POC: appease linter for gh-53

.github/workflows/test-vendor.yml

@@ -29,7 +29,11 @@ jobs:
       - name: Checkout array-api-compat
         uses: actions/checkout@v4
         with:
-          repository: data-apis/array-api-compat
+          # DNM
+          # repository: data-apis/array-api-compat
+          repository: crusaderky/array-api-compat
+          ref: d7ab986843cc9eb20882d7ccbf7248d78fcbd759
+          # /DNM
           path: array-api-compat
 
       - name: Vendor array-api-extra into test package

docs/api-reference.md

@@ -6,6 +6,7 @@
     :nosignatures:
     :toctree: generated
 
+    at
     atleast_nd
     cov
     create_diagonal

pyproject.toml

@@ -26,7 +26,9 @@ classifiers = [
     "Typing :: Typed",
 ]
 dynamic = ["version"]
-dependencies = ["array-api-compat>=1.1.1"]
+# DNM
+# dependencies = ["array-api-compat>=1.1.1"]
+dependencies = []
 
 [project.optional-dependencies]
 tests = [
@@ -63,9 +65,12 @@ platforms = ["linux-64", "osx-arm64", "win-64"]
 
 [tool.pixi.dependencies]
 python = ">=3.10.15,<3.14"
-array-api-compat = ">=1.1.1"
+# array-api-compat = ">=1.1.1"  # DNM
 
 [tool.pixi.pypi-dependencies]
+# DNM main plus #205, #207, #211
+array-api-compat = { git = "https://github.com/crusaderky/array-api-compat.git", rev = "d7ab986843cc9eb20882d7ccbf7248d78fcbd759" }
+
 array-api-extra = { path = ".", editable = true }
 
 [tool.pixi.feature.lint.dependencies]
@@ -190,6 +195,8 @@ reportAny = false
 reportExplicitAny = false
 # data-apis/array-api-strict#6
 reportUnknownMemberType = false
+# no array-api-compat type stubs
+reportUnknownVariableType = false
 
 
 # Ruff

src/array_api_extra/__init__.py

@@ -1,12 +1,22 @@
 from __future__ import annotations  # https://github.com/pylint-dev/pylint/pull/9990
 
-from ._funcs import atleast_nd, cov, create_diagonal, expand_dims, kron, setdiff1d, sinc
+from ._funcs import (
+    at,
+    atleast_nd,
+    cov,
+    create_diagonal,
+    expand_dims,
+    kron,
+    setdiff1d,
+    sinc,
+)
 
 __version__ = "0.3.3.dev0"
 
 # pylint: disable=duplicate-code
 __all__ = [
     "__version__",
+    "at",
     "atleast_nd",
     "cov",
     "create_diagonal",

src/array_api_extra/_funcs.py

@@ -1,15 +1,26 @@
 from __future__ import annotations  # https://github.com/pylint-dev/pylint/pull/9990
 
+import operator
 import typing
 import warnings
 
-if typing.TYPE_CHECKING:
-    from ._lib._typing import Array, ModuleType
+# 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 _utils
-from ._lib._compat import array_namespace
+from ._lib._compat import (
+    array_namespace,
+    is_array_api_obj,
+    is_dask_array,
+    is_writeable_array,
+)
+
+if typing.TYPE_CHECKING:
+    from ._lib._typing import Array, Index, ModuleType, Untyped
 
