x = xp.asarray([0, 1, 2], device=device) + y = one_hot(x, 3) + assert get_device(y) == device + + @pytest.mark.skip_xp_backend( Backend.SPARSE, reason="read-only backend without .at support" ) From d8b9cecc63c9c25693218fdc1db1769f7990407f Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 3 Jun 2025 11:31:01 +0100 Subject: [PATCH 020/104] REL: set version to 0.8.0 --- pixi.lock | 1958 +++++++++++++++---------------- src/array_api_extra/__init__.py | 2 +- 2 files changed, 978 insertions(+), 982 deletions(-) diff --git a/pixi.lock b/pixi.lock index 76ae4833..2e8472f4 100644 --- a/pixi.lock +++ b/pixi.lock @@ -19,8 +19,8 @@ environments: - 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def persistent_id(self, obj: object) -> Literal[0, 1, None]: # pyright: ignore[reportIncompatibleMethodOverride] # numpydoc ignore=GL08 + def persistent_id( + self, obj: object + ) -> Literal[0, 1, None]: # numpydoc ignore=GL08 if isinstance(obj, cls): instances.append(obj) # type: ignore[arg-type] return 0 @@ -483,7 +485,7 @@ class Unpickler(pickle.Unpickler): # numpydoc ignore=GL08 """Mirror of the overridden Pickler in pickle_flatten.""" @override - def persistent_load(self, pid: Literal[0, 1]) -> object: # pyright: ignore[reportIncompatibleMethodOverride] # numpydoc ignore=GL08 + def persistent_load(self, pid: Literal[0, 1]) -> object: # numpydoc ignore=GL08 try: return next(iters[pid]) except StopIteration as e: From 74789e25f0adec785eaedebe1937ab47eaa2b9ea Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 3 Jun 2025 12:10:45 +0100 Subject: [PATCH 022/104] TST: remove sparse `isdtype` xfails --- tests/test_funcs.py | 4 ---- tests/test_helpers.py | 1 - tests/test_testing.py | 18 ++++++------------ 3 files changed, 6 insertions(+), 17 deletions(-) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index c8bea859..891c4c6f 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -404,7 +404,6 @@ def test_none(self, args: tuple[tuple[float | None, ...], ...]): assert actual == expect -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") class TestCov: def test_basic(self, xp: ModuleType): xp_assert_close( @@ -697,7 +696,6 @@ def test_xp(self, xp: ModuleType): @pytest.mark.filterwarnings( # array_api_strictest "ignore:invalid value encountered:RuntimeWarning:array_api_strict" ) -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") class TestIsClose: @pytest.mark.parametrize("swap", [False, True]) @pytest.mark.parametrize( @@ -919,7 +917,6 @@ def test_kron_shape( k = kron(a, b) assert k.shape == expected_shape - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") def test_python_scalar(self, xp: ModuleType): a = 1 # Test no dtype promotion to xp.asarray(a); use b.dtype @@ -1138,7 +1135,6 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(actual, expected) -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") class TestSinc: def test_simple(self, xp: ModuleType): xp_assert_equal(sinc(xp.asarray(0.0)), xp.asarray(1.0)) diff --git a/tests/test_helpers.py b/tests/test_helpers.py index b1b6ddba..74a0ec93 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -79,7 +79,6 @@ def test_xp(self, xp: ModuleType): class TestAsArrays: - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") @pytest.mark.parametrize( ("dtype", "b", "defined"), [ diff --git a/tests/test_testing.py b/tests/test_testing.py index b195a65b..43d6e8ae 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -38,12 +38,7 @@ def test_device(self, xp: ModuleType, device: Device): class TestAssertEqualCloseLess: - pr_assert_close = pytest.param( # pyright: ignore[reportUnannotatedClassAttribute] - xp_assert_close, - marks=pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype"), - ) - - @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close]) + @pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close]) def test_assert_equal_close_basic(self, xp: ModuleType, func: Callable[..., None]): func(xp.asarray(0), xp.asarray(0)) func(xp.asarray([1, 2]), xp.asarray([1, 2])) @@ -75,7 +70,7 @@ def test_namespace(self, xp: ModuleType, func: Callable[..., None]): with pytest.raises(TypeError, match="list is not a supported array type"): func(xp.asarray([0]), [0]) - @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close, xp_assert_less]) + @pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) def test_check_shape(self, xp: ModuleType, func: Callable[..., None]): a = xp.asarray([1] if func is xp_assert_less else [2]) b = xp.asarray(2) @@ -90,7 +85,7 @@ def test_check_shape(self, xp: ModuleType, func: Callable[..., None]): with pytest.raises(AssertionError, match="sizes do not match"): func(a, d, check_shape=False) - @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close, xp_assert_less]) + @pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) def test_check_dtype(self, xp: ModuleType, func: Callable[..., None]): a = xp.asarray(1 if func is xp_assert_less else 2) b = xp.asarray(2, dtype=xp.int16) @@ -102,7 +97,7 @@ def test_check_dtype(self, xp: ModuleType, func: Callable[..., None]): with pytest.raises(AssertionError, match="Mismatched elements"): func(a, c, check_dtype=False) - @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close, xp_assert_less]) + @pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) @pytest.mark.xfail_xp_backend( Backend.SPARSE, reason="sparse [()] returns np.generic" ) @@ -122,7 +117,6 @@ def test_check_scalar( with pytest.raises(AssertionError, match="Mismatched elements"): func(a, c, check_scalar=True) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") @pytest.mark.parametrize("dtype", ["int64", "float64"]) def test_assert_close_tolerance(self, dtype: str, xp: ModuleType): a = xp.asarray([100], dtype=getattr(xp, dtype)) @@ -145,7 +139,7 @@ def test_assert_less(self, xp: ModuleType): with pytest.raises(AssertionError, match="Mismatched elements"): xp_assert_less(xp.asarray([1, 1]), xp.asarray([2, 1])) - @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close, xp_assert_less]) + @pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="index by sparse array") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="boolean indexing") def test_none_shape(self, xp: ModuleType, func: Callable[..., None]): @@ -176,7 +170,7 @@ def test_none_shape(self, xp: ModuleType, func: Callable[..., None]): with pytest.raises(AssertionError, match="Mismatched elements"): func(xp.asarray([4]), a) - @pytest.mark.parametrize("func", [xp_assert_equal, pr_assert_close, xp_assert_less]) + @pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) def test_device(self, xp: ModuleType, device: Device, func: Callable[..., None]): a = xp.asarray([1] if func is xp_assert_less else [2], device=device) b = xp.asarray([2], device=device) From a91beffe21be38c9c3947f4a63b15c99d8c48a97 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 3 Jun 2025 16:33:42 +0100 Subject: [PATCH 023/104] TST: fix up sparse tests --- src/array_api_extra/_lib/_utils/_helpers.py | 6 +++++- tests/test_funcs.py | 9 ++++++++- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 897cdd65..877d9538 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -322,7 +322,11 @@ def capabilities(xp: ModuleType, *, device: Device | None = None) -> dict[str, i """ if is_pydata_sparse_namespace(xp): # No __array_namespace_info__(); no indexing by sparse arrays - return {"boolean indexing": False, "data-dependent shapes": True} + return { + "boolean indexing": False, + "data-dependent shapes": True, + "max dimensions": None, + } out = xp.__array_namespace_info__().capabilities() if is_jax_namespace(xp) and out["boolean indexing"]: # FIXME https://github.com/jax-ml/jax/issues/27418 diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 891c4c6f..99da4a2b 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -416,6 +416,7 @@ def test_complex(self, xp: ModuleType): expect = xp.asarray([[1.0, -1.0j], [1.0j, 1.0]], dtype=xp.complex128) xp_assert_close(actual, expect) + @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="matmul with nan fillvalue") def test_empty(self, xp: ModuleType): with warnings.catch_warnings(record=True): warnings.simplefilter("always", RuntimeWarning) @@ -611,7 +612,6 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(y, xp.asarray([[1, 0], [0, 2]])) -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no __array_namespace_info__") class TestDefaultDType: def test_basic(self, xp: ModuleType): assert default_dtype(xp) == xp.empty(0).dtype @@ -696,6 +696,9 @@ def test_xp(self, xp: ModuleType): @pytest.mark.filterwarnings( # array_api_strictest "ignore:invalid value encountered:RuntimeWarning:array_api_strict" ) +@pytest.mark.filterwarnings( # sparse + "ignore:invalid value encountered:RuntimeWarning:sparse" +) class TestIsClose: @pytest.mark.parametrize("swap", [False, True]) @pytest.mark.parametrize( @@ -813,6 +816,7 @@ def test_bool_dtype(self, xp: ModuleType): isclose(xp.asarray(True), b, atol=1), xp.asarray([True, True, True]) ) + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="index by sparse array") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="unknown shape") def test_none_shape(self, xp: ModuleType): a = xp.asarray([1, 5, 0]) @@ -821,6 +825,7 @@ def test_none_shape(self, xp: ModuleType): a = a[a < 5] xp_assert_equal(isclose(a, b), xp.asarray([True, False])) + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="index by sparse array") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="unknown shape") def test_none_shape_bool(self, xp: ModuleType): a = xp.asarray([True, True, False]) @@ -1136,6 +1141,7 @@ def test_xp(self, xp: ModuleType): class TestSinc: + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no linspace") def test_simple(self, xp: ModuleType): xp_assert_equal(sinc(xp.asarray(0.0)), xp.asarray(1.0)) w = sinc(xp.linspace(-1, 1, 100)) @@ -1147,6 +1153,7 @@ def test_dtype(self, xp: ModuleType, x: int | complex): with pytest.raises(ValueError, match="real floating data type"): _ = sinc(xp.asarray(x)) + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no arange") def test_3d(self, xp: ModuleType): x = xp.reshape(xp.arange(18, dtype=xp.float64), (3, 3, 2)) expected = xp.zeros((3, 3, 2), dtype=xp.float64) From 1cd079a67377d4711eaad9d649e3c61f8e4519f3 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 3 Jun 2025 16:37:27 +0100 Subject: [PATCH 024/104] TYP: fix `capabilities` annotation --- src/array_api_extra/_lib/_utils/_helpers.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 877d9538..3e43fa91 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -301,7 +301,9 @@ def meta_namespace( return array_namespace(*metas) -def capabilities(xp: ModuleType, *, device: Device | None = None) -> dict[str, int]: +def capabilities( + xp: ModuleType, *, device: Device | None = None +) -> dict[str, int | None]: """ Return patched ``xp.__array_namespace_info__().capabilities()``. From 3791c8ad6e1ce1ddb6448586c5d25c06d8355399 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 3 Jun 2025 19:36:05 +0100 Subject: [PATCH 025/104] DEV: set version to 0.8.1.dev0 (#315) --- pixi.lock | 156 ++++++++++++++++---------------- src/array_api_extra/__init__.py | 2 +- 2 files changed, 79 insertions(+), 79 deletions(-) diff --git a/pixi.lock b/pixi.lock index 2e8472f4..0c6f731c 100644 --- a/pixi.lock +++ b/pixi.lock @@ -254,8 +254,8 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/tomlkit-0.13.2-pyha770c72_1.conda - conda: https://prefix.dev/conda-forge/noarch/toolz-1.0.0-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/noarch/traitlets-5.14.3-pyhd8ed1ab_1.conda - - conda: https://prefix.dev/conda-forge/noarch/typing-extensions-4.13.2-h0e9735f_0.conda - - conda: https://prefix.dev/conda-forge/noarch/typing_extensions-4.13.2-pyh29332c3_0.conda + - conda: https://prefix.dev/conda-forge/noarch/typing-extensions-4.14.0-h32cad80_0.conda + - conda: https://prefix.dev/conda-forge/noarch/typing_extensions-4.14.0-pyhe01879c_0.conda - 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pkg:pypi/pytest?source=compressed-mapping size: 275014 @@ -10243,28 +10245,26 @@ packages: - pkg:pypi/triton?source=hash-mapping size: 162861153 timestamp: 1746164354834 -- conda: https://prefix.dev/conda-forge/noarch/typing-extensions-4.13.2-h0e9735f_0.conda - sha256: 4865fce0897d3cb0ffc8998219157a8325f6011c136e6fd740a9a6b169419296 - md5: 568ed1300869dca0ba09fb750cda5dbb +- conda: https://prefix.dev/conda-forge/noarch/typing-extensions-4.14.0-h32cad80_0.conda + sha256: b8cabfa54432b0f124c0af6b6facdf8110892914fa841ac2e80ab65ac52c1ba4 + md5: a1cdd40fc962e2f7944bc19e01c7e584 depends: - - typing_extensions ==4.13.2 pyh29332c3_0 + - typing_extensions ==4.14.0 pyhe01879c_0 license: PSF-2.0 - license_family: PSF purls: [] - size: 89900 - timestamp: 1744302253997 -- conda: https://prefix.dev/conda-forge/noarch/typing_extensions-4.13.2-pyh29332c3_0.conda - sha256: a8aaf351e6461de0d5d47e4911257e25eec2fa409d71f3b643bb2f748bde1c08 - md5: 83fc6ae00127671e301c9f44254c31b8 + size: 90310 + timestamp: 1748959427551 +- conda: https://prefix.dev/conda-forge/noarch/typing_extensions-4.14.0-pyhe01879c_0.conda + sha256: 8561db52f278c5716b436da6d4ee5521712a49e8f3c70fcae5350f5ebb4be41c + md5: 2adcd9bb86f656d3d43bf84af59a1faf depends: - python >=3.9 - python license: PSF-2.0 - license_family: PSF purls: - pkg:pypi/typing-extensions?source=compressed-mapping - size: 52189 - timestamp: 1744302253997 + size: 50978 + timestamp: 1748959427551 - conda: https://prefix.dev/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda sha256: 5aaa366385d716557e365f0a4e9c3fca43ba196872abbbe3d56bb610d131e192 md5: 4222072737ccff51314b5ece9c7d6f5a diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index b5654902..ddfc715e 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -17,7 +17,7 @@ ) from ._lib._lazy import lazy_apply -__version__ = "0.8.0" +__version__ = "0.8.1.dev0" # pylint: disable=duplicate-code __all__ = [ From 460e944ef9a1b432f03f80d307d9c374540de42f Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 4 Jun 2025 04:20:52 +0000 Subject: [PATCH 026/104] deps: Update dependency dask-core to >=2025.5.1 (#316) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pixi.lock b/pixi.lock index 0c6f731c..8ad1d62e 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3936,7 +3936,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 372435cdb1289323015e8675e2d91b881fec3f5f072e3ccedff93528b4800f2c + sha256: 1a38cc67f696d967e9f4281776a5668eb588f710797748c160147da5337035f9 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 84dc07b8..80ba8af5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -65,7 +65,7 @@ array-api-strict = ">=2.3.1" numpy = ">=2.1.3" pytest = ">=8.3.5" hypothesis = ">=6.131.8" -dask-core = ">=2025.5.0" # No distributed, tornado, etc. +dask-core = ">=2025.5.1" # No distributed, tornado, etc. # NOTE: don't add cupy, jax, pytorch, or sparse here, # as they slow down mypy and are not portable across target OSs @@ -105,7 +105,7 @@ myst-parser = ">=4.0.1" sphinx-copybutton = ">=0.5.2" sphinx-autodoc-typehints = ">=1.25.3" # Needed to import parsed modules with autodoc -dask-core = ">=2025.5.0" # No distributed, tornado, etc. +dask-core = ">=2025.5.1" # No distributed, tornado, etc. pytest = ">=8.3.5" typing-extensions = ">=4.13.2" numpy = ">=2.1.3" @@ -135,7 +135,7 @@ numpy = "=1.22.0" # Note: JAX and PyTorch will install CPU variants. [tool.pixi.feature.backends.dependencies] pytorch = ">=2.7.0" -dask-core = ">=2025.5.0" # No distributed, tornado, etc. +dask-core = ">=2025.5.1" # No distributed, tornado, etc. sparse = ">=0.16.0" [tool.pixi.feature.backends.target.linux-64.dependencies] From fb0306315f33e2ad62fba8ca89db97a58f4f38e5 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 4 Jun 2025 14:07:55 +0100 Subject: [PATCH 027/104] deps: Update dependency sparse to >=0.17.0 (#317) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 8ad1d62e..0924ebd5 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3936,7 +3936,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 1a38cc67f696d967e9f4281776a5668eb588f710797748c160147da5337035f9 + sha256: bbde76ca6f19f4e67758fb784655e5a6675dedf135d2ed6f9f50502582dd4e8c requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 80ba8af5..2163aeba 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -136,7 +136,7 @@ numpy = "=1.22.0" [tool.pixi.feature.backends.dependencies] pytorch = ">=2.7.0" dask-core = ">=2025.5.1" # No distributed, tornado, etc. -sparse = ">=0.16.0" +sparse = ">=0.17.0" [tool.pixi.feature.backends.target.linux-64.dependencies] jax = ">=0.5.3" From 8507174cd26569507b6c64be3e962d9c3aa4600d Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Wed, 4 Jun 2025 15:16:00 +0100 Subject: [PATCH 028/104] MAINT: bump to sparse >=0.17 (#318) --- src/array_api_extra/_lib/_utils/_helpers.py | 28 +++++++++++---------- tests/test_funcs.py | 21 ++++++++-------- tests/test_helpers.py | 2 +- tests/test_testing.py | 2 +- 4 files changed, 28 insertions(+), 25 deletions(-) diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 3e43fa91..7851d32f 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -322,26 +322,28 @@ def capabilities( dict Capabilities of the namespace. """ - if is_pydata_sparse_namespace(xp): - # No __array_namespace_info__(); no indexing by sparse arrays - return { - "boolean indexing": False, - "data-dependent shapes": True, - "max dimensions": None, - } out = xp.__array_namespace_info__().capabilities() - if is_jax_namespace(xp) and out["boolean indexing"]: - # FIXME https://github.com/jax-ml/jax/issues/27418 - # Fixed in jax >=0.6.0 - out = out.copy() - out["boolean indexing"] = False - if is_torch_namespace(xp): + if is_pydata_sparse_namespace(xp): + if out["boolean indexing"]: + # FIXME https://github.com/pydata/sparse/issues/876 + # boolean indexing is supported, but not when the index is a sparse array. + # boolean indexing by list or numpy array is not part of the Array API. + out = out.copy() + out["boolean indexing"] = False + elif is_jax_namespace(xp): + if out["boolean indexing"]: # pragma: no cover + # Backwards compatibility with jax <0.6.0 + # https://github.com/jax-ml/jax/issues/27418 + out = out.copy() + out["boolean indexing"] = False + elif is_torch_namespace(xp): # FIXME https://github.com/data-apis/array-api/issues/945 device = xp.get_default_device() if device is None else xp.device(device) if device.type == "meta": # type: ignore[union-attr] # pyright: ignore[reportAttributeAccessIssue,reportOptionalMemberAccess] out = out.copy() out["boolean indexing"] = False out["data-dependent shapes"] = False + return out diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 99da4a2b..88fb580f 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -416,7 +416,7 @@ def test_complex(self, xp: ModuleType): expect = xp.asarray([[1.0, -1.0j], [1.0j, 1.0]], dtype=xp.complex128) xp_assert_close(actual, expect) - @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="matmul with nan fillvalue") + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="sparse#877") def test_empty(self, xp: ModuleType): with warnings.catch_warnings(record=True): warnings.simplefilter("always", RuntimeWarning) @@ -451,7 +451,7 @@ def test_xp(self, xp: ModuleType): ) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="backend doesn't have arange") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no arange", strict=False) class TestOneHot: @pytest.mark.parametrize("n_dim", range(4)) @pytest.mark.parametrize("num_classes", [1, 3, 10]) @@ -816,7 +816,7 @@ def test_bool_dtype(self, xp: ModuleType): isclose(xp.asarray(True), b, atol=1), xp.asarray([True, True, True]) ) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="index by sparse array") + @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="index by sparse array") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="unknown shape") def test_none_shape(self, xp: ModuleType): a = xp.asarray([1, 5, 0]) @@ -825,7 +825,7 @@ def test_none_shape(self, xp: ModuleType): a = a[a < 5] xp_assert_equal(isclose(a, b), xp.asarray([True, False])) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="index by sparse array") + @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="index by sparse array") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="unknown shape") def test_none_shape_bool(self, xp: ModuleType): a = xp.asarray([True, True, False]) @@ -1141,10 +1141,10 @@ def test_xp(self, xp: ModuleType): class TestSinc: - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no linspace") def test_simple(self, xp: ModuleType): xp_assert_equal(sinc(xp.asarray(0.0)), xp.asarray(1.0)) - w = sinc(xp.linspace(-1, 1, 100)) + x = xp.asarray(np.linspace(-1, 1, 100)) + w = sinc(x) # check symmetry xp_assert_close(w, xp.flip(w, axis=0)) @@ -1153,11 +1153,12 @@ def test_dtype(self, xp: ModuleType, x: int | complex): with pytest.raises(ValueError, match="real floating data type"): _ = sinc(xp.asarray(x)) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no arange") def test_3d(self, xp: ModuleType): - x = xp.reshape(xp.arange(18, dtype=xp.float64), (3, 3, 2)) - expected = xp.zeros((3, 3, 2), dtype=xp.float64) - expected = at(expected)[0, 0, 0].set(1.0) + x = np.arange(18, dtype=np.float64).reshape((3, 3, 2)) + expected = np.zeros_like(x) + expected[0, 0, 0] = 1 + x = xp.asarray(x) + expected = xp.asarray(expected) xp_assert_close(sinc(x), expected, atol=1e-15) def test_device(self, xp: ModuleType, device: Device): diff --git a/tests/test_helpers.py b/tests/test_helpers.py index 74a0ec93..4a545df8 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -40,7 +40,7 @@ def override(func): lazy_xp_function(in1d, jax_jit=False) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no unique_inverse") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no unique_inverse") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="no unique_inverse") class TestIn1D: # cover both code paths diff --git a/tests/test_testing.py b/tests/test_testing.py index 43d6e8ae..5a123db9 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -140,7 +140,7 @@ def test_assert_less(self, xp: ModuleType): xp_assert_less(xp.asarray([1, 1]), xp.asarray([2, 1])) @pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close, xp_assert_less]) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="index by sparse array") + @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="index by sparse array") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="boolean indexing") def test_none_shape(self, xp: ModuleType, func: Callable[..., None]): """On Dask and other lazy backends, test that a shape with NaN's or None's From 7b4887e83c01709ef9cb2d7cc3d84af156753461 Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Wed, 4 Jun 2025 15:41:31 +0100 Subject: [PATCH 029/104] docs: add mdhaber as a contributor for test (#319) * docs: update README.md * docs: update CONTRIBUTORS.md * docs: update .all-contributorsrc --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> --- .all-contributorsrc | 3 ++- CONTRIBUTORS.md | 2 +- README.md | 2 +- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index 561259e2..b33d332f 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -38,7 +38,8 @@ "profile": "https://github.com/mdhaber", "contributions": [ "code", - "ideas" + "ideas", + "test" ] }, { diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index b0f2ffb6..cc93de44 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -10,7 +10,7 @@ This project exists thanks to the following contributors Lucas Colley
Lucas Colley
💻 📖 💡 🤔 🚇 🚧 🔧 ⚠️ 🐛 📦 👀 - Matt Haberland
Matt Haberland
💻 🤔 + Matt Haberland
Matt Haberland
💻 🤔 ⚠️ Jake Bowhay
Jake Bowhay
💻 👀 🔧 Aaron Meurer
Aaron Meurer
👀 🤔 🚇 Tim Head
Tim Head
🤔 diff --git a/README.md b/README.md index 65d19699..54f9d3a7 100644 --- a/README.md +++ b/README.md @@ -65,7 +65,7 @@ This project exists thanks to the following contributors Lucas Colley
Lucas Colley
💻 📖 💡 🤔 🚇 🚧 🔧 ⚠️ 🐛 📦 👀 - Matt Haberland
Matt Haberland
💻 🤔 + Matt Haberland
Matt Haberland
💻 🤔 ⚠️ Jake Bowhay
Jake Bowhay
💻 👀 🔧 Aaron Meurer
Aaron Meurer
👀 🤔 🚇 Tim Head
Tim Head
