update: fix all

VsevolodX · VsevolodX · commit 0d0f6f751f02 · 2025-08-06T13:04:09.000-07:00
diff --git a/src/py/mat3ra/made/tools/analyze/crystal_site/adatom_crystal_site_material_analyzer.py b/src/py/mat3ra/made/tools/analyze/crystal_site/adatom_crystal_site_material_analyzer.py
@@ -1,8 +1,8 @@
 from typing import List
 
 from mat3ra.made.material import Material
-
 from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.builder import SlabBuilder
+
 from ...build_components.entities.reusable.two_dimensional.slab_stack.helpers import (
     recreate_slab_with_fractional_layers,
 )
diff --git a/src/py/mat3ra/made/tools/analyze/interface/grain_boundary.py b/src/py/mat3ra/made/tools/analyze/interface/grain_boundary.py
@@ -6,9 +6,9 @@
     SupercellMatrix2DSchema,
 )
 from mat3ra.made.material import Material
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration
 from pydantic import model_validator
 
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration
 from .utils.holders import MatchedSubstrateFilmConfigurationHolder
 from .zsl import ZSLInterfaceAnalyzer
 
diff --git a/src/py/mat3ra/made/tools/analyze/interface/simple.py b/src/py/mat3ra/made/tools/analyze/interface/simple.py
@@ -7,15 +7,13 @@
 from mat3ra.esse.models.materials_category_components.entities.auxiliary.two_dimensional.supercell_matrix_2d import (
     SupercellMatrix2DSchema,
 )
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.build_parameters import SlabBuilderParameters
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.builder import SlabBuilder
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration
 
 from ...build.pristine_structures.two_dimensional.slab_strained_supercell.configuration import (
     SlabStrainedSupercellConfiguration,
 )
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.build_parameters import (
-    SlabBuilderParameters,
-)
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.builder import SlabBuilder
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration
 from ..interface.utils.holders import MatchedSubstrateFilmConfigurationHolder
 
 
diff --git a/src/py/mat3ra/made/tools/analyze/interface/twisted_nanoribbons.py b/src/py/mat3ra/made/tools/analyze/interface/twisted_nanoribbons.py
@@ -1,8 +1,8 @@
 from typing import Tuple
 
 from mat3ra.made.material import Material
-
 from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration
+
 from ...modify import translate_to_center
 from ...operations.core.unary import rotate
 from ..other import get_surface_area
diff --git a/src/py/mat3ra/made/tools/analyze/interface/zsl.py b/src/py/mat3ra/made/tools/analyze/interface/zsl.py
@@ -8,11 +8,11 @@
 from mat3ra.esse.models.materials_category_components.entities.auxiliary.two_dimensional.supercell_matrix_2d import (
     SupercellMatrix2DSchema,
 )
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.builder import SlabBuilder
 from mat3ra.utils.matrix import convert_2x2_to_3x3
 from pymatgen.analysis.interfaces.coherent_interfaces import ZSLGenerator as PymatgenZSLGenerator
 
 from ...build_components import MaterialWithBuildMetadata
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.builder import SlabBuilder
 from ..interface.simple import InterfaceAnalyzer
 from ..interface.utils.holders import MatchedSubstrateFilmConfigurationHolder
 from ..utils import calculate_von_mises_strain
diff --git a/src/py/mat3ra/made/tools/analyze/slab.py b/src/py/mat3ra/made/tools/analyze/slab.py
@@ -2,13 +2,11 @@
 
 from typing import Type
 
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.build_parameters import SlabBuilderParameters
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration
 from mat3ra.made.utils import adjust_material_cell_to_set_gap_along_direction, get_atomic_coordinates_extremum
 
 from ..build_components.entities.core.two_dimensional.vacuum.configuration import VacuumConfiguration
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.build_parameters import (
-    SlabBuilderParameters,
-)
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration
 from ..build_components.metadata import MaterialWithBuildMetadata
 from .build_metadata_analyzer import BuildMetadataAnalyzer
 from .crystal_site.crystal_site_analyzer import CrystalSiteAnalyzer
diff --git a/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/configuration.py b/src/py/mat3ra/made/tools/build/pristine_structures/two_dimensional/slab/configuration.py
@@ -5,7 +5,9 @@
 from mat3ra.made.material import Material
 
 from .....analyze.lattice_planes import CrystalLatticePlanesMaterialAnalyzer
-from .....build_components.entities.reusable.two_dimensional import AtomicLayersUniqueRepeatedConfiguration
+from .....build_components.entities.reusable.two_dimensional.atomic_layers_unique_repeated.configuration import (
+    AtomicLayersUniqueRepeatedConfiguration,
+)
 from .....build_components.metadata import MaterialWithBuildMetadata
 from .....build_components import select_slab_termination
 from .....build_components.operations.core.combinations.stack.configuration import StackConfiguration
diff --git a/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/__init__.py b/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/__init__.py
@@ -1,11 +1,12 @@
 from .atomic_layers_unique_repeated import AtomicLayersUniqueRepeatedBuilder, AtomicLayersUniqueRepeatedConfiguration
 from .crystal_lattice_planes import CrystalLatticePlanesBuilder, CrystalLatticePlanesConfiguration
-from .slab_stack import (
-    SlabStackBuilder,
-    SlabStackConfiguration,
-    create_slab_stack,
-    recreate_slab_with_fractional_layers,
-)
+
+# from .slab_stack import (
+#     SlabStackBuilder,
+#     SlabStackConfiguration,
+#     create_slab_stack,
+#     recreate_slab_with_fractional_layers,
+# )
 
