defragmented temporary memory allocations in sparse_dot_topn routines

Author: ParticularMiner

setup.py

@@ -35,6 +35,7 @@ def finalize_options(self):
                                     './sparse_dot_topn/sparse_dot_topn_source.cpp'
                                 ],
                          extra_compile_args=extra_compile_args,
+                         define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
                          language='c++')
 
 original_ext = Extension('sparse_dot_topn.sparse_dot_topn',
@@ -43,6 +44,7 @@ def finalize_options(self):
                                     './sparse_dot_topn/sparse_dot_topn_source.cpp'
                                 ],
                          extra_compile_args=extra_compile_args,
+                         define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
                          language='c++')
 
 threaded_ext = Extension('sparse_dot_topn.sparse_dot_topn_threaded',
@@ -52,6 +54,7 @@ def finalize_options(self):
                              './sparse_dot_topn/sparse_dot_topn_parallel.cpp'
                             ],
                          extra_compile_args=extra_compile_args,
+                         define_macros=[('NPY_NO_DEPRECATED_API', 'NPY_1_7_API_VERSION')],
                          language='c++')
 
 setup(

sparse_dot_topn/array_wrappers.pxd

@@ -2,17 +2,17 @@ from libcpp.vector cimport vector
 
 # define a Cython array wrapper class to hold a C++ vector of ints, adhering to numpy's buffer protocol:
 cdef class ArrayWrapper_int:
-    cdef int view_count
-    cdef vector[int] vec
-    cdef Py_ssize_t shape[2]
-    cdef Py_ssize_t strides[2]
+	cdef int view_count
+	cdef vector[int] vec
+	cdef Py_ssize_t shape[2]
+	cdef Py_ssize_t strides[2]
 
 
 # define a Cython array wrapper class to hold a C++ vector of doubles, adhering to numpy's buffer protocol:
 cdef class ArrayWrapper_double:
-    cdef int view_count
-    cdef vector[double] vec
-    cdef Py_ssize_t shape[2]
-    cdef Py_ssize_t strides[2]
+	cdef int view_count
+	cdef vector[double] vec
+	cdef Py_ssize_t shape[2]
+	cdef Py_ssize_t strides[2]
 
 

sparse_dot_topn/array_wrappers.pyx

@@ -3,71 +3,71 @@ from libcpp.vector cimport vector
 
 # define a Cython array wrapper class to hold a C++ vector of ints, adhering to numpy's buffer protocol:
 cdef class ArrayWrapper_int:
-    # constructor and destructor are fairly unimportant now since
-    # vec will be destroyed automatically.
+	# constructor and destructor are fairly unimportant now since
+	# vec will be destroyed automatically.
 
-    def __cinit__(self, vector[int]& data):
-        self.vec.swap(data)
-        self.view_count = 0
+	def __cinit__(self, vector[int]& data):
+		self.vec.swap(data)
+		self.view_count = 0
 
-    # now implement the buffer protocol for the class
-    # which makes it generally useful to anything that expects an array
-    def __getbuffer__(self, Py_buffer *buffer, int flags):
-        # relevant documentation http://cython.readthedocs.io/en/latest/src/userguide/buffer.html#a-matrix-class
-        cdef Py_ssize_t itemsize = sizeof(self.vec[0])
+	# now implement the buffer protocol for the class
+	# which makes it generally useful to anything that expects an array
+	def __getbuffer__(self, Py_buffer *buffer, int flags):
+		# relevant documentation http://cython.readthedocs.io/en/latest/src/userguide/buffer.html#a-matrix-class
+		cdef Py_ssize_t itemsize = sizeof(self.vec[0])
 
