Fixed tests

package/MDAnalysis/analysis/diffusionmap.py

@@ -145,7 +145,7 @@
 import logging
 import warnings
 
-import MDAnalysis.Universe as universe
+from MDAnalysis.core.AtomGroup import Universe
 import numpy as np
 
 from .rms import rmsd
@@ -230,11 +230,11 @@ def __init__(self, u, select='all', metric=rmsd, cutoff=1E0-5,
         self._cutoff = cutoff
         self._weights = weights
         self._calculated = False
-        # remember that this must be called before referencing self.nframes
+        # remember that this must be called before referencing self.n_frames
         self._setup_frames(traj, start, stop, step)
 
     def _prepare(self):
-        self.dist_matrix = np.zeros((self.nframes, self.nframes))
+        self.dist_matrix = np.zeros((self.n_frames, self.n_frames))
 
     def _single_frame(self):
         iframe = self._ts.frame
@@ -326,7 +326,7 @@ def __init__(self, u, epsilon=1, **kwargs):
         step : int, optional
             Step between frames to analyse, Default: 1
         """
-        if isinstance(u, universe):
+        if isinstance(u, Universe):
             self._dist_matrix = DistanceMatrix(u, **kwargs)
         elif isinstance(u, DistanceMatrix):
             self._dist_matrix = u
@@ -335,8 +335,8 @@ def __init__(self, u, epsilon=1, **kwargs):
                              " so the DiffusionMap has no data to work with.")
         self._epsilon = epsilon
         # important for transform function and length of .run() method
-        self._nframes = self._dist_matrix.nframes
-        if self._nframes > 5000:
+        self._n_frames = self._dist_matrix.n_frames
+        if self._n_frames > 5000:
             warnings.warn("The distance matrix is very large, and can "
                           "be very slow to compute. Consider picking a larger "
                           "step size in distance matrix initialization.")

testsuite/MDAnalysisTests/analysis/test_diffusionmap.py

@@ -35,20 +35,20 @@ def setUp(self):
 
     def test_eg(self):
         # number of frames is trajectory is now 10 vs. 98
-        assert_equal(self.eigvals.shape, (self.dist.nframes, ))
+        assert_equal(self.eigvals.shape, (self.dist.n_frames, ))
         # makes no sense to test values here, no physical meaning
 
     def test_dist_weights(self):
         backbone = self.u.select_atoms('backbone')
         weights_atoms = np.ones(len(backbone.atoms))
         self.dist = diffusionmap.DistanceMatrix(self.u, select='backbone',
-                                           weights=weights_atoms)
+                                                weights=weights_atoms)
         self.dist.run()
 
     def test_different_steps(self):
         self.dmap = diffusionmap.DiffusionMap(self.u, select='backbone', step=3)
         self.dmap.run()
-    
+
     def test_transform(self):
         self.n_eigenvectors = 4
         self.dmap = diffusionmap.DiffusionMap(self.u)