Merge pull request #1250 from cmu-delphi/release/delphi-epidata-4.1.7

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.1.6
+current_version = 4.1.7
 commit = False
 tag = False
 

.github/workflows/create-release.yml

@@ -39,7 +39,7 @@ jobs:
           base: main
           title: Release Delphi Epidata ${{ steps.version.outputs.next_tag }}
           labels: chore
-          reviewers: krivard
-          assignees: krivard
+          reviewers: melange396
+          assignees: melange396
           body: |
             Releasing Delphi Epidata ${{ steps.version.outputs.next_tag }}.

.github/workflows/dependabot-assignments.yml

@@ -7,11 +7,11 @@ permissions:
 jobs:
   dependabot:
     runs-on: ubuntu-latest
-    env: 
-        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+    env:
+      GH_TOKEN: ${{ secrets.CMU_DELPHI_AUTOMATION_MACHINE_DEPENDABOT_PAT }}
     if: ${{ github.actor == 'dependabot[bot]' }}
     steps:
       - name: Assign team to PR
         run: gh pr edit "$PR_URL" --add-reviewer "cmu-delphi/code-reviewers"
         env:
-          PR_URL: ${{github.event.pull_request.html_url}}
+          PR_URL: ${{github.event.pull_request.html_url}}

.github/workflows/release-helper.yml

@@ -147,7 +147,7 @@ jobs:
           base: dev
           title: "chore: sync main->dev"
           labels: chore
-          reviewers: krivard
-          assignees: krivard
+          reviewers: melange396
+          assignees: melange396
           body: |
             Syncing Main->Dev.

.github/workflows/update_gdocs_data.yml

@@ -31,7 +31,7 @@ jobs:
           commit-message: 'chore: update docs'
           title: Update Google Docs Meta Data
           labels: chore
-          reviewers: krivard
-          assignees: krivard
+          reviewers: melange396
+          assignees: melange396
           body: |
             Updating Google Docs Meta Data

deploy.json

@@ -217,6 +217,16 @@
       "add-header-comment": true
     },
 
+    "// maintenance",
+    {
+      "type": "move",
+      "src": "src/maintenance/",
+      "dst": "[[package]]/maintenance/",
+      "match": "^.*\\.(py)$",
+      "recursive": true,
+      "add-header-comment": true
+    },
+
     "// move flask tests out of the way",
     {
       "type": "move",

dev/local/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 4.1.6
+version = 4.1.7
 
 [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:
 
+- Kobayashi H, Saenz-Escarcega R, Fulk A, Agusto FB (2023). [Understanding
+  mental health trends during COVID-19 pandemic in the United States using
+  network analysis](https://doi.org/10.1371/journal.pone.0286857). *PLoS
+  ONE* 18(6): e0286857. 
 - GK Charles, SP Braunstein, JL Barker, et al (2023). [How do psychobehavioural
   variables shed light on heterogeneity in COVID-19 vaccine acceptance? Evidence
   from United States general population surveys on a probability panel and
@@ -43,7 +47,7 @@ Research publications using the survey data include:
 - M. Rubinstein, A. Haviland, and J. Breslau (2023). [The effect of COVID-19
   vaccinations on self-reported depression and anxiety during February
   2021](https://doi.org/10.1080/2330443X.2023.2190008). *Statistics and Public
-  Policy.*
+  Policy* 10 (1), 2190008.
 - Rönn MM, Menzies NA, Salomon JA (2023). [Vaccination and voting patterns in
   the United States: analysis of COVID-19 and flu surveys from 2010 to
   2022](https://doi.org/10.1016/j.amepre.2023.03.001). *American Journal of
@@ -69,15 +73,15 @@ Research publications using the survey data include:
   over time: Culture, uncertainty avoidance, and vaccine side-effect
   concerns](https://doi.org/10.1037/pspa0000320). *Journal of Personality and
   Social Psychology* 124 (4), 683-706.
+- C. Lupton-Smith, E. Badillo Goicoechea, M. Collins, J. Lessler, M. K.
+  Grabowski & E. A. Stuart (2023). [Consistency between Household and County
+  Measures of Onsite Schooling during the COVID-19
+  Pandemic](https://doi.org/10.1080/19345747.2022.2131660). *Journal of Research
+  on Educational Effectiveness* 16 (3), 419-441.
 - Rader, B., Astley, C.M., Sewalk, K. et al (2022). [Spatial modeling of vaccine
   deserts as barriers to controlling
   SARS-CoV-2](https://doi.org/10.1038/s43856-022-00183-8). *Communications
   Medicine* 2, 141.
-- C. Lupton-Smith, E. Badillo Goicoechea, M. Collins, J. Lessler, M. K.
-  Grabowski & E. A. Stuart (2022). [Consistency between Household and County
-  Measures of Onsite Schooling during the COVID-19
-  Pandemic](https://doi.org/10.1080/19345747.2022.2131660). *Journal of Research
-  on Educational Effectiveness*.
 - Nguyen, Q.C., Yardi, I., Gutierrez, F.X.M. et al. (2022). [Leveraging 13
   million responses to the U.S. COVID-19 Trends and Impact Survey to examine
   vaccine hesitancy, vaccination, and mask wearing, January 2021-February

