Port core module to pytest (#1443)

* Fix test_group_traj_access.py
* Move core to PYTEST_LIST
* Fix test_atom.py
* Fix test_atomgroup.py
* Fix test_atomselections.py
* Fix test_groups.py
* Fix test_index_dtype.py
* Fix test_residue.py
* Fix test_residuegroup.py
* Fix test_segment.py
* Fix test_segmentgroup.py
* Fix test_topology.py
* Fix test_topologyattrs.py
* Fix test_topologyobjects.py
* Fix test_universe.py
* Fix test_updating_atomgroup.py
* Use @pytest.mark.skipif in place of @dec.skipif

.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 core"
+    - NOSE_TEST_LIST="analysis"
     - PYTEST_FLAGS="--disable-pytest-warnings -n 2"
-    - PYTEST_LIST="testsuite/MDAnalysisTests/lib testsuite/MDAnalysisTests/formats testsuite/MDAnalysisTests/coordinates testsuite/MDAnalysisTests/utils testsuite/MDAnalysisTests/topology testsuite/MDAnalysisTests/auxiliary"
+    - PYTEST_LIST="testsuite/MDAnalysisTests/lib testsuite/MDAnalysisTests/formats testsuite/MDAnalysisTests/coordinates testsuite/MDAnalysisTests/utils testsuite/MDAnalysisTests/topology testsuite/MDAnalysisTests/auxiliary testsuite/MDAnalysisTests/core"
     - 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/core/test_atom.py

@@ -21,6 +21,9 @@
 #
 
 from __future__ import absolute_import
+
+from unittest import TestCase
+
 import numpy as np
 from numpy.testing import (
     dec,
@@ -29,6 +32,7 @@
     assert_equal,
     assert_raises,
 )
+import pytest
 
 import MDAnalysis as mda
 from MDAnalysis import NoDataError
@@ -40,11 +44,11 @@
 from MDAnalysisTests import parser_not_found
 
 
-class TestAtom(object):
+class TestAtom(TestCase):
     # Legacy tests from before 363
     """Tests of Atom."""
 
-    @dec.skipif(parser_not_found('DCD'),
+    @pytest.mark.skipif(parser_not_found('DCD'),
                 'DCD parser not available. Are you using python 3?')
     def setUp(self):
         """Set up the standard AdK system in implicit solvent."""
@@ -127,7 +131,7 @@ def test_undefined_occupancy(self):
         self.universe.atoms[0].occupancy
 
 
-class TestAtomNoForceNoVel(object):
+class TestAtomNoForceNoVel(TestCase):
     def setUp(self):
         self.u = mda.Universe(XYZ_mini)
         self.a = self.u.atoms[0]

testsuite/MDAnalysisTests/core/test_atomgroup.py

@@ -25,6 +25,8 @@
 import itertools
 import os
 from os import path
+from unittest import TestCase
+
 import numpy as np
 import warnings
 
@@ -56,35 +58,33 @@
 )
 from MDAnalysisTests import parser_not_found, tempdir, make_Universe
 
+import pytest
+
 # I want to catch all warnings in the tests. If this is not set at the start it
 # could cause test that check for warnings to fail.
 warnings.simplefilter('always')
 
 class TestDeprecationWarnings(object):
-    @staticmethod
-    @dec.skipif(parser_not_found('DCD'),
-                'DCD parser not available. Are you using python 3?')
-    def test_AtomGroupUniverse_usage_warning():
+    @pytest.mark.skipif(parser_not_found('DCD'), reason='DCD parser not available. Are you using python 3?')
+    def test_AtomGroupUniverse_usage_warning(self):
         with warnings.catch_warnings(record=True) as warn:
             warnings.simplefilter('always')
             mda.core.AtomGroup.Universe(PSF, DCD)
         assert_equal(len(warn), 1)
 
