scipy 1.16.0__cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl → 1.16.1__cp312-cp312-manylinux2014_aarch64.manylinux_2_17_aarch64.whl

scipy/__config__.py

@@ -59,7 +59,7 @@ CONFIG = _cleanup(
             },
             "pythran": {
                 "version": r"0.18.0",
-                "include directory": r"../../tmp/build-env-kgwue17m/lib/python3.12/site-packages/pythran"
+                "include directory": r"../../tmp/build-env-1147qsel/lib/python3.12/site-packages/pythran"
             },
         },
         "Machine Information": {
@@ -100,13 +100,13 @@ CONFIG = _cleanup(
             },
             "pybind11": {
                 "name": "pybind11",
-                "version": "2.13.6",
+                "version": "3.0.0",
                 "detection method": "config-tool",
                 "include directory": r"unknown",
             },
         },
         "Python Information": {
-            "path": r"/tmp/build-env-kgwue17m/bin/python",
+            "path": r"/tmp/build-env-1147qsel/bin/python",
             "version": "3.12",
         },
     }

scipy/_lib/_util.py

@@ -351,6 +351,13 @@ def _transition_to_rng(old_name, *, position_num=None, end_version=None,
 
             return fun(*args, **kwargs)
 
+        # Add the old parameter name to the function signature
+        wrapped_signature = inspect.signature(fun)
+        wrapper.__signature__ = wrapped_signature.replace(parameters=[
+            *wrapped_signature.parameters.values(),
+            inspect.Parameter(old_name, inspect.Parameter.KEYWORD_ONLY, default=None),
+        ])
+
         if replace_doc:
             doc = FunctionDoc(wrapper)
             parameter_names = [param.name for param in doc['Parameters']]

scipy/io/matlab/tests/test_streams.py

@@ -2,7 +2,9 @@
 
 """
 
+import platform
 import os
+import sys
 import zlib
 
 from io import BytesIO
@@ -15,6 +17,7 @@ import numpy as np
 
 from numpy.testing import assert_, assert_equal
 from pytest import raises as assert_raises
+import pytest
 
 from scipy.io.matlab._streams import (make_stream,
     GenericStream, ZlibInputStream,
@@ -194,6 +197,9 @@ class TestZlibInputStream:
         stream.seek(1024)
         assert_(stream.all_data_read())
 
+    @pytest.mark.skipif(
+            (platform.system() == 'Windows' and sys.version_info >= (3, 14)),
+            reason='gh-23185')
     def test_all_data_read_overlap(self):
         COMPRESSION_LEVEL = 6
 
@@ -210,6 +216,9 @@ class TestZlibInputStream:
         stream.seek(len(data))
         assert_(stream.all_data_read())
 
+    @pytest.mark.skipif(
+            (platform.system() == 'Windows' and sys.version_info >= (3, 14)),
+            reason='gh-23185')
     def test_all_data_read_bad_checksum(self):
         COMPRESSION_LEVEL = 6
 

scipy/linalg/tests/test_matfuncs.py

@@ -460,6 +460,13 @@ class TestSqrtM:
         np.fill_diagonal(M, 1)
         assert np.isrealobj(sqrtm(M))
 
+    def test_gh23278(self):
+        M = np.array([[1., 0., 0.], [0, 1, -1j], [0, 1j, 2]])
+        sq = sqrtm(M)
+        assert_allclose(sq @ sq, M, atol=1e-14)
+        sq = sqrtm(M.astype(np.complex64))
+        assert_allclose(sq @ sq, M, atol=1e-6)
+
     def test_data_size_preservation_uint_in_float_out(self):
         M = np.eye(10, dtype=np.uint8)
         assert sqrtm(M).dtype == np.float64

