doc/source/_static/mathconf.js

+MathJax.Hub.Config({
+    TeX: {
+        Macros: {
+            bra: ['{\\left\\langle #1\\right|}',1],
+            ket: ['{\\left| #1\\right\\rangle}',1],
+            braket: ['\\left\\langle#1|#2\\right\\rangle', 2],
+            ri: '\\text{i}',
+            rd: '\\text{d}'
+        }
+    }
+});

doc/source/_static/sidebar.js

@@ -97,9 +97,9 @@ $(function() {
     // find the height of the viewport to center the '<<' in the page
     var viewport_height;
     if (window.innerHeight)
- 	  viewport_height = window.innerHeight;
+      viewport_height = window.innerHeight;
     else
-	  viewport_height = $(window).height();
+      viewport_height = $(window).height();
     var sidebar_offset = sidebar.offset().top;
     var sidebar_height = Math.max(bodywrapper.height(), sidebar.height());
     sidebarbutton.find('span').css({

doc/source/conf.py

@@ -11,12 +11,23 @@
 # All configuration values have a default; values that are commented out
 # serve to show the default.
 
-import sys, os
-
+import sys
+import os
+import string
 from distutils.util import get_platform
-sys.path.insert(0, "../../build/lib.{0}-{1}.{2}".format(
-        get_platform(), *sys.version_info[:2]))
+
+package_path = os.path.abspath(
+    "../../build/lib.{0}-{1}.{2}"
+    .format(get_platform(), *sys.version_info[:2]))
+
+# Insert into sys.path so that we can import kwant here
+sys.path.insert(0, package_path)
+# Insert into PYTHONPATH so that jupyter-sphinx will pick it up
+os.environ['PYTHONPATH'] = ':'.join((package_path, os.environ.get('PYTHONPATH','')))
+
 import kwant
+import kwant.qsymm
+import kwant.continuum  # sphinx gets confused with lazy loading
 
 # -- General configuration -----------------------------------------------------
 
@@ -26,8 +37,9 @@ import kwant
 sys.path.insert(0, os.path.abspath('../sphinxext'))
 
 extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary',
-              'sphinx.ext.todo', 'sphinx.ext.pngmath', 'numpydoc',
-              'kwantdoc']
+              'sphinx.ext.todo', 'sphinx.ext.mathjax', 'sphinx.ext.napoleon',
+              'sphinx.ext.linkcode', 'jupyter_sphinx', 'sphinx_togglebutton',
+              'sphinxcontrib.rsvgconverter']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['../templates']
@@ -42,8 +54,8 @@ source_suffix = '.rst'
 master_doc = 'index'
 
 # General information about the project.
-project = u'Kwant'
-copyright = u'2011-2013, C. W. Groth (CEA), M. Wimmer, A. R. Akhmerov, X. Waintal (CEA), and others'
+project = 'Kwant'
+copyright = '2011-2017, 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
@@ -52,12 +64,8 @@ copyright = u'2011-2013, C. W. Groth (CEA), M. Wimmer, A. R. Akhmerov, X. Wainta
 # The full version, including alpha/beta/rc tags.
 release = kwant.__version__
 
-for i, s in enumerate(release):
-    if s not in '0123456790.':
-        break
-
 # The short X.Y version.
-version = release[:i]
+version = release[:len(release) - len(release.lstrip('012345679.'))].rstrip('.')
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -99,22 +107,20 @@ pygments_style = 'sphinx'
 # Do not show all class members automatically in the class documentation
 numpydoc_show_class_members = False
 
-# -- Options for HTML output ---------------------------------------------------
+# Jupyter Sphinx config
 
