Port topology module (#1420)

* Port topology to pytest

testsuite/MDAnalysisTests/topology/base.py

@@ -20,6 +20,9 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from __future__ import absolute_import
+
+from unittest import TestCase
+
 from numpy.testing import (
     assert_,
 )
@@ -28,11 +31,14 @@
 from MDAnalysis.core.topology import Topology
 
 
-class ParserBase(object):
+class ParserBase(TestCase):
     """Base class for testing Topology parsers.
 
     All Parsers must subclass this class!
     """
+
+    __test__ = False
+
     expected_attrs = []
     guessed_attrs = []
 

testsuite/MDAnalysisTests/topology/test_crd.py

@@ -21,6 +21,8 @@
 #
 from __future__ import absolute_import
 
+from unittest import TestCase
+
 import MDAnalysis as mda
 
 from MDAnalysisTests.topology.base import ParserBase
@@ -30,6 +32,9 @@
 
 
 class TestCRDParser(ParserBase):
+
+    __test__ = True
+
     parser = mda.topology.CRDParser.CRDParser
     filename = CRD
     expected_attrs = ['ids', 'names', 'tempfactors',

testsuite/MDAnalysisTests/topology/test_dlpoly.py

@@ -39,11 +39,17 @@
 
 
 class DLPUniverse(ParserBase):
+
+    __test__ = False
+
     def test_creates_universe(self):
         u = mda.Universe(self.filename, topology_format=self.format)
         assert_(isinstance(u, mda.Universe))
-        
+
 class DLPBase2(DLPUniverse):
+
+    __test__ = False
+
     expected_attrs = ['ids', 'names']
     guessed_attrs = ['types', 'masses']
     expected_n_atoms = 216
@@ -56,18 +62,27 @@ def test_names(self):
 
 
 class TestDLPHistoryParser(DLPBase2):
+
+    __test__ = True
+
     parser = mda.topology.DLPolyParser.HistoryParser
     filename = DLP_HISTORY
     format='HISTORY'
 
 
 class TestDLPConfigParser(DLPBase2):
+
+    __test__ = True
+
     parser = mda.topology.DLPolyParser.ConfigParser
     filename = DLP_CONFIG
     format='CONFIG'
 
 
 class DLPBase(DLPUniverse):
+
+    __test__ = False
+
     expected_attrs = ['ids', 'names']
     guessed_attrs = ['types', 'masses']
     expected_n_atoms = 3
@@ -80,24 +95,36 @@ def test_dlp_names(self):
 
 
 class TestDLPConfigMinimal(DLPBase):
+
+    __test__ = True
+
     parser = mda.topology.DLPolyParser.ConfigParser
     filename = DLP_CONFIG_minimal
     format='CONFIG'
 
 
 class TestDLPConfigOrder(DLPBase):
+
+    __test__ = True
+
     parser = mda.topology.DLPolyParser.ConfigParser
     filename = DLP_CONFIG_order
     format='CONFIG'
 
 
 class TestDLPHistoryMinimal(DLPBase):
+
+    __test__ = True
+
     parser = mda.topology.DLPolyParser.HistoryParser
     filename = DLP_HISTORY_minimal
     format='HISTORY'
 
 
 class TestDLPHistoryOrder(DLPBase):
+
+    __test__ = True
+
     parser = mda.topology.DLPolyParser.HistoryParser
     filename = DLP_HISTORY_order
     format='HISTORY'

testsuite/MDAnalysisTests/topology/test_dms.py

@@ -33,6 +33,9 @@
 
 
 class TestDMSParser(ParserBase):
+
+    __test__ = True
+
     parser = mda.topology.DMSParser.DMSParser
     filename = DMS
     expected_attrs = ['ids', 'names', 'bonds', 'charges',

testsuite/MDAnalysisTests/topology/test_gms.py

@@ -36,6 +36,9 @@
 
 
 class GMSBase(ParserBase):
+
+    __test__ = False
+
     parser = mda.topology.GMSParser.GMSParser
     expected_attrs = ['names', 'atomiccharges']
     guessed_attrs = ['masses', 'types']
@@ -44,6 +47,9 @@ class GMSBase(ParserBase):
 
 
 class TestGMSASYMOPT(GMSBase):
+
+    __test__ = True
+
     filename = GMS_ASYMOPT
     expected_n_atoms = 6
 
