add prettier and format code

.gitattributes

@@ -0,0 +1,131 @@
+# These settings are for any web project
+
+# Handle line endings automatically for files detected as text
+# and leave all files detected as binary untouched.
+* text=auto eol=lf
+
+#
+# The above will handle all files NOT found below
+#
+
+#
+## These files are text and should be normalized (Convert crlf => lf)
+#
+
+# source code
+*.php text
+*.css text
+*.sass text
+*.scss text
+*.less text
+*.styl text
+*.js text
+*.ts text
+*.coffee text
+*.json text
+*.htm text
+*.html text
+*.xml text
+*.txt text
+*.ini text
+*.inc text
+*.pl text
+*.rb text
+*.py text
+*.scm text
+*.sql text
+*.sh text eof=LF
+*.bat text
+*.R text
+
+# templates
+*.hbt text
+*.jade text
+*.haml text
+*.hbs text
+*.dot text
+*.tmpl text
+*.phtml text
+
+# server config
+.htaccess text
+
+# git config
+.gitattributes text
+.gitignore text
+
+# code analysis config
+.jshintrc text
+.jscsrc text
+.jshintignore text
+.csslintrc text
+
+# misc config
+*.yaml text
+*.yml text
+*.editorconfig text
+*.toml text
+
+# build config
+*.npmignore text
+*.bowerrc text
+*.prettierignore text
+Dockerfile text eof=LF
+
+# Heroku
+Procfile text
+.slugignore text
+
+# Documentation
+*.md text
+LICENSE text
+AUTHORS text
+
+
+#
+## These files are binary and should be left untouched
+#
+
+# (binary is a macro for -text -diff)
+*.png binary
+*.jpg binary
+*.jpeg binary
+*.gif binary
+*.ico binary
+*.mov binary
+*.mp4 binary
+*.mp3 binary
+*.flv binary
+*.fla binary
+*.swf binary
+*.gz binary
+*.zip binary
+*.7z binary
+*.ttf binary
+*.pyc binary
+*.pdf binary
+
+# Source files
+# ============
+*.pxd		text
+*.py 		text
+*.py3 		text
+*.pyw 		text
+*.pyx  		text
+*.sh        text eol=lf
+*.json      text
+
+# Binary files
+# ============
+*.db		binary
+*.p 		binary
+*.pkl 		binary
+*.pyc 		binary
+*.pyd		binary
+*.pyo 		binary
+
+# Note: .db, .p, and .pkl files are associated
+# with the python modules ``pickle``, ``dbm.*``,
+# ``shelve``, ``marshal``, ``anydbm``, & ``bsddb``
+# (among others).
+*.rda       binary

.github/workflows/ci.yaml

@@ -1,9 +1,9 @@
 on:
   push:
     paths: # run only when an Rmd file changes
-     - '**.Rmd'
-     - 'environment.yml'
-     - '.github/workflows/ci.yaml'
+      - "**.Rmd"
+      - "environment.yml"
+      - ".github/workflows/ci.yaml"
 
 name: ci
 
@@ -17,7 +17,7 @@ jobs:
           fetch-depth: 3
       - name: Cache Conda
         uses: actions/cache@v1
-        with:          
+        with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda6-${{ hashFiles('environment.yml') }}
           restore-keys: |
@@ -50,20 +50,22 @@ jobs:
           restore-keys: |
             ${{ runner.os }}-blogdown2-
       - name: Build site
-        shell: bash -l {0}        
+        shell: bash -l {0}
         run: |
           npm run build:blog
-      
+
       - uses: actions/setup-node@v1
         with:
-          node-version: '12'
+          node-version: "12"
       - uses: actions/cache@v2
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
           restore-keys: |
             ${{ runner.os }}-node-
       - run: npm ci
+      - name: Lint
+        run: npm run lint
       - name: Build
         run: npm run build
 

.github/workflows/ci_fast.yaml

@@ -1,9 +1,9 @@
 on:
   push:
     paths-ignore: # don't run the fast version when an Rmd file changes
-     - '**.Rmd'
-     - 'environment.yml'
-     - '.github/workflows/ci.yaml'
+      - "**.Rmd"
+      - "environment.yml"
+      - ".github/workflows/ci.yaml"
 
 name: ci_fast
 
@@ -14,18 +14,20 @@ jobs:
       - uses: actions/checkout@v2
         with:
           # submodules: true  # Fetch Hugo themes (true OR recursive)
-          fetch-depth: 3    # Fetch all history for .GitInfo and .Lastmod   
-      
+          fetch-depth: 3 # Fetch all history for .GitInfo and .Lastmod
+
       - uses: actions/setup-node@v1
         with:
-          node-version: '12'
+          node-version: "12"
       - uses: actions/cache@v2
         with:
           path: ~/.npm
           key: ${{ runner.os }}-node-${{ hashFiles('**/package-lock.json') }}
           restore-keys: |
             ${{ runner.os }}-node-
       - run: npm ci
+      - name: Lint
+        run: npm run lint
       - name: Build
         run: npm run build
 

.gitignore

@@ -1,7 +1,6 @@
 /public
 /resources/_gen
 *.exe
-/.vscode
 /blogdown
 /.Rhistory
 *_cache

