Fix issues with base classes

testsuite/MDAnalysisTests/coordinates/base.py

@@ -19,6 +19,7 @@
 
 class _SingleFrameReader(TestCase, RefAdKSmall):
     # see TestPDBReader how to set up!
+    __test__ = False
 
     def tearDown(self):
         del self.universe

testsuite/MDAnalysisTests/coordinates/test_dcd.py

@@ -344,6 +344,9 @@ def test_OtherWriter(self):
 
 
 class _TestDCDReader_TriclinicUnitcell(TestCase):
+
+    __test__ = False
+
     def setUp(self):
         self.u = mda.Universe(self.topology, self.trajectory)
         self.tempdir = tempdir.TempDir()
@@ -386,12 +389,12 @@ def test_write_triclinic(self):
 
 class TestDCDReader_CHARMM_Unitcell(_TestDCDReader_TriclinicUnitcell,
                                     RefCHARMMtriclinicDCD):
-    pass
+    __test__ = True
 
 
 class TestDCDReader_NAMD_Unitcell(_TestDCDReader_TriclinicUnitcell,
                                   RefNAMDtriclinicDCD):
-    pass
+    __test__ = True
 
 
 class TestNCDF2DCD(TestCase):

testsuite/MDAnalysisTests/coordinates/test_dlpoly.py

@@ -11,6 +11,7 @@
 from unittest import TestCase
 
 class _DLPConfig(TestCase):
+    __test__ = False
     def setUp(self):
         self.r = mda.coordinates.DLPoly.ConfigReader
         rd = self.rd = self.r(self.f)
@@ -41,17 +42,20 @@ def test_forces(self):
 
 
 class TestConfigReader(_DLPConfig):
+    __test__ = True
     f = DLP_CONFIG
 
     def test_read(self):
         assert_equal(self.rd.title, "DL_POLY: Potassium Chloride Test Case")
 
 
 class TestConfigOrder(_DLPConfig):
+    __test__ = True
     f = DLP_CONFIG_order
 
 
 class TestConfigMinimal(_DLPConfig):
+    __test__ = True
     f = DLP_CONFIG_minimal
 
     def test_read_unitcell(self):
@@ -64,7 +68,10 @@ def test_forces(self):
         assert_raises(AttributeError, getattr, self.ts, "_forces")
 
 
-class _DLPConfig2(object):
+class _DLPConfig2(TestCase):
+
+    __test__ = False
+
     def setUp(self):
         self.u = mda.Universe(self.f, format='CONFIG')
 
@@ -93,10 +100,14 @@ def test_number(self):
 
 
 class TestConfigReader2(_DLPConfig2):
+
+    __test__ = True
     f = DLP_CONFIG_order
 
 
 class TestConfigReaderMinimal2(_DLPConfig2):
+
+    __test__ = True
     f = DLP_CONFIG_minimal
 
     def test_vel(self):
@@ -106,7 +117,10 @@ def test_for(self):
         pass
 
 
-class _DLHistory(object):
+class _DLHistory(TestCase):
+
+    __test__ = False
+
     def setUp(self):
         self.u = mda.Universe(self.f, format='HISTORY')
 
@@ -166,14 +180,17 @@ def test_unitcell(self):
 
 
 class TestDLPolyHistory(_DLHistory):
+    __test__ = True
     f = DLP_HISTORY
 
 
 class TestDLPolyHistoryOrder(_DLHistory):
+    __test__ = True
     f = DLP_HISTORY_order
 
 
 class TestDLPolyHistoryMinimal(_DLHistory):
+    __test__ = True
     f = DLP_HISTORY_minimal
 
     def test_velocity(self):

testsuite/MDAnalysisTests/coordinates/test_gms.py

@@ -6,9 +6,10 @@
 from numpy.testing import (assert_equal, assert_almost_equal)
 
 from MDAnalysisTests.datafiles import (GMS_ASYMOPT, GMS_ASYMSURF, GMS_SYMOPT)
+from unittest import TestCase
 
-
-class _GMSBase(object):
+class _GMSBase(TestCase):
+    __test__ = False
     def tearDown(self):
         del self.u
         del self.n_frames
@@ -68,20 +69,23 @@ def test_step5distances(self):
 
 
 class TestGMSReader(_GMSBase):
+    __test__ = True
     def setUp(self):
         self.u =  mda.Universe(GMS_ASYMOPT)
         self.n_frames = 21
         self.flavour = "GAMESS C1 optimization"
         self.step5d = -0.0484664
 
 class TestGMSReaderSO(_GMSBase):
+    __test__ = True
     def setUp(self):
         self.u = mda.Universe(GMS_SYMOPT)
         self.n_frames = 8
         self.flavour = "GAMESS D4H optimization"
         self.step5d = 0.227637
 
 class TestGMSReaderASS(_GMSBase):
+    __test__ = True
     def setUp(self):
         self.u = mda.Universe(GMS_ASYMSURF)
         self.n_frames = 10

testsuite/MDAnalysisTests/coordinates/test_lammps.py

@@ -28,6 +28,8 @@ class _TestLammpsData_Coords(TestCase):
     All topology loading from MDAnalysisTests.data is done in test_topology
     """
 
+    __test__ = False
+
     def setUp(self):
         self.u = mda.Universe(self.filename)
 
