Fix docstrings (#159)

Adapt docstrings to  ruff format

Author: c-w-feldmann

molpipeline/abstract_pipeline_elements/core.py

@@ -71,9 +71,6 @@ def __init__(self, filter_element_id: str, message: str | None = None) -> None:
         message: str | None, optional
             Optional message why the molecule was removed.
 
-        Returns
-        -------
-        None
         """
         self.filter_element_id = filter_element_id
         self.message = message
@@ -193,10 +190,16 @@ def set_params(self, **parameters: Any) -> Self:
         parameters: Any
             Parameters to be set.
 
+        Raises
+        ------
+        ValueError
+            If the parameter is not a valid parameter of the object.
+
         Returns
         -------
         Self
             Self with updated parameters.
+
         """
         for att_name, att_value in parameters.items():
             if not hasattr(self, att_name):
@@ -225,9 +228,6 @@ def n_jobs(self, n_jobs: int) -> None:
         n_jobs: int
             Number of cores used for processing.
 
-        Returns
-        -------
-        None
         """
         self._n_jobs = check_available_cores(n_jobs)
 
@@ -388,19 +388,22 @@ def parameters(self, **parameters: Any) -> None:
         parameters: Any
             Object parameters as a dictionary.
 
-        Returns
-        -------
-        None
         """
         self.set_params(**parameters)
 
     def copy(self) -> Self:
         """Copy the object.
 
+        Raises
+        ------
+        AssertionError
+            If the object cannot be copied.
+
         Returns
         -------
         Self
             Copy of the object.
+
         """
         recreated_object = self.__class__(**self.parameters)
         for key, value in self.additional_attributes.items():

molpipeline/abstract_pipeline_elements/mol2any/mol2bitvector.py

@@ -155,17 +155,24 @@ def set_params(self, **parameters: Any) -> Self:
         parameters: Any
             Dictionary of parameter names and values.
 
+        Raises
+        ------
+        ValueError
+            If return_as is not one of the allowed values.
+
         Returns
         -------
         Self
             Copied object with updated parameters.
+
         """
         parameter_dict_copy = dict(parameters)
         return_as = parameter_dict_copy.pop("return_as", None)
         if return_as is not None:
             if return_as not in get_args(OutputDatatype):
                 raise ValueError(
-                    f"return_as has to be one of {get_args(OutputDatatype)}! (Received: {return_as})"
+                    f"return_as has to be one of {get_args(OutputDatatype)}! "
+                    f"(Received: {return_as})"
                 )
             self._return_as = return_as
         super().set_params(**parameter_dict_copy)
@@ -373,6 +380,12 @@ def __init__(
             Number of jobs.
         uuid: str | None, optional
             Unique identifier.
+
+        Raises
+        ------
+        ValueError
+            If radius is not a positive integer.
+
         """
         # pylint: disable=R0801
         super().__init__(

molpipeline/abstract_pipeline_elements/mol2mol/filter.py

@@ -187,10 +187,16 @@ def pretransform_single(  # pylint: disable=too-many-return-statements
         value: RDKitMol
             Molecule to check.
 
+        Raises
+        ------
+        ValueError
+            If the mode is not "any" or "all".
+
         Returns
         -------
         OptionalMol
             Molecule that matches defined filter elements, else InvalidInstance.
+
         """
         for filter_element, (lower_limit, upper_limit) in self.filter_elements.items():
             property_value = self._calculate_single_element_value(filter_element, value)
@@ -318,6 +324,12 @@ def patterns_mol_dict(self, patterns: Sequence[str]) -> None:
         ----------
         patterns: Sequence[str]
             List of patterns.
+
+        Raises
+        ------
+        ValueError
+            If the patterns are not valid SMILES or SMARTS.
+
         """
         self._patterns_mol_dict = {pat: self._pattern_to_mol(pat) for pat in patterns}
         failed_patterns = [

molpipeline/error_handling.py

@@ -58,6 +58,11 @@ def __init__(
         uuid: str | None, optional
             UUID of the pipeline element.
 
+        Raises
+        ------
+        ValueError
+            If element_ids is None and filter_everything is False.
+
         """
         super().__init__(name=name, n_jobs=n_jobs, uuid=uuid)
         self.error_indices = []
@@ -134,10 +139,16 @@ def set_params(self, **parameters: Any) -> Self:
         parameters: Any
             Dict of arameters to set.
 
