Merge remote-tracking branch 'origin/dev' into sgratzl/center-of-excellence

Author: sgratzl

.github/workflows/ci.yaml

@@ -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 }}

.gitignore

@@ -13,3 +13,5 @@
 .DS_Store
 *.zip
 *.tgz
+.Rhistory
+*.log

README.md

@@ -3,7 +3,9 @@
 [![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.
 
@@ -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

@@ -61,11 +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"
@@ -91,6 +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"
@@ -137,4 +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/publications/images/causal.jpg

@@ -1,6 +1,12 @@
 ---
 title: Research and White Papers
 papers:
+  - title: "Causal inference in the time of COVID-19"
+    image: causal.jpg
+    authors: Bonvini, Kennedy, Ventura, Wasserman
+    link: https://arxiv.org/abs/2103.04472
+    journal: ArXiv preprint
+    year: 2021
   - title: "Pancasting: forecasting epidemics from provisional data"
     image: pancasting.jpg
     authors: Brooks

content/about/publications/index.md

@@ -285,21 +285,20 @@ can change for _weeks_ as new data arrives:
 ```{r q-versioning, warning=FALSE, message=FALSE, cache=TRUE}
 library(covidcast)
 library(dplyr)
-# DISABLED for now since the API is not ready
 query_date <- "2020-08-01"
-# covidcast_signal(
-#   data_source = "quidel",
-#   signal = "covid_ag_raw_pct_positive",
-#   start_day = query_date,
-#   end_day = query_date,
-#   geo_type = "state",
-#   geo_value = "ny",
-#   issues = c(query_date, "2020-09-04")) %>%
-#     select(time_value, value, sample_size, issue, lag) %>%
-#     distinct(value, .keep_all=TRUE) %>%
-#     knitr::kable("html", digits = 2,
-#                  col.names = c("Test date", "Positivity rate (%)", "Sample size",
-#                                "Issued on", "Lag (days)"))
+covidcast_signal(
+  data_source = "quidel",
+  signal = "covid_ag_raw_pct_positive",
+  start_day = query_date,
+  end_day = query_date,
+  geo_type = "state",
+  geo_value = "ny",
+  issues = c(query_date, "2020-09-04")) %>%
+    select(time_value, value, sample_size, issue, lag) %>%
+    distinct(value, .keep_all=TRUE) %>%
+    knitr::kable("html", digits = 2,
+                 col.names = c("Test date", "Positivity rate (%)", "Sample size",
+                               "Issued on", "Lag (days)"))
 ```
 
 Many data sources are subject to revisions: