documentation fixups prior to release

doc/source/code/figure/closed_system.py.diff

@@ -60,14 +60,9 @@
  #HIDDEN_BEGIN_yvri
  def plot_spectrum(syst, Bfields):
  
-     # In the following, we compute the spectrum of the quantum dot
-     # using dense matrix methods. This works in this toy example, as
-     # the system is tiny. In a real example, one would want to use
-     # sparse matrix methods
- 
      energies = []
      for B in Bfields:
-         # Obtain the Hamiltonian as a dense matrix
+         # Obtain the Hamiltonian as a sparse matrix
          ham_mat = syst.hamiltonian_submatrix(params=dict(B=B), sparse=True)
  
          # we only calculate the 15 lowest eigenvalues

doc/source/pre/whatsnew/1.4.rst

@@ -83,7 +83,9 @@ Here is an example for extracting the symmetry group of a graphene system::
 
 ``kwant.qsymm`` also contains functionality for converting Qsymm models to Kwant Builders,
 and vice versa, and for working with continuum Hamiltonians (such as would be used with
-``kwant.continuum``)
+``kwant.continuum``).
+This integration requires separately installing Qsymm, which is available on the
+`Python Package Index <https://pypi.org/project/qsymm/>`_.
 
 Automatic Peierls phase calculation
 -----------------------------------
@@ -101,8 +103,7 @@ which calculates the Peierls phases for you::
       return -t * peierls(a, b)
 
   syst = make_system(hopping)
-  lead = make_lead(hopping)
-  lead.substituted(peierls='peierls_lead')
+  lead = make_lead(hopping).substituted(peierls='peierls_lead')
   syst.attach_lead(lead)
   syst = syst.finalized()
 
@@ -135,19 +136,19 @@ has a parameter ``V``, and one wishes to have different values for ``V`` in
 the scattering region and leads, one could do the following::
 
    syst = kwant.Builder()
-   syst.fill(model.substituted(V='V_dot', ...))
+   syst.fill(model.substituted(V='V_dot'), ...))
 
    lead = kwant.Builder()
    lead.fill(model.substituted(V='V_lead'), ...)
 
    syst.attach_lead(lead)
-   fsyst = syst.finalized()
+   syst = syst.finalized()
 
    kwant.smatrix(syst, params=dict(V_dot=0, V_lead=1))
 
 Interpolated density plots
 --------------------------
-A new function, `~kwant.plotter.density`, has been added that can be used to
+A new function, `kwant.plotter.density`, has been added that can be used to
 visualize a density defined over the sites of a Kwant system. This convolves
 the "discrete" density (defined over the system sites) with a "bump" function
 in realspace. The output of `~kwant.plotter.density` can be more informative
@@ -166,7 +167,8 @@ but in an inconsistent way (e.g. a parameter 'phi' that is a superconducting
 phase in one value function, but a peierls phase in another). This leads
 to bugs that are confusing and hard to track down.
 
-Concretely, the above means that the following no longer works::
+For this reason value functions may no longer have default values for paramters.
+Concretely this means that the following no longer works::
 
   syst = kwant.Builder()
 
@@ -190,7 +192,7 @@ To deal with many parameters, the following idiom may be useful::
   ...
   smatrix = kwant.smatrix(syst, E, params=dict(defaults, d=4, e=5))
 
-Note that it allows to override defaults as well as to add additional
+Note that this allows to override defaults as well as to add additional
 parameters.
 
 System parameters can now be inspected
@@ -228,9 +230,9 @@ This is a provisional API that may be changed in a future version of Kwant.
 Passing system arguments via ``args`` is deprecated in favor of ``params``
 --------------------------------------------------------------------------
 It is now deprecated to pass arguments to systems by providing the
-``args`` parameter (in ``kwant.smatrix`` and elsewhere). This is
-error prone and requires that all value functions take the same
-formal parameters, even if they do not depend on all of them. The
+``args`` parameter (in ``kwant.smatrix`` and elsewhere). Passing arguments
+via ``args`` is error prone and requires that all value functions take the
+same formal parameters, even if they do not depend on all of them. The
 preferred way of passing parameters to Kwant systems is by passing
 a dictionary using ``params``::
 
@@ -244,7 +246,7 @@ a dictionary using ``params``::
   # Compare this to the deprecated 'args'
   kwant.smatrix(syst, args=(0.5, 0.2))
 
-The ability to provide ``args`` will be removed in a future Kwant version.
+Providing ``args`` will be removed in a future Kwant version.
 
 Finalized Builders keep track of which sites were added when attaching leads
 ----------------------------------------------------------------------------
@@ -261,8 +263,8 @@ that this option is not available in `~kwant.plotter.current`.  In order to use
 it, one has to call ``streamplot`` directly as shown in the docstring of
 ``current``.
 
