.gitignore

@@ -1 +1 @@
-SOURCES/scipy-1.3.1.tar.gz
+SOURCES/scipy-1.5.4.tar.gz

.scipy.metadata

@@ -1 +1 @@
-3c079c09ecb614d8056135edd1cc6da51d18df0a SOURCES/scipy-1.3.1.tar.gz
+ffbc97517d08d8a5b290c7a5dd6cda0c730ed531 SOURCES/scipy-1.5.4.tar.gz

SOURCES/acceptable_failure_rate.patch

@@ -1,28 +0,0 @@
-diff --git a/scipy/conftest.py b/scipy/conftest.py
-index e5fac23..1a971e8 100644
---- a/scipy/conftest.py
-+++ b/scipy/conftest.py
-@@ -3,6 +3,7 @@ from __future__ import division, absolute_import, print_function
- 
- import os
- import pytest
-+import _pytest
- import warnings
- 
- from distutils.version import LooseVersion
-@@ -37,3 +38,15 @@ def check_fpu_mode(request):
-         warnings.warn("FPU mode changed from {0:#x} to {1:#x} during "
-                       "the test".format(old_mode, new_mode),
-                       category=FPUModeChangeWarning, stacklevel=0)
-+
-+
-+ACCEPTABLE_FAILURE_RATE = int(os.environ.get('ACCEPTABLE_FAILURE_RATE', 0))
-+
-+
-+@pytest.hookimpl()
-+def pytest_sessionfinish(session, exitstatus):
-+    if exitstatus != _pytest.main.EXIT_TESTSFAILED:
-+        return
-+    failure_rate = (100.0 * session.testsfailed) / session.testscollected
-+    if failure_rate <= ACCEPTABLE_FAILURE_RATE:
-+        session.exitstatus = 0

SOURCES/ckdtree_bugfix.patch

@@ -1,140 +0,0 @@
-From d945dfa4063c5cd7169acd117c15f23ba68027ed Mon Sep 17 00:00:00 2001
-From: Pauli Virtanen <pav@iki.fi>
-Date: Wed, 31 Jul 2019 23:31:22 +0300
-Subject: [PATCH 1/2] BUG: spatial: use c++11 construct for getting start of
- vector
-
-gcc 9.1.1 on Fedora throws asserts and crashes at runtime on
-`&x.front()` when `x` is empty, so use a different construct for getting
-the beginning of the data block.
----
- scipy/spatial/ckdtree.pyx | 18 +++++++++---------
- 1 file changed, 9 insertions(+), 9 deletions(-)
-
-diff --git a/scipy/spatial/ckdtree.pyx b/scipy/spatial/ckdtree.pyx
-index e2eea8c9097..884d49e1d34 100644
---- a/scipy/spatial/ckdtree.pyx
-+++ b/scipy/spatial/ckdtree.pyx
-@@ -190,7 +190,7 @@ cdef class coo_entries:
-         res_dtype = np.dtype(_dtype, align = True)
-         n = <np.intp_t> self.buf.size()
-         if NPY_LIKELY(n > 0):
--            pr = &self.buf.front()
-+            pr = self.buf.data()
-             uintptr = <np.uintp_t> (<void*> pr)
-             dtype = np.dtype(np.uint8)
-             self.__array_interface__ = dict(
-@@ -213,7 +213,7 @@ cdef class coo_entries:
-             dict res_dict
-         n = <np.intp_t> self.buf.size()
-         if NPY_LIKELY(n > 0):
--            pr = &self.buf.front()
-+            pr = self.buf.data()
-             res_dict = dict()
-             for k in range(n):
-                 i = pr[k].i
-@@ -263,7 +263,7 @@ cdef class ordered_pairs:
-             np.intp_t n
-         n = <np.intp_t> self.buf.size()
-         if NPY_LIKELY(n > 0):
--            pr = &self.buf.front()
-+            pr = self.buf.data()
-             uintptr = <np.uintp_t> (<void*> pr)
-             dtype = np.dtype(np.intp)
-             self.__array_interface__ = dict(
-@@ -284,7 +284,7 @@ cdef class ordered_pairs:
-             np.intp_t i, n
-             set results
-         results = set()
--        pair = &self.buf.front()
-+        pair = self.buf.data()
-         n = <np.intp_t> self.buf.size()
-         if sizeof(long) < sizeof(np.intp_t):
-             # Needed for Python 2.x on Win64
-@@ -593,7 +593,7 @@ cdef class cKDTree:
-         cself = self.cself
-         # finalize the tree points, this calls _post_init_traverse
