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-rw-r--r--tools/allocation_tracking/track_allocations.py10
-rw-r--r--tools/swig/numpy.i24
-rw-r--r--tools/swig/test/Array.i33
-rw-r--r--tools/swig/test/ArrayZ.cxx131
-rw-r--r--tools/swig/test/ArrayZ.h56
-rw-r--r--tools/swig/test/Makefile3
-rwxr-xr-xtools/swig/test/setup.py3
-rwxr-xr-xtools/swig/test/testArray.py101
-rw-r--r--tools/test-installed-numpy.py2
-rwxr-xr-xtools/travis-test.sh9
10 files changed, 353 insertions, 19 deletions
diff --git a/tools/allocation_tracking/track_allocations.py b/tools/allocation_tracking/track_allocations.py
index 2006217c2..dfc354eb5 100644
--- a/tools/allocation_tracking/track_allocations.py
+++ b/tools/allocation_tracking/track_allocations.py
@@ -1,6 +1,7 @@
from __future__ import division, absolute_import, print_function
import numpy as np
+import gc
import inspect
from alloc_hook import NumpyAllocHook
@@ -35,12 +36,21 @@ class AllocationTracker(object):
self.numpy_hook.__exit__()
def hook(self, inptr, outptr, size):
+ # minimize the chances that the garbage collector kicks in during a
+ # cython __dealloc__ call and causes a double delete of the current
+ # object. To avoid this fully the hook would have to avoid all python
+ # api calls, e.g. by being implemented in C like python 3.4's
+ # tracemalloc module
+ gc_on = gc.isenabled()
+ gc.disable()
if outptr == 0: # it's a free
self.free_cb(inptr)
elif inptr != 0: # realloc
self.realloc_cb(inptr, outptr, size)
else: # malloc
self.alloc_cb(outptr, size)
+ if gc_on:
+ gc.enable()
def alloc_cb(self, ptr, size):
if size >= self.threshold:
diff --git a/tools/swig/numpy.i b/tools/swig/numpy.i
index e250e78bf..181625057 100644
--- a/tools/swig/numpy.i
+++ b/tools/swig/numpy.i
@@ -872,7 +872,7 @@
(PyArrayObject* array=NULL, int is_new_object=0)
{
npy_intp size[2] = { -1, -1 };
- array = obj_to_array_contiguous_allow_conversion($input,
+ array = obj_to_array_fortran_allow_conversion($input,
DATA_TYPECODE,
&is_new_object);
if (!array || !require_dimensions(array, 2) ||
@@ -1106,7 +1106,7 @@
(PyArrayObject* array=NULL, int is_new_object=0)
{
npy_intp size[3] = { -1, -1, -1 };
- array = obj_to_array_contiguous_allow_conversion($input,
+ array = obj_to_array_fortran_allow_conversion($input,
DATA_TYPECODE,
&is_new_object);
if (!array || !require_dimensions(array, 3) ||
@@ -1345,7 +1345,7 @@
(PyArrayObject* array=NULL, int is_new_object=0)
{
npy_intp size[4] = { -1, -1, -1 , -1 };
- array = obj_to_array_contiguous_allow_conversion($input, DATA_TYPECODE,
+ array = obj_to_array_fortran_allow_conversion($input, DATA_TYPECODE,
&is_new_object);
if (!array || !require_dimensions(array, 4) ||
!require_size(array, size, 4) || !require_fortran(array)) SWIG_fail;
@@ -3071,15 +3071,13 @@
* %numpy_typemaps(long double, NPY_LONGDOUBLE, int)
*/
-/* ***************************************************************
- * Swig complains about a syntax error for the following macro
- * expansions:
- *
- * %numpy_typemaps(complex float, NPY_CFLOAT , int)
- *
- * %numpy_typemaps(complex double, NPY_CDOUBLE, int)
- *
- * %numpy_typemaps(complex long double, NPY_CLONGDOUBLE, int)
- */
+%#ifdef __cplusplus
+
+%include <std_complex.i>
+
+%numpy_typemaps(std::complex<float>, NPY_CFLOAT , int)
+%numpy_typemaps(std::complex<double>, NPY_CDOUBLE, int)
+
+%#endif
#endif /* SWIGPYTHON */
diff --git a/tools/swig/test/Array.i b/tools/swig/test/Array.i
index 6a8605eb6..64ae57eb0 100644
--- a/tools/swig/test/Array.i
+++ b/tools/swig/test/Array.i
@@ -6,6 +6,7 @@
#define SWIG_FILE_WITH_INIT
#include "Array1.h"
#include "Array2.h"
