scipy 1.15.3__cp312-cp312-win_amd64.whl → 1.16.0rc2__cp312-cp312-win_amd64.whl

scipy/interpolate/tests/test_interpnd.py

@@ -238,8 +238,10 @@ class TestEstimateGradients2DGlobal:
             dz = interpnd.estimate_gradients_2d_global(tri, z, tol=1e-6)
 
             assert dz.shape == (6, 2)
-            xp_assert_close(dz, np.array(grad)[None,:] + 0*dz,
-                            rtol=1e-5, atol=1e-5, err_msg="item %d" % j)
+            xp_assert_close(
+                dz, np.array(grad)[None, :] + 0*dz, rtol=1e-5, atol=1e-5, 
+                err_msg=f"item {j}"
+            )
 
     def test_regression_2359(self):
         # Check regression --- for certain point sets, gradient
@@ -300,17 +302,22 @@ class TestCloughTocher2DInterpolator:
         ]
 
         for j, func in enumerate(funcs):
-            self._check_accuracy(func, tol=1e-13, atol=1e-7, rtol=1e-7,
-                                 err_msg="Function %d" % j)
-            self._check_accuracy(func, tol=1e-13, atol=1e-7, rtol=1e-7,
-                                 alternate=True,
-                                 err_msg="Function (alternate) %d" % j)
+            self._check_accuracy(
+                func, tol=1e-13, atol=1e-7, rtol=1e-7, err_msg=f"Function {j}"
+            )
+            self._check_accuracy(
+                func, tol=1e-13, atol=1e-7, rtol=1e-7, alternate=True, 
+                err_msg=f"Function (alternate) {j}"
+            )
             # check rescaling
-            self._check_accuracy(func, tol=1e-13, atol=1e-7, rtol=1e-7,
-                                 err_msg="Function (rescaled) %d" % j, rescale=True)
-            self._check_accuracy(func, tol=1e-13, atol=1e-7, rtol=1e-7,
-                                 alternate=True, rescale=True,
-                                 err_msg="Function (alternate, rescaled) %d" % j)
+            self._check_accuracy(
+                func, tol=1e-13, atol=1e-7, rtol=1e-7, 
+                err_msg=f"Function (rescaled) {j}", rescale=True
+            )
+            self._check_accuracy(
+                func, tol=1e-13, atol=1e-7, rtol=1e-7, alternate=True, rescale=True, 
+                err_msg=f"Function (alternate, rescaled) {j}"
+            )
 
     def test_quadratic_smoketest(self):
         # Should be reasonably accurate for quadratic functions
@@ -322,10 +329,12 @@ class TestCloughTocher2DInterpolator:
         ]
 
         for j, func in enumerate(funcs):
-            self._check_accuracy(func, tol=1e-9, atol=0.22, rtol=0,
-                                 err_msg="Function %d" % j)
-            self._check_accuracy(func, tol=1e-9, atol=0.22, rtol=0,
-                                 err_msg="Function %d" % j, rescale=True)
+            self._check_accuracy(
+                func, tol=1e-9, atol=0.22, rtol=0, err_msg=f"Function {j}"
+            )
+            self._check_accuracy(
+                func, tol=1e-9, atol=0.22, rtol=0, err_msg=f"Function {j}", rescale=True
+            )
 
     def test_tri_input(self):
         # Test at single points
@@ -379,10 +388,13 @@ class TestCloughTocher2DInterpolator:
                      rng.rand(30*30, 2)]
 
         for j, func in enumerate(funcs):
-            self._check_accuracy(func, x=grid, tol=1e-9, atol=5e-3, rtol=1e-2,
-                                 err_msg="Function %d" % j)
-            self._check_accuracy(func, x=grid, tol=1e-9, atol=5e-3, rtol=1e-2,
-                                 err_msg="Function %d" % j, rescale=True)
+            self._check_accuracy(
+                func, x=grid, tol=1e-9, atol=5e-3, rtol=1e-2, err_msg=f"Function {j}"
+            )
+            self._check_accuracy(
+                func, x=grid, tol=1e-9, atol=5e-3, rtol=1e-2, 
+                err_msg=f"Function {j}", rescale=True
+            )
 
     def test_wrong_ndim(self):
         x = np.random.randn(30, 3)

scipy/interpolate/tests/test_interpolate.py

@@ -906,6 +906,50 @@ class TestAkima1DInterpolator:
         yi[:, 1, 1] = 4. * yi_
         xp_assert_close(ak(xi), yi)
 
