Extend ruff linting (#293)

* Extend ruff linting

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.ci_support/release.py

@@ -15,7 +15,7 @@ def get_setup_version_and_pattern(setup_content):
                     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)}
+    version_high_dict = dict(zip(depend_lst, version_lst))
     return version_high_dict
 
 
@@ -30,13 +30,13 @@ def get_env_version(env_content):
             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 dict(zip(depend_lst, version_lst))
 
 
 def update_dependencies(setup_content, version_low_dict, version_high_dict):
     version_combo_dict = {}
     for dep, ver in version_high_dict.items():
-        if dep in version_low_dict.keys() and version_low_dict[dep] != ver:
+        if dep in version_low_dict and version_low_dict[dep] != ver:
             version_combo_dict[dep] = dep + ">=" + version_low_dict[dep] + ",<=" + ver
         else:
             version_combo_dict[dep] = dep + "==" + ver
@@ -52,10 +52,10 @@ def update_dependencies(setup_content, version_low_dict, version_high_dict):
 
 
 if __name__ == "__main__":
-    with open("pyproject.toml", "r") as f:
+    with open("pyproject.toml") as f:
         setup_content = f.readlines()
 
-    with open("environment.yml", "r") as f:
+    with open("environment.yml") as f:
         env_content = f.readlines()
 
     setup_content_new = update_dependencies(

.pre-commit-config.yaml

@@ -4,7 +4,7 @@ repos:
     hooks:
       - id: ruff
         name: ruff lint
-        args: ["--select", "I", "--fix"]
+        args: ["--fix"]
         files: ^pylammpsmpi/
       - id: ruff-format
         name: ruff format

pylammpsmpi/__init__.py

@@ -4,13 +4,13 @@
 
 from ._version import get_versions
 
-__all__ = [LammpsLibrary, LammpsConcurrent, LammpsBase]
+__all__ = ["LammpsLibrary", "LammpsConcurrent", "LammpsBase"]
 __version__ = get_versions()["version"]
 
 
 try:
     from pylammpsmpi.wrapper.ase import LammpsASELibrary
 
-    __all__ += [LammpsASELibrary]
+    __all__ += ["LammpsASELibrary"]
 except ImportError:
     pass

pylammpsmpi/mpi/lmpmpi.py

@@ -1,4 +1,3 @@
-# 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.
 
@@ -127,7 +126,7 @@ def extract_atom(job, funct_args):
         # extract atoms return an internal data type
         # this has to be reformatted
         name = str(funct_args[0])
-        if name not in atom_properties.keys():
+        if name not in atom_properties:
             return []
 
         # this block prevents error when trying to access values
@@ -166,14 +165,13 @@ def extract_variable(job, funct_args):
         )
         if MPI.COMM_WORLD.rank == 0:
             return np.array(data)
-    else:
-        if MPI.COMM_WORLD.rank == 0:
-            # if type is 1 - reformat file
-            try:
-                data = job.extract_variable(*funct_args)
-            except ValueError:
-                return []
-            return data
+    elif MPI.COMM_WORLD.rank == 0:
+        # if type is 1 - reformat file
+        try:
+            data = job.extract_variable(*funct_args)
+        except ValueError:
+            return []
+        return data
 
 
 def get_natoms(job, funct_args):
@@ -194,7 +192,7 @@ def gather_atoms(job, funct_args):
     # extract atoms return an internal data type
     # this has to be reformatted
     name = str(funct_args[0])
-    if name not in atom_properties.keys():
+    if name not in atom_properties:
         return []
 
     # this block prevents error when trying to access values
@@ -209,18 +207,15 @@ def gather_atoms(job, funct_args):
     # number of atoms - first dimension
     val = list(val)
     dim = atom_properties[name]["dim"]
-    if dim > 1:
-        data = [val[x : x + dim] for x in range(0, len(val), dim)]
-    else:
-        data = list(val)
+    data = [val[x : x + dim] for x in range(0, len(val), dim)] if dim > 1 else list(val)
     return np.array(data)
 
 
 def gather_atoms_concat(job, funct_args):
     # extract atoms return an internal data type
     # this has to be reformatted
     name = str(funct_args[0])
-    if name not in atom_properties.keys():
+    if name not in atom_properties:
         return []
 
     # this block prevents error when trying to access values
@@ -235,10 +230,7 @@ def gather_atoms_concat(job, funct_args):
     # number of atoms - first dimension
     val = list(val)
     dim = atom_properties[name]["dim"]
-    if dim > 1:
-        data = [val[x : x + dim] for x in range(0, len(val), dim)]
-    else:
-        data = list(val)
+    data = [val[x : x + dim] for x in range(0, len(val), dim)] if dim > 1 else list(val)
     return np.array(data)
 
 
@@ -253,7 +245,7 @@ def gather_atoms_subset(job, funct_args):
     for i in range(lenids):
         cids[i] = ids[i]
 
-    if name not in atom_properties.keys():
+    if name not in atom_properties:
         return []
 
     # this block prevents error when trying to access values
@@ -272,10 +264,7 @@ def gather_atoms_subset(job, funct_args):
     # number of atoms - first dimension
     val = list(val)
     dim = atom_properties[name]["dim"]
-    if dim > 1:
-        data = [val[x : x + dim] for x in range(0, len(val), dim)]
-    else:
-        data = list(val)
+    data = [val[x : x + dim] for x in range(0, len(val), dim)] if dim > 1 else list(val)
     return np.array(data)
 
 
@@ -487,7 +476,7 @@ def _run_lammps_mpi(argument_lst):
         else:
             input_dict = None
         input_dict = MPI.COMM_WORLD.bcast(input_dict, root=0)
-        if "shutdown" in input_dict.keys() and input_dict["shutdown"]:
+        if "shutdown" in input_dict and input_dict["shutdown"]:
             job.close()
             if MPI.COMM_WORLD.rank == 0:
                 interface_send(socket=socket, result_dict={"result": True})

pylammpsmpi/wrapper/ase.py

@@ -2,7 +2,7 @@
 import os
 import warnings
 from ctypes import c_double, c_int
-from typing import List, Optional
+from typing import Optional
 
 import numpy as np
 from ase.atoms import Atoms
@@ -45,7 +45,7 @@ def __init__(
             self._interactive_library = library
             self._cores = library.cores
         elif self._cores == 1:
-            lammps = getattr(importlib.import_module("lammps"), "lammps")
+            lammps = importlib.import_module("lammps").lammps
             if disable_log_file:
                 self._interactive_library = lammps(
                     cmdargs=["-screen", "none", "-log", "none"],
@@ -89,7 +89,7 @@ def interactive_positions_getter(self) -> np.ndarray:
             positions = self._prism.vector_to_ase(positions)
         return positions
 
-    def interactive_positions_setter(self, positions: List[List[float]]) -> None:
+    def interactive_positions_setter(self, positions: list[list[float]]) -> None:
         """
         Set the positions of atoms in the interactive library.
 
@@ -142,7 +142,8 @@ def interactive_cells_setter(self, cell: np.ndarray) -> None:
         lx, ly, lz, xy, xz, yz = self._prism.get_lammps_prism()
         if not _check_ortho_prism(prism=self._prism):
             warnings.warn(
-                "Warning: setting upper trangular matrix might slow down the calculation"
+                "Warning: setting upper trangular matrix might slow down the calculation",
+                stacklevel=2,
             )
 
         is_skewed = cell_is_skewed(cell=cell, tolerance=1.0e-8)
@@ -152,19 +153,16 @@ def interactive_cells_setter(self, cell: np.ndarray) -> None:
             if not was_skewed:
                 self.interactive_lib_command(command="change_box all triclinic")
             self.interactive_lib_command(
-                command="change_box all x final 0 %f y final 0 %f z final 0 %f  xy final %f xz final %f yz final %f remap units box"
-                % (lx, ly, lz, xy, xz, yz),
+                command=f"change_box all x final 0 {lx:f} y final 0 {ly:f} z final 0 {lz:f}  xy final {xy:f} xz final {xz:f} yz final {yz:f} remap units box",
             )
         elif was_skewed:
             self.interactive_lib_command(
-                command="change_box all x final 0 %f y final 0 %f z final 0 %f xy final %f xz final %f yz final %f remap units box"
-                % (lx, ly, lz, 0.0, 0.0, 0.0),
+                command=f"change_box all x final 0 {lx:f} y final 0 {ly:f} z final 0 {lz:f} xy final {0.0:f} xz final {0.0:f} yz final {0.0:f} remap units box",
             )
             self.interactive_lib_command(command="change_box all ortho")
         else:
             self.interactive_lib_command(
-                command="change_box all x final 0 %f y final 0 %f z final 0 %f remap units box"
-                % (lx, ly, lz),
+                command=f"change_box all x final 0 {lx:f} y final 0 {ly:f} z final 0 {lz:f} remap units box",
             )
 
     def interactive_volume_getter(self) -> float:
@@ -198,7 +196,7 @@ def interactive_structure_setter(
         dimension: int,
         boundary: str,
         atom_style: str,
-        el_eam_lst: List[str],
+        el_eam_lst: list[str],
         calc_md: bool = True,
     ) -> None:
         """
@@ -224,7 +222,8 @@ def interactive_structure_setter(
         self._prism = Prism(structure.cell)
         if not _check_ortho_prism(prism=self._prism):
             warnings.warn(
-                "Warning: setting upper trangular matrix might slow down the calculation"
+                "Warning: setting upper trangular matrix might slow down the calculation",
+                stacklevel=2,
             )
         xhi, yhi, zhi, xy, xz, yz = self._prism.get_lammps_prism()
         if self._prism.is_skewed():
@@ -274,13 +273,11 @@ def interactive_structure_setter(
         for id_eam, el_eam in enumerate(el_eam_lst):
             if el_eam in el_struct_lst:
                 self.interactive_lib_command(
-                    command="mass {0:3d} {1:f}".format(
-                        id_eam + 1, atomic_masses[atomic_numbers[el_eam]]
-                    ),
+                    command=f"mass {id_eam + 1:3d} {atomic_masses[atomic_numbers[el_eam]]:f}",
                 )
             else:
                 self.interactive_lib_command(
-                    command="mass {0:3d} {1:f}".format(id_eam + 1, 1.00),
+                    command=f"mass {id_eam + 1:3d} {1.00:f}",
                 )
         if not _check_ortho_prism(prism=self._prism):
             positions = self._prism.vector_to_lammps(structure.positions).flatten()
@@ -476,10 +473,7 @@ def cell_is_skewed(cell, tolerance=1.0e-8):
     """
     volume = np.abs(np.linalg.det(cell))
     prod = np.linalg.norm(cell, axis=-1).prod()
-    if volume > 0:
-        if abs(volume - prod) / volume < tolerance:
-            return False
-    return True
+    return not (volume > 0 and abs(volume - prod) / volume < tolerance)
 
