Hacking for Science

Block 3, Session 2: Infrastructure for Team Projects

Matt Bannert (@whatsgoodio)

Today’s Goals

  • find infrastructure for team projects
  • build teams

Introduction to GitHub Pages

Examples

Github Pages in a Nutshell

  • every github repository can opt to have a repository specific website
  • GitHub Pages is designed to document and/or market the software developed in the repo the URL pattern is: user.github.io/repository-name
  • GitHub Pages sites either reside on a separate gh-pages branch or in the docs folder on the main branch.
  • GitHub Pages can be activated through the Github GUI
  • GitHub Pages can host either .md files or .html webpages (including .js and .css)

Introduction to GitHub Actions

What is GitHub Actions?

Example Outline

  • Prepare a task you want to run, e.g., an R script.
  • Configure an environment AND workflow in a simple .yaml text file
  • Push the file to a hidden folder .github/workflows (this won’t be necessary if you edited the file directly on GitHub
  • Use the GitHub web GUI to monitor the process.

https://crontab.guru/

cronjobs - execute on schedule. GitHub Actions docs

Introduction to Shiny

server.R (Why Do I have to Do All the Work ?)

ui.R (I may be late, but I look gooooooood.)

What Does the shiny Framework Do for Us?

  1. create HTML/CSS/Javascript code
  2. start/run a (local) webserver
  3. communication between the R session and the browser

A minimal note on HTML

  • Markup language
  • content is wrapped in tags
<a href="http://somedestination.com">some link</a>
<b>this is bold</b>
<i>this is italic</i>
<div class="some-class">a class with a style</div>

=> shiny functions create these wraps for us.

Breaking Down the Hello World App

ui.R

library(shiny)
shinyUI(fluidPage(
  titlePanel("A random normal"),
  # Sidebar with a slider input for number of bins 
  sidebarLayout(
    sidebarPanel(
      sliderInput("obs",
                  "Number of obs:",
                  min = 1,
                  max = 1000,
                  value = 100)
    ),
    mainPanel(
      plotOutput("randomPlot")
    )
  )
))

Breaking Down the Hello World App

ui.R

library(shiny)
shinyUI(fluidPage(
  titlePanel("A random normal"),
  # Sidebar with a slider input for number of bins 
  sidebarLayout(
    sidebarPanel(
      sliderInput("obs",
                  "Number of obs:",
                  min = 1,
                  max = 1000,
                  value = 100)
    ),
    mainPanel(
      plotOutput("randomPlot")
    )
  )
))

server.R

shinyServer(function(input, output) {
    output$randomPlot <- renderPlot({
    hist(rnorm(input$obs),
         col = 'darkgray',
         border = 'white')
  })
})

Planning the App

This course: dashboard structure

  • sidebar
  • topbar
  • main panel
  • menu buttons / sub pages

The shinydashboard package

library(shinydashboard)
dashboardPage(
  dashboardHeader(),
  dashboardSidebar(),
  dashboardBody()
)

Are you ready for to build a real app?

More Shiny Resources

Basics

Advanced Reads

Hacking for Science by Dr. Matthias Bannert is licensed under CC BY-NC-SA 4.0