Merge pull request #1580 from cmu-delphi/dev

Remove JHU signals from documentation

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.1.27
+current_version = 4.1.28
 commit = False
 tag = False
 

.github/workflows/performance-tests-one-time.yml

@@ -23,14 +23,6 @@ jobs:
       max_time: ${{ steps.output.outputs.max_time }}
       requests_per_sec: ${{ steps.output.outputs.requests_per_sec }}
     steps:
-      - name: Set up WireGuard
-        uses: egor-tensin/[email protected]
-        with:
-          endpoint: '${{ secrets.WG_PERF_ENDPOINT }}'
-          endpoint_public_key: '${{ secrets.WG_PERF_ENDPOINT_PUBLIC_KEY }}'
-          ips: '${{ secrets.WG_PERF_IPS }}'
-          allowed_ips: '${{ secrets.WG_PERF_ALLOWED_IPS }}'
-          private_key: '${{ secrets.WG_PERF_PRIVATE_KEY }}'
       - name: Clean files from previous runs
         uses: AutoModality/action-clean@v1
       - name: Check out repository

.github/workflows/performance-tests.yml

@@ -25,14 +25,6 @@ jobs:
       max_time: ${{ steps.output.outputs.max_time }}
       requests_per_sec: ${{ steps.output.outputs.requests_per_sec }}
     steps:
-      - name: Set up WireGuard
-        uses: egor-tensin/[email protected]
-        with:
-          endpoint: '${{ secrets.WG_PERF_ENDPOINT }}'
-          endpoint_public_key: '${{ secrets.WG_PERF_ENDPOINT_PUBLIC_KEY }}'
-          ips: '${{ secrets.WG_PERF_IPS }}'
-          allowed_ips: '${{ secrets.WG_PERF_ALLOWED_IPS }}'
-          private_key: '${{ secrets.WG_PERF_PRIVATE_KEY }}'
       - name: Clean files from previous runs
         uses: AutoModality/action-clean@v1
       - name: Check out repository

dev/local/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 4.1.27
+version = 4.1.28
 
 [options]
 packages =

docs/api/covidcast-signals/nssp.md

@@ -19,11 +19,8 @@ nav_order: 1
 
 [The National Syndromic Surveillance Program (NSSP)](https://www.cdc.gov/nssp/php/about/index.html) is an effort to track epidemiologically relevant conditions.
 This dataset in particular tracks emergency department (ED) visits arising from a subset of influenza-like illnesses, specifically influenza, COVID-19, and respiratory syncytial virus (RSV).
-Each signal below is derived from one of two following datasets:
-- Primary: [NSSP Emergency Department Visit Trajectories by State and Sub State Regions- COVID-19, Flu, RSV, Combined dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data)
-- Secondary: [2023 Respiratory Virus Response - NSSP Emergency Department Visit Trajectories by State- COVID-19, Flu, RSV, Combined](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/7mra-9cq9/data_preview). Signals derived from the secondary dataset have suffix `_2023RVR` in their signal names.
-
-Both datasets started reporting data in late 2022. As of May 2024, NSSP received data from 78% of US EDs.
+It is derived from the CDC's [Respiratory Virus Response NSSP Emergency Department Visit Trajectories dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data), which started reporting data in late 2022.
+As of May 2024, NSSP received data from 78% of US EDs.
 
 | Signal                          | Description                                                                                                                          |
 |---------------------------------|--------------------------------------------------------------------------------------------------------------------------------------|
@@ -35,10 +32,6 @@ Both datasets started reporting data in late 2022. As of May 2024, NSSP received
 | `smoothed_pct_ed_visits_influenza` | 3 week moving average of `pct_ed_visits_influenza`   <br/> **Earliest date available:** 2022-10-01                                      |
 | `smoothed_pct_ed_visits_rsv`       | 3 week moving average of `pct_ed_visits_rsv`   <br/> **Earliest date available:** 2022-10-01                                            |
 | `smoothed_pct_ed_visits_combined`  | 3 week moving average of `pct_ed_visits_combined`   <br/> **Earliest date available:** 2022-10-01                                       |
-| `pct_ed_visits_covid_2023RVR`              | Percent of ED visits that had a discharge diagnosis code of COVID-19 <br/> **Earliest date available:** 2022-10-01                      |
-| `pct_ed_visits_influenza_2023RVR`          | Percent of ED visits that had a discharge diagnosis code of influenza  <br/> **Earliest date available:** 2022-10-01                 |
-| `pct_ed_visits_rsv_2023RVR`                | Percent of ED visits that had a discharge diagnosis code of rsv  <br/> **Earliest date available:** 2022-10-01                       |
-| `pct_ed_visits_combined_2023RVR`           | Percent of ED visits that had a discharge diagnosis code of COVID-19, influenza, or rsv   <br/> **Earliest date available:** 2022-10-01 |
 
 ## Table of Contents
 {: .no_toc .text-delta}
@@ -49,8 +42,7 @@ Both datasets started reporting data in late 2022. As of May 2024, NSSP received
 ## Estimation
 
 The percent visits signals are calculated as a fraction of visits at facilities reporting to NSSP, rather than all facilities in the area.
-For primary signals, `county`, `state` and `nation` level data is reported as-is from NSSP, without modification, while `hhs`, `hrr` and `msa` are estimated by Delphi.
-For secondary signals, `state`, `hhs` and `nation` level data is reported as-is from NSSP, without modification.
+`county`, `state` and `nation` level data is reported as-is from NSSP, without modification, while `hhs`, `hrr` and `msa` are estimated by Delphi.
 
