Added support for numpy>2.0, and spglib>2.0, fixed warnings with docs…

…tring (#32)

* Added support for numpy>2.0, and spglib>2.0, fixed warnings with docstring.

* Remove unused imports.

docs/assets/conventional_cell_comparison.py

@@ -14,9 +14,9 @@ def get_spglib_conventional(system):
     dataset = spglib.get_symmetry_dataset(cell)
 
     return Atoms(
-        symbols=dataset["std_types"],
-        scaled_positions=dataset["std_positions"],
-        cell=dataset["std_lattice"],
+        symbols=dataset.std_types,
+        scaled_positions=dataset.std_positions,
+        cell=dataset.std_lattice,
     )
 
 # Lets define two variants of NaCl in rocksalt structure

matid/symmetry/symmetryanalyzer.py

@@ -18,6 +18,12 @@
 from ase import Atoms
 
 
+class AttrDict(dict):
+    def __init__(self, *args, **kwargs):
+        super(AttrDict, self).__init__(*args, **kwargs)
+        self.__dict__ = self
+
+
 class SymmetryAnalyzer(object):
     """A base class for getting symmetry related properties of unit cells."""
 
@@ -144,7 +150,7 @@ def get_space_group_number(self):
             int: The space group number.
         """
         dataset = self.get_symmetry_dataset()
-        value = dataset["number"]
+        value = dataset.number
 
         return value
 
@@ -154,7 +160,7 @@ def get_space_group_international_short(self):
             str: The international space group short symbol.
         """
         dataset = self.get_symmetry_dataset()
-        value = dataset["international"]
+        value = dataset.international
 
         return value
 
@@ -164,7 +170,7 @@ def get_hall_symbol(self):
             str: The Hall symbol.
         """
         dataset = self.get_symmetry_dataset()
-        value = dataset["hall"]
+        value = dataset.hall
 
         return value
 
@@ -174,7 +180,7 @@ def get_hall_number(self):
             int: The Hall number.
         """
         dataset = self.get_symmetry_dataset()
-        value = dataset["hall_number"]
+        value = dataset.hall_number
 
         return value
 
@@ -186,7 +192,7 @@ def get_point_group(self):
             str: point group symbol
         """
         dataset = self.get_symmetry_dataset()
-        value = dataset["pointgroup"]
+        value = dataset.pointgroup
 
         return value
 
@@ -367,7 +373,7 @@ def get_conventional_system(self):
             # The index of the originally non-periodic dimension may not correspond
             # to the one in the normalized system, because the normalized system
             # may use a different coordinate system.
-            transformation_matrix = self.get_symmetry_dataset()["transformation_matrix"]
+            transformation_matrix = self.get_symmetry_dataset().transformation_matrix
             nonperiodic_axis = None
             prec = 1e-8
             for i_axis, axis in enumerate(transformation_matrix):
@@ -448,7 +454,7 @@ def get_rotations(self):
             np.ndarray: Rotation matrices.
         """
         dataset = self.get_symmetry_dataset()
-        value = dataset["rotations"]
+        value = dataset.rotations
 
         return value
 
@@ -461,7 +467,7 @@ def get_translations(self):
             np.ndarray: Translation vectors.
         """
         dataset = self.get_symmetry_dataset()
-        value = dataset["translations"]
+        value = dataset.translations
 
         return value
 
@@ -472,7 +478,7 @@ def get_choice(self):
             settings.
         """
         dataset = self.get_symmetry_dataset()
-        value = dataset["choice"]
+        value = dataset.choice
 
         return value
 
@@ -595,6 +601,11 @@ def get_symmetry_dataset(self):
         if symmetry_dataset is None:
             raise CellNormalizationError("Spglib error when finding symmetry dataset.")
 
+        # Prior to spglib 2.5.0 the dataset is returned as a dictionary: this
+        # provides backwards compatibility
+        if isinstance(symmetry_dataset, dict):
+            symmetry_dataset = AttrDict(symmetry_dataset)
+
         self._symmetry_dataset = symmetry_dataset
 
         return symmetry_dataset
@@ -610,9 +621,9 @@ def _get_spglib_conventional_system(self):
             return self._spglib_conventional_system
 
         dataset = self.get_symmetry_dataset()
-        cell = dataset["std_lattice"]
-        pos = dataset["std_positions"]
-        num = dataset["std_types"]
+        cell = dataset.std_lattice
+        pos = dataset.std_positions
+        num = dataset.std_types
         spg_conv_sys = self._spglib_description_to_system((cell, pos, num))
 
         self._spglib_conventional_system = spg_conv_sys
@@ -624,7 +635,7 @@ def _get_spglib_wyckoff_letters_original(self):
             list of str: Wyckoff letters for the atoms in the original system.
         """
         dataset = self.get_symmetry_dataset()
-        value = np.array(dataset["wyckoffs"])
+        value = np.array(dataset.wyckoffs)
 
         return value
 
@@ -640,7 +651,7 @@ def _get_spglib_equivalent_atoms_original(self):
         # equivalent atoms reported by spglib are based on the symmetry of the
         # original cell. Equivalence in crystallographic_orbits is instead
         # based on the primitive cell/conventional cell which is what we want.
-        value = dataset["crystallographic_orbits"]
+        value = dataset.crystallographic_orbits
 