@@ -57,6 +63,9 @@ def test_types(self):
 
 
 class TestGMSSYMOPT(GMSBase):
+
+    __test__ = True
+
     filename = GMS_SYMOPT
     expected_n_atoms = 4
 
@@ -69,4 +78,7 @@ def test_types(self):
                            [6, 6, 1, 1])
 
 class TestGMSASYMSURF(TestGMSASYMOPT):
+
+    __test__ = True
+
     filename = GMS_ASYMSURF

testsuite/MDAnalysisTests/topology/test_gro.py

@@ -40,6 +40,9 @@
 
 
 class TestGROParser(ParserBase):
+
+    __test__ = True
+
     parser = mda.topology.GROParser.GROParser
     filename = GRO
     expected_attrs = ['ids', 'names', 'resids', 'resnames', 'masses']

testsuite/MDAnalysisTests/topology/test_guessers.py

@@ -36,61 +36,50 @@
 from MDAnalysisTests.core.test_fragments import make_starshape
 
 class TestGuessMasses(object):
-    @staticmethod
-    def test_guess_masses():
+    def test_guess_masses(self):
         out = guessers.guess_masses(['C', 'C', 'H'])
 
         assert_(isinstance(out, np.ndarray))
         assert_array_equal(out,
                            np.array([12.011, 12.011, 1.008]))
 
-    @staticmethod
-    def test_guess_masses_warn():
+    def test_guess_masses_warn(self):
         assert_warns(UserWarning, guessers.guess_masses, ['X'])
 
-    @staticmethod
-    def test_guess_masses_miss():
+    def test_guess_masses_miss(self):
         out = guessers.guess_masses(['X', 'Z'])
         assert_array_equal(out, np.array([0.0, 0.0]))
 
-    @staticmethod
-    def test_get_atom_mass():
+    def test_get_atom_mass(self):
         assert_(guessers.get_atom_mass('H') == 1.008)
 
-    @staticmethod
-    def test_get_atom_mass_miss():
+    def test_get_atom_mass_miss(self):
         assert_(guessers.get_atom_mass('XYZ') == 0.0)
 
-    @staticmethod
-    def test_guess_atom_mass():
+    def test_guess_atom_mass(self):
         assert_(guessers.guess_atom_mass('1H') == 1.008)
 
 
 class TestGuessTypes(object):
     # guess_types
     # guess_atom_type
     # guess_atom_element
-    @staticmethod
-    def test_guess_types():
+    def test_guess_types(self):
         out = guessers.guess_types(['MG2+', 'C12'])
 
         assert_(isinstance(out, np.ndarray))
         assert_array_equal(out, np.array(['MG', 'C'], dtype=object))
-
-    @staticmethod
-    def test_guess_atom_element():
+
+    def test_guess_atom_element(self):
         assert_(guessers.guess_atom_element('MG2+') == 'MG')
-
-    @staticmethod
-    def test_guess_atom_element_empty():
+
+    def test_guess_atom_element_empty(self):
         assert_(guessers.guess_atom_element('') == '')
 
-    @staticmethod
-    def test_guess_atom_element_singledigit():
+    def test_guess_atom_element_singledigit(self):
         assert_(guessers.guess_atom_element('1') == '1')
 