-        self.shape[1] = self.vec.size()
-        self.shape[0] = 1
-        self.strides[1] = <Py_ssize_t>(  <char *>&(self.vec[1]) - <char *>&(self.vec[0]))
-        self.strides[0] = self.vec.size() * self.strides[1]
-        buffer.buf = <char *>&(self.vec[0])
-        buffer.format = 'i'
-        buffer.internal = NULL
-        buffer.itemsize = itemsize
-        buffer.len = self.vec.size() * itemsize   # product(shape) * itemsize
-        buffer.ndim = 2
-        buffer.obj = self
-        buffer.readonly = 0
-        buffer.shape = self.shape
-        buffer.strides = self.strides
-        buffer.suboffsets = NULL
-        self.view_count += 1
-        
-    def __releasebuffer__(self, Py_buffer *buffer):
-        self.view_count -= 1
+		self.shape[1] = self.vec.size()
+		self.shape[0] = 1
+		self.strides[1] = <Py_ssize_t>(  <char *>&(self.vec[1]) - <char *>&(self.vec[0]))
+		self.strides[0] = self.vec.size() * self.strides[1]
+		buffer.buf = <char *>&(self.vec[0])
+		buffer.format = 'i'
+		buffer.internal = NULL
+		buffer.itemsize = itemsize
+		buffer.len = self.vec.size() * itemsize   # product(shape) * itemsize
+		buffer.ndim = 2
+		buffer.obj = self
+		buffer.readonly = 0
+		buffer.shape = self.shape
+		buffer.strides = self.strides
+		buffer.suboffsets = NULL
+		self.view_count += 1
+		
+	def __releasebuffer__(self, Py_buffer *buffer):
+		self.view_count -= 1
 
 
 # define a Cython array wrapper class to hold a C++ vector of doubles, adhering to numpy's buffer protocol:
 cdef class ArrayWrapper_double:
-    # constructor and destructor are fairly unimportant now since
-    # vec will be destroyed automatically.
+	# constructor and destructor are fairly unimportant now since
+	# vec will be destroyed automatically.
 
-    def __cinit__(self, vector[double]& data):
-        self.vec.swap(data)
-        self.view_count = 0
+	def __cinit__(self, vector[double]& data):
+		self.vec.swap(data)
+		self.view_count = 0
 
-    # now implement the buffer protocol for the class
-    # which makes it generally useful to anything that expects an array
-    def __getbuffer__(self, Py_buffer *buffer, int flags):
-        # relevant documentation http://cython.readthedocs.io/en/latest/src/userguide/buffer.html#a-matrix-class
-        cdef Py_ssize_t itemsize = sizeof(self.vec[0])
+	# now implement the buffer protocol for the class
+	# which makes it generally useful to anything that expects an array
+	def __getbuffer__(self, Py_buffer *buffer, int flags):
+		# relevant documentation http://cython.readthedocs.io/en/latest/src/userguide/buffer.html#a-matrix-class
+		cdef Py_ssize_t itemsize = sizeof(self.vec[0])
 
-        self.shape[1] = self.vec.size()
-        self.shape[0] = 1
-        self.strides[1] = <Py_ssize_t>(  <char *>&(self.vec[1]) - <char *>&(self.vec[0]))
-        self.strides[0] = self.vec.size() * self.strides[1]
-        buffer.buf = <char *>&(self.vec[0])
-        buffer.format = 'd'
-        buffer.internal = NULL
-        buffer.itemsize = itemsize
-        buffer.len = self.vec.size() * itemsize   # product(shape) * itemsize
-        buffer.ndim = 2
-        buffer.obj = self
-        buffer.readonly = 0
-        buffer.shape = self.shape
-        buffer.strides = self.strides
-        buffer.suboffsets = NULL
-        self.view_count += 1
-        
-    def __releasebuffer__(self, Py_buffer *buffer):
-        self.view_count -= 1
+		self.shape[1] = self.vec.size()
+		self.shape[0] = 1
+		self.strides[1] = <Py_ssize_t>(  <char *>&(self.vec[1]) - <char *>&(self.vec[0]))
+		self.strides[0] = self.vec.size() * self.strides[1]
+		buffer.buf = <char *>&(self.vec[0])
+		buffer.format = 'd'
+		buffer.internal = NULL
+		buffer.itemsize = itemsize
+		buffer.len = self.vec.size() * itemsize   # product(shape) * itemsize
+		buffer.ndim = 2
+		buffer.obj = self
+		buffer.readonly = 0
+		buffer.shape = self.shape
+		buffer.strides = self.strides
+		buffer.suboffsets = NULL
+		self.view_count += 1
+		
+	def __releasebuffer__(self, Py_buffer *buffer):
+		self.view_count -= 1