🤔 From c4b81fa58b7aaa871f79aa19b0fba5f1499c978c Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 5 Jun 2025 13:22:08 +0000 Subject: [PATCH 030/104] deps: Update dependency basedpyright to >=1.29.2 (#320) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 0924ebd5..5201b6b8 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3936,7 +3936,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: bbde76ca6f19f4e67758fb784655e5a6675dedf135d2ed6f9f50502582dd4e8c + sha256: 9e5333f19e26dd1aaeffcff7d9773c8ea8ffaecd16860c0d018fcd480e4aa8cc requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 2163aeba..1db23337 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ typing-extensions = ">=4.13.2" pre-commit = ">=4.2.0" pylint = ">=3.3.7" basedmypy = ">=2.10.0" -basedpyright = ">=1.29.1" +basedpyright = ">=1.29.2" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1" From a127376d44cc6864120b48f5c991e2ba54a38af5 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 10 Jun 2025 04:56:22 +0000 Subject: [PATCH 031/104] deps: Update dependency hypothesis to >=6.131.28 (#328) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pixi.lock b/pixi.lock index 5201b6b8..c5eadf27 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3936,7 +3936,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 9e5333f19e26dd1aaeffcff7d9773c8ea8ffaecd16860c0d018fcd480e4aa8cc + sha256: 9d76fb8805ceb542471e2d82f1aa6b821db5f0a64fe04cc02d3d7c4bb728437e requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 1db23337..7a415f01 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,7 +64,7 @@ numpydoc = ">=1.8.0,<2" array-api-strict = ">=2.3.1" numpy = ">=2.1.3" pytest = ">=8.3.5" -hypothesis = ">=6.131.8" +hypothesis = ">=6.131.28" dask-core = ">=2025.5.1" # No distributed, tornado, etc. # NOTE: don't add cupy, jax, pytorch, or sparse here, # as they slow down mypy and are not portable across target OSs @@ -80,7 +80,7 @@ lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"] , description [tool.pixi.feature.tests.dependencies] pytest = ">=8.3.5" pytest-cov = ">=6.1.1" -hypothesis = ">=6.131.8" +hypothesis = ">=6.131.28" array-api-strict = ">=2.3.1" numpy = ">=1.22.0" From 9375f638607042f35a008e6002d9d95d088afd4c Mon Sep 17 00:00:00 2001 From: crusaderky Date: Tue, 10 Jun 2025 10:05:26 +0100 Subject: [PATCH 032/104] TYP: replace basedmypy with mypy --- pixi.lock | 362 +++++++++++++++++--- pyproject.toml | 11 +- src/array_api_extra/_lib/_at.py | 2 +- src/array_api_extra/_lib/_backends.py | 2 +- src/array_api_extra/_lib/_funcs.py | 12 +- src/array_api_extra/_lib/_lazy.py | 12 +- src/array_api_extra/_lib/_testing.py | 2 +- src/array_api_extra/_lib/_utils/_compat.pyi | 2 +- src/array_api_extra/_lib/_utils/_helpers.py | 8 +- src/array_api_extra/_lib/_utils/_typing.pyi | 4 +- src/array_api_extra/testing.py | 16 +- tests/test_at.py | 10 +- tests/test_funcs.py | 5 +- tests/test_helpers.py | 13 +- tests/test_lazy.py | 2 +- tests/test_testing.py | 3 +- 16 files changed, 359 insertions(+), 107 deletions(-) diff --git a/pixi.lock b/pixi.lock index c5eadf27..03cc1128 100644 --- a/pixi.lock +++ b/pixi.lock @@ -101,9 +101,7 @@ environments: - 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conda: https://prefix.dev/conda-forge/noarch/ptyprocess-0.7.0-pyhd8ed1ab_1.conda sha256: a7713dfe30faf17508ec359e0bc7e0983f5d94682492469bd462cdaae9c64d83 md5: 7d9daffbb8d8e0af0f769dbbcd173a54 diff --git a/pyproject.toml b/pyproject.toml index 7a415f01..36e25425 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -57,7 +57,7 @@ array-api-extra = { path = ".", editable = true } typing-extensions = ">=4.13.2" pre-commit = ">=4.2.0" pylint = ">=3.3.7" -basedmypy = ">=2.10.0" +mypy = ">=1.16.0" basedpyright = ">=1.29.2" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: @@ -227,16 +227,17 @@ python_version = "3.10" warn_unused_configs = true strict = true enable_error_code = ["ignore-without-code", "truthy-bool"] -# https://github.com/data-apis/array-api-typing -disallow_any_expr = false -# false positives with input validation -disable_error_code = ["redundant-expr", "unreachable", "no-any-return"] +disable_error_code = ["no-any-return"] [[tool.mypy.overrides]] # slow or unavailable on Windows; do not add to the lint env module = ["cupy.*", "jax.*", "sparse.*", "torch.*"] ignore_missing_imports = true +[[tool.mypy.overrides]] +module = ["tests/*"] +disable_error_code = ["no-untyped-def"] # test(...) without -> None + # pyright [tool.basedpyright] diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py index 870884b8..fb2d6ab7 100644 --- a/src/array_api_extra/_lib/_at.py +++ b/src/array_api_extra/_lib/_at.py @@ -37,7 +37,7 @@ class _AtOp(Enum): MAX = "max" # @override from Python 3.12 - def __str__(self) -> str: # type: ignore[explicit-override] # pyright: ignore[reportImplicitOverride] + def __str__(self) -> str: # pyright: ignore[reportImplicitOverride] """ Return string representation (useful for pytest logs). diff --git a/src/array_api_extra/_lib/_backends.py b/src/array_api_extra/_lib/_backends.py index f64e1479..68bef24b 100644 --- a/src/array_api_extra/_lib/_backends.py +++ b/src/array_api_extra/_lib/_backends.py @@ -30,7 +30,7 @@ class Backend(Enum): # numpydoc ignore=PR02 JAX = "jax.numpy" JAX_GPU = "jax.numpy:gpu" - def __str__(self) -> str: # type: ignore[explicit-override] # pyright: ignore[reportImplicitOverride] # numpydoc ignore=RT01 + def __str__(self) -> str: # pyright: ignore[reportImplicitOverride] # numpydoc ignore=RT01 """Pretty-print parameterized test names.""" return ( self.name.lower().replace("_gpu", ":gpu").replace("_readonly", ":readonly") diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 69dfe6a4..cf1a894a 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -34,7 +34,7 @@ @overload -def apply_where( # type: ignore[explicit-any,decorated-any] # numpydoc ignore=GL08 +def apply_where( # numpydoc ignore=GL08 cond: Array, args: Array | tuple[Array, ...], f1: Callable[..., Array], @@ -46,7 +46,7 @@ def apply_where( # type: ignore[explicit-any,decorated-any] # numpydoc ignore=G @overload -def apply_where( # type: ignore[explicit-any,decorated-any] # numpydoc ignore=GL08 +def apply_where( # numpydoc ignore=GL08 cond: Array, args: Array | tuple[Array, ...], f1: Callable[..., Array], @@ -57,7 +57,7 @@ def apply_where( # type: ignore[explicit-any,decorated-any] # numpydoc ignore=G ) -> Array: ... -def apply_where( # type: ignore[explicit-any] # numpydoc ignore=PR01,PR02 +def apply_where( # numpydoc ignore=PR01,PR02 cond: Array, args: Array | tuple[Array, ...], f1: Callable[..., Array], @@ -143,7 +143,7 @@ def apply_where( # type: ignore[explicit-any] # numpydoc ignore=PR01,PR02 return _apply_where(cond, f1, f2, fill_value, *args_, xp=xp) -def _apply_where( # type: ignore[explicit-any] # numpydoc ignore=PR01,RT01 +def _apply_where( # numpydoc ignore=PR01,RT01 cond: Array, f1: Callable[..., Array], f2: Callable[..., Array] | None, @@ -813,8 +813,7 @@ def pad( else: pad_width_seq = cast(list[tuple[int, int]], list(pad_width)) - # https://github.com/python/typeshed/issues/13376 - slices: list[slice] = [] # type: ignore[explicit-any] + slices: list[slice] = [] newshape: list[int] = [] for ax, w_tpl in enumerate(pad_width_seq): if len(w_tpl) != 2: @@ -826,6 +825,7 @@ def pad( if w_tpl[0] == 0 and w_tpl[1] == 0: sl = slice(None, None, None) else: + stop: int | None start, stop = w_tpl stop = None if stop == 0 else -stop diff --git a/src/array_api_extra/_lib/_lazy.py b/src/array_api_extra/_lib/_lazy.py index d13d08f8..dc7c0039 100644 --- a/src/array_api_extra/_lib/_lazy.py +++ b/src/array_api_extra/_lib/_lazy.py @@ -22,7 +22,7 @@ import numpy as np from numpy.typing import ArrayLike - NumPyObject: TypeAlias = np.ndarray[Any, Any] | np.generic # type: ignore[explicit-any] + NumPyObject: TypeAlias = np.ndarray[Any, Any] | np.generic else: # Sphinx hack NumPyObject = Any @@ -31,7 +31,7 @@ @overload -def lazy_apply( # type: ignore[decorated-any, valid-type] +def lazy_apply( # type: ignore[valid-type] func: Callable[P, Array | ArrayLike], *args: Array | complex | None, shape: tuple[int | None, ...] | None = None, @@ -43,7 +43,7 @@ def lazy_apply( # type: ignore[decorated-any, valid-type] @overload -def lazy_apply( # type: ignore[decorated-any, valid-type] +def lazy_apply( # type: ignore[valid-type] func: Callable[P, Sequence[Array | ArrayLike]], *args: Array | complex | None, shape: Sequence[tuple[int | None, ...]], @@ -313,7 +313,7 @@ def _is_jax_jit_enabled(xp: ModuleType) -> bool: # numpydoc ignore=PR01,RT01 return True -def _lazy_apply_wrapper( # type: ignore[explicit-any] # numpydoc ignore=PR01,RT01 +def _lazy_apply_wrapper( # numpydoc ignore=PR01,RT01 func: Callable[..., Array | ArrayLike | Sequence[Array | ArrayLike]], as_numpy: bool, multi_output: bool, @@ -331,7 +331,7 @@ def _lazy_apply_wrapper( # type: ignore[explicit-any] # numpydoc ignore=PR01,R # On Dask, @wraps causes the graph key to contain the wrapped function's name @wraps(func) - def wrapper( # type: ignore[decorated-any,explicit-any] + def wrapper( *args: Array | complex | None, **kwargs: Any ) -> tuple[Array, ...]: # numpydoc ignore=GL08 args_list = [] @@ -343,7 +343,7 @@ def wrapper( # type: ignore[decorated-any,explicit-any] if as_numpy: import numpy as np - arg = cast(Array, np.asarray(arg)) # type: ignore[bad-cast] # noqa: PLW2901 + arg = cast(Array, np.asarray(arg)) # noqa: PLW2901 args_list.append(arg) assert device is not None diff --git a/src/array_api_extra/_lib/_testing.py b/src/array_api_extra/_lib/_testing.py index 16a9d102..30e2f1ef 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -110,7 +110,7 @@ def _is_materializable(x: Array) -> bool: return not is_torch_array(x) or x.device.type != "meta" # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] -def as_numpy_array(array: Array, *, xp: ModuleType) -> np.typing.NDArray[Any]: # type: ignore[explicit-any] +def as_numpy_array(array: Array, *, xp: ModuleType) -> np.typing.NDArray[Any]: """ Convert array to NumPy, bypassing GPU-CPU transfer guards and densification guards. """ diff --git a/src/array_api_extra/_lib/_utils/_compat.pyi b/src/array_api_extra/_lib/_utils/_compat.pyi index 48addda4..95c6bc8a 100644 --- a/src/array_api_extra/_lib/_utils/_compat.pyi +++ b/src/array_api_extra/_lib/_utils/_compat.pyi @@ -36,7 +36,7 @@ def is_torch_array(x: object, /) -> TypeGuard[Array]: ... def is_lazy_array(x: object, /) -> TypeGuard[Array]: ... def is_writeable_array(x: object, /) -> TypeGuard[Array]: ... def size(x: Array, /) -> int | None: ... -def to_device( # type: ignore[explicit-any] +def to_device( x: Array, device: Device, # pylint: disable=redefined-outer-name /, diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 7851d32f..d177b376 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -210,7 +210,7 @@ def asarrays( float: ("real floating", "complex floating"), complex: "complex floating", } - kind = same_dtype[type(cast(complex, b))] # type: ignore[index] + kind = same_dtype[type(cast(complex, b))] if xp.isdtype(a.dtype, kind): xb = xp.asarray(b, dtype=a.dtype) else: @@ -458,7 +458,7 @@ def persistent_id( return instances, (f.getvalue(), *rest) -def pickle_unflatten(instances: Iterable[object], rest: FlattenRest) -> Any: # type: ignore[explicit-any] +def pickle_unflatten(instances: Iterable[object], rest: FlattenRest) -> Any: """ Reverse of ``pickle_flatten``. @@ -521,7 +521,7 @@ def __init__(self, obj: T) -> None: # numpydoc ignore=GL08 self.obj = obj @classmethod - def _register(cls): # numpydoc ignore=SS06 + def _register(cls) -> None: # numpydoc ignore=SS06 """ Register upon first use instead of at import time, to avoid globally importing JAX. @@ -583,7 +583,7 @@ def f(x: Array, y: float, plus: bool) -> Array: import jax @jax.jit # type: ignore[misc] # pyright: ignore[reportUntypedFunctionDecorator] - def inner( # type: ignore[decorated-any,explicit-any] # numpydoc ignore=GL08 + def inner( # numpydoc ignore=GL08 wargs: _AutoJITWrapper[Any], ) -> _AutoJITWrapper[T]: args, kwargs = wargs.obj diff --git a/src/array_api_extra/_lib/_utils/_typing.pyi b/src/array_api_extra/_lib/_utils/_typing.pyi index e32a59bd..35c255fc 100644 --- a/src/array_api_extra/_lib/_utils/_typing.pyi +++ b/src/array_api_extra/_lib/_utils/_typing.pyi @@ -95,10 +95,10 @@ class DType(Protocol): # pylint: disable=missing-class-docstring class Device(Protocol): # pylint: disable=missing-class-docstring pass -SetIndex: TypeAlias = ( # type: ignore[explicit-any] +SetIndex: TypeAlias = ( int | slice | EllipsisType | Array | tuple[int | slice | EllipsisType | Array, ...] ) -GetIndex: TypeAlias = ( # type: ignore[explicit-any] +GetIndex: TypeAlias = ( SetIndex | None | tuple[int | slice | EllipsisType | None | Array, ...] ) diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index 3979f9dd..bb310467 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -36,7 +36,7 @@ def override(func): P = ParamSpec("P") T = TypeVar("T") -_ufuncs_tags: dict[object, dict[str, Any]] = {} # type: ignore[explicit-any] +_ufuncs_tags: dict[object, dict[str, Any]] = {} class Deprecated(enum.Enum): @@ -48,7 +48,7 @@ class Deprecated(enum.Enum): DEPRECATED = Deprecated.DEPRECATED -def lazy_xp_function( # type: ignore[explicit-any] +def lazy_xp_function( func: Callable[..., Any], *, allow_dask_compute: bool | int = False, @@ -257,12 +257,12 @@ def xp(request, monkeypatch): mod = cast(ModuleType, request.module) mods = [mod, *cast(list[ModuleType], getattr(mod, "lazy_xp_modules", []))] - def iter_tagged() -> ( # type: ignore[explicit-any] + def iter_tagged() -> ( Iterator[tuple[ModuleType, str, Callable[..., Any], dict[str, Any]]] ): for mod in mods: for name, func in mod.__dict__.items(): - tags: dict[str, Any] | None = None # type: ignore[explicit-any] + tags: dict[str, Any] | None = None with contextlib.suppress(AttributeError): tags = func._lazy_xp_function # pylint: disable=protected-access if tags is None: @@ -313,7 +313,9 @@ def __init__(self, max_count: int, msg: str): # numpydoc ignore=GL08 self.msg = msg @override - def __call__(self, dsk: Graph, keys: Sequence[Key] | Key, **kwargs: Any) -> Any: # type: ignore[decorated-any,explicit-any] # numpydoc ignore=GL08 + def __call__( + self, dsk: Graph, keys: Sequence[Key] | Key, **kwargs: Any + ) -> Any: # numpydoc ignore=GL08 import dask self.count += 1 @@ -321,7 +323,7 @@ def __call__(self, dsk: Graph, keys: Sequence[Key] | Key, **kwargs: Any) -> Any: # offending line in the user's code assert self.count <= self.max_count, self.msg - return dask.get(dsk, keys, **kwargs) # type: ignore[attr-defined,no-untyped-call] # pyright: ignore[reportPrivateImportUsage] + return dask.get(dsk, keys, **kwargs) # type: ignore[attr-defined] # pyright: ignore[reportPrivateImportUsage] def _dask_wrap( @@ -354,7 +356,7 @@ def wrapper(*args: P.args, **kwargs: P.kwargs) -> T: # numpydoc ignore=GL08 # `pytest.raises` and `pytest.warns` to work as expected. Note that this would # not work on scheduler='distributed', as it would not block. arrays, rest = pickle_flatten(out, da.Array) - arrays = dask.persist(arrays, scheduler="threads")[0] # type: ignore[attr-defined,no-untyped-call,func-returns-value,index] # pyright: ignore[reportPrivateImportUsage] + arrays = dask.persist(arrays, scheduler="threads")[0] # type: ignore[attr-defined,no-untyped-call] # pyright: ignore[reportPrivateImportUsage] return pickle_unflatten(arrays, rest) # pyright: ignore[reportUnknownArgumentType] return wrapper diff --git a/tests/test_at.py b/tests/test_at.py index 7294a7c4..04b71b70 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -40,7 +40,7 @@ def at_op( just a workaround for when one wants to apply jax.jit to `at()` directly, which is not a common use case. """ - meth = cast(Callable[..., Array], getattr(at(x, idx), op.value)) # type: ignore[explicit-any] + meth = cast(Callable[..., Array], getattr(at(x, idx), op.value)) return meth(y, copy=copy, xp=xp) @@ -157,7 +157,7 @@ def test_copy_default(xp: ModuleType, library: Backend, op: _AtOp): """ x = xp.asarray([1.0, 10.0, 20.0]) expect_copy = not is_writeable_array(x) - meth = cast(Callable[..., Array], getattr(at(x)[:2], op.value)) # type: ignore[explicit-any] + meth = cast(Callable[..., Array], getattr(at(x)[:2], op.value)) with assert_copy(x, None, expect_copy): _ = meth(2.0) @@ -166,7 +166,7 @@ def test_copy_default(xp: ModuleType, library: Backend, op: _AtOp): # even if the arrays are writeable. expect_copy = not is_writeable_array(x) or library is Backend.DASK idx = xp.asarray([True, True, False]) - meth = cast(Callable[..., Array], getattr(at(x, idx), op.value)) # type: ignore[explicit-any] + meth = cast(Callable[..., Array], getattr(at(x, idx), op.value)) with assert_copy(x, None, expect_copy): _ = meth(2.0) @@ -178,7 +178,7 @@ def test_copy_invalid(): def test_xp(): - a = cast(Array, np.asarray([1, 2, 3])) # type: ignore[bad-cast] + a = cast(Array, np.asarray([1, 2, 3])) _ = at(a, 0).set(4, xp=np) _ = at(a, 0).add(4, xp=np) _ = at(a, 0).subtract(4, xp=np) @@ -190,7 +190,7 @@ def test_xp(): def test_alternate_index_syntax(): - xp = cast(ModuleType, np) # pyright: ignore[reportInvalidCast] + xp = cast(ModuleType, np) # type: ignore[redundant-cast] # pyright: ignore[reportInvalidCast] a = cast(Array, xp.asarray([1, 2, 3])) xp_assert_equal(at(a, 0).set(4, copy=True), xp.asarray([4, 2, 3])) xp_assert_equal(at(a)[0].set(4, copy=True), xp.asarray([4, 2, 3])) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 88fb580f..6e80a61d 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -36,9 +36,6 @@ from .conftest import NUMPY_VERSION -# some xp backends are untyped -# mypy: disable-error-code=no-untyped-def - lazy_xp_function(apply_where) lazy_xp_function(atleast_nd) lazy_xp_function(cov) @@ -213,7 +210,7 @@ def test_device(self, xp: ModuleType, device: Device): p=st.floats(min_value=0, max_value=1), data=st.data(), ) - def test_hypothesis( # type: ignore[explicit-any,decorated-any] + def test_hypothesis( self, n_arrays: int, rng_seed: int, diff --git a/tests/test_helpers.py b/tests/test_helpers.py index 4a545df8..275ca519 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -32,7 +32,6 @@ def override(func): return func -# mypy: disable-error-code=no-untyped-usage T = TypeVar("T") @@ -387,7 +386,7 @@ def test_static_hashable(self, jnp: ModuleType): """Static argument/return value is hashable, but not serializable""" class C: - def __reduce__(self) -> object: # type: ignore[explicit-override,override] # pyright: ignore[reportIncompatibleMethodOverride,reportImplicitOverride] + def __reduce__(self) -> object: # type: ignore[override] # pyright: ignore[reportIncompatibleMethodOverride,reportImplicitOverride] raise Exception() @jax_autojit @@ -399,12 +398,12 @@ def f(x: object) -> object: assert out is inp # Serializable opaque input contains non-serializable object plus array - inp = Wrapper((C(), jnp.asarray([1, 2]))) - out = f(inp) + winp = Wrapper((C(), jnp.asarray([1, 2]))) + out = f(winp) assert isinstance(out, Wrapper) - assert out.x[0] is inp.x[0] - assert out.x[1] is not inp.x[1] - xp_assert_equal(out.x[1], inp.x[1]) # pyright: ignore[reportUnknownArgumentType] + assert out.x[0] is winp.x[0] + assert out.x[1] is not winp.x[1] + xp_assert_equal(out.x[1], winp.x[1]) # pyright: ignore[reportUnknownArgumentType] def test_arraylikes_are_static(self): pytest.importorskip("jax") diff --git a/tests/test_lazy.py b/tests/test_lazy.py index f97062f0..503e180f 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -141,7 +141,7 @@ def f(x: Array) -> Array: xp = array_namespace(x) return xp.sum(x, axis=0) + x - x_np = cast(Array, np.arange(15).reshape(5, 3)) # type: ignore[bad-cast] + x_np = cast(Array, np.arange(15).reshape(5, 3)) expect = da.asarray(f(x_np)) x_da = da.asarray(x_np).rechunk(3) diff --git a/tests/test_testing.py b/tests/test_testing.py index 5a123db9..33c36c12 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -20,7 +20,6 @@ from array_api_extra._lib._utils._typing import Array, Device from array_api_extra.testing import lazy_xp_function -# mypy: disable-error-code="decorated-any, explicit-any" # pyright: reportUnknownParameterType=false,reportMissingParameterType=false @@ -295,7 +294,7 @@ def test_lazy_xp_function_deprecated_static_argnames(): # Test an arbitrary Cython ufunc (@cython.vectorize). # When SCIPY_ARRAY_API is not set, this is the same as # scipy.special.erf. - from scipy.special._ufuncs import erf # type: ignore[import-not-found] + from scipy.special._ufuncs import erf # type: ignore[import-untyped] lazy_xp_function(erf) # pyright: ignore[reportUnknownArgumentType] except ImportError: From 2e336b278bbd1b088ddb2e336e2c4f6e3b60f02b Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sat, 14 Jun 2025 16:24:01 +0000 Subject: [PATCH 033/104] deps: Update jax to >=0.6.0 (#331) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/pixi.lock b/pixi.lock index 03cc1128..abf2341d 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3948,7 +3948,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 026f2389147e594fb81cfd47423eb90f6d7253d12ea1e0e0ea739e6aa4dd2e63 + sha256: 39c5dcdddbee3dd770673f18c2eb0b781a07cb0080dd9ef9bd121ea1a3ba800e requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 36e25425..48182b1a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -139,13 +139,13 @@ dask-core = ">=2025.5.1" # No distributed, tornado, etc. sparse = ">=0.17.0" [tool.pixi.feature.backends.target.linux-64.dependencies] -jax = ">=0.5.3" +jax = ">=0.6.0" [tool.pixi.feature.backends.target.osx-64.dependencies] -jax = ">=0.5.3" +jax = ">=0.6.0" [tool.pixi.feature.backends.target.osx-arm64.dependencies] -jax = ">=0.5.3" +jax = ">=0.6.0" [tool.pixi.feature.backends.target.win-64.dependencies] # jax = "*" # unavailable @@ -161,7 +161,7 @@ system-requirements = { cuda = "12" } [tool.pixi.feature.cuda-backends.target.linux-64.dependencies] cupy = ">=13.4.1" -jaxlib = { version = ">=0.5.3", build = "cuda12*" } +jaxlib = { version = ">=0.6.0", build = "cuda12*" } pytorch = { version = ">=2.7.0", build = "cuda12*" } [tool.pixi.feature.cuda-backends.target.osx-64.dependencies] From 4631572c484d837a7867a71e9491898307c7b787 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sun, 15 Jun 2025 04:22:28 +0000 Subject: [PATCH 034/104] deps: Update codecov/codecov-action action to v5.4.3 (#332) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 73ab37e1..b4558c09 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -69,6 +69,6 @@ jobs: run: pixi run -e ${{ matrix.environment }} tests-ci - name: Upload coverage report - uses: codecov/codecov-action@ad3126e916f78f00edff4ed0317cf185271ccc2d # v5.4.2 + uses: codecov/codecov-action@18283e04ce6e62d37312384ff67231eb8fd56d24 # v5.4.3 with: token: ${{ secrets.CODECOV_TOKEN }} From dbcd7097f13afff0e5e00077b6050c387cc4c30a Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sun, 15 Jun 2025 09:12:48 +0100 Subject: [PATCH 035/104] deps: Update dawidd6/action-download-artifact action to v10 (#333) --- .github/workflows/docs-deploy.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs-deploy.yml b/.github/workflows/docs-deploy.yml index 78a5ada1..25b46467 100644 --- a/.github/workflows/docs-deploy.yml +++ b/.github/workflows/docs-deploy.yml @@ -19,7 +19,7 @@ jobs: steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 - name: Download Artifact - uses: dawidd6/action-download-artifact@07ab29fd4a977ae4d2b275087cf67563dfdf0295 # v9 + uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10 with: workflow: docs-build.yml name: docs-build From 58cf1dbd8582902c9ee8567a14470007386933bc Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 17 Jun 2025 11:11:12 +0100 Subject: [PATCH 036/104] deps: Update dependency pytest to >=8.4.0 (#334) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pixi.lock b/pixi.lock index abf2341d..601133e5 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3948,7 +3948,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 39c5dcdddbee3dd770673f18c2eb0b781a07cb0080dd9ef9bd121ea1a3ba800e + sha256: 538b22782f80a225a957582445ed0772fe7ae71f85fc9f2082dcd71510b976d6 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 48182b1a..611a6a80 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -63,7 +63,7 @@ numpydoc = ">=1.8.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1" numpy = ">=2.1.3" -pytest = ">=8.3.5" +pytest = ">=8.4.0" hypothesis = ">=6.131.28" dask-core = ">=2025.5.1" # No distributed, tornado, etc. # NOTE: don't add cupy, jax, pytorch, or sparse here, @@ -78,7 +78,7 @@ pyright = { cmd = "basedpyright", description = "Type check with basedpyright"} lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"] , description = "Run pre-commit, pylint, mypy, and pyright"} [tool.pixi.feature.tests.dependencies] -pytest = ">=8.3.5" +pytest = ">=8.4.0" pytest-cov = ">=6.1.1" hypothesis = ">=6.131.28" array-api-strict = ">=2.3.1" @@ -106,7 +106,7 @@ sphinx-copybutton = ">=0.5.2" sphinx-autodoc-typehints = ">=1.25.3" # Needed to import parsed modules with autodoc dask-core = ">=2025.5.1" # No distributed, tornado, etc. -pytest = ">=8.3.5" +pytest = ">=8.4.0" typing-extensions = ">=4.13.2" numpy = ">=2.1.3" From dfa980887484499031bf2a023e32b57cf37fdca6 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Tue, 17 Jun 2025 16:19:55 +0100 Subject: [PATCH 037/104] ENH: Free-threading support (#330) * TST: Free-threaded tests * project tag --- .github/workflows/ci.yml | 16 +- pixi.lock | 702 ++++++++++++++++++++++++-- pyproject.toml | 13 +- src/array_api_extra/_lib/_backends.py | 40 +- src/array_api_extra/_lib/_lazy.py | 2 +- src/array_api_extra/testing.py | 73 ++- tests/conftest.py | 38 +- tests/test_at.py | 2 +- tests/test_funcs.py | 4 +- tests/test_helpers.py | 2 +- tests/test_lazy.py | 4 +- tests/test_testing.py | 22 +- 12 files changed, 828 insertions(+), 90 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b4558c09..ebe75372 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -45,13 +45,18 @@ jobs: pixi run -e lint pyright checks: - name: Check ${{ matrix.environment }} + name: Test ${{ matrix.environment }} runs-on: ${{ matrix.runs-on }} needs: [pre-commit-and-lint] strategy: fail-fast: false matrix: - environment: [tests-py310, tests-py313, tests-numpy1, tests-backends] + environment: + - tests-py310 + - tests-py313 + - tests-numpy1 + - tests-backends + - tests-nogil runs-on: [ubuntu-latest] steps: @@ -66,9 +71,16 @@ jobs: environments: ${{ matrix.environment }} - name: Test package + # Save some time; also at the moment of writing coverage crashes on python 3.13t + if: ${{ matrix.environment != 'tests-nogil' }} run: pixi run -e ${{ matrix.environment }} tests-ci + - name: Test free-threading + if: ${{ matrix.environment == 'tests-nogil' }} + run: pixi run -e tests-nogil tests --parallel-threads=4 + - name: Upload coverage report + if: ${{ matrix.environment != 'tests-nogil' }} uses: codecov/codecov-action@18283e04ce6e62d37312384ff67231eb8fd56d24 # v5.4.3 with: token: ${{ secrets.CODECOV_TOKEN }} diff --git a/pixi.lock b/pixi.lock index 601133e5..709ffbe9 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1542,7 +1542,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/noarch/myst-parser-4.0.1-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda - - conda: https://prefix.dev/conda-forge/linux-64/numpy-2.2.6-py313h17eae1a_0.conda + - conda: https://prefix.dev/conda-forge/linux-64/numpy-2.3.0-py313h17eae1a_0.conda - conda: https://prefix.dev/conda-forge/linux-64/openssl-3.5.0-h7b32b05_1.conda - conda: https://prefix.dev/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda - conda: https://prefix.dev/conda-forge/noarch/partd-1.4.2-pyhd8ed1ab_0.conda @@ -1629,7 +1629,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/noarch/myst-parser-4.0.1-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/osx-64/ncurses-6.5-h0622a9a_3.conda - - conda: https://prefix.dev/conda-forge/osx-64/numpy-2.2.6-py313hc518a0f_0.conda + - conda: https://prefix.dev/conda-forge/osx-64/numpy-2.3.0-py313hc518a0f_0.conda - conda: https://prefix.dev/conda-forge/osx-64/openssl-3.5.0-hc426f3f_1.conda - conda: https://prefix.dev/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda - conda: https://prefix.dev/conda-forge/noarch/partd-1.4.2-pyhd8ed1ab_0.conda @@ -1716,7 +1716,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/noarch/myst-parser-4.0.1-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/osx-arm64/ncurses-6.5-h5e97a16_3.conda - - conda: https://prefix.dev/conda-forge/osx-arm64/numpy-2.2.6-py313h41a2e72_0.conda + - conda: https://prefix.dev/conda-forge/osx-arm64/numpy-2.3.0-py313h41a2e72_0.conda - conda: https://prefix.dev/conda-forge/osx-arm64/openssl-3.5.0-h81ee809_1.conda - conda: https://prefix.dev/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda - conda: https://prefix.dev/conda-forge/noarch/partd-1.4.2-pyhd8ed1ab_0.conda @@ -1803,7 +1803,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/mdurl-0.1.2-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/win-64/mkl-2024.2.2-h66d3029_15.conda - conda: https://prefix.dev/conda-forge/noarch/myst-parser-4.0.1-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/win-64/numpy-2.2.6-py313hefb8edb_0.conda + - conda: https://prefix.dev/conda-forge/win-64/numpy-2.3.0-py313hefb8edb_0.conda - conda: https://prefix.dev/conda-forge/win-64/openssl-3.5.0-ha4e3fda_1.conda - conda: https://prefix.dev/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda - conda: https://prefix.dev/conda-forge/noarch/partd-1.4.2-pyhd8ed1ab_0.conda @@ -1921,7 +1921,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/nodeenv-1.9.1-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/linux-64/nodejs-22.13.0-hf235a45_0.conda - conda: https://prefix.dev/conda-forge/noarch/nodejs-wheel-22.16.0-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/numpy-2.2.6-py313h17eae1a_0.conda + - conda: https://prefix.dev/conda-forge/linux-64/numpy-2.3.0-py313h17eae1a_0.conda - conda: https://prefix.dev/conda-forge/noarch/numpydoc-1.8.0-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/linux-64/openssl-3.5.0-h7b32b05_1.conda - conda: