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[Review Needed]Pytest Style topology/test_topology_base.py #1604

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Merged
kain88-de merged 1 commit into from
Aug 13, 2017
Merged

[Review Needed]Pytest Style topology/test_topology_base.py #1604

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31 changes: 15 additions & 16 deletions testsuite/MDAnalysisTests/topology/test_topology_base.py
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Original file line number Diff line number Diff line change
@@ -1,23 +1,22 @@
from __future__ import absolute_import
import numpy as np
from numpy.testing import (
assert_array_equal,
)
from numpy.testing import assert_equal

from MDAnalysis.topology.base import squash_by, change_squash


class TestSquash(object):
atom_resids = np.array([2, 2, 1, 1, 5, 5, 4, 4])
atom_resnames = np.array(['A', 'A', 'B', 'B', 'C', 'C', 'D', 'D'],
dtype=object)

def test_squash(self):
atom_residx, resids, (resnames,) = squash_by(
self.atom_resids, self.atom_resnames)
atom_residx, resids, (resnames, ) = squash_by(self.atom_resids,
self.atom_resnames)

assert_array_equal(atom_residx, np.array([1, 1, 0, 0, 3, 3, 2, 2]))
assert_array_equal(resids, np.array([1, 2, 4, 5]))
assert_array_equal(resnames, np.array(['B', 'A', 'D', 'C']))
assert_equal(atom_residx, np.array([1, 1, 0, 0, 3, 3, 2, 2]))
assert_equal(resids, np.array([1, 2, 4, 5]))
assert_equal(resnames, np.array(['B', 'A', 'D', 'C']))


class TestChangeSquash(object):
Expand All @@ -30,17 +29,17 @@ def test_resid_squash(self):
segids = np.array(['A', 'A', 'A', 'A', 'B', 'B'])

residx, (new_resids, new_resnames, new_segids) = change_squash(
(resids,), (resids, resnames, segids))
(resids, ), (resids, resnames, segids))

assert_array_equal(residx, np.array([0, 0, 1, 1, 2, 2]))
assert_array_equal(new_resids, np.array([2, 3, 2]))
assert_array_equal(new_resnames, np.array(['RsA', 'RsB', 'RsC']))
assert_array_equal(new_segids, np.array(['A', 'A', 'B']))
assert_equal(residx, np.array([0, 0, 1, 1, 2, 2]))
assert_equal(new_resids, np.array([2, 3, 2]))
assert_equal(new_resnames, np.array(['RsA', 'RsB', 'RsC']))
assert_equal(new_segids, np.array(['A', 'A', 'B']))

def test_segid_squash(self):
segids = np.array(['A', 'A', 'B'])

segidx, (new_segids,) = change_squash((segids,), (segids,))
segidx, (new_segids, ) = change_squash((segids, ), (segids, ))

assert_array_equal(segidx, np.array([0, 0, 1]))
assert_array_equal(new_segids, np.array(['A', 'B']))
assert_equal(segidx, np.array([0, 0, 1]))
assert_equal(new_segids, np.array(['A', 'B']))