Move utils module to run with pytest

Get rid of staticmethods

Fixed import ordering

.travis.yml

@@ -23,9 +23,9 @@ env:
     - PYTHON_VERSION=2.7
     - COVERALLS=false
     - NOSE_FLAGS="--processes=2 --process-timeout=400 --no-open-files --with-timer --timer-top-n 50"
-    - NOSE_TEST_LIST="analysis auxiliary core topology utils"
+    - NOSE_TEST_LIST="analysis auxiliary coordinates core topology"
     - PYTEST_FLAGS="--disable-pytest-warnings"
-    - PYTEST_LIST="testsuite/MDAnalysisTests/lib testsuite/MDAnalysisTests/formats testsuite/MDAnalysisTests/coordinates"
+    - PYTEST_LIST="testsuite/MDAnalysisTests/lib testsuite/MDAnalysisTests/formats testsuite/MDAnalysisTests/utils"
     - NOSE_COVERAGE_FILE="nose_coverage"
     - PYTEST_COVERAGE_FILE="pytest_coverage"
     - MAIN_CMD="pytest ${PYTEST_LIST} ${PYTEST_FLAGS}; python ./testsuite/MDAnalysisTests/mda_nosetests ${NOSE_TEST_LIST} ${NOSE_FLAGS}"

testsuite/MDAnalysisTests/utils/test_distances.py

@@ -20,17 +20,18 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from __future__ import division, absolute_import
-
 import MDAnalysis
 import MDAnalysis.lib.distances
+
 import numpy as np
-from MDAnalysis.lib import mdamath
-from MDAnalysis.tests.datafiles import PSF, DCD, TRIC
-from MDAnalysisTests import parser_not_found
-from nose.plugins.attrib import attr
 from numpy.testing import (TestCase, dec, raises, assert_,
-                           assert_almost_equal, assert_equal, assert_raises, )
+                           assert_almost_equal, assert_equal, assert_raises,)
 
+from nose.plugins.attrib import attr
+
+from MDAnalysis.tests.datafiles import PSF, DCD, TRIC
+from MDAnalysis.lib import mdamath
+from MDAnalysisTests import parser_not_found
 
 class _TestDistanceArray(TestCase):
     # override backend in test classes
@@ -121,7 +122,6 @@ def tearDown(self):
         del self.trajectory
         del self.ca
 
-    @attr('issue')
     def test_simple(self):
         U = self.universe
         self.trajectory.rewind()

testsuite/MDAnalysisTests/utils/test_modelling.py

@@ -21,19 +21,30 @@
 #
 from __future__ import absolute_import, print_function
 
-import os
-
 import MDAnalysis
+from MDAnalysis.tests.datafiles import (
+    PSF,
+    DCD,
+    capping_input,
+    capping_output,
+    capping_ace,
+    capping_nma,
+    merge_protein,
+    merge_ligand,
+    merge_water
+)
 import MDAnalysis.core.groups
-from MDAnalysis import Merge
-from MDAnalysis.analysis.align import alignto
 from MDAnalysis.core.groups import AtomGroup
-from MDAnalysis.tests.datafiles import PSF, DCD, capping_input, capping_output, capping_ace, capping_nma, \
-    merge_protein, merge_ligand, merge_water
 from MDAnalysisTests import parser_not_found, tempdir
+
 from numpy.testing import (TestCase, dec, assert_equal, assert_raises, assert_,
                            assert_array_equal)
 
