Merge remote-tracking branch 'origin/dev' into sgratzl/covidcast-dev

Author: sgratzl

.github/workflows/ci.yaml

@@ -24,7 +24,7 @@ jobs:
             ${{ runner.os }}-conda6-
       - uses: conda-incubator/setup-miniconda@v2
         with:
-          python-version: 3.7
+          python-version: 3.9
           mamba-version: "*"
           channels: conda-forge,defaults
           channel-priority: true
@@ -46,14 +46,22 @@ jobs:
         with:
           path: |
             ./blogdown
-          key: ${{ runner.os }}-blogdown2-${{ hashFiles('content/blog/**.Rmd') }}
+          key: ${{ runner.os }}-blogdown2-${{ hashFiles('environment.yml') }}-${{ hashFiles('content/blog/**.Rmd') }}
           restore-keys: |
+            ${{ runner.os }}-blogdown2-${{ hashFiles('environment.yml') }}-
             ${{ runner.os }}-blogdown2-
       - name: Build site
         shell: bash -l {0}
         run: |
           npm run build:blog
 
+      - uses: actions/upload-artifact@v2
+        with:
+          name: blog
+          path: |
+            ./content/blog
+            ./static/blog
+
       - uses: actions/setup-node@v1
         with:
           node-version: "12"

.github/workflows/ci_fast.yaml

@@ -35,39 +35,36 @@ 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: Login to GitHub Container Registry
+        if: (startsWith(github.ref, 'refs/tags/v') || github.ref == 'refs/heads/main' || github.ref == 'refs/heads/dev' || github.ref == 'refs/heads/release') && github.event_name == 'push'
+        uses: docker/login-action@v1
+        with:
+          registry: ghcr.io
+          username: cmu-delphi-deploy-machine
+          password: ${{ secrets.CMU_DELPHI_DEPLOY_MACHINE_PAT }}
 
-      - name: Build, tag, and push image to Amazon ECR
+      - name: Build, tag, and push image to Github
+        if: (startsWith(github.ref, 'refs/tags/v') || github.ref == 'refs/heads/main' || github.ref == 'refs/heads/dev' || github.ref == 'refs/heads/release') && github.event_name == 'push'
         env:
-          ECR_REGISTRY: ${{ steps.login-ecr.outputs.registry }}
-          ECR_REPOSITORY: ${{ github.event.repository.name }}
+          DEVOPS_DOCKER_FILE: ./devops/precompiled.dockerfile
         run: |
           baseRef="${GITHUB_REF#*/}"
           baseRef="${baseRef#*/}"
           case "${baseRef}" in
           main)
-            awsTag="latest"
+            imageTag="latest"
             ;;
           *)
-            awsTag="${baseRef//\//_}" # replace `/` with `_` in branch name
+            imageTag="${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:$awsTag
+          echo "using tag: --${imageTag}--"
+          docker build -t ghcr.io/${{ github.repository }}:$imageTag --file ${DEVOPS_DOCKER_FILE} .
+          docker push ghcr.io/${{ github.repository }}:$imageTag
 
           # 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"
+               -d "repository=ghcr.io/${{ github.repository }}&tag=$imageTag"

.gitignore

@@ -11,3 +11,5 @@
 /assets/jsconfig.json
 /static/uikit/**
 .DS_Store
+*.zip
+*.tgz

.gitpod.yml

@@ -0,0 +1,10 @@
+image:
+  file: ./devops/gitpod.dockerfile
+tasks:
+  - init: npm install && RScript -e "blogdown::install_hugo()"
+  - command: 'echo ''run: "npm start" or "npm run start:blog"'''
+ports:
+  - port: 1313
+vscode:
+  extensions:
+    - [email protected]:SrD06skfmg05hLAerl2aKQ==

.prettierignore

@@ -29,4 +29,7 @@
 *.md
 *.jpeg
 *.ico
-/themes/delphi/layouts/partials/webp-image.html
+*.bib
+/themes/delphi/layouts/partials/webp-image.html
+/themes/delphi/layouts/shortcodes/apireflink.html
+/themes/delphi/layouts/shortcodes/reflink.html

.release-it.json

@@ -0,0 +1,17 @@
+{
+  "hooks": {
+    "before:init": "npm run lint",
+    "before:release": "npm run build && npm run zip",
+    "after:release": "echo Successfully released ${name} v${version}."
+  },
+  "git": {
+    "tagName": "v${version}"
+  },
+  "npm": {
+    "publish": false
+  },
+  "github": {
+    "release": true,
+    "assets": ["website.zip"]
+  }
+}

README.md

@@ -1,5 +1,8 @@
 # Delphi Website
 
+[![Open in Gitpod](https://gitpod.io/button/open-in-gitpod.svg)](https://gitpod.io/#https://github.com/cmu-delpih/www-main)
+
+
 Delphi's homepage at https://cmu-delphi-main.netlify.app/
 
