Bump phonopy from 2.43.2 to 2.43.6 (#412)

* Bump phonopy from 2.43.2 to 2.43.6

Bumps [phonopy](https://github.com/phonopy/phonopy) from 2.43.2 to 2.43.6.
- [Changelog](https://github.com/phonopy/phonopy/blob/develop/doc/changelog.md)
- [Commits](phonopy/phonopy@v2.43.2...v2.43.6)

---
updated-dependencies:
- dependency-name: phonopy
  dependency-version: 2.43.6
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <[email protected]>

* [dependabot skip] Update environment

* fix cell

* fix chemical symbols

* fix positions

---------

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: pyironrunner <[email protected]>
Co-authored-by: Jan Janßen <[email protected]>

Author: 3 people

.ci_support/environment.yml

@@ -10,7 +10,7 @@ dependencies:
 - nglview =3.1.4
 - notebook
 - numpy =2.3.4
-- phonopy =2.43.2
+- phonopy =2.43.6
 - plotly =6.3.1
 - pymatgen =2025.6.14
 - pyscal3 =3.3.0

pyproject.toml

@@ -53,7 +53,7 @@ surface = [
     "pymatgen==2025.6.14",
 ]
 phonopy = [
-    "phonopy==2.43.2",
+    "phonopy==2.43.6",
     "spglib==2.6.0",
 ]
 

structuretoolkit/common/phonopy.py

@@ -11,9 +11,9 @@ def phonopy_to_atoms(ph_atoms) -> Atoms:
 
     """
     return Atoms(
-        symbols=list(ph_atoms.get_chemical_symbols()),
-        positions=list(ph_atoms.get_positions()),
-        cell=list(ph_atoms.get_cell()),
+        symbols=list(ph_atoms.symbols),
+        positions=list(ph_atoms.positions),
+        cell=list(ph_atoms.cell),
         pbc=True,
     )