+import os
+
+from MDAnalysis import Merge
+from MDAnalysis.analysis.align import alignto
+
 
 def capping(ref, ace, nma, output):
     resids = ref.select_atoms("all").resids
@@ -48,12 +59,12 @@ def capping(ref, ace, nma, output):
     # TODO consider a case when the protein resid is 1 and all peptide has to be shifted by +1, put that in docs as a
     #  post-processing step
     alignto(ace, ref, select={
-        "mobile": "resid {0} and backbone".format(resid_min),
-        "reference": "resid {0} and backbone".format(resid_min)},
+            "mobile": "resid {0} and backbone".format(resid_min),
+            "reference": "resid {0} and backbone".format(resid_min)},
             strict=True)
     alignto(nma, ref, select={
-        "mobile": "resid {0} and backbone and not (resname NMA NME)".format(resid_max),
-        "reference": "resid {0} and (backbone or name OT2)".format(resid_max)},
+            "mobile": "resid {0} and backbone and not (resname NMA NME)".format(resid_max),
+            "reference": "resid {0} and (backbone or name OT2)".format(resid_max)},
             strict=True)
 
     #  TODO remove the Hydrogen closest to ACE's oxygen
@@ -152,9 +163,9 @@ def test_merge(self):
         # Check that the output Universe has the same number of residues and
         # segments as the starting AtomGroups
         assert_equal(len(u0.residues), (len(u1.residues) + len(u2.residues) +
-                                        len(u3.residues)))
+                                                           len(u3.residues)))
         assert_equal(len(u0.segments), (len(u1.segments) + len(u2.segments) +
-                                        len(u3.segments)))
+                                                           len(u3.segments)))
 
         # Make sure that all the atoms in the new universe are assigned to only
         # one, new Universe

testsuite/MDAnalysisTests/utils/test_persistence.py

@@ -20,15 +20,20 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from __future__ import absolute_import
+from six.moves import cPickle
+
+import MDAnalysis as mda
+from numpy.testing import (
+    TestCase,
+    assert_array_equal,
+    assert_,
+    assert_raises,
+    assert_equal
+)
 
 import gc
 
-import MDAnalysis as mda
 from MDAnalysisTests.datafiles import PDB_small
-from numpy.testing import (TestCase,
-                           assert_array_equal, assert_, assert_raises,
-                           assert_equal)
-from six.moves import cPickle
 
 
 class TestAtomGroupPickle(TestCase):

testsuite/MDAnalysisTests/utils/test_selections.py

@@ -22,17 +22,19 @@
 
 # Test the selection exporters in MDAnalysis.selections
 from __future__ import absolute_import
+# use StringIO and NamedStream to write to memory instead to temp files
+from six.moves import StringIO
 
 import re
 
-import MDAnalysis
 import numpy as np
-from MDAnalysis.lib.util import NamedStream
+from numpy.testing import TestCase, assert_equal, assert_array_equal, dec
+
 from MDAnalysis.tests.datafiles import PSF, DCD
 from MDAnalysisTests import parser_not_found
-from numpy.testing import TestCase, assert_equal, assert_array_equal, dec
-# use StringIO and NamedStream to write to memory instead to temp files
-from six.moves import StringIO
+
+import MDAnalysis
+from MDAnalysis.lib.util import NamedStream
 
 
 class _SelectionWriter(TestCase):
@@ -105,10 +107,10 @@ class TestSelectionWriter_Gromacs(_SelectionWriter):
     filename = "CA.ndx"
     ref_name = "CA_selection"
     ref_indices = ndx2array(
-        ['5 22 46 65 84 103 122 129 141 153 160 170 \n',
-         '177 199 206 220 237 247 264 284 303 320 335 357 \n',
-         ]
-    )
+        [ '5 22 46 65 84 103 122 129 141 153 160 170 \n',
+          '177 199 206 220 237 247 264 284 303 320 335 357 \n',
+          ]
+        )
 
     def _assert_selectionstring(self):
         header = self.namedfile.readline().strip()
@@ -192,9 +194,9 @@ class TestSelectionWriter_Jmol(_SelectionWriter):
     writer = MDAnalysis.selections.jmol.SelectionWriter
     filename = "CA.spt"
     ref_name, ref_indices = spt2array(
-        ('@~ca ({4 21 45 64 83 102 121 128 140 152 159 169 176 198 205 219 236'
-         ' 246 263 283 302 319 334 356});')
-    )
+        ( '@~ca ({4 21 45 64 83 102 121 128 140 152 159 169 176 198 205 219 236'
+          ' 246 263 283 302 319 334 356});')
+        )
 
