From e5c33723f92829d21b04e5a4c0d6b7746ac3b533 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Wed, 15 Jan 2025 14:40:08 +0000 Subject: [PATCH 001/140] DEV: set version to 0.6.1.dev0 --- RELEASING.md | 4 ++-- pixi.lock | 2 +- src/array_api_extra/__init__.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/RELEASING.md b/RELEASING.md index a9640cb4..564fc682 100644 --- a/RELEASING.md +++ b/RELEASING.md @@ -1,8 +1,8 @@ 1. Update the version in `src/array_api_extra/__init__.py` -2. Update the lockfile with `pixi update` and `pixi install` +2. Update the lockfile with `pixi update && pixi install` 3. Push your changes 4. Cut a release via the GitHub GUI 5. Update the version to `{next micro version}.dev0` -6. Update the lockfile +6. `pixi clean cache --pypi && pixi update && pixi install` 7. Push your changes 8. Merge the automated PR to conda-forge/array-api-extra-feedstock diff --git a/pixi.lock b/pixi.lock index 438cf49e..6955b233 100644 --- a/pixi.lock +++ b/pixi.lock @@ -2466,7 +2466,7 @@ packages: timestamp: 1735201429468 - pypi: . name: array-api-extra - version: 0.6.0 + version: 0.6.1.dev0 sha256: 4ec1183114a670b9c9b9b351826c962ad92ab470b1914a163e4a5ed02d0e04a0 requires_dist: - array-api-compat>=1.10.0,<2 diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index ea660f1e..360097f7 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -13,7 +13,7 @@ sinc, ) -__version__ = "0.6.0" +__version__ = "0.6.1.dev0" # pylint: disable=duplicate-code __all__ = [ From ccc23d7e1557f24153e5279a08e455c66d5a6eab Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Wed, 15 Jan 2025 19:59:12 +0000 Subject: [PATCH 002/140] MAINT: JAX CUDA environment (#95) Co-authored-by: Lucas Colley --- pixi.lock | 4866 +++++++++++++++++++++++++++++++++++++++++++----- pyproject.toml | 15 +- 2 files changed, 4453 insertions(+), 428 deletions(-) diff --git a/pixi.lock b/pixi.lock index 6955b233..f94d86a8 100644 --- a/pixi.lock +++ b/pixi.lock @@ -36,7 +36,7 @@ environments: - 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_your library? Let us know!_ +## Installation + +See https://data-apis.org/array-api-extra/#installation. + +## Versioning + +This project uses [EffVer](https://jacobtomlinson.dev/effver/). TL;DR: + +- To bump from version `x.y.z` to `x.(y+1).0` of array-api-extra, expect that + you may need to put in some work. +- To bump from version `x.y.z` to `x.y.(z+1)`, any work needed on your side + should be minimal. Please open an issue if this is not the case! + ## Contributors This project exists thanks to the following contributors diff --git a/docs/index.md b/docs/index.md index c1998cdd..d15a6247 100644 --- a/docs/index.md +++ b/docs/index.md @@ -112,7 +112,16 @@ 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 + https://github.com/scipy/scipy/blob/main/scipy/_lib/_array_api_compat_vendor.py + +## Versioning + +This project uses [EffVer](https://jacobtomlinson.dev/effver/). TL;DR: + +- To bump from version `x.y.z` to `x.(y+1).0` of array-api-extra, expect that + you may need to put in some work. +- To bump from version `x.y.z` to `x.y.(z+1)`, any work needed on your side + should be minimal. Please open an issue if this is not the case! 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python >=3.8 license: BSD-3-Clause license_family: BSD purls: - pkg:pypi/xyzservices?source=hash-mapping - size: 46860 - timestamp: 1733143536777 + size: 48641 + timestamp: 1737234992057 - conda: https://prefix.dev/conda-forge/linux-64/yaml-0.2.5-h7f98852_2.tar.bz2 sha256: a4e34c710eeb26945bdbdaba82d3d74f60a78f54a874ec10d373811a5d217535 md5: 4cb3ad778ec2d5a7acbdf254eb1c42ae diff --git a/pyproject.toml b/pyproject.toml index 1ad1ca1c..d6ea9805 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -167,7 +167,7 @@ cupy = "*" [tool.pixi.environments] default = { solve-group = "default" } -lint = { features = ["lint"], solve-group = "default" } +lint = { features = ["lint", "backends"], 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" } diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 360097f7..65d2f738 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -1,8 +1,8 @@ """Extra array functions built on top of the array API standard.""" from ._delegation import pad +from ._lib._at import at from ._lib._funcs import ( - at, atleast_nd, cov, create_diagonal, diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py new file mode 100644 index 00000000..f2dd7219 --- /dev/null +++ b/src/array_api_extra/_lib/_at.py @@ -0,0 +1,373 @@ +"""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 ._utils._compat import array_namespace, is_jax_array, is_writeable_array +from ._utils._typing import Array, Index + + +class _AtOp(Enum): + """Operations for use in `xpx.at`.""" + + SET = "set" + ADD = "add" + SUBTRACT = "subtract" + MULTIPLY = "multiply" + DIVIDE = "divide" + POWER = "power" + MIN = "min" + MAX = "max" + + # @override from Python 3.12 + def __str__(self) -> str: # type: ignore[explicit-override] # pyright: ignore[reportImplicitOverride] + """ + Return string representation (useful for pytest logs). + + Returns + ------- + str + The operation's name. + """ + return self.value + + +_undef = object() + + +class at: # pylint: disable=invalid-name # numpydoc ignore=PR02 + """ + Update operations for read-only arrays. + + This implements ``jax.numpy.ndarray.at`` for all writeable + backends (those that support ``__setitem__``) and routes + to the ``.at[]`` method for JAX arrays. + + Parameters + ---------- + x : array + Input array. + idx : index, optional + Only `array API standard compliant indices + `_ + are supported. + + You may use two alternate syntaxes:: + + >>> import array_api_extra as xpx + >>> xpx.at(x, idx).set(value) # or add(value), etc. + >>> xpx.at(x)[idx].set(value) + + copy : bool, optional + None (default) + The array parameter *may* be modified in place if it is + possible and beneficial for performance. + You should not reuse it after calling this function. + True + Ensure that the inputs are not modified. + False + Ensure that the update operation writes back to the input. + Raise ``ValueError`` if a copy cannot be avoided. + + xp : array_namespace, optional + The standard-compatible namespace for `x`. Default: infer. + + Returns + ------- + Updated input array. + + Warnings + -------- + (a) When you omit the ``copy`` parameter, you should never reuse the parameter + array later on; ideally, you should reassign it immediately:: + + >>> import array_api_extra as xpx + >>> x = xpx.at(x, 0).set(2) + + The above best practice pattern ensures that the behaviour won't change depending + on whether ``x`` is writeable or not, as the original ``x`` object is dereferenced + as soon as ``xpx.at`` returns; this way there is no risk to accidentally update it + twice. + + On the reverse, the anti-pattern below must be avoided, as it will result in + different behaviour on read-only versus writeable arrays:: + + >>> x = xp.asarray([0, 0, 0]) + >>> y = xpx.at(x, 0).set(2) + >>> z = xpx.at(x, 1).set(3) + + In the above example, both calls to ``xpx.at`` update ``x`` in place *if possible*. + This causes the behaviour to diverge depending on whether ``x`` is writeable or not: + + - If ``x`` is writeable, then after the snippet above you'll have + ``x == y == z == [2, 3, 0]`` + - If ``x`` is read-only, then you'll end up with + ``x == [0, 0, 0]``, ``y == [2, 0, 0]`` and ``z == [0, 3, 0]``. + + The correct pattern to use if you want diverging outputs from the same input is + to enforce copies:: + + >>> x = xp.asarray([0, 0, 0]) + >>> y = xpx.at(x, 0).set(2, copy=True) # Never updates x + >>> z = xpx.at(x, 1).set(3) # May or may not update x in place + >>> del x # avoid accidental reuse of x as we don't know its state anymore + + (b) The array API standard does not support integer array indices. + The behaviour of update methods when the index is an array of integers is + undefined and will vary between backends; this is particularly true when the + index contains multiple occurrences of the same index, e.g.:: + + >>> import numpy as np + >>> import jax.numpy as jnp + >>> import array_api_extra as xpx + >>> xpx.at(np.asarray([123]), np.asarray([0, 0])).add(1) + array([124]) + >>> xpx.at(jnp.asarray([123]), jnp.asarray([0, 0])).add(1) + Array([125], dtype=int32) + + See Also + -------- + jax.numpy.ndarray.at : Equivalent array method in JAX. + + Notes + ----- + `sparse `_, as well as read-only arrays from libraries + not explicitly covered by ``array-api-compat``, are not supported by update + methods. + + Examples + -------- + Given either of these equivalent expressions:: + + >>> import array_api_extra as xpx + >>> x = xpx.at(x)[1].add(2) + >>> x = xpx.at(x, 1).add(2) + + If x is a JAX array, they are the same as:: + + >>> x = x.at[1].add(2) + + If x is a read-only numpy array, they are the same as:: + + >>> x = x.copy() + >>> x[1] += 2 + + For other known backends, they are the same as:: + + >>> x[1] += 2 + """ + + _x: Array + _idx: Index + __slots__: ClassVar[tuple[str, ...]] = ("_idx", "_x") + + def __init__( + self, x: Array, idx: Index = _undef, / + ) -> None: # numpydoc ignore=GL08 + self._x = x + self._idx = idx + + def __getitem__(self, idx: Index, /) -> at: # numpydoc ignore=PR01,RT01 + """ + Allow for the alternate syntax ``at(x)[start:stop:step]``. + + It looks prettier than ``at(x, slice(start, stop, step))`` + and feels more intuitive coming from the JAX documentation. + """ + if self._idx is not _undef: + msg = "Index has already been set" + raise ValueError(msg) + return at(self._x, idx) + + def _update_common( + self, + at_op: _AtOp, + y: Array, + /, + copy: bool | None, + xp: ModuleType | None, + ) -> tuple[Array, None] | tuple[None, Array]: # numpydoc ignore=PR01 + """ + Perform common prepocessing to all update operations. + + Returns + ------- + tuple + If the operation can be resolved by ``at[]``, ``(return value, None)`` + Otherwise, ``(None, preprocessed x)``. + """ + x, idx = self._x, self._idx + + if idx is _undef: + msg = ( + "Index has not been set.\n" + "Usage: either\n" + " at(x, idx).set(value)\n" + "or\n" + " at(x)[idx].set(value)\n" + "(same for all other methods)." + ) + raise ValueError(msg) + + if copy not in (True, False, None): + msg = f"copy must be True, False, or None; got {copy!r}" + raise ValueError(msg) + + if copy is None: + writeable = is_writeable_array(x) + copy = not writeable + elif copy: + writeable = None + else: + writeable = is_writeable_array(x) + + if copy: + if is_jax_array(x): + # Use JAX's at[] + func = cast(Callable[[Array], Array], getattr(x.at[idx], at_op.value)) + return func(y), None + # Emulate at[] behaviour for non-JAX arrays + # with a copy followed by an update + if xp is None: + xp = array_namespace(x) + x = xp.asarray(x, copy=True) + if writeable is False: + # A copy of a read-only numpy array is writeable + # Note: this assumes that a copy of a writeable array is writeable + writeable = None + + if writeable is None: + writeable = is_writeable_array(x) + if not writeable: + # sparse crashes here + msg = f"Can't update read-only array {x}" + raise ValueError(msg) + + return None, x + + def set( + self, + y: Array, + /, + copy: bool | None = None, + xp: ModuleType | None = None, + ) -> Array: # numpydoc ignore=PR01,RT01 + """Apply ``x[idx] = y`` and return the update array.""" + res, x = self._update_common(_AtOp.SET, y, copy=copy, xp=xp) + if res is not None: + return res + assert x is not None + x[self._idx] = y + return x + + def _iop( + self, + at_op: _AtOp, + elwise_op: Callable[[Array, Array], Array], + y: Array, + /, + copy: bool | None, + xp: ModuleType | None, + ) -> Array: # numpydoc ignore=PR01,RT01 + """ + ``x[idx] += y`` or equivalent in-place operation on a subset of x. + + which is the same as saying + x[idx] = x[idx] + y + Note that this is not the same as + operator.iadd(x[idx], y) + Consider for example when x is a numpy array and idx is a fancy index, which + triggers a deep copy on __getitem__. + """ + res, x = self._update_common(at_op, y, copy=copy, xp=xp) + if res is not None: + return res + assert x is not None + x[self._idx] = elwise_op(x[self._idx], y) + return x + + def add( + self, + y: Array, + /, + copy: bool | None = None, + xp: ModuleType | None = None, + ) -> Array: # numpydoc ignore=PR01,RT01 + """Apply ``x[idx] += y`` and return the updated array.""" + + # Note for this and all other methods based on _iop: + # operator.iadd and operator.add subtly differ in behaviour, as + # only iadd will trigger exceptions when y has an incompatible dtype. + return self._iop(_AtOp.ADD, operator.iadd, y, copy=copy, xp=xp) + + def subtract( + self, + y: Array, + /, + copy: bool | None = None, + xp: ModuleType | None = None, + ) -> Array: # numpydoc ignore=PR01,RT01 + """Apply ``x[idx] -= y`` and return the updated array.""" + return self._iop(_AtOp.SUBTRACT, operator.isub, y, copy=copy, xp=xp) + + def multiply( + self, + y: Array, + /, + copy: bool | None = None, + xp: ModuleType | None = None, + ) -> Array: # numpydoc ignore=PR01,RT01 + """Apply ``x[idx] *= y`` and return the updated array.""" + return self._iop(_AtOp.MULTIPLY, operator.imul, y, copy=copy, xp=xp) + + def divide( + self, + y: Array, + /, + copy: bool | None = None, + xp: ModuleType | None = None, + ) -> Array: # numpydoc ignore=PR01,RT01 + """Apply ``x[idx] /= y`` and return the updated array.""" + return self._iop(_AtOp.DIVIDE, operator.itruediv, y, copy=copy, xp=xp) + + def power( + self, + y: Array, + /, + copy: bool | None = None, + xp: ModuleType | None = None, + ) -> Array: # numpydoc ignore=PR01,RT01 + """Apply ``x[idx] **= y`` and return the updated array.""" + return self._iop(_AtOp.POWER, operator.ipow, y, copy=copy, xp=xp) + + def min( + self, + y: Array, + /, + copy: bool | None = None, + xp: ModuleType | None = None, + ) -> Array: # numpydoc ignore=PR01,RT01 + """Apply ``x[idx] = minimum(x[idx], y)`` and return the updated array.""" + if xp is None: + xp = array_namespace(self._x) + y = xp.asarray(y) + return self._iop(_AtOp.MIN, xp.minimum, y, copy=copy, xp=xp) + + def max( + self, + y: Array, + /, + copy: bool | None = None, + xp: ModuleType | None = None, + ) -> Array: # numpydoc ignore=PR01,RT01 + """Apply ``x[idx] = maximum(x[idx], y)`` and return the updated array.""" + if xp is None: + xp = array_namespace(self._x) + y = xp.asarray(y) + return self._iop(_AtOp.MAX, xp.maximum, y, copy=copy, xp=xp) diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 320e5455..85778356 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -4,19 +4,16 @@ from __future__ import annotations import math -import operator import warnings -from collections.abc import Callable -from enum import Enum from types import ModuleType -from typing import ClassVar, cast +from typing import cast +from ._at import at from ._utils import _compat, _helpers -from ._utils._compat import array_namespace, is_jax_array, is_writeable_array -from ._utils._typing import Array, Index +from ._utils._compat import array_namespace, is_jax_array +from ._utils._typing import Array __all__ = [ - "at", "atleast_nd", "cov", "create_diagonal", @@ -413,6 +410,87 @@ def kron(a: Array, b: Array, /, *, xp: ModuleType | None = None) -> Array: return xp.reshape(result, res_shape) +def nunique(x: Array, /, *, xp: ModuleType | None = None) -> Array: + """ + Count the number of unique elements in an array. + + Compatible with JAX and Dask, whose laziness would be otherwise + problematic. + + Parameters + ---------- + x : Array + Input array. + xp : array_namespace, optional + The standard-compatible namespace for `x`. Default: infer. + + Returns + ------- + array: 0-dimensional integer array + The number of unique elements in `x`. It can be lazy. + """ + if xp is None: + xp = array_namespace(x) + + if is_jax_array(x): + # 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 or math.isnan(n): # e.g. Dask, ndonnx + return xp.astype(counts, xp.bool).sum() + return xp.asarray(n, device=_compat.device(x)) + + +def pad( + x: Array, + pad_width: int | tuple[int, int] | list[tuple[int, int]], + *, + constant_values: bool | int | float | complex = 0, + xp: ModuleType, +) -> Array: # numpydoc ignore=PR01,RT01 + """See docstring in `array_api_extra._delegation.py`.""" + # make pad_width a list of length-2 tuples of ints + x_ndim = cast(int, x.ndim) + if isinstance(pad_width, int): + pad_width = [(pad_width, pad_width)] * x_ndim + if isinstance(pad_width, tuple): + pad_width = [pad_width] * x_ndim + + # https://github.com/python/typeshed/issues/13376 + slices: list[slice] = [] # type: ignore[no-any-explicit] + newshape: list[int] = [] + for ax, w_tpl in enumerate(pad_width): + if len(w_tpl) != 2: + msg = f"expect a 2-tuple (before, after), got {w_tpl}." + raise ValueError(msg) + + sh = x.shape[ax] + if w_tpl[0] == 0 and w_tpl[1] == 0: + sl = slice(None, None, None) + else: + start, stop = w_tpl + stop = None if stop == 0 else -stop + + sl = slice(start, stop, None) + sh += w_tpl[0] + w_tpl[1] + + newshape.append(sh) + slices.append(sl) + + padded = xp.full( + tuple(newshape), + fill_value=constant_values, + dtype=x.dtype, + device=_compat.device(x), + ) + return at(padded, tuple(slices)).set(x) + + def setdiff1d( x1: Array, x2: Array, @@ -553,444 +631,3 @@ def sinc(x: Array, /, *, xp: ModuleType | None = None) -> Array: xp.asarray(xp.finfo(x.dtype).eps, dtype=x.dtype, device=_compat.device(x)), ) return xp.sin(y) / y - - -def pad( - x: Array, - pad_width: int | tuple[int, int] | list[tuple[int, int]], - *, - constant_values: bool | int | float | complex = 0, - xp: ModuleType, -) -> Array: # numpydoc ignore=PR01,RT01 - """See docstring in `array_api_extra._delegation.py`.""" - # make pad_width a list of length-2 tuples of ints - x_ndim = cast(int, x.ndim) - if isinstance(pad_width, int): - pad_width = [(pad_width, pad_width)] * x_ndim - if isinstance(pad_width, tuple): - pad_width = [pad_width] * x_ndim - - # https://github.com/python/typeshed/issues/13376 - slices: list[slice] = [] # type: ignore[no-any-explicit] - newshape: list[int] = [] - for ax, w_tpl in enumerate(pad_width): - if len(w_tpl) != 2: - msg = f"expect a 2-tuple (before, after), got {w_tpl}." - raise ValueError(msg) - - sh = x.shape[ax] - if w_tpl[0] == 0 and w_tpl[1] == 0: - sl = slice(None, None, None) - else: - start, stop = w_tpl - stop = None if stop == 0 else -stop - - sl = slice(start, stop, None) - sh += w_tpl[0] + w_tpl[1] - - newshape.append(sh) - slices.append(sl) - - padded = xp.full( - tuple(newshape), - fill_value=constant_values, - dtype=x.dtype, - device=_compat.device(x), - ) - return at(padded, tuple(slices)).set(x) - - -def nunique(x: Array, /, *, xp: ModuleType | None = None) -> Array: - """ - Count the number of unique elements in an array. - - Compatible with JAX and Dask, whose laziness would be otherwise - problematic. - - Parameters - ---------- - x : Array - Input array. - xp : array_namespace, optional - The standard-compatible namespace for `x`. Default: infer. - - Returns - ------- - array: 0-dimensional integer array - The number of unique elements in `x`. It can be lazy. - """ - if xp is None: - xp = array_namespace(x) - - if is_jax_array(x): - # 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 or math.isnan(n): # e.g. Dask, ndonnx - return xp.astype(counts, xp.bool).sum() - return xp.asarray(n, device=_compat.device(x)) - - -class _AtOp(Enum): - """Operations for use in `xpx.at`.""" - - SET = "set" - ADD = "add" - SUBTRACT = "subtract" - MULTIPLY = "multiply" - DIVIDE = "divide" - POWER = "power" - MIN = "min" - MAX = "max" - - # @override from Python 3.12 - def __str__(self) -> str: # type: ignore[explicit-override] # pyright: ignore[reportImplicitOverride] - """ - Return string representation (useful for pytest logs). - - Returns - ------- - str - The operation's name. - """ - return self.value - - -_undef = object() - - -class at: # pylint: disable=invalid-name # numpydoc ignore=PR02 - """ - Update operations for read-only arrays. - - This implements ``jax.numpy.ndarray.at`` for all writeable - backends (those that support ``__setitem__``) and routes - to the ``.at[]`` method for JAX arrays. - - Parameters - ---------- - x : array - Input array. - idx : index, optional - Only `array API standard compliant indices - `_ - are supported. - - You may use two alternate syntaxes:: - - >>> import array_api_extra as xpx - >>> xpx.at(x, idx).set(value) # or add(value), etc. - >>> xpx.at(x)[idx].set(value) - - copy : bool, optional - None (default) - The array parameter *may* be modified in place if it is - possible and beneficial for performance. - You should not reuse it after calling this function. - True - Ensure that the inputs are not modified. - False - Ensure that the update operation writes back to the input. - Raise ``ValueError`` if a copy cannot be avoided. - - xp : array_namespace, optional - The standard-compatible namespace for `x`. Default: infer. - - Returns - ------- - Updated input array. - - Warnings - -------- - (a) When you omit the ``copy`` parameter, you should never reuse the parameter - array later on; ideally, you should reassign it immediately:: - - >>> import array_api_extra as xpx - >>> x = xpx.at(x, 0).set(2) - - The above best practice pattern ensures that the behaviour won't change depending - on whether ``x`` is writeable or not, as the original ``x`` object is dereferenced - as soon as ``xpx.at`` returns; this way there is no risk to accidentally update it - twice. - - On the reverse, the anti-pattern below must be avoided, as it will result in - different behaviour on read-only versus writeable arrays:: - - >>> x = xp.asarray([0, 0, 0]) - >>> y = xpx.at(x, 0).set(2) - >>> z = xpx.at(x, 1).set(3) - - In the above example, both calls to ``xpx.at`` update ``x`` in place *if possible*. - This causes the behaviour to diverge depending on whether ``x`` is writeable or not: - - - If ``x`` is writeable, then after the snippet above you'll have - ``x == y == z == [2, 3, 0]`` - - If ``x`` is read-only, then you'll end up with - ``x == [0, 0, 0]``, ``y == [2, 0, 0]`` and ``z == [0, 3, 0]``. - - The correct pattern to use if you want diverging outputs from the same input is - to enforce copies:: - - >>> x = xp.asarray([0, 0, 0]) - >>> y = xpx.at(x, 0).set(2, copy=True) # Never updates x - >>> z = xpx.at(x, 1).set(3) # May or may not update x in place - >>> del x # avoid accidental reuse of x as we don't know its state anymore - - (b) The array API standard does not support integer array indices. - The behaviour of update methods when the index is an array of integers is - undefined and will vary between backends; this is particularly true when the - index contains multiple occurrences of the same index, e.g.:: - - >>> import numpy as np - >>> import jax.numpy as jnp - >>> import array_api_extra as xpx - >>> xpx.at(np.asarray([123]), np.asarray([0, 0])).add(1) - array([124]) - >>> xpx.at(jnp.asarray([123]), jnp.asarray([0, 0])).add(1) - Array([125], dtype=int32) - - See Also - -------- - jax.numpy.ndarray.at : Equivalent array method in JAX. - - Notes - ----- - `sparse `_, as well as read-only arrays from libraries - not explicitly covered by ``array-api-compat``, are not supported by update - methods. - - Examples - -------- - Given either of these equivalent expressions:: - - >>> import array_api_extra as xpx - >>> x = xpx.at(x)[1].add(2) - >>> x = xpx.at(x, 1).add(2) - - If x is a JAX array, they are the same as:: - - >>> x = x.at[1].add(2) - - If x is a read-only numpy array, they are the same as:: - - >>> x = x.copy() - >>> x[1] += 2 - - For other known backends, they are the same as:: - - >>> x[1] += 2 - """ - - _x: Array - _idx: Index - __slots__: ClassVar[tuple[str, ...]] = ("_idx", "_x") - - def __init__( - self, x: Array, idx: Index = _undef, / - ) -> None: # numpydoc ignore=GL08 - self._x = x - self._idx = idx - - def __getitem__(self, idx: Index, /) -> at: # numpydoc ignore=PR01,RT01 - """ - Allow for the alternate syntax ``at(x)[start:stop:step]``. - - It looks prettier than ``at(x, slice(start, stop, step))`` - and feels more intuitive coming from the JAX documentation. - """ - if self._idx is not _undef: - msg = "Index has already been set" - raise ValueError(msg) - return at(self._x, idx) - - def _update_common( - self, - at_op: _AtOp, - y: Array, - /, - copy: bool | None, - xp: ModuleType | None, - ) -> tuple[Array, None] | tuple[None, Array]: # numpydoc ignore=PR01 - """ - Perform common prepocessing to all update operations. - - Returns - ------- - tuple - If the operation can be resolved by ``at[]``, ``(return value, None)`` - Otherwise, ``(None, preprocessed x)``. - """ - x, idx = self._x, self._idx - - if idx is _undef: - msg = ( - "Index has not been set.\n" - "Usage: either\n" - " at(x, idx).set(value)\n" - "or\n" - " at(x)[idx].set(value)\n" - "(same for all other methods)." - ) - raise ValueError(msg) - - if copy not in (True, False, None): - msg = f"copy must be True, False, or None; got {copy!r}" - raise ValueError(msg) - - if copy is None: - writeable = is_writeable_array(x) - copy = not writeable - elif copy: - writeable = None - else: - writeable = is_writeable_array(x) - - if copy: - if is_jax_array(x): - # Use JAX's at[] - func = cast(Callable[[Array], Array], getattr(x.at[idx], at_op.value)) - return func(y), None - # Emulate at[] behaviour for non-JAX arrays - # with a copy followed by an update - if xp is None: - xp = array_namespace(x) - x = xp.asarray(x, copy=True) - if writeable is False: - # A copy of a read-only numpy array is writeable - # Note: this assumes that a copy of a writeable array is writeable - writeable = None - - if writeable is None: - writeable = is_writeable_array(x) - if not writeable: - # sparse crashes here - msg = f"Can't update read-only array {x}" - raise ValueError(msg) - - return None, x - - def set( - self, - y: Array, - /, - copy: bool | None = None, - xp: ModuleType | None = None, - ) -> Array: # numpydoc ignore=PR01,RT01 - """Apply ``x[idx] = y`` and return the update array.""" - res, x = self._update_common(_AtOp.SET, y, copy=copy, xp=xp) - if res is not None: - return res - assert x is not None - x[self._idx] = y - return x - - def _iop( - self, - at_op: _AtOp, - elwise_op: Callable[[Array, Array], Array], - y: Array, - /, - copy: bool | None, - xp: ModuleType | None, - ) -> Array: # numpydoc ignore=PR01,RT01 - """ - ``x[idx] += y`` or equivalent in-place operation on a subset of x. - - which is the same as saying - x[idx] = x[idx] + y - Note that this is not the same as - operator.iadd(x[idx], y) - Consider for example when x is a numpy array and idx is a fancy index, which - triggers a deep copy on __getitem__. - """ - res, x = self._update_common(at_op, y, copy=copy, xp=xp) - if res is not None: - return res - assert x is not None - x[self._idx] = elwise_op(x[self._idx], y) - return x - - def add( - self, - y: Array, - /, - copy: bool | None = None, - xp: ModuleType | None = None, - ) -> Array: # numpydoc ignore=PR01,RT01 - """Apply ``x[idx] += y`` and return the updated array.""" - - # Note for this and all other methods based on _iop: - # operator.iadd and operator.add subtly differ in behaviour, as - # only iadd will trigger exceptions when y has an incompatible dtype. - return self._iop(_AtOp.ADD, operator.iadd, y, copy=copy, xp=xp) - - def subtract( - self, - y: Array, - /, - copy: bool | None = None, - xp: ModuleType | None = None, - ) -> Array: # numpydoc ignore=PR01,RT01 - """Apply ``x[idx] -= y`` and return the updated array.""" - return self._iop(_AtOp.SUBTRACT, operator.isub, y, copy=copy, xp=xp) - - def multiply( - self, - y: Array, - /, - copy: bool | None = None, - xp: ModuleType | None = None, - ) -> Array: # numpydoc ignore=PR01,RT01 - """Apply ``x[idx] *= y`` and return the updated array.""" - return self._iop(_AtOp.MULTIPLY, operator.imul, y, copy=copy, xp=xp) - - def divide( - self, - y: Array, - /, - copy: bool | None = None, - xp: ModuleType | None = None, - ) -> Array: # numpydoc ignore=PR01,RT01 - """Apply ``x[idx] /= y`` and return the updated array.""" - return self._iop(_AtOp.DIVIDE, operator.itruediv, y, copy=copy, xp=xp) - - def power( - self, - y: Array, - /, - copy: bool | None = None, - xp: ModuleType | None = None, - ) -> Array: # numpydoc ignore=PR01,RT01 - """Apply ``x[idx] **= y`` and return the updated array.""" - return self._iop(_AtOp.POWER, operator.ipow, y, copy=copy, xp=xp) - - def min( - self, - y: Array, - /, - copy: bool | None = None, - xp: ModuleType | None = None, - ) -> Array: # numpydoc ignore=PR01,RT01 - """Apply ``x[idx] = minimum(x[idx], y)`` and return the updated array.""" - if xp is None: - xp = array_namespace(self._x) - y = xp.asarray(y) - return self._iop(_AtOp.MIN, xp.minimum, y, copy=copy, xp=xp) - - def max( - self, - y: Array, - /, - copy: bool | None = None, - xp: ModuleType | None = None, - ) -> Array: # numpydoc ignore=PR01,RT01 - """Apply ``x[idx] = maximum(x[idx], y)`` and return the updated array.""" - if xp is None: - xp = array_namespace(self._x) - y = xp.asarray(y) - return self._iop(_AtOp.MAX, xp.maximum, y, copy=copy, xp=xp) diff --git a/tests/conftest.py b/tests/conftest.py index c588d802..fa555018 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -105,9 +105,9 @@ def xp(library: Backend) -> ModuleType: # numpydoc ignore=PR01,RT03 return NumPyReadOnly() # type: ignore[return-value] # pyright: ignore[reportReturnType] xp = pytest.importorskip(library.value) if library == Backend.JAX_NUMPY: - import jax # type: ignore[import-not-found] # pyright: ignore[reportMissingImports] + import jax - jax.config.update("jax_enable_x64", True) + jax.config.update("jax_enable_x64", True) # type: ignore[no-untyped-call] # Possibly wrap module with array_api_compat return array_namespace(xp.empty(0)) diff --git a/tests/test_at.py b/tests/test_at.py index 749c1b55..c65a4a0d 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -12,7 +12,7 @@ from array_api_extra import at from array_api_extra._lib import Backend -from array_api_extra._lib._funcs import _AtOp +from array_api_extra._lib._at import _AtOp from array_api_extra._lib._testing import xp_assert_equal from array_api_extra._lib._utils._typing import Array diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 897b7811..3557642b 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -22,6 +22,7 @@ from array_api_extra._lib._utils._compat import device as get_device from array_api_extra._lib._utils._typing import Array, Device +# some xp backends are untyped # mypy: disable-error-code=no-untyped-usage @@ -330,6 +331,74 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(kron(a, b, xp=xp), k) +class TestNUnique: + def test_simple(self, xp: ModuleType): + a = xp.asarray([[1, 1], [0, 2], [2, 2]]) + xp_assert_equal(nunique(a), xp.asarray(3)) + + 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) + assert get_device(nunique(a)) == device + + def test_xp(self, xp: ModuleType): + a = xp.asarray([[1, 1], [0, 2], [2, 2]]) + xp_assert_equal(nunique(a, xp=xp), xp.asarray(3)) + + +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no arange, no device") +class TestPad: + def test_simple(self, xp: ModuleType): + a = xp.arange(1, 4) + padded = pad(a, 2) + xp_assert_equal(padded, xp.asarray([0, 0, 1, 2, 3, 0, 0])) + + def test_fill_value(self, xp: ModuleType): + a = xp.arange(1, 4) + padded = pad(a, 2, constant_values=42) + xp_assert_equal(padded, xp.asarray([42, 42, 1, 2, 3, 42, 42])) + + def test_ndim(self, xp: ModuleType): + a = xp.reshape(xp.arange(2 * 3 * 4), (2, 3, 4)) + padded = pad(a, 2) + assert padded.shape == (6, 7, 8) + + def test_mode_not_implemented(self, xp: ModuleType): + a = xp.arange(3) + with pytest.raises(NotImplementedError, match="Only `'constant'`"): + pad(a, 2, mode="edge") # type: ignore[arg-type] # pyright: ignore[reportArgumentType] + + def test_device(self, xp: ModuleType, device: Device): + a = xp.asarray(0.0, device=device) + assert get_device(pad(a, 2)) == device + + def test_xp(self, xp: ModuleType): + padded = pad(xp.asarray(0), 1, xp=xp) + xp_assert_equal(padded, xp.asarray(0)) + + def test_tuple_width(self, xp: ModuleType): + a = xp.reshape(xp.arange(12), (3, 4)) + padded = pad(a, (1, 0)) + assert padded.shape == (4, 5) + + padded = pad(a, (1, 2)) + assert padded.shape == (6, 7) + + with pytest.raises((ValueError, RuntimeError)): + pad(a, [(1, 2, 3)]) # type: ignore[list-item] # pyright: ignore[reportArgumentType] + + def test_list_of_tuples_width(self, xp: ModuleType): + a = xp.reshape(xp.arange(12), (3, 4)) + padded = pad(a, [(1, 0), (0, 2)]) + assert padded.shape == (4, 6) + + padded = pad(a, [(1, 0), (0, 0)]) + assert padded.shape == (4, 4) + + @pytest.mark.skip_xp_backend(Backend.DASK_ARRAY, reason="no argsort") @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no device") class TestSetDiff1D: @@ -401,71 +470,3 @@ def test_device(self, xp: ModuleType, device: Device): def test_xp(self, xp: ModuleType): xp_assert_equal(sinc(xp.asarray(0.0), xp=xp), xp.asarray(1.0)) - - -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no arange, no device") -class TestPad: - def test_simple(self, xp: ModuleType): - a = xp.arange(1, 4) - padded = pad(a, 2) - xp_assert_equal(padded, xp.asarray([0, 0, 1, 2, 3, 0, 0])) - - def test_fill_value(self, xp: ModuleType): - a = xp.arange(1, 4) - padded = pad(a, 2, constant_values=42) - xp_assert_equal(padded, xp.asarray([42, 42, 1, 2, 3, 42, 42])) - - def test_ndim(self, xp: ModuleType): - a = xp.reshape(xp.arange(2 * 3 * 4), (2, 3, 4)) - padded = pad(a, 2) - assert padded.shape == (6, 7, 8) - - def test_mode_not_implemented(self, xp: ModuleType): - a = xp.arange(3) - with pytest.raises(NotImplementedError, match="Only `'constant'`"): - pad(a, 2, mode="edge") # type: ignore[arg-type] # pyright: ignore[reportArgumentType] - - def test_device(self, xp: ModuleType, device: Device): - a = xp.asarray(0.0, device=device) - assert get_device(pad(a, 2)) == device - - def test_xp(self, xp: ModuleType): - padded = pad(xp.asarray(0), 1, xp=xp) - xp_assert_equal(padded, xp.asarray(0)) - - def test_tuple_width(self, xp: ModuleType): - a = xp.reshape(xp.arange(12), (3, 4)) - padded = pad(a, (1, 0)) - assert padded.shape == (4, 5) - - padded = pad(a, (1, 2)) - assert padded.shape == (6, 7) - - with pytest.raises((ValueError, RuntimeError)): - pad(a, [(1, 2, 3)]) # type: ignore[list-item] # pyright: ignore[reportArgumentType] - - def test_list_of_tuples_width(self, xp: ModuleType): - a = xp.reshape(xp.arange(12), (3, 4)) - padded = pad(a, [(1, 0), (0, 2)]) - assert padded.shape == (4, 6) - - padded = pad(a, [(1, 0), (0, 0)]) - assert padded.shape == (4, 4) - - -class TestNUnique: - def test_simple(self, xp: ModuleType): - a = xp.asarray([[1, 1], [0, 2], [2, 2]]) - xp_assert_equal(nunique(a), xp.asarray(3)) - - 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) - assert get_device(nunique(a)) == device - - def test_xp(self, xp: ModuleType): - a = xp.asarray([[1, 1], [0, 2], [2, 2]]) - xp_assert_equal(nunique(a, xp=xp), xp.asarray(3)) From 70d3e32500328e99d2ec8ea7f432c021c5476c42 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Sun, 19 Jan 2025 19:13:39 +0000 Subject: [PATCH 005/140] clean up pyproject.toml (#102) --- pixi.lock | 168 ++++++++++++++++-------------------------- pyproject.toml | 64 ++++------------ tests/test_testing.py | 9 ++- 3 files changed, 84 insertions(+), 157 deletions(-) diff --git a/pixi.lock b/pixi.lock index 217da68f..33633cc9 100644 --- a/pixi.lock +++ b/pixi.lock @@ -42,10 +42,9 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/coverage-7.6.10-py310h89163eb_0.conda - conda: https://prefix.dev/conda-forge/noarch/cpython-3.10.16-py310hd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/linux-64/cytoolz-1.0.1-py310ha75aee5_0.conda - - conda: https://prefix.dev/conda-forge/noarch/dask-2024.12.1-pyhd8ed1ab_0.conda - - conda: https://prefix.dev/conda-forge/noarch/dask-core-2024.12.1-pyhd8ed1ab_0.conda - 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click >=8.0 - cloudpickle >=3.0.0 - cytoolz >=0.11.2 - - dask-core >=2024.12.1,<2024.12.2.0a0 + - dask-core >=2025.1.0,<2025.1.1.0a0 - jinja2 >=2.10.3 - locket >=1.0.0 - msgpack-python >=1.0.2 @@ -6330,8 +6290,8 @@ packages: license_family: BSD purls: - pkg:pypi/distributed?source=hash-mapping - size: 803908 - timestamp: 1734473202885 + size: 802199 + timestamp: 1737295363044 - conda: https://prefix.dev/conda-forge/noarch/docutils-0.21.2-pyhd8ed1ab_1.conda sha256: fa5966bb1718bbf6967a85075e30e4547901410cc7cb7b16daf68942e9a94823 md5: 24c1ca34138ee57de72a943237cde4cc diff --git a/pyproject.toml b/pyproject.toml index d6ea9805..ffd9ca76 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,21 +28,6 @@ classifiers = [ dynamic = ["version"] dependencies = ["array-api-compat>=1.10.0,<2"] -[project.optional-dependencies] -tests = [ - "pytest >=6", - "pytest-cov >=3", - "array-api-strict", - "numpy", -] -docs = [ - "sphinx>=7.0", - "myst_parser>=0.13", - "sphinx_copybutton", - "sphinx_autodoc_typehints", - "furo>=2023.08.17", -] - [project.urls] Homepage = "https://github.com/data-apis/array-api-extra" "Bug Tracker" = "https://github.com/data-apis/array-api-extra/issues" @@ -178,30 +163,24 @@ ci-py313 = ["py313", "tests"] ci-backends = ["py310", "tests", "backends"] tests-backends = ["py310", "tests", "backends", "cuda-backends"] + # pytest [tool.pytest.ini_options] minversion = "6.0" addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"] xfail_strict = true -filterwarnings = [ - "error", - # TODO: when Python 3.10 is dropped, use `enum.member` in `_delegation.py` - "ignore:functools.partial will be a method descriptor:FutureWarning", -] +filterwarnings = ["error"] log_cli_level = "INFO" testpaths = ["tests"] markers = ["skip_xp_backend(library, *, reason=None): Skip test for a specific backend"] + # Coverage [tool.coverage] run.source = ["array_api_extra"] -report.exclude_also = [ - '\.\.\.', - 'if typing.TYPE_CHECKING:', - 'if TYPE_CHECKING:', -] +report.exclude_also = ['\.\.\.'] # mypy @@ -212,18 +191,11 @@ python_version = "3.10" warn_unused_configs = true strict = true enable_error_code = ["ignore-without-code", "truthy-bool"] -disallow_untyped_defs = false -disallow_incomplete_defs = false -# data-apis/array-api#589 +# https://github.com/data-apis/array-api-typing disallow_any_expr = false # false positives with input validation disable_error_code = ["redundant-expr", "unreachable"] -[[tool.mypy.overrides]] -module = "array_api_extra.*" -disallow_untyped_defs = true -disallow_incomplete_defs = true - # pyright @@ -233,10 +205,10 @@ pythonVersion = "3.10" pythonPlatform = "All" typeCheckingMode = "all" -# data-apis/array-api#589 +# https://github.com/data-apis/array-api-typing reportAny = false reportExplicitAny = false -# data-apis/array-api-strict#6 +# no array-api-strict type stubs reportUnknownMemberType = false # no array-api-compat type stubs reportUnknownVariableType = false @@ -293,25 +265,17 @@ ignore = [ "N806", # Variable in function should be lowercase ] -[tool.ruff.lint.per-file-ignores] -"tests/**" = ["T20"] - # Pylint [tool.pylint] py-version = "3.10" -ignore-paths = [".*/_version.py"] reports.output-format = "colorized" -similarities.ignore-imports = "yes" messages_control.disable = [ - "design", - "fixme", - "line-too-long", - "missing-module-docstring", - "missing-function-docstring", - "too-many-lines", - "wrong-import-position", + "design", # ignore heavily opinionated design checks + "fixme", # allow FIXME comments + "line-too-long", # ruff handles this + "missing-function-docstring", # numpydoc handles this ] @@ -320,9 +284,9 @@ messages_control.disable = [ [tool.numpydoc_validation] checks = [ "all", # report on all checks, except the below - "EX01", - "SA01", - "ES01", + "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_at.