-# http://stackoverflow.com/questions/9728292/creating-latex-math-macros-within-sphinx
-pngmath_latex_preamble = r"""\newcommand{\bra}[1]{\left\langle#1\right|}
-\newcommand{\ket}[1]{\left|#1\right>}
-\newcommand{\braket}[2]{\left\langle#1|#2\right\rangle}
-\newcommand{\ri}{\text{i}}
-\newcommand{\rd}{\text{d}}
-"""
+jupyter_sphinx_thebelab_config = {
+    "binderOptions": {
+        "repo": "kwant-project/binder",
+        "ref": "master",
+    }
+}
+
+# -- Options for HTML output ---------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  Major themes that come with
 # Sphinx are currently 'default' and 'sphinxdoc'.
-html_theme = 'kwantdoctheme'
-html_theme_path = ['..']
-html_theme_options = {'collapsiblesidebar': True}
-html_style = 'kwant.css'
+html_theme = 'sphinx_book_theme'
 
 # Theme options are theme-specific and customize the look and feel of a theme
 # further.  For a list of options available for each theme, see the
@@ -133,7 +139,7 @@ html_style = 'kwant.css'
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
-#html_logo = None
+html_logo = "_static/kwant_logo.png"
 
 # The name of an image file (within the static path) to use as favicon of the
 # docs.  This file should be a Windows icon file (.ico) being 16x16 or 32x32
@@ -183,13 +189,9 @@ html_domain_indices = False
 # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml").
 #html_file_suffix = ''
 
-# Output file base name for HTML help builder.
-htmlhelp_basename = 'kwantdoc'
-
 
 # -- Options for LaTeX output --------------------------------------------------
 
-# http://thread.gmane.org/gmane.comp.python.sphinx.devel/4220/focus=4238
 latex_elements = {'papersize': 'a4paper',
                   'release': '',
                   'releasename': '',
@@ -205,17 +207,29 @@ r"""\makeatletter
     \renewcommand{\footrulewidth}{0.4pt}
   }
 \makeatother
-""" + pngmath_latex_preamble}
+
+\newcommand{\bra}[1]{\left\langle#1\right|}
+\newcommand{\ket}[1]{\left|#1\right>}
+\newcommand{\braket}[2]{\left\langle#1|#2\right\rangle}
+\newcommand{\ri}{\text{i}}
+\newcommand{\rd}{\text{d}}
+
+\usepackage{unicode-math}
+"""}
 
 # Grouping the document tree into LaTeX files. List of tuples
 # (source start file, target name, title, author, documentclass [howto/manual]).
 # 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'),
 ]
 
+latex_engine = 'xelatex'
+
+latex_use_xindy = False  # Xindy not installable in CI environment
+
 # The name of an image file (relative to this directory) to place at the top of
 # the title page.
 #latex_logo = None
@@ -227,9 +241,6 @@ latex_documents = [
 # Documents to append as an appendix to all manuals.
 #latex_appendices = []
 
-# If false, no module index is generated.
-latex_use_modindex = False
-
 # This is needed too.
 latex_domain_indices = False
 
@@ -238,7 +249,9 @@ latex_domain_indices = False
 autosummary_generate = True
 
 autoclass_content = "both"
-autodoc_default_flags = ['show-inheritance']
+autodoc_default_options = {
+    'show-inheritance': True,
+}
 
 # -- Teach Sphinx to document bound methods like functions ---------------------
 import types
@@ -251,11 +264,11 @@ class BoundMethodDocumenter(autodoc.FunctionDocumenter):
     @classmethod
     def can_document_member(cls, member, membername, isattr, parent):
         # Return True iff `member` is a bound method.  Taken from
-        # <http://stackoverflow.com/a/1260881>.
+        # <https://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()
@@ -266,3 +279,56 @@ class BoundMethodDocumenter(autodoc.FunctionDocumenter):
 
