Merge pull request #14937 from rgommers/ci-failures-17x

MAINT: backports for 1.7.2, plus update Pythran min version to 0.9.12

.coveragerc

@@ -5,3 +5,4 @@ omit =
     scipy/setup.py
     scipy/*/setup.py
     scipy/signal/_max_len_seq_inner.py
+disable_warnings = include-ignored

.github/workflows/macos.yml

@@ -81,4 +81,5 @@ jobs:
 
     - name: Test SciPy
       run: |
+        export LIBRARY_PATH="$LIBRARY_PATH:/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib"
         SCIPY_USE_PYTHRAN=`test ${{ matrix.python-version }} != 3.9; echo $?` python -u runtests.py

pyproject.toml

@@ -13,7 +13,7 @@ requires = [
     "setuptools<58.0.0",
     "Cython>=0.29.18,<3.0",
     "pybind11>=2.4.3,<2.8.0",
-    "pythran>=0.9.11,<0.10.0",
+    "pythran>=0.9.12,<0.10.0",
 
     # NumPy dependencies - to update these, sync from
     # https://github.com/scipy/oldest-supported-numpy/, and then

scipy/cluster/_hierarchy.pyx

@@ -11,6 +11,7 @@ cdef extern from "numpy/npy_math.h":
 
 ctypedef unsigned char uchar
 
+np.import_array()
 
 # _hierarchy_distance_update.pxi includes the definition of linkage_distance_update
 # and the distance update functions for the supported linkage methods.

scipy/cluster/_optimal_leaf_ordering.pyx

@@ -32,6 +32,7 @@ from libc.stdlib cimport malloc, free
 
 from scipy.spatial.distance import squareform, is_valid_y, is_valid_dm
 
+np.import_array()
 
 @cython.profile(False)
 @cython.boundscheck(False)

scipy/fftpack/convolve.pyx

@@ -3,6 +3,8 @@ import numpy as np
 cimport numpy as np
 cimport cython
 
+np.import_array()
+
 __all__ = ['destroy_convolve_cache', 'convolve', 'convolve_z',
            'init_convolution_kernel']
 

scipy/interpolate/_bspl.pyx

@@ -8,6 +8,8 @@ cimport numpy as cnp
 
 cimport cython
 
+cnp.import_array()
+
 cdef extern from "src/__fitpack.h":
     void _deBoor_D(const double *t, double x, int k, int ell, int m, double *result) nogil
 

scipy/io/matlab/mio_utils.pyx

@@ -5,6 +5,8 @@
 import numpy as np
 cimport numpy as cnp
 
+cnp.import_array()
+
 
 cpdef object squeeze_element(cnp.ndarray arr):
     ''' Return squeezed element

scipy/ndimage/src/_cytest.pyx

@@ -6,6 +6,7 @@ from cpython.pycapsule cimport (
 cimport numpy as np
 from numpy cimport npy_intp as intp
 
+np.import_array()
 
 cdef void _destructor(obj):
     cdef void *callback_data = PyCapsule_GetContext(obj)

scipy/optimize/_bglu_dense.pyx

@@ -11,6 +11,8 @@ try:
 except ImportError:
     from time import clock as timer
 
+np.import_array()
+
 __all__ = ['LU', 'BGLU']
 
 @cython.boundscheck(False)

scipy/optimize/_group_columns.pyx

@@ -10,6 +10,8 @@ import numpy as np
 cimport numpy as np
 from cpython cimport bool
 
+np.import_array()
+
 
 @cython.boundscheck(False)
 @cython.wraparound(False)

scipy/optimize/_highs/cython/src/_highs_wrapper.pyx

@@ -64,6 +64,8 @@ from .HighsOptions cimport (
 )
 from .HighsModelUtils cimport utilPrimalDualStatusToString
 