-    @staticmethod
-    def test_guess_atom_element_1H():
+    def test_guess_atom_element_1H(self):
         assert_(guessers.guess_atom_element('1H') == 'H')
         assert_(guessers.guess_atom_element('2H') == 'H')
 

testsuite/MDAnalysisTests/topology/test_hoomdxml.py

@@ -33,6 +33,9 @@
 
 
 class TestHoomdXMLParser(ParserBase):
+
+    __test__ = True
+
     parser = mda.topology.HoomdXMLParser.HoomdXMLParser
     filename = HoomdXMLdata
     expected_attrs = ['types', 'masses', 'charges', 'radii',

testsuite/MDAnalysisTests/topology/test_lammpsdata.py

@@ -39,6 +39,9 @@
 
 
 class LammpsBase(ParserBase):
+
+    __test__ = False
+
     parser = mda.topology.LAMMPSParser.DATAParser
     expected_n_segments = 1
     expected_attrs = ['types', 'resids', 'masses', 'charges']
@@ -100,6 +103,9 @@ class TestLammpsData(LammpsBase):
     The reading of coords and velocities is done separately in
     test_coordinates
     """
+
+    __test__ = True
+
     filename = LAMMPSdata
     expected_n_atoms = 18364
     expected_n_atom_types = 10
@@ -114,6 +120,9 @@ class TestLammpsData(LammpsBase):
 
 
 class TestLAMMPSCNT(LammpsBase):
+
+    __test__ = True
+
     filename = LAMMPScnt
     expected_n_atoms = 604
     expected_n_atom_types = 1
@@ -129,10 +138,16 @@ class TestLAMMPSCNT(LammpsBase):
 
 
 class TestLAMMPSCNT2(TestLAMMPSCNT):
+
+    __test__ = True
+
     filename = LAMMPScnt2
 
 
 class TestLAMMPSHYD(LammpsBase):
+
+    __test__ = True
+
     filename = LAMMPShyd
     expected_n_atoms = 2
     expected_n_atom_types = 1
@@ -145,10 +160,16 @@ class TestLAMMPSHYD(LammpsBase):
 
 
 class TestLAMMPSHYD2(TestLAMMPSHYD):
+
+    __test__ = True
+
     filename = LAMMPShyd2
 
 
 class TestLAMMPSDeletedAtoms(LammpsBase):
+
+    __test__ = True
+
     filename = LAMMPSdata_deletedatoms
 
     expected_n_atoms = 10

testsuite/MDAnalysisTests/topology/test_mmtf.py

@@ -12,8 +12,12 @@
 from MDAnalysisTests.topology.base import ParserBase
 from MDAnalysisTests.datafiles import MMTF, MMTF_gz
 
+from unittest import TestCase
+
 
 class TestMMTFParser(ParserBase):
+    __test__ = False
+
     parser = mda.topology.MMTFParser.MMTFParser
     filename = MMTF
     expected_attrs = ['ids', 'names', 'types', 'altLocs',
@@ -27,13 +31,15 @@ class TestMMTFParser(ParserBase):
 
 
 class TestMMTFParser_gz(TestMMTFParser):
+    __test__ = True
+
     filename = MMTF_gz
     expected_n_atoms = 1140
     expected_n_residues = 36
     expected_n_segments = 4
 
 
-class TestMMTFUniverse(object):
+class TestMMTFUniverse(TestCase):
     def setUp(self):
         self.u = mda.Universe(MMTF)
 
@@ -87,7 +93,7 @@ def setUp(self):
         self.u = mda.Universe(top)
 
 
-class TestMMTFgzUniverse(object):
+class TestMMTFgzUniverse(TestCase):
     def setUp(self):
         self.u = mda.Universe(MMTF_gz)
 
@@ -119,9 +125,9 @@ def setUp(self, mock_fetch):
         top = mmtf.parse(MMTF)
         mock_fetch.return_value = top
         self.u = mda.fetch_mmtf('173D')  # string is irrelevant
-
 
-class TestSelectModels(object):
+
+class TestSelectModels(TestCase):
     # tests for 'model' keyword in select_atoms
     def setUp(self):
         self.u = mda.Universe(MMTF_gz)