scipy 1.16.0rc2__cp313-cp313-macosx_14_0_arm64.whl → 1.16.1__cp313-cp313-macosx_14_0_arm64.whl

scipy/__config__.py

@@ -36,7 +36,7 @@ CONFIG = _cleanup(
             "cython": {
                 "name": r"cython",
                 "linker": r"cython",
-                "version": r"3.1.1",
+                "version": r"3.1.2",
                 "commands": r"cython",
                 "args": r"",
                 "linker args": r"",
@@ -52,14 +52,14 @@ CONFIG = _cleanup(
             "fortran": {
                 "name": "gcc",
                 "linker": r"ld64",
-                "version": "13.3.0",
+                "version": "13.4.0",
                 "commands": r"gfortran",
                 "args": r"",
                 "linker args": r"",
             },
             "pythran": {
                 "version": r"0.18.0",
-                "include directory": r"../../../../../../private/var/folders/y6/nj790rtn62lfktb1sh__79hc0000gn/T/pip-build-env-ll1mab9y/overlay/lib/python3.13/site-packages/pythran"
+                "include directory": r"../../../../../../private/var/folders/y6/nj790rtn62lfktb1sh__79hc0000gn/T/build-env-b1iku3ur/lib/python3.13/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"/private/var/folders/y6/nj790rtn62lfktb1sh__79hc0000gn/T/cibw-run-py4859z1/cp313-macosx_arm64/build/venv/bin/python",
+            "path": r"/private/var/folders/y6/nj790rtn62lfktb1sh__79hc0000gn/T/build-env-b1iku3ur/bin/python",
             "version": "3.13",
         },
     }

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/conftest.py

@@ -34,6 +34,31 @@ except Exception:
 
 
 def pytest_configure(config):
+    """
+    Add pytest markers to avoid PytestUnknownMarkWarning
+
+    This needs to contain all markers that are SciPy-specific, as well as
+    dummy fallbacks for markers defined in optional test packages.
+
+    Note that we need both the registration here *and* in `pytest.ini`.
+    """
+    config.addinivalue_line("markers",
+        "slow: Tests that are very slow.")
+    config.addinivalue_line("markers",
+        "xslow: mark test as extremely slow (not run unless explicitly requested)")
+    config.addinivalue_line("markers",
+        "xfail_on_32bit: mark test as failing on 32-bit platforms")
+    config.addinivalue_line("markers",
+        "array_api_backends: test iterates on all array API backends")
+    config.addinivalue_line("markers",
+        ("skip_xp_backends(backends, reason=None, np_only=False, cpu_only=False, " +
+         "eager_only=False, exceptions=None): mark the desired skip configuration " +
+         "for the `skip_xp_backends` fixture"))
+    config.addinivalue_line("markers",
+        ("xfail_xp_backends(backends, reason=None, np_only=False, cpu_only=False, " +
+         "eager_only=False, exceptions=None): mark the desired xfail configuration " +
+         "for the `xfail_xp_backends` fixture"))
+
     try:
         import pytest_timeout  # noqa:F401
     except Exception:

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/blas.py

@@ -45,15 +45,19 @@ BLAS Level 1 functions
 .. autosummary::
    :toctree: generated/
 