 __all__ = [
     # atomic_layers
@@ -16,8 +17,8 @@
     "CrystalLatticePlanesBuilder",
     "CrystalLatticePlanesConfiguration",
     # slab_stack
-    "SlabStackBuilder",
-    "SlabStackConfiguration",
-    "create_slab_stack",
-    "recreate_slab_with_fractional_layers",
+    # "SlabStackBuilder",
+    # "SlabStackConfiguration",
+    # "create_slab_stack",
+    # "recreate_slab_with_fractional_layers",
 ]
diff --git a/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/atomic_layers_unique_repeated/helpers.py b/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/atomic_layers_unique_repeated/helpers.py
@@ -1,9 +1,10 @@
-from typing import Union, Tuple, Optional
+from typing import Optional, Tuple, Union
 
 from mat3ra.made.material import Material
-from .. import AtomicLayersUniqueRepeatedConfiguration, AtomicLayersUniqueRepeatedBuilder
-from ....auxiliary.two_dimensional.termination import Termination
+
 from ..... import MaterialWithBuildMetadata
+from ....auxiliary.two_dimensional.termination import Termination
+from .. import AtomicLayersUniqueRepeatedBuilder, AtomicLayersUniqueRepeatedConfiguration
 
 
 def create_atomic_layers(
diff --git a/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/slab_stack/builder.py b/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/slab_stack/builder.py
@@ -2,9 +2,10 @@
 
 from mat3ra.made.tools.build_components.entities.reusable.base_builder import TypeConfiguration
 
+from ......build.pristine_structures.two_dimensional.slab import SlabBuilder
+from ......build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration
 from ..... import MaterialWithBuildMetadata
 from .....operations.core.combinations.stack.builder import StackNComponentsBuilder
-from ......build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration
 from .configuration import SlabStackConfiguration
 
 
@@ -13,7 +14,6 @@ class SlabStackBuilder(StackNComponentsBuilder):
 
     @property
     def stack_component_types_conversion_map(self):
-        from ......build.pristine_structures.two_dimensional.slab.builder import SlabBuilder
         return {
             **super().stack_component_types_conversion_map,
             SlabConfiguration: SlabBuilder,
diff --git a/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/slab_stack/helpers.py b/src/py/mat3ra/made/tools/build_components/entities/reusable/two_dimensional/slab_stack/helpers.py
@@ -1,11 +1,11 @@
 from mat3ra.esse.models.core.reusable.axis_enum import AxisEnum
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.builder import SlabBuilder
 from sympy import ceiling
 
 from ......analyze.slab import SlabMaterialAnalyzer
 from ......modify import filter_by_box
 from ..... import MaterialWithBuildMetadata
 from ....core.two_dimensional.vacuum.configuration import VacuumConfiguration
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.builder import SlabBuilder
 from .builder import SlabStackBuilder
 from .configuration import SlabStackConfiguration
 
diff --git a/src/py/mat3ra/made/tools/helpers.py b/src/py/mat3ra/made/tools/helpers.py
@@ -1,5 +1,11 @@
 # Defective Structures
 from build_components.entities.reusable.two_dimensional.slab_stack.helpers import create_slab_stack
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.helpers import (
+    create_atomic_layers,
+    create_slab,
+    get_slab_terminations,
+)
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.termination_utils import select_slab_termination
 
 # Compound Pristine Structures
 from .build.compound_pristine_structures.two_dimensional.interface.base.helpers import (
@@ -32,14 +38,6 @@
 from .build.pristine_structures.three_dimensional.ideal_crystal.helpers import create_monolayer
 from .build.pristine_structures.two_dimensional.nanoribbon.helpers import create_nanoribbon
 from .build.pristine_structures.two_dimensional.nanotape.helpers import create_nanotape
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.helpers import (
-    create_atomic_layers,
-    create_slab,
-    get_slab_terminations,
-)
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.termination_utils import (
-    select_slab_termination,
-)
 from .build.pristine_structures.zero_dimensional.nanoparticle.helpers import create_nanoparticle_from_material
 
