diff --git a/doc/Makefile b/doc/Makefile
index c3529688942efc29effcf7c574d861e211ff0c5c..28f86b153fab74b06e65fab437a639e557a48974 100644
--- a/doc/Makefile
+++ b/doc/Makefile
@@ -136,5 +136,5 @@ $(foreach name,$(SCRIPTS),$(eval $(call makedep,$(name))))
# Generation of images
.%_flag: %.py
- cd $(dir $<) && python $(notdir $<)
+ cd $(dir $<) && python3 $(notdir $<)
@touch $@
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 98d2c401804651380e27101374ef1fe6a917cc47..8514d0db295d6641493ce69f077c7c25e9c03cf8 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -42,8 +42,8 @@ source_suffix = '.rst'
master_doc = 'index'
# General information about the project.
-project = u'Kwant'
-copyright = u'2011-2015, C. W. Groth (CEA), M. Wimmer, A. R. Akhmerov, X. Waintal (CEA), and others'
+project = 'Kwant'
+copyright = '2011-2015, C. W. Groth (CEA), M. Wimmer, A. R. Akhmerov, X. Waintal (CEA), and others'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@@ -208,7 +208,7 @@ r"""\makeatletter
# We use "et al." as it is shorter and there's not much space left horizontally.
latex_documents = [
('index', 'kwant.tex', 'Kwant {0} documentation'.format(release),
- u'C. W. Groth, M. Wimmer, A. R. Akhmerov, X. Waintal, et al.',
+ 'C. W. Groth, M. Wimmer, A. R. Akhmerov, X. Waintal, et al.',
'manual'),
]
@@ -249,9 +249,9 @@ class BoundMethodDocumenter(autodoc.FunctionDocumenter):
# Return True iff `member` is a bound method. Taken from
# <http://stackoverflow.com/a/1260881>.
return (isinstance(member, types.MethodType) and
- member.im_self is not None and
- not issubclass(member.im_class, type) and
- member.im_class is not types.ClassType)
+ member.__self__ is not None and
+ not issubclass(member.__self__.__class__, type) and
+ member.__self__.__class__ is not type)
def format_args(self):
args = super(BoundMethodDocumenter, self).format_args()
diff --git a/doc/source/images/graphene.py.diff b/doc/source/images/graphene.py.diff
index 351a717cb0be71fda9a19350434553135950ed9d..d4444aff257eda32e6a21bef257f90dace0790aa 100644
--- a/doc/source/images/graphene.py.diff
+++ b/doc/source/images/graphene.py.diff
@@ -1,14 +1,13 @@
--- original
+++ modified
-@@ -11,6 +11,7 @@
+@@ -11,5 +11,6 @@
# lattice, namely graphene
- from __future__ import division # so that 1/2 == 0.5, and not 0
+import _defs
from math import pi, sqrt, tanh
import kwant
-@@ -97,22 +98,40 @@
+@@ -96,22 +97,40 @@
smatrix = kwant.smatrix(sys, energy)
data.append(smatrix.transmission(0, 1))
@@ -57,7 +56,7 @@
def main():
-@@ -124,8 +143,11 @@
+@@ -123,8 +142,11 @@
def family_colors(site):
return 0 if site.family == a else 1
@@ -71,7 +70,7 @@
# Compute some eigenvalues.
compute_evs(sys.finalized())
-@@ -134,9 +156,11 @@
+@@ -133,9 +155,11 @@
for lead in leads:
sys.attach_lead(lead)
diff --git a/doc/source/tutorial/ab_ring.py b/doc/source/tutorial/ab_ring.py
index 5df7ecda6ef7f2331fc46b0756d7e5f5104cb126..33de87fbee803011e1222787d67577d95840e740 100644
--- a/doc/source/tutorial/ab_ring.py
+++ b/doc/source/tutorial/ab_ring.py
@@ -118,7 +118,7 @@ def main():
# We should see a conductance that is periodic with the flux quantum
plot_conductance(sys, energy=0.15, fluxes=[0.01 * i * 3 * 2 * pi
- for i in xrange(100)])
+ for i in range(100)])
# Call the main function if the script gets executed (as opposed to imported).
diff --git a/doc/source/tutorial/band_structure.py b/doc/source/tutorial/band_structure.py
index ddb9976482783bee6d5d8781d4f2a5d95ab7190c..5b223d3e96f0f474e7b684f2eae779c160698388 100644
--- a/doc/source/tutorial/band_structure.py
+++ b/doc/source/tutorial/band_structure.py
@@ -24,7 +24,7 @@ def make_lead(a=1, t=1.0, W=10):
# build up one unit cell of the lead, and add the hoppings
# to the next unit cell
- for j in xrange(W):
+ for j in range(W):
lead[lat(0, j)] = 4 * t
if j > 0:
diff --git a/doc/source/tutorial/closed_system.py b/doc/source/tutorial/closed_system.py
index 2f54bf046023d678ec9d47873c0c238bccccb077..49d2dc1d460252bde38bf2499190958947a2d01e 100644
--- a/doc/source/tutorial/closed_system.py
+++ b/doc/source/tutorial/closed_system.py
@@ -106,7 +106,7 @@ def main():
try:
# We should observe energy levels that flow towards Landau
# level energies with increasing magnetic field.
- plot_spectrum(sys, [iB * 0.002 for iB in xrange(100)])
+ plot_spectrum(sys, [iB * 0.002 for iB in range(100)])
# Plot an eigenmode of a circular dot. Here we create a larger system for
# better spatial resolution.
@@ -114,8 +114,8 @@ def main():
plot_wave_function(sys)
except ValueError as e:
if e.message == "Input matrix is not real-valued.":
- print "The calculation of eigenvalues failed because of a bug in SciPy 0.9."
- print "Please upgrade to a newer version of SciPy."
+ print("The calculation of eigenvalues failed because of a bug in SciPy 0.9.")
+ print("Please upgrade to a newer version of SciPy.")
else:
raise
diff --git a/doc/source/tutorial/graphene.py b/doc/source/tutorial/graphene.py
index cd0ec2e6939cbd2a54bf7ff87a6e444d0ac34126..31f2c578501323a16983b698e9776a7545c30fff 100644
--- a/doc/source/tutorial/graphene.py
+++ b/doc/source/tutorial/graphene.py
@@ -10,7 +10,6 @@
# - Application of all the aspects of tutorials 1-3 to a more complicated
# lattice, namely graphene
-from __future__ import division # so that 1/2 == 0.5, and not 0
from math import pi, sqrt, tanh
import kwant
@@ -102,7 +101,7 @@ def compute_evs(sys):
sparse_mat = sys.hamiltonian_submatrix(sparse=True)
evs = sla.eigs(sparse_mat, 2)[0]
- print evs.real
+ print(evs.real)
#HIDDEN_END_zydk
@@ -166,11 +165,11 @@ def main():
sys = sys.finalized()
# Compute the band structure of lead 0.
- momenta = [-pi + 0.02 * pi * i for i in xrange(101)]
+ momenta = [-pi + 0.02 * pi * i for i in range(101)]
plot_bandstructure(sys.leads[0], momenta)
# Plot conductance.
- energies = [-2 * pot + 4. / 50. * pot * i for i in xrange(51)]
+ energies = [-2 * pot + 4. / 50. * pot * i for i in range(51)]
plot_conductance(sys, energies)
diff --git a/doc/source/tutorial/quantum_well.py b/doc/source/tutorial/quantum_well.py
index 76ab616624bba5a5cf7cf30254ae9eef6745a102..98309437c614b47418846c04dc7e8167d3a2168b 100644
--- a/doc/source/tutorial/quantum_well.py
+++ b/doc/source/tutorial/quantum_well.py
@@ -43,7 +43,7 @@ def make_system(a=1, t=1.0, W=10, L=30, L_well=10):
#### Define and attach the leads. ####
lead = kwant.Builder(kwant.TranslationalSymmetry((-a, 0)))
- lead[(lat(0, j) for j in xrange(W))] = 4 * t
+ lead[(lat(0, j) for j in range(W))] = 4 * t
lead[lat.neighbors()] = -t
sys.attach_lead(lead)
sys.attach_lead(lead.reversed())
@@ -79,7 +79,7 @@ def main():
# We should see conductance steps.
plot_conductance(sys, energy=0.2,
- welldepths=[0.01 * i for i in xrange(100)])
+ welldepths=[0.01 * i for i in range(100)])
# Call the main function if the script gets executed (as opposed to imported).
diff --git a/doc/source/tutorial/quantum_wire.py b/doc/source/tutorial/quantum_wire.py
index d4d89956c27d9bb322b99660135e2bda1273986c..b32072123c2f65b492c6f5588103ad26cec3f55b 100644
--- a/doc/source/tutorial/quantum_wire.py
+++ b/doc/source/tutorial/quantum_wire.py
@@ -35,8 +35,8 @@ L = 30
# Define the scattering region
-for i in xrange(L):
- for j in xrange(W):
+for i in range(L):
+ for j in range(W):
# On-site Hamiltonian
sys[lat(i, j)] = 4 * t
@@ -59,7 +59,7 @@ left_lead = kwant.Builder(sym_left_lead)
#HIDDEN_END_xcmc
#HIDDEN_BEGIN_ndez
-for j in xrange(W):
+for j in range(W):
left_lead[lat(0, j)] = 4 * t
if j > 0:
left_lead[lat(0, j), lat(0, j - 1)] = -t
@@ -75,7 +75,7 @@ sys.attach_lead(left_lead)
sym_right_lead = kwant.TranslationalSymmetry((a, 0))
right_lead = kwant.Builder(sym_right_lead)
-for j in xrange(W):
+for j in range(W):
right_lead[lat(0, j)] = 4 * t
if j > 0:
right_lead[lat(0, j), lat(0, j - 1)] = -t
@@ -98,7 +98,7 @@ sys = sys.finalized()
#HIDDEN_BEGIN_buzn
energies = []
data = []
-for ie in xrange(100):
+for ie in range(100):
energy = ie * 0.01
# compute the scattering matrix at a given energy
diff --git a/doc/source/tutorial/quantum_wire_revisited.py b/doc/source/tutorial/quantum_wire_revisited.py
index c42912ce10636e3d0f4a08d7015ef60b7df1487c..e21341576d0ed53807c46020ed763eec4cb547cc 100644
--- a/doc/source/tutorial/quantum_wire_revisited.py
+++ b/doc/source/tutorial/quantum_wire_revisited.py
@@ -39,7 +39,7 @@ def make_system(a=1, t=1.0, W=10, L=30):
# Construct the left lead.
#HIDDEN_BEGIN_iepx
lead = kwant.Builder(kwant.TranslationalSymmetry((-a, 0)))
- lead[(lat(0, j) for j in xrange(W))] = 4 * t
+ lead[(lat(0, j) for j in range(W))] = 4 * t
lead[lat.neighbors()] = -t
#HIDDEN_END_iepx
@@ -79,7 +79,7 @@ def main():
sys = sys.finalized()