-   caxpy
-   ccopy
-   cdotc
-   cdotu
-   crotg
-   cscal
-   csrot
-   csscal
-   cswap
+   sasum
+   saxpy
+   scasum
+   scnrm2
+   scopy
+   sdot
+   snrm2
+   srot
+   srotg
+   srotm
+   srotmg
+   sscal
+   sswap
    dasum
    daxpy
    dcopy
@@ -71,19 +75,15 @@ BLAS Level 1 functions
    idamax
    isamax
    izamax
-   sasum
-   saxpy
-   scasum
-   scnrm2
-   scopy
-   sdot
-   snrm2
-   srot
-   srotg
-   srotm
-   srotmg
-   sscal
-   sswap
+   caxpy
+   ccopy
+   cdotc
+   cdotu
+   crotg
+   cscal
+   csrot
+   csscal
+   cswap
    zaxpy
    zcopy
    zdotc
@@ -104,12 +104,15 @@ BLAS Level 2 functions
    sgemv
    sger
    ssbmv
+   sspmv
    sspr
    sspr2
    ssymv
    ssyr
    ssyr2
    stbmv
+   stbsv
+   stpmv
    stpsv
    strmv
    strsv
@@ -117,12 +120,15 @@ BLAS Level 2 functions
    dgemv
    dger
    dsbmv
+   dspmv
    dspr
    dspr2
    dsymv
    dsyr
    dsyr2
    dtbmv
+   dtbsv
+   dtpmv
    dtpsv
    dtrmv
    dtrsv
@@ -137,13 +143,15 @@ BLAS Level 2 functions
    chpmv
    chpr
    chpr2
+   cspmv
+   cspr
+   csyr
    ctbmv
    ctbsv
    ctpmv
    ctpsv
    ctrmv
    ctrsv
-   csyr
    zgbmv
    zgemv
    zgerc
@@ -155,12 +163,15 @@ BLAS Level 2 functions
    zhpmv
    zhpr
    zhpr2
+   zspmv
+   zspr
+   zsyr
    ztbmv
    ztbsv
    ztpmv
+   ztpsv
    ztrmv
    ztrsv
-   zsyr
 
 BLAS Level 3 functions
 ----------------------

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/_lbfgsb_py.py

@@ -42,6 +42,8 @@ from ._optimize import (MemoizeJac, OptimizeResult, _call_callback_maybe_halt,
 from ._constraints import old_bound_to_new
 
 from scipy.sparse.linalg import LinearOperator
+from scipy._lib.deprecation import _NoValue
+import warnings
 
 __all__ = ['fmin_l_bfgs_b', 'LbfgsInvHessProduct']
 
@@ -93,7 +95,7 @@ def fmin_l_bfgs_b(func, x0, fprime=None, args=(),
                   approx_grad=0,
                   bounds=None, m=10, factr=1e7, pgtol=1e-5,
                   epsilon=1e-8,
-                  iprint=-1, maxfun=15000, maxiter=15000, disp=None,
+                  iprint=_NoValue, maxfun=15000, maxiter=15000, disp=_NoValue,
                   callback=None, maxls=20):
     """
     Minimize a function func using the L-BFGS-B algorithm.
@@ -144,7 +146,7 @@ def fmin_l_bfgs_b(func, x0, fprime=None, args=(),
         output and this keyword has no function.
 
         .. deprecated:: 1.15.0
-            This keyword is deprecated and will be removed from SciPy 1.17.0.
+            This keyword is deprecated and will be removed from SciPy 1.18.0.
 
     disp : int, optional
         Deprecated option that previously controlled the text printed on the
@@ -152,7 +154,7 @@ def fmin_l_bfgs_b(func, x0, fprime=None, args=(),
         output and this keyword has no function.
 
         .. deprecated:: 1.15.0
-            This keyword is deprecated and will be removed from SciPy 1.17.0.
+            This keyword is deprecated and will be removed from SciPy 1.18.0.
 
     maxfun : int, optional
         Maximum number of function evaluations. Note that this function
@@ -265,7 +267,9 @@ def fmin_l_bfgs_b(func, x0, fprime=None, args=(),
 
