Merge pull request #753 from cmu-delphi/fix_linting

Update makefiles to fix linting failures not failing

Author: krivard

_delphi_utils_python/Makefile

@@ -11,9 +11,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

_delphi_utils_python/delphi_utils/export.py

@@ -66,5 +66,4 @@ def create_export_csv(
         if remove_null_samples:
             export_df = export_df[export_df["sample_size"].notnull()]
         export_df.to_csv(export_file, index=False, na_rep="NA")
-    
     return dates

_delphi_utils_python/delphi_utils/geomap.py

@@ -306,7 +306,8 @@ def add_geocode(
         df = df.copy()
         from_col = from_code if from_col is None else from_col
         new_col = new_code if new_col is None else new_col
-        assert from_col != new_col, f"Can't use the same column '{from_col}' for both from_col and to_col"
+        assert from_col != new_col, \
+            f"Can't use the same column '{from_col}' for both from_col and to_col"
         state_codes = ["state_code", "state_id", "state_name"]
 
         if not is_string_dtype(df[from_col]):
@@ -325,7 +326,8 @@ def add_geocode(
             return df
         elif new_code == "nation":
             raise ValueError(
-                f"Conversion to the nation level is not supported from {from_code}; try fips, zip, or state_*"
+                f"Conversion to the nation level is not supported "
+                f"from {from_code}; try fips, zip, or state_*"
             )
 
         # state codes are all stored in one table

_template_python/Makefile

@@ -12,9 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

cdc_covidnet/Makefile

@@ -12,9 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

changehc/Makefile

@@ -12,9 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

changehc/delphi_changehc/run.py

@@ -150,10 +150,9 @@ def run_module():
                 su_inst.update_sensor(
                     data,
                     params["export_dir"]
-                )            
+                )
             logger.info("finished processing", geo = geo)
-    
+
     elapsed_time_in_seconds = round(time.time() - start_time, 2)
     logger.info("Completed indicator run",
         elapsed_time_in_seconds = elapsed_time_in_seconds)
-

claims_hosp/Makefile

@@ -12,10 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir)
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

combo_cases_and_deaths/Makefile

@@ -12,9 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

combo_cases_and_deaths/delphi_combo_cases_and_deaths/run.py

@@ -196,7 +196,7 @@ def run_module():
             df[df["timestamp"] == date_][["geo_id", "val", "se", "sample_size", ]].to_csv(
                 f"{export_dir}/{export_fn}", index=False, na_rep="NA"
             )
-    
+
     elapsed_time_in_seconds = round(time.time() - start_time, 2)
     logger.info("Completed indicator run",
         elapsed_time_in_seconds = elapsed_time_in_seconds)

covid_act_now/Makefile

@@ -12,9 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

google_health/Makefile

@@ -12,8 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

google_symptoms/Makefile

@@ -12,13 +12,11 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
-	. env/bin/activate ;\
-	(cd tests && ../env/bin/pytest --cov=$(dir) --cov-report=term-missing)
+	. env/bin/activate ; (cd tests && ../env/bin/pytest --cov=$(dir) --cov-report=term-missing)
 
 clean:
 	rm -rf env

google_symptoms/delphi_google_symptoms/run.py

@@ -4,22 +4,22 @@
 This module should contain a function called `run_module`, that is executed
 when the module is run with `python -m delphi_google_symptoms`.
 """
+import time
 from datetime import datetime
 from itertools import product
 
 import numpy as np
-import time
 from delphi_utils import (
-    read_params, 
-    create_export_csv, 
+    read_params,
+    create_export_csv,
     geomap,
     get_structured_logger
 )
 
-from .pull import pull_gs_data
-from .geo import geo_map
 from .constants import (METRICS, COMBINED_METRIC,
                         GEO_RESOLUTIONS, SMOOTHERS, SMOOTHERS_MAP)
+from .geo import geo_map
+from .pull import pull_gs_data
 
 
 def run_module():
@@ -66,7 +66,7 @@ def run_module():
                 metric=metric.lower(),
                 geo_res=geo_res,
                 sensor=sensor_name)
-            
+
             if not exported_csv_dates.empty:
                 csv_export_count += exported_csv_dates.size
                 if not oldest_final_export_date:

hhs_facilities/Makefile

@@ -12,9 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

hhs_hosp/Makefile

@@ -12,9 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

jhu/Makefile

@@ -12,9 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

nchs_mortality/Makefile

@@ -12,9 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

nowcast/Makefile

@@ -12,9 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir) --match-dir '(?!nowcast_fusion)'
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir) --match-dir '(?!nowcast_fusion)'
 
 test:
 	. env/bin/activate ;\

quidel/Makefile

@@ -12,9 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\

quidel/delphi_quidel/data_tools.py

@@ -6,7 +6,7 @@
 def _prop_var(p, n):
     """
     Calculate variance of proportion.
-    
+
     var(X/n) = 1/(n^2)var(X) = (npq)/(n^2) = pq/n
     """
     return p * (1 - p) / n
@@ -64,7 +64,7 @@ def _slide_window_sum(arr, k):
 
 def _geographical_pooling(tpooled_tests, tpooled_ptests, min_obs, max_borrow_obs):
     """
-    Calculate proportion of parent samples (tests) that must be "borrowed" in order to compute the statistic.
+    Calculate proportion of parent samples (tests) that must be "borrowed" to compute the statistic.
 
