@mat3ra/made 2025.8.9-0 → 2025.8.13-0

package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@mat3ra/made",
-    "version": "2025.8.9-0",
+    "version": "2025.8.13-0",
     "description": "MAterials DEsign library",
     "scripts": {
         "lint": "eslint --cache src/js tests/js && prettier --write src/js tests/js",

package/src/py/mat3ra/made/basis/__init__.py

@@ -184,9 +184,17 @@ class Basis(BasisSchema, InMemoryEntityPydantic):
         self.coordinates.filter_by_ids(ids)
         return self
 
-    def set_labels_from_list(self, labels: List[Union[int, str]]) -> None:
+    def set_labels_from_list(self, labels: Optional[List[Union[int, str]]]) -> None:
+        """
+        Set the labels of the basis from a list of labels (i. e. [1,1,1] for a 3-atom basis).
+            If None or [] are passed, the labels are removed (set to an empty array).
+        """
         num_atoms = len(self.elements.values)
 
+        if labels is None or len(labels) == 0:
+            self.labels = ArrayWithIds.from_values([])
+            return
+
         if len(labels) != num_atoms:
             raise ValueError(f"Number of labels ({len(labels)}) must match number of atoms ({num_atoms})")
 

package/src/py/mat3ra/made/material.py

@@ -1,4 +1,4 @@
-from typing import Any, List, Union
+from typing import Any, List, Optional, Union
 
 from mat3ra.code.constants import AtomicCoordinateUnits, Units
 from mat3ra.code.entity import HasDescriptionHasMetadataNamedDefaultableInMemoryEntityPydantic
@@ -103,7 +103,7 @@ class Material(MaterialSchema, HasDescriptionHasMetadataNamedDefaultableInMemory
     def add_atom(self, element: str, coordinate: List[float], use_cartesian_coordinates: bool = False) -> None:
         self.basis.add_atom(element, coordinate, use_cartesian_coordinates)
 
-    def set_labels_from_list(self, labels: List[Union[int, str]]) -> None:
+    def set_labels_from_list(self, labels: Optional[List[Union[int, str]]]) -> None:
         self.basis.set_labels_from_list(labels)
 
     def set_labels_from_value(self, value: Union[int, str]) -> None:

package/src/py/mat3ra/made/tools/build/compound_pristine_structures/two_dimensional/interface/commensurate/helpers.py

@@ -5,6 +5,7 @@ from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
 
 from mat3ra.made.material import Material
 from .. import InterfaceBuilder, InterfaceConfiguration
+from ......build_components.entities.core.two_dimensional.vacuum.configuration import VacuumConfiguration
 from .....pristine_structures.two_dimensional.slab_strained_supercell.configuration import (
     SlabStrainedSupercellConfiguration,
 )
@@ -142,8 +143,9 @@ def create_interface_commensurate(
         use_conventional_cell=use_conventional_cell,
     )
 
+    vacuum_config = VacuumConfiguration(size=vacuum, crystal=None, direction=direction)
     interface_config = InterfaceConfiguration(
-        stack_components=strained_configs,
+        stack_components=strained_configs + [vacuum_config],
         gaps=ArrayWithIds.from_values([gap, gap]),
         direction=direction,
     )

package/tests/py/unit/test_material.py

@@ -1,8 +1,10 @@
 import numpy as np
+import pytest
 from mat3ra.made.basis import Basis, Coordinates
 from mat3ra.made.lattice import Lattice
 from mat3ra.made.material import Material
 from mat3ra.utils import assertion as assertion_utils
+from unit.fixtures.bulk import BULK_Si_PRIMITIVE
 from unit.fixtures.slab import BULK_Si_CONVENTIONAL
 from unit.utils import assert_two_entities_deep_almost_equal
 
@@ -91,3 +93,28 @@ def test_basis_cell_lattice_sync():
     assertion_utils.assert_deep_almost_equal(new_vectors, material.basis.cell.vector_arrays)
     assertion_utils.assert_deep_almost_equal(new_vectors, material.lattice.vector_arrays)
     # Verify basis coordinates are still correct
+
+
+@pytest.mark.parametrize(
+    "initial_labels, reset_labels, expected_final",
+    [
+        # Test resetting with empty list
+        ([1, 2], [], []),
+        # Test resetting with None
+        ([1, 2], None, []),
+        # Test normal behavior with non-empty lists
+        ([], [1, 2], [1, 2]),
+    ],
+)
+def test_set_labels_from_list(initial_labels, reset_labels, expected_final):
+    material = Material.create(BULK_Si_PRIMITIVE)
+
+    if initial_labels:
+        material.basis.set_labels_from_list(initial_labels)
+        assert len(material.basis.labels.values) == len(initial_labels)
+        assert material.basis.labels.values == initial_labels
+
+    material.basis.set_labels_from_list(reset_labels)
+
+    assert len(material.basis.labels.values) == len(expected_final)
+    assert material.basis.labels.values == expected_final