structuretoolkit 0.0.42__tar.gz → 0.0.44__tar.gz

structuretoolkit-0.0.44/.gitignore

@@ -0,0 +1,217 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[codz]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#   Usually these files are written by a python script from a template
+#   before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py.cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
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+# Sphinx documentation
+docs/_build/
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+# PyBuilder
+.pybuilder/
+target/
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+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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+# Pipfile.lock
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+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
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+#   commonly ignored for libraries.
+# uv.lock
+
+# poetry
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+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+# poetry.lock
+# poetry.toml
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#   pdm recommends including project-wide configuration in pdm.toml, but excluding .pdm-python.
+#   https://pdm-project.org/en/latest/usage/project/#working-with-version-control
+# pdm.lock
+# pdm.toml
+.pdm-python
+.pdm-build/
+
+# pixi
+#   Similar to Pipfile.lock, it is generally recommended to include pixi.lock in version control.
+# pixi.lock
+#   Pixi creates a virtual environment in the .pixi directory, just like venv module creates one
+#   in the .venv directory. It is recommended not to include this directory in version control.
+.pixi
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# Redis
+*.rdb
+*.aof
+*.pid
+
+# RabbitMQ
+mnesia/
+rabbitmq/
+rabbitmq-data/
+
+# ActiveMQ
+activemq-data/
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+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
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+
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+.mypy_cache/
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+
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+#   JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#   be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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+#   option (not recommended) you can uncomment the following to ignore the entire idea folder.
+# .idea/
+
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+#   Abstra is an AI-powered process automation framework.
+#   Ignore directories containing user credentials, local state, and settings.
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+.abstra/
+
+# Visual Studio Code
+#   Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore 
+#   that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
+#   and can be added to the global gitignore or merged into this file. However, if you prefer, 
+#   you could uncomment the following to ignore the entire vscode folder
+# .vscode/
+# Temporary file for partial code execution
+tempCodeRunnerFile.py
+
+# Ruff stuff:
+.ruff_cache/
+
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+
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+marimo/_static/
+marimo/_lsp/
+__marimo__/
+
+# Streamlit
+.streamlit/secrets.toml

{structuretoolkit-0.0.42 → structuretoolkit-0.0.44}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: structuretoolkit
-Version: 0.0.42
+Version: 0.0.44
 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
@@ -41,14 +41,13 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
-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: <3.15,>=3.10
-Requires-Dist: ase<=3.28.0,>=3.20.1
-Requires-Dist: numpy<=2.4.3,>=1.23.5
+Requires-Dist: ase<=3.28.0,>=3.24.0
+Requires-Dist: numpy<=2.4.6,>=1.23.5
 Requires-Dist: scipy<=1.17.1,>=1.15.0
 Provides-Extra: clusters
 Requires-Dist: scikit-learn==1.8.0; extra == 'clusters'
@@ -56,23 +55,23 @@ 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<=2026.3.23,>=2022.2.1; extra == 'grainboundary'
+Requires-Dist: pymatgen==2026.3.23; extra == 'grainboundary'
 Provides-Extra: matplotlib
-Requires-Dist: matplotlib==3.10.8; extra == 'matplotlib'
+Requires-Dist: matplotlib==3.10.9; extra == 'matplotlib'
 Provides-Extra: mp-api
 Requires-Dist: mp-api==0.45.15; extra == 'mp-api'
-Requires-Dist: pymatgen<=2026.3.23,>=2022.2.1; extra == 'mp-api'
+Requires-Dist: pymatgen==2026.3.23; extra == 'mp-api'
 Provides-Extra: nglview
 Requires-Dist: nglview<=4.0.1,>=2.7.7; extra == 'nglview'
 Provides-Extra: phonopy
-Requires-Dist: phonopy<=3.5.0,>=2.16.2; extra == 'phonopy'
+Requires-Dist: phonopy<=4.0.1,>=2.21.2; extra == 'phonopy'
 Requires-Dist: spglib==2.7.0; extra == 'phonopy'
 Provides-Extra: plotly
-Requires-Dist: plotly<=6.6.0,>=4.14.3; extra == 'plotly'
+Requires-Dist: plotly<=6.8.0,>=6.0.0; extra == 'plotly'
 Provides-Extra: pyscal
 Requires-Dist: pyscal3<=3.3.2,>=3.2.5; extra == 'pyscal'
 Provides-Extra: surface
-Requires-Dist: pymatgen<=2026.3.23,>=2022.2.1; extra == 'surface'
+Requires-Dist: pymatgen==2026.3.23; extra == 'surface'
 Requires-Dist: spglib==2.7.0; extra == 'surface'
 Provides-Extra: symmetry
 Requires-Dist: spglib==2.7.0; extra == 'symmetry'