# We should see conductance steps.
- plot_conductance(sys, energies=[0.01 * i for i in xrange(100)])
+ plot_conductance(sys, energies=[0.01 * i for i in range(100)])
#HIDDEN_END_cjel
diff --git a/doc/source/tutorial/spin_orbit.py b/doc/source/tutorial/spin_orbit.py
index 0112d3feb9874e184303327555c4c19c0898fdcb..e9d3f7f4ff73764c3c236d58ce3f60c6b3edab75 100644
--- a/doc/source/tutorial/spin_orbit.py
+++ b/doc/source/tutorial/spin_orbit.py
@@ -55,7 +55,7 @@ def make_system(a=1, t=1.0, alpha=0.5, e_z=0.08, W=10, L=30):
lead = kwant.Builder(kwant.TranslationalSymmetry((-a, 0)))
#HIDDEN_BEGIN_yliu
- lead[(lat(0, j) for j in xrange(W))] = 4 * t * sigma_0 + e_z * sigma_z
+ lead[(lat(0, j) for j in range(W))] = 4 * t * sigma_0 + e_z * sigma_z
# hoppings in x-direction
lead[kwant.builder.HoppingKind((1, 0), lat, lat)] = \
-t * sigma_0 - 1j * alpha * sigma_y
@@ -95,7 +95,7 @@ def main():
sys = sys.finalized()
# We should see non-monotonic conductance steps.
- plot_conductance(sys, energies=[0.01 * i - 0.3 for i in xrange(100)])
+ plot_conductance(sys, energies=[0.01 * i - 0.3 for i in range(100)])
# Call the main function if the script gets executed (as opposed to imported).
diff --git a/doc/source/tutorial/superconductor_band_structure.py b/doc/source/tutorial/superconductor_band_structure.py
index 9f8da5e274daf2dbd884a69099889772ac1cefd6..6a7928363e420abbee4f24c56ac14ebeebe4dcf5 100644
--- a/doc/source/tutorial/superconductor_band_structure.py
+++ b/doc/source/tutorial/superconductor_band_structure.py
@@ -35,7 +35,7 @@ def make_lead(a=1, t=1.0, mu=0.7, Delta=0.1, W=10):
# build up one unit cell of the lead, and add the hoppings
# to the next unit cell
- for j in xrange(W):
+ for j in range(W):
lead[lat(0, j)] = (4 * t - mu) * tau_z + Delta * tau_x
if j > 0:
diff --git a/doc/source/tutorial/superconductor_transport.py b/doc/source/tutorial/superconductor_transport.py
index 505479e28a1989bd94521105d0bb90a70ce88cd6..a8184c95f3b4c5de4ce27855f7bb55fc360d994c 100644
--- a/doc/source/tutorial/superconductor_transport.py
+++ b/doc/source/tutorial/superconductor_transport.py
@@ -55,12 +55,12 @@ def make_system(a=1, W=10, L=10, barrier=1.5, barrierpos=(3, 4),
# left electron lead
lead0 = kwant.Builder(sym_left)
- lead0[(lat_e(0, j) for j in xrange(W))] = 4 * t - mu
+ lead0[(lat_e(0, j) for j in range(W))] = 4 * t - mu
lead0[lat_e.neighbors()] = -t
# left hole lead
lead1 = kwant.Builder(sym_left)
- lead1[(lat_h(0, j) for j in xrange(W))] = mu - 4 * t
+ lead1[(lat_h(0, j) for j in range(W))] = mu - 4 * t
lead1[lat_h.neighbors()] = t
#HIDDEN_END_ttth
@@ -72,7 +72,7 @@ def make_system(a=1, W=10, L=10, barrier=1.5, barrierpos=(3, 4),
lead2 = kwant.Builder(sym_right)
lead2 += lead0
lead2 += lead1
- lead2[((lat_e(0, j), lat_h(0, j)) for j in xrange(W))] = Delta
+ lead2[((lat_e(0, j), lat_h(0, j)) for j in range(W))] = Delta
#HIDDEN_END_mhiw
#### Attach the leads and return the system. ####
@@ -113,7 +113,7 @@ def main():
# Finalize the system.
sys = sys.finalized()
- plot_conductance(sys, energies=[0.002 * i for i in xrange(100)])
+ plot_conductance(sys, energies=[0.002 * i for i in range(100)])
# Call the main function if the script gets executed (as opposed to imported).
diff --git a/examples/3d_plot.py b/examples/3d_plot.py
index 8dcef1f40ca45a341d16afb8a208a9ed523e311a..ed8bccfeaa5bd7ea03cc6236f08a834a0c835f04 100644
--- a/examples/3d_plot.py
+++ b/examples/3d_plot.py
@@ -1,6 +1,6 @@
from math import sqrt
import scipy.sparse.linalg as sla
-import matplotlib.pyplot
+from matplotlib import pyplot
import kwant
sys = kwant.Builder()
@@ -9,11 +9,11 @@ lat = kwant.lattice.general([(1,0,0), (0,1,0), (0,0,1)])
t = 1.0
R = 10
-sys[(lat(x,y,z) for x in xrange(-R-1, R+1)
- for y in xrange(-R-1, R+1) for z in xrange(R+1)
+sys[(lat(x,y,z) for x in range(-R-1, R+1)
+ for y in range(-R-1, R+1) for z in range(R+1)
if sqrt(x**2 + y**2 + z**2) < R + 0.01)] = 4 * t
-sys[(lat(x,y,z) for x in xrange(-2*R, 2*R + 1)
- for y in xrange(-R, R+1) for z in xrange(-R, 0))] = 4 * t
+sys[(lat(x,y,z) for x in range(-2*R, 2*R + 1)
+ for y in range(-R, R+1) for z in range(-R, 0))] = 4 * t
sys[lat.neighbors()] = -t
sys = sys.finalized()
kwant.plot(sys)
diff --git a/examples/advanced_construction.py b/examples/advanced_construction.py
index dcfcfa92e6291fc577cd529732310b26d7b79c00..1d4806bacbd0eb268e0f9c7524a84b91cf98c0a1 100644
--- a/examples/advanced_construction.py
+++ b/examples/advanced_construction.py
@@ -1,6 +1,5 @@
"""An example of advanced system creation."""
-from __future__ import division
from math import tanh
from cmath import exp
import tinyarray as ta
@@ -48,7 +47,7 @@ def make_system(R):
def main():
sys = make_system(100)
- print kwant.smatrix(sys, 1.1, [0.1]).transmission(0, 1)
+ print(kwant.smatrix(sys, 1.1, [0.1]).transmission(0, 1))
if __name__ == '__main__':
diff --git a/examples/logo.py b/examples/logo.py
index c3dcb1f6e59cef8b4e7427895891767f2fb56043..941c613c8c803205d139a91bb24fd6826f960e0b 100644
--- a/examples/logo.py
+++ b/examples/logo.py
@@ -1,12 +1,10 @@
"""The script generating Kwant logo. In addition to Kwant it also needs Python
-image library (PIL)."""
+image library Pillow."""
-import Image
-import ImageFont
-import ImageDraw
+from PIL import Image, ImageFont, ImageDraw
import matplotlib
import numpy as np
-import scipy
+import scipy.misc
import kwant
def main():
@@ -86,7 +84,7 @@ def main():
# result is not too empty or not too dark.
out = np.zeros(textpos.shape)
for i, rho in enumerate(ldos**.2):
- x1, y1 = sys.site(i).tag
+ x1, y1 = sys.sites[i].tag
out[x1, y1] = rho
out = normalize_data(out)
diff --git a/examples/square.py b/examples/square.py
index c7df5d54200b247cb7584db9a7e0a9699ebf2f58..580df113f33af5743bc32140a460aba003aa6ca8 100644
--- a/examples/square.py
+++ b/examples/square.py
@@ -2,7 +2,6 @@
kwant.Builder.
"""
-from __future__ import division
import numpy as np
from matplotlib import pyplot
import kwant
@@ -10,6 +9,7 @@ from kwant.physics.leads import square_selfenergy
__all__ = ['System']
+
class Lead(object):
def __init__(self, width, t, potential):
self.width = width
@@ -20,6 +20,7 @@ class Lead(object):
return square_selfenergy(self.width, self.t,
self.potential + fermi_energy)
+
class System(kwant.system.FiniteSystem):
def __init__(self, shape, hopping,
potential=0, lead_potentials=(0, 0),
@@ -56,7 +57,7 @@ class System(kwant.system.FiniteSystem):
edges[:shape[across], 1] += increment[along]
edges[shape[across]:, (0, 1)] = edges[:shape[across], (1, 0)]
g.add_edges(edges)
- for i in xrange(shape[along] - 2):
+ for i in range(shape[along] - 2):
edges += increment[along]
g.add_edges(edges)
self.graph = g.compressed()
@@ -66,7 +67,7 @@ class System(kwant.system.FiniteSystem):
# We have to use list here, as numpy.array does not understand
# generators.
interface = list(self.nodeid_from_pos((x, y))
- for y in xrange(shape[1]))
+ for y in range(shape[1]))
self.lead_interfaces.append(np.array(interface))
self.leads = [Lead(shape[1], hopping, lead_potentials[i])
@@ -85,7 +86,7 @@ class System(kwant.system.FiniteSystem):
return result
def nodeid_from_pos(self, pos):
- for i in xrange(2):
+ for i in range(2):
assert int(pos[i]) == pos[i]
assert pos[i] >= 0 and pos[i] < self.shape[i]
return pos[0] + pos[1] * self.shape[0]
@@ -98,8 +99,8 @@ class System(kwant.system.FiniteSystem):
def main():
sys = System((10, 5), 1)
- energies = [0.04 * i for i in xrange(100)]
- data = [kwant.smatrix(sys, energy).transmission(1, 0)
+ energies = [0.04 * i for i in range(100)]
+ data = [kwant.greens_function(sys, energy).transmission(1, 0)
for energy in energies]
pyplot.plot(energies, data)
diff --git a/examples/tests/test_square.py b/examples/tests/test_square.py
index 4d605368caa4f43660fbd27ea94587aecf09ef3f..f8654c98a50288f49d55a6b079029a959090d5aa 100644
--- a/examples/tests/test_square.py
+++ b/examples/tests/test_square.py
@@ -4,18 +4,18 @@ from numpy.testing import assert_almost_equal
def test_nodeid_to_from_pos():
s = square.System((3, 4), 1)
- assert_raises(StandardError, s.nodeid_from_pos, (0, -2))
- assert_raises(StandardError, s.nodeid_from_pos, (-1, 3))
- assert_raises(StandardError, s.nodeid_from_pos, (3, 1))
- assert_raises(StandardError, s.pos_from_nodeid, -1)
- assert_raises(StandardError, s.pos_from_nodeid, 12)
+ assert_raises(Exception, s.nodeid_from_pos, (0, -2))
+ assert_raises(Exception, s.nodeid_from_pos, (-1, 3))
+ assert_raises(Exception, s.nodeid_from_pos, (3, 1))
+ assert_raises(Exception, s.pos_from_nodeid, -1)
+ assert_raises(Exception, s.pos_from_nodeid, 12)
assert_equal(s.nodeid_from_pos((0, 0)), 0)
assert_equal(s.nodeid_from_pos(s.pos_from_nodeid(7)), 7)
assert_equal(s.pos_from_nodeid(s.nodeid_from_pos((2, 3))), (2, 3))
def test_hamiltonian():
sys = square.System((4, 5), 1)
- for i in xrange(sys.graph.num_nodes):
+ for i in range(sys.graph.num_nodes):
shape = sys.hamiltonian(i, i).shape
assert_equal(len(shape), 2)
assert_equal(shape[0], 1)
@@ -28,7 +28,7 @@ def test_hamiltonian():
def test_selfenergy():
sys = square.System((2, 4), 1)
- for lead in xrange(len(sys.lead_interfaces)):
+ for lead in range(len(sys.lead_interfaces)):
se = sys.leads[lead].selfenergy(0)
assert_equal(len(se.shape), 2)
assert_equal(se.shape[0], se.shape[1])
diff --git a/kwant/__init__.py b/kwant/__init__.py
index c45de3fd9fac82e270e530bb39c82630e08399a4..74e80f9fb3bb1491cbee5b721c40c0a952fe5165 100644
--- a/kwant/__init__.py
+++ b/kwant/__init__.py
@@ -29,7 +29,7 @@ __all__.append('KwantDeprecationWarning')
from ._common import version as __version__
for module in ['system', 'builder', 'lattice', 'solvers', 'digest', 'rmt']:
- exec 'from . import {0}'.format(module)
+ exec('from . import {0}'.format(module))
