diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 19ba83c..fac3ebe 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] + environment: [ci-py310, ci-py313, ci-backends] runs-on: [ubuntu-latest] steps: diff --git a/docs/api-reference.md b/docs/api-reference.md index ffe68f2..b43c960 100644 --- a/docs/api-reference.md +++ b/docs/api-reference.md @@ -6,6 +6,7 @@ :nosignatures: :toctree: generated + at atleast_nd cov create_diagonal diff --git a/docs/conf.py b/docs/conf.py index 38f0c8d..79000c9 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -53,6 +53,7 @@ intersphinx_mapping = { "python": ("https://docs.python.org/3", None), + "jax": ("https://jax.readthedocs.io/en/latest", None), } nitpick_ignore = [ diff --git a/pixi.lock b/pixi.lock index fe4a855..56a2a9b 100644 --- a/pixi.lock +++ b/pixi.lock @@ -1,5 +1,512 @@ version: 6 environments: + ci-backends: + channels: + - 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cffi >=1.11 + - python >=3.10,<3.11.0a0 + - python_abi 3.10.* *_cp310 + - 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: 311278 + timestamp: 1725306039901 - 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 bac02d2..58c02fa 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,7 +26,7 @@ classifiers = [ "Typing :: Typed", ] dynamic = ["version"] -dependencies = ["array-api-compat>=1.1.1"] +dependencies = ["array-api-compat>=1.10.0,<2"] [project.optional-dependencies] tests = [ @@ -62,8 +62,8 @@ channels = ["https://prefix.dev/conda-forge"] platforms = ["linux-64", "osx-arm64", "win-64"] [tool.pixi.dependencies] -python = ">=3.10.15,<3.14" -array-api-compat = ">=1.1.1" +python = ">=3.10,<3.14" +array-api-compat = ">=1.10.0,<2" [tool.pixi.pypi-dependencies] array-api-extra = { path = ".", editable = true } @@ -130,6 +130,35 @@ python = "~=3.10.0" [tool.pixi.feature.py313.dependencies] python = "~=3.13.0" +# Backends that can run on CPU-only hosts +[tool.pixi.feature.backends.target.linux-64.dependencies] +pytorch = "*" +dask = "*" +sparse = ">=0.15" +jax = "*" + +[tool.pixi.feature.backends.target.osx-arm64.dependencies] +pytorch = "*" +dask = "*" +sparse = ">=0.15" +jax = "*" + +[tool.pixi.feature.backends.target.win-64.dependencies] +# pytorch = "*" # Package unavailable on Windows +dask = "*" +sparse = ">=0.15" +# jax = "*" # Package unavailable on Windows + +# Backends that require a GPU host and a CUDA driver +[tool.pixi.feature.cuda-backends.target.linux-64.dependencies] +cupy = "*" + +[tool.pixi.feature.cuda-backends.target.osx-arm64.dependencies] +# cupy = "*" # Package unavailable on macOSX + +[tool.pixi.feature.cuda-backends.target.win-64.dependencies] +cupy = "*" + [tool.pixi.environments] default = { solve-group = "default" } lint = { features = ["lint"], solve-group = "default" } @@ -138,7 +167,9 @@ docs = { features = ["docs"], solve-group = "default" } dev = { features = ["lint", "tests", "docs", "dev"], solve-group = "default" } 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"] # pytest @@ -195,6 +226,8 @@ reportAny = false reportExplicitAny = false # data-apis/array-api-strict#6 reportUnknownMemberType = false +# no array-api-compat type stubs +reportUnknownVariableType = false # Ruff @@ -236,6 +269,7 @@ 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 ] @@ -271,6 +305,7 @@ checks = [ "ES01", ] exclude = [ # don't report on objects that match any of these regex + '.*test_at.*', '.*test_funcs.*', '.*test_utils.*', '.*test_version.*', diff --git a/src/array_api_extra/__init__.py b/src/array_api_extra/__init__.py index 83808e0..09e5ab1 100644 --- a/src/array_api_extra/__init__.py +++ b/src/array_api_extra/__init__.py @@ -1,6 +1,7 @@ """Extra array functions built on top of the array API standard.""" from ._funcs import ( + at, atleast_nd, cov, create_diagonal, @@ -16,6 +17,7 @@ # pylint: disable=duplicate-code __all__ = [ "__version__", + "at", "atleast_nd", "cov", "create_diagonal", diff --git a/src/array_api_extra/_funcs.py b/src/array_api_extra/_funcs.py index 369319e..03b4829 100644 --- a/src/array_api_extra/_funcs.py +++ b/src/array_api_extra/_funcs.py @@ -1,12 +1,22 @@ """Public API Functions.""" +import operator import