{structuretoolkit-0.0.42 → structuretoolkit-0.0.44}/pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["ase", "numpy", "scipy", "hatchling==1.29.0", "hatch-vcs==0.5.0"]
+requires = ["ase", "numpy", "scipy", "hatchling==1.30.1", "hatch-vcs==0.5.0"]
 build-backend = "hatchling.build"
 
 [project]
@@ -18,14 +18,13 @@ classifiers = [
     "License :: OSI Approved :: BSD License",
     "Intended Audience :: Science/Research",
     "Operating System :: OS Independent",
-    "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,<=3.28.0",
-    "numpy>=1.23.5,<=2.4.3",
+    "ase>=3.24.0,<=3.28.0",
+    "numpy>=1.23.5,<=2.4.6",
     "scipy>=1.15.0,<=1.17.1",
 ]
 dynamic = ["version"]
@@ -39,25 +38,25 @@ Repository = "https://github.com/pyiron/structuretoolkit"
 dscribe = ["dscribe==2.1.2"]
 grainboundary = [
     "aimsgb>=1.0.2,<=1.1.1",
-    "pymatgen>=2022.2.1,<=2026.3.23",
+    "pymatgen==2026.3.23",
 ]
 pyscal = ["pyscal3>=3.2.5,<=3.3.2"]
 nglview = ["nglview>=2.7.7,<=4.0.1"]
-matplotlib = ["matplotlib==3.10.8"]
-plotly = ["plotly>=4.14.3,<=6.6.0"]
+matplotlib = ["matplotlib==3.10.9"]
+plotly = ["plotly>=6.0.0,<=6.8.0"]
 clusters = ["scikit-learn==1.8.0"]
 symmetry = ["spglib==2.7.0"]
 surface = [
     "spglib==2.7.0",
-    "pymatgen>=2022.2.1,<=2026.3.23",
+    "pymatgen==2026.3.23",
 ]
 phonopy = [
-    "phonopy>=2.16.2,<=3.5.0",
+    "phonopy>=2.21.2,<=4.0.1",
     "spglib==2.7.0",
 ]
 mp-api = [
     "mp-api==0.45.15",
-    "pymatgen>=2022.2.1,<=2026.3.23",
+    "pymatgen==2026.3.23",
 ]
 
 [tool.ruff]

structuretoolkit-0.0.44/src/structuretoolkit/_version.py

@@ -0,0 +1,24 @@
+# file generated by vcs-versioning
+# don't change, don't track in version control
+from __future__ import annotations
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
+version: str
+__version__: str
+__version_tuple__: tuple[int | str, ...]
+version_tuple: tuple[int | str, ...]
+commit_id: str | None
+__commit_id__: str | None
+
+__version__ = version = '0.0.44'
+__version_tuple__ = version_tuple = (0, 0, 44)
+
+__commit_id__ = commit_id = None

{structuretoolkit-0.0.42 → structuretoolkit-0.0.44}/src/structuretoolkit/analyse/dscribe.py

@@ -11,7 +11,7 @@ def soap_descriptor_per_atom(
     rbf: str = "gto",
     weighting: np.ndarray | None = None,
     average: str = "off",
-    compression: dict = None,
+    compression: dict | None = None,
     species: list | None = None,
     periodic: bool = True,
     sparse: bool = False,

{structuretoolkit-0.0.42 → structuretoolkit-0.0.44}/src/structuretoolkit/analyse/neighbors.py

