splits BaseReaderTest into BaseReaderTest & MultiframeReaderTest

testsuite/MDAnalysisTests/coordinates/base.py

@@ -5,7 +5,7 @@
 from unittest import TestCase
 from numpy.testing import (assert_equal, assert_raises, assert_almost_equal,
                            assert_array_almost_equal, raises, assert_allclose,
-                           assert_)
+                           assert_, dec)
 
 import MDAnalysis as mda
 from MDAnalysis.coordinates.base import Timestep
@@ -207,33 +207,6 @@ def test_double_close(self):
         self.reader.close()
         self.reader._reopen()
 
-    def test_reopen(self):
-        self.reader.close()
-        self.reader._reopen()
-        ts = self.reader.next()
-        assert_timestep_almost_equal(ts, self.ref.first_frame,
-                                     decimal=self.ref.prec)
-
-    def test_last_frame(self):
-        ts = self.reader[-1]
-        assert_timestep_almost_equal(ts, self.ref.last_frame,
-                                     decimal=self.ref.prec)
-
-    def test_next_gives_second_frame(self):
-        reader = self.ref.reader(self.ref.trajectory)
-        ts = reader.next()
-        assert_timestep_almost_equal(ts, self.ref.second_frame,
-                                     decimal=self.ref.prec)
-
-    @raises(IndexError)
-    def test_go_over_last_frame(self):
-        self.reader[self.ref.n_frames + 1]
-
-    def test_frame_jump(self):
-        ts = self.reader[self.ref.jump_to_frame.frame]
-        assert_timestep_almost_equal(ts, self.ref.jump_to_frame,
-                                     decimal=self.ref.prec)
-
     def test_get_writer_1(self):
         with tempdir.in_tempdir():
             self.outfile = 'test-writer' + self.ref.ext
@@ -338,17 +311,7 @@ def test_iter_as_aux_cutoff(self):
         assert_equal(num_frames, 0, "iter_as_aux should iterate over 0 frames,"
                                     " not {}".format(num_frames))
 
-    def test_rename_aux(self):
-        self.reader.rename_aux('lowf', 'lowf_renamed')
-        # data should now be in aux namespace under new name
-        assert_equal(self.reader.ts.aux.lowf_renamed,
-                     self.ref.aux_lowf_data[0])
-        # old name should be removed
-        assert_raises(AttributeError, getattr, self.reader.ts.aux, 'lowf')
-        # new name should be retained
-        next(self.reader)
-        assert_equal(self.reader.ts.aux.lowf_renamed,
-                     self.ref.aux_lowf_data[1])
+
 
     def test_reload_auxiliaries_from_description(self):
         # get auxiliary desscriptions form existing reader
@@ -374,6 +337,50 @@ def test_stop_iter(self):
         assert_equal(self.reader.frame, 0)
 
 
+class MultiframeReaderTest(BaseReaderTest):
+
+    def test_last_frame(self):
+        ts = self.reader[-1]
+        assert_timestep_almost_equal(ts, self.ref.last_frame,
+                                     decimal=self.ref.prec)
+
+    @raises(IndexError)
+    def test_go_over_last_frame(self):
+        self.reader[self.ref.n_frames + 1]
+
+    def test_frame_jump(self):
+        ts = self.reader[self.ref.jump_to_frame.frame]
+        assert_timestep_almost_equal(ts, self.ref.jump_to_frame,
+                                     decimal=self.ref.prec)
+
+
+    def test_next_gives_second_frame(self):
+        reader = self.ref.reader(self.ref.trajectory)
+        ts = reader.next()
+        assert_timestep_almost_equal(ts, self.ref.second_frame,
+                                     decimal=self.ref.prec)
+
+    def test_reopen(self):
+        self.reader.close()
+        self.reader._reopen()
+        ts = self.reader.next()
+        assert_timestep_almost_equal(ts, self.ref.first_frame,
+                                     decimal=self.ref.prec)
+
+    def test_rename_aux(self):
+        self.reader.rename_aux('lowf', 'lowf_renamed')
+        # data should now be in aux namespace under new name
+        assert_equal(self.reader.ts.aux.lowf_renamed,
+                     self.ref.aux_lowf_data[0])
+        # old name should be removed
+        assert_raises(AttributeError, getattr, self.reader.ts.aux, 'lowf')
+        # new name should be retained
+        next(self.reader)
+        assert_equal(self.reader.ts.aux.lowf_renamed,
+                     self.ref.aux_lowf_data[1])
+
+
+
 class BaseWriterTest(object):
     def __init__(self, reference):
         self.ref = reference

testsuite/MDAnalysisTests/coordinates/test_gro.py

@@ -94,6 +94,8 @@ def test_unitcell(self):
     def test_volume(self):
         # test_volume: reduce precision for Gromacs comparison to 0 decimals
         # (A**3 <--> nm**3!)
+        print(self.ts.volume,
+            self.ref_volume)
         assert_almost_equal(
             self.ts.volume,
             self.ref_volume,

testsuite/MDAnalysisTests/coordinates/test_gro2.py

@@ -1,5 +1,5 @@
 from MDAnalysis.coordinates.GRO import GROReader, GROWriter
-from MDAnalysisTests.coordinates.base import BaseReference, BaseReaderTest
+from MDAnalysisTests.coordinates.base import BaseReference, BaseReaderTest, MultiframeReaderTest
 from MDAnalysisTests.datafiles import COORDINATES_GRO
 import numpy as np
 
@@ -12,6 +12,7 @@ def __init__(self):
         self.reader = GROReader
         self.writer = GROWriter
         self.ext = 'gro'
+        self.n_frames = 1
         # self.volume = 0
         # self.dimensions = np.zeros(6)
         # self.container_format = True

testsuite/MDAnalysisTests/coordinates/test_memory.py

@@ -4,7 +4,7 @@
 from MDAnalysis.coordinates.memory import MemoryReader
 from MDAnalysisTests.datafiles import DCD, PSF
 from MDAnalysisTests.coordinates.base import (BaseReference,
-                                              BaseReaderTest)
+                                              MultiframeReaderTest)
 from MDAnalysis.coordinates.memory import Timestep
 from numpy.testing import assert_equal, dec
 from MDAnalysisTests import parser_not_found
@@ -59,7 +59,7 @@ def iter_ts(self, i):
 
 
 
-class TestMemoryReader(BaseReaderTest):
+class TestMemoryReader(MultiframeReaderTest):
     def __init__(self):
         reference = MemoryReference()
         super(TestMemoryReader, self).__init__(reference)

testsuite/MDAnalysisTests/coordinates/test_xdr.py

@@ -23,7 +23,7 @@
 
 from MDAnalysisTests.datafiles import (COORDINATES_XTC, COORDINATES_TOPOLOGY,
                                        COORDINATES_TRR)
-from MDAnalysisTests.coordinates.base import (BaseReaderTest, BaseReference,
+from MDAnalysisTests.coordinates.base import (MultiframeReaderTest, BaseReference,
                                               BaseWriterTest,
                                               assert_timestep_almost_equal)
 from MDAnalysisTests import tempdir
@@ -619,7 +619,7 @@ def __init__(self):
         self.changing_dimensions = True
 
 
-class TestXTCReader_2(BaseReaderTest):
+class TestXTCReader_2(MultiframeReaderTest):
     def __init__(self, reference=None):
         if reference is None:
             reference = XTCReference()
@@ -679,7 +679,7 @@ def iter_ts(self, i):
         return ts
 
 
-class TestTRRReader_2(BaseReaderTest):
+class TestTRRReader_2(MultiframeReaderTest):
     def __init__(self, reference=None):
         if reference is None:
             reference = TRRReference()

testsuite/MDAnalysisTests/coordinates/test_xyz.py

@@ -13,7 +13,7 @@
 from MDAnalysis.coordinates.XYZ import XYZWriter
 
 from MDAnalysisTests.datafiles import COORDINATES_XYZ, COORDINATES_XYZ_BZ2
-from MDAnalysisTests.coordinates.base import (BaseReaderTest, BaseReference,
+from MDAnalysisTests.coordinates.base import (MultiframeReaderTest, BaseReference,
                                               BaseWriterTest)
 from MDAnalysisTests import tempdir, make_Universe
 
@@ -32,7 +32,7 @@ def __init__(self):
         self.container_format = True
 
 
-class TestXYZReader(BaseReaderTest):
+class TestXYZReader(MultiframeReaderTest):
     def __init__(self, reference=None):
         if reference is None:
             reference = XYZReference()