Merge pull request #303 from cmu-delphi/release/7.3.0

Release 7.3.0

Author: nmdefries

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 7.2.0
+current_version = 7.3.0
 commit = False
 tag = False
 

.github/workflows/ci.yaml

@@ -6,7 +6,7 @@ jobs:
   build:
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
@@ -26,11 +26,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
       - name: Pull Image Data
         run: make pull_data
       - name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           registry: ghcr.io
           username: cmu-delphi-deploy-machine
@@ -48,24 +48,24 @@ jobs:
           if [ "$imageTag" = "main" ] ; then
             imageTag="latest"
           fi
-          echo "::set-output name=tag::$imageTag"
-          echo "::set-output name=repo::ghcr.io/${{ github.repository }}"
+          echo "tag=$imageTag" >> "$GITHUB_OUTPUT"
+          echo "repo=ghcr.io/${{ github.repository }}" >> "$GITHUB_OUTPUT"
       - name: Push Dev Tag
         run: |
           docker tag repo ${{ steps.tagname.outputs.repo }}:${{ steps.tagname.outputs.tag }}
           docker push ${{ steps.tagname.outputs.repo }}:${{ steps.tagname.outputs.tag }}
       - name: Set up Python 3.8
         if: startsWith(github.ref, 'refs/heads/main')
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: Extract version
         if: startsWith(github.ref, 'refs/heads/main')
         id: extract_version
         run: |
           python -m pip install bump2version
-          echo -n "::set-output name=version::"
-          bump2version --dry-run --list patch | grep ^current_version | sed -r s,"^.*=",,
+          currentVersion=`bump2version --dry-run --list patch | grep ^current_version | sed -r s,"^.*=",,`
+          echo "version=$currentVersion" >> "$GITHUB_OUTPUT"
       - name: Trigger Webhook
         run: |
           # trigger a webhook update

.github/workflows/create_release.yml

@@ -20,17 +20,17 @@ jobs:
           git fetch origin dev:dev
           git reset --hard dev
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: Change version number
         id: version
         run: |
           python -m pip install bump2version
-          echo -n "::set-output name=next_tag::"
-          bump2version --list ${{ github.event.inputs.versionName }} | grep new_version | sed -r s,"^.*=",,
+          newVersion=`bump2version --list ${{ github.event.inputs.versionName }} | grep new_version | sed -r s,"^.*=",,`
+          echo "next_tag=$newVersion" >> "$GITHUB_OUTPUT"
       - name: Create pull request into main
-        uses: peter-evans/create-pull-request@v3
+        uses: peter-evans/create-pull-request@v4
         with:
           branch: release/${{ steps.version.outputs.next_tag }}
           commit-message: "chore: release ${{ steps.version.outputs.next_tag }}"

.github/workflows/release_main.yml

@@ -22,15 +22,15 @@ jobs:
       - name: Check out code
         uses: actions/checkout@v3
       - name: Set up Python 3.8
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: Extract version
         id: extract_version
         run: |
           python -m pip install bump2version
-          echo -n "::set-output name=version::"
-          bump2version --dry-run --list patch | grep ^current_version | sed -r s,"^.*=",,
+          currentVersion=`bump2version --dry-run --list patch | grep ^current_version | sed -r s,"^.*=",,`
+          echo "version=$currentVersion" >> "$GITHUB_OUTPUT"
       - name: Create Release
         id: create_release
         uses: release-drafter/release-drafter@v5

.github/workflows/s3_upload_ec2.yml

@@ -25,26 +25,28 @@ jobs:
         run: sudo chown -R $USER:$USER $GITHUB_WORKSPACE
 
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Test AWS cli installation
         run: aws --version
 
       - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v1
+        uses: aws-actions/configure-aws-credentials@v2
         with:
           aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY }}
           aws-secret-access-key: ${{ secrets.AWS_SECRET_KEY }}
           aws-region: ${{ env.AWS_REGION_NAME }}
 
       - name: Login to GitHub Container Registry
-        uses: docker/login-action@v1
+        uses: docker/login-action@v2
         with:
           registry: ghcr.io
           username: cmu-delphi-deploy-machine
           password: ${{ secrets.CMU_DELPHI_DEPLOY_MACHINE_PAT }}
 