@@ -62,13 +64,14 @@ def test_iter(self):
 
 
 class TestLammpsData_Coords(_TestLammpsData_Coords, RefLAMMPSData):
-    pass
+    __test__ = True
 
 
 class TestLammpsDataMini_Coords(_TestLammpsData_Coords, RefLAMMPSDataMini):
-    pass
+    __test__ = True
 
 class _TestLAMMPSDATAWriter(TestCase):
+    __test__ = False
     all_attrs = set(['types', 'bonds', 'angles', 'dihedrals', 'impropers'])
     all_numerical_attrs = set(['masses', 'charges', 'velocities', 'positions'])
 
@@ -124,18 +127,23 @@ def test_Writer_atoms(self):
 
 
 class TestLAMMPSDATAWriter_data(_TestLAMMPSDATAWriter):
+    __test__ = True
     filename = LAMMPSdata
 
 class TestLAMMPSDATAWriter_mini(_TestLAMMPSDATAWriter):
+    __test__ = True
     filename = LAMMPSdata_mini
 
 class TestLAMMPSDATAWriter_cnt(_TestLAMMPSDATAWriter):
+    __test__ = True
     filename = LAMMPScnt
 
 class TestLAMMPSDATAWriter_hyd(_TestLAMMPSDATAWriter):
+    __test__ = True
     filename = LAMMPShyd
 
 class TestLAMMPSDATAWriter_data_partial(_TestLAMMPSDATAWriter):
+    __test__ = True
     filename = LAMMPSdata
     N_kept = 5
 
@@ -170,7 +178,7 @@ def test_Writer_atoms(self):
 
 # need more tests of the LAMMPS DCDReader
 
-class TestLAMMPSDCDReader(RefLAMMPSDataDCD):
+class TestLAMMPSDCDReader(TestCase, RefLAMMPSDataDCD):
     flavor = 'LAMMPS'
 
     def setUp(self):
@@ -232,7 +240,7 @@ def wrong_load(unit="GARBAGE"):
         assert_raises(ValueError, wrong_load)
 
 
-class TestLAMMPSDCDWriter(RefLAMMPSDataDCD):
+class TestLAMMPSDCDWriter(TestCase, RefLAMMPSDataDCD):
     flavor = 'LAMMPS'
 
     def setUp(self):

testsuite/MDAnalysisTests/coordinates/test_netcdf.py

@@ -19,6 +19,8 @@
 
 
 class _NCDFReaderTest(_TRJReaderTest):
+    __test__ = False
+
     @dec.skipif(module_not_found("netCDF4"), "Test skipped because netCDF is not available.")
     def setUp(self):
         self.universe = mda.Universe(self.topology, self.filename)
@@ -60,10 +62,10 @@ def test_read_on_closed(self):
 
 
 class TestNCDFReader(_NCDFReaderTest, RefVGV):
-    pass
+    __test__ = True
 
 class TestNCDFReaderTZ2(_NCDFReaderTest, RefTZ2):
-    pass
+    __test__ = True
 
 
 class TestNCDFReader2(TestCase):

testsuite/MDAnalysisTests/coordinates/test_pdb.py

@@ -24,6 +24,7 @@
 
 
 class TestPDBReader(_SingleFrameReader):
+    __test__ = True
     def setUp(self):
         # can lead to race conditions when testing in parallel
         self.universe = mda.Universe(RefAdKSmall.filename)
@@ -54,6 +55,7 @@ def test_ENT(self):
 
 class _PDBMetadata(TestCase, Ref4e43):
 
+    __test__ = False
 
     def setUp(self):
         self.universe = mda.Universe(self.filename)
@@ -116,6 +118,7 @@ def test_REMARK(self):
 
 
 class TestExtendedPDBReader(_SingleFrameReader):
+    __test__ = True
     def setUp(self):
         self.universe = mda.Universe(PDB_small,
                                      topology_format="XPDB",
@@ -716,6 +719,7 @@ def test_serials(self):
 
 
 class TestPSF_CRDReader(_SingleFrameReader):
+    __test__ = True
     def setUp(self):
         self.universe = mda.Universe(PSF, CRD)
         self.prec = 5  # precision in CRD (at least we are writing %9.5f)

testsuite/MDAnalysisTests/coordinates/test_pqr.py

@@ -15,6 +15,7 @@
 from numpy.testing import TestCase
 
 class TestPQRReader(_SingleFrameReader):
+    __test__ = True
     def setUp(self):
         self.universe = mda.Universe(PQR)
         # 3 decimals in PDB spec
@@ -46,7 +47,7 @@ def test_ProNCharges(self):
             "Charges for N atoms in Pro residues do not match.")
 
 
-class TestPQRWriter(RefAdKSmall):
+class TestPQRWriter(TestCase, RefAdKSmall):
     def setUp(self):
         self.universe = mda.Universe(PQR)
         self.prec = 3

testsuite/MDAnalysisTests/coordinates/test_reader_api.py

@@ -70,6 +70,7 @@ def _read_first_frame(self):
 
 
 class _TestReader(TestCase):
+    __test__ = False
     """Basic API readers"""
     def setUp(self):
         self.reader = self.readerclass('test.txt')
@@ -125,6 +126,7 @@ class _Multi(_TestReader):
 
 
 class TestMultiFrameReader(_Multi):
+    __test__ = True
     def _check_slice(self, start, stop, step):
         """Compare the slice applied to trajectory, to slice of list"""
         res = [ts.frame for ts in self.reader[start:stop:step]]
@@ -232,6 +234,7 @@ class _Single(_TestReader):
 
 
 class TestSingleFrameReader(_Single):
+    __test__ = True
     def test_next(self):
         assert_raises(StopIteration, self.reader.next)