- 
--        cself.ctree = &cself.tree_buffer.front()
-+        cself.ctree = cself.tree_buffer.data()
- 
-         # set the size attribute after tree_buffer is built
-         cself.size = cself.tree_buffer.size()
-@@ -971,7 +971,7 @@ cdef class cKDTree:
-                     m = <np.intp_t> (vvres[i].size())
-                     tmp = m * [None]
- 
--                    cur = &vvres[i].front()
-+                    cur = vvres[i].data()
-                     for j in range(m):
-                         tmp[j] = cur[0]
-                         cur += 1
-@@ -1067,7 +1067,7 @@ cdef class cKDTree:
-                     tmp = m * [None]
-                     with nogil:
-                         sort(vvres[i].begin(), vvres[i].end())
--                    cur = &vvres[i].front()
-+                    cur = vvres[i].data()
-                     for j in range(m):
-                         tmp[j] = cur[0]
-                         cur += 1
-@@ -1492,7 +1492,7 @@ cdef class cKDTree:
-         cdef ckdtree * cself = self.cself
-         size = cself.tree_buffer.size() * sizeof(ckdtreenode)
- 
--        cdef np.ndarray tree = np.asarray(<char[:size]> <char*> &cself.tree_buffer.front())
-+        cdef np.ndarray tree = np.asarray(<char[:size]> <char*> cself.tree_buffer.data())
- 
-         state = (tree.copy(), self.data.copy(), self.n, self.m, self.leafsize,
-                       self.maxes, self.mins, self.indices.copy(),
-@@ -1511,7 +1511,7 @@ cdef class cKDTree:
-         cself.tree_buffer = new vector[ckdtreenode]()
-         cself.tree_buffer.resize(tree.size // sizeof(ckdtreenode))
- 
--        mytree = np.asarray(<char[:tree.size]> <char*> &cself.tree_buffer.front())
-+        mytree = np.asarray(<char[:tree.size]> <char*> cself.tree_buffer.data())
- 
-         # set raw pointers
-         self._pre_init()
-
-From ad0f91438f49bfe277e32d2689aefeb0c11c789f Mon Sep 17 00:00:00 2001
-From: Pauli Virtanen <pav@iki.fi>
-Date: Wed, 31 Jul 2019 23:41:40 +0300
-Subject: [PATCH 2/2] BLD: spatial: set c++ std flags for ckdtree
-
----
- scipy/spatial/setup.py | 11 ++++++++++-
- 1 file changed, 10 insertions(+), 1 deletion(-)
-
-diff --git a/scipy/spatial/setup.py b/scipy/spatial/setup.py
-index d7e334876df..19d78593c5e 100644
---- a/scipy/spatial/setup.py
-+++ b/scipy/spatial/setup.py
-@@ -4,6 +4,13 @@
- import glob
- 
- 
-+def pre_build_hook(build_ext, ext):
-+    from scipy._build_utils.compiler_helper import get_cxx_std_flag
-+    std_flag = get_cxx_std_flag(build_ext._cxx_compiler)
-+    if std_flag is not None:
-+        ext.extra_compile_args.append(std_flag)
-+
-+
- def configuration(parent_package='', top_path=None):
-     from numpy.distutils.misc_util import Configuration, get_numpy_include_dirs
-     from numpy.distutils.misc_util import get_info as get_misc_info
-@@ -55,10 +62,12 @@ def configuration(parent_package='', top_path=None):
-     ckdtree_headers = [join('ckdtree', 'src', x) for x in ckdtree_headers]
- 
-     ckdtree_dep = ['ckdtree.cxx'] + ckdtree_headers + ckdtree_src
--    config.add_extension('ckdtree',
-+    ext = config.add_extension('ckdtree',
-                          sources=['ckdtree.cxx'] + ckdtree_src,
-                          depends=ckdtree_dep,
-                          include_dirs=inc_dirs + [join('ckdtree', 'src')])
-+    ext._pre_build_hook = pre_build_hook
-+
-     # _distance_wrap
-     config.add_extension('_distance_wrap',
-                          sources=[join('src', 'distance_wrap.c')],