+#include "ArrayZ.h"
%}
// Get the NumPy typemaps
@@ -51,6 +52,12 @@
%apply (int* DIM1 , int* DIM2 , long** ARGOUTVIEW_ARRAY2)
{(int* nrows, int* ncols, long** data )};
+// Apply the 1D NumPy typemaps
+%apply (int DIM1 , std::complex<double>* INPLACE_ARRAY1)
+ {(int length, std::complex<double>* data )};
+%apply (std::complex<double>** ARGOUTVIEW_ARRAY1, int* DIM1 )
+ {(std::complex<double>** data , int* length)};
+
// Array1 support
%include "Array1.h"
%extend Array1
@@ -100,3 +107,29 @@
return self->asString();
}
}
+
+// ArrayZ support
+%include "ArrayZ.h"
+%extend ArrayZ
+{
+ void __setitem__(int i, std::complex<double> v)
+ {
+ self->operator[](i) = v;
+ }
+
+ std::complex<double> __getitem__(int i)
+ {
+ return self->operator[](i);
+ }
+
+ int __len__()
+ {
+ return self->length();
+ }
+
+ std::string __str__()
+ {
+ return self->asString();
+ }
+}
+
diff --git a/tools/swig/test/ArrayZ.cxx b/tools/swig/test/ArrayZ.cxx
new file mode 100644
index 000000000..4756c6981
--- /dev/null
+++ b/tools/swig/test/ArrayZ.cxx
@@ -0,0 +1,131 @@
+#include "ArrayZ.h"
+#include <iostream>
+#include <sstream>
+
+// Default/length/array constructor
+ArrayZ::ArrayZ(int length, std::complex<double>* data) :
+ _ownData(false), _length(0), _buffer(0)
+{
+ resize(length, data);
+}
+
+// Copy constructor
+ArrayZ::ArrayZ(const ArrayZ & source) :
+ _length(source._length)
+{
+ allocateMemory();
+ *this = source;
+}
+
+// Destructor
+ArrayZ::~ArrayZ()
+{
+ deallocateMemory();
+}
+
+// Assignment operator
+ArrayZ & ArrayZ::operator=(const ArrayZ & source)
+{
+ int len = _length < source._length ? _length : source._length;
+ for (int i=0; i < len; ++i)
+ {
+ (*this)[i] = source[i];
+ }
+ return *this;
+}
+
+// Equals operator
+bool ArrayZ::operator==(const ArrayZ & other) const
+{
+ if (_length != other._length) return false;
+ for (int i=0; i < _length; ++i)
+ {
+ if ((*this)[i] != other[i]) return false;
+ }
+ return true;
+}
+
+// Length accessor
+int ArrayZ::length() const
+{
+ return _length;
+}
+
+// Resize array
+void ArrayZ::resize(int length, std::complex<double>* data)
+{
+ if (length < 0) throw std::invalid_argument("ArrayZ length less than 0");
+ if (length == _length) return;
+ deallocateMemory();
+ _length = length;
+ if (!data)
+ {
+ allocateMemory();
+ }
+ else
+ {
+ _ownData = false;
+ _buffer = data;
+ }
+}
+
+// Set item accessor
+std::complex<double> & ArrayZ::operator[](int i)
+{
+ if (i < 0 || i >= _length) throw std::out_of_range("ArrayZ index out of range");
+ return _buffer[i];
+}
+
+// Get item accessor
+const std::complex<double> & ArrayZ::operator[](int i) const
+{
+ if (i < 0 || i >= _length) throw std::out_of_range("ArrayZ index out of range");
+ return _buffer[i];
+}
+
+// String output
+std::string ArrayZ::asString() const
+{
+ std::stringstream result;
+ result << "[";
+ for (int i=0; i < _length; ++i)
+ {
+ result << " " << _buffer[i];
+ if (i < _length-1) result << ",";
+ }
+ result << " ]";
+ return result.str();
+}
+
+// Get view
+void ArrayZ::view(std::complex<double>** data, int* length) const
+{
+ *data = _buffer;
+ *length = _length;
+}
+
+// Private methods
+ void ArrayZ::allocateMemory()
+ {
+ if (_length == 0)
+ {
+ _ownData = false;
+ _buffer = 0;
+ }
+ else
+ {
+ _ownData = true;
+ _buffer = new std::complex<double>[_length];
+ }
+ }
+
+ void ArrayZ::deallocateMemory()
+ {
+ if (_ownData && _length && _buffer)
+ {
+ delete [] _buffer;
+ }
+ _ownData = false;
+ _length = 0;
+ _buffer = 0;
+ }
diff --git a/tools/swig/test/ArrayZ.h b/tools/swig/test/ArrayZ.h
new file mode 100644
index 000000000..75abae0b2
