Merge pull request #224 from pyiron/ruff

Add ruff linter

Author: jan-janssen

.ci_support/release.py

@@ -1,12 +1,19 @@
 def get_setup_version_and_pattern(setup_content):
     depend_lst, version_lst = [], []
     for l in setup_content:
-        if '==' in l:
-            lst = l.split('[')[-1].split(']')[0].replace(' ', '').replace('"', '').replace("'", '').split(',')
+        if "==" in l:
+            lst = (
+                l.split("[")[-1]
+                .split("]")[0]
+                .replace(" ", "")
+                .replace('"', "")
+                .replace("'", "")
+                .split(",")
+            )
             for dep in lst:
-                if dep != '\n':
-                    version_lst.append(dep.split('==')[1])
-                    depend_lst.append(dep.split('==')[0])
+                if dep != "\n":
+                    version_lst.append(dep.split("==")[1])
+                    depend_lst.append(dep.split("==")[0])
 
     version_high_dict = {d: v for d, v in zip(depend_lst, version_lst)}
     return version_high_dict
@@ -16,14 +23,14 @@ def get_env_version(env_content):
     read_flag = False
     depend_lst, version_lst = [], []
     for l in env_content:
-        if 'dependencies:' in l:
+        if "dependencies:" in l:
             read_flag = True
         elif read_flag:
-            lst = l.replace('-', '').replace(' ', '').replace('\n', '').split("=")
+            lst = l.replace("-", "").replace(" ", "").replace("\n", "").split("=")
             if len(lst) == 2:
                 depend_lst.append(lst[0])
                 version_lst.append(lst[1])
-    return {d:v for d, v in zip(depend_lst, version_lst)}
+    return {d: v for d, v in zip(depend_lst, version_lst)}
 
 
 def update_dependencies(setup_content, version_low_dict, version_high_dict):
@@ -35,27 +42,29 @@ def update_dependencies(setup_content, version_low_dict, version_high_dict):
             version_combo_dict[dep] = dep + "==" + ver
 
     setup_content_new = ""
-    pattern_dict = {d:d + "==" + v for d, v in version_high_dict.items()}
+    pattern_dict = {d: d + "==" + v for d, v in version_high_dict.items()}
     for l in setup_content:
         for k, v in pattern_dict.items():
             if v in l:
                 l = l.replace(v, version_combo_dict[k])
-        setup_content_new +=l
+        setup_content_new += l
     return setup_content_new
 
 
 if __name__ == "__main__":
-    with open('pyproject.toml', "r") as f:
+    with open("pyproject.toml", "r") as f:
         setup_content = f.readlines()
 
-    with open('environment.yml', "r") as f:
+    with open("environment.yml", "r") as f:
         env_content = f.readlines()
 
     setup_content_new = update_dependencies(
         setup_content=setup_content[2:],
         version_low_dict=get_env_version(env_content=env_content),
-        version_high_dict=get_setup_version_and_pattern(setup_content=setup_content[2:]),
+        version_high_dict=get_setup_version_and_pattern(
+            setup_content=setup_content[2:]
+        ),
     )
 
-    with open('pyproject.toml', "w") as f:
+    with open("pyproject.toml", "w") as f:
         f.writelines("".join(setup_content[:2]) + setup_content_new)

.pre-commit-config.yaml

@@ -0,0 +1,10 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.5.2
+    hooks:
+      - id: ruff
+        name: ruff lint
+        args: ["--select", "I", "--fix"]
+        files: ^structuretoolkit/
+      - id: ruff-format
+        name: ruff format

setup.py

@@ -1,8 +1,7 @@
-from setuptools import setup
-
 import versioneer
+from setuptools import setup
 
 setup(
     version=versioneer.get_version(),
     cmdclass=versioneer.get_cmdclass(),
-)
+)

structuretoolkit/__init__.py

@@ -1,5 +1,3 @@
-from . import _version
-
 # Analyse
 from structuretoolkit.analyse import (
     find_mic,
@@ -25,19 +23,59 @@
     get_voronoi_volumes,
 )
 
