Release v1.12.0

.dockerignore

@@ -0,0 +1,2 @@
+node_modules
+.git

.github/workflows/ci_fast.yaml

@@ -35,3 +35,39 @@ jobs:
         with:
           name: website
           path: ./public
+
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.DELPHI_ECR_ACCESS_ID }}
+          aws-secret-access-key: ${{ secrets.DELPHI_ECR_ACCESS_KEY }}
+          aws-region: us-east-1
+
+      - name: Login to Amazon ECR
+        id: login-ecr
+        uses: aws-actions/amazon-ecr-login@v1
+
+      - name: Build, tag, and push image to Amazon ECR
+        env:
+          ECR_REGISTRY: ${{ steps.login-ecr.outputs.registry }}
+          ECR_REPOSITORY: ${{ github.event.repository.name }}
+        run: |
+          baseRef="${GITHUB_REF#*/}"
+          baseRef="${baseRef#*/}"
+          case "${baseRef}" in
+          main)
+            awsTag="latest"
+            ;;
+          *)
+            awsTag="${baseRef//\//_}" # replace `/` with `_` in branch name
+            ;;
+          esac
+          echo "using tag: --${awsTag}--"
+          docker build -t $ECR_REGISTRY/$ECR_REPOSITORY:$awsTag --file ./devops/precompiled/Dockerfile .
+          docker push $ECR_REGISTRY/$ECR_REPOSITORY:$awsTag
+
+          # trigger a webhook update
+          curl -H "Authorization: Bearer ${{ secrets.DELPHI_DEPLOY_WEBHOOK_TOKEN }}" \
+               -X POST ${{ secrets.DELPHI_DEPLOY_WEBHOOK_URL }} \
+               -H "Content-Type: application/x-www-form-urlencoded" \
+               -d "repository=$ECR_REGISTRY/$ECR_REPOSITORY&tag=$awsTag"

.prettierignore

@@ -24,7 +24,9 @@
 *.woff2
 *.R
 *.xml
+.dockerignore
 *.Rmd
 *.md
 *.jpeg
-*.ico
+*.ico
+/themes/delphi/layouts/partials/webp-image.html

config.toml

@@ -46,16 +46,21 @@ relativeURLs = false
     name = "Surveys"
     url = "/covidcast/surveys"
     weight = 2
+[[menu.main]]
+    parent = "covidcast"
+    name = "Survey Results"
+    url = "/covidcast/survey-results"
+    weight = 3
 [[menu.main]]
     parent = "covidcast"
     name = "Release Log"
     url = "/covidcast/release-log"
-    weight = 3
+    weight = 4
 [[menu.main]]
     parent = "covidcast"
     name = "Terms Of Use"
     url = "/covidcast/terms-of-use"
-    weight = 4
+    weight = 5
 [[menu.main]]
     identifier = "flu"
     name = "Flu and Other Diseases"
@@ -83,6 +88,6 @@ relativeURLs = false
 
 [params]
     description = "Developing the Theory and Practice of Epidemiological Forecasting"
-    mission = "Develop the theory and practice of epidemiological forecasting, with a long-term vision of seeing this technology become as universally accepted and useful as weather forecasting is today."
+    mission = "Develop the theory and practice of epidemiological forecasting, with a long-term vision of making this technology as universally accepted and useful as weather forecasting is today."
     apiUrl = "https://cmu-delphi.github.io/delphi-epidata"
     twitter = "CmuDelphi"

content/_index.md

@@ -4,19 +4,24 @@ description: Developing the Theory and Practice of Epidemiological Forecasting
 layout: landing
 
 carousel:
+  - pre: Our Tools
+    title: National COVID Survey Dashboard
+    ref: covidcast/survey-results
+    alt: Explore the Survey Results
+    image: covidcast_survey.jpg
   - pre: Our Tools
     title: Real-time Indicators of COVID-19 Activity
     ref: covidcast
     alt: Explore COVIDCast
-    image: covidcast_withfill.png
+    image: covidcast_withfill.jpg
   - pre: Our Blog Post
     title: New and improved COVID Symptom Survey Tracks Testing and Mask-Wearing
     ref: 2020-10-06-survey-wave-4
     alt: Learn more
-    image: landing-pg_hero-img-2_New and Improved COVID Symptom Survey Tracks Testing and Mask-Wearing.png
+    image: landing-pg_hero-img-2_New and Improved COVID Symptom Survey Tracks Testing and Mask-Wearing.jpg
   - pre: Our Research and White Papers
     title: "Pancasting: forecasting epidemics from provisional data"
     link: https://delphi.cmu.edu/~lcbrooks/brooks2020pancasting.pdf
     alt: View Paper
-    image: landing-pg_hero-img-2_Pancasting_ forecasting epidemics from provisional data.png
+    image: landing-pg_hero-img-2_Pancasting_ forecasting epidemics from provisional data.jpg
 ---

