When the fundamental domains of the constituent symmetries
of a wrapped around system do not coincide, it was previously
possible for wrapping around to fail when 'keep' was provided,
even if wrapping around succeeded with 'keep=None'.

Rafal Skolasinski authored 7 years ago and Joseph Weston committed 7 years ago

Arguments of "discretize", "discretize_symbolic", and "build_discretized"
that does not represent Hamiltonian or discrete coordinates are now keyword-only.
Also "lattice_constant" argument is renamed to "grid_spacing" in order to
distinguish it from real lattice constant of a crystal. Closes 110.

Closes #113.

This allows to provide a helpful error message when someone tries to
import Kwant with Python 2.

Note that I moved the version code into a module of its own:
kwant.version.  The rationale is to separate this code from unrelated
stuff in kwant._common that requires various external libs.  The
kwant.version module should work on its own without any third-party
libraries.

This makes it possible to use colormaps that are white at zero and still
distinguish areas with and without sites.

This function is adapted to plotting band structure in the case
where the translation symmetry vectors are not orthogonal
(e.g. graphene). It can only handle a very limited subset of
systems (2D lattices in 2D realspace), and most of the time
use of 'plotter.spectrum' should be preferred.

This adds some extra attributed on finalization, which allow the
momentum parameter names and symmetry of the original Builder to
be accessed from the finalized wrapped-around builder.

'plotter.spectrum' can be used to plot the spectrum of
a Hamiltonian as a function of arbitrary parameters. This is
generically useful functionality, so we factor it out.

We build conda packages on 'master' (on all forks) by default.
Builds for branches may be triggered manually.

Conda forge removes support for Python 3.4. If anyone is using
conda then they can easily upgrade to newer Python in any case.

Previously we used 'ssh-keyscan' on every upload, so derived
no security from host key checking. 'ssh-keyscan' caused the CI
server's IP to be blacklisted, so now we just ignore the host key
entirely. We never send private information, so this is fine.

We previously restricted conda package uploading to master branch on the
main Kwant repository, as otherwise this step would fail for forked
repositories without a valid anaconda key. Now we build the conda
packages and upload to anaconda in two separate jobs, and the upload job
is only run on the main Kwant repository.

Previously, if a tuple of floats was passed as the 'domain' argument to
'act' then the tags of the resulting sites would be floats, rather than
integers. This is because the tags of sites created inside 'act' were
not normalized to integers, as they would usually be, and this causes
bugs in other locations where an integer dtype is assumed.

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

Passing arguments via 'args' will be deprecated in a future
release, and will be removed in Kwant 2.0, so any new features
should only support 'params'.

We also now properly 'bind' parameters to the passed operator;
previously the parameters were not passed correctly.

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

the '_defs' module is used solely when generating images
within the tutorial part of the documentation.

Previously, 'syst.fill(template, shape, start)' would return
successfully even if all sites in domain 'start' are outside of 'shape'.
This is in contrast to the behaviour of 'lattice.shape'.
In addition, if the target builder already has sites in the start domain
and `overwrite=False` then we should raise an exception, as this is
probably not what the user expects.

Closes #107

Rafal Skolasinski authored 8 years ago and Joseph Weston committed 8 years ago

Currently when 'build_discretized' receives onsite and hoppings to build
kwant template system it checks if the input expression contains
position operators as symbols. Because at this moment commutative relations
don't play any significant role it is enough to check by symbol names.

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).