structuretoolkit 0.0.29__tar.gz → 0.0.32__tar.gz

{structuretoolkit-0.0.29/structuretoolkit.egg-info → structuretoolkit-0.0.32}/PKG-INFO

@@ -1,6 +1,6 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: structuretoolkit
-Version: 0.0.29
+Version: 0.0.32
 Summary: build, analyse and visualise atomistic structures for materials science
 Author-email: Jan Janssen <janssen@mpie.de>
 License: BSD 3-Clause License
@@ -49,39 +49,40 @@ Classifier: Programming Language :: Python :: 3.12
 Requires-Python: <3.13,>=3.9
 Description-Content-Type: text/markdown
 License-File: LICENSE
-Requires-Dist: ase<=3.24.0,>=3.20.1
+Requires-Dist: ase<=3.25.0,>=3.20.1
 Requires-Dist: numpy<=1.26.4,>=1.23.5
-Requires-Dist: scipy<=1.15.0,>=1.9.3
+Requires-Dist: scipy<=1.15.2,>=1.9.3
 Provides-Extra: dscribe
 Requires-Dist: dscribe==2.1.1; extra == "dscribe"
 Provides-Extra: grainboundary
 Requires-Dist: aimsgb<=1.1.1,>=1.0.2; extra == "grainboundary"
-Requires-Dist: pymatgen<=2024.11.13,>=2022.2.1; extra == "grainboundary"
+Requires-Dist: pymatgen<=2025.3.10,>=2022.2.1; extra == "grainboundary"
 Provides-Extra: pyscal
 Requires-Dist: pyscal3<=3.2.7,>=3.2.5; extra == "pyscal"
 Provides-Extra: nglview
 Requires-Dist: nglview<=3.1.4,>=2.7.7; extra == "nglview"
 Provides-Extra: matplotlib
-Requires-Dist: matplotlib==3.10.0; extra == "matplotlib"
+Requires-Dist: matplotlib==3.10.1; extra == "matplotlib"
 Provides-Extra: plotly
-Requires-Dist: plotly<=5.24.1,>=4.14.3; extra == "plotly"
+Requires-Dist: plotly<=6.0.1,>=4.14.3; extra == "plotly"
 Provides-Extra: clusters
-Requires-Dist: scikit-learn==1.6.0; extra == "clusters"
+Requires-Dist: scikit-learn==1.6.1; extra == "clusters"
 Provides-Extra: symmetry
-Requires-Dist: spglib<=2.5.0,>=1.16.5; extra == "symmetry"
+Requires-Dist: spglib<=2.6.0,>=1.16.5; extra == "symmetry"
 Provides-Extra: surface
-Requires-Dist: spglib<=2.5.0,>=1.16.5; extra == "surface"
-Requires-Dist: pymatgen<=2024.11.13,>=2022.2.1; extra == "surface"
+Requires-Dist: spglib<=2.6.0,>=1.16.5; extra == "surface"
+Requires-Dist: pymatgen<=2025.3.10,>=2022.2.1; extra == "surface"
 Provides-Extra: phonopy
-Requires-Dist: phonopy<=2.34.0,>=2.16.2; extra == "phonopy"
-Requires-Dist: spglib<=2.5.0,>=1.16.5; extra == "phonopy"
+Requires-Dist: phonopy<=2.38.0,>=2.16.2; extra == "phonopy"
+Requires-Dist: spglib<=2.6.0,>=1.16.5; extra == "phonopy"
 Provides-Extra: pyxtal
-Requires-Dist: pyxtal<=1.0.6,>=0.5.5; extra == "pyxtal"
+Requires-Dist: pyxtal<=1.0.7,>=0.5.5; extra == "pyxtal"
+Dynamic: license-file
 
