Merge pull request #1566 from cmu-delphi/release/delphi-epidata-4.1.27

Release Delphi Epidata 4.1.27

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.1.26
+current_version = 4.1.27
 commit = False
 tag = False
 

.github/workflows/missing_signals.yaml

@@ -21,7 +21,7 @@ jobs:
         run: python scripts/report_missing_covidcast_meta.py
       - name: Upload Missing Artifact
         if: failure()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v4
         with:
           name: missing_db_signals.csv
           path:  missing_db_signals.csv

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

@@ -101,7 +101,7 @@ jobs:
               write_float('requests_per_sec', final_line[9])
 
       - name: Archive results as artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: locust-output
           path: |

.github/workflows/performance-tests.yml

@@ -109,7 +109,7 @@ jobs:
               write_float('requests_per_sec', final_line[9])
 
       - name: Archive results as artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: locust-output
           path: |

.github/workflows/release-helper.yml

@@ -89,7 +89,7 @@ jobs:
         working-directory: src/client/packaging/pypi
         run: |
           python -m build --sdist --wheel
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           name: delphi_epidata_py
           path: src/client/packaging/pypi/dist/*.tar.gz
@@ -132,7 +132,7 @@ jobs:
       - run: npm pack
       - name: Rename to a different name
         run: for f in *.tgz; do mv "$f" "$(echo "$f" | sed s/delphi_epidata-/delphi_epidata_js-/)"; done
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v4
         with:
           name: delphi_epidata_js
           path: src/client/packaging/npm/*.tgz

dev/local/setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = Delphi Development
-version = 4.1.26
+version = 4.1.27
 
 [options]
 packages =

docs/about_delphi.md

@@ -0,0 +1,15 @@
+---
+title: About Delphi
+nav_order: 60
+has_children: false
+---
+
+# About The Delphi Group
+
+The Delphi Group's mission is to develop the theory and practice of epidemic detection, tracking and forecasting, and their use in decision making, both public and private.
+
+Our vision is to make this technology as useful as weather forecasting is today. 
+
+Find out more about the Delphi Research Group on our <a href="https://delphi.cmu.edu" target="_blank">offical webpage</a>.
+Please read our <a href="https://delphi.cmu.edu/blog" target="_blank">blog</a> for additional news, findings, and musings from the team.
+

docs/api/README.md

@@ -1,7 +1,7 @@
 ---
 title: Other Endpoints (COVID-19 and Other Diseases)
-nav_order: 3
 has_children: true
+nav_order: 3
 ---
 
 # Other Endpoints (COVID-19 and Other Diseases)
@@ -208,4 +208,4 @@ To access our Epidata API, visit our [Epidata API Client Libraries)](client_libr
 
 # Related Work
 
-Please visit our [related works](related_work.md) page for more information.
+Please visit our [related works](../related_work.md) page for more information.

docs/api/api_keys.md

@@ -1,7 +1,7 @@
 ---
 title: API Keys
+parent: Epidata API Intro
 nav_order: 1
-has_children: true
 ---
 
 # Epidata API Keys
@@ -42,11 +42,12 @@ there are several ways to use your key to authenticate your requests:
 
 ### Using a client
 
-* covidcast
+* [epidatr](https://cmu-delphi.github.io/epidatr/#api-keys)
+* [epidatpy](https://cmu-delphi.github.io/epidatpy/#api-keys)
+* [delphi-epidata](https://cmu-delphi.github.io/delphi-epidata/api/client_libraries.html)
+* covidcast (deprecated in favor of `epidatr` and `epidatpy`)
   * [R client](https://cmu-delphi.github.io/covidcast/covidcastR/reference/covidcast_signal.html#api-keys-1)
   * [Python client](https://cmu-delphi.github.io/covidcast/covidcast-py/html/signals.html#covidcast.use_api_key)
-* [epidatr](https://github.com/cmu-delphi/epidatr#api-keys)
-* [delphi-epidata](https://cmu-delphi.github.io/delphi-epidata/api/client_libraries.html)
 
 ### Via request parameter
 

docs/api/cdc.md

@@ -1,6 +1,8 @@
 ---
-title: CDC
-parent: Other Endpoints (COVID-19 and Other Diseases)
+title: <i>inactive</i> CDC
+parent: Data Sources and Signals
+grand_parent: Other Endpoints (COVID-19 and Other Diseases)
+nav_order: 2
 ---
 
 # CDC

docs/api/client_libraries.md

@@ -1,18 +1,18 @@
 ---
-title: Epidata API Client Libraries
+title: API Clients
 parent: Other Endpoints (COVID-19 and Other Diseases)
 nav_order: 1
 ---
 
-# Epidata API Client Libraries
+# Epidata API Clients
 
 To access Delphi Epidata programmatically, we recommend our client libraries:
 
 - R: [epidatr](https://cmu-delphi.github.io/epidatr/),
-- Python: [delphi-epidata](https://pypi.org/project/delphi-epidata/) (soon to be replaced with [epidatpy](https://github.com/cmu-delphi/epidatpy)),
+- Python: [epidatpy](https://cmu-delphi.github.io/epidatpy/) (recommended) and [delphi-epidata](https://pypi.org/project/delphi-epidata/),
 - Javascript: [delphi-epidata](https://github.com/cmu-delphi/delphi-epidata/blob/master/src/client/delphi_epidata.js).
 