@@ -3,6 +3,7 @@
 
 import itertools
 import warnings
+from typing import Any, cast
 
 import numpy as np
 from ase.atoms import Atoms
@@ -56,18 +57,18 @@ class Tree:
         Args:
             ref_structure (ase.atoms.Atoms): Reference structure.
         """
-        self._distances = None
-        self._vectors = None
-        self._indices = None
+        self._distances: Any = None
+        self._vectors: Any = None
+        self._indices: Any = None
         self._mode = {"filled": True, "ragged": False, "flattened": False}
-        self._extended_positions = None
-        self._positions = None
-        self._wrapped_indices = None
-        self._extended_indices = None
+        self._extended_positions: Any = None
+        self._positions: Any = None
+        self._wrapped_indices: Any = None
+        self._extended_indices: Any = None
         self._ref_structure = ref_structure.copy()
         self.wrap_positions = False
-        self._tree = None
-        self.num_neighbors = None
+        self._tree: Any = None
+        self.num_neighbors: int | None = None
         self.cutoff_radius = np.inf
         self._norm_order = 2
 
@@ -91,6 +92,7 @@ class Tree:
         for k, v in self._mode.items():
             if v:
                 return k
+        raise ValueError("No neighbor representation mode is active")
 
     def _set_mode(self, new_mode: str) -> None:
         """
@@ -172,6 +174,7 @@ class Tree:
             return self._contract(value, ref_vector=ref_vector)
         elif key == "flattened":
             return value[self._distances < np.inf]
+        raise ValueError(f"Unknown neighbor representation mode: {key}")
 
     @property
     def distances(self) -> np.ndarray:
@@ -257,7 +260,7 @@ class Tree:
             + " with the correct norm_order value"
         )
 
-    def _get_max_length(self, ref_vector: np.ndarray | None = None) -> int:
+    def _get_max_length(self, ref_vector: np.ndarray | None = None) -> int | None:
         """
         Get the maximum length of the reference vector.
 
@@ -277,9 +280,7 @@ class Tree:
             return None
         return max(len(dd[dd < np.inf]) for dd in ref_vector)
 
-    def _contract(
-        self, value: np.ndarray, ref_vector: np.ndarray | None = None
-    ) -> np.ndarray:
+    def _contract(self, value: np.ndarray, ref_vector: np.ndarray | None = None):
         """
         Contract the given value based on the specified reference vector.
 
@@ -297,7 +298,7 @@ class Tree:
             for vv, dist in zip(value, self.filled.distances, strict=True)
         ]
 
-    def _allow_ragged_to_mode(self, new_bool: bool) -> str:
+    def _allow_ragged_to_mode(self, new_bool: bool | None) -> str:
         """
         Set the representation mode based on the value of new_bool.
 
@@ -504,6 +505,8 @@ class Tree:
         if self.num_neighbors is None:
             self.num_neighbors = num_neighbors
             self.cutoff_radius = cutoff_radius
+        assert num_neighbors is not None
+        assert self.num_neighbors is not None
         if num_neighbors > self.num_neighbors:
             warnings.warn(
                 "Taking a larger search area after initialization has the risk of "
@@ -582,7 +585,7 @@ class Tree:
     def _get_neighborhood(
         self,
         positions: np.ndarray,
-        num_neighbors: int = 12,
+        num_neighbors: int | None = 12,
         cutoff_radius: float = np.inf,
         exclude_self: bool = False,
         width_buffer: float = 1.2,
@@ -611,7 +614,7 @@ class Tree:
             cutoff_radius=cutoff_radius,
             width_buffer=width_buffer,
         )
-        if num_neighbors is not None:
+        if num_neighbors is not None and self.num_neighbors is not None:
             self.num_neighbors -= 1
         max_column = np.sum(distances < np.inf, axis=-1).max()
         self._distances = distances[..., start_column:max_column]
@@ -620,7 +623,7 @@ class Tree:
         self._positions = positions
         return self
 
-    def _check_width(self, width: float, pbc: list[bool, bool, bool]) -> bool:
+    def _check_width(self, width: float, pbc: np.ndarray) -> bool:
         """
         Check if the width of the layer exceeds the specified value.
 
