1226 Remove duplicates in python docstrings(#1227)

Author: kilianvolmer

pycode/memilio-epidata/memilio/epidata/customPlot.py

@@ -54,11 +54,9 @@ def plot_multiple_series(
     :param innercolor: Inner color of figure. (Default value = 'white')
     :param fig_name: name of the figure to save. (Default value = 'customPlot')
     :param loc_legend:  (Default value = 'upper left')
-    :param fig_size:  (Default value = (10)
-    :param 6): 
+    :param fig_size:  (Default value = (10, 6))
     :param plot_outside:  (Default value = True)
     :param path_rel:  (Default value = 'figures/')
-    :param innercolor:  (Default value = 'white')
 
     """
     fig, ax = plt.subplots(figsize=fig_size, facecolor=outercolor)

pycode/memilio-epidata/memilio/epidata/getCaseData.py

@@ -60,13 +60,9 @@ def check_for_completeness(df: pd.DataFrame,
     Note: There is no check if data for every day and every county is available (which can happen).
 
     :param df: pd.Dataframe. Dataframe to check
-    :param merge_berlin: bool True or False. Defines if Berlin's districts are kept separated or get merged. Default defined in defaultDict.
-    :param merge_eisenach: bool True or False. Defines if Eisenbach districts are kept separated or get merged. Default defined in defaultDict.
+    :param merge_berlin: bool True or False. Defines if Berlin's districts are kept separated or get merged. Default value = false
+    :param merge_eisenach: bool True or False. Defines if Eisenbach districts are kept separated or get merged. Default value = True.
     :param run_checks: bool
-    :param df: pd.DataFrame: 
-    :param run_checks: bool: 
-    :param merge_berlin: bool:  (Default value = False)
-    :param merge_eisenach: bool:  (Default value = True)
     :returns: Boolean to say if data is complete or not
 
     """
@@ -105,10 +101,7 @@ def fetch_case_data(
     :param filename: str
         Name of the full dataset filename
     :param conf_obj: configuration object
-    :param read_data: bool. Defines if data is read from file or downloaded. Default defined in defaultDict.
-    :param directory: str: 
-    :param filename: str: 
-    :param read_data: bool:  (Default value = dd.defaultDict['read_data'])
+    :param read_data: bool. Defines if data is read from file or downloaded. (Default value = dd.defaultDict['read_data'])
     :returns: df pd.Dataframe. Dataframe containing the downloaded case data
 
     """
@@ -201,13 +194,8 @@ def preprocess_case_data(raw_df: pd.DataFrame,
     :param filename: str
         Name of the full dataset filename
     :param conf_obj: configuration object
-    :param split_berlin: bool. Defines if Berlin's disctricts are kept separated or get merged. Default defined in defaultDict.
-    :param rep_date: bool Defines if reporting date or reference date is taken into dataframe. Default defined in defaultDict.
-    :param raw_df: pd.DataFrame: 
-    :param directory: str: 
-    :param filename: str: 
-    :param split_berlin: bool:  (Default value = dd.defaultDict['split_berlin'])
-    :param rep_date: bool:  (Default value = dd.defaultDict['rep_date'])
+    :param split_berlin: bool. Defines if Berlin's disctricts are kept separated or get merged. Default defined in defaultDict. (Default value = dd.defaultDict['split_berlin'])
+    :param rep_date: bool Defines if reporting date or reference date is taken into dataframe. Default defined in defaultDict. (Default value = dd.defaultDict['rep_date'])
     :returns: df pd.Dataframe
 