-For anyone looking for COVIDCast data, please visit our [COVIDCast Libraries](covidcast_clients.md).
+For anyone looking for COVIDCast data, please visit our [COVIDCast API Client Libraries](covidcast_clients.md).
 
 The following samples show how to import the library and fetch Delphi's
 COVID-19 Surveillance Streams from Facebook Survey CLI for county 06001 and days
@@ -23,18 +23,41 @@ COVID-19 Surveillance Streams from Facebook Survey CLI for county 06001 and days
 Install [`epidatr` from CRAN](https://cran.r-project.org/package=epidatr)
 with `install.packages("epidatr")`.
 
-```R
+```r
 # Configure API key interactively, if needed. See
 # https://cmu-delphi.github.io/epidatr/articles/epidatr.html#api-keys for details.
 #save_api_key()
 library(epidatr)
-res <- pub_covidcast('fb-survey', 'smoothed_cli', 'county', 'day', geo_values = '06001',
+data <- pub_covidcast('fb-survey', 'smoothed_cli', 'county', 'day', geo_values = '06001',
                      time_values = c(20200401, 20200405:20200414))
-cat(res)
+cat(data)
 ```
 
 ### Python
 
+The `epidatpy` package will soon be [available on PyPI as `epidatpy`](https://pypi.org/project/epidatpy/).
+Meanwhile, it can be [installed from GitHub](https://github.com/cmu-delphi/epidatpy/) with
+`pip install "git+https://github.com/cmu-delphi/epidatpy.git#egg=epidatpy"`.
+
+```python
+# Configure API key, if needed.
+# https://github.com/cmu-delphi/epidatpy/blob/dev/docs/index.rst#api-keys
+
+from epidatpy import EpiDataContext, EpiRange
+
+# Create the client object.
+epidata = EpiDataContext()
+apicall = epidata.pub_covidcast(
+    data_source="jhu-csse",
+    signals="confirmed_cumulative_num",
+    geo_type="nation",
+    time_type="day",
+    geo_values="us",
+    time_values=EpiRange(20210405, 20210410),
+)
+print(apicall.df())
+```
+
 Install [`delphi-epidata` from PyPI](https://pypi.org/project/delphi-epidata/) with
 `pip install delphi-epidata`.
 

docs/api/covid_hosp.md

@@ -1,6 +1,8 @@
 ---
-title: COVID-19 Reported Patient Impact and Hospital Capacity by State Timeseries
-parent: Other Endpoints (COVID-19 and Other Diseases)
+title: <i>inactive</i> COVID-19 Reported Patient Impact and Hospital Capacity by State Timeseries
+parent: Data Sources and Signals
+grand_parent: Other Endpoints (COVID-19 and Other Diseases)
+nav_order: 2
 ---
 
 # COVID-19 Hospitalization by State
@@ -86,12 +88,19 @@ https://api.delphi.cmu.edu/epidata/covid_hosp_state_timeseries/?states=MA&dates=
 