__all__.append(module)
# Make selected functionality available directly in the root namespace.
@@ -38,7 +38,7 @@ available = [('builder', ['Builder', 'HoppingKind']),
('solvers.default',
['smatrix', 'greens_function', 'ldos', 'wave_function'])]
for module, names in available:
- exec 'from .{0} import {1}'.format(module, ', '.join(names))
+ exec('from .{0} import {1}'.format(module, ', '.join(names)))
__all__.extend(names)
# Importing plotter might not work, but this does not have to be a problem --
diff --git a/kwant/_common.py b/kwant/_common.py
index e050f2edef9923a1aec16cbb46b1a2bb1fe767ff..b67d1326a53d3af9758fb752e27a12924661c9b0 100644
--- a/kwant/_common.py
+++ b/kwant/_common.py
@@ -11,7 +11,9 @@ import os
__all__ = ['version', 'KwantDeprecationWarning']
-distr_root = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
+package_root = os.path.dirname(os.path.realpath(__file__))
+distr_root = os.path.dirname(package_root)
+version_file = '_kwant_version.py'
def get_version_from_git():
try:
@@ -22,8 +24,7 @@ def get_version_from_git():
return
if p.wait() != 0:
return
- # TODO: use os.path.samefile once we depend on Python >= 3.3.
- if os.path.normpath(p.communicate()[0].rstrip('\n')) != distr_root:
+ if not os.path.samefile(p.communicate()[0].decode().rstrip('\n'), distr_root):
# The top-level directory of the current Git repository is not the same
# as the root directory of the Kwant distribution: do not extract the
# version from Git.
@@ -42,7 +43,7 @@ def get_version_from_git():
break
else:
return
- description = p.communicate()[0].strip('v').rstrip('\n')
+ description = p.communicate()[0].decode().strip('v').rstrip('\n')
release, dev, git = description.rsplit('-', 2)
version = [release]
@@ -67,7 +68,11 @@ def get_version_from_git():
-from _kwant_version import version
+# populate the version_info dictionary with values stored in the version file
+version_info = {}
+with open(os.path.join(package_root, version_file), 'r') as f:
+ exec(f.read(), {}, version_info)
+version = version_info['version']
version_is_from_git = (version == "__use_git__")
if version_is_from_git:
version = get_version_from_git()
diff --git a/kwant/_system.pyx b/kwant/_system.pyx
index dc3e665dd3ef9505cacb852226943ca946e82e62..beebd9465866dd61532b1f8d92ef411a9ee07555 100644
--- a/kwant/_system.pyx
+++ b/kwant/_system.pyx
@@ -11,6 +11,7 @@ import tinyarray as ta
import numpy as np
from scipy import sparse as sp
from itertools import chain
+import types
from .graph.core cimport CGraph, gintArraySlice
from .graph.defs cimport gint
@@ -84,8 +85,15 @@ def make_sparse(ham, args, CGraph gr, diag,
rows_cols[1, k] = j + from_off[n_fs]
k += 1
- return sp.coo_matrix((data[:k], rows_cols[:, :k]),
- shape=(to_off[-1], from_off[-1]))
+ # hack around a bug in Scipy + Python 3 + memoryviews
+ # see https://github.com/scipy/scipy/issues/5123 for details
+ np_data = np.asarray(data)
+ np_rows_cols = np.asarray(rows_cols)
+ np_to_off = np.asarray(to_off)
+ np_from_off = np.asarray(from_off)
+
+ return sp.coo_matrix((np_data[:k], np_rows_cols[:, :k]),
+ shape=(np_to_off[-1], np_from_off[-1]))
@cython.boundscheck(False)
@@ -147,8 +155,15 @@ def make_sparse_full(ham, args, CGraph gr, diag,
rows_cols[0, k + 1] = rows_cols[1, k] = j + from_off[fs]
k += 2
- return sp.coo_matrix((data[:k], rows_cols[:, :k]),
- shape=(to_off[-1], from_off[-1]))
+ # hack around a bug in Scipy + Python 3 + memoryviews
+ # see https://github.com/scipy/scipy/issues/5123 for details
+ np_data = np.asarray(data)
+ np_rows_cols = np.asarray(rows_cols)
+ np_to_off = np.asarray(to_off)
+ np_from_off = np.asarray(from_off)
+
+ return sp.coo_matrix((np_data[:k], np_rows_cols[:, :k]),
+ shape=(np_to_off[-1], np_from_off[-1]))
@cython.boundscheck(False)
@@ -327,3 +342,13 @@ def hamiltonian_submatrix(self, args=(), to_sites=None, from_sites=None,
mat = func(ham, args, self.graph, diag, from_sites,
n_by_to_site, to_norb, to_off, from_norb, from_off)
return (mat, to_norb, from_norb) if return_norb else mat
+
+# workaround for Cython functions not having __get__ and
+# Python 3 getting rid of unbound methods
+cdef class HamiltonianSubmatrix:
+
+ def __get__(self, obj, objtype):
+ if obj is None:
+ return hamiltonian_submatrix
+ else:
+ return types.MethodType(hamiltonian_submatrix, obj)
diff --git a/kwant/builder.py b/kwant/builder.py
index c594f7202322e492abfddd78f22f6d85ce09e341..cd83747df7112a8fb35169dd644db138050f5d89 100644
--- a/kwant/builder.py
+++ b/kwant/builder.py
@@ -6,15 +6,13 @@
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
-from __future__ import division
-
__all__ = ['Builder', 'Site', 'SiteFamily', 'SimpleSiteFamily', 'Symmetry',
'HoppingKind', 'Lead', 'BuilderLead', 'SelfEnergyLead', 'ModesLead']
import abc
import warnings
import operator
-from itertools import izip, islice, chain
+from itertools import islice, chain
import tinyarray as ta
import numpy as np
from . import system, graph, KwantDeprecationWarning
@@ -84,7 +82,7 @@ class Site(tuple):
return self.family.pos(self.tag)
-class SiteFamily(object):
+class SiteFamily(object, metaclass=abc.ABCMeta):
"""Abstract base class for site families.
Site families are the 'type' of `Site` objects. Within a family, individual
@@ -107,7 +105,6 @@ class SiteFamily(object):
site belonging to this family with a given tag.
"""
- __metaclass__ = abc.ABCMeta
def __init__(self, canonical_repr, name):
self.canonical_repr = canonical_repr
@@ -224,7 +221,7 @@ def validate_hopping(hopping):
################ Symmetries
-class Symmetry(object):
+class Symmetry(object, metaclass=abc.ABCMeta):
"""Abstract base class for spatial symmetries.
Many physical systems possess a discrete spatial symmetry, which results in
@@ -249,7 +246,6 @@ class Symmetry(object):
typical example of this is when the vector defining a translational
symmetry is not a lattice vector.
"""
- __metaclass__ = abc.ABCMeta
@abc.abstractproperty
def num_directions(self):
@@ -430,7 +426,7 @@ class HermConjOfFunc(object):
################ Leads
-class Lead(object):
+class Lead(object, metaclass=abc.ABCMeta):
"""Abstract base class for leads that can be attached to a `Builder`.
To attach a lead to a builder, append it to the builder's `~Builder.leads`
@@ -442,7 +438,6 @@ class Lead(object):
interface : sequence of sites
"""
- __metaclass__ = abc.ABCMeta
@abc.abstractmethod
def finalized(self):
@@ -567,7 +562,7 @@ def edges(seq):
# izip, when given the same iterator twice, turns a sequence into a
# sequence of pairs.
seq_iter = iter(seq)
- result = izip(seq_iter, seq_iter)
+ result = zip(seq_iter, seq_iter)
next(result) # Skip the special loop edge.
return result
@@ -766,7 +761,7 @@ class Builder(object):
result.H = self.H
return result
- def __nonzero__(self):
+ def __bool__(self):
return bool(self.H)
def expand(self, key):
@@ -974,13 +969,13 @@ class Builder(object):
initially (but always the equivalent ones).
"""
try:
- return self.H.viewkeys()
+ return self.H.keys()
except AttributeError:
return frozenset(self.H)
def site_value_pairs(self):
"""Return an iterator over all (site, value) pairs."""
- for site, hvhv in self.H.iteritems():
+ for site, hvhv in self.H.items():
yield site, hvhv[1]
def hoppings(self):
@@ -990,7 +985,7 @@ class Builder(object):
`Builder` symmetry, and are not necessarily the ones that were set
initially (but always the equivalent ones).
"""
- for tail, hvhv in self.H.iteritems():
+ for tail, hvhv in self.H.items():
for head, value in edges(hvhv):
if value is Other:
continue
@@ -998,7 +993,7 @@ class Builder(object):
def hopping_value_pairs(self):
"""Return an iterator over all (hopping, value) pairs."""
- for tail, hvhv in self.H.iteritems():
+ for tail, hvhv in self.H.items():
for head, value in edges(hvhv):
if value is Other:
continue
@@ -1201,7 +1196,7 @@ class Builder(object):
#### Make graph.
g = graph.Graph()
g.num_nodes = len(sites) # Some sites could not appear in any edge.
- for tail, hvhv in self.H.iteritems():
+ for tail, hvhv in self.H.items():
for head in islice(hvhv, 2, None, 2):
if tail == head:
continue
@@ -1225,7 +1220,7 @@ class Builder(object):
msg = 'When finalizing lead {0}:'.format(lead_nr)
warnings.warn(w.__class__(' '.join((msg,) + w.args)),
stacklevel=3)
- except ValueError, e:
+ except ValueError as e:
# Re-raise the exception with an additional message.
msg = 'Problem finalizing lead {0}:'.format(lead_nr)
e.args = (' '.join((msg,) + e.args),)
diff --git a/kwant/digest.py b/kwant/digest.py
index 8daac5cc6483aad90f12d9788bb75a7235670ec2..0b502d5f2992477ee12d721111a104b0fa481536 100644
--- a/kwant/digest.py
+++ b/kwant/digest.py
@@ -19,8 +19,6 @@ good enough to pass the "dieharder" battery of tests: see the function `test` of
this module.
"""
-from __future__ import division
-
from math import pi, log, sqrt, cos
from hashlib import md5
from struct import unpack
@@ -35,30 +33,22 @@ BPF_MASK = 2**53 - 1
RECIP_BPF = 2**-BPF
-# TODO: Remove the following workaround for Python 2.6 once we do not support it
-# anymore.
-
-if sys.version_info < (2, 7):
- def uniform2(input, salt=''):
- """Return two independent [0,1)-distributed numbers."""
- try:
- input = bytes(buffer(input)) + salt
- except TypeError:
- # Tinyarray does not provide the old buffer protocol, so buffer does
- # not work. However, bytearray does work!