*', diff --git a/tests/test_testing.py b/tests/test_testing.py index 2dbc913a..e0ce66ad 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -1,3 +1,6 @@ +from collections.abc import Callable +from types import ModuleType + import numpy as np import pytest @@ -18,7 +21,7 @@ ), ], ) -def test_assert_close_equal_basic(xp, func): +def test_assert_close_equal_basic(xp: ModuleType, func: Callable[..., None]): # type: ignore[no-any-explicit] func(xp.asarray(0), xp.asarray(0)) func(xp.asarray([1, 2]), xp.asarray([1, 2])) @@ -47,7 +50,7 @@ def test_assert_close_equal_basic(xp, func): ), ], ) -def test_assert_close_equal_namespace(xp, func): +def test_assert_close_equal_namespace(xp: ModuleType, func: Callable[..., None]): # type: ignore[no-any-explicit] with pytest.raises(AssertionError): func(xp.asarray(0), np.asarray(0)) with pytest.raises(TypeError): @@ -57,7 +60,7 @@ def test_assert_close_equal_namespace(xp, func): @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype") -def test_assert_close_tolerance(xp): +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) From 49da2ce1ccfc496242dadf52336569317c2b221d Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Sun, 19 Jan 2025 19:46:36 +0000 Subject: [PATCH 006/140] DOC: contributor docs for delegation --- docs/contributing.md | 36 +++++++++++++++++++++++++++++++++--- 1 file changed, 33 insertions(+), 3 deletions(-) diff --git a/docs/contributing.md b/docs/contributing.md index 221021d0..474fdd49 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -6,11 +6,14 @@ converting code to consume the standard. Thanks to [all contributors](contributors.md) so far! -## How to contribute a function +## How to contribute a new function - [Open an issue](https://github.com/data-apis/array-api-extra/issues/new) to - propose the new function. -- Add the implementation of your function to `src/array_api_extra/_funcs.py`. + propose the new function. You may want to wait for initial feedback on the + issue before diving into an implementation. Feel free to skip this step if + there is already an open issue for the function. +- Add the implementation of your function to + `src/array_api_extra/_lib/_funcs.py`. - Ensure that your function includes type annotations and a [numpydoc-style docstring](https://numpydoc.readthedocs.io/en/latest/format.html). - Add your function to `__all__` at the top of the file. @@ -20,6 +23,33 @@ Thanks to [all contributors](contributors.md) so far! - Add your function to `docs/api-reference.md`. - [Make a PR!](https://github.com/data-apis/array-api-extra/pulls) +## How to add delegation to a function + +See [the tracker for adding delegation][delegation-tracker]. + +[delegation-tracker]: https://github.com/data-apis/array-api-extra/issues/100 + +- If you would like to discuss the task before diving into the implementation, + click on the three dots next to the function on the tracker issue, and choose + "Convert to sub-issue". +- Create a function in `src/array_api_extra/_delegation.py` with a signature + matching the function in `src/array_api_extra/_lib/_funcs.py`, and move the + docstring to the new function. Leave a one-line docstring in `_funcs.py`, + pointing to `_delegation.py` to see the full docstring. +- Also move the initial `array_namespace` call and any input validation over to + the new function. +- Add delegation to backends using the `if _delegate` pattern. See + `src/array_api_extra/_lib/_backends.py` for the full list of backends we have + worked with so far. +- After all delegation layers, return the result from the implementation in + `_funcs`. +- Simplify the signature in `_funcs.py` to remove impossible arguments now that + it is only called internally via `_delegation`. For example, the `xp` + parameter can be changed from type `ModuleType | None` to `ModuleType`. +- Don't worry if you are not sure how to do some of the above steps or think you + might have done something wrong - + [make a PR!](https://github.com/data-apis/array-api-extra/pulls) + ## Development workflow If you are an experienced contributor to Python packages, feel free to develop From 20cb3b9973aa51ffe6dd69e1756f1d2356a06a5e Mon Sep 17 00:00:00 2001 From: crusaderky Date: Mon, 20 Jan 2025 11:49:48 +0000 Subject: [PATCH 007/140] TST:Better pytest short summary info --- src/array_api_extra/_delegation.py | 2 +- src/array_api_extra/_lib/_backends.py | 4 ++-- tests/conftest.py | 2 +- tests/test_at.py | 2 +- tests/test_funcs.py | 32 ++++++++++++++++----------- tests/test_testing.py | 16 +++++++++----- tests/test_utils.py | 18 ++++++++++----- 7 files changed, 48 insertions(+), 28 deletions(-) diff --git a/src/array_api_extra/_delegation.py b/src/array_api_extra/_delegation.py index 4a1740e6..c3d77f8e 100644 --- a/src/array_api_extra/_delegation.py +++ b/src/array_api_extra/_delegation.py @@ -77,7 +77,7 @@ def pad( 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_NUMPY, Backend.CUPY): + if _delegate(xp, Backend.NUMPY, Backend.JAX, Backend.CUPY): 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/_backends.py b/src/array_api_extra/_lib/_backends.py index ee2e051e..f044281a 100644 --- a/src/array_api_extra/_lib/_backends.py +++ b/src/array_api_extra/_lib/_backends.py @@ -28,9 +28,9 @@ 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 - DASK_ARRAY = "dask.array", _compat.is_dask_namespace + DASK = "dask.array", _compat.is_dask_namespace SPARSE = "sparse", _compat.is_pydata_sparse_namespace - JAX_NUMPY = "jax.numpy", _compat.is_jax_namespace + JAX = "jax.numpy", _compat.is_jax_namespace def __new__( cls, value: str, _is_namespace: Callable[[ModuleType], bool] diff --git a/tests/conftest.py b/tests/conftest.py index fa555018..fc2e68e2 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -104,7 +104,7 @@ def xp(library: Backend) -> ModuleType: # numpydoc ignore=PR01,RT03 if library == Backend.NUMPY_READONLY: return NumPyReadOnly() # type: ignore[return-value] # pyright: ignore[reportReturnType] xp = pytest.importorskip(library.value) - if library == Backend.JAX_NUMPY: + if library == Backend.JAX: import jax jax.config.update("jax_enable_x64", True) # type: ignore[no-untyped-call] diff --git a/tests/test_at.py b/tests/test_at.py index c65a4a0d..84aa464c 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -34,7 +34,7 @@ def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: @pytest.mark.skip_xp_backend( - Backend.SPARSE, reason="read-only backend without .at support" + Backend.SPARSE, reason="sparse:read-only backend without .at support" ) @pytest.mark.parametrize( ("kwargs", "expect_copy"), diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 3557642b..692d486b 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -26,7 +26,7 @@ # mypy: disable-error-code=no-untyped-usage -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no expand_dims") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no expand_dims") class TestAtLeastND: def test_0D(self, xp: ModuleType): x = xp.asarray(1.0) @@ -98,7 +98,7 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(y, x) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no isdtype") class TestCov: def test_basic(self, xp: ModuleType): xp_assert_close( @@ -137,7 +137,9 @@ def test_device(self, xp: ModuleType, device: Device): x = xp.asarray([1, 2, 3], device=device) assert get_device(cov(x)) == device - @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY) + @pytest.mark.skip_xp_backend( + Backend.NUMPY_READONLY, reason="numpy_readonly:explicit xp" + ) def test_xp(self, xp: ModuleType): xp_assert_close( cov(xp.asarray([[0.0, 2.0], [1.0, 1.0], [2.0, 0.0]]).T, xp=xp), @@ -145,7 +147,7 @@ def test_xp(self, xp: ModuleType): ) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no device") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no device kwarg in asarray") class TestCreateDiagonal: def test_1d(self, xp: ModuleType): # from np.diag tests @@ -191,10 +193,10 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(y, xp.asarray([[1, 0], [0, 2]])) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no sparse.expand_dims") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no expand_dims") class TestExpandDims: - @pytest.mark.skip_xp_backend(Backend.DASK_ARRAY, reason="tuple index out of range") - @pytest.mark.skip_xp_backend(Backend.TORCH, reason="tuple index out of range") + @pytest.mark.skip_xp_backend(Backend.DASK, reason="dask:tuple index out of range") + @pytest.mark.skip_xp_backend(Backend.TORCH, reason="torch:tuple index out of range") def test_functionality(self, xp: ModuleType): def _squeeze_all(b: Array) -> Array: """Mimics `np.squeeze(b)`. `xpx.squeeze`?""" @@ -252,7 +254,7 @@ def test_xp(self, xp: ModuleType): assert y.shape == (1, 1, 1, 3) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no sparse.expand_dims") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no expand_dims") class TestKron: def test_basic(self, xp: ModuleType): # Using 0-dimensional array @@ -349,7 +351,9 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(nunique(a, xp=xp), xp.asarray(3)) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no arange, no device") +@pytest.mark.skip_xp_backend( + Backend.SPARSE, reason="sparse:no arange, no device kwarg in asarray" +) class TestPad: def test_simple(self, xp: ModuleType): a = xp.arange(1, 4) @@ -399,8 +403,8 @@ def test_list_of_tuples_width(self, xp: ModuleType): assert padded.shape == (4, 4) -@pytest.mark.skip_xp_backend(Backend.DASK_ARRAY, reason="no argsort") -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no device") +@pytest.mark.skip_xp_backend(Backend.DASK, reason="dask:no argsort") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no device kwarg in asarray") class TestSetDiff1D: @pytest.mark.skip_xp_backend( Backend.TORCH, reason="index_select not implemented for uint32" @@ -436,7 +440,9 @@ def test_device(self, xp: ModuleType, device: Device): x2 = xp.asarray([2, 3, 4], device=device) assert get_device(setdiff1d(x1, x2)) == device - @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY) + @pytest.mark.skip_xp_backend( + Backend.NUMPY_READONLY, reason="numpy_readonly:explicit xp" + ) def test_xp(self, xp: ModuleType): x1 = xp.asarray([3, 8, 20]) x2 = xp.asarray([2, 3, 4]) @@ -445,7 +451,7 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(actual, expected) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse: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_testing.py b/tests/test_testing.py index e0ce66ad..41fc6673 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -17,7 +17,9 @@ xp_assert_equal, pytest.param( xp_assert_close, - marks=pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype"), + marks=pytest.mark.skip_xp_backend( + Backend.SPARSE, reason="sparse:no isdtype" + ), ), ], ) @@ -38,15 +40,19 @@ def test_assert_close_equal_basic(xp: ModuleType, func: Callable[..., None]): # func(xp.asarray([1, 2]), xp.asarray([1, 3]), err_msg="hello") -@pytest.mark.skip_xp_backend(Backend.NUMPY) -@pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY) +@pytest.mark.skip_xp_backend(Backend.NUMPY, reason="numpy:test other ns vs. numpy") +@pytest.mark.skip_xp_backend( + Backend.NUMPY_READONLY, reason="numpy_readonly:test other ns vs. numpy" +) @pytest.mark.parametrize( "func", [ xp_assert_equal, pytest.param( xp_assert_close, - marks=pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype"), + marks=pytest.mark.skip_xp_backend( + Backend.SPARSE, reason="sparse:no isdtype" + ), ), ], ) @@ -59,7 +65,7 @@ def test_assert_close_equal_namespace(xp: ModuleType, func: Callable[..., None]) func(xp.asarray([0]), [0]) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse: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): diff --git a/tests/test_utils.py b/tests/test_utils.py index 981d5c03..f053f177 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -12,8 +12,10 @@ class TestIn1D: - @pytest.mark.skip_xp_backend(Backend.DASK_ARRAY, reason="no argsort") - @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no unique_inverse, no device") + @pytest.mark.skip_xp_backend(Backend.DASK, reason="dask:no argsort") + @pytest.mark.skip_xp_backend( + Backend.SPARSE, reason="sparse:no unique_inverse, no device kwarg in asarray" + ) # cover both code paths @pytest.mark.parametrize("n", [9, 15]) def test_no_invert_assume_unique(self, xp: ModuleType, n: int): @@ -23,14 +25,20 @@ def test_no_invert_assume_unique(self, xp: ModuleType, n: int): actual = in1d(x1, x2) xp_assert_equal(actual, expected) - @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no device") + @pytest.mark.skip_xp_backend( + Backend.SPARSE, reason="sparse: no device kwarg in asarray" + ) def test_device(self, xp: ModuleType, device: Device): x1 = xp.asarray([3, 8, 20], device=device) x2 = xp.asarray([2, 3, 4], device=device) assert get_device(in1d(x1, x2)) == device - @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY) - @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no arange, no device") + @pytest.mark.skip_xp_backend( + Backend.NUMPY_READONLY, reason="numpy_readonly:explicit xp" + ) + @pytest.mark.skip_xp_backend( + Backend.SPARSE, reason="sparse:no arange, no device kwarg in asarray" + ) def test_xp(self, xp: ModuleType): x1 = xp.asarray([1, 6]) x2 = xp.arange(5) From 39f6a27a4fd90ff3295db6e1748ea9c57a51fa20 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Mon, 20 Jan 2025 12:24:54 +0000 Subject: [PATCH 008/140] DEV: `pixi run lint` improvements (#104) --- .github/workflows/ci.yml | 2 +- docs/contributing.md | 19 +- pixi.lock | 4665 ++++++++++---------- pyproject.toml | 23 +- src/array_api_extra/_lib/_utils/_compat.py | 4 +- tests/conftest.py | 3 +- tests/test_at.py | 5 +- 7 files changed, 2272 insertions(+), 2449 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index fac3ebe8..d455e389 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -48,7 +48,7 @@ jobs: strategy: fail-fast: false matrix: - environment: [ci-py310, ci-py313, ci-backends] + environment: [tests-py310, tests-py313, tests-backends] runs-on: [ubuntu-latest] steps: diff --git a/docs/contributing.md b/docs/contributing.md index 474fdd49..83db0de4 100644 --- a/docs/contributing.md +++ b/docs/contributing.md @@ -106,7 +106,7 @@ pixi run pre-commit-install - To run the lint suite: ``` -pixi run lint +pixi run -e lint lint ``` - To enter an interactive Python prompt: @@ -118,10 +118,10 @@ pixi run ipython - To run individual parts of the lint suite separately: ``` -pixi run pre-commit -pixi run pylint -pixi run mypy -pixi run pyright +pixi run -e lint pre-commit +pixi run -e lint pylint +pixi run -e lint mypy +pixi run -e lint pyright ``` Alternative environments are available with a subset of the dependencies and @@ -130,5 +130,14 @@ tasks available in the `dev` environment: ``` pixi shell -e docs pixi shell -e tests +pixi shell -e tests-backends pixi shell -e 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 +``` diff --git a/pixi.lock b/pixi.lock index 33633cc9..5ea45749 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,6 +1,71 @@ version: 6 environments: - 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license_family: BSD purls: - pkg:pypi/numpy?source=hash-mapping - size: 5929029 - timestamp: 1734904776467 -- conda: https://prefix.dev/conda-forge/osx-arm64/numpy-2.2.1-py313ha4a2180_0.conda - sha256: c6dafb68d407bd4f34a8e178fe37be0c0c6533e6408a066d2cfcdccd6eb63402 - md5: 186189cd83b1b95e73a805a268bc7a98 + size: 5874341 + timestamp: 1737331525429 +- conda: https://prefix.dev/conda-forge/osx-arm64/numpy-2.2.2-py313h41a2e72_0.conda + sha256: 0e7f27766505a73ceafaf48c2d791e4f1aa197f61456038c9f4ae042b811d5df + md5: e5041789d91a22a14205a69faf4ee324 depends: - __osx >=11.0 - libblas >=3.9.0,<4.0a0 @@ -11036,11 +10802,10 @@ packages: constrains: - numpy-base <0a0 license: BSD-3-Clause - license_family: BSD purls: - pkg:pypi/numpy?source=hash-mapping - size: 6513050 - timestamp: 1734904817005 + size: 6517665 + timestamp: 1737331575921 - conda: https://prefix.dev/conda-forge/win-64/numpy-2.0.2-py310h1ec8c79_1.conda sha256: 2537e8dadd1656d49f55b7f2422bef745a60a308fcf879f2d74dc8338aecb4bb md5: 4f2239328935b02e9024e25dc21840c3 @@ -11081,9 +10846,9 @@ packages: - pkg:pypi/numpy?source=hash-mapping size: 6875358 timestamp: 1732315495587 -- conda: https://prefix.dev/conda-forge/win-64/numpy-2.2.1-py310hb9d903e_0.conda - sha256: 942ec24291d65e00e718765016b1f6b6be9bc5f09137dc14c21e047b94a09d30 - md5: 25361f25ec68789cea29b14b412970e8 +- conda: https://prefix.dev/conda-forge/win-64/numpy-2.2.2-py310h4987827_0.conda + sha256: dcaeba9df1e8ddacdf6f9c31fb11c000bc98795bdfc927568abb15bf55505f97 + md5: 19fe9605ee7deff2a702d2e89efbbb9c depends: - libblas >=3.9.0,<4.0a0 - libcblas >=3.9.0,<4.0a0 @@ -11096,14 +10861,13 @@ packages: constrains: - numpy-base <0a0 license: BSD-3-Clause - license_family: BSD purls: - pkg:pypi/numpy?source=hash-mapping - size: 6420026 - timestamp: 1734905273023 -- conda: https://prefix.dev/conda-forge/win-64/numpy-2.2.1-py313hd65a2fa_0.conda - sha256: a49b54335d97b674bc09dacce0b232cf748e730500dcc45172f8dd9db3c0fb99 - md5: 80b2f22cec897016e76261aea177fde8 + size: 6501890 + timestamp: 1737332099209 +- conda: https://prefix.dev/conda-forge/win-64/numpy-2.2.2-py313hefb8edb_0.conda + sha256: c6a5645d5b7afaafe5d45a5ad7aaad4e47498592da334d41e6d58d724160d7de + md5: f00ff06a249506cab4da50b85e22cadb depends: - libblas >=3.9.0,<4.0a0 - libcblas >=3.9.0,<4.0a0 @@ -11116,11 +10880,10 @@ packages: constrains: - numpy-base <0a0 license: BSD-3-Clause - license_family: BSD purls: - pkg:pypi/numpy?source=hash-mapping - size: 7147174 - timestamp: 1734905243335 + size: 7116196 + timestamp: 1737332125142 - conda: https://prefix.dev/conda-forge/noarch/numpydoc-1.8.0-pyhd8ed1ab_1.conda sha256: d836860163b027622cb59b96b92824dd75196a37d599e8ae69733b31769989a9 md5: 5af206d64d18d6c8dfb3122b4d9e643b @@ -11888,6 +11651,29 @@ packages: purls: [] size: 25756 timestamp: 1737128388939 +- conda: https://prefix.dev/conda-forge/linux-64/pyarrow-core-19.0.0-py310h23ac199_0_cuda.conda + sha256: df5b77ce2ef766d65e4775aeb0f1dafde2ff86ceeb1f94bdf7d007e9e9729f58 + md5: b996dbff06cf1231de8f5190d38fd712 + depends: + - __cuda >=11.8 + - __glibc >=2.17,<3.0.a0 + - libarrow 19.0.0.* *cuda + - libgcc + - libgcc-ng >=12 + - libstdcxx + - libstdcxx-ng >=12 + - libzlib >=1.3.1,<2.0a0 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + constrains: + - numpy >=1.21,<3 + - apache-arrow-proc =*=cuda + license: Apache-2.0 + license_family: APACHE + purls: + - pkg:pypi/pyarrow?source=hash-mapping + size: 5311517 + timestamp: 1737128238259 - conda: https://prefix.dev/conda-forge/linux-64/pyarrow-core-19.0.0-py310hac404ae_0_cpu.conda sha256: 0b7815fab725c33885afe1e8562a199be60f5d2de60ae34e177ad2f91f97a4eb md5: 041f56d6b24eb7b961c43f6fb3949a53 @@ -11928,6 +11714,29 @@ packages: - pkg:pypi/pyarrow?source=hash-mapping size: 5230953 timestamp: 1737128097002 +- conda: https://prefix.dev/conda-forge/linux-64/pyarrow-core-19.0.0-py312h09cf70e_0_cuda.conda + sha256: e9423e2d18d21cbe4b5a3a03307dcfbb129159243bc7212769fd69e6d808381b + md5: f473d99b4c91f3a3715fd11d96ed7963 + depends: + - __cuda >=11.8 + - __glibc >=2.17,<3.0.a0 + - libarrow 19.0.0.* *cuda + - libgcc + - libgcc-ng >=12 + - libstdcxx + - libstdcxx-ng >=12 + - libzlib >=1.3.1,<2.0a0 + - python >=3.12,<3.13.0a0 + - python_abi 3.12.* *_cp312 + constrains: + - apache-arrow-proc =*=cuda + - numpy >=1.21,<3 + license: Apache-2.0 + license_family: APACHE + purls: + - pkg:pypi/pyarrow?source=hash-mapping + size: 5839565 + timestamp: 1737128375591 - conda: https://prefix.dev/conda-forge/osx-arm64/pyarrow-core-19.0.0-py310hc17921c_0_cpu.conda sha256: 3a18a24c8594a89e70aa87e94dd9fd61100244536fc3ed327ffbe86ca32c0cc6 md5: c1d09d52bf69aa807b347ff6f4dc2aef @@ -13247,7 +13056,7 @@ packages: license: MIT license_family: MIT purls: - - pkg:pypi/setuptools?source=hash-mapping + - pkg:pypi/setuptools?source=compressed-mapping size: 775598 timestamp: 1736512753595 - conda: https://prefix.dev/conda-forge/noarch/six-1.17.0-pyhd8ed1ab_0.conda diff --git a/pyproject.toml b/pyproject.toml index ffd9ca76..2fae4f82 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -152,16 +152,16 @@ cupy = "*" [tool.pixi.environments] default = { solve-group = "default" } -lint = { features = ["lint", "backends"], 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"] } -ci-py310 = ["py310", "tests"] -ci-py313 = ["py313", "tests"] -# CUDA not available on free github actions -ci-backends = ["py310", "tests", "backends"] -tests-backends = ["py310", "tests", "backends", "cuda-backends"] +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 @@ -196,6 +196,10 @@ disallow_any_expr = false # false positives with input validation disable_error_code = ["redundant-expr", "unreachable"] +[[tool.mypy.overrides]] +# slow/unavailable on Windows; do not add to the lint env +module = ["dask.*", "jax.*"] +ignore_missing_imports = true # pyright @@ -208,10 +212,13 @@ typeCheckingMode = "all" # https://github.com/data-apis/array-api-typing reportAny = false reportExplicitAny = false -# no array-api-strict type stubs +# no array-api-strict type stubs; pytest fixtures reportUnknownMemberType = false -# no array-api-compat type stubs +# no array-api-compat type stubs; pytest fixtures reportUnknownVariableType = false +# Redundant with mypy checks +reportMissingImports = false +reportMissingTypeStubs = false # false positives for input validation reportUnreachable = false diff --git a/src/array_api_extra/_lib/_utils/_compat.py b/src/array_api_extra/_lib/_utils/_compat.py index d7f7e83a..707e9553 100644 --- a/src/array_api_extra/_lib/_utils/_compat.py +++ b/src/array_api_extra/_lib/_utils/_compat.py @@ -3,7 +3,7 @@ # `array-api-compat` to override the import location try: - from ...._array_api_compat_vendor import ( # pyright: ignore[reportMissingImports] + from ...._array_api_compat_vendor import ( array_namespace, device, is_array_api_strict_namespace, @@ -18,7 +18,7 @@ size, ) except ImportError: - from array_api_compat import ( # pyright: ignore[reportMissingTypeStubs] + from array_api_compat import ( array_namespace, device, is_array_api_strict_namespace, diff --git a/tests/conftest.py b/tests/conftest.py index fa555018..51e30cc6 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -107,7 +107,8 @@ def xp(library: Backend) -> ModuleType: # numpydoc ignore=PR01,RT03 if library == Backend.JAX_NUMPY: import jax - jax.config.update("jax_enable_x64", True) # type: ignore[no-untyped-call] + # 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] # Possibly wrap module with array_api_compat return array_namespace(xp.empty(0)) diff --git a/tests/test_at.py b/tests/test_at.py index c65a4a0d..4bd09c6a 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -5,15 +5,12 @@ import numpy as np import pytest -from array_api_compat import ( # type: ignore[import-untyped] # pyright: ignore[reportMissingTypeStubs] - array_namespace, - is_writeable_array, -) 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._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 From 73452c9c0944159b829e9ddedfbb3cc346d6c06a Mon Sep 17 00:00:00 2001 From: crusaderky Date: Mon, 20 Jan 2025 12:36:09 +0000 Subject: [PATCH 009/140] TST: Less redundant `skip_xp_backends` --- tests/conftest.py | 5 ++++- tests/test_at.py | 2 +- tests/test_funcs.py | 32 +++++++++++++------------------- tests/test_testing.py | 16 +++++----------- tests/test_utils.py | 14 +++++--------- 5 files changed, 28 insertions(+), 41 deletions(-) diff --git a/tests/conftest.py b/tests/conftest.py index 8d3a4f3f..39904ae2 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,6 +1,7 @@ """Pytest fixtures.""" from collections.abc import Callable +from contextlib import suppress from functools import wraps from types import ModuleType from typing import ParamSpec, TypeVar, cast @@ -36,7 +37,9 @@ def library(request: pytest.FixtureRequest) -> Backend: # numpydoc ignore=PR01, msg = "argument of skip_xp_backend must be a Backend enum" raise TypeError(msg) if skip_library == elem: - reason = cast(str, marker.kwargs.get("reason", "skip_xp_backend")) + reason = skip_library.value + with suppress(KeyError): + reason += ":" + cast(str, marker.kwargs["reason"]) pytest.skip(reason=reason) return elem diff --git a/tests/test_at.py b/tests/test_at.py index 49abe0e4..4bd09c6a 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -31,7 +31,7 @@ def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: @pytest.mark.skip_xp_backend( - Backend.SPARSE, reason="sparse:read-only backend without .at support" + Backend.SPARSE, reason="read-only backend without .at support" ) @pytest.mark.parametrize( ("kwargs", "expect_copy"), diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 692d486b..4847cb9f 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -26,7 +26,7 @@ # mypy: disable-error-code=no-untyped-usage -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no expand_dims") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no expand_dims") class TestAtLeastND: def test_0D(self, xp: ModuleType): x = xp.asarray(1.0) @@ -98,7 +98,7 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(y, x) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no isdtype") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype") class TestCov: def test_basic(self, xp: ModuleType): xp_assert_close( @@ -137,9 +137,7 @@ def test_device(self, xp: ModuleType, device: Device): x = xp.asarray([1, 2, 3], device=device) assert get_device(cov(x)) == device - @pytest.mark.skip_xp_backend( - Backend.NUMPY_READONLY, reason="numpy_readonly:explicit xp" - ) + @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="explicit xp") def test_xp(self, xp: ModuleType): xp_assert_close( cov(xp.asarray([[0.0, 2.0], [1.0, 1.0], [2.0, 0.0]]).T, xp=xp), @@ -147,7 +145,7 @@ def test_xp(self, xp: ModuleType): ) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no device kwarg in asarray") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no device") class TestCreateDiagonal: def test_1d(self, xp: ModuleType): # from np.diag tests @@ -193,10 +191,10 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(y, xp.asarray([[1, 0], [0, 2]])) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no expand_dims") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no expand_dims") class TestExpandDims: - @pytest.mark.skip_xp_backend(Backend.DASK, reason="dask:tuple index out of range") - @pytest.mark.skip_xp_backend(Backend.TORCH, reason="torch:tuple index out of range") + @pytest.mark.skip_xp_backend(Backend.DASK, reason="tuple index out of range") + @pytest.mark.skip_xp_backend(Backend.TORCH, reason="tuple index out of range") def test_functionality(self, xp: ModuleType): def _squeeze_all(b: Array) -> Array: """Mimics `np.squeeze(b)`. `xpx.squeeze`?""" @@ -254,7 +252,7 @@ def test_xp(self, xp: ModuleType): assert y.shape == (1, 1, 1, 3) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no expand_dims") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no expand_dims") class TestKron: def test_basic(self, xp: ModuleType): # Using 0-dimensional array @@ -351,9 +349,7 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(nunique(a, xp=xp), xp.asarray(3)) -@pytest.mark.skip_xp_backend( - Backend.SPARSE, reason="sparse:no arange, no device kwarg in asarray" -) +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no arange, no device") class TestPad: def test_simple(self, xp: ModuleType): a = xp.arange(1, 4) @@ -403,8 +399,8 @@ def test_list_of_tuples_width(self, xp: ModuleType): assert padded.shape == (4, 4) -@pytest.mark.skip_xp_backend(Backend.DASK, reason="dask:no argsort") -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no device kwarg in asarray") +@pytest.mark.skip_xp_backend(Backend.DASK, reason="no argsort") +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no device kwarg in asarray") class TestSetDiff1D: @pytest.mark.skip_xp_backend( Backend.TORCH, reason="index_select not implemented for uint32" @@ -440,9 +436,7 @@ def test_device(self, xp: ModuleType, device: Device): x2 = xp.asarray([2, 3, 4], device=device) assert get_device(setdiff1d(x1, x2)) == device - @pytest.mark.skip_xp_backend( - Backend.NUMPY_READONLY, reason="numpy_readonly:explicit xp" - ) + @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="explicit xp") def test_xp(self, xp: ModuleType): x1 = xp.asarray([3, 8, 20]) x2 = xp.asarray([2, 3, 4]) @@ -451,7 +445,7 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(actual, expected) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no isdtype") +@pytest.mark.skip_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_testing.py b/tests/test_testing.py index 41fc6673..dc315663 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -17,9 +17,7 @@ xp_assert_equal, pytest.param( xp_assert_close, - marks=pytest.mark.skip_xp_backend( - Backend.SPARSE, reason="sparse:no isdtype" - ), + marks=pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype"), ), ], ) @@ -40,19 +38,15 @@ def test_assert_close_equal_basic(xp: ModuleType, func: Callable[..., None]): # func(xp.asarray([1, 2]), xp.asarray([1, 3]), err_msg="hello") -@pytest.mark.skip_xp_backend(Backend.NUMPY, reason="numpy:test other ns vs. numpy") -@pytest.mark.skip_xp_backend( - Backend.NUMPY_READONLY, reason="numpy_readonly:test other ns vs. numpy" -) +@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, pytest.param( xp_assert_close, - marks=pytest.mark.skip_xp_backend( - Backend.SPARSE, reason="sparse:no isdtype" - ), + marks=pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype"), ), ], ) @@ -65,7 +59,7 @@ def test_assert_close_equal_namespace(xp: ModuleType, func: Callable[..., None]) func(xp.asarray([0]), [0]) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="sparse:no isdtype") +@pytest.mark.skip_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): diff --git a/tests/test_utils.py b/tests/test_utils.py index f053f177..fff3f0f2 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -12,9 +12,9 @@ class TestIn1D: - @pytest.mark.skip_xp_backend(Backend.DASK, reason="dask:no argsort") + @pytest.mark.skip_xp_backend(Backend.DASK, reason="no argsort") @pytest.mark.skip_xp_backend( - Backend.SPARSE, reason="sparse:no unique_inverse, no device kwarg in asarray" + Backend.SPARSE, reason="no unique_inverse, no device kwarg in asarray" ) # cover both code paths @pytest.mark.parametrize("n", [9, 15]) @@ -25,19 +25,15 @@ def test_no_invert_assume_unique(self, xp: ModuleType, n: int): actual = in1d(x1, x2) xp_assert_equal(actual, expected) - @pytest.mark.skip_xp_backend( - Backend.SPARSE, reason="sparse: no device kwarg in asarray" - ) + @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no device kwarg in asarray") def test_device(self, xp: ModuleType, device: Device): x1 = xp.asarray([3, 8, 20], device=device) x2 = xp.asarray([2, 3, 4], device=device) assert get_device(in1d(x1, x2)) == device + @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="explicit xp") @pytest.mark.skip_xp_backend( - Backend.NUMPY_READONLY, reason="numpy_readonly:explicit xp" - ) - @pytest.mark.skip_xp_backend( - Backend.SPARSE, reason="sparse:no arange, no device kwarg in asarray" + Backend.SPARSE, reason="no arange, no device kwarg in asarray" ) def test_xp(self, xp: ModuleType): x1 = xp.asarray([1, 6]) From 9e50896d8f62404191925075218b6358d99700c4 Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Mon, 20 Jan 2025 14:53:08 +0000 Subject: [PATCH 010/140] docs: add crusaderky as a contributor for bug (#107) 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 c2651c64..f9456f16 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -174,7 +174,8 @@ "doc", "tool", "test", - "example" + "example", + "bug" ] }, { diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index 042541ab..9f14c5ac 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -28,7 +28,7 @@ This project exists thanks to the following contributors Olivier Grisel
Olivier Grisel
💻 - Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 + Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 🐛 Evgeni Burovski
Evgeni Burovski
💻 📖 Jake Vanderplas
Jake Vanderplas
👀 diff --git a/README.md b/README.md index 3ef32b32..66a73d54 100644 --- a/README.md +++ b/README.md @@ -80,7 +80,7 @@ This project exists thanks to the following contributors Olivier Grisel
Olivier Grisel
💻 - Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 + Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 🐛 Evgeni Burovski
Evgeni Burovski
💻 📖 Jake Vanderplas
Jake Vanderplas
👀 From e97918848453af60a950f4c173f2479ac46eab59 Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Mon, 20 Jan 2025 14:57:16 +0000 Subject: [PATCH 011/140] docs: add kotlinisland as a contributor for review (#108) 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 f9456f16..f26838b2 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -196,6 +196,15 @@ "contributions": [ "review" ] + }, + { + "login": "kotlinisland", + "name": "kotlinisland", + "avatar_url": "https://avatars.githubusercontent.com/u/65446343?v=4", + "profile": "https://github.com/KotlinIsland", + "contributions": [ + "review" + ] } ] } diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index 9f14c5ac..ce0b0a40 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -31,6 +31,7 @@ This project exists thanks to the following contributors Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 🐛 Evgeni Burovski
Evgeni Burovski
💻 📖 Jake Vanderplas
Jake Vanderplas
👀 + kotlinisland
kotlinisland
👀 diff --git a/README.md b/README.md index 66a73d54..11eebdb6 100644 --- a/README.md +++ b/README.md @@ -83,6 +83,7 @@ This project exists thanks to the following contributors Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 🐛 Evgeni Burovski
Evgeni Burovski
💻 📖 Jake Vanderplas
Jake Vanderplas
👀 + kotlinisland
kotlinisland
👀 From e4b79bb57d0e480f782256b792d03f8f40f82737 Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Mon, 20 Jan 2025 15:02:08 +0000 Subject: [PATCH 012/140] docs: add detachhead as a contributor for review (#110) 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 f26838b2..bc8b8d33 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -205,6 +205,15 @@ "contributions": [ "review" ] + }, + { + "login": "detachhead", + "name": "detachhead", + "avatar_url": "https://avatars.githubusercontent.com/u/57028336?v=4", + "profile": "https://github.com/DetachHead", + "contributions": [ + "review" + ] } ] } diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index ce0b0a40..5e17e750 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -32,6 +32,7 @@ This project exists thanks to the following contributors Evgeni Burovski
Evgeni Burovski
💻 📖 Jake Vanderplas
Jake Vanderplas
👀 kotlinisland
kotlinisland
👀 + detachhead
detachhead
👀 diff --git a/README.md b/README.md index 11eebdb6..b2e20129 100644 --- a/README.md +++ b/README.md @@ -84,6 +84,7 @@ This project exists thanks to the following contributors Evgeni Burovski
Evgeni Burovski
💻 📖 Jake Vanderplas
Jake Vanderplas
👀 kotlinisland
kotlinisland
👀 + detachhead
detachhead
👀 From 48fb66a763466981416188f74f2b86c7b59acdb2 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Mon, 20 Jan 2025 15:19:52 +0000 Subject: [PATCH 013/140] DOC: tweak all-contributors table (#111) --- .all-contributorsrc | 42 +++++++++++++++++++++--------------------- CONTRIBUTORS.md | 4 ++-- README.md | 4 ++-- 3 files changed, 25 insertions(+), 25 deletions(-) diff --git a/.all-contributorsrc b/.all-contributorsrc index bc8b8d33..e0565ac1 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -90,14 +90,17 @@ ] }, { - "login": "rgommers", - "name": "Ralf Gommers", - "avatar_url": "https://avatars.githubusercontent.com/u/98330?v=4", - "profile": "https://github.com/rgommers/", + "login": "crusaderky", + "name": "Guido Imperiale", + "avatar_url": "https://avatars.githubusercontent.com/u/6213168?v=4", + "profile": "https://github.com/crusaderky", "contributions": [ - "ideas", - "infra", - "review" + "code", + "doc", + "tool", + "test", + "example", + "bug" ] }, { @@ -155,6 +158,17 @@ "code" ] }, + { + "login": "rgommers", + "name": "Ralf Gommers", + "avatar_url": "https://avatars.githubusercontent.com/u/98330?v=4", + "profile": "https://github.com/rgommers/", + "contributions": [ + "ideas", + "infra", + "review" + ] + }, { "login": "ogrisel", "name": "Olivier Grisel", @@ -164,20 +178,6 @@ "code" ] }, - { - "login": "crusaderky", - "name": "Guido Imperiale", - "avatar_url": "https://avatars.githubusercontent.com/u/6213168?v=4", - "profile": "https://github.com/crusaderky", - "contributions": [ - "code", - "doc", - "tool", - "test", - "example", - "bug" - ] - }, { "login": "ev-br", "name": "Evgeni Burovski", diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index 5e17e750..a482691e 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
🤔 - Ralf Gommers
Ralf Gommers
🤔 🚇 👀 + Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 🐛 Joren Hammudoglu
Joren Hammudoglu
👀 Thomas J. Fan
Thomas J. Fan
🤔 Irwin Zaid
Irwin Zaid
🤔 @@ -27,8 +27,8 @@ This project exists thanks to the following contributors Omar Salman
Omar Salman
💻 + Ralf Gommers
Ralf Gommers
🤔 🚇 👀 Olivier Grisel
Olivier Grisel
💻 - Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 🐛 Evgeni Burovski
Evgeni Burovski
💻 📖 Jake Vanderplas
Jake Vanderplas
👀 kotlinisland
kotlinisland
👀 diff --git a/README.md b/README.md index b2e20129..44099678 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
🤔 - Ralf Gommers
Ralf Gommers
🤔 🚇 👀 + Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 🐛 Joren Hammudoglu
Joren Hammudoglu
👀 Thomas J. Fan
Thomas J. Fan
🤔 Irwin Zaid
Irwin Zaid
🤔 @@ -79,8 +79,8 @@ This project exists thanks to the following contributors Omar Salman
Omar Salman
💻 + Ralf Gommers
Ralf Gommers
🤔 🚇 👀 Olivier Grisel
Olivier Grisel
💻 - Guido Imperiale
Guido Imperiale
💻 📖 🔧 ⚠️ 💡 🐛 Evgeni Burovski
Evgeni Burovski
💻 📖 Jake Vanderplas
Jake Vanderplas
👀 kotlinisland
kotlinisland
👀 From 3754e7ccad0f40be39646de16e11bc729ea8a11f Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Mon, 20 Jan 2025 20:20:44 +0000 Subject: [PATCH 014/140] ENH: `pad`: `pad_width` can be any sequence (#114) --- src/array_api_extra/_delegation.py | 7 ++++--- src/array_api_extra/_lib/_funcs.py | 18 +++++++++++++----- tests/test_funcs.py | 8 ++++---- 3 files changed, 21 insertions(+), 12 deletions(-) diff --git a/src/array_api_extra/_delegation.py b/src/array_api_extra/_delegation.py index c3d77f8e..195dd88f 100644 --- a/src/array_api_extra/_delegation.py +++ b/src/array_api_extra/_delegation.py @@ -1,5 +1,6 @@ """Delegation to existing implementations for Public API Functions.""" +from collections.abc import Sequence from types import ModuleType from typing import Literal @@ -31,7 +32,7 @@ def _delegate(xp: ModuleType, *backends: Backend) -> bool: def pad( x: Array, - pad_width: int | tuple[int, int] | list[tuple[int, int]], + pad_width: int | tuple[int, int] | Sequence[tuple[int, int]], mode: Literal["constant"] = "constant", *, constant_values: bool | int | float | complex = 0, @@ -44,9 +45,9 @@ def pad( ---------- x : array Input array. - pad_width : int or tuple of ints or list of pairs of ints + pad_width : int or tuple of ints or sequence of pairs of ints Pad the input array with this many elements from each side. - If a list of tuples, ``[(before_0, after_0), ... (before_N, after_N)]``, + If a sequence of tuples, ``[(before_0, after_0), ... (before_N, after_N)]``, each pair applies to the corresponding axis of ``x``. A single tuple, ``(before, after)``, is equivalent to a list of ``x.ndim`` copies of this tuple. diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 85778356..c1c39f58 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -5,6 +5,7 @@ import math import warnings +from collections.abc import Sequence from types import ModuleType from typing import cast @@ -448,7 +449,7 @@ def nunique(x: Array, /, *, xp: ModuleType | None = None) -> Array: def pad( x: Array, - pad_width: int | tuple[int, int] | list[tuple[int, int]], + pad_width: int | tuple[int, int] | Sequence[tuple[int, int]], *, constant_values: bool | int | float | complex = 0, xp: ModuleType, @@ -456,15 +457,22 @@ def pad( """See docstring in `array_api_extra._delegation.py`.""" # make pad_width a list of length-2 tuples of ints x_ndim = cast(int, x.ndim) + if isinstance(pad_width, int): - pad_width = [(pad_width, pad_width)] * x_ndim - if isinstance(pad_width, tuple): - pad_width = [pad_width] * x_ndim + pad_width_seq = [(pad_width, pad_width)] * x_ndim + elif ( + isinstance(pad_width, tuple) + and len(pad_width) == 2 + and all(isinstance(i, int) for i in pad_width) + ): + pad_width_seq = [cast(tuple[int, int], pad_width)] * x_ndim + else: + pad_width_seq = cast(list[tuple[int, int]], list(pad_width)) # https://github.com/python/typeshed/issues/13376 slices: list[slice] = [] # type: ignore[no-any-explicit] newshape: list[int] = [] - for ax, w_tpl in enumerate(pad_width): + for ax, w_tpl in enumerate(pad_width_seq): if len(w_tpl) != 2: msg = f"expect a 2-tuple (before, after), got {w_tpl}." raise ValueError(msg) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 4847cb9f..9be01508 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -390,12 +390,12 @@ def test_tuple_width(self, xp: ModuleType): with pytest.raises((ValueError, RuntimeError)): pad(a, [(1, 2, 3)]) # type: ignore[list-item] # pyright: ignore[reportArgumentType] - def test_list_of_tuples_width(self, xp: ModuleType): + def test_sequence_of_tuples_width(self, xp: ModuleType): a = xp.reshape(xp.arange(12), (3, 4)) - padded = pad(a, [(1, 0), (0, 2)]) - assert padded.shape == (4, 6) - padded = pad(a, [(1, 0), (0, 0)]) + padded = pad(a, ((1, 0), (0, 2))) + assert padded.shape == (4, 6) + padded = pad(a, ((1, 0), (0, 0))) assert padded.shape == (4, 4) From 6ee70c033a005b823c8d77cf5335a17258aba85c Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Tue, 21 Jan 2025 14:16:55 +0000 Subject: [PATCH 015/140] ENH: new function `isclose` (#113) --- docs/api-reference.md | 1 + pixi.lock | 253 +++++++++++++-------------- src/array_api_extra/__init__.py | 3 +- src/array_api_extra/_delegation.py | 92 +++++++++- src/array_api_extra/_lib/_funcs.py | 34 ++++ src/array_api_extra/_lib/_testing.py | 29 ++- tests/test_funcs.py | 136 +++++++++++++- tests/test_testing.py | 44 +++-- 8 files changed, 447 insertions(+), 145 deletions(-) diff --git a/docs/api-reference.md b/docs/api-reference.md index e2c115c6..32205248 100644 --- a/docs/api-reference.md +++ b/docs/api-reference.md @@ -11,6 +11,7 @@ cov create_diagonal expand_dims + isclose kron nunique pad diff --git a/pixi.lock b/pixi.lock index 5ea45749..db425962 100644 --- a/pixi.lock +++ b/pixi.lock @@ -139,10 +139,10 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/hpack-4.0.0-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/noarch/hyperframe-6.0.1-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/linux-64/icu-75.1-he02047a_0.conda - - conda: https://prefix.dev/conda-forge/noarch/identify-2.6.5-pyhd8ed1ab_0.conda + - conda: https://prefix.dev/conda-forge/noarch/identify-2.6.6-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/noarch/idna-3.10-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/noarch/imagesize-1.4.1-pyhd8ed1ab_0.tar.bz2 - - conda: https://prefix.dev/conda-forge/noarch/importlib-metadata-8.5.0-pyha770c72_1.conda + - conda: https://prefix.dev/conda-forge/noarch/importlib-metadata-8.6.1-pyha770c72_0.conda - conda: https://prefix.dev/conda-forge/noarch/iniconfig-2.0.0-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/noarch/ipython-8.31.0-pyh707e725_0.conda - conda: https://prefix.dev/conda-forge/noarch/isort-5.13.2-pyhd8ed1ab_1.conda @@ -248,8 +248,8 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/pillow-11.1.0-py312h80c1187_0.conda - conda: https://prefix.dev/conda-forge/noarch/platformdirs-4.3.6-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/noarch/pluggy-1.5.0-pyhd8ed1ab_1.conda - - conda: https://prefix.dev/conda-forge/noarch/pre-commit-4.0.1-pyha770c72_1.conda - - conda: https://prefix.dev/conda-forge/noarch/prompt-toolkit-3.0.48-pyha770c72_1.conda + - conda: https://prefix.dev/conda-forge/noarch/pre-commit-4.1.0-pyha770c72_0.conda + - conda: https://prefix.dev/conda-forge/noarch/prompt-toolkit-3.0.50-pyha770c72_0.conda - conda: https://prefix.dev/conda-forge/linux-64/psutil-6.1.1-py312h66e93f0_0.conda - conda: https://prefix.dev/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda - conda: https://prefix.dev/conda-forge/noarch/ptyprocess-0.7.0-pyhd8ed1ab_1.conda @@ -268,7 +268,7 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/python_abi-3.12-5_cp312.conda - conda: https://prefix.dev/conda-forge/linux-64/pytorch-2.5.1-cpu_mkl_py312_hf462abe_109.conda - 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- pkg:pypi/setuptools?source=compressed-mapping + - pkg:pypi/setuptools?source=hash-mapping size: 775598 timestamp: 1736512753595 - conda: https://prefix.dev/conda-forge/noarch/six-1.17.0-pyhd8ed1ab_0.conda diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 65d2f738..840dd8e7 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 pad +from ._delegation import isclose, pad from ._lib._at import at from ._lib._funcs import ( atleast_nd, @@ -23,6 +23,7 @@ "cov", "create_diagonal", "expand_dims", + "isclose", "kron", "nunique", "pad", diff --git a/src/array_api_extra/_delegation.py b/src/array_api_extra/_delegation.py index 195dd88f..b7bc9a84 100644 --- a/src/array_api_extra/_delegation.py +++ b/src/array_api_extra/_delegation.py @@ -8,7 +8,7 @@ from ._lib._utils._compat import array_namespace from ._lib._utils._typing import Array -__all__ = ["pad"] +__all__ = ["isclose", "pad"] def _delegate(xp: ModuleType, *backends: Backend) -> bool: @@ -30,6 +30,96 @@ def _delegate(xp: ModuleType, *backends: Backend) -> bool: return any(backend.is_namespace(xp) for backend in backends) +def isclose( + a: Array, + b: Array, + *, + rtol: float = 1e-05, + atol: float = 1e-08, + equal_nan: bool = False, + xp: ModuleType | None = None, +) -> Array: + """ + Return a boolean array where two arrays are element-wise equal within a tolerance. + + The tolerance values are positive, typically very small numbers. The relative + difference ``(rtol * abs(b))`` and the absolute difference `atol` are added together + to compare against the absolute difference between `a` and `b`. + + NaNs are treated as equal if they are in the same place and if ``equal_nan=True``. + Infs are treated as equal if they are in the same place and of the same sign in both + arrays. + + Parameters + ---------- + a, b : Array + Input arrays to compare. + rtol : array_like, optional + The relative tolerance parameter (see Notes). + atol : array_like, optional + The absolute tolerance parameter (see Notes). + equal_nan : bool, optional + Whether to compare NaN's as equal. If True, NaN's in `a` will be considered + equal to NaN's in `b` in the output array. + xp : array_namespace, optional + The standard-compatible namespace for `a` and `b`. Default: infer. + + Returns + ------- + Array + A boolean array of shape broadcasted from `a` and `b`, containing ``True`` where + `a` is close to `b`, and ``False`` otherwise. + + Warnings + -------- + The default `atol` is not appropriate for comparing numbers with magnitudes much + smaller than one (see notes). + + See Also + -------- + math.isclose : Similar function in stdlib for Python scalars. + + Notes + ----- + For finite values, `isclose` uses the following equation to test whether two + floating point values are equivalent:: + + absolute(a - b) <= (atol + rtol * absolute(b)) + + Unlike the built-in `math.isclose`, + the above equation is not symmetric in `a` and `b`, + so that ``isclose(a, b)`` might be different from ``isclose(b, a)`` in some rare + cases. + + The default value of `atol` is not appropriate when the reference value `b` has + magnitude smaller than one. For example, it is unlikely that ``a = 1e-9`` and + ``b = 2e-9`` should be considered "close", yet ``isclose(1e-9, 2e-9)`` is ``True`` + with default settings. Be sure to select `atol` for the use case at hand, especially + for defining the threshold below which a non-zero value in `a` will be considered + "close" to a very small or zero value in `b`. + + The comparison of `a` and `b` uses standard broadcasting, which means that `a` and + `b` need not have the same shape in order for ``isclose(a, b)`` to evaluate to + ``True``. + + `isclose` is not defined for non-numeric data types. + ``bool`` is considered a numeric data-type for this purpose. + """ + xp = array_namespace(a, b) if xp is None else xp + + if _delegate( + xp, + Backend.NUMPY, + Backend.CUPY, + Backend.DASK, + Backend.JAX, + Backend.TORCH, + ): + 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) + + 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 c1c39f58..0af265e2 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -305,6 +305,40 @@ def expand_dims( return a +def isclose( + a: Array, + b: Array, + *, + rtol: float = 1e-05, + atol: float = 1e-08, + equal_nan: bool = False, + xp: ModuleType, +) -> Array: # numpydoc ignore=PR01,RT01 + """See docstring in array_api_extra._delegation.""" + + 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: + # FIXME: use scipy's lazywhere to suppress warnings on inf + out = xp.abs(a - b) <= (atol + rtol * xp.abs(b)) + out = xp.where(xp.isinf(a) & xp.isinf(b), xp.sign(a) == xp.sign(b), out) + if equal_nan: + out = xp.where(xp.isnan(a) & xp.isnan(b), xp.asarray(True), out) + return out + + if xp.isdtype(a.dtype, "bool") or xp.isdtype(b.dtype, "bool"): + if atol >= 1 or rtol >= 1: + return xp.ones_like(a == b) + return a == b + + # integer types + atol = int(atol) + if rtol == 0: + return xp.abs(a - b) <= atol + nrtol = int(1.0 / rtol) + return xp.abs(a - b) <= (atol + xp.abs(b) // nrtol) + + def kron(a: Array, b: Array, /, *, xp: ModuleType | None = None) -> Array: """ Kronecker product of two arrays. diff --git a/src/array_api_extra/_lib/_testing.py b/src/array_api_extra/_lib/_testing.py index b6993a16..cc0d0559 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -4,11 +4,13 @@ Note that this is private API; don't expect it to be stable. """ +import math from types import ModuleType from ._utils._compat import ( array_namespace, is_cupy_namespace, + is_dask_namespace, is_pydata_sparse_namespace, is_torch_namespace, ) @@ -40,8 +42,16 @@ def _check_ns_shape_dtype( msg = f"namespaces do not match: {actual_xp} != f{desired_xp}" assert actual_xp == desired_xp, msg - msg = f"shapes do not match: {actual.shape} != f{desired.shape}" - assert actual.shape == desired.shape, msg + actual_shape = actual.shape + desired_shape = desired.shape + if is_dask_namespace(desired_xp): + if any(math.isnan(i) for i in actual_shape): + actual_shape = actual.compute().shape + if any(math.isnan(i) for i in desired_shape): + desired_shape = desired.compute().shape + + 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 @@ -61,6 +71,11 @@ 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. + + 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) @@ -112,6 +127,16 @@ def xp_assert_close( Absolute tolerance. Default: 0. err_msg : str, optional Error message to display on failure. + + See Also + -------- + xp_assert_equal : Similar function for exact equality checks. + isclose : Public function for checking closeness. + numpy.testing.assert_allclose : Similar function for NumPy arrays. + + Notes + ----- + The default `atol` and `rtol` differ from `xp.all(xpx.isclose(a, b))`. """ xp = _check_ns_shape_dtype(actual, desired) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 9be01508..fbb530b0 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -11,6 +11,7 @@ cov, create_diagonal, expand_dims, + isclose, kron, nunique, pad, @@ -23,7 +24,7 @@ from array_api_extra._lib._utils._typing import Array, Device # some xp backends are untyped -# mypy: disable-error-code=no-untyped-usage +# mypy: disable-error-code=no-untyped-def @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no expand_dims") @@ -252,6 +253,139 @@ def test_xp(self, xp: ModuleType): assert y.shape == (1, 1, 1, 3) +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype") +class TestIsClose: + # FIXME use lazywhere to avoid warnings on inf + @pytest.mark.filterwarnings("ignore:invalid value encountered") + @pytest.mark.parametrize( + ("a", "b"), + [ + (0.0, 0.0), + (1.0, 1.0), + (1.0, 2.0), + (1.0, -1.0), + (100.0, 101.0), + (0, 0), + (1, 1), + (1, 2), + (1, -1), + (1.0 + 1j, 1.0 + 1j), + (1.0 + 1j, 1.0 - 1j), + (float("inf"), float("inf")), + (float("inf"), 100.0), + (float("inf"), float("-inf")), + (float("nan"), float("nan")), + (float("nan"), 0.0), + (0.0, float("nan")), + (1e6, 1e6 + 1), # True - within rtol + (1e6, 1e6 + 100), # False - outside rtol + (1e-6, 1.1e-6), # False - outside atol + (1e-7, 1.1e-7), # True - outside atol + (1e6 + 0j, 1e6 + 1j), # True - within rtol + (1e6 + 0j, 1e6 + 100j), # False - outside rtol + ], + ) + def test_basic(self, a: float, b: float, xp: ModuleType): + a_xp = xp.asarray(a) + b_xp = xp.asarray(b) + + xp_assert_equal(isclose(a_xp, b_xp), xp.asarray(np.isclose(a, b))) + + with warnings.catch_warnings(): + warnings.simplefilter("ignore") + r_xp = xp.asarray(np.arange(10), dtype=a_xp.dtype) + ar_xp = a_xp * r_xp + br_xp = b_xp * r_xp + ar_np = a * np.arange(10) + br_np = b * np.arange(10) + + xp_assert_equal(isclose(ar_xp, br_xp), xp.asarray(np.isclose(ar_np, br_np))) + + @pytest.mark.parametrize("dtype", ["float32", "int32"]) + def test_broadcast(self, dtype: str, xp: ModuleType): + dtype = getattr(xp, dtype) + a = xp.asarray([1, 2, 3], dtype=dtype) + b = xp.asarray([[1], [5]], dtype=dtype) + actual = isclose(a, b) + expect = xp.asarray( + [[True, False, False], [False, False, False]], dtype=xp.bool + ) + + xp_assert_equal(actual, expect) + + # FIXME use lazywhere to avoid warnings on inf + @pytest.mark.filterwarnings("ignore:invalid value encountered") + def test_some_inf(self, xp: ModuleType): + a = xp.asarray([0.0, 1.0, float("inf"), float("inf"), float("inf")]) + b = xp.asarray([1e-9, 1.0, float("inf"), float("-inf"), 2.0]) + actual = isclose(a, b) + xp_assert_equal(actual, xp.asarray([True, True, True, False, False])) + + def test_equal_nan(self, xp: ModuleType): + a = xp.asarray([float("nan"), float("nan"), 1.0]) + b = xp.asarray([float("nan"), 1.0, float("nan")]) + xp_assert_equal(isclose(a, b), xp.asarray([False, False, False])) + xp_assert_equal(isclose(a, b, equal_nan=True), xp.asarray([True, False, False])) + + @pytest.mark.parametrize("dtype", ["float32", "complex64", "int32"]) + def test_tolerance(self, dtype: str, xp: ModuleType): + dtype = getattr(xp, dtype) + a = xp.asarray([100, 100], dtype=dtype) + b = xp.asarray([101, 102], dtype=dtype) + xp_assert_equal(isclose(a, b), xp.asarray([False, False])) + xp_assert_equal(isclose(a, b, atol=1), xp.asarray([True, False])) + xp_assert_equal(isclose(a, b, rtol=0.01), xp.asarray([True, False])) + + # Attempt to trigger division by 0 in rtol on int dtype + xp_assert_equal(isclose(a, b, rtol=0), xp.asarray([False, False])) + xp_assert_equal(isclose(a, b, atol=1, rtol=0), xp.asarray([True, False])) + + def test_very_small_numbers(self, xp: ModuleType): + a = xp.asarray([1e-9, 1e-9]) + b = xp.asarray([1.0001e-9, 1.00001e-9]) + # Difference is below default atol + xp_assert_equal(isclose(a, b), xp.asarray([True, True])) + # Use only rtol + xp_assert_equal(isclose(a, b, atol=0), xp.asarray([False, True])) + xp_assert_equal(isclose(a, b, atol=0, rtol=0), xp.asarray([False, False])) + + def test_bool_dtype(self, xp: ModuleType): + a = xp.asarray([False, True, False]) + b = xp.asarray([True, True, False]) + xp_assert_equal(isclose(a, b), xp.asarray([False, True, True])) + xp_assert_equal(isclose(a, b, atol=1), xp.asarray([True, True, True])) + xp_assert_equal(isclose(a, b, atol=2), xp.asarray([True, True, True])) + xp_assert_equal(isclose(a, b, rtol=1), xp.asarray([True, True, True])) + xp_assert_equal(isclose(a, b, rtol=2), xp.asarray([True, True, True])) + + # Test broadcasting + xp_assert_equal( + isclose(a, xp.asarray(True), atol=1), xp.asarray([True, True, True]) + ) + xp_assert_equal( + isclose(xp.asarray(True), b, atol=1), xp.asarray([True, True, True]) + ) + + def test_none_shape(self, xp: ModuleType): + a = xp.asarray([1, 5, 0]) + b = xp.asarray([1, 4, 2]) + b = b[a < 5] + a = a[a < 5] + xp_assert_equal(isclose(a, b), xp.asarray([True, False])) + + def test_none_shape_bool(self, xp: ModuleType): + a = xp.asarray([True, True, False]) + b = xp.asarray([True, False, True]) + b = b[a] + a = a[a] + xp_assert_equal(isclose(a, b), xp.asarray([True, False])) + + def test_xp(self, xp: ModuleType): + a = xp.asarray([0.0, 0.0]) + b = xp.asarray([1e-9, 1e-4]) + xp_assert_equal(isclose(a, b, xp=xp), xp.asarray([True, False])) + + @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no expand_dims") class TestKron: def test_basic(self, xp: ModuleType): diff --git a/tests/test_testing.py b/tests/test_testing.py index dc315663..ec5023b9 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -10,8 +10,7 @@ # mypy: disable-error-code=no-any-decorated # pyright: reportUnknownParameterType=false,reportMissingParameterType=false - -@pytest.mark.parametrize( +param_assert_equal_close = pytest.mark.parametrize( "func", [ xp_assert_equal, @@ -21,6 +20,9 @@ ), ], ) + + +@param_assert_equal_close def test_assert_close_equal_basic(xp: ModuleType, func: Callable[..., None]): # type: ignore[no-any-explicit] func(xp.asarray(0), xp.asarray(0)) func(xp.asarray([1, 2]), xp.asarray([1, 2])) @@ -40,16 +42,7 @@ 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, - pytest.param( - xp_assert_close, - marks=pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype"), - ), - ], -) +@param_assert_equal_close def test_assert_close_equal_namespace(xp: ModuleType, func: Callable[..., None]): # type: ignore[no-any-explicit] with pytest.raises(AssertionError): func(xp.asarray(0), np.asarray(0)) @@ -68,3 +61,30 @@ def test_assert_close_tolerance(xp: ModuleType): 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) + + +@param_assert_equal_close +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no bool indexing by sparse arrays") +def test_assert_close_equal_none_shape(xp: ModuleType, func: Callable[..., None]): # type: ignore[no-any-explicit] + """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) From 6f0ef5c3e74fdec16159563ce568e864f697f904 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Tue, 21 Jan 2025 16:40:59 +0000 Subject: [PATCH 016/140] MAINT: Simplify `at` implementation --- src/array_api_extra/_lib/_at.py | 111 +++++++++++++++----------------- 1 file changed, 51 insertions(+), 60 deletions(-) diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py index f2dd7219..927a7300 100644 --- a/src/array_api_extra/_lib/_at.py +++ b/src/array_api_extra/_lib/_at.py @@ -185,22 +185,42 @@ def __getitem__(self, idx: Index, /) -> at: # numpydoc ignore=PR01,RT01 raise ValueError(msg) return at(self._x, idx) - def _update_common( + def _op( self, at_op: _AtOp, - y: Array, + in_place_op: Callable[[Array, Array | object], Array] | None, + y: Array | object, /, copy: bool | None, xp: ModuleType | None, - ) -> tuple[Array, None] | tuple[None, Array]: # numpydoc ignore=PR01 + ) -> Array: """ - Perform common prepocessing to all update operations. + Implement all update operations. + + Parameters + ---------- + at_op : _AtOp + Method of JAX's Array.at[]. + in_place_op : Callable[[Array, Array | object], Array] | None + In-place operation to apply on mutable backends:: + + x[idx] = in_place_op(x[idx], y) + + If None:: + + x[idx] = y + + y : array or object + Right-hand side of the operation. + copy : bool or None + Whether to copy the input array. See the class docstring for details. + xp : array_namespace or None + The array namespace for the input array. Returns ------- - tuple - If the operation can be resolved by ``at[]``, ``(return value, None)`` - Otherwise, ``(None, preprocessed x)``. + Array + Updated `x`. """ x, idx = self._x, self._idx @@ -231,7 +251,7 @@ def _update_common( if is_jax_array(x): # Use JAX's at[] func = cast(Callable[[Array], Array], getattr(x.at[idx], at_op.value)) - return func(y), None + return func(y) # Emulate at[] behaviour for non-JAX arrays # with a copy followed by an update if xp is None: @@ -249,52 +269,25 @@ def _update_common( msg = f"Can't update read-only array {x}" raise ValueError(msg) - return None, x + if in_place_op: + x[self._idx] = in_place_op(x[self._idx], y) + else: # set() + x[self._idx] = y + return x def set( self, - y: Array, + y: Array | object, /, copy: bool | None = None, xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] = y`` and return the update array.""" - res, x = self._update_common(_AtOp.SET, y, copy=copy, xp=xp) - if res is not None: - return res - assert x is not None - x[self._idx] = y - return x - - def _iop( - self, - at_op: _AtOp, - elwise_op: Callable[[Array, Array], Array], - y: Array, - /, - copy: bool | None, - xp: ModuleType | None, - ) -> Array: # numpydoc ignore=PR01,RT01 - """ - ``x[idx] += y`` or equivalent in-place operation on a subset of x. - - which is the same as saying - x[idx] = x[idx] + y - Note that this is not the same as - operator.iadd(x[idx], y) - Consider for example when x is a numpy array and idx is a fancy index, which - triggers a deep copy on __getitem__. - """ - res, x = self._update_common(at_op, y, copy=copy, xp=xp) - if res is not None: - return res - assert x is not None - x[self._idx] = elwise_op(x[self._idx], y) - return x + return self._op(_AtOp.SET, None, y, copy=copy, xp=xp) def add( self, - y: Array, + y: Array | object, /, copy: bool | None = None, xp: ModuleType | None = None, @@ -304,70 +297,68 @@ def add( # Note for this and all other methods based on _iop: # operator.iadd and operator.add subtly differ in behaviour, as # only iadd will trigger exceptions when y has an incompatible dtype. - return self._iop(_AtOp.ADD, operator.iadd, y, copy=copy, xp=xp) + return self._op(_AtOp.ADD, operator.iadd, y, copy=copy, xp=xp) def subtract( self, - y: Array, + y: Array | object, /, copy: bool | None = None, xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] -= y`` and return the updated array.""" - return self._iop(_AtOp.SUBTRACT, operator.isub, y, copy=copy, xp=xp) + return self._op(_AtOp.SUBTRACT, operator.isub, y, copy=copy, xp=xp) def multiply( self, - y: Array, + y: Array | object, /, copy: bool | None = None, xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] *= y`` and return the updated array.""" - return self._iop(_AtOp.MULTIPLY, operator.imul, y, copy=copy, xp=xp) + return self._op(_AtOp.MULTIPLY, operator.imul, y, copy=copy, xp=xp) def divide( self, - y: Array, + y: Array | object, /, copy: bool | None = None, xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] /= y`` and return the updated array.""" - return self._iop(_AtOp.DIVIDE, operator.itruediv, y, copy=copy, xp=xp) + return self._op(_AtOp.DIVIDE, operator.itruediv, y, copy=copy, xp=xp) def power( self, - y: Array, + y: Array | object, /, copy: bool | None = None, xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] **= y`` and return the updated array.""" - return self._iop(_AtOp.POWER, operator.ipow, y, copy=copy, xp=xp) + return self._op(_AtOp.POWER, operator.ipow, y, copy=copy, xp=xp) def min( self, - y: Array, + y: Array | object, /, copy: bool | None = None, xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] = minimum(x[idx], y)`` and return the updated array.""" - if xp is None: - xp = array_namespace(self._x) + xp = array_namespace(self._x) if xp is None else xp y = xp.asarray(y) - return self._iop(_AtOp.MIN, xp.minimum, y, copy=copy, xp=xp) + return self._op(_AtOp.MIN, xp.minimum, y, copy=copy, xp=xp) def max( self, - y: Array, + y: Array | object, /, copy: bool | None = None, xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] = maximum(x[idx], y)`` and return the updated array.""" - if xp is None: - xp = array_namespace(self._x) + xp = array_namespace(self._x) if xp is None else xp y = xp.asarray(y) - return self._iop(_AtOp.MAX, xp.maximum, y, copy=copy, xp=xp) + return self._op(_AtOp.MAX, xp.maximum, y, copy=copy, xp=xp) From 750643bc2e58cb252da8dbfef649e5b8d40fa512 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Fri, 24 Jan 2025 15:16:11 +0000 Subject: [PATCH 017/140] MAINT: bump pixi to 0.40.3 --- .github/workflows/ci.yml | 4 +- .github/workflows/docs-build.yml | 2 +- pixi.lock | 1543 +++++++++++++++--------------- 3 files changed, 791 insertions(+), 758 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index d455e389..4ba1dec5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -32,7 +32,7 @@ jobs: extra_args: --hook-stage manual --all-files - uses: prefix-dev/setup-pixi@v0.8.1 with: - pixi-version: v0.39.0 + pixi-version: v0.40.3 cache: true environments: lint - name: Run Pylint, Mypy & Pyright @@ -58,7 +58,7 @@ jobs: - uses: prefix-dev/setup-pixi@v0.8.1 with: - pixi-version: v0.39.0 + pixi-version: v0.40.3 cache: true environments: ${{ matrix.environment }} diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index b1bfac51..b5145f92 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -9,7 +9,7 @@ jobs: - uses: actions/checkout@v4 - uses: prefix-dev/setup-pixi@v0.8.1 with: - pixi-version: v0.39.0 + pixi-version: v0.40.3 cache: true environments: docs - name: Build Docs diff --git a/pixi.lock b/pixi.lock index db425962..f82df2e4 100644 --- a/pixi.lock +++ b/pixi.lock @@ -19,7 +19,7 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_1.conda - conda: https://prefix.dev/conda-forge/linux-64/liblzma-5.6.3-hb9d3cd8_1.conda - conda: https://prefix.dev/conda-forge/linux-64/libnsl-2.0.1-hd590300_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/libsqlite-3.48.0-hee588c1_0.conda + - conda: https://prefix.dev/conda-forge/linux-64/libsqlite-3.48.0-hee588c1_1.conda - 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conda: https://prefix.dev/conda-forge/noarch/typing_extensions-4.12.2-pyha770c72_1.conda - conda: https://prefix.dev/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda @@ -2098,6 +2169,7 @@ environments: - conda: https://prefix.dev/conda-forge/win-64/vs2015_runtime-14.42.34433-hfef2bbc_24.conda - conda: https://prefix.dev/conda-forge/noarch/win_inet_pton-1.1.0-pyh7428d3b_8.conda - conda: https://prefix.dev/conda-forge/win-64/yaml-0.2.5-h8ffe710_2.tar.bz2 + - conda: https://prefix.dev/conda-forge/noarch/zipp-3.21.0-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/win-64/zstandard-0.23.0-py312h7606c53_1.conda - conda: https://prefix.dev/conda-forge/win-64/zstd-1.5.6-h0ea2cb4_0.conda - pypi: . @@ -3695,7 +3767,7 @@ packages: - pypi: . name: array-api-extra version: 0.6.1.dev0 - sha256: 22c9e9830a088aff4480ecea8495d2ebcf91f65596886a12012bebfb238181d6 + sha256: bb6cd89a7f100a73d3f853de571b2f4fff0e70de8df0d113f2f5c1559744e6b6 requires_dist: - array-api-compat>=1.10.0,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 2fae4f82..d15aba84 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -54,6 +54,7 @@ array-api-compat = ">=1.10.0,<2" array-api-extra = { path = ".", editable = true } [tool.pixi.feature.lint.dependencies] +typing-extensions = "*" pre-commit = "*" pylint = "*" basedmypy = "*" @@ -63,6 +64,9 @@ numpydoc = ">=1.8.0,<2" array-api-strict = "*" numpy = "*" pytest = "*" +dask-core = "*" # 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 [tool.pixi.feature.lint.tasks] pre-commit-install = "pre-commit install" @@ -98,6 +102,10 @@ furo = ">=2023.08.17" myst-parser = ">=0.13" sphinx-copybutton = "*" sphinx-autodoc-typehints = "*" +# Needed to import parsed modules with autodoc +dask-core = "*" +pytest = "*" +typing-extensions = "*" [tool.pixi.feature.docs.tasks] docs = { cmd = "sphinx-build . build/", cwd = "docs" } @@ -180,8 +188,10 @@ markers = ["skip_xp_backend(library, *, reason=None): Skip test for a specific b [tool.coverage] run.source = ["array_api_extra"] -report.exclude_also = ['\.\.\.'] - +report.exclude_also = [ + '\.\.\.', + 'if TYPE_CHECKING:', +] # mypy @@ -221,6 +231,8 @@ reportMissingImports = false reportMissingTypeStubs = false # false positives for input validation reportUnreachable = false +# ruff handles this +reportUnusedParameter = false executionEnvironments = [ { root = "tests", reportPrivateUsage = false }, @@ -282,7 +294,10 @@ 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 ] diff --git a/src/array_api_extra/_lib/_testing.py b/src/array_api_extra/_lib/_testing.py index cc0d0559..ac4ae586 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -2,6 +2,7 @@ Testing utilities. Note that this is private API; don't expect it to be stable. +See also ..testing for public testing utilities. """ import math diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py new file mode 100644 index 00000000..e124ed74 --- /dev/null +++ b/src/array_api_extra/testing.py @@ -0,0 +1,262 @@ +""" +Public testing utilities. + +See also _lib._testing for additional private testing utilities. +""" + +# https://github.com/scikit-learn/scikit-learn/pull/27910#issuecomment-2568023972 +from __future__ import annotations + +from collections.abc import Callable, Iterable, Sequence +from functools import wraps +from types import ModuleType +from typing import TYPE_CHECKING, Any, TypeVar, cast + +import pytest + +from array_api_extra._lib._utils._compat import is_dask_namespace, is_jax_namespace + +__all__ = ["lazy_xp_function", "patch_lazy_xp_functions"] + +if TYPE_CHECKING: + # 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 + + 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 + + def override(func: Callable[P, T]) -> Callable[P, T]: + return func + + +T = TypeVar("T") + + +def lazy_xp_function( # type: ignore[no-any-explicit] + func: Callable[..., Any], + *, + allow_dask_compute: int = 0, + jax_jit: bool = True, + static_argnums: int | Sequence[int] | None = None, + static_argnames: str | Iterable[str] | None = None, +) -> None: # numpydoc ignore=GL07 + """ + Tag a function to be tested on lazy backends. + + Tag a function, which must be imported in the test module globals, so that when any + tests defined in the same module are executed with ``xp=jax.numpy`` the function is + replaced with a jitted version of itself, and when it is executed with + ``xp=dask.array`` the function will raise if it attempts to materialize the graph. + This will be later expanded to provide test coverage for other lazy backends. + + In order for the tag to be effective, the test or a fixture must call + :func:`patch_lazy_xp_functions`. + + Parameters + ---------- + 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()``. + + 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 + 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 + 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 + 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)`. + + See Also + -------- + patch_lazy_xp_functions : Companion function to call from the test or fixture. + jax.jit : JAX function to compile a function for performance. + + Examples + -------- + In ``test_mymodule.py``:: + + from array_api_extra.testing import lazy_xp_function from mymodule import myfunc + + lazy_xp_function(myfunc) + + 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=dask.array, crash on compute() or persist() + b = myfunc(a) + + Notes + ----- + A test function can circumvent this monkey-patching system by calling `func` as an + attribute of the original module. You need to sanitize your code to make sure this + does not happen. + + Example:: + + import mymodule from mymodule import myfunc + + lazy_xp_function(myfunc) + + def test_myfunc(xp): + a = xp.asarray([1, 2]) b = myfunc(a) # This is jitted when xp=jax.numpy c = + mymodule.myfunc(a) # This is not + """ + func.allow_dask_compute = allow_dask_compute # type: ignore[attr-defined] # pyright: ignore[reportFunctionMemberAccess] + if jax_jit: + func.lazy_jax_jit_kwargs = { # type: ignore[attr-defined] # pyright: ignore[reportFunctionMemberAccess] + "static_argnums": static_argnums, + "static_argnames": static_argnames, + } + + +def patch_lazy_xp_functions( + request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch, *, xp: ModuleType +) -> None: + """ + Test lazy execution of functions tagged with :func:`lazy_xp_function`. + + If ``xp==jax.numpy``, search for all functions which have been tagged with + :func:`lazy_xp_function` in the globals of the module that defines the current test + and wrap them with :func:`jax.jit`. Unwrap them at the end of the test. + + If ``xp==dask.array``, wrap the functions with a decorator that disables + ``compute()`` and ``persist()``. + + 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 + + but it can be otherwise be called by the test itself too. + + Parameters + ---------- + 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. + xp : module + Array namespace to be tested. + + See Also + -------- + lazy_xp_function : Tag a function to be tested on lazy backends. + pytest.FixtureRequest : `request` test function parameter. + """ + globals_ = cast("dict[str, Any]", request.module.__dict__) # type: ignore[no-any-explicit] + + if is_dask_namespace(xp): + for name, func in globals_.items(): + n = getattr(func, "allow_dask_compute", None) + if n is not None: + assert isinstance(n, int) + wrapped = _allow_dask_compute(func, n) + monkeypatch.setitem(globals_, name, wrapped) + + elif is_jax_namespace(xp): + import jax + + for name, func in globals_.items(): + kwargs = cast( # type: ignore[no-any-explicit] + "dict[str, Any] | None", getattr(func, "lazy_jax_jit_kwargs", None) + ) + if kwargs is not None: + # suppress unused-ignore to run mypy in -e lint as well as -e dev + wrapped = cast(Callable[..., Any], jax.jit(func, **kwargs)) # type: ignore[no-any-explicit,no-untyped-call,unused-ignore] + monkeypatch.setitem(globals_, name, wrapped) + + +class CountingDaskScheduler(SchedulerGetCallable): + """ + Dask scheduler that counts how many times `dask.compute` is called. + + If the number of times exceeds 'max_count', it raises an error. + This is a wrapper around Dask's own 'synchronous' scheduler. + + Parameters + ---------- + max_count : int + Maximum number of allowed calls to `dask.compute`. + msg : str + Assertion to raise when the count exceeds `max_count`. + """ + + count: int + max_count: int + msg: str + + def __init__(self, max_count: int, msg: str): # numpydoc ignore=GL08 + self.count = 0 + self.max_count = max_count + self.msg = msg + + @override + def __call__(self, dsk: Graph, keys: Sequence[Key] | Key, **kwargs: Any) -> Any: # type: ignore[no-any-decorated,no-any-explicit] # numpydoc ignore=GL08 + import dask + + self.count += 1 + # This should yield a nice traceback to the + # 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] + + +def _allow_dask_compute( + func: Callable[P, T], n: int +) -> Callable[P, T]: # numpydoc ignore=PR01,RT01 + """ + Wrap `func` to raise if it attempts to call `dask.compute` more than `n` times. + """ + import dask.config + + func_name = getattr(func, "__name__", str(func)) + n_str = f"only up to {n}" if n else "no" + msg = ( + f"Called `dask.compute()` or `dask.persist()` {n + 1} times, " + f"but {n_str} calls are allowed. Set " + f"`lazy_xp_function({func_name}, allow_dask_compute={n + 1})` " + "to allow for more (but note that this will harm performance). " + ) + + @wraps(func) + def wrapper(*args: P.args, **kwargs: P.kwargs) -> T: # numpydoc ignore=GL08 + scheduler = CountingDaskScheduler(n, msg) + with dask.config.set({"scheduler": scheduler}): + return func(*args, **kwargs) + + return wrapper diff --git a/tests/conftest.py b/tests/conftest.py index 39904ae2..4402c067 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -13,6 +13,7 @@ from array_api_extra._lib._utils._compat import array_namespace from array_api_extra._lib._utils._compat import device as get_device from array_api_extra._lib._utils._typing import Device +from array_api_extra.testing import patch_lazy_xp_functions T = TypeVar("T") P = ParamSpec("P") @@ -96,7 +97,9 @@ def wrapper(*args: P.args, **kwargs: P.kwargs) -> T: # numpydoc ignore=GL08 @pytest.fixture -def xp(library: Backend) -> ModuleType: # numpydoc ignore=PR01,RT03 +def xp( + library: Backend, request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch +) -> ModuleType: # numpydoc ignore=PR01,RT03 """ Parameterized fixture that iterates on all libraries. @@ -107,6 +110,9 @@ def xp(library: Backend) -> ModuleType: # numpydoc ignore=PR01,RT03 if library == Backend.NUMPY_READONLY: return NumPyReadOnly() # type: ignore[return-value] # pyright: ignore[reportReturnType] xp = pytest.importorskip(library.value) + + patch_lazy_xp_functions(request, monkeypatch, xp=xp) + if library == Backend.JAX: import jax diff --git a/tests/test_at.py b/tests/test_at.py index 4bd09c6a..744e3aaf 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -1,7 +1,8 @@ +import pickle from collections.abc import Callable, Generator from contextlib import contextmanager from types import ModuleType -from typing import cast +from typing import Any, cast import numpy as np import pytest @@ -11,7 +12,46 @@ 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 +from array_api_extra._lib._utils._typing import Array, Index +from array_api_extra.testing import lazy_xp_function + + +def at_op( # type: ignore[no-any-explicit] + x: Array, + idx: Index, + op: _AtOp, + y: Array | object, + **kwargs: Any, # Test the default copy=None +) -> Array: + """ + Wrapper around at(x, idx).op(y, copy=copy, xp=xp). + + This is a hack to allow wrapping `at()` with `lazy_xp_function`. + For clarity, at() itself works inside jax.jit without hacks; this is + 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, **kwargs) + return _at_op(x, idx, None, op, y, **kwargs) + + +def _at_op( # type: ignore[no-any-explicit] + x: Array, + idx: Index | None, + idx_pickle: bytes | None, + op: _AtOp, + y: Array | object, + **kwargs: Any, +) -> Array: + """jitted helper of at_op""" + if idx_pickle: + idx = pickle.loads(idx_pickle) + meth = cast(Callable[..., Array], getattr(at(x, idx), op.value)) # type: ignore[no-any-explicit] + return meth(y, **kwargs) + + +lazy_xp_function(_at_op, static_argnames=("op", "idx_pickle", "copy", "xp")) @contextmanager @@ -43,7 +83,7 @@ def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: ], ) @pytest.mark.parametrize( - ("op", "arg", "expect"), + ("op", "y", "expect"), [ (_AtOp.SET, 40.0, [10.0, 40.0, 40.0]), (_AtOp.ADD, 40.0, [10.0, 60.0, 70.0]), @@ -55,21 +95,52 @@ def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: (_AtOp.MAX, 25.0, [10.0, 25.0, 30.0]), ], ) +@pytest.mark.parametrize( + ("bool_mask", "shaped_y"), + [ + (False, False), + (False, True), + pytest.param( + True, + False, + marks=( + pytest.mark.skip_xp_backend(Backend.JAX, reason="TODO special case"), + pytest.mark.skip_xp_backend(Backend.DASK, reason="TODO special case"), + ), + ), + pytest.param( + True, + True, + marks=( + pytest.mark.skip_xp_backend( + Backend.JAX, reason="bool mask update with shaped rhs" + ), + pytest.mark.skip_xp_backend( + Backend.DASK, reason="bool mask update with shaped rhs" + ), + ), + ), + ], +) def test_update_ops( xp: ModuleType, kwargs: dict[str, bool | None], expect_copy: bool | None, op: _AtOp, - arg: float, + y: float, expect: list[float], + bool_mask: bool, + shaped_y: bool, ): - array = xp.asarray([10.0, 20.0, 30.0]) + x = xp.asarray([10.0, 20.0, 30.0]) + idx = xp.asarray([False, True, True]) if bool_mask else slice(1, None) + if shaped_y: + y = xp.asarray([y, y]) - with assert_copy(array, expect_copy): - func = cast(Callable[..., Array], getattr(at(array)[1:], op.value)) # type: ignore[no-any-explicit] - y = func(arg, **kwargs) - assert isinstance(y, type(array)) - xp_assert_equal(y, xp.asarray(expect)) + with assert_copy(x, expect_copy): + z = at_op(x, idx, op, y, **kwargs) + assert isinstance(z, type(x)) + xp_assert_equal(z, xp.asarray(expect)) def test_copy_invalid(): @@ -121,7 +192,6 @@ def test_iops_incompatible_dtype(op: _AtOp, copy: bool): UFuncTypeError: Cannot cast ufunc 'divide' output from dtype('float64') to dtype('int64') with casting rule 'same_kind' """ - a = np.asarray([2, 4]) - func = cast(Callable[..., Array], getattr(at(a)[:], op.value)) # type: ignore[no-any-explicit] + x = np.asarray([2, 4]) with pytest.raises(TypeError, match="Cannot cast ufunc"): - func(1.1, copy=copy) + at_op(x, slice(None), op, 1.1, copy=copy) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index fbb530b0..ef1a1fc2 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -22,10 +22,24 @@ 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._typing import Array, Device +from array_api_extra.testing import lazy_xp_function # some xp backends are untyped # mypy: disable-error-code=no-untyped-def +lazy_xp_function(atleast_nd, static_argnames=("ndim", "xp")) +lazy_xp_function(cov, static_argnames="xp") +# FIXME .device attribute https://github.com/data-apis/array-api-compat/pull/238 +lazy_xp_function(create_diagonal, jax_jit=False, 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")) +# FIXME calls in1d which calls xp.unique_values without size +lazy_xp_function(setdiff1d, jax_jit=False, static_argnames=("assume_unique", "xp")) +# FIXME .device attribute https://github.com/data-apis/array-api-compat/pull/238 +lazy_xp_function(sinc, jax_jit=False, static_argnames="xp") + @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no expand_dims") class TestAtLeastND: diff --git a/tests/test_testing.py b/tests/test_testing.py index ec5023b9..7d4ed0ad 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -6,6 +6,13 @@ 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 ( + array_namespace, + is_dask_namespace, + is_jax_namespace, +) +from array_api_extra._lib._utils._typing import Array +from array_api_extra.testing import lazy_xp_function # mypy: disable-error-code=no-any-decorated # pyright: reportUnknownParameterType=false,reportMissingParameterType=false @@ -88,3 +95,110 @@ def test_assert_close_equal_none_shape(xp: ModuleType, func: Callable[..., None] func(xp.asarray(2), a) with pytest.raises(AssertionError): func(xp.asarray([3]), a) + + +def good_lazy(x: Array) -> Array: + """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. + """ + xp = array_namespace(x) + # 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) + return x + + +def non_materializable2(x: Array) -> Array: + return non_materializable(x) + + +def non_materializable3(x: Array) -> Array: + return non_materializable(x) + + +def non_materializable4(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) +# Works on JAX, but not Dask +lazy_xp_function(non_materializable3, jax_jit=False, allow_dask_compute=1) +# Works neither on Dask nor JAX +lazy_xp_function(non_materializable4) + + +def test_lazy_xp_function(xp: ModuleType): + x = xp.asarray([1.0, 2.0]) + + xp_assert_equal(good_lazy(x), xp.asarray([2.0, 4.0])) + # Not wrapped + 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])) + + if is_jax_namespace(xp): + xp_assert_equal(non_materializable3(x), xp.asarray([1.0, 2.0])) + with pytest.raises( + TypeError, match="Attempted boolean conversion of traced array" + ): + non_materializable4(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) + with pytest.raises( + AssertionError, + match=r"dask\.compute.* 1 times, but no calls are allowed", + ): + non_materializable4(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])) + + +def static_params(x: Array, n: int, flag: bool = False) -> Array: + """Function with static parameters that must not be jitted""" + if flag and n > 0: # This fails if n or flag are jitted arrays + return x * 2.0 + return x * 3.0 + + +def static_params1(x: Array, n: int, flag: bool = False) -> Array: + return static_params(x, n, flag) + + +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") + + +@pytest.mark.parametrize("func", [static_params1, static_params2, static_params3]) +def test_lazy_xp_function_static_params(xp: ModuleType, func: Callable[..., Array]): # type: ignore[no-any-explicit] + 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])) diff --git a/tests/test_utils.py b/tests/test_utils.py index fff3f0f2..f710056b 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -7,9 +7,13 @@ from array_api_extra._lib._utils._compat import device as get_device from array_api_extra._lib._utils._helpers import in1d from array_api_extra._lib._utils._typing import Device +from array_api_extra.testing import lazy_xp_function # 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")) + class TestIn1D: @pytest.mark.skip_xp_backend(Backend.DASK, reason="no argsort") From 37b116a95568a46b9f04b4a9f1032b662c5b716a Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Sat, 25 Jan 2025 23:13:08 +0000 Subject: [PATCH 019/140] DEV: disable codecov annotations closes gh-125 --- codecov.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/codecov.yml b/codecov.yml index 1a517b3a..d05bc8e2 100644 --- a/codecov.yml +++ b/codecov.yml @@ -1,4 +1,6 @@ comment: false +github_checks: + annotations: false ignore: - "src/array_api_extra/_lib/_compat" - "src/array_api_extra/_lib/_typing" From a5cb116fa57a4564c05210a4d0dfc306f2795c61 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Sat, 25 Jan 2025 23:15:55 +0000 Subject: [PATCH 020/140] ENH: `at` support for bool mask in Dask and JAX (#121) Co-authored-by: Lucas Colley --- src/array_api_extra/_lib/_at.py | 92 ++++++++++++++++++--- src/array_api_extra/_lib/_utils/_compat.py | 3 + src/array_api_extra/_lib/_utils/_compat.pyi | 1 + tests/test_at.py | 87 ++++++++++++++----- vendor_tests/test_vendor.py | 2 + 5 files changed, 153 insertions(+), 32 deletions(-) diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py index 927a7300..e5cb3875 100644 --- a/src/array_api_extra/_lib/_at.py +++ b/src/array_api_extra/_lib/_at.py @@ -9,7 +9,12 @@ from types import ModuleType from typing import ClassVar, cast -from ._utils._compat import array_namespace, is_jax_array, is_writeable_array +from ._utils._compat import ( + array_namespace, + is_dask_array, + is_jax_array, + is_writeable_array, +) from ._utils._typing import Array, Index @@ -141,6 +146,25 @@ class at: # pylint: disable=invalid-name # numpydoc ignore=PR02 not explicitly covered by ``array-api-compat``, are not supported by update methods. + Boolean masks are supported on Dask and jitted JAX arrays exclusively + when `idx` has the same shape as `x` and `y` is 0-dimensional. + Note that this support is not available in JAX's native + ``x.at[mask].set(y)``. + + This pattern:: + + >>> mask = m(x) + >>> x[mask] = f(x[mask]) + + Can't be replaced by `at`, as it won't work on Dask and JAX inside jax.jit:: + + >>> mask = m(x) + >>> x = xpx.at(x, mask).set(f(x[mask]) # Crash on Dask and jax.jit + + You should instead use:: + + >>> x = xp.where(m(x), f(x), x) + Examples -------- Given either of these equivalent expressions:: @@ -189,6 +213,7 @@ def _op( self, at_op: _AtOp, in_place_op: Callable[[Array, Array | object], Array] | None, + out_of_place_op: Callable[[Array, Array], Array] | None, y: Array | object, /, copy: bool | None, @@ -210,6 +235,16 @@ def _op( x[idx] = y + out_of_place_op : Callable[[Array, Array], Array] | None + Out-of-place operation to apply when idx is a boolean mask and the backend + doesn't support in-place updates:: + + x = xp.where(idx, out_of_place_op(x, y), x) + + If None:: + + x = xp.where(idx, y, x) + y : array or object Right-hand side of the operation. copy : bool or None @@ -223,6 +258,7 @@ def _op( Updated `x`. """ x, idx = self._x, self._idx + xp = array_namespace(x, y) if xp is None else xp if idx is _undef: msg = ( @@ -247,15 +283,41 @@ def _op( else: writeable = is_writeable_array(x) + # JAX inside jax.jit and Dask don't support in-place updates with boolean + # mask. However we can handle the common special case of 0-dimensional y + # with where(idx, y, x) instead. + if ( + (is_dask_array(idx) or is_jax_array(idx)) + and idx.dtype == xp.bool + and idx.shape == x.shape + ): + y_xp = xp.asarray(y, dtype=x.dtype) + if y_xp.ndim == 0: + if out_of_place_op: + # FIXME: suppress inf warnings on dask with lazywhere + out = xp.where(idx, out_of_place_op(x, y_xp), x) + # Undo int->float promotion on JAX after _AtOp.DIVIDE + out = xp.astype(out, x.dtype, copy=False) + else: + out = xp.where(idx, y_xp, x) + + if copy: + return out + x[()] = out + return x + # else: this will work on eager JAX and crash on jax.jit and Dask + if copy: if is_jax_array(x): # Use JAX's at[] func = cast(Callable[[Array], Array], getattr(x.at[idx], at_op.value)) - return func(y) + out = func(y) + # Undo int->float promotion on JAX after _AtOp.DIVIDE + return xp.astype(out, x.dtype, copy=False) + # Emulate at[] behaviour for non-JAX arrays # with a copy followed by an update - if xp is None: - xp = array_namespace(x) + x = xp.asarray(x, copy=True) if writeable is False: # A copy of a read-only numpy array is writeable @@ -283,7 +345,7 @@ def set( xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] = y`` and return the update array.""" - return self._op(_AtOp.SET, None, y, copy=copy, xp=xp) + return self._op(_AtOp.SET, None, None, y, copy=copy, xp=xp) def add( self, @@ -297,7 +359,7 @@ def add( # Note for this and all other methods based on _iop: # operator.iadd and operator.add subtly differ in behaviour, as # only iadd will trigger exceptions when y has an incompatible dtype. - return self._op(_AtOp.ADD, operator.iadd, y, copy=copy, xp=xp) + return self._op(_AtOp.ADD, operator.iadd, operator.add, y, copy=copy, xp=xp) def subtract( self, @@ -307,7 +369,9 @@ def subtract( xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] -= y`` and return the updated array.""" - return self._op(_AtOp.SUBTRACT, operator.isub, y, copy=copy, xp=xp) + return self._op( + _AtOp.SUBTRACT, operator.isub, operator.sub, y, copy=copy, xp=xp + ) def multiply( self, @@ -317,7 +381,9 @@ def multiply( xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] *= y`` and return the updated array.""" - return self._op(_AtOp.MULTIPLY, operator.imul, y, copy=copy, xp=xp) + return self._op( + _AtOp.MULTIPLY, operator.imul, operator.mul, y, copy=copy, xp=xp + ) def divide( self, @@ -327,7 +393,9 @@ def divide( xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] /= y`` and return the updated array.""" - return self._op(_AtOp.DIVIDE, operator.itruediv, y, copy=copy, xp=xp) + return self._op( + _AtOp.DIVIDE, operator.itruediv, operator.truediv, y, copy=copy, xp=xp + ) def power( self, @@ -337,7 +405,7 @@ def power( xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] **= y`` and return the updated array.""" - return self._op(_AtOp.POWER, operator.ipow, y, copy=copy, xp=xp) + return self._op(_AtOp.POWER, operator.ipow, operator.pow, y, copy=copy, xp=xp) def min( self, @@ -349,7 +417,7 @@ def min( """Apply ``x[idx] = minimum(x[idx], y)`` and return the updated array.""" xp = array_namespace(self._x) if xp is None else xp y = xp.asarray(y) - return self._op(_AtOp.MIN, xp.minimum, y, copy=copy, xp=xp) + return self._op(_AtOp.MIN, xp.minimum, xp.minimum, y, copy=copy, xp=xp) def max( self, @@ -361,4 +429,4 @@ def max( """Apply ``x[idx] = maximum(x[idx], y)`` and return the updated array.""" xp = array_namespace(self._x) if xp is None else xp y = xp.asarray(y) - return self._op(_AtOp.MAX, xp.maximum, y, copy=copy, xp=xp) + return self._op(_AtOp.MAX, xp.maximum, xp.maximum, y, copy=copy, xp=xp) diff --git a/src/array_api_extra/_lib/_utils/_compat.py b/src/array_api_extra/_lib/_utils/_compat.py index 707e9553..f4def9f3 100644 --- a/src/array_api_extra/_lib/_utils/_compat.py +++ b/src/array_api_extra/_lib/_utils/_compat.py @@ -8,6 +8,7 @@ device, is_array_api_strict_namespace, is_cupy_namespace, + is_dask_array, is_dask_namespace, is_jax_array, is_jax_namespace, @@ -23,6 +24,7 @@ device, is_array_api_strict_namespace, is_cupy_namespace, + is_dask_array, is_dask_namespace, is_jax_array, is_jax_namespace, @@ -38,6 +40,7 @@ "device", "is_array_api_strict_namespace", "is_cupy_namespace", + "is_dask_array", "is_dask_namespace", "is_jax_array", "is_jax_namespace", diff --git a/src/array_api_extra/_lib/_utils/_compat.pyi b/src/array_api_extra/_lib/_utils/_compat.pyi index 1e81c984..e409091e 100644 --- a/src/array_api_extra/_lib/_utils/_compat.pyi +++ b/src/array_api_extra/_lib/_utils/_compat.pyi @@ -25,6 +25,7 @@ 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_dask_array(x: object, /) -> bool: ... def is_jax_array(x: object, /) -> bool: ... def is_writeable_array(x: object, /) -> bool: ... def size(x: Array, /) -> int | None: ... diff --git a/tests/test_at.py b/tests/test_at.py index 744e3aaf..e5c1bbee 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -1,3 +1,4 @@ +import math import pickle from collections.abc import Callable, Generator from contextlib import contextmanager @@ -15,6 +16,12 @@ from array_api_extra._lib._utils._typing import Array, Index from array_api_extra.testing import lazy_xp_function +pytestmark = [ + pytest.mark.skip_xp_backend( + Backend.SPARSE, reason="read-only backend without .at support" + ) +] + def at_op( # type: ignore[no-any-explicit] x: Array, @@ -70,9 +77,6 @@ def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: xp_assert_equal(xp.all(array == array_orig), xp.asarray(copy)) -@pytest.mark.skip_xp_backend( - Backend.SPARSE, reason="read-only backend without .at support" -) @pytest.mark.parametrize( ("kwargs", "expect_copy"), [ @@ -100,14 +104,7 @@ def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: [ (False, False), (False, True), - pytest.param( - True, - False, - marks=( - pytest.mark.skip_xp_backend(Backend.JAX, reason="TODO special case"), - pytest.mark.skip_xp_backend(Backend.DASK, reason="TODO special case"), - ), - ), + (True, False), # Uses xp.where(idx, y, x) on JAX and Dask pytest.param( True, True, @@ -176,15 +173,22 @@ def test_alternate_index_syntax(): at(a, 0)[0].set(4) -@pytest.mark.parametrize("copy", [True, False]) -@pytest.mark.parametrize( - "op", [_AtOp.ADD, _AtOp.SUBTRACT, _AtOp.MULTIPLY, _AtOp.DIVIDE, _AtOp.POWER] -) -def test_iops_incompatible_dtype(op: _AtOp, copy: bool): +@pytest.mark.parametrize("copy", [True, None]) +@pytest.mark.parametrize("bool_mask", [False, True]) +@pytest.mark.parametrize("op", list(_AtOp)) +def test_incompatible_dtype( + xp: ModuleType, library: Backend, op: _AtOp, copy: bool | None, bool_mask: bool +): """Test that at() replicates the backend's behaviour for in-place operations with incompatible dtypes. - Note: + Behavior is backend-specific, but only two behaviors are allowed: + 1. raise an exception, or + 2. return the same dtype as x, disregarding y.dtype (no broadcasting). + + Note that __i__ and ____ behave differently, and we want to + replicate the behavior of __i__: + >>> a = np.asarray([1, 2, 3]) >>> a / 1.5 array([0. , 0.66666667, 1.33333333]) @@ -192,6 +196,49 @@ def test_iops_incompatible_dtype(op: _AtOp, copy: bool): UFuncTypeError: Cannot cast ufunc 'divide' output from dtype('float64') to dtype('int64') with casting rule 'same_kind' """ - x = np.asarray([2, 4]) - with pytest.raises(TypeError, match="Cannot cast ufunc"): - at_op(x, slice(None), op, 1.1, copy=copy) + x = xp.asarray([2, 4]) + idx = xp.asarray([True, False]) if bool_mask else slice(None) + z = None + + if library is 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: + if op in (_AtOp.MIN, _AtOp.MAX): + pytest.xfail(reason="need array-api-compat 1.11") + z = at_op(x, idx, op, 1.1, copy=copy) + + elif library is 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) + + elif op in (_AtOp.SET, _AtOp.MIN, _AtOp.MAX): + # There is no __i__ version of these operations + z = at_op(x, idx, op, 1.1, copy=copy) + + else: + with pytest.raises(Exception, match=r"cast|promote|dtype"): + at_op(x, idx, op, 1.1, copy=copy) + + assert z is None or z.dtype == x.dtype + + +def test_bool_mask_nd(xp: ModuleType): + x = xp.asarray([[1, 2, 3], [4, 5, 6]]) + idx = xp.asarray([[True, False, False], [False, True, True]]) + z = at_op(x, idx, _AtOp.SET, 0) + xp_assert_equal(z, xp.asarray([[0, 2, 3], [4, 0, 0]])) + + +@pytest.mark.skip_xp_backend(Backend.DASK, reason="FIXME need scipy's lazywhere") +@pytest.mark.parametrize("bool_mask", [False, True]) +def test_no_inf_warnings(xp: ModuleType, bool_mask: bool): + x = xp.asarray([math.inf, 1.0, 2.0]) + idx = ~xp.isinf(x) if bool_mask else slice(1, None) + # inf - inf -> nan with a warning + z = at_op(x, idx, _AtOp.SUBTRACT, math.inf) + xp_assert_equal(z, xp.asarray([math.inf, -math.inf, -math.inf])) diff --git a/vendor_tests/test_vendor.py b/vendor_tests/test_vendor.py index 38249378..914a0a1d 100644 --- a/vendor_tests/test_vendor.py +++ b/vendor_tests/test_vendor.py @@ -7,6 +7,7 @@ def test_vendor_compat(): array_namespace, device, is_cupy_namespace, + is_dask_array, is_dask_namespace, is_jax_array, is_jax_namespace, @@ -20,6 +21,7 @@ def test_vendor_compat(): assert array_namespace(x) is xp device(x) assert not is_cupy_namespace(xp) + assert not is_dask_array(x) assert not is_dask_namespace(xp) assert not is_jax_array(x) assert not is_jax_namespace(xp) From 3ca8945d14e0f9c2a23a5d35d0897169d1161a8a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 27 Jan 2025 02:35:38 +0000 Subject: [PATCH 021/140] Bump the actions group with 3 updates Bumps the actions group with 3 updates: [actions/attest-build-provenance](https://github.com/actions/attest-build-provenance), [codecov/codecov-action](https://github.com/codecov/codecov-action) and [dawidd6/action-download-artifact](https://github.com/dawidd6/action-download-artifact). Updates `actions/attest-build-provenance` from 2.1.0 to 2.2.0 - [Release notes](https://github.com/actions/attest-build-provenance/releases) - [Changelog](https://github.com/actions/attest-build-provenance/blob/main/RELEASE.md) - [Commits](https://github.com/actions/attest-build-provenance/compare/v2.1.0...v2.2.0) Updates `codecov/codecov-action` from 5.1.2 to 5.3.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/v5.1.2...v5.3.1) Updates `dawidd6/action-download-artifact` from 7 to 8 - [Release notes](https://github.com/dawidd6/action-download-artifact/releases) - [Commits](https://github.com/dawidd6/action-download-artifact/compare/v7...v8) --- updated-dependencies: - dependency-name: actions/attest-build-provenance dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: dawidd6/action-download-artifact dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] --- .github/workflows/cd.yml | 2 +- .github/workflows/ci.yml | 2 +- .github/workflows/docs-deploy.