https://prefix.dev/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda @@ -2030,7 +2030,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/nodeenv-1.9.1-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/osx-64/nodejs-22.13.0-hffbc63d_0.conda - conda: https://prefix.dev/conda-forge/noarch/nodejs-wheel-22.16.0-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/osx-64/numpy-2.2.6-py313hc518a0f_0.conda + - conda: https://prefix.dev/conda-forge/osx-64/numpy-2.3.0-py313hc518a0f_0.conda - conda: https://prefix.dev/conda-forge/noarch/numpydoc-1.8.0-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/osx-64/openssl-3.5.0-hc426f3f_1.conda - conda: https://prefix.dev/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda @@ -2139,7 +2139,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/nodeenv-1.9.1-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/osx-arm64/nodejs-22.13.0-h02a13b7_0.conda - conda: https://prefix.dev/conda-forge/noarch/nodejs-wheel-22.16.0-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/osx-arm64/numpy-2.2.6-py313h41a2e72_0.conda + - conda: https://prefix.dev/conda-forge/osx-arm64/numpy-2.3.0-py313h41a2e72_0.conda - conda: https://prefix.dev/conda-forge/noarch/numpydoc-1.8.0-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/osx-arm64/openssl-3.5.0-h81ee809_1.conda - conda: https://prefix.dev/conda-forge/noarch/packaging-25.0-pyh29332c3_1.conda @@ -2246,7 +2246,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/nodeenv-1.9.1-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/win-64/nodejs-22.13.0-hfeaa22a_0.conda - conda: https://prefix.dev/conda-forge/noarch/nodejs-wheel-22.16.0-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/win-64/numpy-2.2.6-py313hefb8edb_0.conda + - 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pkg:pypi/zipp?source=compressed-mapping size: 22691 timestamp: 1748277499928 +- conda: https://prefix.dev/conda-forge/noarch/zipp-3.23.0-pyhd8ed1ab_0.conda + sha256: 7560d21e1b021fd40b65bfb72f67945a3fcb83d78ad7ccf37b8b3165ec3b68ad + md5: df5e78d904988eb55042c0c97446079f + depends: + - python >=3.9 + license: MIT + license_family: MIT + purls: + - pkg:pypi/zipp?source=hash-mapping + size: 22963 + timestamp: 1749421737203 - conda: https://prefix.dev/conda-forge/linux-64/zlib-1.3.1-hb9d3cd8_2.conda sha256: 5d7c0e5f0005f74112a34a7425179f4eb6e73c92f5d109e6af4ddeca407c92ab md5: c9f075ab2f33b3bbee9e62d4ad0a6cd8 diff --git a/pyproject.toml b/pyproject.toml index 611a6a80..3d6cbdf4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -23,6 +23,7 @@ classifiers = [ "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", "Programming Language :: Python :: 3.13", + "Programming Language :: Python :: Free Threading :: 3 - Stable", "Typing :: Typed", ] dynamic = ["version"] @@ -47,7 +48,6 @@ channels = ["https://prefix.dev/conda-forge"] platforms = ["linux-64", "osx-64", "osx-arm64", "win-64"] [tool.pixi.dependencies] -python = ">=3.10,<3.14" array-api-compat = ">=1.12.0,<2" [tool.pixi.pypi-dependencies] @@ -179,6 +179,15 @@ cupy = ">=13.4.1" # jaxlib = { version = "*", build = "cuda12*" } # unavailable pytorch = { version = ">=2.7.0", build = "cuda12*" } +[tool.pixi.feature.nogil.dependencies] +python-freethreading = "~=3.13.0" +pytest-run-parallel = ">=0.4.3" +numpy = ">=2.3.0" +# pytorch = "*" # Not available on Python 3.13t yet +dask-core = ">=2025.5.1" # No distributed, tornado, etc. +# sparse = "*" # numba not available on Python 3.13t yet +# jax = "*" # ml_dtypes not available on Python 3.13t yet + [tool.pixi.environments] default = { features = ["py313"], solve-group = "py313" } lint = { features = ["py313", "lint"], solve-group = "py313" } @@ -197,7 +206,7 @@ tests-cuda = { features = ["py310", "tests", "backends", "cuda-backends"], solve # Ungrouped environments tests-numpy1 = ["py310", "tests", "numpy1"] tests-py310 = ["py310", "tests"] - +tests-nogil = ["nogil", "tests"] # pytest diff --git a/src/array_api_extra/_lib/_backends.py b/src/array_api_extra/_lib/_backends.py index 68bef24b..936f5dd0 100644 --- a/src/array_api_extra/_lib/_backends.py +++ b/src/array_api_extra/_lib/_backends.py @@ -3,8 +3,14 @@ from __future__ import annotations from enum import Enum +from typing import Any -__all__ = ["Backend"] +import numpy as np +import pytest + +__all__ = ["NUMPY_VERSION", "Backend"] + +NUMPY_VERSION = tuple(int(v) for v in np.__version__.split(".")[:3]) # pyright: ignore[reportUnknownArgumentType] class Backend(Enum): # numpydoc ignore=PR02 @@ -30,12 +36,6 @@ class Backend(Enum): # numpydoc ignore=PR02 JAX = "jax.numpy" JAX_GPU = "jax.numpy:gpu" - def __str__(self) -> str: # pyright: ignore[reportImplicitOverride] # numpydoc ignore=RT01 - """Pretty-print parameterized test names.""" - return ( - self.name.lower().replace("_gpu", ":gpu").replace("_readonly", ":readonly") - ) - @property def modname(self) -> str: # numpydoc ignore=RT01 """Module name to be imported.""" @@ -44,3 +44,29 @@ def modname(self) -> str: # numpydoc ignore=RT01 def like(self, *others: Backend) -> bool: # numpydoc ignore=PR01,RT01 """Check if this backend uses the same module as others.""" return any(self.modname == other.modname for other in others) + + def pytest_param(self) -> Any: + """ + Backend as a pytest parameter + + Returns + ------- + pytest.mark.ParameterSet + """ + id_ = ( + self.name.lower().replace("_gpu", ":gpu").replace("_readonly", ":readonly") + ) + + marks = [] + if self.like(Backend.ARRAY_API_STRICT): + marks.append( + pytest.mark.skipif( + NUMPY_VERSION < (1, 26), + reason="array_api_strict is untested on NumPy <1.26", + ) + ) + if self.like(Backend.DASK, Backend.JAX): + # Monkey-patched by lazy_xp_function + marks.append(pytest.mark.thread_unsafe) + + return pytest.param(self, id=id_, marks=marks) # pyright: ignore[reportUnknownArgumentType] diff --git a/src/array_api_extra/_lib/_lazy.py b/src/array_api_extra/_lib/_lazy.py index dc7c0039..d5095001 100644 --- a/src/array_api_extra/_lib/_lazy.py +++ b/src/array_api_extra/_lib/_lazy.py @@ -343,7 +343,7 @@ def wrapper( if as_numpy: import numpy as np - arg = cast(Array, np.asarray(arg)) # noqa: PLW2901 + arg = cast(Array, np.asarray(arg)) # pyright: ignore[reportInvalidCast] # noqa: PLW2901 args_list.append(arg) assert device is not None diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index bb310467..47511c75 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -9,7 +9,7 @@ import contextlib import enum import warnings -from collections.abc import Callable, Iterator, Sequence +from collections.abc import Callable, Generator, Iterator, Sequence from functools import wraps from types import ModuleType from typing import TYPE_CHECKING, Any, ParamSpec, TypeVar, cast @@ -216,8 +216,11 @@ def test_myfunc(xp): def patch_lazy_xp_functions( - request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch, *, xp: ModuleType -) -> None: + request: pytest.FixtureRequest, + monkeypatch: pytest.MonkeyPatch | None = None, + *, + xp: ModuleType, +) -> contextlib.AbstractContextManager[None]: """ Test lazy execution of functions tagged with :func:`lazy_xp_function`. @@ -233,10 +236,15 @@ def patch_lazy_xp_functions( This function should be typically called by your library's `xp` fixture that runs tests on multiple backends:: - @pytest.fixture(params=[numpy, array_api_strict, jax.numpy, dask.array]) - def xp(request, monkeypatch): - patch_lazy_xp_functions(request, monkeypatch, xp=request.param) - return request.param + @pytest.fixture(params=[ + numpy, + array_api_strict, + pytest.param(jax.numpy, marks=pytest.mark.thread_unsafe), + pytest.param(dask.array, marks=pytest.mark.thread_unsafe), + ]) + def xp(request): + with patch_lazy_xp_functions(request, xp=request.param): + yield request.param but it can be otherwise be called by the test itself too. @@ -245,7 +253,7 @@ def xp(request, monkeypatch): request : pytest.FixtureRequest Pytest fixture, as acquired by the test itself or by one of its fixtures. monkeypatch : pytest.MonkeyPatch - Pytest fixture, as acquired by the test itself or by one of its fixtures. + Deprecated xp : array_namespace Array namespace to be tested. @@ -253,10 +261,42 @@ def xp(request, monkeypatch): -------- lazy_xp_function : Tag a function to be tested on lazy backends. pytest.FixtureRequest : `request` test function parameter. + + Notes + ----- + This context manager monkey-patches modules and as such is thread unsafe + on Dask and JAX. If you run your test suite with + `pytest-run-parallel `_, + you should mark these backends with ``@pytest.mark.thread_unsafe``, as shown in + the example above. """ mod = cast(ModuleType, request.module) mods = [mod, *cast(list[ModuleType], getattr(mod, "lazy_xp_modules", []))] + to_revert: list[tuple[ModuleType, str, object]] = [] + + def temp_setattr(mod: ModuleType, name: str, func: object) -> None: + """ + Variant of monkeypatch.setattr, which allows monkey-patching only selected + parameters of a test so that pytest-run-parallel can run on the remainder. + """ + assert hasattr(mod, name) + to_revert.append((mod, name, getattr(mod, name))) + setattr(mod, name, func) + + if monkeypatch is not None: + warnings.warn( + ( + "The `monkeypatch` parameter is deprecated and will be removed in a " + "future version. " + "Use `patch_lazy_xp_function` as a context manager instead." + ), + DeprecationWarning, + stacklevel=2, + ) + # Enable using patch_lazy_xp_function not as a context manager + temp_setattr = monkeypatch.setattr # type: ignore[assignment] # pyright: ignore[reportAssignmentType] + def iter_tagged() -> ( Iterator[tuple[ModuleType, str, Callable[..., Any], dict[str, Any]]] ): @@ -279,13 +319,26 @@ def iter_tagged() -> ( elif n is False: n = 0 wrapped = _dask_wrap(func, n) - monkeypatch.setattr(mod, name, wrapped) + temp_setattr(mod, name, wrapped) elif is_jax_namespace(xp): for mod, name, func, tags in iter_tagged(): if tags["jax_jit"]: wrapped = jax_autojit(func) - monkeypatch.setattr(mod, name, wrapped) + temp_setattr(mod, name, wrapped) + + # We can't just decorate patch_lazy_xp_functions with + # @contextlib.contextmanager because it would not work with the + # deprecated monkeypatch when not used as a context manager. + @contextlib.contextmanager + def revert_on_exit() -> Generator[None]: + try: + yield + finally: + for mod, name, orig_func in to_revert: + setattr(mod, name, orig_func) + + return revert_on_exit() class CountingDaskScheduler(SchedulerGetCallable): diff --git a/tests/conftest.py b/tests/conftest.py index 82a0acbb..26b9a816 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -18,11 +18,10 @@ T = TypeVar("T") P = ParamSpec("P") -NUMPY_VERSION = tuple(int(v) for v in np.__version__.split(".")[2]) np_compat = array_namespace(np.empty(0)) # type: ignore[arg-type] # pyright: ignore[reportArgumentType] -@pytest.fixture(params=tuple(Backend)) +@pytest.fixture(params=[b.pytest_param() for b in Backend]) def library(request: pytest.FixtureRequest) -> Backend: # numpydoc ignore=PR01,RT03 """ Parameterized fixture that iterates on all libraries. @@ -112,7 +111,7 @@ def wrapper(*args: P.args, **kwargs: P.kwargs) -> T: # numpydoc ignore=GL08 @pytest.fixture def xp( - library: Backend, request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch + library: Backend, request: pytest.FixtureRequest ) -> Generator[ModuleType]: # numpydoc ignore=PR01,RT03 """ Parameterized fixture that iterates on all libraries. @@ -125,9 +124,6 @@ def xp( yield NumPyReadOnly() # type: ignore[misc] # pyright: ignore[reportReturnType] return - if library.like(Backend.ARRAY_API_STRICT) and NUMPY_VERSION < (1, 26): - pytest.skip("array_api_strict is untested on NumPy <1.26") - xp = pytest.importorskip(library.modname) # Possibly wrap module with array_api_compat xp = array_namespace(xp.empty(0)) @@ -143,16 +139,15 @@ def xp( yield xp return - # On Dask and JAX, monkey-patch all functions tagged by `lazy_xp_function` - # in the global scope of the module containing the test function. - patch_lazy_xp_functions(request, monkeypatch, xp=xp) - if library.like(Backend.JAX): _setup_jax(library) elif library.like(Backend.TORCH): _setup_torch(library) - yield xp + # On Dask and JAX, monkey-patch all functions tagged by `lazy_xp_function` + # in the global scope of the module containing the test function. + with patch_lazy_xp_functions(request, xp=xp): + yield xp def _setup_jax(library: Backend) -> None: @@ -189,26 +184,27 @@ def _setup_torch(library: Backend) -> None: torch.set_default_device("cpu") -@pytest.fixture(params=[Backend.DASK]) # Can select the test with `pytest -k dask` +# Can select the test with `pytest -k dask` +@pytest.fixture(params=[Backend.DASK.pytest_param()]) def da( - request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch -) -> ModuleType: # numpydoc ignore=PR01,RT01 + request: pytest.FixtureRequest, +) -> Generator[ModuleType]: # numpydoc ignore=PR01,RT01 """Variant of the `xp` fixture that only yields dask.array.""" xp = pytest.importorskip("dask.array") xp = array_namespace(xp.empty(0)) - patch_lazy_xp_functions(request, monkeypatch, xp=xp) - return xp + with patch_lazy_xp_functions(request, xp=xp): + yield xp -@pytest.fixture(params=[Backend.JAX, Backend.JAX_GPU]) +@pytest.fixture(params=[Backend.JAX.pytest_param(), Backend.JAX_GPU.pytest_param()]) def jnp( - request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch -) -> ModuleType: # numpydoc ignore=PR01,RT01 + request: pytest.FixtureRequest, +) -> Generator[ModuleType]: # numpydoc ignore=PR01,RT01 """Variant of the `xp` fixture that only yields jax.numpy.""" xp = pytest.importorskip("jax.numpy") _setup_jax(request.param) - patch_lazy_xp_functions(request, monkeypatch, xp=xp) - return xp + with patch_lazy_xp_functions(request, xp=xp): + yield xp @pytest.fixture(params=[Backend.TORCH, Backend.TORCH_GPU]) diff --git a/tests/test_at.py b/tests/test_at.py index 04b71b70..d9e1bdf9 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -178,7 +178,7 @@ def test_copy_invalid(): def test_xp(): - a = cast(Array, np.asarray([1, 2, 3])) + a = cast(Array, np.asarray([1, 2, 3])) # pyright: ignore[reportInvalidCast] _ = at(a, 0).set(4, xp=np) _ = at(a, 0).add(4, xp=np) _ = at(a, 0).subtract(4, xp=np) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 6e80a61d..dc0658ab 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -27,15 +27,13 @@ setdiff1d, sinc, ) -from array_api_extra._lib._backends import Backend +from array_api_extra._lib._backends import NUMPY_VERSION, Backend from array_api_extra._lib._testing import xp_assert_close, xp_assert_equal from array_api_extra._lib._utils._compat import device as get_device from array_api_extra._lib._utils._helpers import eager_shape, ndindex from array_api_extra._lib._utils._typing import Array, Device from array_api_extra.testing import lazy_xp_function -from .conftest import NUMPY_VERSION - lazy_xp_function(apply_where) lazy_xp_function(atleast_nd) lazy_xp_function(cov) diff --git a/tests/test_helpers.py b/tests/test_helpers.py index 275ca519..43ad5dc7 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -24,7 +24,7 @@ from .conftest import np_compat -if TYPE_CHECKING: +if TYPE_CHECKING: # pragma: no cover # TODO import from typing (requires Python >=3.12) from typing_extensions import override else: diff --git a/tests/test_lazy.py b/tests/test_lazy.py index 503e180f..056d608b 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -141,7 +141,7 @@ def f(x: Array) -> Array: xp = array_namespace(x) return xp.sum(x, axis=0) + x - x_np = cast(Array, np.arange(15).reshape(5, 3)) + x_np = cast(Array, np.arange(15).reshape(5, 3)) # pyright: ignore[reportInvalidCast] expect = da.asarray(f(x_np)) x_da = da.asarray(x_np).rechunk(3) @@ -230,7 +230,7 @@ def test_lazy_apply_none_shape_in_args(xp: ModuleType, library: Backend): # Single output with ctx: values = lazy_apply(mxp.unique_values, x, shape=(None,)) - xp_assert_equal(values, xp.asarray([1, 2])) + xp_assert_equal(xp.sort(values), xp.asarray([1, 2])) with ctx: # Multi output diff --git a/tests/test_testing.py b/tests/test_testing.py index 33c36c12..7eda3fb6 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -18,7 +18,7 @@ is_jax_namespace, ) from array_api_extra._lib._utils._typing import Array, Device -from array_api_extra.testing import lazy_xp_function +from array_api_extra.testing import lazy_xp_function, patch_lazy_xp_functions # pyright: reportUnknownParameterType=false,reportMissingParameterType=false @@ -448,3 +448,23 @@ def test_lazy_xp_modules(xp: ModuleType, library: Backend): else: y = wrapped.f(x) xp_assert_equal(y, x) + + +def test_patch_lazy_xp_functions_deprecated_monkeypatch( + request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch +): + xp = pytest.importorskip("dask.array") + + x = xp.asarray([1.0, 2.0]) + y = non_materializable5(x) + xp_assert_equal(y, x) + + with pytest.warns(DeprecationWarning): + _ = patch_lazy_xp_functions(request, monkeypatch, xp=xp) + + with pytest.raises(AssertionError, match=r"dask\.compute.* 1 times"): + _ = non_materializable5(x) + + monkeypatch.undo() + y = non_materializable5(x) + xp_assert_equal(y, x) From 4091d5010c6b2f558055575ea220e8b13eebd3c4 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 17 Jun 2025 18:45:49 +0000 Subject: [PATCH 038/104] deps: Update dependency typing-extensions to >=4.14.0 (#335) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pixi.lock b/pixi.lock index 709ffbe9..f5900d5e 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4196,7 +4196,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: a0415d461d8fb7cff758e3f0148fa44b537702fa0120e3597dde01fb4790694d + sha256: 9bd192b85cf9420c28a5c2b04aaf318ea6344ebb6f8b8cb9dac980ae647ad10d requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 3d6cbdf4..e52621f8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,7 +54,7 @@ array-api-compat = ">=1.12.0,<2" array-api-extra = { path = ".", editable = true } [tool.pixi.feature.lint.dependencies] -typing-extensions = ">=4.13.2" +typing-extensions = ">=4.14.0" pre-commit = ">=4.2.0" pylint = ">=3.3.7" mypy = ">=1.16.0" @@ -107,7 +107,7 @@ sphinx-autodoc-typehints = ">=1.25.3" # Needed to import parsed modules with autodoc dask-core = ">=2025.5.1" # No distributed, tornado, etc. pytest = ">=8.4.0" -typing-extensions = ">=4.13.2" +typing-extensions = ">=4.14.0" numpy = ">=2.1.3" [tool.pixi.feature.docs.tasks] From d4c3dd4307fe13f893413b8f28790af64f4323ad Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 25 Jun 2025 16:12:57 +0000 Subject: [PATCH 039/104] deps: Update dependency pytest-run-parallel to >=0.4.4 (#336) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 20 ++++++++++---------- pyproject.toml | 2 +- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/pixi.lock b/pixi.lock index f5900d5e..2562b093 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3344,7 +3344,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/pygments-2.19.1-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/noarch/pytest-8.4.0-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/noarch/pytest-cov-6.1.1-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/noarch/pytest-run-parallel-0.4.3-pyhd8ed1ab_0.conda + - conda: https://prefix.dev/conda-forge/noarch/pytest-run-parallel-0.4.4-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/linux-64/python-3.13.3-h4724d56_1_cp313t.conda - conda: https://prefix.dev/conda-forge/noarch/python-freethreading-3.13.3-h92d6c8b_1.conda - conda: https://prefix.dev/conda-forge/noarch/python_abi-3.13-7_cp313t.conda @@ -3402,7 +3402,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/pygments-2.19.1-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/noarch/pytest-8.4.0-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/noarch/pytest-cov-6.1.1-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/noarch/pytest-run-parallel-0.4.3-pyhd8ed1ab_0.conda + - conda: https://prefix.dev/conda-forge/noarch/pytest-run-parallel-0.4.4-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/osx-64/python-3.13.3-h2267d90_1_cp313t.conda - conda: https://prefix.dev/conda-forge/noarch/python-freethreading-3.13.3-h92d6c8b_1.conda - conda: https://prefix.dev/conda-forge/noarch/python_abi-3.13-7_cp313t.conda @@ -3460,7 +3460,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/pygments-2.19.1-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/noarch/pytest-8.4.0-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/noarch/pytest-cov-6.1.1-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/noarch/pytest-run-parallel-0.4.3-pyhd8ed1ab_0.conda + - conda: 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https://prefix.dev/conda-forge/noarch/python_abi-3.13-7_cp313t.conda @@ -4196,7 +4196,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 9bd192b85cf9420c28a5c2b04aaf318ea6344ebb6f8b8cb9dac980ae647ad10d + sha256: b08ab7c0e105daa17c6cc9c8cc394274666ce410882dc3a422ae3f2f96938d3f requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' @@ -9669,9 +9669,9 @@ packages: - pkg:pypi/pytest-cov?source=hash-mapping size: 27565 timestamp: 1743886993683 -- conda: https://prefix.dev/conda-forge/noarch/pytest-run-parallel-0.4.3-pyhd8ed1ab_0.conda - sha256: 981deb0bad7e92b78ce8c4b3db99f9c008e37ddb666fc117ec28efe7ec8ad7cd - md5: 4974eeb9e368dca027c3e49c58ced417 +- conda: https://prefix.dev/conda-forge/noarch/pytest-run-parallel-0.4.4-pyhd8ed1ab_0.conda + sha256: 63490d2de6a759fb8c52702a950a4dff5c71b225b8931eeabf01fb841cb939f0 + md5: 8e06da4a4c29963150f5cc140e7c90fb depends: - pytest >=6.2.0 - python >=3.9 @@ -9679,8 +9679,8 @@ packages: license_family: MIT purls: - pkg:pypi/pytest-run-parallel?source=hash-mapping - size: 17692 - timestamp: 1748343358484 + size: 17822 + timestamp: 1749628808758 - conda: https://prefix.dev/conda-forge/linux-64/python-3.10.17-hd6af730_0_cpython.conda sha256: 0ae32507817402bfad08fbf0f4a9b5ae26859d5390b98bc939da85fd0bd4239f md5: 7bb89638dae9ce1b8e051d0b721e83c2 diff --git a/pyproject.toml b/pyproject.toml index e52621f8..1bf9fa72 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -181,7 +181,7 @@ pytorch = { version = ">=2.7.0", build = "cuda12*" } [tool.pixi.feature.nogil.dependencies] python-freethreading = "~=3.13.0" -pytest-run-parallel = ">=0.4.3" +pytest-run-parallel = ">=0.4.4" numpy = ">=2.3.0" # pytorch = "*" # Not available on Python 3.13t yet dask-core = ">=2025.5.1" # No distributed, tornado, etc. From b6487ee2b8106a67ca63d25dcbdee6f8b83e0fd3 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 26 Jun 2025 01:03:59 +0000 Subject: [PATCH 040/104] deps: Update dependency basedpyright to >=1.29.3 (#337) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 36 ++++++++++++++++++------------------ pyproject.toml | 2 +- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/pixi.lock b/pixi.lock index 2562b093..e686bf53 100644 --- a/pixi.lock +++ b/pixi.lock @@ -101,7 +101,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/asttokens-3.0.0-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/noarch/attrs-25.3.0-pyh71513ae_0.conda - conda: https://prefix.dev/conda-forge/noarch/babel-2.17.0-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.29.2-pyhe01879c_0.conda + - conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.29.4-pyhe01879c_0.conda - conda: https://prefix.dev/conda-forge/noarch/beautifulsoup4-4.13.4-pyha770c72_0.conda - conda: 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conda: https://prefix.dev/conda-forge/osx-64/astroid-3.3.10-py313habf4b1d_0.conda - conda: https://prefix.dev/conda-forge/noarch/attrs-25.3.0-pyh71513ae_0.conda - conda: https://prefix.dev/conda-forge/noarch/babel-2.17.0-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.29.2-pyhe01879c_0.conda + - conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.29.4-pyhe01879c_0.conda - conda: https://prefix.dev/conda-forge/osx-64/brotli-python-1.1.0-py313h9ea2907_2.conda - conda: https://prefix.dev/conda-forge/osx-64/bzip2-1.0.8-hfdf4475_7.conda - conda: https://prefix.dev/conda-forge/noarch/ca-certificates-2025.4.26-hbd8a1cb_0.conda @@ -2085,7 +2085,7 @@ environments: - conda: https://prefix.dev/conda-forge/osx-arm64/astroid-3.3.10-py313h8f79df9_0.conda - conda: https://prefix.dev/conda-forge/noarch/attrs-25.3.0-pyh71513ae_0.conda - conda: https://prefix.dev/conda-forge/noarch/babel-2.17.0-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.29.2-pyhe01879c_0.conda + - conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.29.4-pyhe01879c_0.conda - conda: https://prefix.dev/conda-forge/osx-arm64/brotli-python-1.1.0-py313h3579c5c_2.conda - conda: https://prefix.dev/conda-forge/osx-arm64/bzip2-1.0.8-h99b78c6_7.conda - conda: https://prefix.dev/conda-forge/noarch/ca-certificates-2025.4.26-hbd8a1cb_0.conda @@ -2194,7 +2194,7 @@ environments: - conda: https://prefix.dev/conda-forge/win-64/astroid-3.3.10-py313hfa70ccb_0.conda - conda: https://prefix.dev/conda-forge/noarch/attrs-25.3.0-pyh71513ae_0.conda - conda: https://prefix.dev/conda-forge/noarch/babel-2.17.0-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.29.2-pyhe01879c_0.conda + - conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.29.4-pyhe01879c_0.conda - conda: https://prefix.dev/conda-forge/win-64/brotli-python-1.1.0-py313h5813708_2.conda - conda: https://prefix.dev/conda-forge/win-64/bzip2-1.0.8-h2466b09_7.conda - conda: https://prefix.dev/conda-forge/noarch/ca-certificates-2025.4.26-h4c7d964_0.conda @@ -4196,7 +4196,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: b08ab7c0e105daa17c6cc9c8cc394274666ce410882dc3a422ae3f2f96938d3f + sha256: e4f5b99a8d2416d6524c4c22232fdfe0331a93b67b528053532042186e998d66 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' @@ -4361,9 +4361,9 @@ packages: - pkg:pypi/babel?source=compressed-mapping size: 6938256 timestamp: 1738490268466 -- conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.29.2-pyhe01879c_0.conda - sha256: a5e63030159e8c9c65314d0d09d3cc65dcaf0ca2bebb4e396d2deac3351d1ee5 - md5: 39ca9f1815ff1ad3aaf89b21f00487a4 +- conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.29.4-pyhe01879c_0.conda + sha256: 06dceddeb8547cac92a48d1adc0d06201f14a3649757327670f01345ecd99c63 + md5: b130c91f9371a7f8c3709d7b95be8709 depends: - python >=3.9 - nodejs-wheel >=20.13.1 @@ -4371,8 +4371,8 @@ packages: license: MIT AND Apache-2.0 purls: - pkg:pypi/basedpyright?source=hash-mapping - size: 8231612 - timestamp: 1747891728335 + size: 8225473 + timestamp: 1749712419694 - conda: https://prefix.dev/conda-forge/noarch/beautifulsoup4-4.13.4-pyha770c72_0.conda sha256: ddb0df12fd30b2d36272f5daf6b6251c7625d6a99414d7ea930005bbaecad06d md5: 9f07c4fc992adb2d6c30da7fab3959a7 diff --git a/pyproject.toml b/pyproject.toml index 1bf9fa72..7cf724d2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ typing-extensions = ">=4.14.0" pre-commit = ">=4.2.0" pylint = ">=3.3.7" mypy = ">=1.16.0" -basedpyright = ">=1.29.2" +basedpyright = ">=1.29.3" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1" From dc95481e1da671ff8c420f6059131a7f96200944 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 26 Jun 2025 15:53:15 +0000 Subject: [PATCH 041/104] deps: Update dependency basedpyright to >=1.29.4 (#338) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index e686bf53..f73f2e5a 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4196,7 +4196,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: e4f5b99a8d2416d6524c4c22232fdfe0331a93b67b528053532042186e998d66 + sha256: f83e26a4917e36e3729f14eee4af233f02056332e85a601e8731c6e983ede675 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 7cf724d2..428c2338 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ typing-extensions = ">=4.14.0" pre-commit = ">=4.2.0" pylint = ">=3.3.7" mypy = ">=1.16.0" -basedpyright = ">=1.29.3" +basedpyright = ">=1.29.4" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1" 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+ size: 28216 + timestamp: 1749778064293 - conda: https://prefix.dev/conda-forge/noarch/pytest-run-parallel-0.4.4-pyhd8ed1ab_0.conda sha256: 63490d2de6a759fb8c52702a950a4dff5c71b225b8931eeabf01fb841cb939f0 md5: 8e06da4a4c29963150f5cc140e7c90fb diff --git a/pyproject.toml b/pyproject.toml index 428c2338..e7a2bf8b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -79,7 +79,7 @@ lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"] , description [tool.pixi.feature.tests.dependencies] pytest = ">=8.4.0" -pytest-cov = ">=6.1.1" +pytest-cov = ">=6.2.1" hypothesis = ">=6.131.28" array-api-strict = ">=2.3.1" numpy = ">=1.22.0" From 7f523429d752e44eaa1734489d002a5d4308e7eb Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Mon, 30 Jun 2025 21:05:59 +0100 Subject: [PATCH 043/104] DEV: add pull request template (#342) --- .github/pull_request_template.md | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 .github/pull_request_template.md diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 00000000..014064f0 --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,5 @@ + From 973ba8c0d89ea8b79a98a3291fa5b8d12984e75d Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 1 Jul 2025 10:37:09 +0100 Subject: [PATCH 044/104] deps: Update dependency mypy to >=1.16.1 (#345) --- pixi.lock | 108 ++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 55 insertions(+), 55 deletions(-) diff --git a/pixi.lock b/pixi.lock index 115a6c0f..105e58fd 100644 --- a/pixi.lock +++ b/pixi.lock @@ -185,7 +185,7 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/mpc-1.3.1-h24ddda3_1.conda - conda: https://prefix.dev/conda-forge/linux-64/mpfr-4.2.1-h90cbb55_3.conda - conda: https://prefix.dev/conda-forge/noarch/mpmath-1.3.0-pyhd8ed1ab_1.conda - - conda: 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b/pixi.lock index 105e58fd..32a21e2f 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4196,7 +4196,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 2f998a4b4fb32a961ab7097e7c4a9a6cb11ffcf47b702e53cb2649afef406005 + sha256: c77a8e8beae9d2d5dd0910b1bb0563574b908a6112e4ca67dcda5d4799d0bc70 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index b2d7d6dd..c5a9f4da 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,42 +61,42 @@ mypy = ">=1.16.1" basedpyright = ">=1.29.4" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: -array-api-strict = ">=2.3.1" +array-api-strict = ">=2.3.1,<2.4" numpy = ">=2.1.3" pytest = ">=8.4.0" hypothesis = ">=6.131.28" -dask-core = ">=2025.5.1" # No distributed, tornado, etc. +dask-core = ">=2025.5.1" # No distributed, tornado, etc. # NOTE: don't add cupy, jax, pytorch, or sparse here, # as they slow down mypy and are not portable across target OSs [tool.pixi.feature.lint.tasks] -pre-commit-install = { cmd = "pre-commit install", description = "Install pre-commit"} -pre-commit = { cmd = "pre-commit run --all-files", description = "Run pre-commit"} -mypy = { cmd = "mypy", description="Type check with mypy"} -pylint = { cmd = "pylint array_api_extra", cwd = "src" , description = "Lint using pylint"} -pyright = { cmd = "basedpyright", description = "Type check with basedpyright"} -lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"] , description = "Run pre-commit, pylint, mypy, and pyright"} +pre-commit-install = { cmd = "pre-commit install", description = "Install pre-commit" } +pre-commit = { cmd = "pre-commit run --all-files", description = "Run pre-commit" } +mypy = { cmd = "mypy", description = "Type check with mypy" } +pylint = { cmd = "pylint array_api_extra", cwd = "src", description = "Lint using pylint" } +pyright = { cmd = "basedpyright", description = "Type check with basedpyright" } +lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"], description = "Run pre-commit, pylint, mypy, and pyright" } [tool.pixi.feature.tests.dependencies] pytest = ">=8.4.0" pytest-cov = ">=6.2.1" hypothesis = ">=6.131.28" -array-api-strict = ">=2.3.1" +array-api-strict = ">=2.3.1,<2.4" numpy = ">=1.22.0" [tool.pixi.feature.tests.tasks] -tests = { cmd = "pytest -v", description = "Run tests"} -tests-cov = { cmd="pytest -v -ra --cov --cov-report=xml --cov-report=term --durations=20", description = "Run tests with coverage"} +tests = { cmd = "pytest -v", description = "Run tests" } +tests-cov = { cmd = "pytest -v -ra --cov --cov-report=xml --cov-report=term --durations=20", description = "Run tests with coverage" } -clean-vendor-compat = { cmd = "rm -rf vendor_tests/array_api_compat", description = "Delete the existing vendored version of array-api-compat"} -clean-vendor-extra = { cmd = "rm -rf vendor_tests/array_api_extra" , description = "Delete the existing vendored version of array-api-extra"} -copy-vendor-compat = { cmd = "cp -r $(python -c 'import site; print(site.getsitepackages()[0])')/array_api_compat vendor_tests/", depends-on = ["clean-vendor-compat"] , description = "Vendor a clean copy of array-api-compat"} -copy-vendor-extra = { cmd = "cp -r src/array_api_extra vendor_tests/", depends-on = ["clean-vendor-extra"] , description = "Vendor a clean copy of array-api-extra"} -tests-vendor = { cmd = "pytest -v vendor_tests", depends-on = ["copy-vendor-compat", "copy-vendor-extra"] , description = "Check that array-api-extra and array-api-compat can be vendored together" } +clean-vendor-compat = { cmd = "rm -rf vendor_tests/array_api_compat", description = "Delete the existing vendored version of array-api-compat" } +clean-vendor-extra = { cmd = "rm -rf vendor_tests/array_api_extra", description = "Delete the existing vendored version of array-api-extra" } +copy-vendor-compat = { cmd = "cp -r $(python -c 'import site; print(site.getsitepackages()[0])')/array_api_compat vendor_tests/", depends-on = ["clean-vendor-compat"], description = "Vendor a clean copy of array-api-compat" } +copy-vendor-extra = { cmd = "cp -r src/array_api_extra vendor_tests/", depends-on = ["clean-vendor-extra"], description = "Vendor a clean copy of array-api-extra" } +tests-vendor = { cmd = "pytest -v vendor_tests", depends-on = ["copy-vendor-compat", "copy-vendor-extra"], description = "Check that array-api-extra and array-api-compat can be vendored together" } -tests-ci = { depends-on = ["tests-cov", "tests-vendor"] , description = "Run tests with coverage and vendor tests"} -coverage = { cmd = "coverage html", depends-on = ["tests-cov"], description = "Generate test coverage html report"} -open-coverage = { cmd = "open htmlcov/index.html", depends-on = ["coverage"] , description = "Open test coverage report"} +tests-ci = { depends-on = ["tests-cov", "tests-vendor"], description = "Run tests with coverage and vendor tests" } +coverage = { cmd = "coverage html", depends-on = ["tests-cov"], description = "Generate test coverage html report" } +open-coverage = { cmd = "open htmlcov/index.html", depends-on = ["coverage"], description = "Open test coverage report" } [tool.pixi.feature.docs.dependencies] sphinx = ">=7.4.7" @@ -105,20 +105,20 @@ myst-parser = ">=4.0.1" sphinx-copybutton = ">=0.5.2" sphinx-autodoc-typehints = ">=1.25.3" # Needed to import parsed modules with autodoc -dask-core = ">=2025.5.1" # No distributed, tornado, etc. +dask-core = ">=2025.5.1" # No distributed, tornado, etc. pytest = ">=8.4.0" typing-extensions = ">=4.14.0" numpy = ">=2.1.3" [tool.pixi.feature.docs.tasks] -docs = { cmd = "sphinx-build -E -W . build/", cwd = "docs" , description = "Build docs"} -open-docs = { cmd = "open build/index.html", cwd = "docs", depends-on = ["docs"] , description = "Open the generated docs"} +docs = { cmd = "sphinx-build -E -W . build/", cwd = "docs", description = "Build docs" } +open-docs = { cmd = "open build/index.html", cwd = "docs", depends-on = ["docs"], description = "Open the generated docs" } [tool.pixi.feature.dev.dependencies] ipython = ">=7.33.0" [tool.pixi.feature.dev.tasks] -ipython = { cmd = "ipython" , description = "Launch ipython"} +ipython = { cmd = "ipython", description = "Launch ipython" } [tool.pixi.feature.py310.dependencies] python = "~=3.10.0" @@ -135,7 +135,7 @@ numpy = "=1.22.0" # Note: JAX and PyTorch will install CPU variants. [tool.pixi.feature.backends.dependencies] pytorch = ">=2.7.0" -dask-core = ">=2025.5.1" # No distributed, tornado, etc. +dask-core = ">=2025.5.1" # No distributed, tornado, etc. sparse = ">=0.17.0" [tool.pixi.feature.backends.target.linux-64.dependencies] @@ -184,7 +184,7 @@ python-freethreading = "~=3.13.0" pytest-run-parallel = ">=0.4.4" numpy = ">=2.3.0" # pytorch = "*" # Not available on Python 3.13t yet -dask-core = ">=2025.5.1" # No distributed, tornado, etc. +dask-core = ">=2025.5.1" # No distributed, tornado, etc. # sparse = "*" # numba not available on Python 3.13t yet # jax = "*" # ml_dtypes not available on Python 3.13t yet @@ -245,7 +245,7 @@ ignore_missing_imports = true [[tool.mypy.overrides]] module = ["tests/*"] -disable_error_code = ["no-untyped-def"] # test(...) without -> None +disable_error_code = ["no-untyped-def"] # test(...) without -> None # pyright From 83897e599a51e3ef3cb228ba3491fdef8afafe09 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 1 Jul 2025 11:32:05 +0100 Subject: [PATCH 046/104] DEV: replace pre-commit with lefthook+Pixi (#344) --- .dprint.jsonc | 25 + .github/workflows/ci.yml | 17 +- .pre-commit-config.yaml | 84 - README.md | 23 +- docs/contributing.md | 58 +- docs/contributors.md | 1 - docs/index.md | 7 +- lefthook.yml | 43 + pixi.lock | 5360 +++++++++++----------- pyproject.toml | 95 +- renovate.json | 106 +- src/array_api_extra/_lib/_funcs.py | 2 +- src/array_api_extra/testing.py | 6 +- tests/conftest.py | 10 +- tests/test_funcs.py | 10 +- tests/test_helpers.py | 20 +- tests/test_lazy.py | 6 +- tests/test_testing.py | 4 +- typos.toml | 8 + vendor_tests/_array_api_compat_vendor.py | 1 + vendor_tests/test_vendor.py | 8 +- 21 files changed, 2976 insertions(+), 2918 deletions(-) create mode 100644 .dprint.jsonc delete mode 100644 .pre-commit-config.yaml create mode 100644 lefthook.yml create mode 100644 typos.toml diff --git a/.dprint.jsonc b/.dprint.jsonc new file mode 100644 index 00000000..c3642905 --- /dev/null +++ b/.dprint.jsonc @@ -0,0 +1,25 @@ +{ + "json": { + "lineWidth": 100, + "array.preferSingleLine": true, + }, + "markdown": { + "lineWidth": 200, + "emphasisKind": "asterisks", + }, + "toml": { + "lineWidth": 100, + }, + "yaml": { + "printWidth": 100, + "formatComments": true, + "braceSpacing": false, + }, + "excludes": ["**/*-lock.json", "**/*.lock", "**/node_modules/", "dist/"], + "plugins": [ + "https://plugins.dprint.dev/g-plane/pretty_yaml-v0.5.1.wasm", + "https://plugins.dprint.dev/json-0.20.0.wasm", + "https://plugins.dprint.dev/markdown-0.19.0.wasm", + "https://plugins.dprint.dev/toml-0.7.0.wasm", + ], +} diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index ebe75372..3f1fca89 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -20,8 +20,8 @@ env: FORCE_COLOR: 3 jobs: - pre-commit-and-lint: - name: Format + lint: + name: Lint runs-on: ubuntu-latest steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 @@ -30,24 +30,17 @@ jobs: - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0 with: python-version: "3.13.3" - - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 - with: - extra_args: --hook-stage manual --all-files - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 with: - pixi-version: v0.42.1 + pixi-version: v0.49.0 cache: true environments: lint - - name: Run Pylint, Mypy & Pyright - run: | - pixi run -e lint pylint - pixi run -e lint mypy - pixi run -e lint pyright + - name: Lint + run: pixi run -e lint lint checks: name: Test ${{ matrix.environment }} runs-on: ${{ matrix.runs-on }} - needs: [pre-commit-and-lint] strategy: fail-fast: false matrix: diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml deleted file mode 100644 index 7be7a1ca..00000000 --- a/.pre-commit-config.yaml +++ /dev/null @@ -1,84 +0,0 @@ -ci: - autoupdate_commit_msg: "chore: update pre-commit hooks" - autofix_commit_msg: "style: pre-commit fixes" - -exclude: ^.cruft.json|.copier-answers.yml$ - -repos: - - repo: https://github.com/adamchainz/blacken-docs - rev: "1.18.0" - hooks: - - id: blacken-docs - additional_dependencies: [black==24.*] - - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: "v5.0.0" - hooks: - - id: check-added-large-files - - id: check-case-conflict - - id: check-merge-conflict - - id: check-symlinks - - id: check-yaml - - id: debug-statements - - id: end-of-file-fixer - - id: mixed-line-ending - - id: name-tests-test - args: ["--pytest-test-first"] - - id: requirements-txt-fixer - - id: trailing-whitespace - - - repo: https://github.com/pre-commit/pygrep-hooks - rev: "v1.10.0" - hooks: - - id: rst-backticks - - id: rst-directive-colons - - id: rst-inline-touching-normal - - - repo: https://github.com/rbubley/mirrors-prettier - rev: "v3.4.2" - hooks: - - id: prettier - types_or: [yaml, markdown, html, css, scss, javascript, json] - args: [--prose-wrap=always] - - - repo: https://github.com/astral-sh/ruff-pre-commit - rev: "v0.8.2" - hooks: - - id: ruff-format - - id: ruff - args: ["--fix", "--show-fixes"] - - - repo: https://github.com/codespell-project/codespell - rev: "v2.3.0" - hooks: - - id: codespell - exclude: pixi.lock - - - repo: https://github.com/shellcheck-py/shellcheck-py - rev: "v0.10.0.1" - hooks: - - id: shellcheck - - - repo: local - hooks: - - id: disallow-caps - name: Disallow improper capitalization - language: pygrep - entry: PyBind|Numpy|Cmake|CCache|Github|PyTest - exclude: .pre-commit-config.yaml - - - repo: https://github.com/abravalheri/validate-pyproject - rev: "v0.23" - hooks: - - id: validate-pyproject - additional_dependencies: ["validate-pyproject-schema-store[all]"] - - - repo: https://github.com/python-jsonschema/check-jsonschema - rev: "0.30.0" - hooks: - - id: check-github-workflows - - - repo: https://github.com/numpy/numpydoc - rev: "v1.8.0" - hooks: - - id: numpydoc-validation diff --git a/README.md b/README.md index 54f9d3a7..cef223d3 100644 --- a/README.md +++ b/README.md @@ -16,17 +16,18 @@ -[actions-badge]: https://github.com/data-apis/array-api-extra/workflows/CI/badge.svg -[actions-link]: https://github.com/data-apis/array-api-extra/actions -[conda-badge]: https://img.shields.io/conda/vn/conda-forge/array-api-extra -[conda-link]: https://github.com/conda-forge/array-api-extra-feedstock + +[actions-badge]: https://github.com/data-apis/array-api-extra/workflows/CI/badge.svg +[actions-link]: https://github.com/data-apis/array-api-extra/actions +[conda-badge]: https://img.shields.io/conda/vn/conda-forge/array-api-extra +[conda-link]: https://github.com/conda-forge/array-api-extra-feedstock [github-discussions-badge]: https://img.shields.io/static/v1?label=Discussions&message=Ask&color=blue&logo=github -[github-discussions-link]: https://github.com/data-apis/array-api-extra/discussions -[pypi-link]: https://pypi.org/project/array-api-extra/ -[pypi-platforms]: https://img.shields.io/pypi/pyversions/array-api-extra -[pypi-version]: https://img.shields.io/pypi/v/array-api-extra -[docs-badge]: https://img.shields.io/badge/docs-here!-2ea44f -[docs-link]: https://data-apis.org/array-api-extra/index.html +[github-discussions-link]: https://github.com/data-apis/array-api-extra/discussions +[pypi-link]: https://pypi.org/project/array-api-extra/ +[pypi-platforms]: https://img.shields.io/pypi/pyversions/array-api-extra +[pypi-version]: https://img.shields.io/pypi/v/array-api-extra +[docs-badge]: https://img.shields.io/badge/docs-here!-2ea44f +[docs-link]: https://data-apis.org/array-api-extra/index.html @@ -38,7 +39,7 @@ Used by: scientific computing. - [scikit-learn](https://github.com/scikit-learn/scikit-learn) — Machine Learning in Python. -- _your library? Let us know!_ +- *your library? Let us know!* ## Installation diff --git a/docs/contributing.md b/docs/contributing.md index 83db0de4..bfcfd0d0 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -61,7 +61,7 @@ development of array-api-extra is made easy with at . - `cd array-api-extra`. - [Install Pixi](https://pixi.sh/latest/#installation). -- To enter a development environment: +- To enter a development environment (if you prefer this to the `pixi run` interface): ``` pixi shell -e dev @@ -73,71 +73,75 @@ pixi shell -e dev pixi run tests ``` -- To generate the coverage report: +- To build the docs locally: ``` -pixi run coverage +pixi run docs ``` -- To generate and display the coverage report: +- To build and preview the docs locally: ``` -pixi run open-coverage +pixi run open-docs ``` -- To build the docs locally: +- To install pre-commit hooks: ``` -pixi run docs +pixi run hooks ``` -- To build and preview the docs locally: +- To run pre-commit checks on staged files: ``` -pixi run open-docs +pixi run pre-commit ``` -- To install a [pre-commit](https://pre-commit.com) hook: +- To run the full lint suite: ``` -pixi run pre-commit-install +pixi run --environment=lint lint ``` -- To run the lint suite: +- To enter an interactive Python prompt: ``` -pixi run -e lint lint +pixi run ipython ``` -- To enter an interactive Python prompt: +- To run individual parts of the lint suite separately (for example): ``` -pixi run ipython +pixi run --environment=lint pyright +pixi run --environment=lint dprint +``` + +- To generate the coverage report: + +``` +pixi run coverage ``` -- To run individual parts of the lint suite separately: +- To generate and display the coverage report: ``` -pixi run -e lint pre-commit -pixi run -e lint pylint -pixi run -e lint mypy -pixi run -e lint pyright +pixi run open-coverage ``` Alternative environments are available with a subset of the dependencies and tasks available in the `dev` environment: ``` -pixi shell -e docs -pixi shell -e tests -pixi shell -e tests-backends -pixi shell -e lint +pixi shell --environment=docs +pixi shell --environment=tests +pixi shell --environment=tests-backends +pixi shell --environment=lint ``` If you run on a host with CUDA hardware, you can enable extra tests: ``` -pixi shell -e dev-cuda -pixi shell -e tests-cuda -pixi run -e tests-cuda tests +pixi shell --environment=dev-cuda +pixi shell --environment=tests-cuda +pixi run --environment=tests-cuda tests ``` diff --git a/docs/contributors.md b/docs/contributors.md index 724cdb77..c8e001d3 100644 --- a/docs/contributors.md +++ b/docs/contributors.md @@ -1,3 +1,2 @@ ```{include} ../CONTRIBUTORS.md - ``` diff --git a/docs/index.md b/docs/index.md index 59615583..5168e973 100644 --- a/docs/index.md +++ b/docs/index.md @@ -17,7 +17,7 @@ well as delegation to existing implementations for known array library backends. The intended users of this library are "array-consuming" libraries which are using [array-api-compat](https://data-apis.org/array-api-compat/) to make their own library's functions array-agnostic. In this library, they will find a set of -tools which provide _extra_ functionality on top of the array API standard, +tools which provide *extra* functionality on top of the array API standard, which other array-consuming libraries in a similar position have found useful themselves. @@ -27,7 +27,7 @@ It is currently used by: scientific computing. - [scikit-learn](https://github.com/scikit-learn/scikit-learn) — Machine Learning in Python. -- _your library? Let us know!_ +- *your library? Let us know!* (installation)= @@ -114,8 +114,7 @@ def array_namespace(*xs, **kwargs): See [an example of this in SciPy][scipy-vendor-example]. ``` -[scipy-vendor-example]: - https://github.com/scipy/scipy/blob/main/scipy/_lib/_array_api_compat_vendor.py +[scipy-vendor-example]: https://github.com/scipy/scipy/blob/main/scipy/_lib/_array_api_compat_vendor.py ## Versioning diff --git a/lefthook.yml b/lefthook.yml new file mode 100644 index 00000000..4797a99e --- /dev/null +++ b/lefthook.yml @@ -0,0 +1,43 @@ +lefthook: pixi run --environment=lint lefthook + +templates: + run: run --environment=lint + +pre-commit: + parallel: true + jobs: + - name: dprint + glob: "*.{json,jsonc,md,toml,yaml,yml}" + stage_fixed: true + run: pixi {run} dprint + - name: ruff + glob: "*.{py,pyi}" + stage_fixed: true + group: + piped: true + jobs: + - name: ruff check + run: pixi {run} ruff-check {staged_files} + - name: ruff format + run: pixi {run} ruff-format {staged_files} + - name: pyright + glob: "*.{py,pyi}" + run: pixi {run} pyright + - name: mypy + glob: "*.{py,pyi}" + run: pixi {run} mypy + - name: typos + stage_fixed: true + run: pixi {run} typos + - name: actionlint + run: pixi {run} actionlint + - name: blacken-docs + glob: "*.md" + stage_fixed: true + run: pixi {run} blacken-docs {staged_files} + - name: validate-pyproject + glob: "pyproject.toml" + run: pixi {run} validate-pyproject + - name: numpydoc + glob: "*.py" + run: pixi {run} numpydoc {staged_files} diff --git a/pixi.lock b/pixi.lock index 32a21e2f..9c76431a 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,21 +11,21 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.12.0-pyhe01879c_0.conda - conda: https://prefix.dev/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda - - conda: https://prefix.dev/conda-forge/noarch/ca-certificates-2025.4.26-hbd8a1cb_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda + - conda: https://prefix.dev/conda-forge/noarch/ca-certificates-2025.6.15-hbd8a1cb_0.conda + - conda: https://prefix.dev/conda-forge/linux-64/ld_impl_linux-64-2.43-h1423503_5.conda - conda: https://prefix.dev/conda-forge/linux-64/libexpat-2.7.0-h5888daf_0.conda - conda: https://prefix.dev/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda - - conda: https://prefix.dev/conda-forge/linux-64/libgcc-15.1.0-h767d61c_2.conda - - conda: https://prefix.dev/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_2.conda - - conda: https://prefix.dev/conda-forge/linux-64/libgomp-15.1.0-h767d61c_2.conda - - conda: https://prefix.dev/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_1.conda + - conda: https://prefix.dev/conda-forge/linux-64/libgcc-15.1.0-h767d61c_3.conda + - conda: https://prefix.dev/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_3.conda + - conda: https://prefix.dev/conda-forge/linux-64/libgomp-15.1.0-h767d61c_3.conda + - conda: https://prefix.dev/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda - 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# Hatch [tool.hatch] version.path = "src/array_api_extra/__init__.py" +[tool.hatch.build.targets.sdist] +exclude = ["codecov.yml", "pixi.lock", "RELEASING.md", "renovate.json"] -# Pixi +#  Pixi [tool.pixi.project] channels = ["https://prefix.dev/conda-forge"] @@ -55,7 +56,6 @@ array-api-extra = { path = ".", editable = true } [tool.pixi.feature.lint.dependencies] typing-extensions = ">=4.14.0" -pre-commit = ">=4.2.0" pylint = ">=3.3.7" mypy = ">=1.16.1" basedpyright = ">=1.29.4" @@ -63,19 +63,35 @@ numpydoc = ">=1.8.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1,<2.4" numpy = ">=2.1.3" -pytest = ">=8.4.0" hypothesis = ">=6.131.28" -dask-core = ">=2025.5.1" # No distributed, tornado, etc. +dask-core = ">=2025.5.1" # No distributed, tornado, etc. +dprint = ">=0.50.0,<0.51" +lefthook = ">=1.11.14,<2" +ruff = ">=0.12.1,<0.13" +typos = ">=1.34.0,<2" +actionlint = ">=1.7.7,<2" +blacken-docs = ">=1.19.1,<2" +pytest = ">=8.4.1,<9" +validate-pyproject = ">=0.24.1,<0.25" # NOTE: don't add cupy, jax, pytorch, or sparse here, # as they slow down mypy and are not portable across target OSs [tool.pixi.feature.lint.tasks] -pre-commit-install = { cmd = "pre-commit install", description = "Install pre-commit" } -pre-commit = { cmd = "pre-commit run --all-files", description = "Run pre-commit" } +lefthook = { cmd = "lefthook", description = "Run lefthook" } +hooks = { cmd = "lefthook install", description = "Install pre-commit hooks" } +pre-commit = { cmd = "lefthook run pre-commit", description = "Run pre-commit checks" } +pylint = { cmd = "pylint array_api_extra", cwd = "src", description = "Lint with pylint" } mypy = { cmd = "mypy", description = "Type check with mypy" } -pylint = { cmd = "pylint array_api_extra", cwd = "src", description = "Lint using pylint" } pyright = { cmd = "basedpyright", description = "Type check with basedpyright" } -lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"], description = "Run pre-commit, pylint, mypy, and pyright" } +ruff-check = { cmd = "ruff check --fix", description = "Lint with ruff" } +ruff-format = { cmd = "ruff format", description = "Format with ruff" } +dprint = { cmd = "dprint fmt", description = "Format with dprint" } +typos = { cmd = "typos --write-changes --force-exclude", description = "Fix typos" } +actionlint = { cmd = "actionlint", description = "Lint actions with actionlint" } +blacken-docs = { cmd = "blacken-docs", description = "Format Python markdown blocks with Black" } +validate-pyproject = { cmd = "validate-pyproject pyproject.toml", description = "Validate pyproject.toml" } +numpydoc = { cmd = "numpydoc lint", description = "Validate docstrings with numpydoc" } +lint = { cmd = "lefthook run pre-commit --all-files --force", description = "Run all linters" } [tool.pixi.feature.tests.dependencies] pytest = ">=8.4.0" @@ -105,7 +121,7 @@ myst-parser = ">=4.0.1" sphinx-copybutton = ">=0.5.2" sphinx-autodoc-typehints = ">=1.25.3" # Needed to import parsed modules with autodoc -dask-core = ">=2025.5.1" # No distributed, tornado, etc. +dask-core = ">=2025.5.1" # No distributed, tornado, etc. pytest = ">=8.4.0" typing-extensions = ">=4.14.0" numpy = ">=2.1.3" @@ -222,7 +238,6 @@ markers = [ "xfail_xp_backend(library, /, *, reason=None, strict=None): Xfail test for a specific backend", ] - # Coverage [tool.coverage] @@ -275,11 +290,10 @@ reportImportCycles = false reportUnknownLambdaType = false executionEnvironments = [ - { root = "tests", reportPrivateUsage = false }, + { root = "tests", reportPrivateUsage = false, reportUnknownArgumentType = false }, { root = "src" }, ] - # Ruff [tool.ruff] @@ -287,65 +301,64 @@ target-version = "py310" [tool.ruff.lint] extend-select = [ - "B", # flake8-bugbear - "F", # Pyflakes - "I", # isort - "E", # Pycodestyle - "W", # Pycodestyle - "N", # pep8-naming + "B", # flake8-bugbear + "F", # Pyflakes + "I", # isort + "E", # Pycodestyle + "W", # Pycodestyle + "N", # pep8-naming "ARG", # flake8-unused-arguments - "C4", # flake8-comprehensions - "EM", # flake8-errmsg + "C4", # flake8-comprehensions + "EM", # flake8-errmsg "ICN", # flake8-import-conventions "ISC", # flake8-implicit-str-concat - "G", # flake8-logging-format + "G", # flake8-logging-format "PGH", # pygrep-hooks "PIE", # flake8-pie - "PL", # pylint - "PT", # flake8-pytest-style + "PL", # pylint + "PT", # flake8-pytest-style "PTH", # flake8-use-pathlib "RET", # flake8-return "RUF", # Ruff-specific "SIM", # flake8-simplify "T20", # flake8-print - "UP", # pyupgrade + "UP", # pyupgrade "YTT", # flake8-2020 "EXE", # flake8-executable "NPY", # NumPy specific rules - "PD", # pandas-vet - "UP", # Pyupgrade + "PD", # pandas-vet + "UP", # Pyupgrade ] ignore = [ - "PLR09", # Too many <...