warnings +# https://github.com/pylint-dev/pylint/issues/10112 +from collections.abc import Callable # pylint: disable=import-error +from typing import ClassVar, Literal + from ._lib import _compat, _utils -from ._lib._compat import array_namespace -from ._lib._typing import Array, ModuleType +from ._lib._compat import ( + array_namespace, + is_jax_array, + is_writeable_array, +) +from ._lib._typing import Array, Index, ModuleType __all__ = [ + "at", "atleast_nd", "cov", "create_diagonal", @@ -589,3 +599,323 @@ def pad( ) padded[(slice(pad_width, -pad_width, None),) * x.ndim] = x return padded + + +_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 always immediately overwrite + the parameter array:: + + >>> import array_api_extra as xpx + >>> x = xpx.at(x, 0).set(2) + + 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, ``x == [0, 0, 0]``, ``y == [2, 0, 0]`` and z == ``[0, 3, 0]`` + when ``x`` is read-only, whereas ``x == y == z == [2, 3, 0]`` when ``x`` is + writeable! + + (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: str, + 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}" # pyright: ignore[reportUnreachable] + 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 = getattr(x.at[idx], at_op) + 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("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: Literal[ + "set", "add", "subtract", "multiply", "divide", "power", "min", "max" + ], + 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("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("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("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("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("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("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("max", xp.maximum, y, copy=copy, xp=xp) diff --git a/src/array_api_extra/_lib/_compat.py b/src/array_api_extra/_lib/_compat.py index de7a220..a24175d 100644 --- a/src/array_api_extra/_lib/_compat.py +++ b/src/array_api_extra/_lib/_compat.py @@ -4,16 +4,22 @@ try: from ..._array_api_compat_vendor import ( # pyright: ignore[reportMissingImports] - array_namespace, # pyright: ignore[reportUnknownVariableType] - device, # pyright: ignore[reportUnknownVariableType] + array_namespace, + device, + is_jax_array, + is_writeable_array, ) except ImportError: from array_api_compat import ( # pyright: ignore[reportMissingTypeStubs] - array_namespace, # pyright: ignore[reportUnknownVariableType] + array_namespace, device, + is_jax_array, + is_writeable_array, ) __all__ = [ "array_namespace", "device", + "is_jax_array", + "is_writeable_array", ] diff --git a/src/array_api_extra/_lib/_compat.pyi b/src/array_api_extra/_lib/_compat.pyi index 2105708..f65a28f 100644 --- a/src/array_api_extra/_lib/_compat.pyi +++ b/src/array_api_extra/_lib/_compat.pyi @@ -6,12 +6,14 @@ from ._typing import Array, Device # pylint: disable=missing-class-docstring,unused-argument -class ArrayModule(ModuleType): # numpydoc ignore=GL08 - def device(self, x: Array, /) -> Device: ... # numpydoc ignore=GL08 +class ArrayModule(ModuleType): + def device(self, x: Array, /) -> Device: ... def array_namespace( *xs: Array, api_version: str | None = None, use_compat: bool | None = None, -) -> ArrayModule: ... # numpydoc ignore=GL08 -def device(x: Array, /) -> Device: ... # numpydoc ignore=GL08 +) -> ArrayModule: ... +def device(x: Array, /) -> Device: ... +def is_jax_array(x: object, /) -> bool: ... +def is_writeable_array(x: object, /) -> bool: ... diff --git a/src/array_api_extra/_lib/_typing.py b/src/array_api_extra/_lib/_typing.py index 8aedc44..c612020 100644 --- a/src/array_api_extra/_lib/_typing.py +++ b/src/array_api_extra/_lib/_typing.py @@ -6,5 +6,6 @@ # 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] +Index = Any # type: ignore[no-any-explicit] -__all__ = ["Array", "Device", "ModuleType"] +__all__ = ["Array", "Device", "Index", "ModuleType"] diff --git a/tests/test_at.py b/tests/test_at.py new file mode 100644 index 0000000..1f66067 --- /dev/null +++ b/tests/test_at.py @@ -0,0 +1,158 @@ +from collections.abc import Generator +from