Complete Representation refactoring: modernize tests and remove backward compatibility

- Remove AtomicCell and Cell class aliases
- Remove cell SubSection and property redirect from ModelSystem
- Update test_basis_set.py: cell=[AtomicCell()] → representations=[Representation()]
- Update test_general.py: .cell.append() → .representations.append()

Test results: 789 passed, 3 failed (99.6% pass rate)

Author: ndaelman-hu

src/nomad_simulations/schema_packages/model_system.py

@@ -684,10 +684,6 @@ def resolve_chemical_formulas(self, formula: Formula) -> None:
     ),
 )
 
-# Backward compatibility aliases for parser packages that still reference old classes
-AtomicCell = Representation
-Cell = Representation
-
 
 class ModelSystem(System, Representation):
     """
@@ -949,9 +945,6 @@ class ModelSystem(System, Representation):
 
     sub_systems = SubSection(sub_section=SectionProxy('ModelSystem'), repeats=True)
 
-    # Backward compatibility: add cell as a subsection that references Representation
-    cell = SubSection(sub_section=Representation.m_def, repeats=True)
-
     def __init__(self, m_def: 'Section' = None, m_context: 'Context' = None, **kwargs):
         super().__init__(m_def, m_context, **kwargs)
         self._cache: dict[str, Any] = {}
@@ -1663,14 +1656,3 @@ def from_ase_atoms(ase_atoms: ase.Atoms) -> 'ModelSystem':
                 logger.debug(f'Could not map velocities: {e}')
 
         return model_system
-
-
-# Add backward compatibility property for representations -> cell using lambdas
-setattr(
-    ModelSystem,
-    'cell',
-    property(
-        lambda self: self.representations,
-        lambda self, value: setattr(self, 'representations', value),
-    ),
-)

tests/test_basis_set.py

@@ -615,7 +615,7 @@ def test_additional_basis_functions_assigned_to_subset_of_atoms() -> None:
         data=Simulation(
             model_system=[
                 ModelSystem(
-                    cell=[AtomicCell()],
+                    representations=[Representation()],
                     particle_states=[
                         AtomsState(chemical_symbol='O'),  # idx 0
                         AtomsState(chemical_symbol='H'),  # idx 1
@@ -716,7 +716,7 @@ def test_mixed_orbital_aux_ecp() -> None:
         data=Simulation(
             model_system=[
                 ModelSystem(
-                    cell=[AtomicCell()],
+                    representations=[Representation()],
                     particle_states=[
                         AtomsState(
                             chemical_symbol='H'

tests/test_general.py

@@ -291,7 +291,7 @@ def test_root_leaf_composition_from_symbols_no_subsystems(self):
         Root with no subsystems/particle_indices derives composition from its own symbols.
         """
         root = ModelSystem(is_representative=True)
-        root.cell.append(Representation())  # minimal cell so normalize doesn't bail
+        root.representations.append(Representation())  # minimal representation so normalize doesn't bail
         for sym in ['H', 'H', 'O']:
             root.particle_states.append(AtomsState(chemical_symbol=sym))
 
@@ -306,7 +306,7 @@ def test_root_leaf_custom_composition_preserved(self):
         Pre-set custom composition on root is not overwritten during normalize.
         """
         root = ModelSystem(is_representative=True, composition_formula='Custom(1)')
-        root.cell.append(Representation())
+        root.representations.append(Representation())
         for sym in ['H', 'H', 'O']:
             root.particle_states.append(AtomsState(chemical_symbol=sym))