- input = bytearray(input) + salt
- a, b = unpack('qq', md5(input).digest())
- a &= BPF_MASK
- b &= BPF_MASK
- return a * RECIP_BPF, b * RECIP_BPF
-else:
- def uniform2(input, salt=''):
- """Return two independent [0,1)-distributed numbers."""
- input = memoryview(input).tobytes() + salt
- a, b = unpack('qq', md5(input).digest())
- a &= BPF_MASK
- b &= BPF_MASK
- return a * RECIP_BPF, b * RECIP_BPF
+def str_to_bytes(s):
+ """Return bytes if the input is a string, else return the object as-is."""
+ try:
+ return s.encode('utf8')
+ except AttributeError:
+ return s
+
+def uniform2(input, salt=''):
+ """Return two independent [0,1)-distributed numbers."""
+ input = str_to_bytes(input)
+ salt = str_to_bytes(salt)
+ input = memoryview(input).tobytes() + salt
+ a, b = unpack('qq', md5(input).digest())
+ a &= BPF_MASK
+ b &= BPF_MASK
+ return a * RECIP_BPF, b * RECIP_BPF
def uniform(input, salt=''):
@@ -96,8 +86,8 @@ def test(n=20000):
f = tempfile.NamedTemporaryFile(delete=False)
try:
- for x in xrange(n):
- for y in xrange(n):
+ for x in range(n):
+ for y in range(n):
a = array((x, y))
i = int(2**32 * uniform(a))
f.write(pack('I', i))
diff --git a/kwant/graph/__init__.py b/kwant/graph/__init__.py
index dc9463446aae5d3e7152d171442c0ea368838036..2905777027cb8b0672367c507000794e9dde1f1b 100644
--- a/kwant/graph/__init__.py
+++ b/kwant/graph/__init__.py
@@ -11,6 +11,6 @@
# Merge the public interface of all submodules.
__all__ = []
for module in ['core', 'defs', 'slicer', 'utils']:
- exec 'from . import {0}'.format(module)
- exec 'from .{0} import *'.format(module)
- exec '__all__.extend({0}.__all__)'.format(module)
+ exec('from . import {0}'.format(module))
+ exec('from .{0} import *'.format(module))
+ exec('__all__.extend({0}.__all__)'.format(module))
diff --git a/kwant/graph/tests/test_core.py b/kwant/graph/tests/test_core.py
index 967ff6d8ad95043e3515a2d8e6e340f794fa947c..14cdad0ba633b1989a1341450ee82472ba6df86e 100644
--- a/kwant/graph/tests/test_core.py
+++ b/kwant/graph/tests/test_core.py
@@ -6,8 +6,8 @@
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
-from StringIO import StringIO
-from itertools import izip_longest
+from io import StringIO
+from itertools import zip_longest
import numpy as np
from nose.tools import assert_equal, assert_raises
from kwant.graph.core import (Graph, NodeDoesNotExistError,
@@ -41,12 +41,12 @@ def test_num_nodes():
def test_large():
num_edges = 1000
graph = Graph()
- for i in xrange(num_edges):
+ for i in range(num_edges):
graph.add_edge(i, i + 1)
g = graph.compressed()
g2 = graph.compressed(twoway=True)
assert_equal(num_edges, g.num_nodes - 1)
- for i in xrange(num_edges):
+ for i in range(num_edges):
assert_equal(tuple(g.out_neighbors(i)), (i + 1,))
assert_equal(tuple(g2.in_neighbors(i + 1)), (i,))
@@ -71,7 +71,7 @@ def test_small():
check_dot(dot_expect, g)
g = g.compressed(twoway=True)
- for edge_should, edge_is in izip_longest(edges, g):
+ for edge_should, edge_is in zip_longest(edges, g):
assert_equal(edge_should, edge_is)
edge_ids = []
diff --git a/kwant/graph/tests/test_dissection.py b/kwant/graph/tests/test_dissection.py
index cb8fc8f7f1e0209a3eef171b54974fcaeab67516..fb21fe786737a2f784d6d1de09df528ce4dfc1d8 100644
--- a/kwant/graph/tests/test_dissection.py
+++ b/kwant/graph/tests/test_dissection.py
@@ -19,13 +19,13 @@ def _DISABLED_test_edge_dissection():
size = 5
graph = Graph()
- for i in xrange(size - 1):
+ for i in range(size - 1):
offset = i * size
- for j in xrange(size - 1):
+ for j in range(size - 1):
graph.add_edge(offset + j, offset + j + 1)
graph.add_edge(offset + j + 1, offset + j)
if i > 0:
- for j in xrange(size):
+ for j in range(size):
graph.add_edge(offset + j, offset + j - size)
graph.add_edge(offset + j - size, offset + j)
g = graph.compressed()
diff --git a/kwant/graph/tests/test_scotch.py b/kwant/graph/tests/test_scotch.py
index 222ff05f5f9e0b2b1e6a6eaa01c9b217801cc994..2ded31ae2f863eceee4a371b0e2db6a35eb70788 100644
--- a/kwant/graph/tests/test_scotch.py
+++ b/kwant/graph/tests/test_scotch.py
@@ -17,32 +17,32 @@ def _DISABLED_test_bisect():
size = 5
graph = Graph()
- for i in xrange(size-1):
+ for i in range(size - 1):
offset = i * size
- for j in xrange(size-1):
+ for j in range(size - 1):
graph.add_edge(offset + j, offset + j + 1)
graph.add_edge(offset + j + 1, offset + j)
if i > 0:
- for j in xrange(size):
+ for j in range(size):
graph.add_edge(offset + j, offset + j - size)
graph.add_edge(offset + j - size, offset + j)
g = graph.compressed()
parts = bisect(g)
- for i in xrange(g.num_nodes):
+ for i in range(g.num_nodes):
assert_true(parts[i] == 0 or parts[i] == 1)
def _DISABLED_test_reset():
size = 5
graph = Graph()
- for i in xrange(size-1):
+ for i in range(size - 1):
offset = i * size
- for j in xrange(size-1):
+ for j in range(size - 1):
graph.add_edge(offset + j, offset + j + 1)
graph.add_edge(offset + j + 1, offset + j)
if i > 0:
- for j in xrange(size):
+ for j in range(size):
graph.add_edge(offset + j, offset + j - size)
graph.add_edge(offset + j - size, offset + j)
g = graph.compressed()
diff --git a/kwant/graph/tests/test_slicer.py b/kwant/graph/tests/test_slicer.py
index 29e549cbdef4c04e568a6eecbea44e246a046d2d..2191310dbc759c0f64dd8f2ec2224ef5a836a9ad 100644
--- a/kwant/graph/tests/test_slicer.py
+++ b/kwant/graph/tests/test_slicer.py
@@ -11,13 +11,13 @@ from kwant.graph import slicer
def assert_sanity(graph, slices):
# Slices must comprise all of the graph.
- slclist = [slices[j][i] for j in xrange(len(slices))
- for i in xrange(len(slices[j]))]
+ slclist = [slices[j][i] for j in range(len(slices))
+ for i in range(len(slices[j]))]
slclist.sort()
- assert slclist == [i for i in xrange(graph.num_nodes)]
+ assert slclist == [i for i in range(graph.num_nodes)]
# Nodes may only have neighbors in neighboring slices.
- for j in xrange(len(slices)):
+ for j in range(len(slices)):
for node in slices[j]:
for neigh in graph.out_neighbors(node):
if j > 0 and j < len(slices) - 1:
@@ -39,8 +39,8 @@ def test_rectangle():
sys = kwant.Builder()
lead = kwant.Builder(kwant.TranslationalSymmetry((-1, 0)))
lat = kwant.lattice.square()
- lead[(lat(0, i) for i in xrange(w))] = 0
- sys[(lat(j, i) for j in xrange(l) for i in xrange(w))] = 0
+ lead[(lat(0, i) for i in range(w))] = 0
+ sys[(lat(j, i) for j in range(l) for i in range(w))] = 0
for s in [lead, sys]:
for kind in [kwant.builder.HoppingKind((1, 0), lat),
kwant.builder.HoppingKind((0, 1), lat)]:
@@ -57,7 +57,7 @@ def test_rectangle():
# we know that all slices must have the same shape.
assert len(slices) == l
- for j in xrange(l):
+ for j in range(l):
assert len(slices[j]) == w
assert_sanity(fsys.graph, slices)
diff --git a/kwant/graph/tests/test_utils.py b/kwant/graph/tests/test_utils.py
index bea187e5f38344e1407dba3ea277712806eaf67e..0906765e5fd587dfe7fa2345bf06cb44c6dc8748 100644
--- a/kwant/graph/tests/test_utils.py
+++ b/kwant/graph/tests/test_utils.py
@@ -83,7 +83,7 @@ def test_induced_subgraph():
num_nodes = 6
graph = Graph()
- for i in xrange(num_nodes-1):
+ for i in range(num_nodes - 1):
graph.add_edge(i, i + 1)
graph.add_edge(1, 0)
g = graph.compressed()
diff --git a/kwant/lattice.py b/kwant/lattice.py
index 5b55b98890f984aad57944bfc3b1b8bf3d5b580a..e93228980cc7392bcd5f9842f15bae745eb584eb 100644
--- a/kwant/lattice.py
+++ b/kwant/lattice.py
@@ -6,8 +6,6 @@
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
-from __future__ import division
-
__all__ = ['TranslationalSymmetry', 'general', 'Polyatomic', 'Monatomic',
'chain', 'square', 'triangular', 'honeycomb', 'kagome']
@@ -617,7 +615,6 @@ class TranslationalSymmetry(builder.Symmetry):
det_m = int(round(np.linalg.det(m)))
if det_m == 0:
- print m
raise RuntimeError('Adding site family failed.')
det_x_inv_m = np.array(np.round(det_m * np.linalg.inv(m)), dtype=int)
diff --git a/kwant/linalg/__init__.py b/kwant/linalg/__init__.py
index ad60f34fdde3fa5ca390b90a2ea7131204c3c161..cd46cf5aab99934e9c73282c42b1ff3700835433 100644
--- a/kwant/linalg/__init__.py
+++ b/kwant/linalg/__init__.py
@@ -11,6 +11,6 @@ from . import lapack
# Merge the public interface of the other submodules.
for module in ['decomp_lu', 'decomp_ev', 'decomp_schur']:
- exec 'from . import {0}'.format(module)
- exec 'from .{0} import *'.format(module)
- exec '__all__.extend({0}.__all__)'.format(module)
+ exec('from . import {0}'.format(module))
+ exec('from .{0} import *'.format(module))
+ exec('__all__.extend({0}.__all__)'.format(module))
diff --git a/kwant/linalg/decomp_lu.py b/kwant/linalg/decomp_lu.py
index 65bc0fd723ebeb2b2695caf3b09bbae8c007a45d..79accc254feaa53206a9ea2f4a9d977a0d904138 100644
--- a/kwant/linalg/decomp_lu.py
+++ b/kwant/linalg/decomp_lu.py
@@ -61,13 +61,13 @@ def lu_factor(a, overwrite_a=False):
return lapack.cgetrf(a)
-def lu_solve((lu, ipiv, singular), b):
+def lu_solve(matrix_factorization, b):
"""Solve a linear system of equations, a x = b, given the LU
factorization of a
Parameters
----------
- (lu, piv, singular)
+ matrix_factorization
Factorization of the coefficient matrix a, as given by lu_factor
b : array (vector or matrix)
Right-hand side
@@ -77,7 +77,7 @@ def lu_solve((lu, ipiv, singular), b):
x : array (vector or matrix)
Solution to the system
"""
-
+ (lu, ipiv, singular) = matrix_factorization
if singular:
raise RuntimeWarning("In lu_solve: the flag singular indicates "
"a singular matrix. Result of solve step "
@@ -102,7 +102,7 @@ def lu_solve((lu, ipiv, singular), b):
return lapack.cgetrs(lu, ipiv, b)
-def rcond_from_lu((lu, ipiv, singular), norm_a, norm="1"):
+def rcond_from_lu(matrix_factorization, norm_a, norm="1"):
"""Compute the reciprocal condition number from the LU decomposition as
returned from lu_factor(), given additionally the norm of the matrix a in
norm_a.