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 18fd21ee..83087bff 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -37,7 +37,7 @@ jobs: path: dist - name: Generate artifact attestation for sdist and wheel - uses: actions/attest-build-provenance@v2.1.0 + uses: actions/attest-build-provenance@v2.2.0 with: subject-path: "dist/*" diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 4ba1dec5..6ad4e77e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -66,6 +66,6 @@ jobs: run: pixi run -e ${{ matrix.environment }} tests-ci - name: Upload coverage report - uses: codecov/codecov-action@v5.1.2 + uses: codecov/codecov-action@v5.3.1 with: token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/docs-deploy.yml b/.github/workflows/docs-deploy.yml index 65f1286c..a08b2bf4 100644 --- a/.github/workflows/docs-deploy.yml +++ b/.github/workflows/docs-deploy.yml @@ -16,7 +16,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Download Artifact - uses: dawidd6/action-download-artifact@v7 + uses: dawidd6/action-download-artifact@v8 with: workflow: docs-build.yml name: docs-build From b83c85b7f08892b83ed0c38f59f699f0fdc50882 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Mon, 27 Jan 2025 15:24:17 +0000 Subject: [PATCH 022/140] BUG: vendored xpx.testing crashes on import --- src/array_api_extra/testing.py | 2 +- vendor_tests/test_vendor.py | 9 +++++++++ 2 files changed, 10 insertions(+), 1 deletion(-) diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index e124ed74..cc3f01f8 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -14,7 +14,7 @@ import pytest -from array_api_extra._lib._utils._compat import is_dask_namespace, is_jax_namespace +from ._lib._utils._compat import is_dask_namespace, is_jax_namespace __all__ = ["lazy_xp_function", "patch_lazy_xp_functions"] diff --git a/vendor_tests/test_vendor.py b/vendor_tests/test_vendor.py index 914a0a1d..9402217b 100644 --- a/vendor_tests/test_vendor.py +++ b/vendor_tests/test_vendor.py @@ -39,6 +39,15 @@ def test_vendor_extra(): assert_array_equal(y, x) +def test_vendor_extra_testing(): + from .array_api_extra.testing import lazy_xp_function + + def f(x): + return x + + lazy_xp_function(f) + + def test_vendor_extra_uses_vendor_compat(): from ._array_api_compat_vendor import array_namespace as n1 from .array_api_extra._lib._utils._compat import array_namespace as n2 From 6997c91fa3558f5746d87999b0771dc3bd695d43 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Wed, 29 Jan 2025 13:12:49 +0000 Subject: [PATCH 023/140] MAINT: import everything from array-api-compat --- src/array_api_extra/_lib/_utils/_compat.py | 15 +++++++++++++++ src/array_api_extra/_lib/_utils/_compat.pyi | 5 +++++ vendor_tests/test_vendor.py | 14 ++++++++++++++ 3 files changed, 34 insertions(+) diff --git a/src/array_api_extra/_lib/_utils/_compat.py b/src/array_api_extra/_lib/_utils/_compat.py index f4def9f3..34958149 100644 --- a/src/array_api_extra/_lib/_utils/_compat.py +++ b/src/array_api_extra/_lib/_utils/_compat.py @@ -6,14 +6,19 @@ from ...._array_api_compat_vendor import ( array_namespace, device, + is_array_api_obj, is_array_api_strict_namespace, + is_cupy_array, is_cupy_namespace, is_dask_array, is_dask_namespace, is_jax_array, is_jax_namespace, + is_numpy_array, is_numpy_namespace, + is_pydata_sparse_array, is_pydata_sparse_namespace, + is_torch_array, is_torch_namespace, is_writeable_array, size, @@ -22,14 +27,19 @@ from array_api_compat import ( array_namespace, device, + is_array_api_obj, is_array_api_strict_namespace, + is_cupy_array, is_cupy_namespace, is_dask_array, is_dask_namespace, is_jax_array, is_jax_namespace, + is_numpy_array, is_numpy_namespace, + is_pydata_sparse_array, is_pydata_sparse_namespace, + is_torch_array, is_torch_namespace, is_writeable_array, size, @@ -38,14 +48,19 @@ __all__ = [ "array_namespace", "device", + "is_array_api_obj", "is_array_api_strict_namespace", + "is_cupy_array", "is_cupy_namespace", "is_dask_array", "is_dask_namespace", "is_jax_array", "is_jax_namespace", + "is_numpy_array", "is_numpy_namespace", + "is_pydata_sparse_array", "is_pydata_sparse_namespace", + "is_torch_array", "is_torch_namespace", "is_writeable_array", "size", diff --git a/src/array_api_extra/_lib/_utils/_compat.pyi b/src/array_api_extra/_lib/_utils/_compat.pyi index e409091e..5c8b6260 100644 --- a/src/array_api_extra/_lib/_utils/_compat.pyi +++ b/src/array_api_extra/_lib/_utils/_compat.pyi @@ -18,6 +18,7 @@ def array_namespace( use_compat: bool | None = None, ) -> ArrayModule: ... def device(x: Array, /) -> Device: ... +def is_array_api_obj(x: object, /) -> bool: ... def is_array_api_strict_namespace(xp: ModuleType, /) -> bool: ... def is_cupy_namespace(xp: ModuleType, /) -> bool: ... def is_dask_namespace(xp: ModuleType, /) -> bool: ... @@ -25,7 +26,11 @@ 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, /) -> bool: ... def is_dask_array(x: object, /) -> bool: ... def is_jax_array(x: object, /) -> bool: ... +def is_numpy_array(x: object, /) -> bool: ... +def is_pydata_sparse_array(x: object, /) -> bool: ... +def is_torch_array(x: object, /) -> bool: ... def is_writeable_array(x: object, /) -> bool: ... def size(x: Array, /) -> int | None: ... diff --git a/vendor_tests/test_vendor.py b/vendor_tests/test_vendor.py index 9402217b..7aaa9eba 100644 --- a/vendor_tests/test_vendor.py +++ b/vendor_tests/test_vendor.py @@ -6,12 +6,19 @@ def test_vendor_compat(): from ._array_api_compat_vendor import ( # type: ignore[attr-defined] array_namespace, device, + is_array_api_obj, + is_array_api_strict_namespace, + is_cupy_array, is_cupy_namespace, is_dask_array, is_dask_namespace, is_jax_array, is_jax_namespace, + is_numpy_array, + is_numpy_namespace, + is_pydata_sparse_array, is_pydata_sparse_namespace, + is_torch_array, is_torch_namespace, is_writeable_array, size, @@ -20,12 +27,19 @@ def test_vendor_compat(): x = xp.asarray([1, 2, 3]) assert array_namespace(x) is xp device(x) + assert is_array_api_obj(x) + assert is_array_api_strict_namespace(xp) + assert not is_cupy_array(x) assert not is_cupy_namespace(xp) assert not is_dask_array(x) assert not is_dask_namespace(xp) assert not is_jax_array(x) assert not is_jax_namespace(xp) + assert not is_numpy_array(x) + assert not is_numpy_namespace(xp) + assert not is_pydata_sparse_array(x) assert not is_pydata_sparse_namespace(xp) + assert not is_torch_array(x) assert not is_torch_namespace(xp) assert is_writeable_array(x) assert size(x) == 3 From e61c31fa613ff71025ec9f988c5d0c686978cdbd Mon Sep 17 00:00:00 2001 From: crusaderky Date: Wed, 29 Jan 2025 15:25:55 +0000 Subject: [PATCH 024/140] BUG: `setdiff1d` vs. non-1d arrays --- src/array_api_extra/_lib/_funcs.py | 1 + tests/test_funcs.py | 15 +++++++++++++++ 2 files changed, 16 insertions(+) diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 0af265e2..9986569c 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -580,6 +580,7 @@ def setdiff1d( if assume_unique: x1 = xp.reshape(x1, (-1,)) + x2 = xp.reshape(x2, (-1,)) else: x1 = xp.unique_values(x1) x2 = xp.unique_values(x2) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index ef1a1fc2..b31cdfb8 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -579,6 +579,21 @@ def test_assume_unique(self, xp: ModuleType): actual = setdiff1d(x1, x2, assume_unique=True) xp_assert_equal(actual, expected) + @pytest.mark.parametrize("assume_unique", [True, False]) + @pytest.mark.parametrize("shape1", [(), (1,), (1, 1)]) + @pytest.mark.parametrize("shape2", [(), (1,), (1, 1)]) + def test_shapes( + self, + assume_unique: bool, + shape1: tuple[int, ...], + shape2: tuple[int, ...], + xp: ModuleType, + ): + x1 = xp.zeros(shape1) + x2 = xp.zeros(shape2) + actual = setdiff1d(x1, x2, assume_unique=assume_unique) + xp_assert_equal(actual, xp.empty((0,))) + def test_device(self, xp: ModuleType, device: Device): x1 = xp.asarray([3, 8, 20], device=device) x2 = xp.asarray([2, 3, 4], device=device) From c23ac0127d866b93cc89caa4937810d3011fce87 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Wed, 29 Jan 2025 16:08:13 +0000 Subject: [PATCH 025/140] BUG: `isclose` integer overflow (#130) --- src/array_api_extra/_lib/_funcs.py | 8 +++++++- tests/test_funcs.py | 7 +++++++ 2 files changed, 14 insertions(+), 1 deletion(-) diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 9986569c..2fdc084a 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -335,7 +335,13 @@ def isclose( atol = int(atol) if rtol == 0: return xp.abs(a - b) <= atol - nrtol = int(1.0 / rtol) + + try: + nrtol = xp.asarray(int(1.0 / rtol), dtype=b.dtype) + except OverflowError: + # rtol * max_int(dtype) < 1, so it's inconsequential + return xp.abs(a - b) <= atol + return xp.abs(a - b) <= (atol + xp.abs(b) // nrtol) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index b31cdfb8..33a8f36e 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -354,6 +354,13 @@ def test_tolerance(self, dtype: str, xp: ModuleType): xp_assert_equal(isclose(a, b, rtol=0), xp.asarray([False, False])) xp_assert_equal(isclose(a, b, atol=1, rtol=0), xp.asarray([True, False])) + @pytest.mark.parametrize("dtype", ["int8", "uint8"]) + def test_tolerance_integer_overflow(self, dtype: str, xp: ModuleType): + """1/rtol is too large for dtype""" + a = xp.asarray([100, 100], dtype=getattr(xp, dtype)) + b = xp.asarray([100, 101], dtype=getattr(xp, dtype)) + xp_assert_equal(isclose(a, b), xp.asarray([True, False])) + def test_very_small_numbers(self, xp: ModuleType): a = xp.asarray([1e-9, 1e-9]) b = xp.asarray([1.0001e-9, 1.00001e-9]) From 4b0b63c5eb4155bae9e6f5bab22d50fc317c84cf Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Wed, 29 Jan 2025 19:35:29 +0000 Subject: [PATCH 026/140] ENH: Array API 2024.12 binary ops vs. Python scalars (#131) Co-authored-by: Lucas Colley --- docs/conf.py | 1 + src/array_api_extra/_delegation.py | 4 +- src/array_api_extra/_lib/_funcs.py | 11 ++- src/array_api_extra/_lib/_utils/_helpers.py | 84 ++++++++++++++++++ tests/test_funcs.py | 68 ++++++++++++--- tests/test_utils.py | 97 ++++++++++++++++++++- 6 files changed, 246 insertions(+), 19 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index 79000c96..afa3bd5e 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -53,6 +53,7 @@ intersphinx_mapping = { "python": ("https://docs.python.org/3", None), + "array-api": ("https://data-apis.org/array-api/draft", None), "jax": ("https://jax.readthedocs.io/en/latest", None), } diff --git a/src/array_api_extra/_delegation.py b/src/array_api_extra/_delegation.py index b7bc9a84..f3295c45 100644 --- a/src/array_api_extra/_delegation.py +++ b/src/array_api_extra/_delegation.py @@ -52,8 +52,8 @@ def isclose( Parameters ---------- - a, b : Array - Input arrays to compare. + a, b : Array | int | float | complex | bool + Input objects to compare. At least one must be an array. rtol : array_like, optional The relative tolerance parameter (see Notes). atol : array_like, optional diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 2fdc084a..f7eb8c88 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -12,6 +12,7 @@ from ._at import at from ._utils import _compat, _helpers from ._utils._compat import array_namespace, is_jax_array +from ._utils._helpers import asarrays from ._utils._typing import Array __all__ = [ @@ -315,6 +316,7 @@ def isclose( xp: ModuleType, ) -> Array: # numpydoc ignore=PR01,RT01 """See docstring in array_api_extra._delegation.""" + a, b = asarrays(a, b, xp=xp) a_inexact = xp.isdtype(a.dtype, ("real floating", "complex floating")) b_inexact = xp.isdtype(b.dtype, ("real floating", "complex floating")) @@ -356,8 +358,8 @@ def kron(a: Array, b: Array, /, *, xp: ModuleType | None = None) -> Array: Parameters ---------- - a, b : array - Input arrays. + a, b : Array | int | float | complex + Input arrays or scalars. At least one must be an array. xp : array_namespace, optional The standard-compatible namespace for `a` and `b`. Default: infer. @@ -420,10 +422,10 @@ def kron(a: Array, b: Array, /, *, xp: ModuleType | None = None) -> Array: """ if xp is None: xp = array_namespace(a, b) + a, b = asarrays(a, b, xp=xp) - b = xp.asarray(b) singletons = (1,) * (b.ndim - a.ndim) - a = xp.broadcast_to(xp.asarray(a), singletons + a.shape) + a = xp.broadcast_to(a, singletons + a.shape) nd_b, nd_a = b.ndim, a.ndim nd_max = max(nd_b, nd_a) @@ -583,6 +585,7 @@ def setdiff1d( """ if xp is None: xp = array_namespace(x1, x2) + x1, x2 = asarrays(x1, x2, xp=xp) if assume_unique: x1 = xp.reshape(x1, (-1,)) diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 84efcc35..b32a1081 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -4,8 +4,10 @@ from __future__ import annotations from types import ModuleType +from typing import cast from . import _compat +from ._compat import is_array_api_obj, is_numpy_array from ._typing import Array __all__ = ["in1d", "mean"] @@ -91,3 +93,85 @@ def mean( mean_imag = xp.mean(x_imag, axis=axis, keepdims=keepdims) return mean_real + (mean_imag * xp.asarray(1j)) return xp.mean(x, axis=axis, keepdims=keepdims) + + +def is_python_scalar(x: object) -> bool: # numpydoc ignore=PR01,RT01 + """Return True if `x` is a Python scalar, False otherwise.""" + # isinstance(x, float) returns True for np.float64 + # isinstance(x, complex) returns True for np.complex128 + return isinstance(x, int | float | complex | bool) and not is_numpy_array(x) + + +def asarrays( + a: Array | int | float | complex | bool, + b: Array | int | float | complex | bool, + xp: ModuleType, +) -> tuple[Array, Array]: + """ + Ensure both `a` and `b` are arrays. + + If `b` is a python scalar, it is converted to the same dtype as `a`, and vice versa. + + Behavior is not specified when mixing a Python ``float`` and an array with an + integer data type; this may give ``float32``, ``float64``, or raise an exception. + Behavior is implementation-specific. + + Similarly, behavior is not specified when mixing a Python ``complex`` and an array + with a real-valued data type; this may give ``complex64``, ``complex128``, or raise + an exception. Behavior is implementation-specific. + + Parameters + ---------- + a, b : Array | int | float | complex | bool + Input arrays or scalars. At least one must be an array. + xp : ModuleType + The standard-compatible namespace for the returned arrays. + + Returns + ------- + Array, Array + The input arrays, possibly converted to arrays if they were scalars. + + See Also + -------- + mixing-arrays-with-python-scalars : Array API specification for the behavior. + """ + a_scalar = is_python_scalar(a) + b_scalar = is_python_scalar(b) + if not a_scalar and not b_scalar: + return a, b # This includes misc. malformed input e.g. str + + swap = False + if a_scalar: + swap = True + b, a = a, b + + if is_array_api_obj(a): + # a is an Array API object + # b is a int | float | complex | bool + + # pyright doesn't like it if you reuse the same variable name + xa = cast(Array, a) + + # https://data-apis.org/array-api/draft/API_specification/type_promotion.html#mixing-arrays-with-python-scalars + same_dtype = { + bool: "bool", + int: ("integral", "real floating", "complex floating"), + float: ("real floating", "complex floating"), + complex: "complex floating", + } + kind = same_dtype[type(b)] # type: ignore[index] + if xp.isdtype(xa.dtype, kind): + xb = xp.asarray(b, dtype=xa.dtype) + else: + # Undefined behaviour. Let the function deal with it, if it can. + xb = xp.asarray(b) + + else: + # Neither a nor b are Array API objects. + # Note: we can only reach this point when one explicitly passes + # xp=xp to the calling function; otherwise we fail earlier on + # array_namespace(a, b). + xa, xb = xp.asarray(a), xp.asarray(b) + + return (xb, xa) if swap else (xa, xb) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 33a8f36e..2c265b23 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -401,6 +401,24 @@ def test_none_shape_bool(self, xp: ModuleType): a = a[a] xp_assert_equal(isclose(a, b), xp.asarray([True, False])) + @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="xp=xp") + @pytest.mark.skip_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])) + xp_assert_equal(isclose(0.0, a), xp.asarray([True, False])) + + a = xp.asarray([0, 1], dtype=xp.int16) + xp_assert_equal(isclose(a, 0), xp.asarray([True, False])) + xp_assert_equal(isclose(0, a), xp.asarray([True, False])) + + xp_assert_equal(isclose(0, 0, xp=xp), xp.asarray(True)) + xp_assert_equal(isclose(0, 1, xp=xp), xp.asarray(False)) + + def test_all_python_scalars(self): + with pytest.raises(TypeError, match="Unrecognized"): + isclose(0, 0) + def test_xp(self, xp: ModuleType): a = xp.asarray([0.0, 0.0]) b = xp.asarray([1e-9, 1e-4]) @@ -413,30 +431,22 @@ def test_basic(self, xp: ModuleType): # Using 0-dimensional array a = xp.asarray(1) b = xp.asarray([[1, 2], [3, 4]]) - k = xp.asarray([[1, 2], [3, 4]]) - xp_assert_equal(kron(a, b), k) - a = xp.asarray([[1, 2], [3, 4]]) - b = xp.asarray(1) - xp_assert_equal(kron(a, b), k) + xp_assert_equal(kron(a, b), b) + xp_assert_equal(kron(b, a), b) # Using 1-dimensional array a = xp.asarray([3]) b = xp.asarray([[1, 2], [3, 4]]) k = xp.asarray([[3, 6], [9, 12]]) xp_assert_equal(kron(a, b), k) - a = xp.asarray([[1, 2], [3, 4]]) - b = xp.asarray([3]) - xp_assert_equal(kron(a, b), k) + xp_assert_equal(kron(b, a), k) # Using 3-dimensional array a = xp.asarray([[[1]], [[2]]]) b = xp.asarray([[1, 2], [3, 4]]) k = xp.asarray([[[1, 2], [3, 4]], [[2, 4], [6, 8]]]) xp_assert_equal(kron(a, b), k) - a = xp.asarray([[1, 2], [3, 4]]) - b = xp.asarray([[[1]], [[2]]]) - k = xp.asarray([[[1, 2], [3, 4]], [[2, 4], [6, 8]]]) - xp_assert_equal(kron(a, b), k) + xp_assert_equal(kron(b, a), k) def test_kron_smoke(self, xp: ModuleType): a = xp.ones((3, 3)) @@ -474,6 +484,18 @@ def test_kron_shape( k = kron(a, b) assert k.shape == expected_shape + def test_python_scalar(self, xp: ModuleType): + a = 1 + # Test no dtype promotion to xp.asarray(a); use b.dtype + b = xp.asarray([[1, 2], [3, 4]], dtype=xp.int16) + xp_assert_equal(kron(a, b), b) + xp_assert_equal(kron(b, a), b) + xp_assert_equal(kron(1, 1, xp=xp), xp.asarray(1)) + + def test_all_python_scalars(self): + with pytest.raises(TypeError, match="Unrecognized"): + kron(1, 1) + def test_device(self, xp: ModuleType, device: Device): x1 = xp.asarray([1, 2, 3], device=device) x2 = xp.asarray([4, 5], device=device) @@ -601,6 +623,28 @@ def test_shapes( actual = setdiff1d(x1, x2, assume_unique=assume_unique) xp_assert_equal(actual, xp.empty((0,))) + @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="xp=xp") + @pytest.mark.parametrize("assume_unique", [True, False]) + def test_python_scalar(self, xp: ModuleType, assume_unique: bool): + # Test no dtype promotion to xp.asarray(x2); use x1.dtype + x1 = xp.asarray([3, 1, 2], dtype=xp.int16) + x2 = 3 + actual = setdiff1d(x1, x2, assume_unique=assume_unique) + xp_assert_equal(actual, xp.asarray([1, 2], dtype=xp.int16)) + + actual = setdiff1d(x2, x1, assume_unique=assume_unique) + xp_assert_equal(actual, xp.asarray([], dtype=xp.int16)) + + xp_assert_equal( + setdiff1d(0, 0, assume_unique=assume_unique, xp=xp), + xp.asarray([0])[:0], # Default int dtype for backend + ) + + @pytest.mark.parametrize("assume_unique", [True, False]) + def test_all_python_scalars(self, assume_unique: bool): + with pytest.raises(TypeError, match="Unrecognized"): + setdiff1d(0, 0, assume_unique=assume_unique) + def test_device(self, xp: ModuleType, device: Device): x1 = xp.asarray([3, 8, 20], device=device) x2 = xp.asarray([2, 3, 4], device=device) diff --git a/tests/test_utils.py b/tests/test_utils.py index f710056b..d9f50362 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -1,11 +1,12 @@ from types import ModuleType +import numpy as np import pytest from array_api_extra._lib import Backend from array_api_extra._lib._testing import xp_assert_equal from array_api_extra._lib._utils._compat import device as get_device -from array_api_extra._lib._utils._helpers import in1d +from array_api_extra._lib._utils._helpers import asarrays, in1d from array_api_extra._lib._utils._typing import Device from array_api_extra.testing import lazy_xp_function @@ -45,3 +46,97 @@ def test_xp(self, xp: ModuleType): expected = xp.asarray([True, False]) actual = in1d(x1, x2, xp=xp) xp_assert_equal(actual, expected) + + +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype") +@pytest.mark.parametrize( + ("dtype", "b", "defined"), + [ + # Well-defined cases of dtype promotion from Python scalar to Array + # bool vs. bool + ("bool", True, True), + # int vs. xp.*int*, xp.float*, xp.complex* + ("int16", 1, True), + ("uint8", 1, True), + ("float32", 1, True), + ("float64", 1, True), + ("complex64", 1, True), + ("complex128", 1, True), + # float vs. xp.float, xp.complex + ("float32", 1.0, True), + ("float64", 1.0, True), + ("complex64", 1.0, True), + ("complex128", 1.0, True), + # complex vs. xp.complex + ("complex64", 1.0j, True), + ("complex128", 1.0j, True), + # Undefined cases + ("bool", 1, False), + ("int64", 1.0, False), + ("float64", 1.0j, False), + ], +) +def test_asarrays_array_vs_scalar( + dtype: str, b: int | float | complex, defined: bool, xp: ModuleType +): + a = xp.asarray(1, dtype=getattr(xp, dtype)) + + xa, xb = asarrays(a, b, xp) + assert xa.dtype == a.dtype + if defined: + assert xb.dtype == a.dtype + else: + assert xb.dtype == xp.asarray(b).dtype + + xbr, xar = asarrays(b, a, xp) + assert xar.dtype == xa.dtype + assert xbr.dtype == xb.dtype + + +def test_asarrays_scalar_vs_scalar(xp: ModuleType): + a, b = asarrays(1, 2.2, xp=xp) + assert a.dtype == xp.asarray(1).dtype # Default dtype + assert b.dtype == xp.asarray(2.2).dtype # Default dtype; not broadcasted + + +ALL_TYPES = ( + "int8", + "int16", + "int32", + "int64", + "uint8", + "uint16", + "uint32", + "uint64", + "float32", + "float64", + "complex64", + "complex128", + "bool", +) + + +@pytest.mark.parametrize("a_type", ALL_TYPES) +@pytest.mark.parametrize("b_type", ALL_TYPES) +def test_asarrays_array_vs_array(a_type: str, b_type: str, xp: ModuleType): + """ + Test that when both inputs of asarray are already Array API objects, + they are returned unchanged. + """ + a = xp.asarray(1, dtype=getattr(xp, a_type)) + b = xp.asarray(1, dtype=getattr(xp, b_type)) + xa, xb = asarrays(a, b, xp) + assert xa.dtype == a.dtype + assert xb.dtype == b.dtype + + +@pytest.mark.parametrize("dtype", [np.float64, np.complex128]) +def test_asarrays_numpy_generics(dtype: type): + """ + Test special case of np.float64 and np.complex128, + which are subclasses of float and complex. + """ + a = dtype(0) + xa, xb = asarrays(a, 0, xp=np) + assert xa.dtype == dtype + assert xb.dtype == dtype From 27b0bf29d2e44df2dc773c3d4bab63ae5b2c8e3b Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Wed, 5 Feb 2025 13:45:22 +0000 Subject: [PATCH 027/140] TST: `xfail_xp_backend` (#132) * TST: `xfail_xp_backend` * nit * nit * nit * pixi update --- pixi.lock | 3454 ++++++++++++-------------- pyproject.toml | 5 +- src/array_api_extra/_lib/_testing.py | 20 + tests/conftest.py | 27 +- tests/test_at.py | 41 +- tests/test_funcs.py | 69 +- tests/test_testing.py | 14 +- tests/test_utils.py | 27 +- 8 files changed, 1792 insertions(+), 1865 deletions(-) diff --git a/pixi.lock b/pixi.lock index 00c8feef..10e70ff2 100644 --- a/pixi.lock +++ b/pixi.lock @@ -11,20 +11,20 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/_openmp_mutex-4.5-2_kmp_llvm.tar.bz2 - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.10.0-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda - - conda: https://prefix.dev/conda-forge/linux-64/ca-certificates-2024.12.14-hbcca054_0.conda + - conda: https://prefix.dev/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda - conda: https://prefix.dev/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda - conda: https://prefix.dev/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda - conda: https://prefix.dev/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2 - conda: https://prefix.dev/conda-forge/linux-64/libgcc-14.2.0-h77fa898_1.conda - conda: 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c8e9c1c467b5f960b627d7adc1c65fece8e929a3de89967e91ef0f726422fd32 diff --git a/pyproject.toml b/pyproject.toml index d15aba84..ab3b015d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -181,7 +181,10 @@ xfail_strict = true filterwarnings = ["error"] log_cli_level = "INFO" testpaths = ["tests"] -markers = ["skip_xp_backend(library, *, reason=None): Skip test for a specific backend"] +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", +] # Coverage diff --git a/src/array_api_extra/_lib/_testing.py b/src/array_api_extra/_lib/_testing.py index ac4ae586..3cd72942 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -8,6 +8,8 @@ import math from types import ModuleType +import pytest + from ._utils._compat import ( array_namespace, is_cupy_namespace, @@ -170,3 +172,21 @@ def xp_assert_close( np.testing.assert_allclose( actual, desired, rtol=rtol, atol=atol, err_msg=err_msg ) + + +def xfail(request: pytest.FixtureRequest, reason: str) -> None: + """ + XFAIL the currently running test. + + Unlike ``pytest.xfail``, allow rest of test to execute instead of immediately + halting it, so that it may result in a XPASS. + xref https://github.com/pandas-dev/pandas/issues/38902 + + Parameters + ---------- + request : pytest.FixtureRequest + ``request`` argument of the test function. + reason : str + Reason for the expected failure. + """ + request.node.add_marker(pytest.mark.xfail(reason=reason)) diff --git a/tests/conftest.py b/tests/conftest.py index 4402c067..e1a75e2e 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -2,7 +2,7 @@ from collections.abc import Callable from contextlib import suppress -from functools import wraps +from functools import partial, wraps from types import ModuleType from typing import ParamSpec, TypeVar, cast @@ -10,6 +10,7 @@ import pytest from array_api_extra._lib 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 from array_api_extra._lib._utils._typing import Device @@ -32,16 +33,20 @@ def library(request: pytest.FixtureRequest) -> Backend: # numpydoc ignore=PR01, """ elem = cast(Backend, request.param) - for marker in request.node.iter_markers("skip_xp_backend"): - skip_library = marker.kwargs.get("library") or marker.args[0] # type: ignore[no-untyped-usage] - if not isinstance(skip_library, Backend): - msg = "argument of skip_xp_backend must be a Backend enum" - raise TypeError(msg) - if skip_library == elem: - reason = skip_library.value - with suppress(KeyError): - reason += ":" + cast(str, marker.kwargs["reason"]) - pytest.skip(reason=reason) + for marker_name, skip_or_xfail in ( + ("skip_xp_backend", pytest.skip), + ("xfail_xp_backend", partial(xfail, request)), + ): + 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" + raise TypeError(msg) + if library == elem: + reason = library.value + with suppress(KeyError): + reason += ":" + cast(str, marker.kwargs["reason"]) + skip_or_xfail(reason=reason) return elem diff --git a/tests/test_at.py b/tests/test_at.py index e5c1bbee..447b099e 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -11,7 +11,7 @@ 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._testing import xp_assert_equal +from array_api_extra._lib._testing import xfail, 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, Index from array_api_extra.testing import lazy_xp_function @@ -80,10 +80,12 @@ def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: @pytest.mark.parametrize( ("kwargs", "expect_copy"), [ - ({"copy": True}, True), - ({"copy": False}, False), - ({"copy": None}, None), # Behavior is backend-specific - ({}, None), # Test that the copy parameter defaults to None + pytest.param({"copy": True}, True, id="copy=True"), + pytest.param({"copy": False}, False, id="copy=False"), + # Behavior is backend-specific + pytest.param({"copy": None}, None, id="copy=None"), + # Test that the copy parameter defaults to None + pytest.param({}, None, id="no copy kwarg"), ], ) @pytest.mark.parametrize( @@ -109,10 +111,10 @@ def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: True, True, marks=( - pytest.mark.skip_xp_backend( + pytest.mark.skip_xp_backend( # test passes when copy=False Backend.JAX, reason="bool mask update with shaped rhs" ), - pytest.mark.skip_xp_backend( + pytest.mark.xfail_xp_backend( Backend.DASK, reason="bool mask update with shaped rhs" ), ), @@ -177,7 +179,12 @@ def test_alternate_index_syntax(): @pytest.mark.parametrize("bool_mask", [False, True]) @pytest.mark.parametrize("op", list(_AtOp)) def test_incompatible_dtype( - xp: ModuleType, library: Backend, op: _AtOp, copy: bool | None, bool_mask: bool + xp: ModuleType, + library: Backend, + request: pytest.FixtureRequest, + op: _AtOp, + copy: bool | None, + bool_mask: bool, ): """Test that at() replicates the backend's behaviour for in-place operations with incompatible dtypes. @@ -208,8 +215,8 @@ def test_incompatible_dtype( z = at_op(x, idx, op, 1.1, copy=copy) elif library is Backend.DASK: - if op in (_AtOp.MIN, _AtOp.MAX): - pytest.xfail(reason="need array-api-compat 1.11") + if op in (_AtOp.MIN, _AtOp.MAX) and bool_mask: + xfail(request, reason="need array-api-compat 1.11") z = at_op(x, idx, op, 1.1, copy=copy) elif library is Backend.ARRAY_API_STRICT and op is not _AtOp.SET: @@ -234,8 +241,18 @@ def test_bool_mask_nd(xp: ModuleType): xp_assert_equal(z, xp.asarray([[0, 2, 3], [4, 0, 0]])) -@pytest.mark.skip_xp_backend(Backend.DASK, reason="FIXME need scipy's lazywhere") -@pytest.mark.parametrize("bool_mask", [False, True]) +@pytest.mark.parametrize( + "bool_mask", + [ + False, + pytest.param( + True, + marks=pytest.mark.xfail_xp_backend( + Backend.DASK, reason="FIXME need scipy's lazywhere" + ), + ), + ], +) def test_no_inf_warnings(xp: ModuleType, bool_mask: bool): x = xp.asarray([math.inf, 1.0, 2.0]) idx = ~xp.isinf(x) if bool_mask else slice(1, None) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 2c265b23..2b900a85 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -41,7 +41,7 @@ lazy_xp_function(sinc, jax_jit=False, static_argnames="xp") -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no expand_dims") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") class TestAtLeastND: def test_0D(self, xp: ModuleType): x = xp.asarray(1.0) @@ -108,12 +108,12 @@ def test_device(self, xp: ModuleType, device: Device): assert get_device(atleast_nd(x, ndim=2)) == device def test_xp(self, xp: ModuleType): - x = xp.asarray(1) - y = atleast_nd(x, ndim=0, xp=xp) - xp_assert_equal(y, x) + x = xp.asarray(1.0) + y = atleast_nd(x, ndim=1, xp=xp) + xp_assert_equal(y, xp.ones((1,))) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") class TestCov: def test_basic(self, xp: ModuleType): xp_assert_close( @@ -152,7 +152,7 @@ def test_device(self, xp: ModuleType, device: Device): x = xp.asarray([1, 2, 3], device=device) assert get_device(cov(x)) == device - @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="explicit xp") + @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="xp=xp") def test_xp(self, xp: ModuleType): xp_assert_close( cov(xp.asarray([[0.0, 2.0], [1.0, 1.0], [2.0, 0.0]]).T, xp=xp), @@ -160,8 +160,8 @@ def test_xp(self, xp: ModuleType): ) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no device") class TestCreateDiagonal: + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") def test_1d(self, xp: ModuleType): # from np.diag tests vals = 100 * xp.arange(5, dtype=xp.float64) @@ -177,6 +177,7 @@ def test_1d(self, xp: ModuleType): xp_assert_equal(create_diagonal(vals, offset=2), b) xp_assert_equal(create_diagonal(vals, offset=-2), c) + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") @pytest.mark.parametrize("n", range(1, 10)) @pytest.mark.parametrize("offset", range(1, 10)) def test_create_diagonal(self, xp: ModuleType, n: int, offset: int): @@ -196,20 +197,22 @@ def test_2d(self, xp: ModuleType): with pytest.raises(ValueError, match="1-dimensional"): create_diagonal(xp.asarray([[1]])) + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") def test_device(self, xp: ModuleType, device: Device): x = xp.asarray([1, 2, 3], device=device) assert get_device(create_diagonal(x)) == device + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") def test_xp(self, xp: ModuleType): x = xp.asarray([1, 2]) y = create_diagonal(x, xp=xp) xp_assert_equal(y, xp.asarray([[1, 0], [0, 2]])) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no expand_dims") class TestExpandDims: - @pytest.mark.skip_xp_backend(Backend.DASK, reason="tuple index out of range") - @pytest.mark.skip_xp_backend(Backend.TORCH, reason="tuple index out of range") + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") + @pytest.mark.xfail_xp_backend(Backend.DASK, reason="tuple index out of range") + @pytest.mark.xfail_xp_backend(Backend.TORCH, reason="tuple index out of range") def test_functionality(self, xp: ModuleType): def _squeeze_all(b: Array) -> Array: """Mimics `np.squeeze(b)`. `xpx.squeeze`?""" @@ -225,6 +228,7 @@ def _squeeze_all(b: Array) -> Array: assert b.shape[axis] == 1 assert _squeeze_all(b).shape == s + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") def test_axis_tuple(self, xp: ModuleType): a = xp.empty((3, 3, 3)) assert expand_dims(a, axis=(0, 1, 2)).shape == (1, 1, 1, 3, 3, 3) @@ -257,17 +261,19 @@ def test_positive_negative_repeated(self, xp: ModuleType): with pytest.raises(ValueError, match="Duplicate dimensions"): expand_dims(a, axis=(3, -3)) + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") def test_device(self, xp: ModuleType, device: Device): x = xp.asarray([1, 2, 3], device=device) assert get_device(expand_dims(x, axis=0)) == device + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") def test_xp(self, xp: ModuleType): x = xp.asarray([1, 2, 3]) y = expand_dims(x, axis=(0, 1, 2), xp=xp) assert y.shape == (1, 1, 1, 3) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") class TestIsClose: # FIXME use lazywhere to avoid warnings on inf @pytest.mark.filterwarnings("ignore:invalid value encountered") @@ -402,7 +408,7 @@ 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.skip_xp_backend(Backend.TORCH, reason="Array API 2024.12 support") + @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])) @@ -425,7 +431,7 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(isclose(a, b, xp=xp), xp.asarray([True, False])) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no expand_dims") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") class TestKron: def test_basic(self, xp: ModuleType): # Using 0-dimensional array @@ -526,7 +532,7 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(nunique(a, xp=xp), xp.asarray(3)) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no arange, no device") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no arange, no device") class TestPad: def test_simple(self, xp: ModuleType): a = xp.arange(1, 4) @@ -576,10 +582,24 @@ def test_sequence_of_tuples_width(self, xp: ModuleType): assert padded.shape == (4, 4) -@pytest.mark.skip_xp_backend(Backend.DASK, reason="no argsort") -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no device kwarg in asarray") +assume_unique = pytest.mark.parametrize( + "assume_unique", + [ + True, + pytest.param( + False, + marks=pytest.mark.xfail_xp_backend( + Backend.DASK, reason="NaN-shaped arrays" + ), + ), + ], +) + + +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in asarray()") class TestSetDiff1D: - @pytest.mark.skip_xp_backend( + @pytest.mark.xfail_xp_backend(Backend.DASK, reason="NaN-shaped arrays") + @pytest.mark.xfail_xp_backend( Backend.TORCH, reason="index_select not implemented for uint32" ) def test_setdiff1d(self, xp: ModuleType): @@ -608,7 +628,7 @@ def test_assume_unique(self, xp: ModuleType): actual = setdiff1d(x1, x2, assume_unique=True) xp_assert_equal(actual, expected) - @pytest.mark.parametrize("assume_unique", [True, False]) + @assume_unique @pytest.mark.parametrize("shape1", [(), (1,), (1, 1)]) @pytest.mark.parametrize("shape2", [(), (1,), (1, 1)]) def test_shapes( @@ -623,8 +643,8 @@ def test_shapes( actual = setdiff1d(x1, x2, assume_unique=assume_unique) xp_assert_equal(actual, xp.empty((0,))) + @assume_unique @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="xp=xp") - @pytest.mark.parametrize("assume_unique", [True, False]) def test_python_scalar(self, xp: ModuleType, assume_unique: bool): # Test no dtype promotion to xp.asarray(x2); use x1.dtype x1 = xp.asarray([3, 1, 2], dtype=xp.int16) @@ -645,21 +665,22 @@ def test_all_python_scalars(self, assume_unique: bool): with pytest.raises(TypeError, match="Unrecognized"): setdiff1d(0, 0, assume_unique=assume_unique) - def test_device(self, xp: ModuleType, device: Device): + @assume_unique + 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) - assert get_device(setdiff1d(x1, x2)) == device + assert get_device(setdiff1d(x1, x2, assume_unique=assume_unique)) == device - @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="explicit xp") + @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="xp=xp") def test_xp(self, xp: ModuleType): x1 = xp.asarray([3, 8, 20]) x2 = xp.asarray([2, 3, 4]) expected = xp.asarray([8, 20]) - actual = setdiff1d(x1, x2, xp=xp) + actual = setdiff1d(x1, x2, assume_unique=True, xp=xp) xp_assert_equal(actual, expected) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype") +@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_testing.py b/tests/test_testing.py index 7d4ed0ad..c9a1e32f 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -23,7 +23,7 @@ xp_assert_equal, pytest.param( xp_assert_close, - marks=pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype"), + marks=pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype"), ), ], ) @@ -49,17 +49,17 @@ 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") -@param_assert_equal_close +@pytest.mark.parametrize("func", [xp_assert_equal, xp_assert_close]) def test_assert_close_equal_namespace(xp: ModuleType, func: Callable[..., None]): # type: ignore[no-any-explicit] - with pytest.raises(AssertionError): + with pytest.raises(AssertionError, match="namespaces do not match"): func(xp.asarray(0), np.asarray(0)) - with pytest.raises(TypeError): + with pytest.raises(TypeError, match="Unrecognized array input"): func(xp.asarray(0), 0) - with pytest.raises(TypeError): + with pytest.raises(TypeError, match="list is not a supported array type"): func(xp.asarray([0]), [0]) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype") +@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): @@ -71,7 +71,7 @@ def test_assert_close_tolerance(xp: ModuleType): @param_assert_equal_close -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no bool indexing by sparse arrays") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no bool indexing") def test_assert_close_equal_none_shape(xp: ModuleType, func: Callable[..., None]): # type: ignore[no-any-explicit] """On dask and other lazy backends, test that a shape with NaN's or None's can be compared to a real shape. diff --git a/tests/test_utils.py b/tests/test_utils.py index d9f50362..699f25f1 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -17,12 +17,23 @@ class TestIn1D: - @pytest.mark.skip_xp_backend(Backend.DASK, reason="no argsort") - @pytest.mark.skip_xp_backend( - Backend.SPARSE, reason="no unique_inverse, no device kwarg in asarray" + @pytest.mark.xfail_xp_backend( + Backend.SPARSE, reason="no unique_inverse, no device kwarg in asarray()" ) # cover both code paths - @pytest.mark.parametrize("n", [9, 15]) + @pytest.mark.parametrize( + "n", + [ + pytest.param(9, id="fast path"), + pytest.param( + 15, + id="slow path", + marks=pytest.mark.xfail_xp_backend( + Backend.DASK, reason="NaN-shaped array" + ), + ), + ], + ) def test_no_invert_assume_unique(self, xp: ModuleType, n: int): x1 = xp.asarray([3, 8, 20]) x2 = xp.arange(n) @@ -30,14 +41,14 @@ def test_no_invert_assume_unique(self, xp: ModuleType, n: int): actual = in1d(x1, x2) xp_assert_equal(actual, expected) - @pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no device kwarg in asarray") + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in asarray") def test_device(self, xp: ModuleType, device: Device): x1 = xp.asarray([3, 8, 20], device=device) x2 = xp.asarray([2, 3, 4], device=device) assert get_device(in1d(x1, x2)) == device - @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="explicit xp") - @pytest.mark.skip_xp_backend( + @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="xp=xp") + @pytest.mark.xfail_xp_backend( Backend.SPARSE, reason="no arange, no device kwarg in asarray" ) def test_xp(self, xp: ModuleType): @@ -48,7 +59,7 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(actual, expected) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="no isdtype") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") @pytest.mark.parametrize( ("dtype", "b", "defined"), [ From a71bd2e2cbb4e7f010679cb0f9a788235df2e051 Mon Sep 17 00:00:00 2001 From: Neil Girdhar Date: Sat, 8 Feb 2025 09:40:32 -0500 Subject: [PATCH 028/140] DEV: Add editorconfig (#138) * Add editorconfig * match prettier default --------- Co-authored-by: Lucas Colley --- .editorconfig | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 .editorconfig diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 00000000..46f23570 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,14 @@ +root = true + +[*.{py,md}] +indent_style = space +end_of_line = lf +trim_trailing_whitespace = true +insert_final_newline = true + +[*.py] +max_line_length = 88 +indent_size = 4 + +[*.md] +max_line_length = 80 From 03f0b3e19370f1ee287da0bf98ae2cf93ba4f98f Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Tue, 11 Feb 2025 15:41:09 +0000 Subject: [PATCH 029/140] ENH: new function `broadcast_shapes` (#133) * ENH: `broadcast_shapes` * xref broadcast_arrays * mixed nan-none test * add comment * Update src/array_api_extra/_lib/_funcs.py --------- Co-authored-by: Lucas Colley --- docs/api-reference.md | 1 + docs/conf.py | 1 + src/array_api_extra/__init__.py | 2 + src/array_api_extra/_lib/_funcs.py | 64 ++++++++++++++++++++++++++++++ tests/test_funcs.py | 59 +++++++++++++++++++++++++++ 5 files changed, 127 insertions(+) diff --git a/docs/api-reference.md b/docs/api-reference.md index 32205248..2483a55d 100644 --- a/docs/api-reference.md +++ b/docs/api-reference.md @@ -8,6 +8,7 @@ at atleast_nd + broadcast_shapes cov create_diagonal expand_dims diff --git a/docs/conf.py b/docs/conf.py index afa3bd5e..eff2a33d 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -54,6 +54,7 @@ intersphinx_mapping = { "python": ("https://docs.python.org/3", None), "array-api": ("https://data-apis.org/array-api/draft", None), + "numpy": ("https://numpy.org/doc/stable", None), "jax": ("https://jax.readthedocs.io/en/latest", None), } diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 840dd8e7..4a49fd48 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -4,6 +4,7 @@ from ._lib._at import at from ._lib._funcs import ( atleast_nd, + broadcast_shapes, cov, create_diagonal, expand_dims, @@ -20,6 +21,7 @@ "__version__", "at", "atleast_nd", + "broadcast_shapes", "cov", "create_diagonal", "expand_dims", diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index f7eb8c88..a5729559 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -17,6 +17,7 @@ __all__ = [ "atleast_nd", + "broadcast_shapes", "cov", "create_diagonal", "expand_dims", @@ -71,6 +72,69 @@ def atleast_nd(x: Array, /, *, ndim: int, xp: ModuleType | None = None) -> Array return x +# `float` in signature to accept `math.nan` for Dask. +# `int`s are still accepted as `float` is a superclass of `int` in typing +def broadcast_shapes(*shapes: tuple[float | None, ...]) -> tuple[int | None, ...]: + """ + Compute the shape of the broadcasted arrays. + + Duplicates :func:`numpy.broadcast_shapes`, with additional support for + None and NaN sizes. + + This is equivalent to ``xp.broadcast_arrays(arr1, arr2, ...)[0].shape`` + without needing to worry about the backend potentially deep copying + the arrays. + + Parameters + ---------- + *shapes : tuple[int | None, ...] + Shapes of the arrays to broadcast. + + Returns + ------- + tuple[int | None, ...] + The shape of the broadcasted arrays. + + See Also + -------- + numpy.broadcast_shapes : Equivalent NumPy function. + array_api.broadcast_arrays : Function to broadcast actual arrays. + + Notes + ----- + This function accepts the Array API's ``None`` for unknown sizes, + as well as Dask's non-standard ``math.nan``. + Regardless of input, the output always contains ``None`` for unknown sizes. + + Examples + -------- + >>> import array_api_extra as xpx + >>> xpx.broadcast_shapes((2, 3), (2, 1)) + (2, 3) + >>> xpx.broadcast_shapes((4, 2, 3), (2, 1), (1, 3)) + (4, 2, 3) + """ + if not shapes: + return () # Match numpy output + + ndim = max(len(shape) for shape in shapes) + out: list[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 + sizes -= {1, None, math.nan} + if len(sizes) > 1: + msg = ( + "shape mismatch: objects cannot be broadcast to a single shape: " + f"{shapes}." + ) + raise ValueError(msg) + out.append(None if none_size else cast(int, sizes.pop()) if sizes else 1) + + return tuple(out) + + def cov(m: Array, /, *, xp: ModuleType | None = None) -> Array: """ Estimate a covariance matrix. diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 2b900a85..84d2f5d1 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -1,4 +1,5 @@ import contextlib +import math import warnings from types import ModuleType @@ -8,6 +9,7 @@ from array_api_extra import ( at, atleast_nd, + broadcast_shapes, cov, create_diagonal, expand_dims, @@ -113,6 +115,63 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(y, xp.ones((1,))) +class TestBroadcastShapes: + @pytest.mark.parametrize( + "args", + [ + (), + ((),), + ((), ()), + ((1,),), + ((1,), (1,)), + ((2,), (1,)), + ((3, 1, 4), (2, 1)), + ((1, 1, 4), (2, 1)), + ((1,), ()), + ((), (2,), ()), + ((0,),), + ((0,), (1,)), + ((2, 0), (1, 1)), + ((2, 0, 3), (2, 1, 1)), + ], + ) + def test_simple(self, args: tuple[tuple[int, ...], ...]): + expect = np.broadcast_shapes(*args) + actual = broadcast_shapes(*args) + assert actual == expect + + @pytest.mark.parametrize( + "args", + [ + ((2,), (3,)), + ((2, 3), (1, 2)), + ((2,), (0,)), + ((2, 0, 2), (1, 3, 1)), + ], + ) + def test_fail(self, args: tuple[tuple[int, ...], ...]): + match = "cannot be broadcast to a single shape" + with pytest.raises(ValueError, match=match): + _ = np.broadcast_shapes(*args) + with pytest.raises(ValueError, match=match): + _ = broadcast_shapes(*args) + + @pytest.mark.parametrize( + "args", + [ + ((None,), (None,)), + ((math.nan,), (None,)), + ((1, None, 2, 4), (2, 3, None, 1), (2, None, None, 4)), + ((1, math.nan, 2), (4, 2, 3, math.nan), (4, 2, None, None)), + ((math.nan, 1), (None, 2), (None, 2)), + ], + ) + def test_none(self, args: tuple[tuple[float | None, ...], ...]): + expect = args[-1] + actual = broadcast_shapes(*args[:-1]) + assert actual == expect + + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") class TestCov: def test_basic(self, xp: ModuleType): From 253ef87db5f122cde8ca105a6e7a512b5bb5b0ae Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 17 Feb 2025 02:37:05 +0000 Subject: [PATCH 030/140] Bump prefix-dev/setup-pixi from 0.8.1 to 0.8.2 in the actions group Bumps the actions group with 1 update: [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi). Updates `prefix-dev/setup-pixi` from 0.8.1 to 0.8.2 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/v0.8.1...v0.8.2) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] --- .