--- /dev/null
+++ b/tools/swig/test/ArrayZ.h
@@ -0,0 +1,56 @@
+#ifndef ARRAYZ_H
+#define ARRAYZ_H
+
+#include <stdexcept>
+#include <string>
+#include <complex>
+
+class ArrayZ
+{
+public:
+
+ // Default/length/array constructor
+ ArrayZ(int length = 0, std::complex<double>* data = 0);
+
+ // Copy constructor
+ ArrayZ(const ArrayZ & source);
+
+ // Destructor
+ ~ArrayZ();
+
+ // Assignment operator
+ ArrayZ & operator=(const ArrayZ & source);
+
+ // Equals operator
+ bool operator==(const ArrayZ & other) const;
+
+ // Length accessor
+ int length() const;
+
+ // Resize array
+ void resize(int length, std::complex<double>* data = 0);
+
+ // Set item accessor
+ std::complex<double> & operator[](int i);
+
+ // Get item accessor
+ const std::complex<double> & operator[](int i) const;
+
+ // String output
+ std::string asString() const;
+
+ // Get view
+ void view(std::complex<double>** data, int* length) const;
+
+private:
+ // Members
+ bool _ownData;
+ int _length;
+ std::complex<double> * _buffer;
+
+ // Methods
+ void allocateMemory();
+ void deallocateMemory();
+};
+
+#endif
diff --git a/tools/swig/test/Makefile b/tools/swig/test/Makefile
index 5360b1ced..5632e7ad0 100644
--- a/tools/swig/test/Makefile
+++ b/tools/swig/test/Makefile
@@ -5,7 +5,8 @@ PROXIES = $(INTERFACES:.i=.py )
# Default target: build the tests
.PHONY : all
-all: $(WRAPPERS) Array1.cxx Array1.h Farray.cxx Farray.h Vector.cxx Vector.h \
+all: $(WRAPPERS) Array1.cxx Array1.h Array2.cxx Array2.h ArrayZ.cxx ArrayZ.h \
+ Farray.cxx Farray.h Vector.cxx Vector.h \
Matrix.cxx Matrix.h Tensor.cxx Tensor.h Fortran.h Fortran.cxx
./setup.py build_ext -i
diff --git a/tools/swig/test/setup.py b/tools/swig/test/setup.py
index e39114f91..81df1b8ed 100755
--- a/tools/swig/test/setup.py
+++ b/tools/swig/test/setup.py
@@ -15,7 +15,8 @@ numpy_include = numpy.get_include()
_Array = Extension("_Array",
["Array_wrap.cxx",
"Array1.cxx",
- "Array2.cxx"],
+ "Array2.cxx",
+ "ArrayZ.cxx"],
include_dirs = [numpy_include],
)
diff --git a/tools/swig/test/testArray.py b/tools/swig/test/testArray.py
index d986de3b3..2ccca19b4 100755
--- a/tools/swig/test/testArray.py
+++ b/tools/swig/test/testArray.py
@@ -269,12 +269,113 @@ class Array2TestCase(unittest.TestCase):
######################################################################
+class ArrayZTestCase(unittest.TestCase):
+
+ def setUp(self):
+ self.length = 5
+ self.array3 = Array.ArrayZ(self.length)
+
+ def testConstructor0(self):
+ "Test ArrayZ default constructor"
+ a = Array.ArrayZ()
+ self.failUnless(isinstance(a, Array.ArrayZ))
+ self.failUnless(len(a) == 0)
+
+ def testConstructor1(self):
+ "Test ArrayZ length constructor"
+ self.failUnless(isinstance(self.array3, Array.ArrayZ))
+
+ def testConstructor2(self):
+ "Test ArrayZ array constructor"
+ na = np.arange(self.length, dtype=np.complex128)
+ aa = Array.ArrayZ(na)
+ self.failUnless(isinstance(aa, Array.ArrayZ))
+
+ def testConstructor3(self):
+ "Test ArrayZ copy constructor"
+ for i in range(self.array3.length()): self.array3[i] = complex(i,-i)
+ arrayCopy = Array.ArrayZ(self.array3)
+ self.failUnless(arrayCopy == self.array3)
+
+ def testConstructorBad(self):
+ "Test ArrayZ length constructor, negative"
+ self.assertRaises(ValueError, Array.ArrayZ, -4)
+
+ def testLength(self):
+ "Test ArrayZ length method"
+ self.failUnless(self.array3.length() == self.length)
+
+ def testLen(self):
+ "Test ArrayZ __len__ method"
+ self.failUnless(len(self.array3) == self.length)
+
+ def testResize0(self):
+ "Test ArrayZ resize method, length"
+ newLen = 2 * self.length
