Fix linting on delphi utils

_delphi_utils_python/delphi_utils/archive.py

@@ -104,7 +104,8 @@ def run_module(archive_type: str,
     Parameters
     ----------
     archive_type: str
-        Type of ArchiveDiffer to run.  Must be one of ["git", "s3"] which correspond to `GitArchiveDiffer` and `S3ArchiveDiffer`, respectively.
+        Type of ArchiveDiffer to run.  Must be one of ["git", "s3"] which correspond to
+        `GitArchiveDiffer` and `S3ArchiveDiffer`, respectively.
     cache_dir: str
         The directory for storing most recent archived/uploaded CSVs to start diffing from.
     export_dir: str
@@ -351,7 +352,7 @@ def update_cache(self):
 
         self._cache_updated = True
 
-    def archive_exports(self,
+    def archive_exports(self,  # pylint: disable=arguments-differ
         exported_files: Files,
         update_cache: bool = True,
         update_s3: bool = True

_delphi_utils_python/delphi_utils/export.py

@@ -1,3 +1,4 @@
+"""Export data in the format expected by the Delphi API."""
 # -*- coding: utf-8 -*-
 from datetime import datetime
 from os.path import join

_delphi_utils_python/delphi_utils/geomap.py

@@ -9,7 +9,7 @@
 - remove deprecated functions once integration into JHU and Quidel is refactored
   see: https://github.com/cmu-delphi/covidcast-indicators/issues/283
 """
-
+# pylint: disable=too-many-lines
 from os.path import join
 import warnings
 import pkg_resources
@@ -41,7 +41,7 @@
 }
 
 
-class GeoMapper:
+class GeoMapper:  # pylint: disable=too-many-public-methods
     """Geo mapping tools commonly used in Delphi.
 
     The GeoMapper class provides utility functions for translating between different
@@ -301,7 +301,7 @@ def add_geocode(
                 df[from_col] = df[from_col].astype(str)
 
         # Assuming that the passed-in records are all United States data, at the moment
-        if (from_code, new_code) in [("fips", "nation"), ("zip", "nation")]:
+        if (from_code, new_code) in [("fips", "nation"), ("zip", "nation")]: # pylint: disable=no-else-return
             df[new_col] = df[from_col].apply(lambda x: "us")
             return df
         elif new_code == "nation":
@@ -724,7 +724,7 @@ def convert_state_code_to_state_id(
         )
 
         state_table = self._load_crosswalk(from_code="state", to_code="state")
-        state_table = state_table[["state_code", "state_id"]].rename(
+        state_table = state_table[["state_code", "state_id"]].rename(  # pylint: disable=unsubscriptable-object
             columns={"state_id": state_id_col}
         )
         data = data.copy()
@@ -796,7 +796,7 @@ def convert_zip_to_hrr(self, data, zip_col="zip", hrr_col="hrr"):
         return data
 
     def convert_zip_to_msa(
-        self, data, zip_col="zip", msa_col="msa", date_col="date", count_cols=None
+        self, data, zip_col="zip", date_col="date", count_cols=None
     ):
         """DEPRECATED."""
         warnings.warn(
@@ -828,7 +828,6 @@ def zip_to_msa(
         data = self.convert_zip_to_msa(
             data,
             zip_col=zip_col,
-            msa_col=msa_col,
             date_col=date_col,
             count_cols=count_cols,
         )

_delphi_utils_python/delphi_utils/smooth.py

@@ -16,7 +16,7 @@
 import pandas as pd
 
 
-class Smoother:
+class Smoother:  # pylint: disable=too-many-instance-attributes
     """
     This is the smoothing utility class. This class holds the parameter settings for its smoother
     methods and provides reasonable defaults. Basic usage can be found in the examples below.
@@ -66,8 +66,8 @@ class Smoother:
     Methods
     ----------
     smooth: np.ndarray or pd.Series
-        Takes a 1D signal and returns a smoothed version. The input and the output have the same length
-        and type.
+        Takes a 1D signal and returns a smoothed version.
+        The input and the output have the same lengthand type.
 
     Example Usage
     -------------
@@ -244,20 +244,21 @@ def left_gauss_linear_smoother(self, signal):
         )
         n = len(signal)
         signal_smoothed = np.zeros_like(signal)
-        A = np.vstack([np.ones(n), np.arange(n)]).T  # the regression design matrix
+        # A is the regression design matrix
+        A = np.vstack([np.ones(n), np.arange(n)]).T  # pylint: disable=invalid-name
         for idx in range(n):
             weights = np.exp(
                 -((np.arange(idx + 1) - idx) ** 2) / self.gaussian_bandwidth
             )
-            AwA = np.dot(A[: (idx + 1), :].T * weights, A[: (idx + 1), :])
-            Awy = np.dot(
+            AwA = np.dot(A[: (idx + 1), :].T * weights, A[: (idx + 1), :])  # pylint: disable=invalid-name
+            Awy = np.dot(  # pylint: disable=invalid-name
                 A[: (idx + 1), :].T * weights, signal[: (idx + 1)].reshape(-1, 1)
             )
             try:
                 beta = np.linalg.solve(AwA, Awy)
                 signal_smoothed[idx] = np.dot(A[: (idx + 1), :], beta)[-1]
             except np.linalg.LinAlgError:
-                signal_smoothed[idx] = signal[idx] if self.impute else np.nan
+                signal_smoothed[idx] = signal[idx] if self.impute else np.nan  # pylint: disable=using-constant-test
         if self.minval is not None:
             signal_smoothed[signal_smoothed <= self.minval] = self.minval
         return signal_smoothed
@@ -318,7 +319,7 @@ def savgol_coeffs(self, nl, nr):
         if nr > 0:
             raise warnings.warn("The filter is no longer causal.")
 
-        A = np.vstack(
+        A = np.vstack(  # pylint: disable=invalid-name
             [np.arange(nl, nr + 1) ** j for j in range(self.poly_fit_degree + 1)]
         ).T
 
@@ -367,7 +368,7 @@ def savgol_smoother(self, signal):
         # - shortened_window (default) applies savgol with a smaller window to do the fit
         # - identity keeps the original signal (doesn't smooth)
         # - nan writes nans
-        if self.boundary_method == "shortened_window":
+        if self.boundary_method == "shortened_window":  # pylint: disable=no-else-return
             for ix in range(len(self.coeffs)):
                 if ix == 0:
                     signal_smoothed[ix] = signal[ix]

_delphi_utils_python/delphi_utils/utils.py

@@ -1,3 +1,4 @@
+"""Read parameter files containing configuration information."""
 # -*- coding: utf-8 -*-
 from json import load
 from os.path import exists