> + "PLR09", # Too many <...> "PLR2004", # Magic value used in comparison - "ISC001", # Conflicts with formatter - "N801", # Class name should use CapWords convention - "N802", # Function name should be lowercase - "N806", # Variable in function should be lowercase + "ISC001", # Conflicts with formatter + "N801", # Class name should use CapWords convention + "N802", # Function name should be lowercase + "N806", # Variable in function should be lowercase + "PLC0415", # `import` should be at the top-level of a file ] - # Pylint [tool.pylint] py-version = "3.10" reports.output-format = "colorized" messages_control.disable = [ - "design", # ignore heavily opinionated design checks - "fixme", # allow FIXME comments - "line-too-long", # ruff handles this - "unused-argument", # ruff handles this + "design", # ignore heavily opinionated design checks + "fixme", #  allow FIXME comments + "line-too-long", # ruff handles this + "unused-argument", # ruff handles this "missing-function-docstring", # numpydoc handles this - "import-error", # mypy handles this - "import-outside-toplevel", # optional dependencies + "import-error", # mypy handles this + "import-outside-toplevel", # optional dependencies ] - # numpydoc [tool.numpydoc_validation] checks = [ - "all", # report on all checks, except the below + "all", # report on all checks, except the below "EX01", # most docstrings do not need an example "SA01", # data-apis/array-api-extra#87 "ES01", # most docstrings do not need an extended summary diff --git a/renovate.json b/renovate.json index c263292b..a25395b0 100644 --- a/renovate.json +++ b/renovate.json @@ -1,10 +1,6 @@ { "$schema": "https://docs.renovatebot.com/renovate-schema.json", - "extends": [ - "config:recommended", - "helpers:pinGitHubActionDigests", - ":automergeMinor" - ], + "extends": ["config:recommended", "helpers:pinGitHubActionDigests", ":automergeMinor"], "dependencyDashboardTitle": "META: Dependency Dashboard", "commitMessagePrefix": "deps:", "labels": ["dependencies"], @@ -13,59 +9,49 @@ "pixi": ">=v0.45.0" }, "minimumReleaseAge": "14 days", - "packageRules": [ - { - "description": "Do not bump deps pinned with '~=' or '='.", - "matchManagers": ["pixi"], - "matchCurrentValue": "/^~?=/", - "enabled": false - }, - { - "description": "Do not bump Python deps in the manifest or requires-python.", - "matchManagers": ["pixi", "pep621"], - "matchPackageNames": ["python"], - "enabled": false - }, - { - "description": "Schedule automerged GHA updates for the 15th of each month.", - "matchManagers": ["github-actions"], - "groupName": "gha", - "schedule": ["* * 15 * *"], - "automerge": true - }, - { - "description": "Block PRs for updates blocked on dropping Python 3.10.", - "matchManagers": ["pixi"], - "matchPackageNames": ["sphinx", "ipython", "sphinx-autodoc-typehints"], - "enabled": false - }, - { - "description": "Waiting for Numba to support NumPy 2.2.", - "matchManagers": ["pixi"], - "matchPackageNames": ["numpy"], - "enabled": false - }, - { - "description": "Block Python CI updates as setup-python lags behind (gh-194).", - "matchManagers": ["github-actions"], - "matchPackageNames": ["python"], - "enabled": false - }, - { - "description": "Group Dask packages.", - "matchPackageNames": ["dask", "dask-core"], - "groupName": "dask" - }, - { - "description": "Group JAX packages.", - "matchPackageNames": ["jax", "jaxlib"], - "groupName": "jax" - }, - { - "description": "Schedule hypothesis monthly as releases are frequent.", - "matchManagers": ["pixi"], - "matchPackageNames": ["hypothesis"], - "schedule": ["* * 10 * *"] - } - ] + "packageRules": [{ + "description": "Do not bump deps pinned with '~=' or '='.", + "matchManagers": ["pixi"], + "matchCurrentValue": "/^~?=/", + "enabled": false + }, { + "description": "Do not bump Python deps in the manifest or requires-python.", + "matchManagers": ["pixi", "pep621"], + "matchPackageNames": ["python"], + "enabled": false + }, { + "description": "Schedule automerged GHA updates for the 15th of each month.", + "matchManagers": ["github-actions"], + "groupName": "gha", + "schedule": ["* * 15 * *"], + "automerge": true + }, { + "description": "Block PRs for updates blocked on dropping Python 3.10.", + "matchManagers": ["pixi"], + "matchPackageNames": ["sphinx", "ipython", "sphinx-autodoc-typehints"], + "enabled": false + }, { + "description": "Waiting for Numba to support NumPy 2.2.", + "matchManagers": ["pixi"], + "matchPackageNames": ["numpy"], + "enabled": false + }, { + "description": "Block Python CI updates as setup-python lags behind (gh-194).", + "matchManagers": ["github-actions"], + "matchPackageNames": ["python"], + "enabled": false + }, { + "description": "Group Dask packages.", + "matchPackageNames": ["dask", "dask-core"], + "groupName": "dask" + }, { + "description": "Group JAX packages.", + "matchPackageNames": ["jax", "jaxlib"], + "groupName": "jax" + }, { + "description": "Schedule hypothesis monthly as releases are frequent.", + "matchManagers": ["pixi"], + "matchPackageNames": ["hypothesis"], + "schedule": ["* * 10 * *"] + }] } diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index cf1a894a..05db6251 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -268,7 +268,7 @@ def broadcast_shapes(*shapes: tuple[float | None, ...]) -> tuple[int | None, ... for axis in range(-ndim, 0): sizes = {shape[axis] for shape in shapes if axis >= -len(shape)} # Dask uses NaN for unknown shape, which predates the Array API spec for None - none_size = None in sizes or math.nan in sizes + none_size = None in sizes or math.nan in sizes # noqa: PLW0177 sizes -= {1, None, math.nan} if len(sizes) > 1: msg = ( diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index 47511c75..d40fea1a 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -297,9 +297,9 @@ def temp_setattr(mod: ModuleType, name: str, func: object) -> None: # Enable using patch_lazy_xp_function not as a context manager temp_setattr = monkeypatch.setattr # type: ignore[assignment] # pyright: ignore[reportAssignmentType] - def iter_tagged() -> ( - Iterator[tuple[ModuleType, str, Callable[..., Any], dict[str, Any]]] - ): + def iter_tagged() -> Iterator[ + tuple[ModuleType, str, Callable[..., Any], dict[str, Any]] + ]: for mod in mods: for name, func in mod.__dict__.items(): tags: dict[str, Any] | None = None diff --git a/tests/conftest.py b/tests/conftest.py index 26b9a816..76fb7650 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -37,13 +37,13 @@ def library(request: pytest.FixtureRequest) -> Backend: # numpydoc ignore=PR01, ("xfail_xp_backend", partial(xfail, request), {"reason", "strict"}), ): for marker in request.node.iter_markers(marker_name): - if len(marker.args) != 1: # pyright: ignore[reportUnknownArgumentType] + if len(marker.args) != 1: msg = f"Expected exactly one positional argument; got {marker.args}" raise TypeError(msg) if not isinstance(marker.args[0], Backend): msg = f"Argument of {marker_name} must be a Backend enum" raise TypeError(msg) - if invalid_kwargs := set(marker.kwargs) - allow_kwargs: # pyright: ignore[reportUnknownArgumentType] + if invalid_kwargs := set(marker.kwargs) - allow_kwargs: msg = f"Unexpected kwarg(s): {invalid_kwargs}" raise TypeError(msg) @@ -52,9 +52,9 @@ def library(request: pytest.FixtureRequest) -> Backend: # numpydoc ignore=PR01, strict: bool | None = marker.kwargs.get("strict", None) if library == elem: - reason = f"{library}: {reason}" if reason else str(library) # pyright: ignore[reportUnknownArgumentType] + reason = f"{library}: {reason}" if reason else str(library) kwargs = {"strict": strict} if strict is not None else {} - skip_or_xfail(reason=reason, **kwargs) # pyright: ignore[reportUnknownArgumentType] + skip_or_xfail(reason=reason, **kwargs) return elem @@ -98,7 +98,7 @@ def as_readonly(o: T) -> T: # numpydoc ignore=PR01,RT01 # This works with namedtuples too if isinstance(o, tuple | list): - return type(o)(*(as_readonly(i) for i in o)) # type: ignore[arg-type,return-value] # pyright: ignore[reportArgumentType,reportUnknownArgumentType] + return type(o)(*(as_readonly(i) for i in o)) # type: ignore[arg-type,return-value] # pyright: ignore[reportArgumentType] return o diff --git a/tests/test_funcs.py b/tests/test_funcs.py index dc0658ab..769b4119 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -94,8 +94,8 @@ def test_broadcast(self, xp: ModuleType): actual = apply_where( cond, (x, y), - lambda x, _: x, # pyright: ignore[reportUnknownArgumentType] - lambda _, y: y, # pyright: ignore[reportUnknownArgumentType] + lambda x, _: x, + lambda _, y: y, ) expect = xp.where(cond, x, y) xp_assert_equal(actual, expect) @@ -115,7 +115,7 @@ def test_dtype_propagation(self, xp: ModuleType, library: Backend): cond, (x, y), self.f1, - lambda x, y: mxp.astype(x - y, xp.int64), # pyright: ignore[reportArgumentType,reportUnknownArgumentType] + lambda x, y: mxp.astype(x - y, xp.int64), # pyright: ignore[reportArgumentType] ) assert actual.dtype == xp.int64 @@ -162,8 +162,8 @@ def test_dont_run_on_false(self, xp: ModuleType): actual = apply_where( x == 0, (x, y), - lambda x, y: x / y, # pyright: ignore[reportUnknownArgumentType] - lambda x, y: y / x, # pyright: ignore[reportUnknownArgumentType] + lambda x, y: x / y, + lambda x, y: y / x, ) xp_assert_equal(actual, xp.asarray([0.0, 1.5, 0.0])) diff --git a/tests/test_helpers.py b/tests/test_helpers.py index 43ad5dc7..9f5c924d 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -234,10 +234,10 @@ def test_device(self, xp: ModuleType, library: Backend, device: Device): # Test that we're accepting anything that is accepted by the # device= parameter in other functions - actual = capabilities(xp, device=device.type) # type: ignore[attr-defined] # pyright: ignore[reportUnknownArgumentType,reportAttributeAccessIssue] + actual = capabilities(xp, device=device.type) # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] -class Wrapper(Generic[T]): +class Wrapper(Generic[T]): # noqa: PLW1641 """Trivial opaque wrapper. Must be pickleable.""" x: T @@ -263,7 +263,7 @@ def __reduce__(self) -> tuple[object, ...]: # Note: NotHashable() instances can be reduced to an # unserializable local class - class NotHashable: + class NotHashable: # noqa: PLW1641 @override def __eq__(self, other: object) -> bool: return isinstance(other, type(self)) and other.__dict__ == self.__dict__ @@ -331,16 +331,16 @@ def test_flattened_stream(self): obj2 = [Wrapper(2), Wrapper(3)] instances1, rest1 = pickle_flatten(obj1, Wrapper) instances2, rest2 = pickle_flatten(obj2, Wrapper) - it = iter(instances1 + instances2 + [Wrapper(4)]) # pyright: ignore[reportUnknownArgumentType] - assert pickle_unflatten(it, rest1) == obj1 # pyright: ignore[reportUnknownArgumentType] - assert pickle_unflatten(it, rest2) == obj2 # pyright: ignore[reportUnknownArgumentType] - assert list(it) == [Wrapper(4)] # pyright: ignore[reportUnknownArgumentType] + it = iter(instances1 + instances2 + [Wrapper(4)]) + assert pickle_unflatten(it, rest1) == obj1 + assert pickle_unflatten(it, rest2) == obj2 + assert list(it) == [Wrapper(4)] def test_too_short(self): obj = [Wrapper(1), Wrapper(2)] instances, rest = pickle_flatten(obj, Wrapper) with pytest.raises(ValueError, match="Not enough"): - pickle_unflatten(instances[:1], rest) # pyright: ignore[reportUnknownArgumentType] + pickle_unflatten(instances[:1], rest) def test_recursion(self): obj: list[object] = [Wrapper(1)] @@ -349,7 +349,7 @@ def test_recursion(self): instances, rest = pickle_flatten(obj, Wrapper) assert instances == [Wrapper(1)] - obj2 = pickle_unflatten(instances, rest) # pyright: ignore[reportUnknownArgumentType] + obj2 = pickle_unflatten(instances, rest) assert len(obj2) == 2 assert obj2[0] is obj[0] assert obj2[1] is obj2 @@ -403,7 +403,7 @@ def f(x: object) -> object: assert isinstance(out, Wrapper) assert out.x[0] is winp.x[0] assert out.x[1] is not winp.x[1] - xp_assert_equal(out.x[1], winp.x[1]) # pyright: ignore[reportUnknownArgumentType] + xp_assert_equal(out.x[1], winp.x[1]) def test_arraylikes_are_static(self): pytest.importorskip("jax") diff --git a/tests/test_lazy.py b/tests/test_lazy.py index 056d608b..07904a33 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -187,8 +187,8 @@ def f(x: Array) -> Array: return x + 1 y = lazy_apply(f, x_da) - assert array_namespace(y._meta) is cp # type: ignore[attr-defined] # pyright: ignore[reportUnknownArgumentType,reportAttributeAccessIssue] - xp_assert_equal(y.compute(), x_cp + 1) # type: ignore[attr-defined] # pyright: ignore[reportUnknownArgumentType,reportAttributeAccessIssue] + assert array_namespace(y._meta) is cp # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + xp_assert_equal(y.compute(), x_cp + 1) # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] def test_dask_key(da: ModuleType): @@ -396,7 +396,7 @@ def test_lazy_apply_kwargs(xp: ModuleType, library: Backend, as_numpy: bool): with numpy arrays, and leave the rest untouched.""" x = xp.asarray(0) expect_cls = np.ndarray if as_numpy or library is Backend.DASK else type(x) - actual = check_lazy_apply_kwargs(x, expect_cls, as_numpy) # pyright: ignore[reportUnknownArgumentType] + actual = check_lazy_apply_kwargs(x, expect_cls, as_numpy) xp_assert_equal(actual, x + 1) diff --git a/tests/test_testing.py b/tests/test_testing.py index 7eda3fb6..3a93e287 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -296,7 +296,7 @@ def test_lazy_xp_function_deprecated_static_argnames(): # scipy.special.erf. from scipy.special._ufuncs import erf # type: ignore[import-untyped] - lazy_xp_function(erf) # pyright: ignore[reportUnknownArgumentType] + lazy_xp_function(erf) except ImportError: erf = None @@ -459,7 +459,7 @@ def test_patch_lazy_xp_functions_deprecated_monkeypatch( y = non_materializable5(x) xp_assert_equal(y, x) - with pytest.warns(DeprecationWarning): + with pytest.warns(DeprecationWarning, match="`monkeypatch` parameter"): _ = patch_lazy_xp_functions(request, monkeypatch, xp=xp) with pytest.raises(AssertionError, match=r"dask\.compute.* 1 times"): diff --git a/typos.toml b/typos.toml new file mode 100644 index 00000000..34233590 --- /dev/null +++ b/typos.toml @@ -0,0 +1,8 @@ +[files] +extend-exclude = [".git/", ".pixi/"] +ignore-hidden = false + +[default.extend-words] +nd = "nd" +typ = "typ" +cardinalis = "cardinalis" diff --git a/vendor_tests/_array_api_compat_vendor.py b/vendor_tests/_array_api_compat_vendor.py index cd31a9c4..9bc129b5 100644 --- a/vendor_tests/_array_api_compat_vendor.py +++ b/vendor_tests/_array_api_compat_vendor.py @@ -1,4 +1,5 @@ """This file is a hook imported by `src/array_api_extra/_lib/_compat.py`.""" +# pyright: reportUnknownParameterType=false, reportMissingParameterType=false from .array_api_compat import * # noqa: F403 from .array_api_compat import array_namespace as array_namespace_compat diff --git a/vendor_tests/test_vendor.py b/vendor_tests/test_vendor.py index 374cba11..e43c82fb 100644 --- a/vendor_tests/test_vendor.py +++ b/vendor_tests/test_vendor.py @@ -1,3 +1,7 @@ +# pyright: reportAttributeAccessIssue=false + +from typing import Any + import array_api_strict as xp from numpy.testing import assert_array_equal @@ -53,13 +57,13 @@ def test_vendor_extra(): x = xp.asarray(1) y = atleast_nd(x, ndim=0) - assert_array_equal(y, x) + assert_array_equal(y, x) # pyright: ignore[reportUnknownArgumentType] def test_vendor_extra_testing(): from .array_api_extra.testing import lazy_xp_function - def f(x): + def f(x: Any) -> Any: return x lazy_xp_function(f) From 992795fe1c5632910c6e2619769559805b61c4bb Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 2 Jul 2025 22:39:45 +0000 Subject: [PATCH 047/104] deps: Update dependency pytest to >=8.4.1 (#349) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pixi.lock b/pixi.lock index 9c76431a..583815d1 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 4d25cc2efa53002701cb00f6089ceba04b127ce21700f2b01b9e327778c3d54a + sha256: 7e1a92103a20e38d111dc539f7e17ed92e13b27b7c5b09d81a83e96723ca7c4f requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index e200956b..587cc46a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -94,7 +94,7 @@ numpydoc = { cmd = "numpydoc lint", description = "Validate docstrings with nump lint = { cmd = "lefthook run pre-commit --all-files --force", description = "Run all linters" } [tool.pixi.feature.tests.dependencies] -pytest = ">=8.4.0" +pytest = ">=8.4.1" pytest-cov = ">=6.2.1" hypothesis = ">=6.131.28" array-api-strict = ">=2.3.1,<2.4" @@ -122,7 +122,7 @@ sphinx-copybutton = ">=0.5.2" sphinx-autodoc-typehints = ">=1.25.3" # Needed to import parsed modules with autodoc dask-core = ">=2025.5.1" # No distributed, tornado, etc. -pytest = ">=8.4.0" +pytest = ">=8.4.1" typing-extensions = ">=4.14.0" numpy = ">=2.1.3" From ceb14ebc3afd418815960f84add2138a5cedd4a3 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 9 Jul 2025 18:55:11 +0000 Subject: [PATCH 048/104] deps: Update dependency numpydoc to >=1.9.0,<2 (#351) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 583815d1..e6224eed 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 7e1a92103a20e38d111dc539f7e17ed92e13b27b7c5b09d81a83e96723ca7c4f + sha256: b6c53de8343a57b2655aec9ba02089cd55ece9249885734959612f7be8963640 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 587cc46a..12f902fb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -59,7 +59,7 @@ typing-extensions = ">=4.14.0" pylint = ">=3.3.7" mypy = ">=1.16.1" basedpyright = ">=1.29.4" -numpydoc = ">=1.8.0,<2" +numpydoc = ">=1.9.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1,<2.4" numpy = ">=2.1.3" From a89d7d396600b3920f64430f375c90ef69d519a2 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 9 Jul 2025 21:44:11 +0100 Subject: [PATCH 049/104] CI/deps: clean up workflows and renovate config (#352) * CI: remove redundant setup-python * clean up workflows and renovate config --- .github/workflows/ci.yml | 7 +++---- .github/workflows/docs-build.yml | 5 ++++- .github/workflows/docs-deploy.yml | 1 + renovate.json | 15 +++------------ 4 files changed, 11 insertions(+), 17 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 3f1fca89..c8c5f2bd 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -27,14 +27,13 @@ jobs: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 with: fetch-depth: 0 - - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0 - with: - python-version: "3.13.3" + - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 with: pixi-version: v0.49.0 cache: true environments: lint + - name: Lint run: pixi run -e lint lint @@ -59,7 +58,7 @@ jobs: - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 with: - pixi-version: v0.42.1 + pixi-version: v0.49.0 cache: true environments: ${{ matrix.environment }} diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index e9da16ec..dc263cf5 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -10,13 +10,16 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 + - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 with: - pixi-version: v0.42.1 + pixi-version: v0.49.0 cache: true environments: docs + - name: Build Docs run: pixi run -e docs docs + - name: Upload Artifact uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2 with: diff --git a/.github/workflows/docs-deploy.yml b/.github/workflows/docs-deploy.yml index 25b46467..0f928bf6 100644 --- a/.github/workflows/docs-deploy.yml +++ b/.github/workflows/docs-deploy.yml @@ -18,6 +18,7 @@ jobs: name: docs-deploy steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 + - name: Download Artifact uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10 with: diff --git a/renovate.json b/renovate.json index a25395b0..259aa70d 100644 --- a/renovate.json +++ b/renovate.json @@ -15,8 +15,8 @@ "matchCurrentValue": "/^~?=/", "enabled": false }, { - "description": "Do not bump Python deps in the manifest or requires-python.", - "matchManagers": ["pixi", "pep621"], + "description": "Do not bump requires-python.", + "matchManagers": ["pep621"], "matchPackageNames": ["python"], "enabled": false }, { @@ -28,18 +28,9 @@ }, { "description": "Block PRs for updates blocked on dropping Python 3.10.", "matchManagers": ["pixi"], + "matchUpdateTypes": ["major"], "matchPackageNames": ["sphinx", "ipython", "sphinx-autodoc-typehints"], "enabled": false - }, { - "description": "Waiting for Numba to support NumPy 2.2.", - "matchManagers": ["pixi"], - "matchPackageNames": ["numpy"], - "enabled": false - }, { - "description": "Block Python CI updates as setup-python lags behind (gh-194).", - "matchManagers": ["github-actions"], - "matchPackageNames": ["python"], - "enabled": false }, { "description": "Group Dask packages.", "matchPackageNames": ["dask", "dask-core"], From 95a31f41de786f94f39443a748fbf8ff8004acda Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 9 Jul 2025 22:29:51 +0100 Subject: [PATCH 050/104] deps: turn off renovate for `numpy` in `tests` feature (#354) --- renovate.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/renovate.json b/renovate.json index 259aa70d..6efaa5c8 100644 --- a/renovate.json +++ b/renovate.json @@ -25,6 +25,12 @@ "groupName": "gha", "schedule": ["* * 15 * *"], "automerge": true + }, { + "description": "Don't bump test dependencies for oldest Python compatibility.", + "matchManagers": ["pixi"], + "matchDepTypes": ["feature-tests"], + "matchPackageNames": ["numpy"], + "enabled": false }, { "description": "Block PRs for updates blocked on dropping Python 3.10.", "matchManagers": ["pixi"], From 4f2d14d1ddf4e97f6c68dd71fbec60175943bbd7 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 9 Jul 2025 22:40:13 +0100 Subject: [PATCH 051/104] deps: add numpy to 3.10 drop list (#355) --- renovate.json | 8 +------- 1 file changed, 1 insertion(+), 7 deletions(-) diff --git a/renovate.json b/renovate.json index 6efaa5c8..93e09280 100644 --- a/renovate.json +++ b/renovate.json @@ -25,17 +25,11 @@ "groupName": "gha", "schedule": ["* * 15 * *"], "automerge": true - }, { - "description": "Don't bump test dependencies for oldest Python compatibility.", - "matchManagers": ["pixi"], - "matchDepTypes": ["feature-tests"], - "matchPackageNames": ["numpy"], - "enabled": false }, { "description": "Block PRs for updates blocked on dropping Python 3.10.", "matchManagers": ["pixi"], "matchUpdateTypes": ["major"], - "matchPackageNames": ["sphinx", "ipython", "sphinx-autodoc-typehints"], + "matchPackageNames": ["numpy", "sphinx", "ipython", "sphinx-autodoc-typehints"], "enabled": false }, { "description": "Group Dask packages.", From 7e3ac5772134012e061d3196e708ccb0be813f4e Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 9 Jul 2025 22:48:47 +0100 Subject: [PATCH 052/104] deps: also block minor updates for oldest python compat (#356) --- renovate.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/renovate.json b/renovate.json index 93e09280..d81ec2b4 100644 --- a/renovate.json +++ b/renovate.json @@ -28,7 +28,7 @@ }, { "description": "Block PRs for updates blocked on dropping Python 3.10.", "matchManagers": ["pixi"], - "matchUpdateTypes": ["major"], + "matchUpdateTypes": ["major", "minor"], "matchPackageNames": ["numpy", "sphinx", "ipython", "sphinx-autodoc-typehints"], "enabled": false }, { From 14d6cda3ffa8192959b36dc1d2b046287908bd18 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 10 Jul 2025 00:01:39 +0100 Subject: [PATCH 053/104] deps: Update dependency numpy to >=2.3.1 (#353) --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index e6224eed..508108a4 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: b6c53de8343a57b2655aec9ba02089cd55ece9249885734959612f7be8963640 + sha256: bdcbaec13bc57e4b0c6b05d697f1fcaf956ea3c412b0cc47b3ec27cc70ae9fb8 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 12f902fb..0c182a6a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -198,7 +198,7 @@ pytorch = { version = ">=2.7.0", build = "cuda12*" } [tool.pixi.feature.nogil.dependencies] python-freethreading = "~=3.13.0" pytest-run-parallel = ">=0.4.4" -numpy = ">=2.3.0" +numpy = ">=2.3.1" # pytorch = "*" # Not available on Python 3.13t yet dask-core = ">=2025.5.1" # No distributed, tornado, etc. # sparse = "*" # numba not available on Python 3.13t yet From 1da26e8ebb3c3e67485c4a634568a6e7b78ee342 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 10 Jul 2025 04:52:41 +0000 Subject: [PATCH 054/104] deps: Update dependency hypothesis to >=6.135.15 (#357) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pixi.lock b/pixi.lock index 508108a4..334de1df 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: bdcbaec13bc57e4b0c6b05d697f1fcaf956ea3c412b0cc47b3ec27cc70ae9fb8 + sha256: 17ea66b6b47edc3a347d92258dbd798e13ab370d01b7e1c36c5b31be1a737e05 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 0c182a6a..e993dda8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -63,7 +63,7 @@ numpydoc = ">=1.9.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1,<2.4" numpy = ">=2.1.3" -hypothesis = ">=6.131.28" +hypothesis = ">=6.135.15" dask-core = ">=2025.5.1" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.11.14,<2" @@ -96,7 +96,7 @@ lint = { cmd = "lefthook run pre-commit --all-files --force", description = "Run [tool.pixi.feature.tests.dependencies] pytest = ">=8.4.1" pytest-cov = ">=6.2.1" -hypothesis = ">=6.131.28" +hypothesis = ">=6.135.15" array-api-strict = ">=2.3.1,<2.4" numpy = ">=1.22.0" From 7784ba972357f3cb6193258781c630bfd60c5b9a Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 10 Jul 2025 15:49:21 +0000 Subject: [PATCH 055/104] deps: Update dependency hypothesis to >=6.135.16 (#358) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pixi.lock b/pixi.lock index 334de1df..562a5762 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 17ea66b6b47edc3a347d92258dbd798e13ab370d01b7e1c36c5b31be1a737e05 + sha256: 9b790b979ee30cd3120cd86d2f63915ed8b3aa4884d58f0439fcad6479e70852 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index e993dda8..0259021d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -63,7 +63,7 @@ numpydoc = ">=1.9.