Release covidcast-indicators 0.3.45

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.44
+current_version = 0.3.45
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

ansible/templates/sir_complainsalot-params-prod.json.j2

@@ -14,8 +14,7 @@
     },
     "chng": {
       "max_age": 6,
-      "maintainers": ["U01AP8GSWG3","U01069KCRS7"],
-      "retired-signals": ["smoothed_outpatient_covid", "smoothed_adj_outpatient_covid", "smoothed_outpatient_cli", "smoothed_adj_outpatient_cli"]
+      "maintainers": ["U01AP8GSWG3","U01069KCRS7"]
     },
     "google-symptoms": {
       "max_age": 6,

changehc/version.cfg

@@ -1 +1 @@
-current_version = 0.3.44
+current_version = 0.3.45

claims_hosp/version.cfg

@@ -1 +1 @@
-current_version = 0.3.44
+current_version = 0.3.45

doctor_visits/version.cfg

@@ -1 +1 @@
-current_version = 0.3.44
+current_version = 0.3.45

google_symptoms/version.cfg

@@ -1 +1 @@
-current_version = 0.3.44
+current_version = 0.3.45

hhs_hosp/version.cfg

@@ -1 +1 @@
-current_version = 0.3.44
+current_version = 0.3.45

nchs_mortality/version.cfg

@@ -1 +1 @@
-current_version = 0.3.44
+current_version = 0.3.45

nowcast/version.cfg

@@ -1 +1 @@
-current_version = 0.3.44
+current_version = 0.3.45

quidel_covidtest/.pylintrc

@@ -9,6 +9,7 @@ disable=logging-format-interpolation,
     no-self-use,
     # Allow pytest classes to have one test.
     too-few-public-methods
+enable=useless-suppression
 
 [BASIC]
 

quidel_covidtest/delphi_quidel_covidtest/geo_maps.py

@@ -75,11 +75,11 @@ def add_parent_state(data, geo_res, geo_key):
     """
     fips_to_state = GMPR.get_crosswalk(from_code="fips", to_code="state")
     if geo_res == "county":
-        mix_map = fips_to_state[["fips", "state_id"]]  # pylint: disable=unsubscriptable-object
+        mix_map = fips_to_state[["fips", "state_id"]]
     else:
         fips_to_geo_res = GMPR.get_crosswalk(from_code="fips", to_code=geo_res)
         mix_map = fips_to_geo_res[["fips", geo_res]].merge(
-                fips_to_state[["fips", "state_id"]],  # pylint: disable=unsubscriptable-object
+                fips_to_state[["fips", "state_id"]],
                 on="fips",
                 how="inner")
         mix_map = GMPR.add_population_column(mix_map, "fips").groupby(

quidel_covidtest/delphi_quidel_covidtest/run.py

@@ -6,6 +6,7 @@
 """
 import atexit
 from datetime import datetime
+from multiprocessing import Manager, Pool, cpu_count, current_process
 import time
 from typing import Dict, Any
 
@@ -55,6 +56,49 @@ def get_smooth_info(sensors, _SMOOTHERS):
             smoothers[sensor] = smoothers.pop(RAW_TEST_PER_DEVICE)
     return smoothers
 
+def generate_and_export_for_nonparent_geo(geo_groups, res_key, smooth, device,
+                                          first_date, last_date, suffix, # generate args
+                                          geo_res, sensor_name, export_dir,
+                                          export_start_date, export_end_date, # export args
+                                          lock, log_filename, log_exceptions): # logger args
+    """Generate sensors, create export CSV then return stats."""
+    # logger cannot be passed to child processes, so has to be recreated
+    with lock:
+        logger = get_structured_logger(__name__, log_filename, log_exceptions)
+        logger.info("Generating signal and exporting to CSV",
+                geo_res=geo_res,
+                sensor=sensor_name,
+                pid=current_process().pid)
+    res_df = generate_sensor_for_nonparent_geo(geo_groups, res_key, smooth, device,
+                                               first_date, last_date, suffix)
+    dates = create_export_csv(res_df, geo_res=geo_res,
+                              sensor=sensor_name, export_dir=export_dir,
+                              start_date=export_start_date,
+                              end_date=export_end_date)
+    return dates
+
+def generate_and_export_for_parent_geo(geo_groups, geo_data, res_key, smooth, device,
+                                       first_date, last_date, suffix, # generate args
+                                       geo_res, sensor_name, export_dir,
+                                       export_start_date, export_end_date, # export args
+                                       lock, log_filename, log_exceptions): # logger args
+    """Generate sensors, create export CSV then return stats."""
+    # logger cannot be passed to child processes, so has to be recreated
+    with lock:
+        logger = get_structured_logger(__name__, log_filename, log_exceptions)
+        logger.info("Generating signal and exporting to CSV",
+                    geo_res=geo_res,
+                    sensor=sensor_name,
+                    pid=current_process().pid)
+    res_df = generate_sensor_for_parent_geo(geo_groups, geo_data, res_key, smooth, device,
+                                            first_date, last_date, suffix)
+    dates = create_export_csv(res_df, geo_res=geo_res,
+                              sensor=sensor_name, export_dir=export_dir,
+                              start_date=export_start_date,
+                              end_date=export_end_date,
+                              remove_null_samples=True) # for parent geo, remove null sample size
+    return dates
+
 def run_module(params: Dict[str, Any]):
     """Run the quidel_covidtest indicator.
 
