Merge pull request #561 from cmu-delphi/gsymptoms-docs

Get google symptoms to pass pydocstyle

Author: krivard

google_symptoms/Makefile

@@ -13,7 +13,8 @@ install: venv
 
 lint:
 	. env/bin/activate; \
-	pylint $(dir)
+	pylint $(dir); \
+	pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

google_symptoms/delphi_google_symptoms/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
-"""Module to pull and clean indicators from the Google Research's Open
-   COVID-19 Data project.
+"""Module to pull and clean indicators from the Google Research's Open COVID-19 Data project.
+
 This file defines the functions that are made public by the module. As the
 module is intended to be executed though the main method, these are primarily
 for testing.

google_symptoms/delphi_google_symptoms/constants.py

@@ -1,4 +1,4 @@
-"""Registry for constants"""
+"""Registry for constants."""
 from functools import partial
 from datetime import timedelta
 

google_symptoms/delphi_google_symptoms/geo.py

@@ -1,13 +1,15 @@
+"""Functions for mapping between geo regions."""
 # -*- coding: utf-8 -*-
 import numpy as np
 import pandas as pd
 from delphi_utils import GeoMapper
 from .constants import METRICS, COMBINED_METRIC
 
 gmpr = GeoMapper()
+
 def generate_transition_matrix(geo_res):
     """
-    Generate transition matrix from county to msa/hrr
+    Generate transition matrix from county to msa/hrr.
 
     Parameters
     ----------

google_symptoms/delphi_google_symptoms/pull.py

@@ -1,3 +1,4 @@
+"""Retrieve data and wrangle into appropriate format."""
 # -*- coding: utf-8 -*-
 import re
 
@@ -8,6 +9,8 @@
 
 def get_geo_id(region_code):
     """
+    Extract fips code from region code.
+
     There are region code in the format of "US-state" and "US-state-fips". In
     county level report, we only consider rows with fips info provided.
     """
@@ -19,8 +22,7 @@ def get_geo_id(region_code):
 
 def preprocess(df, level):
     """
-    Conforms the pulled data from Google COVID-19 Search Trends symptoms
-    data into a dataset
+    Conforms the pulled data from Google COVID-19 Search Trends symptoms data into a dataset.
 
     The output dataset has:
 
@@ -90,7 +92,9 @@ def preprocess(df, level):
     return df
 
 def pull_gs_data(base_url):
-    """Pulls the latest Google COVID-19 Search Trends symptoms dataset, and
+    """Pull latest dataset and transform it into the appropriate format.
+
+    Pull the latest Google COVID-19 Search Trends symptoms dataset, and
     conforms it into a dataset as described in preprocess function.
 
     Note that we retrieve state level data from "2020_US_daily_symptoms_dataset.csv"

google_symptoms/delphi_google_symptoms/run.py

@@ -17,7 +17,7 @@
 
 
 def run_module():
-
+    """Run Google Symptoms module."""
     params = read_params()
     export_start_date = datetime.strptime(params["export_start_date"], "%Y-%m-%d")
     export_dir = params["export_dir"]

google_symptoms/delphi_google_symptoms/smooth.py

@@ -1,8 +1,9 @@
+"""Functions for smoothing signals."""
 # -*- coding: utf-8 -*-
 import numpy as np
 
 def identity(x):
-    '''Trivial "smoother" that does no smoothing.
+    """Trivial "smoother" that does no smoothing.
 
     Parameters
     ----------
@@ -13,11 +14,11 @@ def identity(x):
     -------
     np.ndarray:
         Same as x
-    '''
+    """
     return x
 
 def kday_moving_average(x, k):
-    '''Compute k-day moving average on x.
+    """Compute k-day moving average on x.
 
     Parameters
     ----------
@@ -28,7 +29,7 @@ def kday_moving_average(x, k):
     -------
     np.ndarray:
         k-day moving average.  The first k-1 entries are np.nan.
-    '''
+    """
     if not isinstance(k, int):
         raise ValueError('k must be int.')
     # temp = np.append(np.zeros(k - 1), x)