Improve type annotations for core.structure

[DanielYang59]

Summary

• Improve type annotations for core.structure
• Fix some type: ignore[reportPossiblyUnboundVariable]

A question from me:

What is the difference between np.ndarray, ArrayLike and NDArray for typing?

ArrayLike: type[Buffer] | type[_SupportsArray[dtype[Any]]] | type[_NestedSequence[_SupportsArray[dtype[Any]]]] | type[bool] | type[int] | type[float] | type[complex] | type[str] | type[bytes] | type[_NestedSequence[bool | int | float | complex | str | bytes]]

NDArray: type[ndarray[Any, dtype[_ScalarType_co@NDArray]]]

[DanielYang59]

@janosh Can you please review this? Thanks.

[janosh]

thanks @DanielYang59! 👍

[DanielYang59]

Thanks for reviewing and the tweaks!

[wortelboer]

Hello,
Today I ran into an issue while using pymatgen 2024.5.31, that I think might be related to this contribution. I am using a fresh conda environment, python 3.11, with pymatgen installed via pip install pymatgen. I get an error when trying to import from pymatgen.core.structure:

>>> from pymatgen.core import Structure
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "~\AppData\Local\miniconda3\envs\test311\Lib\site-packages\pymatgen\core\__init__.py", line 17, in <module>
    from pymatgen.core.structure import IMolecule, IStructure, Molecule, PeriodicNeighbor, SiteCollection, Structure
  File "~\AppData\Local\miniconda3\envs\test311\Lib\site-packages\pymatgen\core\structure.py", line 39, in <module>
    from typing_extensions import Self
ModuleNotFoundError: No module named 'typing_extensions'

If I then install typing-extensions separately, things seem to work fine. In v2024.5.31's setup.py I see that typing-extensions is listed under extras_require["dev"]. My understanding of setup.py is limited though. Should I install pymatgen in a different way?
Thank you in advance.

[DanielYang59]

Hi @wortelboer thanks for asking and sorry for the trouble caused, I forgot to guard a typing_extensions import, and I'm asking Shyue to yank current release and issue a new one to fix this. You could manually install typing-extensions for now, until a new release is up.