scipy/ndimage/_filters.py

@@ -232,7 +232,9 @@ def vectorized_filter(input, function, *, size=None, footprint=None, output=None
         We adjust `size` to the number of dimensions indicated by `axes`.
         For instance, if `axes` is ``(0, 2, 1)`` and ``n`` is passed for ``size``,
         then the effective `size` is ``(n, n, n)``.
-    %(output)s
+    output : array, optional
+        The array in which to place the output. By default, an array of the dtype
+        returned by `function` will be created.
     mode : {'reflect', 'constant', 'nearest', 'mirror', 'wrap'}, optional
         The `mode` parameter determines how the input array is extended
         beyond its boundaries. Default is 'reflect'. Behavior for each valid
@@ -1987,7 +1989,14 @@ def _rank_filter(input, rank, size=None, footprint=None, output=None,
                 "A sequence of modes is not supported by non-separable rank "
                 "filters")
         mode = _ni_support._extend_mode_to_code(mode, is_filter=True)
-        if input.ndim == 1:
+        # Some corner cases are currently not allowed to use the
+        # "new"/fast 1D rank filter code, including when the
+        # footprint is large compared to the array size.
+        # See discussion in gh-23293; longer-term it may be possible
+        # to allow the fast path for these corner cases as well,
+        # if algorithmic fixes are found.
+        lim2 = input.size - ((footprint.size - 1) // 2 - origin)
+        if input.ndim == 1 and ((lim2 >= 0) or (input.size == 1)):
             if input.dtype in (np.int64, np.float64, np.float32):
                 x = input
                 x_out = output

scipy/ndimage/tests/test_filters.py

@@ -3029,3 +3029,55 @@ class TestVectorizedFilter:
 def test_gh_22586_crash_property(x, size, mode):
     # property-based test for median_filter resilience to hard crashing
     ndimage.median_filter(x, size=size, mode=mode)
+
+
+@pytest.mark.parametrize('samples, mode, size, expected', [
+    ([1, 2], "reflect", 5, [2, 1]),
+    ([2], "reflect", 5, [2]), # original failure from gh-23075
+    ([2], "nearest", 5, [2]),
+    ([2], "wrap", 5, [2]),
+    ([2], "mirror", 5, [2]),
+    ([2], "constant", 5, [0]),
+    ([2], "reflect", 1, [2]),
+    ([2], "nearest", 1, [2]),
+    ([2], "wrap", 1, [2]),
+    ([2], "mirror", 1, [2]),
+    ([2], "constant", 1, [2]),
+    ([2], "reflect", 100, [2]),
+    ([2], "nearest", 100, [2]),
+    ([2], "wrap", 100, [2]),
+    ([2], "mirror", 100, [2]),
+    ([2], "constant", 100, [0]),
+])
+def test_gh_23075(samples, mode, size, expected):
+    # results verified against SciPy 1.14.1, before the median_filter
+    # overhaul
+    sample_array = np.asarray(samples, dtype=np.float32)
+    expected = np.asarray(expected, dtype=np.float32)
+    filtered_samples = ndimage.median_filter(sample_array, size=size, mode=mode)
+    xp_assert_close(filtered_samples, expected, check_shape=True, check_dtype=True)
+
+
+@pytest.mark.parametrize('samples, size, cval, expected', [
+    ([2], 5, 17.7, [17.7]),
+    ([2], 1, 0, [2]),
+    ([2], 100, 1.4, [1.4]),
+    ([9], 137, -7807.7, [-7807.7]),
+])
+def test_gh_23075_constant(samples, size, cval, expected):
+    # results verified against SciPy 1.14.1, before the median_filter
+    # overhaul
+    sample_array = np.asarray(samples, dtype=np.single)
+    expected = np.asarray(expected, dtype=np.single)
+    filtered_samples = ndimage.median_filter(sample_array,
+                                             size=size,
+                                             mode="constant",
+                                             cval=cval)
+    xp_assert_close(filtered_samples, expected, check_shape=True, check_dtype=True)
+
+
+def test_median_filter_lim2():
+    sample_array = np.ones(8)
+    expected = np.ones(8)
+    filtered_samples = ndimage.median_filter(sample_array, size=19, mode="reflect")
+    xp_assert_close(filtered_samples, expected, check_shape=True, check_dtype=True)

scipy/optimize/_lsq/least_squares.py

@@ -17,7 +17,7 @@ from .trf import trf
 from .dogbox import dogbox
 from .common import EPS, in_bounds, make_strictly_feasible
 
-    
+
 from scipy.optimize._optimize import _wrap_callback
 
 TERMINATION_MESSAGES = {
@@ -392,7 +392,7 @@ def least_squares(
 
         * For 'trf'    : ``x_scale == 1``
         * For 'dogbox' : ``x_scale == 1``
-        * For 'jac'    : ``x_scale == 'jac'``
+        * For 'lm'     : ``x_scale == 'jac'``
 
