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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
import pytest
import numpy as np
from numpy.testing import assert_equal
from MDAnalysis.lib._cutil import (
unique_int_1d,
find_fragments,
_in2d,
)
@pytest.mark.parametrize(
"values",
(
[], # empty array
[1, 1, 1, 1], # all identical
[2, 3, 5, 7], # all different, monotonic
[5, 2, 7, 3], # all different, non-monotonic
[1, 2, 2, 4, 4, 6], # duplicates, monotonic
[1, 2, 2, 6, 4, 4], # duplicates, non-monotonic
),
)
def test_unique_int_1d(values):
array = np.array(values, dtype=np.intp)
ref = np.unique(array)
res = unique_int_1d(array)
assert_equal(res, ref)
assert type(res) == type(ref)
assert res.dtype == ref.dtype
@pytest.mark.parametrize(
"edges,ref",
[
([[0, 1], [1, 2], [2, 3], [3, 4]], [[0, 1, 2, 3, 4]]), # linear chain
(
[[0, 1], [1, 2], [2, 3], [3, 4], [4, 10]],
[[0, 1, 2, 3, 4]],
), # unused edge (4, 10)
([[0, 1], [1, 2], [2, 3]], [[0, 1, 2, 3], [4]]), # lone atom
(
[[0, 1], [1, 2], [2, 0], [3, 4], [4, 3]],
[[0, 1, 2], [3, 4]],
), # circular
],
)
def test_find_fragments(edges, ref):
atoms = np.arange(5)
fragments = find_fragments(atoms, edges)
assert len(fragments) == len(ref)
for frag, r in zip(fragments, ref):
assert_equal(frag, r)
def test_in2d():
arr1 = np.array([[1, 2], [3, 4], [5, 6]], dtype=np.intp)
arr2 = np.array([[3, 4], [2, 1], [5, 5], [6, 6]], dtype=np.intp)
result = _in2d(arr1, arr2)
assert_equal(result, np.array([False, True, False]))
@pytest.mark.parametrize(
"arr1,arr2",
[
(
np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]], dtype=np.intp),
np.array([[1, 2], [3, 4]], dtype=np.intp),
),
(
np.array([[1, 2], [3, 4]], dtype=np.intp),
np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]], dtype=np.intp),
),
],
)
def test_in2d_VE(arr1, arr2):
with pytest.raises(
ValueError, match=r"Both arrays must be \(n, 2\) arrays"
):
_in2d(arr1, arr2)
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