     def _assert_selectionstring(self):
         header, indices = spt2array(self.namedfile.readline())

testsuite/MDAnalysisTests/utils/test_transformations.py

@@ -21,15 +21,18 @@
 #
 from __future__ import division, absolute_import
 
-import unittest
+from six.moves import range
 from itertools import permutations
-from unittest import TestCase
 
 import numpy as np
-from MDAnalysis.lib import transformations as t
+import unittest
 from numpy.testing import (assert_allclose, assert_equal, assert_almost_equal,
                            assert_array_equal)
-from six.moves import range
+
+from MDAnalysis.lib import transformations as t
+
+from unittest import TestCase
+
 
 """
 Testing transformations is weird because there are 2 versions of many of
@@ -565,7 +568,7 @@ def test_quaternion_from_matrix_2(self):
         q = self.f(np.diag([1., -1., -1., 1.]))
         check = (np.allclose(
             q, [0, 1, 0, 0], atol=_ATOL) or np.allclose(
-            q, [0, -1, 0, 0], atol=_ATOL))
+                q, [0, -1, 0, 0], atol=_ATOL))
         assert_equal(check, True)
 
     def test_quaternion_from_matrix_3(self):
@@ -886,7 +889,7 @@ def test_transformations_old_module():
         raise AssertionError("MDAnalysis.core.transformations not importable. "
                              "Only remove for 1.0")
 
-        # NOTE: removed this test with release 1.0 when we remove the stub
+    # NOTE: removed this test with release 1.0 when we remove the stub
 
 
 def test_rotaxis_equal_vectors():

testsuite/MDAnalysisTests/utils/test_units.py

@@ -30,30 +30,27 @@
 
 
 class TestDefaultUnits(TestCase):
-    @staticmethod
-    def test_length():
+    def test_length(self):
         assert_equal(flags['length_unit'], 'Angstrom',
                      u"The default length unit should be Angstrom (in core.flags)")
-    @staticmethod
-    def test_time():
+
+    def test_time(self):
         assert_equal(flags['time_unit'], 'ps',
                      u"The default length unit should be pico seconds (in core.flags)")
-    @staticmethod
-    def test_convert_gromacs_trajectories():
+
+    def test_convert_gromacs_trajectories(self):
         assert_equal(flags['convert_lengths'], True,
                      u"The default behaviour should be to auto-convert Gromacs trajectories")
 
 
 class TestUnitEncoding(TestCase):
-    @staticmethod
-    def test_unicode():
+    def test_unicode(self):
         try:
             assert_equal(units.lengthUnit_factor[u"\u212b"], 1.0)
         except KeyError:
             raise AssertionError("Unicode symbol for Angtrom not supported")
 
-    @staticmethod
-    def test_unicode_encoding_with_symbol():
+    def test_unicode_encoding_with_symbol(self):
         try:
             assert_equal(units.lengthUnit_factor[u"Å"], 1.0)
         except KeyError:
@@ -106,14 +103,12 @@ def test_force(self):
         yield self._assert_almost_equal_convert, 2.5, 'kJ/(mol*nm)', 'kJ/(mol*A)', 0.25
         yield self._assert_almost_equal_convert, 1, 'kcal/(mol*Angstrom)', 'kJ/(mol*Angstrom)', 4.184
 
-    @staticmethod
-    def test_unit_unknown():
+    def test_unit_unknown(self):
         nm = 12.34567
         assert_raises(ValueError, units.convert, nm, 'Stone', 'nm')
         assert_raises(ValueError, units.convert, nm, 'nm', 'Stone')
-
-    @staticmethod
-    def test_unit_unconvertable():
+
+    def test_unit_unconvertable(self):
         nm = 12.34567
         A = nm * 10.
         assert_raises(ValueError, units.convert, A, 'A', 'ps')