Merge branch 'dev' into c2b_blogpost

Author: Ananya-Joshi

.github/dependabot.yml

@@ -0,0 +1,14 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    target-branch: dev
+    schedule:
+      interval: "weekly"
+  # Maintain dependencies for npm
+  - package-ecosystem: "npm"
+    directory: "/"
+    target-branch: dev
+    schedule:
+      interval: "weekly"

.github/release-drafter.yml

@@ -19,6 +19,7 @@ categories:
     labels:
       - "chore"
       - "documentation"
+      - "dependencies"
 change-template: "- #$NUMBER $TITLE"
 change-title-escapes: '\<*_&`#@'
 template: |

.github/workflows/blog.yaml

@@ -16,7 +16,7 @@ jobs:
           # submodules: true  # Fetch Hugo themes (true OR recursive)
           fetch-depth: 3
       - name: Cache Conda
-        uses: actions/cache@v1
+        uses: actions/cache@v2.1.5
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda6-${{ hashFiles('environment.yml') }}
@@ -42,7 +42,7 @@ jobs:
         run: |
           Rscript ./dependencies.R
       - name: Restore Blogdown Cache
-        uses: actions/cache@v2
+        uses: actions/cache@v2.1.5
         with:
           path: |
             ./blogdown
@@ -62,10 +62,10 @@ jobs:
             ./content/blog
             ./static/blog
 
-      - uses: actions/setup-node@v1
+      - uses: actions/setup-node@v2.1.5
         with:
           node-version: "12"
-      - uses: actions/cache@v2
+      - uses: actions/cache@v2.1.5
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}

.github/workflows/ci.yaml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/[email protected]
         with:
           node-version: "14"
-      - uses: actions/cache@v2
+      - uses: actions/cache@v2.1.5
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node3-${{ hashFiles('**/package-lock.json') }}
@@ -61,23 +61,22 @@ jobs:
           echo "::set-output name=tag::$imageTag"
           echo "::set-output name=repo::ghcr.io/${{ github.repository }}"
       - name: Push Dev Tag
-        if: startsWith(github.ref, 'refs/heads/dev')
         run: |
           docker tag repo ${{ steps.tagname.outputs.repo }}:${{ steps.tagname.outputs.tag }}
           docker push ${{ steps.tagname.outputs.repo }}:${{ steps.tagname.outputs.tag }}
       - name: Extract version
         if: startsWith(github.ref, 'refs/heads/main')
         id: extract_version
         run: node -pe "'::set-output name=version::' + require('./package.json').version"
-      - name: Push Version Tag Tag
-        if: startsWith(github.ref, 'refs/heads/main')
-        run: |
-          docker tag repo ${{ steps.tagname.outputs.repo }}:v{{ steps.extract_version.outputs.version }}
-          docker push ${{ steps.tagname.outputs.repo }}:v{{ steps.extract_version.outputs.version }}
       - name: Trigger Webhook
         run: |
           # trigger a webhook update
           curl -H "Authorization: Bearer ${{ secrets.DELPHI_DEPLOY_WEBHOOK_TOKEN }}" \
                -X POST ${{ secrets.DELPHI_DEPLOY_WEBHOOK_URL }} \
                -H "Content-Type: application/x-www-form-urlencoded" \
                -d "repository=${{ steps.tagname.outputs.repo }}&tag=${{ steps.tagname.outputs.tag }}"
+      - name: Push Version Tag Tag
+        if: startsWith(github.ref, 'refs/heads/main')
+        run: |
+          docker tag repo ${{ steps.tagname.outputs.repo }}:v${{ steps.extract_version.outputs.version }}
+          docker push ${{ steps.tagname.outputs.repo }}:v${{ steps.extract_version.outputs.version }}

.github/workflows/release_main.yml

@@ -18,7 +18,7 @@ jobs:
     steps:
       - name: Check out code
         uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v2.1.5
         with:
           node-version: "14"
       - name: Extract version
@@ -43,11 +43,11 @@ jobs:
     steps:
       - name: Check out code
         uses: actions/checkout@v2
-      - uses: actions/setup-node@v2
+      - uses: actions/setup-node@v2.1.5
         with:
           node-version: "14"
       - name: Cache Node.js modules
-        uses: actions/cache@v2
+        uses: actions/cache@v2.1.5
         with:
           path: ~/.npm # npm cache files are stored in `~/.npm` on Linux/macOS
           key: ${{ runner.OS }}-node2-${{ hashFiles('**/package-lock.json') }}

