Merge branch 'main' into dependabot/pip/numpy-2.2.4

Author: jan-janssen

.ci_support/environment.yml

@@ -11,10 +11,10 @@ dependencies:
 - notebook
 - numpy =2.2.4
 - phonopy =2.38.0
-- plotly =6.0.0
+- plotly =6.0.1
 - pymatgen =2025.3.10
 - pyscal3 =3.2.7
-- pyxtal =1.0.6
+- pyxtal =1.0.7
 - scikit-learn =1.6.1
 - scipy =1.15.2
 - spglib =2.6.0

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.10
+    rev: v0.11.0
     hooks:
       - id: ruff
         name: ruff lint

pyproject.toml

@@ -44,7 +44,7 @@ grainboundary = [
 pyscal = ["pyscal3==3.2.7"]
 nglview = ["nglview==3.1.4"]
 matplotlib = ["matplotlib==3.10.1"]
-plotly = ["plotly==6.0.0"]
+plotly = ["plotly==6.0.1"]
 clusters = ["scikit-learn==1.6.1"]
 symmetry = ["spglib==2.6.0"]
 surface = [
@@ -55,7 +55,7 @@ phonopy = [
     "phonopy==2.38.0",
     "spglib==2.6.0",
 ]
-pyxtal = ["pyxtal==1.0.6"]
+pyxtal = ["pyxtal==1.0.7"]
 
 [tool.setuptools.packages.find]
 include = ["structuretoolkit*"]

structuretoolkit/analyse/neighbors.py

@@ -107,7 +107,7 @@ def _set_mode(self, new_mode: str) -> None:
             raise KeyError(
                 f"{new_mode} not found. Available modes: {', '.join(self._mode.keys())}"
             )
-        self._mode = {key: False for key in self._mode}
+        self._mode = dict.fromkeys(self._mode, False)
         self._mode[new_mode] = True
 
     def __repr__(self) -> str: