Silence diffpy structure 3.4.0 warnings

CHANGELOG.rst

@@ -6,6 +6,13 @@ All user facing changes to this project are documented in this file. The format
 on `Keep a Changelog <https://keepachangelog.com/en/1.0.0/>`__, and this project tries
 its best to adhere to `Semantic Versioning <https://semver.org/spec/v2.0.0.html>`__.
 
+Unreleased
+==========
+
+Fixed
+-----
+- Silenced most warnings from diffpy.structure >= 3.4.
+
 
 2026-06-10 - version 0.15.0
 ===========================

doc/user/installation.rst

@@ -130,6 +130,7 @@ This is a list of required package dependencies:
 * :doc:`matplotlib <matplotlib:index>`: Visualization
 * :doc:`numba <numba:index>`: CPU acceleration
 * :doc:`numpy <numpy:index>`: Handling of N-dimensional arrays
+* :doc:`packaging <packaging:index>`: Version comparison
 * :doc:`pooch <pooch:api/index>`: Downloading and caching of datasets
 * :doc:`scipy <scipy:index>`: Optimization algorithms, filtering and more
 * `tqdm <https://tqdm.github.io/>`__: Progressbars

orix/_utils/_diffpy_structure_utils.py

@@ -0,0 +1,76 @@
+#
+# Copyright 2018-2026 the orix developers
+#
+# This file is part of orix.
+#
+# orix is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# orix is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with orix. If not, see <http://www.gnu.org/licenses/>.
+#
+
+"""Utilities for interfacing with diffpy.structure."""
+
+from typing import Callable
+
+from diffpy.structure import __version__
+from diffpy.structure.lattice import Lattice
+from diffpy.structure.parsers import p_cif
+from diffpy.structure.spacegroups import SpaceGroup
+from diffpy.structure.structure import Structure
+from packaging.version import Version
+
+DIFFPY_STRUCTURE_VERSION = Version(__version__)
+
+# TODO: Remove these checks (and most likely this whole file) once
+# 3.4.0 is the minimal supported version
+
+if DIFFPY_STRUCTURE_VERSION >= Version("3.4.0"):
+    from diffpy.structure import load_structure
+    from diffpy.structure.spacegroups import get_space_group
+else:
+    from diffpy.structure import loadStructure as load_structure
+    from diffpy.structure.spacegroups import GetSpaceGroup as get_space_group
+
+
+def place_in_lattice(structure: Structure, lattice: Lattice) -> Structure:
+    if DIFFPY_STRUCTURE_VERSION >= Version("3.4.0"):
+        return structure.place_in_lattice(lattice)
+    else:
+        return structure.placeInLattice(lattice)
+
+
+def get_cell_parms(lattice: Lattice) -> tuple[float, float, float, float, float, float]:
+    if DIFFPY_STRUCTURE_VERSION >= Version("3.4.0"):
+        return lattice.cell_parms()
+    else:
+        return lattice.abcABG()
+
+
+def get_parser_and_structure_from_cif_file(fname: str) -> tuple[p_cif.P_cif, Structure]:
+    parser = p_cif.P_cif()
+    if DIFFPY_STRUCTURE_VERSION >= Version("3.4.0"):
+        structure = parser.parse_file(fname)
+    else:
+        structure = parser.parseFile(fname)
+    return parser, structure
+
+
+get_space_group: Callable[[str | int], SpaceGroup]
+# Simplified signature for our current use case
+load_structure: Callable[[str], Structure]
+
+__all__ = [
+    "get_space_group",
+    "get_parser_and_structure_from_cif_file",
+    "load_structure",
+    "place_in_lattice",
+]

orix/crystal_map/_phase.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2018-2025 the orix developers
+# Copyright 2018-2026 the orix developers
 #
 # This file is part of orix.
 #
@@ -26,12 +26,17 @@
 import warnings
 
 from diffpy.structure import Lattice, Structure
-from diffpy.structure.parsers import p_cif
-from diffpy.structure.spacegroups import GetSpaceGroup, SpaceGroup
+from diffpy.structure.spacegroups import SpaceGroup
 from diffpy.structure.symmetryutilities import ExpandAsymmetricUnit
 import matplotlib.colors as mcolors
 import numpy as np
 