 ```json
 {
-    "result": 1,
-    "epidata": [
+    "epidata":
+    [
         {
             "state": "MA",
-            "issue": 20201116,
+            "geocoded_state": null,
+            "issue": 20240503,
             "date": 20200510,
+            "critical_staffing_shortage_today_yes": 0,
+            "critical_staffing_shortage_today_no": 0,
+            "critical_staffing_shortage_today_not_reported": 84,
+            "critical_staffing_shortage_anticipated_within_week_yes": 0,
+            "critical_staffing_shortage_anticipated_within_week_no": 0,
+            "critical_staffing_shortage_anticipated_within_week_not_reported": 84,
             "hospital_onset_covid": 53,
             "hospital_onset_covid_coverage": 84,
             "inpatient_beds": 15691,
@@ -139,18 +148,74 @@ https://api.delphi.cmu.edu/epidata/covid_hosp_state_timeseries/?states=MA&dates=
             "adult_icu_bed_utilization_coverage": null,
             "adult_icu_bed_utilization_numerator": null,
             "adult_icu_bed_utilization_denominator": null,
-            "inpatient_beds_utilization": 0.6978504972730191,
-            "percent_of_inpatients_with_covid": 0.2902550897239881,
-            "inpatient_bed_covid_utilization": 0.21056656682174496,
+            "deaths_covid": 48,
+            "deaths_covid_coverage": 73,
+            "icu_patients_confirmed_influenza": null,
+            "icu_patients_confirmed_influenza_coverage": 0,
+            "on_hand_supply_therapeutic_a_casirivimab_imdevimab_courses": null,
+            "on_hand_supply_therapeutic_b_bamlanivimab_courses": null,
+            "on_hand_supply_therapeutic_c_bamlanivimab_etesevimab_courses": null,
+            "previous_day_admission_adult_covid_confirmed_18_19": null,
+            "previous_day_admission_adult_covid_confirmed_18_19_coverage": 0,
+            "previous_day_admission_adult_covid_confirmed_20_29": null,
+            "previous_day_admission_adult_covid_confirmed_20_29_coverage": 0,
+            "previous_day_admission_adult_covid_confirmed_30_39": null,
+            "previous_day_admission_adult_covid_confirmed_30_39_coverage": 0,
+            "previous_day_admission_adult_covid_confirmed_40_49": null,
+            "previous_day_admission_adult_covid_confirmed_40_49_coverage": 0,
+            "previous_day_admission_adult_covid_confirmed_50_59": null,
+            "previous_day_admission_adult_covid_confirmed_50_59_coverage": 0,
+            "previous_day_admission_adult_covid_confirmed_60_69": null,
+            "previous_day_admission_adult_covid_confirmed_60_69_coverage": 0,
+            "previous_day_admission_adult_covid_confirmed_70_79": null,
+            "previous_day_admission_adult_covid_confirmed_70_79_coverage": 0,
+            "previous_day_admission_adult_covid_confirmed_80plus": null,
+            "previous_day_admission_adult_covid_confirmed_80plus_coverage": 0,
+            "previous_day_admission_adult_covid_confirmed_unknown": null,
+            "previous_day_admission_adult_covid_confirmed_unknown_coverage": 0,
+            "previous_day_admission_adult_covid_suspected_18_19": null,
+            "previous_day_admission_adult_covid_suspected_18_19_coverage": 0,
+            "previous_day_admission_adult_covid_suspected_20_29": null,
+            "previous_day_admission_adult_covid_suspected_20_29_coverage": 0,
+            "previous_day_admission_adult_covid_suspected_30_39": null,
+            "previous_day_admission_adult_covid_suspected_30_39_coverage": 0,
+            "previous_day_admission_adult_covid_suspected_40_49": null,
+            "previous_day_admission_adult_covid_suspected_40_49_coverage": 0,
+            "previous_day_admission_adult_covid_suspected_50_59": null,
+            "previous_day_admission_adult_covid_suspected_50_59_coverage": 0,
+            "previous_day_admission_adult_covid_suspected_60_69": null,
+            "previous_day_admission_adult_covid_suspected_60_69_coverage": 0,
+            "previous_day_admission_adult_covid_suspected_70_79": null,
+            "previous_day_admission_adult_covid_suspected_70_79_coverage": 0,
+            "previous_day_admission_adult_covid_suspected_80plus": null,
+            "previous_day_admission_adult_covid_suspected_80plus_coverage": 0,
+            "previous_day_admission_adult_covid_suspected_unknown": null,
+            "previous_day_admission_adult_covid_suspected_unknown_coverage": 0,
+            "previous_day_admission_influenza_confirmed": null,
+            "previous_day_admission_influenza_confirmed_coverage": 0,
+            "previous_day_deaths_covid_and_influenza": null,
+            "previous_day_deaths_covid_and_influenza_coverage": 0,
+            "previous_day_deaths_influenza": null,
+            "previous_day_deaths_influenza_coverage": 0,
+            "previous_week_therapeutic_a_casirivimab_imdevimab_courses_used": null,
+            "previous_week_therapeutic_b_bamlanivimab_courses_used": null,
