builder.fill: Make starting sites that are not in the template a warning, and improve the warning message in this case.

See merge request kwant/kwant!244

We raise a warning and remove the sites from 'start', so as to avoid
cryptic 'KeyError's later.

Also take an early exit if there are no starting sites in the template,
to avoid a spurious warning about all starting sites already being
present in the target.

Closes #224.

This is the standard way to re-raise errors and makes the messages
easier to follow.

Simplifications and optimizations of how parameters are handled

Closes #228

See merge request kwant/kwant!243

Christoph Groth authored 6 years ago and Joseph Weston committed 6 years ago

Co-authored-by: Joseph Weston <joseph@weston.cloud>

Christoph Groth authored 6 years ago and Joseph Weston committed 6 years ago

With this, wrapping parameter-substituted value functions is no longer
necessary and any overhead of using builder parameter substitutions
disappears.

Co-authored-by: Joseph Weston <joseph@weston.cloud>

Christoph Groth authored 6 years ago and Joseph Weston committed 6 years ago

Co-authored-by: Joseph Weston <joseph@weston.cloud>

Christoph Groth authored 6 years ago and Joseph Weston committed 6 years ago

and without default values.

Co-authored-by: Joseph Weston <joseph@weston.cloud>

Christoph Groth authored 6 years ago and Joseph Weston committed 6 years ago

This requires changes to other modules, but these were kept to a
minimum.  The most important one is that
builder._FinalizedBuilderMixin.hamiltonian() now always calls value
functions using *args.

So it's no longer necessary to provide the REFNAME environment variable.
Also the link template string format is now more general to support at
least gitlab github and cgit.

Previously we masked points that are further than a "typical" distance
from any site. This was determined as the minimal nearest-neighbor
distance from 10 arbitrarily chosen sites. Now we mask points where
the bump function is zero (as it has finite support).

Closes #219.

Previously we had forgotten the padding, so the mask was applied
at the wrong position.

The former creates a numpy.matrixlib.matrix object, while the latter a regular
numpy array.

Closes #218

'box-forced' is deprecated as of matplotlib 2.2.

Gitlab now has built-in mirroring, so we don't need to have a CI
step for this now.

Refactor 'plotter.density' into 'plotter.scalarplot' and
fix up plotter docstrings.

Now 'plotter.density' is just the composition of
'interpolate_density' and 'scalarplot', which makes it easier
for users to customise if they need.

See merge request kwant/kwant!223

Previously 'plotter.density' was not as well factored as
'plotter.current', which made it hard to compose, e.g. for
passing custom parameters to 'plotter.interpolate_density'.

Gitlab now has built-in mirroring, so we don't need to have a CI
step for this now.

Allow different lattice spacing in each dimension for 'kwant.continuum'. Also simplify the processing of
'grid' and 'grid_spacing' and fix up some docstrings

Closes #197

See merge request kwant/kwant!220

Python's lack of block scope means that we should avoid
temporaries where they don't significantly clarify meaning

Previously parts of the docstrings for 'density' and 'current'
had been switched.