+        Raises
+        ------
+        TypeError
+            If element_ids is not a set.
+
         Returns
         -------
         Self
             Self with updated parameters.
+
         """
         param_copy = dict(parameters)
         if "element_ids" in param_copy:
@@ -221,10 +232,18 @@ def co_transform(self, values: TypeFixedVarSeq) -> TypeFixedVarSeq:
         values: TypeFixedVarSeq
             Values to be transformed.
 
+        Raises
+        ------
+        ValueError
+            If the length of the values does not match the length of the values in fit.
+        TypeError
+            If the type of values is not a list or numpy array.
+
         Returns
         -------
         TypeFixedVarSeq
             Input where rows are removed.
+
         """
         if self.n_total != len(values):
             raise ValueError("Length of values does not match length of values in fit")
@@ -375,6 +394,14 @@ def register_removed(self, index: int, value: RemovedInstance) -> None:
             Index of the invalid instance.
         value: Any
             Value of the invalid instance.
+
+        Raises
+        ------
+        TypeError
+            If value is not a RemovedInstance.
+        ValueError
+            If value is not captured by any ErrorFilter.
+
         """
         if not isinstance(value, RemovedInstance):
             raise TypeError(f"Unexpected Type: {type(value)}")
@@ -399,9 +426,6 @@ def set_total(self, total: int) -> None:
         total: int
             Total number of instances seen during transformation.
 
-        Returns
-        -------
-        None
         """
         for error_filter in self.error_filter_list:
             error_filter.n_total = total
@@ -531,7 +555,14 @@ def set_params(self, **parameters: Any) -> Self:
 
     @property
     def error_filter(self) -> ErrorFilter:
-        """Get the ErrorFilter connected to this FilterReinserter."""
+        """Get the ErrorFilter connected to this FilterReinserter.
+
+        Raises
+        ------
+        ValueError
+            If the ErrorFilter is not set.
+
+        """
         if self._error_filter is None:
             raise ValueError("ErrorFilter not set")
         return self._error_filter
@@ -555,10 +586,16 @@ def select_error_filter(self, error_filter_list: list[ErrorFilter]) -> Self:
         error_filter_list: list[ErrorFilter]
             List of ErrorFilters to select from.
 
+        Raises
+        ------
+        ValueError
+            If the ErrorFilter with the given id is not found in the list.
+
         Returns
         -------
         Self
             FilterReinserter with updated ErrorFilter.
+
         """
         for error_filter in error_filter_list:
             if error_filter.uuid == self.error_filter_id:
@@ -674,10 +711,16 @@ def transform(
         **params: Any
             Additional keyword arguments.
 
+        Raises
+        ------
+        ValueError
+            If the length of the values does not match the length of the values in fit.
+
         Returns
         -------
         TypeFixedVarSeq
             Iterable where invalid instances were removed.
+
         """
         if len(values) != self.error_filter.n_total - len(
             self.error_filter.error_indices
@@ -696,10 +739,17 @@ def _fill_list(self, list_to_fill: Sequence[_S]) -> Sequence[_S | _T]:
         list_to_fill: list[Number]
             List to fill with dummy values.
 
+        Raises
+        ------
+        AssertionError
+            If the length of the list does not match the expected length.
+
         Returns
         -------
         list[Number]
-            List where dummy values were inserted to replace instances which could not be processed.
+            List where dummy values were inserted to replace instances which could not
+            be processed.
+
         """
         filled_list: list[_S | _T] = []
         next_value_pos = 0
@@ -710,7 +760,9 @@ def _fill_list(self, list_to_fill: Sequence[_S]) -> Sequence[_S | _T]:
                 filled_list.append(list_to_fill[next_value_pos])
                 next_value_pos += 1
         if len(list_to_fill) != next_value_pos:
-            raise AssertionError()
+            raise AssertionError(
+                "Length of list does not match length of values in fit"
+            )
         return filled_list
 
     def _fill_numpy_arr(self, value_array: npt.NDArray[Any]) -> npt.NDArray[Any]:
@@ -753,10 +805,16 @@ def fill_with_dummy(
         value_container: TypeFixedVarSeq
             Iterable to fill with dummy values.
 
+        Raises
+        ------
+        TypeError
+            If value_container is not a list or numpy array.
+
         Returns
         -------
         AnyVarSeq
             Iterable where dummy values were inserted to replace molecules which could not be processed.
+
         """
         if isinstance(value_container, list):
             return self._fill_list(value_container)  # type: ignore