fix multiple warnings (mostly deprecations)

Closes #386

doc/source/conf.py

@@ -38,7 +38,7 @@ sys.path.insert(0, os.path.abspath('../sphinxext'))
 
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary',
               'sphinx.ext.todo', 'sphinx.ext.mathjax', 'numpydoc',
-              'kwantdoc', 'sphinx.ext.linkcode', 'jupyter_sphinx.execute',
+              'kwantdoc', 'sphinx.ext.linkcode', 'jupyter_sphinx',
               'sphinxcontrib.rsvgconverter']
 
 # Add any paths that contain templates here, relative to this directory.

kwant/continuum/discretizer.py

@@ -15,6 +15,7 @@ import numpy as np
 import tinyarray as ta
 
 import sympy
+from sympy.matrices.matrices import MatrixBase
 from sympy.utilities.lambdify import lambdastr
 from sympy.printing.lambdarepr import LambdaPrinter
 from sympy.printing.precedence import precedence
@@ -211,7 +212,7 @@ def discretize_symbolic(hamiltonian, coords=None, *, locals=None):
 
     onsite_zeros = (0,) * len(coords)
 
-    if not isinstance(hamiltonian, sympy.matrices.MatrixBase):
+    if not isinstance(hamiltonian, MatrixBase):
         hamiltonian = sympy.Matrix([hamiltonian])
         _input_format = 'expression'
     else:
@@ -574,7 +575,7 @@ def _return_string(expr, coords):
 
     expr = expr.subs(map_func_calls)
 
-    if isinstance(expr, sympy.matrices.MatrixBase):
+    if isinstance(expr, MatrixBase):
         # express matrix return values in terms of sums of known matrices,
         # which will be assigned to '_cache_n' in the function body.
         mons = monomials(expr, expr.atoms(sympy.Symbol))

kwant/plotter.py

@@ -2179,9 +2179,11 @@ def _spectrum_matplotlib(syst, x, y=None, params=None, mask=None, file=None,
         # plot_surface cannot directly handle rank-3 values, so we
         # explicitly loop over the last axis
         grid = np.meshgrid(*array_values)
-        for i in range(spectrum.shape[-1]):
-            spec = spectrum[:, :, i].transpose()  # row-major to x-y ordering
-            ax.plot_surface(*(grid + [spec]), cstride=1, rstride=1)
+        with warnings.catch_warnings():
+            warnings.filterwarnings('ignore', message='Z contains NaN values')
+            for i in range(spectrum.shape[-1]):
+                spec = spectrum[:, :, i].transpose()  # row-major to x-y ordering
+                ax.plot_surface(*(grid + [spec]), cstride=1, rstride=1)
 
     _maybe_output_fig(fig, file=file, show=show)
 
@@ -2324,8 +2326,13 @@ def _interpolate_field(dim, elements, discrete_field, bbox, width,
 
         # Coordinates of the grid points that are within range of the current
         # hopping.
-        coords = np.meshgrid(*[region[d][field_slice[d]] for d in range(dim)],
-                             sparse=True, indexing='ij')
+        coords = np.array(
+            np.meshgrid(
+                *[region[d][field_slice[d]] for d in range(dim)],
+                sparse=True, indexing='ij'
+            ),
+            dtype=object
+        )
 
         # Convert "coords" into scaled distances from pos_offset
         coords -= pos_offsets[i]

kwant/qsymm.py

@@ -18,12 +18,15 @@ import scipy.linalg as la
 
 try:
     import sympy
+    import sympy.matrices.matrices
     import qsymm
     from qsymm.model import Model, BlochModel, BlochCoeff
     from qsymm.groups import PointGroupElement, ContinuousGroupGenerator
     from qsymm.symmetry_finder import bravais_point_group
     from qsymm.linalg import allclose
     from qsymm.hamiltonian_generator import hamiltonian_from_family
+
+    one = sympy.S.One
 except ImportError as error:
     msg = ("'kwant.qsymm' is not available because one or more of its "
            "dependencies is not installed.")
@@ -346,7 +349,7 @@ def model_to_builder(model, norbs, lat_vecs, atom_coords, *, coeffs=None):
     for atom in atoms:
         if atom not in onsites_dict:
             onsites_dict[atom] = Model(
-                {sympy.numbers.One(): np.zeros((norbs[atom], norbs[atom]))},
+                {one: np.zeros((norbs[atom], norbs[atom]))},
                 momenta=momenta)
 
     # Make the Kwant system, and set all onsites and hoppings.

kwant/solvers/common.py

@@ -841,12 +841,10 @@ class SMatrix(BlockResult):
                 block_offsets.append(block_offset)
         # Symmetry block offsets for all leads - or None if lead does not have
         # blocks.
-        self.block_offsets = block_offsets
+        block_offsets = np.array(block_offsets, dtype=object)
         # Pick out symmetry block offsets for in and out leads
-        self.in_block_offsets = \
-                np.array(self.block_offsets)[list(self.in_leads)]
-        self.out_block_offsets = \
-                np.array(self.block_offsets)[list(self.out_leads)]
+        self._in_block_offsets = block_offsets[list(self.in_leads)]
+        self._out_block_offsets = block_offsets[list(self.out_leads)]
         # Block j of in lead i starts at in_block_offsets[i][j]
 
     def out_block_coords(self, lead_out):
@@ -860,9 +858,9 @@ class SMatrix(BlockResult):
             lead_ind, block_ind = lead_out
             lead_ind = self.out_leads.index(lead_ind)
             return slice(self.out_offsets[lead_ind] +
-                         self.out_block_offsets[lead_ind][block_ind],
+                         self._out_block_offsets[lead_ind][block_ind],
                          self.out_offsets[lead_ind] +
-                         self.out_block_offsets[lead_ind][block_ind + 1])
+                         self._out_block_offsets[lead_ind][block_ind + 1])
 
     def in_block_coords(self, lead_in):
         """
@@ -876,9 +874,9 @@ class SMatrix(BlockResult):
             lead_ind, block_ind = lead_in
             lead_ind = self.in_leads.index(lead_ind)
             return slice(self.in_offsets[lead_ind] +
-                         self.in_block_offsets[lead_ind][block_ind],
+                         self._in_block_offsets[lead_ind][block_ind],
                          self.in_offsets[lead_ind] +
-                         self.in_block_offsets[lead_ind][block_ind + 1])
+                         self._in_block_offsets[lead_ind][block_ind + 1])
 
     def _transmission(self, lead_out, lead_in):
         return np.linalg.norm(self.submatrix(lead_out, lead_in)) ** 2

kwant/tests/test_qsymm.py

@@ -180,7 +180,7 @@ def test_graphene_to_kwant():
         assert allclose(hamiltonian2, hamiltonian3)
 
     # Include random onsites as well
-    one = sympy.numbers.One()
+    one = sympy.S.One
     onsites = [Model({one: np.array([[1, 0], [0, 0]])}, momenta=family[0].momenta),
                Model({one: np.array([[0, 0], [0, 1]])}, momenta=family[0].momenta)]
     family = family + onsites