MAINT: various refactoring (#101)

Author: lucascolley

pixi.lock

@@ -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" }

pyproject.toml

@@ -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,

src/array_api_extra/__init__.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
+        <https://data-apis.org/array-api/latest/API_specification/indexing.html>`_
+        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 <https://sparse.pydata.org/>`_, 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)