@@ -706,26 +709,19 @@ class Tree:
         radius. For automated uses, see Atoms.analyse.pyscal_steinhardt_parameter()
         """
         random_rotation = Rotation.from_mrp(np.random.random(3)).as_matrix()
-        return np.sqrt(
-            4
-            * np.pi
-            / (2 * l + 1)
-            * np.sum(
-                [
-                    np.absolute(
-                        self.get_spherical_harmonics(
-                            l=l,
-                            m=m,
-                            cutoff_radius=cutoff_radius,
-                            rotation=random_rotation,
-                        )
-                    )
-                    ** 2
-                    for m in np.arange(-l, l + 1)
-                ],
-                axis=0,
+        harmonic_values: list[np.ndarray] = [
+            np.absolute(
+                self.get_spherical_harmonics(
+                    l=l,
+                    m=m,
+                    cutoff_radius=cutoff_radius,
+                    rotation=random_rotation,
+                )
             )
-        )
+            ** 2
+            for m in np.arange(-l, l + 1)
+        ]
+        return np.sqrt(4 * np.pi / (2 * l + 1) * np.sum(harmonic_values, axis=0))
 
     @staticmethod
     def _get_all_possible_pairs(l: int) -> np.ndarray:
@@ -827,8 +823,8 @@ class Neighbors(Tree):
         """
         super().__init__(ref_structure=ref_structure)
         self._tolerance = tolerance
-        self._cluster_vecs = None
-        self._cluster_dist = None
+        self._cluster_vecs: Any = None
+        self._cluster_dist: Any = None
 
     def __repr__(self):
         """
@@ -1072,7 +1068,7 @@ class Neighbors(Tree):
 
     def find_neighbors_by_vector(
         self, vector: np.ndarray, return_deviation: bool = False
-    ) -> np.ndarray:
+    ) -> np.ndarray | tuple[np.ndarray, np.ndarray]:
         """
         Args:
             vector (list/np.ndarray): vector by which positions are translated (and neighbors are searched)
@@ -1323,9 +1319,9 @@ class Neighbors(Tree):
         ind_shell = []
         for d, i in zip(dist, ind, strict=True):
             id_list = get_cluster(d[d < radius], i[d < radius])
-            ia_shells_dict = {}
+            ia_shells_dict: dict[str, list[list[int]]] = {}
             for i_shell_list in id_list:
-                ia_shell_dict = {}
+                ia_shell_dict: dict[str, list[int]] = {}
                 for i_s in i_shell_list:
                     el = el_list[i_s]
                     if el not in ia_shell_dict:
@@ -1382,14 +1378,17 @@ def get_neighbors(
     Returns:
         Neighbors: An instance of the Neighbors class with the neighbor indices, distances, and vectors.
     """
-    neigh = _get_neighbors(
-        structure=structure,
-        num_neighbors=num_neighbors,
-        tolerance=tolerance,
-        id_list=id_list,
-        cutoff_radius=cutoff_radius,
-        width_buffer=width_buffer,
-        norm_order=norm_order,
+    neigh = cast(
+        Neighbors,
+        _get_neighbors(
+            structure=structure,
+            num_neighbors=num_neighbors,
+            tolerance=tolerance,
+            id_list=id_list,
+            cutoff_radius=cutoff_radius,
+            width_buffer=width_buffer,
+            norm_order=norm_order,
+        ),
     )
     neigh._set_mode(mode)
     return neigh

{structuretoolkit-0.0.42 → structuretoolkit-0.0.44}/src/structuretoolkit/analyse/phonopy.py

@@ -47,4 +47,6 @@ def get_equivalent_atoms(
     ops = spglib.get_symmetry(
         cell=unitcell.totuple(), symprec=symprec, angle_tolerance=angle_tolerance
     )
+    if ops is None:
+        raise RuntimeError("spglib could not determine symmetry")
     return ops["equivalent_atoms"]

{structuretoolkit-0.0.42 → structuretoolkit-0.0.44}/src/structuretoolkit/analyse/pyscal.py

@@ -27,7 +27,7 @@ def get_steinhardt_parameters(
     n_clusters: int | None = 2,
     q: tuple | None = None,
     averaged: bool = False,
-) -> tuple[np.ndarray] | tuple[np.ndarray, np.ndarray]:
+) -> np.ndarray | tuple[np.ndarray, np.ndarray]:
     """
     Calculate Steinhardts parameters
 
