structuretoolkit 0.0.35__tar.gz → 0.0.36__tar.gz

{structuretoolkit-0.0.35 → structuretoolkit-0.0.36}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: structuretoolkit
-Version: 0.0.35
+Version: 0.0.36
 Summary: build, analyse and visualise atomistic structures for materials science
 Project-URL: Homepage, https://github.com/pyiron/structuretoolkit
 Project-URL: Documentation, https://github.com/pyiron/structuretoolkit
@@ -45,33 +45,32 @@ Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Topic :: Scientific/Engineering :: Physics
-Requires-Python: <3.13,>=3.9
+Requires-Python: <3.14,>=3.9
 Requires-Dist: ase<=3.26.0,>=3.20.1
-Requires-Dist: numpy<=2.3.3,>=1.23.5
-Requires-Dist: scipy<=1.16.2,>=1.9.3
+Requires-Dist: numpy<=2.3.4,>=1.23.5
+Requires-Dist: scipy<=1.16.3,>=1.9.3
 Provides-Extra: clusters
-Requires-Dist: scikit-learn==1.6.1; extra == 'clusters'
+Requires-Dist: scikit-learn==1.7.2; extra == 'clusters'
 Provides-Extra: dscribe
 Requires-Dist: dscribe==2.1.2; extra == 'dscribe'
 Provides-Extra: grainboundary
 Requires-Dist: aimsgb<=1.1.1,>=1.0.2; extra == 'grainboundary'
-Requires-Dist: pymatgen<=2025.3.10,>=2022.2.1; extra == 'grainboundary'
+Requires-Dist: pymatgen<=2025.6.14,>=2022.2.1; extra == 'grainboundary'
 Provides-Extra: matplotlib
-Requires-Dist: matplotlib==3.10.3; extra == 'matplotlib'
+Requires-Dist: matplotlib==3.10.7; extra == 'matplotlib'
 Provides-Extra: nglview
 Requires-Dist: nglview<=3.1.4,>=2.7.7; extra == 'nglview'
 Provides-Extra: phonopy
 Requires-Dist: phonopy<=2.43.2,>=2.16.2; extra == 'phonopy'
 Requires-Dist: spglib<=2.6.0,>=1.16.5; extra == 'phonopy'
 Provides-Extra: plotly
-Requires-Dist: plotly<=6.3.0,>=4.14.3; extra == 'plotly'
+Requires-Dist: plotly<=6.3.1,>=4.14.3; extra == 'plotly'
 Provides-Extra: pyscal
 Requires-Dist: pyscal3<=3.3.0,>=3.2.5; extra == 'pyscal'
-Provides-Extra: pyxtal
-Requires-Dist: pyxtal<=1.1.1,>=0.5.5; extra == 'pyxtal'
 Provides-Extra: surface
-Requires-Dist: pymatgen<=2025.3.10,>=2022.2.1; extra == 'surface'
+Requires-Dist: pymatgen<=2025.6.14,>=2022.2.1; extra == 'surface'
 Requires-Dist: spglib<=2.6.0,>=1.16.5; extra == 'surface'
 Provides-Extra: symmetry
 Requires-Dist: spglib<=2.6.0,>=1.16.5; extra == 'symmetry'
@@ -127,7 +126,6 @@ stk.plot3d(structure)
 * `stk.build.high_index_surface()`
 * `stk.build.get_high_index_surface_info()`
 * `stk.build.sqs_structures()`
-* `stk.build.pyxtal()`
 * `stk.build.B2()`
 * `stk.build.C14()`
 * `stk.build.C15()`

{structuretoolkit-0.0.35 → structuretoolkit-0.0.36}/README.md

@@ -48,7 +48,6 @@ stk.plot3d(structure)
 * `stk.build.high_index_surface()`
 * `stk.build.get_high_index_surface_info()`
 * `stk.build.sqs_structures()`
-* `stk.build.pyxtal()`
 * `stk.build.B2()`
 * `stk.build.C14()`
 * `stk.build.C15()`

{structuretoolkit-0.0.35 → structuretoolkit-0.0.36}/pyproject.toml

@@ -11,7 +11,7 @@ authors = [
 readme = "README.md"
 license = { file = "LICENSE" }
 keywords = ["pyiron"]
-requires-python = ">=3.9, <3.13"
+requires-python = ">=3.9, <3.14"
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Topic :: Scientific/Engineering :: Physics",
@@ -22,11 +22,12 @@ classifiers = [
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
 ]
 dependencies = [
     "ase>=3.20.1,<=3.26.0",
-    "numpy>=1.23.5,<=2.3.3",
-    "scipy>=1.9.3,<=1.16.2",
+    "numpy>=1.23.5,<=2.3.4",
+    "scipy>=1.9.3,<=1.16.3",
 ]
 dynamic = ["version"]
 
@@ -39,23 +40,22 @@ Repository = "https://github.com/pyiron/structuretoolkit"
 dscribe = ["dscribe==2.1.2"]
 grainboundary = [
     "aimsgb>=1.0.2,<=1.1.1",
-    "pymatgen>=2022.2.1,<=2025.3.10",
+    "pymatgen>=2022.2.1,<=2025.6.14",
 ]
 pyscal = ["pyscal3>=3.2.5,<=3.3.0"]
 nglview = ["nglview>=2.7.7,<=3.1.4"]
-matplotlib = ["matplotlib==3.10.3"]
-plotly = ["plotly>=4.14.3,<=6.3.0"]
-clusters = ["scikit-learn==1.6.1"]
+matplotlib = ["matplotlib==3.10.7"]
+plotly = ["plotly>=4.14.3,<=6.3.1"]
+clusters = ["scikit-learn==1.7.2"]
 symmetry = ["spglib>=1.16.5,<=2.6.0"]
 surface = [
     "spglib>=1.16.5,<=2.6.0",
-    "pymatgen>=2022.2.1,<=2025.3.10",
+    "pymatgen>=2022.2.1,<=2025.6.14",
 ]
 phonopy = [
     "phonopy>=2.16.2,<=2.43.2",
     "spglib>=1.16.5,<=2.6.0",
 ]
-pyxtal = ["pyxtal>=0.5.5,<=1.1.1"]
 