-    @staticmethod
-    @dec.skipif(parser_not_found('DCD'),
-                'DCD parser not available. Are you using python 3?')
-    def test_old_AtomGroup_init_warns():
+    @pytest.mark.skipif(parser_not_found('DCD'),
+                reason='DCD parser not available. Are you using python 3?')
+    def test_old_AtomGroup_init_warns(self):
         u = make_Universe(('names',))
         at_list = list(u.atoms[:10])
         with warnings.catch_warnings(record=True) as warn:
             warnings.simplefilter('always')
             ag = mda.core.groups.AtomGroup(at_list)
         assert_equal(len(warn), 1)
 
-    @staticmethod
-    @dec.skipif(parser_not_found('DCD'),
-                'DCD parser not available. Are you using python 3?')
-    def test_old_AtomGroup_init_works():
+    @pytest.mark.skipif(parser_not_found('DCD'),
+                reason='DCD parser not available. Are you using python 3?')
+    def test_old_AtomGroup_init_works(self):
         u = make_Universe(('names',))
         at_list = list(u.atoms[:10])
         ag = mda.core.groups.AtomGroup(at_list)
@@ -93,21 +93,19 @@ def test_old_AtomGroup_init_works():
         assert_(len(ag) == 10)
         assert_equal(ag.names, u.atoms[:10].names)
 
-    @staticmethod
-    @dec.skipif(parser_not_found('DCD'),
-                'DCD parser not available. Are you using python 3?')
-    def test_old_ResidueGroup_init_warns():
+    @pytest.mark.skipif(parser_not_found('DCD'),
+                reason='DCD parser not available. Are you using python 3?')
+    def test_old_ResidueGroup_init_warns(self):
         u = make_Universe(('resnames',))
         res_list = list(u.residues[:10])
         with warnings.catch_warnings(record=True) as warn:
             warnings.simplefilter('always')
             rg = mda.core.groups.ResidueGroup(res_list)
         assert_equal(len(warn), 1)
 
-    @staticmethod
-    @dec.skipif(parser_not_found('DCD'),
-                'DCD parser not available. Are you using python 3?')
-    def test_old_ResidueGroup_init_works():
+    @pytest.mark.skipif(parser_not_found('DCD'),
+                reason='DCD parser not available. Are you using python 3?')
+    def test_old_ResidueGroup_init_works(self):
         u = make_Universe(('resnames',))
         res_list = list(u.residues[:10])
         rg = mda.core.groups.ResidueGroup(res_list)
@@ -116,21 +114,19 @@ def test_old_ResidueGroup_init_works():
         assert_(len(rg) == 10)
         assert_equal(rg.resnames, u.residues[:10].resnames)
 
-    @staticmethod
-    @dec.skipif(parser_not_found('DCD'),
-                'DCD parser not available. Are you using python 3?')
-    def test_old_SegmentGroup_init_warns():
+    @pytest.mark.skipif(parser_not_found('DCD'),
+                reason='DCD parser not available. Are you using python 3?')
+    def test_old_SegmentGroup_init_warns(self):
         u = make_Universe(('segids',))
         seg_list = list(u.segments[:3])
         with warnings.catch_warnings(record=True) as warn:
             warnings.simplefilter('always')
             sg = mda.core.groups.SegmentGroup(seg_list)
         assert_equal(len(warn), 1)
 
-    @staticmethod
-    @dec.skipif(parser_not_found('DCD'),
-                'DCD parser not available. Are you using python 3?')
-    def test_old_SegmentGroup_init_works():
+    @pytest.mark.skipif(parser_not_found('DCD'),
+                reason='DCD parser not available. Are you using python 3?')
+    def test_old_SegmentGroup_init_works(self):
         u = make_Universe(('segids',))
         seg_list = list(u.segments[:3])
         sg = mda.core.groups.SegmentGroup(seg_list)
@@ -142,46 +138,45 @@ def test_old_SegmentGroup_init_works():
 
 class TestAtomGroupToTopology(object):
     """Test the conversion of AtomGroup to TopologyObjects"""
-    @dec.skipif(parser_not_found('DCD'),
-                'DCD parser not available. Are you using python 3?')
-    def setUp(self):
-        self.u = mda.Universe(PSF, DCD)
-
-    def tearDown(self):
-        del self.u
+    @pytest.mark.skipif(parser_not_found('DCD'),'DCD parser not available. Are you using python 3?')
+    @pytest.fixture()
+    def u(self):
+        return mda.Universe(PSF, DCD)
 