 This site is based on [Hugo](https://gohugo.io) and uses [Prettier](https://prettier.io) for formatting.
@@ -38,9 +41,9 @@ In RMarkdown things are slightly more different since the R Markdown parser is u
 **Examples**
 
 ```
-[Facebook](`r blogdown::shortcode_html("ref", "2020-08-26-fb-survey")`)
-[previous exploratory investigations](`r blogdown::shortcode_html("ref", "2020-08-26-fb-survey#some-interesting-examples")`)
-[public API](`r blogdown::shortcode_html("apiref", "api/covidcast.html")`)
+`r blogdown::shortcode_html("reflink", "2020-08-26-fb-survey", "Facebook")`
+`r blogdown::shortcode_html("reflink", "2020-08-26-fb-survey#some-interesting-examples", "previous exploratory investigations")`
+`r blogdown::shortcode_html("apireflink", "api/covidcast.html", "public API")`
 
 ```
 
@@ -53,6 +56,8 @@ In addition, there in the `/data` directory there are the following listings in
 
 ## 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)
+
 ### Web Editor Only
 
 1. Install Node: https://nodejs.org/en/download/
@@ -86,6 +91,7 @@ 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. Alternatively, run `npm run build:blog`
 1. Run Hugo server as usual
 
@@ -98,3 +104,16 @@ In case you use new dependencies don't forget to either edit `environment.yml` o
 A Github action should runs when Rmd files changes so it will verify that the blog post can be built.
 However, the converted HTML file along with all generated images are committed to the repository.
 This simplifies the deployment and ensures that we have a blog post even when the API or data changes.
+
+
+### 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.
+

config.toml

@@ -111,3 +111,9 @@ relativeURLs = false
     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"
+    feedbackForm = "https://docs.google.com/forms/d/e/1FAIpQLSeIeOJtrAhdOriEyiRY7LkpQX8DZBY19dl6De8l56Q9CZhmxw/viewform?usp=pp_url&entry.1245962748="
+    feedbackLikelihoodMobile = 0.2
+    feedbackLikelihoodDesktop = 1
+    feedbackDelayMin = 45  # in sec
+    feedbackDelayMax = 180 # in sec
+    feedbackDuration = 60  # show it for 60sec

content/about/team/index.md

@@ -219,6 +219,13 @@ team:
   note: Core member, May–July 2020
   team:
   - contributors
+- firstName: Sangwon (Justin)
+  lastName: Hyun
+  image: sangwon-justin-hyun-500x500-min.jpg
+  affiliation: USC
+  team:
+  - contributors
+  note: Core member, March–May 2020
 - firstName: Jimi
   lastName: Kim
   image: jimi-kim-500x500-min.jpg
@@ -293,6 +300,13 @@ team:
   team:
   - past
   note: Core member, March–April 2020
+- firstName: David
+  lastName: Farrow
+  image: david-farrow_head-shot.jpg
+  affiliation: Software Engineer
+  team:
+  - past
+  note: Founding member 2012–2016, Core member March–April 2020, Google Fellow October–December 2020
 - firstName: EJ
   lastName: Fox
   image: ej-fox-500x500-min.jpg
@@ -314,13 +328,6 @@ team:
   team:
   - past
   notes: Intern, summer 2020
-- firstName: Sangwon (Justin)
-  lastName: Hyun
-  image: sangwon-justin-hyun-500x500-min.jpg
-  affiliation: USC
-  team:
-  - past
-  note: Core member, March–May 2020; Contributor, May–July 2020
 - firstName: Jaemin
   lastName: Jo
   image: jaemin-jo-500x500-min.jpg
@@ -456,13 +463,6 @@ team:
   affiliation: Software Engineer
   team:
   - google
-- firstName: David
-  lastName: Farrow
-  image: david-farrow_head-shot.jpg
-  affiliation: Software Engineer
-  team:
-  - google
-  note: Founding member 2012–2016, Core member March–April 2020
 - firstName: Shreenath
   lastName: Regunathan
   image: shreenath-regunathan-head-shot.jpg

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.jpg
-heroImageThumb: /blog/images/blog-thumb-img_hello-world.jpg
+heroImage: /blog/images/blog-lg-img_hello-world.jpg # size: 1120x440 jpg and webp format
+heroImageThumb: /blog/images/blog-thumb-img_hello-world.jpg # size: 300x200 jpg and webp format
 summary: |
   Blog summary, the first 150 characters are used for the blog list
 acknowledgements: |
@@ -110,12 +110,12 @@ suggest we consider the following tags as base tags:
 
 ### Linking to other pages and blog posts:
 
-using the file name and the Hugo shortcodes, e.g.: [Facebook Post](`r blogdown::shortcode_html("relref", "2020-08-26-fb-survey")`).
+using the file name and the Hugo shortcodes, e.g.: `r blogdown::shortcode_html("reflink", "2020-08-26-fb-survey", "Facebook Post")`.
 Jumping to a specific section/anchor is supported too: 
-[previous exploratory investigations](`r blogdown::shortcode_html("relref", "2020-08-26-fb-survey#some-interesting-examples")`)
+`r blogdown::shortcode_html("reflink", "2020-08-26-fb-survey#some-interesting-examples", "previous exploratory investigations")`
 
 ### Linking to the API doc:
 
 there is another shortcode for creating an api link, e.g. 
-[public API](`r blogdown::shortcode_html("apiref", "/")`) or
-[Doctor's Visits signal](`r blogdown::shortcode_html("apiref", "api/covidcast-signals/doctor-visits.html")`) 
+`r blogdown::shortcode_html("apireflink", "/", "public API")` or
+`r blogdown::shortcode_html("apireflink", "api/covidcast-signals/doctor-visits.html", "Doctor's Visits signal")`