API: Cleaning numpy/__init__.py and main namespace - Part 4 [NEP 52] (#24445)

mtsokol · web-flow · commit 2f0bd6e86a77 · 2023-09-05T21:58:22.000+02:00
[skip ci]
diff --git a/doc/release/upcoming_changes/24445.deprecation.rst b/doc/release/upcoming_changes/24445.deprecation.rst
@@ -0,0 +1,5 @@
+* ``np.trapz`` has been deprecated. Use ``scipy.interpolate.trapezoid`` instead.
+
+* ``np.in1d`` has been deprecated. Use ``np.isin`` instead.
+
+* Alias ``np.row_stack`` has been deprecated. Use ``np.vstack`` directly.
diff --git a/doc/source/reference/routines.array-manipulation.rst b/doc/source/reference/routines.array-manipulation.rst
@@ -72,7 +72,6 @@ Joining arrays
    hstack
    dstack
    column_stack
-   row_stack
 
 Splitting arrays
 ================
diff --git a/doc/source/reference/routines.ma.rst b/doc/source/reference/routines.ma.rst
@@ -145,7 +145,6 @@ Changing the number of dimensions
    ma.hstack
    ma.hsplit
    ma.mr_
-   ma.row_stack
    ma.vstack
 
 
diff --git a/doc/source/reference/routines.math.rst b/doc/source/reference/routines.math.rst
@@ -64,7 +64,6 @@ Sums, products, differences
    ediff1d
    gradient
    cross
-   trapz
 
 Exponents and logarithms
 ------------------------
diff --git a/doc/source/user/quickstart.rst b/doc/source/user/quickstart.rst
@@ -767,14 +767,6 @@ It is equivalent to `hstack` only for 2D arrays::
     array([[4., 3.],
            [2., 8.]])
 
-On the other hand, the function `row_stack` is equivalent to `vstack`
-for any input arrays. In fact, `row_stack` is an alias for `vstack`::
-
-    >>> np.column_stack is np.hstack
-    False
-    >>> np.row_stack is np.vstack
-    True
-
 In general, for arrays with more than two dimensions,
 `hstack` stacks along their second
 axes, `vstack` stacks along their
diff --git a/numpy/core/fromnumeric.py b/numpy/core/fromnumeric.py
@@ -2241,8 +2241,6 @@ def sum(a, axis=None, dtype=None, out=None, keepdims=np._NoValue,
 
     cumsum : Cumulative sum of array elements.
 
-    trapz : Integration of array values using the composite trapezoidal rule.
-
     mean, average
 
     Notes
@@ -2544,7 +2542,6 @@ def cumsum(a, axis=None, dtype=None, out=None):
     See Also
     --------
     sum : Sum array elements.
-    trapz : Integration of array values using the composite trapezoidal rule.
     diff : Calculate the n-th discrete difference along given axis.
 
     Notes
diff --git a/numpy/core/shape_base.py b/numpy/core/shape_base.py
@@ -230,8 +230,6 @@ def vstack(tup, *, dtype=None, casting="same_kind"):
     and r/g/b channels (third axis). The functions `concatenate`, `stack` and
     `block` provide more general stacking and concatenation operations.
 
-    ``np.row_stack`` is an alias for `vstack`. They are the same function.
-
     Parameters
     ----------
     tup : sequence of ndarrays
diff --git a/numpy/core/tests/test_deprecations.py b/numpy/core/tests/test_deprecations.py
@@ -755,6 +755,7 @@ def test_lib_functions_deprecation_call(self):
         from numpy.lib._shape_base_impl import get_array_wrap
         from numpy.core.numerictypes import maximum_sctype
         from numpy.lib.tests.test_io import TextIO
+        from numpy import in1d, row_stack, trapz
         
         self.assert_deprecated(lambda: safe_eval("None"))
 
@@ -766,3 +767,7 @@ def test_lib_functions_deprecation_call(self):
         self.assert_deprecated(lambda: disp("test"))
         self.assert_deprecated(lambda: get_array_wrap())
         self.assert_deprecated(lambda: maximum_sctype(int))
+
+        self.assert_deprecated(lambda: in1d([1], [1]))
+        self.assert_deprecated(lambda: row_stack([[]]))
+        self.assert_deprecated(lambda: trapz([1], [1]))
diff --git a/numpy/core/tests/test_overrides.py b/numpy/core/tests/test_overrides.py
@@ -737,24 +737,3 @@ def __array__(self):
     bound = np.mean.__get__(MyClass)  # classmethod
     with pytest.raises(TypeError, match="unsupported operand type"):
         bound()
-
-
-def test_scipy_trapz_support_shim():
-    # SciPy 1.10 and earlier "clone" trapz in this way, so we have a
-    # support shim in place: https://github.com/scipy/scipy/issues/17811
-    # That should be removed eventually.  This test copies what SciPy does.
-    # Hopefully removable 1 year after SciPy 1.11; shim added to NumPy 1.25.
-    import types
-    import functools
-
-    def _copy_func(f):
-        # Based on http://stackoverflow.com/a/6528148/190597 (Glenn Maynard)
-        g = types.FunctionType(f.__code__, f.__globals__, name=f.__name__,
-                            argdefs=f.__defaults__, closure=f.__closure__)
-        g = functools.update_wrapper(g, f)
-        g.__kwdefaults__ = f.__kwdefaults__
-        return g
-
-    trapezoid = _copy_func(np.trapz)
-
-    assert np.trapz([1, 2]) == trapezoid([1, 2])
diff --git a/numpy/lib/_arraysetops_impl.py b/numpy/lib/_arraysetops_impl.py
@@ -15,6 +15,7 @@
 
 """
 import functools
+import warnings
 
 import numpy as np
 from numpy.core import overrides
@@ -518,11 +519,12 @@ def in1d(ar1, ar2, assume_unique=False, invert=False, *, kind=None):
     """
     Test whether each element of a 1-D array is also present in a second array.
 