@@ -112,7 +112,7 @@ def rcond_from_lu((lu, ipiv, singular), norm_a, norm="1"):
Parameters
----------
- (lu, piv, singular)
+ matrix_factorization
Factorization of the matrix a, as given by lu_factor
norm_a : float or complex
norm of the original matrix a (type of norm is specified in norm)
@@ -126,9 +126,10 @@ def rcond_from_lu((lu, ipiv, singular), norm_a, norm="1"):
reciprocal condition number of a with respect to the type of matrix
norm specified in norm
"""
-
+ (lu, ipiv, singular) = matrix_factorization
if not norm in ("1", "I"):
raise ValueError("norm in rcond_from_lu must be either '1' or 'I'")
+ norm = norm.encode('utf8') # lapack expects bytes
ltype, lu = lapack.prepare_for_lapack(False, lu)
diff --git a/kwant/linalg/fortran_helpers.py b/kwant/linalg/fortran_helpers.py
index 2f82b26db9410d919981677692df5b7cfdec7b38..39ec639e606264e8dc14d85e06284c4aa51b86e6 100644
--- a/kwant/linalg/fortran_helpers.py
+++ b/kwant/linalg/fortran_helpers.py
@@ -36,7 +36,7 @@ def prepare_for_fortran(overwrite, *args):
# Make sure we have NumPy arrays
mats = [None]*len(args)
- for i in xrange(len(args)):
+ for i in range(len(args)):
if args[i] is not None:
arr = np.asanyarray(args[i])
if not np.issubdtype(arr.dtype, np.number):
diff --git a/kwant/linalg/lapack.pyx b/kwant/linalg/lapack.pyx
index 5ad31afc254a3b087307b6d1d77b724303487019..da74fbc51b1fc457a21247129c12d07abcc31012 100644
--- a/kwant/linalg/lapack.pyx
+++ b/kwant/linalg/lapack.pyx
@@ -245,7 +245,7 @@ def zgetrs(np.ndarray[np.complex128_t, ndim=2] LU,
# Wrappers for xGECON
def sgecon(np.ndarray[np.float32_t, ndim=2] LU,
- float normA, char *norm = "1"):
+ float normA, char *norm = b"1"):
cdef l_int N, info
cdef float rcond
cdef np.ndarray[np.float32_t, ndim=1] work
@@ -266,7 +266,7 @@ def sgecon(np.ndarray[np.float32_t, ndim=2] LU,
return rcond
def dgecon(np.ndarray[np.float64_t, ndim=2] LU,
- double normA, char *norm = "1"):
+ double normA, char *norm = b"1"):
cdef l_int N, info
cdef double rcond
cdef np.ndarray[np.float64_t, ndim=1] work
@@ -287,7 +287,7 @@ def dgecon(np.ndarray[np.float64_t, ndim=2] LU,
return rcond
def cgecon(np.ndarray[np.complex64_t, ndim=2] LU,
- float normA, char *norm = "1"):
+ float normA, char *norm = b"1"):
cdef l_int N, info
cdef float rcond
cdef np.ndarray[np.complex64_t, ndim=1] work
@@ -308,7 +308,7 @@ def cgecon(np.ndarray[np.complex64_t, ndim=2] LU,
return rcond
def zgecon(np.ndarray[np.complex128_t, ndim=2] LU,
- double normA, char *norm = "1"):
+ double normA, char *norm = b"1"):
cdef l_int N, info
cdef double rcond
cdef np.ndarray[np.complex128_t, ndim=1] work
diff --git a/kwant/linalg/lll.py b/kwant/linalg/lll.py
index 17b353ca11fea6f39487fc527af1ef3636d76ddc..c9f2540fc68056234bc03056ae3f89d862483590 100644
--- a/kwant/linalg/lll.py
+++ b/kwant/linalg/lll.py
@@ -6,13 +6,12 @@
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
-from __future__ import division
-
__all__ = ['lll', 'cvp', 'voronoi']
import numpy as np
from itertools import product
+
def gs_coefficient(a, b):
"""Gram-Schmidt coefficient."""
return np.dot(a, b) / np.linalg.norm(b)**2
diff --git a/kwant/linalg/tests/_test_utils.py b/kwant/linalg/tests/_test_utils.py
index 8f76e8150f5b04ed8ae5435f6065460b4f09bd7c..5ada76379e8b6a42dc5f7ace060213384de5ed90 100644
--- a/kwant/linalg/tests/_test_utils.py
+++ b/kwant/linalg/tests/_test_utils.py
@@ -43,16 +43,16 @@ class _Random:
mat = np.empty((n, m), dtype = dtype)
if issubclass(dtype, np.complexfloating):
- for i in xrange(n):
- for j in xrange(m):
+ for i in range(n):
+ for j in range(m):
mat[i,j] = self._randf() + 1j * self._randf()
elif issubclass(dtype, np.floating):
- for i in xrange(n):
- for j in xrange(m):
+ for i in range(n):
+ for j in range(m):
mat[i,j] = self._randf()
elif issubclass(dtype, np.integer):
- for i in xrange(n):
- for j in xrange(m):
+ for i in range(n):
+ for j in range(m):
mat[i,j] = self._randi()
return mat
@@ -61,13 +61,13 @@ class _Random:
vec = np.empty(n, dtype = dtype)
if issubclass(dtype, np.complexfloating):
- for i in xrange(n):
+ for i in range(n):
vec[i] = self._randf() + 1j * self._randf()
elif issubclass(dtype, np.floating):
- for i in xrange(n):
+ for i in range(n):
vec[i] = self._randf()
elif issubclass(dtype, np.integer):
- for i in xrange(n):
+ for i in range(n):
vec[i] = self._randi()
return vec
diff --git a/kwant/linalg/tests/test_linalg.py b/kwant/linalg/tests/test_linalg.py
index f059580af1545f27123aa30af48ba7fb2740a778..7b70728ced8dae5d91de80c7d32e42aea0a2ceeb 100644
--- a/kwant/linalg/tests/test_linalg.py
+++ b/kwant/linalg/tests/test_linalg.py
@@ -12,7 +12,7 @@ from kwant.linalg import (
convert_r2c_gen_schur, order_gen_schur, evecs_from_gen_schur)
from nose.tools import assert_equal, assert_true
import numpy as np
-from _test_utils import _Random, assert_array_almost_equal
+from ._test_utils import _Random, assert_array_almost_equal
def test_gen_eig():
def _test_gen_eig(dtype):
diff --git a/kwant/linalg/tests/test_lll.py b/kwant/linalg/tests/test_lll.py
index e11627aee7cdd48da595de150a4fc8d3434b7d45..cb04809046d722b061bdd9435c35205f15e00b65 100644
--- a/kwant/linalg/tests/test_lll.py
+++ b/kwant/linalg/tests/test_lll.py
@@ -6,7 +6,7 @@
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
-from __future__ import division
+
import numpy as np
from kwant.linalg import lll
diff --git a/kwant/linalg/tests/test_mumps.py b/kwant/linalg/tests/test_mumps.py
index 8991a7d2c4899e2783d94b0c07a758789709c3e3..bfb5028a75e8937514127bcf221d621bd5fc7c12 100644
--- a/kwant/linalg/tests/test_mumps.py
+++ b/kwant/linalg/tests/test_mumps.py
@@ -17,7 +17,7 @@ from kwant.builder import Builder, HoppingKind
from numpy.testing.decorators import skipif
import numpy as np
import scipy.sparse as sp
-from _test_utils import _Random, assert_array_almost_equal
+from ._test_utils import _Random, assert_array_almost_equal
@skipif(no_mumps)
def test_lu_with_dense():
@@ -53,7 +53,7 @@ def test_schur_complement_with_dense():
def _test_schur_complement_with_dense(dtype):
rand = _Random()
a = rand.randmat(10, 10, dtype)
- s = schur_complement(sp.coo_matrix(a), range(3))
+ s = schur_complement(sp.coo_matrix(a), list(range(3)))
assert_array_almost_equal(dtype, np.linalg.inv(s),
np.linalg.inv(a)[:3, :3])
diff --git a/kwant/physics/__init__.py b/kwant/physics/__init__.py
index 1c463828c1133793242c7a31af708d204ef170eb..10edc954d7d06fb5223c49b57895fa51723dd77b 100644
--- a/kwant/physics/__init__.py
+++ b/kwant/physics/__init__.py
@@ -11,6 +11,6 @@
# Merge the public interface of all submodules.
__all__ = []
for module in ['leads', 'dispersion', 'noise']:
- exec 'from . import {0}'.format(module)
- exec 'from .{0} import *'.format(module)
- exec '__all__.extend({0}.__all__)'.format(module)
+ exec('from . import {0}'.format(module))
+ exec('from .{0} import *'.format(module))
+ exec('__all__.extend({0}.__all__)'.format(module))
diff --git a/kwant/physics/leads.py b/kwant/physics/leads.py
index 586eaaed21ecd620400334a0ffe0351218a74a72..edacd0bfb58110f1fc40cb9d7a4c46ce42350094 100644
--- a/kwant/physics/leads.py
+++ b/kwant/physics/leads.py
@@ -6,10 +6,10 @@
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
-from __future__ import division
+
from math import sin, cos, sqrt, pi, copysign
from collections import namedtuple
-from itertools import izip
+
import numpy as np
import numpy.linalg as npl
import scipy.linalg as la
@@ -434,7 +434,7 @@ def make_proper_modes(lmbdainv, psi, extract, tol=1e6):
if boundaries.shape == (0,) and len(angles):
boundaries = np.array([0, len(angles)])
- for interval in izip(boundaries[:-1], boundaries[1:]):
+ for interval in zip(boundaries[:-1], boundaries[1:]):
if interval[1] > boundaries[0] + len(angles):
break
@@ -661,8 +661,8 @@ def square_selfenergy(width, hopping, fermi_energy):
psi_p_i = np.empty((width, width))
factor = pi / (width + 1)
prefactor = sqrt(2 / (width + 1))
- for p in xrange(width):
- for i in xrange(width):
+ for p in range(width):
+ for i in range(width):
psi_p_i[p, i] = prefactor * sin(factor * (p + 1) * (i + 1))
# Precalculate the integrals of the longitudinal wave functions.
@@ -672,15 +672,15 @@ def square_selfenergy(width, hopping, fermi_energy):
else:
return q/2 - copysign(sqrt((q / 2) ** 2 - 1), q)
f_p = np.empty((width,), dtype=complex)
- for p in xrange(width):
+ for p in range(width):
e = 2 * hopping * (1 - cos(factor * (p + 1)))
q = (fermi_energy - e) / hopping - 2
f_p[p] = f(q)
# Put everything together into the self energy and return it.
result = np.empty((width, width), dtype=complex)
- for i in xrange(width):
- for j in xrange(width):
+ for i in range(width):
+ for j in range(width):
result[i, j] = hopping * (
psi_p_i[:, i] * psi_p_i[:, j].conj() * f_p).sum()
return result
diff --git a/kwant/physics/tests/test_leads.py b/kwant/physics/tests/test_leads.py
index fb7a5b33c7d4866128d5a46a08b958ce96b3313b..15da9dc3d1e92e9e3be7c6065cd7a435b63624db 100644
--- a/kwant/physics/tests/test_leads.py
+++ b/kwant/physics/tests/test_leads.py
@@ -6,9 +6,9 @@
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
-from __future__ import division
+
import numpy as np
-from itertools import product, izip
+from itertools import product
from numpy.testing import assert_almost_equal
from kwant.physics import leads
import kwant
@@ -273,14 +273,14 @@ def test_algorithm_equivalence():
evan_vecs.append(full_vecs[:, 2 * result.nmodes :])
msg = 'Stabilization {0} failed.'
