Merge branch 'master' into master

.github/workflows/issue-metrics.yml

@@ -9,6 +9,8 @@ permissions:
 
 jobs:
   build:
+    # prevent this action from running on forks
+    if: github.repository == 'materialsproject/pymatgen'
     name: issue metrics
     runs-on: ubuntu-latest
     permissions:

.pre-commit-config.yaml

@@ -2,16 +2,16 @@ exclude: ^(docs|tests/files|tasks.py)
 
 ci:
   autoupdate_schedule: monthly
-  skip: [ mypy, pyright ]
+  skip: [mypy, pyright]
   autofix_commit_msg: pre-commit auto-fixes
   autoupdate_commit_msg: pre-commit autoupdate
 
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.4
+    rev: v0.5.6
     hooks:
       - id: ruff
-        args: [ --fix, --unsafe-fixes ]
+        args: [--fix, --unsafe-fixes]
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
@@ -22,24 +22,24 @@ repos:
       - id: trailing-whitespace
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.11.0
+    rev: v1.11.1
     hooks:
       - id: mypy
 
   - repo: https://github.com/codespell-project/codespell
     rev: v2.3.0
     hooks:
       - id: codespell
-        stages: [ commit, commit-msg ]
-        exclude_types: [ html ]
-        additional_dependencies: [ tomli ] # needed to read pyproject.toml below py3.11
+        stages: [commit, commit-msg]
+        exclude_types: [html]
+        additional_dependencies: [tomli] # needed to read pyproject.toml below py3.11
         exclude: src/pymatgen/analysis/aflow_prototypes.json
 
   - repo: https://github.com/MarcoGorelli/cython-lint
     rev: v0.16.2
     hooks:
       - id: cython-lint
-        args: [ --no-pycodestyle ]
+        args: [--no-pycodestyle]
       - id: double-quote-cython-strings
 
   - repo: https://github.com/adamchainz/blacken-docs
@@ -56,15 +56,15 @@ repos:
         # MD033: no inline HTML
         # MD041: first line in a file should be a top-level heading
         # MD025: single title
-        args: [ --disable, MD013, MD024, MD025, MD033, MD041, "--" ]
+        args: [--disable, MD013, MD024, MD025, MD033, MD041, "--"]
 
   - repo: https://github.com/kynan/nbstripout
     rev: 0.7.1
     hooks:
       - id: nbstripout
-        args: [ --drop-empty-cells, --keep-output ]
+        args: [--drop-empty-cells, --keep-output]
 
   - repo: https://github.com/RobertCraigie/pyright-python
-    rev: v1.1.373
+    rev: v1.1.374
     hooks:
       - id: pyright

dev_scripts/chemenv/explicit_permutations.py

@@ -10,6 +10,7 @@
 import os
 
 import numpy as np
+
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
     AllCoordinationGeometries,
     ExplicitPermutationsAlgorithm,

dev_scripts/chemenv/explicit_permutations_plane_algorithm.py

@@ -9,6 +9,7 @@
 import json
 
 import numpy as np
+
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,

dev_scripts/chemenv/get_plane_permutations_optimized.py

@@ -15,6 +15,7 @@
 
 import numpy as np
 import tabulate
+
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,

dev_scripts/chemenv/strategies/multi_weights_strategy_parameters.py

@@ -8,6 +8,7 @@
 
 import matplotlib.pyplot as plt
 import numpy as np
+
 from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
     AngleNbSetWeight,
     CNBiasNbSetWeight,
@@ -50,7 +51,9 @@ def __init__(self, initial_environment_symbol, expected_final_environment_symbol
         self.abstract_geometry = AbstractGeometry.from_cg(self.coordination_geometry)
 
     @classmethod
-    def simple_expansion(cls, initial_environment_symbol, expected_final_environment_symbol, neighbors_indices):
+    def simple_expansion(
+        cls, initial_environment_symbol, expected_final_environment_symbol, neighbors_indices
+    ) -> CoordinationEnvironmentMorphing:
         """Simple expansion of a coordination environment.
 
         Args:

dev_scripts/chemenv/test_algos.py

@@ -8,6 +8,7 @@
 from random import shuffle
 
 import numpy as np
+
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import AllCoordinationGeometries
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import (
     AbstractGeometry,

dev_scripts/chemenv/view_environment.py

@@ -3,6 +3,7 @@
 from __future__ import annotations
 
 import numpy as np
+
 from pymatgen.analysis.chemenv.coordination_environments.coordination_geometries import (
     SEPARATION_PLANE,
     AllCoordinationGeometries,

dev_scripts/potcar_scrambler.py

@@ -9,6 +9,7 @@
 import numpy as np
 from monty.os.path import zpath
 from monty.serialization import zopen
+
 from pymatgen.core import SETTINGS
 from pymatgen.io.vasp import Potcar, PotcarSingle
 from pymatgen.io.vasp.sets import _load_yaml_config

dev_scripts/update_pt_data.py

@@ -11,9 +11,10 @@
 import requests
 from monty.dev import requires
 from monty.serialization import dumpfn, loadfn
-from pymatgen.core import Element, get_el_sp
 from ruamel import yaml
 
+from pymatgen.core import Element, get_el_sp
+
 try:
     from bs4 import BeautifulSoup
 except ImportError:

dev_scripts/update_spacegroup_data.py

@@ -12,6 +12,7 @@
 import sys
 
 from monty.serialization import dumpfn, loadfn
+
 from pymatgen.symmetry.groups import PointGroup
 
 __author__ = "Katharina Ueltzen @kaueltzen"
@@ -29,7 +30,7 @@ def convert_symmops_to_sg_encoding(symbol: str) -> str:
     Args:
         symbol (str): "hermann_mauguin" or "universal_h_m" key of symmops.json
     Returns:
-        symbol in the format of SYMM_DATA["space_group_encoding"] keys
+        str: symbol in the format of SYMM_DATA["space_group_encoding"] keys
     """
     symbol_representation = symbol.split(":")
     representation = ":" + "".join(symbol_representation[1].split(" ")) if len(symbol_representation) > 1 else ""
@@ -50,7 +51,7 @@ def remove_identity_from_full_hermann_mauguin(symbol: str) -> str:
     Args:
         symbol (str): "hermann_mauguin" key of symmops.json
     Returns:
-        short "hermann_mauguin" key
+        str: short "hermann_mauguin" key
     """
     if symbol in ("P 1", "C 1", "P 1 "):
         return symbol