add changes from out_dim PR (#74 in python-chebai)

Author: sfluegel05

chebai/preprocessing/datasets/deepGO/go_uniprot.py

@@ -770,7 +770,7 @@ def _name(self) -> str:
         return f"{threshold_part}{self.max_sequence_length}"
 
     # ------------------------------ Phase: Prepare data -----------------------------------
-    def prepare_data(self, *args: Any, **kwargs: Any) -> None:
+    def _perform_data_preparation(self, *args: Any, **kwargs: Any) -> None:
         """
         Checks for the existence of migrated DeepGO data in the specified directory.
         Raises an error if the required data file is not found, prompting

chebai/preprocessing/datasets/deepGO/protein_pretraining.py

@@ -55,7 +55,7 @@ def __init__(self, **kwargs):
             )
 
     # ------------------------------ Phase: Prepare data -----------------------------------
-    def prepare_data(self, *args: Any, **kwargs: Any) -> None:
+    def _perform_data_preparation(self, *args: Any, **kwargs: Any) -> None:
         """
         Prepares the data by downloading and parsing Swiss-Prot data if not already available. Saves the processed data
         for further use.