 def setup(app):
     app.add_autodocumenter(BoundMethodDocumenter)
+
+
+# By default linkcheck only tries once, but experience has shown us that this test is
+# very non-specific for detecting dead links. Trying a few times should significantly
+# lower the probability of false positives.
+linkcheck_retries = 5
+# Some websites (particularly IoP) take a long time to respond. The combination of
+# this timeout and the retries should make this check sufficiently specific.
+linkcheck_timeout = 10
+
+nitpick_ignore = [('py:class', 'Warning'), ('py:class', 'Exception'),
+                  ('py:class', 'object'), ('py:class', 'tuple'),
+                  ('py:class', 'kwant.operator._LocalOperator'),
+                  ('py:class', 'numpy.ndarray'),
+                  ('py:class', 'kwant.solvers.common.BlockResult'),
+                  ('py:class', 'kwant.builder._FinalizedBuilderMixin')]
+
+
+# -- Make Sphinx insert source code links --------------------------------------
+def linkcode_resolve(domain, info):
+    def find_source():
+        # try to find the file and line number, based on code from numpy:
+        # https://github.com/numpy/numpy/blob/master/doc/source/conf.py#L286
+        obj = sys.modules[info['module']]
+        for part in info['fullname'].split('.'):
+            obj = getattr(obj, part)
+        import inspect
+        fn = inspect.getsourcefile(obj)
+        fn = os.path.relpath(fn, start=os.path.dirname(kwant.__file__))
+        source, lineno = inspect.getsourcelines(obj)
+        return fn, lineno, lineno + len(source) - 1
+
+    if domain != 'py' or not info['module']:
+        return None
+    try:
+        filename = 'kwant/%s#L%d-%d' % find_source()
+    except Exception:
+        filename = info['module'].replace('.', '/') + '.py'
+
+    # The following relies on the documented format of kwant.__version__.
+    rel = release.rstrip('.dirty')
+    if '.dev' in rel:
+        try:
+            refname = rel[rel.index('+g') + 2:]
+        except ValueError:
+            return
+    else:
+        refname = 'v' + rel
+
+    templ = os.environ.get(
+        "SOURCE_LINK_TEMPLATE",
+        "https://gitlab.kwant-project.org/kwant/kwant/blob/$r/$f")
+    return string.Template(templ).safe_substitute(r=refname, f=filename)

doc/source/images/ab_ring_sketch.svg → doc/source/figure/ab_ring_sketch.svg

@@ -3,7 +3,7 @@
 
 <svg
    xmlns:dc="http://purl.org/dc/elements/1.1/"
-   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:cc="https://creativecommons.org/ns#"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:svg="http://www.w3.org/2000/svg"
    xmlns="http://www.w3.org/2000/svg"

doc/source/images/ab_ring_sketch2.svg → doc/source/figure/ab_ring_sketch2.svg

@@ -3,7 +3,7 @@
 
 <svg
    xmlns:dc="http://purl.org/dc/elements/1.1/"
-   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:cc="https://creativecommons.org/ns#"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:svg="http://www.w3.org/2000/svg"
    xmlns="http://www.w3.org/2000/svg"

doc/source/images/superconductor_transport_sketch.svg → doc/source/figure/superconductor_transport_sketch.svg

@@ -3,7 +3,7 @@
 
 <svg
    xmlns:dc="http://purl.org/dc/elements/1.1/"
-   xmlns:cc="http://creativecommons.org/ns#"
+   xmlns:cc="https://creativecommons.org/ns#"
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:svg="http://www.w3.org/2000/svg"
    xmlns="http://www.w3.org/2000/svg"

doc/source/images/_defs.py

-################################################################
-# Make matplotlib work without X11
-################################################################
-import matplotlib
-matplotlib.use('Agg')
-
-################################################################
-# Prepend Kwant's build directory to sys.path
-################################################################
-import sys
-from distutils.util import get_platform
-sys.path.insert(0, "../../../build/lib.{0}-{1}.{2}".format(
-        get_platform(), *sys.version_info[:2]))
-
-################################################################
-# Define constants for plotting
-################################################################
-pt_to_in = 1. / 72.
-
-# Default width of figures in pts
-figwidth_pt = 600
-figwidth_in = figwidth_pt * pt_to_in
-
-# Width for smaller figures
-figwidth_small_pt = 400
-figwidth_small_in = figwidth_small_pt * pt_to_in
-
-# Sizes for matplotlib figures
-mpl_width_in = figwidth_pt * pt_to_in
-mpl_label_size = None  # font sizes in points
-mpl_tick_size = None
-
-# dpi for conversion from inches
-dpi = 90

doc/source/images/ab_ring.py.diff

---- original
-+++ modified
-@@ -12,6 +12,7 @@
- #    example, but in the tutorial main text)
- #  - Modifcations of hoppings/sites after they have been added
- 
-+import _defs
- from cmath import exp
- from math import pi
- 
-@@ -40,12 +41,13 @@
-     sys[lat.shape(ring, (0, r1 + 1))] = 4 * t
-     sys[lat.neighbors()] = -t
- 
--    # In order to introduce a flux through the ring, we introduce a phase on
--    # the hoppings on the line cut through one of the arms.  Since we want to
--    # change the flux without modifying the Builder instance repeatedly, we
--    # define the modified hoppings as a function that takes the flux as its
--    # parameter phi.
--    def fluxphase(site1, site2, phi):
-+    # In order to introduce a flux through the ring, we introduce a phase
-+    # on the hoppings on the line cut through one of the arms
-+
-+    # since we want to change the flux without modifying Builder repeatedly,
-+    # we define the modified hoppings as a function that takes the flux
-+    # through the argument phi.
-+    def fluxphase(site1, site2, phi=0):
-         return exp(1j * phi)
- 
-     def crosses_branchcut(hop):
-@@ -81,6 +83,50 @@
-     return sys
- 
- 
-+def make_system_note1(a=1, t=1.0, W=10, r1=10, r2=20):
-+    lat = kwant.lattice.square(a)
-+    sys = kwant.Builder()
-+    def ring(pos):
-+        (x, y) = pos
-+        rsq = x**2 + y**2
-+        return ( r1**2 < rsq < r2**2)
-+    sys[lat.shape(ring, (0, 11))] = 4 * t
-+    sys[lat.neighbors()] = -t
-+    sym_lead0 = kwant.TranslationalSymmetry((-a, 0))
-+    lead0 = kwant.Builder(sym_lead0)
-+    def lead_shape(pos):
-+        (x, y) = pos
-+        return (-1 < x < 1) and ( 0.5 * W < y < 1.5 * W )
-+    lead0[lat.shape(lead_shape, (0, W))] = 4 * t
-+    lead0[lat.neighbors()] = -t
-+    lead1 = lead0.reversed()
-+    sys.attach_lead(lead0)
-+    sys.attach_lead(lead1)
-+    return sys
-+
-+
-+def make_system_note2(a=1, t=1.0, W=10, r1=10, r2=20):
-+    lat = kwant.lattice.square(a)
-+    sys = kwant.Builder()
-+    def ring(pos):
-+        (x, y) = pos
-+        rsq = x**2 + y**2
-+        return ( r1**2 < rsq < r2**2)
-+    sys[lat.shape(ring, (0, 11))] = 4 * t
-+    sys[lat.neighbors()] = -t
-+    sym_lead0 = kwant.TranslationalSymmetry((-a, 0))
-+    lead0 = kwant.Builder(sym_lead0)
-+    def lead_shape(pos):
-+        (x, y) = pos
-+        return (-1 < x < 1) and ( -W/2 < y < W/2  )
-+    lead0[lat.shape(lead_shape, (0, 0))] = 4 * t
-+    lead0[lat.neighbors()] = -t
-+    lead1 = lead0.reversed()
-+    sys.attach_lead(lead0)
-+    sys.attach_lead(lead1, lat(0, 0))
-+    return sys
-+
-+
- def plot_conductance(sys, energy, fluxes):
-     # compute conductance
- 
-@@ -90,18 +136,31 @@
-         smatrix = kwant.smatrix(sys, energy, args=[flux])
-         data.append(smatrix.transmission(1, 0))
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(normalized_fluxes, data)
--    pyplot.xlabel("flux [flux quantum]")
--    pyplot.ylabel("conductance [e^2/h]")
--    pyplot.show()
-+    pyplot.xlabel("flux [flux quantum]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("conductance [e^2/h]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    fig.savefig("ab_ring_result.pdf")
-+    fig.savefig("ab_ring_result.png", dpi=_defs.dpi)
- 
- 
- def main():
-     sys = make_system()
- 
-     # Check that the system looks as intended.
--    kwant.plot(sys)
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(sys, file="ab_ring_sys." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
-+
- 
-     # Finalize the system.
-     sys = sys.finalized()
-@@ -111,6 +170,17 @@
-                                                 for i in xrange(100)])
- 
- 
-+    # Finally, some plots needed for the notes
-+    sys = make_system_note1()
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(sys, file="ab_ring_note1." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
-+    sys = make_system_note2()
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(sys, file="ab_ring_note2." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
-+
-+
- # Call the main function if the script gets executed (as opposed to imported).
- # See <http://docs.python.org/library/__main__.html>.
- if __name__ == '__main__':

