Release Delphi Epidata 4.1.38

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.1.37
+current_version = 4.1.38
 commit = False
 tag = False
 

dev/local/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 4.1.37
+version = 4.1.38
 
 [options]
 packages =

docs/symptom-survey/publications.md

@@ -26,6 +26,10 @@ Pandemic"](https://www.pnas.org/topic/548) in *PNAS*:
 
 Research publications using the survey data include:
 
+- S. Pampati, E.A. Stuart, J. Lessler et al (2024). [Impact of School-Based
+  Infection Prevention Strategies on Household COVID-19 and Respiratory
+  Disease Outcomes: a Cross-Sectional Study](https://doi.org/10.1016/j.annepidem.2025.10.019).
+  *Annals of Epidemiology*.
 - K.B. Smith, S. Shen, and B.T. Denton (2025). [Can past variants of SARS-CoV-2
   predict the impact of future variants? Machine learning for early warning
   of US counties at risk](https://doi.org/10.1007/s10729-025-09728-4).

src/acquisition/fluview/impute_missing_values.py

@@ -293,7 +293,11 @@ def impute_missing_values(database, test_mode=False):
             known_values["pr"] = (0, 0, 0)
 
         # get the imputation matrix and lists of known and unknown locations
-        F, known, unknown = get_fusion_parameters(known_values.keys())
+        try:
+            F, known, unknown = get_fusion_parameters(known_values.keys())
+        except StatespaceException as e:
+            print(e)
+            continue
 
         # finally, impute the missing values
         z = np.array([known_values[k] for k in known])

src/client/delphi_epidata.R

@@ -15,7 +15,7 @@ Epidata <- (function() {
   # API base url
   BASE_URL <- getOption('epidata.url', default = 'https://api.delphi.cmu.edu/epidata/')
 
-  client_version <- '4.1.37'
+  client_version <- '4.1.38'
 
   auth <- getOption("epidata.auth", default = NA)
 

src/client/delphi_epidata.js

@@ -22,7 +22,7 @@
   }
 })(this, function (exports, fetchImpl, jQuery) {
   const BASE_URL = "https://api.delphi.cmu.edu/epidata/";
-  const client_version = "4.1.37";
+  const client_version = "4.1.38";
 
   // Helper function to cast values and/or ranges to strings
   function _listitem(value) {

src/client/packaging/npm/package.json

@@ -2,7 +2,7 @@
   "name": "delphi_epidata",
   "description": "Delphi Epidata API Client",
   "authors": "Delphi Group",
-  "version": "4.1.37",
+  "version": "4.1.38",
   "license": "MIT",
   "homepage": "https://github.com/cmu-delphi/delphi-epidata",
   "bugs": {

src/ddl/migrations/flusurv_age_sex_race_strata.sql

@@ -1,23 +1,23 @@
 -- Add new age, race, and sex strata, and season descriptor (YYYY-YY format)
 ALTER TABLE `flusurv` ADD (
-  `rate_age_18t29` double DEFAULT NULL,
-  `rate_age_30t39` double DEFAULT NULL,
-  `rate_age_40t49` double DEFAULT NULL,
-  `rate_age_5t11` double DEFAULT NULL,
-  `rate_age_12t17` double DEFAULT NULL,
-  `rate_age_lt18` double DEFAULT NULL,
-  `rate_age_gte18` double DEFAULT NULL,
-  `rate_race_white` double DEFAULT NULL,
-  `rate_race_black` double DEFAULT NULL,
-  `rate_race_hisp` double DEFAULT NULL,
-  `rate_race_asian` double DEFAULT NULL,
-  `rate_race_natamer` double DEFAULT NULL,
-  `rate_sex_male` double DEFAULT NULL,
-  `rate_sex_female` double DEFAULT NULL,
-  `rate_age_0tlt1` double DEFAULT NULL,
-  `rate_age_1t4` double DEFAULT NULL,
-  `rate_age_gte75` double DEFAULT NULL,
-  `rate_flu_a` double DEFAULT NULL,
-  `rate_flu_b` double DEFAULT NULL,
-  `season` char(7) DEFAULT NULL,
+    `season` char(7) DEFAULT NULL,
+    `rate_age_18t29` double DEFAULT NULL,
+    `rate_age_30t39` double DEFAULT NULL,
+    `rate_age_40t49` double DEFAULT NULL,
+    `rate_age_5t11` double DEFAULT NULL,
+    `rate_age_12t17` double DEFAULT NULL,
+    `rate_age_lt18` double DEFAULT NULL,
+    `rate_age_gte18` double DEFAULT NULL,
+    `rate_age_1t4` double DEFAULT NULL,
+    `rate_age_gte75` double DEFAULT NULL,
+    `rate_age_0tlt1` double DEFAULT NULL,
+    `rate_race_white` double DEFAULT NULL,
+    `rate_race_black` double DEFAULT NULL,
+    `rate_race_hisp` double DEFAULT NULL,
+    `rate_race_asian` double DEFAULT NULL,
+    `rate_race_natamer` double DEFAULT NULL,
+    `rate_sex_male` double DEFAULT NULL,
+    `rate_sex_female` double DEFAULT NULL,
+    `rate_flu_a` double DEFAULT NULL,
+    `rate_flu_b` double DEFAULT NULL
 );

src/server/_config.py

@@ -7,7 +7,7 @@
 
 load_dotenv()
 
-VERSION = "4.1.37"
+VERSION = "4.1.38"
 
 MAX_RESULTS = int(10e6)
 MAX_COMPATIBILITY_RESULTS = int(3650)

tests/acquisition/fluview/test_impute_missing_values.py

@@ -2,16 +2,17 @@
 
 # standard library
 import argparse
+import sys
 import unittest
 from unittest.mock import MagicMock
+from io import StringIO
 
 # first party
 from delphi.utils.geo.locations import Locations
 from delphi.epidata.acquisition.fluview.impute_missing_values import (
     get_argument_parser,
     get_lag_and_ili,
     impute_missing_values,
-    StatespaceException,
 )
 
 # py3tester coverage target
@@ -87,8 +88,12 @@ def test_impute_missing_values_vipr(self):
         db.get_known_values.return_value = known_data
 
         db.find_missing_rows.return_value = [(201340, 201340)]
-        with self.assertRaises(Exception):
-            impute_missing_values(db, test_mode=True)
+
+        capturedOutput = StringIO()
+        sys.stdout = capturedOutput
+        impute_missing_values(db, test_mode=True)
+        sys.stdout = sys.__stdout__
+        self.assertTrue("system is underdetermined" in capturedOutput.getvalue().split("\n"))
 
         db.find_missing_rows.return_value = [(201339, 201339)]
         impute_missing_values(db, test_mode=True)
@@ -131,5 +136,8 @@ def test_impute_missing_values_underdetermined(self):
         db.find_missing_rows.return_value = [(201740, 201740)]
         db.get_known_values.return_value = known_data
 
-        with self.assertRaises(StatespaceException):
-            impute_missing_values(db, test_mode=True)
+        capturedOutput = StringIO()
+        sys.stdout = capturedOutput
+        impute_missing_values(db, test_mode=True)
+        sys.stdout = sys.__stdout__
+        self.assertTrue("system is underdetermined" in capturedOutput.getvalue().split("\n"))