+    .. deprecated:: 2.0
+        Use :func:`isin` instead of `in1d` for new code.
+
     Returns a boolean array the same length as `ar1` that is True
     where an element of `ar1` is in `ar2` and False otherwise.
 
-    We recommend using :func:`isin` instead of `in1d` for new code.
-
     Parameters
     ----------
     ar1 : (M,) array_like
@@ -604,6 +606,18 @@ def in1d(ar1, ar2, assume_unique=False, invert=False, *, kind=None):
     >>> test[mask]
     array([1, 5])
     """
+
+    # Deprecated in NumPy 2.0, 2023-08-18
+    warnings.warn(
+        "`in1d` is deprecated. Use `np.isin` instead.",
+        DeprecationWarning,
+        stacklevel=2
+    )
+
+    return _in1d(ar1, ar2, assume_unique, invert, kind=kind)
+
+
+def _in1d(ar1, ar2, assume_unique=False, invert=False, *, kind=None):
     # Ravel both arrays, behavior for the first array could be different
     ar1 = np.asarray(ar1).ravel()
     ar2 = np.asarray(ar2).ravel()
@@ -805,10 +819,6 @@ def isin(element, test_elements, assume_unique=False, invert=False, *,
         Has the same shape as `element`. The values `element[isin]`
         are in `test_elements`.
 
-    See Also
-    --------
-    in1d                  : Flattened version of this function.
-
     Notes
     -----
 
@@ -876,8 +886,8 @@ def isin(element, test_elements, assume_unique=False, invert=False, *,
            [ True, False]])
     """
     element = np.asarray(element)
-    return in1d(element, test_elements, assume_unique=assume_unique,
-                invert=invert, kind=kind).reshape(element.shape)
+    return _in1d(element, test_elements, assume_unique=assume_unique,
+                 invert=invert, kind=kind).reshape(element.shape)
 
 
 def _union1d_dispatcher(ar1, ar2):
@@ -957,4 +967,4 @@ def setdiff1d(ar1, ar2, assume_unique=False):
     else:
         ar1 = unique(ar1)
         ar2 = unique(ar2)
-    return ar1[in1d(ar1, ar2, assume_unique=True, invert=True)]
+    return ar1[_in1d(ar1, ar2, assume_unique=True, invert=True)]
diff --git a/numpy/lib/_function_base_impl.py b/numpy/lib/_function_base_impl.py
@@ -4783,6 +4783,9 @@ def trapz(y, x=None, dx=1.0, axis=-1):
     r"""
     Integrate along the given axis using the composite trapezoidal rule.
 
+    .. deprecated:: 2.0
+        Use `scipy.integrate.trapezoid` instead.
+
     If `x` is provided, the integration happens in sequence along its
     elements - they are not sorted.
 
@@ -4880,6 +4883,14 @@ def trapz(y, x=None, dx=1.0, axis=-1):
     >>> np.trapz(a, axis=1)
     array([2.,  8.])
     """
+
+    # Deprecated in NumPy 2.0, 2023-08-18
+    warnings.warn(
+        "`trapz` is deprecated. Use `scipy.integrate.trapezoid` instead.",
+        DeprecationWarning,
+        stacklevel=2
+    )
+
     y = asanyarray(y)
     if x is None:
         d = dx
diff --git a/numpy/lib/_shape_base_impl.py b/numpy/lib/_shape_base_impl.py
@@ -604,7 +604,19 @@ def expand_dims(a, axis):
     return a.reshape(shape)
 
 
-row_stack = vstack
+# TODO: Remove once deprecation period passes
+def row_stack(tup, *, dtype=None, casting="same_kind"):
+    # Deprecated in NumPy 2.0, 2023-08-18
+    warnings.warn(
+        "`row_stack` alias is deprecated. "
+        "Use `np.vstack` directly.",
+        DeprecationWarning,
+        stacklevel=2
+    )
+    return vstack(tup, dtype=dtype, casting=casting)
+
+
+row_stack.__doc__ = vstack.__doc__
 
 
 def _column_stack_dispatcher(tup):
diff --git a/numpy/lib/tests/test_arraysetops.py b/numpy/lib/tests/test_arraysetops.py
diff --git a/numpy/lib/tests/test_function_base.py b/numpy/lib/tests/test_function_base.py
diff --git a/numpy/matrixlib/tests/test_interaction.py b/numpy/matrixlib/tests/test_interaction.py
diff --git a/numpy/tests/test_public_api.py b/numpy/tests/test_public_api.py
diff --git a/numpy/typing/tests/data/reveal/arraysetops.pyi b/numpy/typing/tests/data/reveal/arraysetops.pyi
diff --git a/numpy/typing/tests/data/reveal/shape_base.pyi b/numpy/typing/tests/data/reveal/shape_base.pyi
