doc/source/reference/kwant.builder.rst

@@ -11,10 +11,11 @@ Types
    Builder
    Site
    HoppingKind
-   SimpleSiteFamily
    BuilderLead
    SelfEnergyLead
    ModesLead
+   FiniteSystem
+   InfiniteSystem
 
 Abstract base classes
 ---------------------
@@ -24,3 +25,10 @@ Abstract base classes
    SiteFamily
    Symmetry
    Lead
+
+Functions
+---------
+.. autosummary::
+   :toctree: generated/
+
+   add_peierls_phase

doc/source/reference/kwant.continuum.rst

+:mod:`kwant.continuum` -- Tools for continuum systems
+=====================================================
+
+.. module:: kwant.continuum
+
+Discretizer
+-----------
+.. autosummary::
+    :toctree: generated/
+
+    discretize
+    discretize_symbolic
+    build_discretized
+    discretize_landau
+
+Symbolic helpers
+----------------
+.. autosummary::
+    :toctree: generated/
+
+    sympify
+    lambdify
+    to_landau_basis
+
+Other
+-----
+.. autosummary::
+    :toctree: generated/
+
+    LandauLattice

doc/source/reference/kwant.graph.rst

@@ -76,19 +76,8 @@ Graph types
    Graph
    CGraph
 
-Graph algorithms
-----------------
-.. autosummary::
-   :toctree: generated/
-
-   slice
-   make_undirected
-   remove_duplicates
-   induced_subgraph
-   print_graph
-
 Other
 -----
-+--------------+------------------------------------------+
-| `gint_dtype` | Data type used for graph nodes and edges |
-+--------------+------------------------------------------+
++----------------+------------------------------------------+
+| ``gint_dtype`` | Data type used for graph nodes and edges |
++----------------+------------------------------------------+

doc/source/reference/kwant.kpm.rst

+:mod:`kwant.kpm` -- Kernel Polynomial Method
+============================================
+
+.. automodule:: kwant.kpm
+   :members:
+   :special-members:
+   :exclude-members: __weakref__, __init__

doc/source/reference/kwant.lattice.rst

@@ -20,6 +20,7 @@ Library of lattices
 
    chain
    square
+   cubic
    triangular
    honeycomb
    kagome

doc/source/reference/kwant.operator.rst

+:mod:`kwant.operator` -- Operators and Observables
+==================================================
+
+.. module:: kwant.operator
+
+Observables
+-----------
+.. autosummary::
+   :toctree: generated/
+   :template: autosummary/functor.rst
+
+   Density
+   Current
+   Source

doc/source/reference/kwant.physics.rst

@@ -14,3 +14,19 @@ Leads
    two_terminal_shotnoise
    PropagatingModes
    StabilizedModes
+
+Symmetry
+--------
+.. autosummary::
+   :toctree: generated/
+
+   DiscreteSymmetry
+
+Computation of magnetic field gauge
+-----------------------------------
+
+.. autosummary::
+   :toctree: generated/
+   :template: autosummary/functor.rst
+
+   magnetic_gauge

doc/source/reference/kwant.plotter.rst

@@ -4,20 +4,27 @@
 .. module:: kwant.plotter
 
 
-Plotting routine
-----------------
+Plotting routines
+-----------------
 .. autosummary::
    :toctree: generated/
 
    plot
    map
+   density
+   current
    bands
+   spectrum
+   streamplot
+   scalarplot
 
-Data-generating functions
--------------------------
+Helper functions
+----------------
 .. autosummary::
    :toctree: generated/
 
+   interpolate_current
+   interpolate_density
    sys_leads_sites
    sys_leads_hoppings
    sys_leads_pos

doc/source/reference/kwant.qsymm.rst

+:mod:`kwant.qsymm` -- Integration with `Qsymm <https://gitlab.kwant-project.org/qt/qsymm>`_
+===========================================================================================
+
+.. automodule:: kwant.qsymm
+   :members:
+   :special-members:
+   :exclude-members: __weakref__

doc/source/reference/kwant.rst

@@ -3,9 +3,20 @@
 
 .. module:: kwant
 
-The top-level Kwant package serves as a container for sub-packages and does not
-have any functions of its own.  For convenience, short names are provided for a
-few widely used objects from the sub-packages:
+For convenience, short names are provided for a few widely used objects from
+the sub-packages.
+Otherwise, this package has only very limited functionality of its own.
+
+Generic functionality
+---------------------
+
+.. autodata:: kwant.__version__
+
+.. autosummary::
+   :toctree: generated/
+
+   KwantDeprecationWarning
+   UserCodeError
 
 .. currentmodule:: kwant.builder
 
@@ -43,7 +54,3 @@ From `kwant.solvers.default`
    ldos
    smatrix
    wave_function
-
-Version information
--------------------
-The version of Kwant is available under the name ``__version__``.