+ self.array3.resize(newLen)
+ self.failUnless(len(self.array3) == newLen)
+
+ def testResize1(self):
+ "Test ArrayZ resize method, array"
+ a = np.zeros((2*self.length,), dtype=np.complex128)
+ self.array3.resize(a)
+ self.failUnless(len(self.array3) == a.size)
+
+ def testResizeBad(self):
+ "Test ArrayZ resize method, negative length"
+ self.assertRaises(ValueError, self.array3.resize, -5)
+
+ def testSetGet(self):
+ "Test ArrayZ __setitem__, __getitem__ methods"
+ n = self.length
+ for i in range(n):
+ self.array3[i] = i*i
+ for i in range(n):
+ self.failUnless(self.array3[i] == i*i)
+
+ def testSetBad1(self):
+ "Test ArrayZ __setitem__ method, negative index"
+ self.assertRaises(IndexError, self.array3.__setitem__, -1, 0)
+
+ def testSetBad2(self):
+ "Test ArrayZ __setitem__ method, out-of-range index"
+ self.assertRaises(IndexError, self.array3.__setitem__, self.length+1, 0)
+
+ def testGetBad1(self):
+ "Test ArrayZ __getitem__ method, negative index"
+ self.assertRaises(IndexError, self.array3.__getitem__, -1)
+
+ def testGetBad2(self):
+ "Test ArrayZ __getitem__ method, out-of-range index"
+ self.assertRaises(IndexError, self.array3.__getitem__, self.length+1)
+
+ def testAsString(self):
+ "Test ArrayZ asString method"
+ for i in range(self.array3.length()): self.array3[i] = complex(i+1,-i-1)
+ self.failUnless(self.array3.asString() == "[ (1,-1), (2,-2), (3,-3), (4,-4), (5,-5) ]")
+
+ def testStr(self):
+ "Test ArrayZ __str__ method"
+ for i in range(self.array3.length()): self.array3[i] = complex(i-2,(i-2)*2)
+ self.failUnless(str(self.array3) == "[ (-2,-4), (-1,-2), (0,0), (1,2), (2,4) ]")
+
+ def testView(self):
+ "Test ArrayZ view method"
+ for i in range(self.array3.length()): self.array3[i] = complex(i+1,i+2)
+ a = self.array3.view()
+ self.failUnless(isinstance(a, np.ndarray))
+ self.failUnless(len(a) == self.length)
+ self.failUnless((a == [1+2j, 2+3j, 3+4j, 4+5j, 5+6j]).all())
+
+######################################################################
+
if __name__ == "__main__":
# Build the test suite
suite = unittest.TestSuite()
suite.addTest(unittest.makeSuite(Array1TestCase))
suite.addTest(unittest.makeSuite(Array2TestCase))
+ suite.addTest(unittest.makeSuite(ArrayZTestCase))
# Execute the test suite
print("Testing Classes of Module Array")
diff --git a/tools/test-installed-numpy.py b/tools/test-installed-numpy.py
index 0174e0708..26a50b2fa 100644
--- a/tools/test-installed-numpy.py
+++ b/tools/test-installed-numpy.py
@@ -38,7 +38,7 @@ import numpy
# Check that NPY_RELAXED_STRIDES_CHECKING is active when set.
# The same flags check is also used in the tests to switch behavior.
-if (os.environ.get('NPY_RELAXED_STRIDES_CHECKING', "0") != "0"):
+if (os.environ.get('NPY_RELAXED_STRIDES_CHECKING', "1") != "0"):
if not numpy.ones((10, 1), order='C').flags.f_contiguous:
print('NPY_RELAXED_STRIDES_CHECKING set, but not active.')
sys.exit(1)
diff --git a/tools/travis-test.sh b/tools/travis-test.sh
index de078edf7..3981c3b58 100755
--- a/tools/travis-test.sh
+++ b/tools/travis-test.sh
@@ -1,6 +1,9 @@
#!/bin/sh
set -ex
+# travis boxes give you 1.5 cpus
+export NPY_NUM_BUILD_JOBS=2
+
# setup env
if [ -r /usr/lib/libeatmydata/libeatmydata.so ]; then
# much faster package installation
@@ -59,9 +62,9 @@ setup_bento()
cd ..
# Waf
- wget http://waf.googlecode.com/files/waf-1.7.13.tar.bz2
- tar xjvf waf-1.7.13.tar.bz2
- cd waf-1.7.13
+ wget http://ftp.waf.io/pub/release/waf-1.7.16.tar.bz2
+ tar xjvf waf-1.7.16.tar.bz2
+ cd waf-1.7.16
python waf-light
export WAFDIR=$PWD
cd ..
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