Migrate spglib to new SpglibDataset format with version 2.5.0 (#3923)

* increment spglig min version

* re-enable part of the test

* use dot notation and tweak code format

* add types for SpacegroupAnalyzer, mypy error to fix

* final round of format tweaks

* re-enable unit test for invalid spg number

* fix mypy errors

* migrate one more in unit test

* add types for PointGroupAnalyzer

* add types for remaining of analyzer

Author: DanielYang59

pyproject.toml

@@ -69,7 +69,7 @@ dependencies = [
     "requests>=2.32",
     "ruamel.yaml>=0.17.0",
     "scipy>=1.13.0",
-    "spglib>=2.0.2",
+    "spglib>=2.5.0",
     "sympy>=1.2",
     "tabulate>=0.9",
     "tqdm>=4.60",