doc/source/images/band_structure.py.diff

---- original
-+++ modified
-@@ -9,6 +9,7 @@
- # --------------------------
- #  - Computing the band structure of a finalized lead.
- 
-+import _defs
- import kwant
- 
- # For plotting.
-@@ -36,10 +37,19 @@
- 
- def main():
-     lead = make_lead().finalized()
--    kwant.plotter.bands(lead, show=False)
--    pyplot.xlabel("momentum [(lattice constant)^-1]")
--    pyplot.ylabel("energy [t]")
--    pyplot.show()
-+    fig = kwant.plotter.bands(lead, show=False)
-+    pyplot.xlabel("momentum [(lattice constant)^-1]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("energy [t]", fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("band_structure_result." + extension, dpi=_defs.dpi)
-+
- 
- 
- # Call the main function if the script gets executed (as opposed to imported).

doc/source/images/closed_system.py.diff

---- original
-+++ modified
-@@ -11,6 +11,7 @@
- #  - Use of `hamiltonian_submatrix` in order to obtain a Hamiltonian
- #    matrix.
- 
-+import _defs
- from cmath import exp
- import numpy as np
- import kwant
-@@ -68,29 +69,39 @@
- 
-         energies.append(ev)
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(Bfields, energies)
--    pyplot.xlabel("magnetic field [arbitrary units]")
--    pyplot.ylabel("energy [t]")
--    pyplot.show()
-+    pyplot.xlabel("magnetic field [arbitrary units]",
-+                  fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("energy [t]", fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+                fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+                fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("closed_system_result." + extension, dpi=_defs.dpi)
- 
- 
- def plot_wave_function(sys):
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+
-     # Calculate the wave functions in the system.
-     ham_mat = sys.hamiltonian_submatrix(sparse=True)
-     evecs = sla.eigsh(ham_mat, k=20, which='SM')[1]
- 
-     # Plot the probability density of the 10th eigenmode.
--    kwant.plotter.map(sys, np.abs(evecs[:, 9])**2,
--                      colorbar=False, oversampling=1)
-+    for extension in ('pdf', 'png'):
-+        kwant.plotter.map(
-+            sys, np.abs(evecs[:, 9])**2, colorbar=False, oversampling=1,
-+            file="closed_system_eigenvector." + extension,
-+            fig_size=size, dpi=_defs.dpi)
- 
- 
- def main():
-     sys = make_system()
- 
--    # Check that the system looks as intended.
--    kwant.plot(sys)
--
-     # Finalize the system.
-     sys = sys.finalized()
- 

doc/source/images/generate-diffs.sh

-# !/bin/sh
-
-# This script regenerates the .diff files in this directory.  It's these files
-# that are kept under vesion control instead of the scripts themselves.
-
-for f in [a-zA-Z]*.py; do
-    # We use custom labels to suppress the time stamps which are unnecessary
-    # here and would only lead to noise in version control.
-    grep -v '#HIDDEN' ../tutorial/$f |
-    diff -u --label original --label modified - $f >$f.diff_
-    if cmp $f.diff_ $f.diff >/dev/null 2>&1; then
-        rm $f.diff_
-    else
-        mv $f.diff_ $f.diff
-    fi
-done