SOURCES/numpy-deprecation-warnings.patch

@@ -1,589 +0,0 @@
-diff -ru scipy-1.2.1/scipy/odr/__odrpack.c scipy-1.2.1_patched/scipy/odr/__odrpack.c
---- scipy-1.2.1/scipy/odr/__odrpack.c	2019-01-28 04:57:51.000000000 +0100
-+++ scipy-1.2.1_patched/scipy/odr/__odrpack.c	2019-06-06 16:11:32.947892754 +0200
-@@ -9,6 +9,8 @@
-  *
-  */
- 
-+#define PY_SSIZE_T_CLEAN
-+#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
- #include "odrpack.h"
- 
- 
-@@ -44,7 +46,7 @@
-                   double *fjacb, double *fjacd, int *istop)
- {
-   PyObject *arg01, *arglist;
--  PyObject *result;
-+  PyObject *result = NULL;
-   PyArrayObject *result_array = NULL;
-   PyArrayObject *pyXplusD;
-   void *beta_dst;
-@@ -57,14 +59,14 @@
-       dim2[0] = *m;
-       dim2[1] = *n;
-       pyXplusD = (PyArrayObject *) PyArray_SimpleNew(2, dim2, NPY_DOUBLE);
--      memcpy(pyXplusD->data, (void *)xplusd, (*m) * (*n) * sizeof(double));
-+      memcpy(PyArray_DATA(pyXplusD), (void *)xplusd, (*m) * (*n) * sizeof(double));
-     }
-   else
-     {
-       npy_intp dim1[1];
-       dim1[0] = *n;
-       pyXplusD = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_DOUBLE);
--      memcpy(pyXplusD->data, (void *)xplusd, (*n) * sizeof(double));
-+      memcpy(PyArray_DATA(pyXplusD), (void *)xplusd, (*n) * sizeof(double));
-     }
- 
-   PyTuple_SetItem(arg01, 0, odr_global.pyBeta);
-@@ -84,7 +86,7 @@
-   Py_DECREF(arg01);
-   *istop = 0;
- 
--  beta_dst = ((PyArrayObject *) (odr_global.pyBeta))->data;
-+  beta_dst = (PyArray_DATA((PyArrayObject *) odr_global.pyBeta));
-   if (beta != beta_dst) {
-       memcpy(beta_dst, (void *)beta, (*np) * sizeof(double));
-   }
-@@ -121,7 +123,7 @@
-                  "Result from function call is not a proper array of floats.");
-         }
- 
--      memcpy((void *)f, result_array->data, (*n) * (*nq) * sizeof(double));
-+      memcpy((void *)f, PyArray_DATA(result_array), (*n) * (*nq) * sizeof(double));
-       Py_DECREF(result_array);
-     }
- 
-@@ -161,7 +163,7 @@
-         {
-           /* result_array should be rank-3 */
- 
--          if (result_array->nd != 3)
-+          if (PyArray_NDIM(result_array) != 3)
-             {
-               Py_DECREF(result_array);
-               PYERR2(odr_error, "Beta Jacobian is not rank-3");
-@@ -171,14 +173,14 @@
-         {
-           /* result_array should be rank-2 */
- 
--          if (result_array->nd != 2)
-+          if (PyArray_NDIM(result_array) != 2)
-             {
-               Py_DECREF(result_array);
-               PYERR2(odr_error, "Beta Jacobian is not rank-2");
-             }
-         }
- 
--      memcpy((void *)fjacb, result_array->data,
-+      memcpy((void *)fjacb, PyArray_DATA(result_array),
-              (*n) * (*nq) * (*np) * sizeof(double));
-       Py_DECREF(result_array);
- 
-@@ -220,7 +222,7 @@
-         {
-           /* result_array should be rank-3 */
- 
--          if (result_array->nd != 3)
-+          if (PyArray_NDIM(result_array) != 3)
-             {
-               Py_DECREF(result_array);
-               PYERR2(odr_error, "xplusd Jacobian is not rank-3");
-@@ -230,7 +232,7 @@
-         {
-           /* result_array should be rank-2 */
- 
--          if (result_array->nd != 2)
-+          if (PyArray_NDIM(result_array) != 2)
-             {
-               Py_DECREF(result_array);
-               PYERR2(odr_error, "xplusd Jacobian is not rank-2");
-@@ -240,14 +242,14 @@
-         {
-           /* result_array should be rank-1 */
- 
--          if (result_array->nd != 1)
-+          if (PyArray_NDIM(result_array) != 1)
-             {
-               Py_DECREF(result_array);
-               PYERR2(odr_error, "xplusd Jacobian is not rank-1");
-             }
-         }
- 
--      memcpy((void *)fjacd, result_array->data,
-+      memcpy((void *)fjacd, PyArray_DATA(result_array),
-              (*n) * (*nq) * (*m) * sizeof(double));
-       Py_DECREF(result_array);
-     }
-@@ -291,7 +293,7 @@
-       return NULL;
-   }
- 
--  lwkmn = work->dimensions[0];
-+  lwkmn = PyArray_DIMS(work)[0];
- 
-   F_FUNC(dwinf,DWINF)(&n, &m, &np, &nq, &ldwe, &ld2we, &isodr,
-         &delta, &eps, &xplus, &fn, &sd, &vcv, &rvar, &wss, &wssde,
-@@ -352,15 +354,15 @@
-   wrk6--;
-   wrk7--;
- 
--  dim1[0] = beta->dimensions[0];
-+  dim1[0] = PyArray_DIMS(beta)[0];
-   sd_beta = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_DOUBLE);
--  dim2[0] = beta->dimensions[0];
--  dim2[1] = beta->dimensions[0];
-+  dim2[0] = PyArray_DIMS(beta)[0];
-+  dim2[1] = PyArray_DIMS(beta)[0];
-   cov_beta = (PyArrayObject *) PyArray_SimpleNew(2, dim2, NPY_DOUBLE);
- 
--  memcpy(sd_beta->data, (void *)((double *)(work->data) + sd),
-+  memcpy(PyArray_DATA(sd_beta), (void *)((double *)(PyArray_DATA(work)) + sd),
-          np * sizeof(double));
--  memcpy(cov_beta->data, (void *)((double *)(work->data) + vcv),
-+  memcpy(PyArray_DATA(cov_beta), (void *)((double *)(PyArray_DATA(work)) + vcv),
-          np * np * sizeof(double));
- 
-   if (!full_output)
-@@ -427,21 +429,21 @@
-           fnA = (PyArrayObject *) PyArray_SimpleNew(2, dim2, NPY_DOUBLE);
-         }
- 
--      memcpy(deltaA->data, (void *)((double *)(work->data) + delta),
-+      memcpy(PyArray_DATA(deltaA), (void *)((double *)(PyArray_DATA(work)) + delta),
-              m * n * sizeof(double));
--      memcpy(epsA->data, (void *)((double *)(work->data) + eps),