       - name: Deploy score files to S3 bucket
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         run: |
           make deploy
 

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: forecasteval
 Title: Forecast Evaluation Dashboard
-Version: 7.2.0
+Version: 7.3.0
 Authors@R: c(person("Kate", "Harwood", role = "aut"),
 	   person("Chris", "Scott", role = "ctb"),
 	   person("Jed", "Grabman", role = "ctb"),

Makefile

@@ -4,6 +4,8 @@ PWD=$(shell pwd)
 .DEFAULT_GOAL:=build
 S3_URL=https://forecast-eval.s3.us-east-2.amazonaws.com
 S3_BUCKET=s3://forecast-eval
+# If not already set in calling environment, set PAT to an empty value.
+GITHUB_PAT?=
 
 # Change `imageTag` during `make` call via `make <command> imageTag=<tag name>`
 #
@@ -46,6 +48,7 @@ score_forecast: r_build dist pull_data
 		-v ${PWD}/Report:/var/forecast-eval \
 		-v ${PWD}/dist:/var/dist \
 		-w /var/forecast-eval \
+		-e GITHUB_PAT \
 		forecast-eval-build \
 		Rscript create_reports.R --dir /var/dist
 

Report/create_reports.R

@@ -30,22 +30,29 @@ prediction_cards_filepath <- case_when(
 
 options(warn = 1)
 
-# Requested forecasters that do not get included in final scores:
-#    Auquan-SEIR: Only predicts cumulative deaths
-#    CDDEP-ABM: No longer on Forecast Hub. Causes some warnings when trying to download.
-#    CDDEP-SEIR_MCMC: County-level predictions only
-#    CUBoulder-COVIDLSTM: County-level predictions only
-#    FAIR-NRAR: County-level predictions only
-#    HKUST-DNN: Only predicts cumulative deaths
-#    ISUandPKU-vSEIdR: Folder but no forecasts on Forecast Hub
-#    PandemicCentral-COVIDForest: County-level predictions only
-#    UT_GISAG-SPDM: County-level predictions only
-#    WalmartLabsML-LogForecasting: Only predicts cumulative deaths
-#    Yu_Group-CLEP: County-level predictions only
 forecasters <- unique(c(
   get_covidhub_forecaster_names(designations = c("primary", "secondary")),
   "COVIDhub-baseline", "COVIDhub-trained_ensemble", "COVIDhub-4_week_ensemble"
-))
+)) %>%
+  # Drop invalid forecasters
+  setdiff(c(
+    # Forecasters that have no data on Forecast Hub
+    "CDDEP-ABM", # No longer on Forecast Hub. Causes some warnings when trying to download.
+    "ISUandPKU-vSEIdR", # Folder but no forecasts on Forecast Hub
+
+    # Forecasters that don't qualify for inclusion in the dashboard (wrong geo
+    # level, wrong target variable)
+    "Auquan-SEIR", # Only predicts cumulative deaths
+    "CDDEP-SEIR_MCMC", # County-level predictions only
+    "CUBoulder-COVIDLSTM", # County-level predictions only
+    "FAIR-NRAR", # County-level predictions only
+    "HKUST-DNN", # Only predicts cumulative deaths
+    "PandemicCentral-COVIDForest", # County-level predictions only
+    "UT_GISAG-SPDM", # County-level predictions only
+    "WalmartLabsML-LogForecasting", # Only predicts cumulative deaths
+    "Yu_Group-CLEP" # County-level predictions only
+  ))
+
 locations <- covidHubUtils::hub_locations
 
 # also includes "us", which is national level data

app/global.R

@@ -10,7 +10,7 @@ library(tsibble)
 library(covidcast)
 library(data.table)
 
-appVersion <- "7.2.0"
+appVersion <- "7.3.0"
 
 COVERAGE_INTERVALS <- c("10", "20", "30", "40", "50", "60", "70", "80", "90", "95", "98")
 CASES_DEATHS_TARGET_DAY <- "Saturday"