+    def test_linear_interpolant_edge_case_1d(self):
+        x = np.array([0.0, 1.0], dtype=float)
+        y = np.array([0.5, 1.0])
+        akima = Akima1DInterpolator(x, y, axis=0, extrapolate=None)
+        xp_assert_close(akima(0.45), np.array(0.725))
+
+    def test_linear_interpolant_edge_case_2d(self):
+        x = np.array([0., 1.])
+        y = np.column_stack((x, 2. * x, 3. * x, 4. * x))
+
+        ak = Akima1DInterpolator(x, y)
+        xi = np.array([0.5, 1.])
+        yi = np.array([[0.5, 1., 1.5, 2. ],
+                       [1., 2., 3., 4.]])
+        xp_assert_close(ak(xi), yi)
+
+        ak = Akima1DInterpolator(x, y.T, axis=1)
+        xp_assert_close(ak(xi), yi.T)
+
+    def test_linear_interpolant_edge_case_3d(self):
+        x = np.arange(0., 2.)
+        y_ = np.array([0., 1.])
+        y = np.empty((2, 2, 2))
+        y[:, 0, 0] = y_
+        y[:, 1, 0] = 2. * y_
+        y[:, 0, 1] = 3. * y_
+        y[:, 1, 1] = 4. * y_
+        ak = Akima1DInterpolator(x, y)
+        yi_ = np.array([0.5, 1.])
+        yi = np.empty((2, 2, 2))
+        yi[:, 0, 0] = yi_
+        yi[:, 1, 0] = 2. * yi_
+        yi[:, 0, 1] = 3. * yi_
+        yi[:, 1, 1] = 4. * yi_
+        xi = yi_
+        xp_assert_close(ak(xi), yi)
+
+        ak = Akima1DInterpolator(x, y.transpose(1, 0, 2), axis=1)
+        xp_assert_close(ak(xi), yi.transpose(1, 0, 2))
+
+        ak = Akima1DInterpolator(x, y.transpose(2, 1, 0), axis=2)
+        xp_assert_close(ak(xi), yi.transpose(2, 1, 0))
+
+
     def test_degenerate_case_multidimensional(self):
         # This test is for issue #5683.
         x = np.array([0, 1, 2])
@@ -1354,8 +1398,7 @@ class TestPPoly:
 
         xi = np.linspace(0, 1, 200)
         for dx in range(0, 10):
-            xp_assert_close(pp(xi, dx), pp.derivative(dx)(xi),
-                            err_msg="dx=%d" % (dx,))
+            xp_assert_close(pp(xi, dx), pp.derivative(dx)(xi), err_msg=f"dx={dx}")
 
     def test_antiderivative_of_constant(self):
         # https://github.com/scipy/scipy/issues/4216
@@ -1418,8 +1461,9 @@ class TestPPoly:
                 r = 1e-13
                 endpoint = r*pp2.x[:-1] + (1 - r)*pp2.x[1:]
 
-                xp_assert_close(pp2(pp2.x[1:]), pp2(endpoint),
-                                rtol=1e-7, err_msg="dx=%d k=%d" % (dx, k))
+                xp_assert_close(
+                    pp2(pp2.x[1:]), pp2(endpoint), rtol=1e-7, err_msg=f"dx={dx} k={k}"
+                )
 
     def test_antiderivative_vs_spline(self):
         rng = np.random.RandomState(1234)

scipy/interpolate/tests/test_rgi.py

@@ -4,6 +4,8 @@ import pytest
 import numpy as np
 
 from numpy.testing import assert_warns
+from numpy.exceptions import ComplexWarning
+
 from scipy._lib._array_api import (
     xp_assert_equal, xp_assert_close, assert_array_almost_equal
 )
@@ -16,7 +18,6 @@ from scipy.interpolate import (RegularGridInterpolator, interpn,
                                NearestNDInterpolator, LinearNDInterpolator)
 
 from scipy.sparse._sputils import matrix
-from scipy._lib._util import ComplexWarning
 from scipy._lib._testutils import _run_concurrent_barrier
 
