Replace object with TestCase

testsuite/MDAnalysisTests/coordinates/base.py

@@ -469,7 +469,7 @@ def test_write_not_changing_ts(self):
             assert_timestep_almost_equal(copy_ts, ts)
 
 
-class BaseTimestepTest(object):
+class BaseTimestepTest(TestCase):
     """Test all the base functionality of a Timestep
 
     All Timesteps must pass these tests!

testsuite/MDAnalysisTests/coordinates/test_crd.py

@@ -12,8 +12,9 @@
 from MDAnalysisTests.datafiles import CRD
 from MDAnalysisTests import tempdir, make_Universe
 
+from unittest import TestCase
 
-class TestCRDWriter(object):
+class TestCRDWriter(TestCase):
     def setUp(self):
         self.u = mda.Universe(CRD)
         self.tmpdir = tempdir.TempDir()

testsuite/MDAnalysisTests/coordinates/test_dcd.py

@@ -43,7 +43,7 @@ def test_with_statement(self):
             err_msg="with_statement: DCDReader does not read all frames")
 
 
-class TestDCDReader(object):
+class TestDCDReader(TestCase):
     def setUp(self):
         self.universe = mda.Universe(PSF, DCD)
         self.dcd = self.universe.trajectory

testsuite/MDAnalysisTests/coordinates/test_dlpoly.py

@@ -8,9 +8,9 @@
                                        DLP_CONFIG_order, DLP_HISTORY,
                                        DLP_HISTORY_minimal, DLP_HISTORY_order)
 from MDAnalysisTests.coordinates.base import BaseTimestepTest
+from unittest import TestCase
 
-
-class _DLPConfig(object):
+class _DLPConfig(TestCase):
     def setUp(self):
         self.r = mda.coordinates.DLPoly.ConfigReader
         rd = self.rd = self.r(self.f)

testsuite/MDAnalysisTests/coordinates/test_gro.py

@@ -163,7 +163,7 @@ def test_volume(self):
             err_msg="wrong volume for unitcell (rhombic dodecahedron)")
 
 
-class TestGROIncompleteVels(object):
+class TestGROIncompleteVels(TestCase):
     def setUp(self):
         self.u = mda.Universe(GRO_incomplete_vels)
 
@@ -341,7 +341,7 @@ def test_writer_large_residue_count(self):
 
 
 
-class TestGROWriterVels(object):
+class TestGROWriterVels(TestCase):
     def setUp(self):
         self.tmpdir = tempdir.TempDir()
         self.outfile = self.tmpdir.name + '/gro-writervels.gro'

testsuite/MDAnalysisTests/coordinates/test_lammps.py

@@ -15,13 +15,14 @@
     LAMMPScnt, LAMMPShyd, LAMMPSdata, LAMMPSdata_mini
 )
 
+from unittest import TestCase
 
 def test_datareader_ValueError():
     from MDAnalysis.coordinates.LAMMPS import DATAReader
     assert_raises(ValueError, DATAReader, 'filename')
 
 
-class _TestLammpsData_Coords(object):
+class _TestLammpsData_Coords(TestCase):
     """Tests using a .data file for loading single frame.
 
     All topology loading from MDAnalysisTests.data is done in test_topology
@@ -67,7 +68,7 @@ class TestLammpsData_Coords(_TestLammpsData_Coords, RefLAMMPSData):
 class TestLammpsDataMini_Coords(_TestLammpsData_Coords, RefLAMMPSDataMini):
     pass
 
-class _TestLAMMPSDATAWriter(object):
+class _TestLAMMPSDATAWriter(TestCase):
     all_attrs = set(['types', 'bonds', 'angles', 'dihedrals', 'impropers'])
     all_numerical_attrs = set(['masses', 'charges', 'velocities', 'positions'])
 
@@ -293,7 +294,7 @@ def test_OtherWriter(self):
                             self.u.trajectory[0].positions,
                             6, err_msg="coordinate mismatch between corresponding frames")
 
-class TestLAMMPSDCDWriterClass(object):
+class TestLAMMPSDCDWriterClass(TestCase):
     flavor = 'LAMMPS'
 
     def setUp(self):
@@ -339,7 +340,7 @@ def wrong_load(unit="GARBAGE"):
         assert_raises(ValueError, wrong_load)
 
 
-class TestLammpsDataTriclinic(object):
+class TestLammpsDataTriclinic(TestCase):
     def setUp(self):
         self.u = mda.Universe(LAMMPScnt)
 
@@ -351,7 +352,7 @@ def test_triclinicness(self):
         assert_(self.u.dimensions[4] == 90.)
         assert_(self.u.dimensions[5] == 120.)
 
