Fix typing_extension ImportError in downstream packages

[janosh]

closes #3751

Summary by CodeRabbit

• Refactor

  • Improved code readability by consolidating imports in core modules.
  • Enhanced type hinting and conditional type checking across various modules.

• Tests

  • Updated test functions with specific error messages for better clarity.

• Chores

  • Updated revision of pre-commit hooks to ensure code quality.

[coderabbitai]

Walkthrough

The recent updates to the pymatgen codebase involve enhancing type handling and code readability. Changes include updating the ruff-pre-commit repository version, consolidating imports in core modules, and adding conditional imports for improved type checking.

Changes

File Path	Change Summary
.pre-commit-config.yaml	Updated ruff-pre-commit repository to v0.3.7
pymatgen/core/...	Grouped imports for better readability
pymatgen/analysis/... pymatgen/ext/... pymatgen/io/abinit/...	Added TYPE_CHECKING and conditional Self imports
tests/io/test_packmol.py	Added import re, error message constant, and test modifications
tests/transformations/...	Removed unnecessary comment directive

Assessment against linked issues

Objective	Addressed	Explanation
Import typing_extension at runtime causing ImportError [#3751]	✅

Poem

🐇 Hop, hop, hooray! Let's celebrate today,
Code has been groomed, with imports well-tuned.
From Self imports sly, to a version bump high,
Every line and dot, makes our code a top-notch spot!
🚀 Let's code away, in a much smoother way!

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Recent Review Details

Configuration used: CodeRabbit UI

Commits

Files that changed from the base of the PR and between 666db91 and 16af9e4.

Files selected for processing (1)

• tests/io/test_packmol.py (4 hunks)

Files skipped from review as they are similar to previous changes (1)

• tests/io/test_packmol.py

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[kavanase]

Hi @janosh @DanielYang59 !
Sorry to be the bearer of bad news, but this issue has cropped up again in the recent release of pymatgen, which again is causing failures in our CI for doped/ShakeNBreak (and I imagine other downstream packages of pymatgen).
(https://github.com/SMTG-Bham/ShakeNBreak/actions/runs/9323684325/job/25667402879, https://github.com/SMTG-Bham/doped/actions/runs/9323686497).

The issue is that typing_extensions is now imported before the TYPE_CHECKING block in pymatgen.core.structure, added in this commit: d0ad785
As far as I can tell, it's correctly imported in the TYPE_CHECKING block in all other usages, but might be worth a quick check.

[janosh]

sorry for the trouble!

we'll get a fix in asap ofc but really we need to setup CI that only installs non-optional deps so we catch these mistakes in the future.

[kavanase]

Also minor issue that doesn't really matter but might be useful to know about, pymatgen.core.periodic_table uses the monty.dev @deprecated() decorator with the deadline keyword argument, but this was only added by @DanielYang59 in v2024.3.31 of monty, but this isn't a version requirement of pymatgen, so when I updated to the new pymatgen it was throwing top_level_collect error messages about this until I upgrade monty.
So probably worth adding monty>=2024.3.31 to the dependencies!

[janosh]

that should be easy to prevent in future since we use uv which offers --resolution=lowest to install the oldest allowed versions of all packages

[DanielYang59]

Sorry for the trouble, again. And I really want some automated import guard against TYPE_CHECKING only imports #3827, which would prevent such issues.

Also minor issue that doesn't really matter but might be useful to know about, pymatgen.core.periodic_table uses the monty.dev @deprecated() decorator with the deadline keyword argument, but this was only added by @DanielYang59 in v2024.3.31 of monty, but this isn't a version requirement of pymatgen, so when I updated to the new pymatgen it was throwing top_level_collect error messages about this until I upgrade monty. So probably worth adding monty>=2024.3.31 to the dependencies!

Looks like I forgot about the monty version in setup.py:

pymatgen/setup.py

Lines 30 to 32 in 2982968

	install_requires=[
	"matplotlib>=1.5",
	"monty>=2024.2.2",

And updated the monty version in requirements.txt alone:

pymatgen/requirements.txt

Line 4 in 2982968

monty==2024.5.24

Perhaps we should reuse requirements.txt in setup.py instead of having duplicates? Maybe there are reasons that I'm not aware of?

[janosh]

Perhaps we should reuse requirements.txt in setup.py instead of having duplicates? Maybe there are reasons that I'm not aware of?

better yet, get rid of requirements.txt as i've been saying for years. no good reasons for keeping it imo

[JaGeo]

I would also be pro removing. Would it actually make sense to have a pymatgen[strict] similar to atomate2[strict] to have exact version numbers of all packages as well?