 # structuretoolkit 
 
-[![Unittests](https://github.com/pyiron/structuretoolkit/actions/workflows/unittests.yml/badge.svg)](https://github.com/pyiron/structuretoolkit/actions/workflows/unittests.yml)
-[![Coverage Status](https://coveralls.io/repos/github/pyiron/structuretoolkit/badge.svg?branch=main)](https://coveralls.io/github/pyiron/structuretoolkit?branch=main)
+[![Pipeline](https://github.com/pyiron/structuretoolkit/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pyiron/structuretoolkit/actions/workflows/pipeline.yml)
+[![codecov](https://codecov.io/gh/pyiron/structuretoolkit/graph/badge.svg?token=B6I4OACKND)](https://codecov.io/gh/pyiron/structuretoolkit)
 
 Originally developed as part of the `pyiron_atomistics` module the `structuretoolkit` was release as standalone library
 for analysing, building and visualising atomistic structures. Internally it uses the `ase.atoms.Atoms` class to 

{structuretoolkit-0.0.29 → structuretoolkit-0.0.32}/README.md

@@ -1,7 +1,7 @@
 # structuretoolkit 
 
-[![Unittests](https://github.com/pyiron/structuretoolkit/actions/workflows/unittests.yml/badge.svg)](https://github.com/pyiron/structuretoolkit/actions/workflows/unittests.yml)
-[![Coverage Status](https://coveralls.io/repos/github/pyiron/structuretoolkit/badge.svg?branch=main)](https://coveralls.io/github/pyiron/structuretoolkit?branch=main)
+[![Pipeline](https://github.com/pyiron/structuretoolkit/actions/workflows/pipeline.yml/badge.svg)](https://github.com/pyiron/structuretoolkit/actions/workflows/pipeline.yml)
+[![codecov](https://codecov.io/gh/pyiron/structuretoolkit/graph/badge.svg?token=B6I4OACKND)](https://codecov.io/gh/pyiron/structuretoolkit)
 
 Originally developed as part of the `pyiron_atomistics` module the `structuretoolkit` was release as standalone library
 for analysing, building and visualising atomistic structures. Internally it uses the `ase.atoms.Atoms` class to 

{structuretoolkit-0.0.29 → structuretoolkit-0.0.32}/pyproject.toml

@@ -24,9 +24,9 @@ classifiers = [
     "Programming Language :: Python :: 3.12",
 ]
 dependencies = [
-    "ase>=3.20.1,<=3.24.0",
+    "ase>=3.20.1,<=3.25.0",
     "numpy>=1.23.5,<=1.26.4",
-    "scipy>=1.9.3,<=1.15.0",
+    "scipy>=1.9.3,<=1.15.2",
 ]
 dynamic = ["version"]
 
@@ -39,23 +39,23 @@ Repository = "https://github.com/pyiron/structuretoolkit"
 dscribe = ["dscribe==2.1.1"]
 grainboundary = [
     "aimsgb>=1.0.2,<=1.1.1",
-    "pymatgen>=2022.2.1,<=2024.11.13",
+    "pymatgen>=2022.2.1,<=2025.3.10",
 ]
 pyscal = ["pyscal3>=3.2.5,<=3.2.7"]
 nglview = ["nglview>=2.7.7,<=3.1.4"]
-matplotlib = ["matplotlib==3.10.0"]
-plotly = ["plotly>=4.14.3,<=5.24.1"]
-clusters = ["scikit-learn==1.6.0"]
-symmetry = ["spglib>=1.16.5,<=2.5.0"]
+matplotlib = ["matplotlib==3.10.1"]
+plotly = ["plotly>=4.14.3,<=6.0.1"]
+clusters = ["scikit-learn==1.6.1"]
+symmetry = ["spglib>=1.16.5,<=2.6.0"]
 surface = [
-    "spglib>=1.16.5,<=2.5.0",
-    "pymatgen>=2022.2.1,<=2024.11.13",
+    "spglib>=1.16.5,<=2.6.0",
+    "pymatgen>=2022.2.1,<=2025.3.10",
 ]
 phonopy = [
-    "phonopy>=2.16.2,<=2.34.0",
-    "spglib>=1.16.5,<=2.5.0",
+    "phonopy>=2.16.2,<=2.38.0",
+    "spglib>=1.16.5,<=2.6.0",
 ]
-pyxtal = ["pyxtal>=0.5.5,<=1.0.6"]
+pyxtal = ["pyxtal>=0.5.5,<=1.0.7"]
 