- for vecs, algo in izip(prop_vecs, algos):
+ for vecs, algo in zip(prop_vecs, algos):
# Propagating modes should have identical ordering, and only vary
# By a phase
np.testing.assert_allclose(np.abs(np.sum(vecs/prop_vecs[0],
axis=0)), vecs.shape[0],
err_msg=msg.format(algo))
- for vecs, algo in izip(evan_vecs, algos):
+ for vecs, algo in zip(evan_vecs, algos):
# Evanescent modes must span the same linear space.
assert (np.linalg.matrix_rank(np.c_[vecs, evan_vecs[0]], tol=1e-12) ==
vecs.shape[1]), msg.format(algo)
diff --git a/kwant/plotter.py b/kwant/plotter.py
index 42ba2bfb99fc4d3dbc8b40ae9434c1526bb4f5c9..22bd311c1b4db700653ba67c02f6f278b4834871 100644
--- a/kwant/plotter.py
+++ b/kwant/plotter.py
@@ -69,7 +69,7 @@ if mpl_enabled:
# Collections that allow for symbols and linewiths to be given in data space
# (not for general use, only implement what's needed for plotter)
def isarray(var):
- if hasattr(var, '__getitem__') and not isinstance(var, basestring):
+ if hasattr(var, '__getitem__') and not isinstance(var, str):
return True
else:
return False
@@ -717,18 +717,18 @@ def sys_leads_sites(sys, num_lead_cells=2):
if hasattr(lead, 'builder') and len(lead.interface):
sites.extend(((site, leadnr, i) for site in
lead.builder.sites() for i in
- xrange(num_lead_cells)))
+ range(num_lead_cells)))
lead_cells.append(slice(start, len(sites)))
elif isinstance(sys, system.FiniteSystem):
- sites = [(i, None, 0) for i in xrange(sys.graph.num_nodes)]
+ sites = [(i, None, 0) for i in range(sys.graph.num_nodes)]
for leadnr, lead in enumerate(sys.leads):
start = len(sites)
# We will only plot leads with a graph and with a symmetry.
if (hasattr(lead, 'graph') and hasattr(lead, 'symmetry') and
len(sys.lead_interfaces[leadnr])):
sites.extend(((site, leadnr, i) for site in
- xrange(lead.cell_size) for i in
- xrange(num_lead_cells)))
+ range(lead.cell_size) for i in
+ range(num_lead_cells)))
lead_cells.append(slice(start, len(sites)))
else:
raise TypeError('Unrecognized system type.')
@@ -796,10 +796,10 @@ def sys_leads_pos(sys, site_lead_nr):
# Conversion to numpy array here useful for efficiency
vec = np.array(sym.periods)[0]
return vec, dom
- vecs_doms = dict((i, get_vec_domain(i)) for i in xrange(len(sys.leads)))
+ vecs_doms = dict((i, get_vec_domain(i)) for i in range(len(sys.leads)))
vecs_doms[None] = np.zeros((dim,)), 0
- for k, v in vecs_doms.iteritems():
- vecs_doms[k] = [v[0] * i for i in xrange(v[1], v[1] + num_lead_cells)]
+ for k, v in vecs_doms.items():
+ vecs_doms[k] = [v[0] * i for i in range(v[1], v[1] + num_lead_cells)]
pos += [vecs_doms[i[1]][i[2]] for i in site_lead_nr]
return pos
@@ -856,11 +856,11 @@ def sys_leads_hoppings(sys, num_lead_cells=2):
if hasattr(lead, 'builder') and len(lead.interface):
hoppings.extend(((hop, leadnr, i) for hop in
lead_hoppings(lead.builder) for i in
- xrange(num_lead_cells)))
+ range(num_lead_cells)))
lead_cells.append(slice(start, len(hoppings)))
elif isinstance(sys, system.System):
def ll_hoppings(sys):
- for i in xrange(sys.graph.num_nodes):
+ for i in range(sys.graph.num_nodes):
for j in sys.graph.out_neighbors(i):
if i < j:
yield i, j
@@ -872,7 +872,7 @@ def sys_leads_hoppings(sys, num_lead_cells=2):
if (hasattr(lead, 'graph') and hasattr(lead, 'symmetry') and
len(sys.lead_interfaces[leadnr])):
hoppings.extend(((hop, leadnr, i) for hop in ll_hoppings(lead)
- for i in xrange(num_lead_cells)))
+ for i in range(num_lead_cells)))
lead_cells.append(slice(start, len(hoppings)))
else:
raise TypeError('Unrecognized system type.')
@@ -942,12 +942,12 @@ def sys_leads_hopping_pos(sys, hop_lead_nr):
vec = np.array(sym.periods)[0]
return np.r_[vec, vec], dom
- vecs_doms = dict((i, get_vec_domain(i)) for i in xrange(len(sys.leads)))
+ vecs_doms = dict((i, get_vec_domain(i)) for i in range(len(sys.leads)))
vecs_doms[None] = np.zeros((dim,)), 0
- for k, v in vecs_doms.iteritems():
- vecs_doms[k] = [v[0] * i for i in xrange(v[1], v[1] + num_lead_cells)]
+ for k, v in vecs_doms.items():
+ vecs_doms[k] = [v[0] * i for i in range(v[1], v[1] + num_lead_cells)]
pos += [vecs_doms[i[1]][i[2]] for i in hop_lead_nr]
- return np.copy(pos[:, : dim / 2]), np.copy(pos[:, dim / 2:])
+ return np.copy(pos[:, : dim // 2]), np.copy(pos[:, dim // 2:])
# Useful plot functions (to be extended).
@@ -1136,7 +1136,7 @@ def plot(sys, num_lead_cells=2, unit='nn',
if name in ('site_size', 'site_lw') and isinstance(value, tuple):
raise TypeError('{0} may not be a tuple, use list or '
'array instead.'.format(name))
- if isinstance(value, (basestring, tuple)):
+ if isinstance(value, (str, tuple)):
return
try:
if len(value) != n_sys_sites:
@@ -1226,7 +1226,7 @@ def plot(sys, num_lead_cells=2, unit='nn',
for i, symbol in enumerate(site_symbol):
symbol_dict[symbol].append(i)
symbol_slcs = []
- for symbol, indx in symbol_dict.iteritems():
+ for symbol, indx in symbol_dict.items():
symbol_slcs.append((symbol, np.array(indx)))
fancy_indexing = True
else:
@@ -1285,7 +1285,7 @@ def plot(sys, num_lead_cells=2, unit='nn',
else defaults['hop_lw'][dim])
hop_cmap = None
- if not isinstance(cmap, basestring):
+ if not isinstance(cmap, str):
try:
cmap, hop_cmap = cmap
except TypeError:
diff --git a/kwant/rmt.py b/kwant/rmt.py
index cff30d4fc381884c6092f410d42bc723e5ace17a..6442fc0a90e220277086f35a9a07576f327e4299 100644
--- a/kwant/rmt.py
+++ b/kwant/rmt.py
@@ -6,8 +6,6 @@
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
-from __future__ import division
-
__all__ = ['gaussian', 'circular']
import numpy as np
diff --git a/kwant/solvers/common.py b/kwant/solvers/common.py
index d74a9473a225c6d2b41ab2c6d5cf481047931c22..0d59ce553d97f0620b9e2425565e7e91c7acf1b1 100644
--- a/kwant/solvers/common.py
+++ b/kwant/solvers/common.py
@@ -15,6 +15,7 @@ import numpy as np
import scipy.sparse as sp
from .._common import ensure_isinstance
from .. import system
+from functools import reduce
# Currently, scipy.sparse does not support matrices with one dimension being
# zero: http://projects.scipy.org/scipy/ticket/1602 We use NumPy dense matrices
@@ -28,7 +29,7 @@ from .. import system
LinearSys = namedtuple('LinearSys', ['lhs', 'rhs', 'indices', 'num_orb'])
-class SparseSolver(object):
+class SparseSolver(object, metaclass=abc.ABCMeta):
"""Solver class for computing physical quantities based on solving
a liner system of equations.
@@ -51,7 +52,6 @@ class SparseSolver(object):
too avoid excessive memory usage, but for some solvers not too small for
performance reasons.
"""
- __metaclass__ = abc.ABCMeta
@abc.abstractmethod
def _factorized(self, a):
@@ -333,11 +333,11 @@ class SparseSolver(object):
n = len(sys.lead_interfaces)
if in_leads is None:
- in_leads = range(n)
+ in_leads = list(range(n))
else:
in_leads = list(in_leads)
if out_leads is None:
- out_leads = range(n)
+ out_leads = list(range(n))
else:
out_leads = list(out_leads)
if (np.any(np.diff(in_leads) <= 0) or np.any(np.diff(out_leads) <= 0)):
@@ -420,11 +420,11 @@ class SparseSolver(object):
n = len(sys.lead_interfaces)
if in_leads is None:
- in_leads = range(n)
+ in_leads = list(range(n))
else:
in_leads = list(in_leads)
if out_leads is None:
- out_leads = range(n)
+ out_leads = list(range(n))
else:
out_leads = list(out_leads)
if (np.any(np.diff(in_leads) <= 0) or np.any(np.diff(out_leads) <= 0)):
@@ -489,7 +489,7 @@ class SparseSolver(object):
raise NotImplementedError("ldos for leads with only "
"self-energy is not implemented yet.")
- linsys = self._make_linear_sys(sys, xrange(len(sys.leads)), energy,
+ linsys = self._make_linear_sys(sys, range(len(sys.leads)), energy,
args, check_hermiticity)[0]
ldos = np.zeros(linsys.num_orb, float)
@@ -503,7 +503,7 @@ class SparseSolver(object):
# See comment about zero-shaped sparse matrices at the top of common.py.
rhs = sp.bmat([[i for i in linsys.rhs if i.shape[1]]],
format=self.rhsformat)
- for j in xrange(0, rhs.shape[1], self.nrhs):
+ for j in range(0, rhs.shape[1], self.nrhs):
jend = min(j + self.nrhs, rhs.shape[1])
psi = self._solve_linear_sys(factored, rhs[:, j:jend],
slice(linsys.num_orb))
@@ -555,7 +555,7 @@ class WaveFunction(object):
msg = ('Wave functions for leads with only self-energy'
' are not available yet.')
raise NotImplementedError(msg)
- linsys = solver._make_linear_sys(sys, xrange(len(sys.leads)), energy,
+ linsys = solver._make_linear_sys(sys, range(len(sys.leads)), energy,
args, check_hermiticity)[0]
self.solve = solver._solve_linear_sys
self.rhs = linsys.rhs
@@ -568,11 +568,10 @@ class WaveFunction(object):
return result.transpose()
-class BlockResult(object):
+class BlockResult(object, metaclass=abc.ABCMeta):
"""
ABC for a linear system solution with variable grouping.
