From 70c7c8092d665c1556f6cd9ab819e266c5d88674 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 18 Mar 2025 23:09:04 +0000 Subject: [PATCH 001/131] DEV: bump version to 0.7.1.dev0 --- pixi.lock | 2 +- src/array_api_extra/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index ee40d532..54635581 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3884,7 +3884,7 @@ packages: timestamp: 1742159192304 - pypi: . name: array-api-extra - version: 0.7.0 + version: 0.7.1.dev0 sha256: 03300616865414593ebd17cd40b2c63d372e276398f319c1dbe8f7ae2ad11bed requires_dist: - array-api-compat>=1.11,<2 diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 21e7620e..879d49b5 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__ = "0.7.0" +__version__ = "0.7.1.dev0" # pylint: disable=duplicate-code __all__ = [ From 438310cef14741294ad1f1b61edceedc8361b225 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Wed, 19 Mar 2025 15:32:18 +0000 Subject: [PATCH 002/131] BUG: `isclose` PyTorch Array API 2024.12 compliance --- src/array_api_extra/_delegation.py | 14 ++++++-------- tests/test_funcs.py | 1 - 2 files changed, 6 insertions(+), 9 deletions(-) diff --git a/src/array_api_extra/_delegation.py b/src/array_api_extra/_delegation.py index b6e58688..bb11b7ee 100644 --- a/src/array_api_extra/_delegation.py +++ b/src/array_api_extra/_delegation.py @@ -6,6 +6,7 @@ from ._lib import Backend, _funcs from ._lib._utils._compat import array_namespace +from ._lib._utils._helpers import asarrays from ._lib._utils._typing import Array __all__ = ["isclose", "pad"] @@ -107,14 +108,11 @@ def isclose( """ xp = array_namespace(a, b) if xp is None else xp - if _delegate( - xp, - Backend.NUMPY, - Backend.CUPY, - Backend.DASK, - Backend.JAX, - Backend.TORCH, - ): + if _delegate(xp, Backend.NUMPY, Backend.CUPY, Backend.DASK, Backend.JAX): + return xp.isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan) + + if _delegate(xp, Backend.TORCH): + a, b = asarrays(a, b, xp=xp) # Array API 2024.12 support return xp.isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan) return _funcs.isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan, xp=xp) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 23344f62..a6b3711b 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -689,7 +689,6 @@ def test_none_shape_bool(self, xp: ModuleType): xp_assert_equal(isclose(a, b), xp.asarray([True, False])) @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="xp=xp") - @pytest.mark.xfail_xp_backend(Backend.TORCH, reason="Array API 2024.12 support") def test_python_scalar(self, xp: ModuleType): a = xp.asarray([0.0, 0.1], dtype=xp.float32) xp_assert_equal(isclose(a, 0.0), xp.asarray([True, False])) From 212809dcf22bd1523e8a1fe72889f0e6b62fd7cd Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 19 Mar 2025 16:27:28 +0000 Subject: [PATCH 003/131] DOC: fix copyright (#168) --- docs/conf.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/conf.py b/docs/conf.py index 64389f80..e2cab35b 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -4,6 +4,8 @@ from typing import Any project = "array-api-extra" +copyright = "Consortium for Python Data API Standards" +author = "Consortium for Python Data API Standards" version = release = importlib.metadata.version("array_api_extra") extensions = [ From 3db7f7502ce158392e8d369b4906d473ec85faeb Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Wed, 19 Mar 2025 16:44:33 +0000 Subject: [PATCH 004/131] TST: NumPy 1.x support (#169) * TST: NumPy 1.x support * Downgrade to oldest SPEC0 --- .github/workflows/ci.yml | 2 +- pixi.lock | 1141 ++++++++++++++++++- pyproject.toml | 6 + src/array_api_extra/_lib/_funcs.py | 9 +- src/array_api_extra/_lib/_utils/_helpers.py | 3 +- tests/test_funcs.py | 10 + tests/test_helpers.py | 6 +- tests/test_lazy.py | 9 +- 8 files changed, 1167 insertions(+), 19 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a3ce6620..de8250cd 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -48,7 +48,7 @@ jobs: strategy: fail-fast: false matrix: - environment: [tests-py310, tests-py313, tests-backends] + environment: [tests-py310, tests-py313, tests-numpy1, tests-backends] runs-on: [ubuntu-latest] steps: diff --git a/pixi.lock b/pixi.lock index 54635581..6d5ba70d 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1614,6 +1614,399 @@ environments: - conda: https://prefix.dev/conda-forge/win-64/zstd-1.5.7-hbeecb71_1.conda - pypi: https://files.pythonhosted.org/packages/82/84/de41ad6793c584a9b92935c4541744c169f7b6ce9ca69e98a147c412ed4a/sparse-0.16.0b3-py2.py3-none-any.whl - pypi: . + dev-numpy1: + channels: + - url: https://prefix.dev/conda-forge/ + indexes: + - https://pypi.org/simple + packages: + 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/alabaster-1.0.0-pyhd8ed1ab_1.conda + - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.11.1-pyh29332c3_1.conda + - 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b) <= atol - try: - nrtol = xp.asarray(int(1.0 / rtol), dtype=b.dtype) - except OverflowError: - # rtol * max_int(dtype) < 1, so it's inconsequential + # Don't rely on OverflowError, as it is not guaranteed by the Array API. + nrtol = int(1.0 / rtol) + if nrtol > xp.iinfo(b.dtype).max: + # rtol * max_int < 1, so it's inconsequential return xp.abs(a - b) <= atol - return xp.abs(a - b) <= (atol + xp.abs(b) // nrtol) diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 7ac97033..3734130b 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -245,8 +245,7 @@ def eager_shape(x: Array, /) -> tuple[int, ...]: def meta_namespace( - *arrays: Array | int | float | complex | bool | None, - xp: ModuleType | None = None, + *arrays: Array | complex | None, xp: ModuleType | None = None ) -> ModuleType: """ Get the namespace of Dask chunks. diff --git a/tests/test_funcs.py b/tests/test_funcs.py index a6b3711b..997411cc 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -48,6 +48,9 @@ lazy_xp_function(sinc, static_argnames="xp") +NUMPY_GE2 = int(np.__version__.split(".")[0]) >= 2 + + @pytest.mark.skip_xp_backend( Backend.SPARSE, reason="read-only backend without .at support" ) @@ -213,6 +216,13 @@ def test_hypothesis( # type: ignore[explicit-any,decorated-any] xp: ModuleType, library: Backend, ): + if ( + library in (Backend.NUMPY, Backend.NUMPY_READONLY) + and not NUMPY_GE2 + and dtype is np.float32 + ): + pytest.xfail(reason="NumPy 1.x dtype promotion for scalars") + mbs = npst.mutually_broadcastable_shapes(num_shapes=n_arrays + 1, min_side=0) input_shapes, _ = data.draw(mbs) cond_shape, *shapes = input_shapes diff --git a/tests/test_helpers.py b/tests/test_helpers.py index 2fc21735..81b11d1f 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -18,9 +18,9 @@ from array_api_extra._lib._utils._typing import Array, Device, DType from array_api_extra.testing import lazy_xp_function -# mypy: disable-error-code=no-untyped-usage +from .conftest import np_compat -np_compat = array_namespace(np.empty(0)) # type: ignore[arg-type] # pyright: ignore[reportArgumentType] +# mypy: disable-error-code=no-untyped-usage # FIXME calls xp.unique_values without size lazy_xp_function(in1d, jax_jit=False, static_argnames=("assume_unique", "invert", "xp")) @@ -149,7 +149,7 @@ def test_numpy_generics(self, dtype: DType): which are subclasses of float and complex. """ a = cast(Array, dtype(0)) # type: ignore[operator] # pyright: ignore[reportCallIssue] - xa, xb = asarrays(a, 0, xp=np) + xa, xb = asarrays(a, 0, xp=np_compat) assert xa.dtype == dtype assert xb.dtype == dtype diff --git a/tests/test_lazy.py b/tests/test_lazy.py index fcee38b0..647132e9 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -94,12 +94,7 @@ def f(x: Array) -> tuple[Array, Array]: @pytest.mark.parametrize( "as_numpy", [ - pytest.param( - False, - marks=pytest.mark.xfail_xp_backend( - Backend.TORCH, reason="illegal dtype promotion" - ), - ), + False, pytest.param( True, marks=[ @@ -119,7 +114,7 @@ def f(x: Array, y: Array) -> tuple[Array, Array]: return x + y, x - y x = xp.asarray([1, 2], dtype=xp.float32) - y = xp.asarray(3, dtype=xp.float64) + y = xp.asarray([3], dtype=xp.float64) expect = ( xp.asarray([4, 5], dtype=xp.float64), xp.asarray([-2, -1], dtype=xp.float64), From ca0c1d2746c19dd7daa43d7ec68ea0e58d1bbcf5 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Thu, 20 Mar 2025 13:02:44 +0000 Subject: [PATCH 005/131] MAINT: drop Python 3.9 informal support --- pixi.lock | 2 +- pyproject.toml | 2 +- src/array_api_extra/_lib/_at.py | 11 +++++++---- src/array_api_extra/_lib/_funcs.py | 3 --- src/array_api_extra/_lib/_lazy.py | 15 +++------------ src/array_api_extra/_lib/_utils/_helpers.py | 1 - src/array_api_extra/testing.py | 19 +++++-------------- 7 files changed, 17 insertions(+), 36 deletions(-) diff --git a/pixi.lock b/pixi.lock index 6d5ba70d..c111514b 100644 --- a/pixi.lock +++ b/pixi.lock @@ -4419,7 +4419,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.1.dev0 - sha256: f78ab5cbb082bc05c77354eea2778c551b79283b5c89c3ec12a31c149f83f9bc + sha256: 33748bc31a54e83a22964d3d80a9894b64868c3f040a285e5e66af27f744b230 requires_dist: - array-api-compat>=1.11,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 25905209..2bd16b53 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -111,7 +111,7 @@ typing-extensions = "*" numpy = "*" [tool.pixi.feature.docs.tasks] -docs = { cmd = "sphinx-build . build/", cwd = "docs" } +docs = { cmd = "sphinx-build -E -W . build/", cwd = "docs" } open-docs = { cmd = "open build/index.html", cwd = "docs", depends-on = ["docs"] } [tool.pixi.feature.dev.dependencies] diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py index 25d764e3..aa323d78 100644 --- a/src/array_api_extra/_lib/_at.py +++ b/src/array_api_extra/_lib/_at.py @@ -1,13 +1,12 @@ """Update operations for read-only arrays.""" -# https://github.com/scikit-learn/scikit-learn/pull/27910#issuecomment-2568023972 from __future__ import annotations import operator from collections.abc import Callable from enum import Enum from types import ModuleType -from typing import ClassVar, cast +from typing import TYPE_CHECKING, ClassVar, cast from ._utils._compat import ( array_namespace, @@ -18,6 +17,10 @@ from ._utils._helpers import meta_namespace from ._utils._typing import Array, SetIndex +if TYPE_CHECKING: # pragma: no cover + # TODO import from typing (requires Python >=3.11) + from typing_extensions import Self + class _AtOp(Enum): """Operations for use in `xpx.at`.""" @@ -204,7 +207,7 @@ def __init__( self._x = x self._idx = idx - def __getitem__(self, idx: SetIndex, /) -> at: # numpydoc ignore=PR01,RT01 + def __getitem__(self, idx: SetIndex, /) -> Self: # numpydoc ignore=PR01,RT01 """ Allow for the alternate syntax ``at(x)[start:stop:step]``. @@ -214,7 +217,7 @@ def __getitem__(self, idx: SetIndex, /) -> at: # numpydoc ignore=PR01,RT01 if self._idx is not _undef: msg = "Index has already been set" raise ValueError(msg) - return at(self._x, idx) + return type(self)(self._x, idx) def _op( self, diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 1ccfbceb..f1ea6543 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -1,8 +1,5 @@ """Array-agnostic implementations for the public API.""" -# https://github.com/scikit-learn/scikit-learn/pull/27910#issuecomment-2568023972 -from __future__ import annotations - import math import warnings from collections.abc import Callable, Sequence diff --git a/src/array_api_extra/_lib/_lazy.py b/src/array_api_extra/_lib/_lazy.py index 14117634..767bb6de 100644 --- a/src/array_api_extra/_lib/_lazy.py +++ b/src/array_api_extra/_lib/_lazy.py @@ -1,13 +1,12 @@ """Public API Functions.""" -# https://github.com/scikit-learn/scikit-learn/pull/27910#issuecomment-2568023972 from __future__ import annotations import math from collections.abc import Callable, Sequence from functools import partial, wraps from types import ModuleType -from typing import TYPE_CHECKING, Any, cast, overload +from typing import TYPE_CHECKING, Any, ParamSpec, TypeAlias, cast, overload from ._funcs import broadcast_shapes from ._utils import _compat @@ -20,23 +19,15 @@ from ._utils._typing import Array, DType if TYPE_CHECKING: # pragma: no cover - # TODO move outside TYPE_CHECKING - # depends on scikit-learn abandoning Python 3.9 - # https://github.com/scikit-learn/scikit-learn/pull/27910#issuecomment-2568023972 - from typing import ParamSpec, TypeAlias - import numpy as np from numpy.typing import ArrayLike NumPyObject: TypeAlias = np.ndarray[Any, Any] | np.generic # type: ignore[explicit-any] - P = ParamSpec("P") else: - # Sphinx hacks + # Sphinx hack NumPyObject = Any - class P: # pylint: disable=missing-class-docstring - args: tuple - kwargs: dict +P = ParamSpec("P") @overload diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 3734130b..9882d72e 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -1,6 +1,5 @@ """Helper functions used by `array_api_extra/_funcs.py`.""" -# https://github.com/scikit-learn/scikit-learn/pull/27910#issuecomment-2568023972 from __future__ import annotations import math diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index 4417b648..867f0226 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -4,42 +4,33 @@ See also _lib._testing for additional private testing utilities. """ -# https://github.com/scikit-learn/scikit-learn/pull/27910#issuecomment-2568023972 from __future__ import annotations import contextlib from collections.abc import Callable, Iterable, Iterator, Sequence from functools import wraps from types import ModuleType -from typing import TYPE_CHECKING, Any, TypeVar, cast +from typing import TYPE_CHECKING, Any, ParamSpec, TypeVar, cast from ._lib._utils._compat import is_dask_namespace, is_jax_namespace __all__ = ["lazy_xp_function", "patch_lazy_xp_functions"] if TYPE_CHECKING: # pragma: no cover - # TODO move ParamSpec outside TYPE_CHECKING - # depends on scikit-learn abandoning Python 3.9 - # https://github.com/scikit-learn/scikit-learn/pull/27910#issuecomment-2568023972 - from typing import ParamSpec - + # TODO import override from typing (requires Python >=3.12) import pytest from dask.typing import Graph, Key, SchedulerGetCallable from typing_extensions import override - P = ParamSpec("P") else: - SchedulerGetCallable = object - # Sphinx hacks - class P: # pylint: disable=missing-class-docstring - args: tuple - kwargs: dict + SchedulerGetCallable = object - def override(func: Callable[P, T]) -> Callable[P, T]: + def override(func: object) -> object: return func +P = ParamSpec("P") T = TypeVar("T") _ufuncs_tags: dict[object, dict[str, Any]] = {} # type: ignore[explicit-any] From 23edd303b00a1fcbe2cee7d4e866c2e5d9a218a2 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Thu, 20 Mar 2025 18:27:32 +0000 Subject: [PATCH 006/131] MAINT: capitalization nits --- src/array_api_extra/_lib/_at.py | 4 ++-- src/array_api_extra/_lib/_funcs.py | 4 ++-- src/array_api_extra/_lib/_lazy.py | 8 ++++---- src/array_api_extra/testing.py | 4 ++-- tests/conftest.py | 2 +- tests/test_at.py | 2 +- tests/test_lazy.py | 8 ++++---- tests/test_testing.py | 18 +++++++++--------- 8 files changed, 25 insertions(+), 25 deletions(-) diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py index aa323d78..22e18d2c 100644 --- a/src/array_api_extra/_lib/_at.py +++ b/src/array_api_extra/_lib/_at.py @@ -187,7 +187,7 @@ class at: # pylint: disable=invalid-name # numpydoc ignore=PR02 >>> x = x.at[1].add(2) - If x is a read-only numpy array, they are the same as:: + If x is a read-only NumPy array, they are the same as:: >>> x = x.copy() >>> x[1] += 2 @@ -430,7 +430,7 @@ def min( """Apply ``x[idx] = minimum(x[idx], y)`` and return the updated array.""" # On Dask, this function runs on the chunks, so we need to determine the # namespace that Dask is wrapping. - # Note that da.minimum _incidentally_ works on numpy, cupy, and sparse + # Note that da.minimum _incidentally_ works on NumPy, CuPy, and sparse # thanks to all these meta-namespaces implementing the __array_ufunc__ # interface, but there's no guarantee that it will work for other # wrapped libraries in the future. diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index f1ea6543..d0b67388 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -260,7 +260,7 @@ def broadcast_shapes(*shapes: tuple[float | None, ...]) -> tuple[int | None, ... (4, 2, 3) """ if not shapes: - return () # Match numpy output + return () # Match NumPy output ndim = max(len(shape) for shape in shapes) out: list[int | None] = [] @@ -538,7 +538,7 @@ def isclose( a_inexact = xp.isdtype(a.dtype, ("real floating", "complex floating")) b_inexact = xp.isdtype(b.dtype, ("real floating", "complex floating")) if a_inexact or b_inexact: - # prevent warnings on numpy and dask on inf - inf + # prevent warnings on NumPy and Dask on inf - inf mxp = meta_namespace(a, b, xp=xp) out = apply_where( xp.isinf(a) | xp.isinf(b), diff --git a/src/array_api_extra/_lib/_lazy.py b/src/array_api_extra/_lib/_lazy.py index 767bb6de..f7cc2a58 100644 --- a/src/array_api_extra/_lib/_lazy.py +++ b/src/array_api_extra/_lib/_lazy.py @@ -86,7 +86,7 @@ def lazy_apply( # type: ignore[valid-type] # numpydoc ignore=GL07,SA04 One or more Array API compliant arrays, Python scalars, or None's. If `as_numpy=True`, you need to be able to apply :func:`numpy.asarray` to - non-None args to convert them to numpy; read notes below about specific + non-None args to convert them to NumPy; read notes below about specific backends. shape : tuple[int | None, ...] | Sequence[tuple[int | None, ...]], optional Output shape or sequence of output shapes, one for each output of `func`. @@ -97,7 +97,7 @@ def lazy_apply( # type: ignore[valid-type] # numpydoc ignore=GL07,SA04 Default: infer the result type(s) from the input arrays. as_numpy : bool, optional If True, convert the input arrays to NumPy before passing them to `func`. - This is particularly useful to make numpy-only functions, e.g. written in Cython + This is particularly useful to make NumPy-only functions, e.g. written in Cython or Numba, work transparently with array API-compliant arrays. Default: False. xp : array_namespace, optional @@ -143,8 +143,8 @@ def lazy_apply( # type: ignore[valid-type] # numpydoc ignore=GL07,SA04 `_. Dask - This allows applying eager functions to dask arrays. - The dask graph won't be computed. + This allows applying eager functions to Dask arrays. + The Dask graph won't be computed. `lazy_apply` doesn't know if `func` reduces along any axes; also, shape changes are non-trivial in chunked Dask arrays. For these reasons, all inputs diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index 867f0226..4f8288cf 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -63,12 +63,12 @@ def lazy_xp_function( # type: ignore[explicit-any] Number of times `func` is allowed to internally materialize the Dask graph. This is typically triggered by ``bool()``, ``float()``, or ``np.asarray()``. - Set to 1 if you are aware that `func` converts the input parameters to numpy and + Set to 1 if you are aware that `func` converts the input parameters to NumPy and want to let it do so at least for the time being, knowing that it is going to be extremely detrimental for performance. If a test needs values higher than 1 to pass, it is a canary that the conversion - to numpy/bool/float is happening multiple times, which translates to multiple + to NumPy/bool/float is happening multiple times, which translates to multiple computations of the whole graph. Short of making the function fully lazy, you should at least add explicit calls to ``np.asarray()`` early in the function. *Note:* the counter of `allow_dask_compute` resets after each call to `func`, so diff --git a/tests/conftest.py b/tests/conftest.py index 6cb4e433..b4d07df8 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -55,7 +55,7 @@ class NumPyReadOnly: """ Variant of array_api_compat.numpy producing read-only arrays. - Read-only numpy arrays fail on `__iadd__` etc., whereas read-only libraries such as + Read-only NumPy arrays fail on `__iadd__` etc., whereas read-only libraries such as JAX and Sparse simply don't define those methods, which makes calls to `+=` fall back to `__add__`. diff --git a/tests/test_at.py b/tests/test_at.py index 07ea2d3b..555e48af 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -318,7 +318,7 @@ def test_gh134(xp: ModuleType, bool_mask: bool, copy: bool | None): """ x = xp.zeros(1) - # In numpy, we have a writeable np.ndarray in input and a read-only np.generic in + # In NumPy, we have a writeable np.ndarray in input and a read-only np.generic in # output. As both are Arrays, this behaviour is Array API compliant. # In Dask, we have a writeable da.Array on both sides, and if you call __setitem__ # on it all seems fine, but when you compute() your graph is corrupted. diff --git a/tests/test_lazy.py b/tests/test_lazy.py index 647132e9..ea5b9ae1 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -47,7 +47,7 @@ def f(x: Array) -> Array: assert xp2 is xp y = xp2.broadcast_to(xp2.astype(x + 1, getattr(xp2, dtype)), shape) - return xp2.asarray(y, copy=True) # Torch: ensure writeable numpy array + return xp2.asarray(y, copy=True) # PyTorch: ensure writeable NumPy array x = xp.asarray([1, 2], dtype=xp.int16) expect = xp.broadcast_to(xp.astype(x + 1, getattr(xp, dtype)), shape) @@ -74,7 +74,7 @@ def f(x: Array) -> tuple[Array, Array]: xp2 = array_namespace(x) y = x + xp2.asarray(2, dtype=xp2.int8) # Sparse: bad dtype propagation z = xp2.broadcast_to(xp2.astype(x + 1, xp2.int16), (3, 2)) - z = xp2.asarray(z, copy=True) # Torch: ensure writeable numpy array + z = xp2.asarray(z, copy=True) # PyTorch: ensure writeable NumPy array return y, z x = xp.asarray([1, 2], dtype=xp.int8) @@ -166,8 +166,8 @@ def f(x: Array) -> Array: def test_lazy_apply_dask_non_numpy_meta(da: ModuleType): - """Test dask wrapping around a meta-namespace other than numpy.""" - # At the moment of writing, of all Array API namespaces cupy is + """Test Dask wrapping around a meta-namespace other than numpy.""" + # At the moment of writing, of all Array API namespaces CuPy is # the only one that Dask supports. # For this reason, we can only test as_numpy=False since # np.asarray(cp.Array) is blocked by the transfer guard. diff --git a/tests/test_testing.py b/tests/test_testing.py index 566e795f..47eaa4dd 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -74,7 +74,7 @@ def test_assert_close_tolerance(xp: ModuleType): @param_assert_equal_close @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="index by sparse array") 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 + """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]) @@ -99,18 +99,18 @@ def test_assert_close_equal_none_shape(xp: ModuleType, func: Callable[..., None] def good_lazy(x: Array) -> Array: - """A function that behaves well in dask and jax.jit""" + """A function that behaves well in Dask and jax.jit""" return x * 2.0 def non_materializable(x: Array) -> Array: """ This function materializes the input array, so it will fail when wrapped in jax.jit - and it will trigger an expensive computation in dask. + and it will trigger an expensive computation in Dask. """ xp = array_namespace(x) # Crashes inside jax.jit - # On dask, this triggers two computations of the whole graph + # On Dask, this triggers two computations of the whole graph if xp.any(x < 0.0) or xp.any(x > 10.0): msg = "Values must be in the [0, 10] range" raise ValueError(msg) @@ -217,20 +217,20 @@ def test_lazy_xp_function_static_params(xp: ModuleType, func: Callable[..., Arra erf = None -@pytest.mark.filterwarnings("ignore:__array_wrap__:DeprecationWarning") # torch +@pytest.mark.filterwarnings("ignore:__array_wrap__:DeprecationWarning") # PyTorch def test_lazy_xp_function_cython_ufuncs(xp: ModuleType, library: Backend): pytest.importorskip("scipy") assert erf is not None x = xp.asarray([6.0, 7.0]) if library in (Backend.ARRAY_API_STRICT, Backend.JAX): - # array-api-strict arrays are auto-converted to numpy + # array-api-strict arrays are auto-converted to NumPy # which results in an assertion error for mismatched namespaces - # eager jax arrays are auto-converted to numpy in eager jax + # eager JAX arrays are auto-converted to NumPy in eager JAX # and fail in jax.jit (which lazy_xp_function tests here) with pytest.raises((TypeError, AssertionError)): xp_assert_equal(cast(Array, erf(x)), xp.asarray([1.0, 1.0])) else: - # cupy, dask and sparse define __array_ufunc__ and dispatch accordingly + # CuPy, Dask and sparse define __array_ufunc__ and dispatch accordingly # note that when sparse reduces to scalar it returns a np.generic, which # would make xp_assert_equal fail. xp_assert_equal(cast(Array, erf(x)), xp.asarray([1.0, 1.0])) @@ -271,7 +271,7 @@ def test_lazy_xp_function_eagerly_raises(da: ModuleType): def f(x: Array) -> Array: xp = array_namespace(x) - # Crash in jax.jit and trigger compute() on dask + # Crash in jax.jit and trigger compute() on Dask if not xp.all(x): msg = "Values must be non-zero" raise ValueError(msg) From 696ec8e562c552fb4c5a9b1d0f89d0ce7eeb9fb5 Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Sat, 22 Mar 2025 16:41:52 +0000 Subject: [PATCH 007/131] docs: add crusaderky as a contributor for ideas, review, and maintenance (#173) * 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 | 5 ++++- CONTRIBUTORS.md | 2 +- README.md | 2 +- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index f91258c2..281b770f 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -101,7 +101,10 @@ "tool", "test", "example", - "bug" + "bug", + "ideas", + "review", + "maintenance" ] }, { diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index fef09188..9d195237 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -18,7 +18,7 @@ This project exists thanks to the following contributors Carlos Ramos Carreño
