3d plots of unit cells

[argerlt]

Breaking out this part of #563 into it's own PR. It can be pushed before or after #647.

Description of the change

Adds the unit cell plotting tool originally mentioned in #563 before that spiraled out into a bigger topic. I can add examples now if we want, but similar to #647, it might make more sense to add examples as part of #563 while replacing the related tutorial notebooks.

Progress of the PR

• Docstrings for all functions
• Unit tests with pytest for all lines
• Clean code style by running black via pre-commit

Minimal example of the bug fix or new feature

import orix.crystal_map as ocm
import matplotlib.pyplot as plt
import diffpy.structure as dst

# define two different phases slightly different ways.

# Alumina first
Al2O3_atoms = [
    dst.Atom("Al", [1 / 3, 2 / 3, 0.815]),
    dst.Atom("O", [0.361, 1 / 3, 0.583]),
]
Al2O3_lattice = dst.Lattice(0.481, 0.481, 1.391, 90, 90, 120)
Al2O3_structure = dst.Structure(atoms=Al2O3_atoms, lattice=Al2O3_lattice)
Al2O3_phase = ocm.Phase(
    name="Alumina",
    space_group=167,
    structure=Al2O3_structure,
    color="red",
).expand_asymmetric_unit()

# Then alpha iron
Fe_atoms = [
    dst.Atom("Fe", [0, 0, 0]),
    dst.Atom("Fe", [1, 0, 0]),
    dst.Atom("Fe", [0, 1, 0]),
    dst.Atom("Fe", [0, 0, 1]),
    dst.Atom("Fe", [0, 1, 1]),
    dst.Atom("Fe", [1, 0, 1]),
    dst.Atom("Fe", [1, 1, 0]),
    dst.Atom("Fe", [1, 1, 1]),
    dst.Atom("Fe", [1 / 2, 1 / 2, 1 / 2]),
]
Fe_lattice = dst.Lattice(1, 1, 1, 90, 90, 90)
Fe_structure = dst.Structure(atoms=Fe_atoms, lattice=Fe_lattice)
Fe_phase = ocm.Phase(point_group="m3m", structure=Fe_structure)

# For both, make a standard plot, as well as a nicer one.
for p in [Al2O3_phase, Fe_phase]:
    fig1 = p.plot_unit_cell(figsize=[5, 4], return_figure=True)
    p.plot_unit_cell(show_xyz=True, show_atoms=True, show_uvw_labels=True)

For reviewers

• The PR title is short, concise, and will make sense 1 year later.
• New functions are imported in corresponding __init__.py.
• New features, API changes, and deprecations are mentioned in the unreleased
  section in CHANGELOG.rst.
• Contributor(s) are listed correctly in __credits__ in orix/__init__.py and in
  .zenodo.json.

[argerlt]

pre-commit.ci autofix

[CSSFrancis]

I've been playing around with creating a new plotting library backend for hyperspy and other related EM packages. I wonder if it might be useful here eventually.

https://cssfrancis.github.io/anyplotlib/dev/auto_examples/plot_3d.html

I might need to add additional functionality but I don't think it should be too difficult to support something like this.

[argerlt]

I've been playing around with creating a new plotting library backend for hyperspy and other related EM packages. I wonder if it might be useful here eventually.

https://cssfrancis.github.io/anyplotlib/dev/auto_examples/plot_3d.html

I think what I'm doing here is too basic for anyplotlib, and I also want to keep dependencies as low as possible so I can use this feature later on as an overlay for crystal map plots.

That said, keeping this as a mental note for when I finally get around to adding ODF's. Half the battle there is making interactive plots that don't look like garbage when embedded in a readthedocs.