Added description to Symmetry.resolve_analyzed_atomic_cell

Added typing in methods

simulationdataschema/model_system.py

@@ -37,6 +37,8 @@
 import re
 import numpy as np
 import ase
+from typing import Union, Tuple
+from structlog.stdlib import BoundLogger
 
 from matid import SymmetryAnalyzer, Classifier  # pylint: disable=import-error
 from matid.classification.classifications import (
@@ -178,13 +180,13 @@ class AtomicCell(GeometricSpace):
         """,
     )
 
-    def to_ase_atoms(self, logger):
+    def to_ase_atoms(self, logger: BoundLogger) -> Union[ase.Atoms, None]:
         """
         Generates an ASE Atoms object with the most basic information from the parsed `AtomicCell`
         section (labels, periodic_boundary_conditions, positions, and lattice_vectors).
 
         Returns:
-            ase.Atoms: The ASE Atoms object with the basic information from the `AtomicCell`.
+            Union[ase.Atoms, None]: The ASE Atoms object with the basic information from the `AtomicCell`.
         """
         # Initialize ase.Atoms object with labels
         ase_atoms = ase.Atoms(symbols=self.labels)
@@ -203,11 +205,11 @@ def to_ase_atoms(self, logger):
                 logger.error(
                     "Length of `AtomicCell.positions` does not coincide with the length of the `AtomicCell.labels`."
                 )
-                return
+                return None
             ase_atoms.set_positions(self.positions.to("angstrom").magnitude)
         else:
             logger.error("Could not find `AtomicCell.positions`.")
-            return
+            return None
 
         # Lattice vectors
         if self.lattice_vectors is not None:
@@ -364,13 +366,25 @@ class Symmetry(ArchiveSection):
     )
 
     def resolve_analyzed_atomic_cell(
-        self, symmetry_analyzer: SymmetryAnalyzer, cell_type: str, logger
-    ):
+        self, symmetry_analyzer: SymmetryAnalyzer, cell_type: str, logger: BoundLogger
+    ) -> Union[AtomicCell, None]:
+        """
+        Resolves the `AtomicCell` section from the `SymmetryAnalyzer` object and the cell_type
+        (primitive or conventional).
+
+        Args:
+            symmetry_analyzer (SymmetryAnalyzer): The `SymmetryAnalyzer` object used to resolve.
+            cell_type (str): The type of cell to resolve, either 'primitive' or 'conventional'.
+
+        Returns:
+            Union[AtomicCell, None]: The resolved `AtomicCell` section or None if the cell_type
+            is not recognized.
+        """
         if cell_type not in ["primitive", "conventional"]:
             logger.error(
                 "Cell type not recognized, only 'primitive' and 'conventional' are allowed."
             )
-            return
+            return None
         wyckoff = getattr(symmetry_analyzer, f"get_wyckoff_letters_{cell_type}")()
         equivalent_atoms = getattr(
             symmetry_analyzer, f"get_equivalent_atoms_{cell_type}"
@@ -392,7 +406,9 @@ def resolve_analyzed_atomic_cell(
         atomic_cell.get_geometric_space_for_atomic_cell(logger)
         return atomic_cell
 
-    def resolve_bulk_symmetry(self, original_atomic_cell, logger):
+    def resolve_bulk_symmetry(
+        self, original_atomic_cell: AtomicCell, logger: BoundLogger
+    ) -> Tuple[Union[AtomicCell, None], Union[AtomicCell, None]]:
         """
         Resolves the symmetry of the material being simulated using MatID and the
         originally parsed data under original_atomic_cell. It generates two other
@@ -416,10 +432,10 @@ def resolve_bulk_symmetry(self, original_atomic_cell, logger):
             logger.debug(
                 "Symmetry analysis with MatID is not available.", details=str(e)
             )
-            return
+            return None, None
         except Exception as e:
             logger.warning("Symmetry analysis with MatID failed.", exc_info=e)
-            return
+            return None, None
 
         # We store symmetry_analyzer info in a dictionary
         symmetry["bravais_lattice"] = symmetry_analyzer.get_bravais_lattice()
@@ -746,7 +762,9 @@ class ModelSystem(System):
 
     model_system = SubSection(sub_section=SectionProxy("ModelSystem"), repeats=True)
 
-    def resolve_system_type_and_dimensionality(self, ase_atoms):
+    def resolve_system_type_and_dimensionality(
+        self, ase_atoms: ase.Atoms
+    ) -> Tuple[str, int]:
         """
         Determine the ModelSystem.type and ModelSystem.dimensionality using MatID classification analyzer:
 

simulationdataschema/model_system_review.py

@@ -37,6 +37,8 @@
 import re
 import numpy as np
 import ase
+from typing import Union, Tuple
+from structlog.stdlib import BoundLogger
 
 from matid import SymmetryAnalyzer, Classifier  # pylint: disable=import-error
 from matid.classification.classifications import (
@@ -59,7 +61,7 @@
 from nomad.datamodel.metainfo.basesections import System, GeometricSpace
 from nomad.datamodel.metainfo.annotations import ELNAnnotation
 
-from ..utils import get_sub_section_from_section_parent
+from .utils import get_sub_section_from_section_parent
 
 
 class AtomicCell(GeometricSpace):
@@ -178,13 +180,13 @@ class AtomicCell(GeometricSpace):
         """,
     )
 
-    def to_ase_atoms(self, logger):
+    def to_ase_atoms(self, logger: BoundLogger) -> Union[ase.Atoms, None]:
         """
         Generates an ASE Atoms object with the most basic information from the parsed `AtomicCell`
         section (labels, periodic_boundary_conditions, positions, and lattice_vectors).
 
         Returns:
-            ase.Atoms: The ASE Atoms object with the basic information from the `AtomicCell`.
+            Union[ase.Atoms, None]: The ASE Atoms object with the basic information from the `AtomicCell`.
         """
         # Initialize ase.Atoms object with labels
         ase_atoms = ase.Atoms(symbols=self.labels)
@@ -203,11 +205,11 @@ def to_ase_atoms(self, logger):
                 logger.error(
                     "Length of `AtomicCell.positions` does not coincide with the length of the `AtomicCell.labels`."
                 )
-                return
+                return None
             ase_atoms.set_positions(self.positions.to("angstrom").magnitude)
         else:
             logger.error("Could not find `AtomicCell.positions`.")
-            return
+            return None
 
         # Lattice vectors
         if self.lattice_vectors is not None:
@@ -364,13 +366,25 @@ class Symmetry(ArchiveSection):
     )
 
     def resolve_analyzed_atomic_cell(
-        self, symmetry_analyzer: SymmetryAnalyzer, cell_type: str, logger
-    ):
+        self, symmetry_analyzer: SymmetryAnalyzer, cell_type: str, logger: BoundLogger
+    ) -> Union[AtomicCell, None]:
+        """
+        Resolves the `AtomicCell` section from the `SymmetryAnalyzer` object and the cell_type
+        (primitive or conventional).
+
+        Args:
+            symmetry_analyzer (SymmetryAnalyzer): The `SymmetryAnalyzer` object used to resolve.
+            cell_type (str): The type of cell to resolve, either 'primitive' or 'conventional'.
+
+        Returns:
+            Union[AtomicCell, None]: The resolved `AtomicCell` section or None if the cell_type
+            is not recognized.
+        """
         if cell_type not in ["primitive", "conventional"]:
             logger.error(
                 "Cell type not recognized, only 'primitive' and 'conventional' are allowed."
             )
-            return
+            return None
         wyckoff = getattr(symmetry_analyzer, f"get_wyckoff_letters_{cell_type}")()
         equivalent_atoms = getattr(
             symmetry_analyzer, f"get_equivalent_atoms_{cell_type}"
@@ -392,7 +406,9 @@ def resolve_analyzed_atomic_cell(
         atomic_cell.get_geometric_space_for_atomic_cell(logger)
         return atomic_cell
 
-    def resolve_bulk_symmetry(self, original_atomic_cell, logger):
+    def resolve_bulk_symmetry(
+        self, original_atomic_cell: AtomicCell, logger: BoundLogger
+    ) -> Tuple[Union[AtomicCell, None], Union[AtomicCell, None]]:
         """
         Resolves the symmetry of the material being simulated using MatID and the
         originally parsed data under original_atomic_cell. It generates two other
@@ -416,10 +432,10 @@ def resolve_bulk_symmetry(self, original_atomic_cell, logger):
             logger.debug(
                 "Symmetry analysis with MatID is not available.", details=str(e)
             )
-            return
+            return None, None
         except Exception as e:
             logger.warning("Symmetry analysis with MatID failed.", exc_info=e)
-            return
+            return None, None
 
         # We store symmetry_analyzer info in a dictionary
         symmetry["bravais_lattice"] = symmetry_analyzer.get_bravais_lattice()
@@ -555,7 +571,7 @@ class ChemicalFormula(ArchiveSection):
         """,
     )
 
-    def resolve_chemical_formulas(self, formula):
+    def resolve_chemical_formulas(self, formula: Formula):
         """
         Resolves the chemical formulas of the `ModelSystem` in different formats.
 
@@ -746,7 +762,9 @@ class ModelSystem(System):
 
     model_system = SubSection(sub_section=SectionProxy("ModelSystem"), repeats=True)
 
-    def resolve_system_type_and_dimensionality(self, ase_atoms):
+    def resolve_system_type_and_dimensionality(
+        self, ase_atoms: ase.Atoms
+    ) -> Tuple[str, int]:
         """
         Determine the ModelSystem.type and ModelSystem.dimensionality using MatID classification analyzer:
 
@@ -833,15 +851,13 @@ def normalize(self, archive, logger):
             ) = self.resolve_system_type_and_dimensionality(ase_atoms)
             # Creating and normalizing Symmetry section
             if self.type == "bulk" and self.symmetry is not None:
-                sec_symmetry = Symmetry()
+                sec_symmetry = self.m_create(Symmetry)
                 sec_symmetry.normalize(archive, logger)
-                self.symmetry.append(sec_symmetry)
 
         # Creating and normalizing ChemicalFormula section
         # TODO add support for fractional formulas (possibly add `AtomicCell.concentrations` for each species)
-        sec_chemical_formula = ChemicalFormula()
+        sec_chemical_formula = self.m_create(ChemicalFormula)
         sec_chemical_formula.normalize(archive, logger)
-        self.chemical_formula.append(sec_chemical_formula)
         if sec_chemical_formula.m_cache:
             self.elemental_composition = sec_chemical_formula.m_cache.get(
                 "elemental_composition", []