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1,<2.4" numpy = ">=2.1.3" -hypothesis = ">=6.135.15" +hypothesis = ">=6.135.16" dask-core = ">=2025.5.1" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.11.14,<2" @@ -96,7 +96,7 @@ lint = { cmd = "lefthook run pre-commit --all-files --force", description = "Run [tool.pixi.feature.tests.dependencies] pytest = ">=8.4.1" pytest-cov = ">=6.2.1" -hypothesis = ">=6.135.15" +hypothesis = ">=6.135.16" array-api-strict = ">=2.3.1,<2.4" numpy = ">=1.22.0" From 4b486994be9d05f3b8722134ab6f4f3dcaccc379 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Mon, 14 Jul 2025 21:39:02 +0000 Subject: [PATCH 056/104] deps: Update dependency basedpyright to >=1.29.5 (#361) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 562a5762..78fde7bb 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 9b790b979ee30cd3120cd86d2f63915ed8b3aa4884d58f0439fcad6479e70852 + sha256: 61e2ab615bffd7a7de08369000f63712da0adcb91d71ebf6d86cc6ec01862109 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 0259021d..69c080e4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ array-api-extra = { path = ".", editable = true } typing-extensions = ">=4.14.0" pylint = ">=3.3.7" mypy = ">=1.16.1" -basedpyright = ">=1.29.4" +basedpyright = ">=1.29.5" numpydoc = ">=1.9.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1,<2.4" From cbbb302344bfaf86aa2670d47598f99c8d60a9c2 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 15 Jul 2025 05:00:06 +0000 Subject: [PATCH 057/104] deps: Update gha (#362) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/cd.yml | 4 ++-- .github/workflows/ci.yml | 4 ++-- .github/workflows/docs-build.yml | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index c57eeb4d..68bd3738 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -21,7 +21,7 @@ jobs: with: fetch-depth: 0 - - uses: hynek/build-and-inspect-python-package@b5076c307dc91924a82ad150cdd1533b444d3310 # v2.12.0 + - uses: hynek/build-and-inspect-python-package@c52c3a4710070b50470d903818a7b25115dcd076 # v2.13.0 publish: needs: [dist] @@ -40,7 +40,7 @@ jobs: path: dist - name: Generate artifact attestation for sdist and wheel - uses: actions/attest-build-provenance@db473fddc028af60658334401dc6fa3ffd8669fd # v2.3.0 + uses: actions/attest-build-provenance@e8998f949152b193b063cb0ec769d69d929409be # v2.4.0 with: subject-path: "dist/*" diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index c8c5f2bd..7ed9676d 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -28,7 +28,7 @@ jobs: with: fetch-depth: 0 - - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 + - uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961 # v0.8.10 with: pixi-version: v0.49.0 cache: true @@ -56,7 +56,7 @@ jobs: with: fetch-depth: 0 - - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 + - uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961 # v0.8.10 with: pixi-version: v0.49.0 cache: true diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index dc263cf5..81073742 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -11,7 +11,7 @@ jobs: steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 - - uses: prefix-dev/setup-pixi@19eac09b398e3d0c747adc7921926a6d802df4da # v0.8.8 + - uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961 # v0.8.10 with: pixi-version: v0.49.0 cache: true From e89ebb5853f95c50316c4371b9afeebb4c90cabc Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 15 Jul 2025 10:35:11 +0000 Subject: [PATCH 058/104] deps: Update dawidd6/action-download-artifact action to v11 (#363) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/docs-deploy.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/docs-deploy.yml b/.github/workflows/docs-deploy.yml index 0f928bf6..844031bd 100644 --- a/.github/workflows/docs-deploy.yml +++ b/.github/workflows/docs-deploy.yml @@ -20,7 +20,7 @@ jobs: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 - name: Download Artifact - uses: dawidd6/action-download-artifact@4c1e823582f43b179e2cbb49c3eade4e41f992e2 # v10 + uses: dawidd6/action-download-artifact@ac66b43f0e6a346234dd65d4d0c8fbb31cb316e5 # v11 with: workflow: docs-build.yml name: docs-build From 546a33674d0270de03e881afb24a9717907e11b4 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 15 Jul 2025 21:50:06 +0100 Subject: [PATCH 059/104] DOC: organise README badges (#364) --- .github/workflows/ci.yml | 2 +- README.md | 11 +++++------ lefthook.yml | 17 +++++++++++++++-- 3 files changed, 21 insertions(+), 9 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 7ed9676d..bcbc67e9 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -34,7 +34,7 @@ jobs: cache: true environments: lint - - name: Lint + - name: Lint (if this step fails, please 'pixi run lint' locally and push the changes) run: pixi run -e lint lint checks: diff --git a/README.md b/README.md index cef223d3..1b33322a 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,14 @@ # array-api-extra -[![Actions Status][actions-badge]][actions-link] [![docs - here!][docs-badge]][docs-link] -[![Pixi Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json)](https://pixi.sh) -[![All Contributors](https://img.shields.io/github/all-contributors/data-apis/array-api-extra?color=ee8449&style=flat-square)](#contributors) -[![Typing](https://img.shields.io/pypi/types/array-api-extra)](https://typing.python.org/) -[![codecov](https://codecov.io/github/data-apis/array-api-extra/graph/badge.svg)](https://codecov.io/github/data-apis/array-api-extra) - [![PyPI version][pypi-version]][pypi-link] [![Conda-Forge][conda-badge]][conda-link] [![PyPI platforms][pypi-platforms]][pypi-link] +[![All Contributors](https://img.shields.io/github/all-contributors/data-apis/array-api-extra?color=ee8449&style=flat-square)](#contributors) + +[![Pixi Badge](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/prefix-dev/pixi/main/assets/badge/v0.json)](https://pixi.sh) +[![Typing](https://img.shields.io/pypi/types/array-api-extra)](https://typing.python.org/) +[![codecov](https://codecov.io/github/data-apis/array-api-extra/graph/badge.svg)](https://codecov.io/github/data-apis/array-api-extra) [![EffVer Versioning](https://img.shields.io/badge/version_scheme-EffVer-0097a7)](https://jacobtomlinson.dev/effver) [![SPEC 8 — Securing the Release Process](https://img.shields.io/badge/SPEC-8-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/spec-0008/) diff --git a/lefthook.yml b/lefthook.yml index 4797a99e..3ae3197d 100644 --- a/lefthook.yml +++ b/lefthook.yml @@ -1,7 +1,20 @@ -lefthook: pixi run --environment=lint lefthook +lefthook: pixi run --no-progress --environment=lint lefthook templates: - run: run --environment=lint + run: run --quiet --no-progress --environment=lint + +colors: true + +output: + - meta # Print lefthook version + - summary # Print summary block (successful and failed steps) + - empty_summary # Print summary heading when there are no steps to run + # - success # Print successful steps + # - failure # Print failed steps printing + # - execution # Print any execution logs + # - execution_out # Print execution output + # - execution_info # Print `EXECUTE > ...` logging + - skips # Print "skip" (i.e. no files matched) pre-commit: parallel: true From 8bff45965efe28e56323b1b1566f4d7058c716f2 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 17 Jul 2025 18:55:33 +0000 Subject: [PATCH 060/104] deps: Update dependency lefthook to >=1.11.15,<2 (#365) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 71 +++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 37 insertions(+), 36 deletions(-) diff --git a/pixi.lock b/pixi.lock index 78fde7bb..85ad460b 100644 --- a/pixi.lock +++ b/pixi.lock @@ -146,7 +146,7 @@ environments: - 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python >=3.9 + - python + license: PSF-2.0 + license_family: PSF + purls: + - pkg:pypi/typing-extensions?source=hash-mapping + size: 51065 + timestamp: 1751643513473 - conda: https://prefix.dev/conda-forge/linux-64/typos-1.34.0-h8fae777_0.conda sha256: b8ebacc5a6971149fb4eec067d48d1243995de8fdb92145eadd12f94bf538ab9 md5: e31ae446eb567b9f330a894453b11086 diff --git a/pyproject.toml b/pyproject.toml index 7a1a21fe..54b9059c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -55,7 +55,7 @@ array-api-compat = ">=1.12.0,<2" array-api-extra = { path = ".", editable = true } [tool.pixi.feature.lint.dependencies] -typing-extensions = ">=4.14.0" +typing-extensions = ">=4.14.1" pylint = ">=3.3.7" mypy = ">=1.16.1" basedpyright = ">=1.29.5" @@ -123,7 +123,7 @@ sphinx-autodoc-typehints = ">=1.25.3" # Needed to import parsed modules with autodoc dask-core = ">=2025.5.1" # No distributed, tornado, etc. pytest = ">=8.4.1" -typing-extensions = ">=4.14.0" +typing-extensions = ">=4.14.1" numpy = ">=2.1.3" [tool.pixi.feature.docs.tasks] From f8723678eb8d9289b7809cb4a0f67fe7deb93489 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 23 Jul 2025 01:15:23 +0000 Subject: [PATCH 063/104] deps: Update dependency lefthook to >=1.11.16,<2 (#369) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index a52800e7..01864e22 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: ae38ad7436631cc98ee7a1b6b9723789bb2207f6fb62fc18556fcabc85034f4e + sha256: ba92d7ddd4ad19a471c16057d755b0883a440e92b130696c57f5f97d4f011be7 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 54b9059c..00ede73b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,7 +66,7 @@ numpy = ">=2.1.3" hypothesis = ">=6.135.16" dask-core = ">=2025.5.1" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" -lefthook = ">=1.11.15,<2" +lefthook = ">=1.11.16,<2" ruff = ">=0.12.2,<0.13" typos = ">=1.34.0,<2" actionlint = ">=1.7.7,<2" From d05e61c9707b3056d1c4d37e04913224fc1847e9 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 23 Jul 2025 16:07:07 +0000 Subject: [PATCH 064/104] deps: Update dependency lefthook to >=1.12.0,<2 (#370) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 01864e22..8d84463e 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: ba92d7ddd4ad19a471c16057d755b0883a440e92b130696c57f5f97d4f011be7 + sha256: e9a271f263b2a72833a9016a49fb6e40fe62379fcb0dea611faf8592e2a5780e requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 00ede73b..6a39627e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,7 +66,7 @@ numpy = ">=2.1.3" hypothesis = ">=6.135.16" dask-core = ">=2025.5.1" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" -lefthook = ">=1.11.16,<2" +lefthook = ">=1.12.0,<2" ruff = ">=0.12.2,<0.13" typos = ">=1.34.0,<2" actionlint = ">=1.7.7,<2" From 3663f2042a1fd597cfaae833db20029eb80233b5 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 23 Jul 2025 19:26:38 +0000 Subject: [PATCH 065/104] deps: Update dependency basedpyright to >=1.30.0 (#371) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 36 ++++++++++++++++++------------------ pyproject.toml | 2 +- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/pixi.lock b/pixi.lock index 8d84463e..0183f204 100644 --- a/pixi.lock +++ b/pixi.lock @@ -102,7 +102,7 @@ environments: - 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conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.31.0-pyhe01879c_0.conda - conda: https://prefix.dev/conda-forge/osx-arm64/black-25.1.0-py313h8f79df9_0.conda - conda: https://prefix.dev/conda-forge/noarch/blacken-docs-1.19.1-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/osx-arm64/brotli-python-1.1.0-py313h928ef07_3.conda @@ -2203,7 +2203,7 @@ environments: - conda: https://prefix.dev/conda-forge/win-64/astroid-3.3.10-py313hfa70ccb_0.conda - conda: https://prefix.dev/conda-forge/noarch/attrs-25.3.0-pyh71513ae_0.conda - conda: https://prefix.dev/conda-forge/noarch/babel-2.17.0-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.29.5-pyhe01879c_0.conda + - conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.31.0-pyhe01879c_0.conda - conda: https://prefix.dev/conda-forge/noarch/black-25.1.0-pyh866005b_0.conda - conda: https://prefix.dev/conda-forge/noarch/blacken-docs-1.19.1-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/win-64/brotli-python-1.1.0-py313h5813708_3.conda @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: e9a271f263b2a72833a9016a49fb6e40fe62379fcb0dea611faf8592e2a5780e + sha256: 01d7ae36773c7e54547d4d024b588cf9f26bb5ba7b3b74bb0c4c314fbc2c5355 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' @@ -4418,9 +4418,9 @@ packages: - pkg:pypi/babel?source=compressed-mapping size: 6938256 timestamp: 1738490268466 -- conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.29.5-pyhe01879c_0.conda - sha256: 75ad1b095f3bed6962d6fea8c197a718df6751dfa0c92016647fe341d9426793 - md5: f493f7a303f65470586f4ad0f74bc4e7 +- conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.31.0-pyhe01879c_0.conda + sha256: cac9f946958cfb1ac67bc5e4cf96ec2e212132763b256699b16f37eb004698ae + md5: 37b50852c793b39b2b3ec44229e019b7 depends: - python >=3.9 - nodejs-wheel >=20.13.1 @@ -4428,8 +4428,8 @@ packages: license: MIT AND Apache-2.0 purls: - pkg:pypi/basedpyright?source=hash-mapping - size: 8225085 - timestamp: 1751294452624 + size: 8255872 + timestamp: 1752676975836 - conda: https://prefix.dev/conda-forge/noarch/beautifulsoup4-4.13.4-pyha770c72_0.conda sha256: ddb0df12fd30b2d36272f5daf6b6251c7625d6a99414d7ea930005bbaecad06d md5: 9f07c4fc992adb2d6c30da7fab3959a7 diff --git a/pyproject.toml b/pyproject.toml index 6a39627e..480ec641 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ array-api-extra = { path = ".", editable = true } typing-extensions = ">=4.14.1" pylint = ">=3.3.7" mypy = ">=1.16.1" -basedpyright = ">=1.29.5" +basedpyright = ">=1.30.0" numpydoc = ">=1.9.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1,<2.4" From c09fa870a687420ff1a53433b2b6fc3af1916bb8 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 24 Jul 2025 01:47:08 +0000 Subject: [PATCH 066/104] deps: Update dependency lefthook to >=1.12.1,<2 (#372) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 0183f204..5645b9fd 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 01d7ae36773c7e54547d4d024b588cf9f26bb5ba7b3b74bb0c4c314fbc2c5355 + sha256: f4ecdd7317a97d0a487fe3bd8f6720b4590c4f1d94b09097697d7a975dcba1c2 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 480ec641..64650376 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,7 +66,7 @@ numpy = ">=2.1.3" hypothesis = ">=6.135.16" dask-core = ">=2025.5.1" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" -lefthook = ">=1.12.0,<2" +lefthook = ">=1.12.1,<2" ruff = ">=0.12.2,<0.13" typos = ">=1.34.0,<2" actionlint = ">=1.7.7,<2" From e568ac3a67ac8511aa07e4fb6fefaf9e38a22c26 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 24 Jul 2025 19:02:35 +0000 Subject: [PATCH 067/104] deps: Update dependency basedpyright to >=1.30.1 (#373) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 5645b9fd..47969ec0 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: f4ecdd7317a97d0a487fe3bd8f6720b4590c4f1d94b09097697d7a975dcba1c2 + sha256: bb7866b60526563fe6c8fb94bd0afbe450bc852e84cdf603040c863930380fd6 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 64650376..7eefe2db 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ array-api-extra = { path = ".", editable = true } typing-extensions = ">=4.14.1" pylint = ">=3.3.7" mypy = ">=1.16.1" -basedpyright = ">=1.30.0" +basedpyright = ">=1.30.1" numpydoc = ">=1.9.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1,<2.4" From 41594d48ef0e47a754a5140ff3a54d970a8138ae Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sat, 26 Jul 2025 00:36:11 +0000 Subject: [PATCH 068/104] deps: Update dependency lefthook to >=1.12.2,<2 (#374) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 47969ec0..50c0cff2 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: bb7866b60526563fe6c8fb94bd0afbe450bc852e84cdf603040c863930380fd6 + sha256: 4a1f0d658501c0d9f94c6482d5be8cf5e4203496b6ae1649634f3cf668cb6a73 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 7eefe2db..025183e9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,7 +66,7 @@ numpy = ">=2.1.3" hypothesis = ">=6.135.16" dask-core = ">=2025.5.1" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" -lefthook = ">=1.12.1,<2" +lefthook = ">=1.12.2,<2" ruff = ">=0.12.2,<0.13" typos = ">=1.34.0,<2" actionlint = ">=1.7.7,<2" From 52f7ee34c7bf99ae3a0c35a1638d04c9558abcaf Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sat, 26 Jul 2025 08:22:57 +0000 Subject: [PATCH 069/104] deps: Update dependency ruff to >=0.12.3,<0.13 (#375) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 50c0cff2..c6f82a30 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4253,7 +4253,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 4a1f0d658501c0d9f94c6482d5be8cf5e4203496b6ae1649634f3cf668cb6a73 + sha256: fe8e82ce1aaa8c17aac35e3210ae85c52dff38064917da9f6da44354fbd2de23 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 025183e9..bf21d6dd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,7 +67,7 @@ hypothesis = ">=6.135.16" dask-core = ">=2025.5.1" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.12.2,<2" -ruff = ">=0.12.2,<0.13" +ruff = ">=0.12.3,<0.13" typos = ">=1.34.0,<2" actionlint = ">=1.7.7,<2" blacken-docs = ">=1.19.1,<2" From cbd065c8fda1c4de688807bae6a96442ff868326 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Mon, 28 Jul 2025 05:09:41 +0000 Subject: [PATCH 070/104] deps: Update dependency cupy to >=13.5.1 (#376) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 112 ++++++++++++++++++++++++------------------------- pyproject.toml | 4 +- 2 files changed, 58 insertions(+), 58 deletions(-) diff --git a/pixi.lock b/pixi.lock index c6f82a30..4c0826fe 100644 --- a/pixi.lock +++ b/pixi.lock @@ -802,8 +802,8 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/cuda-nvvm-tools-12.9.86-he02047a_1.conda - conda: https://prefix.dev/conda-forge/noarch/cuda-version-12.9-h4f385c5_3.conda - conda: https://prefix.dev/conda-forge/linux-64/cudnn-9.10.1.4-h7646684_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/cupy-13.4.1-py310hab14140_1.conda - - conda: https://prefix.dev/conda-forge/linux-64/cupy-core-13.4.1-py310h4564b94_1.conda + - conda: https://prefix.dev/conda-forge/linux-64/cupy-13.5.1-py310h8c3aed4_1.conda + - conda: https://prefix.dev/conda-forge/linux-64/cupy-core-13.5.1-py310h1ea0ae5_1.conda - conda: https://prefix.dev/conda-forge/noarch/dask-core-2025.5.1-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/noarch/decorator-5.2.1-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/noarch/dill-0.4.0-pyhd8ed1ab_0.conda @@ -900,7 +900,7 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/mypy-1.16.1-py310ha75aee5_0.conda - conda: https://prefix.dev/conda-forge/noarch/mypy_extensions-1.1.0-pyha770c72_0.conda - 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[tool.pixi.feature.backends.dependencies] pytorch = ">=2.7.0" -dask-core = ">=2025.5.1" # No distributed, tornado, etc. +dask-core = ">=2025.7.0" # No distributed, tornado, etc. sparse = ">=0.17.0" [tool.pixi.feature.backends.target.linux-64.dependencies] @@ -200,7 +200,7 @@ python-freethreading = "~=3.13.0" pytest-run-parallel = ">=0.4.4" numpy = ">=2.3.1" # pytorch = "*" # Not available on Python 3.13t yet -dask-core = ">=2025.5.1" # No distributed, tornado, etc. +dask-core = ">=2025.7.0" # No distributed, tornado, etc. # sparse = "*" # numba not available on Python 3.13t yet # jax = "*" # ml_dtypes not available on Python 3.13t yet From 8b291c42054a54cad90ad6d033250f98635505df Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 29 Jul 2025 08:45:12 +0000 Subject: [PATCH 072/104] deps: Update dependency mypy to >=1.17.0 (#378) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 118 ++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 60 insertions(+), 60 deletions(-) diff --git a/pixi.lock b/pixi.lock index 2e0aed7d..674715a6 100644 --- a/pixi.lock +++ b/pixi.lock @@ -187,7 +187,7 @@ environments: - 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mypy_extensions >=1.0.0 - pathspec >=0.9.0 @@ -8592,17 +8592,17 @@ packages: - tomli >=1.1.0 - typing_extensions >=4.6.0 - ucrt >=10.0.20348.0 - - vc >=14.2,<15 - - vc14_runtime >=14.29.30139 + - vc >=14.3,<15 + - vc14_runtime >=14.44.35208 license: MIT license_family: MIT purls: - pkg:pypi/mypy?source=hash-mapping - size: 9640121 - timestamp: 1750118532736 -- conda: https://prefix.dev/conda-forge/win-64/mypy-1.16.1-py313ha7868ed_0.conda - sha256: d915755801ee459c174dcd7d40ddc6b1a4b0e96fa161c686582223a3b51077f2 - md5: 7c94601304b4e66c082e9c86ad219cea + size: 9611357 + timestamp: 1752534665931 +- conda: https://prefix.dev/conda-forge/win-64/mypy-1.17.0-py313h5ea7bf4_0.conda + sha256: 7af3ee6404a28a66cafe6e246eb2292763986c28c1e6189396527659f8f12501 + md5: f2348acb29874c7cb197ede0574ef95a depends: - mypy_extensions >=1.0.0 - pathspec >=0.9.0 @@ -8611,14 +8611,14 @@ packages: - python_abi 3.13.* *_cp313 - typing_extensions >=4.6.0 - ucrt >=10.0.20348.0 - - vc >=14.2,<15 - - vc14_runtime >=14.29.30139 + - vc >=14.3,<15 + - vc14_runtime >=14.44.35208 license: MIT license_family: MIT purls: - pkg:pypi/mypy?source=hash-mapping - size: 8494415 - timestamp: 1750118712013 + size: 8456330 + timestamp: 1752534865671 - conda: https://prefix.dev/conda-forge/noarch/mypy_extensions-1.1.0-pyha770c72_0.conda sha256: 6ed158e4e5dd8f6a10ad9e525631e35cee8557718f83de7a4e3966b1f772c4b1 md5: e9c622e0d00fa24a6292279af3ab6d06 diff --git a/pyproject.toml b/pyproject.toml index c5ec4409..10d0a6e3 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -57,7 +57,7 @@ array-api-extra = { path = ".", editable = true } [tool.pixi.feature.lint.dependencies] typing-extensions = ">=4.14.1" pylint = ">=3.3.7" -mypy = ">=1.16.1" +mypy = ">=1.17.0" basedpyright = ">=1.30.1" numpydoc = ">=1.9.0,<2" # import dependencies for mypy: From 68b98003150036cfd1d2ff015287ad628ff0d297 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Tue, 29 Jul 2025 11:24:44 +0100 Subject: [PATCH 073/104] deps: Upgrade to array-api-strict 2.4.1 (#379) --- .github/workflows/ci.yml | 4 +- .github/workflows/docs-build.yml | 2 +- pixi.lock | 3570 +++++++++++++++--------------- pyproject.toml | 10 +- tests/test_at.py | 8 +- 5 files changed, 1794 insertions(+), 1800 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index bcbc67e9..e92e284c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -30,7 +30,7 @@ jobs: - uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961 # v0.8.10 with: - pixi-version: v0.49.0 + pixi-version: v0.50.2 cache: true environments: lint @@ -58,7 +58,7 @@ jobs: - uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961 # v0.8.10 with: - pixi-version: v0.49.0 + pixi-version: v0.50.2 cache: true environments: ${{ matrix.environment }} diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index 81073742..95340c82 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -13,7 +13,7 @@ jobs: - uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961 # v0.8.10 with: - pixi-version: v0.49.0 + pixi-version: v0.50.2 cache: true environments: docs diff --git a/pixi.lock b/pixi.lock index 674715a6..62e131bf 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,22 +11,25 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.12.0-pyhe01879c_0.conda - 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md5: c989e0295dcbdc08106fe5d9e935f0b9 - depends: - - __osx >=10.13 - - libzlib 1.3.1 hd23fc13_2 - license: Zlib - license_family: Other - purls: [] - size: 88544 - timestamp: 1727963189976 -- conda: https://prefix.dev/conda-forge/osx-arm64/zlib-1.3.1-h8359307_2.conda - sha256: 58f8860756680a4831c1bf4f294e2354d187f2e999791d53b1941834c4b37430 - md5: e3170d898ca6cb48f1bb567afb92f775 - depends: - - __osx >=11.0 - - libzlib 1.3.1 h8359307_2 - license: Zlib - license_family: Other - purls: [] - size: 77606 - timestamp: 1727963209370 - conda: https://prefix.dev/conda-forge/linux-64/zstandard-0.23.0-py310ha75aee5_2.conda sha256: f9b76c2f8a0f96e656843553272e547170182f5b8aba1a6bcba28f7611d87c23 md5: f9254b5b0193982416b91edcb4b2676f diff --git a/pyproject.toml b/pyproject.toml index 10d0a6e3..a8138baf 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,7 +61,7 @@ mypy = ">=1.17.0" basedpyright = ">=1.30.1" numpydoc = ">=1.9.0,<2" # import dependencies for mypy: -array-api-strict = ">=2.3.1,<2.4" +array-api-strict = ">=2.4.1,<2.5" numpy = ">=2.1.3" hypothesis = ">=6.135.16" dask-core = ">=2025.7.0" # No distributed, tornado, etc. @@ -97,7 +97,7 @@ lint = { cmd = "lefthook run pre-commit --all-files --force", description = "Run pytest = ">=8.4.1" pytest-cov = ">=6.2.1" hypothesis = ">=6.135.16" -array-api-strict = ">=2.3.1,<2.4" +array-api-strict = ">=2.4.1,<2.5" numpy = ">=1.22.0" [tool.pixi.feature.tests.tasks] @@ -155,13 +155,13 @@ dask-core = ">=2025.7.0" # No distributed, tornado, etc. sparse = ">=0.17.0" [tool.pixi.feature.backends.target.linux-64.dependencies] -jax = ">=0.6.0" +jax = ">=0.6.0,!=0.6.2" # 0.6.2 segfaults on Linux CUDA [tool.pixi.feature.backends.target.osx-64.dependencies] -jax = ">=0.6.0" +jax = ">=0.6.0,!=0.6.2" [tool.pixi.feature.backends.target.osx-arm64.dependencies] -jax = ">=0.6.0" +jax = ">=0.6.0,!