Fix phase list when initializing CrystalMap with a sparse phase list

[hakonanes]

Description of the change

This is a fix for a bug spotted by @Erlendos12 in pyxem/kikuchipy#620. When a CrystalMap is initialized with a phase ID array with more IDs than there are phases in the given phase list, the returned map does not link the phase ID array with the correct phase in the phase list. It does with this fix. See below for an example.

I'd like to release a 0.11.1 patch with this fix as soon as this PR is merged onto main, if that is OK with people.

Progress of the PR

• Docstrings for all functions
• Unit tests with pytest for all lines
• Clean code style by running black via pre-commit
• Fix docs (https://readthedocs.org/projects/orix/builds/19674675/), see "icon_links" required in html_theme_options in v0.13.0 pydata/pydata-sphinx-theme#1220

Minimal example of the bug fix or new feature

>>> import numpy as np
>>> from orix.crystal_map import CrystalMap, PhaseList
>>> from orix.quaternion import Rotation
>>> pl = PhaseList(ids=[1], names=["b"], space_groups=[225])
>>> pl
Id  Name  Space group  Point group  Proper point group     Color
 1     b        Fm-3m         m-3m                 432  tab:blue
>>> phase_id = np.array([0, 0, 1, 1, 1, 3])
>>> xmap = CrystalMap(
...     rotations=Rotation.identity(phase_id.size),
...     is_in_data=phase_id == 1,
...     phase_list=pl,
...     phase_id=phase_id,
... )

# Output with 0.11.0

>>> xmap
Phase  Orientations  Name  Space group  Point group  Proper point group       Color
    1    3 (100.0%)  None         None         None                None  tab:orange
Properties: 
Scan unit: px
>>> xmap.phases
Id  Name  Space group  Point group  Proper point group       Color
 0     b        Fm-3m         m-3m                 432    tab:blue
 1  None         None         None                None  tab:orange
 3  None         None         None                None   tab:green


# Output after fix (with upcoming 0.11.1)

>>> xmap
Phase  Orientations  Name  Space group  Point group  Proper point group     Color
    1    3 (100.0%)     b        Fm-3m         m-3m                 432  tab:blue
Properties: 
Scan unit: px
>>> xmap.phases
Id  Name  Space group  Point group  Proper point group       Color
 0  None         None         None                None  tab:orange
 1     b        Fm-3m         m-3m                 432    tab:blue
 3  None         None         None                None   tab:green

This example is also an added test.

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.

[harripj]

Thanks for the ping! Looks good to me, also happy with the patch release. I'll leave the merge to you 😊

[hakonanes]

Thanks, Patrick! Tomorrow, Wednesday, I'll update the changelog date, merge and release.