 [tool.setuptools.packages.find]
 include = ["structuretoolkit*"]
@@ -63,6 +63,53 @@ include = ["structuretoolkit*"]
 [tool.setuptools.dynamic]
 version = {attr = "structuretoolkit.__version__"}
 
+[tool.ruff]
+exclude = [".ci_support", "tests", "setup.py", "_version.py"]
+
+[tool.ruff.lint]
+select = [
+    # pycodestyle
+    "E",
+    # Pyflakes
+    "F",
+    # pyupgrade
+    "UP",
+    # flake8-bugbear
+    "B",
+    # flake8-simplify
+    "SIM",
+    # isort
+    "I",
+    # flake8-comprehensions
+    "C4",
+    # eradicate
+    "ERA",
+    # pylint
+    "PL",
+]
+ignore = [
+    # ignore functions in argument defaults
+    "B008",
+    # ignore exception naming
+    "B904",
+    # ignore line-length violations
+    "E501",
+    # ignore equality comparisons for numpy arrays
+    "E712",
+    # ignore bare except
+    "E722",
+    # ignore ambiguous variable name
+    "E741",
+    # Too many arguments in function definition
+    "PLR0913",
+    # Magic value used in comparison
+    "PLR2004",
+    # Too many branches
+    "PLR0912",
+    # Too many statements
+    "PLR0915",
+]
+
 [tool.versioneer]
 VCS = "git"
 style = "pep440-pre"

{structuretoolkit-0.0.29 → structuretoolkit-0.0.32}/structuretoolkit/__init__.py

@@ -98,4 +98,62 @@ from structuretoolkit.visualize import plot3d
 
 from . import _version
 
+__all__ = [
+    "find_mic",
+    "find_solids",
+    "get_adaptive_cna_descriptors",
+    "get_average_of_unique_labels",
+    "get_centro_symmetry_descriptors",
+    "get_cluster_positions",
+    "get_delaunay_neighbors",
+    "get_diamond_structure_descriptors",
+    "get_distances_array",
+    "get_equivalent_atoms",
+    "get_interstitials",
+    "get_layers",
+    "get_mean_positions",
+    "get_neighborhood",
+    "get_neighbors",
+    "get_steinhardt_parameters",
+    "get_strain",
+    "get_symmetry",
+    "get_voronoi_neighbors",
+    "get_voronoi_vertices",
+    "get_voronoi_volumes",
+    "analyse_find_solids",
+    "analyse_cna_adaptive",
+    "analyse_centro_symmetry",
+    "cluster_positions",
+    "analyse_diamond_structure",
+    "analyse_phonopy_equivalent_atoms",
+    "get_steinhardt_parameter_structure",
+    "analyse_voronoi_volume",
+    "B2",
+    "C14",
+    "C15",
+    "C36",
+    "D03",
+    "create_mesh",
+    "get_grainboundary_info",
+    "get_high_index_surface_info",
+    "grainboundary",
+    "high_index_surface",
+    "sqs_structures",
+    "grainboundary_info",
+    "high_index_surface_info",
+    "grainboundary_build",
+    "get_sqs_structures",
+    "SymmetryError",
+    "apply_strain",
+    "ase_to_pymatgen",
+    "ase_to_pyscal",
+    "center_coordinates_in_unit_cell",
+    "get_cell",
+    "get_extended_positions",
+    "get_vertical_length",
+    "get_wrapped_coordinates",
+    "pymatgen_to_ase",
+    "select_index",
+    "plot3d",
+]
 __version__ = _version.get_versions()["version"]

{structuretoolkit-0.0.29 → structuretoolkit-0.0.32}/structuretoolkit/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-01-08T12:24:58+0100",
+ "date": "2025-04-13T08:36:36+0200",
  "dirty": true,
  "error": null,
- "full-revisionid": "1d3dc72ffec6f8278719c0551754cf405880e393",
- "version": "0.0.29"
+ "full-revisionid": "6a0b89e67ab34d999e56a93afceaa1fbedf249bc",
+ "version": "0.0.32"
 }
 '''  # END VERSION_JSON
 

