Revert "Add Structure.get_symmetry_dataset convenience method (#4268)"

pyproject.toml

@@ -68,7 +68,7 @@ dependencies = [
     # scipy<1.14.1 is incompatible with NumPy 2.0 on Windows
     # https://github.com/scipy/scipy/issues/21052
     "scipy>=1.14.1; platform_system == 'Windows'",
-    "spglib>=2.5",
+    "spglib>=2.5.0",
     "sympy>=1.3",  # PR #4116
     "tabulate>=0.9",
     "tqdm>=4.60",
@@ -89,7 +89,7 @@ Pypi = "https://pypi.org/project/pymatgen"
 [project.optional-dependencies]
 abinit = ["netcdf4>=1.7.2"]
 ase = ["ase>=3.23.0"]
-ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8", "pymatgen[symmetry]"]
+ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]
 electronic_structure = ["fdint>=2.0.2"]
 mlp = ["chgnet>=0.3.8", "matgl>=1.1.3"]
@@ -110,8 +110,6 @@ optional = [
     "phonopy>=2.33.3",
     "seekpath>=2.0.1",
 ]
-# moyopy[interface] includes ase
-symmetry = ["moyopy[interface]>=0.3", "spglib>=2.5"]
 # tblite only support Python 3.12+ through conda-forge
 # https://github.com/tblite/tblite/issues/175
 tblite = [ "tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'"]

src/pymatgen/core/structure.py

@@ -20,7 +20,7 @@
 from abc import ABC, abstractmethod
 from collections import defaultdict
 from fnmatch import fnmatch
-from typing import TYPE_CHECKING, Literal, cast, get_args, overload
+from typing import TYPE_CHECKING, Literal, cast, get_args
 
 import numpy as np
 from monty.dev import deprecated
@@ -43,15 +43,12 @@
 from pymatgen.electronic_structure.core import Magmom
 from pymatgen.symmetry.maggroups import MagneticSpaceGroup
 from pymatgen.util.coord import all_distances, get_angle, lattice_points_in_supercell
-from pymatgen.util.due import Doi, due
 
 if TYPE_CHECKING:
     from collections.abc import Callable, Iterable, Iterator, Sequence
     from typing import Any, ClassVar, SupportsIndex, TypeAlias
 
-    import moyopy
     import pandas as pd
-    import spglib
     from ase import Atoms
     from ase.calculators.calculator import Calculator
     from ase.io.trajectory import Trajectory
@@ -3341,61 +3338,6 @@ def to_conventional(self, **kwargs) -> Structure:
         """
         return self.to_cell("conventional", **kwargs)
 
-    @overload
-    def get_symmetry_dataset(self, backend: Literal["moyopy"], **kwargs) -> moyopy.MoyoDataset: ...
-
-    @due.dcite(
-        Doi("10.1080/27660400.2024.2384822"),
-        description="Spglib: a software library for crystal symmetry search",
-    )
-    @overload
-    def get_symmetry_dataset(self, backend: Literal["spglib"], **kwargs) -> spglib.SpglibDataset: ...
-
-    def get_symmetry_dataset(
-        self, backend: Literal["moyopy", "spglib"] = "spglib", **kwargs
-    ) -> moyopy.MoyoDataset | spglib.SpglibDataset:
-        """Get a symmetry dataset from the structure using either moyopy or spglib backend.
-
-        If using the spglib backend (default), please cite:
-
-        Togo, A., Shinohara, K., & Tanaka, I. (2024). Spglib: a software library for crystal
-        symmetry search. Science and Technology of Advanced Materials: Methods, 4(1), 2384822-2384836.
-        https://doi.org/10.1080/27660400.2024.2384822
-
-        Args:
-            backend ("moyopy" | "spglib"): Which symmetry analysis backend to use.
-                Defaults to "spglib".
-            **kwargs: Additional arguments passed to the respective backend's constructor.
-                For spglib, these are passed to SpacegroupAnalyzer (e.g. symprec, angle_tolerance).
-                For moyopy, these are passed to MoyoDataset constructor.
-
-        Returns:
-            MoyoDataset | SpglibDataset: Symmetry dataset from the chosen backend.
-
-        Raises:
-            ImportError: If the requested backend is not installed.
-            ValueError: If an invalid backend is specified.
-        """
-        if backend == "moyopy":
-            try:
-                import moyopy
-                import moyopy.interface
-            except ImportError:
-                raise ImportError("moyopy is not installed. Run pip install moyopy.")
-
-            # Convert structure to MoyoDataset format
-            moyo_cell = moyopy.interface.MoyoAdapter.from_structure(self)
-            return moyopy.MoyoDataset(cell=moyo_cell, **kwargs)
-
-        if backend == "spglib":
-            from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
-
-            sga = SpacegroupAnalyzer(self, **kwargs)
-            return sga.get_symmetry_dataset()
-
-        valid_backends = ("moyopy", "spglib")
-        raise ValueError(f"Invalid {backend=}, must be one of {valid_backends}")
-
 
 class IMolecule(SiteCollection, MSONable):
     """Basic immutable Molecule object without periodicity. Essentially a

tests/core/test_structure.py

@@ -6,7 +6,6 @@
 from fractions import Fraction
 from pathlib import Path
 from shutil import which
-from unittest import mock
 
 import numpy as np
 import pytest
@@ -966,32 +965,6 @@ def test_sites_setter(self):
         struct.sites = new_sites
         assert struct.sites == new_sites
 
-    def test_get_symmetry_dataset(self):
-        """Test getting symmetry dataset from structure using different backends."""
-        # Test spglib backend
-        dataset = self.struct.get_symmetry_dataset(backend="spglib")
-        assert dataset.number == 227  # Fd-3m space group
-        assert dataset.international == "Fd-3m"
-        assert len(dataset.rotations) > 0
-        assert len(dataset.translations) > 0
-
-        # Test moyopy backend if available
-        moyopy = pytest.importorskip("moyopy")
-        dataset = self.struct.get_symmetry_dataset(backend="moyopy")
-        assert isinstance(dataset, moyopy.MoyoDataset)
-        assert dataset.prim_std_cell.numbers == [14, 14]  # Si atomic number is 14
-
-        # Test import error
-        with (
-            mock.patch.dict("sys.modules", {"moyopy": None}),
-            pytest.raises(ImportError, match="moyopy is not installed. Run pip install moyopy."),
-        ):
-            self.struct.get_symmetry_dataset(backend="moyopy")
-
-        # Test invalid backend
-        with pytest.raises(ValueError, match="Invalid backend='42'"):
-            self.struct.get_symmetry_dataset(backend="42")
-
 
 class TestStructure(PymatgenTest):
     def setUp(self):