doc/source/images/graphene.py.diff

---- original
-+++ modified
-@@ -11,6 +11,7 @@
- #    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 @@
-         smatrix = kwant.smatrix(sys, energy)
-         data.append(smatrix.transmission(0, 1))
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(energies, data)
--    pyplot.xlabel("energy [t]")
--    pyplot.ylabel("conductance [e^2/h]")
--    pyplot.show()
-+    pyplot.xlabel("energy [t]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("conductance [e^2/h]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("graphene_result." + extension, dpi=_defs.dpi)
- 
- 
- def plot_bandstructure(flead, momenta):
-     bands = kwant.physics.Bands(flead)
-     energies = [bands(k) for k in momenta]
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(momenta, energies)
--    pyplot.xlabel("momentum [(lattice constant)^-1]")
--    pyplot.ylabel("energy [t]")
--    pyplot.show()
-+    pyplot.xlabel("momentum [(lattice constant)^-1]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("energy [t]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("graphene_bs." + extension, dpi=_defs.dpi)
- 
- 
- def main():
-@@ -124,8 +143,11 @@
-     def family_colors(site):
-         return 0 if site.family == a else 1
- 
--    # Plot the closed system without leads.
--    kwant.plot(sys, site_color=family_colors, site_lw=0.1, colorbar=False)
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(sys, site_color=family_colors, site_lw=0.1, colorbar=False,
-+                   file="graphene_sys1." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
-     # Compute some eigenvalues.
-     compute_evs(sys.finalized())
-@@ -134,9 +156,11 @@
-     for lead in leads:
-         sys.attach_lead(lead)
- 
--    # Then, plot the system with leads.
--    kwant.plot(sys, site_color=family_colors, site_lw=0.1,
--               lead_site_lw=0, colorbar=False)
-+    size = (_defs.figwidth_in, 0.9 * _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(sys, site_color=family_colors, colorbar=False, site_lw=0.1,
-+                   file="graphene_sys2." + extension,
-+                   fig_size=size, dpi=_defs.dpi, lead_site_lw=0)
- 
-     # Finalize the system.
-     sys = sys.finalized()

doc/source/images/plot_graphene.py.diff

---- original
-+++ modified
-@@ -9,6 +9,7 @@
- # --------------------------
- #  - demonstrate different ways of plotting
- 
-+import _defs
- import kwant
- from matplotlib import pyplot
- 
-@@ -22,7 +23,7 @@
-         return x**2 + y**2 < r**2
- 
-     sys = kwant.Builder()
--    sys[lat.shape(circle, (0, 0))] = 0
-+    sys[lat.shape(circle, (0,0))] = 0
-     sys[lat.neighbors()] = t
-     sys.eradicate_dangling()
-     if tp:
-@@ -32,9 +33,11 @@
- 
- 
- def plot_system(sys):
--    kwant.plot(sys)
--    # the standard plot is ok, but not very intelligible. One can do
--    # better by playing wioth colors and linewidths
-+    # standard plot - not very intelligible for this particular situation
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(sys, file="plot_graphene_sys1." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
-     # use color and linewidths to get a better plot
-     def family_color(site):
-@@ -43,7 +46,11 @@
-     def hopping_lw(site1, site2):
-         return 0.04 if site1.family == site2.family else 0.1
- 
--    kwant.plot(sys, site_lw=0.1, site_color=family_color, hop_lw=hopping_lw)
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(sys, site_lw=0.1, site_color=family_color,
-+                   hop_lw=hopping_lw, file="plot_graphene_sys2." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
- 
- def plot_data(sys, n):
-@@ -58,7 +65,11 @@
-     # the usual - works great in general, looks just a bit crufty for
-     # small systems
- 
--    kwant.plotter.map(sys, wf, oversampling=10, cmap='gist_heat_r')
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plotter.map(sys, wf, oversampling=10, cmap='gist_heat_r',
-+                          file="plot_graphene_data1." + extension,
-+                          fig_size=size, dpi=_defs.dpi)
- 
-     # use two different sort of triangles to cleanly fill the space
-     def family_shape(i):
-@@ -68,15 +79,22 @@
-     def family_color(i):
-         return 'black' if sys.site(i).family == a else 'white'
- 
--    kwant.plot(sys, site_color=wf, site_symbol=family_shape,
--               site_size=0.5, hop_lw=0, cmap='gist_heat_r')
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(sys, site_color=wf, site_symbol=family_shape,
-+                   site_size=0.5, hop_lw=0, cmap='gist_heat_r',
-+                   file="plot_graphene_data2." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
-     # plot by changing the symbols itself
-     def site_size(i):
-         return 3 * wf[i] / wf.max()
- 
--    kwant.plot(sys, site_size=site_size, site_color=(0, 0, 1, 0.3),
--               hop_lw=0.1)
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(sys, site_size=site_size, site_color=(0,0,1,0.3),
-+                   hop_lw=0.1, file="plot_graphene_data3." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
- 
- def main():