 

scipy/io/_fast_matrix_market/__init__.py

@@ -194,6 +194,8 @@ def _get_read_cursor(source, parallelism=None):
             source = bz2.BZ2File(path, 'rb')
             ret_stream_to_close = source
         else:
+            if not os.path.exists(path):
+                raise FileNotFoundError(f"The source file does not exist: {path}")
             return _fmm_core.open_read_file(path, parallelism), ret_stream_to_close
 
     # Stream object.

scipy/io/_harwell_boeing/_fortran_format_parser.py

@@ -72,20 +72,20 @@ class IntFormat:
     def __repr__(self):
         r = "IntFormat("
         if self.repeat:
-            r += "%d" % self.repeat
-        r += "I%d" % self.width
+            r += f"{self.repeat}"
+        r += f"I{self.width}"
         if self.min:
-            r += ".%d" % self.min
+            r += f".{self.min}"
         return r + ")"
 
     @property
     def fortran_format(self):
         r = "("
         if self.repeat:
-            r += "%d" % self.repeat
-        r += "I%d" % self.width
+            r += f"{self.repeat}"
+        r += f"I{self.width}"
         if self.min:
-            r += ".%d" % self.min
+            r += f".{self.min}"
         return r + ")"
 
     @property
@@ -145,20 +145,20 @@ class ExpFormat:
     def __repr__(self):
         r = "ExpFormat("
         if self.repeat:
-            r += "%d" % self.repeat
-        r += "E%d.%d" % (self.width, self.significand)
+            r += f"{self.repeat}"
+        r += f"E{self.width}.{self.significand}"
         if self.min:
-            r += "E%d" % self.min
+            r += f"E{self.min}"
         return r + ")"
 
     @property
     def fortran_format(self):
         r = "("
         if self.repeat:
-            r += "%d" % self.repeat
-        r += "E%d.%d" % (self.width, self.significand)
+            r += f"{self.repeat}"
+        r += f"E{self.width}.{self.significand}"
         if self.min:
-            r += "E%d" % self.min
+            r += f"E{self.min}"
         return r + ")"
 
     @property
@@ -200,8 +200,10 @@ class Tokenizer:
                 else:
                     self.curpos = m.end()
                     return Token(self.tokens[i], m.group(), self.curpos)
-            raise SyntaxError("Unknown character at position %d (%s)"
-                              % (self.curpos, self.data[curpos]))
+            raise SyntaxError(
+                f"Unknown character at position {self.curpos} "
+                f"({self.data[self.curpos]})"
+            )
 
 
 # Grammar for fortran format:
@@ -263,8 +265,9 @@ class FortranFormatParser:
 
     def _parse_format(self, tokens):
         if not tokens[0].type == "LPAR":
-            raise SyntaxError("Expected left parenthesis at position "
-                              "%d (got '%s')" % (0, tokens[0].value))
+            raise SyntaxError(
+                f"Expected left parenthesis at position {0} (got '{tokens[0].value}')"
+            )
         elif not tokens[-1].type == "RPAR":
             raise SyntaxError("Expected right parenthesis at position "
                               f"{len(tokens)} (got '{tokens[-1].value}')")

scipy/io/_harwell_boeing/hb.py

@@ -189,9 +189,10 @@ class HBInfo:
         nnon_zeros = _expect_int(line[42:56])
         nelementals = _expect_int(line[56:70])
         if not nelementals == 0:
-            raise ValueError("Unexpected value %d for nltvl (last entry of line 3)"
-                             % nelementals)
-
+            raise ValueError(
+                f"Unexpected value {nelementals} for nltvl (last entry of line 3)"
+            )
+        
         # Fourth line
         line = fid.readline().strip("\n")
 
@@ -282,18 +283,13 @@ class HBInfo:
         """Gives the header corresponding to this instance as a string."""
         header = [self.title.ljust(72) + self.key.ljust(8)]
 
