pylint fixed

.style.yapf

@@ -9,4 +9,5 @@ BLANK_LINE_BEFORE_CLASS_DOCSTRING = true
 BLANK_LINE_BEFORE_MODULE_DOCSTRING = true
 BLANK_LINE_BEFORE_NESTED_CLASS_OR_DEF = true
 BLANK_LINES_AROUND_TOP_LEVEL_DEFINITION = 3
-SPLIT_PENALTY_IMPORT_NAMES=1000
+SPLIT_PENALTY_IMPORT_NAMES=1000
+SPACES_BEFORE_COMMENT=2

PQAnalysis/analysis/rdf/rdf_output_file_writer.py

@@ -15,7 +15,9 @@
 from .rdf import RDF
 
 
+
 class RDFDataWriter(BaseWriter):
+
     """
     Class for writing the data of an 
     :py:class:`~PQAnalysis.analysis.rdf.rdf.RDF`
@@ -34,14 +36,14 @@ def __init__(self, filename: str) -> None:
         super().__init__(filename)
 
     @runtime_type_checking
-    def write(self,
-              data: Tuple[Np1DNumberArray,
-                          Np1DNumberArray,
-                          Np1DNumberArray,
-                          Np1DNumberArray,
-                          Np1DNumberArray
-                          ]
-              ):
+    def write(
+        self,
+        data: Tuple[Np1DNumberArray,
+        Np1DNumberArray,
+        Np1DNumberArray,
+        Np1DNumberArray,
+        Np1DNumberArray]
+    ):
         """
         Writes the data to the file.
 
@@ -55,12 +57,19 @@ def write(self,
 
         for i in range(len(data[0])):
             print(
-                f"{data[0][i]} {data[1][i]} {data[2][i]} {data[3][i]} {data[4][i]}", file=self.file)
+                (
+                f"{data[0][i]} {data[1][i]} {data[2][i]} "
+                f"{data[3][i]} {data[4][i]}"
+                ),
+                file=self.file
+            )
 
         super().close()
 
 
+
 class RDFLogWriter(BaseWriter):
+
     """
     Class for writing the log (setup parameters) of an 
     :py:class:`~PQAnalysis.analysis.rdf.rdf.RDF` analysis

PQAnalysis/core/atom/atom.py

@@ -106,8 +106,9 @@ def __init__(
             If his parameter is not given, the name parameter is used to determine 
             the element type of the atom_type.
         use_guess_element : bool, optional
-            Whether to use the guess_element function to determine the element type of the atom_type 
-            by its name, by default True
+            Whether to use the guess_element function to determine
+            the element type of the atom_type by its name,
+            by default True
 
         Raises
         ------

PQAnalysis/formats.py

@@ -6,7 +6,9 @@
 from beartype.typing import Any, List
 
 
+
 class BaseEnumFormat(Enum):
+
     """
     An enumeration super class of the various supported trajectory formats.
     """
@@ -27,7 +29,8 @@ def member_repr(cls) -> str:
     @classmethod
     def value_repr(cls) -> str:
         """
-        This method returns a string representation of the values of the members of the enumeration.
+        This method returns a string representation of
+        the values of the members of the enumeration.
 
         Returns
         -------

PQAnalysis/io/conversion_api.py

@@ -160,7 +160,8 @@ def traj2box(
     mode: FileWritingMode | str = "w"
 ) -> None:
     """
-    Converts multiple trajectory files to a box file and prints it to stdout or writes it to a file.
+    Converts multiple trajectory files to a box file and 
+    prints it to stdout or writes it to a file.
 
     Without the vmd option the output is printed in a data file format.
     The first column represents the step starting from 1, the second to fourth column

PQAnalysis/io/input_file_reader/pq_analysis/pqanalysis_input_file_reader.py

@@ -5,14 +5,15 @@
 
 from beartype.typing import List
 
-from PQAnalysis.io.input_file_reader.exceptions import InputFileError, InputFileWarning
+from PQAnalysis.io.input_file_reader.exceptions import InputFileError
 from PQAnalysis.io.input_file_reader.input_file_parser import InputFileParser
 from PQAnalysis.io.input_file_reader.formats import InputFileFormat
+from PQAnalysis.utils.custom_logging import setup_logger
+from PQAnalysis import __package_name__
+
 from ._file_mixin import _FileMixin
 from ._selection_mixin import _SelectionMixin
 from ._positions_mixin import _PositionsMixin
-from PQAnalysis.utils.custom_logging import setup_logger
-from PQAnalysis import __package_name__
 
 
 

PQAnalysis/io/traj_file/frame_reader.py

@@ -19,7 +19,9 @@
 from .exceptions import FrameReaderError
 
 
+
 class _FrameReader:
+
     """
     This class provides methods for reading a frame from a string.
     The string can be a single frame or a whole trajectory.
@@ -36,7 +38,10 @@ class can be used to read a whole trajectory as well as
     logger = logging.getLogger(__package_name__).getChild(__qualname__)
     logger = setup_logger(logger)
 