content/about/publications/index.md

@@ -2,49 +2,49 @@
 title: Research and White Papers
 papers:
   - title: "Pancasting: forecasting epidemics from provisional data"
-    image: pancasting.png
+    image: pancasting.jpg
     authors: Brooks
     link: https://delphi.cmu.edu/~lcbrooks/brooks2020pancasting.pdf
     journal: PhD thesis
     year: 2020
   - title: "Kalman filter, sensor fusion, and constrained regression: equivalences and insights"
-    image: kalman_filter.png
+    image: kalman_filter.jpg
     authors: Jahja, Farrow, Rosenfeld, Tibshirani
     link: https://papers.nips.cc/paper/9475-kalman-filter-sensor-fusion-and-constrained-regression-equivalences-and-insights
     journal: Neural Information Processing Systems
     year: 2019
   - title: "Nonmechanistic forecasts of seasonal influenza with iterative one-week-ahead distributions"
-    image: nonmechanistic_forecasts.png
+    image: nonmechanistic_forecasts.jpg
     authors: Brooks, Farrow, Hyun, Tibshirani, Rosenfeld
     link: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006134
     journal: PLOS Computational Biology
     year: 2018
   - title: "A human judgment approach to epidemiological forecasting"
-    image: human.png
+    image: human.jpg
     authors: Farrow, Brooks, Hyun, Tibshirani, Burke, Rosenfeld
     link: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005248
     journal: PLOS Computational Biology
     year: 2017
   - title: "Modeling the past, present, and future of influenza"
-    image: modeling.png
+    image: modeling.jpg
     authors: Farrow
     link: https://delphi.cmu.edu/~dfarrow/thesis.pdf
     journal: PhD thesis
     year: 2016
   - title: "Flexible modeling of epidemics with an empirical Bayes framework"
-    image: flexible_modeling.png
+    image: flexible_modeling.jpg
     authors: Brooks, Farrow, Hyun, Tibshirani, Rosenfeld
     link: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004382
     journal: PLOS Computational Biology
     year: 2015
   - title: "Predicting the predictable"
-    image: predicting.png
+    image: predicting.jpg
     authors: Rosenfeld
     link: https://delphi.cmu.edu/files/PredictingThePredictable_13-04-03.pdf
     journal: presentation
     year: 2013
   - title: "A proposal for standardized evaluation of epidemiological models"
-    image: evaluation.png
+    image: evaluation.jpg
     authors: Rosenfeld, Grefenstette, Burke
     link: http://www.cs.cmu.edu/~roni/standardized-evaluation-of-epi-models-rev-09nov2012.pdf
     journal: White paper

content/about/team/index.md

@@ -235,8 +235,8 @@ team:
   note: Intern, Summer 2020
 - firstName: Kenneth
   lastName: Lee
-  image: profile-placeholder.png
-  affiliation:
+  image: lee-kenneth.png
+  affiliation: UC Davis
   team:
   - contributors
 - firstName: Natalia

content/blog/2015-07-23-template-post.Rmd

@@ -9,8 +9,8 @@ tags:
 draft: true # remove this line in new blog posts
 authors: # list of author keys, see /data/authors.yaml
   - frida
-heroImage: /blog/images/blog-lg-img_hello-world.png
-heroImageThumb: /blog/images/blog-thumb-img_hello-world.png
+heroImage: /blog/images/blog-lg-img_hello-world.jpg
+heroImageThumb: /blog/images/blog-thumb-img_hello-world.jpg
 summary: |
   Blog summary, the first 150 characters are used for the blog list
 acknowledgements: |

content/blog/2015-07-23-template-post.html

@@ -9,8 +9,8 @@
 draft: true # remove this line in new blog posts
 authors: # list of author keys, see /data/authors.yaml
   - frida
-heroImage: /blog/images/blog-lg-img_hello-world.png
-heroImageThumb: /blog/images/blog-thumb-img_hello-world.png
+heroImage: /blog/images/blog-lg-img_hello-world.jpg
+heroImageThumb: /blog/images/blog-thumb-img_hello-world.jpg
 summary: |
   Blog summary, the first 150 characters are used for the blog list
 acknowledgements: |
@@ -49,21 +49,21 @@
 see <a href="http://rmarkdown.rstudio.com" class="uri">http://rmarkdown.rstudio.com</a>.</p>
 <p>You can embed an R code chunk like this:</p>
 <pre class="r"><code>summary(cars)
-##      speed           dist       
-##  Min.   : 4.0   Min.   :  2.00  
-##  1st Qu.:12.0   1st Qu.: 26.00  
-##  Median :15.0   Median : 36.00  
-##  Mean   :15.4   Mean   : 42.98  
-##  3rd Qu.:19.0   3rd Qu.: 56.00  
+##      speed           dist
+##  Min.   : 4.0   Min.   :  2.00
+##  1st Qu.:12.0   1st Qu.: 26.00
+##  Median :15.0   Median : 36.00
+##  Mean   :15.4   Mean   : 42.98
+##  3rd Qu.:19.0   3rd Qu.: 56.00
 ##  Max.   :25.0   Max.   :120.00
 fit &lt;- lm(dist ~ speed, data = cars)
 fit
-## 
+##
 ## Call:
 ## lm(formula = dist ~ speed, data = cars)
-## 
+##
 ## Coefficients:
-## (Intercept)        speed  
+## (Intercept)        speed
 ##     -17.579        3.932</code></pre>
 <div id="including-plots" class="section level2">
 <h2>Including Plots</h2>