         .. versionchanged:: 1.16.0
             The default keyword value is changed from 1 to None to indicate that

scipy/optimize/_minimize.py

@@ -188,7 +188,6 @@ def minimize(fun, x0, args=(), method=None, jac=None, hess=None,
 
         Equality constraint means that the constraint function result is to
         be zero whereas inequality means that it is to be non-negative.
-        Note that COBYLA only supports inequality constraints.
 
     tol : float, optional
         Tolerance for termination. When `tol` is specified, the selected

scipy/optimize/_shgo_lib/_complex.py

@@ -183,6 +183,7 @@ class Complex:
             self.V = VertexCacheIndex()
 
         self.V_non_symm = []  # List of non-symmetric vertices
+        self.split_edge = cache(self._split_edge)
 
     def __call__(self):
         return self.H
@@ -995,8 +996,7 @@ class Complex:
                 d_v0v1.connect(d_v1v2)
         return
 
-    @cache
-    def split_edge(self, v1, v2):
+    def _split_edge(self, v1, v2):
         v1 = self.V[v1]
         v2 = self.V[v2]
         # Destroy original edge, if it exists:

scipy/signal/_filter_design.py

@@ -60,6 +60,17 @@ def _is_int_type(x):
         return True
 
 
+def _real_dtype_for_complex(dtyp, *, xp):
+    if xp.isdtype(dtyp, 'real floating'):
+        return dtyp
+    if dtyp == xp.complex64:
+        return xp.float32
+    elif dtyp == xp.complex128:
+        return xp.float64
+    else:
+        raise ValueError(f"Unknown dtype {dtyp}.")
+
+
 # https://github.com/numpy/numpy/blob/v2.2.0/numpy/_core/function_base.py#L195-L302
 def _logspace(start, stop, num=50, endpoint=True, base=10.0, dtype=None, *, xp):
     if not isinstance(base, float | int) and xp.asarray(base).ndim > 0:
@@ -488,6 +499,7 @@ def freqz(b, a=1, worN=512, whole=False, plot=None, fs=2*pi,
     if xp.isdtype(a.dtype, 'integral'):
         a = xp.astype(a, xp_default_dtype(xp))
     res_dtype = xp.result_type(b, a)
+    real_dtype = _real_dtype_for_complex(res_dtype, xp=xp)
 
     b = xpx.atleast_nd(b, ndim=1, xp=xp)
     a = xpx.atleast_nd(a, ndim=1, xp=xp)
@@ -509,7 +521,7 @@ def freqz(b, a=1, worN=512, whole=False, plot=None, fs=2*pi,
         # if include_nyquist is true and whole is false, w should
         # include end point
         w = xp.linspace(0, lastpoint, N,
-                        endpoint=include_nyquist and not whole, dtype=res_dtype)
+                        endpoint=include_nyquist and not whole, dtype=real_dtype)
         n_fft = N if whole else 2 * (N - 1) if include_nyquist else 2 * N
         if (xp_size(a) == 1 and (b.ndim == 1 or (b.shape[-1] == 1))
                 and n_fft >= b.shape[0]

scipy/signal/_fir_filter_design.py

@@ -834,7 +834,7 @@ def remez(numtaps, bands, desired, *, weight=None, type='bandpass',
     xp = array_namespace(bands, desired, weight)
     bands = np.asarray(bands)
     desired = np.asarray(desired)
-    if weight:
+    if weight is not None:
         weight = np.asarray(weight)
 
     fs = _validate_fs(fs, allow_none=True)

scipy/signal/_polyutils.py

@@ -117,7 +117,7 @@ def poly(seq_of_zeros, *, xp):
     if xp.isdtype(a.dtype, 'complex floating'):
         # if complex roots are all complex conjugates, the roots are real.
         roots = xp.asarray(seq_of_zeros, dtype=xp.complex128)
-        if xp.all(_sort_cmplx(roots, xp) == _sort_cmplx(xp.conj(roots), xp)):
+        if xp.all(xp.sort(xp.imag(roots)) == xp.sort(xp.imag(xp.conj(roots)))):
             a = xp.asarray(xp.real(a), copy=True)
 
     return a

scipy/signal/tests/test_filter_design.py

@@ -382,6 +382,19 @@ class TestTf2Sos:
         sos2 = tf2sos(b, a, analog=analog)
         assert_array_almost_equal(sos, sos2, decimal=4)
 