-+      memcpy(PyArray_DATA(epsA), (void *)((double *)(PyArray_DATA(work)) + eps),
-              nq * n * sizeof(double));
--      memcpy(xplusA->data, (void *)((double *)(work->data) + xplus),
-+      memcpy(PyArray_DATA(xplusA), (void *)((double *)(PyArray_DATA(work)) + xplus),
-              m * n * sizeof(double));
--      memcpy(fnA->data, (void *)((double *)(work->data) + fn),
-+      memcpy(PyArray_DATA(fnA), (void *)((double *)(PyArray_DATA(work)) + fn),
-              nq * n * sizeof(double));
- 
--      res_var = *((double *)(work->data) + rvar);
--      sum_square = *((double *)(work->data) + wss);
--      sum_square_delta = *((double *)(work->data) + wssde);
--      sum_square_eps = *((double *)(work->data) + wssep);
--      inv_condnum = *((double *)(work->data) + rcond);
--      rel_error = *((double *)(work->data) + eta);
-+      res_var = *((double *)(PyArray_DATA(work)) + rvar);
-+      sum_square = *((double *)(PyArray_DATA(work)) + wss);
-+      sum_square_delta = *((double *)(PyArray_DATA(work)) + wssde);
-+      sum_square_eps = *((double *)(PyArray_DATA(work)) + wssep);
-+      inv_condnum = *((double *)(PyArray_DATA(work)) + rcond);
-+      rel_error = *((double *)(PyArray_DATA(work)) + eta);
- 
-       retobj =
-         Py_BuildValue
-@@ -623,7 +625,7 @@
-           PYERR(PyExc_ValueError,
-                 "y could not be made into a suitable array");
-         }
--      n = y->dimensions[y->nd - 1];     /* pick the last dimension */
-+      n = PyArray_DIMS(y)[PyArray_NDIM(y) - 1];     /* pick the last dimension */
-       if ((x =
-            (PyArrayObject *) PyArray_CopyFromObject(px, NPY_DOUBLE, 1,
-                                                     2)) == NULL)
-@@ -631,18 +633,18 @@
-           PYERR(PyExc_ValueError,
-                 "x could not be made into a suitable array");
-         }
--      if (n != x->dimensions[x->nd - 1])
-+      if (n != PyArray_DIMS(x)[PyArray_NDIM(x) - 1])
-         {
-           PYERR(PyExc_ValueError,
-                 "x and y don't have matching numbers of observations");
-         }
--      if (y->nd == 1)
-+      if (PyArray_NDIM(y) == 1)
-         {
-           nq = 1;
-         }
-       else
-         {
--          nq = y->dimensions[0];
-+          nq = PyArray_DIMS(y)[0];
-         }
- 
-       ldx = ldy = n;
-@@ -664,17 +666,17 @@
-                 "x could not be made into a suitable array");
-         }
- 
--      n = x->dimensions[x->nd - 1];
-+      n = PyArray_DIMS(x)[PyArray_NDIM(x) - 1];
-       ldx = n;
-     }
- 
--  if (x->nd == 1)
-+  if (PyArray_NDIM(x) == 1)
-     {
-       m = 1;
-     }
-   else
-     {
--      m = x->dimensions[0];
-+      m = PyArray_DIMS(x)[0];
-     }                           /* x, y */
- 
-   if ((beta =
-@@ -684,14 +686,14 @@
-       PYERR(PyExc_ValueError,
-             "initbeta could not be made into a suitable array");
-     }
--  np = beta->dimensions[0];
-+  np = PyArray_DIMS(beta)[0];
- 
-   if (pwe == NULL)
-     {
-       ldwe = ld2we = 1;
-       dim1[0] = n;
-       we = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_DOUBLE);
--      ((double *)(we->data))[0] = -1.0;
-+      ((double *)(PyArray_DATA(we)))[0] = -1.0;
-     }
-   else if (PyNumber_Check(pwe) && !PyArray_Check(pwe))
-     {
-@@ -711,11 +713,11 @@
-       we = (PyArrayObject *) PyArray_SimpleNew(3, dim3, NPY_DOUBLE);
-       if (implicit)
-         {
--          ((double *)(we->data))[0] = val;
-+          ((double *)(PyArray_DATA(we)))[0] = val;
-         }
-       else
-         {
--          ((double *)(we->data))[0] = -val;
-+          ((double *)(PyArray_DATA(we)))[0] = -val;
-         }
-       ldwe = ld2we = 1;
-     }
-@@ -730,29 +732,29 @@
-           PYERR(PyExc_ValueError, "could not convert we to a suitable array");
-         }
- 
--      if (we->nd == 1 && nq == 1)
-+      if (PyArray_NDIM(we) == 1 && nq == 1)
-         {
- 
-           ldwe = n;
-           ld2we = 1;
-         }
--      else if (we->nd == 1 && we->dimensions[0] == nq)
-+      else if (PyArray_NDIM(we) == 1 && PyArray_DIMS(we)[0] == nq)
-         {
-           /* we is a rank-1 array with diagonal weightings to be broadcast 
-            * to all observations */
-           ldwe = 1;
-           ld2we = 1;
-         }
--      else if (we->nd == 3 && we->dimensions[0] == nq
--               && we->dimensions[1] == nq && we->dimensions[2] == 1)
-+      else if (PyArray_NDIM(we) == 3 && PyArray_DIMS(we)[0] == nq
-+               && PyArray_DIMS(we)[1] == nq && PyArray_DIMS(we)[2] == 1)
-         {
-           /* we is a rank-3 array with the covariant weightings 
-              to be broadcast to all observations */
-           ldwe = 1;
-           ld2we = nq;
-         }
--      else if (we->nd == 2 && we->dimensions[0] == nq
--               && we->dimensions[1] == nq)
-+      else if (PyArray_NDIM(we) == 2 && PyArray_DIMS(we)[0] == nq
-+               && PyArray_DIMS(we)[1] == nq)
-         {
-           /* we is a rank-2 array with the full covariant weightings 
-              to be broadcast to all observations */
-@@ -760,16 +762,16 @@
-           ld2we = nq;
-         }
- 
--      else if (we->nd == 2 && we->dimensions[0] == nq
--               && we->dimensions[1] == n)
-+      else if (PyArray_NDIM(we) == 2 && PyArray_DIMS(we)[0] == nq
-+               && PyArray_DIMS(we)[1] == n)
-         {
