This is to work around
https://github.com/cython/cython/issues/4153

Update to upstream version '1.4.4'
with Debian dir 8def8a542b2194d410ecd66e752084f9dfd4a1ed

Kostas Vilkelis authored 2 years ago and Anton Akhmerov committed 1 year ago

closes #418

Sympy used to implicitly cast Symbol to Function but stopped in v1.10.
Our tests (but not code) relied on the casting behavior, and here we fix
this ambiguity.

See
- https://github.com/scipy/scipy/pull/15220
- https://github.com/scipy/scipy/issues/14360


Currently, it gives the following error message:
```
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
Input In [29], in <module>
----> 1 from scipy.sparse.linalg import linsolve

ImportError: cannot import name 'linsolve' from 'scipy.sparse.linalg' (/nfshome/basnijholt/mambaforge/envs/qms-lab-20220224-main/lib/python3.9/site-packages/scipy/sparse/linalg/__init__.py)
```

With this change, the following warning is emitted:
```
/tmp/scratch/basnijholt/ipykernel_59547/2794395227.py:1: DeprecationWarning: The module `scipy.sparse.linalg.dsolve.linsolve` is deprecated. All public names must be imported directly from the `scipy.sparse.linalg` namespace.
  from scipy.sparse.linalg.dsolve import linsolve
```

The following gives no warning:
```
from scipy.sparse.linalg._dsolve import linsolve
```

However, we should reconsider using private features.

Fix Numpy-related deprecation warnings

See merge request kwant!397

Anton Akhmerov authored 4 years ago and Viacheslav Ostroukh committed 3 years ago

Closes #386

Sympy 1.7 broke alias `sympy.numbers` and `sympy.core.numbers` should be used
instead. Second alias, however, can't be used in eariler Sympy version. This
fix uses one of them, dependent on what attribute is present.

Backport Matplotlib fixes from master

See merge request kwant!395

Viacheslav Ostroukh authored 3 years ago and Viacheslav Ostroukh committed 3 years ago

`renderer` argument of mplot3d's `do_3d_projection()` is deprecated in
Matplotlib 3.4. This commit switches from using (also deprecated) `renderer.M`
to `self.axes.M`.

A warning about `renderer` being deprecated is still emitted, but we still
need to keep `renderer=None` statements for reverse compatibility.

The issue is in Matplotlib. This is a temporary solution before [1] is merged.

Fixes #407.

[1] https://github.com/matplotlib/matplotlib/pull/20416

Transpose array-like in herm_conj

See merge request kwant!387

If value passed to `herm_conj()` function can't be conjugated as an
array or a number, attempt to convert it to a tinyarray is performed.
In that way array-like list of lists/tuples can also be conjugated
correctly.

Fixes #406

If onsite/hopping value was supplied to the builder as array-like instead of
proper array, Hamiltonian could be generated silently without any Hermitian
conjugation, if required.

To expose this, `test_builder.py::test_hermitian_conjugation` is
parametrized with different types of values to ensure that Numpy arrays,
tinyarrays, lists and tuples are all conjugated properly.

See issue #406.

Merge CI fixes from master

See merge request kwant!392

This is done instead of picking all changes that were commited to master
and not reflected in stable.

Current master revision is 8a6d320be25dc30b38064bb02341ea2458ebf77a.