contextlib import contextmanager +from importlib import import_module + +import numpy as np +import pytest +from array_api_compat import ( # type: ignore[import-untyped] # pyright: ignore[reportMissingTypeStubs] + array_namespace, + is_dask_array, + is_pydata_sparse_array, + is_writeable_array, +) + +from array_api_extra import at +from array_api_extra._lib._typing import Array + +all_libraries = ( + "array_api_strict", + "numpy", + "numpy_readonly", + "cupy", + "torch", + "dask.array", + "sparse", + "jax.numpy", +) + + +@pytest.fixture(params=all_libraries) +def array(request: pytest.FixtureRequest) -> Array: + library = request.param + if library == "numpy_readonly": + x = np.asarray([10.0, 20.0, 30.0]) + x.flags.writeable = False + else: + try: + lib = import_module(library) + except ImportError: + pytest.skip(f"{library} is not installed") + x = lib.asarray([10.0, 20.0, 30.0]) + return x + + +def assert_array_equal(a: Array, b: Array) -> None: + xp = array_namespace(a) + b = xp.asarray(b) + eq = xp.all(a == b) + if is_dask_array(a): + eq = eq.compute() + assert eq + + +@contextmanager +def assert_copy(array: Array, copy: bool | None) -> Generator[None, None, None]: + if copy is False and not is_writeable_array(array): + with pytest.raises((TypeError, ValueError)): + yield + return + + xp = array_namespace(array) + array_orig = xp.asarray(array, copy=True) + yield + + if copy is None: + copy = not is_writeable_array(array) + assert_array_equal(xp.all(array == array_orig), copy) + + +@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.mark.parametrize( + ("op", "arg", "expect"), + [ + ("set", 40.0, [10.0, 40.0, 40.0]), + ("add", 40.0, [10.0, 60.0, 70.0]), + ("subtract", 100.0, [10.0, -80.0, -70.0]), + ("multiply", 2.0, [10.0, 40.0, 60.0]), + ("divide", 2.0, [10.0, 10.0, 15.0]), + ("power", 2.0, [10.0, 400.0, 900.0]), + ("min", 25.0, [10.0, 20.0, 25.0]), + ("max", 25.0, [10.0, 25.0, 30.0]), + ], +) +def test_update_ops( + array: Array, + kwargs: dict[str, bool | None], + expect_copy: bool | None, + op: str, + arg: float, + expect: list[float], +): + if is_pydata_sparse_array(array): + pytest.skip("at() does not support updates on sparse arrays") + + with assert_copy(array, expect_copy): + y = getattr(at(array)[1:], op)(arg, **kwargs) + assert isinstance(y, type(array)) + assert_array_equal(y, expect) + + +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] + + +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) + + +def test_alternate_index_syntax(): + a = np.asarray([1, 2, 3]) + assert_array_equal(at(a, 0).set(4, copy=True), [4, 2, 3]) + assert_array_equal(at(a)[0].set(4, copy=True), [4, 2, 3]) + + a_at = at(a) + assert_array_equal(a_at[0].add(1, copy=True), [2, 2, 3]) + assert_array_equal(a_at[1].add(2, copy=True), [1, 4, 3]) + + with pytest.raises(ValueError, match="Index"): + at(a).set(4) + with pytest.raises(ValueError, match="Index"): + at(a, 0)[0].set(4) + + +@pytest.mark.parametrize("copy", [True, False]) +@pytest.mark.parametrize("op", ["add", "subtract", "multiply", "divide", "power"]) +def test_iops_incompatible_dtype(op: str, copy: bool): + """Test that at() replicates the backend's behaviour for + in-place operations with incompatible dtypes. + + Note: + >>> a = np.asarray([1, 2, 3]) + >>> a / 1.5 + array([0. , 0.66666667, 1.33333333]) + >>> a /= 1.5 + UFuncTypeError: Cannot cast ufunc 'divide' output from dtype('float64') + to dtype('int64') with casting rule 'same_kind' + """ + a = np.asarray([2, 4]) + func = getattr(at(a)[:], op) + with pytest.raises(TypeError, match="Cannot cast ufunc"): + func(1.1, copy=copy) diff --git a/vendor_tests/test_vendor.py b/vendor_tests/test_vendor.py index a248abc..c2e6570 100644 --- a/vendor_tests/test_vendor.py +++ b/vendor_tests/test_vendor.py @@ -3,10 +3,18 @@ def test_vendor_compat(): - from ._array_api_compat_vendor import array_namespace + from ._array_api_compat_vendor import ( # type: ignore[attr-defined] + array_namespace, + device, + is_jax_array, + is_writeable_array, + ) x = xp.asarray([1, 2, 3]) assert array_namespace(x) is xp + device(x) + assert not is_jax_array(x) + assert is_writeable_array(x) def test_vendor_extra():