-    def test_bond(self):
-        ag = self.u.atoms[:2]
+    def test_bond(self, u):
+        ag = u.atoms[:2]
         bond = ag.bond
         assert_(isinstance(bond, Bond))
 
-    def test_angle(self):
-        ag = self.u.atoms[:3]
+    def test_angle(self, u):
+        ag = u.atoms[:3]
         angle = ag.angle
         assert_(isinstance(angle, Angle))
 
-    def test_dihedral(self):
-        ag = self.u.atoms[:4]
+    def test_dihedral(self, u):
+        ag = u.atoms[:4]
         dih = ag.dihedral
         assert_(isinstance(dih, Dihedral))
 
-    def test_improper(self):
-        ag = self.u.atoms[:4]
+    def test_improper(self, u):
+        ag = u.atoms[:4]
         imp = ag.improper
         assert_(isinstance(imp, ImproperDihedral))
 
-    def _check_VE(self, btype):
-        ag = self.u.atoms[:10]
+    @pytest.mark.parametrize('btype,', [
+        'bond',
+        'angle',
+        'dihedral',
+        'improper'
+    ])
+    def test_VE(self, btype, u):
+        ag = u.atoms[:10]
 
         assert_raises(ValueError, getattr, ag, btype)
 
-    def test_VEs(self):
-        for btype in ('bond', 'angle', 'dihedral', 'improper'):
-            yield self._check_VE, btype
 
-
-class TestAtomGroupWriting(object):
-    @dec.skipif(parser_not_found('DCD'),
+class TestAtomGroupWriting(TestCase):
+    @pytest.mark.skipif(parser_not_found('DCD'),
                 'DCD parser not available. Are you using python 3?')
     def setUp(self):
         self.u = mda.Universe(PSF, DCD)
@@ -217,12 +212,15 @@ def test_bogus_kwarg_pdb(self):
             with assert_raises(TypeError):
                 self.u.atoms.write('dummy.pdb', bogus="what?")
 
-class _WriteAtoms(object):
+class _WriteAtoms(TestCase):
     """Set up the standard AdK system in implicit solvent."""
+
+    __test__ = False
+
     ext = None  # override to test various output writers
     precision = 3
 
-    @dec.skipif(parser_not_found('DCD'),
+    @pytest.mark.skipif(parser_not_found('DCD'),
                 'DCD parser not available. Are you using python 3?')
     def setUp(self):
         self.universe = mda.Universe(PSF, DCD)
@@ -313,11 +311,17 @@ def test_write_Universe(self):
 
 
 class TestWritePDB(_WriteAtoms):
+
+    __test__ = True
+
     ext = "pdb"
     precision = 3
 
 
 class TestWriteGRO(_WriteAtoms):
+
+    __test__ = True
+
     ext = "gro"
     precision = 2
 
@@ -328,8 +332,8 @@ def test_flag_convert_length(self):
                      " in the testing suite.)")
 
 
-class TestAtomGroupTransformations(object):
-    @dec.skipif(parser_not_found('DCD'),
+class TestAtomGroupTransformations(TestCase):
+    @pytest.mark.skipif(parser_not_found('DCD'),
                 'DCD parser not available. Are you using python 3?')
     def setUp(self):
         self.u = mda.Universe(PSF, DCD)
@@ -455,7 +459,8 @@ def test_transform_translation_and_rotation(self):
                                                     np.sin(angle) + 1,
                                                     1])
 
-class TestCenter(object):
+
+class TestCenter(TestCase):
     def setUp(self):
         self.u = make_Universe(trajectory=True)
         self.ag = self.u.atoms[10:30]
@@ -487,8 +492,8 @@ def test_center_wrong_shape(self):
         assert_raises(TypeError, self.ag.center, weights)
 