doc/source/images/plot_zincblende.py.diff

---- original
-+++ modified
-@@ -9,6 +9,7 @@
- # --------------------------
- #  - demonstrate different ways of plotting in 3D
- 
-+import _defs
- import kwant
- from matplotlib import pyplot
- 
-@@ -33,7 +34,10 @@
-     # checking shapes:
-     sys = make_cuboid()
- 
--    kwant.plot(sys)
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(sys, file="plot_zincblende_sys1." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
-     # visualize the crystal structure better for a very small system
-     sys = make_cuboid(a=1.5, b=1.5, c=1.5)
-@@ -41,8 +45,12 @@
-     def family_colors(site):
-         return 'r' if site.family == a else 'g'
- 
--    kwant.plot(sys, site_size=0.18, site_lw=0.01, hop_lw=0.05,
--               site_color=family_colors)
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(sys, site_size=0.18, site_lw=0.01, hop_lw=0.05,
-+                   site_color=family_colors,
-+                   file="plot_zincblende_sys2." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
- 
- # Call the main function if the script gets executed (as opposed to imported).

doc/source/images/quantum_well.py.diff

---- original
-+++ modified
-@@ -9,6 +9,7 @@
- # --------------------------
- #  - Functions as values in Builder
- 
-+import _defs
- import kwant
- 
- # For plotting
-@@ -55,19 +56,25 @@
-         smatrix = kwant.smatrix(sys, energy, args=[-welldepth])
-         data.append(smatrix.transmission(1, 0))
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(welldepths, data)
--    pyplot.xlabel("well depth [t]")
--    pyplot.ylabel("conductance [e^2/h]")
--    pyplot.show()
-+    pyplot.xlabel("well depth [t]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("conductance [e^2/h]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("quantum_well_result." + extension, dpi=_defs.dpi)
- 
- 
- def main():
-     sys = make_system()
- 
--    # Check that the system looks as intended.
--    kwant.plot(sys)
--
-     # Finalize the system.
-     sys = sys.finalized()
- 