Carlos Ramos Carreño
🤔 - Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 🐛 + Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 🐛 🤔 👀 🚧 Joren Hammudoglu
Joren Hammudoglu
👀 Thomas J. Fan
Thomas J. Fan
🤔 Irwin Zaid
Irwin Zaid
🤔 diff --git a/README.md b/README.md index 8d11a67e..8524d28a 100644 --- a/README.md +++ b/README.md @@ -70,7 +70,7 @@ This project exists thanks to the following contributors Carlos Ramos Carreño
Carlos Ramos Carreño
🤔 - Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 🐛 + Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 🐛 🤔 👀 🚧 Joren Hammudoglu
Joren Hammudoglu
👀 Thomas J. Fan
Thomas J. Fan
🤔 Irwin Zaid
Irwin Zaid
🤔 From 114a3ec4d870db6a0decb4b583ca69d4c902f2ce Mon Sep 17 00:00:00 2001 From: crusaderky Date: Sun, 23 Mar 2025 19:16:35 +0000 Subject: [PATCH 008/131] MAINT: test vs. NumPy 1.22 --- pixi.lock | 808 ++++++++++++++-------------------------------- pyproject.toml | 5 +- tests/conftest.py | 3 + 3 files changed, 241 insertions(+), 575 deletions(-) diff --git a/pixi.lock b/pixi.lock index c111514b..6dbaed87 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1626,24 +1626,24 @@ 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-1.11.1-pyh29332c3_1.conda - conda: https://prefix.dev/conda-forge/noarch/array-api-strict-2.3-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/astroid-3.3.9-py311h38be061_0.conda + - conda: https://prefix.dev/conda-forge/linux-64/astroid-3.3.9-py310hff52083_0.conda - conda: https://prefix.dev/conda-forge/noarch/asttokens-3.0.0-pyhd8ed1ab_1.conda - 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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) -[![Scientific Python Ecosystem Coordination](https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/) +[![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] @@ -33,8 +33,10 @@ Extra array functions built on top of the array API standard. Used by: -- [SciPy](https://github.com/scipy/scipy) - Fundamental algorithms for +- [SciPy](https://github.com/scipy/scipy) — Fundamental algorithms for scientific computing. +- [scikit-learn](https://github.com/scikit-learn/scikit-learn) — Machine + Learning in Python. - _your library? Let us know!_ ## Installation From 52f8466682e9f0cd21758a8633450a194815a243 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Tue, 25 Mar 2025 13:48:32 +0000 Subject: [PATCH 010/131] MAINT: general deps bump --- pixi.lock | 4420 +++++++------------------- pyproject.toml | 27 +- src/array_api_extra/_lib/_lazy.py | 2 +- src/array_api_extra/_lib/_testing.py | 2 +- tests/test_at.py | 2 +- tests/test_funcs.py | 10 +- tests/test_lazy.py | 4 +- 7 files changed, 1256 insertions(+), 3211 deletions(-) diff --git a/pixi.lock b/pixi.lock index 6dbaed87..1daa6d96 100644 --- a/pixi.lock +++ b/pixi.lock @@ -7,8 +7,9 @@ environments: - https://pypi.org/simple packages: linux-64: - - conda: https://prefix.dev/conda-forge/linux-64/_openmp_mutex-4.5-3_kmp_llvm.conda - - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.11.1-pyh29332c3_1.conda + - 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 + - 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libzlib >=1.3.1,<2.0a0 - ucrt >=10.0.20348.0 @@ -15002,5 +13046,5 @@ packages: license: BSD-3-Clause license_family: BSD purls: [] - size: 353182 - timestamp: 1740255407949 + size: 354697 + timestamp: 1742433568506 diff --git a/pyproject.toml b/pyproject.toml index d6e77bc8..75d67d5d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -136,6 +136,7 @@ numpy = "=1.22.0" pytorch = "*" dask = "*" numba = "*" # sparse dependency +llvmlite = "*" # sparse dependency [tool.pixi.feature.backends.pypi-dependencies] sparse = { version = ">= 0.16.0b3" } @@ -166,19 +167,23 @@ cupy = "*" # jaxlib = { version = "*", build = "cuda12*" } # unavailable [tool.pixi.environments] -default = { solve-group = "default" } -lint = { features = ["lint"], solve-group = "default" } -tests = { features = ["tests"], solve-group = "default" } -docs = { features = ["docs"], solve-group = "default" } -dev = { features = ["lint", "tests", "docs", "dev", "backends"], solve-group = "default" } -dev-cuda = { features = ["lint", "tests", "docs", "dev", "backends", "cuda-backends"] } -dev-numpy1 = { features = ["lint", "tests", "dev", "numpy1"] } +default = { features = ["py313"], solve-group = "py313" } +lint = { features = ["py313", "lint"], solve-group = "py313" } +docs = { features = ["py313", "docs"], solve-group = "py313" } +tests = { features = ["py313", "tests"], solve-group = "py313" } +tests-py313 = { features = ["py313", "tests"], solve-group = "py313" } # alias of tests + +# Some backends may pin numpy; use separate solve-group +dev = { features = ["py310", "lint", "tests", "docs", "dev", "backends"], solve-group = "backends" } +tests-backends = { features = ["py310", "tests", "backends"], solve-group = "backends" } + +# CUDA not available on free github actions and on some developers' PCs +dev-cuda = { features = ["py310", "lint", "tests", "docs", "dev", "backends", "cuda-backends"], solve-group = "cuda" } +tests-cuda = { features = ["py310", "tests", "backends", "cuda-backends"], solve-group = "cuda" } + +# Ungrouped environments tests-numpy1 = ["py310", "tests", "numpy1"] tests-py310 = ["py310", "tests"] -tests-py313 = ["py313", "tests"] -# CUDA not available on free github actions and on some developers' PCs -tests-backends = ["py310", "tests", "backends"] -tests-cuda = ["py310", "tests", "backends", "cuda-backends"] # pytest diff --git a/src/array_api_extra/_lib/_lazy.py b/src/array_api_extra/_lib/_lazy.py index f7cc2a58..7b45eff9 100644 --- a/src/array_api_extra/_lib/_lazy.py +++ b/src/array_api_extra/_lib/_lazy.py @@ -338,7 +338,7 @@ 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 # pyright: ignore[reportInvalidCast] + arg = cast(Array, np.asarray(arg)) # type: ignore[bad-cast] # 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 87de688d..f592eb45 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -106,7 +106,7 @@ def xp_assert_equal(actual: Array, desired: Array, err_msg: str = "") -> None: desired = desired.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] # JAX uses `np.testing` - np.testing.assert_array_equal(actual, desired, err_msg=err_msg) # type: ignore[arg-type] # pyright: ignore[reportArgumentType] + np.testing.assert_array_equal(actual, desired, err_msg=err_msg) # pyright: ignore[reportUnknownArgumentType] def xp_assert_close( diff --git a/tests/test_at.py b/tests/test_at.py index 555e48af..d9a58549 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -187,7 +187,7 @@ def test_copy_invalid(): def test_xp(): - a = cast(Array, np.asarray([1, 2, 3])) # type: ignore[bad-cast] # pyright: ignore[reportInvalidCast] + a = cast(Array, np.asarray([1, 2, 3])) # type: ignore[bad-cast] _ = 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 997411cc..b93cc7c9 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -28,7 +28,7 @@ from array_api_extra._lib import 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 asarrays, eager_shape, ndindex +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 @@ -193,7 +193,7 @@ def test_device(self, xp: ModuleType, device: Device): assert get_device(y) == device @pytest.mark.filterwarnings("ignore::RuntimeWarning") # overflows, etc. - @hypothesis.settings( # pyright: ignore[reportArgumentType] + @hypothesis.settings( # The xp and library fixtures are not regenerated between hypothesis iterations suppress_health_check=[hypothesis.HealthCheck.function_scoped_fixture], # JAX can take a long time to initialize on the first call @@ -262,11 +262,7 @@ def f2(*args: Array) -> Array: ref1 = xp.where(cond, f1(*arrays), fill_value) ref2 = xp.where(cond, f1(*arrays), f2(*arrays)) - if library is Backend.ARRAY_API_STRICT: - # FIXME https://github.com/data-apis/array-api-strict/issues/131 - ref3 = xp.where(cond, *asarrays(f1(*arrays), float_fill_value, xp=xp)) - else: - ref3 = xp.where(cond, f1(*arrays), float_fill_value) + ref3 = xp.where(cond, f1(*arrays), float_fill_value) xp_assert_close(res1, ref1, rtol=2e-16) xp_assert_equal(res2, ref2) diff --git a/tests/test_lazy.py b/tests/test_lazy.py index ea5b9ae1..91cfed72 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -136,7 +136,7 @@ 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] # pyright: ignore[reportInvalidCast] + x_np = cast(Array, np.arange(15).reshape(5, 3)) # type: ignore[bad-cast] expect = da.asarray(f(x_np)) x_da = da.asarray(x_np).rechunk(3) @@ -419,6 +419,6 @@ def f(x: Array) -> Array: with pytest.raises(ValueError, match="multiple shapes but only one dtype"): _ = lazy_apply(f, x, shape=[(1,), (2,)], dtype=np.int32) # type: ignore[call-overload] # pyright: ignore[reportCallIssue,reportArgumentType] with pytest.raises(ValueError, match="single shape but multiple dtypes"): - _ = lazy_apply(f, x, shape=(1,), dtype=[np.int32, np.int64]) + _ = lazy_apply(f, x, shape=(1,), dtype=[np.int32, np.int64]) # pyright: ignore[reportCallIssue,reportArgumentType] with pytest.raises(ValueError, match="2 shapes and 1 dtypes"): _ = lazy_apply(f, x, shape=[(1,), (2,)], dtype=[np.int32]) # type: ignore[arg-type] # pyright: ignore[reportCallIssue,reportArgumentType] From 74e5f27299cb92edd4e8e2b107f43d95cd773348 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 25 Mar 2025 17:22:02 +0000 Subject: [PATCH 011/131] DOC: update homepage --- docs/index.md | 4 +++- pixi.lock | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/index.md b/docs/index.md index d72c40ef..59615583 100644 --- a/docs/index.md +++ b/docs/index.md @@ -23,8 +23,10 @@ themselves. It is currently used by: -- [SciPy](https://github.com/scipy/scipy) - Fundamental algorithms for +- [SciPy](https://github.com/scipy/scipy) — Fundamental algorithms for scientific computing. +- [scikit-learn](https://github.com/scikit-learn/scikit-learn) — Machine + Learning in Python. - _your library? Let us know!_ (installation)= diff --git a/pixi.lock b/pixi.lock index 1daa6d96..ad46cac7 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11726,7 +11726,7 @@ packages: license: MIT license_family: MIT purls: - - pkg:pypi/pytz?source=compressed-mapping + - pkg:pypi/pytz?source=hash-mapping size: 186859 timestamp: 1738317649432 - conda: https://prefix.dev/conda-forge/linux-64/pyyaml-6.0.2-py310h89163eb_2.conda From f55076f3fc66facd0e41174356769d868dd5ff7d Mon Sep 17 00:00:00 2001 From: Thomas Li <47963215+lithomas1@users.noreply.github.com> Date: Tue, 25 Mar 2025 13:57:23 -0400 Subject: [PATCH 012/131] BUG: isclose: fix multidevice for `equal_nan=True` (#177) * BUG: Fix isclose multidevice * test the right way * fix pre-commit * convert to CPU in xp_assert_equal * fixes * fix tests --------- Co-authored-by: Lucas Colley --- src/array_api_extra/_lib/_funcs.py | 2 +- src/array_api_extra/_lib/_testing.py | 34 +++++++++++++++++++++++----- tests/test_funcs.py | 10 ++++++++ 3 files changed, 39 insertions(+), 7 deletions(-) diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index d0b67388..efe2f377 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -549,7 +549,7 @@ def isclose( xp=xp, ) if equal_nan: - out = xp.where(xp.isnan(a) & xp.isnan(b), xp.asarray(True), out) + out = xp.where(xp.isnan(a) & xp.isnan(b), True, out) return out if xp.isdtype(a.dtype, "bool") or xp.isdtype(b.dtype, "bool"): diff --git a/src/array_api_extra/_lib/_testing.py b/src/array_api_extra/_lib/_testing.py index f592eb45..e5ec16a6 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -13,6 +13,7 @@ from ._utils._compat import ( array_namespace, + is_array_api_strict_namespace, is_cupy_namespace, is_dask_namespace, is_pydata_sparse_namespace, @@ -105,8 +106,18 @@ def xp_assert_equal(actual: Array, desired: Array, err_msg: str = "") -> None: actual = actual.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] desired = desired.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] - # JAX uses `np.testing` - np.testing.assert_array_equal(actual, desired, err_msg=err_msg) # pyright: ignore[reportUnknownArgumentType] + actual_np = None + desired_np = None + if is_array_api_strict_namespace(xp): + # __array__ doesn't work on array-api-strict device arrays + # We need to convert to the CPU device first + actual_np = np.asarray(xp.asarray(actual, device=xp.Device("CPU_DEVICE"))) + desired_np = np.asarray(xp.asarray(desired, device=xp.Device("CPU_DEVICE"))) + + # JAX/Dask arrays work with `np.testing` + actual_np = actual if actual_np is None else actual_np + desired_np = desired if desired_np is None else desired_np + np.testing.assert_array_equal(actual_np, desired_np, err_msg=err_msg) # pyright: ignore[reportUnknownArgumentType] def xp_assert_close( @@ -169,14 +180,25 @@ def xp_assert_close( actual = actual.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] desired = desired.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] - # JAX uses `np.testing` + actual_np = None + desired_np = None + if is_array_api_strict_namespace(xp): + # __array__ doesn't work on array-api-strict device arrays + # We need to convert to the CPU device first + actual_np = np.asarray(xp.asarray(actual, device=xp.Device("CPU_DEVICE"))) + desired_np = np.asarray(xp.asarray(desired, device=xp.Device("CPU_DEVICE"))) + + # JAX/Dask arrays work with `np.testing` + actual_np = actual if actual_np is None else actual_np + desired_np = desired if desired_np is None else desired_np + assert isinstance(rtol, float) np.testing.assert_allclose( # pyright: ignore[reportCallIssue] - actual, # pyright: ignore[reportArgumentType] - desired, # pyright: ignore[reportArgumentType] + actual_np, # type: ignore[arg-type] # pyright: ignore[reportArgumentType] + desired_np, # type: ignore[arg-type] # pyright: ignore[reportArgumentType] rtol=rtol, atol=atol, - err_msg=err_msg, # type: ignore[call-overload] + err_msg=err_msg, ) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index b93cc7c9..46591ed6 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -716,6 +716,16 @@ def test_xp(self, xp: ModuleType): b = xp.asarray([1e-9, 1e-4]) xp_assert_equal(isclose(a, b, xp=xp), xp.asarray([True, False])) + @pytest.mark.parametrize("equal_nan", [True, False]) + def test_device(self, xp: ModuleType, device: Device, equal_nan: bool): + a = xp.asarray([0.0, 0.0, xp.nan], device=device) + 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: def test_basic(self, xp: ModuleType): From 3a822e2a4ae8d6c3a75ce5d07cbdbdefa008fa7b Mon Sep 17 00:00:00 2001 From: crusaderky Date: Tue, 25 Mar 2025 18:19:57 +0000 Subject: [PATCH 013/131] TST: `at`: add test for device --- tests/test_at.py | 15 ++++++++++++++- 1 file changed, 14 insertions(+), 1 deletion(-) diff --git a/tests/test_at.py b/tests/test_at.py index d9a58549..218b05b2 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -13,7 +13,8 @@ from array_api_extra._lib._at import _AtOp from array_api_extra._lib._testing import xp_assert_equal from array_api_extra._lib._utils._compat import array_namespace, is_writeable_array -from array_api_extra._lib._utils._typing import Array, SetIndex +from array_api_extra._lib._utils._compat import device as get_device +from array_api_extra._lib._utils._typing import Array, Device, SetIndex from array_api_extra.testing import lazy_xp_function pytestmark = [ @@ -327,3 +328,15 @@ def test_gh134(xp: ModuleType, bool_mask: bool, copy: bool | None): idx = xp.asarray(True) if bool_mask else () z = at_op(y, idx, _AtOp.SET, 1, copy=copy) xp_assert_equal(z, xp.asarray(1, dtype=x.dtype)) + + +def test_device(xp: ModuleType, device: Device): + x = xp.asarray([1, 2, 3], device=device) + + y = xp.asarray([4, 5], device=device) + z = at(x)[:2].set(y) + assert get_device(z) == get_device(x) + + idx = xp.asarray([True, False, True], device=device) + z = at(x)[idx].set(4) + assert get_device(z) == get_device(x) From c07f084cde2161371b978f9b3133858f6d6ad0cf Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Tue, 25 Mar 2025 18:29:57 +0000 Subject: [PATCH 014/131] docs: add lithomas1 as a contributor for bug (#181) * 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 | 3 +++ README.md | 3 +++ 3 files changed, 15 insertions(+) diff --git a/.all-contributorsrc b/.all-contributorsrc index 281b770f..93880be6 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -228,6 +228,15 @@ "code", "test" ] + }, + { + "login": "lithomas1", + "name": "Thomas Li", + "avatar_url": "https://avatars.githubusercontent.com/u/47963215?v=4", + "profile": "https://github.com/lithomas1", + "contributions": [ + "bug" + ] } ] } diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index 9d195237..c2914370 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -35,6 +35,9 @@ This project exists thanks to the following contributors detachhead
detachhead
👀 Neil Girdhar
Neil Girdhar
💻 ⚠️ + + Thomas Li
Thomas Li
🐛 + diff --git a/README.md b/README.md index 0f80c9e4..acf94182 100644 --- a/README.md +++ b/README.md @@ -89,6 +89,9 @@ This project exists thanks to the following contributors detachhead
detachhead
👀 Neil Girdhar
Neil Girdhar
💻 ⚠️ + + Thomas Li
Thomas Li
🐛 + From fd6a2c3adf6998c43bac738c970e8e95061dd577 Mon Sep 17 00:00:00 2001 From: Thomas Li <47963215+lithomas1@users.noreply.github.com> Date: Tue, 25 Mar 2025 18:23:54 -0400 Subject: [PATCH 015/131] DEV: Configure pixi for Intel Macs --- pixi.lock | 3269 +++++++++++++++++++++++++++++++++++++++++++++++- pyproject.toml | 2 +- 2 files changed, 3242 insertions(+), 29 deletions(-) diff --git a/pixi.lock b/pixi.lock index ad46cac7..38af268a 100644 --- a/pixi.lock +++ b/pixi.lock @@ -31,6 +31,24 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda - conda: https://prefix.dev/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda - pypi: . + osx-64: + - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.11.2-pyh29332c3_0.conda + - conda: https://prefix.dev/conda-forge/osx-64/bzip2-1.0.8-hfdf4475_7.conda + - conda: https://prefix.dev/conda-forge/osx-64/ca-certificates-2025.1.31-h8857fd0_0.conda + - conda: https://prefix.dev/conda-forge/osx-64/libexpat-2.6.4-h240833e_0.conda + - 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"bug" + "bug", + "tool" ] } ] diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index c2914370..7d095124 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -36,7 +36,7 @@ This project exists thanks to the following contributors Neil Girdhar
Neil Girdhar
💻 ⚠️ - Thomas Li
Thomas Li
🐛 + Thomas Li
Thomas Li
🐛 🔧 diff --git a/README.md b/README.md index acf94182..ab42dfa0 100644 --- a/README.md +++ b/README.md @@ -90,7 +90,7 @@ This project exists thanks to the following contributors Neil Girdhar
Neil Girdhar
💻 ⚠️ - Thomas Li
Thomas Li
🐛 + Thomas Li
Thomas Li