@@ -162,7 +162,7 @@ def get_diamond_structure_descriptors(
 
 def get_adaptive_cna_descriptors(
     structure: Atoms, mode: str = "total", ovito_compatibility: bool = False
-) -> np.ndarray:
+) -> dict | np.ndarray:
     """
     Use common neighbor analysis
 

{structuretoolkit-0.0.42 → structuretoolkit-0.0.44}/src/structuretoolkit/analyse/snap.py

@@ -63,7 +63,7 @@ def get_snap_descriptors_per_atom(
     structure: Atoms,
     atom_types: list[str],
     twojmax: int = 6,
-    element_radius: list[int] = None,
+    element_radius: list[float] | None = None,
     rcutfac: float = 1.0,
     rfac0: float = 0.99363,
     rmin0: float = 0.0,
@@ -114,7 +114,7 @@ def get_snap_descriptor_derivatives(
     structure: Atoms,
     atom_types: list[str],
     twojmax: int = 6,
-    element_radius: list[int] = None,
+    element_radius: list[float] | None = None,
     rcutfac: float = 1.0,
     rfac0: float = 0.99363,
     rmin0: float = 0.0,
@@ -161,7 +161,7 @@ def get_snap_descriptor_derivatives(
     )
 
 
-def get_snap_descriptor_names(twojmax: int) -> np.ndarray:
+def get_snap_descriptor_names(twojmax: int) -> list[list[float]]:
     """
     Get names of the SNAP descriptors
 
@@ -548,7 +548,7 @@ def _extract_computes_snap(
         np.ndarray: Output of the LAMMPS compute command
     """
     lmp_atom_ids = lmp.numpy.extract_atom_iarray("id", num_atoms).flatten()
-    cond = np.all(lmp_atom_ids == 1 + np.arange(num_atoms))
+    cond = bool(np.all(lmp_atom_ids == 1 + np.arange(num_atoms)))
     assert cond, "LAMMPS seems to have lost atoms"
 
     # Extract types
@@ -556,7 +556,7 @@ def _extract_computes_snap(
     lmp_volume = lmp.get_thermo("vol")
 
     # Extract Bsum
-    _extract_compute_np(lmp, "b_sum", 0, 1, (n_coeff))
+    _extract_compute_np(lmp, "b_sum", 0, 1, (n_coeff,))
 
     # Extract B
     lmp_barr = _extract_compute_np(lmp, "b", 1, 2, (num_atoms, n_coeff))
@@ -571,13 +571,13 @@ def _extract_computes_snap(
 
     lmp_dbarr = _extract_compute_np(lmp, "db", 1, 2, (num_atoms, num_types, 3, n_coeff))
     lmp_dbsum = _extract_compute_np(lmp, "db_sum", 0, 1, (num_types, 3, n_coeff))
-    cond = np.allclose(lmp_dbsum, lmp_dbarr.sum(axis=0), rtol=1e-12, atol=1e-12)
+    cond = bool(np.allclose(lmp_dbsum, lmp_dbarr.sum(axis=0), rtol=1e-12, atol=1e-12))
     assert cond, "db_sum doesn't match sum of db"
     db_atom = np.transpose(lmp_dbarr, (0, 2, 1, 3))
 
     lmp_vbarr = _extract_compute_np(lmp, "vb", 1, 2, (num_atoms, num_types, 6, n_coeff))
     lmp_vbsum = _extract_compute_np(lmp, "vb_sum", 0, 1, (num_types, 6, n_coeff))
-    cond = np.allclose(lmp_vbsum, lmp_vbarr.sum(axis=0), rtol=1e-12, atol=1e-12)
+    cond = bool(np.allclose(lmp_vbsum, lmp_vbarr.sum(axis=0), rtol=1e-12, atol=1e-12))
     assert cond, "vb_sum doesn't match sum of vb"
     vb_sum = np.transpose(lmp_vbsum, (1, 0, 2)) / lmp_volume * eV_div_A3_to_bar