Re-enable some useful ruff rules

[DanielYang59]

Re-enable some useful ruff rules

• COM812: missing-trailing-comma: no change to code base
• ISC001: single-line-implicit-string-concatenation: might conflict with other ruff rules sometimes
• RUF012: mutable-class-default
• PLC1901: compare-to-empty-string: no change to code base
• PYI024collections-named-tuple: make typing of namedtuple possible

REVERTED

• C408: unnecessary-collection-call (confirmed no comment is dropped)

[coderabbitai]

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Walkthrough

The recent updates across various files in the pymatgen library primarily involve the introduction of ClassVar type annotations to class attributes, enhancing clarity on which variables are class-level constants. This change streamlines the handling of configurations and settings across the library, ensuring that these attributes are correctly recognized as static properties of their respective classes.

Changes

Files	Change Summary
.../chemenv/..., .../eos.py, .../composition.py, .../xcfunc.py, .../molecule_structure_comparator.py	Added ClassVar to class dictionary attributes to clarify their usage as static class properties.
.../io/abinit/..., .../io/adf.py, .../io/icet.py, .../io/nwchem.py, .../io/pwscf.py, .../io/vasp/inputs.py	Introduction of ClassVar annotations for various class attributes to enforce their static nature.
.../symmetry/groups.py	Type annotations (ClassVar) added to dictionaries to explicitly define them as class-level attributes.
pyproject.toml	Modifications in linting rules, including the removal of specific checks and adjustments in documentation and exception handling practices.

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[DanielYang59]

@coderabbitai ignore

[coderabbitai]

Actionable comments posted: 0

Out of diff range and nitpick comments (5)

pymatgen/io/vasp/inputs.py (5)

Line range hint 1747-1765: Ensure consistent use of ClassVar for class-level constants.

-    functional_dir: ClassVar = {
+    functional_dir: ClassVar[dict[str, str]] = {

---

Line range hint 1766-1780: Ensure consistent use of ClassVar for class-level constants.

-    functional_tags: ClassVar = {
+    functional_tags: ClassVar[dict[str, dict[str, str]]] = {

---

Line range hint 1780-1804: Ensure consistent use of ClassVar for class-level constants.

-    parse_functions: ClassVar = {
+    parse_functions: ClassVar[dict[str, Callable[[str], Any]]] = {

---

Line range hint 1804-1823: Consider adding type hints to the constructor parameters for clarity.

-    def __init__(self, data: str, symbol: str | None = None) -> None:
+    def __init__(self, data: str, symbol: Optional[str] = None) -> None:

---

Line range hint 1823-1842: Consider adding type hints to the constructor parameters for clarity.

-    def __init__(self, incar: dict | Incar, kpoints: Kpoints | None, poscar: Poscar, potcar: Potcar | None, optional_files: dict[PathLike, object] | None = None, **kwargs) -> None:
+    def __init__(self, incar: Union[dict, Incar], kpoints: Optional[Kpoints], poscar: Poscar, potcar: Optional[Potcar], optional_files: Optional[dict[PathLike, object]] = None, **kwargs) -> None:

[coderabbitai]

@coderabbitai ignore

Actions Performed

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[janosh]

i actually often prefer the dict(foo=bar) version over {"foo": bar} since it's more compact due to not needing so many quotes. this sometimes avoids a line break which imo helps readability. i'd vote to keep C408 in the ignore list

[DanielYang59]

i actually often prefer the dict(foo=bar) version over {"foo": bar} since it's more compact due to not needing so many quotes. this sometimes avoids a line break which imo helps readability.

dict(foo=bar) has one more character than {"foo": bar} including the whitespace. So I assume there is no reason dict() is more compact than {}?

And it seems {} should be faster than dict():

It's unnecessary to call, e.g., dict() as opposed to using an empty literal ({}). The former is slower because the name dict must be looked up in the global scope in case it has been rebound.

[DanielYang59]

It should be ready for review now @janosh. Thanks. Let me know if want to enable any more/less ruff rules.

I tried to enable:

pymatgen/pyproject.toml

Line 72 in 46b018d

"PERF401", # manual-list-comprehension (TODO fix these or wait for autofix)

But it seems to force all kind of list builder into list comprehensions (especially some nested conditions list), which would greatly reduce readability.

[janosh]

dict(foo=bar) is 13 characters and {"foo": bar} is 12 (including the whitespace).

that inverts once you have 2 or more keys in your dict. at that point the collection call is shorter

[DanielYang59]

dict(foo=bar) is 13 characters and {"foo": bar} is 12 (including the whitespace).

that inverts once you have 2 or more keys in your dict. at that point the collection call is shorter

That's true. But if you look into the commit 38a5aa7, it appears among all changes, this case you mentioned (where a line is broken by extra characters) only happened once for:

pymatgen/pymatgen/io/vasp/sets.py

Line 2219 in 46b018d

updates = dict(LCHARG=False, NELM=60, PREC="Normal", EDIFFG=-0.02, ICHARG=0, NSW=200, EDIFF=0.0001)

And all other changes didn't introduce any additional line.

But anyway, feel free to revert that commit if you really prefer not to change that (it's all automatically changed by ruff so wasn't any effort from me). But at least we should search and replace some list() or dict().

[janosh]

thanks @DanielYang59, lgtm! 👍

[DanielYang59]

Beautiful. Thanks for reviewing @janosh Appreciate it.

[DanielYang59]

I forgot to remove this TODO tag for PERF401, would do it in another PR.

I'm pretty sure we don't really want to enable this rule:

it seems to force all kind of list builder into list comprehensions (especially some nested conditions list), which would greatly reduce readability.

[DanielYang59]

I just look into this speed comparison between dict() and {}, and it surprised me as the speed improvement seems quite significant (could be more than 2x the time for dict()). I thought it was just minor improvement like ~10%.