Previously the testing/importing 'continuum' would fail if sympy was not
installed. Now we do the following:

    * add sympy as an optional dependency in 'extras_require'
    * force pytest to ignore tests in packages that have uninstalled
      dependencies by defining a hook in 'conftest.py'
    * use the 'class as a module' hack when importing 'continuum'.
      When sympy is not installed the continuum module will be replaced
      with an instance of 'ExtensionUnavailable' that will raise a runtime
      error on attribute access.
    * no warning is raised if sympy is not installed (it is an
      optional dependency).

The check 'if vec' is changed to 'if vec is not None', as the
truth value of an array is ambiguous.

Numpy's leastsquares implementation sometimes produces memory errors,
but Scipy's appears to be unaffected (at least for the cases seen
thus far).

So far substitutions were accepted in form ''string key: sympy expression'',
which was extended to accept form of ''string key: string expression'.
Also 'substitutions' were only used when input 'hamiltonian' was not a sympy
object already, which got alternated to apply them always. Closes #97.

No extra logic is added to wraparound, we just transfer over extra
Builder attributes to the wrapped around system, being careful to
set TR and PH symmetry to None (for the k-space Hamiltonian these
are only satisfied at special points in the Brillouin zone, and
currently there is no way in Kwant to specify that symmetries only
appear for certain parameter values).

No change in functionality.  Split tests out into a separate module
remove (for now) functionality for plotting 2D band structures for
wrapped-around systems.

Fixes #92.

Previously, the API was formally incompatible, as user-provided
mode/selfenergy functions required a 'params' keyword argument,
which was not required by the API in Kwant 1.2. Fixes #96.

original repository: https://gitlab.kwant-project.org/r-j-skolasinski/discretizer
base commit: 2ca27cd988f13925ef78202136712843a0c06162
developed by: Rafal Skolasinski and Sebastian Rubbert

Pablo Piskunow authored 8 years ago and Joseph Weston committed 8 years ago

Also refactor '_update_moments_list' and add some tests
to check for when an odd number of KPM moments is used.

Hamiltonian value functions may now have signatures that depend on
different parameters. On finalization, Builders now inspect all of their
value functions and store the names of the parameters on which the value
function depends. Then, when evaluating the Hamiltonian, a particular
value function is only passed the parameters on which it depends.

'System.hamiltonian' has been updated to accept an extra keyword-only
parameter, 'params', which is a dictionary mapping parameter names to
values. This is mutually exclusive with the existing '*args'. All
top-level API that takes an 'args' parameter now also takes a
keyword-only parameter, 'params'

Pablo Piskunow authored 8 years ago and Joseph Weston committed 8 years ago

Now, the tolerance to which the spectral bounds of the Hamiltonian
are calculated is set by 'epsilon', which also controls the
rescaling of the Hamiltonian to ensure that the spectral bounds are
strictly between (-1, 1). Also the spectral bounds are only calculated
*once* (if not provided by the user).

Tómas authored 8 years ago and Joseph Weston committed 8 years ago

Uses the new conservation law and discrete symmetry interface
to Builder, and illustrates the separation of the scattering matrix into
blocks depending on conservation law eigenvalue.

Also improve the documentation for operators in general.

special methods are not included by autodocs by default, and
as class documentation pages are generated by autosummary,
we cannot just explicitly include __call__. We get around this
by using a custom autosummary template for the operator classes.

For cython extension modules, the method signature for __call__
is still not embedded properly.
See https://github.com/cython/cython/issues/1577.

This patch fixes the reasons for compiler warnings in
 - partitioner (signed unsigned comparison),
 - graph/util (maybe uninitialized),
 - operator (maybe uninitialized).