Merge branch 'main' into dev

PQAnalysis/atomic_system/_decorators.py

@@ -24,9 +24,7 @@
 from decorator import decorator
 
 from .exceptions import (
-    AtomicSystemPositionsError,
-    AtomicSystemMassError,
-    AtomicSystemError
+    AtomicSystemPositionsError, AtomicSystemMassError, AtomicSystemError
 )
 
 
@@ -54,17 +52,12 @@ def check_atom_number_setters(func, self, arg_to_set: Any) -> None:
     AtomicSystemError
         If the number of atoms is not equal the number of positions.
     """
-    print("test")
-    print(func.__name__, file=sys.stderr)
-    print(self.logger)
-    print(arg_to_set)
     if self.n_atoms != np.shape(arg_to_set)[0]:
-        print("test")
         self.logger.error(
             (
-            "The number of atoms in the AtomicSystem object have "
-            "to be equal to the number of atoms in the new array "
-            "in order to set the property."
+                "The number of atoms in the AtomicSystem object have "
+                "to be equal to the number of atoms in the new array "
+                "in order to set the property."
             ),
             exception=AtomicSystemError
         )
@@ -129,8 +122,7 @@ def check_atoms_has_mass(func, *args, **kwargs):
 
     if not all(atom.mass is not None for atom in self.atoms):
         self.logger.error(
-            AtomicSystemMassError.message,
-            exception=AtomicSystemMassError
+            AtomicSystemMassError.message, exception=AtomicSystemMassError
         )
 
     return func(*args, **kwargs)

PQAnalysis/core/cell/cell.py

@@ -277,9 +277,6 @@ def init_from_box_matrix(cls, box_matrix: Np3x3NumberArray) -> "Cell":
             ) / (y * z)
         )
 
-        print(alpha, beta, gamma)
-        print(np.rad2deg(alpha), np.rad2deg(beta), np.rad2deg(gamma))
-
         return cls(
             x, y, z, np.rad2deg(alpha), np.rad2deg(beta), np.rad2deg(gamma)
         )

PQAnalysis/io/formats.py

@@ -140,8 +140,6 @@ def infer_format_from_extension(cls, file_path: str) -> "OutputFileFormat":
 
         file_extension = "." + file_path.split(".")[-1]
 
-        print(file_extension)
-
         if file_extension in cls.file_extensions()[cls.XYZ.value]:
             return cls.XYZ
 

PQAnalysis/io/input_file_reader/pq/pq_input_file_reader.py

@@ -132,33 +132,28 @@ def continue_input_file(self, n: PositiveInt):
                 if key in self.dictionary.keys():
 
                     new_filename = self.dictionary[key][0].replace(
-                        self.actual_n,
-                        new_actual_n
+                        self.actual_n, new_actual_n
                     )
 
                     new_raw_input_file = new_raw_input_file.replace(
-                        self.dictionary[key][0],
-                        new_filename
+                        self.dictionary[key][0], new_filename
                     )
 
             # replace digit strings in output files
             for key in self.start_file_keys:
                 if key in self.dictionary.keys():
 
                     new_filename = self.dictionary[key][0].replace(
-                        self.start_n,
-                        new_start_n
+                        self.start_n, new_start_n
                     )
 
                     new_raw_input_file = new_raw_input_file.replace(
-                        self.dictionary[key][0],
-                        new_filename
+                        self.dictionary[key][0], new_filename
                     )
 
             # create new input file and write new_raw_input_file to it
             new_filename = self.filename.replace(
-                self.input_file_n,
-                new_input_file_n
+                self.input_file_n, new_input_file_n
             )
 
             with open(new_filename, "w", encoding="utf-8") as file:
@@ -191,8 +186,10 @@ def _parse_start_n(self) -> str:
 
         if self.is_rpmd_start_file_defined:
             # add "." to match also files without extension
-            if (_n := _get_digit_string_from_filename(self.rpmd_start_file +
-                '.')) != n:
+            if (
+                _n :=
+                _get_digit_string_from_filename(self.rpmd_start_file + '.')
+            ) != n:
                 self.logger.error(
                     f"N from start_file ({n}) and rpmd_start_file ({_n}) do not match.",
                     exception=PQValueError
@@ -226,7 +223,6 @@ def _parse_actual_n(self) -> str:
                 )
 
                 if _n != n and n is not None:
-                    print(_n, n, key)
                     self.logger.error(
                         "Actual n in output files is not consistent.",
                         exception=PQValueError
@@ -324,8 +320,8 @@ def _get_digit_string_from_filename(filename: str) -> str:
     if (regex := re.search(r"\d+.", filename)) is None:
         PQInputFileReader.logger.error(
             (
-            f"Filename {filename} does not contain a number to be "
-            "continued from. It has to be of the form \"...<number>.<extension>\"."
+                f"Filename {filename} does not contain a number to be "
+                "continued from. It has to be of the form \"...<number>.<extension>\"."
             ),
             exception=PQValueError
         )