=0.6.2" [tool.pixi.feature.backends.target.win-64.dependencies] # jax = "*" # unavailable diff --git a/tests/test_at.py b/tests/test_at.py index d9e1bdf9..9558f7b8 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -246,12 +246,16 @@ def test_incompatible_dtype( elif library.like(Backend.DASK): z = at_op(x, idx, op, 1.1, copy=copy) - elif library.like(Backend.ARRAY_API_STRICT) and op is not _AtOp.SET: + elif library.like(Backend.ARRAY_API_STRICT): with pytest.raises(Exception, match=r"cast|promote|dtype"): _ = at_op(x, idx, op, 1.1, copy=copy) elif op in (_AtOp.SET, _AtOp.MIN, _AtOp.MAX): - # There is no __i__ version of these operations + # There is no __i__ version of min/max. + # libraries other than array-api-strict are happy with + # int[:] = float + # int[:] = min(int[:], float) + # int[:] = max(int[:], float) z = at_op(x, idx, op, 1.1, copy=copy) else: From 42995668d513d8e484dab197b0e4e99f4dc1a1bd Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 29 Jul 2025 19:31:47 +0000 Subject: [PATCH 074/104] deps: Update dependency pytorch to >=2.7.1 (#380) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pixi.lock b/pixi.lock index 62e131bf..983d3b18 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4279,7 +4279,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: e0b0d16f52c57ee04df4720729c1d0b0759c607019ba4aa5c38a2831293b89d4 + sha256: 4f3bbe7c191529a40b4e5d42e0a8cb1d1f357a11f956f341f3c34ebda070cb28 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index a8138baf..d22f95cb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -150,7 +150,7 @@ numpy = "=1.22.0" # Backends that can run on CPU-only hosts # Note: JAX and PyTorch will install CPU variants. [tool.pixi.feature.backends.dependencies] -pytorch = ">=2.7.0" +pytorch = ">=2.7.1" dask-core = ">=2025.7.0" # No distributed, tornado, etc. sparse = ">=0.17.0" @@ -178,7 +178,7 @@ system-requirements = { cuda = "12" } [tool.pixi.feature.cuda-backends.target.linux-64.dependencies] cupy = ">=13.5.1" jaxlib = { version = ">=0.6.0", build = "cuda12*" } -pytorch = { version = ">=2.7.0", build = "cuda12*" } +pytorch = { version = ">=2.7.1", build = "cuda12*" } [tool.pixi.feature.cuda-backends.target.osx-64.dependencies] # cupy = "*" # unavailable @@ -193,7 +193,7 @@ pytorch = { version = ">=2.7.0", build = "cuda12*" } [tool.pixi.feature.cuda-backends.target.win-64.dependencies] cupy = ">=13.5.1" # jaxlib = { version = "*", build = "cuda12*" } # unavailable -pytorch = { version = ">=2.7.0", build = "cuda12*" } +pytorch = { version = ">=2.7.1", build = "cuda12*" } [tool.pixi.feature.nogil.dependencies] python-freethreading = "~=3.13.0" From decdbb0d453654df6a553b5fa155cbeab5dfee57 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 30 Jul 2025 21:25:17 +0000 Subject: [PATCH 075/104] deps: Update dependency basedpyright to >=1.31.0 (#381) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 983d3b18..ebbb2e73 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4279,7 +4279,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 4f3bbe7c191529a40b4e5d42e0a8cb1d1f357a11f956f341f3c34ebda070cb28 + sha256: bd71c29d957296645d11a2b45963ad66bfa4345e922db299b9c531e1a0583405 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index d22f95cb..95b3b43c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ array-api-extra = { path = ".", editable = true } typing-extensions = ">=4.14.1" pylint = ">=3.3.7" mypy = ">=1.17.0" -basedpyright = ">=1.30.1" +basedpyright = ">=1.31.0" numpydoc = ">=1.9.0,<2" # import dependencies for mypy: array-api-strict = ">=2.4.1,<2.5" From 5cf753c07c6526820b6b96be9a7352b1e8cde4bc Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 1 Aug 2025 04:29:56 +0000 Subject: [PATCH 076/104] deps: Update dependency ruff to >=0.12.4,<0.13 (#382) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index ebbb2e73..3a3e9077 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4279,7 +4279,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: bd71c29d957296645d11a2b45963ad66bfa4345e922db299b9c531e1a0583405 + sha256: f4b98abbfac34e7970b331cca6339d38fee2b52b7b021c198228f4e1d1b42171 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 95b3b43c..76187b9e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,7 +67,7 @@ hypothesis = ">=6.135.16" dask-core = ">=2025.7.0" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.12.2,<2" -ruff = ">=0.12.3,<0.13" +ruff = ">=0.12.4,<0.13" typos = ">=1.34.0,<2" actionlint = ">=1.7.7,<2" blacken-docs = ">=1.19.1,<2" From b5a436871c604ef590e8111209d1048506e067da Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 5 Aug 2025 12:21:16 +0000 Subject: [PATCH 077/104] deps: Update dependency pytest-run-parallel to >=0.5.0 (#383) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 3a3e9077..bdad36a6 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4279,7 +4279,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: f4b98abbfac34e7970b331cca6339d38fee2b52b7b021c198228f4e1d1b42171 + sha256: 7d997dc40f8585e186d5dffd8fdbff817429717e37fd96aa08e2f8a6f27648f1 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 76187b9e..eb58d456 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -197,7 +197,7 @@ pytorch = { version = ">=2.7.1", build = "cuda12*" } [tool.pixi.feature.nogil.dependencies] python-freethreading = "~=3.13.0" -pytest-run-parallel = ">=0.4.4" +pytest-run-parallel = ">=0.5.0" numpy = ">=2.3.1" # pytorch = "*" # Not available on Python 3.13t yet dask-core = ">=2025.7.0" # No distributed, tornado, etc. From fe45b1467ca7f6df5e42ce0f3c5e740f1c94c607 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 8 Aug 2025 08:22:01 +0000 Subject: [PATCH 078/104] deps: Update dependency numpy to >=2.3.2 (#384) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index bdad36a6..a5567a81 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4279,7 +4279,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 7d997dc40f8585e186d5dffd8fdbff817429717e37fd96aa08e2f8a6f27648f1 + sha256: 8a6caaa05807cf8f059bd6990cbd23a02035ef828c1e0f1a3cd8340301bfb766 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index eb58d456..7b64a755 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -198,7 +198,7 @@ pytorch = { version = ">=2.7.1", build = "cuda12*" } [tool.pixi.feature.nogil.dependencies] python-freethreading = "~=3.13.0" pytest-run-parallel = ">=0.5.0" -numpy = ">=2.3.1" +numpy = ">=2.3.2" # pytorch = "*" # Not available on Python 3.13t yet dask-core = ">=2025.7.0" # No distributed, tornado, etc. # sparse = "*" # numba not available on Python 3.13t yet From 4cf19c65d24e731e6855e663b0e0f028bae57ad6 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 8 Aug 2025 12:21:30 +0000 Subject: [PATCH 079/104] deps: Update dependency ruff to >=0.12.5,<0.13 (#385) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index a5567a81..5d4db067 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4279,7 +4279,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 8a6caaa05807cf8f059bd6990cbd23a02035ef828c1e0f1a3cd8340301bfb766 + sha256: a15ec1b7e82c6b8f3eb17bce01a864caf770a29b6d24b1cff79c0e7c3cb5117d requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 7b64a755..6feb40ff 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,7 +67,7 @@ hypothesis = ">=6.135.16" dask-core = ">=2025.7.0" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.12.2,<2" -ruff = ">=0.12.4,<0.13" +ruff = ">=0.12.5,<0.13" typos = ">=1.34.0,<2" actionlint = ">=1.7.7,<2" blacken-docs = ">=1.19.1,<2" From 4c500c72ac81ce15454bcce38289923ecab4197a Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sun, 10 Aug 2025 04:21:06 +0000 Subject: [PATCH 080/104] deps: Update dependency hypothesis to >=6.136.4 (#387) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pixi.lock b/pixi.lock index 5d4db067..27b0fa1f 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4279,7 +4279,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: a15ec1b7e82c6b8f3eb17bce01a864caf770a29b6d24b1cff79c0e7c3cb5117d + sha256: f310d5b4b0c22e02452981a83b9bad9627ebcd5558e4258c8ea98cd06121d7cf requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 6feb40ff..69f1fca6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -63,7 +63,7 @@ numpydoc = ">=1.9.0,<2" # import dependencies for mypy: array-api-strict = ">=2.4.1,<2.5" numpy = ">=2.1.3" -hypothesis = ">=6.135.16" +hypothesis = ">=6.136.4" dask-core = ">=2025.7.0" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.12.2,<2" @@ -96,7 +96,7 @@ lint = { cmd = "lefthook run pre-commit --all-files --force", description = "Run [tool.pixi.feature.tests.dependencies] pytest = ">=8.4.1" pytest-cov = ">=6.2.1" -hypothesis = ">=6.135.16" +hypothesis = ">=6.136.4" array-api-strict = ">=2.4.1,<2.5" numpy = ">=1.22.0" From f95e867000834f30cb5364b284d6b8a39c3670b3 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 14 Aug 2025 09:11:15 +0000 Subject: [PATCH 081/104] deps: Update dependency ruff to >=0.12.7,<0.13 (#388) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 74 ++++++++++++++++++++++++++------------------------ pyproject.toml | 2 +- 2 files changed, 40 insertions(+), 36 deletions(-) diff --git a/pixi.lock b/pixi.lock index 27b0fa1f..6db7a5a9 100644 --- a/pixi.lock +++ b/pixi.lock @@ -235,7 +235,7 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/re2-2025.06.26-h9925aae_0.conda - conda: https://prefix.dev/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda - conda: https://prefix.dev/conda-forge/noarch/requests-2.32.4-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/ruff-0.12.5-hf9daec2_0.conda + - conda: https://prefix.dev/conda-forge/linux-64/ruff-0.12.8-hf9daec2_0.conda - conda: https://prefix.dev/conda-forge/linux-64/scipy-1.15.2-py310h1d65ade_0.conda - conda: https://prefix.dev/conda-forge/noarch/setuptools-80.9.0-pyhff2d567_0.conda - conda: https://prefix.dev/conda-forge/linux-64/sleef-3.8-h1b44611_0.conda @@ -402,7 +402,7 @@ environments: - conda: https://prefix.dev/conda-forge/osx-64/re2-2025.06.26-ha5e900a_0.conda - conda: https://prefix.dev/conda-forge/osx-64/readline-8.2-h7cca4af_2.conda - conda: https://prefix.dev/conda-forge/noarch/requests-2.32.4-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/osx-64/ruff-0.12.5-h6cc4cfe_0.conda + - conda: https://prefix.dev/conda-forge/osx-64/ruff-0.12.8-h6cc4cfe_0.conda - 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conda: https://prefix.dev/conda-forge/win-64/pyyaml-6.0.2-py310h38315fa_2.conda - conda: https://prefix.dev/conda-forge/noarch/requests-2.32.4-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/win-64/ruff-0.12.5-hd40eec1_0.conda + - conda: https://prefix.dev/conda-forge/win-64/ruff-0.12.8-hd40eec1_0.conda - conda: https://prefix.dev/conda-forge/noarch/setuptools-80.9.0-pyhff2d567_0.conda - conda: https://prefix.dev/conda-forge/win-64/sleef-3.8-h7e360cc_0.conda - conda: https://prefix.dev/conda-forge/noarch/snowballstemmer-3.0.1-pyhd8ed1ab_0.conda @@ -944,7 +944,7 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/re2-2025.06.26-h9925aae_0.conda - conda: https://prefix.dev/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda - conda: https://prefix.dev/conda-forge/noarch/requests-2.32.4-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/ruff-0.12.5-hf9daec2_0.conda + - conda: https://prefix.dev/conda-forge/linux-64/ruff-0.12.8-hf9daec2_0.conda - conda: https://prefix.dev/conda-forge/linux-64/scipy-1.15.2-py310h1d65ade_0.conda - conda: https://prefix.dev/conda-forge/noarch/setuptools-80.9.0-pyhff2d567_0.conda - conda: https://prefix.dev/conda-forge/linux-64/sleef-3.8-h1b44611_0.conda @@ -1113,7 +1113,7 @@ environments: - conda: https://prefix.dev/conda-forge/osx-64/re2-2025.06.26-ha5e900a_0.conda - conda: https://prefix.dev/conda-forge/osx-64/readline-8.2-h7cca4af_2.conda - conda: https://prefix.dev/conda-forge/noarch/requests-2.32.4-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/osx-64/ruff-0.12.5-h6cc4cfe_0.conda + - conda: https://prefix.dev/conda-forge/osx-64/ruff-0.12.8-h6cc4cfe_0.conda - conda: https://prefix.dev/conda-forge/osx-64/scipy-1.15.2-py310hef62574_0.conda - conda: https://prefix.dev/conda-forge/noarch/setuptools-80.9.0-pyhff2d567_0.conda - conda: https://prefix.dev/conda-forge/osx-64/sleef-3.8-hfe0d17b_0.conda @@ -1278,7 +1278,7 @@ environments: - conda: https://prefix.dev/conda-forge/osx-arm64/re2-2025.06.26-h6589ca4_0.conda - conda: https://prefix.dev/conda-forge/osx-arm64/readline-8.2-h1d1bf99_2.conda - conda: https://prefix.dev/conda-forge/noarch/requests-2.32.4-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/osx-arm64/ruff-0.12.5-h575f11b_0.conda + - conda: https://prefix.dev/conda-forge/osx-arm64/ruff-0.12.8-h575f11b_0.conda - conda: https://prefix.dev/conda-forge/osx-arm64/scipy-1.15.2-py310h32ab4ed_0.conda - conda: https://prefix.dev/conda-forge/noarch/setuptools-80.9.0-pyhff2d567_0.conda - conda: https://prefix.dev/conda-forge/osx-arm64/sleef-3.8-h8391f65_0.conda @@ -1448,7 +1448,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/pytz-2025.2-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/win-64/pyyaml-6.0.2-py310h38315fa_2.conda - conda: https://prefix.dev/conda-forge/noarch/requests-2.32.4-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/win-64/ruff-0.12.5-hd40eec1_0.conda + - conda: https://prefix.dev/conda-forge/win-64/ruff-0.12.8-hd40eec1_0.conda - conda: https://prefix.dev/conda-forge/noarch/setuptools-80.9.0-pyhff2d567_0.conda - conda: https://prefix.dev/conda-forge/win-64/sleef-3.8-h7e360cc_0.conda - conda: https://prefix.dev/conda-forge/noarch/snowballstemmer-3.0.1-pyhd8ed1ab_0.conda @@ -1955,7 +1955,7 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/readline-8.2-h8c095d6_2.conda - conda: https://prefix.dev/conda-forge/noarch/requests-2.32.4-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/noarch/roman-numerals-py-3.1.0-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/ruff-0.12.5-hf9daec2_0.conda + - conda: https://prefix.dev/conda-forge/linux-64/ruff-0.12.8-hf9daec2_0.conda - conda: https://prefix.dev/conda-forge/noarch/setuptools-80.9.0-pyhff2d567_0.conda - conda: https://prefix.dev/conda-forge/noarch/snowballstemmer-3.0.1-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/noarch/sortedcontainers-2.4.0-pyhd8ed1ab_1.conda @@ -2063,7 +2063,7 @@ environments: - conda: https://prefix.dev/conda-forge/osx-64/readline-8.2-h7cca4af_2.conda - 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pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: f310d5b4b0c22e02452981a83b9bad9627ebcd5558e4258c8ea98cd06121d7cf + sha256: d2b15f9e0b18a4fa822220123a96a15c76fb97c72657252d30e1a763eba5d004 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' @@ -10607,63 +10607,67 @@ packages: - pkg:pypi/roman-numerals-py?source=hash-mapping size: 13348 timestamp: 1740240332327 -- conda: https://prefix.dev/conda-forge/linux-64/ruff-0.12.5-hf9daec2_0.conda +- conda: https://prefix.dev/conda-forge/linux-64/ruff-0.12.8-hf9daec2_0.conda noarch: python - sha256: e0383ea982545b0836771b58cd6d5e516f722d02b899f5bf325a54c8f6ef73b4 - md5: 37a142ca01da7f87652d55a1fb5043e8 + sha256: a1489605292241b0f1d52cca9eab762e92ac8d37ed26ee7472b6637cc591889d + md5: cdd4c26d70310431c77a530174e4fe8e depends: - python - - __glibc >=2.17,<3.0.a0 - libgcc >=14 + - __glibc >=2.17,<3.0.a0 constrains: - __glibc >=2.17 license: MIT + license_family: MIT purls: - - pkg:pypi/ruff?source=compressed-mapping - size: 10477480 - timestamp: 1753401049977 -- conda: https://prefix.dev/conda-forge/osx-64/ruff-0.12.5-h6cc4cfe_0.conda + - pkg:pypi/ruff?source=hash-mapping + size: 10492379 + timestamp: 1754600833195 +- conda: https://prefix.dev/conda-forge/osx-64/ruff-0.12.8-h6cc4cfe_0.conda noarch: python - sha256: 13bc134e829fb3bd716d3028c6aa7938b6fcdaae620000afea83a0e7a4e2e2fd - md5: 5f63b268b1ca853a3894f2f697b0f5ce + sha256: 220d7055c88eb31d39d18e7af58451229ec129707ef882a5413e2b8e798299d9 + md5: 3330f8fc08f9ea8357e02b3de6df5f42 depends: - python - __osx >=10.13 constrains: - __osx >=10.13 license: MIT + license_family: MIT purls: - pkg:pypi/ruff?source=hash-mapping - size: 10494874 - timestamp: 1753401117063 -- conda: https://prefix.dev/conda-forge/osx-arm64/ruff-0.12.5-h575f11b_0.conda + size: 10472014 + timestamp: 1754600887628 +- conda: https://prefix.dev/conda-forge/osx-arm64/ruff-0.12.8-h575f11b_0.conda noarch: python - sha256: 18eb56cfd7c3d5f07ea2459c9b94ac1cfc5ded2072385ec3b784eaf0d00baece - md5: 950f9ba560c91bb5785e5f388774799c + sha256: 02ca99095cc5b4dff0a7c7b980a18fcfa4f78d14764598dcebb5d6cf75ef6952 + md5: 7c0ecef473bba6d40f7f7c3635f24dfa depends: - python - __osx >=11.0 constrains: - __osx >=11.0 license: MIT + license_family: MIT purls: - pkg:pypi/ruff?source=hash-mapping - size: 9692798 - timestamp: 1753401120925 -- conda: https://prefix.dev/conda-forge/win-64/ruff-0.12.5-hd40eec1_0.conda + size: 9712438 + timestamp: 1754600916793 +- conda: https://prefix.dev/conda-forge/win-64/ruff-0.12.8-hd40eec1_0.conda noarch: python - sha256: 2971f92b4bbcb6cff9e70c1cd0f006cef4297731d11c922a65d11444ed15b44c - md5: 77b150d20b480e26a401a3bb752e36eb + sha256: eba7c047e23a7ba5410c8b9a36007f807bef1d99cd0ec304cfe350f840aba9d5 + md5: 4597f39a03982885c89c9ffa6394de1a depends: - python - vc >=14.3,<15 - vc14_runtime >=14.44.35208 - ucrt >=10.0.20348.0 license: MIT + license_family: MIT purls: - pkg:pypi/ruff?source=hash-mapping - size: 10837184 - timestamp: 1753401075216 + size: 10821904 + timestamp: 1754600827894 - conda: https://prefix.dev/conda-forge/linux-64/scipy-1.15.2-py310h1d65ade_0.conda sha256: 4cb98641f870666d365594013701d5691205a0fe81ac3ba7778a23b1cc2caa8e md5: 8c29cd33b64b2eb78597fa28b5595c8d diff --git a/pyproject.toml b/pyproject.toml index 69f1fca6..82f8a972 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,7 +67,7 @@ hypothesis = ">=6.136.4" dask-core = ">=2025.7.0" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.12.2,<2" -ruff = ">=0.12.5,<0.13" +ruff = ">=0.12.7,<0.13" typos = ">=1.34.0,<2" actionlint = ">=1.7.7,<2" blacken-docs = ">=1.19.1,<2" From 3155318db64716d41c0c39bd6a01fadc4c04670d Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 15 Aug 2025 04:21:07 +0000 Subject: [PATCH 082/104] deps: Update dependency mypy to >=1.17.1 (#389) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 106 ++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 54 insertions(+), 54 deletions(-) diff --git a/pixi.lock b/pixi.lock index 6db7a5a9..1c6f3eb6 100644 --- a/pixi.lock +++ b/pixi.lock @@ -193,7 +193,7 @@ environments: - 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- uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961 # v0.8.10 + - uses: prefix-dev/setup-pixi@8ca4608ef7f4daeb54f5205b20d0b7cb42f11143 # v0.8.14 with: pixi-version: v0.50.2 cache: true @@ -56,7 +56,7 @@ jobs: with: fetch-depth: 0 - - uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961 # v0.8.10 + - uses: prefix-dev/setup-pixi@8ca4608ef7f4daeb54f5205b20d0b7cb42f11143 # v0.8.14 with: pixi-version: v0.50.2 cache: true diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index 95340c82..df2c2f9b 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -11,7 +11,7 @@ jobs: steps: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 - - uses: prefix-dev/setup-pixi@14c8aabd75893f83f4ab30c03e7cf853c8208961 # v0.8.10 + - uses: prefix-dev/setup-pixi@8ca4608ef7f4daeb54f5205b20d0b7cb42f11143 # v0.8.14 with: pixi-version: v0.50.2 cache: true From d59cc8a2e21967d8d350dd67a4c3a280d52075ca Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sat, 16 Aug 2025 04:21:11 +0000 Subject: [PATCH 084/104] deps: Update dependency pytest-run-parallel to >=0.6.0 (#391) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 20 ++++++++++---------- pyproject.toml | 2 +- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/pixi.lock b/pixi.lock index 1c6f3eb6..ca33e0c0 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3362,7 +3362,7 @@ environments: - 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pkg:pypi/pytest-cov?source=hash-mapping size: 28216 timestamp: 1749778064293 -- conda: https://prefix.dev/conda-forge/noarch/pytest-run-parallel-0.5.0-pyhd8ed1ab_0.conda - sha256: b822dfd698ccfc33497cca1de5be75febd929e6d7b5703f498c3e5471eb3ec1a - md5: 42c3ecce76d724043ae0878bf5c5a3b7 +- conda: https://prefix.dev/conda-forge/noarch/pytest-run-parallel-0.6.1-pyhd8ed1ab_0.conda + sha256: ad3bcc53283512c34933012243756668b5631ef371468090121ec2fef8029261 + md5: 4bc53a42b6c9f9f9e89b478d05091743 depends: - pytest >=6.2.0 - python >=3.9 @@ -9735,8 +9735,8 @@ packages: license_family: MIT purls: - pkg:pypi/pytest-run-parallel?source=hash-mapping - size: 19108 - timestamp: 1753164017992 + size: 20705 + timestamp: 1755134346338 - conda: https://prefix.dev/conda-forge/linux-64/python-3.10.18-hd6af730_0_cpython.conda sha256: 4111e5504fa4f4fb431d3a73fa606daccaf23a5a1da0f17a30db70ffad9336a7 md5: 4ea0c77cdcb0b81813a0436b162d7316 diff --git a/pyproject.toml b/pyproject.toml index c1e88893..9e095398 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -197,7 +197,7 @@ pytorch = { version = ">=2.7.1", build = "cuda12*" } [tool.pixi.feature.nogil.dependencies] python-freethreading = "~=3.13.0" -pytest-run-parallel = ">=0.5.0" +pytest-run-parallel = ">=0.6.0" numpy = ">=2.3.2" # pytorch = "*" # Not available on Python 3.13t yet dask-core = ">=2025.7.0" # No distributed, tornado, etc. From a5deb100cca8ac4adbbc3ade914f4303dd619bd2 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sun, 17 Aug 2025 20:21:50 +0000 Subject: [PATCH 085/104] deps: Update dependency basedpyright to >=1.31.1 (#393) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 36 ++++++++++++++++++------------------ pyproject.toml | 2 +- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/pixi.lock b/pixi.lock index ca33e0c0..d619f5cd 100644 --- a/pixi.lock +++ b/pixi.lock @@ -108,7 +108,7 @@ environments: - 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pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: e24f608587961124bb17a27702c794b00ea89f0eb7300bf69ca168927dbd1e00 + sha256: 0aacf2aef668067243698baea22d07e68b355e1eb7ddbb1a42186f3282e98556 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' @@ -4444,9 +4444,9 @@ packages: - pkg:pypi/babel?source=hash-mapping size: 6938256 timestamp: 1738490268466 -- conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.31.0-pyhe01879c_0.conda - sha256: cac9f946958cfb1ac67bc5e4cf96ec2e212132763b256699b16f37eb004698ae - md5: 37b50852c793b39b2b3ec44229e019b7 +- conda: https://prefix.dev/conda-forge/noarch/basedpyright-1.31.2-pyhe01879c_0.conda + sha256: 44f543bedfb0be916a95bf6301fbd6d73a5a5c28a4f2072029c1fb5778880fa7 + md5: 34e0903b71e592c18dcb4c8567862f1d depends: - python >=3.9 - nodejs-wheel >=20.13.1 @@ -4454,8 +4454,8 @@ packages: license: MIT AND Apache-2.0 purls: - pkg:pypi/basedpyright?source=hash-mapping - size: 8255872 - timestamp: 1752676975836 + size: 8256728 + timestamp: 1755106603278 - conda: https://prefix.dev/conda-forge/noarch/beautifulsoup4-4.13.4-pyha770c72_0.conda sha256: ddb0df12fd30b2d36272f5daf6b6251c7625d6a99414d7ea930005bbaecad06d md5: 9f07c4fc992adb2d6c30da7fab3959a7 diff --git a/pyproject.toml b/pyproject.toml index 9e095398..3b2dd73c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ array-api-extra = { path = ".", editable = true } typing-extensions = ">=4.14.1" pylint = ">=3.3.7" mypy = ">=1.17.1" -basedpyright = ">=1.31.0" +basedpyright = ">=1.31.1" numpydoc = ">=1.9.0,<2" # import dependencies for mypy: array-api-strict = ">=2.4.1,<2.5" From cd3b49fb9f7bfe35c9fe749bc6ed40fc304a050e Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 19 Aug 2025 08:24:02 +0000 Subject: [PATCH 086/104] deps: Update dependency typos to >=1.35.1,<2 (#394) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 68 +++++++++++++++++++++++++------------------------- pyproject.toml | 2 +- 2 files changed, 35 insertions(+), 35 deletions(-) diff --git a/pixi.lock b/pixi.lock index d619f5cd..e09c6d95 100644 --- a/pixi.lock +++ b/pixi.lock @@ -264,7 +264,7 @@ environments: - 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sha256: 8e96013ebff778f2e5b017d83718ce860c1011c1631defb88e616e0b23d19a4f - md5: b5aa9a717a8da26210330b75ff31b716 + size: 3400833 + timestamp: 1755559185815 +- conda: https://prefix.dev/conda-forge/osx-64/typos-1.35.5-hb440939_0.conda + sha256: 6463aef1b401e05f38a17d8489975411ddb927d4142a02e07e5520ca6a925ee6 + md5: 6733052db82afe61b288dc56d3744386 depends: - __osx >=10.13 constrains: @@ -11263,11 +11263,11 @@ packages: license: MIT license_family: MIT purls: [] - size: 2774035 - timestamp: 1751305502248 -- conda: https://prefix.dev/conda-forge/osx-arm64/typos-1.34.0-h0716509_0.conda - sha256: 0309323403793e346c39e8680c40031ba8801422077459164b5285d9807149c0 - md5: 5ce04c5014a1ae8c97c8ebfaa2c252b6 + size: 2723507 + timestamp: 1755559451900 +- conda: https://prefix.dev/conda-forge/osx-arm64/typos-1.35.5-h0ca00b2_0.conda + sha256: 97d5a14c0ba602513af0cbca5b86c5d454909d78ec2ff7f46943e440dc5b10f8 + md5: f3c3ae98f6166a6eb6ad2a75218bd83a depends: - __osx >=11.0 constrains: @@ -11275,11 +11275,11 @@ packages: license: MIT license_family: MIT purls: [] - size: 2737457 - timestamp: 1751305859246 -- conda: https://prefix.dev/conda-forge/win-64/typos-1.34.0-h77a83cd_0.conda - sha256: b5eb9835ed565944db42b62aeec1098e80ec18b6108c07af0ee085b6abecfc21 - md5: c39c84a3eb9967bdbec425338997e5cd + size: 2682680 + timestamp: 1755559601530 +- conda: https://prefix.dev/conda-forge/win-64/typos-1.35.5-h77a83cd_0.conda + sha256: 8952109cb6e3e940f5629a7178990f40bcca60e6998ae51d430032b372b49a51 + md5: 1de577934b7084cd0a814060f0a0c9d7 depends: - ucrt >=10.0.20348.0 - vc >=14.3,<15 @@ -11287,8 +11287,8 @@ packages: license: MIT license_family: MIT purls: [] - size: 2586327 - timestamp: 1751305889847 + size: 2533104 + timestamp: 1755559549226 - conda: https://prefix.dev/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda sha256: 5aaa366385d716557e365f0a4e9c3fca43ba196872abbbe3d56bb610d131e192 md5: 4222072737ccff51314b5ece9c7d6f5a diff --git a/pyproject.toml b/pyproject.toml index 3b2dd73c..f98f19dc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -68,7 +68,7 @@ dask-core = ">=2025.7.0" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.12.2,<2" ruff = ">=0.12.7,<0.13" -typos = ">=1.34.0,<2" +typos = ">=1.35.1,<2" actionlint = ">=1.7.7,<2" blacken-docs = ">=1.19.1,<2" pytest = ">=8.4.1,<9" From 52270638812c471ca91a3d91e6958f5c0e998dd2 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 22 Aug 2025 00:29:56 +0000 Subject: [PATCH 087/104] deps: Update dependency ruff to >=0.12.8,<0.13 (#396) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index e09c6d95..44296a51 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4279,7 +4279,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 23718ce691255c0af22aaf4dafda7fa46e1bca23dc973cc954689e0914882cf4 + sha256: f662e636983b880bcac25f05207f2c2f63a8481aebf11cf3248539f43b24d6ba requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index f98f19dc..d23e0167 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,7 +67,7 @@ hypothesis = ">=6.136.4" dask-core = ">=2025.7.0" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.12.2,<2" -ruff = ">=0.12.7,<0.13" +ruff = ">=0.12.8,<0.13" typos = ">=1.35.1,<2" actionlint = ">=1.7.7,<2" blacken-docs = ">=1.19.1,<2" From 9adefe1bfeafdc962ddfad2f3f0440cd28edee77 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sun, 24 Aug 2025 08:23:09 +0000 Subject: [PATCH 088/104] deps: Update dependency pylint to >=3.3.8 (#399) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 36 ++++++++++++++++++------------------ pyproject.toml | 2 +- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/pixi.lock b/pixi.lock index 44296a51..44d7e2b8 100644 --- a/pixi.lock +++ b/pixi.lock @@ -222,7 +222,7 @@ environments: - 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pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: f662e636983b880bcac25f05207f2c2f63a8481aebf11cf3248539f43b24d6ba + sha256: 24a77cb224cff02d6246f517584afc13df07572fa384d7862a201edce5c567fe requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' @@ -9645,9 +9645,9 @@ packages: - pkg:pypi/pygments?source=hash-mapping size: 889287 timestamp: 1750615908735 -- conda: https://prefix.dev/conda-forge/noarch/pylint-3.3.7-pyhe01879c_0.conda - sha256: 6a1dc262763220c9dc046400d8655ebe58ad4d81e872be7264af5137f906e220 - md5: fad6b90165dcf39e3ac79de5dbc030a8 +- conda: https://prefix.dev/conda-forge/noarch/pylint-3.3.8-pyhe01879c_0.conda + sha256: 5b19f8113694ff4e4f0d0870cf38357d9e84330ff6c2516127a65764289b6743 + md5: f5ba3b2c52e855b67fc0abedcebc9675 depends: - astroid >=3.3.8,<3.4.0-dev0 - colorama >=0.4.5 @@ -9664,8 +9664,8 @@ packages: license_family: GPL purls: - pkg:pypi/pylint?source=hash-mapping - size: 380752 - timestamp: 1746387959153 + size: 381472 + timestamp: 1754751762506 - conda: https://prefix.dev/conda-forge/noarch/pysocks-1.7.1-pyh09c184e_7.conda sha256: d016e04b0e12063fbee4a2d5fbb9b39a8d191b5a0042f0b8459188aedeabb0ca md5: e2fd202833c4a981ce8a65974fe4abd1 diff --git a/pyproject.toml b/pyproject.toml index d23e0167..38a887f6 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -56,7 +56,7 @@ array-api-extra = { path = ".", editable = true } [tool.pixi.feature.lint.dependencies] typing-extensions = ">=4.14.1" -pylint = ">=3.3.7" +pylint = ">=3.3.8" mypy = ">=1.17.1" basedpyright = ">=1.31.1" numpydoc = ">=1.9.0,<2" From d3b779d75ffc8553fc32d20642dbb6d458e671fd Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sun, 24 Aug 2025 11:15:53 +0200 Subject: [PATCH 089/104] deps: Update dependency typos to >=1.35.3,<2 (#400) --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 