         return value
 
@@ -653,7 +664,7 @@ def _get_spglib_wyckoff_letters_conventional(self):
         if self._spglib_wyckoff_letters_conventional is None:
             wyckoff_letters_primitive = self._get_spglib_wyckoff_letters_primitive()
             dataset = self.get_symmetry_dataset()
-            mapping = dataset["std_mapping_to_primitive"]
+            mapping = dataset.std_mapping_to_primitive
             self._spglib_wyckoff_letters_conventional = wyckoff_letters_primitive[
                 mapping
             ]
@@ -668,7 +679,7 @@ def _get_spglib_equivalent_atoms_conventional(self):
         if self._spglib_equivalent_atoms_conventional is None:
             equivalent_atoms_primitive = self._get_spglib_equivalent_atoms_primitive()
             dataset = self.get_symmetry_dataset()
-            mapping = dataset["std_mapping_to_primitive"]
+            mapping = dataset.std_mapping_to_primitive
             self._spglib_equivalent_atoms_conventional = equivalent_atoms_primitive[
                 mapping
             ]
@@ -690,7 +701,7 @@ def _get_spglib_origin_shift(self):
             3*1 np.ndarray: The shift of the origin as a vector.
         """
         dataset = self.get_symmetry_dataset()
-        value = dataset["origin_shift"]
+        value = dataset.origin_shift
 
         return value
 
@@ -707,8 +718,8 @@ def get_symmetry_operations(self):
         """
         dataset = self.get_symmetry_dataset()
         operations = {
-            "rotations": dataset["rotations"],
-            "translations": dataset["translations"],
+            "rotations": dataset.rotations,
+            "translations": dataset.translations,
         }
 
         return operations
@@ -728,7 +739,7 @@ def _get_spglib_transformation_matrix(self):
             3x3 np.ndarray:
         """
         dataset = self.get_symmetry_dataset()
-        value = dataset["transformation_matrix"]
+        value = dataset.transformation_matrix
 
         return value
 
@@ -802,7 +813,7 @@ def _get_spglib_primitive_to_original_mapping(self):
         """
         if self._spglib_primitive_to_original_mapping is None:
             dataset = self.get_symmetry_dataset()
-            mapping = dataset["mapping_to_primitive"]
+            mapping = dataset.mapping_to_primitive
             _, indices = np.unique(mapping, return_index=True)
             self._spglib_primitive_to_original_mapping = indices
 
@@ -896,7 +907,7 @@ def _get_primitive_system(
         # Keep one occurrence for each atom that should be within the cell and
         # wrap it's position to tbe inside the primitive cell.
         conv_num = conv_system.get_atomic_numbers()
-        conv_to_prim_map = self._symmetry_dataset["std_mapping_to_primitive"]
+        conv_to_prim_map = self._symmetry_dataset.std_mapping_to_primitive
         _, inside_mask = np.unique(conv_to_prim_map, return_index=True)
         prim_pos = prim_pos[inside_mask]
         prim_num = conv_num[inside_mask]
@@ -1204,7 +1215,7 @@ def _get_wyckoff_sets(
         precision,
         return_parameters,
     ):
-        """Used to get detailed information about about the sets of equivalent
+        r"""Used to get detailed information about about the sets of equivalent
         atoms. The detected Wyckoff set variables (x, y, z) are reported
         consistenly by selecting the variable sets that has lowest x value, then
         lowest y and finally lowest z.

matid/utils/symmetry_info_generation/query_conventional_transform_info.py

@@ -15,7 +15,7 @@
 
 for hall_number in range(1, 531):
     dataset = spglib.get_spacegroup_type(hall_number)
-    number = dataset["number"]
+    number = dataset.number
     space_hall_map[number].append(hall_number)
 
 degenerate_spgs = []
@@ -26,7 +26,7 @@
     degenerate_spgs.append(key)
     first_hall = value[0]
     dataset = spglib.get_spacegroup_type(first_hall)
-    choice = dataset["choice"]
+    choice = dataset.choice
 
     # try:
     # origin = int(choice)

matid/utils/symmetry_info_generation/query_space_group_info.py

@@ -12,8 +12,8 @@
 
 for hall_number in range(1, 531):
     dataset = spglib.get_spacegroup_type(hall_number)
-    number = dataset["number"]
-    international_short = dataset["international_short"]
+    number = dataset.number
+    international_short = dataset.international_short
 
     # Check that the spglib data has no two different international symbols for
     # the same space group number
@@ -28,7 +28,7 @@
         # Point group. There actually seeems to be a bug in spglib 1.9.4, where
         # the Hermann-Mauguin point group symbol is in the plalce of Schonflies
         # data and vice versa.
-        pointgroup = dataset["pointgroup_schoenflies"]
+        pointgroup = dataset.pointgroup_schoenflies
         space_group_database[number]["pointgroup"] = pointgroup
 
         # Crystal system

pyproject.toml

@@ -1,19 +1,19 @@
 [build-system]
-requires = ["setuptools", "wheel", "pybind11~=2.11.1"]
+requires = ["setuptools", "wheel", "pybind11~=2.13.6"]
 build-backend = "setuptools.build_meta"
 
 [project]
 name = 'matid'
-version = '2.1.4'
+version = '2.1.5'
 description = 'MatID is a Python package for identifying and analyzing atomistic systems based on their structure.'
 readme = "README.md"
 authors = [{ name = "Lauri Himanen" }]
 license = { file = "LICENSE" }
 requires-python = ">=3.8"
 dependencies = [
-    "numpy<2.0.0",
+    "numpy",
     "ase",
-    "spglib>=1.15.0",
+    "spglib>=2.0.0",
     "scikit-learn",
     "networkx>=2.4",
 ]