W#03 Recap: Our Toolkit and the git-GitHub dance

Jan Lorenz

Git and GitHub

  • Git the version control system
    • somehow like Track Changes in Microsoft Word
    • somehow like “Save as …” for multiple files in a folder (with old versions saved)
  • Developed 2005 by Linus Torvalds to maintain the Linux kernel

  • GitHub our home for Git-based projects on the internet – a bit like DropBox but for code files
  • The platform for web hosting, collaboration, and as our course management system in this course

The git-GitHub dance

Happens with your individual repositories in the GitHub-Organization.

The git-GitHub dance

We only use only a few of the various git commands.1

The git-GitHub dance

You git clone your private repositories to your computer.

The git-GitHub dance

git add, git commit, git push your work, git pull other’s work

Programming languages

Definition: Systems of rules which can process instructions to be executed by the computer.

Our two programming languages are:

 

In R:

do_this(to_this)
do_that(to_this, with_those)
to_this |> do_this() |> do_that(with_those) 
store <- do_that(to_this)

In python:

to_this.do_this()
to_this.do_this(with_those)
to_this.do_this().do_that(with_those)
store = do_that(to_this)

Syntax and Packages

In R:

do_this(to_this)
do_that(to_this, with_those)
to_this |> do_this() |> do_that(with_those) 
store <- do_that(to_this)

In python:

to_this.do_this()
to_this.do_this(with_those)
to_this.do_this().do_that(with_those)
store = do_that(to_this)
  • The role of brackets {,[,(, dots ., spaces, special words, and so on is the syntax of a language.
    • Wrong syntax is a common cause of error.
    • Learning syntax is annoying, but there is no way around.
  • Essential part of the game: Installing and using libraries/packages.
    In R:
    install.packages("tidyverse") (called once to install) and
    library(tidyverse) (in the code before using its commands)

Integrated development environment

IDEs provide terminals, a source code editor, an object browser (the environment), output and help view, tools for rendering and version control, and more to help in the workflow. Our IDEs are:

  VS Code

Editors delight us with

  • syntax highlighting Then we see if code looks good
c(1O, Text, true, 10,"Text",TRUE)
  • code completion Start writing, and press Tab to see options
  • automatic indentation, brace matching, keyboard shortcuts, …

Learn to customize and use IDEs ever better and better!

Publishing system

Weaves together text and code to produces good-looking formatted scientific or technical output.

 

A YAML header and Markdown text with code chunks is rendered to a document in several formats.

Notebooks are a similar concept: text and executable code mixed together in a browser tab. Notebooks (e.g. .ipynb-files) Can be rendered by quarto. Popular in the python world.

Main difference between notebook and quarto-output: Code in the notebook can be executed. The page is not static.

quarto Documents

YAML Header: with title, author, document-wide specifications. Body:

  • Parts of plain text with formatting syntax like **bold** for bold, and other for headers, lists, and so on. Good idea: Occassionally spend a few minutes to look up and learn some formatting rules for markdown.
  • Code chunks where the programming happens!
    • Beginning with ```{r}
    • Then optional chunk specifications. For example
      • #| label: NAME to cross-reference it in the text
      • #| echo: false to not show code in output
      • #| warning: false to not show the warnings you would see in the Console
    • Then comes the code itself. By default, every command which creates some print output or shows a graphic will make this appear in your output-document.
    • Ending with ```

What is an Enviroment, and why you should know it

  • Environment can be understood as the surrounding conditions in which code is executed.
    • In RStudio: There is an Environment-Tab.
    • Most important: Shows the variables currently accessible from the Console.
  • The environment of your quarto document is different from that of the Console! Remember this! It will be a source of confusion.