Add type annotations for io.vasp.inputs/optics

[DanielYang59]

Summary

• Add type annotations for io.vasp.inputs/optics
• Replace str as path type with PathLike
• Docstring tweaks

Originally

Proposed by @janosh in #3739 (comment).

• Run ruff check . --select ANN204 --unsafe-fixes to auto-fix "ANN204", to experiment on auto typing fix with ruff.
• 135 mypy errors were dug out and need to be fixed.

ANN204 refers to:

Checks that "special" methods, like __init__, __new__, and __call__, have return type annotations.

Summary by CodeRabbit

• New Features

  • Added a 60-second timeout to HTTP requests across various modules to improve system reliability during data fetching.

• Refactor

  • Enhanced code clarity by specifying explicit types for various attributes and variables across multiple modules.

• Bug Fixes

  • Adjusted handling of subprocess output and method argument defaults to prevent errors and improve data handling.

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Commits

Files that changed from the base of the PR and between 2954c80 and 2991771.

Walkthrough

This update primarily focuses on enhancing code clarity and reliability across the pymatgen library and associated scripts. Key changes include the introduction of explicit type annotations for variables and attributes, the addition of timeouts to HTTP requests to prevent hanging processes, and minor adjustments such as renaming variables and updating method signatures. These modifications aim to improve the maintainability and performance of the codebase, ensuring more robust and clear code structure.

Changes

File Path	Change Summary
dev_scripts/update_pt_data.py	Added a 60-second timeout to HTTP requests.
pymatgen/.../filters.py, transmuters.py	Specified structure_list and structure_data as lists.
pymatgen/analysis/...	Updated various attributes to explicitly specify types such as lists and dictionaries.
pymatgen/apps/..., pymatgen/command_line/...	Enhanced clarity with type hints and modified variable handling.
pymatgen/ext/..., pymatgen/io/...	Added timeouts to HTTP requests, updated type annotations in various I/O related files.
pymatgen/transformations/..., pymatgen/vis/...	Updated type specifications for attributes and parameters.
tasks.py, tests/ext/...	Standardized the addition of a 60-second timeout across various test and task scripts.
tests/io/vasp/test_outputs.py	Applied @pytest.mark.skip() decorator to skip certain tests, no significant functionality changes.

This table groups files with similar changes, focusing on type annotations and the addition of timeouts, which are prevalent throughout this update.

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[DanielYang59]

@janosh I re-visited this PR and realized it might not be a good idea to work on a single method globally like this, we should push the type annotation effort module by module.

Though I agree ruff auto-fix is looking promising but we should not run it globally.

My reason being: by working like this, we're just adding types for a single (or very few) function among many other un-typed functions. But as the types within a module heavily depend on others, it would either dig out huge amount of extra work, or make the type very loose.

I would prefer close this and push our type-annotation effort module by module as discussed previously (starting for core, io.vasp, electronic, phonon and such). What do you think?

[janosh]

going folder by folder sounds good. no need to close this PR though, we can just start with pymatgen/io/vasp in this one.

i just reverted the initial

ruff check . --select ANN204 --unsafe-fixes --fix

and force pushed

ruff check pymatgen/io/vasp --select ANN204 --unsafe-fixes --fix

instead and keeping your manual fixes. you just need to run git reset --hard @{u} to get back to the tip of this branch

[DanielYang59]

going folder by folder sounds good. no need to close this PR though, we can just start with pymatgen/io/vasp in this one.

Good point. Let's do it.

instead and keeping your manual fixes. you just need to run git reset --hard @{u} to get back to the tip of this branch

There aren't many valuable fixes though. Thanks for the tip!

[DanielYang59]

The default value of default_names seems inconsistent in:

pymatgen/pymatgen/core/structure.py

Lines 2860 to 2863 in 7f96ef2

	elif fmt_low == "poscar":
	from pymatgen.io.vasp import Poscar
	struct = Poscar.from_str(input_string, default_names=False, read_velocities=False, **kwargs).structure

Changed to None in 1a1752a.

And

pymatgen/pymatgen/io/vasp/inputs.py

Lines 273 to 306 in 7f96ef2

	@classmethod
	def from_str(cls, data, default_names=None, read_velocities=True) -> Self:
	"""
	Reads a Poscar from a string.
	The code will try its best to determine the elements in the POSCAR in
	the following order:
	1. If default_names are supplied and valid, it will use those. Usually,
	default names comes from an external source, such as a POTCAR in the
	same directory.
	2. If there are no valid default names but the input file is VASP5-like
	and contains element symbols in the 6th line, the code will use that.
	3. Failing (2), the code will check if a symbol is provided at the end
	of each coordinate.
	If all else fails, the code will just assign the first n elements in
	increasing atomic number, where n is the number of species, to the
	Poscar. For example, H, He, Li, .... This will ensure at least a
	unique element is assigned to each site and any analysis that does not
	require specific elemental properties should work fine.
	Args:
	data (str): String containing Poscar data.
	default_names ([str]): Default symbols for the POSCAR file,
	usually coming from a POTCAR in the same directory.
	read_velocities (bool): Whether to read or not velocities if they
	are present in the POSCAR. Default is True.
	Returns:
	Poscar object.
	"""

[DanielYang59]

I'm trying to relocate the class methods such that dunder methods and properties come first. But this seems to pollute git history. Wondering if there is a way to relocate codes without such side effect?

[DanielYang59]

Can you please review this @janosh? I decided to separate the work for different modules as there are too many changes. Some return types are removed for completely un-typed __init__ in io.vasp.outputs to avoid mypy checking for now, I would work on it later.

There is one minor fix for the default value of default_names in #3740 (comment).

UPDATE: And there are two requests for changing the default values for type compatibility in #3740 (comment).

Other than these two, I don't expect further functional changes (the unit test failure is related to the requested default value change, I would need your confirmation before I could change the unit test :) ). Thanks!

[janosh]

Wondering if there is a way to relocate codes without such side effect?

not really. have a look at this video which doesn't solve your problem but is slightly relevant

[DanielYang59]

Wondering if there is a way to relocate codes without such side effect?

not really. have a look at this video which doesn't solve your problem but is slightly relevant

Thanks. It's always great to know more tips :)

Should be ready for reviewing then. I reverted the default values to None. Thanks!

[janosh]

can we make the types more specific? list/dict/set/... alone don't add any information for the reader. dict[str, CoordinationGeometry], list[Structure], etc. is more helpful

[DanielYang59]

can we make the types more specific? list/dict/set/... alone don't add any information for the reader. dict[str, CoordinationGeometry], list[Structure], etc. is more helpful

Yes this is very true. But in this PR I was working on adding types for io.vasp, sometimes mypy would complain about other unrelated modules (with need annotation for some line) which I haven't yet got time to look closer into. So in these case I just put a general type to stop mypy from complaining (if I look closely into every module, then the work can never be done).

But I would keep this in mind and try to more specific types :)

[janosh]

thanks so much @DanielYang59! 🙏

given the generic type annotations like var_name: list = [] are easy to find and fix later, we can merge this now

[DanielYang59]

Thanks for reviewing!

given the generic type annotations like var_name: list = [] are easy to find and fix later

Yes I don't know how mypy made those decisions, but it seems to require type annotations for some unrelated and un-typed code sections. Such general types were added to stop such mypy complaints :)