+# Analyse - for backwards compatibility
+from structuretoolkit.analyse import (
+    find_solids as analyse_find_solids,
+)
+from structuretoolkit.analyse import (
+    get_adaptive_cna_descriptors as analyse_cna_adaptive,
+)
+from structuretoolkit.analyse import (
+    get_centro_symmetry_descriptors as analyse_centro_symmetry,
+)
+from structuretoolkit.analyse import (
+    get_cluster_positions as cluster_positions,
+)
+from structuretoolkit.analyse import (
+    get_diamond_structure_descriptors as analyse_diamond_structure,
+)
+from structuretoolkit.analyse import (
+    get_equivalent_atoms as analyse_phonopy_equivalent_atoms,
+)
+from structuretoolkit.analyse import (
+    get_steinhardt_parameters as get_steinhardt_parameter_structure,
+)
+from structuretoolkit.analyse import (
+    get_voronoi_volumes as analyse_voronoi_volume,
+)
+
 # Build
 from structuretoolkit.build import (
     B2,
     C14,
     C15,
     C36,
     D03,
+    create_mesh,
     get_grainboundary_info,
     get_high_index_surface_info,
     grainboundary,
     high_index_surface,
     sqs_structures,
-    create_mesh,
+)
+
+# Build - for backwards compatibility
+from structuretoolkit.build import (
+    get_grainboundary_info as grainboundary_info,
+)
+from structuretoolkit.build import (
+    get_high_index_surface_info as high_index_surface_info,
+)
+from structuretoolkit.build import (
+    grainboundary as grainboundary_build,
+)
+from structuretoolkit.build import (
+    sqs_structures as get_sqs_structures,
 )
 
 # Common
@@ -47,35 +85,17 @@
     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,
-    get_cell,
 )
 
 # Visualize
 from structuretoolkit.visualize import plot3d
 
-# Analyse - for backwards compatibility
-from structuretoolkit.analyse import (
-    find_solids as analyse_find_solids,
-    get_adaptive_cna_descriptors as analyse_cna_adaptive,
-    get_centro_symmetry_descriptors as analyse_centro_symmetry,
-    get_cluster_positions as cluster_positions,
-    get_diamond_structure_descriptors as analyse_diamond_structure,
-    get_equivalent_atoms as analyse_phonopy_equivalent_atoms,
-    get_steinhardt_parameters as get_steinhardt_parameter_structure,
-    get_voronoi_volumes as analyse_voronoi_volume,
-)
-
-# Build - for backwards compatibility
-from structuretoolkit.build import (
-    get_grainboundary_info as grainboundary_info,
-    get_high_index_surface_info as high_index_surface_info,
-    grainboundary as grainboundary_build,
-    sqs_structures as get_sqs_structures,
-)
+from . import _version
 
 __version__ = _version.get_versions()["version"]

structuretoolkit/_version.py

@@ -11,12 +11,12 @@
 """Git implementation of _version.py."""
 
 import errno
+import functools
 import os
 import re
 import subprocess
 import sys
 from typing import Any, Callable, Dict, List, Optional, Tuple
-import functools
 
 
 def get_keywords() -> Dict[str, str]:

structuretoolkit/analyse/__init__.py

@@ -12,6 +12,11 @@
     get_steinhardt_parameters,
     get_voronoi_volumes,
 )
+from structuretoolkit.analyse.snap import (
+    get_snap_descriptor_derivatives,
+    get_snap_descriptor_names,
+    get_snap_descriptors_per_atom,
+)
 from structuretoolkit.analyse.spatial import (
     get_average_of_unique_labels,
     get_cluster_positions,
@@ -23,11 +28,6 @@
     get_voronoi_vertices,
 )
 from structuretoolkit.analyse.strain import get_strain
-from structuretoolkit.analyse.snap import (
-    get_snap_descriptor_names,
-    get_snap_descriptors_per_atom,
-    get_snap_descriptor_derivatives,
-)
 
 
 def get_symmetry(

structuretoolkit/analyse/distance.py

@@ -1,6 +1,7 @@
 from typing import Optional
-from ase.atoms import Atoms
+
 import numpy as np
+from ase.atoms import Atoms
 
 
 def get_distances_array(

structuretoolkit/analyse/dscribe.py

@@ -1,6 +1,7 @@
+from typing import Optional
+
 import numpy as np
 from ase.atoms import Atoms
-from typing import Optional
 
 
 def soap_descriptor_per_atom(

structuretoolkit/analyse/neighbors.py

@@ -6,8 +6,8 @@
 import warnings
 from typing import Optional
 
-from ase.atoms import Atoms
 import numpy as np
+from ase.atoms import Atoms
 from scipy.sparse import coo_matrix
 from scipy.spatial import cKDTree
 from scipy.spatial.transform import Rotation

structuretoolkit/analyse/phonopy.py

@@ -2,8 +2,8 @@
 # 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 ase.atoms import Atoms
 import numpy as np
+from ase.atoms import Atoms
 
 __author__ = "Osamu Waseda"
 __copyright__ = (

structuretoolkit/analyse/pyscal.py

@@ -3,6 +3,7 @@
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
 from typing import Optional
+
 import numpy as np
 from ase.atoms import Atoms
 

structuretoolkit/analyse/snap.py

@@ -1,7 +1,8 @@
-from ase.atoms import Atoms
+from ctypes import POINTER, c_double, c_int, cast
 from typing import Optional, Union
-from ctypes import c_double, c_int, cast, POINTER
+
 import numpy as np
+from ase.atoms import Atoms
 from scipy.constants import physical_constants
 
 eV_div_A3_to_bar = 1e25 / physical_constants["joule-electron volt relationship"][0]

structuretoolkit/analyse/spatial.py

@@ -2,11 +2,12 @@
 # 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 ase.atoms import Atoms
+from typing import Optional
+
 import numpy as np
+from ase.atoms import Atoms
 from scipy.sparse import coo_matrix
 from scipy.spatial import ConvexHull, Delaunay, Voronoi
-from typing import Optional
 
 from structuretoolkit.analyse.neighbors import get_neighborhood, get_neighbors
 from structuretoolkit.common.helper import (

structuretoolkit/analyse/strain.py

@@ -1,7 +1,8 @@
-from ase.atoms import Atoms
+from typing import Optional
+
 import numpy as np
+from ase.atoms import Atoms
 from scipy.spatial.transform import Rotation
-from typing import Optional
 
 from structuretoolkit.analyse.neighbors import get_neighbors
 from structuretoolkit.analyse.pyscal import get_adaptive_cna_descriptors

structuretoolkit/analyse/symmetry.py

@@ -3,14 +3,14 @@
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
 import ast
+import string
+from functools import cached_property
+from typing import Optional
 
-from ase.atoms import Atoms
 import numpy as np
 import spglib
+from ase.atoms import Atoms
 from scipy.spatial import cKDTree
-from typing import Optional
-import string
-from functools import cached_property
 
 import structuretoolkit.common.helper
 from structuretoolkit.common.error import SymmetryError

structuretoolkit/build/__init__.py

@@ -1,12 +1,9 @@
-from structuretoolkit.build.aimsgb import (
-    grainboundary,
-    get_grainboundary_info
-)
+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,
     high_index_surface,
-    get_high_index_surface_info
 )
-from structuretoolkit.build.mesh import create_mesh

structuretoolkit/build/aimsgb.py

@@ -5,8 +5,9 @@
 from typing import Optional
 from warnings import warn
 
-from ase.atoms import Atoms
 import numpy as np
+from ase.atoms import Atoms
+
 from structuretoolkit.common.pymatgen import ase_to_pymatgen, pymatgen_to_ase
 
 __author__ = "Ujjal Saikia"
@@ -42,6 +43,7 @@ def get_grainboundary_info(axis: np.ndarray, max_sigma: int):
     GBBuilder.gb_build() function along with the rotational axis and initial bulk structure.
     """
     from aimsgb import GBInformation
+
     return GBInformation(axis=axis, max_sigma=max_sigma)
 
 
@@ -91,7 +93,7 @@ def grainboundary(
     Returns:
         :class:`ase.Atoms`: final grain boundary structure
     """
-    from aimsgb import GrainBoundary, Grain
+    from aimsgb import Grain, GrainBoundary
 
     if add_if_dist is not None:
         warn("`add_if_dist` is deprecated, please use `gap` instead.")