Major refactor for improved documentation and readability

src/submissions/backend/excel/__init__.py

@@ -1,43 +1,50 @@
-from pandas import DataFrame
-import re
+'''
+Contains pandas convenience functions for interacting with excel workbooks
+'''
+
+from .reports import *
+from .parser import *
+
+# from pandas import DataFrame
+# import re
 
 
-def get_unique_values_in_df_column(df: DataFrame, column_name: str) -> list:
-    """
-    get all unique values in a dataframe column by name
+# def get_unique_values_in_df_column(df: DataFrame, column_name: str) -> list:
+#     """
+#     get all unique values in a dataframe column by name
 
-    Args:
-        df (DataFrame): input dataframe
-        column_name (str): name of column of interest
+#     Args:
+#         df (DataFrame): input dataframe
+#         column_name (str): name of column of interest
 
-    Returns:
-        list: sorted list of unique values
-    """    
-    return sorted(df[column_name].unique())
+#     Returns:
+#         list: sorted list of unique values
+#     """    
+#     return sorted(df[column_name].unique())
 
 
-def drop_reruns_from_df(ctx:dict, df: DataFrame) -> DataFrame:
-    """
-    Removes semi-duplicates from dataframe after finding sequencing repeats.
+# def drop_reruns_from_df(ctx:dict, df: DataFrame) -> DataFrame:
+#     """
+#     Removes semi-duplicates from dataframe after finding sequencing repeats.
 
-    Args:
-        settings (dict): settings passed from gui
-        df (DataFrame): initial dataframe
+#     Args:
+#         settings (dict): settings passed from gui
+#         df (DataFrame): initial dataframe
 
-    Returns:
-        DataFrame: dataframe with originals removed in favour of repeats.
-    """    
-    sample_names = get_unique_values_in_df_column(df, column_name="name")
-    if 'rerun_regex' in ctx:
-        # logger.debug(f"Compiling regex from: {settings['rerun_regex']}")
-        rerun_regex = re.compile(fr"{ctx['rerun_regex']}")
-        for sample in sample_names:
-            # logger.debug(f'Running search on {sample}')
-            if rerun_regex.search(sample):
-                # logger.debug(f'Match on {sample}')
-                first_run = re.sub(rerun_regex, "", sample)
-                # logger.debug(f"First run: {first_run}")
-                df = df.drop(df[df.name == first_run].index)
-        return df
-    else:
-        return None
+#     Returns:
+#         DataFrame: dataframe with originals removed in favour of repeats.
+#     """    
+#     sample_names = get_unique_values_in_df_column(df, column_name="name")
+#     if 'rerun_regex' in ctx:
+#         # logger.debug(f"Compiling regex from: {settings['rerun_regex']}")
+#         rerun_regex = re.compile(fr"{ctx['rerun_regex']}")
+#         for sample in sample_names:
+#             # logger.debug(f'Running search on {sample}')
+#             if rerun_regex.search(sample):
+#                 # logger.debug(f'Match on {sample}')
+#                 first_run = re.sub(rerun_regex, "", sample)
+#                 # logger.debug(f"First run: {first_run}")
+#                 df = df.drop(df[df.name == first_run].index)
+#         return df
+#     else:
+#         return None