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 6ad4e77e..2ca14085 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -30,7 +30,7 @@ jobs: - uses: pre-commit/action@v3.0.1 with: extra_args: --hook-stage manual --all-files - - uses: prefix-dev/setup-pixi@v0.8.1 + - uses: prefix-dev/setup-pixi@v0.8.2 with: pixi-version: v0.40.3 cache: true @@ -56,7 +56,7 @@ jobs: with: fetch-depth: 0 - - uses: prefix-dev/setup-pixi@v0.8.1 + - uses: prefix-dev/setup-pixi@v0.8.2 with: pixi-version: v0.40.3 cache: true diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index b5145f92..8f86bc95 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -7,7 +7,7 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - uses: prefix-dev/setup-pixi@v0.8.1 + - uses: prefix-dev/setup-pixi@v0.8.2 with: pixi-version: v0.40.3 cache: true From 116558ab043a119f76bce1d32c0aa96fd5da7ae7 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Tue, 18 Feb 2025 13:53:38 +0000 Subject: [PATCH 031/140] BUG: `isclose` finite vs. infinite --- src/array_api_extra/_lib/_funcs.py | 8 ++++++-- tests/test_funcs.py | 22 ++++++++++++---------- 2 files changed, 18 insertions(+), 12 deletions(-) diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index a5729559..bd1b5f06 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -386,8 +386,12 @@ def isclose( b_inexact = xp.isdtype(b.dtype, ("real floating", "complex floating")) if a_inexact or b_inexact: # FIXME: use scipy's lazywhere to suppress warnings on inf - out = xp.abs(a - b) <= (atol + rtol * xp.abs(b)) - out = xp.where(xp.isinf(a) & xp.isinf(b), xp.sign(a) == xp.sign(b), out) + out = xp.where( + xp.isinf(a) | xp.isinf(b), + xp.isinf(a) & xp.isinf(b) & (xp.sign(a) == xp.sign(b)), + # Note: inf <= inf is True! + xp.abs(a - b) <= (atol + rtol * xp.abs(b)), + ) if equal_nan: out = xp.where(xp.isnan(a) & xp.isnan(b), xp.asarray(True), out) return out diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 84d2f5d1..f7a2c4fb 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -336,6 +336,7 @@ def test_xp(self, xp: ModuleType): class TestIsClose: # FIXME use lazywhere to avoid warnings on inf @pytest.mark.filterwarnings("ignore:invalid value encountered") + @pytest.mark.parametrize("swap", [False, True]) @pytest.mark.parametrize( ("a", "b"), [ @@ -353,9 +354,9 @@ class TestIsClose: (float("inf"), float("inf")), (float("inf"), 100.0), (float("inf"), float("-inf")), + (float("-inf"), float("-inf")), (float("nan"), float("nan")), - (float("nan"), 0.0), - (0.0, float("nan")), + (float("nan"), 100.0), (1e6, 1e6 + 1), # True - within rtol (1e6, 1e6 + 100), # False - outside rtol (1e-6, 1.1e-6), # False - outside atol @@ -364,7 +365,9 @@ class TestIsClose: (1e6 + 0j, 1e6 + 100j), # False - outside rtol ], ) - def test_basic(self, a: float, b: float, xp: ModuleType): + def test_basic(self, a: float, b: float, swap: bool, xp: ModuleType): + if swap: + b, a = a, b a_xp = xp.asarray(a) b_xp = xp.asarray(b) @@ -372,11 +375,10 @@ def test_basic(self, a: float, b: float, xp: ModuleType): with warnings.catch_warnings(): warnings.simplefilter("ignore") - r_xp = xp.asarray(np.arange(10), dtype=a_xp.dtype) - ar_xp = a_xp * r_xp - br_xp = b_xp * r_xp ar_np = a * np.arange(10) br_np = b * np.arange(10) + ar_xp = xp.asarray(ar_np) + br_xp = xp.asarray(br_np) xp_assert_equal(isclose(ar_xp, br_xp), xp.asarray(np.isclose(ar_np, br_np))) @@ -395,14 +397,14 @@ def test_broadcast(self, dtype: str, xp: ModuleType): # FIXME use lazywhere to avoid warnings on inf @pytest.mark.filterwarnings("ignore:invalid value encountered") def test_some_inf(self, xp: ModuleType): - a = xp.asarray([0.0, 1.0, float("inf"), float("inf"), float("inf")]) - b = xp.asarray([1e-9, 1.0, float("inf"), float("-inf"), 2.0]) + a = xp.asarray([0.0, 1.0, xp.inf, xp.inf, xp.inf]) + b = xp.asarray([1e-9, 1.0, xp.inf, -xp.inf, 2.0]) actual = isclose(a, b) xp_assert_equal(actual, xp.asarray([True, True, True, False, False])) def test_equal_nan(self, xp: ModuleType): - a = xp.asarray([float("nan"), float("nan"), 1.0]) - b = xp.asarray([float("nan"), 1.0, float("nan")]) + a = xp.asarray([xp.nan, xp.nan, 1.0]) + b = xp.asarray([xp.nan, 1.0, xp.nan]) xp_assert_equal(isclose(a, b), xp.asarray([False, False, False])) xp_assert_equal(isclose(a, b, equal_nan=True), xp.asarray([True, False, False])) From 45c9fbbe7b8f7045db8c64fe70aa6a1a677cdb71 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Thu, 20 Feb 2025 13:07:17 +0000 Subject: [PATCH 032/140] MAINT: backports and tweaks --- docs/conf.py | 1 + pixi.lock | 5322 +++++++++++-------- pyproject.toml | 11 +- src/array_api_extra/_lib/_at.py | 4 +- src/array_api_extra/_lib/_utils/_helpers.py | 12 +- src/array_api_extra/_lib/_utils/_typing.py | 3 +- src/array_api_extra/testing.py | 4 +- tests/conftest.py | 18 +- 8 files changed, 3148 insertions(+), 2227 deletions(-) diff --git a/docs/conf.py b/docs/conf.py index eff2a33d..64389f80 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -54,6 +54,7 @@ intersphinx_mapping = { "python": ("https://docs.python.org/3", None), "array-api": ("https://data-apis.org/array-api/draft", None), + "dask": ("https://docs.dask.org/en/stable", None), "numpy": ("https://numpy.org/doc/stable", None), "jax": ("https://jax.readthedocs.io/en/latest", None), } diff --git a/pixi.lock b/pixi.lock index 10e70ff2..6a417843 100644 --- a/pixi.lock +++ b/pixi.lock @@ -14,19 +14,19 @@ environments: - 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__glibc >=2.17,<3.0.a0 + - libgcc >=13 + - libstdcxx >=13 + - libzlib >=1.3.1,<2.0a0 + license: BSD-3-Clause + purls: [] + size: 564076 + timestamp: 1740024448267 - conda: https://prefix.dev/conda-forge/osx-arm64/zstd-1.5.6-hb46c0d2_0.conda sha256: 2d4fd1ff7ee79cd954ca8e81abf11d9d49954dd1fef80f27289e2402ae9c2e09 md5: d96942c06c3e84bfcc5efb038724a7fd diff --git a/pyproject.toml b/pyproject.toml index ab3b015d..2c33b4b1 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -191,10 +191,6 @@ markers = [ [tool.coverage] run.source = ["array_api_extra"] -report.exclude_also = [ - '\.\.\.', - 'if TYPE_CHECKING:', -] # mypy @@ -314,10 +310,5 @@ checks = [ "ES01", # most docstrings do not need an extended summary ] exclude = [ # don't report on objects that match any of these regex - '.*test_at.*', - '.*test_funcs.*', - '.*test_testing.*', - '.*test_utils.*', - '.*test_version.*', - '.*test_vendor.*', + '.*test_*', ] diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py index e5cb3875..1915da5c 100644 --- a/src/array_api_extra/_lib/_at.py +++ b/src/array_api_extra/_lib/_at.py @@ -249,8 +249,8 @@ def _op( Right-hand side of the operation. copy : bool or None Whether to copy the input array. See the class docstring for details. - xp : array_namespace or None - The array namespace for the input array. + xp : array_namespace, optional + The array namespace for the input array. Default: infer. Returns ------- diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index b32a1081..accae896 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -7,10 +7,10 @@ from typing import cast from . import _compat -from ._compat import is_array_api_obj, is_numpy_array +from ._compat import array_namespace, is_array_api_obj, is_numpy_array from ._typing import Array -__all__ = ["in1d", "mean"] +__all__ = ["asarrays", "in1d", "is_python_scalar", "mean"] def in1d( @@ -33,7 +33,7 @@ def in1d( https://github.com/numpy/numpy/blob/v1.26.0/numpy/lib/arraysetops.py#L524-L758 """ if xp is None: - xp = _compat.array_namespace(x1, x2) + xp = array_namespace(x1, x2) # This code is run to make the code significantly faster if x2.shape[0] < 10 * x1.shape[0] ** 0.145: @@ -84,7 +84,7 @@ def mean( Complex mean, https://github.com/data-apis/array-api/issues/846. """ if xp is None: - xp = _compat.array_namespace(x) + xp = array_namespace(x) if xp.isdtype(x.dtype, "complex floating"): x_real = xp.real(x) @@ -124,8 +124,8 @@ def asarrays( ---------- a, b : Array | int | float | complex | bool Input arrays or scalars. At least one must be an array. - xp : ModuleType - The standard-compatible namespace for the returned arrays. + xp : array_namespace, optional + The standard-compatible namespace for `x`. Default: infer. Returns ------- diff --git a/src/array_api_extra/_lib/_utils/_typing.py b/src/array_api_extra/_lib/_utils/_typing.py index 83b51d04..95f29f79 100644 --- a/src/array_api_extra/_lib/_utils/_typing.py +++ b/src/array_api_extra/_lib/_utils/_typing.py @@ -5,6 +5,7 @@ # To be changed to a Protocol later (see data-apis/array-api#589) Array = Any # type: ignore[no-any-explicit] Device = Any # type: ignore[no-any-explicit] +DType = Any # type: ignore[no-any-explicit] Index = Any # type: ignore[no-any-explicit] -__all__ = ["Array", "Device", "Index"] +__all__ = ["Array", "DType", "Device", "Index"] diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index cc3f01f8..65362382 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -18,7 +18,7 @@ __all__ = ["lazy_xp_function", "patch_lazy_xp_functions"] -if TYPE_CHECKING: +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 @@ -169,7 +169,7 @@ def xp(request, monkeypatch): 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. - xp : module + xp : array_namespace Array namespace to be tested. See Also diff --git a/tests/conftest.py b/tests/conftest.py index e1a75e2e..5ba6dca6 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -115,7 +115,11 @@ def xp( if library == Backend.NUMPY_READONLY: return NumPyReadOnly() # type: ignore[return-value] # pyright: ignore[reportReturnType] xp = pytest.importorskip(library.value) + # Possibly wrap module with array_api_compat + xp = array_namespace(xp.empty(0)) + # 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.JAX: @@ -124,8 +128,18 @@ def xp( # 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] - # Possibly wrap module with array_api_compat - return array_namespace(xp.empty(0)) + return xp + + +@pytest.fixture(params=[Backend.DASK]) # Can select the test with `pytest -k dask` +def da( + request: pytest.FixtureRequest, monkeypatch: pytest.MonkeyPatch +) -> 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 @pytest.fixture From 273ff4ebd5a798cb936028f90257ce576979cd6a Mon Sep 17 00:00:00 2001 From: crusaderky Date: Thu, 20 Feb 2025 13:03:23 +0000 Subject: [PATCH 033/140] rename test_utils -> test_helpers --- tests/{test_utils.py => test_helpers.py} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename tests/{test_utils.py => test_helpers.py} (100%) diff --git a/tests/test_utils.py b/tests/test_helpers.py similarity index 100% rename from tests/test_utils.py rename to tests/test_helpers.py From 7b90a4e4f2cbe7d5234773119980a739d0d05e93 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Thu, 20 Feb 2025 13:05:27 +0000 Subject: [PATCH 034/140] refactor tests for asarrays --- tests/test_helpers.py | 181 +++++++++++++++++++++--------------------- 1 file changed, 89 insertions(+), 92 deletions(-) diff --git a/tests/test_helpers.py b/tests/test_helpers.py index 699f25f1..f0d8224f 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -59,95 +59,92 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(actual, expected) -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") -@pytest.mark.parametrize( - ("dtype", "b", "defined"), - [ - # Well-defined cases of dtype promotion from Python scalar to Array - # bool vs. bool - ("bool", True, True), - # int vs. xp.*int*, xp.float*, xp.complex* - ("int16", 1, True), - ("uint8", 1, True), - ("float32", 1, True), - ("float64", 1, True), - ("complex64", 1, True), - ("complex128", 1, True), - # float vs. xp.float, xp.complex - ("float32", 1.0, True), - ("float64", 1.0, True), - ("complex64", 1.0, True), - ("complex128", 1.0, True), - # complex vs. xp.complex - ("complex64", 1.0j, True), - ("complex128", 1.0j, True), - # Undefined cases - ("bool", 1, False), - ("int64", 1.0, False), - ("float64", 1.0j, False), - ], -) -def test_asarrays_array_vs_scalar( - dtype: str, b: int | float | complex, defined: bool, xp: ModuleType -): - a = xp.asarray(1, dtype=getattr(xp, dtype)) - - xa, xb = asarrays(a, b, xp) - assert xa.dtype == a.dtype - if defined: - assert xb.dtype == a.dtype - else: - assert xb.dtype == xp.asarray(b).dtype - - xbr, xar = asarrays(b, a, xp) - assert xar.dtype == xa.dtype - assert xbr.dtype == xb.dtype - - -def test_asarrays_scalar_vs_scalar(xp: ModuleType): - a, b = asarrays(1, 2.2, xp=xp) - assert a.dtype == xp.asarray(1).dtype # Default dtype - assert b.dtype == xp.asarray(2.2).dtype # Default dtype; not broadcasted - - -ALL_TYPES = ( - "int8", - "int16", - "int32", - "int64", - "uint8", - "uint16", - "uint32", - "uint64", - "float32", - "float64", - "complex64", - "complex128", - "bool", -) - - -@pytest.mark.parametrize("a_type", ALL_TYPES) -@pytest.mark.parametrize("b_type", ALL_TYPES) -def test_asarrays_array_vs_array(a_type: str, b_type: str, xp: ModuleType): - """ - Test that when both inputs of asarray are already Array API objects, - they are returned unchanged. - """ - a = xp.asarray(1, dtype=getattr(xp, a_type)) - b = xp.asarray(1, dtype=getattr(xp, b_type)) - xa, xb = asarrays(a, b, xp) - assert xa.dtype == a.dtype - assert xb.dtype == b.dtype - - -@pytest.mark.parametrize("dtype", [np.float64, np.complex128]) -def test_asarrays_numpy_generics(dtype: type): - """ - Test special case of np.float64 and np.complex128, - which are subclasses of float and complex. - """ - a = dtype(0) - xa, xb = asarrays(a, 0, xp=np) - assert xa.dtype == dtype - assert xb.dtype == dtype +class TestAsArrays: + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") + @pytest.mark.parametrize( + ("dtype", "b", "defined"), + [ + # Well-defined cases of dtype promotion from Python scalar to Array + # bool vs. bool + ("bool", True, True), + # int vs. xp.*int*, xp.float*, xp.complex* + ("int16", 1, True), + ("uint8", 1, True), + ("float32", 1, True), + ("float64", 1, True), + ("complex64", 1, True), + ("complex128", 1, True), + # float vs. xp.float, xp.complex + ("float32", 1.0, True), + ("float64", 1.0, True), + ("complex64", 1.0, True), + ("complex128", 1.0, True), + # complex vs. xp.complex + ("complex64", 1.0j, True), + ("complex128", 1.0j, True), + # Undefined cases + ("bool", 1, False), + ("int64", 1.0, False), + ("float64", 1.0j, False), + ], + ) + def test_array_vs_scalar( + self, dtype: str, b: int | float | complex, defined: bool, xp: ModuleType + ): + a = xp.asarray(1, dtype=getattr(xp, dtype)) + + xa, xb = asarrays(a, b, xp) + assert xa.dtype == a.dtype + if defined: + assert xb.dtype == a.dtype + else: + assert xb.dtype == xp.asarray(b).dtype + + xbr, xar = asarrays(b, a, xp) + assert xar.dtype == xa.dtype + assert xbr.dtype == xb.dtype + + def test_scalar_vs_scalar(self, xp: ModuleType): + a, b = asarrays(1, 2.2, xp=xp) + assert a.dtype == xp.asarray(1).dtype # Default dtype + assert b.dtype == xp.asarray(2.2).dtype # Default dtype; not broadcasted + + ALL_TYPES: tuple[str, ...] = ( + "int8", + "int16", + "int32", + "int64", + "uint8", + "uint16", + "uint32", + "uint64", + "float32", + "float64", + "complex64", + "complex128", + "bool", + ) + + @pytest.mark.parametrize("a_type", ALL_TYPES) + @pytest.mark.parametrize("b_type", ALL_TYPES) + def test_array_vs_array(self, a_type: str, b_type: str, xp: ModuleType): + """ + Test that when both inputs of asarray are already Array API objects, + they are returned unchanged. + """ + a = xp.asarray(1, dtype=getattr(xp, a_type)) + b = xp.asarray(1, dtype=getattr(xp, b_type)) + xa, xb = asarrays(a, b, xp) + assert xa.dtype == a.dtype + assert xb.dtype == b.dtype + + @pytest.mark.parametrize("dtype", [np.float64, np.complex128]) + def test_numpy_generics(self, dtype: type): + """ + Test special case of np.float64 and np.complex128, + which are subclasses of float and complex. + """ + a = dtype(0) + xa, xb = asarrays(a, 0, xp=np) + assert xa.dtype == dtype + assert xb.dtype == dtype From 95abaed8d233a8e6ee4b847b4e2c2de903a898c3 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Thu, 20 Feb 2025 13:26:58 +0000 Subject: [PATCH 035/140] BUG: `at` should not force overwrite in Dask when copy=None --- src/array_api_extra/_lib/_at.py | 30 +++--- tests/test_at.py | 159 ++++++++++++++++++++++++-------- 2 files changed, 133 insertions(+), 56 deletions(-) diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py index 1915da5c..a008efa9 100644 --- a/src/array_api_extra/_lib/_at.py +++ b/src/array_api_extra/_lib/_at.py @@ -275,16 +275,11 @@ def _op( msg = f"copy must be True, False, or None; got {copy!r}" raise ValueError(msg) - if copy is None: - writeable = is_writeable_array(x) - copy = not writeable - elif copy: - writeable = None - else: - writeable = is_writeable_array(x) + writeable = None if copy else is_writeable_array(x) - # JAX inside jax.jit and Dask don't support in-place updates with boolean - # mask. However we can handle the common special case of 0-dimensional y + # JAX inside jax.jit doesn't support in-place updates with boolean + # masks; Dask exclusively supports __setitem__ but not iops. + # We can handle the common special case of 0-dimensional y # with where(idx, y, x) instead. if ( (is_dask_array(idx) or is_jax_array(idx)) @@ -293,21 +288,22 @@ def _op( ): y_xp = xp.asarray(y, dtype=x.dtype) if y_xp.ndim == 0: - if out_of_place_op: + if out_of_place_op: # add(), subtract(), ... # FIXME: suppress inf warnings on dask with lazywhere out = xp.where(idx, out_of_place_op(x, y_xp), x) # Undo int->float promotion on JAX after _AtOp.DIVIDE out = xp.astype(out, x.dtype, copy=False) - else: + else: # set() out = xp.where(idx, y_xp, x) - if copy: - return out - x[()] = out - return x + if copy is False: + x[()] = out + return x + return out + # else: this will work on eager JAX and crash on jax.jit and Dask - if copy: + if copy or (copy is None and not writeable): if is_jax_array(x): # Use JAX's at[] func = cast(Callable[[Array], Array], getattr(x.at[idx], at_op.value)) @@ -331,7 +327,7 @@ def _op( msg = f"Can't update read-only array {x}" raise ValueError(msg) - if in_place_op: + if in_place_op: # add(), subtract(), ... x[self._idx] = in_place_op(x[self._idx], y) else: # set() x[self._idx] = y diff --git a/tests/test_at.py b/tests/test_at.py index 447b099e..ce27fbff 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -3,7 +3,7 @@ from collections.abc import Callable, Generator from contextlib import contextmanager from types import ModuleType -from typing import Any, cast +from typing import cast import numpy as np import pytest @@ -23,12 +23,13 @@ ] -def at_op( # type: ignore[no-any-explicit] +def at_op( x: Array, idx: Index, op: _AtOp, y: Array | object, - **kwargs: Any, # Test the default copy=None + copy: bool | None = None, + xp: ModuleType | None = None, ) -> Array: """ Wrapper around at(x, idx).op(y, copy=copy, xp=xp). @@ -39,30 +40,33 @@ def at_op( # type: ignore[no-any-explicit] which is not a common use case. """ if isinstance(idx, (slice | tuple)): - return _at_op(x, None, pickle.dumps(idx), op, y, **kwargs) - return _at_op(x, idx, None, op, y, **kwargs) + 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( # type: ignore[no-any-explicit] +def _at_op( x: Array, idx: Index | None, idx_pickle: bytes | None, op: _AtOp, y: Array | object, - **kwargs: Any, + 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, idx), op.value)) # type: ignore[no-any-explicit] - return meth(y, **kwargs) + return meth(y, copy=copy, xp=xp) lazy_xp_function(_at_op, static_argnames=("op", "idx_pickle", "copy", "xp")) @contextmanager -def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: +def assert_copy( + array: Array, copy: bool | None, expect_copy: bool | None = None +) -> Generator[None, None, None]: if copy is False and not is_writeable_array(array): with pytest.raises((TypeError, ValueError)): yield @@ -72,24 +76,23 @@ def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: array_orig = xp.asarray(array, copy=True) yield - if copy is None: - copy = not is_writeable_array(array) - xp_assert_equal(xp.all(array == array_orig), xp.asarray(copy)) + if expect_copy is None: + expect_copy = copy + if expect_copy: + # Original has not been modified + xp_assert_equal(array, array_orig) + elif expect_copy is False: + # Original has been modified + with pytest.raises(AssertionError): + xp_assert_equal(array, array_orig) + # Test nothing for copy=None. Dask changes behaviour depending on + # whether it's a special case of a bool mask with scalar RHS or not. + +@pytest.mark.parametrize("copy", [False, True, None]) @pytest.mark.parametrize( - ("kwargs", "expect_copy"), - [ - pytest.param({"copy": True}, True, id="copy=True"), - pytest.param({"copy": False}, False, id="copy=False"), - # Behavior is backend-specific - pytest.param({"copy": None}, None, id="copy=None"), - # Test that the copy parameter defaults to None - pytest.param({}, None, id="no copy kwarg"), - ], -) -@pytest.mark.parametrize( - ("op", "y", "expect"), + ("op", "y", "expect_list"), [ (_AtOp.SET, 40.0, [10.0, 40.0, 40.0]), (_AtOp.ADD, 40.0, [10.0, 60.0, 70.0]), @@ -102,14 +105,13 @@ def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: ], ) @pytest.mark.parametrize( - ("bool_mask", "shaped_y"), + ("bool_mask", "x_ndim", "y_ndim"), [ - (False, False), - (False, True), - (True, False), # Uses xp.where(idx, y, x) on JAX and Dask + (False, 1, 0), + (False, 1, 1), + (True, 1, 0), # Uses xp.where(idx, y, x) on JAX and Dask pytest.param( - True, - True, + *(True, 1, 1), marks=( pytest.mark.skip_xp_backend( # test passes when copy=False Backend.JAX, reason="bool mask update with shaped rhs" @@ -119,29 +121,65 @@ def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: ), ), ), + (False, 0, 0), + (True, 0, 0), ], ) def test_update_ops( xp: ModuleType, - kwargs: dict[str, bool | None], - expect_copy: bool | None, + copy: bool | None, op: _AtOp, y: float, - expect: list[float], + expect_list: list[float], bool_mask: bool, - shaped_y: bool, + x_ndim: int, + y_ndim: int, ): - x = xp.asarray([10.0, 20.0, 30.0]) - idx = xp.asarray([False, True, True]) if bool_mask else slice(1, None) - if shaped_y: + if x_ndim == 1: + x = xp.asarray([10.0, 20.0, 30.0]) + idx = xp.asarray([False, True, True]) if bool_mask else slice(1, None) + expect: list[float] | float = expect_list + else: + idx = xp.asarray(True) if bool_mask else () + # Pick an element that does change with the operation + if op is _AtOp.MIN: + x = xp.asarray(30.0) + expect = expect_list[2] + else: + x = xp.asarray(20.0) + expect = expect_list[1] + + if y_ndim == 1: y = xp.asarray([y, y]) - with assert_copy(x, expect_copy): - z = at_op(x, idx, op, y, **kwargs) + with assert_copy(x, copy): + z = at_op(x, idx, op, y, copy=copy) assert isinstance(z, type(x)) xp_assert_equal(z, xp.asarray(expect)) +@pytest.mark.parametrize("op", list(_AtOp)) +def test_copy_default(xp: ModuleType, library: Backend, op: _AtOp): + """ + Test that the default copy behaviour is False for writeable arrays + and True for read-only ones. + """ + 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[no-any-explicit] + with assert_copy(x, None, expect_copy): + _ = meth(2.0) + + x = xp.asarray([1.0, 10.0, 20.0]) + # Dask's default copy value is True for bool masks, + # 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[no-any-explicit] + with assert_copy(x, None, expect_copy): + _ = meth(2.0) + + def test_copy_invalid(): a = np.asarray([1, 2, 3]) with pytest.raises(ValueError, match="copy"): @@ -259,3 +297,46 @@ def test_no_inf_warnings(xp: ModuleType, bool_mask: bool): # inf - inf -> nan with a warning z = at_op(x, idx, _AtOp.SUBTRACT, math.inf) xp_assert_equal(z, xp.asarray([math.inf, -math.inf, -math.inf])) + + +@pytest.mark.parametrize( + "copy", + [ + None, + pytest.param( + False, + marks=[ + pytest.mark.skip_xp_backend( + Backend.NUMPY, reason="np.generic is read-only" + ), + pytest.mark.skip_xp_backend( + Backend.NUMPY_READONLY, reason="read-only backend" + ), + pytest.mark.skip_xp_backend(Backend.JAX, reason="read-only backend"), + pytest.mark.skip_xp_backend(Backend.SPARSE, reason="read-only backend"), + ], + ), + ], +) +@pytest.mark.parametrize("bool_mask", [False, True]) +def test_gh134(xp: ModuleType, bool_mask: bool, copy: bool | None): + """ + Test that xpx.at doesn't encroach in a bug of dask.array.Array.__setitem__, which + blindly assumes that chunk contents are writeable np.ndarray objects: + + https://github.com/dask/dask/issues/11722 + + In other words: when special-casing bool masks for Dask, unless the user explicitly + asks for copy=False, do not needlessly write back to the input. + """ + x = xp.zeros(1) + + # 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. + y = x[0] + + 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)) From ea42de83dd2953d97b34d3bb8f77094c8becda22 Mon Sep 17 00:00:00 2001 From: Neil Girdhar Date: Fri, 7 Feb 2025 02:22:14 -0500 Subject: [PATCH 036/140] Make create_diagonal support broadcasting --- src/array_api_extra/_lib/_funcs.py | 32 ++++++++++--------- src/array_api_extra/_lib/_utils/_helpers.py | 24 ++++++++++++++ tests/test_funcs.py | 35 +++++++++++++++++---- tests/test_helpers.py | 9 +++++- 4 files changed, 79 insertions(+), 21 deletions(-) diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index bd1b5f06..2c2e5a7a 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -12,7 +12,7 @@ from ._at import at from ._utils import _compat, _helpers from ._utils._compat import array_namespace, is_jax_array -from ._utils._helpers import asarrays +from ._utils._helpers import asarrays, ndindex from ._utils._typing import Array __all__ = [ @@ -236,7 +236,7 @@ def create_diagonal( Parameters ---------- x : array - A 1-D array. + An array having shape ``(*batch_dims, k)``. offset : int, optional Offset from the leading diagonal (default is ``0``). Use positive ints for diagonals above the leading diagonal, @@ -247,7 +247,8 @@ def create_diagonal( Returns ------- array - A 2-D array with `x` on the diagonal (offset by `offset`). + An array having shape ``(*batch_dims, k+abs(offset), k+abs(offset))`` with `x` + on the diagonal (offset by `offset`). Examples -------- @@ -270,18 +271,21 @@ def create_diagonal( if xp is None: xp = array_namespace(x) - if x.ndim != 1: - err_msg = "`x` must be 1-dimensional." + if x.ndim == 0: + err_msg = "`x` must be at least 1-dimensional." raise ValueError(err_msg) - n = x.shape[0] + abs(offset) - diag = xp.zeros(n**2, dtype=x.dtype, device=_compat.device(x)) - - start = offset if offset >= 0 else abs(offset) * n - stop = min(n * (n - offset), diag.shape[0]) - step = n + 1 - diag = at(diag)[start:stop:step].set(x) - - return xp.reshape(diag, (n, n)) + batch_dims = x.shape[:-1] + n = x.shape[-1] + abs(offset) + diag = xp.zeros((*batch_dims, n**2), dtype=x.dtype, device=_compat.device(x)) + + target_slice = slice( + offset if offset >= 0 else abs(offset) * n, + min(n * (n - offset), diag.shape[-1]), + n + 1, + ) + for index in ndindex(*batch_dims): + diag = at(diag)[(*index, target_slice)].set(x[(*index, slice(None))]) + return xp.reshape(diag, (*batch_dims, n, n)) def expand_dims( diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index accae896..e8419f24 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -3,6 +3,7 @@ # https://github.com/scikit-learn/scikit-learn/pull/27910#issuecomment-2568023972 from __future__ import annotations +from collections.abc import Generator from types import ModuleType from typing import cast @@ -175,3 +176,26 @@ def asarrays( xa, xb = xp.asarray(a), xp.asarray(b) return (xb, xa) if swap else (xa, xb) + + +def ndindex(*x: int) -> Generator[tuple[int, ...]]: + """ + Generate all N-dimensional indices for a given array shape. + + Given the shape of an array, an ndindex instance iterates over the N-dimensional + index of the array. At each iteration a tuple of indices is returned, the last + dimension is iterated over first. + + This has an identical API to numpy.ndindex. + + Parameters + ---------- + *x : int + The shape of the array. + """ + if not x: + yield () + return + for i in ndindex(*x[:-1]): + for j in range(x[-1]): + yield *i, j diff --git a/tests/test_funcs.py b/tests/test_funcs.py index f7a2c4fb..e24a7c0e 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -23,6 +23,7 @@ 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 ndindex from array_api_extra._lib._utils._typing import Array, Device from array_api_extra.testing import lazy_xp_function @@ -221,7 +222,7 @@ def test_xp(self, xp: ModuleType): class TestCreateDiagonal: @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") - def test_1d(self, xp: ModuleType): + def test_1d_from_numpy(self, xp: ModuleType): # from np.diag tests vals = 100 * xp.arange(5, dtype=xp.float64) b = xp.zeros((5, 5), dtype=xp.float64) @@ -239,7 +240,7 @@ def test_1d(self, xp: ModuleType): @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") @pytest.mark.parametrize("n", range(1, 10)) @pytest.mark.parametrize("offset", range(1, 10)) - def test_create_diagonal(self, xp: ModuleType, n: int, offset: int): + def test_1d_from_scipy(self, xp: ModuleType, n: int, offset: int): # from scipy._lib tests rng = np.random.default_rng(2347823) one = xp.asarray(1.0) @@ -248,13 +249,35 @@ def test_create_diagonal(self, xp: ModuleType, n: int, offset: int): B = xp.asarray(np.diag(x, offset), dtype=one.dtype) xp_assert_equal(A, B) - def test_0d(self, xp: ModuleType): + def test_0d_raises(self, xp: ModuleType): with pytest.raises(ValueError, match="1-dimensional"): create_diagonal(xp.asarray(1)) - def test_2d(self, xp: ModuleType): - with pytest.raises(ValueError, match="1-dimensional"): - create_diagonal(xp.asarray([[1]])) + @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") + @pytest.mark.parametrize( + "shape", + [ + (0,), + (10,), + (0, 1), + (1, 0), + (0, 0), + (4, 2, 1), + (1, 1, 7), + (0, 0, 1), + (3, 2, 4, 5), + ], + ) + def test_nd(self, xp: ModuleType, shape: tuple[int, ...]): + rng = np.random.default_rng(2347823) + b = xp.asarray( + rng.integers((1 << 64) - 1, size=shape, dtype=np.uint64), dtype=xp.uint64 + ) + c = create_diagonal(b) + zero = xp.zeros((), dtype=xp.uint64) + assert c.shape == (*b.shape, b.shape[-1]) + for i in ndindex(*c.shape): + xp_assert_equal(c[i], b[i[:-1]] if i[-2] == i[-1] else zero) @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") def test_device(self, xp: ModuleType, device: Device): diff --git a/tests/test_helpers.py b/tests/test_helpers.py index f0d8224f..1710ff84 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -6,7 +6,7 @@ from array_api_extra._lib import Backend from array_api_extra._lib._testing import xp_assert_equal from array_api_extra._lib._utils._compat import device as get_device -from array_api_extra._lib._utils._helpers import asarrays, in1d +from array_api_extra._lib._utils._helpers import asarrays, in1d, ndindex from array_api_extra._lib._utils._typing import Device from array_api_extra.testing import lazy_xp_function @@ -148,3 +148,10 @@ def test_numpy_generics(self, dtype: type): xa, xb = asarrays(a, 0, xp=np) assert xa.dtype == dtype assert xb.dtype == dtype + + +@pytest.mark.parametrize( + "shape", [(), (1,), (5,), (2, 3), (5, 3, 8), (0,), (3, 0), (0, 0, 1)] +) +def test_ndindex(shape: tuple[int, ...]): + assert tuple(ndindex(*shape)) == tuple(np.ndindex(*shape)) From 69db2e20548748eea09f9f50afca5e91dfc3b8a9 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 24 Feb 2025 02:27:06 +0000 Subject: [PATCH 037/140] Bump prefix-dev/setup-pixi from 0.8.2 to 0.8.3 in the actions group Bumps the actions group with 1 update: [prefix-dev/setup-pixi](https://github.com/prefix-dev/setup-pixi). Updates `prefix-dev/setup-pixi` from 0.8.2 to 0.8.3 - [Release notes](https://github.com/prefix-dev/setup-pixi/releases) - [Commits](https://github.com/prefix-dev/setup-pixi/compare/v0.8.2...v0.8.3) --- updated-dependencies: - dependency-name: prefix-dev/setup-pixi dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] --- .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 2ca14085..e7fba8db 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -30,7 +30,7 @@ jobs: - uses: pre-commit/action@v3.0.1 with: extra_args: --hook-stage manual --all-files - - uses: prefix-dev/setup-pixi@v0.8.2 + - uses: prefix-dev/setup-pixi@v0.8.3 with: pixi-version: v0.40.3 cache: true @@ -56,7 +56,7 @@ jobs: with: fetch-depth: 0 - - uses: prefix-dev/setup-pixi@v0.8.2 + - uses: prefix-dev/setup-pixi@v0.8.3 with: pixi-version: v0.40.3 cache: true diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index 8f86bc95..8e12580f 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -7,7 +7,7 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v4 - - uses: prefix-dev/setup-pixi@v0.8.2 + - uses: prefix-dev/setup-pixi@v0.8.3 with: pixi-version: v0.40.3 cache: true From e31736bfb423260fe79a6fca5675e9f2f2ff3996 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Thu, 27 Feb 2025 16:09:41 +0000 Subject: [PATCH 038/140] REL: set version to 0.6.1 (#148) --- pixi.lock | 1163 ++++++++++++++++--------------- src/array_api_extra/__init__.py | 2 +- 2 files changed, 586 insertions(+), 579 deletions(-) diff --git a/pixi.lock b/pixi.lock index 6a417843..511891d2 100644 --- a/pixi.lock +++ b/pixi.lock @@ -12,11 +12,11 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.10.0-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda - conda: https://prefix.dev/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_2.conda + - conda: https://prefix.dev/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda - conda: https://prefix.dev/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda - 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conda: https://prefix.dev/conda-forge/win-64/psutil-7.0.0-py312h4389bb4_0.conda - conda: https://prefix.dev/conda-forge/win-64/pthread-stubs-0.4-h0e40799_1002.conda - conda: https://prefix.dev/conda-forge/noarch/pure_eval-0.2.3-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/win-64/pyarrow-19.0.1-py312h2e8e312_0.conda @@ -2809,7 +2809,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/partd-1.4.2-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/win-64/pillow-11.1.0-py310h9595edc_0.conda - conda: https://prefix.dev/conda-forge/noarch/pluggy-1.5.0-pyhd8ed1ab_1.conda - - conda: https://prefix.dev/conda-forge/win-64/psutil-6.1.1-py310ha8f682b_0.conda + - conda: https://prefix.dev/conda-forge/win-64/psutil-7.0.0-py310ha8f682b_0.conda - conda: https://prefix.dev/conda-forge/win-64/pthread-stubs-0.4-h0e40799_1002.conda - conda: https://prefix.dev/conda-forge/win-64/pyarrow-19.0.1-py310h5588dad_0.conda - conda: https://prefix.dev/conda-forge/win-64/pyarrow-core-19.0.1-py310h399dd74_0_cpu.conda @@ -3411,7 +3411,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/partd-1.4.2-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/win-64/pillow-11.1.0-py310h9595edc_0.conda - conda: https://prefix.dev/conda-forge/noarch/pluggy-1.5.0-pyhd8ed1ab_1.conda - - conda: https://prefix.dev/conda-forge/win-64/psutil-6.1.1-py310ha8f682b_0.conda + - conda: https://prefix.dev/conda-forge/win-64/psutil-7.0.0-py310ha8f682b_0.conda - conda: https://prefix.dev/conda-forge/win-64/pthread-stubs-0.4-h0e40799_1002.conda - conda: https://prefix.dev/conda-forge/win-64/pyarrow-19.0.1-py310h5588dad_0.conda - conda: https://prefix.dev/conda-forge/win-64/pyarrow-core-19.0.1-py310h8b91b4e_0_cuda.conda @@ -3789,7 +3789,7 @@ packages: timestamp: 1735201429468 - pypi: . name: array-api-extra - version: 0.6.1 + version: 0.7.0.dev0 sha256: 9ff14035e127fef2de7e6c05ca1474ff1780e81e4480c8741f612e115d346f7e requires_dist: - array-api-compat>=1.10.0,<2 @@ -12080,9 +12080,9 @@ packages: - pkg:pypi/psutil?source=hash-mapping size: 484139 timestamp: 1740663381126 -- conda: https://prefix.dev/conda-forge/win-64/psutil-6.1.1-py310ha8f682b_0.conda - sha256: 88ed52584b3d838ec10c10ad445823bb9b52a0002071e79c9bb63433ff934026 - md5: e7da623f94edbf9c66f816bee03432a2 +- conda: https://prefix.dev/conda-forge/win-64/psutil-7.0.0-py310ha8f682b_0.conda + sha256: 61c016c40848168bc565ceb8f3a78ad2d9288ffbe4236bcec312ef554f1caef2 + md5: ec78bb694e0ea34958e8f479e723499e depends: - python >=3.10,<3.11.0a0 - python_abi 3.10.* *_cp310 @@ -12093,11 +12093,11 @@ packages: license_family: BSD purls: - pkg:pypi/psutil?source=hash-mapping - size: 386297 - timestamp: 1735327974109 -- conda: https://prefix.dev/conda-forge/win-64/psutil-6.1.1-py312h4389bb4_0.conda - sha256: 420c86339a8a6c225a79499e9d580df4a23ccbeca6cae4d44fe4fc365654881c - md5: f27ba9579b607b6678d8ac296bbd8603 + size: 369926 + timestamp: 1740663706146 +- conda: https://prefix.dev/conda-forge/win-64/psutil-7.0.0-py312h4389bb4_0.conda + sha256: 088451ee2c9a349e1168f70afe275e58f86350faffb09c032cff76f97d4fb7bb + md5: f5b86d6e2e645ee276febe79a310b640 depends: - python >=3.12,<3.13.0a0 - python_abi 3.12.* *_cp312 @@ -12108,11 +12108,11 @@ packages: license_family: BSD purls: - pkg:pypi/psutil?source=hash-mapping - size: 504977 - timestamp: 1735327974160 -- conda: https://prefix.dev/conda-forge/win-64/psutil-6.1.1-py313ha7868ed_0.conda - sha256: a9141ee67dcf85c4b6eb333ff3dbcd4e2cd4d592f768740703cf89b56eda9d68 - md5: 8a948151d6f16d6cef5318b66c86b972 + size: 484682 + timestamp: 1740663813103 +- conda: https://prefix.dev/conda-forge/win-64/psutil-7.0.0-py313ha7868ed_0.conda + sha256: d8e5d86e939d5f308c7922835a94458afb29d81c90b5d43c43a5537c9c7adbc1 + md5: 3cdf99cf98b01856af9f26c5d8036353 depends: - python >=3.13,<3.14.0a0 - python_abi 3.13.* *_cp313 @@ -12123,8 +12123,8 @@ packages: license_family: BSD purls: - pkg:pypi/psutil?source=hash-mapping - size: 511743 - timestamp: 1735327885260 + size: 491314 + timestamp: 1740663777370 - conda: https://prefix.dev/conda-forge/linux-64/pthread-stubs-0.4-hb9d3cd8_1002.conda sha256: 9c88f8c64590e9567c6c80823f0328e58d3b1efb0e1c539c0315ceca764e0973 md5: b3c17d95b5a10c6e64a21fa17573e70e diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 88222ea9..70310ea9 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -14,7 +14,7 @@ sinc, ) -__version__ = "0.6.1" +__version__ = "0.7.0.dev0" # pylint: disable=duplicate-code __all__ = [ From 1daa76d899746f4b334b69c4e1594a1d4f2400d6 Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Thu, 27 Feb 2025 16:21:14 +0000 Subject: [PATCH 040/140] docs: add NeilGirdhar as a contributor for code, and test (#149) --- .all-contributorsrc | 10 ++++++++++ CONTRIBUTORS.md | 1 + README.md | 1 + 3 files changed, 12 insertions(+) diff --git a/.all-contributorsrc b/.all-contributorsrc index e0565ac1..08df82c1 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -214,6 +214,16 @@ "contributions": [ "review" ] + }, + { + "login": "NeilGirdhar", + "name": "Neil Girdhar", + "avatar_url": "https://avatars.githubusercontent.com/u/730137?v=4", + "profile": "https://github.com/NeilGirdhar", + "contributions": [ + "code", + "test" + ] } ] } diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index a482691e..fe523669 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -33,6 +33,7 @@ This project exists thanks to the following contributors Jake Vanderplas
Jake Vanderplas
👀 kotlinisland
kotlinisland
👀 detachhead
detachhead
👀 + Neil Girdhar
Neil Girdhar
💻 ⚠️ diff --git a/README.md b/README.md index 44099678..7905b9a8 100644 --- a/README.md +++ b/README.md @@ -85,6 +85,7 @@ This project exists thanks to the following contributors Jake Vanderplas
Jake Vanderplas
👀 kotlinisland
kotlinisland
👀 detachhead
detachhead
👀 + Neil Girdhar
Neil Girdhar
💻 ⚠️ From 7806a3d76d7673850df429c60ef0306e41b35be2 Mon Sep 17 00:00:00 2001 From: "allcontributors[bot]" <46447321+allcontributors[bot]@users.noreply.github.com> Date: Fri, 28 Feb 2025 10:25:05 +0000 Subject: [PATCH 041/140] docs: add lucascolley as a contributor for review (#150) 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 08df82c1..f91258c2 100644 --- a/.all-contributorsrc +++ b/.all-contributorsrc @@ -27,7 +27,8 @@ "tool", "test", "bug", - "platform" + "platform", + "review" ] }, { diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md index fe523669..fef09188 100644 --- a/CONTRIBUTORS.md +++ b/CONTRIBUTORS.md @@ -9,7 +9,7 @@ This project exists thanks to the following contributors - + diff --git a/README.md b/README.md index 7905b9a8..8d11a67e 100644 --- a/README.md +++ b/README.md @@ -61,7 +61,7 @@ This project exists thanks to the following contributors
Lucas Colley
Lucas Colley
💻 📖 💡 🤔 🚇 🚧 🔧 ⚠️ 🐛 📦		Lucas Colley
Lucas Colley
💻 📖 💡 🤔 🚇 🚧 🔧 ⚠️ 🐛 📦 👀		 Matt Haberland
Matt Haberland
💻 🤔		 Jake Bowhay
Jake Bowhay
💻 👀		 Aaron Meurer
Aaron Meurer
👀 🤔 🚇