{structuretoolkit-0.0.29 → structuretoolkit-0.0.32}/structuretoolkit/analyse/__init__.py

@@ -254,3 +254,39 @@ def get_ir_reciprocal_mesh(
         is_shift=is_shift,
         is_time_reversal=is_time_reversal,
     )
+
+
+__all__ = [
+    "find_mic",
+    "get_distances_array",
+    "soap_descriptor_per_atom",
+    "get_neighborhood",
+    "get_neighbors",
+    "get_equivalent_atoms",
+    "find_solids",
+    "get_adaptive_cna_descriptors",
+    "get_centro_symmetry_descriptors",
+    "get_diamond_structure_descriptors",
+    "get_steinhardt_parameters",
+    "get_voronoi_volumes",
+    "get_snap_descriptor_derivatives",
+    "get_snap_descriptor_names",
+    "get_snap_descriptors_per_atom",
+    "get_average_of_unique_labels",
+    "get_cluster_positions",
+    "get_delaunay_neighbors",
+    "get_interstitials",
+    "get_layers",
+    "get_mean_positions",
+    "get_voronoi_neighbors",
+    "get_voronoi_vertices",
+    "get_strain",
+    "get_ir_reciprocal_mesh",
+    "get_symmetry",
+    "symmetrize_vectors",
+    "group_points_by_symmetry",
+    "get_primitive_cell",
+    "get_spacegroup",
+    "get_symmetry_dataset",
+    "get_equivalent_points",
+]

{structuretoolkit-0.0.29 → structuretoolkit-0.0.32}/structuretoolkit/analyse/dscribe.py

@@ -13,7 +13,7 @@ def soap_descriptor_per_atom(
     rbf: str = "gto",
     weighting: Optional[np.ndarray] = None,
     average: str = "off",
-    compression: dict = {"mode": "off", "species_weighting": None},
+    compression: dict = None,
     species: Optional[list] = None,
     periodic: bool = True,
     sparse: bool = False,
@@ -50,6 +50,8 @@ def soap_descriptor_per_atom(
     """
     from dscribe.descriptors import SOAP
 
+    if compression is None:
+        compression = {"mode": "off", "species_weighting": None}
     if species is None:
         species = list(set(structure.get_chemical_symbols()))
     periodic_soap = SOAP(

{structuretoolkit-0.0.29 → structuretoolkit-0.0.32}/structuretoolkit/analyse/neighbors.py

@@ -1,10 +1,9 @@
-# coding: utf-8
 # 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 itertools
 import warnings
-from typing import Dict, List, Optional, Tuple, Union
+from typing import Optional, Union
 
 import numpy as np
 from ase.atoms import Atoms
@@ -104,11 +103,11 @@ class Tree:
         Raises:
             KeyError: If the new mode is not found in the available modes.
         """
-        if new_mode not in self._mode.keys():
+        if new_mode not in self._mode:
             raise KeyError(
                 f"{new_mode} not found. Available modes: {', '.join(self._mode.keys())}"
             )
-        self._mode = {key: False for key in self._mode.keys()}
+        self._mode = dict.fromkeys(self._mode, False)
         self._mode[new_mode] = True
 
     def __repr__(self) -> str:
@@ -366,7 +365,7 @@ class Tree:
         num_neighbors: Optional[int] = None,
         cutoff_radius: float = np.inf,
         width_buffer: float = 1.2,
-    ) -> Tuple[np.ndarray, np.ndarray]:
+    ) -> tuple[np.ndarray, np.ndarray]:
         """
         Get the distances and indices of the neighbors for the given positions.
 