-    def __init__(self, md_format: MDEngineFormat | str = MDEngineFormat.PQ) -> None:
+    def __init__(
+        self,
+        md_format: MDEngineFormat | str = MDEngineFormat.PQ
+    ) -> None:
         """
         Parameters
         ----------
@@ -46,10 +51,12 @@ def __init__(self, md_format: MDEngineFormat | str = MDEngineFormat.PQ) -> None:
         self.md_format = MDEngineFormat(md_format)
         self.topology = None
 
-    def read(self, frame_string: str,
-             topology: Topology | None = None,
-             traj_format: TrajectoryFormat | str = TrajectoryFormat.XYZ
-             ) -> AtomicSystem:
+    def read(
+        self,
+        frame_string: str,
+        topology: Topology | None = None,
+        traj_format: TrajectoryFormat | str = TrajectoryFormat.XYZ
+    ) -> AtomicSystem:
         """
         Reads a frame from a string.
 
@@ -204,10 +211,12 @@ def read_charges(self, frame_string: str) -> AtomicSystem:
 
         return AtomicSystem(topology=topology, charges=charges, cell=cell)
 
-    def _check_qmcfc(self,
-                     atoms: List[str],
-                     value: Np1DNumberArray | Np2DNumberArray
-                     ) -> Tuple[Np1DNumberArray | Np2DNumberArray, List[str]]:
+    def _check_qmcfc(
+        self,
+        atoms: List[str],
+        value: Np1DNumberArray | Np2DNumberArray
+    ) -> Tuple[Np1DNumberArray | Np2DNumberArray,
+        List[str]]:
         """
         Check if the first atom is X for QMCFC. If it is, remove it from the list and array.
 
@@ -233,8 +242,8 @@ def _check_qmcfc(self,
             if atoms[0].upper() != 'X':
                 self.logger.error(
                     (
-                        'The first atom in one of the frames is not X. '
-                        'Please use PQ (default) md engine instead'
+                    'The first atom in one of the frames is not X. '
+                    'Please use PQ (default) md engine instead'
                     ),
                     exception=FrameReaderError
                 )
@@ -243,7 +252,11 @@ def _check_qmcfc(self,
 
         return value, atoms
 
-    def _get_topology(self, atoms: List[str], topology: Topology | None) -> Topology:
+    def _get_topology(
+        self,
+        atoms: List[str],
+        topology: Topology | None
+    ) -> Topology:
         """
         Returns the topology of the frame.
 
@@ -258,21 +271,20 @@ def _get_topology(self, atoms: List[str], topology: Topology | None) -> Topology
 
                 topology = Topology(
                     atoms=[
-                        Atom(atom, disable_type_checking=True)
-                        for atom in atoms
+                    Atom(atom,
+                    disable_type_checking=True) for atom in atoms
                     ]
                 )
 
             except ElementNotFoundError:
 
                 topology = Topology(
                     atoms=[
-                        Atom(
-                            atom,
-                            use_guess_element=False,
-                            disable_type_checking=True
-                        )
-                        for atom in atoms
+                    Atom(
+                    atom,
+                    use_guess_element=False,
+                    disable_type_checking=True
+                    ) for atom in atoms
                     ]
                 )
 
@@ -327,9 +339,9 @@ def _read_header_line(self, header_line: str) -> Tuple[int, Cell]:
         return n_atoms, cell
 
     def _read_xyz(self,
-                  splitted_frame_string: List[str],
-                  n_atoms: int
-                  ) -> Tuple[Np2DNumberArray, List[str]]:
+        splitted_frame_string: List[str],
+        n_atoms: int) -> Tuple[Np2DNumberArray,
+        List[str]]:
         """
         Reads the xyz coordinates and the atom names from the given string.
 
@@ -358,22 +370,22 @@ def _read_xyz(self,
             atoms = [None] * n_atoms
 
             # Fill xyz and atoms in a single loop
-            for i, line in enumerate(splitted_frame_string[2:2+n_atoms]):
+            for i, line in enumerate(splitted_frame_string[2:2 + n_atoms]):
                 split_line = line.split()
                 atoms[i] = split_line[0]
                 xyz[i] = split_line[1:4]
 
             return xyz, atoms
-        except ValueError as e:
+        except ValueError:
             self.logger.error(
                 'Invalid file format in xyz coordinates of Frame.',
                 exception=FrameReaderError
             )
 
     def _read_scalar(self,
-                     splitted_frame_string: List[str],
-                     n_atoms: int
-                     ) -> Tuple[Np1DNumberArray, List[str]]:
+        splitted_frame_string: List[str],
+        n_atoms: int) -> Tuple[Np1DNumberArray,
+        List[str]]:
         """
         Reads the scalar values and the atom names from the given string.
 
@@ -400,7 +412,7 @@ def _read_scalar(self,
         scalar = np.zeros((n_atoms))
         atoms = []
         for i in range(n_atoms):
-            line = splitted_frame_string[2+i]
+            line = splitted_frame_string[2 + i]
 
             if len(line.split()) != 2:
                 self.logger.error(