-           /* we is a rank-2 array with the diagonal elements of the 
-              covariant weightings for each observation */
-           ldwe = n;
-           ld2we = 1;
-         }
--      else if (we->nd == 3 && we->dimensions[0] == nq
--               && we->dimensions[1] == nq && we->dimensions[2] == n)
-+      else if (PyArray_NDIM(we) == 3 && PyArray_DIMS(we)[0] == nq
-+               && PyArray_DIMS(we)[1] == nq && PyArray_DIMS(we)[2] == n)
-         {
-           /* we is the full specification of the covariant weights
-              for each observation */
-@@ -788,7 +790,7 @@
- 
-       dim1[0] = m;
-       wd = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_DOUBLE);
--      ((double *)(wd->data))[0] = -1.0;
-+      ((double *)(PyArray_DATA(wd)))[0] = -1.0;
-     }
-   else if (PyNumber_Check(pwd) && !PyArray_Check(pwd))
-     {
-@@ -806,7 +808,7 @@
-       dim3[1] = 1;
-       dim3[2] = m;
-       wd = (PyArrayObject *) PyArray_SimpleNew(3, dim3, NPY_DOUBLE);
--      ((double *)(wd->data))[0] = -val;
-+      ((double *)(PyArray_DATA(wd)))[0] = -val;
-       ldwd = ld2wd = 1;
-     }
-   else if (PySequence_Check(pwd))
-@@ -820,12 +822,12 @@
-           PYERR(PyExc_ValueError, "could not convert wd to a suitable array");
-         }
- 
--      if (wd->nd == 1 && m == 1)
-+      if (PyArray_NDIM(wd) == 1 && m == 1)
-         {
-           ldwd = n;
-           ld2wd = 1;
-         }
--      else if (wd->nd == 1 && wd->dimensions[0] == m)
-+      else if (PyArray_NDIM(wd) == 1 && PyArray_DIMS(wd)[0] == m)
-         {
-           /* wd is a rank-1 array with diagonal weightings to be broadcast 
-            * to all observations */
-@@ -833,16 +835,16 @@
-           ld2wd = 1;
-         }
- 
--      else if (wd->nd == 3 && wd->dimensions[0] == m
--               && wd->dimensions[1] == m && wd->dimensions[2] == 1)
-+      else if (PyArray_NDIM(wd) == 3 && PyArray_DIMS(wd)[0] == m
-+               && PyArray_DIMS(wd)[1] == m && PyArray_DIMS(wd)[2] == 1)
-         {
-           /* wd is a rank-3 array with the covariant wdightings 
-              to be broadcast to all observations */
-           ldwd = 1;
-           ld2wd = m;
-         }
--      else if (wd->nd == 2 && wd->dimensions[0] == m
--               && wd->dimensions[1] == m)
-+      else if (PyArray_NDIM(wd) == 2 && PyArray_DIMS(wd)[0] == m
-+               && PyArray_DIMS(wd)[1] == m)
-         {
-           /* wd is a rank-2 array with the full covariant weightings 
-              to be broadcast to all observations */
-@@ -850,16 +852,16 @@
-           ld2wd = m;
-         }
- 
--      else if (wd->nd == 2 && wd->dimensions[0] == m
--               && wd->dimensions[1] == n)
-+      else if (PyArray_NDIM(wd) == 2 && PyArray_DIMS(wd)[0] == m
-+               && PyArray_DIMS(wd)[1] == n)
-         {
-           /* wd is a rank-2 array with the diagonal elements of the 
-              covariant weightings for each observation */
-           ldwd = n;
-           ld2wd = 1;
-         }
--      else if (wd->nd == 3 && wd->dimensions[0] == m
--               && wd->dimensions[1] == m && wd->dimensions[2] == n)
-+      else if (PyArray_NDIM(wd) == 3 && PyArray_DIMS(wd)[0] == m
-+               && PyArray_DIMS(wd)[1] == m && PyArray_DIMS(wd)[2] == n)
-         {
-           /* wd is the full specification of the covariant weights
-              for each observation */
-@@ -878,7 +880,7 @@
-     {
-       dim1[0] = np;
-       ifixb = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_INT);
--      *(int *)(ifixb->data) = -1;      /* set first element negative */
-+      *(int *)(PyArray_DATA(ifixb)) = -1;      /* set first element negative */
-     }
-   else
-     {
-@@ -892,7 +894,7 @@
-                 "could not convert ifixb to a suitable array");
-         }
- 
--      if (ifixb->dimensions[0] != np)
-+      if (PyArray_DIMS(ifixb)[0] != np)
-         {
-           PYERR(PyExc_ValueError,
-                 "could not convert ifixb to a suitable array");
-@@ -904,7 +906,7 @@
-       dim2[0] = m;
-       dim2[1] = 1;
-       ifixx = (PyArrayObject *) PyArray_SimpleNew(2, dim2, NPY_INT);
--      *(int *)(ifixx->data) = -1;      /* set first element negative */
-+      *(int *)(PyArray_DATA(ifixx)) = -1;      /* set first element negative */
-       ldifx = 1;
-     }
-   else
-@@ -919,16 +921,16 @@
-                 "could not convert ifixx to a suitable array");
-         }
- 
--      if (ifixx->nd == 1 && ifixx->dimensions[0] == m)
-+      if (PyArray_NDIM(ifixx) == 1 && PyArray_DIMS(ifixx)[0] == m)
-         {
-           ldifx = 1;
-         }
--      else if (ifixx->nd == 1 && ifixx->dimensions[0] == n && m == 1)
-+      else if (PyArray_NDIM(ifixx) == 1 && PyArray_DIMS(ifixx)[0] == n && m == 1)
-         {
-           ldifx = n;
-         }
--      else if (ifixx->nd == 2 && ifixx->dimensions[0] == m
--               && ifixx->dimensions[1] == n)
-+      else if (PyArray_NDIM(ifixx) == 2 && PyArray_DIMS(ifixx)[0] == m
-+               && PyArray_DIMS(ifixx)[1] == n)
-         {
-           ldifx = n;
-         }
-@@ -957,14 +959,14 @@
-     {
-       dim1[0] = np;
-       stpb = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_DOUBLE);
--      *(double *)(stpb->data) = 0.0;
-+      *(double *)(PyArray_DATA(stpb)) = 0.0;
-     }
-   else                          /* pstpb is a sequence */
-     {
-       if ((stpb =
-            (PyArrayObject *) PyArray_CopyFromObject(pstpb, NPY_DOUBLE, 1,
-                                                     1)) == NULL
--          || stpb->dimensions[0] != np)
-+          || PyArray_DIMS(stpb)[0] != np)
-         {
-           PYERR(PyExc_ValueError,
-                 "could not convert stpb to a suitable array");
-@@ -976,7 +978,7 @@
-       dim2[0] = 1;
-       dim2[1] = m;
-       stpd = (PyArrayObject *) PyArray_SimpleNew(2, dim2, NPY_DOUBLE);
--      *(double *)(stpd->data) = 0.0;
-+      *(double *)(PyArray_DATA(stpd)) = 0.0;
-       ldstpd = 1;
-     }
-   else
-@@ -989,16 +991,16 @@
-                 "could not convert stpb to a suitable array");
-         }
- 
--      if (stpd->nd == 1 && stpd->dimensions[0] == m)
-+      if (PyArray_NDIM(stpd) == 1 && PyArray_DIMS(stpd)[0] == m)
-         {
-           ldstpd = 1;
-         }
--      else if (stpd->nd == 1 && stpd->dimensions[0] == n && m == 1)
-+      else if (PyArray_NDIM(stpd) == 1 && PyArray_DIMS(stpd)[0] == n && m == 1)
-         {
-           ldstpd = n;
-         }
--      else if (stpd->nd == 2 && stpd->dimensions[0] == n &&
--               stpd->dimensions[1] == m)
-+      else if (PyArray_NDIM(stpd) == 2 && PyArray_DIMS(stpd)[0] == n &&
-+               PyArray_DIMS(stpd)[1] == m)
-         {
-           ldstpd = n;
-         }
-@@ -1008,14 +1010,14 @@
-     {
-       dim1[0] = np;
-       sclb = (PyArrayObject *) PyArray_SimpleNew(1, dim1, NPY_DOUBLE);
--      *(double *)(sclb->data) = 0.0;
-+      *(double *)(PyArray_DATA(sclb)) = 0.0;
-     }
-   else                          /* psclb is a sequence */
-     {
-       if ((sclb =
-            (PyArrayObject *) PyArray_CopyFromObject(psclb, NPY_DOUBLE, 1,
-                                                     1)) == NULL
--          || sclb->dimensions[0] != np)
-+          || PyArray_DIMS(sclb)[0] != np)
-         {
-           PYERR(PyExc_ValueError,
-                 "could not convert sclb to a suitable array");
-@@ -1027,7 +1029,7 @@
-       dim2[0] = 1;
-       dim2[1] = n;
-       scld = (PyArrayObject *) PyArray_SimpleNew(2, dim2, NPY_DOUBLE);
--      *(double *)(scld->data) = 0.0;
-+      *(double *)(PyArray_DATA(scld)) = 0.0;
-       ldscld = 1;
-     }
-   else
-@@ -1040,16 +1042,16 @@
-                 "could not convert stpb to a suitable array");
-         }
- 
--      if (scld->nd == 1 && scld->dimensions[0] == m)
-+      if (PyArray_NDIM(scld) == 1 && PyArray_DIMS(scld)[0] == m)
-         {
-           ldscld = 1;
-         }
--      else if (scld->nd == 1 && scld->dimensions[0] == n && m == 1)
-+      else if (PyArray_NDIM(scld) == 1 && PyArray_DIMS(scld)[0] == n && m == 1)
-         {
-           ldscld = n;
-         }
--      else if (scld->nd == 2 && scld->dimensions[0] == n &&
--               scld->dimensions[1] == m)
-+      else if (PyArray_NDIM(scld) == 2 && PyArray_DIMS(scld)[0] == n &&
-+               PyArray_DIMS(scld)[1] == m)
-         {
-           ldscld = n;
-         }
-@@ -1110,9 +1112,9 @@
-           PYERR(PyExc_ValueError,
-                 "could not convert work to a suitable array");
-         }
--      if (work->dimensions[0] < lwork)
-+      if (PyArray_DIMS(work)[0] < lwork)
-         {
--            printf("%d %d\n", work->dimensions[0], lwork);
-+            printf("%ld %d\n", PyArray_DIMS(work)[0], lwork);
-           PYERR(PyExc_ValueError, "work is too small");
-         }
-     }
-@@ -1133,7 +1135,7 @@
-                 "could not convert iwork to a suitable array");
-         }
- 
--      if (iwork->dimensions[0] < liwork)
-+      if (PyArray_DIMS(iwork)[0] < liwork)
-         {
-           PYERR(PyExc_ValueError, "iwork is too small");
-         }
-@@ -1170,19 +1172,18 @@
-   Py_INCREF(beta);
-   odr_global.extra_args = extra_args;
-   Py_XINCREF(extra_args);
--
--  /* now call DODRC */
--  F_FUNC(dodrc,DODRC)(fcn_callback, &n, &m, &np, &nq, (double *)(beta->data),
--        (double *)(y->data), &ldy, (double *)(x->data), &ldx,
--        (double *)(we->data), &ldwe, &ld2we,
--        (double *)(wd->data), &ldwd, &ld2wd,
--        (int *)(ifixb->data), (int *)(ifixx->data), &ldifx,
--        &job, &ndigit, &taufac, &sstol, &partol, &maxit,
--        &iprint, &lunerr, &lunrpt,
--        (double *)(stpb->data), (double *)(stpd->data), &ldstpd,
--        (double *)(sclb->data), (double *)(scld->data), &ldscld,
--        (double *)(work->data), &lwork, (int *)(iwork->data), &liwork,
--        &info);
-+   /* now call DODRC */
-+   F_FUNC(dodrc,DODRC)(fcn_callback, &n, &m, &np, &nq, (double *)(PyArray_DATA(beta)),
-+         (double *)(PyArray_DATA(y)), &ldy, (double *)(PyArray_DATA(x)), &ldx,
-+         (double *)(PyArray_DATA(we)), &ldwe, &ld2we,
-+         (double *)(PyArray_DATA(wd)), &ldwd, &ld2wd,
-+         (int *)(PyArray_DATA(ifixb)), (int *)(PyArray_DATA(ifixx)), &ldifx,
-+         &job, &ndigit, &taufac, &sstol, &partol, &maxit,
-+         &iprint, &lunerr, &lunrpt,
-+         (double *)(PyArray_DATA(stpb)), (double *)(PyArray_DATA(stpd)), &ldstpd,
-+         (double *)(PyArray_DATA(sclb)), (double *)(PyArray_DATA(scld)), &ldscld,
-+         (double *)(PyArray_DATA(work)), &lwork, (int *)(PyArray_DATA(iwork)), &liwork,
-+         &info);
- 
-   result = gen_output(n, m, np, nq, ldwe, ld2we,
-                       beta, work, iwork, isodr, info, full_output);

SOURCES/skip-certain-tests-on-32-bit-arches.patch

@@ -0,0 +1,47 @@
+From ea0a77cf8761a8b8636b93314139ed0fc0a9d1db Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Nikola=20Forr=C3=B3?= <nforro@redhat.com>
+Date: Wed, 30 Sep 2020 11:44:25 +0200
+Subject: [PATCH] TST: make a couple of tests expected to fail on 32-bit
+ architectures
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+In TestConstructUtils.test_concatenate_int32_overflow
+and test_nnz_overflow, on a 32-bit architecture, in case
+check_free_memory() passes, ValueError is raised on an attempt
+to create a numpy array too large for a 32-bit architecture.
+
+Signed-off-by: Nikola Forró <nforro@redhat.com>
+---
+ scipy/sparse/tests/test_construct.py   | 1 +
+ scipy/sparse/tests/test_sparsetools.py | 1 +
+ 2 files changed, 2 insertions(+)
+
+diff --git a/scipy/sparse/tests/test_construct.py b/scipy/sparse/tests/test_construct.py
+index 3a882c6cc..5a2b92667 100644
+--- a/scipy/sparse/tests/test_construct.py
++++ b/scipy/sparse/tests/test_construct.py
+@@ -378,6 +378,7 @@ class TestConstructUtils(object):
+         excinfo.match(r'Got blocks\[0,1\]\.shape\[0\] == 1, expected 2')
+ 
+     @pytest.mark.slow
++    @pytest.mark.xfail_on_32bit("Can't create large array for test")
+     def test_concatenate_int32_overflow(self):
+         """ test for indptr overflow when concatenating matrices """
+         check_free_memory(30000)
+diff --git a/scipy/sparse/tests/test_sparsetools.py b/scipy/sparse/tests/test_sparsetools.py
+index 0c208ef44..e95df1ba0 100644
+--- a/scipy/sparse/tests/test_sparsetools.py
++++ b/scipy/sparse/tests/test_sparsetools.py
+@@ -61,6 +61,7 @@ def test_regression_std_vector_dtypes():
+ 
+ 
+ @pytest.mark.slow
++@pytest.mark.xfail_on_32bit("Can't create large array for test")
+ def test_nnz_overflow():
+     # Regression test for gh-7230 / gh-7871, checking that coo_todense
+     # with nnz > int32max doesn't overflow.
+-- 
+2.26.2
+

SPECS/scipy.spec

@@ -1,15 +1,18 @@
 # without means enabled
 %bcond_with doc
-
+# RHEL8: Tests disabled due to missing dependencies
 %bcond_with tests
 
 # Set to pre-release version suffix if building pre-release, else %%{nil}
 %global rcver %{nil}
 
+%global blaslib openblas
+%global blasvar p
+
 Summary:    Scientific Tools for Python
 Name:       scipy
-Version:    1.3.1
-Release:    5%{?dist}
+Version:    1.5.4
+Release:    3%{?dist}
 
 # BSD -- whole package except:
 # Boost -- scipy/special/cephes/scipy_iv.c
@@ -18,42 +21,27 @@ License:    BSD and Boost and Public Domain
 Url:        http://www.scipy.org/scipylib/index.html
 Source0:    https://github.com/scipy/scipy/releases/download/v%{version}/scipy-%{version}.tar.gz
 
-# Previously we ignored the tests results, because they don't always pass
-# Instead of ignoring the results entirely, we allow certain failure rate
-# https://stackoverflow.com/a/47731333/1839451
-Patch0:     acceptable_failure_rate.patch
-
-# The C API of PyArrayObject has changed in Python 3.8 and the
-# structure fields accessed in __odrpack.c are now deprecated.
-Patch1:     numpy-deprecation-warnings.patch
-
-# Bugfix of cKDTree
-# PR: https://github.com/scipy/scipy/pull/10567
-# Issue: https://github.com/scipy/scipy/issues/11021
-Patch2:     ckdtree_bugfix.patch
-
 # Exclude i686 arch. Due to a modularity issue it's being added to the
 # x86_64 compose of CRB, but we don't want to ship it at all.
 # See: https://projects.engineering.redhat.com/browse/RCM-72605
 ExcludeArch: i686
 
-BuildRequires: fftw-devel, blas-devel, lapack-devel, suitesparse-devel
-%ifarch %{openblas_arches}
-BuildRequires: openblas-devel
-%else
-BuildRequires: atlas-devel
-%endif
+# https://github.com/scipy/scipy/pull/12899
+Patch0:     skip-certain-tests-on-32-bit-arches.patch
+
+BuildRequires: fftw-devel, suitesparse-devel
+BuildRequires: %{blaslib}-devel
 BuildRequires: gcc-gfortran, swig, gcc-c++
 BuildRequires: qhull-devel
-BuildRequires: /usr/bin/pathfix3.8.py
 
+BuildRequires:  python%{python3_pkgversion}-pybind11-devel
+BuildRequires:  python%{python3_pkgversion}-pybind11 >= 2.4.0
 BuildRequires:  python%{python3_pkgversion}-devel
+BuildRequires:  python%{python3_pkgversion}-rpm-macros
 BuildRequires:  python%{python3_pkgversion}-numpy
 BuildRequires:  python%{python3_pkgversion}-numpy-f2py
 BuildRequires:  python%{python3_pkgversion}-setuptools
 BuildRequires:  python%{python3_pkgversion}-Cython
-BuildRequires:  python%{python3_pkgversion}-rpm-macros
-
 %if %{with tests}
 BuildRequires:  python%{python3_pkgversion}-pytest
 BuildRequires:  python%{python3_pkgversion}-pytest-xdist
@@ -61,9 +49,9 @@ BuildRequires:  python%{python3_pkgversion}-pytest-timeout
 %endif
 
 %if %{with doc}
-BuildRequires:  python%{python3_pkgversion}-sphinx
-BuildRequires:  python%{python3_pkgversion}-matplotlib
-BuildRequires:  python%{python3_pkgversion}-numpydoc
+BuildRequires:  python3-sphinx
+BuildRequires:  python3-matplotlib
+BuildRequires:  python3-numpydoc
 %endif
 
 %global _description %{expand:
@@ -108,11 +96,9 @@ library_dirs = %{_libdir}
 include_dirs = /usr/include/suitesparse
 umfpack_libs = umfpack
 
-%ifarch %{openblas_arches}
 [openblas]
-libraries = openblasp
+libraries = %{blaslib}%{blasvar}
 library_dirs = %{_libdir}
-%endif
 EOF
 
 # Docs won't build unless the .dat files are specified here
@@ -125,9 +111,12 @@ rm $(grep -rl '/\* Generated by Cython') PKG-INFO
 
 %build
 for PY in %{python3_version}; do
+  # Adding -fallow-argument-mismatch workaround for https://github.com/scipy/scipy/issues/11611
   env CFLAGS="$RPM_OPT_FLAGS -lm" \
-      FFLAGS="$RPM_OPT_FLAGS -fPIC -cpp" \
-      LDFLAGS="$RPM_LD_FLAGS -shared" \
+    FFLAGS="$RPM_OPT_FLAGS -fPIC -cpp" \
+    LDFLAGS="$RPM_LD_FLAGS -shared" \
+    OPENBLAS=%{_libdir} \
+    FFTW=%{_libdir} BLAS=%{_libdir} LAPACK=%{_libdir} \
     %{_bindir}/python$PY setup.py config_fc \
     --fcompiler=gnu95 --noarch \
     build
@@ -145,43 +134,36 @@ done
 %install
 %py3_install
 # Some files got ambiguous python shebangs, we fix them after everything else is done
-pathfix3.8.py -pni "%{__python3} %{py3_shbang_opts}" %{buildroot}%{python3_sitearch}
+pathfix%{python3_version}.py -pni "%{__python3} %{py3_shbang_opts}" %{buildroot}%{python3_sitearch}
 
 %if %{with tests}
 %check
-# Skip all tests on s390x because they hangs unexpectedly and randomly
-# and pytest-timeout has no effect. Note that the outcome of the tests
-# was previously ignored anyway so by disabling the test for s390x we
-# are not doing anything more dangerous.
+# check against the reference BLAS/LAPACK
+export FLEXIBLAS=netlib
+
 %ifarch s390x
-exit 0
+# skip failing tests on s390x for now
+export PYTEST_ADDOPTS="-k '\
+    not (TestNoData and test_nodata) and \
+    not test_fortranfile_read_mixed_record and \
+    not test_kde_1d and \
+    not test_kde_1d_weighted and \
+    not test_kde_2d and \
+    not test_kde_2d_weighted and \
+    not test_gaussian_kde_subclassing and \
+    not test_gaussian_kde_covariance_caching and \
+    not test_kde_integer_input and \
+    not test_pdf_logpdf and \
+    not test_pdf_logpdf_weighted'"
 %endif
 
-%ifarch x86_64
-export ACCEPTABLE_FAILURE_RATE=0
-%else
-# there are usually 10-21 test failing, so we allow 1% failure rate
-export ACCEPTABLE_FAILURE_RATE=1
-%endif
-
-%ifarch ppc64le
-# test_decomp segfaults on ppc64le
-export k="not test_denormals and not test_decomp"
-%else
-# test_denormals tends to stuck
-export k="not test_denormals"
-%endif
-
-# Do not create -PYTEST.pyc files
-export PYTHONDONTWRITEBYTECODE=1
-
 pushd %{buildroot}/%{python3_sitearch}
-# TODO TestIQR.test_scale fails on Python 3.8+ due to some warnings, investigate
-%{__python3} -m pytest --timeout=300 -k "$k and not (TestIQR and test_scale)" scipy --numprocesses=auto
+%{pytest} --timeout=500 scipy --numprocesses=auto
 # Remove test remnants
 rm -rf gram{A,B}
 popd
-%endif
+%endif # with tests
+
 
 %files -n python%{python3_pkgversion}-scipy
 %doc LICENSE.txt
@@ -195,20 +177,54 @@ popd
 %endif
 
 %changelog
-* Fri Jul 14 2023 Charalampos Stratakis <cstratak@redhat.com> - 1.3.1-5
-- Remove RPATH from certain shared object files
-- Resolves: rhbz#2222717
-
-* Thu Dec 12 2019 Tomas Orsava <torsava@redhat.com> - 1.3.1-4
-- Exclude unsupported i686 arch
-
-* Tue Dec 03 2019 Lumír Balhar <lbalhar@redhat.com> - 1.3.1-3
+* Mon Jan 18 2021 Tomas Orsava <torsava@redhat.com> - 1.5.4-3
 - Specify LDFLAGS explicitly
 - Force preprocessing of Fortran sources to make annobin record proper flags
-- Resolves: rhbz#1778983
+- Resolves: rhbz#1778983 rhbz#1877430
 
-* Thu Nov 21 2019 Lumír Balhar <lbalhar@redhat.com> - 1.3.1-2
-- Adjusted for Python 3.8 module in RHEL 8
+* Mon Jan 18 2021 Tomas Orsava <torsava@redhat.com> - 1.5.4-2
+- Convert from Fedora to the python39 module in RHEL8
+- Resolves: rhbz#1877430
+
+* Thu Nov 05 2020 Nikola Forró <nforro@redhat.com> - 1.5.4-1
+- New upstream release 1.5.4
+- Increase test timeout, 300 seconds is not always enough
+  for test_logpdf_overflow on s390x
+  resolves: #1894887
+
+* Mon Oct 19 2020 Nikola Forró <nforro@redhat.com> - 1.5.3-1
+- New upstream release 1.5.3
+  resolves: #1889132
+
+* Wed Sep 30 2020 Nikola Forró <nforro@redhat.com> - 1.5.2-2
+- Skip one more test expected to fail on 32-bit architectures
+
+* Mon Aug 31 2020 Nikola Forró <nforro@redhat.com> - 1.5.2-1
+- New upstream release 1.5.2
+  resolves: #1853871 and #1840077
+
+* Sun Aug 16 2020 Iñaki Úcar <iucar@fedoraproject.org> - 1.5.0-4
+- https://fedoraproject.org/wiki/Changes/FlexiBLAS_as_BLAS/LAPACK_manager
+
+* Sat Aug 01 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.5.0-3
+- Second attempt - Rebuilt for
+  https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Wed Jul 29 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.5.0-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild
+
+* Tue Jun 23 2020 Elliott Sales de Andrade <quantum.analyst@gmail.com> - 1.5.0-1
+- Update to latest version
+
+* Mon May 25 2020 Miro Hrončok <mhroncok@redhat.com> - 1.4.1-2
+- Rebuilt for Python 3.9
+
+* Sun Mar 01 2020 Orion Poplawski <orion@nwra.com> - 1.4.1-1
+- Update to 1.4.1 (bz#1771154)
+- Workaround FTBFS with gcc 10 (bz#1800078)
+
+* Thu Jan 30 2020 Fedora Release Engineering <releng@fedoraproject.org> - 1.3.1-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild
 
 * Fri Oct 18 2019 Miro Hrončok <mhroncok@redhat.com> - 1.3.1-1
 - Update to 1.3.1 (#1674101)