"""
- __metaclass__ = abc.ABCMeta
def __init__(self, data, lead_info, out_leads, in_leads, sizes,
current_conserving=False):
@@ -676,7 +675,7 @@ class BlockResult(object):
Section 2.4 of the book by S. Datta.
"""
n = len(self.lead_info)
- rn = xrange(n)
+ rn = range(n)
result = np.array([[-self.transmission(i, j) if i != j else 0
for j in rn] for i in rn])
# Set the diagonal elements such that the sums of columns are zero.
diff --git a/kwant/solvers/mumps.py b/kwant/solvers/mumps.py
index fc4b0e8a14f12b96dc320c6a81094e28c81891c1..f0b9ac0c5286e462dff87ca48c15e52efd6bfdcf 100644
--- a/kwant/solvers/mumps.py
+++ b/kwant/solvers/mumps.py
@@ -84,14 +84,14 @@ class Solver(common.SparseSolver):
self.nrhs = nrhs
if ordering is not None:
- if ordering not in mumps.orderings.keys() + ['kwant_decides']:
- raise ValueError("Invalid ordering: " + ordering)
if ordering == 'kwant_decides':
# Choose what is considered to be the best ordering.
sorted_orderings = [order
for order in ['metis', 'scotch', 'auto']
if order in mumps.possible_orderings()]
ordering = sorted_orderings[0]
+ elif ordering not in mumps.orderings:
+ raise ValueError("Invalid ordering: " + ordering)
self.ordering = ordering
if sparse_rhs is not None:
@@ -111,7 +111,7 @@ class Solver(common.SparseSolver):
solve = factorized_a.solve
sols = []
- for j in xrange(0, b.shape[1], self.nrhs):
+ for j in range(0, b.shape[1], self.nrhs):
tmprhs = b[:, j:min(j + self.nrhs, b.shape[1])]
if not self.sparse_rhs:
diff --git a/kwant/solvers/sparse.py b/kwant/solvers/sparse.py
index 044ebc269bab15677e4d89d786469ef5e7a7f3e0..69f9a3a83534eb37885c6488d543c35edcaa55fc 100644
--- a/kwant/solvers/sparse.py
+++ b/kwant/solvers/sparse.py
@@ -110,7 +110,7 @@ class Solver(common.SparseSolver):
sols = []
vec = np.empty(b.shape[0], complex)
- for j in xrange(b.shape[1]):
+ for j in range(b.shape[1]):
vec[:] = b[:, j].todense().flatten()
sols.append(factorized_a(vec)[kept_vars])
diff --git a/kwant/solvers/tests/_test_sparse.py b/kwant/solvers/tests/_test_sparse.py
index 5eaa20b1d4af9b2e131efe5e29d5eca2fc5514f6..3c26d263be9fae52e85fba704318e91331bf5130 100644
--- a/kwant/solvers/tests/_test_sparse.py
+++ b/kwant/solvers/tests/_test_sparse.py
@@ -6,7 +6,7 @@
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
-from __future__ import division
+
from math import cos, sin
import numpy as np
from nose.tools import assert_raises
@@ -263,18 +263,18 @@ def test_tricky_singular_hopping(smatrix):
lead = kwant.Builder(kwant.TranslationalSymmetry((4, 0)))
interface = []
- for i in xrange(n):
+ for i in range(n):
site = sq(-1, i)
interface.append(site)
system[site] = 0
- for j in xrange(4):
+ for j in range(4):
lead[sq(j, i)] = 0
- for i in xrange(n-1):
+ for i in range(n-1):
system[sq(-1, i), sq(-1, i+1)] = -1
- for j in xrange(4):
+ for j in range(4):
lead[sq(j, i), sq(j, i+1)] = -1
- for i in xrange(n):
- for j in xrange(4):
+ for i in range(n):
+ for j in range(4):
lead[sq(j, i), sq(j+1, i)] = -1
del lead[sq(1, 0), sq(2, 0)]
@@ -300,10 +300,10 @@ def test_many_leads(*factories):
# Build a square system with four leads and a hole in the center.
sys = kwant.Builder()
- sys[(sq(x, y) for x in xrange(-4, 4) for y in xrange(-4, 4)
+ sys[(sq(x, y) for x in range(-4, 4) for y in range(-4, 4)
if x**2 + y**2 >= 2)] = 3
sys[sq.neighbors()] = phase
- for r in [xrange(-4, -1), xrange(4)]:
+ for r in [range(-4, -1), range(4)]:
lead = kwant.Builder(kwant.TranslationalSymmetry([-1, 0]))
lead[(sq(0, y) for y in r)] = 4
lead[sq.neighbors()] = phase
@@ -311,7 +311,7 @@ def test_many_leads(*factories):
sys.attach_lead(lead.reversed())
sys = sys.finalized()
- r4 = range(4)
+ r4 = list(range(4))
br = factories[0](sys, E, out_leads=r4, in_leads=r4)
trans = np.array([[br._transmission(i, j) for j in r4] for i in r4])
cmat = br.conductance_matrix()
@@ -480,7 +480,7 @@ def test_wavefunc_ldos_consistency(wave_function, ldos):
for energy in [0, 1000]:
wf = wave_function(sys, energy)
ldos2 = np.zeros(wf.num_orb, float)
- for lead in xrange(len(sys.leads)):
+ for lead in range(len(sys.leads)):
temp = abs(wf(lead))
temp **= 2
ldos2 += temp.sum(axis=0)
diff --git a/kwant/solvers/tests/test_mumps.py b/kwant/solvers/tests/test_mumps.py
index a185a04c64f63b862ddb7de9827177fd3221a2d8..e07aa120162d69304f405eaeef9443ff60a050fd 100644
--- a/kwant/solvers/tests/test_mumps.py
+++ b/kwant/solvers/tests/test_mumps.py
@@ -11,7 +11,7 @@ from numpy.testing.decorators import skipif
try:
from kwant.solvers.mumps import (
smatrix, greens_function, ldos, wave_function, options, reset_options)
- import _test_sparse
+ from . import _test_sparse
no_mumps = False
except ImportError:
no_mumps = True
diff --git a/kwant/solvers/tests/test_sparse.py b/kwant/solvers/tests/test_sparse.py
index c9920f9d8acd42f9bbd162788ea9cef9a30e429a..f93d7771f9c88f3d287539dec47f647e4f32f7e7 100644
--- a/kwant/solvers/tests/test_sparse.py
+++ b/kwant/solvers/tests/test_sparse.py
@@ -9,7 +9,7 @@
from nose.plugins.skip import SkipTest
from kwant.solvers.sparse import smatrix, greens_function, ldos, wave_function
import kwant.solvers.sparse
-import _test_sparse
+from . import _test_sparse
def test_output():
_test_sparse.test_output(smatrix)
diff --git a/kwant/system.py b/kwant/system.py
index a323eebe4f36882c746d336e6735f02e1f11cf0c..ca541b4ad9c832d3971b75fe61afe707b7e27230 100644
--- a/kwant/system.py
+++ b/kwant/system.py
@@ -8,7 +8,6 @@
"""Low-level interface of systems"""
-from __future__ import division
__all__ = ['System', 'FiniteSystem', 'InfiniteSystem']
import abc
@@ -17,7 +16,7 @@ from copy import copy
from . import _system
-class System(object):
+class System(object, metaclass=abc.ABCMeta):
"""Abstract general low-level system.
Attributes
@@ -33,7 +32,6 @@ class System(object):
Optionally, a class derived from `System` can provide a method `pos` which
is assumed to return the real-space position of a site given its index.
"""
- __metaclass__ = abc.ABCMeta
@abc.abstractmethod
def hamiltonian(self, i, j, *args):
@@ -49,11 +47,10 @@ class System(object):
pass
# Add a C-implemented function as an unbound method to class System.
-System.hamiltonian_submatrix = types.MethodType(
- _system.hamiltonian_submatrix, None, System)
+System.hamiltonian_submatrix = _system.HamiltonianSubmatrix()
-class FiniteSystem(System):
+class FiniteSystem(System, metaclass=abc.ABCMeta):
"""Abstract finite low-level system, possibly with leads.
Attributes
@@ -80,7 +77,6 @@ class FiniteSystem(System):
the first ``len(lead_interfaces[n])`` sites of the InfiniteSystem.
"""
- __metaclass__ = abc.ABCMeta
def precalculate(self, energy=0, args=(), leads=None,
what='modes'):
@@ -123,7 +119,7 @@ class FiniteSystem(System):
result = copy(self)
if leads is None:
- leads = range(len(self.leads))
+ leads = list(range(len(self.leads)))
new_leads = []
for nr, lead in enumerate(self.leads):
if nr not in leads:
@@ -141,7 +137,7 @@ class FiniteSystem(System):
result.leads = new_leads
return result
-class InfiniteSystem(System):
+class InfiniteSystem(System, metaclass=abc.ABCMeta):
"""
Abstract infinite low-level system.
@@ -183,18 +179,17 @@ class InfiniteSystem(System):
infinite system. The other scheme has the numbers of site 0 and 1
exchanged, as well as of site 3 and 4.
"""
- __metaclass__ = abc.ABCMeta
def cell_hamiltonian(self, args=(), sparse=False):
"""Hamiltonian of a single cell of the infinite system."""
- cell_sites = xrange(self.cell_size)
+ cell_sites = range(self.cell_size)
return self.hamiltonian_submatrix(args, cell_sites, cell_sites,
sparse=sparse)
def inter_cell_hopping(self, args=(), sparse=False):
"""Hopping Hamiltonian between two cells of the infinite system."""