+from orix._utils._diffpy_structure_utils import (
+    get_cell_parms,
+    get_parser_and_structure_from_cif_file,
+    get_space_group,
+    place_in_lattice,
+)
 from orix.plot._util.color import get_matplotlib_color
 from orix.quaternion.symmetry import (
     _EDAX_POINT_GROUP_ALIASES,
@@ -142,7 +147,7 @@ def structure(self, value: Structure) -> None:
         new_value = value.copy()
 
         # Ensure atom positions are expressed in the new basis
-        new_value.placeInLattice(Lattice(base=new_matrix))
+        new_value = place_in_lattice(new_value, Lattice(base=new_matrix))
 
         # Store old lattice for expand_asymmetric_unit
         self._diffpy_lattice = old_matrix
@@ -207,7 +212,7 @@ def space_group(self) -> SpaceGroup | None:
     def space_group(self, value: int | SpaceGroup | None) -> None:
         """Set the space group."""
         if isinstance(value, int):
-            value = GetSpaceGroup(value)
+            value = get_space_group(value)
         if not isinstance(value, SpaceGroup) and value is not None:
             raise ValueError(
                 f"{value!r} must be of type {SpaceGroup}, an integer 1-230, or None"
@@ -265,7 +270,7 @@ def is_hexagonal(self) -> bool:
         """Return whether the crystal structure is hexagonal/trigonal or
         not.
         """
-        return np.allclose(self.structure.lattice.abcABG()[3:], [90, 90, 120])
+        return np.allclose(get_cell_parms(self.structure.lattice)[3:], [90, 90, 120])
 
     @property
     def a_axis(self) -> Miller:
@@ -350,14 +355,13 @@ def from_cif(cls, filename: str | Path) -> Phase:
         file format.
         """
         path = Path(filename)
-        parser = p_cif.P_cif()
-        name = path.stem
-        structure = parser.parseFile(str(path))
+        parser, structure = get_parser_and_structure_from_cif_file(str(path))
         try:
             space_group = parser.spacegroup.number
         except AttributeError:  # pragma: no cover
             space_group = None
             warnings.warn(f"Could not read space group from CIF file {path!r}")
+        name = path.stem
         return cls(name, space_group, structure=structure)
 
     def deepcopy(self) -> Phase:
@@ -401,7 +405,9 @@ def expand_asymmetric_unit(self) -> Phase:
 
         # Ensure atom positions are expressed in diffpy's convention
         diffpy_structure = self.structure.copy()
-        diffpy_structure.placeInLattice(Lattice(base=self._diffpy_lattice))
+        diffpy_structure = place_in_lattice(
+            diffpy_structure, Lattice(base=self._diffpy_lattice)
+        )
         xyz = diffpy_structure.xyz
         diffpy_structure.clear()
 

orix/io/plugins/ang.py

@@ -29,6 +29,7 @@
 import numpy as np
 
 from orix import __version__
+from orix._utils._diffpy_structure_utils import get_cell_parms
 from orix.crystal_map._phase_list import PhaseList
 from orix.crystal_map.crystal_map import CrystalMap, create_coordinate_arrays
 from orix.quaternion.rotation import Rotation
@@ -618,7 +619,7 @@ def _get_header_from_phases(xmap: CrystalMap) -> str:
     # Phase IDs are reversed because EDAX TSL OIM Analysis v7.2.0
     # assumes a reversed phase order in the header
     for i, (_, phase) in reversed(list(enumerate(pl))):
-        lattice_constants = phase.structure.lattice.abcABG()
+        lattice_constants = get_cell_parms(phase.structure.lattice)
         lattice_constants = " ".join([f"{float(val):.3f}" for val in lattice_constants])
         phase_id = i + 1
         phase_name = phase.name

orix/io/plugins/orix_hdf5.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2018-2025 the orix developers
+# Copyright 2018-2026 the orix developers
 #
 # This file is part of orix.
 #
@@ -28,6 +28,7 @@
 from h5py import File, Group
 import numpy as np
 
