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Add patch to bugfix cKDTree

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This commit is contained in:
Lumir Balhar 2019-11-07 13:53:05 +01:00
parent 70ed1cdf04
commit 0516e73d2e
2 changed files with 146 additions and 0 deletions
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140
ckdtree_bugfix.patch Normal file
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@ -0,0 +1,140 @@
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')],

6
scipy.spec
View File

@ -25,6 +25,11 @@ Patch0: acceptable_failure_rate.patch
# 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
BuildRequires: fftw-devel, blas-devel, lapack-devel, suitesparse-devel
%ifarch %{openblas_arches}
BuildRequires: openblas-devel
@ -184,6 +189,7 @@ popd
* Fri Oct 18 2019 Miro Hrončok <mhroncok@redhat.com> - 1.3.1-1
- Update to 1.3.1 (#1674101)
- Drop Python 2 packages (not supported by SciPy >= 1.3)
- Backported upstream patch for cKDTree (fixes FTBFS)
* Thu Oct 03 2019 Miro Hrončok <mhroncok@redhat.com> - 1.2.1-8
- Rebuilt for Python 3.8.0rc1 (#1748018)