resolved comments of bernardo

docs/source/rst_doc_files/classes/design/experimentsample.rst

@@ -126,7 +126,7 @@ A reference (:code:`Path`) will be saved to the :attr:`~f3dasm.design.Experiment
  └── jobs.pkl
 
 
-In the :attr:`~f3dasm.design.ExperimentData.output_data`, a reference to the stored object (e.g. :code:`/output_numpy/0.npy`) will be automatically appended to the parameter.
+In the output data of the :class:`~f3dasm.design.experimentdata.ExperimentData` object, a reference path (e.g. :code:`/output_numpy/0.npy`) to the stored object will be saved.
 
 
 :mod:`f3dasm` has built-in storing functions for numpy :class:`~numpy.ndarray`, pandas :class:`~pandas.DataFrame` and xarray :class:`~xarray.DataArray` and :class:`~xarray.Dataset`. 

src/f3dasm/_src/datageneration/abaqus/abaqus_functions.py

@@ -4,10 +4,10 @@
 Note
 ----
 I'm assuming that every process could have a different pre-processing,
- execution and post-processing function.
+execution and post-processing function.
 But they are used in that order and only once.
 If multiple e.g. pre_process steps need to be taken, then they should
- be combined in one function.
+be combined in one function.
 """
 
 # Modules
@@ -41,22 +41,22 @@ def pre_process(
  ----------
  experiment_sample : ExperimentSample
  The design to run the data generator on. Will be handled by
-  the pipeline.
+ the pipeline.
  folder_path : str
  Path of the folder where the python script is located
  python_file : str
  Name of the python file to be executed
  function_name : str, optional
  Name of the function within the python file to be executed,
-  by default "main"
+ by default "main"
  name : str, optional
  Name of the job, by default "job"
  remove_temp_files : bool, optional
 
  Note
  ----
  The python file should create an .inp input-file based on the
-  information of the experiment sample named <job_number>.inp.
+ information of the experiment sample named <job_number>.inp.
  """
 
  sim_info = kwargs
@@ -100,14 +100,14 @@ def post_process(
  ----------
  experiment_sample : ExperimentSample
  The design to run the data generator on.
-  Will be handled by the pipeline.
+ Will be handled by the pipeline.
  folder_path : str
  Path of the folder where the python script is located
  python_file : str
  Name of the python file to be executed
  function_name : str, optional
  Name of the function within the python file to be executed,
-  by default "main"
+ by default "main"
  name : str, optional
  Name of the job, by default "job"
  remove_temp_files : bool, optional
@@ -116,7 +116,7 @@ def post_process(
  Note
  ----
  The post-processing python file should write the results of your
-  simulation to a pickle file
+ simulation to a pickle file
  with the name: results.pkl. This file will be handled by the pipeline.
  """
 

src/f3dasm/_src/datageneration/functions/adapters/augmentor.py

@@ -6,7 +6,7 @@
 # Standard
 from abc import ABC, abstractmethod
 from copy import copy
-from typing import List
+from typing import List, Optional
 
 # Third-party
 import autograd.numpy as np
@@ -136,22 +136,25 @@ class FunctionAugmentor:
  """Combination of Augmentors that can change the input and
  output of an objective function
 
- Args:
- input_augmentors (List[Augmentor]): list of input augmentors
- output_augmentors (List[Augmentor]): list of output augmentors
+ Parameters
+ ----------
+ input_augmentors : List[Augmentor]
+ list of input augmentors
+ outpu_augmentors : List[Augmentor]
+ list of output augmentors
  """
 
  def __init__(
- self, input_augmentors: List[_Augmentor] = None,
- output_augmentors: List[_Augmentor] = None):
+ self, input_augmentors: Optional[List[_Augmentor]] = None,
+ output_augmentors: Optional[List[_Augmentor]] = None):
  """Combination of augmentors that can change the input and output of
  an objective function
 
  Parameters
  ----------
- input_augmentors, optional
+ input_augmentors : Optional[List[_Augmentor]]
  list of input augmentors, by default None
- output_augmentors, optional
+ output_augmentors: Optional[List[_Augmentor]]
  list of output augmentors, by default None
  """
  self.input_augmentors = [] if \
@@ -262,10 +265,36 @@ def augment_reverse_output(self, y: np.ndarray) -> np.ndarray:
 
 
 def _scale_vector(x: np.ndarray, scale: np.ndarray) -> np.ndarray:
- """Scale a vector x to a given scale"""
+ """Scale a vector x to a given scale
+
+ Parameters
+ ----------
+ x : np.ndarray
+ vector to be scaled
+ scale : np.ndarray
+ scale to be scaled towards
+
+ Returns
+ -------
+ np.ndarray
+ scaled vector
+ """
  return (scale[:, 1] - scale[:, 0]) * x + scale[:, 0]
 
 
 def _descale_vector(x: np.ndarray, scale: np.ndarray) -> np.ndarray:
- """Inverse of the _scale_vector() function"""
+ """Inverse of the _scale_vector() function
+
+ Parameters
+ ----------
+ x : np.ndarray
+ scaled vector
+ scale : np.ndarray
+ scale to be scaled towards
+
+ Returns
+ -------
+ np.ndarray
+ descaled vector
+ """
  return (x - scale[:, 0]) / (scale[:, 1] - scale[:, 0])

src/f3dasm/_src/experimentdata/_io.py

@@ -42,59 +42,141 @@
 # Storing methods
 # =============================================================================
 