.prettierignore

@@ -28,6 +28,7 @@
 *.Rmd
 *.md
 *.jpeg
+*.csv
 *.ico
 *.bib
 *.xcf

README.md

@@ -1,9 +1,11 @@
 # Delphi Website
 
-[![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/cmu-delpih/www-main)
+[![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/cmu-delphi/www-main)
 
 
-Delphi's homepage at https://cmu-delphi-main.netlify.app/
+The current stable `main` version is deployed at https://delphi.cmu.edu and https://cmu-delphi-main.netlify.app/.
+
+The next `dev` version is deployed at https://staging.delphi.cmu.edu/ and https://dev--cmu-delphi-main.netlify.app/.
 
 This site is based on [Hugo](https://gohugo.io) and uses [Prettier](https://prettier.io) for formatting.
 
@@ -49,7 +51,7 @@ In RMarkdown things are slightly more different since the R Markdown parser is u
 
 ## Development Environment
 
-One click: [![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/cmu-delpih/www-main)
+One click: [![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/cmu-delphi/www-main)
 
 ### Web Editor Only
 
@@ -84,7 +86,7 @@ In order to convert the Rmd files to HTML files for Hugo you also need to:
    - `local=TRUE` similar to `-D` to process draft files
    - `run_hugo=FALSE` to manually run hugo
    - `build_rmd=TRUE` force a (re)build of the Rmd pages
-1. Run blogdown to convert a single file to HTML: `Rscript -e 'blogdown::build_site(local=TRUE, run_hugo=FALSE, build_rmd="content/blog/<NAME>.Rmd")'`
+1. Run blogdown to convert a single file to HTML: `Rscript -e 'blogdown::build_site(local=TRUE, run_hugo=FALSE, build_rmd="content/blog/<NAME>.Rmd")'` where `<NAME>` should be replaced by the name of the Rmd file.
 1. Alternatively, run `npm run build:blog`
 1. Run Hugo server as usual
 
@@ -101,12 +103,16 @@ This simplifies the deployment and ensures that we have a blog post even when th
 
 ### Release Process
 
-The release process is based on [release-it](https://github.com/release-it/release-it). To create a release, run
-
-1. create/checkout the release branch `release` and push to origin
-1. run `npm run release` and publish the release
-1. create a PR that merges the `release` branch in the `main` branch
-1. create a PR that merges the `main` branch back into the `dev` branch
-
-Then go to the release page and update short description of the changes made.
+The release consists of multiple steps which can be all done via the GitHub website:
+
+1. Go to [create_release GitHub Action](https://github.com/cmu-delphi/www-main/actions/workflows/create_release.yml) and click the `Run workflow` button. Enter the next version number or one of the magic keywords (patch, minor, major) and hit the green `Run workflow` button.
+1. The action will prepare a new release and will end up with a new [Pull Request](https://github.com/cmu-delphi/www-main/pulls)
+1. Let the code owner review the PR and its changes and let the CI check whether everything builds successfully
+1. Once approved and merged, another GitHub action job starts which automatically will
+   1. create a git tag
+   1. create another [Pull Request](https://github.com/cmu-delphi/www-main/pulls) to merge the changes back to the `dev` branch
+   1. create a [GitHub release](https://github.com/cmu-delphi/www-main/releases) with automatically derived release notes
+   1. create docker image and the production system will be notified to pull this update
+1. Once the jobs are completed the new release should be available at https://delphi.cmu.edu within minutes.
+1. Done
 

