Merge branch 'release/0.1.0'

Makefile

@@ -1,7 +1,6 @@
 buildcython:
 	cython -v -t --cplus pyemd/emd.pyx
 	python setup.py build_ext --inplace
-	mv emd*.so pyemd/emd.so
 
 clean:
 	rm -rf pyemd/emd.so

pyemd/__init__.py

@@ -50,7 +50,7 @@
 """
 
 __title__ = 'pyemd'
-__version__ = '0.0.10'
+__version__ = '0.1.0'
 __author__ = 'Will Mayner'
 __author_email__ = 'wmayner@gmail.com'
 __author_website__ = 'http://willmayner.com'

pyemd/emd.pyx

@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
 # distutils: language = c++
 
 from libcpp.vector cimport vector
@@ -20,46 +22,31 @@ cdef extern from "lib/emd_hat.hpp":
 # NumPy array to C++ vector conversion
 # ====================================
 
-# See http://stackoverflow.com/a/2434208/1085344
-cdef vector[double] _c_array_to_vector(double* array, int length):
-    cdef vector[double] output_vector
-    output_vector.reserve(length)
-    output_vector.assign(array, array + length)
-    return output_vector
-
-
 # See https://github.com/cython/cython/wiki/tutorials-NumpyPointerToC
 @cython.boundscheck(False)
 @cython.wraparound(False)
-def _np_array_to_vector(np.ndarray[double, ndim=1, mode="c"] array):
+cdef vector[double] _np_array_to_vector(
+    np.ndarray[double, ndim=1, mode="c"] array):
     """Convert a 1D numpy array to a C++ vector.
 
     :param array: A 1D numpy array of ``np.double``.
-
     """
     cdef vector[double] output_vector
-    cdef int length
-    length = array.size
-
-    # Pass pointer to beginning of numpy array data
-    output_vector = _c_array_to_vector(&array[0], length)
-
+    output_vector.reserve(array.size)
+    output_vector.assign(&array[0], &array[0] + array.size)
     return output_vector
 
 
 def _2d_np_array_to_2d_vector(np.ndarray[double, ndim=2, mode="c"] matrix):
     """Convert a 2D numpy array to a C++ vector of vectors.
 
     :param array: A 2D numpy array of ``np.double``.
-
     """
     cdef vector[vector[double]] output_matrix
+    output_matrix.resize(array.shape[0])
     cdef vector[double] c_row
-
-    for row in matrix:
-        c_row = _np_array_to_vector(row)
-        output_matrix.push_back(c_row)
-
+    for i in range(matrix.shape[0]):
+        output_matrix[i] = _np_array_to_vector(row)
     return output_matrix
 
 
@@ -78,33 +65,13 @@ def emd(np.ndarray[double, ndim=1, mode="c"] first_signature,
         :math:`N`..
     :param distance_matrix: A 2D numpy array of ``np.double``, of size
         :math:`N \cross N`.
-
     """
-    # Validation
-    if ([arg.dtype for arg in [first_signature, second_signature,
-                               distance_matrix]] != [np.dtype('float64')] * 3):
-        raise ValueError("Signatures and ditance matrix must be of dtype " +
-                         "'float64'.")
-    N = first_signature.shape[0]
-    if (N != second_signature.shape[0]):
-        raise ValueError("Signatures must be the same size.")
-    if ((N != distance_matrix.shape[0]) or (N != distance_matrix.shape[1])):
-        raise ValueError("Distance matrix must be NxN, where N is the length of" +
-                         "the signatures.")
-    if (first_signature.ndim != 1) or (first_signature.ndim !=
-                                       second_signature.ndim):
-        raise ValueError("Signatures must be 1-dimensional.")
-    if (distance_matrix.ndim != 2):
-        raise ValueError("Distance matrix must be 2-dimensional.")
-
-    # Convert numpy input to C++ vectors
     cdef vector[double] c_first_signature
     cdef vector[double] c_second_signature
     cdef vector[vector[double]] c_distance_matrix
     c_first_signature = _np_array_to_vector(first_signature)
     c_second_signature = _np_array_to_vector(second_signature)
     c_distance_matrix = _2d_np_array_to_2d_vector(distance_matrix)
-
     return emd_hat_gd_metric_double(c_first_signature,
                                     c_second_signature,
                                     c_distance_matrix)

requirements.txt

@@ -1,6 +1,6 @@
-Cython==0.20.1
-numpy==1.8.0
-py==1.4.20
-pytest==2.5.2
-wheel==0.23.0
-twine==1.3.0
+Cython>=0.20.2
+numpy>=1.8.0, <2.0.0
+py>=1.4.20
+pytest>=2.5.2
+wheel>=0.23.0
+twine>=1.3.0

setup.py

@@ -19,11 +19,11 @@ def finalize_options(self):
 with open('README.rst') as f:
     readme = f.read()
 