 # Processed Structures
diff --git a/tests/py/unit/test_tools_analyze_interface.py b/tests/py/unit/test_tools_analyze_interface.py
@@ -5,9 +5,7 @@
 import pytest
 from mat3ra.made.tools.analyze.interface import InterfaceAnalyzer
 from mat3ra.made.tools.analyze.interface.commensurate import CommensurateLatticeInterfaceAnalyzer
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import (
-    SlabConfiguration,
-)
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import SlabConfiguration
 from unit.fixtures.bulk import BULK_Ge_CONVENTIONAL, BULK_Si_CONVENTIONAL
 
 from .fixtures.monolayer import GRAPHENE
diff --git a/tests/py/unit/test_tools_analyze_interface_zsl.py b/tests/py/unit/test_tools_analyze_interface_zsl.py
@@ -4,12 +4,10 @@
 import numpy as np
 import pytest
 from mat3ra.made.tools.analyze.interface.zsl import ZSLInterfaceAnalyzer
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import SlabConfiguration
 from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab_strained_supercell.builder import (
     SlabStrainedSupercellBuilder,
 )
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import (
-    SlabConfiguration,
-)
 from mat3ra.made.tools.utils import supercell_matrix_2d_schema_to_list, unwrap
 from mat3ra.standata.materials import Materials
 from mat3ra.utils.matrix import convert_2x2_to_3x3
diff --git a/tests/py/unit/test_tools_build_interface.py b/tests/py/unit/test_tools_build_interface.py
@@ -23,11 +23,8 @@
     create_twisted_interface,
 )
 from mat3ra.made.tools.build.pristine_structures.two_dimensional.nanoribbon.helpers import create_nanoribbon
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import SlabBuilder, SlabConfiguration
 from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.helpers import create_slab
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import SlabBuilder
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import (
-    SlabConfiguration,
-)
 from mat3ra.standata.materials import Materials
 from unit.fixtures.bulk import BULK_Ge_CONVENTIONAL, BULK_Si_CONVENTIONAL
 
diff --git a/tests/py/unit/test_tools_build_interface_zsl.py b/tests/py/unit/test_tools_build_interface_zsl.py
@@ -10,11 +10,8 @@
     create_zsl_interface,
     create_zsl_interface_between_slabs,
 )
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import SlabBuilder, SlabConfiguration
 from mat3ra.made.tools.build_components.entities.core.two_dimensional.vacuum.configuration import VacuumConfiguration
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import SlabBuilder
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import (
-    SlabConfiguration,
-)
 from mat3ra.standata.materials import Materials
 
 from .fixtures.interface.gr_ni_111_top_hcp import (
diff --git a/tests/py/unit/test_tools_build_slab.py b/tests/py/unit/test_tools_build_slab.py
@@ -12,30 +12,23 @@
 from mat3ra.made.tools.analyze.interface.utils.vector import align_first_vector_to_x_2d_right_handed
 from mat3ra.made.tools.analyze.lattice_planes import CrystalLatticePlanesMaterialAnalyzer
 from mat3ra.made.tools.build import MaterialWithBuildMetadata
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.helpers import (
-    create_slab,
-    get_slab_terminations,
-)
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.termination_utils import (
-    select_slab_termination,
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import (
+    SlabBuilder,
+    SlabBuilderParameters,
+    SlabConfiguration,
 )
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.helpers import create_slab, get_slab_terminations
+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.termination_utils import select_slab_termination
 from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab_strained_supercell.builder import (
     SlabStrainedSupercellBuilder,
 )
 from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab_strained_supercell.configuration import (
     SlabStrainedSupercellConfiguration,
 )
 from mat3ra.made.tools.build_components.entities.core.two_dimensional.vacuum.configuration import VacuumConfiguration
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import (
-    SlabBuilderParameters,
-)
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import SlabBuilder
-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab import (
-    SlabConfiguration,
-)
 from mat3ra.made.tools.build_components.entities.reusable.two_dimensional import (
-    AtomicLayersUniqueRepeatedConfiguration,
     AtomicLayersUniqueRepeatedBuilder,
+    AtomicLayersUniqueRepeatedConfiguration,
 )
 from mat3ra.made.utils import AXIS_TO_INDEX_MAP, adjust_material_cell_to_set_gap_along_direction
 from mat3ra.utils import assertion

Original file line number	Diff line number	Diff line change
`@@ -1,8 +1,8 @@`
`1`	`1`	`from typing import List`
`2`	`2`
`3`	`3`	`from mat3ra.made.material import Material`
`4`		`-`
`5`	`4`	`from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.builder import SlabBuilder`
	`5`	`+`
`6`	`6`	`from ...build_components.entities.reusable.two_dimensional.slab_stack.helpers import (`
`7`	`7`	`recreate_slab_with_fractional_layers,`
`8`	`8`	`)`
Original file line number	Diff line number	Diff line change
`@@ -6,9 +6,9 @@`
`6`	`6`	`SupercellMatrix2DSchema,`
`7`	`7`	`)`
`8`	`8`	`from mat3ra.made.material import Material`
	`9`	`+from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration`
`9`	`10`	`from pydantic import model_validator`
`10`	`11`
`11`		`-from mat3ra.made.tools.build.pristine_structures.two_dimensional.slab.configuration import SlabConfiguration`
`12`	`12`	`from .utils.holders import MatchedSubstrateFilmConfigurationHolder`
`13`	`13`	`from .zsl import ZSLInterfaceAnalyzer`
`14`	`14`