-kwant.continuum.discretize can be used with rectangular lattices
-----------------------------------------------------------------
+`kwant.continuum.discretize` can be used with rectangular lattices
+------------------------------------------------------------------
 Previously the discretizer could only be used with lattices with the same
 lattice constant in all directions. Now it is possible to pass rectangular
 lattices to the discretizer::

doc/source/reference/kwant.kpm.rst

@@ -4,4 +4,4 @@
 .. automodule:: kwant.kpm
    :members:
    :special-members:
-   :exclude-members: __weakref__
+   :exclude-members: __weakref__, __init__

doc/source/reference/kwant.physics.rst

@@ -27,5 +27,6 @@ Computation of magnetic field gauge
 
 .. autosummary::
    :toctree: generated/
+   :template: autosummary/functor.rst
 
    magnetic_gauge

doc/source/tutorial/discretize.rst

@@ -161,8 +161,8 @@ energy eigenstates:
 .. image:: /code/figure/discretizer_gs.*
 
 Note in the above that we pass the spatially varying potential *function*
-to our system via a parameter called ``V``, because the symbol $V$
-was used in the intial, symbolic, definition of the Hamiltonian.
+to our system via a parameter called ``V``, because the symbol :math:`V`
+was used in the initial, symbolic, definition of the Hamiltonian.
 
 In addition, the function passed as ``V`` expects two input parameters ``x``
 and ``y``, the same as in the initial continuum Hamiltonian.

doc/source/tutorial/faq.rst

@@ -423,7 +423,7 @@ the modes are sorted in the following way:
     + Positive velocity modes are ordered by *decreasing* momentum
 
 For more complicated systems and band structures this can lead to some
-possibly unintuitive orderings:
+unintuitive orderings:
 
 .. image:: /code/figure/faq_pm2.*
 
@@ -437,9 +437,9 @@ infinity" (*not* towards the system) which means that the incoming modes are
 those that have *negative* velocities.
 
 This means that for a lead attached on the left of a scattering region (with
-symmetry vector $(-1, 0)$, for example), the
-positive $k$ direction (when inspecting the lead's band structure) actually
-corresponds to the *negative* $x$ direction.
+symmetry vector :math:`(-1, 0)`, for example), the
+positive :math:`k` direction (when inspecting the lead's band structure) actually
+corresponds to the *negative* :math:`x` direction.
 
 
 How does Kwant order components of an individual wavefunction?

doc/source/tutorial/graphene.rst

@@ -112,9 +112,6 @@ in the following piece of code:
     :start-after: #HIDDEN_BEGIN_zydk
     :end-before: #HIDDEN_END_zydk
 
-Here we use in contrast to the previous example a sparse matrix and
-the sparse linear algebra functionality of SciPy.
-
 The code for computing the band structure and the conductance is identical
 to the previous examples, and needs not be further explained here.
 

doc/source/tutorial/kpm.rst

@@ -340,7 +340,7 @@ vectors
 Note that the Kubo conductivity must be normalized with the area covered
 by the vectors. In this case, each local vector represents a site, and
 covers an area of half a unit cell, while the sum covers one unit cell.
-It is possible to use random vectors to get an average spectation
+It is possible to use random vectors to get an average expectation
 value of the conductivity over large parts of the system. In this
 case, the area that normalizes the result, is the area covered by
 the random vectors.

doc/source/tutorial/spectrum.rst

@@ -122,7 +122,7 @@ better for the special case of a square lattice.
 
 
 As our model breaks time reversal symmetry (because of the applied magnetic
-field) we can also see an intereting property of the eigenstates, namely
+field) we can also see an interesting property of the eigenstates, namely
 that they can have *non-zero* local current. We can calculate the local
 current due to a state by using `kwant.operator.Current` and plotting
 it using `kwant.plotter.current`:

kwant/kpm.py

@@ -41,7 +41,7 @@ class SpectralDensity:
     .. math::
        ρ_A(E) = ρ(E) A(E),
 
-    where :math:`ρ(E) = \\sum_{k=0}^{D-1} δ(E-E_k)` is the density of
+    where :math:`ρ(E) = \sum_{k=0}^{D-1} δ(E-E_k)` is the density of
     states, and :math:`A(E)` is the expectation value of :math:`A` for
     all the eigenstates with energy :math:`E`.
 
@@ -253,11 +253,9 @@ class SpectralDensity:
 
         Returns
         -------
-        ``(energies, densities)`` if the ``energy`` parameter is not
-        provided, else ``densities``.
-
         energies : array of floats
             Drawn from the nodes of the highest Chebyshev polynomial.
+            Not returned if 'energy' was not provided
         densities : float or array of floats
             single ``float`` if the ``energy`` parameter is a single
             ``float``, else an array of ``float``.
@@ -593,7 +591,7 @@ class Correlator:
         self._build_integral_factor()
 
     def __call__(self, mu=0, temperature=0):
-        """Returns the linear response χ_{α β}(µ, T)
+        """Returns the linear response :math:`χ_{α β}(µ, T)`
 
         Parameters
         ----------

kwant/physics/gauge.py

@@ -944,7 +944,7 @@ class magnetic_gauge:
 
     Parameters
     ----------
-    syst : kwant.builder.FiniteSystem or kwant.builder.InfiniteSystem
+    syst : `kwant.builder.FiniteSystem` or `kwant.builder.InfiniteSystem`
 
     Examples
     --------
@@ -1027,7 +1027,7 @@ class magnetic_gauge:
             The first callable computes the Peierls phase in the scattering
             region and the remaining callables compute the Peierls phases
             in each of the leads. Each callable takes a pair of
-            `~kwant.builder.Site`s 'a, b' and returns a unit complex
+            `~kwant.builder.Site` (a hopping) and returns a unit complex
             number (Peierls phase) that multiplies that hopping.
         """
         return self._peierls(syst_field, *lead_fields, tol=tol, average=False)