+np.import_array()
+
 # options to reference for default values and bounds;
 # make a map to quickly lookup
 cdef HighsOptions _ref_opts

scipy/optimize/_trlib/_trlib.pyx

@@ -6,6 +6,7 @@ cimport numpy as np
 
 from scipy._lib.messagestream cimport MessageStream
 
+np.import_array()
 
 class TRLIBQuadraticSubproblem(BaseQuadraticSubproblem):
 

scipy/signal/_max_len_seq_inner.pyx

@@ -5,6 +5,7 @@ import numpy as np
 cimport numpy as np
 cimport cython
 
+np.import_array()
 
 # Fast inner loop of max_len_seq.
 @cython.cdivision(True)  # faster modulo

scipy/signal/_peak_finding_utils.pyx

@@ -11,6 +11,7 @@ import numpy as np
 cimport numpy as np
 from libc.math cimport ceil
 
+np.import_array()
 
 __all__ = ['_local_maxima_1d', '_select_by_peak_distance', '_peak_prominences',
            '_peak_widths']

scipy/signal/_sosfilt.pyx

@@ -1,6 +1,8 @@
 cimport numpy as np
 cimport cython
 
+np.import_array()
+
 ctypedef fused DTYPE_floating_t:
     float
     float complex

scipy/signal/_spectral.pyx

@@ -7,6 +7,8 @@ import numpy as np
 cimport numpy as np
 cimport cython
 
+np.import_array()
+
 __all__ = ['_lombscargle']
 
 

scipy/signal/_upfirdn_apply.pyx

@@ -40,6 +40,7 @@ from cython import bint  # boolean integer type
 from libc.stdlib cimport malloc, free
 from libc.string cimport memset
 
+np.import_array()
 
 ctypedef double complex double_complex
 ctypedef float complex float_complex

scipy/sparse/csgraph/_flow.pyx

@@ -7,6 +7,8 @@ cimport numpy as np
 
 include 'parameters.pxi'
 
+np.import_array()
+
 
 class MaximumFlowResult:
     """Represents the result of a maximum flow calculation.

scipy/sparse/csgraph/_matching.pyx

@@ -9,6 +9,8 @@ from numpy.math cimport INFINITY
 from scipy.sparse import (csr_matrix,
                           isspmatrix_coo, isspmatrix_csc, isspmatrix_csr)
 
+np.import_array()
+
 include "parameters.pxi"
 
 

scipy/sparse/csgraph/_min_spanning_tree.pyx

@@ -8,6 +8,8 @@ cimport cython
 from scipy.sparse import csr_matrix, isspmatrix_csc, isspmatrix
 from scipy.sparse.csgraph._validation import validate_graph
 
+np.import_array()
+
 include 'parameters.pxi'
 
 def minimum_spanning_tree(csgraph, overwrite=False):

scipy/sparse/csgraph/_reordering.pyx

@@ -10,6 +10,7 @@ from scipy.sparse import (csc_matrix, csr_matrix, isspmatrix, isspmatrix_coo,
                           SparseEfficiencyWarning)
 from . import maximum_bipartite_matching
 
+np.import_array()
 
 include 'parameters.pxi'
 

scipy/sparse/csgraph/_shortest_path.pyx

@@ -22,6 +22,8 @@ cimport cython
 from libc.stdlib cimport malloc, free
 from numpy.math cimport INFINITY
 
+np.import_array()
+
 include 'parameters.pxi'
 
 

scipy/sparse/csgraph/_tools.pyx

@@ -11,6 +11,8 @@ cimport numpy as np
 from scipy.sparse import csr_matrix, isspmatrix,\
     isspmatrix_csr, isspmatrix_csc, isspmatrix_lil
 
+np.import_array()
+
 include 'parameters.pxi'
 
 def csgraph_from_masked(graph):

scipy/sparse/csgraph/_traversal.pyx

@@ -15,6 +15,8 @@ from scipy.sparse.csgraph._tools import reconstruct_path
 cimport cython
 from libc cimport stdlib
 
+np.import_array()
+
 include 'parameters.pxi'
 
 def connected_components(csgraph, directed=True, connection='weak',

scipy/spatial/_hausdorff.pyx

@@ -15,6 +15,8 @@ cimport numpy as np
 cimport cython
 from libc.math cimport sqrt
 