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__osx >=10.13 + - libblas >=3.9.0,<4.0a0 + - libcblas >=3.9.0,<4.0a0 + - libcxx >=18 + - libgfortran 5.* + - libgfortran5 >=13.2.0 + - liblapack >=3.9.0,<4.0a0 + - numpy <2.5 + - numpy >=1.19,<3 + - numpy >=1.23.5 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + license: BSD-3-Clause + license_family: BSD + purls: + - pkg:pypi/scipy?source=hash-mapping + size: 14682985 + timestamp: 1739792429025 - conda: https://prefix.dev/conda-forge/osx-arm64/scipy-1.15.2-py310h32ab4ed_0.conda sha256: f6ff2c1ba4775300199e8bc0331d2e2ccb5906f58f3835c5426ddc591c9ad7bf md5: a389f540c808b22b3c696d7aea791a41 diff --git a/pyproject.toml b/pyproject.toml index 5b2494eb..4394b4cb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -144,6 +144,9 @@ sparse = { version = ">= 0.16.0b3" } [tool.pixi.feature.backends.target.linux-64.dependencies] jax = "*" +[tool.pixi.feature.backends.target.osx-64.dependencies] +jax = "*" + [tool.pixi.feature.backends.target.osx-arm64.dependencies] jax = "*" @@ -158,6 +161,10 @@ system-requirements = { cuda = "12" } cupy = "*" jaxlib = { version = "*", build = "cuda12*" } +[tool.pixi.feature.cuda-backends.target.osx-64.dependencies] +# cupy = "*" # unavailable +# jaxlib = { version = "*", build = "cuda12*" } # unavailable + [tool.pixi.feature.cuda-backends.target.osx-arm64.dependencies] # cupy = "*" # unavailable # jaxlib = { version = "*", build = "cuda12*" } # unavailable From 9677f81d655bf0989e2454b67cba7a2bc87adbb4 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Wed, 26 Mar 2025 14:05:17 +0000 Subject: [PATCH 018/131] DEV: pin CUDA variant for PyTorch (#186) * DEV: remove redundant CUDA pins for JAX * Revert JAX and make torch explicit too --- pixi.lock | 2 +- pyproject.toml | 12 +++++++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 4bab4907..8c0a6b3b 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.1.dev0 - sha256: 54fed5ddb6a0d325790f34dd81b796833e3772fcb2b9a81511f26b1ebf32df25 + sha256: 676a791c66366ceb58f64f5bff8010d4f3c1077846f7b9c411883b46eb55fd38 requires_dist: - array-api-compat>=1.11,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 4394b4cb..0aabf345 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -132,6 +132,7 @@ python = "~=3.13.0" 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 = "*" dask = "*" @@ -153,25 +154,34 @@ jax = "*" [tool.pixi.feature.backends.target.win-64.dependencies] # jax = "*" # unavailable -# Backends that require a GPU host and a CUDA driver +# Backends that require a GPU host and a CUDA driver. +# Note that JAX and PyTorch automatically prefer CUDA variants +# thanks to the `system-requirements` below, *if available*. +# We request them explicitly below to ensure that we don't +# quietly revert to CPU-only in the future, e.g. when CUDA 13 +# is released and CUDA 12 builds are dropped upstream. [tool.pixi.feature.cuda-backends] system-requirements = { cuda = "12" } [tool.pixi.feature.cuda-backends.target.linux-64.dependencies] cupy = "*" jaxlib = { version = "*", build = "cuda12*" } +pytorch = { version = "*", build = "cuda12*" } [tool.pixi.feature.cuda-backends.target.osx-64.dependencies] # cupy = "*" # unavailable # jaxlib = { version = "*", build = "cuda12*" } # unavailable +# pytorch = { version = "*", build = "cuda12*" } # unavailable [tool.pixi.feature.cuda-backends.target.osx-arm64.dependencies] # cupy = "*" # unavailable # jaxlib = { version = "*", build = "cuda12*" } # unavailable +# pytorch = { version = "*", build = "cuda12*" } # unavailable [tool.pixi.feature.cuda-backends.target.win-64.dependencies] cupy = "*" # jaxlib = { version = "*", build = "cuda12*" } # unavailable +pytorch = { version = "*", build = "cuda12*" } [tool.pixi.environments] default = { features = ["py313"], solve-group = "py313" } From 0d26a7462a3fbf5ed9e42e261bdb3b39f25e2faf Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 26 Mar 2025 14:17:00 +0000 Subject: [PATCH 019/131] REL: set version to 0.7.1 (#187) --- pixi.lock | 2 +- src/array_api_extra/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 8c0a6b3b..68733839 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5231,7 +5231,7 @@ packages: timestamp: 1742509526028 - pypi: . name: array-api-extra - version: 0.7.1.dev0 + version: 0.7.1 sha256: 676a791c66366ceb58f64f5bff8010d4f3c1077846f7b9c411883b46eb55fd38 requires_dist: - array-api-compat>=1.11,<2 diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 879d49b5..924c23b9 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__ = "0.7.1.dev0" +__version__ = "0.7.1" # pylint: disable=duplicate-code __all__ = [ From 5326cbd00027db8296a5c1a6e6f56c667cef8b42 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 26 Mar 2025 14:23:46 +0000 Subject: [PATCH 020/131] DEV: bump version to 0.7.2.dev0 (#188) --- pixi.lock | 2 +- src/array_api_extra/__init__.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 68733839..6dfdbf39 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5231,7 +5231,7 @@ packages: timestamp: 1742509526028 - pypi: . name: array-api-extra - version: 0.7.1 + version: 0.7.2.dev0 sha256: 676a791c66366ceb58f64f5bff8010d4f3c1077846f7b9c411883b46eb55fd38 requires_dist: - array-api-compat>=1.11,<2 diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 924c23b9..aa0a484a 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__ = "0.7.1" +__version__ = "0.7.2.dev0" # pylint: disable=duplicate-code __all__ = [ From fcddde32eb53ecd9339470cf251e67dd905b9106 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Thu, 27 Mar 2025 12:39:24 +0000 Subject: [PATCH 021/131] MAINT: add Dask note to `lazy_apply` --- src/array_api_extra/_lib/_lazy.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/src/array_api_extra/_lib/_lazy.py b/src/array_api_extra/_lib/_lazy.py index 7b45eff9..d13d08f8 100644 --- a/src/array_api_extra/_lib/_lazy.py +++ b/src/array_api_extra/_lib/_lazy.py @@ -144,7 +144,12 @@ def lazy_apply( # type: ignore[valid-type] # numpydoc ignore=GL07,SA04 Dask This allows applying eager functions to Dask arrays. - The Dask graph won't be computed. + The Dask graph won't be computed until the user calls ``compute()`` or + ``persist()`` down the line. + + The function name will be prominently visible on the user-facing Dask + dashboard and on Prometheus metrics, so it is recommended for it to be + meaningful. `lazy_apply` doesn't know if `func` reduces along any axes; also, shape changes are non-trivial in chunked Dask arrays. For these reasons, all inputs From 76d614501671c2e64d0586387910a763cf530e55 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Thu, 27 Mar 2025 13:18:53 +0000 Subject: [PATCH 022/131] TST: add test for Dask keys in lazy_apply --- tests/test_lazy.py | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/tests/test_lazy.py b/tests/test_lazy.py index 91cfed72..7057af80 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -186,6 +186,27 @@ def f(x: Array) -> Array: xp_assert_equal(y.compute(), x_cp + 1) # type: ignore[attr-defined] # pyright: ignore[reportUnknownArgumentType,reportAttributeAccessIssue] +def test_dask_key(da: ModuleType): + """Test that the function name is visible on the Dask dashboard and in metrics.""" + + def helloworld(x: Array) -> Array: + return x + 1 + + x = da.asarray([1, 2]) + # Use full namespace to bypass monkey-patching by lazy_xp_function, + # which calls persist() to materialize exceptions and warnings and in + # doing so squashes the graph. + y = xpx.lazy_apply(helloworld, x) + + prefixes = set() + for key in y.__dask_graph__(): # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + name = key[0] if isinstance(key, tuple) else key + assert isinstance(name, str) + prefixes.add(name.split("-")[0]) + + assert "helloworld" in prefixes + + def test_lazy_apply_none_shape_in_args(xp: ModuleType, library: Backend): x = xp.asarray([1, 1, 2, 2, 2]) From b41da86663ef7a6d695595df4e11384f58358ce2 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Thu, 27 Mar 2025 18:55:28 +0000 Subject: [PATCH 023/131] ENH/TST: tougher restrictions on array_api_strict (#179) * ENH: tougher restrictions on array_api_strict * Clean up Backend tests * Code review --- src/array_api_extra/_lib/_at.py | 1 + src/array_api_extra/_lib/_backends.py | 21 +++++++-- src/array_api_extra/_lib/_funcs.py | 51 +++++++++++++++------ src/array_api_extra/_lib/_utils/_helpers.py | 36 +++++++++++++++ tests/conftest.py | 32 +++++++++---- tests/test_at.py | 5 +- tests/test_funcs.py | 50 ++++++++++++++++---- tests/test_helpers.py | 12 ++++- tests/test_lazy.py | 28 ++++++----- tests/test_testing.py | 5 +- 10 files changed, 184 insertions(+), 57 deletions(-) diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py index 22e18d2c..736f77bd 100644 --- a/src/array_api_extra/_lib/_at.py +++ b/src/array_api_extra/_lib/_at.py @@ -344,6 +344,7 @@ def _op( msg = f"Can't update read-only array {x}" raise ValueError(msg) + # Backends without boolean indexing (other than JAX) crash here if in_place_op: # add(), subtract(), ... x[idx] = in_place_op(x[idx], y) else: # set() diff --git a/src/array_api_extra/_lib/_backends.py b/src/array_api_extra/_lib/_backends.py index f044281a..3beb676d 100644 --- a/src/array_api_extra/_lib/_backends.py +++ b/src/array_api_extra/_lib/_backends.py @@ -1,9 +1,10 @@ """Backends with which array-api-extra interacts in delegation and testing.""" +from __future__ import annotations + from collections.abc import Callable from enum import Enum from types import ModuleType -from typing import cast from ._utils import _compat @@ -23,9 +24,14 @@ class Backend(Enum): # numpydoc ignore=PR01,PR02 # type: ignore[no-subclass-an corresponding to the backend. """ + # Use : to prevent Enum from deduplicating items with the same value ARRAY_API_STRICT = "array_api_strict", _compat.is_array_api_strict_namespace + ARRAY_API_STRICTEST = ( + "array_api_strict:strictest", + _compat.is_array_api_strict_namespace, + ) NUMPY = "numpy", _compat.is_numpy_namespace - NUMPY_READONLY = "numpy_readonly", _compat.is_numpy_namespace + NUMPY_READONLY = "numpy:readonly", _compat.is_numpy_namespace CUPY = "cupy", _compat.is_cupy_namespace TORCH = "torch", _compat.is_torch_namespace DASK = "dask.array", _compat.is_dask_namespace @@ -48,4 +54,13 @@ def __init__( def __str__(self) -> str: # type: ignore[explicit-override] # pyright: ignore[reportImplicitOverride] # numpydoc ignore=RT01 """Pretty-print parameterized test names.""" - return cast(str, self.value) + return self.name.lower() + + @property + def modname(self) -> str: # numpydoc ignore=RT01 + """Module name to be imported.""" + return self.value.split(":")[0] + + 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) diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index efe2f377..e552392b 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -8,13 +8,14 @@ from ._at import at from ._utils import _compat, _helpers -from ._utils._compat import ( - array_namespace, - is_dask_namespace, - is_jax_array, - is_jax_namespace, +from ._utils._compat import array_namespace, is_dask_namespace, is_jax_array +from ._utils._helpers import ( + asarrays, + capabilities, + eager_shape, + meta_namespace, + ndindex, ) -from ._utils._helpers import asarrays, eager_shape, meta_namespace, ndindex from ._utils._typing import Array __all__ = [ @@ -152,7 +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 is_jax_namespace(xp): + if not capabilities(xp)["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) @@ -708,14 +709,34 @@ def nunique(x: Array, /, *, xp: ModuleType | None = None) -> Array: # size= is JAX-specific # https://github.com/data-apis/array-api/issues/883 _, counts = xp.unique_counts(x, size=_compat.size(x)) - return xp.astype(counts, xp.bool).sum() - - _, counts = xp.unique_counts(x) - n = _compat.size(counts) - # FIXME https://github.com/data-apis/array-api-compat/pull/231 - if n is None: # e.g. Dask, ndonnx - return xp.astype(counts, xp.bool).sum() - return xp.asarray(n, device=_compat.device(x)) + return (counts > 0).sum() + + # There are 3 general use cases: + # 1. backend has unique_counts and it returns an array with known shape + # 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"]: + # xp has unique_counts; O(n) complexity + _, counts = xp.unique_counts(x) + n = _compat.size(counts) + if n is None: + return xp.sum(xp.ones_like(counts)) + 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)) + mask = x != xp.roll(x, -1) + default_int = xp.__array_namespace_info__().default_dtypes( + device=_compat.device(x) + )["integral"] + return xp.maximum( + # Special cases: + # - array is size 0 + # - array has all elements equal to each other + xp.astype(xp.any(~mask), default_int), + xp.sum(xp.astype(mask, default_int)), + ) def pad( diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 9882d72e..64006270 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -12,7 +12,9 @@ array_namespace, is_array_api_obj, is_dask_namespace, + is_jax_namespace, is_numpy_array, + is_pydata_sparse_namespace, ) from ._typing import Array @@ -23,6 +25,7 @@ __all__ = [ "asarrays", + "capabilities", "eager_shape", "in1d", "is_python_scalar", @@ -270,3 +273,36 @@ def meta_namespace( # Quietly skip scalars and None's metas = [cast(Array | None, getattr(a, "_meta", None)) for a in arrays] return array_namespace(*metas) + + +def capabilities(xp: ModuleType) -> dict[str, int]: + """ + Return patched ``xp.__array_namespace_info__().capabilities()``. + + TODO this helper should be eventually removed once all the special cases + it handles are fixed in the respective backends. + + Parameters + ---------- + xp : array_namespace + The standard-compatible namespace. + + Returns + ------- + 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} + out = xp.__array_namespace_info__().capabilities() + if is_jax_namespace(xp): + # FIXME https://github.com/jax-ml/jax/issues/27418 + 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 diff --git a/tests/conftest.py b/tests/conftest.py index 54e2a23a..4e368850 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,6 +1,6 @@ """Pytest fixtures.""" -from collections.abc import Callable +from collections.abc import Callable, Generator from contextlib import suppress from functools import partial, wraps from types import ModuleType @@ -19,6 +19,7 @@ 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] @@ -43,7 +44,7 @@ def library(request: pytest.FixtureRequest) -> Backend: # numpydoc ignore=PR01, msg = f"argument of {marker_name} must be a Backend enum" raise TypeError(msg) if library == elem: - reason = library.value + reason = str(library) with suppress(KeyError): reason += ":" + cast(str, marker.kwargs["reason"]) skip_or_xfail(reason=reason) @@ -104,7 +105,7 @@ def wrapper(*args: P.args, **kwargs: P.kwargs) -> T: # numpydoc ignore=GL08 @pytest.fixture def xp( library: Backend, request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch -) -> ModuleType: # numpydoc ignore=PR01,RT03 +) -> Generator[ModuleType]: # numpydoc ignore=PR01,RT03 """ Parameterized fixture that iterates on all libraries. @@ -113,25 +114,38 @@ def xp( The current array namespace. """ if library == Backend.NUMPY_READONLY: - return NumPyReadOnly() # type: ignore[return-value] # pyright: ignore[reportReturnType] - xp = pytest.importorskip(library.value) + 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)) + if library == Backend.ARRAY_API_STRICTEST: + with xp.ArrayAPIStrictFlags( + boolean_indexing=False, + data_dependent_shapes=False, + # writeable=False, # TODO implement in array-api-strict + # lazy=True, # TODO implement in array-api-strict + enabled_extensions=(), + ): + 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 == Backend.ARRAY_API_STRICT and np.__version__ < "1.26": - pytest.skip("array_api_strict is untested on NumPy <1.26") - if library == 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] - return xp + yield xp @pytest.fixture(params=[Backend.DASK]) # Can select the test with `pytest -k dask` diff --git a/tests/test_at.py b/tests/test_at.py index 218b05b2..4bde5ce2 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -20,7 +20,8 @@ pytestmark = [ pytest.mark.skip_xp_backend( Backend.SPARSE, reason="read-only backend without .at support" - ) + ), + pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="boolean indexing"), ] @@ -256,7 +257,7 @@ def test_incompatible_dtype( elif library is Backend.DASK: z = at_op(x, idx, op, 1.1, copy=copy) - elif library is Backend.ARRAY_API_STRICT and op is not _AtOp.SET: + elif library.like(Backend.ARRAY_API_STRICT) and op is not _AtOp.SET: with pytest.raises(Exception, match=r"cast|promote|dtype"): _ = at_op(x, idx, op, 1.1, copy=copy) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 46591ed6..48ad7b06 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -32,6 +32,8 @@ from array_api_extra._lib._utils._typing import Array, Device from array_api_extra.testing import lazy_xp_function +from .conftest import NUMPY_VERSION + # some xp backends are untyped # mypy: disable-error-code=no-untyped-def @@ -48,12 +50,6 @@ lazy_xp_function(sinc, static_argnames="xp") -NUMPY_GE2 = int(np.__version__.split(".")[0]) >= 2 - - -@pytest.mark.skip_xp_backend( - Backend.SPARSE, reason="read-only backend without .at support" -) class TestApplyWhere: @staticmethod def f1(x: Array, y: Array | int = 10) -> Array: @@ -153,6 +149,14 @@ def test_dont_overwrite_fill_value(self, xp: ModuleType): xp_assert_equal(actual, xp.asarray([100, 12])) xp_assert_equal(fill_value, xp.asarray([100, 200])) + @pytest.mark.skip_xp_backend( + Backend.ARRAY_API_STRICTEST, + reason="no boolean indexing -> run everywhere", + ) + @pytest.mark.skip_xp_backend( + Backend.SPARSE, + reason="no indexing by sparse array -> run everywhere", + ) def test_dont_run_on_false(self, xp: ModuleType): x = xp.asarray([1.0, 2.0, 0.0]) y = xp.asarray([0.0, 3.0, 4.0]) @@ -192,6 +196,7 @@ 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.skip_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 @@ -217,8 +222,8 @@ def test_hypothesis( # type: ignore[explicit-any,decorated-any] library: Backend, ): if ( - library in (Backend.NUMPY, Backend.NUMPY_READONLY) - and not NUMPY_GE2 + library.like(Backend.NUMPY) + and NUMPY_VERSION < (2, 0) and dtype is np.float32 ): pytest.xfail(reason="NumPy 1.x dtype promotion for scalars") @@ -562,6 +567,9 @@ def test_xp(self, xp: ModuleType): assert y.shape == (1, 1, 1, 3) +@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]) @@ -680,6 +688,7 @@ def test_bool_dtype(self, xp: ModuleType): isclose(xp.asarray(True), b, atol=1), xp.asarray([True, True, True]) ) + @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]) b = xp.asarray([1, 4, 2]) @@ -687,6 +696,7 @@ def test_none_shape(self, xp: ModuleType): a = a[a < 5] xp_assert_equal(isclose(a, b), xp.asarray([True, False])) + @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]) b = xp.asarray([True, False, True]) @@ -819,8 +829,27 @@ def test_empty(self, xp: ModuleType): a = xp.asarray([]) xp_assert_equal(nunique(a), xp.asarray(0)) - def test_device(self, xp: ModuleType, device: Device): - a = xp.asarray(0.0, device=device) + def test_size1(self, xp: ModuleType): + a = xp.asarray([123]) + xp_assert_equal(nunique(a), xp.asarray(1)) + + def test_all_equal(self, xp: ModuleType): + a = xp.asarray([123, 123, 123]) + xp_assert_equal(nunique(a), xp.asarray(1)) + + @pytest.mark.xfail_xp_backend(Backend.DASK, reason="No equal_nan kwarg in unique") + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="sparse#855") + def test_nan(self, xp: ModuleType, library: Backend): + if library.like(Backend.NUMPY) and NUMPY_VERSION < (1, 24): + pytest.xfail("NumPy <1.24 has no equal_nan kwarg in unique") + + # Each NaN is counted separately + a = xp.asarray([xp.nan, 123.0, xp.nan]) + xp_assert_equal(nunique(a), xp.asarray(3)) + + @pytest.mark.parametrize("size", [0, 1, 2]) + def test_device(self, xp: ModuleType, device: Device, size: int): + a = xp.asarray([0.0] * size, device=device) assert get_device(nunique(a)) == device def test_xp(self, xp: ModuleType): @@ -895,6 +924,7 @@ def test_sequence_of_tuples_width(self, xp: ModuleType): @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no argsort") +@pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="no unique_values") class TestSetDiff1D: @pytest.mark.xfail_xp_backend(Backend.DASK, reason="NaN-shaped arrays") @pytest.mark.xfail_xp_backend( diff --git a/tests/test_helpers.py b/tests/test_helpers.py index 81b11d1f..c7d271ca 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -10,6 +10,7 @@ from array_api_extra._lib._utils._compat import device as get_device from array_api_extra._lib._utils._helpers import ( asarrays, + capabilities, eager_shape, in1d, meta_namespace, @@ -27,6 +28,7 @@ @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 @pytest.mark.parametrize( @@ -161,7 +163,8 @@ def test_ndindex(shape: tuple[int, ...]): assert tuple(ndindex(*shape)) == tuple(np.ndindex(*shape)) -@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_eager_shape(xp: ModuleType, library: Backend): a = xp.asarray([1, 2, 3]) # Lazy arrays, like Dask, have an eager shape until you slice them with @@ -194,3 +197,10 @@ def test_dask_metas(self, da: ModuleType): def test_xp(self, xp: ModuleType): args = None, xp.asarray(0), 1 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 diff --git a/tests/test_lazy.py b/tests/test_lazy.py index 7057af80..d360e50d 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -1,3 +1,4 @@ +import contextlib from types import ModuleType from typing import cast @@ -214,24 +215,20 @@ def test_lazy_apply_none_shape_in_args(xp: ModuleType, library: Backend): mxp = np if library is Backend.DASK else xp int_type = xp.asarray(0).dtype + ctx: contextlib.AbstractContextManager[object] if library is Backend.JAX: - # Single output - with pytest.raises(ValueError, match="Output shape must be fully known"): - _ = lazy_apply(mxp.unique_values, x, shape=(None,)) - - # Multi output - with pytest.raises(ValueError, match="Output shape must be fully known"): - _ = lazy_apply( - mxp.unique_counts, - x, - shape=((None,), (None,)), - dtype=(x.dtype, int_type), - ) + ctx = pytest.raises(ValueError, match="Output shape must be fully known") + elif library is Backend.ARRAY_API_STRICTEST: + ctx = pytest.raises(RuntimeError, match="data-dependent shapes") else: - # Single output + ctx = contextlib.nullcontext() + + # Single output + with ctx: values = lazy_apply(mxp.unique_values, x, shape=(None,)) xp_assert_equal(values, xp.asarray([1, 2])) + with ctx: # Multi output values, counts = lazy_apply( mxp.unique_counts, @@ -255,8 +252,9 @@ def f(x: Array) -> Array: lazy_xp_function(check_lazy_apply_none_shape_broadcast) -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="bool mask") -@pytest.mark.xfail_xp_backend(Backend.JAX, reason="unknown shape") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="index by sparse array") +@pytest.mark.skip_xp_backend(Backend.JAX, reason="boolean indexing") +@pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="boolean indexing") def test_lazy_apply_none_shape_broadcast(xp: ModuleType): """Broadcast from input array with unknown shape""" x = xp.asarray([1, 2, 2]) diff --git a/tests/test_testing.py b/tests/test_testing.py index 47eaa4dd..10ce7ab3 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -72,7 +72,8 @@ def test_assert_close_tolerance(xp: ModuleType): @param_assert_equal_close -@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_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. @@ -222,7 +223,7 @@ def test_lazy_xp_function_cython_ufuncs(xp: ModuleType, library: Backend): pytest.importorskip("scipy") assert erf is not None x = xp.asarray([6.0, 7.0]) - if library in (Backend.ARRAY_API_STRICT, Backend.JAX): + if library.like(Backend.ARRAY_API_STRICT, Backend.JAX): # array-api-strict arrays are auto-converted to NumPy # which results in an assertion error for mismatched namespaces # eager JAX arrays are auto-converted to NumPy in eager JAX From c4a3df67933173fdf45e2fac0e320022ee08d9a9 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Sun, 30 Mar 2025 11:25:47 +0100 Subject: [PATCH 024/131] REL: implement SPEC 8 (#166) * CI: use hashes for actions * CI: restrict permissions * DOC: add SPEC 8 badge * lint --- .github/workflows/cd.yml | 13 ++++++++----- .github/workflows/ci.yml | 17 ++++++++++------- .github/workflows/dependabot-auto-merge.yml | 2 +- .github/workflows/docs-build.yml | 7 +++++-- .github/workflows/docs-deploy.yml | 9 ++++++--- README.md | 1 + 6 files changed, 31 insertions(+), 18 deletions(-) diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 3c045cbe..1fc044c8 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -1,5 +1,8 @@ name: CD +permissions: + contents: read + on: workflow_dispatch: