refactor: unify and modernize periodic table utilities and typing

- Replace atomsymb and atommass tuples with AtomInfo dataclass and PTable enum for atomic data
- Refactor all usages to access atomic symbol and mass via PTable methods
- Remove nptyping dependency, switch to numpy.typing for type annotations
- Update molecule and atom classes to use new typing and atomic data access
- Bump numpy version to 2.x and remove nptyping from dependencies

pyproject.toml

@@ -18,11 +18,10 @@ version = "0.0.0"
 
 
 [tool.poetry.dependencies]
-numpy = "^1.26.4"
+numpy = "^2.0.2"
 argparse = "^1.4.0"
 setproctitle = "^1.3.2"
 pyyaml = "^6.0"
-nptyping = "^2.5.0"
 pydantic = "^2.12.5"
 typing-extensions = "^4.15.0"
 
@@ -65,6 +64,9 @@ omit = [
 # Linters
 [tool.ruff.lint]
 extend-select = ["I"]
+ignore = [
+    "E741" # ambiguous variable name 'l', 'O', or 'I'
+]
 
 [tool.ruff.lint.isort]
 known-first-party = ["jambo"]