content/blog/2020-08-10-hello-world.Rmd

@@ -7,8 +7,8 @@ tags:
 authors:
   - roni
   - ryan
-heroImage: /blog/images/blog-lg-img_hello-world.png
-heroImageThumb: /blog/images/blog-thumb-img_hello-world.png
+heroImage: /blog/images/blog-lg-img_hello-world.jpg
+heroImageThumb: /blog/images/blog-thumb-img_hello-world.jpg
 summary: |
   Hello from the Delphi research group at Carnegie Mellon University!
   We're a group of faculty, students, and staff, based primarily out of CMU

content/blog/2020-08-10-hello-world.html

@@ -7,18 +7,18 @@
 authors:
   - roni
   - ryan
-heroImage: /blog/images/blog-lg-img_hello-world.png
-heroImageThumb: /blog/images/blog-thumb-img_hello-world.png
+heroImage: /blog/images/blog-lg-img_hello-world.jpg
+heroImageThumb: /blog/images/blog-thumb-img_hello-world.jpg
 summary: |
   Hello from the Delphi research group at Carnegie Mellon University!
   We're a group of faculty, students, and staff, based primarily out of CMU
   together with strong collaborators from other universities and industry.
-  Our group was founded in 2012 to advance the theory and practice of epidemic 
-  forecasting. Since March 2020, we have refocused efforts towards helping combat 
+  Our group was founded in 2012 to advance the theory and practice of epidemic
+  forecasting. Since March 2020, we have refocused efforts towards helping combat
   the COVID-19 pandemic, by supporting informed decision-making at federal, state,
   and local levels of government and in the healthcare sector. Until now, we've
-  been pretty “heads down” with our work, and slow to communicate what we've been 
-  up to. But at last ... Delphi finally has a blog! This first post serves as an 
+  been pretty “heads down” with our work, and slow to communicate what we've been
+  up to. But at last ... Delphi finally has a blog! This first post serves as an
   introduction of sorts. Future posts will dive deeper into our various projects.
 output:
   blogdown::html_page:

content/blog/2020-08-26-fb-survey.Rmd

@@ -9,8 +9,8 @@ tags:
 authors:
   - alex
   - ryan
-heroImage: /blog/images/blog-lg-img_facebook-survey-post.png
-heroImageThumb: /blog/images/blog-thumb-img_facebook-survey-post.png
+heroImage: /blog/images/blog-lg-img_facebook-survey-post.jpg
+heroImageThumb: /blog/images/blog-thumb-img_facebook-survey-post.jpg
 summary: |
   Since April 2020, in collaboration with Facebook,
   partner universities, and public health officials,

content/blog/2020-08-26-fb-survey.html

@@ -9,8 +9,8 @@
 authors:
   - alex
   - ryan
-heroImage: /blog/images/blog-lg-img_facebook-survey-post.png
-heroImageThumb: /blog/images/blog-thumb-img_facebook-survey-post.png
+heroImage: /blog/images/blog-lg-img_facebook-survey-post.jpg
+heroImageThumb: /blog/images/blog-thumb-img_facebook-survey-post.jpg
 summary: |
   Since April 2020, in collaboration with Facebook,
   partner universities, and public health officials,
@@ -36,7 +36,7 @@
   survey data. The COVIDcast API, which serves these estimates and is updated
   daily, is a much larger effort run by the Delphi group, and our entire
   engineering team is owed a lot of credit here. Ryan came up with the
-  idea of running the surveys, and worked with Facebook to make this a reality. 
+  idea of running the surveys, and worked with Facebook to make this a reality.
   On the Facebook side, Curtiss Cobb and Jonathan McKay played big roles. The
   University of Maryland team, including Adrianne Bradford and Samantha Chiu and
   led by Frauke Kreuter, made many contributions to the survey design.

content/blog/2020-08-28-api.Rmd

@@ -10,8 +10,8 @@ tags:
 authors:
   - kathryn
   - alex
-heroImage: /blog/images/blog-lg-img_Accessing Open COVID-19.png
-heroImageThumb: /blog/images/blog-thumb-img_Accessing Open COVID-19.png
+heroImage: /blog/images/blog-lg-img_Accessing Open COVID-19.jpg
+heroImageThumb: /blog/images/blog-thumb-img_Accessing Open COVID-19.jpg
 summary: |
   One of our primary initiatives at the Delphi COVIDcast project
   has been to curate a diverse set of COVID-related data streams,

content/blog/2020-08-28-api.html

@@ -10,8 +10,8 @@
 authors:
   - kathryn
   - alex
-heroImage: /blog/images/blog-lg-img_Accessing Open COVID-19.png
-heroImageThumb: /blog/images/blog-thumb-img_Accessing Open COVID-19.png
+heroImage: /blog/images/blog-lg-img_Accessing Open COVID-19.jpg
+heroImageThumb: /blog/images/blog-thumb-img_Accessing Open COVID-19.jpg
 summary: |
   One of our primary initiatives at the Delphi COVIDcast project
   has been to curate a diverse set of COVID-related data streams,

content/blog/2020-09-18-google-survey.Rmd

@@ -8,8 +8,8 @@ tags:
   - R
 authors:
   - ryan
-heroImage: /blog/images/blog-lg-img_google-survey-post.png
-heroImageThumb: /blog/images/blog-thumb-img_google-survey-post.png
+heroImage: /blog/images/blog-lg-img_google-survey-post.jpg
+heroImageThumb: /blog/images/blog-thumb-img_google-survey-post.jpg
 summary: |
   Since April 2020, in addition to our massive daily survey advertised on 
   Facebook, we've been running (even-more-massive) surveys through Google to 

content/blog/2020-09-18-google-survey.html

@@ -8,30 +8,30 @@
   - R
 authors:
   - ryan
-heroImage: /blog/images/blog-lg-img_google-survey-post.png
-heroImageThumb: /blog/images/blog-thumb-img_google-survey-post.png
+heroImage: /blog/images/blog-lg-img_google-survey-post.jpg
+heroImageThumb: /blog/images/blog-thumb-img_google-survey-post.jpg
 summary: |
-  Since April 2020, in addition to our massive daily survey advertised on 
-  Facebook, we've been running (even-more-massive) surveys through Google to 
-  track the spread of COVID-19 in the United States. 
-  At its peak, our Google survey was taken by over 1.2 million people in a single 
-  day, and over its first month in operation, averaged over 600,000 daily 
-  respondents. In mid-May, we paused daily dissemination of this survey in order 
+  Since April 2020, in addition to our massive daily survey advertised on
+  Facebook, we've been running (even-more-massive) surveys through Google to
+  track the spread of COVID-19 in the United States.
+  At its peak, our Google survey was taken by over 1.2 million people in a single
+  day, and over its first month in operation, averaged over 600,000 daily
+  respondents. In mid-May, we paused daily dissemination of this survey in order
   to focus on our (longer, more complex) survey through Facebook,
-  but we plan to bring back the Google survey this fall. 
-  This short post covers some key differences between our Google and Facebook 
+  but we plan to bring back the Google survey this fall.
+  This short post covers some key differences between our Google and Facebook
   surveys, explains the backstory behind the "CLI-in-community" question
-  as it arose through our collaboration with Google, 
+  as it arose through our collaboration with Google,
   and shares some of our thinking about next steps for the Google survey.
 acknowledgements: |
-  Ryan Tibshirani wrote the initial code for producing 
-  estimates from the aggregated survey data. Sangwon Hyun, Natalia Lombardi de 
+  Ryan Tibshirani wrote the initial code for producing
+  estimates from the aggregated survey data. Sangwon Hyun, Natalia Lombardi de
   Oliveira, and Lester Mackey greatly extended and improved this codebase, and
-  they developed, along with Ryan, the underlying statistical methodology. Ryan 
-  came up with the idea of running the surveys, and worked with Google to make 
-  this a reality. On the Google side, Brett Slatkin and Hal Varian have been key 
-  collaborators; Brett wrote the code to get daily survey data over to Delphi's 
-  estimation pipeline; and both contributed numerous important ideas at various 
+  they developed, along with Ryan, the underlying statistical methodology. Ryan
+  came up with the idea of running the surveys, and worked with Google to make
+  this a reality. On the Google side, Brett Slatkin and Hal Varian have been key
+  collaborators; Brett wrote the code to get daily survey data over to Delphi's
+  estimation pipeline; and both contributed numerous important ideas at various
   stages of the project.
 output:
   html_document: