Update quidel docstrings to pass pydocstyle

quidel/delphi_quidel/constants.py

@@ -1,4 +1,4 @@
-"""Registry for constants"""
+"""Registry for constants."""
 # global constants
 MIN_OBS = 50  # minimum number of observations in order to compute a proportion.
 MAX_BORROW_OBS = 20 # maximum number of observations can be borrowed in geographical pooling

quidel/delphi_quidel/export.py

@@ -1,11 +1,11 @@
 # -*- coding: utf-8 -*-
-"""Function to export the dataset in the format expected of the API.
-"""
+"""Function to export the dataset in the format expected of the API."""
 import numpy as np
 import pandas as pd
 
 def export_csv(df, geo_name, sensor, receiving_dir, start_date, end_date):
-    """Export data set in format expected for injestion by the API
+    """Export data set in format expected for ingestion by the API.
+
     Parameters
     ----------
     df: pd.DataFrame
@@ -23,7 +23,6 @@ def export_csv(df, geo_name, sensor, receiving_dir, start_date, end_date):
     end_date: datetime.datetime
         The last date to report
     """
-
     df = df.copy()
     df = df[np.logical_and(df["timestamp"] >= start_date,
                            df["timestamp"] <= end_date)]

quidel/delphi_quidel/generate_sensor.py

@@ -1,7 +1,5 @@
 # -*- coding: utf-8 -*-
-"""
-Functions to help generate sensor for different geographical levels
-"""
+"""Functions to help generate sensor for different geographical levels."""
 import pandas as pd
 from .data_tools import (fill_dates, raw_positive_prop,
                          smoothed_positive_prop,
@@ -11,7 +9,8 @@
 
 def generate_sensor_for_states(state_groups, smooth, device, first_date, last_date):
     """
-    fit over states
+    Fit over states.
+
     Args:
         state_groups: pd.groupby.generic.DataFrameGroupBy
         state_key: "state_id"
@@ -70,7 +69,8 @@ def generate_sensor_for_states(state_groups, smooth, device, first_date, last_da
 def generate_sensor_for_other_geores(state_groups, data, res_key, smooth,
                                      device, first_date, last_date):
     """
-    fit over counties/HRRs/MSAs
+    Fit over counties/HRRs/MSAs.
+
     Args:
         data: pd.DataFrame
         res_key: "fips", "cbsa_id" or "hrrnum"

quidel/delphi_quidel/handle_wip_sensor.py

@@ -1,8 +1,9 @@
-"""This file checks the wip status of signals"""
+"""This file checks the wip status of signals."""
 import covidcast
 
 def add_prefix(signal_names, wip_signal, prefix):
-    """Adds prefix to signal if there is a WIP signal
+    """Add prefix to signal if there is a WIP signal.
+
     Parameters
     ----------
     signal_names: List[str]
@@ -18,7 +19,6 @@ def add_prefix(signal_names, wip_signal, prefix):
     List of signal names
         wip/non wip signals for further computation
     """
-
     if wip_signal is True:
         return [prefix + signal for signal in signal_names]
     if isinstance(wip_signal, list):
@@ -37,7 +37,8 @@ def add_prefix(signal_names, wip_signal, prefix):
 
 
 def public_signal(signal_):
-    """Checks if the signal name is already public using COVIDcast
+    """Check if the signal name is already public using COVIDcast.
+
     Parameters
     ----------
     signal_ : str

quidel/delphi_quidel/pull.py

@@ -1,5 +1,6 @@
 # -*- coding: utf-8 -*-
 """Simply downloads email attachments.
+
 Uses this handy package: https://pypi.org/project/imap-tools/
 """
 import io
@@ -26,6 +27,7 @@
 def compare_dates(date1, date2, flag):
     """
     Compare two dates.
+
     If op == "l" return the larger date
     If op == "s" return the smaller date
     """
@@ -39,20 +41,15 @@ def compare_dates(date1, date2, flag):
         return date1
 
 def check_whether_date_in_range(search_date, start_date, end_date):
-    """
-    Check whether the search date is in a valid time range
-    """
+    """Check whether the search date is in a valid time range."""
     if search_date > end_date:
         return False
     if search_date < start_date:
         return False
     return True
 