- cell_sites = xrange(self.cell_size)
- interface_sites = xrange(self.cell_size, self.graph.num_nodes)
+ cell_sites = range(self.cell_size)
+ interface_sites = range(self.cell_size, self.graph.num_nodes)
return self.hamiltonian_submatrix(args, cell_sites, interface_sites,
sparse=sparse)
diff --git a/kwant/tests/test_builder.py b/kwant/tests/test_builder.py
index d60d0884e4ac06c54cbaef9b68ed6331b6327a86..11b95c4b3be0d1e0572ffee7f65d5eb8892a60f2 100644
--- a/kwant/tests/test_builder.py
+++ b/kwant/tests/test_builder.py
@@ -6,7 +6,6 @@
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
-from __future__ import division
import warnings
from random import Random
from nose.tools import assert_raises
@@ -84,7 +83,7 @@ def test_bad_keys():
try:
assert_raises(error, func, key)
except AssertionError:
- print func, error, key
+ print(func, error, key)
raise
@@ -259,14 +258,14 @@ def random_hopping_integral(rng):
def check_onsite(fsys, sites, subset=False, check_values=True):
freq = {}
- for node in xrange(fsys.graph.num_nodes):
+ for node in range(fsys.graph.num_nodes):
site = fsys.sites[node].tag
freq[site] = freq.get(site, 0) + 1
if check_values and site in sites:
assert fsys.onsite_hamiltonians[node] is sites[site]
if not subset:
# Check that all sites of `fsys` are in `sites`.
- for site in freq.iterkeys():
+ for site in freq.keys():
assert site in sites
# Check that all sites of `sites` are in `fsys`.
for site in sites:
@@ -302,7 +301,7 @@ def test_finalization():
def set_hops(dest, sites):
while len(dest) < n_hops:
- a, b = rng.sample(sites, 2)
+ a, b = rng.sample(list(sites), 2)
if (a, b) not in dest and (b, a) not in dest:
dest[a, b] = random_hopping_integral(rng)
@@ -327,7 +326,7 @@ def test_finalization():
set_hops(lead_hops, lead_sites)
lead_sites_list = list(lead_sites)
neighbors = set()
- for i in xrange(n_hops):
+ for i in range(n_hops):
while True:
a = rng.choice(lead_sites_list)
b = rng.choice(possible_neighbors)
@@ -343,9 +342,9 @@ def test_finalization():
# Build scattering region from blueprint and test it.
sys = builder.Builder()
fam = kwant.lattice.general(ta.identity(2))
- for site, value in sr_sites.iteritems():
+ for site, value in sr_sites.items():
sys[fam(*site)] = value
- for hop, value in sr_hops.iteritems():
+ for hop, value in sr_hops.items():
sys[fam(*hop[0]), fam(*hop[1])] = value
fsys = sys.finalized()
check_onsite(fsys, sr_sites)
@@ -353,7 +352,7 @@ def test_finalization():
# Build lead from blueprint and test it.
lead = builder.Builder(kwant.TranslationalSymmetry((size, 0)))
- for site, value in lead_sites.iteritems():
+ for site, value in lead_sites.items():
shift = rng.randrange(-5, 6) * size
site = site[0] + shift, site[1]
lead[fam(*site)] = value
@@ -363,7 +362,7 @@ def test_finalization():
assert_equal(len(w), 1)
assert issubclass(w[0].category, RuntimeWarning)
assert "disconnected" in str(w[0].message)
- for (a, b), value in lead_hops.iteritems():
+ for (a, b), value in lead_hops.items():
shift = rng.randrange(-5, 6) * size
a = a[0] + shift, a[1]
b = b[0] + shift, b[1]
@@ -645,21 +644,21 @@ def test_ModesLead_and_SelfEnergyLead():
energies = [0.9, 1.7]
sys = builder.Builder()
- for x in xrange(L):
- for y in xrange(L):
+ for x in range(L):
+ for y in range(L):
sys[lat(x, y)] = 4 * t + rng.random() - 0.5
sys[hoppings] = -t
# Attach a lead from the left.
lead = builder.Builder(VerySimpleSymmetry(-1))
- for y in xrange(L):
+ for y in range(L):
lead[lat(0, y)] = 4 * t
lead[hoppings] = -t
sys.attach_lead(lead)
# Make the right lead and attach it.
lead = builder.Builder(VerySimpleSymmetry(1))
- for y in xrange(L):
+ for y in range(L):
lead[lat(0, y)] = 4 * t
lead[hoppings] = -t
sys.attach_lead(lead)
@@ -669,7 +668,7 @@ def test_ModesLead_and_SelfEnergyLead():
# Replace lead with it's finalized copy.
lead = fsys.leads[1]
- interface = [lat(L-1, lead.sites[i].tag[1]) for i in xrange(L)]
+ interface = [lat(L-1, lead.sites[i].tag[1]) for i in range(L)]
# Re-attach right lead as ModesLead.
sys.leads[1] = builder.ModesLead(lead.modes, interface)
diff --git a/kwant/tests/test_lattice.py b/kwant/tests/test_lattice.py
index 5b389d370d80289c724ec83c8d1b02389f5e579a..f2169863a75a48aa91fc6c7c2d3229433fec08ba 100644
--- a/kwant/tests/test_lattice.py
+++ b/kwant/tests/test_lattice.py
@@ -6,7 +6,6 @@
# the file AUTHORS.rst at the top-level directory of this distribution and at
# http://kwant-project.org/authors.
-from __future__ import division
from math import sqrt
import numpy as np
import tinyarray as ta
@@ -63,15 +62,15 @@ def test_shape():
sites = list(lat.shape(in_circle, (0, 0))())
sites_alt = list()
sl0, sl1 = lat.sublattices
- for x in xrange(-2, 3):
- for y in xrange(-2, 3):
+ for x in range(-2, 3):
+ for y in range(-2, 3):
tag = (x, y)
for site in (sl0(*tag), sl1(*tag)):
if in_circle(site.pos):
sites_alt.append(site)
assert len(sites) == len(sites_alt)
assert_equal(set(sites), set(sites_alt))
- assert_raises(ValueError, lat.shape(in_circle, (10, 10))().next)
+ assert_raises(ValueError, lat.shape(in_circle, (10, 10))().__next__)
# Check if narrow ribbons work.
for period in (0, 1), (1, 0), (1, -1):
diff --git a/kwant/tests/test_plotter.py b/kwant/tests/test_plotter.py
index d3074b0cb99e46690ed15f84cb18ba1e5ef51a05..e34d1aeb14c7d647817850eb30e408ca94e0e806 100644
--- a/kwant/tests/test_plotter.py
+++ b/kwant/tests/test_plotter.py
@@ -31,7 +31,7 @@ def test_importable_without_matplotlib():
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
- exec code # Trigger the warning.
+ exec(code) # Trigger the warning.
nose.tools.assert_equal(len(w), 1)
assert issubclass(w[0].category, RuntimeWarning)
assert "only iterator-providing functions" in str(w[0].message)
@@ -103,7 +103,7 @@ def test_plot():
for sys in (sys2d, sys3d):
fig = plot(sys, site_color=color, cmap='binary', file=out)
if (color != 'k' and
- isinstance(color(iter(sys2d.sites()).next()), float)):
+ isinstance(color(next(iter(sys2d.sites()))), float)):
assert fig.axes[0].collections[0].get_array() is not None
assert len(fig.axes[0].collections) == (8 if sys is sys2d else
6)
@@ -114,7 +114,7 @@ def test_plot():
for sys in (sys2d, sys3d):
fig = plot(sys2d, hop_color=color, cmap='binary', file=out,
fig_size=(2, 10), dpi=30)
- if color != 'k' and isinstance(color(iter(sys2d.sites()).next(),
+ if color != 'k' and isinstance(color(next(iter(sys2d.sites())),
None), float):
assert fig.axes[0].collections[1].get_array() is not None
@@ -150,10 +150,10 @@ def test_map():
pos_transform=bad_transform, file=out)
with warnings.catch_warnings():
warnings.simplefilter("ignore")
- plotter.map(sys.finalized(), xrange(len(sys.sites())),
+ plotter.map(sys.finalized(), range(len(sys.sites())),
file=out)
nose.tools.assert_raises(ValueError, plotter.map, sys,
- xrange(len(sys.sites())), file=out)
+ range(len(sys.sites())), file=out)
def test_mask_interpolate():
diff --git a/kwant/tests/test_system.py b/kwant/tests/test_system.py
index 29af26c2eb6e6043141536fe3605777af84a5a7f..3eb1e15b6100364bd27ff5d6712a35bb9dd010a4 100644
--- a/kwant/tests/test_system.py
+++ b/kwant/tests/test_system.py
@@ -14,9 +14,9 @@ import kwant
def test_hamiltonian_submatrix():
sys = kwant.Builder()
chain = kwant.lattice.chain()
- for i in xrange(3):
+ for i in range(3):
sys[chain(i)] = 0.5 * i
- for i in xrange(2):
+ for i in range(2):
sys[chain(i), chain(i + 1)] = 1j * (i + 1)
sys2 = sys.finalized()
@@ -87,8 +87,8 @@ def test_hamiltonian_submatrix():
return p1 - p2
sys = kwant.Builder()
- sys[(chain(i) for i in xrange(3))] = onsite
- sys[((chain(i), chain(i + 1)) for i in xrange(2))] = hopping
+ sys[(chain(i) for i in range(3))] = onsite
+ sys[((chain(i), chain(i + 1)) for i in range(2))] = hopping
sys2 = sys.finalized()
mat = sys2.hamiltonian_submatrix((2, 1))
mat_should_be = [[3, 1, 0], [1, 4, 1], [0, 1, 5]]
diff --git a/setup.py b/setup.py
index 3b884b97e239eedb01950de25217d13d3deb39f4..2d14a51675cd70641d6fe87a7ef2e806a6282b02 100755
--- a/setup.py
+++ b/setup.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
# Copyright 2011-2015 Kwant authors.
#
@@ -16,7 +16,7 @@ import os
import glob
import imp
import subprocess
-import ConfigParser
+import configparser
from setuptools import setup, find_packages, Extension, Command
from sysconfig import get_platform
from distutils.errors import DistutilsError, DistutilsModuleError, \
@@ -42,16 +42,23 @@ CYTHON_OPTION = '--cython'
TUT_DIR = 'tutorial'
TUT_GLOB = 'doc/source/tutorial/*.py'
TUT_HIDDEN_PREFIX = '#HIDDEN'
+CLASSIFIERS = """\
+ Development Status :: 5 - Production/Stable
+ Intended Audience :: Science/Research
+ Intended Audience :: Developers
+ Programming Language :: Python :: 3 :: Only
+ Topic :: Software Development
+ Topic :: Scientific/Engineering
+ Operating System :: POSIX
+ Operating System :: Unix
+ Operating System :: MacOS :: MacOS X
+ Operating System :: Microsoft :: Windows"""
+
# Let Kwant itself determine its own version. We cannot simply import kwant, as
# it is not built yet.
_dont_write_bytecode_saved = sys.dont_write_bytecode
sys.dont_write_bytecode = True
-try:
- imp.load_source(STATIC_VERSION_PATH[-1].split('.')[0],
- os.path.join(*STATIC_VERSION_PATH))
-except IOError:
- pass
_common = imp.load_source('_common', 'kwant/_common.py')
sys.dont_write_bytecode = _dont_write_bytecode_saved
@@ -166,7 +173,7 @@ def git_lsfiles():
if p.wait() != 0:
return
- return p.communicate()[0].split('\n')[:-1]
+ return p.communicate()[0].decode().split('\n')[:-1]
# Make the command "sdist" depend on "build". This verifies that the
@@ -263,7 +270,7 @@ def search_mumps():
except OSError:
pass
else:
- p.communicate(input='int main() {}\n')
+ p.communicate(input=b'int main() {}\n')
if p.wait() == 0:
return {'libraries': libs}
return {}
@@ -297,7 +304,7 @@ def extensions():
'kwant/graph/c_slicer/slicer.h']})]
#### Add components of Kwant with external compile-time dependencies.
- config = ConfigParser.ConfigParser()
+ config = configparser.ConfigParser()
try:
with open(CONFIG_FILE) as f:
config.readfp(f)
@@ -334,7 +341,7 @@ def extensions():
if kwrds:
build_summary.append('Auto-configured MUMPS')
if kwrds:
- for name, value in lapack.iteritems():
+ for name, value in lapack.items():
kwrds.setdefault(name, []).extend(value)
kwrds.setdefault('depends', []).extend(
[CONFIG_FILE, 'kwant/linalg/cmumps.pxd'])
@@ -467,7 +474,8 @@ def main():
include_dirs=include_dirs,
setup_requires=['numpy > 1.6.1', 'nose >= 1.0'],
install_requires=['numpy > 1.6.1', 'scipy >= 0.9', 'tinyarray'],
- extras_require={'plotting': 'matplotlib >= 1.2'})
+ extras_require={'plotting': 'matplotlib >= 1.2'},
+ classifiers=[c.strip() for c in CLASSIFIERS.split('\n')])
if __name__ == '__main__':
main()