     """
@@ -319,25 +307,15 @@ def write_case_data(df: pd.DataFrame,
         Path to the output directory
     :param conf_obj: configuration object
     :param file_format: str
-        File format which is used for writing the data. Default defined in defaultDict.
+        File format which is used for writing the data. Default defined in defaultDict. (Default value = dd.defaultDict['file_format'])
     :param start_date: date
-        Date of first date in dataframe. Default 2020-01-01.
-    :param end_date: date. Date of last date in dataframe. Default defined in defaultDict.
-    :param impute_dates: bool True or False. Defines if values for dates without new information are imputed. Default defined in defaultDict.
-    :param moving_average: int Integers >=0. Applies an 'moving_average'-days moving average on all time series smooth out effects of irregular reporting. Default defined in defaultDict.
-    :param split_berlin: bool True or False. Defines if Berlin's districts are kept separated or get merged. Default defined in defaultDict.
-    :param rep_date: bool True or False. Defines if reporting date or reference date is taken into dataframe. Default defined in defaultDict.
+        Date of first date in dataframe. Default 2020-01-01. (Default value = dd.defaultDict['start_date'])
+    :param end_date: date. Date of last date in dataframe. Default defined in defaultDict. (Default value = dd.defaultDict['end_date'])
+    :param impute_dates: bool True or False. Defines if values for dates without new information are imputed. Default defined in defaultDict. (Default value = dd.defaultDict['impute_dates']) 
+    :param moving_average: int Integers >=0. Applies an 'moving_average'-days moving average on all time series smooth out effects of irregular reporting. Default defined in defaultDict. (Default value = dd.defaultDict['moving_average'])
+    :param split_berlin: bool True or False. Defines if Berlin's districts are kept separated or get merged. Default defined in defaultDict. (Default value = dd.defaultDict['split_berlin'])
+    :param rep_date: bool True or False. Defines if reporting date or reference date is taken into dataframe. Default defined in defaultDict. (Default value = dd.defaultDict['rep_date'])
     :param files: list. List of strings or 'All' or 'Plot'. Defines which files should be provided (and plotted). Default 'All'.
-    :param df: pd.DataFrame: 
-    :param directory: str: 
-    :param file_format: str:  (Default value = dd.defaultDict['file_format'])
-    :param start_date: date:  (Default value = dd.defaultDict['start_date'])
-    :param end_date: date:  (Default value = dd.defaultDict['end_date'])
-    :param impute_dates: bool:  (Default value = dd.defaultDict['impute_dates'])
-    :param moving_average: int:  (Default value = dd.defaultDict['moving_average'])
-    :param split_berlin: bool:  (Default value = dd.defaultDict['split_berlin'])
-    :param rep_date: bool:  (Default value = dd.defaultDict['rep_date'])
-    :param files: str or list:  (Default value = 'All')
     :returns: None
 
     """
@@ -513,31 +491,17 @@ def get_case_data(read_data: bool = dd.defaultDict['read_data'],
         - Infected, deaths and recovered split for state and age are stored in "cases_all_state_age"
         - Infected, deaths and recovered split for county and age are stored in "cases_all_county_age(_split_berlin)"
 
-    :param read_data: True or False. Defines if data is read from file or downloaded. Default defined in defaultDict.
-    :param file_format: File format which is used for writing the data. Default defined in defaultDict.
-    :param out_folder: Folder where data is written to. Default defined in defaultDict.
-    :param start_date: Date of first date in dataframe. Default 2020-01-01.
-    :param end_date: Date of last date in dataframe. Default defined in defaultDict.
-    :param impute_dates: True or False. Defines if values for dates without new information are imputed. Default defined in defaultDict.
+    :param read_data: True or False. Defines if data is read from file or downloaded. Default defined in defaultDict. (Default value = dd.defaultDict['read_data'])
+    :param file_format: File format which is used for writing the data. Default defined in defaultDict. (Default value = dd.defaultDict['file_format'])
+    :param out_folder: Folder where data is written to. Default defined in defaultDict. (Default value = dd.defaultDict['out_folder'])
+    :param start_date: Date of first date in dataframe. (Default value = dd.defaultDict['start_date'])
+    :param end_date: Date of last date in dataframe. Default defined in defaultDict. (Default value = dd.defaultDict['end_date'])
+    :param impute_dates: True or False. Defines if values for dates without new information are imputed. Default defined in defaultDict. (Default value = dd.defaultDict['impute_dates'])
     :param moving_average: Integers >=0. Applies an 'moving_average'-days moving average on all time series
-        to smooth out effects of irregular reporting. Default defined in defaultDict.
-    :param split_berlin: True or False. Defines if Berlin's disctricts are kept separated or get merged. Default defined in defaultDict.
-    :param rep_date: True or False. Defines if reporting date or reference date is taken into dataframe. Default defined in defaultDict.
+        to smooth out effects of irregular reporting. Default defined in defaultDict. (Default value = dd.defaultDict['moving_average'])
+    :param split_berlin: True or False. Defines if Berlin's disctricts are kept separated or get merged. Default defined in defaultDict. (Default value = dd.defaultDict['split_berlin'])
+    :param rep_date: True or False. Defines if reporting date or reference date is taken into dataframe. Default defined in defaultDict. (Default value = dd.defaultDict['rep_date'])
     :param files: List of strings or 'All' or 'Plot'. Defnies which files should be provided (and plotted). Default 'All'.
-    :param to_dataset: bool True or False. Whether to return the dataframe as an object instead of json file.
-        If True - returns objects with dataframes
-        If False - write dataframes into files
-        Default defined in defaultDict.
-    :param read_data: bool:  (Default value = dd.defaultDict['read_data'])
-    :param out_folder: str:  (Default value = dd.defaultDict['out_folder'])
-    :param file_format: str:  (Default value = dd.defaultDict['file_format'])
-    :param start_date: date:  (Default value = dd.defaultDict['start_date'])
-    :param end_date: date:  (Default value = dd.defaultDict['end_date'])
-    :param impute_dates: bool:  (Default value = dd.defaultDict['impute_dates'])
-    :param moving_average: int:  (Default value = dd.defaultDict['moving_average'])
-    :param split_berlin: bool:  (Default value = dd.defaultDict['split_berlin'])
-    :param rep_date: bool:  (Default value = dd.defaultDict['rep_date'])
-    :param files: str or list:  (Default value = 'All')
     :param **kwargs: 
     :returns: None
 