 [tool.ruff]
 exclude = [".ci_support", "tests", "setup.py", "_version.py"]

{structuretoolkit-0.0.35 → structuretoolkit-0.0.36}/structuretoolkit/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '0.0.35'
-__version_tuple__ = version_tuple = (0, 0, 35)
+__version__ = version = '0.0.36'
+__version_tuple__ = version_tuple = (0, 0, 36)
 
 __commit_id__ = commit_id = None

{structuretoolkit-0.0.35 → structuretoolkit-0.0.36}/structuretoolkit/build/__init__.py

@@ -1,7 +1,6 @@
 from structuretoolkit.build.aimsgb import get_grainboundary_info, grainboundary
 from structuretoolkit.build.compound import B2, C14, C15, C36, D03
 from structuretoolkit.build.mesh import create_mesh
-from structuretoolkit.build.random import pyxtal
 from structuretoolkit.build.sqs import sqs_structures
 from structuretoolkit.build.surface import (
     get_high_index_surface_info,
@@ -17,7 +16,6 @@ __all__ = [
     "C36",
     "D03",
     "create_mesh",
-    "pyxtal",
     "sqs_structures",
     "get_high_index_surface_info",
     "high_index_surface",

structuretoolkit-0.0.35/structuretoolkit/build/random.py

@@ -1,107 +0,0 @@
-# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
-# Distributed under the terms of "New BSD License", see the LICENSE file.
-
-import warnings
-from typing import Union
-
-try:
-    from tqdm.auto import tqdm
-except ImportError:
-
-    def tqdm(x):
-        return x
-
-
-from ase import Atoms
-
-from structuretoolkit.common.helper import center_coordinates_in_unit_cell
-
-
-def pyxtal(
-    group: Union[int, list[int]],
-    species: tuple[str],
-    num_ions: tuple[int],
-    dim=3,
-    repeat=1,
-    allow_exceptions=True,
-    **kwargs,
-) -> Union[Atoms, list[dict]]:
-    """
-    Generate random crystal structures with PyXtal.
-
-    `group` must be between 1 and the largest possible value for the given dimensionality:
-        dim=3 => 1 - 230 (space groups)
-        dim=2 => 1 -  80 (layer groups)
-        dim=1 => 1 -  75 (rod groups)
-        dim=0 => 1 -  58 (point groups)
-
-    When `group` is passed as a list of integers or `repeat>1`, generate multiple structures and return them in a list
-    of dicts containing the keys `atoms`, `symmetry` and `repeat` for the ASE structure, the symmetry group
-    number and which iteration it is, respectively.
-
-    Args:
-        group (list of int, or int): the symmetry group to generate or a list of them
-        species (tuple of str): which species to include, defines the stoichiometry together with `num_ions`
-        num_ions (tuple of int): how many of each species to include, defines the stoichiometry together with `species`
-        dim (int): dimensionality of the symmetry group, 0 is point groups, 1 is rod groups, 2 is layer groups and 3 is space groups
-        repeat (int): how many random structures to generate
-        allow_exceptions (bool): when generating multiple structures, silence errors when the requested stoichiometry and symmetry group are incompatible
-        **kwargs: passed to `pyxtal.pyxtal` function verbatim
-
-    Returns:
-        :class:`~.Atoms`: the generated structure, if repeat==1 and only one symmetry group is requested
-        list of dict of all generated structures, if repeat>1 or multiple symmetry groups are requested
-
-    Raises:
-        ValueError: if `species` and `num_ions` are not of the same length
-        ValueError: if stoichiometry and symmetry group are incompatible and allow_exceptions==False or only one structure is requested
-    """
-    from pyxtal import pyxtal as _pyxtal
-    from pyxtal.msg import Comp_CompatibilityError
-
-    if len(species) != len(num_ions):
-        raise ValueError(
-            "species and num_ions must be of same length, "
-            f"not {species} and {num_ions}!"
-        )
-    stoich = "".join(f"{s}{n}" for s, n in zip(species, num_ions))
-
-    def generate(group):
-        s = _pyxtal()
-        try:
-            s.from_random(
-                dim=dim, group=group, species=species, numIons=num_ions, **kwargs
-            )
-        except Comp_CompatibilityError:
-            if not allow_exceptions:
-                raise ValueError(
-                    f"Symmetry group {group} incompatible with stoichiometry {stoich}!"
-                ) from None
-            else:
-                return None
-        s = s.to_ase()
-        s = center_coordinates_in_unit_cell(structure=s)
-        return s
-
-    # return a single structure
-    if repeat == 1 and isinstance(group, int):
-        allow_exceptions = False
-        return generate(group)
-    else:
-        structures = []
-        if isinstance(group, int):
-            group = [group]
-        failed_groups = []
-        for g in tqdm(group, desc="Spacegroups"):
-            for i in range(repeat):
-                s = generate(g)
-                if s is None:
-                    failed_groups.append(g)
-                    continue
-                structures.append({"atoms": s, "symmetry": g, "repeat": i})
-        if len(failed_groups) > 0:
-            warnings.warn(
-                f"Groups [{', '.join(map(str, failed_groups))}] could not be generated with stoichiometry {stoich}!",
-                stacklevel=2,
-            )
-        return structures