-class TestDataWriterErrors(object):
+class TestDataWriterErrors(TestCase):
     def setUp(self):
         self.tmpdir = tempdir.TempDir()
         self.outfile = os.path.join(self.tmpdir.name, 'out.data')

testsuite/MDAnalysisTests/coordinates/test_mmtf.py

@@ -7,9 +7,9 @@
 from MDAnalysisTests.datafiles import MMTF, MMTF_gz
 
 from MDAnalysis.coordinates.MMTF import MMTFReader
+from numpy.testing import TestCase
 
-
-class TestMMTFReader(object):
+class TestMMTFReader(TestCase):
     def setUp(self):
         self.r = MMTFReader(MMTF)
 
@@ -37,7 +37,7 @@ def test_len(self):
         # should be single frame
         assert_(len(self.r) == 1)
 
-class TestMMTFReaderGZ(object):
+class TestMMTFReaderGZ(TestCase):
     def setUp(self):
         self.r = MMTFReader(MMTF_gz)
 

testsuite/MDAnalysisTests/coordinates/test_netcdf.py

@@ -417,7 +417,7 @@ def test_import_netcdfwriter(self):
                 raise AssertionError
 
 
-class TestNCDFWriterErrors(object):
+class TestNCDFWriterErrors(TestCase):
     @dec.skipif(module_not_found("netCDF4"), "Test skipped because netCDF is not available.")
     def setUp(self):
         self.tmpdir = tempdir.TempDir()

testsuite/MDAnalysisTests/coordinates/test_null.py

@@ -23,9 +23,9 @@
 import MDAnalysis as mda
 
 from MDAnalysisTests.datafiles import (TPR, XTC)
+from numpy.testing import TestCase
 
-
-class TestNullWriter(object):
+class TestNullWriter(TestCase):
     def setUp(self):
         self.universe = mda.Universe(TPR, XTC)
 

testsuite/MDAnalysisTests/coordinates/test_pdb.py

@@ -641,7 +641,7 @@ def test_first_residue(self):
         assert_(len(self.universe.residues[0].atoms) == 19)
 
 
-class TestIncompletePDB(object):
+class TestIncompletePDB(TestCase):
     """Tests for Issue #396
 
     Reads an incomplete (but still intelligible) PDB file
@@ -689,7 +689,7 @@ def test_reading_trajectory(self):
             pass
 
 
-class TestPDBXLSerial(object):
+class TestPDBXLSerial(TestCase):
     """For Issue #446"""
 
     def setUp(self):
@@ -735,7 +735,7 @@ def test_uses_PDBReader(self):
                 "failed to choose PDBReader")
 
 
-class TestPDBWriterOccupancies(object):
+class TestPDBWriterOccupancies(TestCase):
     """Tests for Issue #620"""
     def setUp(self):
         self.tempdir = tempdir.TempDir()

testsuite/MDAnalysisTests/coordinates/test_pdbqt.py

@@ -33,9 +33,9 @@
 
 import os
 from MDAnalysisTests import tempdir, make_Universe
+from numpy.testing import TestCase
 
-
-class TestPDBQT(object):
+class TestPDBQT(TestCase):
     def setUp(self):
         """Set up the standard AdK system in implicit solvent."""
         self.universe = mda.Universe(PDBQT_input)  # PDBQT
@@ -85,7 +85,7 @@ def test_frame(self):
                      "wrong frame number (0-based, should be 0 for single frame readers)")
 