@@ -406,7 +405,8 @@ class Tree:
             warnings.warn(
                 "Number of neighbors found within the cutoff_radius is equal to (estimated) "
                 + "num_neighbors. Increase num_neighbors (or set it to None) or "
-                + "width_buffer to find all neighbors within cutoff_radius."
+                + "width_buffer to find all neighbors within cutoff_radius.",
+                stacklevel=2,
             )
         self._extended_indices = indices.copy()
         indices[distances < np.inf] = self._get_wrapped_indices()[
@@ -508,7 +508,8 @@ class Tree:
         if num_neighbors > self.num_neighbors:
             warnings.warn(
                 "Taking a larger search area after initialization has the risk of "
-                + "missing neighborhood atoms"
+                + "missing neighborhood atoms",
+                stacklevel=2,
             )
         return num_neighbors
 
@@ -632,15 +633,14 @@ class Tree:
             bool: True if the width exceeds the specified value, False otherwise.
 
         """
-        if any(pbc) and np.prod(self.filled.distances.shape) > 0:
-            if (
-                np.linalg.norm(
-                    self.flattened.vecs[..., pbc], axis=-1, ord=self.norm_order
-                ).max()
-                > width
-            ):
-                return True
-        return False
+        return bool(
+            any(pbc)
+            and np.prod(self.filled.distances.shape) > 0
+            and np.linalg.norm(
+                self.flattened.vecs[..., pbc], axis=-1, ord=self.norm_order
+            ).max()
+            > width
+        )
 
     def get_spherical_harmonics(
         self,
@@ -811,9 +811,9 @@ class Mode:
     def __dir__(self):
         """Show value names which are available for different filling modes."""
         return list(
-            set(
-                ["distances", "vecs", "indices", "shells", "atom_numbers"]
-            ).intersection(self.ref_neigh.__dir__())
+            {"distances", "vecs", "indices", "shells", "atom_numbers"}.intersection(
+                self.ref_neigh.__dir__()
+            )
         )
 
 
@@ -1008,7 +1008,7 @@ class Neighbors(Tree):
 
     def get_shell_matrix(
         self,
-        chemical_pair: Optional[List[str]] = None,
+        chemical_pair: Optional[list[str]] = None,
         cluster_by_distances: bool = False,
         cluster_by_vecs: bool = False,
     ):
@@ -1225,7 +1225,7 @@ class Neighbors(Tree):
 
     def cluster_analysis(
         self, id_list: list, return_cluster_sizes: bool = False
-    ) -> Union[Dict[int, List[int]], Tuple[Dict[int, List[int]], List[int]]]:
+    ) -> Union[dict[int, list[int]], tuple[dict[int, list[int]], list[int]]]:
         """
         Perform cluster analysis on a list of atom IDs.
 
@@ -1240,11 +1240,8 @@ class Neighbors(Tree):
         """
         self._cluster = [0] * len(self._ref_structure)
         c_count = 1
-        # element_list = self.get_atomic_numbers()
         for ia in id_list:
-            # el0 = element_list[ia]
             nbrs = self.ragged.indices[ia]
-            # print ("nbrs: ", ia, nbrs)
             if self._cluster[ia] == 0:
                 self._cluster[ia] = c_count
                 self.__probe_cluster(c_count, nbrs, id_list)
@@ -1261,7 +1258,7 @@ class Neighbors(Tree):
         return cluster_dict  # sizes
 
     def __probe_cluster(
-        self, c_count: int, neighbors: List[int], id_list: List[int]
+        self, c_count: int, neighbors: list[int], id_list: list[int]
     ) -> None:
         """
         Recursively probe the cluster and assign cluster IDs to neighbors.
@@ -1275,11 +1272,12 @@ class Neighbors(Tree):
             None
         """
         for nbr_id in neighbors:
-            if self._cluster[nbr_id] == 0:
-                if nbr_id in id_list:  # TODO: check also for ordered structures
-                    self._cluster[nbr_id] = c_count
-                    nbrs = self.ragged.indices[nbr_id]
-                    self.__probe_cluster(c_count, nbrs, id_list)
+            if (
+                self._cluster[nbr_id] == 0 and nbr_id in id_list
+            ):  # TODO: check also for ordered structures
+                self._cluster[nbr_id] = c_count
+                nbrs = self.ragged.indices[nbr_id]
+                self.__probe_cluster(c_count, nbrs, id_list)
 
     # TODO: combine with corresponding routine in plot3d
     def get_bonds(
@@ -1287,7 +1285,7 @@ class Neighbors(Tree):
         radius: float = np.inf,
         max_shells: Optional[int] = None,
         prec: float = 0.1,
-    ) -> List[Dict[str, List[List[int]]]]:
+    ) -> list[dict[str, list[list[int]]]]:
         """
         Get the bonds in the structure.
 