     # build options
     callback = _wrap_callback(callback)
-    opts = {'maxcor': m,
+    opts = {'disp': disp,
+            'iprint': iprint,
+            'maxcor': m,
             'ftol': factr * np.finfo(float).eps,
             'gtol': pgtol,
             'eps': epsilon,
@@ -288,9 +292,9 @@ def fmin_l_bfgs_b(func, x0, fprime=None, args=(),
 
 
 def _minimize_lbfgsb(fun, x0, args=(), jac=None, bounds=None,
-                     disp=None, maxcor=10, ftol=2.2204460492503131e-09,
+                     disp=_NoValue, maxcor=10, ftol=2.2204460492503131e-09,
                      gtol=1e-5, eps=1e-8, maxfun=15000, maxiter=15000,
-                     iprint=-1, callback=None, maxls=20,
+                     iprint=_NoValue, callback=None, maxls=20,
                      finite_diff_rel_step=None, workers=None,
                      **unknown_options):
     """
@@ -305,7 +309,7 @@ def _minimize_lbfgsb(fun, x0, args=(), jac=None, bounds=None,
         output and this keyword has no function.
 
         .. deprecated:: 1.15.0
-            This keyword is deprecated and will be removed from SciPy 1.17.0.
+            This keyword is deprecated and will be removed from SciPy 1.18.0.
 
     maxcor : int
         The maximum number of variable metric corrections used to
@@ -334,7 +338,7 @@ def _minimize_lbfgsb(fun, x0, args=(), jac=None, bounds=None,
         output and this keyword has no function.
 
         .. deprecated:: 1.15.0
-            This keyword is deprecated and will be removed from SciPy 1.17.0.
+            This keyword is deprecated and will be removed from SciPy 1.18.0.
 
     maxls : int, optional
         Maximum number of line search steps (per iteration). Default is 20.
@@ -373,6 +377,17 @@ def _minimize_lbfgsb(fun, x0, args=(), jac=None, bounds=None,
 
     x0 = asarray(x0).ravel()
     n, = x0.shape
+    if disp is not _NoValue:
+        warnings.warn("scipy.optimize: The `disp` and `iprint` options of the "
+                      "L-BFGS-B solver are deprecated and will be removed in "
+                      "SciPy 1.18.0.",
+                      DeprecationWarning, stacklevel=3)
+
+    if iprint is not _NoValue:
+        warnings.warn("scipy.optimize: The `disp` and `iprint` options of the "
+                      "L-BFGS-B solver are deprecated and will be removed in "
+                      "SciPy 1.18.0.",
+                      DeprecationWarning, stacklevel=3)
 
     # historically old-style bounds were/are expected by lbfgsb.
     # That's still the case but we'll deal with new-style from here on,

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/optimize/tests/test_optimize.py

@@ -1126,7 +1126,7 @@ class TestOptimizeSimple(CheckOptimize):
 
     def test_minimize_l_bfgs_b(self):
         # Minimize with L-BFGS-B method
-        opts = {'disp': False, 'maxiter': self.maxiter}
+        opts = {'maxiter': self.maxiter}
         r = optimize.minimize(self.func, self.startparams,
                               method='L-BFGS-B', jac=self.grad,
                               options=opts)
@@ -1156,7 +1156,7 @@ class TestOptimizeSimple(CheckOptimize):
         # Check that the `ftol` parameter in l_bfgs_b works as expected
         v0 = None
         for tol in [1e-1, 1e-4, 1e-7, 1e-10]:
-            opts = {'disp': False, 'maxiter': self.maxiter, 'ftol': tol}
+            opts = {'maxiter': self.maxiter, 'ftol': tol}
             sol = optimize.minimize(self.func, self.startparams,
                                     method='L-BFGS-B', jac=self.grad,
                                     options=opts)
@@ -1173,7 +1173,7 @@ class TestOptimizeSimple(CheckOptimize):
         # check that the maxls is passed down to the Fortran routine
         sol = optimize.minimize(optimize.rosen, np.array([-1.2, 1.0]),
                                 method='L-BFGS-B', jac=optimize.rosen_der,
-                                options={'disp': False, 'maxls': 1})
+                                options={'maxls': 1})
         assert not sol.success
 
     def test_minimize_l_bfgs_b_maxfun_interruption(self):