 
-class TestPDBQTWriter(object):
+class TestPDBQTWriter(TestCase):
     def setUp(self):
         self.reqd_attributes = ['names', 'types', 'resids', 'resnames', 'radii', 'charges']
         self.tmpdir = tempdir.TempDir()

testsuite/MDAnalysisTests/coordinates/test_pqr.py

@@ -12,7 +12,7 @@
 from MDAnalysisTests.coordinates.base import _SingleFrameReader
 from MDAnalysisTests.datafiles import PQR
 from MDAnalysisTests import tempdir, make_Universe
-
+from numpy.testing import TestCase
 
 class TestPQRReader(_SingleFrameReader):
     def setUp(self):
@@ -113,7 +113,7 @@ def test_total_charge(self):
             u.atoms.total_charge(), self.ref_charmm_totalcharge, 3,
             "Total charge (in CHARMM) does not match expected value.")
 
-class TestPQRWriterMissingAttrs(object):
+class TestPQRWriterMissingAttrs(TestCase):
     # pqr requires names, resids, resnames, segids, radii, charges
     def setUp(self):
         self.reqd_attributes = ['names', 'resids', 'resnames', 'radii', 'charges']

testsuite/MDAnalysisTests/coordinates/test_reader_api.py

@@ -24,7 +24,7 @@
 
 from numpy.testing import assert_equal, assert_raises
 import numpy as np
-
+from numpy.testing import TestCase
 """
 Isolate the API definitions of Readers independent of implementations
 """
@@ -69,7 +69,7 @@ def _read_first_frame(self):
         self.ts.frame = 0
 
 
-class _TestReader(object):
+class _TestReader(TestCase):
     """Basic API readers"""
     def setUp(self):
         self.reader = self.readerclass('test.txt')

testsuite/MDAnalysisTests/coordinates/test_timestep_api.py

@@ -38,7 +38,7 @@
                                        NCDF, TRZ_psf, TRZ)
 
 from MDAnalysisTests.coordinates.base import BaseTimestepTest
-
+from numpy.testing import TestCase
 
 # Can add in custom tests for a given Timestep here!
 class TestBaseTimestep(BaseTimestepTest):
@@ -66,7 +66,7 @@ def test_other_timestep(self):
 # TODO: Merge this into generic Reader tests
 # These tests are all included in BaseReaderTest
 # Once Readers use that TestClass, delete this one
-class BaseTimestepInterfaceTest(object):
+class BaseTimestepInterfaceTest(TestCase):
     """Test the Timesteps created by Readers
 
     This checks that Readers are creating correct Timestep objects,

testsuite/MDAnalysisTests/coordinates/test_trj.py

@@ -7,9 +7,9 @@
 from MDAnalysisTests.coordinates.reference import RefACHE, RefCappedAla
 from MDAnalysisTests.datafiles import (PRM, TRJ, TRJ_bz2, PRMpbc, TRJpbc_bz2)
 from MDAnalysisTests.coordinates.base import BaseTimestepTest
+from numpy.testing import TestCase
 
-
-class _TRJReaderTest(object):
+class _TRJReaderTest(TestCase):
     # use as a base class (override setUp()) and mixin a reference
     def tearDown(self):
         del self.universe

testsuite/MDAnalysisTests/coordinates/test_trz.py

@@ -184,7 +184,7 @@ def test_long_title(self):
                       self.Writer, self.outfile, self.ref_n_atoms, title=title)
 
 
-class TestTRZWriter2(object):
+class TestTRZWriter2(TestCase):
     def setUp(self):
         self.u = mda.Universe(two_water_gro)
 

testsuite/MDAnalysisTests/coordinates/test_xyz.py

@@ -16,7 +16,7 @@
 from MDAnalysisTests.coordinates.base import (BaseReaderTest, BaseReference,
                                               BaseWriterTest)
 from MDAnalysisTests import tempdir, make_Universe
-
+from numpy.testing import TestCase
 
 class XYZReference(BaseReference):
     def __init__(self):
@@ -101,7 +101,7 @@ def __init__(self):
         super(Test_XYZBZWriter, self).__init__(XYZ_BZ_Reference())
 
 
-class TestXYZWriterNames(object):
+class TestXYZWriterNames(TestCase):
     def setUp(self):
         self.tmpdir = tempdir.TempDir()
         self.outfile = self.tmpdir.name + '/outfile.xyz'