Shell and Filesystems

Session 2

September 7, 2023

Review of last session

• What questions do you have?
• What happened as you were trying to re-organize projects or R code?
  • Victories?
  • Stumbling blocks?

Learning objectives

• Understand the what and why of the shell
• Use the shell to navigate your computer’s file system
• Use R projects to simplify file system navigation
• Know your options for finding help

What is the shell?

• Command-line interface, in contrast to a GUI

Why learn the shell?

• Be able to work with tools that don’t have a GUI
• Batch large tasks (e.g. renaming files)
• Interact with remote computers like the University HPC

Shell in this workshop

• git/GitHub (next 2 lessons)
• Navigating your file system
• Quarto (lesson 9)

Let’s get set up!

• macOS comes with a shell (usually Bash or Zsh) built-in

• Windows need to install GitBash (includes Bash shell and git, which we will use later)

• Breakout rooms

  • Mac users go with Kristina
  • Windows users go with Renata

Data download

• Download shell-lesson-data.zip
  • Instructions here: https://swcarpentry.github.io/shell-novice/index.html#download-files
• Save it to your Desktop and unzip it.

Coding time

• RStudio panes
• Set up Terminal in RStudio
• Navigation using Terminal and Files pane

Example file system

Example file system

Syntax of a shell command

Coding time

• Synchronize working directories between Terminal, Files Pane, and R working directory

Coding time

• Use an R project to simplify working directories
• Copy shell_lesson_data to your R project

Getting help

ls --help
man ls

Getting help

git --help

Getting help

Getting help

Getting help

Getting help

Beware of stochastic parrots

• LLMs don’t understand, but are good at mimicry
• Use with care:
  • May be wrong
  • May be inconsistent

Beware of stochastic parrots

• Tools like ChatGPT pose ethical issues
  • Plagiarism
  • Labor conditions
  • Inputs may be sent to parent companies

Getting help: fellow humans

Getting help: fellow humans

Takeaways

• The shell is a command-line interface to the computer
• The file system the shell sees is the same as your File Explorer tab
• We can use the shell from the Terminal pane in RStudio
• Find help from built-in manual pages, Google, (maybe) AI tools, or community

Homework for next time

• Read “Excuse me, do you have a moment to talk about version control?”
• Create a diagram of your file system and note your most frequently used directories

Resources: Shell

• Software Carpentry Unix Shell episode #1
• Software Carpentry Unix Shell episode #2
• Software Carpentry Unix Shell episode #3

Resources: AI tools

• https://ecoevo.social/@cboettig/110934209180569370
• https://www.infoworld.com/article/3694611/8-chatgpt-tools-for-r-programming.html
• https://en.wikipedia.org/wiki/Stochastic_parrot
• https://dl.acm.org/doi/abs/10.1145/3442188.3445922
• https://medium.com/@konstantine_45825/chatgpt-is-no-stochastic-parrot-but-it-also-claims-that-1-is-greater-than-1-e3cd1fc303e0

Resources: UA community

• UA Data Science Institute
• UA Data Science Slack
• CCT Drop-in Hours, 9-10 on Tuesdays