@@ -123,53 +167,71 @@ def run_module(params: Dict[str, Any]):
                          wip_signal=params["indicator"]["wip_signal"],
                          prefix="wip_")
     smoothers = get_smooth_info(sensors, SMOOTHERS)
-    for geo_res in NONPARENT_GEO_RESOLUTIONS:
-        geo_data, res_key = geo_map(geo_res, data)
-        geo_groups = geo_data.groupby(res_key)
-        for agegroup in AGE_GROUPS:
-            for sensor in sensors:
-                if agegroup == "total":
-                    sensor_name = sensor
-                else:
-                    sensor_name = "_".join([sensor, agegroup])
-                logger.info("Generating signal and exporting to CSV",
-                            geo_res=geo_res,
-                            sensor=sensor_name)
-                state_df = generate_sensor_for_nonparent_geo(
-                    geo_groups, res_key, smooth=smoothers[sensor][1],
-                    device=smoothers[sensor][0], first_date=first_date,
-                    last_date=last_date, suffix=agegroup)
-                dates = create_export_csv(
-                    state_df,
-                    geo_res=geo_res,
-                    sensor=sensor_name,
-                    export_dir=export_dir,
-                    start_date=export_start_date,
-                    end_date=export_end_date)
-                if len(dates) > 0:
-                    stats.append((max(dates), len(dates)))
-    assert geo_res == "state" # Make sure geo_groups is for state level
-    # County/HRR/MSA level
-    for geo_res in PARENT_GEO_RESOLUTIONS:
-        geo_data, res_key = geo_map(geo_res, data)
-        for agegroup in AGE_GROUPS:
-            for sensor in sensors:
-                if agegroup == "total":
-                    sensor_name = sensor
-                else:
-                    sensor_name = "_".join([sensor, agegroup])
-                logger.info("Generating signal and exporting to CSV",
-                            geo_res=geo_res,
-                            sensor=sensor_name)
-                res_df = generate_sensor_for_parent_geo(
-                    geo_groups, geo_data, res_key, smooth=smoothers[sensor][1],
-                    device=smoothers[sensor][0], first_date=first_date,
-                    last_date=last_date, suffix=agegroup)
-                dates = create_export_csv(res_df, geo_res=geo_res,
-                                          sensor=sensor_name, export_dir=export_dir,
-                                          start_date=export_start_date,
-                                          end_date=export_end_date,
-                                          remove_null_samples=True)
+    n_cpu = min(8, cpu_count()) # for parallelization
+    with Manager() as manager:
+        # for using loggers in multiple threads
+        # disabled due to a Pylint bug, resolved by version bump (#1886)
+        lock = manager.Lock() # pylint: disable=no-member
+        logger.info("Parallelizing sensor generation", n_cpu=n_cpu)
+        with Pool(n_cpu) as pool:
+            pool_results = []
+            for geo_res in NONPARENT_GEO_RESOLUTIONS:
+                geo_data, res_key = geo_map(geo_res, data)
+                geo_groups = geo_data.groupby(res_key)
+                for agegroup in AGE_GROUPS:
+                    for sensor in sensors:
+                        if agegroup == "total":
+                            sensor_name = sensor
+                        else:
+                            sensor_name = "_".join([sensor, agegroup])
+                        pool_results.append(
+                            pool.apply_async(
+                                generate_and_export_for_nonparent_geo,
+                                args=(
+                                    # generate_sensors_for_parent_geo
+                                    geo_groups, res_key,
+                                    smoothers[sensor][1], smoothers[sensor][0],
+                                    first_date, last_date, agegroup,
+                                    # create_export_csv
+                                    geo_res, sensor_name, export_dir,
+                                    export_start_date, export_end_date,
+                                    # logger params
+                                    lock,
+                                    params["common"].get("log_filename"),
+                                    params["common"].get("log_exceptions", True)
+                                )
+                            )
+                        )
+            assert geo_res == "state" # Make sure geo_groups is for state level
+            # County/HRR/MSA level
+            for geo_res in PARENT_GEO_RESOLUTIONS:
+                geo_data, res_key = geo_map(geo_res, data) # using the last geo_groups
+                for agegroup in AGE_GROUPS:
+                    for sensor in sensors:
+                        if agegroup == "total":
+                            sensor_name = sensor
+                        else:
+                            sensor_name = "_".join([sensor, agegroup])
+                        pool_results.append(
+                            pool.apply_async(
+                                generate_and_export_for_parent_geo,
+                                args=(
+                                    # generate_sensors_for_parent_geo
+                                    geo_groups, geo_data, res_key,
+                                    smoothers[sensor][1], smoothers[sensor][0],
+                                    first_date, last_date, agegroup,
+                                    # create_export_csv
+                                    geo_res, sensor_name, export_dir,
+                                    export_start_date, export_end_date,
+                                    # logger params
+                                    lock,
+                                    params["common"].get("log_filename"),
+                                    params["common"].get("log_exceptions", True)
+                                )
+                            )
+                        )
+            pool_results = [proc.get() for proc in pool_results]
+            for dates in pool_results:
                 if len(dates) > 0:
                     stats.append((max(dates), len(dates)))
 

quidel_covidtest/version.cfg

@@ -1 +1 @@
-current_version = 0.3.44
+current_version = 0.3.45

sir_complainsalot/version.cfg

@@ -1 +1 @@
-current_version = 0.3.44
+current_version = 0.3.45