pull_request: @@ -14,11 +17,11 @@ jobs: dist: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 with: fetch-depth: 0 - - uses: hynek/build-and-inspect-python-package@v2 + - uses: hynek/build-and-inspect-python-package@b5076c307dc91924a82ad150cdd1533b444d3310 # v2.12.0 publish: needs: [dist] @@ -31,14 +34,14 @@ jobs: if: github.event_name == 'release' && github.event.action == 'published' steps: - - uses: actions/download-artifact@v4 + - uses: actions/download-artifact@b14cf4c92620c250e1c074ab0a5800e37df86765 # v4.2.0 with: name: Packages path: dist - name: Generate artifact attestation for sdist and wheel - uses: actions/attest-build-provenance@v2.2.3 + uses: actions/attest-build-provenance@c074443f1aee8d4aeeae555aebba3282517141b2 # v2.2.3 with: subject-path: "dist/*" - - uses: pypa/gh-action-pypi-publish@release/v1 + - uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc # v1.12.4 diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index de8250cd..96b16c28 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -1,5 +1,8 @@ name: CI +permissions: + contents: read + on: workflow_dispatch: pull_request: @@ -21,16 +24,16 @@ jobs: name: Format runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 with: fetch-depth: 0 - - uses: actions/setup-python@v5 + - uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0 with: python-version: "3.x" - - uses: pre-commit/action@v3.0.1 + - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 with: extra_args: --hook-stage manual --all-files - - uses: prefix-dev/setup-pixi@v0.8.3 + - uses: prefix-dev/setup-pixi@92815284c57faa15cd896c4d5cfb2d59f32dc43d # v0.8.3 with: pixi-version: v0.42.1 cache: true @@ -52,11 +55,11 @@ jobs: runs-on: [ubuntu-latest] steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 with: fetch-depth: 0 - - uses: prefix-dev/setup-pixi@v0.8.3 + - uses: prefix-dev/setup-pixi@92815284c57faa15cd896c4d5cfb2d59f32dc43d # v0.8.3 with: pixi-version: v0.42.1 cache: true @@ -66,6 +69,6 @@ jobs: run: pixi run -e ${{ matrix.environment }} tests-ci - name: Upload coverage report - uses: codecov/codecov-action@v5.4.0 + uses: codecov/codecov-action@0565863a31f2c772f9f0395002a31e3f06189574 # v5.4.0 with: token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/dependabot-auto-merge.yml b/.github/workflows/dependabot-auto-merge.yml index bd29e25b..d6ac394d 100644 --- a/.github/workflows/dependabot-auto-merge.yml +++ b/.github/workflows/dependabot-auto-merge.yml @@ -13,7 +13,7 @@ jobs: steps: - name: Dependabot metadata id: metadata - uses: dependabot/fetch-metadata@v2 + uses: dependabot/fetch-metadata@d7267f607e9d3fb96fc2fbe83e0af444713e90b7 # v2.3.0 with: github-token: "${{ secrets.GITHUB_TOKEN }}" - name: Enable auto-merge for Dependabot PRs diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index c850c851..1637878d 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -1,12 +1,15 @@ name: Docs Build +permissions: + contents: read + on: [push, pull_request] jobs: docs-build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 - uses: prefix-dev/setup-pixi@v0.8.3 with: pixi-version: v0.42.1 @@ -15,7 +18,7 @@ jobs: - name: Build Docs run: pixi run -e docs docs - name: Upload Artifact - uses: actions/upload-artifact@v4 + uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4.6.1 with: name: docs-build path: docs/build/ diff --git a/.github/workflows/docs-deploy.yml b/.github/workflows/docs-deploy.yml index a7a8cb1c..3f7e6ed0 100644 --- a/.github/workflows/docs-deploy.yml +++ b/.github/workflows/docs-deploy.yml @@ -1,5 +1,8 @@ name: Docs Deploy +permissions: + contents: read + on: workflow_run: workflows: ["Docs Build"] @@ -14,9 +17,9 @@ jobs: environment: name: docs-deploy steps: - - uses: actions/checkout@v4 + - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 - name: Download Artifact - uses: dawidd6/action-download-artifact@v9 + uses: dawidd6/action-download-artifact@07ab29fd4a977ae4d2b275087cf67563dfdf0295 # v9 with: workflow: docs-build.yml name: docs-build @@ -26,7 +29,7 @@ jobs: # See # https://github.com/JamesIves/github-pages-deploy-action/tree/dev#using-an-ssh-deploy-key- - name: Deploy - uses: JamesIves/github-pages-deploy-action@v4 + uses: JamesIves/github-pages-deploy-action@6c2d9db40f9296374acc17b90404b6e8864128c8 # v4.7.3 with: folder: docs/build/ ssh-key: ${{ secrets.DEPLOY_KEY }} diff --git a/README.md b/README.md index ab42dfa0..739fdc5f 100644 --- a/README.md +++ b/README.md @@ -11,6 +11,7 @@ [![Conda-Forge][conda-badge]][conda-link] [![PyPI platforms][pypi-platforms]][pypi-link] [![EffVer Versioning](https://img.shields.io/badge/version_scheme-EffVer-0097a7)](https://jacobtomlinson.dev/effver) +[![SPEC 0 — Minimum Supported Dependencies](https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/spec-0000/) From e4281ef91a4fed0fb86dd1a265921270d06772c3 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Sun, 30 Mar 2025 11:31:18 +0100 Subject: [PATCH 025/131] DOC: fix SPEC 0 -> 8 (#191) --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 739fdc5f..9220d693 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ [![Conda-Forge][conda-badge]][conda-link] [![PyPI platforms][pypi-platforms]][pypi-link] [![EffVer Versioning](https://img.shields.io/badge/version_scheme-EffVer-0097a7)](https://jacobtomlinson.dev/effver) -[![SPEC 0 — Minimum Supported Dependencies](https://img.shields.io/badge/SPEC-0-green?labelColor=%23004811&color=%235CA038)](https://scientific-python.org/specs/spec-0000/) +[![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/) From 66e9282df165df219797f65f1cc061665fe7e95f Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 31 Mar 2025 10:17:15 +0100 Subject: [PATCH 026/131] Bump the actions group with 3 updates (#192) Bumps the actions group with 3 updates: [actions/download-artifact](https://github.com/actions/download-artifact), [actions/setup-python](https://github.com/actions/setup-python) and [actions/upload-artifact](https://github.com/actions/upload-artifact). Updates `actions/download-artifact` from 4.2.0 to 4.2.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/b14cf4c92620c250e1c074ab0a5800e37df86765...95815c38cf2ff2164869cbab79da8d1f422bc89e) Updates `actions/setup-python` from 5.4.0 to 5.5.0 - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](https://github.com/actions/setup-python/compare/42375524e23c412d93fb67b49958b491fce71c38...8d9ed9ac5c53483de85588cdf95a591a75ab9f55) Updates `actions/upload-artifact` from 4.6.1 to 4.6.2 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1...ea165f8d65b6e75b540449e92b4886f43607fa02) --- updated-dependencies: - dependency-name: actions/download-artifact dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/setup-python dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/cd.yml | 2 +- .github/workflows/ci.yml | 2 +- .github/workflows/docs-build.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 1fc044c8..13411752 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -34,7 +34,7 @@ jobs: if: github.event_name == 'release' && github.event.action == 'published' steps: - - uses: actions/download-artifact@b14cf4c92620c250e1c074ab0a5800e37df86765 # v4.2.0 + - uses: actions/download-artifact@95815c38cf2ff2164869cbab79da8d1f422bc89e # v4.2.1 with: name: Packages path: dist diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 96b16c28..be483847 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -27,7 +27,7 @@ jobs: - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2 with: fetch-depth: 0 - - uses: actions/setup-python@42375524e23c412d93fb67b49958b491fce71c38 # v5.4.0 + - uses: actions/setup-python@8d9ed9ac5c53483de85588cdf95a591a75ab9f55 # v5.5.0 with: python-version: "3.x" - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index 1637878d..1a74d2e8 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -18,7 +18,7 @@ jobs: - name: Build Docs run: pixi run -e docs docs - name: Upload Artifact - uses: actions/upload-artifact@4cec3d8aa04e39d1a68397de0c4cd6fb9dce8ec1 # v4.6.1 + uses: actions/upload-artifact@ea165f8d65b6e75b540449e92b4886f43607fa02 # v4.6.2 with: name: docs-build path: docs/build/ From 582176ff753726436c44d78ad0cbc6f5b8ac233e Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sun, 6 Apr 2025 12:22:40 +0100 Subject: [PATCH 027/131] DEV: Configure Renovate (#198) * Add renovate.json * lint --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Lucas Colley --- renovate.json | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 renovate.json diff --git a/renovate.json b/renovate.json new file mode 100644 index 00000000..22a99432 --- /dev/null +++ b/renovate.json @@ -0,0 +1,4 @@ +{ + "$schema": "https://docs.renovatebot.com/renovate-schema.json", + "extends": ["config:recommended"] +} From bb854b4c6f79a981819cf90f1161df24690d8443 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sun, 6 Apr 2025 12:29:19 +0100 Subject: [PATCH 028/131] Update prefix-dev/setup-pixi action to v0.8.4 (#199) * Update prefix-dev/setup-pixi action to v0.8.4 * use full hash everywhere --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Lucas Colley --- .github/workflows/ci.yml | 4 ++-- .github/workflows/docs-build.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index be483847..22b71c35 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,7 +33,7 @@ jobs: - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 with: extra_args: --hook-stage manual --all-files - - uses: prefix-dev/setup-pixi@92815284c57faa15cd896c4d5cfb2d59f32dc43d # v0.8.3 + - uses: prefix-dev/setup-pixi@8eaba7c61d661f73d558b0b477156b7b62667fa4 # v0.8.4 with: pixi-version: v0.42.1 cache: true @@ -59,7 +59,7 @@ jobs: with: fetch-depth: 0 - - uses: prefix-dev/setup-pixi@92815284c57faa15cd896c4d5cfb2d59f32dc43d # v0.8.3 + - uses: prefix-dev/setup-pixi@8eaba7c61d661f73d558b0b477156b7b62667fa4 # v0.8.4 with: pixi-version: v0.42.1 cache: true diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index 1a74d2e8..6cdb2327 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@v0.8.3 + - uses: prefix-dev/setup-pixi@8eaba7c61d661f73d558b0b477156b7b62667fa4 # v0.8.4 with: pixi-version: v0.42.1 cache: true From 9f25be56560e1a49416f1ae6a7e1d536254ac741 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Sun, 6 Apr 2025 12:56:29 +0100 Subject: [PATCH 029/131] DEV: remove dependabot (#201) --- .github/dependabot.yml | 11 ---------- .github/workflows/dependabot-auto-merge.yml | 23 --------------------- .pre-commit-config.yaml | 1 - 3 files changed, 35 deletions(-) delete mode 100644 .github/dependabot.yml delete mode 100644 .github/workflows/dependabot-auto-merge.yml diff --git a/.github/dependabot.yml b/.github/dependabot.yml deleted file mode 100644 index 6c4b3695..00000000 --- a/.github/dependabot.yml +++ /dev/null @@ -1,11 +0,0 @@ -version: 2 -updates: - # Maintain dependencies for GitHub Actions - - package-ecosystem: "github-actions" - directory: "/" - schedule: - interval: "weekly" - groups: - actions: - patterns: - - "*" diff --git a/.github/workflows/dependabot-auto-merge.yml b/.github/workflows/dependabot-auto-merge.yml deleted file mode 100644 index d6ac394d..00000000 --- a/.github/workflows/dependabot-auto-merge.yml +++ /dev/null @@ -1,23 +0,0 @@ -# https://docs.github.com/en/code-security/dependabot/working-with-dependabot/automating-dependabot-with-github-actions#approve-a-pull-request -name: Dependabot auto-merge -on: pull_request - -permissions: - contents: write - pull-requests: write - -jobs: - dependabot: - runs-on: ubuntu-latest - if: github.actor == 'dependabot[bot]' - steps: - - name: Dependabot metadata - id: metadata - uses: dependabot/fetch-metadata@d7267f607e9d3fb96fc2fbe83e0af444713e90b7 # v2.3.0 - with: - github-token: "${{ secrets.GITHUB_TOKEN }}" - - name: Enable auto-merge for Dependabot PRs - run: gh pr merge --auto --merge "$PR_URL" - env: - PR_URL: ${{github.event.pull_request.html_url}} - GH_TOKEN: ${{secrets.GITHUB_TOKEN}} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 655be69a..7be7a1ca 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -76,7 +76,6 @@ repos: - repo: https://github.com/python-jsonschema/check-jsonschema rev: "0.30.0" hooks: - - id: check-dependabot - id: check-github-workflows - repo: https://github.com/numpy/numpydoc From 46301610d3c3c8a4ae0d3d4a4e3b6e84762ed2fa Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Sun, 6 Apr 2025 13:01:21 +0100 Subject: [PATCH 030/131] DEV: set dependency dashboard title (#203) --- renovate.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/renovate.json b/renovate.json index 22a99432..3e01b486 100644 --- a/renovate.json +++ b/renovate.json @@ -1,4 +1,5 @@ { "$schema": "https://docs.renovatebot.com/renovate-schema.json", - "extends": ["config:recommended"] + "extends": ["config:recommended"], + "dependencyDashboardTitle": "META: Dependency Dashboard" } From f87ec1f9927fa5f29fb1dfd5a4cf767bdd5029ae Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 13:48:52 +0100 Subject: [PATCH 031/131] Update prefix-dev/setup-pixi action to v0.8.5 (#204) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/ci.yml | 4 ++-- .github/workflows/docs-build.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 22b71c35..edcbc0eb 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -33,7 +33,7 @@ jobs: - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 with: extra_args: --hook-stage manual --all-files - - uses: prefix-dev/setup-pixi@8eaba7c61d661f73d558b0b477156b7b62667fa4 # v0.8.4 + - uses: prefix-dev/setup-pixi@dbaed5efa0bd33d6bd6d162bec8a06d8fc43c807 # v0.8.5 with: pixi-version: v0.42.1 cache: true @@ -59,7 +59,7 @@ jobs: with: fetch-depth: 0 - 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pypi: . osx-64: - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.11.2-pyh29332c3_0.conda @@ -4244,7 +4244,7 @@ environments: - conda: https://prefix.dev/conda-forge/osx-64/zlib-1.3.1-hd23fc13_2.conda - conda: https://prefix.dev/conda-forge/osx-64/zstandard-0.23.0-py310hbb8c376_1.conda - conda: https://prefix.dev/conda-forge/osx-64/zstd-1.5.7-h8210216_2.conda - - pypi: https://files.pythonhosted.org/packages/2f/ff/dededd0b4492b796a22aa3606a38b2427360107e3a95f1f2cda63ba10445/sparse-0.16.0b4-py2.py3-none-any.whl + - pypi: https://files.pythonhosted.org/packages/ca/4a/e59e0968ad52460bb997221fdf5a77d1385b0258f37bfbc84675977b0a62/sparse-0.16.0-py2.py3-none-any.whl - pypi: . osx-arm64: - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.11.2-pyh29332c3_0.conda @@ -4425,7 +4425,7 @@ environments: - conda: https://prefix.dev/conda-forge/osx-arm64/zlib-1.3.1-h8359307_2.conda - conda: https://prefix.dev/conda-forge/osx-arm64/zstandard-0.23.0-py310h078409c_1.conda - 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pypi: . tests-numpy1: channels: @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 676a791c66366ceb58f64f5bff8010d4f3c1077846f7b9c411883b46eb55fd38 + sha256: 3576781bec620c950ae16518c5695b9d79ef1c385f18d2e9d0afc8fbe838ef3b requires_dist: - array-api-compat>=1.11,<2 requires_python: '>=3.10' @@ -15243,10 +15243,10 @@ packages: - pkg:pypi/soupsieve?source=hash-mapping size: 36754 timestamp: 1693929424267 -- pypi: https://files.pythonhosted.org/packages/2f/ff/dededd0b4492b796a22aa3606a38b2427360107e3a95f1f2cda63ba10445/sparse-0.16.0b4-py2.py3-none-any.whl +- pypi: https://files.pythonhosted.org/packages/ca/4a/e59e0968ad52460bb997221fdf5a77d1385b0258f37bfbc84675977b0a62/sparse-0.16.0-py2.py3-none-any.whl name: sparse - version: 0.16.0b4 - sha256: ede7c659fa269845243c5231c8498de0a17d03040a63f6e21c020bad48de5248 + version: 0.16.0 + sha256: 25d4463cf36315ee16a19b6951f1d6b8e9128a07dafd58f846eb6dfb4cd5b9d8 requires_dist: - numpy>=1.17 - numba>=0.49 @@ -15275,7 +15275,7 @@ packages: - matplotlib ; extra == 'notebooks' - sparse[docs,mlir,notebooks,tox] ; extra == 'all' - matrepr ; extra == 'all' - - finch-tensor>=0.2.9 ; extra == 'finch' + - finch-tensor>=0.2.10 ; extra == 'finch' - finch-mlir>=0.0.2 ; extra == 'mlir' requires_python: '>=3.10' - conda: https://prefix.dev/conda-forge/noarch/sphinx-8.1.3-pyhd8ed1ab_1.conda diff --git a/pyproject.toml b/pyproject.toml index 0aabf345..71a97122 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -140,7 +140,7 @@ numba = "*" # sparse dependency llvmlite = "*" # sparse dependency [tool.pixi.feature.backends.pypi-dependencies] -sparse = { version = ">= 0.16.0b3" } +sparse = { version = ">=0.16.0" } [tool.pixi.feature.backends.target.linux-64.dependencies] jax = "*" From 52d12371d5857b63af3353dd91d25aa4fd23677b Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 16:16:37 +0100 Subject: [PATCH 035/131] Update dependency basedmypy to >=2.10.0 (#215) 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 56d8c13a..72d74d69 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 3576781bec620c950ae16518c5695b9d79ef1c385f18d2e9d0afc8fbe838ef3b + sha256: 0a4bc34e8dd37b621bf159e2ced23c938dabdd5deac52a5e79656cbb28e7c302 requires_dist: - array-api-compat>=1.11,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 71a97122..fc1c5f1a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -57,7 +57,7 @@ array-api-extra = { path = ".", editable = true } typing-extensions = "*" pre-commit = "*" pylint = "*" -basedmypy = "*" +basedmypy = ">=2.10.0" basedpyright = "*" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: From 1501bf336a904089672dce2bf10ef1ef22fe46fd Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 16:24:45 +0100 Subject: [PATCH 036/131] Update dependency array-api-compat to >=1.11.2,<2 (#212) --- pixi.lock | 4 ++-- pyproject.toml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pixi.lock b/pixi.lock index 72d74d69..b15108f5 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,9 +5232,9 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 0a4bc34e8dd37b621bf159e2ced23c938dabdd5deac52a5e79656cbb28e7c302 + sha256: 671006024258074a30f40b61e94dadf3280234c2645ee4d0791fdcf445d919a8 requires_dist: - - array-api-compat>=1.11,<2 + - array-api-compat>=1.11.2,<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 fc1c5f1a..19d496ee 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,7 +26,7 @@ classifiers = [ "Typing :: Typed", ] dynamic = ["version"] -dependencies = ["array-api-compat>=1.11,<2"] +dependencies = ["array-api-compat>=1.11.2,<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" +array-api-compat = ">=1.11.2,<2" [tool.pixi.pypi-dependencies] array-api-extra = { path = ".", editable = true } From 77b2b28469977a39c9761f7ca922127c44e220a1 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 16:33:25 +0100 Subject: [PATCH 037/131] Update dependency array-api-strict to >=1.1.1 (#214) 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 b15108f5..b886982c 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 671006024258074a30f40b61e94dadf3280234c2645ee4d0791fdcf445d919a8 + sha256: be7523c2bc2519d23eb7e92abc0466bbb70d37728f0b677e5acfd67350a2e212 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 19d496ee..507f38c9 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,7 +61,7 @@ basedmypy = ">=2.10.0" basedpyright = "*" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: -array-api-strict = "*" +array-api-strict = ">=1.1.1" numpy = "*" pytest = "*" hypothesis = "*" @@ -81,7 +81,7 @@ lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"] } pytest = ">=6" pytest-cov = ">=3" hypothesis = "*" -array-api-strict = "*" +array-api-strict = ">=1.1.1" numpy = "*" [tool.pixi.feature.tests.tasks] From 03c8e60c09cacaf940ad489d34328249d6dd17af Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 18:02:39 +0100 Subject: [PATCH 038/131] Update dependency cupy to v13 (#219) 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 b886982c..3c3dcf62 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: be7523c2bc2519d23eb7e92abc0466bbb70d37728f0b677e5acfd67350a2e212 + sha256: 7726fff031ff7d628043f99194e7ad89c7ac6fa8fea838fbec4a4a1e0dfc5028 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 507f38c9..3e7fa7ed 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -164,7 +164,7 @@ jax = "*" system-requirements = { cuda = "12" } [tool.pixi.feature.cuda-backends.target.linux-64.dependencies] -cupy = "*" +cupy = ">=13.4.1" jaxlib = { version = "*", build = "cuda12*" } pytorch = { version = "*", build = "cuda12*" } @@ -179,7 +179,7 @@ pytorch = { version = "*", build = "cuda12*" } # pytorch = { version = "*", build = "cuda12*" } # unavailable [tool.pixi.feature.cuda-backends.target.win-64.dependencies] -cupy = "*" +cupy = ">=13.4.1" # jaxlib = { version = "*", build = "cuda12*" } # unavailable pytorch = { version = "*", build = "cuda12*" } From 767f429465ce609cec2e21ed5048d506c7811901 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 18:11:47 +0100 Subject: [PATCH 039/131] Update dependency dask to v2025 (#220) 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 3c3dcf62..5cbdcf92 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 7726fff031ff7d628043f99194e7ad89c7ac6fa8fea838fbec4a4a1e0dfc5028 + sha256: e8180ee635cf120975d7c32dcd09946df033b53de129d9f4f01ce7dd6ca83f5d requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 3e7fa7ed..1a43092f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -135,7 +135,7 @@ numpy = "=1.22.0" # Note: JAX and PyTorch will install CPU variants. [tool.pixi.feature.backends.dependencies] pytorch = "*" -dask = "*" +dask = ">=2025.3.0" numba = "*" # sparse dependency llvmlite = "*" # sparse dependency From 4bb063b63dc672569f5646440ff11f8ec423e9f0 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 18:19:30 +0100 Subject: [PATCH 040/131] Update dependency array-api-strict to v2 (#218) 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 5cbdcf92..dd8482ed 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: e8180ee635cf120975d7c32dcd09946df033b53de129d9f4f01ce7dd6ca83f5d + sha256: 5903d9459bdb738a19a239b5a816a18a374e7f5d00b1f493c1d436f60f9fc0cf requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 1a43092f..1ee87cc5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -61,7 +61,7 @@ basedmypy = ">=2.10.0" basedpyright = "*" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: -array-api-strict = ">=1.1.1" +array-api-strict = ">=2.3.1" numpy = "*" pytest = "*" hypothesis = "*" @@ -81,7 +81,7 @@ lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"] } pytest = ">=6" pytest-cov = ">=3" hypothesis = "*" -array-api-strict = ">=1.1.1" +array-api-strict = ">=2.3.1" numpy = "*" [tool.pixi.feature.tests.tasks] From 3f3a5d4296d8bae479d4882221f886fcb3d5d79d Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 18:30:24 +0100 Subject: [PATCH 041/131] Update dependency dask-core to v2025 (#225) 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 dd8482ed..cf752631 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 5903d9459bdb738a19a239b5a816a18a374e7f5d00b1f493c1d436f60f9fc0cf + sha256: e080746bb84b4917e2dac5c8bb100673d0472c2ce6a4a6636c0d2bb3a1a8a1d1 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 1ee87cc5..3750cf13 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -65,7 +65,7 @@ array-api-strict = ">=2.3.1" numpy = "*" pytest = "*" hypothesis = "*" -dask-core = "*" # No