 def read_historical_data():
-    """
-    Read historical flu antigen test data stored in
-    midas /common/quidel-historical-raw
-    """
+    """Read historical flu antigen test data stored in midas /common/quidel-historical-raw."""
     pull_dir = "/common/quidel-historical-raw"
     columns = ['SofiaSerNum', 'TestDate', 'Facility', 'ZipCode',
                                'FluA', 'FluB', 'StorageDate']
@@ -66,9 +63,10 @@ def read_historical_data():
 
 def regulate_column_names(df, test_type):
     """
-    Regulate column names for flu_ag test data since Quidel changed their
-    column names multiple times. We want to finalize the column name list
-    to be:
+    Regulate column names for flu_ag test data.
+
+    This is done since Quidel changed their column names multiple times.
+    We want to finalize the column name list to be:
         ['SofiaSerNum', 'TestDate', 'Facility',
         'Zip', 'FluA', 'FluB', 'StorageDate']
     """
@@ -88,7 +86,7 @@ def regulate_column_names(df, test_type):
 def get_from_email(column_names, start_dates, end_dates, mail_server,
                    account, sender, password):
     """
-    Get raw data from email account
+    Get raw data from email account.
 
     Parameters:
         start_date: datetime.datetime
@@ -146,9 +144,7 @@ def get_from_email(column_names, start_dates, end_dates, mail_server,
     return dfs, time_flag
 
 def fix_zipcode(df):
-    """
-    Fix zipcode that is 9 digit instead of 5 digit
-    """
+    """Fix zipcode that is 9 digit instead of 5 digit."""
     zipcode5 = []
     fixnum = 0
     for zipcode in df['Zip'].values:
@@ -164,6 +160,8 @@ def fix_zipcode(df):
 
 def fix_date(df):
     """
+    Adjust tests based on their test and storage dates.
+
     Quidel antigen tests are labeled with Test Date and Storage Date. In principle,
     the TestDate should reflect when the test was performed and the StorageDate
     when the test was logged in the MyVirena cloud storage device. We expect
@@ -191,6 +189,7 @@ def preprocess_new_data(start_dates, end_dates, mail_server, account,
                         sender, password, test_mode):
     """
     Pull and pre-process Quidel Antigen Test data from datadrop email.
+
     Drop unnecessary columns. Temporarily consider the positive rate
     sensor only which is related to number of total tests and number
     of positive tests.
@@ -286,7 +285,7 @@ def preprocess_new_data(start_dates, end_dates, mail_server, account,
 
 def check_intermediate_file(cache_dir, pull_start_dates):
     """
-    Check whether there is a cache file containing historical data already
+    Check whether there is a cache file containing historical data already.
 
     Parameters:
         cache_dir: str
@@ -314,8 +313,10 @@ def check_intermediate_file(cache_dir, pull_start_dates):
 
 def pull_quidel_data(params):
     """
-    Pull the quidel test data. Decide whether to combine the newly
-    received data with stored historical records in ./cache
+    Pull the quidel test data.
+
+    Decide whether to combine the newly received data with
+    stored historical records in ./cache
 
     Parameters:
         params: dict
@@ -372,7 +373,8 @@ def pull_quidel_data(params):
 def check_export_end_date(input_export_end_dates, _end_date,
                           END_FROM_TODAY_MINUS):
     """
-    Update the export_end_date according to the data received
+    Update the export_end_date according to the data received.
+
     By default, set the export end date to be the last pulling date - 5 days
     (END_FROM_TODAY_MINUS = 5).
     Otherwise, use the required date if it is earlier than the default one.
@@ -405,6 +407,8 @@ def check_export_end_date(input_export_end_dates, _end_date,
 def check_export_start_date(export_start_dates, export_end_dates,
                             EXPORT_DAY_RANGE):
     """
+    Update the export_start_date according to the export_end_date and date range.
+
     Update the export_start_date according to the export_end_date so that it
     could be export_end_date - EXPORT_DAY_RANGE
 
@@ -439,7 +443,7 @@ def check_export_start_date(export_start_dates, export_end_dates,
 
 def update_cache_file(dfs, _end_date, cache_dir):
     """
-    Update cache file. Remove the old one, export the new one
+    Update cache file. Remove the old one, export the new one.
 
     Parameter:
         df: pd.DataFrame

quidel/delphi_quidel/run.py

@@ -22,6 +22,7 @@
 from .handle_wip_sensor import add_prefix
 
 def run_module():
+    """Run module for processing Quidel test data."""
     params = read_params()
     cache_dir = params["cache_dir"]
     export_dir = params["export_dir"]