doc/source/images/quantum_wire.py.diff

---- original
-+++ modified
-@@ -11,6 +11,7 @@
- #  - Making scattering region and leads
- #  - Using the simple sparse solver for computing Landauer conductance
- 
-+import _defs
- from matplotlib import pyplot
- import kwant
- 
-@@ -69,7 +70,10 @@
- sys.attach_lead(right_lead)
- 
- # Plot it, to make sure it's OK
--kwant.plot(sys)
-+size = (_defs.figwidth_in, 0.3 * _defs.figwidth_in)
-+for extension in ('pdf', 'png'):
-+    kwant.plot(sys, file="quantum_wire_sys." + extension,
-+               fig_size=size, dpi=_defs.dpi)
- 
- # Finalize the system
- sys = sys.finalized()
-@@ -90,8 +94,13 @@
- 
- # Use matplotlib to write output
- # We should see conductance steps
--pyplot.figure()
-+fig = pyplot.figure()
- pyplot.plot(energies, data)
--pyplot.xlabel("energy [t]")
--pyplot.ylabel("conductance [e^2/h]")
--pyplot.show()
-+pyplot.xlabel("energy [t]", fontsize=_defs.mpl_label_size)
-+pyplot.ylabel("conductance [e^2/h]", fontsize=_defs.mpl_label_size)
-+pyplot.setp(fig.get_axes()[0].get_xticklabels(), fontsize=_defs.mpl_tick_size)
-+pyplot.setp(fig.get_axes()[0].get_yticklabels(), fontsize=_defs.mpl_tick_size)
-+fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+for extension in ('pdf', 'png'):
-+    fig.savefig("quantum_wire_result." + extension, dpi=_defs.dpi)

doc/source/images/spin_orbit.py.diff

---- original
-+++ modified
-@@ -13,6 +13,7 @@
- # --------------------------
- #  - Numpy matrices as values in Builder
- 
-+import _defs
- import kwant
- 
- # For plotting
-@@ -70,19 +71,24 @@
-         smatrix = kwant.smatrix(sys, energy)
-         data.append(smatrix.transmission(1, 0))
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(energies, data)
--    pyplot.xlabel("energy [t]")
--    pyplot.ylabel("conductance [e^2/h]")
--    pyplot.show()
-+    pyplot.xlabel("energy [t]", fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("conductance [e^2/h]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("spin_orbit_result." + extension, dpi=_defs.dpi)
- 
- 
- def main():
-     sys = make_system()
- 
--    # Check that the system looks as intended.
--    kwant.plot(sys)
--
-     # Finalize the system.
-     sys = sys.finalized()
- 

doc/source/images/superconductor_band_structure.py.diff

---- original
-+++ modified
-@@ -13,6 +13,7 @@
- #  - Main motivation is to contrast to the implementation of superconductivity
- #    in tutorial5b.py
- 
-+import _defs
- import kwant
- 
- import numpy as np
-@@ -49,11 +50,20 @@
-     # Make system and finalize it right away.
-     lead = make_lead().finalized()
- 
--    kwant.plotter.bands(lead, momenta=np.linspace(-1.5, 1.5, 101), show=False)
-+    fig = kwant.plotter.bands(lead, momenta=np.linspace(-1.5, 1.5, 101),
-+                              show=False)
-     pyplot.xlabel("momentum [(lattice constant)^-1]")
-     pyplot.ylabel("energy [t]")
-     pyplot.ylim([-0.8, 0.8])
--    pyplot.show()
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("superconductor_band_structure_result." + extension,
-+                    dpi=_defs.dpi)
- 
- 
- # Call the main function if the script gets executed (as opposed to imported).

doc/source/images/superconductor_transport.py.diff

---- original
-+++ modified
-@@ -10,6 +10,7 @@
- # - Implementing electron and hole ("orbital") degrees of freedom
- #   using different lattices
- 
-+import _defs
- import kwant
- 
- # For plotting
-@@ -85,19 +86,24 @@
-                     smatrix.transmission(0, 0) +
-                     smatrix.transmission(1, 0))
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(energies, data)
-     pyplot.xlabel("energy [t]")
-     pyplot.ylabel("conductance [e^2/h]")
--    pyplot.show()
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("superconductor_transport_result." + extension,
-+                    dpi=_defs.dpi)
- 
- 
- def main():
-     sys = make_system()
- 
--    # Check that the system looks as intended.
--    kwant.plot(sys)
--
-     # Finalize the system.
-     sys = sys.finalized()
- 

doc/source/index.rst

@@ -4,7 +4,7 @@ Kwant |release| documentation
 
 .. toctree::
    :maxdepth: 2
-   :numbered: 3
+   :numbered: 2
 
    pre/index
    tutorial/index