Fix Numpy-related deprecation warnings

See merge request kwant/kwant!397

Anton Akhmerov authored Aug 30, 2020 and Viacheslav Ostroukh committed Jun 22, 2021

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/kwant!395

Viacheslav Ostroukh authored Jun 14, 2021 and Viacheslav Ostroukh committed Jun 18, 2021

`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

Improvements in documentation automated build

See merge request kwant/kwant!391

Sphinx-4.0 fails to correctly process attributes docstrings/doc comments.
Using unreleased Sphinx-4.1 will allow to properly document class attributes,
escpecially it is benefitial in the case of documenting inherited attributes.

Napoleon Sphinx extension seems to be a drop-in replacement, which handles attributes' documentation better.

Transpose array-like in herm_conj

See merge request kwant/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/kwant!392

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

Current master revision is 8a6d320b.

Clean up linear algebra (related to modes)

See merge request kwant/kwant!389

`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

Merge request !370 was supposed to make Python 3.7 minimal required version,
but in some places 3.6 sneaked from attention. This commit fixes that.

In many cases bug [1] causes `scipy.sparse.coo_matrix` to cast complex matrix to float.

[1] https://github.com/scipy/scipy/issues/13585