integrations/acquisition/covidcast/test_covidcast_meta_caching.py

@@ -13,7 +13,7 @@
 from delphi.epidata.client.delphi_epidata import Epidata
 import delphi.operations.secrets as secrets
 import delphi.epidata.acquisition.covidcast.database as live
-from delphi.epidata.acquisition.covidcast.covidcast_meta_cache_updater import main
+from delphi.epidata.maintenance.covidcast_meta_cache_updater import main
 
 # py3tester coverage target (equivalent to `import *`)
 __test_target__ = (

integrations/client/test_delphi_epidata.py

@@ -11,7 +11,7 @@
 
 # third party
 import delphi.operations.secrets as secrets
-from delphi.epidata.acquisition.covidcast.covidcast_meta_cache_updater import main as update_covidcast_meta_cache
+from delphi.epidata.maintenance.covidcast_meta_cache_updater import main as update_covidcast_meta_cache
 from delphi.epidata.acquisition.covidcast.test_utils import CovidcastBase, CovidcastTestRow, FIPS, MSA
 from delphi.epidata.client.delphi_epidata import Epidata
 from delphi_utils import Nans

integrations/server/test_covidcast_endpoints.py

@@ -9,7 +9,7 @@
 import requests
 import pandas as pd
 
-from delphi.epidata.acquisition.covidcast.covidcast_meta_cache_updater import main as update_cache
+from delphi.epidata.maintenance.covidcast_meta_cache_updater import main as update_cache
 from delphi.epidata.acquisition.covidcast.test_utils import CovidcastBase, CovidcastTestRow
 
 # use the local instance of the Epidata API

integrations/server/test_covidcast_meta.py

@@ -9,7 +9,7 @@
 
 #first party
 from delphi_utils import Nans
-from delphi.epidata.acquisition.covidcast.covidcast_meta_cache_updater import main as update_cache
+from delphi.epidata.maintenance.covidcast_meta_cache_updater import main as update_cache
 import delphi.operations.secrets as secrets
 
 # use the local instance of the Epidata API

requirements.dev.txt

@@ -1,4 +1,4 @@
-aiohttp==3.8.3
+aiohttp==3.8.5
 black>=20.8b1
 bump2version==1.0.1
 covidcast==0.1.5

src/acquisition/covidcast/database.py

@@ -526,13 +526,7 @@ def worker():
       t.join()
     logger.info("all threads terminated")
 
-    # sort the metadata because threaded workers dgaf
-    sorting_fields = "data_source signal time_type geo_type".split()
-    sortable_fields_fn = lambda x: [(field, x[field]) for field in sorting_fields]
-    prepended_sortables_fn = lambda x: sortable_fields_fn(x) + list(x.items())
-    tuple_representation = list(map(prepended_sortables_fn, meta))
-    tuple_representation.sort()
-    meta = list(map(dict, tuple_representation)) # back to dict form
+    meta = sorted(meta, key=lambda x: (x['data_source'], x['signal'], x['time_type'], x['geo_type']))
 
     return meta