 
-class TestSplit(object):
-    @dec.skipif(parser_not_found('DCD'),
+class TestSplit(TestCase):
+    @pytest.mark.skipif(parser_not_found('DCD'),
                 'DCD parser not available. Are you using python 3?')
     def setUp(self):
         self.universe = mda.Universe(PSF, DCD)
@@ -535,8 +540,8 @@ def test_split_VE(self):
         assert_raises(ValueError, ag.split, 'something')
 
 
-class TestWrap(object):
-    @dec.skipif(parser_not_found('TRZ'),
+class TestWrap(TestCase):
+    @pytest.mark.skipif(parser_not_found('TRZ'),
                 'TRZ parser not available. Are you using python 3?')
     def setUp(self):
         self.u = mda.Universe(TRZ_psf, TRZ)
@@ -638,7 +643,7 @@ def _change_atom_check_ag(self, att, atts, vals, ag):
         assert_equal(vals, other,
                      err_msg="Change to Atoms not reflected in AtomGroup for property: {0}".format(att))
 
-    @dec.skipif(parser_not_found('DCD'),
+    @pytest.mark.skipif(parser_not_found('DCD'),
                 'DCD parser not available. Are you using python 3?')
     def test_attributes(self):
         u = make_Universe(('names', 'resids', 'segids', 'types', 'altLocs',
@@ -727,8 +732,8 @@ def test_adding_empty_ags(self):
         assert_(len(u.atoms[:3] + u.atoms[[]]) == 3)
 
 
-class TestDihedralSelections(object):
-    @dec.skipif(parser_not_found('DCD'),
+class TestDihedralSelections(TestCase):
+    @pytest.mark.skipif(parser_not_found('DCD'),
                 'DCD parser not available. Are you using python 3?')
     def setUp(self):
         self.universe = mda.Universe(PSF, DCD)
@@ -799,8 +804,8 @@ def test_dihedral_chi1(self):
         assert_almost_equal(sel.dihedral.value(), -58.428127, self.dih_prec)
 
 
-class TestPBCFlag(object):
-    @dec.skipif(parser_not_found('TRZ'),
+class TestPBCFlag(TestCase):
+    @pytest.mark.skipif(parser_not_found('TRZ'),
                 'TRZ parser not available. Are you using python 3?')
     def setUp(self):
         self.prec = 3
@@ -910,22 +915,22 @@ def test_override_flag(self):
         mda.core.flags['use_pbc'] = False
 
 
-@dec.skipif(parser_not_found('DCD'),
-            'DCD parser not available. Are you using python 3?')
+@pytest.mark.skipif(parser_not_found('DCD'),
+            reason='DCD parser not available. Are you using python 3?')
 def test_instantselection_termini():
     """Test that instant selections work, even for residues that are also termini (Issue 70)"""
     universe = mda.Universe(PSF, DCD)
     assert_equal(universe.residues[20].CA.name, 'CA', "CA of MET21 is not selected correctly")
     del universe
 
 
-class TestAtomGroup(object):
+class TestAtomGroup(TestCase):
     """Tests of AtomGroup; selections are tested separately.
 
     These are from before the big topology rework (aka #363) but are still valid.
     There is likely lots of duplication between here and other tests.
     """
-    @dec.skipif(parser_not_found('DCD'),
+    @pytest.mark.skipif(parser_not_found('DCD'),
                 'DCD parser not available. Are you using python 3?')
     def setUp(self):
         """Set up the standard AdK system in implicit solvent."""
@@ -1286,10 +1291,10 @@ def test_atom_order(self):
                      sorted(self.universe.atoms.indices))
 
 
-class TestAtomGroupTimestep(object):
+class TestAtomGroupTimestep(TestCase):
     """Tests the AtomGroup.ts attribute (partial timestep)"""
 
-    @dec.skipif(parser_not_found('TRZ'),
+    @pytest.mark.skipif(parser_not_found('TRZ'),
                 'TRZ parser not available. Are you using python 3?')
     def setUp(self):
         self.universe = mda.Universe(TRZ_psf, TRZ)