-requires = ['numpy >=1.8.0, < 2.0.0']
+requires = ['numpy >=1.8.0, <2.0.0']
 
 setup(
     name='pyemd',
-    version='0.0.10',
+    version='0.1.0',
     description=("A Python wrapper for Ofir Pele and Michael Werman's " +
                  "implementation of the Earth Mover's Distance."),
     long_description=readme,

test/test_pyemd.py

@@ -1,62 +1,29 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 
-import unittest
 import numpy as np
 from pyemd import emd
 
 
-class TestEmd(unittest.TestCase):
+def test_case_1():
+    first_signature = np.array([0.0, 1.0])
+    second_signature = np.array([5.0, 3.0])
+    distance_matrix = np.array([[0.0, 0.5],
+                                [0.5, 0.0]])
+    assert 3.5 == emd(first_signature, second_signature, distance_matrix)
 
-    def test_case_1(self):
-        first_signature = np.array([0.0, 1.0])
-        second_signature = np.array([5.0, 3.0])
-        distance_matrix = np.array([[0.0, 0.5],
-                                   [0.5, 0.0]])
-        assert 3.5 == emd(first_signature, second_signature, distance_matrix)
 
-    def test_case_2(self):
-        first_signature = np.array([1.0, 1.0])
-        second_signature = np.array([1.0, 1.0])
-        distance_matrix = np.array([[0.0, 1.0],
-                                   [1.0, 0.0]])
-        assert 0.0 == emd(first_signature, second_signature, distance_matrix)
+def test_case_2():
+    first_signature = np.array([1.0, 1.0])
+    second_signature = np.array([1.0, 1.0])
+    distance_matrix = np.array([[0.0, 1.0],
+                                [1.0, 0.0]])
+    assert 0.0 == emd(first_signature, second_signature, distance_matrix)
 
-    def test_case_3(self):
-        first_signature = np.array([6.0, 1.0])
-        second_signature = np.array([1.0, 7.0])
-        distance_matrix = np.array([[0.0, 0.0],
-                                   [0.0, 0.0]])
-        assert 0.0 == emd(first_signature, second_signature, distance_matrix)
 
-    def test_error_different_signature_lengths(self):
-        first_signature = np.array([6.0, 1.0, 9.0])
-        second_signature = np.array([1.0, 7.0])
-        distance_matrix = np.array([[0.0, 1.0],
-                                    [1.0, 0.0]])
-        with self.assertRaises(ValueError):
-            emd(first_signature, second_signature, distance_matrix)
-
-    def test_error_wrong_distance_matrix_shape(self):
-        first_signature = np.array([6.0, 1.0])
-        second_signature = np.array([1.0, 7.0])
-        distance_matrix = np.array([[0.0, 1.0, 0.4],
-                                    [1.0, 0.0]])
-        with self.assertRaises(ValueError):
-            emd(first_signature, second_signature, distance_matrix)
-
-    def test_error_wrong_signature_ndim(self):
-        first_signature = np.array([[6.0, 1.0]])
-        second_signature = np.array([1.0, 7.0])
-        distance_matrix = np.array([[0.0, 1.0],
-                                    [1.0, 0.0]])
-        with self.assertRaises(ValueError):
-            emd(first_signature, second_signature, distance_matrix)
-
-    def test_error_wrong_distance_matrix_ndim(self):
-        first_signature = np.array([6.0, 1.0])
-        second_signature = np.array([1.0, 7.0])
-        distance_matrix = np.array([[[0.0, 1.0],
-                                    [1.0, 0.0]]])
-        with self.assertRaises(ValueError):
-            emd(first_signature, second_signature, distance_matrix)
+def test_case_3():
+    first_signature = np.array([6.0, 1.0])
+    second_signature = np.array([1.0, 7.0])
+    distance_matrix = np.array([[0.0, 0.0],
+                                [0.0, 0.0]])
+    assert 0.0 == emd(first_signature, second_signature, distance_matrix)