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.

Closes #207.

pyplot "attaches" a figure to a backend on calling pyplot.figure. Previously we
implemented a hack that worked around this limitation in case the user did not
import pyplot. However this hack is fragile and breaks new things with newer
matplotlib versions. Now we detect whether the figure is intended for pyplot
and import pyplot directly if it is.

This change also allows us to simplify the interface and the implementation of
output_fig, but this is permitted because it is an internal function.

clarify usage of pseudoinverse, and factor out
rank checks for primitive lattice vectors

Closes #209.

See merge request kwant/kwant!231

Rafal Skolasinski authored 6 years ago and Joseph Weston committed 6 years ago

Currently code that do constraints check on "prim_vecs" during lattice
creation is doubled. In addition to factoring it out into separate
function this commit also adds check if "prim_vecs" are linearly independent.

This was always what was meant semantically; newer versions
of Scipy are stricter about what they accept for row/column
indices for COO matrices.

Closes #211.

Kwant no longer builds with Cython 0.22, and our oldest
supported operating systems ship with at least 0.24.3
as of now.

Closes #204

In the future numpy will not allow multidimensional slices that
are specified as sequences other than tuples.

Closes #210.

Fix compatibility issues with Sympy 1.2.

Closes #203.

See merge request kwant/kwant!228

Rafal Skolasinski authored 6 years ago and Joseph Weston committed 6 years ago

Previously we were manually computing the position from
the site tag an an extra 'grid_spacing' parameter. Even
though we now have one additional Python function call,
using the position as determined by the underlying lattice
is less susceptible to bugs.

Closes #199.

Rafal Skolasinski authored 6 years ago and Joseph Weston committed 6 years ago

SymPy 1.2 brought changes to LambdaPrinter that broke kwant.continuum
for inputs containing functions like "sin", "cos", or constant "pi".
By this fix we assert that "kwant.continuum.sympify" represents in
its output all functions as AppliedUndef in favour to built-in SymPy
functions. We also put a hard constaint that all functions and constants
in the input expression (with except to pi) must be provided through params.

Backport of commit 499f3d91 to stable branch.
Closes #208.