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

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mdsuite/calculators/green_kubo_distinct_diffusion_coefficients.py

@@ -57,7 +57,8 @@ class Args:
 
 class GreenKuboDistinctDiffusionCoefficients(TrajectoryCalculator, ABC):
     """
-    Class for the Green-Kubo diffusion coefficient implementation
+    Class for the Green-Kubo diffusion coefficient implementation.
+
     Attributes
     ----------
     experiment :  object
@@ -211,7 +212,8 @@ def _map_over_particles(self, ds_a: np.ndarray, ds_b: np.ndarray) -> np.ndarray:
 
         def ref_conf_map(ref_dataset, full_ds):
             """
-            Maps over the atoms axis in dataset
+            Maps over the atoms axis in dataset.
+
             Parameters
             ----------
             dataset

mdsuite/calculators/green_kubo_self_diffusion_coefficients.py

@@ -59,7 +59,8 @@ class Args:
 
 class GreenKuboDiffusionCoefficients(TrajectoryCalculator, ABC):
     """
-    Class for the Green-Kubo diffusion coefficient implementation
+    Class for the Green-Kubo diffusion coefficient implementation.
+
     Attributes
     ----------
     experiment :  object

mdsuite/calculators/radial_distribution_function.py

@@ -738,6 +738,7 @@ def _spherical_symmetry(data: np.array) -> np.array:  # TODO make it a property
             ----------
             data : np.array
                     tensor_values on which to operate
+
             Returns
             -------
             function_values : np.array
@@ -751,6 +752,7 @@ def _correction_1(data: np.array) -> np.array:
 
             tensor_values : np.array
                     tensor_values on which to operate
+
             Returns
             -------
             function_values : np.array
@@ -765,6 +767,7 @@ def _correction_2(data: np.array) -> np.array:
 
             tensor_values : np.array
                     tensor_values on which to operate
+
             Returns
             -------
             function_values : np.array
@@ -785,7 +788,8 @@ def _correction_2(data: np.array) -> np.array:
 
         def _piecewise(data: np.array) -> np.array:
             """
-            Return a piecewise operation on a set of tensor_values
+            Return a piecewise operation on a set of tensor_values.
+
             Parameters
             ----------
             data : np.array

mdsuite/calculators/spatial_distribution_function.py

@@ -168,6 +168,7 @@ def _load_positions(self, indices: list, species: str) -> tf.Tensor:
                 List of indices to take from the database_path
         species: str
                 The species to load the positions from
+
         Returns
         -------
         loaded_data : tf.Tensor

mdsuite/database/data_manager.py

@@ -175,6 +175,7 @@ def generator(
                     Path to the tensor_values in the database_path
             dictionary : bool
                     If true, tensor_values is returned in a dictionary
+
             Returns
             -------
             """
@@ -242,6 +243,7 @@ def atom_generator(
                     Path to the tensor_values in the database_path
             dictionary : bool
                     If true, tensor_values is returned in a dictionary
+
             Returns
             -------
             """
@@ -308,7 +310,8 @@ def ensemble_generator(self, system: bool = False, glob_data: dict = None) -> tu
 
         def dictionary_generator(ensemble_loop, correlation_time, data_range):
             """
-            Generator for the ensemble loop
+            Generator for the ensemble loop.
+
             Parameters
             ----------
             ensemble_loop : int
@@ -317,6 +320,7 @@ def dictionary_generator(ensemble_loop, correlation_time, data_range):
                     Distance between ensembles
             data_range : int
                     Size of each ensemble
+
             Returns
             -------
             None.

mdsuite/database/simulation_database.py

@@ -196,7 +196,8 @@ def __init__(self, species_list: List[SpeciesInfo], chunk_size: int):
 
     def add_data(self, data: np.ndarray, config_idx, species_name, property_name):
         """
-        Add configuration data to the chunk
+        Add configuration data to the chunk.
+
         Parameters
         ----------
         data:

mdsuite/experiment/experiment.py

@@ -470,7 +470,8 @@ def add_data(
         appropriate file reader with its default arguments. If you have a custom data
         format with its own reader or want to use non-default arguments for your reader,
         instantiate the reader and pass it to this method.
-        TODO reference online documentation of data loading in the error messages
+        TODO reference online documentation of data loading in the error messages.
+
         Parameters
         ----------
         simulation_data : str or pathlib.Path or mdsuite.file_io.file_read.FileProcessor
@@ -688,7 +689,8 @@ def update_species_attributes_with_pubchempy(species_list: List[SpeciesInfo]):
 def _species_list_to_architecture_dict(species_list, n_configurations):
     # TODO let the database handler use the species list directly instead of the dict
     """
-    converter from species list to legacy architecture dict
+    converter from species list to legacy architecture dict.
+
     Parameters
     ----------
     species_list

mdsuite/experiment/run_module.py

@@ -43,7 +43,8 @@ class RunModule:
     """
 
     def __init__(self, parent, module_dict, **kwargs):
-        """Initialize the attributes
+        """Initialize the attributes.
+
         Parameters
         ----------
         parent: Experiment

mdsuite/file_io/extxyz_files.py

@@ -257,6 +257,7 @@ def _get_property_to_column_idx_dict(
         header to analyse
     var_names:
         dict of translations from MDsuite property names to extxyz property names
+
     Returns
     -------
     species_index: int

mdsuite/file_io/lammps_flux_files.py

@@ -64,7 +64,8 @@ def __init__(
         """
         Initialize the lammps flux reader. Since the flux file does not have a fixed
         expected content, you need to provide the necessary metadata
-        (sample_rate, box_l) here manually
+        (sample_rate, box_l) here manually.
+
         Parameters
         ----------
         file_path

mdsuite/file_io/script_input.py

@@ -15,7 +15,8 @@ def __init__(
         self, data: TrajectoryChunkData, metadata: TrajectoryMetadata, name: str
     ):
         """
-        Provide all the data needed for this class to act as a FileProcessor
+        Provide all the data needed for this class to act as a FileProcessor.
+
         Parameters
         ----------
         data

mdsuite/file_io/tabular_text_files.py

@@ -71,7 +71,8 @@ def __init__(
         Init, also handles the combination of file_format_column_names and
         custom_column_names.
         The result, self._column_name_dict is supposed to be used by child functions to
-        create their TabularTextFileReaderData
+        create their TabularTextFileReaderData.
+
         Parameters
         ----------
         file_path:
@@ -164,7 +165,8 @@ def _read_process_n_configurations(
         n_header_lines: int = 0,
     ) -> mdsuite.database.simulation_database.TrajectoryChunkData:
         """
-        Read n configurations and package them into a trajectory chunk of the right format
+        Read n configurations and package them into a trajectory chunk of the right format.
+
         Parameters
         ----------
         file:
@@ -223,7 +225,8 @@ def _read_process_n_configurations(
 def read_n_lines(file, n_lines: int, start_at: int = None) -> list:
     """
     Get n_lines lines, starting at line number start_at.
-    If start_at is None, read from the current file state
+    If start_at is None, read from the current file state.
+
     Returns
     -------
     A list of strings, one string for each line.
@@ -236,7 +239,8 @@ def read_n_lines(file, n_lines: int, start_at: int = None) -> list:
 
 def skip_n_lines(file, n_lines: int) -> None:
     """
-    skip n_lines in file
+    skip n_lines in file.
+
     Parameters
     ----------
     file: the file where we skip lines

mdsuite/memory_management/memory_manager.py

@@ -355,6 +355,7 @@ def get_ensemble_loop(
                 Data range to be used in the analysis.
         correlation_time : int
                 Correlation time to be considered when looping over the tensor_values
+
         Returns
         -------
         data_range_partitions : int

mdsuite/project/project.py

@@ -273,6 +273,7 @@ def disable_experiments(self, names: Union[str, list]):
         ----------
         names: Name or list of names of experiments that should be instantiated
                and loaded into self.experiments
+
         Returns
         -------
 
@@ -297,6 +298,7 @@ def add_data(self, data_sets: dict):
             values: str or mdsuite.file_io.file_read.FileProcessor
                 refer to mdsuite.experiment.add_data() for an explanation of the file
                 specification options
+
         Returns
         -------
         Updates the experiment classes.

mdsuite/transformations/transformations.py

@@ -178,7 +178,8 @@ def _save_output(
         Save the tensor_values into the database_path
         # todo for the future: this should not be part of the transformation.
         # the transformation should yield a batch and the experiment should take care of
-        # storing it in the correct place, just as with file inputs
+        # storing it in the correct place, just as with file inputs.
+
         Returns
         -------
         saves the tensor_values to the database_path.
@@ -446,7 +447,8 @@ class SingleSpeciesTrafo(Transformations):
     def run_transformation(self, species: typing.Iterable[str] = None):
         """
         Perform the batching and data loading for the transformation,
-        then calls transform_batch
+        then calls transform_batch.
+
         Parameters
         ----------
         species : Iterable[str]
@@ -553,7 +555,8 @@ class MultiSpeciesTrafo(Transformations):
     def run_transformation(self, species: typing.Iterable[str] = None) -> None:
         """
         Perform the batching and data loading for the transformation,
-        then calls transform_batch
+        then calls transform_batch.
+
         Parameters
         ----------
         species : Iterable[str]

mdsuite/utils/meta_functions.py

@@ -467,7 +467,8 @@ def get_nearest_divisor(a: int, b: int) -> int:
 
 def split_array(data: np.array, condition: np.array) -> list:
     """
-    split an array by a condition
+    split an array by a condition.
+
     Parameters
     ----------
     data : np.array

mdsuite/utils/scale_functions.py

@@ -81,6 +81,7 @@ def quadratic_scale_function(
             Scalar scaling factor for the inner multiplication
     outer_scale_factor : int
             Scalar scaling factor for the outer multiplication
+
     Returns
     -------
     scaled_memory : int