Add utils to CI and fix some linting

Author: chinandrew

.github/workflows/python-ci.yml

@@ -16,8 +16,7 @@ jobs:
     if: github.event.pull_request.draft == false
     strategy:
       matrix:
-        #packages: [_delphi_utils_python, cdc_covidnet, claims_hosp, combo_cases_and_deaths, google_symptoms, jhu, nchs_mortality, quidel, quidel_covidtest, safegraph, safegraph_patterns, usafacts]
-        packages: [cdc_covidnet, claims_hosp, combo_cases_and_deaths, google_symptoms, jhu, nchs_mortality, quidel, quidel_covidtest, safegraph, safegraph_patterns, usafacts]
+        packages: [_delphi_utils_python, cdc_covidnet, claims_hosp, combo_cases_and_deaths, google_symptoms, jhu, nchs_mortality, quidel, quidel_covidtest, safegraph, safegraph_patterns, usafacts]
     defaults:
       run:
         working-directory: ${{ matrix.packages }}

_delphi_utils_python/delphi_utils/smooth.py

@@ -150,7 +150,9 @@ def __init__(
         else:
             self.coeffs = None
 
-    def smooth(self, signal: Union[np.ndarray, pd.Series], impute_order=2) -> Union[np.ndarray, pd.Series]:
+    def smooth(self,
+               signal: Union[np.ndarray, pd.Series],
+               impute_order=2) -> Union[np.ndarray, pd.Series]:
         """Apply a smoother to a signal.
 
         The major workhorse smoothing function. Imputes the nans and then applies
@@ -368,7 +370,7 @@ def savgol_coeffs(self, nl, nr, poly_fit_degree):
         if nr > 0:
             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(poly_fit_degree + 1)]
         ).T
 
@@ -385,7 +387,7 @@ def savgol_coeffs(self, nl, nr, poly_fit_degree):
             coeffs[i] = (mat_inverse @ basis_vector)[0]
         return coeffs
 
-    def savgol_smoother(self, signal):
+    def savgol_smoother(self, signal):  # pylint: disable=inconsistent-return-statements
         """Smooth signal with the savgol smoother.
 
         Returns a convolution of the 1D signal with the Savitzky-Golay coefficients, respecting