.prettierignore

@@ -0,0 +1,26 @@
+*.toml
+*.jpg
+*.png
+*.rda
+*.rdx
+*.RData
+*.svg
+/blogdown
+/.htaccess
+/.Rhistory
+.gitignore
+.prettierignore
+/.gitattributes
+/LICENSE
+/package-lock.json
+/content/blog/**/*.html
+/static
+/public
+/Dockerfile
+/resources
+/assets
+*.woff
+*.ttf
+*.woff2
+*.R
+*.xml

.prettierrc.js

@@ -0,0 +1,20 @@
+module.exports = {
+  printWidth: 120,
+  semi: true,
+  trailingComma: "es5",
+
+  overrides: [
+    {
+      files: ["*.html"],
+      options: {
+        parser: "go-template",
+      },
+    },
+    {
+      files: ["*.Rmd"],
+      options: {
+        parser: "markdown",
+      },
+    },
+  ],
+};

.vscode/extensions.json

@@ -0,0 +1,3 @@
+{
+  "recommendations": ["esbenp.prettier-vscode"]
+}

.vscode/settings.json

@@ -0,0 +1,7 @@
+{
+  "editor.formatOnSave": true,
+  "editor.trimAutoWhitespace": false,
+  "editor.formatOnPaste": true,
+  "editor.formatOnSaveMode": "modifications",
+  "editor.defaultFormatter": "esbenp.prettier-vscode"
+}

README.md

@@ -14,7 +14,8 @@ This site is based on [Hugo](https://gohugo.io).
 #### Commands
 
 1. run `npm start` to create a development Hugo server
-1. run `npm build` to build a minified build in `/public`
+1. run `npm run format` to run prettier and format files
+1. run `npm run build` to build a minified build in `/public`
 
 ### Blog Editor
 
@@ -38,9 +39,11 @@ 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. Alternatively, run `npm run build:blog`
 1. Run Hugo server as usual
 
-blogdown also has an integrated server `blogdown::serve_site()` which will render RMarkdown files on the fly and does a similar thing as `hugo server -D`
+blogdown also has an integrated server `blogdown::serve_site()` which will render RMarkdown files on the fly and does a similar thing as `hugo server -D`.
+A shortcut is available through `npm run start:blog`.
 
 #### Adding a new blog post
 

_output.yml

@@ -1,3 +1,3 @@
 blogdown::html_page:
   # force svglite device, since cairo is a mess
-  dev: "svglite"
+  dev: svglite

content/about/_index.md

@@ -23,10 +23,10 @@ Public health authorities (federal, state, local), fellow researchers (working o
 
 - Since March 2020, we've created and maintained the [nation's largest public repository of diverse, geographically-detailed, real-time indicators of COVID-19 activity]({{< relref "covidcast" >}}) in the U.S. Our indicators cover every rung of the [severity pyramid](https://docs.google.com/presentation/d/1jvIycxDRMEIozKIowv2UyvSqZyF5y6jR8EAXUEK22D4/edit?usp=sharing), and they're freely available through a [public API]({{< apiref "api/covidcast.html" >}}).
 
-- Several of the underlying data sources (on which these indicators are built) would not exist or be publicly available without our efforts. This includes: 
+- Several of the underlying data sources (on which these indicators are built) would not exist or be publicly available without our efforts. This includes:
 
-    * A massive [national daily survey]({{< relref "surveys">}}) we're running in [partnership with Facebook](https://covid-survey.dataforgood.fb.com/survey_and_map_data.html). This has reached over 12 million Americans since April, providing real-time insights into, e.g., [self-reported symptoms]({{< relref "2020-08-26-fb-survey#whats-in-the-survey" >}}), [mask wearing]({{< relref "2020-10-06-survey-wave-4.html#mask-wearing" >}}), [testing]({{< relref "2020-10-06-survey-wave-4#testing" >}}), and contacts, all broken down by various demographics.
+  - A massive [national daily survey]({{< relref "surveys">}}) we're running in [partnership with Facebook](https://covid-survey.dataforgood.fb.com/survey_and_map_data.html). This has reached over 12 million Americans since April, providing real-time insights into, e.g., [self-reported symptoms]({{< relref "2020-08-26-fb-survey#whats-in-the-survey" >}}), [mask wearing]({{< relref "2020-10-06-survey-wave-4.html#mask-wearing" >}}), [testing]({{< relref "2020-10-06-survey-wave-4#testing" >}}), and contacts, all broken down by various demographics.
 
-    * An enormous database of de-identified medical insurance claims, covering more than half the US population, made possible through health system partners including Change Healthcare. We use this to produce a new [syndromic COVID-19 indicator based on doctor visits]({{< relref "2020-10-14-dv-signal" >}}), and other indicators based on hospitalizations and ICU admissions.
+  - An enormous database of de-identified medical insurance claims, covering more than half the US population, made possible through health system partners including Change Healthcare. We use this to produce a new [syndromic COVID-19 indicator based on doctor visits]({{< relref "2020-10-14-dv-signal" >}}), and other indicators based on hospitalizations and ICU admissions.
 
 - Since April 2020, we've been supporting and advising the CDC in their community-driven COVID-19 forecasting effort, which includes [creating and evaluating an ensemble forecast]({{< relref "2020-09-21-forecast-demo" >}}) from the 70+ forecasts under submission that serves as the basis for the [CDC's official COVID-19 forecast communications](https://www.cdc.gov/coronavirus/2019-ncov/covid-data/forecasting-us.html). We also contribute our own short-term forecasts of COVID-19 cases and deaths, which can be found in the [COVID-19 Forecast Hub](https://covid19forecasthub.org).