add pylintrc file to each indicator

_delphi_utils_python/.pylintrc

@@ -1,8 +1,21 @@
-[DESIGN]
 
-min-public-methods=1
+[MESSAGES CONTROL]
 
+disable=logging-format-interpolation,
+    too-many-locals,
+    too-many-arguments,
+    # Allow pytest functions to be part of a class.
+    no-self-use,
+    # Allow pytest classes to have one test.
+    too-few-public-methods
 
-[MESSAGES CONTROL]
+[BASIC]
+
+# Allow arbitrarily short-named variables.
+variable-rgx=[a-z_][a-z0-9_]*
+argument-rgx=[a-z_][a-z0-9_]*
+
+[DESIGN]
 
-disable=R0801, C0330, E1101, E0611, C0114, C0116, C0103, R0913, R0914, W0702
+# Don't complain about pytest "unused" arguments.
+ignored-argument-names=(_.*|run_as_module)

_template_python/.pylintrc

@@ -0,0 +1,21 @@
+
+[MESSAGES CONTROL]
+
+disable=logging-format-interpolation,
+    too-many-locals,
+    too-many-arguments,
+    # Allow pytest functions to be part of a class.
+    no-self-use,
+    # Allow pytest classes to have one test.
+    too-few-public-methods
+
+[BASIC]
+
+# Allow arbitrarily short-named variables.
+variable-rgx=[a-z_][a-z0-9_]*
+argument-rgx=[a-z_][a-z0-9_]*
+
+[DESIGN]
+
+# Don't complain about pytest "unused" arguments.
+ignored-argument-names=(_.*|run_as_module)

cdc_covidnet/.pylintrc

@@ -0,0 +1,21 @@
+
+[MESSAGES CONTROL]
+
+disable=logging-format-interpolation,
+    too-many-locals,
+    too-many-arguments,
+    # Allow pytest functions to be part of a class.
+    no-self-use,
+    # Allow pytest classes to have one test.
+    too-few-public-methods
+
+[BASIC]
+
+# Allow arbitrarily short-named variables.
+variable-rgx=[a-z_][a-z0-9_]*
+argument-rgx=[a-z_][a-z0-9_]*
+
+[DESIGN]
+
+# Don't complain about pytest "unused" arguments.
+ignored-argument-names=(_.*|run_as_module)

changehc/.pylintrc

@@ -0,0 +1,21 @@
+
+[MESSAGES CONTROL]
+
+disable=logging-format-interpolation,
+    too-many-locals,
+    too-many-arguments,
+    # Allow pytest functions to be part of a class.
+    no-self-use,
+    # Allow pytest classes to have one test.
+    too-few-public-methods
+
+[BASIC]
+
+# Allow arbitrarily short-named variables.
+variable-rgx=[a-z_][a-z0-9_]*
+argument-rgx=[a-z_][a-z0-9_]*
+
+[DESIGN]
+
+# Don't complain about pytest "unused" arguments.
+ignored-argument-names=(_.*|run_as_module)

claims_hosp/.pylintrc

@@ -0,0 +1,21 @@
+
+[MESSAGES CONTROL]
+
+disable=logging-format-interpolation,
+    too-many-locals,
+    too-many-arguments,
+    # Allow pytest functions to be part of a class.
+    no-self-use,
+    # Allow pytest classes to have one test.
+    too-few-public-methods
+
+[BASIC]
+
+# Allow arbitrarily short-named variables.
+variable-rgx=[a-z_][a-z0-9_]*
+argument-rgx=[a-z_][a-z0-9_]*
+
+[DESIGN]
+
+# Don't complain about pytest "unused" arguments.
+ignored-argument-names=(_.*|run_as_module)

combo_cases_and_deaths/.pylintrc

@@ -0,0 +1,21 @@
+
+[MESSAGES CONTROL]
+
+disable=logging-format-interpolation,
+    too-many-locals,
+    too-many-arguments,
+    # Allow pytest functions to be part of a class.
+    no-self-use,
+    # Allow pytest classes to have one test.
+    too-few-public-methods
+
+[BASIC]
+
+# Allow arbitrarily short-named variables.
+variable-rgx=[a-z_][a-z0-9_]*
+argument-rgx=[a-z_][a-z0-9_]*
+
+[DESIGN]
+
+# Don't complain about pytest "unused" arguments.
+ignored-argument-names=(_.*|run_as_module)

