Merge branch 'bugfix/no-numpy-matrices' into 'master'

maint: clear up warnings in tests

See merge request kwant/kwant!270

.gitlab-ci.yml

@@ -165,7 +165,7 @@ check for dependencies installed:
 .test: &test
   stage: test
   script:
-    - py.test -r w --cov=kwant --cov-report term --cov-report html --flakes kwant --junitxml=tests.xml
+    - py.test -r w --cov=kwant --cov-report term --cov-report html --flakes kwant --junitxml=tests.xml --durations=10
   artifacts:
     paths:
       - htmlcov

kwant/_plotter.py

@@ -119,9 +119,12 @@ if mpl_available:
 
         phi = np.linspace(0, pi, 21)
         xyz = np.c_[np.cos(phi), np.sin(phi), 0 * phi].T.reshape(-1, 1, 21)
-        unit_sphere = np.bmat([[xyz[0], xyz[2]], [xyz[1], xyz[0]],
-                                [xyz[2], xyz[1]]])
-        unit_sphere = np.asarray(unit_sphere)
+        # TODO: use np.block once we depend on numpy >= 1.13.
+        unit_sphere = np.vstack([
+            np.hstack([xyz[0], xyz[2]]),
+            np.hstack([xyz[1], xyz[0]]),
+            np.hstack([xyz[2], xyz[1]]),
+        ])
 
         def projected_length(ax, length):
             rc = np.array([ax.get_xlim3d(), ax.get_ylim3d(), ax.get_zlim3d()])

kwant/physics/noise.py

@@ -13,7 +13,7 @@ __all__ = ['two_terminal_shotnoise']
 
 
 def two_terminal_shotnoise(smatrix):
-    """Compute the shot-noise in a two-terminal setup.
+    r"""Compute the shot-noise in a two-terminal setup.
 
     In a two terminal system the shot noise is given by `tr((1 - t*t^\dagger) *
     t*t^\dagger)`.

kwant/physics/symmetry.py

@@ -16,6 +16,18 @@ def almost_identity(mat):
     return np.all(abs(mat - identity(mat.shape[0])).data < 1e-10)
 
 
+def _column_sum(matrix):
+    """Sum the columns of a sparse matrix.
+
+    This is fully analogous to ``matrix.sum(0)``, and uses an implementation
+    similar to that in scipy v1.1.0, however it avoids using ``numpy.matrix``
+    interface and therefore does not raise a ``PendingDeprecationWarning``.
+    This should be removed once we depend on scipy v1.2.0, where the warning is
+    silenced.
+    """
+    return matrix.T @ np.ones(matrix.shape[0])
+
+
 def cond_conj(op, conj):
     return op.conj() if conj else op
 
@@ -106,8 +118,9 @@ class DiscreteSymmetry:
             symms[i] = symm
 
         if projectors is not None:
-            projectors = [p[:, np.asarray(abs(p).sum(0)).flatten() > 1e-10]
-                          for p in projectors]
+            projectors = [
+                p[:, _column_sum(abs(p)) > 1e-10] for p in projectors
+            ]
             if not almost_identity(sum(projector.dot(projector.conj().T) for
                                        projector in projectors)):
                 raise ValueError("Projectors should stack to a unitary matrix.")

kwant/plotter.py

@@ -1302,6 +1302,7 @@ def map(sys, value, colorbar=True, cmap=None, vmin=None, vmax=None, a=None,
     # Calculate the min/max bounds for the colormap.
     # User-provided values take precedence.
     unmasked_data = img[~img.mask].data.flatten()
+    unmasked_data = unmasked_data[~np.isnan(unmasked_data)]
     new_vmin, new_vmax = percentile_bound(unmasked_data, vmin, vmax)
     overflow_pct = 100 * np.sum(unmasked_data > new_vmax) / len(unmasked_data)
     underflow_pct = 100 * np.sum(unmasked_data < new_vmin) / len(unmasked_data)

kwant/solvers/common.py

@@ -555,7 +555,7 @@ class SparseSolver(metaclass=abc.ABCMeta):
 
     def wave_function(self, sys, energy=0, args=(), check_hermiticity=True,
                       *, params=None):
-        """
+        r"""
         Return a callable object for the computation of the wave function
         inside the scattering region.
 

kwant/tests/test_operator.py

@@ -77,7 +77,6 @@ def test_operator_construction():
             raises(ValueError, a, ket)
             raises(ValueError, a, ket, ket)
             raises(ValueError, a.act, ket)
-            raises(ValueError, a.act, ket, ket)
 
     # Test failure on non-hermitian
     for A in (ops.Density, ops.Current, ops.Source):

kwant/tests/test_plotter.py

@@ -261,7 +261,7 @@ def test_spectrum():
                              params=dict(c=1), fig_size=(10, 10), file=out)
 
         # test 2D plot and explicitly passing axis
-        fig = pyplot.Figure()
+        fig = pyplot.figure()
         ax = fig.add_subplot(1, 1, 1, projection='3d')
         plotter.spectrum(ham_1d, ('a', vals), ('b', 2 * vals),
                          params=dict(c=1), ax=ax, file=out)

kwant/tests/test_wraparound.py

@@ -166,7 +166,8 @@ def test_symmetry():
         syst.particle_hole = ph
         syst.time_reversal = tr
 
-        wrapped = wraparound(syst)
+        with pytest.warns(RuntimeWarning):
+            wrapped = wraparound(syst)
 
         assert wrapped.time_reversal is None
         assert wrapped.particle_hole is None