+    def test_gh_23221(self):
+        # Tests that this tf2sos call below does not produce ComplexWarnings
+        # This test is specific for scipy==1.16.0: later scipy versions do not produce
+        # the warning.
+        with suppress_warnings():
+            warnings.simplefilter("error")
+            tf2sos([0.21860986786301265, -0.4372197357260253, -0.2186098678630126,
+                    0.8744394714520509,  -0.21860986786301248, -0.4372197357260253,
+                    0.21860986786301265],
+                   [1., -4.18323041786553, 6.829924151626914, -5.407777865686045,
+                    2.0773105450802336,  -0.33482732571537893,  0.0186009178695853 ]
+            )
+
 
 @skip_xp_backends(
     cpu_only=True, reason="XXX zpk2sos is numpy-only", exceptions=['cupy']
@@ -754,6 +767,12 @@ class TestFreqz:
         xp_assert_equal(w, xp.asarray([0. , 0.1]))
         xp_assert_equal(h, xp.asarray([1.+0.j, 1.+0.j]))
 
+    def test_gh_23277(self):
+        # backwards compatibility: `w` array must be real, not complex
+        filt = [0.5 + 0.0j, 0.5 + 0.0j]
+        w, _ = freqz(filt, worN=8)
+        assert w.dtype == np.float64
+
     def test_basic(self, xp):
         w, h = freqz(xp.asarray([1.0]), worN=8)
         assert_array_almost_equal(w, xp.pi * xp.arange(8, dtype=w.dtype) / 8.)

scipy/signal/tests/test_fir_filter_design.py

@@ -546,6 +546,11 @@ class TestRemez:
         with pytest.raises(ValueError, match="Sampling.*single scalar"):
             remez(11, .1, 1, fs=np.array([10, 20]))
 
+    def test_gh_23266(self, xp):
+        bands = xp.asarray([0.0, 0.2, 0.3, 0.5])
+        desired = xp.asarray([1.0, 0.0])
+        weight = xp.asarray([1.0, 2.0])
+        remez(21, bands, desired, weight=weight)
 
 
 @skip_xp_backends(cpu_only=True, reason="lstsq")

scipy/sparse/_base.py

@@ -494,7 +494,10 @@ class _spbase(SparseABC):
             return self._mul_scalar(other)
 
         if self.ndim < 3:
-            return self.tocsr()._multiply_2d_with_broadcasting(other)
+            try:
+                return self._multiply_2d_with_broadcasting(other)
+            except AttributeError:
+                return self.tocsr()._multiply_2d_with_broadcasting(other)
 
         if not (issparse(other) or isdense(other)):
             # If it's a list or whatever, treat it like an array

scipy/sparse/tests/test_base.py

@@ -1624,6 +1624,9 @@ class _TestCommon:
         B = array([[0,7,0],[0,-4,0]])
         Asp = self.spcreator(A)
         Bsp = self.spcreator(B)
+        # check output format
+        out_fmt = Asp.format if Asp.format in ('csc', 'dia', 'bsr') else 'csr'
+        assert (Asp.multiply(Bsp)).format == out_fmt
         assert_almost_equal(Asp.multiply(Bsp).toarray(), A*B)  # sparse/sparse
         assert_almost_equal(Asp.multiply(B).toarray(), A*B)  # sparse/dense
 

scipy/stats/_continuous_distns.py

@@ -935,23 +935,26 @@ class beta_gen(rv_continuous):
             log_term = sum_ab*np.log1p(a/b) + np.log(b) - 2*np.log(sum_ab)
             return t1 + t2 + log_term
 