+            "previous_week_therapeutic_c_bamlanivimab_etesevimab_courses_used": null,
+            "total_patients_hospitalized_confirmed_influenza": null,
+            "total_patients_hospitalized_confirmed_influenza_coverage": 0,
+            "total_patients_hospitalized_confirmed_influenza_covid": null,
+            "total_patients_hospitalized_confirmed_influenza_covid_coverage": null,
+            "inpatient_beds_utilization": 0.697850497273019,
+            "percent_of_inpatients_with_covid": 0.290255089723988,
+            "inpatient_bed_covid_utilization": 0.210566566821745,
             "adult_icu_bed_covid_utilization": null,
             "adult_icu_bed_utilization": null
         }
     ],
+    "result": 1,
     "message": "success"
 }
 ```
 
-
 # Code Samples
 
 Libraries are available for [JavaScript](https://github.com/cmu-delphi/delphi-epidata/blob/main/src/client/delphi_epidata.js), [Python](https://pypi.org/project/delphi-epidata/), and [R](https://github.com/cmu-delphi/delphi-epidata/blob/dev/src/client/delphi_epidata.R).

docs/api/covid_hosp_facility.md

@@ -1,6 +1,8 @@
 ---
-title: COVID-19 Reported Patient Impact and Hospital Capacity by Facility
-parent: Other Endpoints (COVID-19 and Other Diseases)
+title: <i>inactive</i> COVID-19 Reported Patient Impact and Hospital Capacity by Facility
+parent: Data Sources and Signals
+grand_parent: Other Endpoints (COVID-19 and Other Diseases)
+nav_order: 2
 ---
 
 # COVID-19 Hospitalization by Facility

docs/api/covid_hosp_facility_lookup.md

@@ -1,6 +1,8 @@
 ---
-title: COVID-19 Reported Patient Impact and Hospital Capacity - Facility lookup
-parent: Other Endpoints (COVID-19 and Other Diseases)
+title: <i>inactive</i> COVID-19 Reported Patient Impact and Hospital Capacity - Facility lookup
+parent: Data Sources and Signals
+grand_parent: Other Endpoints (COVID-19 and Other Diseases)
+nav_order: 2
 ---
 
 # COVID-19 Hospitalization: Facility Lookup

docs/api/covidcast-signals/_source-template.md

@@ -1,7 +1,7 @@
 ---
 title: SOURCE NAME
 parent: Data Sources and Signals
-grand_parent: COVIDcast Main Endpoint
+grand_parent: Main Endpoint (COVIDcast)
 ---
 
 # SOURCE NAME

docs/api/covidcast-signals/chng.md

@@ -1,7 +1,8 @@
 ---
 title: Change Healthcare
 parent: Data Sources and Signals
-grand_parent: COVIDcast Main Endpoint
+grand_parent: Main Endpoint (COVIDcast)
+nav_order: 1
 ---
 
 # Change Healthcare
@@ -29,6 +30,8 @@ commercial purposes.
 
 | Signal | Description |
 | --- | --- |
+| `7dav_inpatient_covid` | Ratio of inpatient hospitalizations associated with COVID-19, based on Change Healthcare claims data that has been de-identified in accordance with HIPAA privacy regulations, smoothed in time with a trailing 7 day average. This historical signal is no longer updated. <br/> **Earliest date available:** 2020-01-01 |
+| `7dav_outpatient_covid` | Ratio of outpatient doctor visits with confirmed COVID-19, based on Change Healthcare claims data that has been de-identified in accordance with HIPAA privacy regulations, smoothed in time with a trailing 7 day average. This historical signal is no longer updated. <br/> **Earliest date available:** 2020-01-01 |
 | `smoothed_outpatient_covid` | Estimated percentage of outpatient doctor visits with confirmed COVID-19, based on Change Healthcare claims data that has been de-identified in accordance with HIPAA privacy regulations, smoothed in time using a Gaussian linear smoother <br/> **Earliest date available:** 2020-02-01 |
 | `smoothed_adj_outpatient_covid` | Same, but with systematic day-of-week effects removed; see [details below](#day-of-week-adjustment) <br/> **Earliest date available:** 2020-02-01 |
 | `smoothed_outpatient_cli` | Estimated percentage of outpatient doctor visits primarily about COVID-related symptoms, based on Change Healthcare claims data that has been de-identified in accordance with HIPAA privacy regulations, smoothed in time using a Gaussian linear smoother <br/> **Earliest date available:** 2020-02-01 |

docs/api/covidcast-signals/covid-act-now.md

@@ -1,7 +1,8 @@
 ---
-title: COVID Act Now
-parent: Inactive Signals
-grand_parent: COVIDcast Main Endpoint
+title: <i>inactive</i> COVID Act Now
+parent: Data Sources and Signals
+grand_parent: Main Endpoint (COVIDcast)
+nav_order: 2
 ---
 
 # COVID Act Now (CAN)

docs/api/covidcast-signals/doctor-visits.md

@@ -1,7 +1,8 @@
 ---
 title: Doctor Visits
 parent: Data Sources and Signals
-grand_parent: COVIDcast Main Endpoint
+grand_parent: Main Endpoint (COVIDcast)
+nav_order: 1
 ---
 
 # Doctor Visits

docs/api/covidcast-signals/dsew-cpr.md

@@ -1,7 +1,8 @@
 ---
-title: Data Strategy and Execution Workgroup Community Profile Report
-parent: Inactive Signals
-grand_parent: COVIDcast Main Endpoint
+title: <i>inactive</i> Data Strategy and Execution Workgroup Community Profile Report
+parent: Data Sources and Signals
+grand_parent: Main Endpoint (COVIDcast)
+nav_order: 2
 ---
 
 # Data Strategy and Execution Workgroup Community Profile Report (CPR)