 ### Geographic weighting
 As the original data is a percentage and raw case counts are not available, `hrr`,`msa`, and `hhs` values are computed from county-level data using a weighted mean. Each county is assigned a weight equal to its population in the last census (2020). Unreported counties are implicitly treated as having a weight of 0 or a value equal to the group mean.
@@ -112,4 +104,4 @@ Some low population counties occasionally report outliers, e.g. 33.33%, 50%, 100
 This source is derived from the CDC's [Respiratory Virus Response NSSP Emergency Department Visit Trajectories dataset](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/rdmq-nq56/about_data).
 There is another version of the dataset that includes [state data only](https://data.cdc.gov/Public-Health-Surveillance/2023-Respiratory-Virus-Response-NSSP-Emergency-Dep/7mra-9cq9/about_data).
 
-This data was originally published by the CDC, and is made available here as a convenience to the forecasting community under the terms of the original license, which is [U.S. Government Public Domain](https://www.usa.gov/government-copyright).
+This data was originally published by the CDC, and is made available here as a convenience to the forecasting community under the terms of the original license, which is [U.S. Government Public Domain](https://www.usa.gov/government-copyright).

docs/symptom-survey/publications.md

@@ -26,17 +26,24 @@ Pandemic"](https://www.pnas.org/topic/548) in *PNAS*:
 
 Research publications using the survey data include:
 
+- S. Santos, M. Humbard, A. Lambrou et al. (2025). [The SARS-CoV-2 test
+  scale-up in the USA: an analysis of the number of tests produced and used
+  over time and their modelled impact on the COVID-19 pandemic](https://doi.org/10.1016/S2468-2667(24)00279-2).
+  *The Lancet Public Health* 10 (1), e47-e57.
+- H. Bui, S. Ekşioğlu, R. Proano, and S. N. Pinkley (2025). [An Analysis of
+  COVID-19 Vaccine Hesitancy in the U.S.](https://doi.org/10.1080/24725854.2024.2301966).
+  *IISE Transactions* 57 (3), 246-260.
 - K.M. Geffel, H.P. Dyer, A.D. Casas, S.N. Christian-Afflu, D.D. Méndez, and
   T.L. Gary-Webb (2024). [COVID-19 vaccine uptake and intention of Black adults:
   A county-wide analysis of an online survey](https://doi.org/10.1016/j.jnma.2024.07.007).
-  *Journal of the National Medical Association*.
+  *Journal of the National Medical Association* 116 (5), 526-538.
 - C.K. Ettman, E. Badillo-Goicoechea, E.A. Stuart, and L.T. Dean (2024).
   [Area-level credit scores and symptoms of depression and anxiety in adults](https://doi.org/10.1093/aje/kwae275).
   *American Journal of Epidemiology* kwae275.
 - C.K. Ettman, E. Badillo-Goicoechea, E.A. Stuart (2024). [Financial
   strain, schooling modality and mental health of US adults living
   with children during the COVID-19 pandemic](https://doi.org/10.1136/jech-2023-221672).
-  *Journal of Epidemiology & Community Health*.
+  *Journal of Epidemiology & Community Health* 78 (10), 662-668.
 - K. Sasse, R. Mahabir, O. Gkountouna, A. Crooks, A. Croitoru (2024).
   [Understanding the determinants of vaccine hesitancy in the United
   States: A comparison of social surveys and social media](https://doi.org/10.1371/journal.pone.0301488).
@@ -68,10 +75,8 @@ Research publications using the survey data include:
   *Social Science & Medicine* 348, 116775.
 - R.R. Andridge (2024). [Using proxy pattern-mixture models to explain bias in
   estimates of COVID-19 vaccine uptake from two large surveys](https://doi.org/10.1093/jrsssa/qnae005).
-  *Journal of the Royal Statistical Society Series A: Statistics in Society*.
-- H. Bui, S. Ekşioğlu, R. Proano, and S. N. Pinkley (2024). [An Analysis of
-  COVID-19 Vaccine Hesitancy in the U.S.](https://doi.org/10.1080/24725854.2024.2301966).
-  *IISE Transactions*.
+  *Journal of the Royal Statistical Society Series A: Statistics in Society*
+  187 (3), 831-843.
 - de Vries, M., Kim, J.Y. & Han, H. (2023). [The unequal landscape of civic
   opportunity in America](https://doi.org/10.1038/s41562-023-01743-1). *Nature
   Human Behavior* 8, 256-263. 

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 <- '4.1.27'
+  client_version <- '4.1.28'
 
   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 = "4.1.27";
+  const client_version = "4.1.28";
 
   // 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": "4.1.27",
+  "version": "4.1.28",
   "license": "MIT",
   "homepage": "https://github.com/cmu-delphi/delphi-epidata",
   "bugs": {

src/server/_config.py

@@ -7,7 +7,7 @@
 
 load_dotenv()
 
-VERSION = "4.1.27"
+VERSION = "4.1.28"
 
 MAX_RESULTS = int(10e6)
 MAX_COMPATIBILITY_RESULTS = int(3650)

tests/server/test_pandas.py

@@ -2,7 +2,7 @@
 
 # standard library
 import unittest
-from mock import patch, sentinel, ANY
+from unittest.mock import patch, sentinel, ANY
 
 # first party
 from delphi.epidata.server.main import app