- + From fe3c46a906d3cb6a67b55806bfc6427344926d13 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 3 Mar 2025 02:30:49 +0000 Subject: [PATCH 042/140] Bump the actions group with 3 updates Bumps the actions group with 3 updates: [actions/attest-build-provenance](https://github.com/actions/attest-build-provenance), [codecov/codecov-action](https://github.com/codecov/codecov-action) and [dawidd6/action-download-artifact](https://github.com/dawidd6/action-download-artifact). Updates `actions/attest-build-provenance` from 2.2.0 to 2.2.2 - [Release notes](https://github.com/actions/attest-build-provenance/releases) - [Changelog](https://github.com/actions/attest-build-provenance/blob/main/RELEASE.md) - [Commits](https://github.com/actions/attest-build-provenance/compare/v2.2.0...v2.2.2) Updates `codecov/codecov-action` from 5.3.1 to 5.4.0 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/v5.3.1...v5.4.0) Updates `dawidd6/action-download-artifact` from 8 to 9 - [Release notes](https://github.com/dawidd6/action-download-artifact/releases) - [Commits](https://github.com/dawidd6/action-download-artifact/compare/v8...v9) --- updated-dependencies: - dependency-name: actions/attest-build-provenance dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: dawidd6/action-download-artifact dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions ... Signed-off-by: dependabot[bot] --- .github/workflows/cd.yml | 2 +- .github/workflows/ci.yml | 2 +- .github/workflows/docs-deploy.yml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 83087bff..2017bf29 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -37,7 +37,7 @@ jobs: path: dist - name: Generate artifact attestation for sdist and wheel - uses: actions/attest-build-provenance@v2.2.0 + uses: actions/attest-build-provenance@v2.2.2 with: subject-path: "dist/*" diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index e7fba8db..fc43be95 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -66,6 +66,6 @@ jobs: run: pixi run -e ${{ matrix.environment }} tests-ci - name: Upload coverage report - uses: codecov/codecov-action@v5.3.1 + uses: codecov/codecov-action@v5.4.0 with: token: ${{ secrets.CODECOV_TOKEN }} diff --git a/.github/workflows/docs-deploy.yml b/.github/workflows/docs-deploy.yml index a08b2bf4..a7a8cb1c 100644 --- a/.github/workflows/docs-deploy.yml +++ b/.github/workflows/docs-deploy.yml @@ -16,7 +16,7 @@ jobs: steps: - uses: actions/checkout@v4 - name: Download Artifact - uses: dawidd6/action-download-artifact@v8 + uses: dawidd6/action-download-artifact@v9 with: workflow: docs-build.yml name: docs-build From 86bdec2d4f718951f0371ae3ba5dac9ab3f7bff9 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Wed, 5 Mar 2025 12:42:41 +0000 Subject: [PATCH 043/140] Bump array-api-compat to 1.11 --- pixi.lock | 1482 +++++++------------ pyproject.toml | 4 +- src/array_api_extra/_lib/_funcs.py | 2 +- src/array_api_extra/_lib/_utils/_compat.py | 3 + src/array_api_extra/_lib/_utils/_compat.pyi | 1 + tests/test_at.py | 5 +- tests/test_funcs.py | 6 +- vendor_tests/test_vendor.py | 2 + 8 files changed, 548 insertions(+), 957 deletions(-) diff --git a/pixi.lock b/pixi.lock index 0548b92e..7310e5af 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_kmp_llvm.tar.bz2 - - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.10.0-pyhd8ed1ab_0.conda + - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.11.1-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/linux-64/bzip2-1.0.8-h4bc722e_7.conda - conda: https://prefix.dev/conda-forge/linux-64/ca-certificates-2025.1.31-hbcca054_0.conda - conda: https://prefix.dev/conda-forge/linux-64/ld_impl_linux-64-2.43-h712a8e2_4.conda @@ -32,7 +32,7 @@ environments: - conda: https://prefix.dev/conda-forge/noarch/tzdata-2025a-h78e105d_0.conda - pypi: . osx-arm64: - - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.10.0-pyhd8ed1ab_0.conda + - conda: https://prefix.dev/conda-forge/noarch/array-api-compat-1.11.1-pyhd8ed1ab_0.conda - conda: https://prefix.dev/conda-forge/osx-arm64/bzip2-1.0.8-h99b78c6_7.conda - conda: https://prefix.dev/conda-forge/osx-arm64/ca-certificates-2025.1.31-hf0a4a13_0.conda - conda: https://prefix.dev/conda-forge/osx-arm64/libexpat-2.6.4-h286801f_0.conda @@ -50,7 +50,7 @@ environments: - 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depends: - - cffi >=1.11 - - python >=3.12,<3.13.0a0 - - python_abi 3.12.* *_cp312 - - ucrt >=10.0.20348.0 - - vc >=14.2,<15 - - vc14_runtime >=14.29.30139 - - zstd >=1.5.6,<1.5.7.0a0 - - zstd >=1.5.6,<1.6.0a0 - license: BSD-3-Clause - license_family: BSD - purls: - - pkg:pypi/zstandard?source=hash-mapping - size: 320624 - timestamp: 1725305934189 - conda: https://prefix.dev/conda-forge/win-64/zstandard-0.23.0-py313h574b89f_1.conda sha256: 1d2744ec0e91da267ce749e19142081472539cb140a7dad0646cd249246691fe md5: 8e017aca933f4dd25491151edd3e7820 diff --git a/pyproject.toml b/pyproject.toml index 2c33b4b1..63682d9d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,7 +26,7 @@ classifiers = [ "Typing :: Typed", ] dynamic = ["version"] -dependencies = ["array-api-compat>=1.10.0,<2"] +dependencies = ["array-api-compat>=1.11,<2"] [project.urls] Homepage = "https://github.com/data-apis/array-api-extra" @@ -48,7 +48,7 @@ platforms = ["linux-64", "osx-arm64", "win-64"] [tool.pixi.dependencies] python = ">=3.10,<3.14" -array-api-compat = ">=1.10.0,<2" +array-api-compat = ">=1.11,<2" [tool.pixi.pypi-dependencies] array-api-extra = { path = ".", editable = true } diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 2c2e5a7a..5621017a 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -556,7 +556,7 @@ def nunique(x: Array, /, *, xp: ModuleType | None = None) -> Array: _, counts = xp.unique_counts(x) n = _compat.size(counts) # FIXME https://github.com/data-apis/array-api-compat/pull/231 - if n is None or math.isnan(n): # e.g. Dask, ndonnx + if n is None: # e.g. Dask, ndonnx return xp.astype(counts, xp.bool).sum() return xp.asarray(n, device=_compat.device(x)) diff --git a/src/array_api_extra/_lib/_utils/_compat.py b/src/array_api_extra/_lib/_utils/_compat.py index 34958149..b9997450 100644 --- a/src/array_api_extra/_lib/_utils/_compat.py +++ b/src/array_api_extra/_lib/_utils/_compat.py @@ -14,6 +14,7 @@ is_dask_namespace, is_jax_array, is_jax_namespace, + is_lazy_array, is_numpy_array, is_numpy_namespace, is_pydata_sparse_array, @@ -35,6 +36,7 @@ is_dask_namespace, is_jax_array, is_jax_namespace, + is_lazy_array, is_numpy_array, is_numpy_namespace, is_pydata_sparse_array, @@ -56,6 +58,7 @@ "is_dask_namespace", "is_jax_array", "is_jax_namespace", + "is_lazy_array", "is_numpy_array", "is_numpy_namespace", "is_pydata_sparse_array", diff --git a/src/array_api_extra/_lib/_utils/_compat.pyi b/src/array_api_extra/_lib/_utils/_compat.pyi index 5c8b6260..1f585a38 100644 --- a/src/array_api_extra/_lib/_utils/_compat.pyi +++ b/src/array_api_extra/_lib/_utils/_compat.pyi @@ -32,5 +32,6 @@ def is_jax_array(x: object, /) -> bool: ... def is_numpy_array(x: object, /) -> bool: ... def is_pydata_sparse_array(x: object, /) -> bool: ... def is_torch_array(x: object, /) -> bool: ... +def is_lazy_array(x: object, /) -> bool: ... def is_writeable_array(x: object, /) -> bool: ... def size(x: Array, /) -> int | None: ... diff --git a/tests/test_at.py b/tests/test_at.py index ce27fbff..e13a691a 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -11,7 +11,7 @@ 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._testing import xfail, xp_assert_equal +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, Index from array_api_extra.testing import lazy_xp_function @@ -219,7 +219,6 @@ def test_alternate_index_syntax(): def test_incompatible_dtype( xp: ModuleType, library: Backend, - request: pytest.FixtureRequest, op: _AtOp, copy: bool | None, bool_mask: bool, @@ -253,8 +252,6 @@ def test_incompatible_dtype( z = at_op(x, idx, op, 1.1, copy=copy) elif library is Backend.DASK: - if op in (_AtOp.MIN, _AtOp.MAX) and bool_mask: - xfail(request, reason="need array-api-compat 1.11") z = at_op(x, idx, op, 1.1, copy=copy) elif library is Backend.ARRAY_API_STRICT and op is not _AtOp.SET: diff --git a/tests/test_funcs.py b/tests/test_funcs.py index e24a7c0e..27318281 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -32,16 +32,14 @@ lazy_xp_function(atleast_nd, static_argnames=("ndim", "xp")) lazy_xp_function(cov, static_argnames="xp") -# FIXME .device attribute https://github.com/data-apis/array-api-compat/pull/238 -lazy_xp_function(create_diagonal, jax_jit=False, static_argnames=("offset", "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")) # FIXME calls in1d which calls xp.unique_values without size lazy_xp_function(setdiff1d, jax_jit=False, static_argnames=("assume_unique", "xp")) -# FIXME .device attribute https://github.com/data-apis/array-api-compat/pull/238 -lazy_xp_function(sinc, jax_jit=False, static_argnames="xp") +lazy_xp_function(sinc, static_argnames="xp") @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") diff --git a/vendor_tests/test_vendor.py b/vendor_tests/test_vendor.py index 7aaa9eba..4613edc7 100644 --- a/vendor_tests/test_vendor.py +++ b/vendor_tests/test_vendor.py @@ -14,6 +14,7 @@ def test_vendor_compat(): is_dask_namespace, is_jax_array, is_jax_namespace, + is_lazy_array, is_numpy_array, is_numpy_namespace, is_pydata_sparse_array, @@ -35,6 +36,7 @@ def test_vendor_compat(): assert not is_dask_namespace(xp) assert not is_jax_array(x) assert not is_jax_namespace(xp) + assert not is_lazy_array(x) assert not is_numpy_array(x) assert not is_numpy_namespace(xp) assert not is_pydata_sparse_array(x) From 2bea9dbb0a4c84a3b85de1dcf423b713c2784092 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 10 Mar 2025 02:54:08 +0000 Subject: [PATCH 044/140] Bump actions/attest-build-provenance in the actions group Bumps the actions group with 1 update: [actions/attest-build-provenance](https://github.com/actions/attest-build-provenance). Updates `actions/attest-build-provenance` from 2.2.2 to 2.2.3 - [Release notes](https://github.com/actions/attest-build-provenance/releases) - [Changelog](https://github.com/actions/attest-build-provenance/blob/main/RELEASE.md) - [Commits](https://github.com/actions/attest-build-provenance/compare/v2.2.2...v2.2.3) --- updated-dependencies: - dependency-name: actions/attest-build-provenance dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] --- .github/workflows/cd.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml index 2017bf29..3c045cbe 100644 --- a/.github/workflows/cd.yml +++ b/.github/workflows/cd.yml @@ -37,7 +37,7 @@ jobs: path: dist - name: Generate artifact attestation for sdist and wheel - uses: actions/attest-build-provenance@v2.2.2 + uses: actions/attest-build-provenance@v2.2.3 with: subject-path: "dist/*" From b24c218871757b11a8e14ab401233cd91c99f329 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Wed, 12 Mar 2025 21:00:30 +0000 Subject: [PATCH 045/140] BUG: `lazy_xp_function` crashes with Cython ufuncs (#153) * BUG: lazy_xp_function crashes with ufuncs * elaborate on comment --------- Co-authored-by: Lucas Colley --- src/array_api_extra/testing.py | 58 +++++++++++++++++++++++----------- tests/test_testing.py | 30 ++++++++++++++++++ 2 files changed, 69 insertions(+), 19 deletions(-) diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index 65362382..1007fa1a 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -7,7 +7,8 @@ # https://github.com/scikit-learn/scikit-learn/pull/27910#issuecomment-2568023972 from __future__ import annotations -from collections.abc import Callable, Iterable, Sequence +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 @@ -42,6 +43,8 @@ def override(func: Callable[P, T]) -> Callable[P, T]: T = TypeVar("T") +_ufuncs_tags: dict[object, dict[str, Any]] = {} # type: ignore[no-any-explicit] + def lazy_xp_function( # type: ignore[no-any-explicit] func: Callable[..., Any], @@ -132,12 +135,16 @@ def test_myfunc(xp): a = xp.asarray([1, 2]) b = myfunc(a) # This is jitted when xp=jax.numpy c = mymodule.myfunc(a) # This is not """ - func.allow_dask_compute = allow_dask_compute # type: ignore[attr-defined] # pyright: ignore[reportFunctionMemberAccess] - if jax_jit: - func.lazy_jax_jit_kwargs = { # type: ignore[attr-defined] # pyright: ignore[reportFunctionMemberAccess] - "static_argnums": static_argnums, - "static_argnames": static_argnames, - } + 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 + _ufuncs_tags[func] = tags def patch_lazy_xp_functions( @@ -179,24 +186,37 @@ def xp(request, monkeypatch): """ globals_ = cast("dict[str, Any]", request.module.__dict__) # type: ignore[no-any-explicit] - if is_dask_namespace(xp): + def iter_tagged() -> Iterator[tuple[str, Callable[..., Any], dict[str, Any]]]: # type: ignore[no-any-explicit] for name, func in globals_.items(): - n = getattr(func, "allow_dask_compute", None) - if n is not None: - assert isinstance(n, int) - wrapped = _allow_dask_compute(func, n) - monkeypatch.setitem(globals_, name, wrapped) + tags: dict[str, Any] | None = None # type: ignore[no-any-explicit] + with contextlib.suppress(AttributeError): + tags = func._lazy_xp_function # pylint: disable=protected-access + if tags is None: + with contextlib.suppress(KeyError, TypeError): + tags = _ufuncs_tags[func] + if tags is not None: + yield name, func, tags + + if is_dask_namespace(xp): + for name, func, tags in iter_tagged(): + n = tags["allow_dask_compute"] + wrapped = _allow_dask_compute(func, n) + monkeypatch.setitem(globals_, name, wrapped) elif is_jax_namespace(xp): import jax - for name, func in globals_.items(): - kwargs = cast( # type: ignore[no-any-explicit] - "dict[str, Any] | None", getattr(func, "lazy_jax_jit_kwargs", None) - ) - if kwargs is not None: + for 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(Callable[..., Any], jax.jit(func, **kwargs)) # type: ignore[no-any-explicit,no-untyped-call,unused-ignore] + wrapped = cast( # type: ignore[no-any-explicit] + Callable[..., Any], + jax.jit( + func, + static_argnums=tags["static_argnums"], + static_argnames=tags["static_argnames"], + ), + ) monkeypatch.setitem(globals_, name, wrapped) diff --git a/tests/test_testing.py b/tests/test_testing.py index c9a1e32f..aa7faaf8 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -202,3 +202,33 @@ def test_lazy_xp_function_static_params(xp: ModuleType, func: Callable[..., Arra 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])) + + +try: + # 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] + + lazy_xp_function(erf) # pyright: ignore[reportUnknownArgumentType] +except ImportError: + erf = None + + +@pytest.mark.filterwarnings("ignore:__array_wrap__:DeprecationWarning") # torch +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 + # which results in an assertion error for mismatched namespaces + # 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(erf(x), xp.asarray([1.0, 1.0])) + else: + # 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(erf(x), xp.asarray([1.0, 1.0])) From a925bf9ed5bf8a4b9ef80283882e95d800e4e19d Mon Sep 17 00:00:00 2001 From: crusaderky Date: Thu, 13 Mar 2025 11:48:56 +0000 Subject: [PATCH 046/140] ENH: `lazy_xp_function` to materialize exceptions on Dask --- src/array_api_extra/testing.py | 17 ++++++++++++----- tests/test_testing.py | 29 +++++++++++++++++++++++++++++ 2 files changed, 41 insertions(+), 5 deletions(-) diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index 1007fa1a..550665ae 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -200,7 +200,7 @@ def iter_tagged() -> Iterator[tuple[str, Callable[..., Any], dict[str, Any]]]: if is_dask_namespace(xp): for name, func, tags in iter_tagged(): n = tags["allow_dask_compute"] - wrapped = _allow_dask_compute(func, n) + wrapped = _dask_wrap(func, n) monkeypatch.setitem(globals_, name, wrapped) elif is_jax_namespace(xp): @@ -256,13 +256,15 @@ def __call__(self, dsk: Graph, keys: Sequence[Key] | Key, **kwargs: Any) -> Any: return dask.get(dsk, keys, **kwargs) # type: ignore[attr-defined,no-untyped-call] # pyright: ignore[reportPrivateImportUsage] -def _allow_dask_compute( +def _dask_wrap( func: Callable[P, T], n: int ) -> Callable[P, T]: # numpydoc ignore=PR01,RT01 """ Wrap `func` to raise if it attempts to call `dask.compute` more than `n` times. + + After the function returns, materialize the graph in order to re-raise exceptions. """ - import dask.config + import dask func_name = getattr(func, "__name__", str(func)) n_str = f"only up to {n}" if n else "no" @@ -276,7 +278,12 @@ def _allow_dask_compute( @wraps(func) def wrapper(*args: P.args, **kwargs: P.kwargs) -> T: # numpydoc ignore=GL08 scheduler = CountingDaskScheduler(n, msg) - with dask.config.set({"scheduler": scheduler}): - return func(*args, **kwargs) + with dask.config.set({"scheduler": scheduler}): # pyright: ignore[reportPrivateImportUsage] + out = func(*args, **kwargs) + + # 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[no-any-return,attr-defined,no-untyped-call,func-returns-value,index] # pyright: ignore[reportPrivateImportUsage] return wrapper diff --git a/tests/test_testing.py b/tests/test_testing.py index aa7faaf8..1649dd86 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -232,3 +232,32 @@ def test_lazy_xp_function_cython_ufuncs(xp: ModuleType, library: Backend): # note that when sparse reduces to scalar it returns a np.generic, which # would make xp_assert_equal fail. xp_assert_equal(erf(x), xp.asarray([1.0, 1.0])) + + +def dask_raises(x: Array) -> Array: + def _raises(x: Array) -> Array: + # Test that map_blocks doesn't eagerly call the function; + # dtype and meta should be sufficient to skip the trial run. + assert x.shape == (3,) + msg = "Hello world" + raise ValueError(msg) + + return x.map_blocks(_raises, dtype=x.dtype, meta=x._meta) + + +lazy_xp_function(dask_raises) + + +def test_lazy_xp_function_eagerly_raises(da: ModuleType): + """Test that the pattern:: + + with pytest.raises(Exception): + func(x) + + works with Dask, even though it normally wouldn't as we're disregarding the func + output so the graph would not be ordinarily materialized. + lazy_xp_function contains ad-hoc code to materialize and reraise exceptions. + """ + x = da.arange(3) + with pytest.raises(ValueError, match="Hello world"): + dask_raises(x) From 17740374cd72def41386e76ff4b3be3f9b36a49e Mon Sep 17 00:00:00 2001 From: crusaderky Date: Fri, 14 Mar 2025 09:40:13 +0000 Subject: [PATCH 047/140] MAINT: Allow `import xpx.testing` outside of test modules --- src/array_api_extra/testing.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index 550665ae..8aca160f 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -13,8 +13,6 @@ from types import ModuleType from typing import TYPE_CHECKING, Any, TypeVar, cast -import pytest - from ._lib._utils._compat import is_dask_namespace, is_jax_namespace __all__ = ["lazy_xp_function", "patch_lazy_xp_functions"] @@ -25,6 +23,7 @@ # https://github.com/scikit-learn/scikit-learn/pull/27910#issuecomment-2568023972 from typing import ParamSpec + import pytest from dask.typing import Graph, Key, SchedulerGetCallable from typing_extensions import override From 2f7b4d9febadf9f5a57b719c1b7658dcc61bb0f7 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Mon, 17 Mar 2025 15:13:05 +0000 Subject: [PATCH 048/140] MAINT: Array API 2024.12 typing nits (#156) * MAINT: Array API 2024.12 typing nits * update docstrings * Update src/array_api_extra/_lib/_utils/_helpers.py Co-authored-by: Lucas Colley * Add xref to pyright bug --------- Co-authored-by: Lucas Colley --- docs/index.md | 2 +- src/array_api_extra/_delegation.py | 4 +-- src/array_api_extra/_lib/_funcs.py | 36 +++++++++++++++++---- src/array_api_extra/_lib/_utils/_compat.pyi | 25 +++++++------- src/array_api_extra/_lib/_utils/_helpers.py | 24 ++++++++------ 5 files changed, 60 insertions(+), 31 deletions(-) diff --git a/docs/index.md b/docs/index.md index f7c51574..ae15c7f4 100644 --- a/docs/index.md +++ b/docs/index.md @@ -185,7 +185,7 @@ increase performance. In particular, the following kinds of function are also in-scope: - Functions which implement - [array API standard extension](https://data-apis.org/array-api/2023.12/extensions/index.html) + [array API standard extension](https://data-apis.org/array-api/latest/extensions/index.html) functions in terms of functions from the base standard. - Functions which add functionality (e.g. extra parameters) to functions from the standard. diff --git a/src/array_api_extra/_delegation.py b/src/array_api_extra/_delegation.py index f3295c45..0c455ae1 100644 --- a/src/array_api_extra/_delegation.py +++ b/src/array_api_extra/_delegation.py @@ -31,8 +31,8 @@ def _delegate(xp: ModuleType, *backends: Backend) -> bool: def isclose( - a: Array, - b: Array, + a: Array | complex, + b: Array | complex, *, rtol: float = 1e-05, atol: float = 1e-08, diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 5621017a..cf06dd55 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -7,7 +7,7 @@ import warnings from collections.abc import Sequence from types import ModuleType -from typing import cast +from typing import TYPE_CHECKING, cast from ._at import at from ._utils import _compat, _helpers @@ -375,8 +375,8 @@ def expand_dims( def isclose( - a: Array, - b: Array, + a: Array | complex, + b: Array | complex, *, rtol: float = 1e-05, atol: float = 1e-08, @@ -385,6 +385,10 @@ def isclose( ) -> Array: # numpydoc ignore=PR01,RT01 """See docstring in array_api_extra._delegation.""" a, b = asarrays(a, b, xp=xp) + # FIXME https://github.com/microsoft/pyright/issues/10085 + if TYPE_CHECKING: # pragma: nocover + assert _compat.is_array_api_obj(a) + assert _compat.is_array_api_obj(b) a_inexact = xp.isdtype(a.dtype, ("real floating", "complex floating")) b_inexact = xp.isdtype(b.dtype, ("real floating", "complex floating")) @@ -419,7 +423,13 @@ def isclose( return xp.abs(a - b) <= (atol + xp.abs(b) // nrtol) -def kron(a: Array, b: Array, /, *, xp: ModuleType | None = None) -> Array: +def kron( + a: Array | complex, + b: Array | complex, + /, + *, + xp: ModuleType | None = None, +) -> Array: """ Kronecker product of two arrays. @@ -495,9 +505,16 @@ def kron(a: Array, b: Array, /, *, xp: ModuleType | None = None) -> Array: if xp is None: xp = array_namespace(a, b) a, b = asarrays(a, b, xp=xp) + # FIXME https://github.com/microsoft/pyright/issues/10085 + if TYPE_CHECKING: # pragma: nocover + assert _compat.is_array_api_obj(a) + assert _compat.is_array_api_obj(b) singletons = (1,) * (b.ndim - a.ndim) a = xp.broadcast_to(a, singletons + a.shape) + # FIXME https://github.com/microsoft/pyright/issues/10085 + if TYPE_CHECKING: # pragma: nocover + assert _compat.is_array_api_obj(a) nd_b, nd_a = b.ndim, a.ndim nd_max = max(nd_b, nd_a) @@ -614,8 +631,8 @@ def pad( def setdiff1d( - x1: Array, - x2: Array, + x1: Array | complex, + x2: Array | complex, /, *, assume_unique: bool = False, @@ -628,7 +645,7 @@ def setdiff1d( Parameters ---------- - x1 : array + x1 : array | int | float | complex | bool Input array. x2 : array Input comparison array. @@ -665,6 +682,11 @@ def setdiff1d( else: x1 = xp.unique_values(x1) x2 = xp.unique_values(x2) + + # FIXME https://github.com/microsoft/pyright/issues/10085 + if TYPE_CHECKING: # pragma: nocover + assert _compat.is_array_api_obj(x1) + return x1[_helpers.in1d(x1, x2, assume_unique=True, invert=True, xp=xp)] diff --git a/src/array_api_extra/_lib/_utils/_compat.pyi b/src/array_api_extra/_lib/_utils/_compat.pyi index 1f585a38..66134fae 100644 --- a/src/array_api_extra/_lib/_utils/_compat.pyi +++ b/src/array_api_extra/_lib/_utils/_compat.pyi @@ -5,27 +5,30 @@ from __future__ import annotations from types import ModuleType +# TODO import from typing (requires Python >=3.13) +from typing_extensions import TypeIs + from ._typing import Array, Device # pylint: disable=missing-class-docstring,unused-argument -class ArrayModule(ModuleType): +class Namespace(ModuleType): def device(self, x: Array, /) -> Device: ... def array_namespace( - *xs: Array, + *xs: Array | complex | None, api_version: str | None = None, use_compat: bool | None = None, -) -> ArrayModule: ... +) -> Namespace: ... def device(x: Array, /) -> Device: ... -def is_array_api_obj(x: object, /) -> bool: ... -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_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, /) -> bool: ... def is_dask_array(x: object, /) -> bool: ... def is_jax_array(x: object, /) -> bool: ... diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index e8419f24..594b6e12 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -5,12 +5,17 @@ from collections.abc import Generator from types import ModuleType -from typing import cast +from typing import TYPE_CHECKING from . import _compat from ._compat import array_namespace, is_array_api_obj, is_numpy_array from ._typing import Array +if TYPE_CHECKING: # pragma: no cover + # TODO import from typing (requires Python >=3.13) + from typing_extensions import TypeIs + + __all__ = ["asarrays", "in1d", "is_python_scalar", "mean"] @@ -96,16 +101,17 @@ def mean( return xp.mean(x, axis=axis, keepdims=keepdims) -def is_python_scalar(x: object) -> bool: # numpydoc ignore=PR01,RT01 +def is_python_scalar(x: object) -> TypeIs[complex]: # numpydoc ignore=PR01,RT01 """Return True if `x` is a Python scalar, False otherwise.""" # isinstance(x, float) returns True for np.float64 # isinstance(x, complex) returns True for np.complex128 - return isinstance(x, int | float | complex | bool) and not is_numpy_array(x) + # bool is a subclass of int + return isinstance(x, int | float | complex) and not is_numpy_array(x) def asarrays( - a: Array | int | float | complex | bool, - b: Array | int | float | complex | bool, + a: Array | complex, + b: Array | complex, xp: ModuleType, ) -> tuple[Array, Array]: """ @@ -150,9 +156,7 @@ def asarrays( if is_array_api_obj(a): # a is an Array API object # b is a int | float | complex | bool - - # pyright doesn't like it if you reuse the same variable name - xa = cast(Array, a) + xa = a # https://data-apis.org/array-api/draft/API_specification/type_promotion.html#mixing-arrays-with-python-scalars same_dtype = { @@ -162,8 +166,8 @@ def asarrays( complex: "complex floating", } kind = same_dtype[type(b)] # type: ignore[index] - if xp.isdtype(xa.dtype, kind): - xb = xp.asarray(b, dtype=xa.dtype) + if xp.isdtype(a.dtype, kind): + xb = xp.asarray(b, dtype=a.dtype) else: # Undefined behaviour. Let the function deal with it, if it can. xb = xp.asarray(b) From 8cac0e47b6251b65ddfee434949e2f277c001f19 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Fri, 14 Mar 2025 10:19:33 +0000 Subject: [PATCH 049/140] ENH: `lazy_xp_function` namespaces support --- src/array_api_extra/testing.py | 101 ++++++++++++++++++++++++--------- tests/test_testing.py | 37 ++++++++++++ 2 files changed, 110 insertions(+), 28 deletions(-) diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index 8aca160f..a0f97a81 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -56,9 +56,8 @@ def lazy_xp_function( # type: ignore[no-any-explicit] """ Tag a function to be tested on lazy backends. - Tag a function, which must be imported in the test module globals, so that when any - tests defined in the same module are executed with ``xp=jax.numpy`` the function is - replaced with a jitted version of itself, and when it is executed with + Tag a function so that when any tests are executed with ``xp=jax.numpy`` the + function is replaced with a jitted version of itself, and when it is executed with ``xp=dask.array`` the function will raise if it attempts to materialize the graph. This will be later expanded to provide test coverage for other lazy backends. @@ -120,19 +119,59 @@ def test_myfunc(xp): Notes ----- - A test function can circumvent this monkey-patching system by calling `func` as an - attribute of the original module. You need to sanitize your code to make sure this - does not happen. + In order for this tag to be effective, the test function must be imported into the + test module globals without its namespace; alternatively its namespace must be + declared in a ``lazy_xp_modules`` list in the test module globals. - Example:: + Example 1:: - import mymodule from mymodule import myfunc + from mymodule import myfunc lazy_xp_function(myfunc) def test_myfunc(xp): - a = xp.asarray([1, 2]) b = myfunc(a) # This is jitted when xp=jax.numpy c = - mymodule.myfunc(a) # This is not + x = myfunc(xp.asarray([1, 2])) + + Example 2:: + + import mymodule + + lazy_xp_modules = [mymodule] + lazy_xp_function(mymodule.myfunc) + + def test_myfunc(xp): + x = mymodule.myfunc(xp.asarray([1, 2])) + + A test function can circumvent this monkey-patching system by using a namespace + outside of the two above patterns. You need to sanitize your code to make sure this + only happens intentionally. + + Example 1:: + + import mymodule + from mymodule import myfunc + + lazy_xp_function(myfunc) + + def test_myfunc(xp): + a = xp.asarray([1, 2]) + b = myfunc(a) # This is wrapped when xp=jax.numpy or xp=dask.array + c = mymodule.myfunc(a) # This is not + + Example 2:: + + import mymodule + + class naked: + myfunc = mymodule.myfunc + + lazy_xp_modules = [mymodule] + lazy_xp_function(mymodule.myfunc) + + def test_myfunc(xp): + a = xp.asarray([1, 2]) + b = mymodule.myfunc(a) # This is wrapped when xp=jax.numpy or xp=dask.array + c = naked.myfunc(a) # This is not """ tags = { "allow_dask_compute": allow_dask_compute, @@ -153,11 +192,13 @@ def patch_lazy_xp_functions( Test lazy execution of functions tagged with :func:`lazy_xp_function`. If ``xp==jax.numpy``, search for all functions which have been tagged with - :func:`lazy_xp_function` in the globals of the module that defines the current test + :func:`lazy_xp_function` in the globals of the module that defines the current test, + as well as in the ``lazy_xp_modules`` list in the globals of the same module, and wrap them with :func:`jax.jit`. Unwrap them at the end of the test. If ``xp==dask.array``, wrap the functions with a decorator that disables - ``compute()`` and ``persist()``. + ``compute()`` and ``persist()`` and ensures that exceptions and warnings are raised + eagerly. This function should be typically called by your library's `xp` fixture that runs tests on multiple backends:: @@ -183,29 +224,33 @@ def xp(request, monkeypatch): lazy_xp_function : Tag a function to be tested on lazy backends. pytest.FixtureRequest : `request` test function parameter. """ - globals_ = cast("dict[str, Any]", request.module.__dict__) # type: ignore[no-any-explicit] - - def iter_tagged() -> Iterator[tuple[str, Callable[..., Any], dict[str, Any]]]: # type: ignore[no-any-explicit] - for name, func in globals_.items(): - tags: dict[str, Any] | None = None # type: ignore[no-any-explicit] - with contextlib.suppress(AttributeError): - tags = func._lazy_xp_function # pylint: disable=protected-access - if tags is None: - with contextlib.suppress(KeyError, TypeError): - tags = _ufuncs_tags[func] - if tags is not None: - yield name, func, tags + mod = cast(ModuleType, request.module) + mods = [mod, *cast(list[ModuleType], getattr(mod, "lazy_xp_modules", []))] + + def iter_tagged() -> ( # type: ignore[no-any-explicit] + 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[no-any-explicit] + with contextlib.suppress(AttributeError): + tags = func._lazy_xp_function # pylint: disable=protected-access + if tags is None: + with contextlib.suppress(KeyError, TypeError): + tags = _ufuncs_tags[func] + if tags is not None: + yield mod, name, func, tags if is_dask_namespace(xp): - for name, func, tags in iter_tagged(): + for mod, name, func, tags in iter_tagged(): n = tags["allow_dask_compute"] wrapped = _dask_wrap(func, n) - monkeypatch.setitem(globals_, name, wrapped) + monkeypatch.setattr(mod, name, wrapped) elif is_jax_namespace(xp): import jax - for name, func, tags in iter_tagged(): + 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[no-any-explicit] @@ -216,7 +261,7 @@ def iter_tagged() -> Iterator[tuple[str, Callable[..., Any], dict[str, Any]]]: static_argnames=tags["static_argnames"], ), ) - monkeypatch.setitem(globals_, name, wrapped) + monkeypatch.setattr(mod, name, wrapped) class CountingDaskScheduler(SchedulerGetCallable): diff --git a/tests/test_testing.py b/tests/test_testing.py index 1649dd86..ed21feb2 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -108,6 +108,7 @@ def non_materializable(x: Array) -> Array: 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 if xp.any(x < 0.0) or xp.any(x > 10.0): msg = "Values must be in the [0, 10] range" @@ -261,3 +262,39 @@ def test_lazy_xp_function_eagerly_raises(da: ModuleType): x = da.arange(3) with pytest.raises(ValueError, match="Hello world"): dask_raises(x) + + +class Wrapped: + def f(x: Array) -> Array: # noqa: N805 # pyright: ignore[reportSelfClsParameterName] + xp = array_namespace(x) + # Crash in jax.jit and trigger compute() on dask + if not xp.all(x): + msg = "Values must be non-zero" + raise ValueError(msg) + return x + + +class Naked: + f = Wrapped.f # pyright: ignore[reportUnannotatedClassAttribute] + + +lazy_xp_function(Wrapped.f) +lazy_xp_modules = [Wrapped] + + +def test_lazy_xp_modules(xp: ModuleType, library: Backend): + x = xp.asarray([1.0, 2.0]) + y = Naked.f(x) + xp_assert_equal(y, x) + + if library is Backend.JAX: + with pytest.raises( + TypeError, match="Attempted boolean conversion of traced array" + ): + Wrapped.f(x) + elif library is Backend.DASK: + with pytest.raises(AssertionError, match=r"dask\.compute"): + Wrapped.f(x) + else: + y = Wrapped.f(x) + xp_assert_equal(y, x) From 308fc1ff2361799ab9d745f0ca1e18835add2341 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Mon, 17 Mar 2025 17:55:13 +0000 Subject: [PATCH 050/140] TYP: Full annotations for Array objects (#159) * ENH: Fully annotate Array * Update src/array_api_extra/_lib/_funcs.py * More compact _typing.py --- pixi.lock | 2 +- pyproject.toml | 2 +- src/array_api_extra/_lib/_at.py | 59 ++++++----- src/array_api_extra/_lib/_funcs.py | 59 +++++------ src/array_api_extra/_lib/_testing.py | 28 ++++-- src/array_api_extra/_lib/_utils/_compat.pyi | 16 +-- src/array_api_extra/_lib/_utils/_helpers.py | 43 ++++++-- src/array_api_extra/_lib/_utils/_typing.py | 17 ++-- src/array_api_extra/_lib/_utils/_typing.pyi | 105 ++++++++++++++++++++ src/array_api_extra/testing.py | 2 +- tests/conftest.py | 2 +- tests/test_at.py | 47 ++++----- tests/test_funcs.py | 30 +++--- tests/test_helpers.py | 26 ++++- tests/test_testing.py | 51 +++++----- 15 files changed, 324 insertions(+), 165 deletions(-) create mode 100644 src/array_api_extra/_lib/_utils/_typing.pyi diff --git a/pixi.lock b/pixi.lock index 7310e5af..c2071402 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3788,7 +3788,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.0.dev0 - sha256: 88f998278ea7742857d385d2171ce91fe8ffde2d36416810070e15d523f5d0bf + sha256: af349b53edfb4298b00cbb25c5e3d68fa41ae6abcca3d0a7032f4423fe8bcd14 requires_dist: - array-api-compat>=1.11,<2 requires_python: '>=3.10' diff --git a/pyproject.toml b/pyproject.toml index 63682d9d..78ab718f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -203,7 +203,7 @@ 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"] +disable_error_code = ["redundant-expr", "unreachable", "no-any-return"] [[tool.mypy.overrides]] # slow/unavailable on Windows; do not add to the lint env diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py index a008efa9..11c8ff6c 100644 --- a/src/array_api_extra/_lib/_at.py +++ b/src/array_api_extra/_lib/_at.py @@ -15,7 +15,7 @@ is_jax_array, is_writeable_array, ) -from ._utils._typing import Array, Index +from ._utils._typing import Array, SetIndex class _AtOp(Enum): @@ -43,7 +43,13 @@ def __str__(self) -> str: # type: ignore[explicit-override] # pyright: ignore[ return self.value -_undef = object() +class Undef(Enum): + """Sentinel for undefined values.""" + + UNDEF = 0 + + +_undef = Undef.UNDEF class at: # pylint: disable=invalid-name # numpydoc ignore=PR02 @@ -188,16 +194,16 @@ class at: # pylint: disable=invalid-name # numpydoc ignore=PR02 """ _x: Array - _idx: Index + _idx: SetIndex | Undef __slots__: ClassVar[tuple[str, ...]] = ("_idx", "_x") def __init__( - self, x: Array, idx: Index = _undef, / + self, x: Array, idx: SetIndex | Undef = _undef, / ) -> None: # numpydoc ignore=GL08 self._x = x self._idx = idx - def __getitem__(self, idx: Index, /) -> at: # numpydoc ignore=PR01,RT01 + def __getitem__(self, idx: SetIndex, /) -> at: # numpydoc ignore=PR01,RT01 """ Allow for the alternate syntax ``at(x)[start:stop:step]``. @@ -212,9 +218,9 @@ def __getitem__(self, idx: Index, /) -> at: # numpydoc ignore=PR01,RT01 def _op( self, at_op: _AtOp, - in_place_op: Callable[[Array, Array | object], Array] | None, + in_place_op: Callable[[Array, Array | complex], Array] | None, out_of_place_op: Callable[[Array, Array], Array] | None, - y: Array | object, + y: Array | complex, /, copy: bool | None, xp: ModuleType | None, @@ -226,7 +232,7 @@ def _op( ---------- at_op : _AtOp Method of JAX's Array.at[]. - in_place_op : Callable[[Array, Array | object], Array] | None + in_place_op : Callable[[Array, Array | complex], Array] | None In-place operation to apply on mutable backends:: x[idx] = in_place_op(x[idx], y) @@ -245,7 +251,7 @@ def _op( x = xp.where(idx, y, x) - y : array or object + y : array or complex Right-hand side of the operation. copy : bool or None Whether to copy the input array. See the class docstring for details. @@ -260,7 +266,7 @@ def _op( x, idx = self._x, self._idx xp = array_namespace(x, y) if xp is None else xp - if idx is _undef: + if isinstance(idx, Undef): msg = ( "Index has not been set.\n" "Usage: either\n" @@ -306,7 +312,10 @@ def _op( if copy or (copy is None and not writeable): if is_jax_array(x): # Use JAX's at[] - func = cast(Callable[[Array], Array], getattr(x.at[idx], at_op.value)) + func = cast( + Callable[[Array | complex], Array], + getattr(x.at[idx], at_op.value), # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue,reportUnknownArgumentType] + ) out = func(y) # Undo int->float promotion on JAX after _AtOp.DIVIDE return xp.astype(out, x.dtype, copy=False) @@ -315,10 +324,10 @@ def _op( # with a copy followed by an update x = xp.asarray(x, copy=True) - if writeable is False: - # A copy of a read-only numpy array is writeable - # Note: this assumes that a copy of a writeable array is writeable - writeable = None + # A copy of a read-only numpy array is writeable + # Note: this assumes that a copy of a writeable array is writeable + assert not writeable + writeable = None if writeable is None: writeable = is_writeable_array(x) @@ -328,14 +337,14 @@ def _op( raise ValueError(msg) if in_place_op: # add(), subtract(), ... - x[self._idx] = in_place_op(x[self._idx], y) + x[idx] = in_place_op(x[idx], y) else: # set() - x[self._idx] = y + x[idx] = y return x def set( self, - y: Array | object, + y: Array | complex, /, copy: bool | None = None, xp: ModuleType | None = None, @@ -345,7 +354,7 @@ def set( def add( self, - y: Array | object, + y: Array | complex, /, copy: bool | None = None, xp: ModuleType | None = None, @@ -359,7 +368,7 @@ def add( def subtract( self, - y: Array | object, + y: Array | complex, /, copy: bool | None = None, xp: ModuleType | None = None, @@ -371,7 +380,7 @@ def subtract( def multiply( self, - y: Array | object, + y: Array | complex, /, copy: bool | None = None, xp: ModuleType | None = None, @@ -383,7 +392,7 @@ def multiply( def divide( self, - y: Array | object, + y: Array | complex, /, copy: bool | None = None, xp: ModuleType | None = None, @@ -395,7 +404,7 @@ def divide( def power( self, - y: Array | object, + y: Array | complex, /, copy: bool | None = None, xp: ModuleType | None = None, @@ -405,7 +414,7 @@ def power( def min( self, - y: Array | object, + y: Array | complex, /, copy: bool | None = None, xp: ModuleType | None = None, @@ -417,7 +426,7 @@ def min( def max( self, - y: Array | object, + y: Array | complex, /, copy: bool | None = None, xp: ModuleType | None = None, diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index cf06dd55..43698c42 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -7,12 +7,12 @@ import warnings from collections.abc import Sequence from types import ModuleType -from typing import TYPE_CHECKING, cast +from typing import cast from ._at import at from ._utils import _compat, _helpers from ._utils._compat import array_namespace, is_jax_array -from ._utils._helpers import asarrays, ndindex +from ._utils._helpers import asarrays, eager_shape, ndindex from ._utils._typing import Array __all__ = [ @@ -211,11 +211,13 @@ def cov(m: Array, /, *, xp: ModuleType | None = None) -> Array: m = xp.astype(m, dtype) avg = _helpers.mean(m, axis=1, xp=xp) - fact = m.shape[1] - 1 + + m_shape = eager_shape(m) + fact = m_shape[1] - 1 if fact <= 0: warnings.warn("Degrees of freedom <= 0 for slice", RuntimeWarning, stacklevel=2) - fact = 0.0 + fact = 0 m -= avg[:, None] m_transpose = m.T @@ -274,8 +276,10 @@ def create_diagonal( if x.ndim == 0: err_msg = "`x` must be at least 1-dimensional." raise ValueError(err_msg) - batch_dims = x.shape[:-1] - n = x.shape[-1] + abs(offset) + + x_shape = eager_shape(x) + batch_dims = x_shape[:-1] + n = x_shape[-1] + abs(offset) diag = xp.zeros((*batch_dims, n**2), dtype=x.dtype, device=_compat.device(x)) target_slice = slice( @@ -385,10 +389,6 @@ def isclose( ) -> Array: # numpydoc ignore=PR01,RT01 """See docstring in array_api_extra._delegation.""" a, b = asarrays(a, b, xp=xp) - # FIXME https://github.com/microsoft/pyright/issues/10085 - if TYPE_CHECKING: # pragma: nocover - assert _compat.is_array_api_obj(a) - assert _compat.is_array_api_obj(b) a_inexact = xp.isdtype(a.dtype, ("real floating", "complex floating")) b_inexact = xp.isdtype(b.dtype, ("real floating", "complex floating")) @@ -505,24 +505,17 @@ def kron( if xp is None: xp = array_namespace(a, b) a, b = asarrays(a, b, xp=xp) - # FIXME https://github.com/microsoft/pyright/issues/10085 - if TYPE_CHECKING: # pragma: nocover - assert _compat.is_array_api_obj(a) - assert _compat.is_array_api_obj(b) singletons = (1,) * (b.ndim - a.ndim) - a = xp.broadcast_to(a, singletons + a.shape) - # FIXME https://github.com/microsoft/pyright/issues/10085 - if TYPE_CHECKING: # pragma: nocover - assert _compat.is_array_api_obj(a) + a = cast(Array, xp.broadcast_to(a, singletons + a.shape)) nd_b, nd_a = b.ndim, a.ndim nd_max = max(nd_b, nd_a) if nd_a == 0 or nd_b == 0: return xp.multiply(a, b) - a_shape = a.shape - b_shape = b.shape + a_shape = eager_shape(a) + b_shape = eager_shape(b) # Equalise the shapes by prepending smaller one with 1s a_shape = (1,) * max(0, nd_b - nd_a) + a_shape @@ -587,16 +580,14 @@ def pad( ) -> Array: # numpydoc ignore=PR01,RT01 """See docstring in `array_api_extra._delegation.py`.""" # make pad_width a list of length-2 tuples of ints - x_ndim = cast(int, x.ndim) - if isinstance(pad_width, int): - pad_width_seq = [(pad_width, pad_width)] * x_ndim + pad_width_seq = [(pad_width, pad_width)] * x.ndim elif ( isinstance(pad_width, tuple) and len(pad_width) == 2 and all(isinstance(i, int) for i in pad_width) ): - pad_width_seq = [cast(tuple[int, int], pad_width)] * x_ndim + pad_width_seq = [cast(tuple[int, int], pad_width)] * x.ndim else: pad_width_seq = cast(list[tuple[int, int]], list(pad_width)) @@ -608,7 +599,8 @@ def pad( msg = f"expect a 2-tuple (before, after), got {w_tpl}." raise ValueError(msg) - sh = x.shape[ax] + sh = eager_shape(x)[ax] + if w_tpl[0] == 0 and w_tpl[1] == 0: sl = slice(None, None, None) else: @@ -674,20 +666,17 @@ def setdiff1d( """ if xp is None: xp = array_namespace(x1, x2) - x1, x2 = asarrays(x1, x2, xp=xp) + # https://github.com/microsoft/pyright/issues/10103 + x1_, x2_ = asarrays(x1, x2, xp=xp) if assume_unique: - x1 = xp.reshape(x1, (-1,)) - x2 = xp.reshape(x2, (-1,)) + x1_ = xp.reshape(x1_, (-1,)) + x2_ = xp.reshape(x2_, (-1,)) else: - x1 = xp.unique_values(x1) - x2 = xp.unique_values(x2) - - # FIXME https://github.com/microsoft/pyright/issues/10085 - if TYPE_CHECKING: # pragma: nocover - assert _compat.is_array_api_obj(x1) + x1_ = xp.unique_values(x1_) + x2_ = xp.unique_values(x2_) - return x1[_helpers.in1d(x1, x2, assume_unique=True, invert=True, xp=xp)] + return x1_[_helpers.in1d(x1_, x2_, assume_unique=True, invert=True, xp=xp)] def sinc(x: Array, /, *, xp: ModuleType | None = None) -> Array: diff --git a/src/array_api_extra/_lib/_testing.py b/src/array_api_extra/_lib/_testing.py index 3cd72942..c6be5e97 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -7,6 +7,7 @@ import math from types import ModuleType +from typing import cast import pytest @@ -48,10 +49,11 @@ def _check_ns_shape_dtype( actual_shape = actual.shape desired_shape = desired.shape if is_dask_namespace(desired_xp): - if any(math.isnan(i) for i in actual_shape): - actual_shape = actual.compute().shape - if any(math.isnan(i) for i in desired_shape): - desired_shape = desired.compute().shape + # 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 @@ -100,11 +102,11 @@ def xp_assert_equal(actual: Array, desired: Array, err_msg: str = "") -> None: import numpy as np # pylint: disable=import-outside-toplevel if is_pydata_sparse_namespace(xp): - actual = actual.todense() - desired = desired.todense() + 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) + np.testing.assert_array_equal(actual, desired, err_msg=err_msg) # type: ignore[arg-type] # pyright: ignore[reportArgumentType] def xp_assert_close( @@ -164,13 +166,17 @@ def xp_assert_close( import numpy as np # pylint: disable=import-outside-toplevel if is_pydata_sparse_namespace(xp): - actual = actual.to_dense() - desired = desired.to_dense() + actual = actual.to_dense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + desired = desired.to_dense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] # JAX uses `np.testing` assert isinstance(rtol, float) - np.testing.assert_allclose( - actual, desired, rtol=rtol, atol=atol, err_msg=err_msg + np.testing.assert_allclose( # pyright: ignore[reportCallIssue] + actual, # pyright: ignore[reportArgumentType] + desired, # pyright: ignore[reportArgumentType] + rtol=rtol, + atol=atol, + err_msg=err_msg, # type: ignore[call-overload] ) diff --git a/src/array_api_extra/_lib/_utils/_compat.pyi b/src/array_api_extra/_lib/_utils/_compat.pyi index 66134fae..f40d7556 100644 --- a/src/array_api_extra/_lib/_utils/_compat.pyi +++ b/src/array_api_extra/_lib/_utils/_compat.pyi @@ -29,12 +29,12 @@ 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, /) -> bool: ... -def is_dask_array(x: object, /) -> bool: ... -def is_jax_array(x: object, /) -> bool: ... -def is_numpy_array(x: object, /) -> bool: ... -def is_pydata_sparse_array(x: object, /) -> bool: ... -def is_torch_array(x: object, /) -> bool: ... -def is_lazy_array(x: object, /) -> bool: ... -def is_writeable_array(x: object, /) -> bool: ... +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 size(x: Array, /) -> int | None: ... diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index 594b6e12..b0e39d06 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -3,9 +3,10 @@ # https://github.com/scikit-learn/scikit-learn/pull/27910#issuecomment-2568023972 from __future__ import annotations -from collections.abc import Generator +import math +from collections.abc import Generator, Iterable from types import ModuleType -from typing import TYPE_CHECKING +from typing import TYPE_CHECKING, cast from . import _compat from ._compat import array_namespace, is_array_api_obj, is_numpy_array @@ -16,7 +17,7 @@ from typing_extensions import TypeIs -__all__ = ["asarrays", "in1d", "is_python_scalar", "mean"] +__all__ = ["asarrays", "eager_shape", "in1d", "is_python_scalar", "mean"] def in1d( @@ -41,14 +42,17 @@ def in1d( if xp is None: xp = array_namespace(x1, x2) + x1_shape = eager_shape(x1) + x2_shape = eager_shape(x2) + # This code is run to make the code significantly faster - if x2.shape[0] < 10 * x1.shape[0] ** 0.145: + if x2_shape[0] < 10 * x1_shape[0] ** 0.145 and isinstance(x2, Iterable): if invert: - mask = xp.ones(x1.shape[0], dtype=xp.bool, device=_compat.device(x1)) + mask = xp.ones(x1_shape[0], dtype=xp.bool, device=_compat.device(x1)) for a in x2: mask &= x1 != a else: - mask = xp.zeros(x1.shape[0], dtype=xp.bool, device=_compat.device(x1)) + mask = xp.zeros(x1_shape[0], dtype=xp.bool, device=_compat.device(x1)) for a in x2: mask |= x1 == a return mask @@ -146,7 +150,8 @@ def asarrays( a_scalar = is_python_scalar(a) b_scalar = is_python_scalar(b) if not a_scalar and not b_scalar: - return a, b # This includes misc. malformed input e.g. str + # This includes misc. malformed input e.g. str + return a, b # type: ignore[return-value] swap = False if a_scalar: @@ -165,7 +170,7 @@ def asarrays( float: ("real floating", "complex floating"), complex: "complex floating", } - kind = same_dtype[type(b)] # type: ignore[index] + kind = same_dtype[type(cast(complex, b))] # type: ignore[index] if xp.isdtype(a.dtype, kind): xb = xp.asarray(b, dtype=a.dtype) else: @@ -203,3 +208,25 @@ def ndindex(*x: int) -> Generator[tuple[int, ...]]: for i in ndindex(*x[:-1]): for j in range(x[-1]): yield *i, j + + +def eager_shape(x: Array, /) -> tuple[int, ...]: + """ + Return shape of an array. Raise if shape is not fully defined. + + Parameters + ---------- + x : Array + Input array. + + Returns + ------- + tuple[int, ...] + Shape of the array. + """ + shape = x.shape + # Dask arrays uses non-standard NaN instead of None + if any(s is None or math.isnan(s) for s in shape): + msg = "Unsupported lazy shape" + raise TypeError(msg) + return cast(tuple[int, ...], shape) diff --git a/src/array_api_extra/_lib/_utils/_typing.py b/src/array_api_extra/_lib/_utils/_typing.py index 95f29f79..d32a3a07 100644 --- a/src/array_api_extra/_lib/_utils/_typing.py +++ b/src/array_api_extra/_lib/_utils/_typing.py @@ -1,11 +1,10 @@ -"""Static typing helpers.""" +# numpydoc ignore=GL08 +# pylint: disable=missing-module-docstring -from typing import Any +Array = object +DType = object +Device = object +GetIndex = object +SetIndex = object -# To be changed to a Protocol later (see data-apis/array-api#589) -Array = Any # type: ignore[no-any-explicit] -Device = Any # type: ignore[no-any-explicit] -DType = Any # type: ignore[no-any-explicit] -Index = Any # type: ignore[no-any-explicit] - -__all__ = ["Array", "DType", "Device", "Index"] +__all__ = ["Array", "DType", "Device", "GetIndex", "SetIndex"] diff --git a/src/array_api_extra/_lib/_utils/_typing.pyi b/src/array_api_extra/_lib/_utils/_typing.pyi new file mode 100644 index 00000000..9ef06162 --- /dev/null +++ b/src/array_api_extra/_lib/_utils/_typing.pyi @@ -0,0 +1,105 @@ +"""Static typing helpers.""" + +from __future__ import annotations + +from types import EllipsisType +from typing import Protocol, TypeAlias + +# TODO import from typing (requires Python >=3.12) +from typing_extensions import override + +# TODO: use array-api-typing once it is available + +class Array(Protocol): # pylint: disable=missing-class-docstring + # Unary operations + def __abs__(self) -> Array: ... + def __pos__(self) -> Array: ... + def __neg__(self) -> Array: ... + def __invert__(self) -> Array: ... + # Binary operations + def __add__(self, other: Array | complex, /) -> Array: ... + def __sub__(self, other: Array | complex, /) -> Array: ... + def __mul__(self, other: Array | complex, /) -> Array: ... + def __truediv__(self, other: Array | complex, /) -> Array: ... + def __floordiv__(self, other: Array | complex, /) -> Array: ... + def __mod__(self, other: Array | complex, /) -> Array: ... + def __pow__(self, other: Array | complex, /) -> Array: ... + def __matmul__(self, other: Array, /) -> Array: ... + def __and__(self, other: Array | int, /) -> Array: ... + def __or__(self, other: Array | int, /) -> Array: ... + def __xor__(self, other: Array | int, /) -> Array: ... + def __lshift__(self, other: Array | int, /) -> Array: ... + def __rshift__(self, other: Array | int, /) -> Array: ... + def __lt__(self, other: Array | complex, /) -> Array: ... + def __le__(self, other: Array | complex, /) -> Array: ... + def __gt__(self, other: Array | complex, /) -> Array: ... + def __ge__(self, other: Array | complex, /) -> Array: ... + @override + def __eq__(self, other: Array | complex, /) -> Array: ... # type: ignore[override] # pyright: ignore[reportIncompatibleMethodOverride] + @override + def __ne__(self, other: Array | complex, /) -> Array: ... # type: ignore[override] # pyright: ignore[reportIncompatibleMethodOverride] + # Reflected operations + def __radd__(self, other: Array | complex, /) -> Array: ... + def __rsub__(self, other: Array | complex, /) -> Array: ... + def __rmul__(self, other: Array | complex, /) -> Array: ... + def __rtruediv__(self, other: Array | complex, /) -> Array: ... + def __rfloordiv__(self, other: Array | complex, /) -> Array: ... + def __rmod__(self, other: Array | complex, /) -> Array: ... + def __rpow__(self, other: Array | complex, /) -> Array: ... + def __rmatmul__(self, other: Array, /) -> Array: ... + def __rand__(self, other: Array | int, /) -> Array: ... + def __ror__(self, other: Array | int, /) -> Array: ... + def __rxor__(self, other: Array | int, /) -> Array: ... + def __rlshift__(self, other: Array | int, /) -> Array: ... + def __rrshift__(self, other: Array | int, /) -> Array: ... + # Attributes + @property + def dtype(self) -> DType: ... + @property + def device(self) -> Device: ... + @property + def mT(self) -> Array: ... # pylint: disable=invalid-name + @property + def ndim(self) -> int: ... + @property + def shape(self) -> tuple[int | None, ...]: ... + @property + def size(self) -> int | None: ... + @property + def T(self) -> Array: ... # pylint: disable=invalid-name + # Collection operations (note: an Array does not have to be Sized or Iterable) + def __getitem__(self, key: GetIndex, /) -> Array: ... + def __setitem__(self, key: SetIndex, value: Array | complex, /) -> None: ... + # Materialization methods (may raise on lazy arrays) + def __bool__(self) -> bool: ... + def __complex__(self) -> complex: ... + def __float__(self) -> float: ... + def __index__(self) -> int: ... + def __int__(self) -> int: ... + + # Misc methods (frequently not implemented in Arrays wrapped by array-api-compat) + # def __array_namespace__(*, api_version: str | None) -> ModuleType: ... + # def __dlpack__( + # *, + # stream: int | Any | None = None, + # max_version: tuple[int, int] | None = None, + # dl_device: tuple[int, int] | None = None, # tuple[Enum, int] + # copy: bool | None = None, + # ) -> Any: ... + # def __dlpack_device__() -> tuple[int, int]: ... # tuple[Enum, int] + # def to_device(device: Device, /, *, stream: int | Any | None = None) -> Array: ... + +class DType(Protocol): # pylint: disable=missing-class-docstring + pass + +class Device(Protocol): # pylint: disable=missing-class-docstring + pass + +SetIndex: TypeAlias = ( # type: ignore[no-any-explicit] + int | slice | EllipsisType | Array | tuple[int | slice | EllipsisType | Array, ...] +) +GetIndex: TypeAlias = ( # type: ignore[no-any-explicit] + SetIndex | None | tuple[int | slice | EllipsisType | None | Array, ...] +) + +__all__ = ["Array", "DType", "Device", "GetIndex", "SetIndex"] diff --git a/src/array_api_extra/testing.py b/src/array_api_extra/testing.py index a0f97a81..b3782090 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -328,6 +328,6 @@ 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[no-any-return,attr-defined,no-untyped-call,func-returns-value,index] # pyright: ignore[reportPrivateImportUsage] + return dask.persist(out, scheduler="threads")[0] # type: ignore[attr-defined,no-untyped-call,func-returns-value,index] # pyright: ignore[reportPrivateImportUsage] return wrapper diff --git a/tests/conftest.py b/tests/conftest.py index 5ba6dca6..6cb4e433 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -19,7 +19,7 @@ T = TypeVar("T") P = ParamSpec("P") -np_compat = array_namespace(np.empty(0)) +np_compat = array_namespace(np.empty(0)) # type: ignore[arg-type] # pyright: ignore[reportArgumentType] @pytest.fixture(params=tuple(Backend)) diff --git a/tests/test_at.py b/tests/test_at.py index e13a691a..9484a481 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -13,7 +13,7 @@ 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, Index +from array_api_extra._lib._utils._typing import Array, SetIndex from array_api_extra.testing import lazy_xp_function pytestmark = [ @@ -25,7 +25,7 @@ def at_op( x: Array, - idx: Index, + idx: SetIndex, op: _AtOp, y: Array | object, copy: bool | None = None, @@ -46,7 +46,7 @@ def at_op( def _at_op( x: Array, - idx: Index | None, + idx: SetIndex | None, idx_pickle: bytes | None, op: _AtOp, y: Array | object, @@ -56,7 +56,7 @@ def _at_op( """jitted helper of at_op""" if idx_pickle: idx = pickle.loads(idx_pickle) - meth = cast(Callable[..., Array], getattr(at(x, idx), op.value)) # type: ignore[no-any-explicit] + meth = cast(Callable[..., Array], getattr(at(x, cast(SetIndex, idx)), op.value)) # type: ignore[no-any-explicit] return meth(y, copy=copy, xp=xp) @@ -183,34 +183,35 @@ def test_copy_default(xp: ModuleType, library: Backend, op: _AtOp): def test_copy_invalid(): a = np.asarray([1, 2, 3]) with pytest.raises(ValueError, match="copy"): - at(a, 0).set(4, copy="invalid") # type: ignore[arg-type] # pyright: ignore[reportArgumentType] + _ = at(a, 0).set(4, copy="invalid") # type: ignore[arg-type] # pyright: ignore[reportArgumentType] def test_xp(): - a = 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) - at(a, 0).multiply(4, xp=np) - at(a, 0).divide(4, xp=np) - at(a, 0).power(4, xp=np) - at(a, 0).min(4, xp=np) - at(a, 0).max(4, xp=np) + a = cast(Array, np.asarray([1, 2, 3])) # type: ignore[bad-cast] # pyright: ignore[reportInvalidCast] + _ = at(a, 0).set(4, xp=np) + _ = at(a, 0).add(4, xp=np) + _ = at(a, 0).subtract(4, xp=np) + _ = at(a, 0).multiply(4, xp=np) + _ = at(a, 0).divide(4, xp=np) + _ = at(a, 0).power(4, xp=np) + _ = at(a, 0).min(4, xp=np) + _ = at(a, 0).max(4, xp=np) def test_alternate_index_syntax(): - a = np.asarray([1, 2, 3]) - xp_assert_equal(at(a, 0).set(4, copy=True), np.asarray([4, 2, 3])) - xp_assert_equal(at(a)[0].set(4, copy=True), np.asarray([4, 2, 3])) + xp = cast(ModuleType, np) # 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])) a_at = at(a) - xp_assert_equal(a_at[0].add(1, copy=True), np.asarray([2, 2, 3])) - xp_assert_equal(a_at[1].add(2, copy=True), np.asarray([1, 4, 3])) + xp_assert_equal(a_at[0].add(1, copy=True), xp.asarray([2, 2, 3])) + xp_assert_equal(a_at[1].add(2, copy=True), xp.asarray([1, 4, 3])) with pytest.raises(ValueError, match="Index"): - at(a).set(4) + _ = at(a).set(4) with pytest.raises(ValueError, match="Index"): - at(a, 0)[0].set(4) + _ = at(a, 0)[0].set(4) @pytest.mark.parametrize("copy", [True, None]) @@ -256,7 +257,7 @@ def test_incompatible_dtype( elif library is 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) + _ = at_op(x, idx, op, 1.1, copy=copy) elif op in (_AtOp.SET, _AtOp.MIN, _AtOp.MAX): # There is no __i__ version of these operations @@ -264,7 +265,7 @@ def test_incompatible_dtype( else: with pytest.raises(Exception, match=r"cast|promote|dtype"): - at_op(x, idx, op, 1.1, copy=copy) + _ = at_op(x, idx, op, 1.1, copy=copy) assert z is None or z.dtype == x.dtype diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 27318281..65d19aaa 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -23,7 +23,7 @@ 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 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 @@ -249,7 +249,7 @@ def test_1d_from_scipy(self, xp: ModuleType, n: int, offset: int): def test_0d_raises(self, xp: ModuleType): with pytest.raises(ValueError, match="1-dimensional"): - create_diagonal(xp.asarray(1)) + _ = create_diagonal(xp.asarray(1)) @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") @pytest.mark.parametrize( @@ -274,7 +274,7 @@ def test_nd(self, xp: ModuleType, shape: tuple[int, ...]): c = create_diagonal(b) zero = xp.zeros((), dtype=xp.uint64) assert c.shape == (*b.shape, b.shape[-1]) - for i in ndindex(*c.shape): + for i in ndindex(*eager_shape(c)): xp_assert_equal(c[i], b[i[:-1]] if i[-2] == i[-1] else zero) @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") @@ -320,26 +320,26 @@ def test_axis_out_of_range(self, xp: ModuleType): s = (2, 3, 4, 5) a = xp.empty(s) with pytest.raises(IndexError, match="out of bounds"): - expand_dims(a, axis=-6) + _ = expand_dims(a, axis=-6) with pytest.raises(IndexError, match="out of bounds"): - expand_dims(a, axis=5) + _ = expand_dims(a, axis=5) a = xp.empty((3, 3, 3)) with pytest.raises(IndexError, match="out of bounds"): - expand_dims(a, axis=(0, -6)) + _ = expand_dims(a, axis=(0, -6)) with pytest.raises(IndexError, match="out of bounds"): - expand_dims(a, axis=(0, 5)) + _ = expand_dims(a, axis=(0, 5)) def test_repeated_axis(self, xp: ModuleType): a = xp.empty((3, 3, 3)) with pytest.raises(ValueError, match="Duplicate dimensions"): - expand_dims(a, axis=(1, 1)) + _ = expand_dims(a, axis=(1, 1)) def test_positive_negative_repeated(self, xp: ModuleType): # https://github.com/data-apis/array-api/issues/760#issuecomment-1989449817 a = xp.empty((2, 3, 4, 5)) with pytest.raises(ValueError, match="Duplicate dimensions"): - expand_dims(a, axis=(3, -3)) + _ = expand_dims(a, axis=(3, -3)) @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") def test_device(self, xp: ModuleType, device: Device): @@ -505,7 +505,7 @@ def test_python_scalar(self, xp: ModuleType): def test_all_python_scalars(self): with pytest.raises(TypeError, match="Unrecognized"): - isclose(0, 0) + _ = isclose(0, 0) def test_xp(self, xp: ModuleType): a = xp.asarray([0.0, 0.0]) @@ -582,7 +582,7 @@ def test_python_scalar(self, xp: ModuleType): def test_all_python_scalars(self): with pytest.raises(TypeError, match="Unrecognized"): - kron(1, 1) + _ = kron(1, 1) def test_device(self, xp: ModuleType, device: Device): x1 = xp.asarray([1, 2, 3], device=device) @@ -634,7 +634,7 @@ def test_ndim(self, xp: ModuleType): def test_mode_not_implemented(self, xp: ModuleType): a = xp.arange(3) with pytest.raises(NotImplementedError, match="Only `'constant'`"): - pad(a, 2, mode="edge") # type: ignore[arg-type] # pyright: ignore[reportArgumentType] + _ = pad(a, 2, mode="edge") # type: ignore[arg-type] # pyright: ignore[reportArgumentType] def test_device(self, xp: ModuleType, device: Device): a = xp.asarray(0.0, device=device) @@ -653,7 +653,7 @@ def test_tuple_width(self, xp: ModuleType): assert padded.shape == (6, 7) with pytest.raises((ValueError, RuntimeError)): - pad(a, [(1, 2, 3)]) # type: ignore[list-item] # pyright: ignore[reportArgumentType] + _ = pad(a, [(1, 2, 3)]) # type: ignore[list-item] # pyright: ignore[reportArgumentType] def test_sequence_of_tuples_width(self, xp: ModuleType): a = xp.reshape(xp.arange(12), (3, 4)) @@ -745,7 +745,7 @@ def test_python_scalar(self, xp: ModuleType, assume_unique: bool): @pytest.mark.parametrize("assume_unique", [True, False]) def test_all_python_scalars(self, assume_unique: bool): with pytest.raises(TypeError, match="Unrecognized"): - setdiff1d(0, 0, assume_unique=assume_unique) + _ = setdiff1d(0, 0, assume_unique=assume_unique) @assume_unique def test_device(self, xp: ModuleType, device: Device, assume_unique: bool): @@ -773,7 +773,7 @@ def test_simple(self, xp: ModuleType): @pytest.mark.parametrize("x", [0, 1 + 3j]) def test_dtype(self, xp: ModuleType, x: int | complex): with pytest.raises(ValueError, match="real floating data type"): - sinc(xp.asarray(x)) + _ = sinc(xp.asarray(x)) def test_3d(self, xp: ModuleType): x = xp.reshape(xp.arange(18, dtype=xp.float64), (3, 3, 2)) diff --git a/tests/test_helpers.py b/tests/test_helpers.py index 1710ff84..9895e2c5 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -1,4 +1,5 @@ from types import ModuleType +from typing import cast import numpy as np import pytest @@ -6,8 +7,8 @@ from array_api_extra._lib import Backend from array_api_extra._lib._testing import xp_assert_equal from array_api_extra._lib._utils._compat import device as get_device -from array_api_extra._lib._utils._helpers import asarrays, in1d, ndindex -from array_api_extra._lib._utils._typing import Device +from array_api_extra._lib._utils._helpers import asarrays, eager_shape, in1d, ndindex +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 @@ -139,12 +140,12 @@ def test_array_vs_array(self, a_type: str, b_type: str, xp: ModuleType): assert xb.dtype == b.dtype @pytest.mark.parametrize("dtype", [np.float64, np.complex128]) - def test_numpy_generics(self, dtype: type): + def test_numpy_generics(self, dtype: DType): """ Test special case of np.float64 and np.complex128, which are subclasses of float and complex. """ - a = dtype(0) + a = cast(Array, dtype(0)) # type: ignore[operator] # pyright: ignore[reportCallIssue] xa, xb = asarrays(a, 0, xp=np) assert xa.dtype == dtype assert xb.dtype == dtype @@ -155,3 +156,20 @@ def test_numpy_generics(self, dtype: type): ) def test_ndindex(shape: tuple[int, ...]): assert tuple(ndindex(*shape)) == tuple(np.ndindex(*shape)) + + +@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="index by sparse array") +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 + # a lazy boolean mask + assert eager_shape(a) == a.shape == (3,) + + b = a[a > 2] + if library is Backend.DASK: + with pytest.raises(TypeError, match="Unsupported lazy shape"): + _ = eager_shape(b) + # FIXME can't test use case for None in the shape until we add support for + # other lazy backends + else: + assert eager_shape(b) == b.shape == (1,) diff --git a/tests/test_testing.py b/tests/test_testing.py index ed21feb2..b5ec7d85 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -1,5 +1,6 @@ from collections.abc import Callable from types import ModuleType +from typing import cast import numpy as np import pytest @@ -151,19 +152,19 @@ def test_lazy_xp_function(xp: ModuleType): with pytest.raises( TypeError, match="Attempted boolean conversion of traced array" ): - non_materializable4(x) # Wrapped + _ = non_materializable4(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_materializable3(x) with pytest.raises( AssertionError, match=r"dask\.compute.* 1 times, but no calls are allowed", ): - non_materializable4(x) + _ = non_materializable4(x) else: xp_assert_equal(non_materializable3(x), xp.asarray([1.0, 2.0])) @@ -227,12 +228,12 @@ def test_lazy_xp_function_cython_ufuncs(xp: ModuleType, library: Backend): # 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(erf(x), xp.asarray([1.0, 1.0])) + xp_assert_equal(cast(Array, erf(x)), xp.asarray([1.0, 1.0])) else: # 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(erf(x), xp.asarray([1.0, 1.0])) + xp_assert_equal(cast(Array, erf(x)), xp.asarray([1.0, 1.0])) def dask_raises(x: Array) -> Array: @@ -243,7 +244,7 @@ def _raises(x: Array) -> Array: msg = "Hello world" raise ValueError(msg) - return x.map_blocks(_raises, dtype=x.dtype, meta=x._meta) + return x.map_blocks(_raises, dtype=x.dtype, meta=x._meta) # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] lazy_xp_function(dask_raises) @@ -261,40 +262,44 @@ def test_lazy_xp_function_eagerly_raises(da: ModuleType): """ x = da.arange(3) with pytest.raises(ValueError, match="Hello world"): - dask_raises(x) + _ = dask_raises(x) -class Wrapped: - def f(x: Array) -> Array: # noqa: N805 # pyright: ignore[reportSelfClsParameterName] - xp = array_namespace(x) - # Crash in jax.jit and trigger compute() on dask - if not xp.all(x): - msg = "Values must be non-zero" - raise ValueError(msg) - return x +wrapped = ModuleType("wrapped") +naked = ModuleType("naked") -class Naked: - f = Wrapped.f # pyright: ignore[reportUnannotatedClassAttribute] +def f(x: Array) -> Array: + xp = array_namespace(x) + # Crash in jax.jit and trigger compute() on dask + if not xp.all(x): + msg = "Values must be non-zero" + raise ValueError(msg) + return x + + +wrapped.f = f # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] +naked.f = f # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] +del f -lazy_xp_function(Wrapped.f) -lazy_xp_modules = [Wrapped] +lazy_xp_function(wrapped.f) +lazy_xp_modules = [wrapped] def test_lazy_xp_modules(xp: ModuleType, library: Backend): x = xp.asarray([1.0, 2.0]) - y = Naked.f(x) + y = naked.f(x) xp_assert_equal(y, x) if library is Backend.JAX: with pytest.raises( TypeError, match="Attempted boolean conversion of traced array" ): - Wrapped.f(x) + wrapped.f(x) elif library is Backend.DASK: with pytest.raises(AssertionError, match=r"dask\.compute"): - Wrapped.f(x) + wrapped.f(x) else: - y = Wrapped.f(x) + y = wrapped.f(x) xp_assert_equal(y, x) From 64378b7a1ba8cbb6eb53baf467fb0cf0e78a39c1 Mon Sep 17 00:00:00 2001 From: crusaderky Date: Tue, 18 Mar 2025 16:54:00 +0000 Subject: [PATCH 051/140] TST: fix failures in `expand_dims` test --- tests/test_funcs.py | 24 ++++++------------------ 1 file changed, 6 insertions(+), 18 deletions(-) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 65d19aaa..66d53b90 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -1,4 +1,3 @@ -import contextlib import math import warnings from types import ModuleType @@ -24,7 +23,7 @@ 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._lib._utils._typing import Device from array_api_extra.testing import lazy_xp_function # some xp backends are untyped @@ -291,22 +290,12 @@ def test_xp(self, xp: ModuleType): class TestExpandDims: @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") - 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conda: https://prefix.dev/conda-forge/noarch/sphinx-8.2.3-pyhd8ed1ab_0.conda sha256: 995f58c662db0197d681fa345522fd9e7ac5f05330d3dff095ab2f102e260ab0 md5: f7af826063ed569bb13f7207d6f949b0 diff --git a/pyproject.toml b/pyproject.toml index 78ab718f..2fc2fb93 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -124,22 +124,21 @@ python = "~=3.10.0" python = "~=3.13.0" # Backends that can run on CPU-only hosts -[tool.pixi.feature.backends.target.linux-64.dependencies] +[tool.pixi.feature.backends.dependencies] pytorch = "*" dask = "*" -sparse = ">=0.15" +numba = "*" # sparse dependency + +[tool.pixi.feature.backends.pypi-dependencies] +sparse = { version = ">= 0.16.0b3" } + +[tool.pixi.feature.backends.target.linux-64.dependencies] jax = "*" [tool.pixi.feature.backends.target.osx-arm64.dependencies] -pytorch = "*" -dask = "*" -sparse = ">=0.15" jax = "*" [tool.pixi.feature.backends.target.win-64.dependencies] -pytorch = "*" -dask = "*" -sparse = ">=0.15" # jax = "*" # unavailable # Backends that require a GPU host and a CUDA driver diff --git a/src/array_api_extra/_delegation.py b/src/array_api_extra/_delegation.py index 0c455ae1..b6e58688 100644 --- a/src/array_api_extra/_delegation.py +++ b/src/array_api_extra/_delegation.py @@ -125,7 +125,7 @@ def pad( pad_width: int | tuple[int, int] | Sequence[tuple[int, int]], mode: Literal["constant"] = "constant", *, - constant_values: bool | int | float | complex = 0, + constant_values: complex = 0, xp: ModuleType | None = None, ) -> Array: """ @@ -168,7 +168,7 @@ def pad( 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): + 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/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 43698c42..9833577a 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -575,7 +575,7 @@ def pad( x: Array, pad_width: int | tuple[int, int] | Sequence[tuple[int, int]], *, - constant_values: bool | int | float | complex = 0, + constant_values: complex = 0, xp: ModuleType, ) -> Array: # numpydoc ignore=PR01,RT01 """See docstring in `array_api_extra._delegation.py`.""" diff --git a/src/array_api_extra/_lib/_testing.py b/src/array_api_extra/_lib/_testing.py index c6be5e97..87de688d 100644 --- a/src/array_api_extra/_lib/_testing.py +++ b/src/array_api_extra/_lib/_testing.py @@ -166,8 +166,8 @@ def xp_assert_close( import numpy as np # pylint: disable=import-outside-toplevel if is_pydata_sparse_namespace(xp): - actual = actual.to_dense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] - desired = desired.to_dense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + actual = actual.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] + desired = desired.todense() # type: ignore[attr-defined] # pyright: ignore[reportAttributeAccessIssue] # JAX uses `np.testing` assert isinstance(rtol, float) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 66d53b90..4ab8eb97 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -41,7 +41,6 @@ lazy_xp_function(sinc, static_argnames="xp") -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") class TestAtLeastND: def test_0D(self, xp: ModuleType): x = xp.asarray(1.0) @@ -68,7 +67,7 @@ def test_1D(self, xp: ModuleType): xp_assert_equal(y, xp.asarray([[0, 1]])) y = atleast_nd(x, ndim=5) - xp_assert_equal(y, xp.reshape(xp.arange(2), (1, 1, 1, 1, 2))) + xp_assert_equal(y, xp.asarray([[[[[0, 1]]]]])) def test_2D(self, xp: ModuleType): x = xp.asarray([[3.0]]) @@ -217,8 +216,10 @@ def test_xp(self, xp: ModuleType): ) +@pytest.mark.skip_xp_backend( + Backend.SPARSE, reason="read-only backend without .at support" +) class TestCreateDiagonal: - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") def test_1d_from_numpy(self, xp: ModuleType): # from np.diag tests vals = 100 * xp.arange(5, dtype=xp.float64) @@ -234,7 +235,6 @@ def test_1d_from_numpy(self, xp: ModuleType): xp_assert_equal(create_diagonal(vals, offset=2), b) xp_assert_equal(create_diagonal(vals, offset=-2), c) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") @pytest.mark.parametrize("n", range(1, 10)) @pytest.mark.parametrize("offset", range(1, 10)) def test_1d_from_scipy(self, xp: ModuleType, n: int, offset: int): @@ -250,7 +250,6 @@ def test_0d_raises(self, xp: ModuleType): with pytest.raises(ValueError, match="1-dimensional"): _ = create_diagonal(xp.asarray(1)) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") @pytest.mark.parametrize( "shape", [ @@ -276,12 +275,10 @@ def test_nd(self, xp: ModuleType, shape: tuple[int, ...]): for i in ndindex(*eager_shape(c)): xp_assert_equal(c[i], b[i[:-1]] if i[-2] == i[-1] else zero) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") def test_device(self, xp: ModuleType, device: Device): x = xp.asarray([1, 2, 3], device=device) assert get_device(create_diagonal(x)) == device - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in zeros()") def test_xp(self, xp: ModuleType): x = xp.asarray([1, 2]) y = create_diagonal(x, xp=xp) @@ -289,7 +286,6 @@ def test_xp(self, xp: ModuleType): class TestExpandDims: - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") 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)) @@ -297,7 +293,6 @@ def test_single_axis(self, xp: ModuleType): b = expand_dims(a, axis=axis) xp_assert_equal(b, xp.expand_dims(a, axis=axis)) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") def test_axis_tuple(self, xp: ModuleType): a = xp.empty((3, 3, 3)) assert expand_dims(a, axis=(0, 1, 2)).shape == (1, 1, 1, 3, 3, 3) @@ -329,12 +324,10 @@ def test_positive_negative_repeated(self, xp: ModuleType): with pytest.raises(ValueError, match="Duplicate dimensions"): _ = expand_dims(a, axis=(3, -3)) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") def test_device(self, xp: ModuleType, device: Device): x = xp.asarray([1, 2, 3], device=device) assert get_device(expand_dims(x, axis=0)) == device - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") def test_xp(self, xp: ModuleType): x = xp.asarray([1, 2, 3]) y = expand_dims(x, axis=(0, 1, 2), xp=xp) @@ -501,7 +494,6 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(isclose(a, b, xp=xp), xp.asarray([True, False])) -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no expand_dims") class TestKron: def test_basic(self, xp: ModuleType): # Using 0-dimensional array @@ -560,6 +552,7 @@ 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 @@ -602,25 +595,27 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(nunique(a, xp=xp), xp.asarray(3)) -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no arange, no device") class TestPad: def test_simple(self, xp: ModuleType): - a = xp.arange(1, 4) + a = xp.asarray([1, 2, 3]) padded = pad(a, 2) xp_assert_equal(padded, xp.asarray([0, 0, 1, 2, 3, 0, 0])) + @pytest.mark.xfail_xp_backend( + Backend.SPARSE, reason="constant_values can only be equal to fill value" + ) def test_fill_value(self, xp: ModuleType): - a = xp.arange(1, 4) + a = xp.asarray([1, 2, 3]) padded = pad(a, 2, constant_values=42) xp_assert_equal(padded, xp.asarray([42, 42, 1, 2, 3, 42, 42])) def test_ndim(self, xp: ModuleType): - a = xp.reshape(xp.arange(2 * 3 * 4), (2, 3, 4)) + a = xp.asarray(np.reshape(np.arange(2 * 3 * 4), (2, 3, 4))) padded = pad(a, 2) assert padded.shape == (6, 7, 8) def test_mode_not_implemented(self, xp: ModuleType): - a = xp.arange(3) + a = xp.asarray([1, 2, 3]) with pytest.raises(NotImplementedError, match="Only `'constant'`"): _ = pad(a, 2, mode="edge") # type: ignore[arg-type] # pyright: ignore[reportArgumentType] @@ -633,7 +628,7 @@ def test_xp(self, xp: ModuleType): xp_assert_equal(padded, xp.asarray(0)) def test_tuple_width(self, xp: ModuleType): - a = xp.reshape(xp.arange(12), (3, 4)) + a = xp.asarray(np.reshape(np.arange(12), (3, 4))) padded = pad(a, (1, 0)) assert padded.shape == (4, 5) @@ -644,7 +639,7 @@ def test_tuple_width(self, xp: ModuleType): _ = pad(a, [(1, 2, 3)]) # type: ignore[list-item] # pyright: ignore[reportArgumentType] def test_sequence_of_tuples_width(self, xp: ModuleType): - a = xp.reshape(xp.arange(12), (3, 4)) + a = xp.asarray(np.reshape(np.arange(12), (3, 4))) padded = pad(a, ((1, 0), (0, 2))) assert padded.shape == (4, 6) @@ -666,7 +661,7 @@ def test_sequence_of_tuples_width(self, xp: ModuleType): ) -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in asarray()") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no argsort") 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 9895e2c5..606f837a 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -17,10 +17,8 @@ lazy_xp_function(in1d, jax_jit=False, static_argnames=("assume_unique", "invert", "xp")) +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no unique_inverse") class TestIn1D: - @pytest.mark.xfail_xp_backend( - Backend.SPARSE, reason="no unique_inverse, no device kwarg in asarray()" - ) # cover both code paths @pytest.mark.parametrize( "n", @@ -42,19 +40,15 @@ def test_no_invert_assume_unique(self, xp: ModuleType, n: int): actual = in1d(x1, x2) xp_assert_equal(actual, expected) - @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no device kwarg in asarray") def test_device(self, xp: ModuleType, device: Device): x1 = xp.asarray([3, 8, 20], device=device) x2 = xp.asarray([2, 3, 4], device=device) assert get_device(in1d(x1, x2)) == device @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="xp=xp") - @pytest.mark.xfail_xp_backend( - Backend.SPARSE, reason="no arange, no device kwarg in asarray" - ) def test_xp(self, xp: ModuleType): x1 = xp.asarray([1, 6]) - x2 = xp.arange(5) + x2 = xp.asarray([0, 1, 2, 3, 4]) expected = xp.asarray([True, False]) actual = in1d(x1, x2, xp=xp) xp_assert_equal(actual, expected) @@ -90,7 +84,7 @@ class TestAsArrays: ], ) def test_array_vs_scalar( - self, dtype: str, b: int | float | complex, defined: bool, xp: ModuleType + self, dtype: str, b: complex, defined: bool, xp: ModuleType ): a = xp.asarray(1, dtype=getattr(xp, dtype)) @@ -158,7 +152,7 @@ def test_ndindex(shape: tuple[int, ...]): assert tuple(ndindex(*shape)) == tuple(np.ndindex(*shape)) -@pytest.mark.skip_xp_backend(Backend.SPARSE, reason="index by sparse array") +@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="index by sparse array") 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 diff --git a/tests/test_testing.py b/tests/test_testing.py index b5ec7d85..1968eded 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -72,7 +72,7 @@ def test_assert_close_tolerance(xp: ModuleType): @param_assert_equal_close -@pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no bool indexing") +@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[no-any-explicit] """On dask and other lazy backends, test that a shape with NaN's or None's can be compared to a real shape. From f74d71af4489c615b42c2f8c2c636a58b8b61c6a Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Tue, 18 Mar 2025 18:39:32 +0000 Subject: [PATCH 053/140] ENH: `apply_where` (migrate `lazywhere` from scipy) (#141) * ENH: apply_where (migrate _lazywhere from scipy) * Code review * merge main * tweak sparse skip --- docs/api-reference.md | 1 + pixi.lock | 107 ++++++++- pyproject.toml | 6 + src/array_api_extra/__init__.py | 2 + src/array_api_extra/_lib/_at.py | 22 +- src/array_api_extra/_lib/_funcs.py | 169 +++++++++++++- src/array_api_extra/_lib/_utils/_helpers.py | 46 +++- tests/test_at.py | 13 +- tests/test_funcs.py | 230 +++++++++++++++++++- tests/test_helpers.py | 29 ++- 10 files changed, 590 insertions(+), 35 deletions(-) diff --git a/docs/api-reference.md b/docs/api-reference.md index 2483a55d..ee33a819 100644 --- a/docs/api-reference.md +++ b/docs/api-reference.md @@ -6,6 +6,7 @@ :nosignatures: :toctree: generated + apply_where at atleast_nd broadcast_shapes diff --git a/pixi.lock b/pixi.lock index 331d7b1c..f07416e6 100644 --- a/pixi.lock +++ b/pixi.lock @@ -82,6 +82,7 @@ environments: - 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conda: https://prefix.dev/conda-forge/win-64/python-3.13.2-h261c0b1_101_cp313.conda - conda: https://prefix.dev/conda-forge/win-64/python_abi-3.13-5_cp313.conda + - conda: https://prefix.dev/conda-forge/noarch/setuptools-75.8.2-pyhff2d567_0.conda + - conda: https://prefix.dev/conda-forge/noarch/sortedcontainers-2.4.0-pyhd8ed1ab_1.conda - conda: https://prefix.dev/conda-forge/win-64/tbb-2021.13.0-h62715c5_1.conda - conda: https://prefix.dev/conda-forge/win-64/tk-8.6.13-h5226925_1.conda - conda: https://prefix.dev/conda-forge/noarch/toml-0.10.2-pyhd8ed1ab_1.conda @@ -3784,7 +3862,7 @@ packages: - pypi: . name: array-api-extra version: 0.7.0.dev0 - sha256: 18b0cdd4c0d1503890ea125b0cb9ec618e6d9d6eb255a6bbce7da7351e784af2 + sha256: 29cc92fbbfb1a7505af089b6c0e62ea8a39673a0266a9413dcf5d5942e9304be requires_dist: - array-api-compat>=1.11,<2 requires_python: '>=3.10' @@ -3873,6 +3951,17 @@ packages: purls: [] size: 71042 timestamp: 1660065501192 +- conda: https://prefix.dev/conda-forge/noarch/attrs-25.1.0-pyh71513ae_0.conda + sha256: 1f267886522dfb9ae4e5ebbc3135b5eb13cff27bdbfe8d881a4d893459166ab4 + md5: 2cc3f588512f04f3a0c64b4e9bedc02d + depends: + - python >=3.9 + license: MIT + license_family: MIT + purls: + - pkg:pypi/attrs?source=compressed-mapping + size: 56370 + timestamp: 1737819298139 - conda: https://prefix.dev/conda-forge/linux-64/aws-c-auth-0.8.1-h205f482_0.conda sha256: ebe5e33249f37f6bb481de99581ebdc92dbfcf1b6915609bcf3c9e78661d6352 md5: 9c500858e88df50af3cc883d194de78a @@ -6393,6 +6482,22 @@ packages: - pkg:pypi/hyperframe?source=hash-mapping size: 17397 timestamp: 1737618427549 +- conda: https://prefix.dev/conda-forge/noarch/hypothesis-6.127.2-pyha770c72_0.conda + sha256: 866f4ff72d7b2f29ba1dc336dc368f7338292e2cf1e410efbe5031cb5a0a1d9e + md5: 31e22fccc611d01cce671c1ae6fbfce7 + depends: + - attrs >=22.2.0 + - click >=7.0 + - exceptiongroup >=1.0.0 + - python >=3.9 + - setuptools + - sortedcontainers >=2.1.0,<3.0.0 + license: MPL-2.0 + license_family: MOZILLA + purls: + - pkg:pypi/hypothesis?source=hash-mapping + size: 344084 + timestamp: 1740463712685 - 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 2fc2fb93..d6836064 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,6 +64,7 @@ numpydoc = ">=1.8.0,<2" array-api-strict = "*" numpy = "*" pytest = "*" +hypothesis = "*" dask-core = "*" # 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 @@ -79,6 +80,7 @@ lint = { depends-on = ["pre-commit", "pylint", "mypy", "pyright"] } [tool.pixi.feature.tests.dependencies] pytest = ">=6" pytest-cov = ">=3" +hypothesis = "*" array-api-strict = "*" numpy = "*" @@ -231,6 +233,10 @@ reportMissingTypeStubs = false reportUnreachable = false # ruff handles this reportUnusedParameter = false +# cyclic imports inside function bodies +reportImportCycles = false +# PyRight can't trace types in lambdas +reportUnknownLambdaType = false executionEnvironments = [ { root = "tests", reportPrivateUsage = false }, diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 70310ea9..634835a8 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -3,6 +3,7 @@ from ._delegation import isclose, pad from ._lib._at import at from ._lib._funcs import ( + apply_where, atleast_nd, broadcast_shapes, cov, @@ -19,6 +20,7 @@ # pylint: disable=duplicate-code __all__ = [ "__version__", + "apply_where", "at", "atleast_nd", "broadcast_shapes", diff --git a/src/array_api_extra/_lib/_at.py b/src/array_api_extra/_lib/_at.py index 11c8ff6c..25d764e3 100644 --- a/src/array_api_extra/_lib/_at.py +++ b/src/array_api_extra/_lib/_at.py @@ -15,6 +15,7 @@ is_jax_array, is_writeable_array, ) +from ._utils._helpers import meta_namespace from ._utils._typing import Array, SetIndex @@ -263,6 +264,8 @@ def _op( Array Updated `x`. """ + from ._funcs import apply_where # pylint: disable=cyclic-import + x, idx = self._x, self._idx xp = array_namespace(x, y) if xp is None else xp @@ -295,8 +298,10 @@ def _op( y_xp = xp.asarray(y, dtype=x.dtype) if y_xp.ndim == 0: if out_of_place_op: # add(), subtract(), ... - # FIXME: suppress inf warnings on dask with lazywhere - out = xp.where(idx, out_of_place_op(x, y_xp), x) + # suppress inf warnings on Dask + out = apply_where( + idx, (x, y_xp), out_of_place_op, fill_value=x, xp=xp + ) # Undo int->float promotion on JAX after _AtOp.DIVIDE out = xp.astype(out, x.dtype, copy=False) else: # set() @@ -420,9 +425,16 @@ def min( xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """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 + # 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. xp = array_namespace(self._x) if xp is None else xp + mxp = meta_namespace(self._x, xp=xp) y = xp.asarray(y) - return self._op(_AtOp.MIN, xp.minimum, xp.minimum, y, copy=copy, xp=xp) + return self._op(_AtOp.MIN, mxp.minimum, mxp.minimum, y, copy=copy, xp=xp) def max( self, @@ -432,6 +444,8 @@ def max( xp: ModuleType | None = None, ) -> Array: # numpydoc ignore=PR01,RT01 """Apply ``x[idx] = maximum(x[idx], y)`` and return the updated array.""" + # See note on min() xp = array_namespace(self._x) if xp is None else xp + mxp = meta_namespace(self._x, xp=xp) y = xp.asarray(y) - return self._op(_AtOp.MAX, xp.maximum, xp.maximum, y, copy=copy, xp=xp) + return self._op(_AtOp.MAX, mxp.maximum, mxp.maximum, y, copy=copy, xp=xp) diff --git a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 9833577a..83f550af 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -5,17 +5,23 @@ import math import warnings -from collections.abc import Sequence -from types import ModuleType -from typing import cast +from collections.abc import Callable, Sequence +from types import ModuleType, NoneType +from typing import cast, overload from ._at import at from ._utils import _compat, _helpers -from ._utils._compat import array_namespace, is_jax_array -from ._utils._helpers import asarrays, eager_shape, ndindex +from ._utils._compat import ( + array_namespace, + is_dask_namespace, + is_jax_array, + is_jax_namespace, +) +from ._utils._helpers import asarrays, eager_shape, meta_namespace, ndindex from ._utils._typing import Array __all__ = [ + "apply_where", "atleast_nd", "broadcast_shapes", "cov", @@ -29,6 +35,148 @@ ] +@overload +def apply_where( # type: ignore[no-any-explicit,no-any-decorated] # numpydoc ignore=GL08 + cond: Array, + args: Array | tuple[Array, ...], + f1: Callable[..., Array], + f2: Callable[..., Array], + /, + *, + xp: ModuleType | None = None, +) -> Array: ... + + +@overload +def apply_where( # type: ignore[no-any-explicit,no-any-decorated] # numpydoc ignore=GL08 + cond: Array, + args: Array | tuple[Array, ...], + f1: Callable[..., Array], + /, + *, + fill_value: Array | complex, + xp: ModuleType | None = None, +) -> Array: ... + + +def apply_where( # type: ignore[no-any-explicit] # numpydoc ignore=PR01,PR02 + cond: Array, + args: Array | tuple[Array, ...], + f1: Callable[..., Array], + f2: Callable[..., Array] | None = None, + /, + *, + fill_value: Array | complex | None = None, + xp: ModuleType | None = None, +) -> Array: + """ + Run one of two elementwise functions depending on a condition. + + Equivalent to ``f1(*args) if cond else fill_value`` performed elementwise + when `fill_value` is defined, otherwise to ``f1(*args) if cond else f2(*args)``. + + Parameters + ---------- + cond : array + The condition, expressed as a boolean array. + args : Array or tuple of Arrays + Argument(s) to `f1` (and `f2`). Must be broadcastable with `cond`. + f1 : callable + Elementwise function of `args`, returning a single array. + Where `cond` is True, output will be ``f1(arg0[cond], arg1[cond], ...)``. + f2 : callable, optional + Elementwise function of `args`, returning a single array. + Where `cond` is False, output will be ``f2(arg0[cond], arg1[cond], ...)``. + Mutually exclusive with `fill_value`. + fill_value : Array or scalar, optional + If provided, value with which to fill output array where `cond` is False. + It does not need to be scalar; it needs however to be broadcastable with + `cond` and `args`. + Mutually exclusive with `f2`. You must provide one or the other. + xp : array_namespace, optional + The standard-compatible namespace for `cond` and `args`. Default: infer. + + Returns + ------- + Array + An array with elements from the output of `f1` where `cond` is True and either + the output of `f2` or `fill_value` where `cond` is False. The returned array has + data type determined by type promotion rules between the output of `f1` and + either `fill_value` or the output of `f2`. + + Notes + ----- + ``xp.where(cond, f1(*args), f2(*args))`` requires explicitly evaluating `f1` even + when `cond` is False, and `f2` when cond is True. This function evaluates each + function only for their matching condition, if the backend allows for it. + + On Dask, `f1` and `f2` are applied to the individual chunks and should use functions + from the namespace of the chunks. + + Examples + -------- + >>> import array_api_strict as xp + >>> import array_api_extra as xpx + >>> a = xp.asarray([5, 4, 3]) + >>> b = xp.asarray([0, 2, 2]) + >>> def f(a, b): + ... return a // b + >>> xpx.apply_where(b != 0, (a, b), f, fill_value=xp.nan) + array([ nan, 2., 1.]) + """ + # Parse and normalize arguments + if (f2 is None) == (fill_value is None): + msg = "Exactly one of `fill_value` or `f2` must be given." + raise TypeError(msg) + args_ = list(args) if isinstance(args, tuple) else [args] + del args + + xp = array_namespace(cond, fill_value, *args_) if xp is None else xp + + if isinstance(fill_value, int | float | complex | NoneType): + cond, *args_ = xp.broadcast_arrays(cond, *args_) + else: + cond, fill_value, *args_ = xp.broadcast_arrays(cond, fill_value, *args_) + + if is_dask_namespace(xp): + meta_xp = meta_namespace(cond, fill_value, *args_, xp=xp) + # map_blocks doesn't descend into tuples of Arrays + return xp.map_blocks(_apply_where, cond, f1, f2, fill_value, *args_, xp=meta_xp) + return _apply_where(cond, f1, f2, fill_value, *args_, xp=xp) + + +def _apply_where( # type: ignore[no-any-explicit] # numpydoc ignore=PR01,RT01 + cond: Array, + f1: Callable[..., Array], + f2: Callable[..., Array] | None, + fill_value: Array | int | float | complex | bool | None, + *args: Array, + xp: ModuleType, +) -> Array: + """Helper of `apply_where`. On Dask, this runs on a single chunk.""" + + if is_jax_namespace(xp): + # 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) + + temp1 = f1(*(arr[cond] for arr in args)) + + if f2 is None: + dtype = xp.result_type(temp1, fill_value) + if isinstance(fill_value, int | float | complex): + out = xp.full_like(cond, dtype=dtype, fill_value=fill_value) + else: + out = xp.astype(fill_value, dtype, copy=True) + else: + ncond = ~cond + temp2 = f2(*(arr[ncond] for arr in args)) + dtype = xp.result_type(temp1, temp2) + out = xp.empty_like(cond, dtype=dtype) + out = at(out, ncond).set(temp2) + + return at(out, cond).set(temp1) + + def atleast_nd(x: Array, /, *, ndim: int, xp: ModuleType | None = None) -> Array: """ Recursively expand the dimension of an array to at least `ndim`. @@ -393,12 +541,15 @@ 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: - # FIXME: use scipy's lazywhere to suppress warnings on inf - out = xp.where( + # 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), - xp.isinf(a) & xp.isinf(b) & (xp.sign(a) == xp.sign(b)), + (a, b), + lambda a, b: mxp.isinf(a) & mxp.isinf(b) & (mxp.sign(a) == mxp.sign(b)), # pyright: ignore[reportUnknownArgumentType] # Note: inf <= inf is True! - xp.abs(a - b) <= (atol + rtol * xp.abs(b)), + lambda a, b: mxp.abs(a - b) <= (atol + rtol * mxp.abs(b)), # pyright: ignore[reportUnknownArgumentType] + xp=xp, ) if equal_nan: out = xp.where(xp.isnan(a) & xp.isnan(b), xp.asarray(True), out) diff --git a/src/array_api_extra/_lib/_utils/_helpers.py b/src/array_api_extra/_lib/_utils/_helpers.py index b0e39d06..7ac97033 100644 --- a/src/array_api_extra/_lib/_utils/_helpers.py +++ b/src/array_api_extra/_lib/_utils/_helpers.py @@ -9,7 +9,12 @@ from typing import TYPE_CHECKING, cast from . import _compat -from ._compat import array_namespace, is_array_api_obj, is_numpy_array +from ._compat import ( + array_namespace, + is_array_api_obj, + is_dask_namespace, + is_numpy_array, +) from ._typing import Array if TYPE_CHECKING: # pragma: no cover @@ -17,7 +22,14 @@ from typing_extensions import TypeIs -__all__ = ["asarrays", "eager_shape", "in1d", "is_python_scalar", "mean"] +__all__ = [ + "asarrays", + "eager_shape", + "in1d", + "is_python_scalar", + "mean", + "meta_namespace", +] def in1d( @@ -230,3 +242,33 @@ def eager_shape(x: Array, /) -> tuple[int, ...]: msg = "Unsupported lazy shape" raise TypeError(msg) return cast(tuple[int, ...], shape) + + +def meta_namespace( + *arrays: Array | int | float | complex | bool | None, + xp: ModuleType | None = None, +) -> ModuleType: + """ + Get the namespace of Dask chunks. + + On all other backends, just return the namespace of the arrays. + + Parameters + ---------- + *arrays : Array | int | float | complex | bool | None + Input arrays. + xp : array_namespace, optional + The standard-compatible namespace for the input arrays. Default: infer. + + Returns + ------- + array_namespace + If xp is Dask, the namespace of the Dask chunks; + otherwise, the namespace of the arrays. + """ + xp = array_namespace(*arrays) if xp is None else xp + if not is_dask_namespace(xp): + return xp + # Quietly skip scalars and None's + metas = [cast(Array | None, getattr(a, "_meta", None)) for a in arrays] + return array_namespace(*metas) diff --git a/tests/test_at.py b/tests/test_at.py index 9484a481..2a4a1947 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -277,18 +277,7 @@ def test_bool_mask_nd(xp: ModuleType): xp_assert_equal(z, xp.asarray([[0, 2, 3], [4, 0, 0]])) -@pytest.mark.parametrize( - "bool_mask", - [ - False, - pytest.param( - True, - marks=pytest.mark.xfail_xp_backend( - Backend.DASK, reason="FIXME need scipy's lazywhere" - ), - ), - ], -) +@pytest.mark.parametrize("bool_mask", [False, True]) def test_no_inf_warnings(xp: ModuleType, bool_mask: bool): x = xp.asarray([math.inf, 1.0, 2.0]) idx = ~xp.isinf(x) if bool_mask else slice(1, None) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index 4ab8eb97..d269b2ca 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -1,11 +1,17 @@ import math import warnings from types import ModuleType +from typing import Any, cast +import hypothesis +import hypothesis.extra.numpy as npst import numpy as np import pytest +from hypothesis import given +from hypothesis import strategies as st from array_api_extra import ( + apply_where, at, atleast_nd, broadcast_shapes, @@ -22,13 +28,14 @@ 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 eager_shape, ndindex -from array_api_extra._lib._utils._typing import Device +from array_api_extra._lib._utils._helpers import asarrays, eager_shape, ndindex +from array_api_extra._lib._utils._typing import Array, Device from array_api_extra.testing import lazy_xp_function # 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")) @@ -41,6 +48,221 @@ lazy_xp_function(sinc, static_argnames="xp") +@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: + return x + y + + @staticmethod + def f2(x: Array, y: Array | int = 10) -> Array: + return x - y + + def test_f1_f2(self, xp: ModuleType): + x = xp.asarray([1, 2, 3, 4]) + cond = x % 2 == 0 + actual = apply_where(cond, x, self.f1, self.f2) + expect = xp.where(cond, self.f1(x), self.f2(x)) + xp_assert_equal(actual, expect) + + def test_fill_value(self, xp: ModuleType): + x = xp.asarray([1, 2, 3, 4]) + cond = x % 2 == 0 + actual = apply_where(x % 2 == 0, x, self.f1, fill_value=0) + expect = xp.where(cond, self.f1(x), xp.asarray(0)) + xp_assert_equal(actual, expect) + + actual = apply_where(x % 2 == 0, x, self.f1, fill_value=xp.asarray(0)) + xp_assert_equal(actual, expect) + + def test_args_tuple(self, xp: ModuleType): + x = xp.asarray([1, 2, 3, 4]) + y = xp.asarray([10, 20, 30, 40]) + cond = x % 2 == 0 + actual = apply_where(cond, (x, y), self.f1, self.f2) + expect = xp.where(cond, self.f1(x, y), self.f2(x, y)) + xp_assert_equal(actual, expect) + + def test_broadcast(self, xp: ModuleType): + x = xp.asarray([1, 2]) + y = xp.asarray([[10], [20], [30]]) + cond = xp.broadcast_to(xp.asarray(True), (4, 1, 1)) + + actual = apply_where(cond, (x, y), self.f1, self.f2) + expect = xp.where(cond, self.f1(x, y), self.f2(x, y)) + xp_assert_equal(actual, expect) + + actual = apply_where( + cond, + (x, y), + lambda x, _: x, # pyright: ignore[reportUnknownArgumentType] + lambda _, y: y, # pyright: ignore[reportUnknownArgumentType] + ) + expect = xp.where(cond, x, y) + xp_assert_equal(actual, expect) + + # Shaped fill_value + actual = apply_where(cond, x, self.f1, fill_value=y) + expect = xp.where(cond, self.f1(x), y) + xp_assert_equal(actual, expect) + + def test_dtype_propagation(self, xp: ModuleType, library: Backend): + x = xp.asarray([1, 2], dtype=xp.int8) + y = xp.asarray([3, 4], dtype=xp.int16) + cond = x % 2 == 0 + + mxp = np if library is Backend.DASK else xp + actual = apply_where( + cond, + (x, y), + self.f1, + lambda x, y: mxp.astype(x - y, xp.int64), # pyright: ignore[reportArgumentType,reportUnknownArgumentType] + ) + assert actual.dtype == xp.int64 + + actual = apply_where(cond, y, self.f1, fill_value=5) + assert actual.dtype == xp.int16 + + @pytest.mark.parametrize("fill_value_raw", [3, [3, 4]]) + @pytest.mark.parametrize( + ("fill_value_dtype", "expect_dtype"), [("int32", "int32"), ("int8", "int16")] + ) + def test_dtype_propagation_fill_value( + self, + xp: ModuleType, + fill_value_raw: int | list[int], + fill_value_dtype: str, + expect_dtype: str, + ): + x = xp.asarray([1, 2], dtype=xp.int16) + cond = x % 2 == 0 + fill_value = xp.asarray(fill_value_raw, dtype=getattr(xp, fill_value_dtype)) + + actual = apply_where(cond, x, self.f1, fill_value=fill_value) + assert actual.dtype == getattr(xp, expect_dtype) + + def test_dont_overwrite_fill_value(self, xp: ModuleType): + x = xp.asarray([1, 2]) + fill_value = xp.asarray([100, 200]) + actual = apply_where(x % 2 == 0, x, self.f1, fill_value=fill_value) + xp_assert_equal(actual, xp.asarray([100, 12])) + xp_assert_equal(fill_value, xp.asarray([100, 