merge bugfix release 0.2.1 into 0.3 development branch

kwant/lattice.py

@@ -118,12 +118,13 @@ class PolyatomicLattice(object):
         Site = builder.Site
 
         dim = len(start)
+        num_vecs = len(self.prim_vecs)
         if dim != self.prim_vecs.shape[1]:
             raise ValueError('Dimensionality of start position does not match'
                              ' the space dimensionality.')
         sls = self.sublattices
-        deltas = [ta.array(i * (0,) + (1,) + (dim - 1 - i) * (0,))
-                  for i in xrange(dim)]
+        deltas = [ta.array(i * (0,) + (1,) + (num_vecs - 1 - i) * (0,))
+                  for i in xrange(num_vecs)]
         deltas += [-delta for delta in deltas]
 
         # Check if no sites are going to be added, to catch a common error.
@@ -218,6 +219,7 @@ class MonatomicLattice(builder.SiteGroup, PolyatomicLattice):
                                          repr(self.name))
         intern(self.canonical_repr)
         self.dim = dim
+        self._lattice_dim = len(prim_vecs)
 
         def short_array_str(array):
             full = ', '.join([i.lstrip() for i in str(array).split('\n')])
@@ -238,7 +240,7 @@ class MonatomicLattice(builder.SiteGroup, PolyatomicLattice):
 
     def normalize_tag(self, tag):
         tag = ta.array(tag, int)
-        if len(tag) != self.dim:
+        if len(tag) != self._lattice_dim:
             raise ValueError("Dimensionality mismatch.")
         return tag
 

kwant/plotter.py

@@ -201,7 +201,7 @@ def lines3d(axes, x0, x1, y0, y1, z0, z1,
 
     if len(x0) == 0:
         coll = mplot3d.art3d.Line3DCollection([], linestyles=linestyles)
-        axes.add_collection(coll)
+        axes.add_collection3d(coll)
         return coll
 
     segments = [(i[: 3], i[3:]) for
@@ -209,7 +209,7 @@ def lines3d(axes, x0, x1, y0, y1, z0, z1,
     coll = mplot3d.art3d.Line3DCollection(segments, linestyles=linestyles)
     set_edge_colors(colors, coll, cmap, norm)
     coll.update(kwargs)
-    axes.add_collection(coll)
+    axes.add_collection3d(coll)
 
     min_max = lambda a, b: np.array(min(a.min(), b.min()),
                                     max(a.max(), b.max()))
@@ -249,9 +249,6 @@ def output_fig(fig, output_mode='auto', file=None, savefile_opts=None,
 
     Notes
     -----
-    For IPython with inline plotting, automatic mode selects 'return', since
-    there is a better way to show a figure by just calling `display(figure)`.
-
     The behavior of this function producing a file is different from that of
     matplotlib in that the `dpi` attribute of the figure is used by defaul
     instead of the matplotlib config setting.
@@ -263,11 +260,8 @@ def output_fig(fig, output_mode='auto', file=None, savefile_opts=None,
             output_mode = 'file'
         else:
             try:
-                if matplotlib.pyplot.get_backend() != \
-                     'module://IPython.zmq.pylab.backend_inline':
-                    output_mode = 'pyplot'
-                else:
-                    output_mode = 'return'
+                matplotlib.pyplot.get_backend()
+                output_mode = 'pyplot'
             except AttributeError:
                 output_mode = 'pyplot'
     if output_mode == 'pyplot':
@@ -670,7 +664,9 @@ def plot(sys, n_lead_copies=2, site_color='b', hop_color='b', cmap='gray',
                        cmap='gist_yarg_r', s=size ** 2,
                        norm=matplotlib.colors.Normalize(-1, n_lead_copies + 1))
         else:
-            ax.add_collection(mplot3d.art3d.Patch3DCollection([]))
+            col = mplot3d.art3d.Patch3DCollection([])
+            col.set_3d_properties([], 'z')
+            ax.add_collection3d(col)
         lead_hop_colors = np.array([i[2] for i in
                                      hops if i[1] is not None], dtype=float)
         lead_hop_colors = 1 / np.sqrt(1. + lead_hop_colors)

kwant/tests/test_lattice.py

@@ -24,6 +24,11 @@ def test_general():
             site = sl(*tag)
             assert_equal(tag, sl.closest(site.pos))
 
+    # Test 2D lattice with 1 vector.
+    lat = lattice.make_lattice([[1, 0]])
+    site = lat(0)
+    assert_raises(ValueError, lat, 0, 1)
+
 
 def test_shape():
     def in_circle(pos):