 
 def _check_ortho_prism(prism, rtol=0.0, atol=1e-08):
@@ -553,11 +547,11 @@ def get_fixed_atom_boolean_vector(structure):
             fixed_atom_vector[c_dict["kwargs"]["indices"]] = [True, True, True]
         elif c_dict["name"] == "FixedPlane":
             if all(np.isin(c_dict["kwargs"]["direction"], [0, 1])):
-                if "indices" in c_dict["kwargs"].keys():
+                if "indices" in c_dict["kwargs"]:
                     fixed_atom_vector[c_dict["kwargs"]["indices"]] = np.array(
                         c_dict["kwargs"]["direction"]
                     ).astype(bool)
-                elif "a" in c_dict["kwargs"].keys():
+                elif "a" in c_dict["kwargs"]:
                     fixed_atom_vector[c_dict["kwargs"]["a"]] = np.array(
                         c_dict["kwargs"]["direction"]
                     ).astype(bool)

pylammpsmpi/wrapper/base.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 List, Union
+from typing import Union
 
 from pylammpsmpi.wrapper.concurrent import LammpsConcurrent
 
@@ -72,7 +71,7 @@ def extract_global(self, name: str) -> Union[int, float, str]:
         """
         return super().extract_global(name=name).result()
 
-    def extract_box(self) -> List[Union[float, List[float], List[int]]]:
+    def extract_box(self) -> list[Union[float, list[float], list[int]]]:
         """
         Get the simulation box
 
@@ -87,7 +86,7 @@ def extract_box(self) -> List[Union[float, List[float], List[int]]]:
         """
         return super().extract_box().result()
 
-    def extract_atom(self, name: str) -> Union[List[int], List[float]]:
+    def extract_atom(self, name: str) -> Union[list[int], list[float]]:
         """
         Extract a property of the atoms
 
@@ -102,7 +101,7 @@ def extract_atom(self, name: str) -> Union[List[int], List[float]]:
         """
         return super().extract_atom(name=name).result()
 
-    def extract_fix(self, *args) -> Union[int, float, List[Union[int, float]]]:
+    def extract_fix(self, *args) -> Union[int, float, list[Union[int, float]]]:
         """
         Extract a fix value
 
@@ -116,7 +115,7 @@ def extract_fix(self, *args) -> Union[int, float, List[Union[int, float]]]:
         """
         return super().extract_fix(*args).result()
 
-    def extract_variable(self, *args) -> Union[int, float, List[Union[int, float]]]:
+    def extract_variable(self, *args) -> Union[int, float, list[Union[int, float]]]:
         """
         Extract the value of a variable
 
@@ -180,11 +179,11 @@ def reset_box(self, *args) -> None:
 
     def generate_atoms(
         self,
-        ids: List[int] = None,
-        type: List[int] = None,
-        x: List[float] = None,
-        v: List[float] = None,
-        image: List[int] = None,
+        ids: list[int] = None,
+        type: list[int] = None,
+        x: list[float] = None,
+        v: list[float] = None,
+        image: list[int] = None,
         shrinkexceed: bool = False,
     ) -> None:
         """
@@ -224,11 +223,11 @@ def generate_atoms(
     def create_atoms(
         self,
         n: int,
-        id: List[int],
-        type: List[int],
-        x: List[float],
-        v: List[float] = None,
-        image: List[int] = None,
+        id: list[int],
+        type: list[int],
+        x: list[float],
+        v: list[float] = None,
+        image: list[int] = None,
         shrinkexceed: bool = False,
     ) -> None:
         """
@@ -290,7 +289,7 @@ def has_ffmpeg_support(self) -> bool:
         return super().has_ffmpeg_support.result()
 
     @property
-    def installed_packages(self) -> List[str]:
+    def installed_packages(self) -> list[str]:
         return super().installed_packages.result()
 
     def set_fix_external_callback(self, *args) -> None:
@@ -305,7 +304,7 @@ def get_neighlist(self, *args):
         """
         return super().get_neighlist(*args).result()
 
-    def find_pair_neighlist(self, style: str) -> int:
+    def find_pair_neighlist(self, *args) -> int:
         """Find neighbor list index of pair style neighbor list
         Try finding pair instance that matches style. If exact is set, the pair must
         match style exactly. If exact is 0, style must only be contained. If pair is