Computational Skills for Researchers

University of Arizona

Dec 9-10, 2023

9:00 am - 5:00 pm

Instructors: Christian Ayala Ortiz, Michele Cosi, Uwe Hilgert, Brenda Huppenthal, Megh Krishnaswamy, Carlos Lizarraga, Mithun Paul, Sarah Roberts

Helpers: Avichal Kaul, Elijah Keeswood, Josie Mazzone, elango munusamy, Caitlin Tribelhorn, Hoi Kei Woo

Apply for the workshop at

General Information

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 novices - participants don't need to have any previous knowledge of the tools that will be presented at the workshop. The workshop targets researchers, including graduate students, postdocs, research staff, PIs, etc. Undergraduate students can be admitted by special request.

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

When: Dec 9-10, 2023. 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 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.


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

Pre-workshop Survey

Post-workshop Survey


Saturday, December 9, 2023

Before Pre-workshop survey
09:00 Navigate The Unix Shell
10:30 Morning break
10:45 Automate Tasks With The Unix Shell
12:00 Lunch break
13:00 Understand Programming With Python
14:30 Afternoon break
14:45 Build Programs With Python
16:30 Wrap-up
17:00 END

Sunday, December 10, 2023

09:00 Version Control With Git & GitHub
10:30 Morning break
10:45 Version Control with Git & GitHub (Continued)
12:00 Lunch break
13:00 Visualize Data
14:30 Afternoon break
14:45 Bringing it Together
16:30 Wrap-up
16:50 Post-workshop Survey
17:00 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

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

Analyse scientific data with Python

  • Use libraries
  • Work with arrays
  • Read and plot data
  • Create and use functions
  • Use loops and conditionals
  • Use Python from the command line
  • Defensive programming

Syllabus subject to change if necessary.


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 some versions of macOS is Bash, and 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 and you can run Bash by typing bash

If you want to change your default shell, see this Apple Support article and follow the instructions on "How to change your default shell".

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 a terminal and press the Enter key. If the message printed does not end with '/bash' then your default is something else and you can run Bash by typing bash.


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 You will need a supported web browser.

You will need an account at 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.


Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine).

During the workshop we will teach Python using a cloud-based environment. While not needed for the workshop, the following instructions will allow you to download and install a version of Python that uses the Jupyter Notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

  1. Open with your web browser.
  2. Download the Anaconda for Windows installer with Python 3. (If you are not sure which version to choose, you probably want the 64-bit Graphical Installer Anaconda3-...-Windows-x86_64.exe)
  3. Install Python 3 by running the Anaconda Installer, using all of the defaults for installation except make sure to check Add Anaconda to my PATH environment variable.

Video Tutorial

  1. Open with your web browser.
  2. Download the Anaconda Installer with Python 3 for macOS (you can either use the Graphical or the Command Line Installer).
  3. Install Python 3 by running the Anaconda Installer using all of the defaults for installation.

Video Tutorial

  1. Open with your web browser.
  2. Download the Anaconda Installer with Python 3 for Linux.
    (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
  3. Open a terminal window and navigate to the directory where the executable is downloaded (e.g., `cd ~/Downloads`).
  4. Type
    bash Anaconda3-
    and then press Tab to autocomplete the full file name. The name of file you just downloaded should appear.
  5. Press Enter (or Return depending on your keyboard). You will follow the text-only prompts. To move through the text, press Spacebar. Type yes and press enter to approve the license. Press Enter (or Return) to approve the default location for the files. Type yes and press Enter (or Return) to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).
  6. Close the terminal window.