emr_hosp/.pylintrc

@@ -0,0 +1,21 @@
+
+[MESSAGES CONTROL]
+
+disable=logging-format-interpolation,
+    too-many-locals,
+    too-many-arguments,
+    # Allow pytest functions to be part of a class.
+    no-self-use,
+    # Allow pytest classes to have one test.
+    too-few-public-methods
+
+[BASIC]
+
+# Allow arbitrarily short-named variables.
+variable-rgx=[a-z_][a-z0-9_]*
+argument-rgx=[a-z_][a-z0-9_]*
+
+[DESIGN]
+
+# Don't complain about pytest "unused" arguments.
+ignored-argument-names=(_.*|run_as_module)

google_health/.pylintrc

@@ -1,8 +1,21 @@
-[DESIGN]
 
-min-public-methods=1
+[MESSAGES CONTROL]
 
+disable=logging-format-interpolation,
+    too-many-locals,
+    too-many-arguments,
+    # Allow pytest functions to be part of a class.
+    no-self-use,
+    # Allow pytest classes to have one test.
+    too-few-public-methods
 
-[MESSAGES CONTROL]
+[BASIC]
+
+# Allow arbitrarily short-named variables.
+variable-rgx=[a-z_][a-z0-9_]*
+argument-rgx=[a-z_][a-z0-9_]*
+
+[DESIGN]
 
-disable=R0801, C0330, E1101, E0611, C0114, C0116, C0103, R0913, R0914, W0702
+# Don't complain about pytest "unused" arguments.
+ignored-argument-names=(_.*|run_as_module)

google_health/delphi_google_health/pull_api.py

@@ -77,7 +77,7 @@ def query(self, start_date: str, end_date: str, geo_id, dma=False) -> dict:
             start_date,
             end_date,
         )
-        data = self.service.getTimelinesForHealth(**params).execute()
+        data = self.service.getTimelinesForHealth(**params).execute() #pylint: disable=no-member
 
         return data
 

google_health/delphi_google_health/smooth.py

@@ -60,11 +60,12 @@ def _left_gauss_linear(s: np.ndarray, h=10, impute=False, minval=None) -> np.nda
 
     n = len(s)
     t = np.zeros_like(s, dtype=np.float64)
-    X = np.vstack([np.ones(n), np.arange(n)]).T
+    X = np.vstack([np.ones(n), np.arange(n)]).T #pylint: disable=invalid-name
     for idx in range(n):
         wts = np.exp(-((np.arange(idx + 1) - idx) ** 2) / (h ** 2))
-        XwX = np.dot(X[: (idx + 1), :].T * wts, X[: (idx + 1), :])
-        Xwy = np.dot(X[: (idx + 1), :].T * wts, s[: (idx + 1)].reshape(-1, 1))
+        XwX = np.dot(X[: (idx + 1), :].T * wts, X[: (idx + 1), :]) #pylint: disable=invalid-name
+        Xwy = np.dot(X[: (idx + 1), :].T * wts, #pylint: disable=invalid-name
+                     s[: (idx + 1)].reshape(-1, 1))
         try:
             beta = np.linalg.solve(XwX, Xwy)
             t[idx] = np.dot(X[: (idx + 1), :], beta)[-1]

jhu/.pylintrc

@@ -1,8 +1,21 @@
-[DESIGN]
 
-min-public-methods=1
+[MESSAGES CONTROL]
 
+disable=logging-format-interpolation,
+    too-many-locals,
+    too-many-arguments,
+    # Allow pytest functions to be part of a class.
+    no-self-use,
+    # Allow pytest classes to have one test.
+    too-few-public-methods
 
-[MESSAGES CONTROL]
+[BASIC]
+
+# Allow arbitrarily short-named variables.
+variable-rgx=[a-z_][a-z0-9_]*
+argument-rgx=[a-z_][a-z0-9_]*
+
+[DESIGN]
 
-disable=R0801, C0330, E1101, E0611, C0114, C0116, C0103, R0913, R0914, W0702
+# Don't complain about pytest "unused" arguments.
+ignored-argument-names=(_.*|run_as_module)

jhu/delphi_jhu/geo.py

@@ -1,7 +1,9 @@
 # -*- coding: utf-8 -*-
+"""Functions for translating between geocodes."""
 import pandas as pd
 from delphi_utils import GeoMapper
 
