University of Arizona

Feb 17-18, 2024

9:00 am - 5:00 pm

Instructors: Salena Ashton, Uwe Hilgert, Avichal Kaul, Torbet McNeil

Helpers: Devin Bayly, Rishabh Bhonsle, Visalakshi Iyer, Brandon Jernigan, Chinmay Joshi, Ashvini Kabadi, Josie Mazzone, John Menassa, Mario Morales, Caitlin Tribelhorn

Apply for the workshop at https://bit.ly/476LJXY.

General Information

The Carpentries project comprises the Software Carpentry, Data Carpentry, and Library Carpentry communities of Instructors, Trainers, Maintainers, helpers, and supporters who share a mission to teach foundational computational and data science skills to researchers.

Want to learn more and stay engaged with The Carpentries? Carpentries Clippings is The Carpentries' biweekly newsletter, where we share community news, community job postings, and more. Sign up to receive future editions and read our full archive: https://carpentries.org/newsletter/

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Tucson, AZ. Get directions with OpenStreetMap or Google Maps.

When: Feb 17-18, 2024. Add to your Google Calendar.

Requirements: Participants must bring a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. They should have a few specific software packages installed (listed below).

Accessibility: We are committed to making this workshop accessible to everybody. For workshops at a physical location, the workshop organizers have checked that:

If we can help making learning easier for you (e.g. sign-language interpreters, lactation facilities) please get in touch (using contact details below) and we will attempt to provide them.

Contact: Please email hilgert@bio5.org for more information.

Roles: To learn more about the roles at the workshop (who will be doing what), refer to our Workshop FAQ.


Code of Conduct

Everyone who participates in Carpentries activities is required to conform to the Code of Conduct. This document also outlines how to report an incident if needed.


Collaborative Notes

We will use this collaborative document for chatting, taking notes, and sharing URLs and bits of code.


Surveys

Please be sure to complete these surveys before and after the workshop.

Pre-workshop Survey

Post-workshop Survey


Schedule

Day 1

Before Pre-workshop survey
09:00 Automating Tasks with the Unix Shell
10:30 Morning break
10:45 Automating Tasks with the Unix Shell (Continued)
12:00 Lunch break
13:00 Building Programs with R
14:30 Afternoon break
14:45 Building Programs with R (Continued)
16:30 Wrap-up
17:00 END

Day 2

09:00 Version Control with Git
10:30 Morning break
10:45 Version Control with Git (Continued)
12:00 Lunch break
13:00 Visualize Data
14:30 Afternoon break
14:45 Bringing It All Together
16:15 Post-workshop Survey
16:30 END

Syllabus & Learning Objectives

Take control with the Bash Shell (Command Line/Shell/Unix)

  • Work in vs. work below the GUI
  • Navigate the shell
  • Find, create, copy, move and delete folders and files
  • Shell over GUI: Command history and tab completion
  • Connect commands into workflows: pipes and redirection
  • Automate repetitive tasks: loops
  • Save and run workflows in scripts
Resources:

Collaborate with git/GitHub

  • Access a repository and pull files
  • Create a repository
  • Record changes: add, commit, ...
  • View changes: status, diff, ...
  • Ignore files
  • Work on the web: clone, pull, push, ...
  • Resolve conflicts
Resources:

Syllabus subject to change if necessary.


Setup

To participate in a Software Carpentry workshop, you will need access to software as described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do tasks more quickly.