distributed, tornado, etc. +dask-core = ">=2025.3.0" # 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 = ">=0.13" sphinx-copybutton = "*" sphinx-autodoc-typehints = "*" # Needed to import parsed modules with autodoc -dask-core = "*" +dask-core = ">=2025.3.0" pytest = "*" typing-extensions = "*" numpy = "*" From 9ae2d5c3cbb131d11c2df55926ec8df16260c275 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 18:36:36 +0100 Subject: [PATCH 042/131] Update dependency basedpyright to >=1.28.3 (#216) 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 cf752631..feff109f 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: e080746bb84b4917e2dac5c8bb100673d0472c2ce6a4a6636c0d2bb3a1a8a1d1 + sha256: 94aa031e277458721e30ccb00f7305fe83fdd61174c88c588d98f663353aed6f requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 3750cf13..41eae83a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ typing-extensions = "*" pre-commit = "*" pylint = "*" basedmypy = ">=2.10.0" -basedpyright = "*" +basedpyright = ">=1.28.3" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1" From 0c79d3e13652c4d0b51de7ad570f2c34b81f940f Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 18:55:57 +0100 Subject: [PATCH 043/131] Update dependency pytest to v8 (#226) 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 feff109f..df9f33ba 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 94aa031e277458721e30ccb00f7305fe83fdd61174c88c588d98f663353aed6f + sha256: 9af8c361fe340a365eae218d62bcef9b9bb1df07486b9612a37ba67aea1a8aee requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 41eae83a..88be4ad3 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 = "*" -pytest = "*" +pytest = ">=8.3.5" hypothesis = "*" dask-core = ">=2025.3.0" # No distributed, tornado, etc. # NOTE: don't add jax, pytorch, sparse, cupy here @@ -78,7 +78,7 @@ pyright = "basedpyright" lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"] } [tool.pixi.feature.tests.dependencies] -pytest = ">=6" +pytest = ">=8.3.5" pytest-cov = ">=3" hypothesis = "*" array-api-strict = ">=2.3.1" @@ -106,7 +106,7 @@ sphinx-copybutton = "*" sphinx-autodoc-typehints = "*" # Needed to import parsed modules with autodoc dask-core = ">=2025.3.0" -pytest = "*" +pytest = ">=8.3.5" typing-extensions = "*" numpy = "*" From d2fcd5a2a91af48c8319a65d7e09023c90bf96ca Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 18:59:17 +0100 Subject: [PATCH 044/131] Update dependency furo to v2024 (#227) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- docs/requirements.txt | 2 +- pixi.lock | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 77237968..2b8ce60d 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,4 +1,4 @@ -furo>=2023.08.17 +furo>=2024.8.6 myst_parser>=0.13 sphinx>=7.0 sphinx_autodoc_typehints diff --git a/pixi.lock b/pixi.lock index df9f33ba..dc4cc3c4 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 9af8c361fe340a365eae218d62bcef9b9bb1df07486b9612a37ba67aea1a8aee + sha256: a4d40ff8215cfef283dcc9bbf73d23703b0cb47c3916f6d60eabef225b0d6add requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 88be4ad3..c49db8fc 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -100,7 +100,7 @@ open-coverage = { cmd = "open htmlcov/index.html", depends-on = ["coverage"] } [tool.pixi.feature.docs.dependencies] sphinx = ">=7.0" -furo = ">=2023.08.17" +furo = ">=2024.8.6" myst-parser = ">=0.13" sphinx-copybutton = "*" sphinx-autodoc-typehints = "*" From b3e14fdaa9d77f98c79bc2dfcbb1b287f6c8c882 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 8 Apr 2025 19:07:33 +0100 Subject: [PATCH 045/131] DEV: set some temporary renovate groups (#228) --- renovate.json | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/renovate.json b/renovate.json index 32b78c39..313bff7a 100644 --- a/renovate.json +++ b/renovate.json @@ -8,6 +8,20 @@ "matchManagers": ["pixi"], "matchCurrentValue": "/^~?=/", "enabled": false + }, + { + "matchPackageNames": [ + "/myst-parser|myst_parser|sphinx|sphinx-autodoc-typehints|sphinx-copybutton/" + ], + "groupName": "docs" + }, + { + "matchPackageNames": ["/pylint|pre-commit|typing-extensions/"], + "groupName": "lint" + }, + { + "matchPackageNames": ["/pytest-cov|hypothesis|ipython|jax|pytorch/"], + "groupName": "tests" } ] } From 8ed3e43b2c851390c6b3934e75429015157d73dc Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 19:12:04 +0100 Subject: [PATCH 046/131] Update dependency llvmlite to >=0.44.0 (#229) 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 dc4cc3c4..7527d846 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: a4d40ff8215cfef283dcc9bbf73d23703b0cb47c3916f6d60eabef225b0d6add + sha256: c3afa72d55dabb18f42583be70bf352f35d84b471fe8733b98cb7701fb5ee768 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index c49db8fc..5109ce09 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -137,7 +137,7 @@ numpy = "=1.22.0" pytorch = "*" dask = ">=2025.3.0" numba = "*" # sparse dependency -llvmlite = "*" # sparse dependency +llvmlite = ">=0.44.0" # sparse dependency [tool.pixi.feature.backends.pypi-dependencies] sparse = { version = ">=0.16.0" } From b9482e08221bd17c172fc24aa7e0c7f52381326d Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 19:20:46 +0100 Subject: [PATCH 047/131] Update dependency numba to >=0.61.0 (#230) --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 7527d846..477b2533 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: c3afa72d55dabb18f42583be70bf352f35d84b471fe8733b98cb7701fb5ee768 + sha256: bab05d6092e374ace29c91044b6e29949ba239e4d65a835bea6192da6632650c requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 5109ce09..4f7c805c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -136,7 +136,7 @@ numpy = "=1.22.0" [tool.pixi.feature.backends.dependencies] pytorch = "*" dask = ">=2025.3.0" -numba = "*" # sparse dependency +numba = ">=0.61.0" # sparse dependency llvmlite = ">=0.44.0" # sparse dependency [tool.pixi.feature.backends.pypi-dependencies] From 91788288c166ed5b2fc3c57d66a9f1c36e0b4b9a Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 19:34:07 +0100 Subject: [PATCH 048/131] Update lint (#232) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 158 ++++++++++++++++++++++++------------------------- pyproject.toml | 8 +-- 2 files changed, 83 insertions(+), 83 deletions(-) diff --git a/pixi.lock b/pixi.lock index 477b2533..689733d8 100644 --- a/pixi.lock +++ b/pixi.lock @@ -285,7 +285,7 @@ environments: - 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sha256: 337be7af5af8b2817f115b3b68870208b30c31d3439bec07bfb2d8f4823e3568 - md5: d17f13df8b65464ca316cbc000a3cb64 + size: 89685 + timestamp: 1743820059977 +- conda: https://prefix.dev/conda-forge/noarch/typing_extensions-4.13.1-pyh29332c3_0.conda + sha256: 78a5efbf86eca68b5f9e58f0dc7e56dcfa96d1dcba5c7f5f37d2c0444de22085 + md5: 5710c79a5fb0a6bfdba0a887f90583b1 depends: - python >=3.9 + - python license: PSF-2.0 license_family: PSF purls: - - pkg:pypi/typing-extensions?source=hash-mapping - size: 39637 - timestamp: 1733188758212 + - pkg:pypi/typing-extensions?source=compressed-mapping + size: 52170 + timestamp: 1743820059977 - 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 4f7c805c..6d3e9f7f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,9 +54,9 @@ array-api-compat = ">=1.11.2,<2" array-api-extra = { path = ".", editable = true } [tool.pixi.feature.lint.dependencies] -typing-extensions = "*" -pre-commit = "*" -pylint = "*" +typing-extensions = ">=4.13.1" +pre-commit = ">=4.2.0" +pylint = ">=3.3.6" basedmypy = ">=2.10.0" basedpyright = ">=1.28.3" numpydoc = ">=1.8.0,<2" @@ -107,7 +107,7 @@ sphinx-autodoc-typehints = "*" # Needed to import parsed modules with autodoc dask-core = ">=2025.3.0" pytest = ">=8.3.5" -typing-extensions = "*" +typing-extensions = ">=4.13.1" numpy = "*" [tool.pixi.feature.docs.tasks] From 1ed40f479846d9b07be92ed1bb5fb3890fe3c68f Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 20:23:28 +0100 Subject: [PATCH 049/131] Update dependency numpy to >=1.26.4 (#233) * Update dependency numpy to >=1.26.4 * Update pyproject.toml * update lock file --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Lucas Colley --- pixi.lock | 2 +- pyproject.toml | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/pixi.lock b/pixi.lock index 689733d8..46f046e7 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 4d7c16b9e1c87048a679ebcb0e72b07624bc8633caa5c221fb87ecbb47c57ec8 + sha256: ac4ddf62fc1119c489439a90bb7cdd847926d5462cf7cffaaf2f9bcd8a2ef831 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 6d3e9f7f..a542faf8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -62,7 +62,7 @@ basedpyright = ">=1.28.3" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1" -numpy = "*" +numpy = ">=1.26.4" pytest = ">=8.3.5" hypothesis = "*" dask-core = ">=2025.3.0" # No distributed, tornado, etc. @@ -82,7 +82,7 @@ pytest = ">=8.3.5" pytest-cov = ">=3" hypothesis = "*" array-api-strict = ">=2.3.1" -numpy = "*" +numpy = ">=1.22.0" [tool.pixi.feature.tests.tasks] tests = "pytest -v" @@ -108,7 +108,7 @@ sphinx-autodoc-typehints = "*" dask-core = ">=2025.3.0" pytest = ">=8.3.5" typing-extensions = ">=4.13.1" -numpy = "*" +numpy = ">=1.26.4" [tool.pixi.feature.docs.tasks] docs = { cmd = "sphinx-build -E -W . build/", cwd = "docs" } From 90352ab62f7c52c24c2a9a12969602e898c02f93 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 20:27:56 +0100 Subject: [PATCH 050/131] Update dependency python to v3.13.2 (#234) * Update dependency python to v3.13.2 * Update pyproject.toml --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Lucas Colley --- .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 edcbc0eb..d030beff 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -29,7 +29,7 @@ jobs: fetch-depth: 0 - uses: actions/setup-python@8d9ed9ac5c53483de85588cdf95a591a75ab9f55 # v5.5.0 with: - python-version: "3.x" + python-version: "3.13.2" - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 with: extra_args: --hook-stage manual --all-files From fb49408fd4fe3c19eb6e51f5660480d2d2e1ce09 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 20:41:27 +0100 Subject: [PATCH 051/131] Update tests (#235) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 2 +- pyproject.toml | 18 +++++++++--------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/pixi.lock b/pixi.lock index 46f046e7..5ba1b013 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: ac4ddf62fc1119c489439a90bb7cdd847926d5462cf7cffaaf2f9bcd8a2ef831 + sha256: 9caaf6a80751c89c1693ce901b4d31202552ea7af0cd3f37564d406d6565c051 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index a542faf8..1e93cbe4 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,7 +64,7 @@ numpydoc = ">=1.8.0,<2" array-api-strict = ">=2.3.1" numpy = ">=1.26.4" pytest = ">=8.3.5" -hypothesis = "*" +hypothesis = ">=3.88.3" dask-core = ">=2025.3.0" # 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 @@ -80,7 +80,7 @@ lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"] } [tool.pixi.feature.tests.dependencies] pytest = ">=8.3.5" pytest-cov = ">=3" -hypothesis = "*" +hypothesis = ">=3.88.3" array-api-strict = ">=2.3.1" numpy = ">=1.22.0" @@ -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 = "*" +pytorch = ">=1.13.1" dask = ">=2025.3.0" numba = ">=0.61.0" # sparse dependency llvmlite = ">=0.44.0" # sparse dependency @@ -143,13 +143,13 @@ llvmlite = ">=0.44.0" # sparse dependency sparse = { version = ">=0.16.0" } [tool.pixi.feature.backends.target.linux-64.dependencies] -jax = "*" +jax = ">=0.5.2" [tool.pixi.feature.backends.target.osx-64.dependencies] -jax = "*" +jax = ">=0.5.2" [tool.pixi.feature.backends.target.osx-arm64.dependencies] -jax = "*" +jax = ">=0.5.2" [tool.pixi.feature.backends.target.win-64.dependencies] # jax = "*" # unavailable @@ -165,8 +165,8 @@ system-requirements = { cuda = "12" } [tool.pixi.feature.cuda-backends.target.linux-64.dependencies] cupy = ">=13.4.1" -jaxlib = { version = "*", build = "cuda12*" } -pytorch = { version = "*", build = "cuda12*" } +jaxlib = { version = ">=0.5.2", build = "cuda12*" } +pytorch = { version = ">=1.13.1", build = "cuda12*" } [tool.pixi.feature.cuda-backends.target.osx-64.dependencies] # cupy = "*" # unavailable @@ -181,7 +181,7 @@ pytorch = { version = "*", build = "cuda12*" } [tool.pixi.feature.cuda-backends.target.win-64.dependencies] cupy = ">=13.4.1" # jaxlib = { version = "*", build = "cuda12*" } # unavailable -pytorch = { version = "*", build = "cuda12*" } +pytorch = { version = ">=1.13.1", build = "cuda12*" } [tool.pixi.environments] default = { features = ["py313"], solve-group = "py313" } From d3801e74e34b1b981f6c8552b165bc1ca2e0780d Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 20:55:39 +0100 Subject: [PATCH 052/131] Update docs (#236) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- docs/requirements.txt | 4 ++-- pixi.lock | 2 +- pyproject.toml | 8 ++++---- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 2b8ce60d..611d1123 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,5 +1,5 @@ furo>=2024.8.6 -myst_parser>=0.13 -sphinx>=7.0 +myst_parser>=0.19.2 +sphinx>=7.4.7 sphinx_autodoc_typehints sphinx_copybutton diff --git a/pixi.lock b/pixi.lock index 5ba1b013..6e015f7b 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 9caaf6a80751c89c1693ce901b4d31202552ea7af0cd3f37564d406d6565c051 + sha256: 9561cf7cf4532ba7a62260a3cc427e4b22c3730b7449295b71513bd42408a356 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 1e93cbe4..2c2efda2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -99,11 +99,11 @@ coverage = { cmd = "coverage html", depends-on = ["tests-cov"] } open-coverage = { cmd = "open htmlcov/index.html", depends-on = ["coverage"] } [tool.pixi.feature.docs.dependencies] -sphinx = ">=7.0" +sphinx = ">=7.4.7" furo = ">=2024.8.6" -myst-parser = ">=0.13" -sphinx-copybutton = "*" -sphinx-autodoc-typehints = "*" +myst-parser = ">=0.19.1" +sphinx-copybutton = ">=0.5.2" +sphinx-autodoc-typehints = ">=1.25.3" # Needed to import parsed modules with autodoc dask-core = ">=2025.3.0" pytest = ">=8.3.5" From e0662915520d2ea4b40e9ff6198221ec7e8f668b Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 8 Apr 2025 20:56:12 +0100 Subject: [PATCH 053/131] DEV: iterate on renovate config (#237) * set `constraints.pixi` * ignore python pixi deps * update groups --- renovate.json | 18 ++++++++++++------ 1 file changed, 12 insertions(+), 6 deletions(-) diff --git a/renovate.json b/renovate.json index 313bff7a..d5c98cc9 100644 --- a/renovate.json +++ b/renovate.json @@ -3,6 +3,7 @@ "extends": ["config:recommended"], "dependencyDashboardTitle": "META: Dependency Dashboard", "rangeStrategy": "bump", + "constraints.pixi": ">=0.45.0", "packageRules": [ { "matchManagers": ["pixi"], @@ -10,17 +11,22 @@ "enabled": false }, { - "matchPackageNames": [ - "/myst-parser|myst_parser|sphinx|sphinx-autodoc-typehints|sphinx-copybutton/" - ], + "matchManagers": ["pixi"], + "matchPackageNames": ["python"], + "enabled": false + }, + { + "matchPackageNames": ["/myst-parser|myst_parser/"], "groupName": "docs" }, { - "matchPackageNames": ["/pylint|pre-commit|typing-extensions/"], - "groupName": "lint" + "matchPackageNames": [ + "/sphinx|sphinx-autodoc-typehints|sphinx-copybutton/" + ], + "groupName": "sphinx" }, { - "matchPackageNames": ["/pytest-cov|hypothesis|ipython|jax|pytorch/"], + "matchPackageNames": ["/pytest-cov|hypothesis/"], "groupName": "tests" } ] From 3bb800b82d90192dc5544b397c5d11d2b9733df6 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 8 Apr 2025 21:05:44 +0100 Subject: [PATCH 054/131] DEV: try to fix renovate config (#238) --- renovate.json | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/renovate.json b/renovate.json index d5c98cc9..2d52cfe5 100644 --- a/renovate.json +++ b/renovate.json @@ -3,7 +3,9 @@ "extends": ["config:recommended"], "dependencyDashboardTitle": "META: Dependency Dashboard", "rangeStrategy": "bump", - "constraints.pixi": ">=0.45.0", + "constraints": { + "pixi": ">=0.45.0" + }, "packageRules": [ { "matchManagers": ["pixi"], From df1d1675a1aec16665e45b724441d6eb094aea66 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 21:08:23 +0100 Subject: [PATCH 055/131] Update dependency ipython to >=4.2.1 (#239) 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 6e015f7b..612ec955 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 9561cf7cf4532ba7a62260a3cc427e4b22c3730b7449295b71513bd42408a356 + sha256: dec3f5c0e283642441e3d0d2d24133e081494bb26fc1b8b4e33e1cc5eae06162 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 2c2efda2..7d81fe17 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -115,7 +115,7 @@ docs = { cmd = "sphinx-build -E -W . build/", cwd = "docs" } open-docs = { cmd = "open build/index.html", cwd = "docs", depends-on = ["docs"] } [tool.pixi.feature.dev.dependencies] -ipython = "*" +ipython = ">=4.2.1" [tool.pixi.feature.dev.tasks] ipython = { cmd = "ipython" } From e9d5cb5bfae534f162de98fc68bf3453953940b7 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 21:23:07 +0100 Subject: [PATCH 056/131] Update dependency pytorch to v2 (#241) 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 612ec955..fc819575 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: dec3f5c0e283642441e3d0d2d24133e081494bb26fc1b8b4e33e1cc5eae06162 + sha256: 3fad55a80a112d7bbf96ef291d9d500be2a20e5b72f3f17159f6cdb9d083e40a requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 7d81fe17..39bc5bea 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 = ">=1.13.1" +pytorch = ">=2.6.0" dask = ">=2025.3.0" numba = ">=0.61.0" # sparse dependency llvmlite = ">=0.44.0" # sparse dependency @@ -166,7 +166,7 @@ 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 = ">=1.13.1", build = "cuda12*" } +pytorch = { version = ">=2.6.0", build = "cuda12*" } [tool.pixi.feature.cuda-backends.target.osx-64.dependencies] # cupy = "*" # unavailable @@ -181,7 +181,7 @@ pytorch = { version = ">=1.13.1", build = "cuda12*" } [tool.pixi.feature.cuda-backends.target.win-64.dependencies] cupy = ">=13.4.1" # jaxlib = { version = "*", build = "cuda12*" } # unavailable -pytorch = { version = ">=1.13.1", build = "cuda12*" } +pytorch = { version = ">=2.6.0", build = "cuda12*" } [tool.pixi.environments] default = { features = ["py313"], solve-group = "py313" } From ba2208bc4118feed2e1509886e2f0e0f603f23dc Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 22:32:48 +0100 Subject: [PATCH 057/131] Update tests to v6 (#244) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 159 +++++++++++++++++++++++++------------------------ pyproject.toml | 6 +- 2 files changed, 83 insertions(+), 82 deletions(-) diff --git a/pixi.lock b/pixi.lock index fc819575..5fec73f8 100644 --- a/pixi.lock +++ b/pixi.lock @@ -159,7 +159,7 @@ environments: - 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attrs >=22.2.0 - click >=7.0 @@ -7987,10 +7987,11 @@ packages: - setuptools - sortedcontainers >=2.1.0,<3.0.0 license: MPL-2.0 + license_family: MOZILLA purls: - pkg:pypi/hypothesis?source=hash-mapping - size: 350305 - timestamp: 1742900979687 + size: 351225 + timestamp: 1744050198261 - conda: https://prefix.dev/conda-forge/linux-64/icu-75.1-he02047a_0.conda sha256: 71e750d509f5fa3421087ba88ef9a7b9be11c53174af3aa4d06aff4c18b38e8e md5: 8b189310083baabfb622af68fd9d3ae3 @@ -14179,9 +14180,9 @@ packages: - pkg:pypi/pytest?source=hash-mapping size: 259816 timestamp: 1740946648058 -- conda: https://prefix.dev/conda-forge/noarch/pytest-cov-6.0.0-pyhd8ed1ab_1.conda - sha256: 09acac1974e10a639415be4be326dd21fa6d66ca51a01fb71532263fba6dccf6 - md5: 79963c319d1be62c8fd3e34555816e01 +- conda: https://prefix.dev/conda-forge/noarch/pytest-cov-6.1.1-pyhd8ed1ab_0.conda + sha256: 9961a1524f63d10bc29efdc52013ec06b0e95fb2619a250e250ff3618261d5cd + md5: 1e35d8f975bc0e984a19819aa91c440a depends: - coverage >=7.5 - pytest >=4.6 @@ -14191,8 +14192,8 @@ packages: license_family: MIT purls: - pkg:pypi/pytest-cov?source=hash-mapping - size: 26256 - timestamp: 1733223113491 + size: 27565 + timestamp: 1743886993683 - conda: https://prefix.dev/conda-forge/linux-64/python-3.10.16-he725a3c_1_cpython.conda build_number: 1 sha256: 3f90a2d5062a73cd2dd8a0027718aee1db93f7975b9cfe529e2c9aeec2db262e diff --git a/pyproject.toml b/pyproject.toml index 39bc5bea..f2858f22 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,7 +64,7 @@ numpydoc = ">=1.8.0,<2" array-api-strict = ">=2.3.1" numpy = ">=1.26.4" pytest = ">=8.3.5" -hypothesis = ">=3.88.3" +hypothesis = ">=6.130.10" dask-core = ">=2025.3.0" # 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 @@ -79,8 +79,8 @@ lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"] } [tool.pixi.feature.tests.dependencies] pytest = ">=8.3.5" -pytest-cov = ">=3" -hypothesis = ">=3.88.3" +pytest-cov = ">=6.1.1" +hypothesis = ">=6.130.10" array-api-strict = ">=2.3.1" numpy = ">=1.22.0" From fe805829175228cf5b28d3202595e0f9ef01cc02 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Apr 2025 22:38:12 +0100 Subject: [PATCH 058/131] Update docs to v4 (#243) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- docs/requirements.txt | 2 +- pixi.lock | 2 +- pyproject.toml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index 611d1123..f5ef400a 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,5 +1,5 @@ furo>=2024.8.6 -myst_parser>=0.19.2 +myst_parser>=4.0.1 sphinx>=7.4.7 sphinx_autodoc_typehints sphinx_copybutton diff --git a/pixi.lock b/pixi.lock index 5fec73f8..1209730f 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 841ed3c6d16ad2db082fae003d779d0b6ee28cf01bd1eecce6e029f55dace211 + sha256: 1eb727e3c349b3467ef8e57414c9399d844c70326c2f9665dba61c2972adce55 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index f2858f22..804cd9db 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -101,7 +101,7 @@ open-coverage = { cmd = "open htmlcov/index.html", depends-on = ["coverage"] } [tool.pixi.feature.docs.dependencies] sphinx = ">=7.4.7" furo = ">=2024.8.6" -myst-parser = ">=0.19.1" +myst-parser = ">=4.0.1" sphinx-copybutton = ">=0.5.2" sphinx-autodoc-typehints = ">=1.25.3" # Needed to import parsed modules with autodoc From 4968db93cdae227e29f9adbb9b734c524a81524e Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 9 Apr 2025 09:02:38 +0100 Subject: [PATCH 059/131] Update dependency hypothesis to >=6.130.11 (#246) --- pixi.lock | 84 +++++++++++++++++++++++++------------------------- pyproject.toml | 4 +-- 2 files changed, 44 insertions(+), 44 deletions(-) diff --git a/pixi.lock b/pixi.lock index 1209730f..6c62c123 100644 --- a/pixi.lock +++ b/pixi.lock @@ -159,7 +159,7 @@ environments: - 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pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 1eb727e3c349b3467ef8e57414c9399d844c70326c2f9665dba61c2972adce55 + sha256: d53e5f8e1370010bb7e1ffa7aea4f3a45707893800c3e539f896b20f7e66111a requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' @@ -7976,9 +7976,9 @@ packages: - pkg:pypi/hyperframe?source=hash-mapping size: 17397 timestamp: 1737618427549 -- conda: https://prefix.dev/conda-forge/noarch/hypothesis-6.130.10-pyha770c72_0.conda - sha256: cbe404289cf09c4a0a3be0b865a4461b2516270c7fe6c418641b176cf95cf087 - md5: 256c1054a1039b67b2709ae4a6772b63 +- conda: https://prefix.dev/conda-forge/noarch/hypothesis-6.130.11-pyha770c72_0.conda + sha256: fd6747793ed84005f56e2acc11721835e7fd3393dfec7bd02f89ecfe9138eee8 + md5: a8619ef32d8b2495a138a48b046ebf86 depends: - attrs >=22.2.0 - click >=7.0 @@ -7990,8 +7990,8 @@ packages: license_family: MOZILLA purls: - pkg:pypi/hypothesis?source=hash-mapping - size: 351225 - timestamp: 1744050198261 + size: 352077 + timestamp: 1744148568706 - conda: https://prefix.dev/conda-forge/linux-64/icu-75.1-he02047a_0.conda sha256: 71e750d509f5fa3421087ba88ef9a7b9be11c53174af3aa4d06aff4c18b38e8e md5: 8b189310083baabfb622af68fd9d3ae3 diff --git a/pyproject.toml b/pyproject.toml index 804cd9db..94dfdde2 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,7 +64,7 @@ numpydoc = ">=1.8.0,<2" array-api-strict = ">=2.3.1" numpy = ">=1.26.4" pytest = ">=8.3.5" -hypothesis = ">=6.130.10" +hypothesis = ">=6.130.11" dask-core = ">=2025.3.0" # 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 @@ -80,7 +80,7 @@ lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"] } [tool.pixi.feature.tests.dependencies] pytest = ">=8.3.5" pytest-cov = ">=6.1.1" -hypothesis = ">=6.130.10" +hypothesis = ">=6.130.11" array-api-strict = ">=2.3.1" numpy = ">=1.22.0" From da087e7a0371c51280643f66853436690af844be Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 9 Apr 2025 09:06:11 +0100 Subject: [PATCH 060/131] Update dependency ipython to >=7.33.0 (#249) --- pixi.lock | 2 +- pyproject.