+VALID_GEO_RES = ("county", "state", "msa", "hrr")
 INCIDENCE_BASE = 100000
 
 def geo_map(df: pd.DataFrame, geo_res: str):
@@ -27,7 +29,6 @@ def geo_map(df: pd.DataFrame, geo_res: str):
         Columns: geo_id, timestamp, ...
     """
     df = df.copy()
-    VALID_GEO_RES = ("county", "state", "msa", "hrr")
     if geo_res not in VALID_GEO_RES:
         raise ValueError(f"geo_res must be one of {VALID_GEO_RES}")
 

jhu/delphi_jhu/pull.py

@@ -1,4 +1,5 @@
 # -*- coding: utf-8 -*-
+"""Functions to pull data from JHU website."""
 
 import pandas as pd
 import numpy as np

jhu/delphi_jhu/run.py

@@ -66,7 +66,7 @@
 
 
 def run_module():
-
+    """Run the JHU indicator module."""
     params = read_params()
     export_start_date = params["export_start_date"]
     export_dir = params["export_dir"]

jhu/delphi_jhu/smooth.py

@@ -1,4 +1,6 @@
 # -*- coding: utf-8 -*-
+'''Functions to smooth signals.'''
+
 import numpy as np
 
 def identity(x):

nchs_mortality/.pylintrc

@@ -1,8 +1,21 @@
-[DESIGN]
 
-min-public-methods=1
+[MESSAGES CONTROL]
 
+disable=logging-format-interpolation,
+    too-many-locals,
+    too-many-arguments,
+    # Allow pytest functions to be part of a class.
+    no-self-use,
+    # Allow pytest classes to have one test.
+    too-few-public-methods
 
-[MESSAGES CONTROL]
+[BASIC]
+
+# Allow arbitrarily short-named variables.
+variable-rgx=[a-z_][a-z0-9_]*
+argument-rgx=[a-z_][a-z0-9_]*
+
+[DESIGN]
 
-disable=R0801, C0330, E1101, E0611, C0114, C0116, C0103, R0913, R0914, W0702
+# Don't complain about pytest "unused" arguments.
+ignored-argument-names=(_.*|run_as_module)

quidel/.pylintrc

@@ -0,0 +1,21 @@
+
+[MESSAGES CONTROL]
+
+disable=logging-format-interpolation,
+    too-many-locals,
+    too-many-arguments,
+    # Allow pytest functions to be part of a class.
+    no-self-use,
+    # Allow pytest classes to have one test.
+    too-few-public-methods
+
+[BASIC]
+
+# Allow arbitrarily short-named variables.
+variable-rgx=[a-z_][a-z0-9_]*
+argument-rgx=[a-z_][a-z0-9_]*
+
+[DESIGN]
+
+# Don't complain about pytest "unused" arguments.
+ignored-argument-names=(_.*|run_as_module)

quidel_covidtest/.pylintrc

@@ -1,8 +1,21 @@
-[DESIGN]
 
-min-public-methods=1
+[MESSAGES CONTROL]
 
+disable=logging-format-interpolation,
+    too-many-locals,
+    too-many-arguments,
+    # Allow pytest functions to be part of a class.
+    no-self-use,
+    # Allow pytest classes to have one test.
+    too-few-public-methods
 
-[MESSAGES CONTROL]
+[BASIC]
+
+# Allow arbitrarily short-named variables.
+variable-rgx=[a-z_][a-z0-9_]*
+argument-rgx=[a-z_][a-z0-9_]*
+
+[DESIGN]
 
-disable=R0801, C0330, E1101, E0611, C0114, C0116, C0103, R0913, R0914, W0702
+# Don't complain about pytest "unused" arguments.
+ignored-argument-names=(_.*|run_as_module)

quidel_covidtest/delphi_quidel_covidtest/generate_sensor.py

@@ -93,7 +93,7 @@ def generate_sensor_for_other_geores(state_groups, data, res_key, smooth,
             res_group = res_group.merge(parent_group, how="left",
                                         on="timestamp", suffixes=('', '_parent'))
             res_group = res_group.drop(columns=[res_key, "state_id", "state_id" + '_parent'])
-        except:
+        except KeyError:
             has_parent = False
             res_group = res_group.drop(columns=[res_key, "state_id"])
         res_group.set_index("timestamp", inplace=True)