+
 class _Store:
+ """Base class for storing and loading output data from disk"""
  suffix: int
 
  def __init__(self, object: Any, path: Path):
+ """
+ Protocol class for storing and loading output data from disk
+
+ Parameters
+ ----------
+ object : Any
+ object to store
+ path : Path
+ location to store the object to
+ """
  self.path = path
  self.object = object
 
  def store(self) -> None:
+ """
+ Protocol class for storing objects to disk
+
+ Raises
+ ------
+ NotImplementedError
+ Raises if the method is not implemented
+ """
  raise NotImplementedError()
 
  def load(self) -> Any:
+ """
+ Protocol class for loading objects to disk
+
+ Returns
+ -------
+ Any
+ The loaded object
+
+ Raises
+ ------
+ NotImplementedError
+ Raises if the method is not implemented
+ """
  raise NotImplementedError()
 
 
 class PickleStore(_Store):
+ """Class to store and load objects using the pickle protocol"""
  suffix: str = '.pkl'
 
  def store(self) -> None:
+ """
+ Store the object to disk using the pickle protocol
+ """
  with open(self.path.with_suffix(self.suffix), 'wb') as file:
  pickle.dump(self.object, file)
 
  def load(self) -> Any:
+ """
+ Load the object from disk using the pickle protocol
+
+ Returns
+ -------
+ Any
+ The loaded object
+
+ """
  with open(self.path.with_suffix(self.suffix), 'rb') as file:
  return pickle.load(file)
 
 
 class NumpyStore(_Store):
+ """Class to store and load objects using the numpy protocol"""
  suffix: int = '.npy'
 
  def store(self) -> None:
+ """
+ Store the object to disk using the numpy protocol
+ """
  np.save(file=self.path.with_suffix(self.suffix), arr=self.object)
 
  def load(self) -> np.ndarray:
+ """
+ Load the object from disk using the numpy protocol
+
+ Returns
+ -------
+ np.ndarray
+ The loaded object
+ """
  return np.load(file=self.path.with_suffix(self.suffix))
 
 
 class PandasStore(_Store):
+ """Class to store and load objects using the pandas protocol"""
  suffix: int = '.csv'
 
  def store(self) -> None:
+ """
+ Store the object to disk using the pandas protocol
+ """
  self.object.to_csv(self.path.with_suffix(self.suffix))
 
  def load(self) -> pd.DataFrame:
+ """
+ Load the object from disk using the pandas protocol
+
+ Returns
+ -------
+ pd.DataFrame
+ The loaded object
+ """
  return pd.read_csv(self.path.with_suffix(self.suffix))
 
 
 class XarrayStore(_Store):
+ """Class to store and load objects using the xarray protocol"""
  suffix: int = '.nc'
 
  def store(self) -> None:
+ """
+ Store the object to disk using the xarray protocol
+ """
  self.object.to_netcdf(self.path.with_suffix(self.suffix))
 
  def load(self) -> xr.DataArray | xr.Dataset:
+ """
+ Load the object from disk using the xarray protocol
+
+ Returns
+ -------
+ xr.DataArray | xr.Dataset
+ The loaded object
+ """
  return xr.open_dataset(self.path.with_suffix(self.suffix))
 
 
@@ -112,6 +194,35 @@ def load(self) -> xr.DataArray | xr.Dataset:
 
 def load_object(path: Path, experimentdata_directory: Path,
  store_method: Type[_Store] = PickleStore) -> Any:
+ """
+ Load an object from disk from a given path and storing method
+
+ Parameters
+ ----------
+ path : Path
+ path of the object to load
+ experimentdata_directory : Path
+ path of the f3dasm project directory
+ store_method : Type[_Store], optional
+ storage method protocol, by default PickleStore
+
+ Returns
+ -------
+ Any
+ the object loaded from disk
+
+ Raises
+ ------
+ ValueError
+ Raises if no matching store type is found
+
+ Note
+ ----
+ If no store method is provided, the function will try to find a matching
+ store type based on the suffix of the item's path. If no matching store
+ type is found, the function will raise a ValueError. By default, the
+ function will use the PickleStore protocol to load the object from disk.
+ """
 
  _path = experimentdata_directory / path