     If there are no samples available in the parent, the borrow_prop is 0.  If the parent does not
     have enough samples, we return a borrow_prop of 1, and the fact that the
@@ -119,7 +119,7 @@ def _geographical_pooling(tpooled_tests, tpooled_ptests, min_obs, max_borrow_obs
 
 def raw_positive_prop(positives, tests, min_obs):
     """
-    Calculate the proportion of positive tests for a single geographic location, without any temporal smoothing.
+    Calculate proportion of positive tests for a single location with no temporal smoothing.
 
     If on any day t, tests[t] < min_obs, then we report np.nan.
 
@@ -172,7 +172,7 @@ def raw_positive_prop(positives, tests, min_obs):
 def smoothed_positive_prop(positives, tests, min_obs, max_borrow_obs, pool_days,
                            parent_positives=None, parent_tests=None):
     """
-    Calculate the proportion of negative tests for a single geographic location, with temporal smoothing.
+    Calculate the proportion of negative tests for a single location with temporal smoothing.
 
     For a given day t, if sum(tests[(t-pool_days+1):(t+1)]) < min_obs, then we
     'borrow' min_obs - sum(tests[(t-pool_days+1):(t+1)]) observations from the
@@ -307,7 +307,7 @@ def raw_tests_per_device(devices, tests, min_obs):
 def smoothed_tests_per_device(devices, tests, min_obs, max_borrow_obs, pool_days,
                               parent_devices=None, parent_tests=None):
     """
-    Calculate the ratio of tests per device for a single geographic location, with temporal smoothing.
+    Calculate the ratio of tests per device for a single location with temporal smoothing.
 
     For a given day t, if sum(tests[(t-pool_days+1):(t+1)]) < min_obs, then we
     'borrow' min_obs - sum(tests[(t-pool_days+1):(t+1)]) observations from the

quidel/delphi_quidel/pull.py

@@ -62,7 +62,7 @@ def read_historical_data():
 
 def regulate_column_names(df, test_type):
     """
-    Regulate column names for flu_ag test data since Quidel changed their column names multiple times.
+    Regulate column names for flu_ag test data since Quidel changed the column names multiple times.
 
     We want to finalize the column name list to be:
         ['SofiaSerNum', 'TestDate', 'Facility',
@@ -311,7 +311,7 @@ def check_intermediate_file(cache_dir, pull_start_dates):
 
 def pull_quidel_data(params):
     """
-    Pull the quidel test data and decide whether to combine the new data with stored historical records in ./cache.
+    Pull new quidel test data and decide whether to combine it with historical records in ./cache.
 
     Parameters:
         params: dict
@@ -402,7 +402,10 @@ def check_export_end_date(input_export_end_dates, _end_date,
 def check_export_start_date(export_start_dates, export_end_dates,
                             export_day_range):
     """
-    Update export_start_date according to the export_end_date so that it could be export_end_date - EXPORT_DAY_RANGE.
+    Update export_start_date according to the export_end_date.
+
+    Update export_start_date according to the export_end_date so that
+    it could be export_end_date - EXPORT_DAY_RANGE.
 
     Parameters:
         export_start_date: dict

quidel/delphi_quidel/run.py

@@ -4,26 +4,27 @@
 This module should contain a function called `run_module`, that is executed
 when the module is run with `python -m MODULE_NAME`.
 """
+import time
 from os.path import join
 
 import pandas as pd
-import time
 from delphi_utils import (
     read_params,
     add_prefix,
     create_export_csv,
     get_structured_logger
 )
 
+from .constants import (END_FROM_TODAY_MINUS, EXPORT_DAY_RANGE,
+                        GEO_RESOLUTIONS, SENSORS)
+from .generate_sensor import (generate_sensor_for_states,
+                              generate_sensor_for_other_geores)
 from .geo_maps import geo_map
 from .pull import (pull_quidel_data,
                    check_export_start_date,
                    check_export_end_date,
                    update_cache_file)
-from .generate_sensor import (generate_sensor_for_states,
-                              generate_sensor_for_other_geores)
-from .constants import (END_FROM_TODAY_MINUS, EXPORT_DAY_RANGE,
-                        GEO_RESOLUTIONS, SENSORS)
+
 
 def run_module():
     """Run Quidel flu test module."""

quidel_covidtest/Makefile

@@ -12,9 +12,8 @@ install: venv
 	pip install -e .
 
 lint:
-	. env/bin/activate; \
-	pylint $(dir); \
-	pydocstyle $(dir)
+	. env/bin/activate; pylint $(dir)
+	. env/bin/activate; pydocstyle $(dir)
 
 test:
 	. env/bin/activate ;\