doc/source/reference/kwant.solvers.mumps.rst

@@ -3,7 +3,7 @@
 
 .. module:: kwant.solvers.mumps
 
-This solver uses `MUMPS <http://graal.ens-lyon.fr/MUMPS/>`_.  (Only the
+This solver uses `MUMPS <https://graal.ens-lyon.fr/MUMPS/>`_.  (Only the
 sequential, single core version of MUMPS is used.)  MUMPS is a very efficient
 direct sparse solver that can take advantage of memory beyond 3GiB for the
 solution of large problems.  Furthermore, it offers a choice of several

doc/source/reference/kwant.solvers.sparse.rst

@@ -4,7 +4,7 @@
 .. module:: kwant.solvers.sparse
 
 This solver uses SciPy's `scipy.sparse.linalg
-<http://docs.scipy.org/doc/scipy/reference/sparse.linalg.html>`_.  The
+<https://docs.scipy.org/doc/scipy/reference/sparse.linalg.html>`_.  The
 interface is identical to that of the :mod:`default solver
 <kwant.solvers.default>`.
 

doc/source/reference/kwant.system.rst

 :mod:`kwant.system` -- Low-level interface of systems
 *****************************************************
 
-.. currentmodule:: kwant.system
+.. automodule:: kwant.system
 
 This module is the binding link between constructing tight-binding systems and
 doing calculations with these systems.  It defines the interface which any
@@ -14,6 +14,11 @@ Any system which is provided to a solver should be derived from the appropriate
 class in this module, and every solver can assume that its input corresponds to
 the interface defined here.
 
+In practice, very often Kwant systems are finalized
+`builders <kwant.builder.Builder>` (i.e.
+`kwant.builder.FiniteSystem` or `kwant.builder.InfiniteSystem`) and offer some
+additional attributes.
+
 .. autosummary::
    :toctree: generated/
 

doc/source/reference/kwant.wraparound.rst

+:mod:`kwant.wraparound` -- Wrapping around translational symmetries
+===================================================================
+.. module:: kwant.wraparound
+.. autosummary::
+   :toctree: generated/
+
+   wraparound
+   plot_2d_bands

doc/source/tutorial/README

-Note for Kwant developers
--------------------------
-
-Say you have modified SCRIPT.py in this directory.  Make sure that the tutorial
-image generation patches still apply by deleting doc/source/images/SCRIPT.py
-and running ``make doc/source/images/SCRIPT.py`` in doc.  Now examine the newly
-created doc/source/images/SCRIPT.py.  If you do not like the result or the
-patch did not apply, edit doc/source/images/SCRIPT.py until you like it.  You
-can run `make html` during your edits to check things.  Finally, even if you
-did not edit the script, execute generate-diffs.sh in doc/source/images.  If
-the patches applied cleanly the diff files will usually stay unchanged.

doc/source/tutorial/band_structure.py

-# Tutorial 2.4.1. Band structure calculations
-# ===========================================
-#
-# Physics background
-# ------------------
-#  band structure of a simple quantum wire in tight-binding approximation
-#
-# Kwant features highlighted
-# --------------------------
-#  - Computing the band structure of a finalized lead.
-
-import kwant
-
-# For plotting.
-from matplotlib import pyplot
-
-#HIDDEN_BEGIN_zxip
-def make_lead(a=1, t=1.0, W=10):
-    # Start with an empty lead with a single square lattice
-    lat = kwant.lattice.square(a)
-
-    sym_lead = kwant.TranslationalSymmetry((-a, 0))
-    lead = kwant.Builder(sym_lead)
-
-    # build up one unit cell of the lead, and add the hoppings
-    # to the next unit cell
-    for j in xrange(W):
-        lead[lat(0, j)] = 4 * t
-
-        if j > 0:
-            lead[lat(0, j), lat(0, j - 1)] = -t
-
-        lead[lat(1, j), lat(0, j)] = -t
-
-    return lead
-#HIDDEN_END_zxip
-
-
-#HIDDEN_BEGIN_pejz
-def main():
-    lead = make_lead().finalized()
-    kwant.plotter.bands(lead, show=False)
-    pyplot.xlabel("momentum [(lattice constant)^-1]")
-    pyplot.ylabel("energy [t]")
-    pyplot.show()
-#HIDDEN_END_pejz
-
-
-# Call the main function if the script gets executed (as opposed to imported).
-# See <http://docs.python.org/library/__main__.html>.
-if __name__ == '__main__':
-    main()

doc/source/tutorial/boilerplate.py

+import matplotlib
+import matplotlib.pyplot
+from matplotlib_inline.backend_inline import set_matplotlib_formats
+
+matplotlib.rcParams['figure.figsize'] = matplotlib.pyplot.figaspect(1) * 2
+set_matplotlib_formats('svg')