+np.import_array()
+
 __all__ = ['directed_hausdorff']
 
 @cython.boundscheck(False)

scipy/spatial/_voronoi.pyx

@@ -14,6 +14,8 @@ import numpy as np
 cimport numpy as np
 cimport cython
 
+np.import_array()
+
 __all__ = ['sort_vertices_of_regions']
 
 # array-filling placeholder that can never occur

scipy/spatial/ckdtree.pyx

@@ -23,6 +23,8 @@ import threading
 import operator
 import warnings
 
+np.import_array()
+
 cdef extern from "<limits.h>":
     long LONG_MAX
 

scipy/spatial/qhull.pyx

@@ -23,6 +23,8 @@ import os
 import sys
 import tempfile
 
+np.import_array()
+
 cdef extern from "numpy/npy_math.h":
     double nan "NPY_NAN"
 

scipy/spatial/src/distance_pybind.cpp

@@ -225,6 +225,13 @@ ArrayDescriptor get_descriptor(const py::array& arr) {
     const auto arr_strides = arr.strides();
     desc.strides.assign(arr_strides, arr_strides + ndim);
     for (intptr_t i = 0; i < ndim; ++i) {
+        if (arr_shape[i] <= 1) {
+            // Under NumPy's relaxed stride checking, dimensions with
+            // 1 or fewer elements are ignored.
+            desc.strides[i] = 0;
+            continue;
+        }
+
         if (desc.strides[i] % desc.element_size != 0) {
             throw std::runtime_error("Arrays must be aligned");
         }

scipy/spatial/transform/rotation.pyx

@@ -10,6 +10,8 @@ from cython.view cimport array
 from libc.math cimport sqrt, sin, cos, atan2, acos
 from numpy.math cimport PI as pi, NAN, isnan # avoid MSVC error
 
+np.import_array()
+
 # utilities for empty array initialization
 cdef inline double[:] _empty1(int n):
     return array(shape=(n,), itemsize=sizeof(double), format=b"d")

scipy/stats/_multivariate.py

@@ -396,8 +396,8 @@ def _process_parameters(self, dim, mean, cov):
         cov = np.asarray(cov, dtype=float)
 
         if dim == 1:
-            mean.shape = (1,)
-            cov.shape = (1, 1)
+            mean = mean.reshape(1)
+            cov = cov.reshape(1, 1)
 
         if mean.ndim != 1 or mean.shape[0] != dim:
             raise ValueError("Array 'mean' must be a vector of length %d." %
@@ -4125,8 +4125,8 @@ def _process_parameters(self, loc, shape, df):
             dim = loc.size
 
         if dim == 1:
-            loc.shape = (1,)
-            shape.shape = (1, 1)
+            loc = loc.reshape(1)
+            shape = shape.reshape(1, 1)
 
         if loc.ndim != 1 or loc.shape[0] != dim:
             raise ValueError("Array 'loc' must be a vector of length %d." %

scipy/stats/_sobol.pyx

@@ -6,6 +6,8 @@ cimport numpy as cnp
 import os
 import numpy as np
 
+cnp.import_array()
+
 # Parameters are linked to the direction numbers list.
 # See `initialize_direction_numbers` for more details.
 # Declared using DEF to be known at compilation time for ``poly`` et ``vinit``

scipy/stats/_stats.pyx

@@ -12,6 +12,7 @@ import numpy as np
 import scipy.stats, scipy.special
 cimport scipy.special.cython_special as cs
 
+np.import_array()
 
 cdef double von_mises_cdf_series(double k, double x, unsigned int p):
     cdef double s, c, sn, cn, R, V

scipy/stats/biasedurn.pyx.templ

@@ -7,6 +7,8 @@ cimport numpy as np
 import numpy as np
 from libcpp.memory cimport unique_ptr
 
+np.import_array()
+
 IF not NPY_OLD:
     from numpy.random cimport bitgen_t
     from cpython.pycapsule cimport PyCapsule_GetPointer, PyCapsule_IsValid