-        header.append("%14d%14d%14d%14d" %
-                      (self.total_nlines, self.pointer_nlines,
-                       self.indices_nlines, self.values_nlines))
-        header.append("%14s%14d%14d%14d%14d" %
-                      (self.mxtype.fortran_format.ljust(14), self.nrows,
-                       self.ncols, self.nnon_zeros, 0))
+        header.append(f"{self.total_nlines:14d}{self.pointer_nlines:14d}{self.indices_nlines:14d}{self.values_nlines:14d}")
+        header.append(f"{self.mxtype.fortran_format.ljust(14):14s}{self.nrows:14d}{self.ncols:14d}{self.nnon_zeros:14d}{0:14d}")
 
         pffmt = self.pointer_format.fortran_format
         iffmt = self.indices_format.fortran_format
         vffmt = self.values_format.fortran_format
-        header.append("%16s%16s%20s" %
-                      (pffmt.ljust(16), iffmt.ljust(16), vffmt.ljust(20)))
+        header.append(f"{pffmt.ljust(16):16s}{iffmt.ljust(16):16s}{vffmt.ljust(20):20s}")
         return "\n".join(header)
 
 

scipy/io/_idl.py

@@ -217,7 +217,7 @@ def _read_data(f, dtype):
     elif dtype == 15:
         return _read_uint64(f)
     else:
-        raise Exception("Unknown IDL type: %i - please report this" % dtype)
+        raise Exception(f"Unknown IDL type: {dtype} - please report this")
 
 
 def _read_structure(f, array_desc, struct_desc):
@@ -238,8 +238,7 @@ def _read_structure(f, array_desc, struct_desc):
                 dtype.append(((col['name'].lower(), col['name']),
                                     DTYPE_DICT[col['typecode']]))
             else:
-                raise Exception("Variable type %i not implemented" %
-                                                            col['typecode'])
+                raise Exception(f"Variable type {col['typecode']} not implemented")
 
     structure = np.rec.recarray((nrows, ), dtype=dtype)
 
@@ -324,7 +323,7 @@ def _read_record(f):
     _skip_bytes(f, 4)
 
     if record['rectype'] not in RECTYPE_DICT:
-        raise Exception("Unknown RECTYPE: %i" % record['rectype'])
+        raise Exception(f"Unknown RECTYPE: {record['rectype']}")
 
     record['rectype'] = RECTYPE_DICT[record['rectype']]
 
@@ -482,8 +481,7 @@ def _read_arraydesc(f):
             arraydesc['dims'].append(_read_long(f))
 
     else:
-
-        raise Exception("Unknown ARRSTART: %i" % arraydesc['arrstart'])
+        raise Exception(f"Unknown ARRSTART: {arraydesc['arrstart']}")
 
     return arraydesc
 
@@ -902,7 +900,7 @@ def readsav(file_name, idict=None, python_dict=False,
 
         for rt in set(rectypes):
             if rt != 'END_MARKER':
-                print(" - %i are of type %s" % (rectypes.count(rt), rt))
+                print(f" - {rectypes.count(rt)} are of type {rt}")
         print("-"*50)
 
         if 'VARIABLE' in rectypes:

scipy/io/_netcdf.py

@@ -132,9 +132,13 @@ class netcdf_file:
 
     Notes
     -----
+    This module is derived from
+    `pupynere <https://bitbucket.org/robertodealmeida/pupynere/>`_.
     The major advantage of this module over other modules is that it doesn't
-    require the code to be linked to the NetCDF libraries. This module is
-    derived from `pupynere <https://bitbucket.org/robertodealmeida/pupynere/>`_.
+    require the code to be linked to the NetCDF libraries. However, for a more
+    recent version of the NetCDF standard and additional features, please consider
+    the permissively-licensed
+    `netcdf4-python <https://unidata.github.io/netcdf4-python/>`_.
 
     NetCDF files are a self-describing binary data format. The file contains
     metadata that describes the dimensions and variables in the file. More
@@ -563,7 +567,7 @@ class netcdf_file:
             types = [(int, NC_INT), (float, NC_FLOAT), (str, NC_CHAR)]
 
             # bytes index into scalars in py3k. Check for "string" types
-            if isinstance(values, (str, bytes)):
+            if isinstance(values, str | bytes):
                 sample = values
             else:
                 try:
@@ -682,8 +686,8 @@ class netcdf_file:
                     actual_size = reduce(mul, (1,) + shape[1:]) * size
                     padding = -actual_size % 4
                     if padding:
-                        dtypes['names'].append('_padding_%d' % var)
-                        dtypes['formats'].append('(%d,)>b' % padding)
+                        dtypes['names'].append(f'_padding_{var}')
+                        dtypes['formats'].append(f'({padding},)>b')
 