44d7e2b8..36b19ca4 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4279,7 +4279,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.8.1.dev0 - sha256: 24a77cb224cff02d6246f517584afc13df07572fa384d7862a201edce5c567fe + sha256: b631ec9d573799efac8de0bc7a3ac6e7904368cc9b2c4dee83ddc4d2c4a21e71 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 38a887f6..24a6bb2c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -68,7 +68,7 @@ dask-core = ">=2025.7.0" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.12.2,<2" ruff = ">=0.12.8,<0.13" -typos = ">=1.35.1,<2" +typos = ">=1.35.3,<2" actionlint = ">=1.7.7,<2" blacken-docs = ">=1.19.1,<2" pytest = ">=8.4.1,<9" From aed27d99116cb6e4f9e3fe3f070621eac08da888 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 26 Aug 2025 16:15:10 +0100 Subject: [PATCH 090/104] REL: v0.8.1 (#401) --- pixi.lock | 3717 ++++++++++++++++--------------- src/array_api_extra/__init__.py | 2 +- 2 files changed, 1864 insertions(+), 1855 deletions(-) diff --git a/pixi.lock b/pixi.lock index 36b19ca4..8af1aee4 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,23 +11,20 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/_openmp_mutex-4.5-2_gnu.tar.bz2 - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.12.0-pyhe01879c_0.conda - conda: https://prefix.dev/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda - - conda: https://prefix.dev/conda-forge/noarch/ca-certificates-2025.7.14-hbd8a1cb_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/icu-75.1-he02047a_0.conda + - conda: https://prefix.dev/conda-forge/noarch/ca-certificates-2025.8.3-hbd8a1cb_0.conda - conda: https://prefix.dev/conda-forge/linux-64/ld_impl_linux-64-2.44-h1423503_1.conda - conda: https://prefix.dev/conda-forge/linux-64/libexpat-2.7.1-hecca717_0.conda - conda: https://prefix.dev/conda-forge/linux-64/libffi-3.4.6-h2dba641_1.conda - - conda: https://prefix.dev/conda-forge/linux-64/libgcc-15.1.0-h767d61c_3.conda - - conda: https://prefix.dev/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_3.conda - - conda: https://prefix.dev/conda-forge/linux-64/libgomp-15.1.0-h767d61c_3.conda + - conda: https://prefix.dev/conda-forge/linux-64/libgcc-15.1.0-h767d61c_4.conda + - conda: https://prefix.dev/conda-forge/linux-64/libgcc-ng-15.1.0-h69a702a_4.conda + - conda: https://prefix.dev/conda-forge/linux-64/libgomp-15.1.0-h767d61c_4.conda - conda: https://prefix.dev/conda-forge/linux-64/liblzma-5.8.1-hb9d3cd8_2.conda - conda: https://prefix.dev/conda-forge/linux-64/libmpdec-4.0.0-hb9d3cd8_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/libsqlite-3.50.3-hee844dc_1.conda - - conda: https://prefix.dev/conda-forge/linux-64/libstdcxx-15.1.0-h8f9b012_3.conda - - conda: https://prefix.dev/conda-forge/linux-64/libstdcxx-ng-15.1.0-h4852527_3.conda + - conda: https://prefix.dev/conda-forge/linux-64/libsqlite-3.50.4-h0c1763c_0.conda - conda: https://prefix.dev/conda-forge/linux-64/libuuid-2.38.1-h0b41bf4_0.conda - conda: https://prefix.dev/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda - conda: https://prefix.dev/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda - - conda: https://prefix.dev/conda-forge/linux-64/openssl-3.5.1-h7b32b05_0.conda + - 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pkg:pypi/zstandard?source=hash-mapping - size: 449871 - timestamp: 1745870298072 + size: 347160 + timestamp: 1756075776191 - conda: https://prefix.dev/conda-forge/linux-64/zstd-1.5.7-hb8e6e7a_2.conda sha256: a4166e3d8ff4e35932510aaff7aa90772f84b4d07e9f6f83c614cba7ceefe0eb md5: 6432cb5d4ac0046c3ac0a8a0f95842f9 diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index ddfc715e..0e63c849 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -17,7 +17,7 @@ ) from ._lib._lazy import lazy_apply -__version__ = "0.8.1.dev0" +__version__ = "0.8.1" # pylint: disable=duplicate-code __all__ = [ From b1fa4183901c6e4f8f73146f1a384659e2362635 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 26 Aug 2025 16:24:15 +0100 Subject: [PATCH 091/104] DEV: bump version to v0.9.0.dev0 (#402) --- RELEASING.md | 4 ++-- pixi.lock | 2 +- src/array_api_extra/__init__.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/RELEASING.md b/RELEASING.md index 564fc682..9b5d4ff5 100644 --- a/RELEASING.md +++ b/RELEASING.md @@ -1,8 +1,8 @@ 1. Update the version in `src/array_api_extra/__init__.py` -2. Update the lockfile with `pixi update && pixi install` +2. Update the lockfile with `pixi update; pixi install` 3. Push your changes 4. Cut a release via the GitHub GUI 5. Update the version to `{next micro version}.dev0` -6. `pixi clean cache --pypi && pixi update && pixi install` +6. `pixi clean cache --pypi; pixi update; pixi install` 7. Push your changes 8. Merge the automated PR to conda-forge/array-api-extra-feedstock diff --git a/pixi.lock b/pixi.lock index 8af1aee4..31b3e728 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4257,7 +4257,7 @@ packages: timestamp: 1747403732947 - pypi: ./ name: array-api-extra - version: 0.8.1 + version: 0.9.0.dev0 sha256: b631ec9d573799efac8de0bc7a3ac6e7904368cc9b2c4dee83ddc4d2c4a21e71 requires_dist: - array-api-compat>=1.12.0,<2 diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 0e63c849..caa0526f 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -17,7 +17,7 @@ ) from ._lib._lazy import lazy_apply -__version__ = "0.8.1" +__version__ = "0.9.0.dev0" # pylint: disable=duplicate-code __all__ = [ From 49f6ca8c07c0f75171a69932212fc9774c416962 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 26 Aug 2025 15:25:09 +0000 Subject: [PATCH 092/104] deps: Update dependency lefthook to >=1.12.3,<2 (#403) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 31b3e728..79223f1f 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4258,7 +4258,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.9.0.dev0 - sha256: b631ec9d573799efac8de0bc7a3ac6e7904368cc9b2c4dee83ddc4d2c4a21e71 + sha256: afe6a4ae3becab53d8442bc1fcc4690cce470380449c428b3debda66c23e4e37 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 24a6bb2c..d02cd4ed 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -66,7 +66,7 @@ numpy = ">=2.1.3" hypothesis = ">=6.136.4" dask-core = ">=2025.7.0" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" -lefthook = ">=1.12.2,<2" +lefthook = ">=1.12.3,<2" ruff = ">=0.12.8,<0.13" typos = ">=1.35.3,<2" actionlint = ">=1.7.7,<2" From 064f9a15f51bb1a2693f3269ec0c4607a0575074 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 27 Aug 2025 00:23:21 +0000 Subject: [PATCH 093/104] deps: Update dependency typos to >=1.35.4,<2 (#404) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 79223f1f..6ce2d713 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4258,7 +4258,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.9.0.dev0 - sha256: afe6a4ae3becab53d8442bc1fcc4690cce470380449c428b3debda66c23e4e37 + sha256: 49fd097c31b08695df2e5351330944ed9dc38ee00b082bf57750a09341b6a46d requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index d02cd4ed..027e47d2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -68,7 +68,7 @@ dask-core = ">=2025.7.0" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.12.3,<2" ruff = ">=0.12.8,<0.13" -typos = ">=1.35.3,<2" +typos = ">=1.35.4,<2" actionlint = ">=1.7.7,<2" blacken-docs = ">=1.19.1,<2" pytest = ">=8.4.1,<9" From b8426ef133fbcf7593ece4b94027a4f62bbeee3d Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 27 Aug 2025 04:21:15 +0000 Subject: [PATCH 094/104] deps: Update dependency typos to >=1.35.5,<2 (#405) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 6ce2d713..50269d6f 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4258,7 +4258,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.9.0.dev0 - sha256: 49fd097c31b08695df2e5351330944ed9dc38ee00b082bf57750a09341b6a46d + sha256: 57393d05751698a82239e9154e8f81e433651ef9d5878cae43294d628ccf4b71 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 027e47d2..19a60433 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -68,7 +68,7 @@ dask-core = ">=2025.7.0" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.12.3,<2" ruff = ">=0.12.8,<0.13" -typos = ">=1.35.4,<2" +typos = ">=1.35.5,<2" actionlint = ">=1.7.7,<2" blacken-docs = ">=1.19.1,<2" pytest = ">=8.4.1,<9" From a2891f78931322c42ad715798e9f7f0c66d5a1a9 Mon Sep 17 00:00:00 2001 From: "Patrick J. Roddy" Date: Wed, 27 Aug 2025 18:10:00 +0100 Subject: [PATCH 095/104] ENH: Implement `nan_to_num` function (#398) Co-authored-by: Lucas Colley --- docs/api-reference.md | 1 + src/array_api_extra/__init__.py | 3 +- src/array_api_extra/_delegation.py | 81 ++++++++++++++++- src/array_api_extra/_lib/_funcs.py | 41 +++++++++ tests/conftest.py | 8 ++ tests/test_funcs.py | 136 +++++++++++++++++++++++++++++ 6 files changed, 268 insertions(+), 2 deletions(-) diff --git a/docs/api-reference.md b/docs/api-reference.md index 38d0d26e..61e09e2d 100644 --- a/docs/api-reference.md +++ b/docs/api-reference.md @@ -16,6 +16,7 @@ expand_dims isclose kron + nan_to_num nunique one_hot pad diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index caa0526f..bcb0b3bd 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -1,6 +1,6 @@ """Extra array functions built on top of the array API standard.""" -from ._delegation import isclose, one_hot, pad +from ._delegation import isclose, nan_to_num, one_hot, pad from ._lib._at import at from ._lib._funcs import ( apply_where, @@ -33,6 +33,7 @@ "isclose", "kron", "lazy_apply", + "nan_to_num", "nunique", "one_hot", "pad", diff --git a/src/array_api_extra/_delegation.py b/src/array_api_extra/_delegation.py index 756841c8..2c061e36 100644 --- a/src/array_api_extra/_delegation.py +++ b/src/array_api_extra/_delegation.py @@ -18,7 +18,7 @@ from ._lib._utils._helpers import asarrays from ._lib._utils._typing import Array, DType -__all__ = ["isclose", "one_hot", "pad"] +__all__ = ["isclose", "nan_to_num", "one_hot", "pad"] def isclose( @@ -113,6 +113,85 @@ def isclose( return _funcs.isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan, xp=xp) +def nan_to_num( + x: Array | float | complex, + /, + *, + fill_value: int | float = 0.0, + xp: ModuleType | None = None, +) -> Array: + """ + Replace NaN with zero and infinity with large finite numbers (default behaviour). + + If `x` is inexact, NaN is replaced by zero or by the user defined value in the + `fill_value` keyword, infinity is replaced by the largest finite floating + point value representable by ``x.dtype``, and -infinity is replaced by the + most negative finite floating point value representable by ``x.dtype``. + + For complex dtypes, the above is applied to each of the real and + imaginary components of `x` separately. + + Parameters + ---------- + x : array | float | complex + Input data. + fill_value : int | float, optional + Value to be used to fill NaN values. If no value is passed + then NaN values will be replaced with 0.0. + xp : array_namespace, optional + The standard-compatible namespace for `x`. Default: infer. + + Returns + ------- + array + `x`, with the non-finite values replaced. + + See Also + -------- + array_api.isnan : Shows which elements are Not a Number (NaN). + + Examples + -------- + >>> import array_api_extra as xpx + >>> import array_api_strict as xp + >>> xpx.nan_to_num(xp.inf) + 1.7976931348623157e+308 + >>> xpx.nan_to_num(-xp.inf) + -1.7976931348623157e+308 + >>> xpx.nan_to_num(xp.nan) + 0.0 + >>> x = xp.asarray([xp.inf, -xp.inf, xp.nan, -128, 128]) + >>> xpx.nan_to_num(x) + array([ 1.79769313e+308, -1.79769313e+308, 0.00000000e+000, # may vary + -1.28000000e+002, 1.28000000e+002]) + >>> y = xp.asarray([complex(xp.inf, xp.nan), xp.nan, complex(xp.nan, xp.inf)]) + array([ 1.79769313e+308, -1.79769313e+308, 0.00000000e+000, # may vary + -1.28000000e+002, 1.28000000e+002]) + >>> xpx.nan_to_num(y) + array([ 1.79769313e+308 +0.00000000e+000j, # may vary + 0.00000000e+000 +0.00000000e+000j, + 0.00000000e+000 +1.79769313e+308j]) + """ + if isinstance(fill_value, complex): + msg = "Complex fill values are not supported." + raise TypeError(msg) + + xp = array_namespace(x) if xp is None else xp + + # for scalars we want to output an array + y = xp.asarray(x) + + if ( + is_cupy_namespace(xp) + or is_jax_namespace(xp) + or is_numpy_namespace(xp) + or is_torch_namespace(xp) + ): + return xp.nan_to_num(y, nan=fill_value) + + return _funcs.nan_to_num(y, fill_value=fill_value, xp=xp) + + def one_hot( x: Array, /, diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 05db6251..cbcbe0ff 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -738,6 +738,47 @@ def kron( return xp.reshape(result, res_shape) +def nan_to_num( # numpydoc ignore=PR01,RT01 + x: Array, + /, + fill_value: int | float = 0.0, + *, + xp: ModuleType, +) -> Array: + """See docstring in `array_api_extra._delegation.py`.""" + + def perform_replacements( # numpydoc ignore=PR01,RT01 + x: Array, + fill_value: int | float, + xp: ModuleType, + ) -> Array: + """Internal function to perform the replacements.""" + x = xp.where(xp.isnan(x), fill_value, x) + + # convert infinities to finite values + finfo = xp.finfo(x.dtype) + idx_posinf = xp.isinf(x) & ~xp.signbit(x) + idx_neginf = xp.isinf(x) & xp.signbit(x) + x = xp.where(idx_posinf, finfo.max, x) + return xp.where(idx_neginf, finfo.min, x) + + if xp.isdtype(x.dtype, "complex floating"): + return perform_replacements( + xp.real(x), + fill_value, + xp, + ) + 1j * perform_replacements( + xp.imag(x), + fill_value, + xp, + ) + + if xp.isdtype(x.dtype, "numeric"): + return perform_replacements(x, fill_value, xp) + + return x + + def nunique(x: Array, /, *, xp: ModuleType | None = None) -> Array: """ Count the number of unique elements in an array. diff --git a/tests/conftest.py b/tests/conftest.py index 76fb7650..df703b97 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -232,3 +232,11 @@ def device( if library == Backend.TORCH_GPU: return xp.device("cpu") return get_device(xp.empty(0)) + + +@pytest.fixture +def infinity(library: Backend) -> float: + """Retrieve the positive infinity value for the given backend.""" + if library in (Backend.TORCH, Backend.TORCH_GPU): + return 3.4028235e38 + return 1.7976931348623157e308 diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 769b4119..8304b848 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -21,6 +21,7 @@ expand_dims, isclose, kron, + nan_to_num, nunique, one_hot, pad, @@ -40,6 +41,7 @@ lazy_xp_function(create_diagonal) lazy_xp_function(expand_dims) lazy_xp_function(kron) +lazy_xp_function(nan_to_num) lazy_xp_function(nunique) lazy_xp_function(one_hot) lazy_xp_function(pad) @@ -941,6 +943,140 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(kron(a, b, xp=xp), k) +class TestNanToNum: + def test_bool(self, xp: ModuleType) -> None: + a = xp.asarray([True]) + xp_assert_equal(nan_to_num(a, xp=xp), a) + + def test_scalar_pos_inf(self, xp: ModuleType, infinity: float) -> None: + a = xp.inf + xp_assert_equal(nan_to_num(a, xp=xp), xp.asarray(infinity)) + + def test_scalar_neg_inf(self, xp: ModuleType, infinity: float) -> None: + a = -xp.inf + xp_assert_equal(nan_to_num(a, xp=xp), -xp.asarray(infinity)) + + def test_scalar_nan(self, xp: ModuleType) -> None: + a = xp.nan + xp_assert_equal(nan_to_num(a, xp=xp), xp.asarray(0.0)) + + def test_real(self, xp: ModuleType, infinity: float) -> None: + a = xp.asarray([xp.inf, -xp.inf, xp.nan, -128, 128]) + xp_assert_equal( + nan_to_num(a, xp=xp), + xp.asarray( + [ + infinity, + -infinity, + 0.0, + -128, + 128, + ] + ), + ) + + def test_complex(self, xp: ModuleType, infinity: float) -> None: + a = xp.asarray( + [ + complex(xp.inf, xp.nan), + xp.nan, + complex(xp.nan, xp.inf), + ] + ) + xp_assert_equal( + nan_to_num(a), + xp.asarray([complex(infinity, 0), complex(0, 0), complex(0, infinity)]), + ) + + def test_empty_array(self, xp: ModuleType) -> None: + a = xp.asarray([], dtype=xp.float32) # forced dtype due to torch + xp_assert_equal(nan_to_num(a, xp=xp), a) + assert xp.isdtype(nan_to_num(a, xp=xp).dtype, xp.float32) + + @pytest.mark.parametrize( + ("in_vals", "fill_value", "out_vals"), + [ + ([1, 2, np.nan, 4], 3, [1.0, 2.0, 3.0, 4.0]), + ([1, 2, np.nan, 4], 3.0, [1.0, 2.0, 3.0, 4.0]), + ( + [ + complex(1, 1), + complex(2, 2), + complex(np.nan, 0), + complex(4, 4), + ], + 3, + [ + complex(1.0, 1.0), + complex(2.0, 2.0), + complex(3.0, 0.0), + complex(4.0, 4.0), + ], + ), + ( + [ + complex(1, 1), + complex(2, 2), + complex(0, np.nan), + complex(4, 4), + ], + 3.0, + [ + complex(1.0, 1.0), + complex(2.0, 2.0), + complex(0.0, 3.0), + complex(4.0, 4.0), + ], + ), + ( + [ + complex(1, 1), + complex(2, 2), + complex(np.nan, np.nan), + complex(4, 4), + ], + 3.0, + [ + complex(1.0, 1.0), + complex(2.0, 2.0), + complex(3.0, 3.0), + complex(4.0, 4.0), + ], + ), + ], + ) + def test_fill_value_success( + self, + xp: ModuleType, + in_vals: Array, + fill_value: int | float, + out_vals: Array, + ) -> None: + a = xp.asarray(in_vals) + xp_assert_equal( + nan_to_num(a, fill_value=fill_value, xp=xp), + xp.asarray(out_vals), + ) + + def test_fill_value_failure(self, xp: ModuleType) -> None: + a = xp.asarray( + [ + complex(1, 1), + complex(xp.nan, xp.nan), + complex(3, 3), + ] + ) + with pytest.raises( + TypeError, + match="Complex fill values are not supported", + ): + _ = nan_to_num( + a, + fill_value=complex(2, 2), # type: ignore[arg-type] # pyright: ignore[reportArgumentType] + xp=xp, + ) + + class TestNUnique: def test_simple(self, xp: ModuleType): a = xp.asarray([[1, 1], [0, 2], [2, 2]]) From 2f778af196747f98bb2e4109728e6eabe5ac4183 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 27 Aug 2025 20:20:47 +0100 Subject: [PATCH 096/104] DOC: add paddy to all contributors (#406) --- .all-contributorsrc | 12 ++++++++++++ CONTRIBUTORS.md | 1 + README.md | 1 + 3 files changed, 14 insertions(+) diff --git a/.all-contributorsrc b/.all-contributorsrc index b33d332f..5585299e 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -249,6 +249,18 @@ "contributions": [ "review" ] + }, + { + "login": "paddyroddy", + "name": "Patrick J. Roddy", + "avatar_url": "https://avatars.githubusercontent.com/u/15052188?v=4", + "profile": "https://paddyroddy.github.io/", + "contributions": [ + "code", + "doc", + "example", + "test" + ] } ] } diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index cc93de44..900b1819 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -38,6 +38,7 @@ This project exists thanks to the following contributors Thomas Li
Thomas Li
🐛 🔧 Pearu Peterson
Pearu Peterson
👀 + Patrick J. Roddy
Patrick J. Roddy
💻 📖 💡 ⚠️ diff --git a/README.md b/README.md index 1b33322a..3ed766eb 100644 --- a/README.md +++ b/README.md @@ -93,6 +93,7 @@ This project exists thanks to the following contributors Thomas Li
Thomas Li
🐛 🔧 Pearu Peterson
Pearu Peterson
👀 + Patrick J. Roddy
Patrick J. Roddy
💻 📖 💡 ⚠️ From e859d775524897759d4ac44d0529f0651cdc0c1d Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 27 Aug 2025 19:21:40 +0000 Subject: [PATCH 097/104] deps: Update dependency basedpyright to >=1.31.2 (#407) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 50269d6f..1d957144 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4258,7 +4258,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.9.0.dev0 - sha256: 57393d05751698a82239e9154e8f81e433651ef9d5878cae43294d628ccf4b71 + sha256: c8906ad8a53818a8e2ac02e860eb8ce2d34eed356ab4e541c031120d107ceb7e requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 19a60433..ac4cb084 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ array-api-extra = { path = ".", editable = true } typing-extensions = ">=4.14.1" pylint = ">=3.3.8" mypy = ">=1.17.1" -basedpyright = ">=1.31.1" +basedpyright = ">=1.31.2" numpydoc = ">=1.9.0,<2" # import dependencies for mypy: array-api-strict = ">=2.4.1,<2.5" From b91a4a6d7e95f41c8fcc960b429e983ec21bd376 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 27 Aug 2025 19:23:47 +0000 Subject: [PATCH 098/104] deps: Update dependency basedpyright to >=1.31.3 (#408) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 1d957144..6118adfb 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4258,7 +4258,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.9.0.dev0 - sha256: c8906ad8a53818a8e2ac02e860eb8ce2d34eed356ab4e541c031120d107ceb7e + sha256: c0997beab6e59ec06538ca122d77aaad514e84a530ca54cfe1653934d8e012ab requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index ac4cb084..5d4b505a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ array-api-extra = { path = ".", editable = true } typing-extensions = ">=4.14.1" pylint = ">=3.3.8" mypy = ">=1.17.1" -basedpyright = ">=1.31.2" +basedpyright = ">=1.31.3" numpydoc = ">=1.9.0,<2" # import dependencies for mypy: array-api-strict = ">=2.4.1,<2.5" From 1194565830146c59d0f3ba8f4dcb3034273106c5 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 27 Aug 2025 21:56:02 +0100 Subject: [PATCH 099/104] REL: v0.8.2 (#409) --- pixi.lock | 596 ++++++++++++++++---------------- src/array_api_extra/__init__.py | 2 +- 2 files changed, 296 insertions(+), 302 deletions(-) diff --git a/pixi.lock b/pixi.lock index 6118adfb..ead68cad 100644 --- a/pixi.lock +++ b/pixi.lock @@ -176,7 +176,7 @@ environments: - 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pypi: ./ name: array-api-extra - version: 0.8.2 + version: 0.9.0.dev0 sha256: c0997beab6e59ec06538ca122d77aaad514e84a530ca54cfe1653934d8e012ab requires_dist: - array-api-compat>=1.12.0,<2 diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 3dcacaae..bcb0b3bd 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -17,7 +17,7 @@ ) from ._lib._lazy import lazy_apply -__version__ = "0.8.2" +__version__ = "0.9.0.dev0" # pylint: disable=duplicate-code __all__ = [ From 0b7aa9e7a7df72c262d9598e2bdf9bdf8f5285d3 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 28 Aug 2025 04:33:14 +0000 Subject: [PATCH 101/104] deps: Update dependency pytest-run-parallel to >=0.6.1 (#411) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index c2b4ac65..59ff2716 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4258,7 +4258,7 @@ packages: - 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pypi: ./ name: array-api-extra version: 0.9.0.dev0 - sha256: e917c80e998aa7d10c639c3d4ae5f9939950e24e438149d3ce734115e4859240 + sha256: 8a7fc03bff6f259deb690be98e654e3463db97a42a4ba31625fbf8b1080a9f87 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' @@ -10605,26 +10605,26 @@ packages: - pkg:pypi/roman-numerals-py?source=hash-mapping size: 13348 timestamp: 1740240332327 -- conda: https://prefix.dev/conda-forge/linux-64/ruff-0.12.10-h718f522_0.conda +- conda: https://prefix.dev/conda-forge/linux-64/ruff-0.12.11-h718f522_0.conda noarch: python - sha256: f7cdb61d8e758d47500b6f45e6c2685a275ca65d1cb9c8bd094fcea227e8b318 - md5: 356a5e0f6531b190b002f7257675074d + sha256: a58f23fa525db63aec3681c4408826563bfc32278010d083e4e0bdc1605577ae + md5: e67207c97cf1abc164eaeba433ad758e depends: - python - - libgcc >=14 - __glibc >=2.17,<3.0.a0 + - libgcc >=14 constrains: - __glibc >=2.17 license: MIT license_family: MIT purls: - - pkg:pypi/ruff?source=compressed-mapping - size: 10661766 - timestamp: 1755823612718 -- conda: https://prefix.dev/conda-forge/osx-64/ruff-0.12.10-hab3cb23_0.conda + - pkg:pypi/ruff?source=hash-mapping + size: 10720449 + timestamp: 1756401197056 +- conda: https://prefix.dev/conda-forge/osx-64/ruff-0.12.11-hab3cb23_0.conda noarch: python - sha256: a5dd1d849b51c32f32c05d0a0ed36631c9047c387cc6759728072438e7e4e3ca - md5: 42bacf6b1ba6d0aa0501f08cfe5161ed + sha256: 3e8ac878c4c95dcbcf022c30d0f8402478fe3639596e7531876921de1372da45 + md5: 9f3382e12db2ae55d55e6aac3fe7ee7e depends: - python - __osx >=10.13 @@ -10634,12 +10634,12 @@ packages: license_family: MIT purls: - pkg:pypi/ruff?source=hash-mapping - size: 10670425 - timestamp: 1755823705979 -- conda: https://prefix.dev/conda-forge/osx-arm64/ruff-0.12.10-h23cf233_0.conda + size: 10719173 + timestamp: 1756401244780 +- conda: https://prefix.dev/conda-forge/osx-arm64/ruff-0.12.11-h23cf233_0.conda noarch: python - sha256: e0142dda1cd36ec73741a1267b61b627ee6549dd6345ced9d707ebd2468e064d - md5: 779b2cda23580d1fc93a0534ec4c60d9 + sha256: e4ce9663231c73a41434b5a51d16a00be054805f618bd0abb6c6d8d80b8410fc + md5: 9b8428d5c969b1cbdba77f9fdd20f909 depends: - python - __osx >=11.0 @@ -10648,13 +10648,13 @@ packages: license: MIT license_family: MIT purls: - - pkg:pypi/ruff?source=compressed-mapping - size: 9876853 - timestamp: 1755823708465 -- conda: https://prefix.dev/conda-forge/win-64/ruff-0.12.10-h429b229_0.conda + - pkg:pypi/ruff?source=hash-mapping + size: 9939501 + timestamp: 1756401265661 +- conda: https://prefix.dev/conda-forge/win-64/ruff-0.12.11-h429b229_0.conda noarch: python - sha256: fabd95186f2e4c3239ff3ad139ff62f1c3523189f3187397d94734f8acfc281a - md5: aeac13adbe43735128768c89574c1e11 + sha256: dae4bc01c5eb4f0b56f3c4482df551ed897d0f048586e9f38ddef7feb42cd790 + md5: 990b0da068b053390c935491da9cddcf depends: - python - vc >=14.3,<15 @@ -10664,8 +10664,8 @@ packages: license_family: MIT purls: - pkg:pypi/ruff?source=hash-mapping - size: 10954968 - timestamp: 1755823643535 + size: 10999317 + timestamp: 1756401205961 - conda: https://prefix.dev/conda-forge/linux-64/scipy-1.15.2-py310h1d65ade_0.conda sha256: 4cb98641f870666d365594013701d5691205a0fe81ac3ba7778a23b1cc2caa8e md5: 8c29cd33b64b2eb78597fa28b5595c8d diff --git a/pyproject.toml b/pyproject.toml index 912d3db8..d662f126 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,7 +67,7 @@ hypothesis = ">=6.136.4" dask-core = ">=2025.7.0" # No distributed, tornado, etc. dprint = ">=0.50.0,<0.51" lefthook = ">=1.12.3,<2" -ruff = ">=0.12.9,<0.13" +ruff = ">=0.12.11,<0.13" typos = ">=1.35.5,<2" actionlint = ">=1.7.7,<2" blacken-docs = ">=1.19.1,<2" From 03e9fd5898a1d9dce0c80d9959ac871687e4650f Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 2 Sep 2025 19:14:02 +0100 Subject: [PATCH 104/104] deps: Update dependency cupy to >=13.6.0 (#414) --- pixi.lock | 2 +- pyproject.toml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/pixi.lock b/pixi.lock index d6f93c28..e11e3e4d 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4258,7 +4258,7 @@ packages: - pypi: ./ name: array-api-extra version: 0.9.0.dev0 - sha256: 8a7fc03bff6f259deb690be98e654e3463db97a42a4ba31625fbf8b1080a9f87 + sha256: f8fc778f97b74d7f786917903904fc73f65f6a58b403c7f6817d9668c0bc57a6 requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index d662f126..0d58cc5f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -176,7 +176,7 @@ jax = ">=0.6.0,!=0.6.2" system-requirements = { cuda = "12" } [tool.pixi.feature.cuda-backends.target.linux-64.dependencies] -cupy = ">=13.5.1" +cupy = ">=13.6.0" jaxlib = { version = ">=0.6.0", build = "cuda12*" } pytorch = { version = ">=2.7.1", build = "cuda12*" } @@ -191,7 +191,7 @@ pytorch = { version = ">=2.7.1", build = "cuda12*" } # pytorch = { version = "*", build = "cuda12*" } # unavailable [tool.pixi.feature.cuda-backends.target.win-64.dependencies] -cupy = ">=13.5.1" +cupy = ">=13.6.0" # jaxlib = { version = "*", build = "cuda12*" } # unavailable pytorch = { version = ">=2.7.1", build = "cuda12*" }