+from orix._utils._diffpy_structure_utils import get_cell_parms
 from orix.crystal_map._phase import Phase
 from orix.crystal_map._phase_list import PhaseList
 from orix.crystal_map.crystal_map import CrystalMap
@@ -445,7 +446,7 @@ def lattice2dict(lattice: Lattice, dictionary: dict | None = None) -> dict:
     """
     if dictionary is None:
         dictionary = {}
-    dictionary["abcABG"] = np.array(lattice.abcABG())
+    dictionary["abcABG"] = np.array(get_cell_parms(lattice))
     dictionary["baserot"] = lattice.baserot
     return dictionary
 

orix/quaternion/symmetry.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2018-2025 the orix developers
+# Copyright 2018-2026 the orix developers
 #
 # This file is part of orix.
 #
@@ -21,10 +21,10 @@
 
 from typing import TYPE_CHECKING, Literal
 
-from diffpy.structure.spacegroups import GetSpaceGroup
 import matplotlib.figure as mfigure
 import numpy as np
 
+from orix._utils._diffpy_structure_utils import get_space_group
 from orix.quaternion.rotation import Rotation
 from orix.vector.vector3d import Vector3d
 
@@ -815,8 +815,8 @@ def get_point_group(space_group_number: int, proper: bool = False) -> Symmetry:
     >>> pgO.name
     '432'
     """
-    spg = GetSpaceGroup(space_group_number)
-    pgn = spg.point_group_name
+    spg = get_space_group(space_group_number)
+    pgn: str = spg.point_group_name
     if proper:
         return spacegroup2pointgroup_dict[pgn]["proper"]
     else:

orix/tests/conftest.py

@@ -26,7 +26,7 @@
 
 from collections import OrderedDict
 from numbers import Number
-from typing import Callable
+from typing import Callable, Generator
 
 from diffpy.structure import Atom, Lattice, Structure
 from h5py import File
@@ -1088,7 +1088,7 @@ def temp_bruker_h5ebsd_file(tmpdir, request):
 
 
 @pytest.fixture
-def cif_file(tmpdir):
+def cif_file(tmpdir) -> Generator[str, None, None]:
     """Actual CIF file of beta double prime phase often seen in Al-Mg-Si
     alloys.
     """

orix/tests/test_crystal_map/test_phase.py

@@ -1,5 +1,5 @@
 #
-# Copyright 2018-2025 the orix developers
+# Copyright 2018-2026 the orix developers
 #
 # This file is part of orix.
 #
@@ -17,10 +17,15 @@
 # along with orix. If not, see <http://www.gnu.org/licenses/>.
 #
 
-from diffpy.structure import Atom, Lattice, Structure, loadStructure
+from diffpy.structure import Atom, Lattice, Structure
 import numpy as np
 import pytest
 
+from orix._utils._diffpy_structure_utils import (
+    get_cell_parms,
+    load_structure,
+    place_in_lattice,
+)
 from orix.crystal_map import Phase
 from orix.crystal_map._phase import default_lattice, new_structure_matrix_from_alignment
 from orix.quaternion.symmetry import O, Symmetry
@@ -113,7 +118,9 @@ def test_copy_constructor_phase(self):
         assert p1.structure[0].element == p2.structure[0].element
         assert tuple(p1.structure[0].xyz) == tuple(p2.structure[0].xyz)
         assert p1.structure[0] is not p2.structure[0]
-        assert p1.structure.lattice.abcABG() == p2.structure.lattice.abcABG()
+        assert get_cell_parms(p1.structure.lattice) == get_cell_parms(
+            p2.structure.lattice
+        )
         assert p1.structure.lattice is not p2.structure.lattice
 