@@ -1303,7 +1301,7 @@ class Neighbors(Tree):
 
         def get_cluster(
             dist_vec: np.ndarray, ind_vec: np.ndarray, prec: float = prec
-        ) -> List[np.ndarray]:
+        ) -> list[np.ndarray]:
             """
             Get clusters from a distance vector and index vector.
 
@@ -1326,7 +1324,6 @@ class Neighbors(Tree):
         ind_shell = []
         for d, i in zip(dist, ind):
             id_list = get_cluster(d[d < radius], i[d < radius])
-            # print ("id: ", d[d<radius], id_list, dist_lst)
             ia_shells_dict = {}
             for i_shell_list in id_list:
                 ia_shell_dict = {}
@@ -1338,9 +1335,11 @@ class Neighbors(Tree):
                 for el, ia_lst in ia_shell_dict.items():
                     if el not in ia_shells_dict:
                         ia_shells_dict[el] = []
-                    if max_shells is not None:
-                        if len(ia_shells_dict[el]) + 1 > max_shells:
-                            continue
+                    if (
+                        max_shells is not None
+                        and len(ia_shells_dict[el]) + 1 > max_shells
+                    ):
+                        continue
                     ia_shells_dict[el].append(ia_lst)
             ind_shell.append(ia_shells_dict)
         return ind_shell
@@ -1457,7 +1456,8 @@ def _get_neighbors(
     if neigh._check_width(width=width, pbc=structure.pbc):
         warnings.warn(
             "width_buffer may have been too small - "
-            "most likely not all neighbors properly assigned"
+            "most likely not all neighbors properly assigned",
+            stacklevel=2,
         )
     return neigh
 

{structuretoolkit-0.0.29 → structuretoolkit-0.0.32}/structuretoolkit/analyse/phonopy.py

@@ -1,8 +1,6 @@
-# coding: utf-8
 # 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.
 
-from typing import List
 
 import numpy as np
 from ase.atoms import Atoms
@@ -21,7 +19,7 @@ __date__ = "Sep 1, 2018"
 
 def get_equivalent_atoms(
     structure: Atoms, symprec: float = 1e-5, angle_tolerance: float = -1.0
-) -> List[int]:
+) -> list[int]:
     """
     Get the indices of atoms that are equivalent under symmetry operations.
 

{structuretoolkit-0.0.29 → structuretoolkit-0.0.32}/structuretoolkit/analyse/pyscal.py

@@ -1,8 +1,7 @@
-# coding: utf-8
 # 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.
 
-from typing import Any, Dict, Optional, Tuple, Union
+from typing import Any, Optional, Union
 
 import numpy as np
 from ase.atoms import Atoms
@@ -28,7 +27,7 @@ def get_steinhardt_parameters(
     n_clusters: Optional[int] = 2,
     q: Optional[tuple] = None,
     averaged: bool = False,
-) -> Union[Tuple[np.ndarray], Tuple[np.ndarray, np.ndarray]]:
+) -> Union[tuple[np.ndarray], tuple[np.ndarray, np.ndarray]]:
     """
     Calculate Steinhardts parameters
 
@@ -81,7 +80,7 @@ def get_centro_symmetry_descriptors(
 
 def get_diamond_structure_descriptors(
     structure: Atoms, mode: str = "total", ovito_compatibility: bool = False
-) -> Union[Dict[str, int], np.ndarray]:
+) -> Union[dict[str, int], np.ndarray]:
     """
     Analyse diamond structure
 

{structuretoolkit-0.0.29 → structuretoolkit-0.0.32}/structuretoolkit/analyse/snap.py

