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')],