200])) + + 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]) + # On NumPy, division by zero will trigger warnings + actual = apply_where( + x == 0, + (x, y), + lambda x, y: x / y, # pyright: ignore[reportUnknownArgumentType] + lambda x, y: y / x, # pyright: ignore[reportUnknownArgumentType] + ) + xp_assert_equal(actual, xp.asarray([0.0, 1.5, 0.0])) + + def test_bad_args(self, xp: ModuleType): + x = xp.asarray([1, 2, 3, 4]) + cond = x % 2 == 0 + # Neither f2 nor fill_value + with pytest.raises(TypeError, match="Exactly one of"): + apply_where(cond, x, self.f1) # type: ignore[call-overload] # pyright: ignore[reportCallIssue] + # Both f2 and fill_value + with pytest.raises(TypeError, match="Exactly one of"): + apply_where(cond, x, self.f1, self.f2, fill_value=0) # type: ignore[call-overload] # pyright: ignore[reportCallIssue] + + @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="xp=xp") + def test_xp(self, xp: ModuleType): + x = xp.asarray([1, 2, 3, 4]) + cond = x % 2 == 0 + actual = apply_where(cond, x, self.f1, self.f2, xp=xp) + expect = xp.where(cond, self.f1(x), self.f2(x)) + xp_assert_equal(actual, expect) + + def test_device(self, xp: ModuleType, device: Device): + x = xp.asarray([1, 2, 3, 4], device=device) + y = apply_where(x % 2 == 0, x, self.f1, self.f2) + assert get_device(y) == device + y = apply_where(x % 2 == 0, x, self.f1, fill_value=0) + assert get_device(y) == device + y = apply_where(x % 2 == 0, x, self.f1, fill_value=x) + assert get_device(y) == device + + @pytest.mark.filterwarnings("ignore::RuntimeWarning") # overflows, etc. + @hypothesis.settings( # pyright: ignore[reportArgumentType] + # 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 + deadline=None, + ) + @given( + n_arrays=st.integers(min_value=1, max_value=3), + rng_seed=st.integers(min_value=1000000000, max_value=9999999999), + dtype=st.sampled_from((np.float32, np.float64)), + p=st.floats(min_value=0, max_value=1), + data=st.data(), + ) + def test_hypothesis( # type: ignore[no-any-explicit,no-any-decorated] + self, + n_arrays: int, + rng_seed: int, + dtype: np.dtype[Any], + p: float, + data: st.DataObject, + xp: ModuleType, + library: Backend, + ): + mbs = npst.mutually_broadcastable_shapes(num_shapes=n_arrays + 1, min_side=0) + input_shapes, _ = data.draw(mbs) + cond_shape, *shapes = input_shapes + + # cupy/cupy#8382 + # https://github.com/jax-ml/jax/issues/26658 + elements = {"allow_subnormal": library not in (Backend.CUPY, Backend.JAX)} + + fill_value = xp.asarray( + data.draw(npst.arrays(dtype=dtype, shape=(), elements=elements)) + ) + float_fill_value = float(fill_value) + if library is Backend.CUPY and dtype is np.float32: + # Avoid data-dependent dtype promotion when encountering subnormals + # close to the max float32 value + float_fill_value = float(np.clip(float_fill_value, -1e38, 1e38)) + + arrays = tuple( + xp.asarray( + data.draw(npst.arrays(dtype=dtype, shape=shape, elements=elements)) + ) + for shape in shapes + ) + + def f1(*args: Array) -> Array: + return cast(Array, sum(args)) + + def f2(*args: Array) -> Array: + return cast(Array, sum(args) / 2) + + rng = np.random.default_rng(rng_seed) + cond = xp.asarray(rng.random(size=cond_shape) > p) + + res1 = apply_where(cond, arrays, f1, fill_value=fill_value) + res2 = apply_where(cond, arrays, f1, f2) + res3 = apply_where(cond, arrays, f1, fill_value=float_fill_value) + + 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) + + xp_assert_close(res1, ref1, rtol=2e-16) + xp_assert_equal(res2, ref2) + xp_assert_equal(res3, ref3) + + class TestAtLeastND: def test_0D(self, xp: ModuleType): x = xp.asarray(1.0) @@ -336,8 +558,6 @@ def test_xp(self, xp: ModuleType): @pytest.mark.xfail_xp_backend(Backend.SPARSE, reason="no isdtype") class TestIsClose: - # FIXME use lazywhere to avoid warnings on inf - @pytest.mark.filterwarnings("ignore:invalid value encountered") @pytest.mark.parametrize("swap", [False, True]) @pytest.mark.parametrize( ("a", "b"), @@ -396,8 +616,6 @@ def test_broadcast(self, dtype: str, xp: ModuleType): xp_assert_equal(actual, expect) - # FIXME use lazywhere to avoid warnings on inf - @pytest.mark.filterwarnings("ignore:invalid value encountered") def test_some_inf(self, xp: ModuleType): a = xp.asarray([0.0, 1.0, xp.inf, xp.inf, xp.inf]) b = xp.asarray([1e-9, 1.0, xp.inf, -xp.inf, 2.0]) diff --git a/tests/test_helpers.py b/tests/test_helpers.py index 606f837a..2fc21735 100644 --- a/tests/test_helpers.py +++ b/tests/test_helpers.py @@ -6,13 +6,22 @@ from array_api_extra._lib 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 -from array_api_extra._lib._utils._helpers import asarrays, eager_shape, in1d, ndindex +from array_api_extra._lib._utils._helpers import ( + asarrays, + eager_shape, + in1d, + meta_namespace, + ndindex, +) 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 +np_compat = array_namespace(np.empty(0)) # type: ignore[arg-type] # pyright: ignore[reportArgumentType] + # FIXME calls xp.unique_values without size lazy_xp_function(in1d, jax_jit=False, static_argnames=("assume_unique", "invert", "xp")) @@ -167,3 +176,21 @@ def test_eager_shape(xp: ModuleType, library: Backend): # other lazy backends else: assert eager_shape(b) == b.shape == (1,) + + +class TestMetaNamespace: + @pytest.mark.skip_xp_backend(Backend.NUMPY_READONLY, reason="namespace tests") + def test_basic(self, xp: ModuleType, library: Backend): + args = None, xp.asarray(0), 1 + expect = np_compat if library is Backend.DASK else xp + assert meta_namespace(*args) is expect + + def test_dask_metas(self, da: ModuleType): + cp = pytest.importorskip("cupy") + cp_compat = array_namespace(cp.empty(0)) + args = None, da.from_array(cp.asarray(0)), 1 + assert meta_namespace(*args) is cp_compat + + def test_xp(self, xp: ModuleType): + args = None, xp.asarray(0), 1 + assert meta_namespace(*args, xp=xp) in (xp, np_compat) From 87fe423a252ed9625cd36108ed4604b6ef8dfe52 Mon Sep 17 00:00:00 2001 From: Guido Imperiale Date: Tue, 18 Mar 2025 22:14:28 +0000 Subject: [PATCH 054/140] ENH: `lazy_apply` (#86) * ENH: New function `lazy_apply` * Update docs/api-lazy.md Co-authored-by: Ralf Gommers * Update src/array_api_extra/_lib/_lazy.py Co-authored-by: Ralf Gommers * Code review * Remove kwargs introspection; support None | complex args * Don't always import numpy * update lockfile * appease mypy --------- Co-authored-by: Ralf Gommers Co-authored-by: Lucas Colley --- docs/api-lazy.md | 15 + docs/index.md | 2 +- docs/testing-utils.md | 14 - pixi.lock | 5459 +++++++++---------- pyproject.toml | 1 + src/array_api_extra/__init__.py | 2 + src/array_api_extra/_lib/_funcs.py | 10 +- src/array_api_extra/_lib/_lazy.py | 361 ++ src/array_api_extra/_lib/_utils/_typing.pyi | 4 +- src/array_api_extra/testing.py | 12 +- tests/test_at.py | 6 +- tests/test_funcs.py | 2 +- tests/test_lazy.py | 429 ++ tests/test_testing.py | 10 +- 14 files changed, 3339 insertions(+), 2988 deletions(-) create mode 100644 docs/api-lazy.md delete mode 100644 docs/testing-utils.md create mode 100644 src/array_api_extra/_lib/_lazy.py create mode 100644 tests/test_lazy.py diff --git a/docs/api-lazy.md b/docs/api-lazy.md new file mode 100644 index 00000000..abea5cbb --- /dev/null +++ b/docs/api-lazy.md @@ -0,0 +1,15 @@ +# Tools for lazy backends + +These additional functions are meant to be used to support compatibility with +lazy backends, e.g. Dask or JAX: + +```{eval-rst} +.. currentmodule:: array_api_extra +.. autosummary:: + :nosignatures: + :toctree: generated + + lazy_apply + testing.lazy_xp_function + testing.patch_lazy_xp_functions +``` diff --git a/docs/index.md b/docs/index.md index ae15c7f4..d72c40ef 100644 --- a/docs/index.md +++ b/docs/index.md @@ -5,7 +5,7 @@ :hidden: self api-reference.md -testing-utils.md +api-lazy.md contributing.md contributors.md ``` diff --git a/docs/testing-utils.md b/docs/testing-utils.md deleted file mode 100644 index 49aeb306..00000000 --- a/docs/testing-utils.md +++ /dev/null @@ -1,14 +0,0 @@ -# Testing Utilities - -These additional functions are meant to be used while unit testing Array API -compliant packages: - -```{eval-rst} -.. currentmodule:: array_api_extra.testing -.. autosummary:: - :nosignatures: - :toctree: generated - - lazy_xp_function - patch_lazy_xp_functions -``` diff --git a/pixi.lock b/pixi.lock index f07416e6..37b2ca15 100644 --- a/pixi.lock +++ b/pixi.lock @@ -7,9 +7,8 @@ environments: - https://pypi.org/simple packages: linux-64: - - conda: 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a/src/array_api_extra/_lib/_funcs.py b/src/array_api_extra/_lib/_funcs.py index 83f550af..7b0783a3 100644 --- a/src/array_api_extra/_lib/_funcs.py +++ b/src/array_api_extra/_lib/_funcs.py @@ -36,7 +36,7 @@ @overload -def apply_where( # type: ignore[no-any-explicit,no-any-decorated] # numpydoc ignore=GL08 +def apply_where( # type: ignore[explicit-any,decorated-any] # numpydoc ignore=GL08 cond: Array, args: Array | tuple[Array, ...], f1: Callable[..., Array], @@ -48,7 +48,7 @@ def apply_where( # type: ignore[no-any-explicit,no-any-decorated] # numpydoc ig @overload -def apply_where( # type: ignore[no-any-explicit,no-any-decorated] # numpydoc ignore=GL08 +def apply_where( # type: ignore[explicit-any,decorated-any] # numpydoc ignore=GL08 cond: Array, args: Array | tuple[Array, ...], f1: Callable[..., Array], @@ -59,7 +59,7 @@ def apply_where( # type: ignore[no-any-explicit,no-any-decorated] # numpydoc ig ) -> Array: ... -def apply_where( # type: ignore[no-any-explicit] # numpydoc ignore=PR01,PR02 +def apply_where( # type: ignore[explicit-any] # numpydoc ignore=PR01,PR02 cond: Array, args: Array | tuple[Array, ...], f1: Callable[..., Array], @@ -145,7 +145,7 @@ def apply_where( # type: ignore[no-any-explicit] # numpydoc ignore=PR01,PR02 return _apply_where(cond, f1, f2, fill_value, *args_, xp=xp) -def _apply_where( # type: ignore[no-any-explicit] # numpydoc ignore=PR01,RT01 +def _apply_where( # type: ignore[explicit-any] # numpydoc ignore=PR01,RT01 cond: Array, f1: Callable[..., Array], f2: Callable[..., Array] | None, @@ -743,7 +743,7 @@ def pad( pad_width_seq = cast(list[tuple[int, int]], list(pad_width)) # https://github.com/python/typeshed/issues/13376 - slices: list[slice] = [] # type: ignore[no-any-explicit] + slices: list[slice] = [] # type: ignore[explicit-any] newshape: list[int] = [] for ax, w_tpl in enumerate(pad_width_seq): if len(w_tpl) != 2: diff --git a/src/array_api_extra/_lib/_lazy.py b/src/array_api_extra/_lib/_lazy.py new file mode 100644 index 00000000..14117634 --- /dev/null +++ b/src/array_api_extra/_lib/_lazy.py @@ -0,0 +1,361 @@ +"""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 ._funcs import broadcast_shapes +from ._utils import _compat +from ._utils._compat import ( + array_namespace, + is_dask_namespace, + is_jax_namespace, +) +from ._utils._helpers import is_python_scalar +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 + NumPyObject = Any + + class P: # pylint: disable=missing-class-docstring + args: tuple + kwargs: dict + + +@overload +def lazy_apply( # type: ignore[decorated-any, valid-type] + func: Callable[P, Array | ArrayLike], + *args: Array | complex | None, + shape: tuple[int | None, ...] | None = None, + dtype: DType | None = None, + as_numpy: bool = False, + xp: ModuleType | None = None, + **kwargs: P.kwargs, # pyright: ignore[reportGeneralTypeIssues] +) -> Array: ... # numpydoc ignore=GL08 + + +@overload +def lazy_apply( # type: ignore[decorated-any, valid-type] + func: Callable[P, Sequence[Array | ArrayLike]], + *args: Array | complex | None, + shape: Sequence[tuple[int | None, ...]], + dtype: Sequence[DType] | None = None, + as_numpy: bool = False, + xp: ModuleType | None = None, + **kwargs: P.kwargs, # pyright: ignore[reportGeneralTypeIssues] +) -> tuple[Array, ...]: ... # numpydoc ignore=GL08 + + +def lazy_apply( # type: ignore[valid-type] # numpydoc ignore=GL07,SA04 + func: Callable[P, Array | ArrayLike | Sequence[Array | ArrayLike]], + *args: Array | complex | None, + shape: tuple[int | None, ...] | Sequence[tuple[int | None, ...]] | None = None, + dtype: DType | Sequence[DType] | None = None, + as_numpy: bool = False, + xp: ModuleType | None = None, + **kwargs: P.kwargs, # pyright: ignore[reportGeneralTypeIssues] +) -> Array | tuple[Array, ...]: + """ + Lazily apply an eager function. + + If the backend of the input arrays is lazy, e.g. Dask or jitted JAX, the execution + of the function is delayed until the graph is materialized; if it's eager, the + function is executed immediately. + + Parameters + ---------- + func : callable + The function to apply. + + It must accept one or more array API compliant arrays as positional arguments. + If `as_numpy=True`, inputs are converted to NumPy before they are passed to + `func`. + It must return either a single array-like or a sequence of array-likes. + + `func` must be a pure function, i.e. without side effects, as depending on the + backend it may be executed more than once or never. + *args : Array | int | float | complex | bool | None + 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 + backends. + shape : tuple[int | None, ...] | Sequence[tuple[int | None, ...]], optional + Output shape or sequence of output shapes, one for each output of `func`. + Default: assume single output and broadcast shapes of the input arrays. + dtype : DType | Sequence[DType], optional + Output dtype or sequence of output dtypes, one for each output of `func`. + dtype(s) must belong to the same array namespace as the input arrays. + 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 + or Numba, work transparently with array API-compliant arrays. + Default: False. + xp : array_namespace, optional + The standard-compatible namespace for `args`. Default: infer. + **kwargs : Any, optional + Additional keyword arguments to pass verbatim to `func`. + They cannot contain Array objects. + + Returns + ------- + Array | tuple[Array, ...] + The result(s) of `func` applied to the input arrays, wrapped in the same + array namespace as the inputs. + If shape is omitted or a single `tuple[int | None, ...]`, return a single array. + Otherwise, return a tuple of arrays. + + Notes + ----- + JAX + This allows applying eager functions to jitted JAX arrays, which are lazy. + The function won't be applied until the JAX array is materialized. + When running inside ``jax.jit``, `shape` must be fully known, i.e. it cannot + contain any `None` elements. + + .. warning:: + + `func` must never raise inside ``jax.jit``, as the resulting behavior is + undefined. + + Using this with `as_numpy=False` is particularly useful to apply non-jittable + JAX functions to arrays on GPU devices. + If ``as_numpy=True``, the :doc:`jax:transfer_guard` may prevent arrays on a GPU + device from being transferred back to CPU. This is treated as an implicit + transfer. + + PyTorch, CuPy + If ``as_numpy=True``, these backends raise by default if you attempt to convert + arrays on a GPU device to NumPy. + + Sparse + If ``as_numpy=True``, by default sparse prevents implicit densification through + :func:`numpy.asarray`. `This safety mechanism can be disabled + `_. + + Dask + 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 + will be rechunked into a single chunk. + + .. warning:: + + The whole operation needs to fit in memory all at once on a single worker. + + The outputs will also be returned as a single chunk and you should consider + rechunking them into smaller chunks afterwards. + + If you want to distribute the calculation across multiple workers, you + should use :func:`dask.array.map_blocks`, :func:`dask.array.map_overlap`, + :func:`dask.array.blockwise`, or a native Dask wrapper instead of + `lazy_apply`. + + Dask wrapping around other backends + If ``as_numpy=False``, `func` will receive in input eager arrays of the meta + namespace, as defined by the ``._meta`` attribute of the input Dask arrays. + The outputs of `func` will be wrapped by the meta namespace, and then wrapped + again by Dask. + + Raises + ------ + ValueError + When ``xp=jax.numpy``, the output `shape` is unknown (it contains ``None`` on + one or more axes) and this function was called inside ``jax.jit``. + RuntimeError + When ``xp=sparse`` and auto-densification is disabled. + Exception (backend-specific) + When the backend disallows implicit device to host transfers and the input + arrays are on a non-CPU device, e.g. on GPU. + + See Also + -------- + jax.transfer_guard + jax.pure_callback + dask.array.map_blocks + dask.array.map_overlap + dask.array.blockwise + """ + args_not_none = [arg for arg in args if arg is not None] + array_args = [arg for arg in args_not_none if not is_python_scalar(arg)] + if not array_args: + msg = "Must have at least one argument array" + raise ValueError(msg) + if xp is None: + xp = array_namespace(*args) + + # Normalize and validate shape and dtype + shapes: list[tuple[int | None, ...]] + dtypes: list[DType] + multi_output = False + + if shape is None: + shapes = [broadcast_shapes(*(arg.shape for arg in array_args))] + elif all(isinstance(s, int | None) for s in shape): + # Do not test for shape to be a tuple + # https://github.com/data-apis/array-api/issues/891#issuecomment-2637430522 + shapes = [cast(tuple[int | None, ...], shape)] + else: + shapes = list(shape) # type: ignore[arg-type] # pyright: ignore[reportAssignmentType] + multi_output = True + + if dtype is None: + dtypes = [xp.result_type(*args_not_none)] * len(shapes) + elif multi_output: + if not isinstance(dtype, Sequence): + msg = "Got multiple shapes but only one dtype" + raise ValueError(msg) + dtypes = list(dtype) # pyright: ignore[reportUnknownArgumentType] + else: + if isinstance(dtype, Sequence): + msg = "Got single shape but multiple dtypes" + raise ValueError(msg) + + dtypes = [dtype] + + if len(shapes) != len(dtypes): + msg = f"Got {len(shapes)} shapes and {len(dtypes)} dtypes" + raise ValueError(msg) + del shape + del dtype + # End of shape and dtype parsing + + # Backend-specific branches + if is_dask_namespace(xp): + import dask + + metas: list[Array] = [arg._meta for arg in array_args] # pylint: disable=protected-access # pyright: ignore[reportAttributeAccessIssue] + meta_xp = array_namespace(*metas) + + wrapped = dask.delayed( # type: ignore[attr-defined] # pyright: ignore[reportPrivateImportUsage] + _lazy_apply_wrapper(func, as_numpy, multi_output, meta_xp), + pure=True, + ) + # This finalizes each arg, which is the same as arg.rechunk(-1). + # Please read docstring above for why we're not using + # dask.array.map_blocks or dask.array.blockwise! + delayed_out = wrapped(*args, **kwargs) + + out = tuple( + xp.from_delayed( + delayed_out[i], # pyright: ignore[reportIndexIssue] + # Dask's unknown shapes diverge from the Array API specification + shape=tuple(math.nan if s is None else s for s in shape), + dtype=dtype, + meta=metas[0], + ) + for i, (shape, dtype) in enumerate(zip(shapes, dtypes, strict=True)) + ) + + elif is_jax_namespace(xp) and _is_jax_jit_enabled(xp): + # Delay calling func with jax.pure_callback, which will forward to func eager + # JAX arrays. Do not use jax.pure_callback when running outside of the JIT, + # as it does not support raising exceptions: + # https://github.com/jax-ml/jax/issues/26102 + import jax + + if any(None in shape for shape in shapes): + msg = "Output shape must be fully known when running inside jax.jit" + raise ValueError(msg) + + # Shield kwargs from being coerced into JAX arrays. + # jax.pure_callback calls jax.jit under the hood, but without the chance of + # passing static_argnames / static_argnums. + wrapped = _lazy_apply_wrapper( + partial(func, **kwargs), as_numpy, multi_output, xp + ) + + # suppress unused-ignore to run mypy in -e lint as well as -e dev + out = cast( # type: ignore[bad-cast,unused-ignore] + tuple[Array, ...], + jax.pure_callback( + wrapped, + tuple( + jax.ShapeDtypeStruct(shape, dtype) # pyright: ignore[reportUnknownArgumentType] + for shape, dtype in zip(shapes, dtypes, strict=True) + ), + *args, + ), + ) + + else: + # Eager backends, including non-jitted JAX + wrapped = _lazy_apply_wrapper(func, as_numpy, multi_output, xp) + out = wrapped(*args, **kwargs) + + return out if multi_output else out[0] + + +def _is_jax_jit_enabled(xp: ModuleType) -> bool: # numpydoc ignore=PR01,RT01 + """Return True if this function is being called inside ``jax.jit``.""" + import jax # pylint: disable=import-outside-toplevel + + x = xp.asarray(False) + try: + return bool(x) + except jax.errors.TracerBoolConversionError: + return True + + +def _lazy_apply_wrapper( # type: ignore[explicit-any] # numpydoc ignore=PR01,RT01 + func: Callable[..., Array | ArrayLike | Sequence[Array | ArrayLike]], + as_numpy: bool, + multi_output: bool, + xp: ModuleType, +) -> Callable[..., tuple[Array, ...]]: + """ + Helper of `lazy_apply`. + + Given a function that accepts one or more arrays as positional arguments and returns + a single array-like or a sequence of array-likes, return a function that accepts the + same number of Array API arrays and always returns a tuple of Array API array. + + Any keyword arguments are passed through verbatim to the wrapped function. + """ + + # On Dask, @wraps causes the graph key to contain the wrapped function's name + @wraps(func) + def wrapper( # type: ignore[decorated-any,explicit-any] + *args: Array | complex | None, **kwargs: Any + ) -> tuple[Array, ...]: # numpydoc ignore=GL08 + args_list = [] + device = None + for arg in args: + if arg is not None and not is_python_scalar(arg): + if device is None: + device = _compat.device(arg) + if as_numpy: + import numpy as np + + arg = cast(Array, np.asarray(arg)) # type: ignore[bad-cast] # noqa: PLW2901 # pyright: ignore[reportInvalidCast] + args_list.append(arg) + assert device is not None + + out = func(*args_list, **kwargs) + + if multi_output: + assert isinstance(out, Sequence) + return tuple(xp.asarray(o, device=device) for o in out) + return (xp.asarray(out, device=device),) + + return wrapper diff --git a/src/array_api_extra/_lib/_utils/_typing.pyi b/src/array_api_extra/_lib/_utils/_typing.pyi index 9ef06162..e32a59bd 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[no-any-explicit] +SetIndex: TypeAlias = ( # type: ignore[explicit-any] int | slice | EllipsisType | Array | tuple[int | slice | EllipsisType | Array, ...] ) -GetIndex: TypeAlias = ( # type: ignore[no-any-explicit] +GetIndex: TypeAlias = ( # type: ignore[explicit-any] 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 b3782090..4417b648 100644 --- a/src/array_api_extra/testing.py +++ b/src/array_api_extra/testing.py @@ -42,10 +42,10 @@ def override(func: Callable[P, T]) -> Callable[P, T]: T = TypeVar("T") -_ufuncs_tags: dict[object, dict[str, Any]] = {} # type: ignore[no-any-explicit] +_ufuncs_tags: dict[object, dict[str, Any]] = {} # type: ignore[explicit-any] -def lazy_xp_function( # type: ignore[no-any-explicit] +def lazy_xp_function( # type: ignore[explicit-any] func: Callable[..., Any], *, allow_dask_compute: int = 0, @@ -227,12 +227,12 @@ def xp(request, monkeypatch): mod = cast(ModuleType, request.module) mods = [mod, *cast(list[ModuleType], getattr(mod, "lazy_xp_modules", []))] - def iter_tagged() -> ( # type: ignore[no-any-explicit] + def iter_tagged() -> ( # type: ignore[explicit-any] 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[no-any-explicit] + tags: dict[str, Any] | None = None # type: ignore[explicit-any] with contextlib.suppress(AttributeError): tags = func._lazy_xp_function # pylint: disable=protected-access if tags is None: @@ -253,7 +253,7 @@ def iter_tagged() -> ( # type: ignore[no-any-explicit] 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[no-any-explicit] + wrapped = cast( # type: ignore[explicit-any] Callable[..., Any], jax.jit( func, @@ -289,7 +289,7 @@ 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[no-any-decorated,no-any-explicit] # numpydoc ignore=GL08 + def __call__(self, dsk: Graph, keys: Sequence[Key] | Key, **kwargs: Any) -> Any: # type: ignore[decorated-any,explicit-any] # numpydoc ignore=GL08 import dask self.count += 1 diff --git a/tests/test_at.py b/tests/test_at.py index 2a4a1947..07ea2d3b 100644 --- a/tests/test_at.py +++ b/tests/test_at.py @@ -56,7 +56,7 @@ def _at_op( """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[no-any-explicit] + meth = cast(Callable[..., Array], getattr(at(x, cast(SetIndex, idx)), op.value)) # type: ignore[explicit-any] return meth(y, copy=copy, xp=xp) @@ -166,7 +166,7 @@ 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[no-any-explicit] + meth = cast(Callable[..., Array], getattr(at(x)[:2], op.value)) # type: ignore[explicit-any] with assert_copy(x, None, expect_copy): _ = meth(2.0) @@ -175,7 +175,7 @@ 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[no-any-explicit] + meth = cast(Callable[..., Array], getattr(at(x, idx), op.value)) # type: ignore[explicit-any] with assert_copy(x, None, expect_copy): _ = meth(2.0) diff --git a/tests/test_funcs.py b/tests/test_funcs.py index d269b2ca..23344f62 100644 --- a/tests/test_funcs.py +++ b/tests/test_funcs.py @@ -203,7 +203,7 @@ 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[no-any-explicit,no-any-decorated] + def test_hypothesis( # type: ignore[explicit-any,decorated-any] self, n_arrays: int, rng_seed: int, diff --git a/tests/test_lazy.py b/tests/test_lazy.py new file mode 100644 index 00000000..fcee38b0 --- /dev/null +++ b/tests/test_lazy.py @@ -0,0 +1,429 @@ +from types import ModuleType +from typing import cast + +import numpy as np +import pytest + +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._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 +from array_api_extra._lib._utils._helpers import eager_shape +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") +) + +as_numpy = pytest.mark.parametrize( + "as_numpy", + [ + False, + pytest.param( + True, + marks=[ + pytest.mark.skip_xp_backend(Backend.CUPY, reason="device->host copy"), + pytest.mark.skip_xp_backend(Backend.SPARSE, reason="densification"), + ], + ), + ], +) + + +@as_numpy +@pytest.mark.parametrize("shape", [(2,), (3, 2)]) +@pytest.mark.parametrize("dtype", ["int32", "float64"]) +def test_lazy_apply_simple( + xp: ModuleType, library: Backend, shape: tuple[int, ...], dtype: str, as_numpy: bool +): + def f(x: Array) -> Array: + xp2 = array_namespace(x) + if as_numpy or library in (Backend.NUMPY_READONLY, Backend.DASK): + assert isinstance(x, np.ndarray) + else: + 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 + + x = xp.asarray([1, 2], dtype=xp.int16) + expect = xp.broadcast_to(xp.astype(x + 1, getattr(xp, dtype)), shape) + actual = lazy_apply(f, x, shape=shape, dtype=getattr(xp, dtype), as_numpy=as_numpy) + xp_assert_equal(actual, expect) + + +@as_numpy +def test_lazy_apply_broadcast(xp: ModuleType, as_numpy: bool): + """Test that default shape and dtype are broadcasted from the inputs.""" + + def f(x: Array, y: Array) -> Array: + return x + y + + x = xp.asarray([1, 2], dtype=xp.int16) + y = xp.asarray([[4], [5], [6]], dtype=xp.int32) + z = lazy_apply(f, x, y, as_numpy=as_numpy) + xp_assert_equal(z, x + y) + + +@as_numpy +def test_lazy_apply_multi_output(xp: ModuleType, as_numpy: bool): + 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 + return y, z + + x = xp.asarray([1, 2], dtype=xp.int8) + expect = ( + xp.asarray([3, 4], dtype=xp.int8), + xp.asarray([[2, 3], [2, 3], [2, 3]], dtype=xp.int16), + ) + actual = lazy_apply( + f, x, shape=((2,), (3, 2)), dtype=(xp.int8, xp.int16), as_numpy=as_numpy + ) + assert isinstance(actual, tuple) + assert len(actual) == 2 + xp_assert_equal(actual[0], expect[0]) + xp_assert_equal(actual[1], expect[1]) + + +@pytest.mark.parametrize( + "as_numpy", + [ + pytest.param( + False, + marks=pytest.mark.xfail_xp_backend( + Backend.TORCH, reason="illegal dtype promotion" + ), + ), + pytest.param( + True, + marks=[ + pytest.mark.skip_xp_backend(Backend.CUPY, reason="device->host copy"), + pytest.mark.skip_xp_backend(Backend.SPARSE, reason="densification"), + ], + ), + ], +) +def test_lazy_apply_multi_output_broadcast_dtype(xp: ModuleType, as_numpy: bool): + """ + If dtype is omitted and there are multiple shapes, use the same + dtype for all output arrays, broadcasted from the inputs + """ + + 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) + expect = ( + xp.asarray([4, 5], dtype=xp.float64), + xp.asarray([-2, -1], dtype=xp.float64), + ) + actual = lazy_apply(f, x, y, shape=((2,), (2,)), as_numpy=as_numpy) + assert isinstance(actual, tuple) + assert len(actual) == 2 + xp_assert_equal(actual[0], expect[0]) + xp_assert_equal(actual[1], expect[1]) + + +def test_lazy_apply_core_indices(da: ModuleType): + """ + Test that a function that performs reductions along axes does so + globally and not locally to each Dask chunk. + """ + + 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] + expect = da.asarray(f(x_np)) + x_da = da.asarray(x_np).rechunk(3) + + # A naive map_blocks fails because it applies f to each chunk separately, + # but f needs to reduce along axis 0 which is broken into multiple chunks. + # axis 0 is a "core axis" or "core index" (from xarray.apply_ufunc's + # "core dimension"). + with pytest.raises(AssertionError): + xp_assert_equal(da.map_blocks(f, x_da), expect) + + xp_assert_equal(lazy_apply(f, x_da), expect) + + +def test_lazy_apply_dont_run_on_meta(da: ModuleType): + """Test that Dask won't try running func on the meta array, + as it may have minimum size requirements. + """ + + def f(x: Array) -> Array: + assert x.size + return x + 1 + + x = da.arange(10) + assert not x._meta.size + y = lazy_apply(f, x) + xp_assert_equal(y, x + 1) + + +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 + # 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. + + cp = pytest.importorskip("cupy") + cp = array_namespace(cp.empty(0)) + x_cp = cp.asarray([1, 2, 3]) + x_da = da.asarray([1, 2, 3]).map_blocks(cp.asarray) + assert array_namespace(x_da._meta) is cp + + 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] + + +def test_lazy_apply_none_shape_in_args(xp: ModuleType, library: Backend): + x = xp.asarray([1, 1, 2, 2, 2]) + + # TODO mxp = meta_namespace(x, xp=xp) + mxp = np if library is Backend.DASK else xp + int_type = xp.asarray(0).dtype + + 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), + ) + else: + # Single output + values = lazy_apply(mxp.unique_values, x, shape=(None,)) + xp_assert_equal(values, xp.asarray([1, 2])) + + # Multi output + values, counts = lazy_apply( + mxp.unique_counts, + x, + shape=((None,), (None,)), + dtype=(x.dtype, int_type), + ) + xp_assert_equal(values, xp.asarray([1, 2])) + xp_assert_equal(counts, xp.asarray([2, 3])) + + +def check_lazy_apply_none_shape_broadcast(x: Array) -> Array: + def f(x: Array) -> Array: + return x + + x = x[x > 1] + # Use explicit namespace to bypass monkey-patching by lazy_xp_function + return xpx.lazy_apply(f, x) + + +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") +def test_lazy_apply_none_shape_broadcast(xp: ModuleType): + """Broadcast from input array with unknown shape""" + x = xp.asarray([1, 2, 2]) + actual = check_lazy_apply_none_shape_broadcast(x) + xp_assert_equal(actual, xp.asarray([2, 2])) + + +@pytest.mark.parametrize( + "as_numpy", + [ + False, + pytest.param( + True, + marks=[ + pytest.mark.skip_xp_backend( + 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.SPARSE, reason="densification"), + ], + ), + ], +) +def test_lazy_apply_device(xp: ModuleType, as_numpy: bool, device: Device): + def f(x: Array) -> Array: + xp2 = array_namespace(x) + # Deliberately forgetting to add device here to test that the + # output is transferred to the right device. This is necessary when + # as_numpy=True anyway. + return xp2.zeros(x.shape, dtype=x.dtype) + + x = xp.asarray([1, 2], device=device) + y = lazy_apply(f, x, as_numpy=as_numpy) + assert _compat.device(y) == device + + +def test_lazy_apply_arraylike(xp: ModuleType): + """Wrapped func returns an array-like""" + x = xp.asarray([1, 2, 3]) + + # Single output + def f(x: Array) -> int: + shape = eager_shape(x) + return shape[0] + + expect = xp.asarray(3) + actual = lazy_apply(f, x, shape=(), dtype=expect.dtype) + xp_assert_equal(actual, expect) + + # Multi output + def g(x: Array) -> tuple[int, list[int]]: + shape = eager_shape(x) + return shape[0], list(shape) + + actual2 = lazy_apply(g, x, shape=((), (1,)), dtype=(expect.dtype, expect.dtype)) + xp_assert_equal(actual2[0], xp.asarray(3)) + xp_assert_equal(actual2[1], xp.asarray([3])) + + +def test_lazy_apply_scalars_and_nones(xp: ModuleType, library: Backend): + def f(x: Array, y: None, z: int | Array) -> Array: + mxp = array_namespace(x, y, z) + mtyp = type(mxp.asarray(0)) + 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) + return x + z + + x = xp.asarray([1, 2]) + w = lazy_apply(f, x, None, 3) + xp_assert_equal(w, x + 3) + + +def check_lazy_apply_kwargs(x: Array, expect_cls: type, as_numpy: bool) -> Array: + is_dask = is_dask_array(x) + recursive: list[object] = [] + if not is_dask: # dask.delayed crashes on recursion + recursive.append(recursive) + + def eager( + x: Array, + z: dict[int, list[int]], + msg: str, + msgs: list[str], + scalar: int, + recursive: list[list[object]], + ) -> Array: + assert isinstance(x, expect_cls) + # JAX will crash if x isn't material + assert int(x) == 0 + # Did we re-wrap the namedtuple correctly, or did it get + # accidentally changed to a basic tuple? + assert z == {0: [1, 2]} + assert msg == "Hello World" # must be hidden from JAX + assert msgs[0] == "Hello World" # must be hidden from JAX + assert isinstance(msg, str) + assert isinstance(msgs[0], str) + assert scalar == 1 # must be hidden from JAX + assert isinstance(scalar, int) + assert isinstance(recursive, list) + if not is_dask: + assert recursive[0][0] is recursive[0] + return x + 1 + + # Use explicit namespace to bypass monkey-patching by lazy_xp_function + return xpx.lazy_apply( # pyright: ignore[reportCallIssue] + eager, + x, + z={0: [1, 2]}, + msg="Hello World", + msgs=["Hello World"], + # This will be automatically cast to jax.Array if we don't wrap it + scalar=1, + recursive=recursive, + shape=x.shape, + dtype=x.dtype, + as_numpy=as_numpy, + ) + + +lazy_xp_function(check_lazy_apply_kwargs, static_argnames=("expect_cls", "as_numpy")) + + +@as_numpy +def test_lazy_apply_kwargs(xp: ModuleType, library: Backend, as_numpy: bool): + """When as_numpy=True, search and replace arrays in the (nested) keywords arguments + 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] + xp_assert_equal(actual, x + 1) + + +class CustomError(Exception): + pass + + +def raises(x: Array) -> Array: + def eager(_: Array) -> Array: + msg = "Hello World" + raise CustomError(msg) + + # Use explicit namespace to bypass monkey-patching by lazy_xp_function + return xpx.lazy_apply(eager, x, shape=x.shape, dtype=x.dtype) + + +# jax.pure_callback does not support raising +# https://github.com/jax-ml/jax/issues/26102 +lazy_xp_function(raises, jax_jit=False) + + +def test_lazy_apply_raises(xp: ModuleType): + """ + See Also + -------- + test_testing.py::test_lazy_xp_function_eagerly_raises + """ + x = xp.asarray(0) + + with pytest.raises(CustomError, match="Hello World"): + # Here we are disregarding the return value, which would + # normally cause the graph not to materialize and the + # exception not to be raised. + # However, lazy_xp_function will do it for us on function exit. + _ = raises(x) + + +def test_invalid_args(): + def f(x: Array) -> Array: + return x + + x = np.asarray(1) + + with pytest.raises(ValueError, match="at least one argument array"): + _ = lazy_apply(f, shape=(1,), dtype=np.int32, xp=np) + with pytest.raises(ValueError, match="at least one argument array"): + _ = lazy_apply(f, 1, shape=(1,), dtype=np.int32, xp=np) + with pytest.raises(ValueError, match="at least one argument array"): + _ = lazy_apply(f, shape=(1,), dtype=np.int32) + 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]) + 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] diff --git a/tests/test_testing.py b/tests/test_testing.py index 1968eded..566e795f 100644 --- a/tests/test_testing.py +++ b/tests/test_testing.py @@ -15,7 +15,7 @@ from array_api_extra._lib._utils._typing import Array from array_api_extra.testing import lazy_xp_function -# mypy: disable-error-code=no-any-decorated +# mypy: disable-error-code=decorated-any # pyright: reportUnknownParameterType=false,reportMissingParameterType=false param_assert_equal_close = pytest.mark.parametrize( @@ -31,7 +31,7 @@ @param_assert_equal_close -def test_assert_close_equal_basic(xp: ModuleType, func: Callable[..., None]): # type: ignore[no-any-explicit] +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])) @@ -51,7 +51,7 @@ 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[no-any-explicit] +def test_assert_close_equal_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"): @@ -73,7 +73,7 @@ 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[no-any-explicit] +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. """ @@ -196,7 +196,7 @@ def static_params3(x: Array, n: int, flag: bool = False) -> Array: @pytest.mark.parametrize("func", [static_params1, static_params2, static_params3]) -def test_lazy_xp_function_static_params(xp: ModuleType, func: Callable[..., Array]): # type: ignore[no-any-explicit] +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])) From 1a479365ed93c3c5b65fe6204174a664f080ab70 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 18 Mar 2025 22:44:47 +0000 Subject: [PATCH 055/140] CI: bump pixi --- .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 fc43be95..a3ce6620 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -32,7 +32,7 @@ jobs: extra_args: --hook-stage manual --all-files - uses: prefix-dev/setup-pixi@v0.8.3 with: - pixi-version: v0.40.3 + pixi-version: v0.42.1 cache: true environments: lint - name: Run Pylint, Mypy & Pyright @@ -58,7 +58,7 @@ jobs: - uses: prefix-dev/setup-pixi@v0.8.3 with: - pixi-version: v0.40.3 + pixi-version: v0.42.1 cache: true environments: ${{ matrix.environment }} diff --git a/.github/workflows/docs-build.yml b/.github/workflows/docs-build.yml index 8e12580f..c850c851 100644 --- a/.github/workflows/docs-build.yml +++ b/.github/workflows/docs-build.yml @@ -9,7 +9,7 @@ jobs: - uses: actions/checkout@v4 - uses: prefix-dev/setup-pixi@v0.8.3 with: - pixi-version: v0.40.3 + pixi-version: v0.42.1 cache: true environments: docs - name: Build Docs From b155cad1b9cab02b0709233c81f87013983196d8 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 18 Mar 2025 22:48:05 +0000 Subject: [PATCH 056/140] REL: bump version to 0.7.0 --- 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 37b2ca15..ee40d532 100644 --- a/pixi.lock +++ b/pixi.lock @@ -3884,7 +3884,7 @@ packages: timestamp: 1742159192304 - pypi: . name: array-api-extra - version: 0.7.0.dev0 + version: 0.7.0 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 84cc4303..21e7620e 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.dev0" +__version__ = "0.7.0" # pylint: disable=duplicate-code __all__ = [ From 70c7c8092d665c1556f6cd9ab819e266c5d88674 Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Tue, 18 Mar 2025 23:09:04 +0000 Subject: [PATCH 057/140] 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 058/140] 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 059/140] 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 060/140] 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 061/140] 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 062/140] 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 063/140] 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 - + 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 - + From 114a3ec4d870db6a0decb4b583ca69d4c902f2ce Mon Sep 17 00:00:00 2001 From: crusaderky Date: Sun, 23 Mar 2025 19:16:35 +0000 Subject: [PATCH 064/140] 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 - 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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 066/140] 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 067/140] 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 068/140] 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 069/140] 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 070/140] 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 + + +
Lucas Colley
Lucas Colley
💻 📖 💡 🤔 🚇 🚧 🔧 ⚠️ 🐛 📦		Lucas Colley
Lucas Colley
💻 📖 💡 🤔 🚇 🚧 🔧 ⚠️ 🐛 📦 👀		 Matt Haberland
Matt Haberland
💻 🤔		 Jake Bowhay
Jake Bowhay
💻 👀		 Aaron Meurer
Aaron Meurer
👀 🤔 🚇		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
🤔		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
🤔		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 071/140] 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 074/140] 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 075/140] 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 076/140] 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 077/140] 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 078/140] 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 079/140] 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 080/140] 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 081/140] 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 082/140] 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 083/140] 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 084/140] 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 085/140] 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: ${{secrets.GITHUB_TOKEN}} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 655be69a..7be7a1ca 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -76,7 +76,6 @@ repos: - repo: https://github.com/python-jsonschema/check-jsonschema rev: "0.30.0" hooks: - - id: check-dependabot - id: check-github-workflows - repo: https://github.com/numpy/numpydoc From 46301610d3c3c8a4ae0d3d4a4e3b6e84762ed2fa Mon Sep 17 00:00:00 2001 From: Lucas Colley Date: Sun, 6 Apr 2025 13:01:21 +0100 Subject: [PATCH 086/140] DEV: set dependency dashboard title (#203) --- renovate.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/renovate.json b/renovate.json index 22a99432..3e01b486 100644 --- a/renovate.json +++ b/renovate.json @@ -1,4 +1,5 @@ { "$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 087/140] 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 091/140] 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 092/140] 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 093/140] 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 094/140] 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 095/140] 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 096/140] 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 097/140] 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 098/140] 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 099/140] 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 100/140] 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 101/140] 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 102/140] 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 103/140] 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 104/140] 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 105/140] 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 106/140] 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 107/140] 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 108/140] 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 109/140] 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 110/140] 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 111/140] 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 112/140] 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 113/140] 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 114/140] 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 115/140] 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 116/140] 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 117/140] 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 118/140] 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 119/140] 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 120/140] 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 121/140] 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 122/140] 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 123/140] 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(-) diff --git a/pixi.lock b/pixi.lock index 71b1afc2..56ee7c56 100644 --- a/pixi.lock +++ b/pixi.lock @@ -25,7 +25,7 @@ environments: - conda: https://prefix.dev/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda - conda: https://prefix.dev/conda-forge/linux-64/ncurses-6.5-h2d0b736_3.conda - conda: https://prefix.dev/conda-forge/linux-64/openssl-3.5.0-h7b32b05_0.conda - - conda: https://prefix.dev/conda-forge/linux-64/python-3.13.2-hf636f53_101_cp313.conda + - conda: https://prefix.dev/conda-forge/linux-64/python-3.13.3-hf636f53_101_cp313.conda - conda: https://prefix.dev/conda-forge/linux-64/python_abi-3.13-6_cp313.conda - 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 @@ -43,7 +43,7 @@ environments: - conda: https://prefix.dev/conda-forge/osx-64/libzlib-1.3.1-hd23fc13_2.conda - conda: https://prefix.dev/conda-forge/osx-64/ncurses-6.5-h0622a9a_3.conda - conda: 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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 124/140] 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 125/140] 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 126/140] 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 127/140] 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 128/140] 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 129/140] 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 130/140] 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 131/140] 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 132/140] 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 133/140] 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 134/140] 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 135/140] 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 136/140] 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 137/140] 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 138/140] 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 139/140] 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 140/140] 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 },