@@ -64,7 +64,7 @@ def get_snap_descriptors_per_atom(
     structure: Atoms,
     atom_types: list[str],
     twojmax: int = 6,
-    element_radius: list[int] = [4.0],
+    element_radius: list[int] = None,
     rcutfac: float = 1.0,
     rfac0: float = 0.99363,
     rmin0: float = 0.0,
@@ -92,6 +92,8 @@ def get_snap_descriptors_per_atom(
     Returns:
         np.ndarray: Numpy array with the calculated descriptor derivatives
     """
+    if element_radius is None:
+        element_radius = [4.0]
     lmp, bispec_options, cutoff = _get_default_parameters(
         atom_types=atom_types,
         twojmax=twojmax,
@@ -113,7 +115,7 @@ def get_snap_descriptor_derivatives(
     structure: Atoms,
     atom_types: list[str],
     twojmax: int = 6,
-    element_radius: list[int] = [4.0],
+    element_radius: list[int] = None,
     rcutfac: float = 1.0,
     rfac0: float = 0.99363,
     rmin0: float = 0.0,
@@ -141,6 +143,8 @@ def get_snap_descriptor_derivatives(
     Returns:
         np.ndarray: Numpy array with the calculated descriptor derivatives
     """
+    if element_radius is None:
+        element_radius = [4.0]
     lmp, bispec_options, cutoff = _get_default_parameters(
         atom_types=atom_types,
         twojmax=twojmax,
@@ -420,7 +424,7 @@ def _calc_snap_per_atom(
         return np.array([])
     else:
         if (
-            "quadraticflag" in bispec_options.keys()
+            "quadraticflag" in bispec_options
             and int(bispec_options["quadraticflag"]) == 1
         ):
             return _extract_compute_np(
@@ -521,7 +525,7 @@ def _set_computes_snap(lmp, bispec_options: dict):
     kw_substrings = [f"{k} {v}" for k, v in kw_options.items()]
     kwargs = " ".join(kw_substrings)
 
-    for op, base in zip(("b", "db", "vb"), (base_b, base_db, base_vb)):
+    for _op, base in zip(("b", "db", "vb"), (base_b, base_db, base_vb)):
         command = f"{base} {radelem} {wj} {kwargs}"
         lmp.command(command)
 
@@ -545,16 +549,15 @@ def _extract_computes_snap(
         np.ndarray: Output of the LAMMPS compute command
     """
     lmp_atom_ids = lmp.numpy.extract_atom_iarray("id", num_atoms).flatten()
-    assert np.all(
-        lmp_atom_ids == 1 + np.arange(num_atoms)
-    ), "LAMMPS seems to have lost atoms"
+    cond = np.all(lmp_atom_ids == 1 + np.arange(num_atoms))
+    assert cond, "LAMMPS seems to have lost atoms"
 
     # Extract types
     lmp_types = lmp.numpy.extract_atom_iarray(name="type", nelem=num_atoms).flatten()
     lmp_volume = lmp.get_thermo("vol")
 
     # Extract Bsum
-    lmp_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))
@@ -569,16 +572,14 @@ 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))
-    assert np.allclose(
-        lmp_dbsum, lmp_dbarr.sum(axis=0), rtol=1e-12, atol=1e-12
-    ), "db_sum doesn't match sum of db"
+    cond = 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))
-    assert np.allclose(
-        lmp_vbsum, lmp_vbarr.sum(axis=0), rtol=1e-12, atol=1e-12
-    ), "vb_sum doesn't match sum of vb"
+    cond = 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
 
     dbatom_shape = db_atom.shape
@@ -631,7 +632,7 @@ def _calc_snap_derivatives(
         return np.array([])
     else:
         if (
-            "quadraticflag" in bispec_options.keys()
+            "quadraticflag" in bispec_options
             and int(bispec_options["quadraticflag"]) == 1
         ):
             return _extract_computes_snap(
@@ -681,10 +682,7 @@ def _get_default_parameters(
     """
     from lammps import lammps
 
-    if weights is None:
-        wj = [1.0] * len(atom_types)
-    else:
-        wj = weights
+    wj = [1.0] * len(atom_types) if weights is None else weights
     if isinstance(element_radius, float):
         radelem = [element_radius] * len(atom_types)
     else: