Merge pull request #235 from cmu-delphi/release

Release v1.12.5

Author: tildechris

.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

@@ -36,38 +36,33 @@ jobs:
           name: website
           path: ./public
 
-      - name: Configure AWS credentials
-        uses: aws-actions/configure-aws-credentials@v1
+      - name: Login to GitHub Container Registry
+        uses: docker/login-action@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
+          registry: ghcr.io
+          username: cmu-delphi-deploy-machine
+          password: ${{ secrets.CMU_DELPHI_DEPLOY_MACHINE_PAT }}
 
-      - name: Login to Amazon ECR
-        id: login-ecr
-        uses: aws-actions/amazon-ecr-login@v1
-
-      - name: Build, tag, and push image to Amazon ECR
+      - name: Build, tag, and push image to Github
         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/
@@ -98,3 +103,16 @@ 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.
+

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")` 

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

@@ -23,8 +23,6 @@
 ---
 
 <script src="/rmarkdown-libs/header-attrs/header-attrs.js"></script>
-<link href="/rmarkdown-libs/anchor-sections/anchor-sections.css" rel="stylesheet" />
-<script src="/rmarkdown-libs/anchor-sections/anchor-sections.js"></script>
 
 <div id="TOC">
 <ul>
@@ -49,21 +47,21 @@
 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>
@@ -142,14 +140,14 @@ <h3>Tags</h3>
 <h2>Linking</h2>
 <div id="linking-to-other-pages-and-blog-posts" class="section level3">
 <h3>Linking to other pages and blog posts:</h3>
-<p>using the file name and the Hugo shortcodes, e.g.: <a href="{{< relref "2020-08-26-fb-survey" >}}">Facebook Post</a>.
+<p>using the file name and the Hugo shortcodes, e.g.: {{< reflink "2020-08-26-fb-survey" "Facebook Post" >}}.
 Jumping to a specific section/anchor is supported too:
-<a href="{{< relref "2020-08-26-fb-survey#some-interesting-examples" >}}">previous exploratory investigations</a></p>
+{{< reflink "2020-08-26-fb-survey#some-interesting-examples" "previous exploratory investigations" >}}</p>
 </div>
 <div id="linking-to-the-api-doc" class="section level3">
 <h3>Linking to the API doc:</h3>
 <p>there is another shortcode for creating an api link, e.g. 
-<a href="{{< apiref "/" >}}">public API</a> or
-<a href="{{< apiref "api/covidcast-signals/doctor-visits.html" >}}">Doctor’s Visits signal</a></p>
+{{< apireflink "/" "public API" >}} or
+{{< apireflink "api/covidcast-signals/doctor-visits.html" "Doctor's Visits signal" >}}</p>
 </div>
 </div>

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

@@ -59,7 +59,7 @@ and making headway into dengue and norovirus.
 To learn about the work our group has done in the past,
 including some papers we've written, software tools we've built,
 and the real-time epidemiological data server we've been deploying since 2016,
-check out [our website](`r blogdown::shortcode("ref", "/")`).
+check out `r blogdown::shortcode_html("reflink", "/", "our website")`.
 
 When the COVID-19 pandemic arrived, we focused all our attention on it.
 Our Delphi team
@@ -70,7 +70,7 @@ including Stanford, UC Davis, and USC, and also from industry.
 The pace has been intense and dizzying at times,
 and we're infinitely grateful for the contributions
 and commitment of all our new members---we'd be nowhere without them.
-See [here](`r blogdown::shortcode("ref", "team")`)
+See `r blogdown::shortcode_html("reflink", "team", "here")`
 for a list of the Delphi team members.
 
 With new members comes a new breadth of expertise:
@@ -145,14 +145,12 @@ Here's a quick summary:
   aggregated counts from massive medical claims data sets through partners like
   Change Healthcare.
 
-- We've built a [public
-  API](`r blogdown::shortcode_html("apiref", "api/covidcast.html")`),
-  and [R and Python
-  packages](`r blogdown::shortcode_html("apiref", "api/covidcast_clients.html")`),
+- We've built a `r blogdown::shortcode_html("apireflink", "api/covidcast.html", "public API")`,
+  and `r blogdown::shortcode_html("apireflink", "api/covidcast_clients.html", "R and Python packages")`,
   to serve our indicators to researchers and the public. This API provides new
   data daily.
 
-- We've built [interactive maps and graphics](`r blogdown::shortcode("ref", "covidcast")`) to
+- We've built `r blogdown::shortcode_html("reflink", "covidcast", "interactive maps and graphics")` to
   display our indicators, and better inform the public and decision-makers.
 
 - We've developed forecasts of the future spread of the pandemic,