From 4f1548e93552adff82ccf165fc1b59a7fc9df2ea Mon Sep 17 00:00:00 2001 From: andrew Date: Mon, 9 Nov 2020 08:33:54 -0800 Subject: [PATCH] fix linting --- _delphi_utils_python/delphi_utils/archive.py | 5 +++-- _delphi_utils_python/delphi_utils/export.py | 1 + _delphi_utils_python/delphi_utils/geomap.py | 11 +++++------ _delphi_utils_python/delphi_utils/smooth.py | 19 ++++++++++--------- _delphi_utils_python/delphi_utils/utils.py | 1 + 5 files changed, 20 insertions(+), 17 deletions(-) diff --git a/_delphi_utils_python/delphi_utils/archive.py b/_delphi_utils_python/delphi_utils/archive.py index 7c0e8be06..84f22f03d 100644 --- a/_delphi_utils_python/delphi_utils/archive.py +++ b/_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 diff --git a/_delphi_utils_python/delphi_utils/export.py b/_delphi_utils_python/delphi_utils/export.py index 47f4a7604..b6bd041c4 100644 --- a/_delphi_utils_python/delphi_utils/export.py +++ b/_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 diff --git a/_delphi_utils_python/delphi_utils/geomap.py b/_delphi_utils_python/delphi_utils/geomap.py index 25af29a0b..0d6da3c28 100644 --- a/_delphi_utils_python/delphi_utils/geomap.py +++ b/_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, ) diff --git a/_delphi_utils_python/delphi_utils/smooth.py b/_delphi_utils_python/delphi_utils/smooth.py index 44c7ad032..05bc9ae41 100644 --- a/_delphi_utils_python/delphi_utils/smooth.py +++ b/_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] diff --git a/_delphi_utils_python/delphi_utils/utils.py b/_delphi_utils_python/delphi_utils/utils.py index c6023e4a4..8de61aa37 100644 --- a/_delphi_utils_python/delphi_utils/utils.py +++ b/_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