def test_KDTree_neighbour(self): for i in range(0, 10): self.assertTrue(_neighbor_test(nr_points, dim, bucket_size, radius))
# This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. try: import numpy except ImportError: from Bio import MissingExternalDependencyError raise MissingExternalDependencyError(\ "Install NumPy if you want to use Bio.KDTree.") from Bio.KDTree.KDTree import _neighbor_test, _test nr_points=5000 dim=3 bucket_size=5 radius=0.01 for i in range(0, 10): _neighbor_test(nr_points, dim, bucket_size, radius) _test(nr_points, dim, bucket_size, radius)
#TODO - What if numpy was installed after Biopython, #meaning KDTree's C code hasn't been compiled? try: import numpy except ImportError: from Bio import MissingExternalDependencyError raise MissingExternalDependencyError(\ "Install NumPy if you want to use Bio.KDTree.") from Bio.KDTree.KDTree import _neighbor_test, _test nr_points = 5000 dim = 3 bucket_size = 5 radius = 0.01 for i in range(0, 10): _neighbor_test(nr_points, dim, bucket_size, radius) _test(nr_points, dim, bucket_size, radius)