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on "Next" four times (two times if you've previously installed Git). You don't need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu, "Choosing the default editor used by Git", select "Use the Nano editor by default" (NOTE: you will need to scroll up to find it) and click on "Next".
    3. On the page that says "Adjusting the name of the initial branch in new repositories", ensure that "Let Git decide" is selected. This will ensure the highest level of compatibility for our lessons.
    4. On the page that says "Adjusting your PATH environment", ensure that "Git from the command line and also from 3rd-party software" is selected and click on "Next". (If you don't do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the "Git from the command line and also from 3rd-party software" option.)
    5. On the page that says "Choosing the SSH executable", ensure that "Use bundled OpenSSH" is selected and click on "Next".
    6. On the page that says "Choosing HTTPS transport backend", ensure that "Use the native Windows Secure Channel Library" is selected and click on "Next".
    7. On the page that says "Configuring the line ending conversions", ensure that "Checkout Windows-style, commit Unix-style line endings" is selected and click on "Next".
    8. On the page that says "Configuring the terminal emulator to use with Git Bash", ensure that "Use Windows' default console window" is selected and click on "Next".
    9. On the page that says "Choose the default behavior of 'git pull'", ensure that "Default (fast-forward or merge) is selected and click on "Next".
    10. On the page that says "Choose a credential helper", ensure that "Git Credential Manager" is selected and click on "Next".
    11. On the page that says "Configuring extra options", ensure that "Enable file system caching" is selected and click on "Next".
    12. On the page that says "Configuring experimental options", click on "Install".
    13. On the page that says "Completing the Git Setup Wizard", uncheck the "View Release Notes" option and click on "Finish" (or "Next", if that's what the button says).
  3. If your "HOME" environment variable is not set (or you don't know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press Enter)
    2. Type the following line into the command prompt window exactly as shown:

      setx HOME "%USERPROFILE%"

    3. Press Enter, you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing Enter

This will provide you with both Git and Bash in the Git Bash program.

Video Tutorial

(The tutorial could be a little outdated, so take with a grain of salt; however, it includes a nice test section for whether your installation was successful at 2:10 min for bash and at 4:00 min for the nano editor.)

The default shell in Mac OS X Ventura and newer versions is Zsh, but Bash is available in all versions, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

To see if your default shell is Bash type echo $SHELL in Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else, you can change your current shell to Bash by typing bash and then pressing Return. To check your current shell type echo $0 and press Return.

To change your default shell to Bash type chsh -s /bin/bash and press the Return key, then reboot for the change to take effect. To change your default back to Zsh, type chsh -s /bin/zsh, press the Return key and reboot. To check available shells, type cat /etc/shells.

Video Tutorial

The default shell is usually Bash and there is usually no need to install anything.

To see if your default shell is Bash type echo $SHELL in Terminal and press the Return key. If the message printed does not end with '/bash' then your default is something else, you can change your current shell to Bash by typing bash and then pressing Return. To check your current shell type echo $0 and press Return.

To change your default shell to Bash type chsh -s /bin/bash and press the Return key, then reboot for the change to take effect. To change your default back to Zsh, type chsh -s /bin/zsh, press the Return key and reboot. To check available shells, type cat /etc/shells.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser.

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

For macOS, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled "snow-leopard" available here.

Video Tutorial

If Git is not already available on your machine you can try to install it via your distro's package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default used in this workshop is 'nano', a basic editor that is installed along with the Bash Shell above. Often, the default text editor is set to Vim,, especially on macOS and Linux. Vim is not famous for being intuitive. If you accidentally open 'Vim' and find yourself stuck in it, hit the Esc key, followed by :+Q+! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

nano is a basic editor and the default that instructors use in the workshop. It is installed along with Git.

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

R

R is a programming language that is especially powerful for data exploration, visualization, and statistical analysis. To interact with R, we use RStudio.

Install R by downloading and running this .exe file from CRAN. Also, please install the RStudio IDE. Note that if you have separate user and admin accounts, you should run the installers as administrator (right-click on .exe file and select "Run as administrator" instead of double-clicking). Otherwise problems may occur later, for example when installing R packages.

Video Tutorial

Instructions for R installation on various Linux platforms (debian, fedora, redhat, and ubuntu) can be found at <https://cran.r-project.org/bin/linux/>. These will instruct you to use your package manager (e.g. for Fedora run sudo dnf install R and for Debian/Ubuntu, add a ppa repository and then run sudo apt-get install r-base). Also, please install the RStudio IDE.