config.toml

@@ -25,6 +25,11 @@ relativeURLs = false
     name = "Team"
     url = "/about/team"
     weight = 2
+[[menu.main]]
+    parent = "about"
+    name = "Center of Excellence"
+    url = "/about/center-of-excellence"
+    weight = 3
 [[menu.main]]
     parent = "about"
     name = "Publications"
@@ -56,11 +61,16 @@ relativeURLs = false
     name = "Explore an Indicator"
     url = "/covidcast/indicator"
     weight = 3
+[[menu.main]]
+    parent = "covidcast"
+    name = "Explore Correlations"
+    url = "/covidcast/correlation"
+    weight = 4
 [[menu.main]]
     parent = "covidcast"
     name = "Classic Map"
     url = "/covidcast/classic"
-    weight = 4
+    weight = 30
 [[menu.main]]
     parent = "covidcast"
     name = "Forecast Evaluation"
@@ -86,6 +96,11 @@ relativeURLs = false
     name = "Export Data"
     url = "/covidcast/export"
     weight = 70
+[[menu.main]]
+    parent = "covidcast"
+    name = "Data Anomalies"
+    url = "/covidcast/data-anomalies"
+    weight = 71
 [[menu.main]]
     parent = "covidcast"
     name = "Release Log"
@@ -132,4 +147,4 @@ relativeURLs = false
     feedbackDelayMin = 45  # in sec
     feedbackDelayMax = 180 # in sec
     feedbackDuration = 60  # show it for 60sec
-    highlightLinks = "/covidcast/,/covidcast/summary,/covidcast/indicator,/signals-dashboard/,/forecast-eval/"
+    highlightLinks = "/covidcast/correlation,/covidcast/data-anomalies"

content/about/_index.md

@@ -32,7 +32,7 @@ Public health authorities (federal, state, local), the healthcare industry, the
 
 ### Delphi's milestones
 
-- Since 2013, we've supported U.S. CDC's Influenza Division in advancing and growing a [scientific community around flu forecasting](https://www.cdc.gov/flu/weekly/flusight/index.html). We've been perennial leaders in forecasting accuracy.
+- Since 2013, we've supported U.S. CDC's Influenza Division in advancing and growing a [scientific community around flu forecasting](https://www.cdc.gov/flu/weekly/flusight/index.html). We've been [perennial leaders in forecasting accuracy](https://www.cs.cmu.edu/~roni/CDC%20Flu%20Challenge%202014-2018%20Results.pdf).
 
 - Since 2016, we've developed the [Delphi Epidata API]({{< apiref "/" >}}), which provides real-time access to epidemiological surveillance data.
 

content/about/center-of-excellence/index.md

@@ -0,0 +1,56 @@
+---
+title: Delphi National Center of Excellence for Epidemic Forecasting
+layout: coe
+members:
+- name: Carnegie Mellon University
+  group: DELPHI Research Group
+  link: /
+  location: Pittsburgh, Pennsylvania, United States
+  pi:
+   - ryan # people keys
+   - roni
+- name: Carnegie Mellon University
+  group: EPP
+  link: https://www.cmu.edu/epp
+  location: Pittsburgh, Pennsylvania, United States
+  pi:
+    - fischhoff
+- name: University of Pittsburgh
+  group: GSPH
+  link: https://publichealth.pitt.edu/
+  location: Pittsburgh, Pennsylvania, United States
+  pi:
+    - burke
+    - panhuis
+- name: Harvard University
+  group: CCDD
+  link: https://www.hsph.harvard.edu/
+  location: Cambridge, Massachusetts, United States
+  pi:
+    - lipsitch
+
+sisters:
+- name: CDC's Influence Division
+  description: Our funders and collaborators at the [CDC's Influenza Division](https://www.cdc.gov/ncird/flu.html), specially the Influenza Applied Research & Modeling team at the [Epidemiology and Prevention branch](https://www.cdc.gov/hiv/dhap/eb/index.html).
+  link: https://www.cdc.gov/ncird/flu.html
+  img: logos/cdc.png
+- name: University of Massachusetts Amherst
+  description: Our sister organization, the [Influenza Forecasting Center of Excellence at UMass Amherst](https://reichlab.io/).
+  link: https://reichlab.io/
+  img: logos/reichlab.png
+
+supporters:
+- Allegheny County Dept of Health
+- Change Healthcare
+- DTRA
+- Facebook
+- Kaiser Permanente Washington Health Research Institute
+- Massachusetts Dept of Public Health
+- Microsoft Azure
+- Pennsylvania Dept. of Health
+- Quidel Inc.
+- UnitedHealth / Optum
+- UPMC
+---
+
+The Delphi National Center of Excellence for Influenza Forecasting was established in 2019. It is a CDC funded and CDC-designated center working on advancing influenza forecasting, and enabling and improving the usefulness of forecasts of both seasonal and pandemic influenza. During the 2020 pandemic, the center expanded to include real-time tracking ("nowcasting") and forecasting of COVID-19, giving rise to the COVIDcast project.  Our goal is to inform public health responses and policy development at the national, state and local levels. Another goal is to inform and empower the general public, providing trustworthy information and reliable short term forecasts that increase the credibility of and trust in public health authorities.