-        def threshold_large(v):
-            if v == 1.0:
-                return 1000
-
-            j = np.log10(v)
-            digits = int(j)
-            d = int(v / 10 ** digits) + 2
-            return d*10**(7 + j)
-
-        if a >= 4.96e6 and b >= 4.96e6:
-            return asymptotic_ab_large(a, b)
-        elif a <= 4.9e6 and b - a >= 1e6 and b >= threshold_large(a):
-            return asymptotic_b_large(a, b)
-        elif b <= 4.9e6 and a - b >= 1e6 and a >= threshold_large(b):
+        def asymptotic_a_large(a, b):
             return asymptotic_b_large(b, a)
-        else:
-            return regular(a, b)
+
+        def threshold_large(v):
+            j = np.floor(np.log10(v))
+            d = np.floor(v / 10 ** j) + 2
+            return xpx.apply_where(v != 1.0, (d, j), lambda d_, j_: d_ * 10**(7 + j_),
+                                   fill_value=1000)
+
+        threshold_a = threshold_large(a)
+        threshold_b = threshold_large(b)
+        return _lazyselect([(a >= 4.96e6) & (b >= 4.96e6),
+                            (a <= 4.9e6) & (b - a >= 1e6) & (b >= threshold_a),
+                            (b <= 4.9e6) & (a - b >= 1e6) & (a >= threshold_b),
+                            (a < 4.9e6) & (b < 4.9e6)
+                           ],
+                           [asymptotic_ab_large, asymptotic_b_large,
+                            asymptotic_a_large, regular],
+                           [a, b]
+        )
 
 
 beta = beta_gen(a=0.0, b=1.0, name='beta')

scipy/stats/tests/test_distributions.py

@@ -5003,6 +5003,19 @@ class TestBeta:
         #     return float(entropy)
         assert_allclose(stats.beta(a, b).entropy(), ref, rtol=tol)
 
+    def test_entropy_broadcasting(self):
+        # gh-23127 reported that the entropy method of the beta
+        # distribution did not broadcast correctly.
+        Beta = stats.make_distribution(stats.beta)
+        a = np.asarray([5e6, 100, 1e9, 10])
+        b = np.asarray([5e6, 1e9, 100, 20])
+        res = Beta(a=a, b=b).entropy()
+        ref = np.asarray([Beta(a=a[0], b=b[0]).entropy(),
+                          Beta(a=a[1], b=b[1]).entropy(),
+                          Beta(a=a[2], b=b[2]).entropy(),
+                          Beta(a=a[3], b=b[3]).entropy()])
+        assert_allclose(res, ref)
+
 
 class TestBetaPrime:
     # the test values are used in test_cdf_gh_17631 / test_ppf_gh_17631

scipy/stats/tests/test_fast_gen_inversion.py

@@ -6,6 +6,7 @@ from numpy.testing import (assert_array_equal, assert_allclose,
 from copy import deepcopy
 from scipy.stats.sampling import FastGeneratorInversion
 from scipy import stats
+from scipy._lib._testutils import IS_MUSL
 
 
 def test_bad_args():
@@ -142,6 +143,7 @@ def test_geninvgauss_uerror():
 
 
 # TODO: add more distributions
+@pytest.mark.skipif(IS_MUSL, reason="Hits RecursionError, see gh-23172")
 @pytest.mark.fail_slow(5)
 @pytest.mark.parametrize(("distname, args"), [("beta", (0.11, 0.11))])
 def test_error_extreme_params(distname, args):

scipy/version.py

@@ -2,10 +2,10 @@
 """
 Module to expose more detailed version info for the installed `scipy`
 """
-version = "1.16.0"
+version = "1.16.1"
 full_version = version
 short_version = version.split('.dev')[0]
-git_revision = "4d3dcc103612a2edaec7069638b7f8d0d75cab8b"
+git_revision = "0cf8e9541b1a2457992bf4ec2c0c669da373e497"
 release = 'dev' not in version and '+' not in version
 
 if not release:

{scipy-1.16.0.dist-info → scipy-1.16.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scipy
-Version: 1.16.0
+Version: 1.16.1
 Summary: Fundamental algorithms for scientific computing in Python
 Maintainer-Email: SciPy Developers <scipy-dev@python.org>
 License: Copyright (c) 2001-2002 Enthought, Inc. 2003, SciPy Developers.
@@ -948,6 +948,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Topic :: Software Development :: Libraries
 Classifier: Topic :: Scientific/Engineering
 Classifier: Operating System :: Microsoft :: Windows