up_sample

Author: jmmshn

pymatgen/analysis/defects/ccd.py

@@ -4,7 +4,7 @@
 import logging
 from dataclasses import dataclass
 from itertools import groupby
-from typing import TYPE_CHECKING, Optional, Sequence, Tuple
+from typing import TYPE_CHECKING
 
 import numpy as np
 from monty.json import MSONable
@@ -20,6 +20,7 @@
 if TYPE_CHECKING:
     from ctypes import Structure
     from pathlib import Path
+    from typing import Optional, Sequence, Tuple
 
     import numpy.typing as npt
     from matplotlib.axes import Axes
@@ -65,9 +66,9 @@ class HarmonicDefect(MSONable):
     charge_state: int
     ispin: int
     vrun: Optional[Vasprun] = None
-    distortions: Optional[list[float]] = None
-    structures: Optional[list[Structure]] = None
-    energies: Optional[list[float]] = None
+    distortions: Optional[Sequence[float]] = None
+    structures: Optional[Sequence[Structure]] = None
+    energies: Optional[Sequence[float]] = None
     defect_band: Optional[Sequence[tuple]] = None
     relaxed_index: Optional[int] = None
     relaxed_bandstructure: Optional[BandStructure] = None
@@ -234,7 +235,7 @@ def _parse_vasprun(vasprun: Vasprun):
             omega=omega,
             charge_state=charge_state,
             ispin=ispin,
-            structures=structures,
+            structures=list(structures),
             distortions=distortions,
             energies=energies,
             defect_band=defect_band,
@@ -313,7 +314,7 @@ def occupation(self, t: npt.ArrayLike | float) -> npt.ArrayLike:
         return 1.0 / (1 - np.exp(-self.omega_eV / KB * t))
 
     def read_wswqs(
-        self, directory: Path, distortions: list[float] | None = None
+        self, directory: Path, distortions: Sequence[float] | None = None
     ) -> None:
         """Read the WSWQ files from a directory.
 

pymatgen/analysis/defects/plotting/phases.py

@@ -90,8 +90,8 @@ def plot_chempot_2d(
     )
     ax.add_patch(patch)
 
-    ax.set_xlabel(f"$\Delta\mu_{{{x_element}}}$ (eV)")
-    ax.set_ylabel(f"$\Delta\mu_{{{y_element}}}$ (eV)")
+    ax.set_xlabel(rf"$\Delta\mu_{{{x_element}}}$ (eV)")
+    ax.set_ylabel(rf"$\Delta\mu_{{{y_element}}}$ (eV)")
     ax.set_xlim(x_min - PLOT_PADDING, 0 + PLOT_PADDING)
     ax.set_ylim(y_min - PLOT_PADDING, 0 + PLOT_PADDING)
     if label_lines:
@@ -102,7 +102,7 @@ def _convex_hull_2d(
     points: list[dict],
     x_element: Element,
     y_element: Element,
-    competing_phases: list = None,
+    competing_phases: list | None = None,
 ) -> list[dict]:
     """Compute the convex hull of a set of points in 2D.
 

pymatgen/analysis/defects/utils.py

@@ -904,7 +904,7 @@ def get_localized_states(
 
 def sort_positive_definite(
     list_in: list, ref1: Any, ref2: Any, dist: Callable
-) -> tuple[list, list[float]]:
+) -> tuple[tuple, tuple[float]]:
     """Sort a list where we can only compute a positive-definite distance.
 
     Sometimes, we can only compute a positive-definite distance between two objects.

pyproject.toml

@@ -100,6 +100,9 @@ line-length = 88
 indent-width = 4
 
 
+
+[tool.ruff.lint]
+# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`).
 # By default, ruff only uses all "E" (pycodestyle) and "F" (pyflakes) rules.
 # Here we append to the defaults.
 select = [
@@ -127,9 +130,6 @@ select = [
   # (ruff-specific) Enable all ruff-specific checks (i.e. not ports of
   # functionality from an existing linter).
   "RUF",
-  # (private member access) Flag access to `_`-prefixed symbols. By default the various special
-  # methods on `NamedTuple` are ignored (e.g. `_replace`).
-  "SLF001",
   # (flake8-type-checking) Auto-sort imports into TYPE_CHECKING blocks depending on whether
   # they are runtime or type-only imports.
   "TCH",
@@ -142,14 +142,10 @@ select = [
   # (invalid escape sequence) flag errant backslashes
   "W605",
 ]
-
-[tool.ruff.lint]
-# Enable Pyflakes (`F`) and a subset of the pycodestyle (`E`).
-select = ["E4", "E7", "E9", "F", "D", "I001", "TCH"]
 ignore = ["E203", "E501", "F401"]
 
 # Allow fix for all enabled rules (when `--fix`) is provided.
-fixable = ["ALL", "TCH"]
+fixable = ["ALL"]
 unfixable = []
 
 # Allow unused variables when underscore-prefixed.