pycode/memilio-epidata/memilio/epidata/getCommuterMobility.py

@@ -60,7 +60,6 @@ def assign_geographical_entities(countykey_list, govkey_list, run_checks):
 
     Keyword arguments:
 
-    :param setup_dict: dictionary with necessary values
     :param countykey_list: List of county regional keys.
     :param govkey_list: List of governing regions regional keys.
     :param run_checks: 
@@ -146,9 +145,9 @@ def get_commuter_data(read_data=dd.defaultDict['read_data'],
     Keyword arguments:
 
     :param read_data: True or False. Defines if data is read from file or downloaded.
-        Only for population data. Commuter data is always downloaded. Default defined in defaultDict.
-    :param file_format: File format which is used for writing the data. Default defined in defaultDict.
-    :param out_folder: Folder where data is written to. Default defined in defaultDict.
+        Only for population data. Commuter data is always downloaded. Default defined in defaultDict. (Default value = dd.defaultDict['read_data'])
+    :param file_format: File format which is used for writing the data. Default defined in defaultDict. (Default value = dd.defaultDict['file_format'])
+    :param out_folder: Folder where data is written to. Default defined in defaultDict. (Default value = dd.defaultDict['out_folder'])
     :param setup_dict: dictionary with necessary values:
         'path': String with datapath where mobility files can be found
         'abs_tol': tolerated undetected people

pycode/memilio-epidata/memilio/epidata/getDIVIData.py

@@ -67,12 +67,8 @@ def fetch_divi_data(
     :param conf_obj: configuration object
     :param filename: str
         File format which is used for writing the data. Default defined in defaultDict.
-    :param read_data: bool. True or False. Defines if data is read from file or downloaded. Default defined in defaultDict.
-    :param file_format: str. File format which is used for writing the data. Default defined in defaultDict.
-    :param directory: str: 
-    :param filename: str: 
-    :param read_data: bool:  (Default value = dd.defaultDict['read_data'])
-    :param file_format: str:  (Default value = dd.defaultDict['file_format'])
+    :param read_data: bool. True or False. Defines if data is read from file or downloaded. Default defined in defaultDict. (Default value = dd.defaultDict['read_data'])
+    :param file_format: str. File format which is used for writing the data. Default defined in defaultDict. (Default value = dd.defaultDict['file_format'])
     :returns: Tuple[df_raw, start_date] Tuple. Contains the fetched data as well as the adjusted starting date
 
     """
@@ -109,17 +105,10 @@ def preprocess_divi_data(df_raw: pd.DataFrame,
 
     :param df_raw: pd.DataFrame
     :param conf_obj: configuration object
-    :param start_date: date  The first date in dataframe. Default defined in defaultDict.
-    :param end_date: date The last date in dataframe. Default defined in defaultDict.
-    :param impute_dates: bool  Defines if values for dates without new information are imputed. Default defined in defaultDict.
-    :param moving_average: int  Integers >=0.Applies an 'moving_average'-days moving average on all time seriesto smooth out effects of irregular reporting. Default defined in defaultDict.
-    :param df_raw: pd.DataFrame: 
-    :param start_date: date:  (Default value = date(2020)
-    :param 4: 
-    :param 24): 
-    :param end_date: date:  (Default value = dd.defaultDict['end_date'])
-    :param impute_dates: bool:  (Default value = dd.defaultDict['impute_dates'])
-    :param moving_average: int:  (Default value = dd.defaultDict['moving_average'])
+    :param start_date: date  The first date in dataframe. Default value = date(2020, 4, 24).
+    :param end_date: date The last date in dataframe. Default defined in defaultDict. (Default value = dd.defaultDict['end_date'])
+    :param impute_dates: bool  Defines if values for dates without new information are imputed. Default defined in defaultDict. (Default value = dd.defaultDict['impute_dates'])
+    :param moving_average: int  Integers >=0.Applies an 'moving_average'-days moving average on all time seriesto smooth out effects of irregular reporting. Default defined in defaultDict. (Default value = dd.defaultDict['moving_average'])
     :returns: df pd.DataFrame  processed divi data
 
     """
@@ -201,14 +190,9 @@ def write_divi_data(df: pd.DataFrame,
     :param directory: str
         Path to the output directory
     :param conf_obj: configuration object
-    :param file_format: str. File format which is used for writing the data. Default defined in defaultDict.
-    :param impute_dates: bool True or False. Defines if values for dates without new information are imputed. Default defined in defaultDict.
-    :param moving_average: int Integers >=0. Applies an 'moving_average'-days moving average on all time series to smooth out effects of irregular reporting. Default defined in defaultDict.
-    :param df: pd.DataFrame: 
-    :param directory: str: 
-    :param file_format: str:  (Default value = dd.defaultDict['file_format'])
-    :param impute_dates: bool:  (Default value = dd.defaultDict['impute_dates'])
-    :param moving_average: int:  (Default value = dd.defaultDict['moving_average'])
+    :param file_format: str. File format which is used for writing the data. Default defined in defaultDict. (Default value = dd.defaultDict['file_format'])
+    :param impute_dates: bool True or False. Defines if values for dates without new information are imputed. Default defined in defaultDict. (Default value = dd.defaultDict['impute_dates'])
+    :param moving_average: int Integers >=0. Applies an 'moving_average'-days moving average on all time series to smooth out effects of irregular reporting. Default defined in defaultDict. (Default value = dd.defaultDict['moving_average'])
     :returns: data_dict Dict Dictionary containing datasets at county, state and national level
 
     """
@@ -284,27 +268,14 @@ def get_divi_data(read_data: bool = dd.defaultDict['read_data'],
     stored in the files "county_divi".json", "state_divi.json" and "germany_divi.json"
     for counties, states and whole Germany, respectively.
 
-    :param read_data: True or False. Defines if data is read from file or downloaded. Default defined in defaultDict.
-    :param file_format: File format which is used for writing the data. Default defined in defaultDict.
-    :param out_folder: Folder where data is written to. Default defined in defaultDict.
-    :param start_date: Date of first date in dataframe. Default defined in defaultDict.
-    :param end_date: Date of last date in dataframe. Default defined in defaultDict.
-    :param impute_dates: True or False. Defines if values for dates without new information are imputed. Default defined in defaultDict.
+    :param read_data: True or False. Defines if data is read from file or downloaded. Default defined in defaultDict. (Default value = dd.defaultDict['read_data'])
+    :param file_format: File format which is used for writing the data. Default defined in defaultDict. (Default value = dd.defaultDict['file_format'])
+    :param out_folder: Folder where data is written to. Default defined in defaultDict. (Default value = dd.defaultDict['out_folder'])
+    :param start_date: Date of first date in dataframe. Default value = ``date(2020, 4, 24)``.
+    :param end_date: Date of last date in dataframe. Default defined in defaultDict. (Default value = dd.defaultDict['end_date'])
+    :param impute_dates: True or False. Defines if values for dates without new information are imputed. Default defined in defaultDict. (Default value = dd.defaultDict['impute_dates'])
     :param moving_average: Integers >=0. Applies an 'moving_average'-days moving average on all time series
-        to smooth out effects of irregular reporting. Default defined in defaultDict.
-    :param to_dataset: bool True or False. Whether to return the dataframe as an object instead of json file.
-        If True - returns objects with dataframes
-        If False - write dataframes into files
-        Default defined in defaultDict.
-    :param read_data: bool:  (Default value = dd.defaultDict['read_data'])
-    :param file_format: str:  (Default value = dd.defaultDict['file_format'])
-    :param out_folder: str:  (Default value = dd.defaultDict['out_folder'])
-    :param start_date: date:  (Default value = date(2020)
-    :param 4: 
-    :param 24): 
-    :param end_date: date:  (Default value = dd.defaultDict['end_date'])
-    :param impute_dates: bool:  (Default value = dd.defaultDict['impute_dates'])
-    :param moving_average: int:  (Default value = dd.defaultDict['moving_average'])
+        to smooth out effects of irregular reporting. Default defined in defaultDict. (Default value = dd.defaultDict['moving_average'])
     :param **kwargs: 
 
     """
@@ -351,8 +322,7 @@ def divi_data_sanity_checks(df: pd.DataFrame) -> None:
     Checks if the headers of the dataframe are those which are needed
     Checks if the size of the dataframe is not unusual
 
-    :param df: The dataframe which has to be checked
-    :param df: pd.DataFrame: 
+    :param df: The dataframe which has to be checked pd.DataFrame
 
     """
     # there should be 13 headers