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/pixi.lock b/pixi.lock index 6c62c123..b449958d 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5232,7 +5232,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: d53e5f8e1370010bb7e1ffa7aea4f3a45707893800c3e539f896b20f7e66111a + sha256: b7eeff1644a4f8d706d88a1f5336cfd50a6c6a9083f080e8dc722430c6a81d26 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 94dfdde2..72bc1ed5 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -115,7 +115,7 @@ docs = { cmd = "sphinx-build -E -W . build/", cwd = "docs" } open-docs = { cmd = "open build/index.html", cwd = "docs", depends-on = ["docs"] } [tool.pixi.feature.dev.dependencies] -ipython = ">=4.2.1" +ipython = ">=7.33.0" [tool.pixi.feature.dev.tasks] ipython = { cmd = "ipython" } From f9fcb3d5098b8e4ade1f139db53eca27eb2cbe86 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 9 Apr 2025 11:06:31 +0100 Subject: [PATCH 061/131] DEV: address renovate config wishlist (#253) --- renovate.json | 30 ++++++++++++++++-------------- 1 file changed, 16 insertions(+), 14 deletions(-) diff --git a/renovate.json b/renovate.json index 2d52cfe5..88188297 100644 --- a/renovate.json +++ b/renovate.json @@ -1,35 +1,37 @@ { "$schema": "https://docs.renovatebot.com/renovate-schema.json", - "extends": ["config:recommended"], + "extends": [ + "config:recommended", + "helpers:pinGitHubActionDigests", + ":automergeMinor" + ], "dependencyDashboardTitle": "META: Dependency Dashboard", + "commitMessagePrefix": "deps:", + "labels": ["dependencies"], "rangeStrategy": "bump", "constraints": { - "pixi": ">=0.45.0" + "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.", "matchManagers": ["pixi"], "matchPackageNames": ["python"], "enabled": false }, { - "matchPackageNames": ["/myst-parser|myst_parser/"], - "groupName": "docs" - }, - { - "matchPackageNames": [ - "/sphinx|sphinx-autodoc-typehints|sphinx-copybutton/" - ], - "groupName": "sphinx" - }, - { - "matchPackageNames": ["/pytest-cov|hypothesis/"], - "groupName": "tests" + "description": "Schedule automerged GHA updates for the 15th of each month.", + "matchManagers": ["github-actions"], + "groupName": "gha", + "schedule": ["* * 15 * *"], + "automerge": true } ] } From 06addad7eccd95aae5a23879c6f70179da16db60 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 9 Apr 2025 12:30:12 +0100 Subject: [PATCH 062/131] deps: Update dependency numpy to >=2.2.4 (#258) --- pixi.lock | 4170 ++++++++++++++++++++++++------------------------ pyproject.toml | 136 +- 2 files changed, 2177 insertions(+), 2129 deletions(-) diff --git a/pixi.lock b/pixi.lock index b449958d..c2890eee 100644 --- a/pixi.lock +++ b/pixi.lock @@ -13,20 +13,20 @@ environments: - 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{ name = "Lucas Colley", email = "lucas.colley8@gmail.com" }, - # { name = "Open Source Contributors" }, # https://github.com/pypi/warehouse/issues/14813 + { name = "Lucas Colley", email = "lucas.colley8@gmail.com" }, + # { name = "Open Source Contributors" }, # https://github.com/pypi/warehouse/issues/14813 ] description = "Extra array functions built on top of the array API standard." readme = "README.md" license.file = "LICENSE" requires-python = ">=3.10" classifiers = [ - "Intended Audience :: Developers", - "License :: OSI Approved :: MIT License", - "Operating System :: OS Independent", - "Programming Language :: Python", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3 :: Only", - "Programming Language :: Python :: 3.10", - "Programming Language :: Python :: 3.11", - "Programming Language :: Python :: 3.12", - "Programming Language :: Python :: 3.13", - "Typing :: Typed", + "Intended Audience :: Developers", + "License :: OSI Approved :: MIT License", + "Operating System :: OS Independent", + "Programming Language :: Python", + "Programming Language :: Python :: 3", + "Programming Language :: Python :: 3 :: Only", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", + "Programming Language :: Python :: 3.12", + "Programming Language :: Python :: 3.13", + "Typing :: Typed", ] dynamic = ["version"] dependencies = ["array-api-compat>=1.11.2,<2"] @@ -62,10 +62,10 @@ basedpyright = ">=1.28.3" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1" -numpy = ">=1.26.4" +numpy = ">=2.1.3" pytest = ">=8.3.5" hypothesis = ">=6.130.11" -dask-core = ">=2025.3.0" # No distributed, tornado, etc. +dask-core = ">=2025.3.0" # 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 @@ -108,7 +108,7 @@ sphinx-autodoc-typehints = ">=1.25.3" dask-core = ">=2025.3.0" pytest = ">=8.3.5" typing-extensions = ">=4.13.1" -numpy = ">=1.26.4" +numpy = ">=2.1.3" [tool.pixi.feature.docs.tasks] docs = { cmd = "sphinx-build -E -W . build/", cwd = "docs" } @@ -136,8 +136,8 @@ numpy = "=1.22.0" [tool.pixi.feature.backends.dependencies] pytorch = ">=2.6.0" dask = ">=2025.3.0" -numba = ">=0.61.0" # sparse dependency -llvmlite = ">=0.44.0" # sparse dependency +numba = ">=0.61.0" # sparse dependency +llvmlite = ">=0.44.0" # sparse dependency [tool.pixi.feature.backends.pypi-dependencies] sparse = { version = ">=0.16.0" } @@ -188,7 +188,7 @@ default = { features = ["py313"], solve-group = "py313" } lint = { features = ["py313", "lint"], solve-group = "py313" } docs = { features = ["py313", "docs"], solve-group = "py313" } tests = { features = ["py313", "tests"], solve-group = "py313" } -tests-py313 = { features = ["py313", "tests"], solve-group = "py313" } # alias of tests +tests-py313 = { features = ["py313", "tests"], solve-group = "py313" } # alias of tests # Some backends may pin numpy; use separate solve-group dev = { features = ["py310", "lint", "tests", "docs", "dev", "backends"], solve-group = "backends" } @@ -213,8 +213,8 @@ filterwarnings = ["error"] log_cli_level = "INFO" testpaths = ["tests"] markers = [ - "skip_xp_backend(library, *, reason=None): Skip test for a specific backend", - "xfail_xp_backend(library, *, reason=None): Xfail test for a specific backend", + "skip_xp_backend(library, *, reason=None): Skip test for a specific backend", + "xfail_xp_backend(library, *, reason=None): Xfail test for a specific backend", ] @@ -269,8 +269,8 @@ reportImportCycles = false reportUnknownLambdaType = false executionEnvironments = [ - { root = "tests", reportPrivateUsage = false }, - { root = "src" }, + { root = "tests", reportPrivateUsage = false }, + { root = "src" }, ] @@ -281,41 +281,41 @@ target-version = "py310" [tool.ruff.lint] extend-select = [ - "B", # flake8-bugbear - "F", # Pyflakes - "I", # isort - "E", # Pycodestyle - "W", # Pycodestyle - "N", # pep8-naming - "ARG", # flake8-unused-arguments - "C4", # flake8-comprehensions - "EM", # flake8-errmsg - "ICN", # flake8-import-conventions - "ISC", # flake8-implicit-str-concat - "G", # flake8-logging-format - "PGH", # pygrep-hooks - "PIE", # flake8-pie - "PL", # pylint - "PT", # flake8-pytest-style - "PTH", # flake8-use-pathlib - "RET", # flake8-return - "RUF", # Ruff-specific - "SIM", # flake8-simplify - "T20", # flake8-print - "UP", # pyupgrade - "YTT", # flake8-2020 - "EXE", # flake8-executable - "NPY", # NumPy specific rules - "PD", # pandas-vet - "UP", # Pyupgrade + "B", # flake8-bugbear + "F", # Pyflakes + "I", # isort + "E", # Pycodestyle + "W", # Pycodestyle + "N", # pep8-naming + "ARG", # flake8-unused-arguments + "C4", # flake8-comprehensions + "EM", # flake8-errmsg + "ICN", # flake8-import-conventions + "ISC", # flake8-implicit-str-concat + "G", # flake8-logging-format + "PGH", # pygrep-hooks + "PIE", # flake8-pie + "PL", # pylint + "PT", # flake8-pytest-style + "PTH", # flake8-use-pathlib + "RET", # flake8-return + "RUF", # Ruff-specific + "SIM", # flake8-simplify + "T20", # flake8-print + "UP", # pyupgrade + "YTT", # flake8-2020 + "EXE", # flake8-executable + "NPY", # NumPy specific rules + "PD", # pandas-vet + "UP", # Pyupgrade ] ignore = [ - "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 + "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 ] @@ -325,13 +325,13 @@ ignore = [ 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 - "missing-function-docstring", # numpydoc handles this - "import-error", # mypy handles this - "import-outside-toplevel", # optional dependencies + "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 ] @@ -339,11 +339,11 @@ messages_control.disable = [ [tool.numpydoc_validation] checks = [ - "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 + "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 ] exclude = [ # don't report on objects that match any of these regex - '.*test_*', + '.*test_*', ] From bab2d202c203605bd4b4fdcb3bc7cc82657c8cf1 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 9 Apr 2025 12:47:03 +0100 Subject: [PATCH 063/131] DEV: renovate: ignore some blocked updates (#260) --- renovate.json | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/renovate.json b/renovate.json index 88188297..10ea8ab9 100644 --- a/renovate.json +++ b/renovate.json @@ -32,6 +32,24 @@ "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 } ] } From 4fa8883f08e2733c1eea24e4061063fc46543c81 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 9 Apr 2025 14:13:03 +0100 Subject: [PATCH 064/131] deps: Update dependency sphinx to v8 (#261) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- docs/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/requirements.txt b/docs/requirements.txt index f5ef400a..539b79ef 100644 --- a/docs/requirements.txt +++ b/docs/requirements.txt @@ -1,5 +1,5 @@ furo>=2024.8.6 myst_parser>=4.0.1 -sphinx>=7.4.7 +sphinx>=8.2.3 sphinx_autodoc_typehints sphinx_copybutton From 06c430832f18b9a2bdfbeeec0ed4a9cfd384cd27 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 9 Apr 2025 14:45:45 +0100 Subject: [PATCH 065/131] MAINT: remove obsolete `docs/requirements.txt` (#262) --- docs/requirements.txt | 5 ----- 1 file changed, 5 deletions(-) delete mode 100644 docs/requirements.txt diff --git a/docs/requirements.txt b/docs/requirements.txt deleted file mode 100644 index 539b79ef..00000000 --- a/docs/requirements.txt +++ /dev/null @@ -1,5 +0,0 @@ -furo>=2024.8.6 -myst_parser>=4.0.1 -sphinx>=8.2.3 -sphinx_autodoc_typehints -sphinx_copybutton From d3f6f67f3e21f1b77a99d34976634b0eb1b871f8 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Tue, 15 Apr 2025 12:48:18 +0100 Subject: [PATCH 066/131] TST: run tests on CPU+GPU (#221) * TST: run tests on CPU+GPU * lock * Simplify conftest * capitalisation --- pixi.lock | 2 +- pyproject.toml | 2 +- src/array_api_extra/_lib/_at.py | 10 ++++- src/array_api_extra/_lib/_backends.py | 6 ++- src/array_api_extra/_lib/_testing.py | 63 ++++++++++++--------------- tests/conftest.py | 21 ++++++++- tests/test_at.py | 10 ++++- tests/test_funcs.py | 5 ++- tests/test_lazy.py | 14 +++++- tests/test_testing.py | 5 ++- 10 files changed, 91 insertions(+), 47 deletions(-) diff --git a/pixi.lock b/pixi.lock index c2890eee..71b1afc2 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5256,7 +5256,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 038ce201a10c2f3747ee69453356a561627455e1caa462151433eaeea9bdcea6 + sha256: a46c6db2ae9462de7b2b2078ea507a1bd7e21f2a6170bfed292f306878055331 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 0471921e..473e933e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -238,7 +238,7 @@ 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.*"] +module = ["dask.*", "jax.*", "torch.*"] ignore_missing_imports = true # pyright diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py index 736f77bd..870884b8 100644 --- a/src/array_api_extra/_lib/_at.py +++ b/src/array_api_extra/_lib/_at.py @@ -8,10 +8,12 @@ from types import ModuleType from typing import TYPE_CHECKING, ClassVar, cast +from ._utils import _compat from ._utils._compat import ( array_namespace, is_dask_array, is_jax_array, + is_torch_array, is_writeable_array, ) from ._utils._helpers import meta_namespace @@ -298,7 +300,7 @@ def _op( and idx.dtype == xp.bool and idx.shape == x.shape ): - y_xp = xp.asarray(y, dtype=x.dtype) + y_xp = xp.asarray(y, dtype=x.dtype, device=_compat.device(x)) if y_xp.ndim == 0: if out_of_place_op: # add(), subtract(), ... # suppress inf warnings on Dask @@ -344,6 +346,12 @@ def _op( msg = f"Can't update read-only array {x}" raise ValueError(msg) + # Work around bug in PyTorch where __setitem__ doesn't + # always support mismatched dtypes + # https://github.com/pytorch/pytorch/issues/150017 + if is_torch_array(y): + y = xp.astype(y, x.dtype, copy=False) + # Backends without boolean indexing (other than JAX) crash here if in_place_op: # add(), subtract(), ... x[idx] = in_place_op(x[idx], y) diff --git a/src/array_api_extra/_lib/_backends.py b/src/array_api_extra/_lib/_backends.py index 3beb676d..e30afd55 100644 --- a/src/array_api_extra/_lib/_backends.py +++ b/src/array_api_extra/_lib/_backends.py @@ -34,9 +34,11 @@ class Backend(Enum): # numpydoc ignore=PR01,PR02 # type: ignore[no-subclass-an NUMPY_READONLY = "numpy:readonly", _compat.is_numpy_namespace CUPY = "cupy", _compat.is_cupy_namespace TORCH = "torch", _compat.is_torch_namespace + TORCH_GPU = "torch:gpu", _compat.is_torch_namespace DASK = "dask.array", _compat.is_dask_namespace SPARSE = "sparse", _compat.is_pydata_sparse_namespace JAX = "jax.numpy", _compat.is_jax_namespace + JAX_GPU = "jax.numpy:gpu", _compat.is_jax_namespace def __new__( cls, value: str, _is_namespace: Callable[[ModuleType], bool] @@ -54,7 +56,9 @@ def __init__( def __str__(self) -> str: # type: ignore[explicit-override] # pyright: ignore[reportImplicitOverride] # numpydoc ignore=RT01 """Pretty-print parameterized test names.""" - return self.name.lower() + return ( + self.name.lower().replace("_gpu", ":gpu").replace("_readonly", ":readonly") + ) @property def modname(self) -> str: # numpydoc ignore=RT01 diff --git a/src/array_api_extra/_lib/_testing.py b/src/array_api_extra/_lib/_testing.py index e5ec16a6..319297c8 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -65,6 +65,24 @@ def _check_ns_shape_dtype( return desired_xp +def _prepare_for_test(array: Array, xp: ModuleType) -> Array: + """ + 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. + """ + if is_torch_namespace(xp): + return array.cpu() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + if is_pydata_sparse_namespace(xp): + return array.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + 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 + + def xp_assert_equal(actual: Array, desired: Array, err_msg: str = "") -> None: """ Array-API compatible version of `np.testing.assert_array_equal`. @@ -84,6 +102,8 @@ def xp_assert_equal(actual: Array, desired: Array, err_msg: str = "") -> None: 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) if is_cupy_namespace(xp): xp.testing.assert_array_equal(actual, desired, err_msg=err_msg) @@ -102,22 +122,7 @@ def xp_assert_equal(actual: Array, desired: Array, err_msg: str = "") -> None: else: import numpy as np # pylint: disable=import-outside-toplevel - if is_pydata_sparse_namespace(xp): - actual = actual.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] - desired = desired.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] - - actual_np = None - desired_np = None - if is_array_api_strict_namespace(xp): - # __array__ doesn't work on array-api-strict device arrays - # We need to convert to the CPU device first - actual_np = np.asarray(xp.asarray(actual, device=xp.Device("CPU_DEVICE"))) - desired_np = np.asarray(xp.asarray(desired, device=xp.Device("CPU_DEVICE"))) - - # JAX/Dask arrays work with `np.testing` - actual_np = actual if actual_np is None else actual_np - desired_np = desired if desired_np is None else desired_np - np.testing.assert_array_equal(actual_np, desired_np, err_msg=err_msg) # pyright: ignore[reportUnknownArgumentType] + np.testing.assert_array_equal(actual, desired, err_msg=err_msg) def xp_assert_close( @@ -165,6 +170,9 @@ def xp_assert_close( 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 @@ -176,26 +184,11 @@ def xp_assert_close( else: import numpy as np # pylint: disable=import-outside-toplevel - if is_pydata_sparse_namespace(xp): - actual = actual.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] - desired = desired.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] - - actual_np = None - desired_np = None - if is_array_api_strict_namespace(xp): - # __array__ doesn't work on array-api-strict device arrays - # We need to convert to the CPU device first - actual_np = np.asarray(xp.asarray(actual, device=xp.Device("CPU_DEVICE"))) - desired_np = np.asarray(xp.asarray(desired, device=xp.Device("CPU_DEVICE"))) - - # JAX/Dask arrays work with `np.testing` - actual_np = actual if actual_np is None else actual_np - desired_np = desired if desired_np is None else desired_np - + # JAX/Dask arrays work directly with `np.testing` assert isinstance(rtol, float) - np.testing.assert_allclose( # pyright: ignore[reportCallIssue] - actual_np, # type: ignore[arg-type] # pyright: ignore[reportArgumentType] - desired_np, # type: ignore[arg-type] # pyright: ignore[reportArgumentType] + 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, diff --git a/tests/conftest.py b/tests/conftest.py index 4e368850..70854249 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -139,12 +139,31 @@ def xp( # in the global scope of the module containing the test function. patch_lazy_xp_functions(request, monkeypatch, xp=xp) - if library == Backend.JAX: + 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) + + 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") + yield xp diff --git a/tests/test_at.py b/tests/test_at.py index 4bde5ce2..926685cb 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -118,6 +118,9 @@ def assert_copy( pytest.mark.skip_xp_backend( # test passes when copy=False Backend.JAX, reason="bool mask update with shaped rhs" ), + pytest.mark.skip_xp_backend( # test passes when copy=False + Backend.JAX_GPU, reason="bool mask update with shaped rhs" + ), pytest.mark.xfail_xp_backend( Backend.DASK, reason="bool mask update with shaped rhs" ), @@ -247,14 +250,14 @@ def test_incompatible_dtype( idx = xp.asarray([True, False]) if bool_mask else slice(None) z = None - if library is Backend.JAX: + if library.like(Backend.JAX): if bool_mask: z = at_op(x, idx, op, 1.1, copy=copy) else: with pytest.warns(FutureWarning, match="cannot safely cast"): z = at_op(x, idx, op, 1.1, copy=copy) - elif library is Backend.DASK: + 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: @@ -302,6 +305,9 @@ def test_no_inf_warnings(xp: ModuleType, bool_mask: bool): Backend.NUMPY_READONLY, reason="read-only backend" ), pytest.mark.skip_xp_backend(Backend.JAX, reason="read-only backend"), + pytest.mark.skip_xp_backend( + Backend.JAX_GPU, reason="read-only backend" + ), pytest.mark.skip_xp_backend(Backend.SPARSE, reason="read-only backend"), ], ), diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 48ad7b06..553df5dc 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -234,7 +234,7 @@ def test_hypothesis( # type: ignore[explicit-any,decorated-any] # cupy/cupy#8382 # https://github.com/jax-ml/jax/issues/26658 - elements = {"allow_subnormal": library not in (Backend.CUPY, Backend.JAX)} + elements = {"allow_subnormal": not library.like(Backend.CUPY, Backend.JAX)} fill_value = xp.asarray( data.draw(npst.arrays(dtype=dtype, shape=(), elements=elements)) @@ -930,6 +930,9 @@ class TestSetDiff1D: @pytest.mark.xfail_xp_backend( Backend.TORCH, reason="index_select not implemented for uint32" ) + @pytest.mark.xfail_xp_backend( + Backend.TORCH_GPU, reason="index_select not implemented for uint32" + ) def test_setdiff1d(self, xp: ModuleType): x1 = xp.asarray([6, 5, 4, 7, 1, 2, 7, 4]) x2 = xp.asarray([2, 4, 3, 3, 2, 1, 5]) diff --git a/tests/test_lazy.py b/tests/test_lazy.py index d360e50d..8690c33e 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -27,6 +27,9 @@ True, marks=[ pytest.mark.skip_xp_backend(Backend.CUPY, reason="device->host copy"), + pytest.mark.skip_xp_backend( + Backend.TORCH_GPU, reason="device->host copy" + ), pytest.mark.skip_xp_backend(Backend.SPARSE, reason="densification"), ], ), @@ -100,6 +103,9 @@ def f(x: Array) -> tuple[Array, Array]: True, marks=[ pytest.mark.skip_xp_backend(Backend.CUPY, reason="device->host copy"), + pytest.mark.skip_xp_backend( + Backend.TORCH_GPU, reason="device->host copy" + ), pytest.mark.skip_xp_backend(Backend.SPARSE, reason="densification"), ], ), @@ -216,7 +222,7 @@ def test_lazy_apply_none_shape_in_args(xp: ModuleType, library: Backend): int_type = xp.asarray(0).dtype ctx: contextlib.AbstractContextManager[object] - if library is Backend.JAX: + if library.like(Backend.JAX): ctx = pytest.raises(ValueError, match="Output shape must be fully known") elif library is Backend.ARRAY_API_STRICTEST: ctx = pytest.raises(RuntimeError, match="data-dependent shapes") @@ -254,6 +260,7 @@ def f(x: Array) -> Array: @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="index by sparse array") @pytest.mark.skip_xp_backend(Backend.JAX, reason="boolean indexing") +@pytest.mark.skip_xp_backend(Backend.JAX_GPU, reason="boolean indexing") @pytest.mark.skip_xp_backend(Backend.ARRAY_API_STRICTEST, reason="boolean indexing") def test_lazy_apply_none_shape_broadcast(xp: ModuleType): """Broadcast from input array with unknown shape""" @@ -273,6 +280,9 @@ 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_GPU, reason="device->host copy" + ), pytest.mark.skip_xp_backend(Backend.SPARSE, reason="densification"), ], ), @@ -321,7 +331,7 @@ def f(x: Array, y: None, z: int | Array) -> Array: assert isinstance(x, mtyp) assert y is None # jax.pure_callback wraps scalar args - assert isinstance(z, mtyp if library is Backend.JAX else int) + assert isinstance(z, mtyp if library.like(Backend.JAX) else int) return x + z x = xp.asarray([1, 2]) diff --git a/tests/test_testing.py b/tests/test_testing.py index 10ce7ab3..9976e6fd 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -218,6 +218,7 @@ def test_lazy_xp_function_static_params(xp: ModuleType, func: Callable[..., Arra erf = None +@pytest.mark.skip_xp_backend(Backend.TORCH_GPU, reason="device->host copy") @pytest.mark.filterwarnings("ignore:__array_wrap__:DeprecationWarning") # PyTorch def test_lazy_xp_function_cython_ufuncs(xp: ModuleType, library: Backend): pytest.importorskip("scipy") @@ -293,12 +294,12 @@ def test_lazy_xp_modules(xp: ModuleType, library: Backend): y = naked.f(x) xp_assert_equal(y, x) - if library is Backend.JAX: + if library.like(Backend.JAX): with pytest.raises( TypeError, match="Attempted boolean conversion of traced array" ): wrapped.f(x) - elif library is Backend.DASK: + elif library.like(Backend.DASK): with pytest.raises(AssertionError, match=r"dask\.compute"): wrapped.f(x) else: From f24a4d596d58fe1b4d50a0524a5f612b92e95e3d Mon Sep 17 00:00:00 2001 From: Jake Bowhay <60778417+j-bowhay@users.noreply.github.com> Date: Tue, 15 Apr 2025 12:52:03 +0100 Subject: [PATCH 067/131] DEV: add Pixi task descriptions (#263) * DEV: add Pixi task descriptions * update lock file --------- Co-authored-by: Lucas Colley --- pixi.lock | 1511 ++++++++++++++++++++++++------------------------ pyproject.toml | 38 +- 2 files changed, 781 insertions(+), 768 deletions(-) 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pkg:pypi/pytz?source=hash-mapping - size: 188538 - timestamp: 1706886944988 + size: 22880687 + timestamp: 1744263487205 - conda: https://prefix.dev/conda-forge/noarch/pytz-2025.2-pyhd8ed1ab_0.conda sha256: 8d2a8bf110cc1fc3df6904091dead158ba3e614d8402a83e51ed3a8aa93cdeb0 md5: bc8e3267d44011051f2eb14d22fb0960 @@ -15780,19 +15793,19 @@ packages: - pkg:pypi/triton?source=hash-mapping size: 102101472 timestamp: 1741776175758 -- conda: https://prefix.dev/conda-forge/noarch/typing-extensions-4.13.1-hf5ce1d7_0.conda - sha256: f38c8a4cb27155a3c0d2853683569b1b1b38b31aa17195c23789367868d2125e - md5: e37cf790f710cf72fd13dcb6b2d4370c +- conda: https://prefix.dev/conda-forge/noarch/typing-extensions-4.13.2-h0e9735f_0.conda + sha256: 4865fce0897d3cb0ffc8998219157a8325f6011c136e6fd740a9a6b169419296 + md5: 568ed1300869dca0ba09fb750cda5dbb depends: - - typing_extensions ==4.13.1 pyh29332c3_0 + - typing_extensions ==4.13.2 pyh29332c3_0 license: PSF-2.0 license_family: PSF purls: [] - size: 89685 - timestamp: 1743820059977 -- conda: https://prefix.dev/conda-forge/noarch/typing_extensions-4.13.1-pyh29332c3_0.conda - sha256: 78a5efbf86eca68b5f9e58f0dc7e56dcfa96d1dcba5c7f5f37d2c0444de22085 - md5: 5710c79a5fb0a6bfdba0a887f90583b1 + size: 89900 + timestamp: 1744302253997 +- conda: https://prefix.dev/conda-forge/noarch/typing_extensions-4.13.2-pyh29332c3_0.conda + sha256: a8aaf351e6461de0d5d47e4911257e25eec2fa409d71f3b643bb2f748bde1c08 + md5: 83fc6ae00127671e301c9f44254c31b8 depends: - python >=3.9 - python @@ -15800,8 +15813,8 @@ packages: license_family: PSF purls: - pkg:pypi/typing-extensions?source=compressed-mapping - size: 52170 - timestamp: 1743820059977 + size: 52189 + timestamp: 1744302253997 - conda: https://prefix.dev/conda-forge/noarch/tzdata-2025b-h78e105d_0.conda sha256: 5aaa366385d716557e365f0a4e9c3fca43ba196872abbbe3d56bb610d131e192 md5: 4222072737ccff51314b5ece9c7d6f5a @@ -15944,9 +15957,9 @@ packages: - pkg:pypi/ukkonen?source=hash-mapping size: 17210 timestamp: 1725784604368 -- conda: https://prefix.dev/conda-forge/noarch/urllib3-2.3.0-pyhd8ed1ab_0.conda - sha256: 114919ffa80c328127dab9c8e7a38f9d563c617691fb81fccb11c1e86763727e - md5: 32674f8dbfb7b26410ed580dd3c10a29 +- conda: https://prefix.dev/conda-forge/noarch/urllib3-2.4.0-pyhd8ed1ab_0.conda + sha256: a25403b76f7f03ca1a906e1ef0f88521edded991b9897e7fed56a3e334b3db8c + md5: c1e349028e0052c4eea844e94f773065 depends: - brotli-python >=1.0.9 - h2 >=4,<5 @@ -15957,8 +15970,8 @@ packages: license_family: MIT purls: - pkg:pypi/urllib3?source=hash-mapping - size: 100102 - timestamp: 1734859520452 + size: 100791 + timestamp: 1744323705540 - conda: https://prefix.dev/conda-forge/win-64/vc-14.3-h2b53caa_26.conda sha256: 7a685b5c37e9713fa314a0d26b8b1d7a2e6de5ab758698199b5d5b6dba2e3ce1 md5: d3f0381e38093bde620a8d85f266ae55 diff --git a/pyproject.toml b/pyproject.toml index 473e933e..67651904 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -70,12 +70,12 @@ dask-core = ">=2025.3.0" # No distributed, tornado, etc. # as they slow down mypy and are not portable across target OSs [tool.pixi.feature.lint.tasks] -pre-commit-install = "pre-commit install" -pre-commit = "pre-commit run --all-files" -mypy = "mypy" -pylint = { cmd = "pylint array_api_extra", cwd = "src" } -pyright = "basedpyright" -lint = { depends-on = ["pre-commit", "pylint", "mypy", "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 = ">=8.3.5" @@ -85,18 +85,18 @@ array-api-strict = ">=2.3.1" numpy = ">=1.22.0" [tool.pixi.feature.tests.tasks] -tests = "pytest -v" -tests-cov = "pytest -v -ra --cov --cov-report=xml --cov-report=term --durations=20" +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 = "rm -rf vendor_tests/array_api_compat" -clean-vendor-extra = "rm -rf vendor_tests/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"] } -copy-vendor-extra = { cmd = "cp -r src/array_api_extra vendor_tests/", depends-on = ["clean-vendor-extra"] } -tests-vendor = { cmd = "pytest -v vendor_tests", depends-on = ["copy-vendor-compat", "copy-vendor-extra"] } +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"] } -coverage = { cmd = "coverage html", depends-on = ["tests-cov"] } -open-coverage = { cmd = "open htmlcov/index.html", depends-on = ["coverage"] } +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" @@ -111,14 +111,14 @@ typing-extensions = ">=4.13.1" numpy = ">=2.1.3" [tool.pixi.feature.docs.tasks] -docs = { cmd = "sphinx-build -E -W . build/", cwd = "docs" } -open-docs = { cmd = "open build/index.html", cwd = "docs", depends-on = ["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" } +ipython = { cmd = "ipython" , description = "Launch ipython"} [tool.pixi.feature.py310.dependencies] python = "~=3.10.0" From c1cd43e7495e278c2bd28cf7d1feec23949f9344 Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Tue, 15 Apr 2025 12:53:39 +0100 Subject: [PATCH 068/131] docs: add j-bowhay as a contributor for tool (#264) * 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 4c24b4a8..5e5e6b0b 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -48,7 +48,8 @@ "profile": "https://github.com/j-bowhay", "contributions": [ "code", - "review" + "review", + "tool" ] }, { diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index 7d095124..36d50b0d 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -11,7 +11,7 @@ This project exists thanks to the following contributors Lucas Colley
Lucas Colley
💻 📖 💡 🤔 🚇 🚧 🔧 ⚠️ 🐛 📦 👀 Matt Haberland
Matt Haberland
💻 🤔 - Jake Bowhay
Jake Bowhay
💻 👀 + Jake Bowhay
Jake Bowhay
💻 👀 🔧 Aaron Meurer
Aaron Meurer
👀 🤔 🚇 Tim Head
Tim Head
🤔 Athan
Athan
👀 🤔 diff --git a/README.md b/README.md index 9220d693..3fe7e3eb 100644 --- a/README.md +++ b/README.md @@ -66,7 +66,7 @@ This project exists thanks to the following contributors Lucas Colley
Lucas Colley
💻 📖 💡 🤔 🚇 🚧 🔧 ⚠️ 🐛 📦 👀 Matt Haberland
Matt Haberland
💻 🤔 - Jake Bowhay
Jake Bowhay
💻 👀 + Jake Bowhay
Jake Bowhay
💻 👀 🔧 Aaron Meurer
Aaron Meurer
👀 🤔 🚇 Tim Head
Tim Head
🤔 Athan
Athan
👀 🤔 From 6e3ad0f37d887f87d75de84e39148f50724a8c7a Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Tue, 15 Apr 2025 17:31:40 +0100 Subject: [PATCH 069/131] MAINT: Don't use `Backend` for delegation (#265) * MAINT: don't use `Backend` for delegation * Update src/array_api_extra/_lib/_backends.py Co-authored-by: Lucas Colley --------- Co-authored-by: Lucas Colley --- src/array_api_extra/_delegation.py | 53 +++++++++++++-------------- src/array_api_extra/_lib/__init__.py | 4 -- src/array_api_extra/_lib/_backends.py | 52 +++++++------------------- tests/conftest.py | 2 +- tests/test_at.py | 2 +- tests/test_funcs.py | 2 +- tests/test_helpers.py | 2 +- tests/test_lazy.py | 2 +- tests/test_testing.py | 2 +- 9 files changed, 46 insertions(+), 75 deletions(-) diff --git a/src/array_api_extra/_delegation.py b/src/array_api_extra/_delegation.py index bb11b7ee..b52c23ae 100644 --- a/src/array_api_extra/_delegation.py +++ b/src/array_api_extra/_delegation.py @@ -4,33 +4,22 @@ from types import ModuleType from typing import Literal -from ._lib import Backend, _funcs -from ._lib._utils._compat import array_namespace +from ._lib import _funcs +from ._lib._utils._compat import ( + array_namespace, + is_cupy_namespace, + is_dask_namespace, + is_jax_namespace, + is_numpy_namespace, + is_pydata_sparse_namespace, + is_torch_namespace, +) from ._lib._utils._helpers import asarrays from ._lib._utils._typing import Array __all__ = ["isclose", "pad"] -def _delegate(xp: ModuleType, *backends: Backend) -> bool: - """ - Check whether `xp` is one of the `backends` to delegate to. - - Parameters - ---------- - xp : array_namespace - Array namespace to check. - *backends : IsNamespace - Arbitrarily many backends (from the ``IsNamespace`` enum) to check. - - Returns - ------- - bool - ``True`` if `xp` matches one of the `backends`, ``False`` otherwise. - """ - return any(backend.is_namespace(xp) for backend in backends) - - def isclose( a: Array | complex, b: Array | complex, @@ -108,10 +97,15 @@ def isclose( """ xp = array_namespace(a, b) if xp is None else xp - if _delegate(xp, Backend.NUMPY, Backend.CUPY, Backend.DASK, Backend.JAX): + if ( + is_numpy_namespace(xp) + or is_cupy_namespace(xp) + or is_dask_namespace(xp) + or is_jax_namespace(xp) + ): return xp.isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan) - if _delegate(xp, Backend.TORCH): + if is_torch_namespace(xp): a, b = asarrays(a, b, xp=xp) # Array API 2024.12 support return xp.isclose(a, b, rtol=rtol, atol=atol, equal_nan=equal_nan) @@ -159,14 +153,19 @@ def pad( msg = "Only `'constant'` mode is currently supported" raise NotImplementedError(msg) + if ( + is_numpy_namespace(xp) + or is_cupy_namespace(xp) + or is_jax_namespace(xp) + or is_pydata_sparse_namespace(xp) + ): + return xp.pad(x, pad_width, mode, constant_values=constant_values) + # https://github.com/pytorch/pytorch/blob/cf76c05b4dc629ac989d1fb8e789d4fac04a095a/torch/_numpy/_funcs_impl.py#L2045-L2056 - if _delegate(xp, Backend.TORCH): + if is_torch_namespace(xp): pad_width = xp.asarray(pad_width) pad_width = xp.broadcast_to(pad_width, (x.ndim, 2)) pad_width = xp.flip(pad_width, axis=(0,)).flatten() return xp.nn.functional.pad(x, tuple(pad_width), value=constant_values) # type: ignore[arg-type] # pyright: ignore[reportArgumentType] - if _delegate(xp, Backend.NUMPY, Backend.JAX, Backend.CUPY, Backend.SPARSE): - return xp.pad(x, pad_width, mode, constant_values=constant_values) - return _funcs.pad(x, pad_width, constant_values=constant_values, xp=xp) diff --git a/src/array_api_extra/_lib/__init__.py b/src/array_api_extra/_lib/__init__.py index b83d7e8c..d7b32033 100644 --- a/src/array_api_extra/_lib/__init__.py +++ b/src/array_api_extra/_lib/__init__.py @@ -1,5 +1 @@ """Internals of array-api-extra.""" - -from ._backends import Backend - -__all__ = ["Backend"] diff --git a/src/array_api_extra/_lib/_backends.py b/src/array_api_extra/_lib/_backends.py index e30afd55..f64e1479 100644 --- a/src/array_api_extra/_lib/_backends.py +++ b/src/array_api_extra/_lib/_backends.py @@ -1,58 +1,34 @@ -"""Backends with which array-api-extra interacts in delegation and testing.""" +"""Backends against which array-api-extra runs its tests.""" from __future__ import annotations -from collections.abc import Callable from enum import Enum -from types import ModuleType - -from ._utils import _compat __all__ = ["Backend"] -class Backend(Enum): # numpydoc ignore=PR01,PR02 # type: ignore[no-subclass-any] +class Backend(Enum): # numpydoc ignore=PR02 """ All array library backends explicitly tested by array-api-extra. Parameters ---------- value : str - Name of the backend's module. - is_namespace : Callable[[ModuleType], bool] - Function to check whether an input module is the array namespace - corresponding to the backend. + Tag of the backend's module, in the format ``[:]``. """ # Use : to prevent Enum from deduplicating items with the same value - ARRAY_API_STRICT = "array_api_strict", _compat.is_array_api_strict_namespace - ARRAY_API_STRICTEST = ( - "array_api_strict:strictest", - _compat.is_array_api_strict_namespace, - ) - NUMPY = "numpy", _compat.is_numpy_namespace - NUMPY_READONLY = "numpy:readonly", _compat.is_numpy_namespace - CUPY = "cupy", _compat.is_cupy_namespace - TORCH = "torch", _compat.is_torch_namespace - TORCH_GPU = "torch:gpu", _compat.is_torch_namespace - DASK = "dask.array", _compat.is_dask_namespace - SPARSE = "sparse", _compat.is_pydata_sparse_namespace - JAX = "jax.numpy", _compat.is_jax_namespace - JAX_GPU = "jax.numpy:gpu", _compat.is_jax_namespace - - def __new__( - cls, value: str, _is_namespace: Callable[[ModuleType], bool] - ): # numpydoc ignore=GL08 - obj = object.__new__(cls) - obj._value_ = value - return obj - - def __init__( - self, - value: str, # noqa: ARG002 # pylint: disable=unused-argument - is_namespace: Callable[[ModuleType], bool], - ): # numpydoc ignore=GL08 - self.is_namespace = is_namespace + ARRAY_API_STRICT = "array_api_strict" + ARRAY_API_STRICTEST = "array_api_strict:strictest" + NUMPY = "numpy" + NUMPY_READONLY = "numpy:readonly" + CUPY = "cupy" + TORCH = "torch" + TORCH_GPU = "torch:gpu" + DASK = "dask.array" + SPARSE = "sparse" + JAX = "jax.numpy" + JAX_GPU = "jax.numpy:gpu" def __str__(self) -> str: # type: ignore[explicit-override] # pyright: ignore[reportImplicitOverride] # numpydoc ignore=RT01 """Pretty-print parameterized test names.""" diff --git a/tests/conftest.py b/tests/conftest.py index 70854249..410a87ff 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -9,7 +9,7 @@ import numpy as np import pytest -from array_api_extra._lib import Backend +from array_api_extra._lib._backends import Backend from array_api_extra._lib._testing import xfail from array_api_extra._lib._utils._compat import array_namespace from array_api_extra._lib._utils._compat import device as get_device diff --git a/tests/test_at.py b/tests/test_at.py index 926685cb..4ccf584e 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -9,8 +9,8 @@ import pytest from array_api_extra import at -from array_api_extra._lib import Backend from array_api_extra._lib._at import _AtOp +from array_api_extra._lib._backends import Backend from array_api_extra._lib._testing import xp_assert_equal from array_api_extra._lib._utils._compat import array_namespace, is_writeable_array from array_api_extra._lib._utils._compat import device as get_device diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 553df5dc..4e40f09b 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -25,7 +25,7 @@ setdiff1d, sinc, ) -from array_api_extra._lib import Backend +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._utils._compat import device as get_device from array_api_extra._lib._utils._helpers import eager_shape, ndindex diff --git a/tests/test_helpers.py b/tests/test_helpers.py index c7d271ca..ebd4811f 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -4,7 +4,7 @@ import numpy as np import pytest -from array_api_extra._lib import Backend +from array_api_extra._lib._backends import Backend from array_api_extra._lib._testing import xp_assert_equal from array_api_extra._lib._utils._compat import array_namespace from array_api_extra._lib._utils._compat import device as get_device diff --git a/tests/test_lazy.py b/tests/test_lazy.py index 8690c33e..f40df277 100644 --- a/tests/test_lazy.py +++ b/tests/test_lazy.py @@ -7,7 +7,7 @@ import array_api_extra as xpx # Let some tests bypass lazy_xp_function from array_api_extra import lazy_apply -from array_api_extra._lib import Backend +from array_api_extra._lib._backends import Backend from array_api_extra._lib._testing import xp_assert_equal from array_api_extra._lib._utils import _compat from array_api_extra._lib._utils._compat import array_namespace, is_dask_array diff --git a/tests/test_testing.py b/tests/test_testing.py index 9976e6fd..ff67121b 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -5,7 +5,7 @@ import numpy as np import pytest -from array_api_extra._lib import Backend +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._utils._compat import ( array_namespace, From 9c9326adb81efa1b48b2ab1cc7f91c4916e2d7f1 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Mon, 21 Apr 2025 15:55:57 +0100 Subject: [PATCH 070/131] TST: `xfail_xp_backend(strict=False)` (#269) --- pixi.lock | 2 +- pyproject.toml | 4 ++-- src/array_api_extra/_lib/_testing.py | 14 +++++++++++-- tests/conftest.py | 30 ++++++++++++++++++---------- tests/test_at.py | 12 +++++++---- tests/test_funcs.py | 2 +- tests/test_helpers.py | 2 +- 7 files changed, 44 insertions(+), 22 deletions(-) diff --git a/pixi.lock b/pixi.lock index 56ee7c56..2153c4e2 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5256,7 +5256,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 74777bddfe6ab8d3ced9e5d1c645cb95c637707a45de9e96c88fc3b41723e3af + sha256: 68490b5f2feb7687422f882f54bb2a93c687425b984a69ecd58c9d6d73653139 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 67651904..9d897cc0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -213,8 +213,8 @@ filterwarnings = ["error"] log_cli_level = "INFO" testpaths = ["tests"] markers = [ - "skip_xp_backend(library, *, reason=None): Skip test for a specific backend", - "xfail_xp_backend(library, *, reason=None): Xfail test for a specific backend", + "skip_xp_backend(library, /, *, reason=None): Skip test for a specific backend", + "xfail_xp_backend(library, /, *, reason=None, strict=None): Xfail test for a specific backend", ] diff --git a/src/array_api_extra/_lib/_testing.py b/src/array_api_extra/_lib/_testing.py index 319297c8..301a851f 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -195,7 +195,9 @@ def xp_assert_close( ) -def xfail(request: pytest.FixtureRequest, reason: str) -> None: +def xfail( + request: pytest.FixtureRequest, *, reason: str, strict: bool | None = None +) -> None: """ XFAIL the currently running test. @@ -209,5 +211,13 @@ def xfail(request: pytest.FixtureRequest, reason: str) -> None: ``request`` argument of the test function. reason : str Reason for the expected failure. + strict: bool, optional + If True, the test will be marked as failed if it passes. + If False, the test will be marked as passed if it fails. + Default: ``xfail_strict`` value in ``pyproject.toml``, or False if absent. """ - request.node.add_marker(pytest.mark.xfail(reason=reason)) + if strict is not None: + marker = pytest.mark.xfail(reason=reason, strict=strict) + else: + marker = pytest.mark.xfail(reason=reason) + request.node.add_marker(marker) diff --git a/tests/conftest.py b/tests/conftest.py index 410a87ff..5676cc0d 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,7 +1,6 @@ """Pytest fixtures.""" from collections.abc import Callable, Generator -from contextlib import suppress from functools import partial, wraps from types import ModuleType from typing import ParamSpec, TypeVar, cast @@ -34,20 +33,29 @@ def library(request: pytest.FixtureRequest) -> Backend: # numpydoc ignore=PR01, """ elem = cast(Backend, request.param) - for marker_name, skip_or_xfail in ( - ("skip_xp_backend", pytest.skip), - ("xfail_xp_backend", partial(xfail, request)), + for marker_name, skip_or_xfail, allow_kwargs in ( + ("skip_xp_backend", pytest.skip, {"reason"}), + ("xfail_xp_backend", partial(xfail, request), {"reason", "strict"}), ): for marker in request.node.iter_markers(marker_name): - library = marker.kwargs.get("library") or marker.args[0] # type: ignore[no-untyped-usage] - if not isinstance(library, Backend): - msg = f"argument of {marker_name} must be a Backend enum" + if len(marker.args) != 1: # pyright: ignore[reportUnknownArgumentType] + 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] + msg = f"Unexpected kwarg(s): {invalid_kwargs}" + raise TypeError(msg) + + library: Backend = marker.args[0] + reason: str | None = marker.kwargs.get("reason", None) + strict: bool | None = marker.kwargs.get("strict", None) + if library == elem: - reason = str(library) - with suppress(KeyError): - reason += ":" + cast(str, marker.kwargs["reason"]) - skip_or_xfail(reason=reason) + reason = f"{library}: {reason}" if reason else str(library) # pyright: ignore[reportUnknownArgumentType] + kwargs = {"strict": strict} if strict is not None else {} + skip_or_xfail(reason=reason, **kwargs) # pyright: ignore[reportUnknownArgumentType] return elem diff --git a/tests/test_at.py b/tests/test_at.py index 4ccf584e..fa9bcdc8 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -115,11 +115,15 @@ def assert_copy( pytest.param( *(True, 1, 1), marks=( - pytest.mark.skip_xp_backend( # test passes when copy=False - Backend.JAX, reason="bool mask update with shaped rhs" + pytest.mark.xfail_xp_backend( + Backend.JAX, + reason="bool mask update with shaped rhs", + strict=False, # test passes when copy=False ), - pytest.mark.skip_xp_backend( # test passes when copy=False - Backend.JAX_GPU, reason="bool mask update with shaped rhs" + pytest.mark.xfail_xp_backend( + Backend.JAX_GPU, + reason="bool mask update with shaped rhs", + strict=False, # test passes when copy=False ), pytest.mark.xfail_xp_backend( Backend.DASK, reason="bool mask update with shaped rhs" diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 4e40f09b..652e12ef 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -196,7 +196,7 @@ 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.skip_xp_backend(Backend.SPARSE, reason="no isdtype") + @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_helpers.py b/tests/test_helpers.py index ebd4811f..a104e93c 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -27,7 +27,7 @@ lazy_xp_function(in1d, jax_jit=False, static_argnames=("assume_unique", "invert", "xp")) -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no unique_inverse") +@pytest.mark.skip_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 From 6998deb01f5a78d2f0c1285c10c110eb698cf8e2 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Tue, 22 Apr 2025 16:50:28 +0100 Subject: [PATCH 071/131] TST: flaky `test_single_axis` (#272) --- tests/test_funcs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 652e12ef..0cee0b4d 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -521,7 +521,7 @@ def test_xp(self, xp: ModuleType): class TestExpandDims: def test_single_axis(self, xp: ModuleType): """Trivial case where xpx.expand_dims doesn't add anything to xp.expand_dims""" - a = xp.empty((2, 3, 4, 5)) + a = xp.asarray(np.reshape(np.arange(2 * 3 * 4 * 5), (2, 3, 4, 5))) for axis in range(-5, 4): b = expand_dims(a, axis=axis) xp_assert_equal(b, xp.expand_dims(a, axis=axis)) From 2ba372c6b08ad32fcabef58403d33114c500e9a5 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 22 Apr 2025 20:29:41 +0100 Subject: [PATCH 072/131] CD: fix docs deployment (#273) closes gh-266 --- .