Merge pull request #569 from cmu-delphi/chc-docs

Get CHC to pass pydocstyle

Author: krivard

changehc/Makefile

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

changehc/delphi_changehc/config.py

@@ -9,8 +9,7 @@
 
 
 class Config:
-    """Static configuration variables.
-    """
+    """Static configuration variables."""
 
     ## dates
     FIRST_DATA_DATE = datetime(2020, 1, 1)
@@ -59,9 +58,11 @@ class Config:
 
 class Constants:
     """
-    Contains the maximum number of geo units for each geo type
+    Contains the maximum number of geo units for each geo type.
+
     Used for sanity checks
     """
+
     # number of counties in usa, including megacounties
     NUM_COUNTIES = 3141 + 52
     NUM_HRRS = 308

changehc/delphi_changehc/constants.py

@@ -1,4 +1,4 @@
-"""Registry for signal names and geo types"""
+"""Registry for signal names and geo types."""
 SMOOTHED = "smoothed_outpatient_covid"
 SMOOTHED_ADJ = "smoothed_adj_outpatient_covid"
 SMOOTHED_CLI = "smoothed_outpatient_cli"

changehc/delphi_changehc/download_ftp_files.py

@@ -1,5 +1,4 @@
-"""
-Downloads files modified in the last 24 hours from the specified ftp server."""
+"""Download files modified in the last 24 hours from the specified ftp server."""
 
 # standard
 import datetime
@@ -11,19 +10,19 @@
 
 
 def print_callback(filename, bytes_so_far, bytes_total):
-    """Log file transfer progress"""
+    """Log file transfer progress."""
     rough_percent_transferred = int(100 * (bytes_so_far / bytes_total))
     if (rough_percent_transferred % 25) == 0:
         print(f'{filename} transfer: {rough_percent_transferred}%')
 
 
 def get_files_from_dir(sftp, out_path):
-    """Download files from sftp server that have been uploaded in last day
+    """Download files from sftp server that have been uploaded in last day.
+
     Args:
         sftp: SFTP Session from Paramiko client
         out_path: Path to local directory into which to download the files
     """
-
     current_time = datetime.datetime.now()
 
     # go through files in recieving dir
@@ -45,12 +44,12 @@ def get_files_from_dir(sftp, out_path):
 
 
 def download_covid(out_path, ftp_conn):
-    """Downloads files necessary to create chng-covid signal from ftp server.
+    """Download files necessary to create chng-covid signal from ftp server.
+
     Args:
         out_path: Path to local directory into which to download the files
         ftp_conn: Dict containing login credentials to ftp server
     """
-
     # open client
     try:
         client = paramiko.SSHClient()
@@ -74,12 +73,12 @@ def download_covid(out_path, ftp_conn):
 
 
 def download_cli(out_path, ftp_conn):
-    """Downloads files necessary to create chng-cli signal from ftp server.
+    """Download files necessary to create chng-cli signal from ftp server.
+
     Args:
         out_path: Path to local directory into which to download the files
         ftp_conn: Dict containing login credentials to ftp server
     """
-
     # open client
     try:
         client = paramiko.SSHClient()

changehc/delphi_changehc/load_data.py

@@ -27,7 +27,6 @@ def load_chng_data(filepath, dropdate, base_geo,
     Returns:
         cleaned dataframe
     """
-
     assert base_geo == "fips", "base unit must be 'fips'"
     count_flag = False
     date_flag = False

changehc/delphi_changehc/run.py

@@ -19,8 +19,7 @@
 from .update_sensor import CHCSensorUpdator
 
 def retrieve_files(params, filedate):
-    """Return filenames of relevant files, downloading them if necessary
-    """
+    """Return filenames of relevant files, downloading them if necessary."""
     files = params["input_files"]
     if files["denom"] is None:
 
@@ -57,8 +56,7 @@ def retrieve_files(params, filedate):
 
 
 def make_asserts(params):
-    """Assert that for each type, filenames are either all present or all absent
-    """
+    """Assert that for each type, filenames are either all present or all absent."""
     files = params["input_files"]
     if "covid" in params["types"]:
         assert (files["denom"] is None) == (files["covid"] is None), \
@@ -79,9 +77,7 @@ def make_asserts(params):
 
 
 def run_module():
-    """Run the delphi_changehc module.
-    """
-
+    """Run the delphi_changehc module."""
     params = read_params()
 
     logging.basicConfig(level=logging.DEBUG)

changehc/delphi_changehc/sensor.py

@@ -20,19 +20,19 @@
 
 
 class CHCSensor:
-    """Sensor class to fit a signal using Covid counts from Change HC outpatient data.
-    """
+    """Sensor class to fit a signal using Covid counts from Change HC outpatient data."""
+
     smoother = Smoother("savgol",
                         poly_fit_degree=1,
                         gaussian_bandwidth=Config.SMOOTHER_BANDWIDTH)
 
     @staticmethod
     def gauss_smooth(count,total):
-        """smooth using the left_gauss_linear
+        """Smooth using the left_gauss_linear.
 