 __all__ = [
+    "at",
     "atleast_nd",
     "cov",
     "create_diagonal",
@@ -548,3 +559,278 @@ def sinc(x: Array, /, *, xp: ModuleType | None = None) -> Array:
         xp.asarray(xp.finfo(x.dtype).eps, dtype=x.dtype, device=x.device),
     )
     return xp.sin(y) / y
+
+
+_undef = object()
+
+
+class at:  # pylint: disable=invalid-name
+    """
+    Update operations for read-only arrays.
+
+    This implements ``jax.numpy.ndarray.at`` for all backends.
+
+    Parameters
+    ----------
+    x : array
+        Input array.
+    idx : index, optional
+        You may use two alternate syntaxes::
+
+          at(x, idx).set(value)  # or get(), add(), etc.
+          at(x)[idx].set(value)
+
+    copy : bool, optional
+        True (default)
+            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.
+        None
+            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.
+    xp : array_namespace, optional
+        The standard-compatible namespace for `x`. Default: infer
+
+    **kwargs:
+        If the backend supports an `at` method, any additional keyword
+        arguments are passed to it verbatim; e.g. this allows passing
+        ``indices_are_sorted=True`` to JAX.
+
+    Returns
+    -------
+    Updated input array.
+
+    Examples
+    --------
+    Given either of these equivalent expressions::
+
+      x = at(x)[1].add(2, copy=None)
+      x = at(x, 1).add(2, copy=None)
+
+    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
+
+    Otherwise, they are the same as::
+
+      x[1] += 2
+
+    Warning
+    -------
+    When you use copy=None, you should always immediately overwrite
+    the parameter array::
+
+        x = at(x, 0).set(2, copy=None)
+
+    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 = at(x, 0).set(2, copy=None)
+        z = at(x, 1).set(3, copy=None)
+
+    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!
+
+    Warning
+    -------
+    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; this is particularly true when the index contains multiple
+    occurrences of the same index, e.g. ``at(x, [0, 0]).set(2)``.
+
+    Note
+    ----
+    `sparse <https://sparse.pydata.org/>`_ is not supported by update methods yet.
+
+    See Also
+    --------
+    `jax.numpy.ndarray.at <https://jax.readthedocs.io/en/latest/_autosummary/jax.numpy.ndarray.at.html>`_
+    """
+
+    x: Array
+    idx: Index
+    __slots__: ClassVar[tuple[str, str]] = ("idx", "x")
+
+    def __init__(self, x: Array, idx: Index = _undef, /) -> None:
+        self.x = x
+        self.idx = idx
+
+    def __getitem__(self, idx: Index, /) -> at:
+        """Allow for the alternate syntax ``at(x)[start:stop:step]``,
+        which 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)
+        self.idx = idx
+        return self
+
+    def _common(
+        self,
+        at_op: str,
+        y: Array = _undef,
+        /,
+        copy: bool | None = True,
+        xp: ModuleType | None = None,
+        _is_update: bool = True,
+        **kwargs: Untyped,
+    ) -> tuple[Untyped, None] | tuple[None, Array]:
+        """Perform common prepocessing.
+
+        Returns
+        -------
+        If the operation can be resolved by at[], (return value, None)
+        Otherwise, (None, preprocessed x)
+        """
+        if self.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 TypeError(msg)
+
+        x = self.x
+
+        if copy is None:
+            writeable = is_writeable_array(x)
+            copy = _is_update and not writeable
+        elif copy:
+            writeable = None
+        else:
+            writeable = is_writeable_array(x)
+            if not writeable:
+                msg = "Cannot modify parameter in place"
+                raise ValueError(msg)
+
+        if copy:
+            try:
+                at_ = x.at
+            except AttributeError:
+                # Emulate at[] behaviour for non-JAX arrays
+                # with a copy followed by an update
+                if xp is None:
+                    xp = array_namespace(x)
+                # Create writeable copy of read-only numpy array
+                x = xp.asarray(x, copy=True)
+                if writeable is False:
+                    # A copy of a read-only numpy array is writeable
+                    writeable = None
+            else:
+                # Use JAX's at[] or other library that with the same duck-type API
+                args = (y,) if y is not _undef else ()
+                return getattr(at_[self.idx], at_op)(*args, **kwargs), None
+
+        if _is_update:
+            if writeable is None:
+                writeable = is_writeable_array(x)
+            if not writeable:
+                # sparse crashes here
+                msg = f"Array {x} has no `at` method and is read-only"
+                raise ValueError(msg)
+
+        return None, x
+
+    def get(self, **kwargs: Untyped) -> Untyped:
+        """Return ``x[idx]``. In addition to plain ``__getitem__``, this allows ensuring
+        that the output is either a copy or a view; it also allows passing
+        keyword arguments to the backend.
+        """
+        if kwargs.get("copy") is False:
+            if is_array_api_obj(self.idx):
+                # Boolean index. Note that the array API spec
+                # https://data-apis.org/array-api/latest/API_specification/indexing.html
+                # does not allow for list, tuple, and tuples of slices plus one or more
+                # one-dimensional array indices, although many backends support them.
+                # So this check will encounter a lot of false negatives in real life,
+                # which can be caught by testing the user code vs. array-api-strict.
+                msg = "get() with an array index always returns a copy"
+                raise ValueError(msg)
+            if is_dask_array(self.x):
+                msg = "get() on Dask arrays always returns a copy"
+                raise ValueError(msg)
+
+        res, x = self._common("get", _is_update=False, **kwargs)
+        if res is not None:
+            return res
+        assert x is not None
+        return x[self.idx]
+
+    def set(self, y: Array, /, **kwargs: Untyped) -> Array:
+        """Apply ``x[idx] = y`` and return the update array"""
+        res, x = self._common("set", y, **kwargs)
+        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,
+        /,
+        **kwargs: Untyped,
+    ) -> Array:
+        """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._common(at_op, y, **kwargs)
+        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, /, **kwargs: Untyped) -> Array:
+        """Apply ``x[idx] += y`` and return the updated array"""
+        return self._iop("add", operator.add, y, **kwargs)
+
+    def subtract(self, y: Array, /, **kwargs: Untyped) -> Array:
+        """Apply ``x[idx] -= y`` and return the updated array"""
+        return self._iop("subtract", operator.sub, y, **kwargs)
+
+    def multiply(self, y: Array, /, **kwargs: Untyped) -> Array:
+        """Apply ``x[idx] *= y`` and return the updated array"""
+        return self._iop("multiply", operator.mul, y, **kwargs)
+
+    def divide(self, y: Array, /, **kwargs: Untyped) -> Array:
+        """Apply ``x[idx] /= y`` and return the updated array"""
+        return self._iop("divide", operator.truediv, y, **kwargs)
+
+    def power(self, y: Array, /, **kwargs: Untyped) -> Array:
+        """Apply ``x[idx] **= y`` and return the updated array"""
+        return self._iop("power", operator.pow, y, **kwargs)
+
+    def min(self, y: Array, /, **kwargs: Untyped) -> Array:
+        """Apply ``x[idx] = minimum(x[idx], y)`` and return the updated array"""
+        xp = array_namespace(self.x)
+        y = xp.asarray(y)
+        return self._iop("min", xp.minimum, y, **kwargs)
+
+    def max(self, y: Array, /, **kwargs: Untyped) -> Array:
+        """Apply ``x[idx] = maximum(x[idx], y)`` and return the updated array"""
+        xp = array_namespace(self.x)
+        y = xp.asarray(y)
+        return self._iop("max", xp.maximum, y, **kwargs)