                 # Data will be set later.
                 data = None
@@ -856,6 +860,12 @@ class netcdf_variable:
     --------
     isrec, shape
 
+    Notes
+    -----
+    For a more recent version of the NetCDF standard and additional features, please
+    consider the permissively-licensed
+    `netcdf4-python <https://unidata.github.io/netcdf4-python/>`_.
+
     """
     def __init__(self, data, typecode, size, shape, dimensions,
                  attributes=None,

scipy/io/arff/tests/test_arffread.py

@@ -40,8 +40,8 @@ expected_types = ['numeric', 'numeric', 'numeric', 'numeric', 'nominal']
 missing = pjoin(data_path, 'missing.arff')
 expect_missing_raw = np.array([[1, 5], [2, 4], [np.nan, np.nan]])
 expect_missing = np.empty(3, [('yop', float), ('yap', float)])
-expect_missing['yop'] = expect_missing_raw[:, 0]  # type: ignore[call-overload]
-expect_missing['yap'] = expect_missing_raw[:, 1]  # type: ignore[call-overload]
+expect_missing['yop'] = expect_missing_raw[:, 0]
+expect_missing['yap'] = expect_missing_raw[:, 1]
 
 
 class TestData:
@@ -147,7 +147,7 @@ class TestHeader:
         # Test numerical attributes
         assert_(len(attrs) == 5)
         for i in range(4):
-            assert_(attrs[i].name == 'attr%d' % i)
+            assert_(attrs[i].name == f'attr{i}')
             assert_(attrs[i].type_name == 'numeric')
 
         # Test nominal attribute

scipy/io/matlab/__init__.py

@@ -14,6 +14,7 @@ and writing MATLAB files.
    MatReadError - Exception indicating a read issue
    MatReadWarning - Warning class for read issues
    MatWriteError - Exception indicating a write issue
+   MatWriteWarning - Warning class for write issues
    mat_struct - Class used when ``struct_as_record=False``
    varmats_from_mat - Pull variables out of mat 5 file as a sequence of mat file objects
 
@@ -38,7 +39,7 @@ namespace also exist in this namespace:
 
 Notes
 -----
-MATLAB(R) is a registered trademark of The MathWorks, Inc., 3 Apple Hill
+MATLAB® is a registered trademark of The MathWorks, Inc., 3 Apple Hill
 Drive, Natick, MA 01760-2098, USA.
 
 """
@@ -47,7 +48,7 @@ from ._mio import loadmat, savemat, whosmat
 from ._mio5 import MatlabFunction, varmats_from_mat
 from ._mio5_params import MatlabObject, MatlabOpaque, mat_struct
 from ._miobase import (matfile_version, MatReadError, MatReadWarning,
-                      MatWriteError)
+                      MatWriteError, MatWriteWarning)
 
 # Deprecated namespaces, to be removed in v2.0.0
 from .import (mio, mio5, mio5_params, mio4, byteordercodes,
@@ -56,7 +57,8 @@ from .import (mio, mio5, mio5_params, mio4, byteordercodes,
 __all__ = [
     'loadmat', 'savemat', 'whosmat', 'MatlabObject',
     'matfile_version', 'MatReadError', 'MatReadWarning',
-    'MatWriteError', 'mat_struct', 'MatlabOpaque', 'MatlabFunction', 'varmats_from_mat',
+    'MatWriteError', 'MatWriteWarning', 'mat_struct', 'MatlabOpaque',
+    'MatlabFunction', 'varmats_from_mat',
 ]
 
 from scipy._lib._testutils import PytestTester

scipy/io/matlab/_mio.py

@@ -267,7 +267,10 @@ def savemat(file_name, mdict,
         True``).
         Can also pass open file_like object.
     mdict : dict
-        Dictionary from which to save matfile variables.
+        Dictionary from which to save matfile variables. Note that if this dict
+        has a key starting with ``_`` or a sub-dict has a key starting with ``_``
+        or a digit, these key's items will not be saved in the mat file and
+        `MatWriteWarning` will be issued.
     appendmat : bool, optional
         True (the default) to append the .mat extension to the end of the
         given filename, if not already present.