         Args:
             count, total: array
-            """
+        """
         count_smooth = CHCSensor.smoother.smooth(count)
         total_smooth = CHCSensor.smoother.smooth(total)
         total_clip = np.clip(total_smooth, 0, None)
@@ -46,12 +46,12 @@ def backfill(
             k=Config.MAX_BACKFILL_WINDOW,
             min_visits_to_fill=Config.MIN_CUM_VISITS):
         """
-        Adjust for backfill (retroactively added observations) by using a
-         variable length smoother, which starts from the RHS and moves
-         leftwards (backwards through time). We cumulatively sum the total
-         visits (denominator), until we have observed some minimum number of
-         counts, then calculate the sum over that bin. We restrict the
-         bin size so to avoid inluding long-past values.
+        Adjust for retroactively added observations (backfill) by using a variable length smoother.
+
+        The smoother starts from the RHS and moves leftwards (backwards through time).
+        We cumulatively sum the total visits (denominator), until we have observed some minimum number of
+        counts, then calculate the sum over that bin. We restrict the
+        bin size so to avoid including long-past values.
 
         Args:
             num: array of covid counts

changehc/delphi_changehc/update_sensor.py

@@ -1,5 +1,6 @@
 """
 Generate CHC sensors.
+
 Author: Aaron Rumack
 Created: 2020-10-14
 """
@@ -21,6 +22,7 @@
 
 def write_to_csv(output_dict, write_se, out_name, output_path="."):
     """Write sensor values to csv.
+
     Args:
         output_dict: dictionary containing sensor rates, se, unique dates, and unique geo_id
         write_se: boolean to write out standard errors, if true, use an obfuscated name
@@ -72,8 +74,7 @@ def write_to_csv(output_dict, write_se, out_name, output_path="."):
 
 
 class CHCSensorUpdator:  # pylint: disable=too-many-instance-attributes
-    """Contains methods to update sensor and write results to csv
-    """
+    """Contains methods to update sensor and write results to csv."""
 
     def __init__(self,
                  startdate,
@@ -84,7 +85,8 @@ def __init__(self,
                  weekday,
                  numtype,
                  se):
-        """Init Sensor Updator
+        """Init Sensor Updator.
+
         Args:
             startdate: first sensor date (YYYY-mm-dd)
             enddate: last sensor date (YYYY-mm-dd)
@@ -123,8 +125,7 @@ def __init__(self,
         self.sensor_dates = None
 
     def shift_dates(self):
-        """shift estimates forward to account for time lag, compute burnindates, sensordates
-        """
+        """Shift estimates forward to account for time lag, compute burnindates, sensordates."""
         drange = lambda s, e: pd.date_range(start=s,periods=(e-s).days,freq='D')
         self.startdate = self.startdate - Config.DAY_SHIFT
         self.burnindate = self.startdate - Config.BURN_IN_PERIOD
@@ -134,7 +135,8 @@ def shift_dates(self):
         return True
 
     def geo_reindex(self, data):
-        """Reindex based on geography, include all date, geo pairs
+        """Reindex based on geography, include all date, geo pairs.
+
         Args:
             data: dataframe, the output of loadcombineddata
         Returns:
@@ -178,6 +180,7 @@ def update_sensor(self,
             data,
             outpath):
         """Generate sensor values, and write to csv format.
+
         Args:
             data: pd.DataFrame with columns num and den
             outpath: output path for the csv results

changehc/delphi_changehc/weekday.py

@@ -55,7 +55,6 @@ def get_params(data):
         Return a matrix of parameters: the entire vector of betas, for each time
         series column in the data.
         """
-
         tmp = data.reset_index()
         denoms = tmp.groupby(Config.DATE_COL).sum()["den"]
         nums = tmp.groupby(Config.DATE_COL).sum()["num"]
@@ -113,7 +112,6 @@ def calc_adjustment(params, sub_data):
         -- this has the same effect.
 
         """
-
         tmp = sub_data.reset_index()
 
         wd_correction = np.zeros((len(tmp["num"])))