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 3f7e6ed0..78a5ada1 100644 --- a/.github/workflows/docs-deploy.yml +++ b/.github/workflows/docs-deploy.yml @@ -1,7 +1,7 @@ name: Docs Deploy permissions: - contents: read + contents: write # needed for the deploy step on: workflow_run: From 675582f74420ed260d8d079b8d5244d26aa660c0 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 23 Apr 2025 15:06:07 +0100 Subject: [PATCH 073/131] deps: add dep groups for dask and jax (#275) --- renovate.json | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/renovate.json b/renovate.json index 10ea8ab9..473f963c 100644 --- a/renovate.json +++ b/renovate.json @@ -50,6 +50,14 @@ "matchManagers": ["github-actions"], "matchPackageNames": ["python"], "enabled": false + }, + { + "matchPackageNames": ["dask", "dask-core"], + "groupName": "dask" + }, + { + "matchPackageNames": ["jax", "jaxlib"], + "groupName": "jax" } ] } From 143ff393c57516c914e786ddb6309a5a32b477ab Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 23 Apr 2025 14:19:07 +0000 Subject: [PATCH 074/131] deps: Update dependency hypothesis to >=6.130.12 (#274) 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 2153c4e2..487c161a 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5256,7 +5256,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 68490b5f2feb7687422f882f54bb2a93c687425b984a69ecd58c9d6d73653139 + sha256: ba6f94790cc0ad792e4857f421b2bed4c62892f2bc923db0108ff6b34c92ddef requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 9d897cc0..058b2467 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 = ">=6.130.11" +hypothesis = ">=6.130.12" dask-core = ">=2025.3.0" # 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 @@ -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 = ">=6.130.11" +hypothesis = ">=6.130.12" array-api-strict = ">=2.3.1" numpy = ">=1.22.0" From 53db9db57c60abd52614afe8b51208e20d09c2f3 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 23 Apr 2025 15:22:02 +0100 Subject: [PATCH 075/131] DEV: disable codecov project status (#276) this avoids failing statuses on PRs due to having to wait for test-backends in unrelated areas of the codebase --- codecov.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/codecov.yml b/codecov.yml index d05bc8e2..dc9b47cd 100644 --- a/codecov.yml +++ b/codecov.yml @@ -4,3 +4,6 @@ github_checks: ignore: - "src/array_api_extra/_lib/_compat" - "src/array_api_extra/_lib/_typing" +coverage: + status: + project: off From 54aaf84ebc90465249ad14d6784ae373ca68ef8f Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 24 Apr 2025 04:21:04 +0000 Subject: [PATCH 076/131] deps: Update dependency basedpyright to >=1.28.5 (#277) 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 487c161a..aeb86565 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5256,7 +5256,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: ba6f94790cc0ad792e4857f421b2bed4c62892f2bc923db0108ff6b34c92ddef + sha256: e0b7b737906dee4bde7c104b7c777f78a22a1b296f32ba74da5b72cce828eb63 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 058b2467..82290941 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -58,7 +58,7 @@ typing-extensions = ">=4.13.1" pre-commit = ">=4.2.0" pylint = ">=3.3.6" basedmypy = ">=2.10.0" -basedpyright = ">=1.28.3" +basedpyright = ">=1.28.5" numpydoc = ">=1.8.0,<2" # import dependencies for mypy: array-api-strict = ">=2.3.1" From ebcdaca65bbf5fa78dd76ef16afeb3e51937badb Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 24 Apr 2025 10:58:24 +0000 Subject: [PATCH 077/131] deps: Update dependency numba to >=0.61.2 (#278) 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 aeb86565..58f0ca0f 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5256,7 +5256,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: e0b7b737906dee4bde7c104b7c777f78a22a1b296f32ba74da5b72cce828eb63 + sha256: 620e3454c349ccc780eefd0a1aa3ab21e1e574465484b43c089402f12f71e3e6 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 82290941..df9b6b0e 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -136,7 +136,7 @@ numpy = "=1.22.0" [tool.pixi.feature.backends.dependencies] pytorch = ">=2.6.0" dask = ">=2025.3.0" -numba = ">=0.61.0" # sparse dependency +numba = ">=0.61.2" # sparse dependency llvmlite = ">=0.44.0" # sparse dependency [tool.pixi.feature.backends.pypi-dependencies] From 9a425121bbf6afb5bd155e137ac65b8aa5494926 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 24 Apr 2025 20:49:58 +0000 Subject: [PATCH 078/131] deps: Update dependency typing-extensions to >=4.13.2 (#279) 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 58f0ca0f..fbe6f8b8 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5256,7 +5256,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 620e3454c349ccc780eefd0a1aa3ab21e1e574465484b43c089402f12f71e3e6 + sha256: 3c9987a48df7f5e5f16e25b7b14512512f23c4438e62c85f5c830973620138ca requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index df9b6b0e..e560ff2d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,7 +54,7 @@ array-api-compat = ">=1.11.2,<2" array-api-extra = { path = ".", editable = true } [tool.pixi.feature.lint.dependencies] -typing-extensions = ">=4.13.1" +typing-extensions = ">=4.13.2" pre-commit = ">=4.2.0" pylint = ">=3.3.6" basedmypy = ">=2.10.0" @@ -107,7 +107,7 @@ sphinx-autodoc-typehints = ">=1.25.3" # Needed to import parsed modules with autodoc dask-core = ">=2025.3.0" pytest = ">=8.3.5" -typing-extensions = ">=4.13.1" +typing-extensions = ">=4.13.2" numpy = ">=2.1.3" [tool.pixi.feature.docs.tasks] From 375429280779ac8b0d6bef508a695428cba626f9 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 24 Apr 2025 21:51:55 +0100 Subject: [PATCH 079/131] deps: Update dependency hypothesis to >=6.131.0 (#280) 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 fbe6f8b8..098b77a2 100644 --- a/pixi.lock +++ b/pixi.lock @@ -5256,7 +5256,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 3c9987a48df7f5e5f16e25b7b14512512f23c4438e62c85f5c830973620138ca + sha256: 9d5f699a813b67c48b9b575fcc37ccd15092cfbf685005c28ab952d29096d05b requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index e560ff2d..b87bfc57 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 = ">=6.130.12" +hypothesis = ">=6.131.0" dask-core = ">=2025.3.0" # 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 @@ -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 = ">=6.130.12" +hypothesis = ">=6.131.0" array-api-strict = ">=2.3.1" numpy = ">=1.22.0" From 22234b4593be902efd494909705fbe321613c1f5 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Thu, 24 Apr 2025 21:52:22 +0100 Subject: [PATCH 080/131] deps: schedule hypothesis monthly (#281) releases are very frequent, causing noise --- renovate.json | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/renovate.json b/renovate.json index 473f963c..05342e62 100644 --- a/renovate.json +++ b/renovate.json @@ -52,12 +52,20 @@ "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 * *"] } ] } From 93763994120c4c57b53f4d65d59f5dc21cfa9f16 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 24 Apr 2025 22:02:38 +0100 Subject: [PATCH 081/131] deps: Update dependency hypothesis to >=6.131.8 (#282) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- pixi.lock | 85 +++++++++++++++++++++++++------------------------- pyproject.toml | 4 +-- 2 files changed, 44 insertions(+), 45 deletions(-) diff --git a/pixi.lock b/pixi.lock index 098b77a2..61b1f717 100644 --- a/pixi.lock +++ b/pixi.lock @@ -159,7 +159,7 @@ environments: - 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pypi: . name: array-api-extra version: 0.7.2.dev0 - sha256: 9d5f699a813b67c48b9b575fcc37ccd15092cfbf685005c28ab952d29096d05b + sha256: eb518a1094740e5a41c947fb7b93845d39c8c52fd03755313440f3771ecad7f6 requires_dist: - array-api-compat>=1.11.2,<2 requires_python: '>=3.10' @@ -8001,9 +8001,9 @@ packages: - pkg:pypi/hyperframe?source=hash-mapping size: 17397 timestamp: 1737618427549 -- conda: https://prefix.dev/conda-forge/noarch/hypothesis-6.131.0-pyha770c72_0.conda - sha256: 10ba30fee960f8e02b49f030d1272e41694752ed6bd6260be611611c5f03d376 - md5: fdb4b15c1f542fb91da87f8b6f6535de +- conda: https://prefix.dev/conda-forge/noarch/hypothesis-6.131.8-pyha770c72_0.conda + sha256: 420637353239732b2649bf3ed6039bf7e12f09f595752a67d5d27be72b88e86b + md5: 09f4414e824e694fb3b89b25421b27df depends: - attrs >=22.2.0 - click >=7.0 @@ -8012,11 +8012,10 @@ packages: - setuptools - sortedcontainers >=2.1.0,<3.0.0 license: MPL-2.0 - license_family: MOZILLA purls: - pkg:pypi/hypothesis?source=hash-mapping - size: 352719 - timestamp: 1744300918665 + size: 356193 + timestamp: 1745475780825 - conda: https://prefix.dev/conda-forge/linux-64/icu-75.1-he02047a_0.conda sha256: 71e750d509f5fa3421087ba88ef9a7b9be11c53174af3aa4d06aff4c18b38e8e md5: 8b189310083baabfb622af68fd9d3ae3 diff --git a/pyproject.toml b/pyproject.toml index b87bfc57..cba9c4cf 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 = ">=6.131.0" +hypothesis = ">=6.131.8" dask-core = ">=2025.3.0" # 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 @@ -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 = ">=6.131.0" +hypothesis = ">=6.131.8" array-api-strict = ">=2.3.1" numpy = ">=1.22.0" From 4425d149867770a28b316fd98133c2b4584bfc48 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Fri, 25 Apr 2025 13:18:52 +0100 Subject: [PATCH 082/131] ENH: `allow_dask_compute=True` instead of 999 (#283) --- src/array_api_extra/testing.py | 18 +++++++++++++----- tests/test_testing.py | 20 +++++++++++++------- 2 files changed, 26 insertions(+), 12 deletions(-) diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index 4f8288cf..37e8e69e 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -39,7 +39,7 @@ def override(func: object) -> object: def lazy_xp_function( # type: ignore[explicit-any] func: Callable[..., Any], *, - allow_dask_compute: int = 0, + allow_dask_compute: bool | int = False, jax_jit: bool = True, static_argnums: int | Sequence[int] | None = None, static_argnames: str | Iterable[str] | None = None, @@ -59,9 +59,10 @@ def lazy_xp_function( # type: ignore[explicit-any] ---------- func : callable Function to be tested. - allow_dask_compute : int, optional - Number of times `func` is allowed to internally materialize the Dask graph. This - is typically triggered by ``bool()``, ``float()``, or ``np.asarray()``. + allow_dask_compute : bool | int, optional + Whether `func` is allowed to internally materialize the Dask graph, or maximum + number of times it is allowed to do so. This is typically triggered by + ``bool()``, ``float()``, or ``np.asarray()``. Set to 1 if you are aware that `func` converts the input parameters to NumPy and want to let it do so at least for the time being, knowing that it is going to be @@ -75,7 +76,10 @@ def lazy_xp_function( # type: ignore[explicit-any] a test function that invokes `func` multiple times should still work with this parameter set to 1. - Default: 0, meaning that `func` must be fully lazy and never materialize the + Set to True to allow `func` to materialize the graph an unlimited number + of times. + + 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 @@ -235,6 +239,10 @@ def iter_tagged() -> ( # type: ignore[explicit-any] if is_dask_namespace(xp): for mod, name, func, tags in iter_tagged(): n = tags["allow_dask_compute"] + if n is True: + n = 1_000_000 + elif n is False: + n = 0 wrapped = _dask_wrap(func, n) monkeypatch.setattr(mod, name, wrapped) diff --git a/tests/test_testing.py b/tests/test_testing.py index ff67121b..fb9ba581 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -130,13 +130,18 @@ def non_materializable4(x: Array) -> Array: return non_materializable(x) +def non_materializable5(x: Array) -> Array: + return non_materializable(x) + + lazy_xp_function(good_lazy) # Works on JAX and Dask lazy_xp_function(non_materializable2, jax_jit=False, allow_dask_compute=2) +lazy_xp_function(non_materializable3, jax_jit=False, allow_dask_compute=True) # Works on JAX, but not Dask -lazy_xp_function(non_materializable3, jax_jit=False, allow_dask_compute=1) +lazy_xp_function(non_materializable4, jax_jit=False, allow_dask_compute=1) # Works neither on Dask nor JAX -lazy_xp_function(non_materializable4) +lazy_xp_function(non_materializable5) def test_lazy_xp_function(xp: ModuleType): @@ -147,29 +152,30 @@ def test_lazy_xp_function(xp: ModuleType): xp_assert_equal(non_materializable(x), xp.asarray([1.0, 2.0])) # Wrapping explicitly disabled xp_assert_equal(non_materializable2(x), xp.asarray([1.0, 2.0])) + xp_assert_equal(non_materializable3(x), xp.asarray([1.0, 2.0])) if is_jax_namespace(xp): - xp_assert_equal(non_materializable3(x), xp.asarray([1.0, 2.0])) + xp_assert_equal(non_materializable4(x), xp.asarray([1.0, 2.0])) with pytest.raises( TypeError, match="Attempted boolean conversion of traced array" ): - _ = non_materializable4(x) # Wrapped + _ = non_materializable5(x) # Wrapped elif is_dask_namespace(xp): with pytest.raises( AssertionError, match=r"dask\.compute.* 2 times, but only up to 1 calls are allowed", ): - _ = non_materializable3(x) + _ = non_materializable4(x) with pytest.raises( AssertionError, match=r"dask\.compute.* 1 times, but no calls are allowed", ): - _ = non_materializable4(x) + _ = non_materializable5(x) else: - xp_assert_equal(non_materializable3(x), xp.asarray([1.0, 2.0])) xp_assert_equal(non_materializable4(x), xp.asarray([1.0, 2.0])) + xp_assert_equal(non_materializable5(x), xp.asarray([1.0, 2.0])) def static_params(x: Array, n: int, flag: bool = False) -> Array: From bb6129b1bfe344b9807a2f28451fe9211efe0b1b Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Fri, 25 Apr 2025 15:57:08 +0100 Subject: [PATCH 083/131] MAINT: array_api_compat tweaks (#285) --- src/array_api_extra/_lib/_utils/_compat.py | 3 ++ src/array_api_extra/_lib/_utils/_compat.pyi | 43 ++++++++++++--------- vendor_tests/test_vendor.py | 3 +- 3 files changed, 29 insertions(+), 20 deletions(-) diff --git a/src/array_api_extra/_lib/_utils/_compat.py b/src/array_api_extra/_lib/_utils/_compat.py index b9997450..c6eec4cd 100644 --- a/src/array_api_extra/_lib/_utils/_compat.py +++ b/src/array_api_extra/_lib/_utils/_compat.py @@ -23,6 +23,7 @@ is_torch_namespace, is_writeable_array, size, + to_device, ) except ImportError: from array_api_compat import ( @@ -45,6 +46,7 @@ is_torch_namespace, is_writeable_array, size, + to_device, ) __all__ = [ @@ -67,4 +69,5 @@ "is_torch_namespace", "is_writeable_array", "size", + "to_device", ] diff --git a/src/array_api_extra/_lib/_utils/_compat.pyi b/src/array_api_extra/_lib/_utils/_compat.pyi index f40d7556..48addda4 100644 --- a/src/array_api_extra/_lib/_utils/_compat.pyi +++ b/src/array_api_extra/_lib/_utils/_compat.pyi @@ -4,6 +4,7 @@ from __future__ import annotations from types import ModuleType +from typing import Any, TypeGuard # TODO import from typing (requires Python >=3.13) from typing_extensions import TypeIs @@ -12,29 +13,33 @@ from ._typing import Array, Device # pylint: disable=missing-class-docstring,unused-argument -class Namespace(ModuleType): - def device(self, x: Array, /) -> Device: ... - def array_namespace( *xs: Array | complex | None, api_version: str | None = None, use_compat: bool | None = None, -) -> Namespace: ... +) -> ModuleType: ... def device(x: Array, /) -> Device: ... def is_array_api_obj(x: object, /) -> TypeIs[Array]: ... -def is_array_api_strict_namespace(xp: ModuleType, /) -> TypeIs[Namespace]: ... -def is_cupy_namespace(xp: ModuleType, /) -> TypeIs[Namespace]: ... -def is_dask_namespace(xp: ModuleType, /) -> TypeIs[Namespace]: ... -def is_jax_namespace(xp: ModuleType, /) -> TypeIs[Namespace]: ... -def is_numpy_namespace(xp: ModuleType, /) -> TypeIs[Namespace]: ... -def is_pydata_sparse_namespace(xp: ModuleType, /) -> TypeIs[Namespace]: ... -def is_torch_namespace(xp: ModuleType, /) -> TypeIs[Namespace]: ... -def is_cupy_array(x: object, /) -> TypeIs[Array]: ... -def is_dask_array(x: object, /) -> TypeIs[Array]: ... -def is_jax_array(x: object, /) -> TypeIs[Array]: ... -def is_numpy_array(x: object, /) -> TypeIs[Array]: ... -def is_pydata_sparse_array(x: object, /) -> TypeIs[Array]: ... -def is_torch_array(x: object, /) -> TypeIs[Array]: ... -def is_lazy_array(x: object, /) -> TypeIs[Array]: ... -def is_writeable_array(x: object, /) -> TypeIs[Array]: ... +def is_array_api_strict_namespace(xp: ModuleType, /) -> bool: ... +def is_cupy_namespace(xp: ModuleType, /) -> bool: ... +def is_dask_namespace(xp: ModuleType, /) -> bool: ... +def is_jax_namespace(xp: ModuleType, /) -> bool: ... +def is_numpy_namespace(xp: ModuleType, /) -> bool: ... +def is_pydata_sparse_namespace(xp: ModuleType, /) -> bool: ... +def is_torch_namespace(xp: ModuleType, /) -> bool: ... +def is_cupy_array(x: object, /) -> TypeGuard[Array]: ... +def is_dask_array(x: object, /) -> TypeGuard[Array]: ... +def is_jax_array(x: object, /) -> TypeGuard[Array]: ... +def is_numpy_array(x: object, /) -> TypeGuard[Array]: ... +def is_pydata_sparse_array(x: object, /) -> TypeGuard[Array]: ... +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] + x: Array, + device: Device, # pylint: disable=redefined-outer-name + /, + *, + stream: int | Any | None = None, +) -> Array: ... diff --git a/vendor_tests/test_vendor.py b/vendor_tests/test_vendor.py index 4613edc7..374cba11 100644 --- a/vendor_tests/test_vendor.py +++ b/vendor_tests/test_vendor.py @@ -23,11 +23,12 @@ def test_vendor_compat(): is_torch_namespace, is_writeable_array, size, + to_device, ) x = xp.asarray([1, 2, 3]) assert array_namespace(x) is xp - device(x) + to_device(x, device(x)) assert is_array_api_obj(x) assert is_array_api_strict_namespace(xp) assert not is_cupy_array(x) From c3ba802c2625064d993c271e281d2543a1638e32 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 30 Apr 2025 15:16:32 +0100 Subject: [PATCH 084/131] deps: disable requires-python updates (#288) --- renovate.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/renovate.json b/renovate.json index 05342e62..c263292b 100644 --- a/renovate.json +++ b/renovate.json @@ -21,8 +21,8 @@ "enabled": false }, { - "description": "Do not bump Python deps in the manifest.", - "matchManagers": ["pixi"], + "description": "Do not bump Python deps in the manifest or requires-python.", + "matchManagers": ["pixi", "pep621"], "matchPackageNames": ["python"], "enabled": false }, From b56aeba0223cbe0585d2018ec6566dea8c57aa55 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Sun, 11 May 2025 23:08:07 +0100 Subject: [PATCH 085/131] REL: prepare 0.7.2 release (#289) * REL: bump version to 0.7.2 * update lock file --- pixi.lock | 7190 +++++++++++++++---------------- src/array_api_extra/__init__.py | 2 +- 2 files changed, 3595 insertions(+), 3597 deletions(-) diff --git a/pixi.lock b/pixi.lock index 61b1f717..ac0d48f9 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,22 +11,22 @@ environments: - 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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 087/131] 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 088/131] 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 089/131] 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 090/131] 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 091/131] 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 092/131] 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 093/131] 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 094/131] 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 095/131] 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 096/131] 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 097/131] 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 098/131] 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 099/131] 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 100/131] 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 101/131] 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 102/131] 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 103/131] 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 104/131] 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 105/131] 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 107/131] 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 108/131] 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 109/131] 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 110/131] 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 111/131] 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 112/131] 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 113/131] 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 114/131] 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 115/131] 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 116/131] 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 117/131] 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 118/131] 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 119/131] 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 120/131] 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 121/131] 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 122/131] 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 123/131] 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 124/131] 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 125/131] 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 126/131] 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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version: 0.8.1.dev0 - sha256: f83e26a4917e36e3729f14eee4af233f02056332e85a601e8731c6e983ede675 + sha256: 8236f595888133a239f0b7b6a6ee07a83c143c6bb09bb8b26ffff0309336f27b requires_dist: - array-api-compat>=1.12.0,<2 requires_python: '>=3.10' @@ -9655,9 +9655,9 @@ packages: - pkg:pypi/pytest?source=compressed-mapping size: 275014 timestamp: 1748907618871 -- conda: https://prefix.dev/conda-forge/noarch/pytest-cov-6.1.1-pyhd8ed1ab_0.conda - sha256: 9961a1524f63d10bc29efdc52013ec06b0e95fb2619a250e250ff3618261d5cd - md5: 1e35d8f975bc0e984a19819aa91c440a +- conda: https://prefix.dev/conda-forge/noarch/pytest-cov-6.2.1-pyhd8ed1ab_0.conda + sha256: 3a9fc07be76bc67aef355b78816b5117bfe686e7d8c6f28b45a1f89afe104761 + md5: ce978e1b9ed8b8d49164e90a5cdc94cd depends: - coverage >=7.5 - pytest >=4.6 @@ -9666,9 +9666,9 @@ packages: license: MIT license_family: MIT purls: - - pkg:pypi/pytest-cov?source=hash-mapping - size: 27565 - timestamp: 1743886993683 + - pkg:pypi/pytest-cov?source=compressed-mapping + 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 128/131] 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 129/131] 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 131/131] 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)