     @pytest.mark.parametrize("name", [None, "al", 1, np.arange(2)])
@@ -272,7 +279,7 @@ def test_structure_matrix(self):
         lattice = phase.structure.lattice
 
         # Lattice parameters are unchanged
-        assert np.allclose(lattice.abcABG(), [1.7, 1.7, 1.4, 90, 90, 120])
+        assert np.allclose(get_cell_parms(lattice), [1.7, 1.7, 1.4, 90, 90, 120])
 
         # Structure matrix has changed internally, but not the input
         # `Lattice` instance
@@ -412,14 +419,14 @@ def test_from_cif(self, cif_file):
         assert phase.point_group.name == "2/m"
         assert len(phase.structure) == 22  # Number of atoms
         lattice = phase.structure.lattice
-        assert np.allclose(lattice.abcABG(), [15.5, 4.05, 6.74, 90, 105.3, 90])
+        assert np.allclose(get_cell_parms(lattice), [15.5, 4.05, 6.74, 90, 105.3, 90])
         assert np.allclose(
             lattice.base, [[15.5, 0, 0], [0, 4.05, 0], [-1.779, 0, 6.501]], atol=1e-3
         )
 
-    def test_from_cif_same_structure(self, cif_file):
+    def test_from_cif_same_structure(self, cif_file: str):
         phase1 = Phase.from_cif(cif_file)
-        structure = loadStructure(cif_file)
+        structure = load_structure(cif_file)
         phase2 = Phase(structure=structure)
         assert np.allclose(phase1.structure.lattice.base, phase2.structure.lattice.base)
         assert np.allclose(phase1.structure.xyz, phase2.structure.xyz)
@@ -563,7 +570,7 @@ def test_expand_asymmetric_unit(
         # Check atom positions in ORIGINAL lattice alignment
         # Doing the check in orix's alignment makes independently computing expected sites difficult
         s = exp.structure.copy()
-        s.placeInLattice(Lattice(base=phase._diffpy_lattice))
+        s = place_in_lattice(s, Lattice(base=phase._diffpy_lattice))
         # Use set to avoid having to ensure the order is the same
         assert set(tuple(xyz.round(8).tolist()) for xyz in s.xyz) == set(
             expected_atom_positions
@@ -574,7 +581,7 @@ def test_expand_asymmetric_unit(
         assert np.array_equal(base, exp2.structure.lattice.base)
         assert len(exp2.structure) == len(expected_atom_positions)
         s = exp2.structure.copy()
-        s.placeInLattice(Lattice(base=phase._diffpy_lattice))
+        s = place_in_lattice(s, Lattice(base=phase._diffpy_lattice))
         assert set(tuple(xyz.round(8).tolist()) for xyz in s.xyz) == set(
             expected_atom_positions
         )
@@ -969,12 +976,12 @@ def test_expand_asymmetric_unit_raise_if_no_point_group(self):
     def test_default_lattice(self):
         for S in ["1", "2", "222", "422", "432"]:
             phase = Phase(point_group=S)
-            lattice_parameters = phase.structure.lattice.abcABG()
+            lattice_parameters = get_cell_parms(phase.structure.lattice)
             assert np.allclose([1, 1, 1, 90, 90, 90], lattice_parameters)
 
         for S in ["3", "622"]:
             phase = Phase(point_group=S)
-            lattice_parameters = phase.structure.lattice.abcABG()
+            lattice_parameters = get_cell_parms(phase.structure.lattice)
             assert np.allclose([1, 1, 1, 90, 90, 120], lattice_parameters)
 
     def test_default_lattice_raises(self):