Merge pull request #1744 from cmu-delphi/release/indicators_v0.3.28_utils_v0.3.7

Release covidcast-indicators 0.3.28

Author: krivard

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.27
+current_version = 0.3.28
 commit = True
 message = chore: bump covidcast-indicators to {new_version}
 tag = False

.github/workflows/create-release.yml

@@ -58,7 +58,13 @@ jobs:
         id: indicators
         run: |
           echo -n "::set-output name=version::"
-          bump2version --list ${{ github.event.inputs.versionName }} | grep ^new_version | sed -r s,"^.*=",,       
+          bump2version --list ${{ github.event.inputs.versionName }} | grep ^new_version | sed -r s,"^.*=",,
+      - name: Copy version to indicator directory
+        run: |
+          indicator_list=("changehc" "claims_hosp" "doctor_visits" "dsew_community_profile" "google_symptoms" "hhs_hosp" "jhu" "nchs_mortality" "nowcast" "quidel_covidtest" "sir_complainsalot")
+          for path in ${indicator_list[@]}; do
+            echo "current_version = ${{ steps.indicators.outputs.version }}" > $path/version.cfg
+          done
       - name: Create pull request into prod
         uses: peter-evans/create-pull-request@v3
         with:

_delphi_utils_python/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.6
+current_version = 0.3.7
 commit = True
 message = chore: bump delphi_utils to {new_version}
 tag = False

_delphi_utils_python/delphi_utils/__init__.py

@@ -15,4 +15,4 @@
 from .nancodes import Nans
 from .weekday import Weekday
 
-__version__ = "0.3.6"
+__version__ = "0.3.7"

_delphi_utils_python/delphi_utils/runner.py

@@ -1,6 +1,7 @@
 """Indicator running utilities."""
 import argparse as ap
 import importlib
+import os
 from typing import Any, Callable, Dict, Optional
 from .archive import ArchiveDiffer, archiver_from_params
 from .logger import get_structured_logger
@@ -40,6 +41,21 @@ def run_indicator_pipeline(indicator_fn:  Callable[[Params], None],
         name=indicator_fn.__module__,
         filename=params["common"].get("log_filename", None),
         log_exceptions=params["common"].get("log_exceptions", True))
+
+    #Get version and indicator name for startup
+    ind_name = indicator_fn.__module__.replace(".run", "")
+    #Check for version.cfg in indicator directory
+    if os.path.exists("version.cfg"):
+        with open("version.cfg") as ver_file:
+            current_version = "not found"
+            for line in ver_file:
+                if "current_version" in line:
+                    current_version = str.strip(line)
+                    current_version = current_version.replace("current_version = ", "")
+    #Logging - Starting Indicator
+        logger.info(f"Started {ind_name} with covidcast-indicators version {current_version}")
+    else: logger.info(f"Started {ind_name} without version.cfg")
+
     indicator_fn(params)
     validator = validator_fn(params)
     archiver = archiver_fn(params)

_delphi_utils_python/setup.py

@@ -26,7 +26,7 @@
 
 setup(
     name="delphi_utils",
-    version="0.3.6",
+    version="0.3.7",
     description="Shared Utility Functions for Indicators",
     long_description=long_description,
     long_description_content_type="text/markdown",

changehc/version.cfg

@@ -0,0 +1 @@
+current_version = 0.3.28

claims_hosp/version.cfg

@@ -0,0 +1 @@
+current_version = 0.3.28

doctor_visits/version.cfg

@@ -0,0 +1 @@
+current_version = 0.3.28

dsew_community_profile/version.cfg

@@ -0,0 +1 @@
+current_version = 0.3.28

google_symptoms/delphi_google_symptoms/constants.py

@@ -45,7 +45,10 @@
                                    impute_method='zeros'), lambda d: d)
 }
 
-
+DTYPE_CONVERSIONS = {'open_covid_region_code':'string','date': 'datetime64'}
+for index, symptom in enumerate(METRICS):
+    key = "symptom_" + METRICS[index].replace(" ","_")
+    DTYPE_CONVERSIONS[key] = "float"
 
 STATE_TO_ABBREV = {'Alabama': 'al',
                    'Alaska': 'ak',

google_symptoms/delphi_google_symptoms/pull.py

@@ -7,7 +7,7 @@
 import numpy as np
 import pandas as pd
 
-from .constants import DC_FIPS, METRICS, COMBINED_METRIC, SYMPTOM_SETS
+from .constants import DC_FIPS, METRICS, COMBINED_METRIC, SYMPTOM_SETS, DTYPE_CONVERSIONS
 
 
 # Create map of BigQuery symptom column names to desired column names.
@@ -223,7 +223,7 @@ def pull_gs_data_one_geolevel(level, date_range):
     """
     query = produce_query(level, date_range)
 
-    df = pandas_gbq.read_gbq(query, progress_bar_type=None)
+    df = pandas_gbq.read_gbq(query, progress_bar_type=None, dtypes = DTYPE_CONVERSIONS)
 
     if len(df) == 0:
         df = pd.DataFrame(

google_symptoms/version.cfg

@@ -0,0 +1 @@
+current_version = 0.3.28

hhs_hosp/version.cfg

@@ -0,0 +1 @@
+current_version = 0.3.28

jhu/version.cfg

@@ -0,0 +1 @@
+current_version = 0.3.28

nchs_mortality/version.cfg

@@ -0,0 +1 @@
+current_version = 0.3.28

nowcast/version.cfg

@@ -0,0 +1 @@
+current_version = 0.3.28

quidel_covidtest/version.cfg

@@ -0,0 +1 @@
+current_version = 0.3.28

sir_complainsalot/version.cfg

@@ -0,0 +1 @@
+current_version = 0.3.28