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