scipy/io/matlab/_mio5.py

@@ -87,7 +87,7 @@ from ._byteordercodes import native_code, swapped_code
 
 from ._miobase import (MatFileReader, docfiller, matdims, read_dtype,
                       arr_to_chars, arr_dtype_number, MatWriteError,
-                      MatReadError, MatReadWarning)
+                      MatReadError, MatReadWarning, MatWriteWarning)
 
 # Reader object for matlab 5 format variables
 from ._mio5_utils import VarReader5
@@ -221,7 +221,7 @@ class MatFile5Reader(MatFileReader):
         hdict['__header__'] = hdr['description'].item().strip(b' \t\n\000')
         v_major = hdr['version'] >> 8
         v_minor = hdr['version'] & 0xFF
-        hdict['__version__'] = '%d.%d' % (v_major, v_minor)
+        hdict['__version__'] = f'{v_major}.{v_minor}'
         return hdict
 
     def initialize_read(self):
@@ -267,7 +267,7 @@ class MatFile5Reader(MatFileReader):
             check_stream_limit = False
             self._matrix_reader.set_stream(self.mat_stream)
         if not mdtype == miMATRIX:
-            raise TypeError('Expecting miMATRIX type here, got %d' % mdtype)
+            raise TypeError(f'Expecting miMATRIX type here, got {mdtype}')
         header = self._matrix_reader.read_header(check_stream_limit)
         return header, next_pos
 
@@ -482,10 +482,14 @@ def to_writeable(source):
         dtype = []
         values = []
         for field, value in source.items():
-            if (isinstance(field, str) and
-                    field[0] not in '_0123456789'):
-                dtype.append((str(field), object))
-                values.append(value)
+            if isinstance(field, str):
+                if field[0] not in '_0123456789':
+                    dtype.append((str(field), object))
+                    values.append(value)
+                else:
+                    msg = (f"Starting field name with a underscore "
+                           f"or a digit ({field}) is ignored")
+                    warnings.warn(msg, MatWriteWarning, stacklevel=2)
         if dtype:
             return np.array([tuple(values)], dtype)
         else:
@@ -512,7 +516,7 @@ NDT_ARRAY_FLAGS = MDTYPES[native_code]['dtypes']['array_flags']
 class VarWriter5:
     ''' Generic matlab matrix writing class '''
     mat_tag = np.zeros((), NDT_TAG_FULL)
-    mat_tag['mdtype'] = miMATRIX  # type: ignore[call-overload]
+    mat_tag['mdtype'] = miMATRIX
 
     def __init__(self, file_writer):
         self.file_stream = file_writer.file_stream
@@ -789,12 +793,11 @@ class VarWriter5:
         length = max([len(fieldname) for fieldname in fieldnames])+1
         max_length = (self.long_field_names and 64) or 32
         if length > max_length:
-            raise ValueError("Field names are restricted to %d characters" %
-                             (max_length-1))
+            raise ValueError(
+                f"Field names are restricted to {max_length - 1} characters"
+            )
         self.write_element(np.array([length], dtype='i4'))
-        self.write_element(
-            np.array(fieldnames, dtype='S%d' % (length)),
-            mdtype=miINT8)
+        self.write_element(np.array(fieldnames, dtype=f'S{length}'), mdtype=miINT8)
         A = np.atleast_2d(arr).flatten('F')
         for el in A:
             for f in fieldnames:
@@ -879,6 +882,9 @@ class MatFile5Writer:
         self._matrix_writer = VarWriter5(self)
         for name, var in mdict.items():
             if name[0] == '_':
+                msg = (f"Starting field name with a "
+                       f"underscore ({name}) is ignored")
+                warnings.warn(msg, MatWriteWarning, stacklevel=2)
                 continue
             is_global = name in self.global_vars
             if self.do_compression:

scipy/io/matlab/_miobase.py

@@ -14,7 +14,7 @@ from scipy._lib import doccer
 from . import _byteordercodes as boc
 
 __all__ = [
-    'MatReadError', 'MatReadWarning', 'MatWriteError',
+    'MatReadError', 'MatReadWarning', 'MatWriteError', 'MatWriteWarning',
 ]
 
 class MatReadError(Exception):
@@ -28,6 +28,9 @@ class MatWriteError(Exception):
 class MatReadWarning(UserWarning):
     """Warning class for read issues."""
 
+class MatWriteWarning(UserWarning):
+    """Warning class for write issues."""
+
 
 doc_dict = \
     {'file_arg':